Tag: Microbiome

Phase Genomics’ Technology Powers New Anti-Microbiota Vaccine with the Potential to Ease Global Environmental Impacts of Salmon Farming

Posted on July 23, 2024 by - Uncategorized

Salmon with vaccine and salmon lice swimming away

 

Data shows proprietary technology enables lower cost and higher efficacy through new induced-dysbiosis vaccine targeting a parasite’s microbiome

 

The salmon aquaculture industry has – to put it mildly – a lousy problem. 

 

Sea lice have been sucking salmon dry at facilities across Europe and the Americas at a rate of more than 70 times their wild cousins1, costing the industry a billion dollars annually and wreaking havoc on the natural environment. But researchers at the Universidad de Concepción in Chile recently developed a method to bite back through what could be the world’s first induced-dysbiosis vaccine. A team led by Phase Genomics’ longtime collaborator Dr. Cristian Gallardo Escárate spent the last half-decade creating a vaccine that rids salmon of their lice oppressors by knocking out a key component of the parasite’s microbiome. 

 

The new, less expensive and more effective vaccine could produce major economic and environmental benefits. Farmed Atlantic salmon are Chile’s second largest export after copper. In 2021, salmon shipped out of the country were valued at almost $5 billion, according to the USDA. Yet infestations by the sea louse, Caligus rogercresseyi, in salmon aquaculture facilities dampen productivity, spread disease, threaten native fish and reduce profits. Like all sea lice, Caligus are crustaceans, not insects. The parasites attach themselves to their unfortunate fish hosts, feeding on blood and mucus. Lice keep salmon from growing and building muscle. They can also transmit pathogens, including an infectious viral anemia that can spread to native fish. Chilean salmon farms spend hundreds of millions of dollars trying to beat back C. rogercresseyi infestations with increasingly ineffective treatments.

 

The breakthrough from Gallardo Escárate’s lab at Chile’s Interdisciplinary Center for Aquaculture Research, which is nearing commercialization now, could become the first commercial example of a vaccine against a target’s microbiome. And Phase Genomics’ platform for metagenomics unlocked the new dimension of microbiome biology to drive the keystone discovery in salmon sea louse hologenomics. 

 

Slashing costs and scaling back environmental impact with proximity ligation 

Phase Genomics used its proximity ligation metagenomics technology to assemble and annotate the genomes of the entire sea louse, including the myriad microbes living within the parasite. Dr. Gallardo Escárate and his team combed through the never-before-seen data delivered by Phase Genomics to latch onto a key discovery: They realized that one bacterium was providing its louse host with a key metabolite, in this case iron, that the louse could not acquire on its own. The team’s resulting vaccine directly targets that microbe, creating a dysbiosis within the sea louse’s microbiota to turn off the louse’s metabolite tap, killing the pest in the process while saving the salmon.

 

 

Field tests show that salmon administered the anti-microbiota vaccine were essentially free of sea lice. If widely applied, Chile’s salmon aquaculture industry may find itself with extra biomass to export, fewer sea lice to cross-contaminate the natural environment, and more money in the bank. The initial findings, detailed recently in The Economist, show that vaccinated salmon are 90-95% louse free and more effective than fish managed using conventional antiparasitics. The new method also lowers the environmental impact from salmon farming, which accounts for 70% of all salmon consumed2. 

 

Cover image of an issue of The Economist with an image of a globe. Image of an article from The Economist with an image of salmon

 

Phase Genomics’ proximity ligation unlocks anti-microbiota pest control from fish to farm for sustainable

Salmon farms in Canada, Great Britain and Scandinavia also suffer from sea lice, but a different species called Lepeophtheirus salmonis. Dr. Gallardo Escárate cites similar findings around common bacteria core among Chilean sea lice ectoparasites which he believes could present a common vulnerability to the current immune dysbiosis vaccine across species.

 

 

This is not only the first time metagenomic data have been used to create a vaccine against the microbiome of a target, Dr. Gallardo Escárate also believes this proximity ligation approach could serve as a template for the development of vaccines that protect against other parasitic ne’er-do-wells, whether they’re nibbling away at fish in the sea or four-legged farm animals on land. 

 

“Without this detailed knowledge of this parasite and its microbiome, this vaccine would not exist – and we would not have a blueprint to look for this same phenomenon in other species,” says Phase Genomics founder and CEO Ivan Liachko. “This study nicely demonstrates why we need next-generation metagenomics: It has the power not just to solve problems in one or two economically important industries, but to reveal the patterns and leads that will transform dozens of industries. The days of blunt instruments are over. We now can target with surgical precision.”

 

Dr. Gallardo Escárate is currently conducting the largest study to date of the vaccine in one million salmon in the waters off of Chile.

 

1 https://www.captainjacksalaska.com/seafood/pc/catalog/salmon_diseases.pdf

2 https://www.worldwildlife.org/industries/farmed-salmon 

Far and wide: New technology reveals the long arm of viruses in microbial ecosystems

Posted on May 30, 2023 by - Metagenomics

Hydrothermal vent on ocean floor depicting the microbial environment of the featured study

Hydrothermal mat sampling aboard R/V Roger Revelle using ROV Jason. Credit: R/V Roger Revelle, Scripps institute of Oceanography.

 

For decades, biologists largely studied microbes and their viruses in isolation, nurtured in laboratory cultures. Yet, to paraphrase the poet John Donne, no microbe is an island. In recent years, scientists have recognized this by studying microbes not as individual species, but as part of the larger microbiome: the communal ecosystems, each home to many different types of bacteria and archaea, in which most microbes reside. It is in these realms that microbes display their collective might. From guts to geysers, tiny tales of competition and cooperation within microbiomes have big effects on our health and environment — such as the spread of antibiotic resistance and the stability of food webs.

 

Revealing microbiome mechanics

Traditional, laboratory-based methods struggle to probe the individual components of the microbiome. But “metagenomics” allows us to study the community at large. Metagenomics is the sequencing of DNA from microbial communities, and metagenome-assembled genomes — or MAGs — put together using ever-more sensitive tools and processes, are increasingly able to resolve the inner workings of these complex ecosystems.

Recently, a collaboration between Phase Genomics and a team at Harvard University on a metagenomics project showed that phages — viruses that infect bacteria and archaea — have a surprisingly broad impact on the microbiome of a seafloor hydrothermal vent. Using a technique called proximity ligation (Hi-C), which cross-links DNA strands from the same cell before DNA extraction and sequencing, researchers reconstructed MAGs in this community and found that diverse microbes, including bacteria and archaea separated by billions of years of evolution, sported records of past encounters with the same phages. One explanation is that the phages have an unheard-of level of host diversity — one certainly not predicted by laboratory experiments. Another is that these deep-sea microbes may somehow “share” adaptive immunity across broad and deep evolutionary gulfs.

If phages have similarly broad impacts far above the ocean floor, scientists may have to rethink how communication, cooperation and evolution shape microbiomes — and how they impact the larger creatures, like us, that depend on them.

 

Tapping the archive

Microbiomes teem with phages. But deciphering their reach is no easy task. Thankfully, some bacteria and archaea are hoarders. Their CRISPR-based immune responses record past phage infections by inserting short fragments of phage genomes into a specific region of their own genome. Some studies have even sought to reconstruct the reach of phages in a microbiome by probing the content of these areas — known as spacer regions. Yet, the approach has its drawbacks.

“Spacer regions are rich in repeats, so they don’t get sorted well in the MAG assembly process,” said Yunha Hwang, a doctoral student at Harvard University. “That creates a bias regarding which spacers and phage fragments are ultimately assembled into MAGs.”

Hwang has studied these genetic archives of microbial immunity, and previously reported that, in a desert microbiome, phages may have broad host ranges.

“It was a preliminary result, but very exciting,” said Hwang. “I wanted to see if this was a wider feature of microbiomes, and I wanted to avoid that assembly bias.”

 

Achieving Hi-C depth in deep oceans

Hwang and Peter Girguis, a professor at Harvard, worked with Phase Genomics to employ a metagenomic approach centered on Hi-C, which, by preserving physical linkages between DNA fragments present in the same cell, eases the process of resolving repeat-rich regions like CRISPR spacers.

Hwang collected samples from the microbiome near a hydrothermal vent in the Gulf of California’s Guyamas Basin. Microbial communities like this employ “alternative” metabolic pathways — relying on the plume’s rich geochemical outflow for nutrients, energy and raw materials instead of the sun-based food webs more familiar to surface-dwellers. As soon as she reached port in San Diego, Hwang shipped the microbiome samples to Phase Genomics for cross-linking, DNA extraction, sequencing and MAG assembly.

The spacer regions of the MAGs assembled via Hi-C showed similar profiles of past phage infection compared to conventional spacer-sequencing and assembly. But the higher-quality Hi-C MAGs also eased the search for phage fragments within CRISPR spacers. And, as in Hwang’s study of desert microbiomes, individual phages in the hydrothermal vent microbiome had a broad reach — including bacteria to archaea.

“This was so baffling to us, because these are two separate domains of life,” said Hwang. “The ability for a phage to infect a host depends on fundamental properties of cell biology, and bacteria and archaea are so different — their membranes, their proteins, their genomes. So, what does this mean?”

Another puzzle is that bacteria and archaea that are linked by symbiotic relationships — such as eating one another’s metabolic leftovers — were also more likely to harbor genomic fragments of the same phages in their CRISPR spacers.

 

Spread the word

One theory to explain these findings is that phages within microbiomes, which can be hard-pressed for space in these close-knit communities, have evolved to infect hosts with radically diverse membrane compositions, host defenses and cell biology. But that is not the only possibility. Another is that symbiotic partners, separated by billions of years of evolution but united at the dinner table, may be sharing more than just a meal.

“In symbiotic microbes, when one population or species gets infected by a phage, there could be a selective advantage in sharing that adaptive, genetically encoded immunity with your partners,” said Hwang.

Future metagenomic studies of other microbiomes may help resolve these theories, or sire new ones. But the eventual explanations will undoubtedly force scientists to rethink how genetic information flows within microbiomes.

“How do bacteria and archaea build up ‘resilience’ in such closely packed communities?” said Hwang. “Perhaps one way that happens through selective pressure to share records of past phage infections widely. Keeping your neighbor healthy keeps you healthy.”

 

Sounds familiar

Once upon a time, far above the ocean floor, children played a game called “telephone”: passing a phrase from one person to another — in the form of a whisper — to see how the message changed as it is heard by each ear and transmitted by each voice.

It seems that bacteria, archaea and phages play similar games, which is just the latest surprise that metagenomics has revealed about microbiomes. It will certainly not be the last.

Pass it on.

 

 

Better together: long-range and long-read DNA sequencing methods close age-old blindspots in microbiome research

Posted on January 19, 2022 by - Hi-C, Metagenomics, ProxiMeta

 

Since its debut, next-generation sequencing has not rested on its laurels. Improved sequencing platforms have reduced error and lengthened reads into the tens of thousands of bases. The debut of ultra-long-range sequencing methods that are based on proximity ligation (aka Hi-C) has brought a new order-of-magnitude into reach by linking DNA strands with their neighbors before sequencing.

Rapid progress in this field has birthed genome-resolved metagenomics, the sequencing and assembly of genomes from environmental samples to study ecosystem dynamics. But metagenomic experiments often undersample microbial diversity, missing rare residents, overlooking closely related organisms (like bacterial strains), losing rich genetic data (like viruses and metabolite gene clusters), and ignoring host-viral or host-plasmid interactions.

 

A revolution within a revolution

New sequencing platforms and methods can reform metagenomics from within. Phase Genomics has been a leader in genome-resolved metagenomics with its ProxiMeta™ platform, which leverages a method that physically connects DNA molecules inside cells before sequencing to generate highly complete genomes for novel bacteria and viruses. Boosting proximity-fueled methods with long-read platforms, such as the PacBio® Sequel® IIe system that can yield HiFi reads of up to 15,000 base pairs with error rates below 1%, could stretch its potential even further.

In a study published in Nature Biotechnology, a team — led by Dr. Timothy Smith and Dr. Derek Bickhart at the U.S. Department of Agriculture and Dr. Pavel Pevzner at the University of California, San Diego — employed both PacBio HiFi sequencing and ProxiMeta in a deep sequencing experiment to uncover record levels of microbial diversity from a fecal sample of a Katahdin lamb. Combined, PacBio HiFi sequencing and ProxiMeta eased assembly, recovered rare microbes, resolved hundreds of strains and their haplotypes, and revealed hundreds of novel plasmid and viral interactions.

 

Deeper diversity

The team constructed SMRTbell® libraries to generate HiFi data, and ProxiMeta™ libraries to generate long-range sequencing data. The two datasets allowed them to assemble contigs and create draft genomes without manual curation.

Researchers compared the breadth and depth of HiFi data-derived metagenome-assembled genomes, or MAGs, to control MAGs from assemblies of the same sample made using long, more error-prone reads. HiFi data yielded 428 complete MAGs from bacteria and archaea — a record number from a single sample. HiFi data also generated more low-prevalence MAGs, capturing a larger slice of the community’s diversity by picking up more genomes from less common residents.

 

The hidden actors

But no assembly method could be considered “complete” if it overlooked viruses, the most numerous members of virtually all ecological niches on Earth. These tiny players shape microbial communities in ways scientists are still trying to understand. For example, as agents of horizontal gene transfer, they help spread antibiotic resistance genes. And conversely, they have recently grown in popularity as a means to kill resistant bacteria in our ever-waging war against antibiotic resistance.

Phase Genomics’ ProxiPhage™ tool can already assemble high-fidelity viral genomes from microbial communities, even using only short-read sequencing data. But the new study shows that having HiFi helps considerably. The team identified 424 unique viral-host interactions, including 60 between viruses and archaea, which is a more than 7-fold increase over control samples. In total, the HiFi library included nearly 400 viral contigs, more than half of which came from a single family that infects bacteria and archaea. The ability to connect viruses with their microbial hosts in vivo is a unique property of Phase Genomics’ technology.

 

HiFi family trees

The long-range ProxiMeta libraries contained information that yielded more than 1,400 complete and 350 partial sets of gene clusters from archaea and bacteria for synthesizing metabolites such as proteasome inhibitors — the most uncovered to date. These clusters likely help some of these microbes colonize the gut. HiFi data picked up about 40% more clusters than control MAGs, illustrating just how much data is lost when long reads aren’t also highly accurate reads.

The team also used the HiFi-based MAGs to trace lineages within the community. They computationally resolved 220 MAGs into strain haplotypes, based largely on variations within single-copy genes. One MAG had 25 different haplotypes, which are likely strains of the same genus or species.

ProxiMeta ultra-long-range sequencing also linked nearly 300 HiFi-assembled plasmids to specific MAGs — revealing the species that hosted them in vivo. One plasmid, for example, was found in bacteria from 13 different genera. Long-range data also identified the first plasmids associated with three archaea, including Methanobrevibacter and Methanosphaera.

 

What’s around the bend?

This study has lessons beyond one lamb’s gastrointestinal tract. It shows decisively that the discovery power innate to long-range sequencing methods like ProxiMeta are greatly enhanced when wedded to high-accuracy sequencing methods like HiFi. Together, the two generate increasingly sophisticated metagenome assemblies for biologists to interrogate.

Applied to other environmental samples, this platform could illuminate the diversity and complexity of other microbial communities — from the bottom of the sea to mountain peaks, and within the body of every human being. It could probe pressing issues of our day, such as disease, soil health, and antibiotic resistance, a scourge whose spread and potential solutions — such as phage therapy — can only be forged through a thorough understanding of microbial diversity, interactions, and ecology.

Inside the Microbiome Startup Industry

Posted on November 10, 2021 by - Webinar

 

“The microbiome is a very special opportunity because it allows you to create products that potentially have the efficacy of a drug, but the safety of a probiotic”
-Colleen Cutcliffe, PhD

 

The Fall 2021 Genome Startup Day event, Inside the Microbiome, took a deep dive into the origins of several microbiome startups. Starting with a fireside chat, Ivan Liachko, PhD, cofounder and CEO of Phase Genomics, and Dr. Christopher Mason, Professor at Weill Cornell Medicine and cofounder of several startups, discussed Mason’s passion and recent projects relating to the microbiome. From children licking their way around their environment to sending fecal samples into space, Mason described his journey into the emerging field of the microbiome. He continued onto some of the early challenges in transitioning from academia to industry and shared his advice to any graduate students attempting to do the same. Mason also noted the improvements being made in this field, making it easier for startups to collaborate and progress.

 

“It’s become much more of a startup-friendly, entrepreneurial ecosystem in most academic centers”
-Christopher Mason, PhD

 

Next, Dr. Kirsten Sanford, host of This Week in Science, led the panelist discussion. Colleen Cutcliffe, PhD, cofounder and CEO of Pendulum Therapeutics, described her motivation to begin a microbiome company. She began with an anecdote about her daughter overcoming illness and inspiring her shift in focus from publishing papers to creating health solutions. Momchilo Vuyisich, PhD, cofounder and CSO at Viome Inc., shared similar experiences he had aiding people to improve their health in miraculous circumstances. Coming from a different field of study, Nick Greenfield, Head of Microbiome at Invitae, described his experience breaking into the industry and how he founded his initial startup, One Codex.

 

View the event recording below for the full conversation and more insights into the world of microbiome startups.

Stay up to date with Genome Startup Day on Twitter and watch previous events on the Genome Startup Day website.

Transcription

Ok. Welcome, everybody. We’re going to get started here for today. Sorry, I had to close my other tab. So good afternoon, everyone. My name is Kayla Young, and I am the chief operating officer at Phase Genomics. Thank you for being here.

Our next Genome Startup Day event. So, for those of you that are new to our events, Genome Startup Day, it’s designed to be a community building catalyst for genomics startups, founders, investors, service providers, media, and jobseekers. So please stay connected with us via Twitter.

@GenomeStartup I also put that in the messages and keep up to date for future events so quickly for kind of some run of show things and housekeeping. We will do question and answer at the end of both the fireside as well as the panel.

So please put those questions into the chat box on the right side of your screen. Additionally, for every question asked will be entered into win Phase Genomics socks, so we will announce those winners throughout the sessions. But I will follow up after to coordinate that.

So, ask those questions and join the conversation. And then finally, last but not least, I would like to extend a very big thank you to all our sponsors that make this happen primarily s2s PR, which helps put on these events for us, but also Agilent, Illumina, Pacific Biosciences, Alexandria LaunchLabs and CoMotion without this sponsorship.

This would not be possible. So, with all of that behind us, I would like to introduce our fireside chatters and my boss, Ivan Liachko, CEO and co-founder of Phase Genomics, who will be talking with Dr Chris Mason. So, Ivan over to you.

Hello, everyone, thank you for coming. Thanks, Kayla, for the intro. As you can see by my fancy attire that we’re having a fireside chat and I’m very lucky today to have with me Chris Mason, who many of you are familiar with.

Chris Computers Chris is an Associate Professor of genomics, physiology and biophysics at the Weill Cornell Medicine and director of World Quant Initiative for Quantitative Prediction, as well as an affiliate of Memorial Sloan-Kettering Cancer Center. Rockefeller, Harvard Med School, Yale Law School.

And there’s like three more pages of this stuff. If you’re not familiar with Chris, Chris is super engaging speaker. I’ve seen him talk many times at different conferences. He addresses really cool topics, most notably his interaction with Nassau and Nassau, not Nassau, NASA and the others, the space poop work he’s done with Kelley twins and

others. And of course, recently a lot of microbiomes of sort of cities and built environments. He can see, I’m just trying to read something. He’s got like 1,000,000 awards. He has been on like ABC, NBC, CBS, Fox, CNN, PBS, Nat Geo.

He’s also one of the reasons why I like to have. I like to, you know, I wanted to have Chris on here is because the purpose of this event is really it’s a startup event, but it’s a little bit different because the goal was not so much to educate people about, like how to raise money and how

to do startup mechanics. But really about that transition for scientists, that has to happen at some point between academia and industry. Like at some point we as geneticists have to come out of our earlier kind of academic shell and decide to spin out companies.

And there are so many challenges. And this event was really about talking about it, not about so much educating you, how to do it and filling out the forms and IP and all that stuff. But really like, what’s it like?

And what’s cool about Chris is that he’s a super accomplished faculty. He’s doing tons of science. He’s in the news all the time, but he’s also very involved in the commercialization of technology is associated with lots of startups, and that’s why I really wanted to bring him in here.

A lot of times what we do is we have founders who a lot of times they’re like juniors and we get their perspective, but of course, they interact their faculty all the time. And so, I want to know what it’s like from a faculty perspective and faculty, as Chris, as you know, range all over the place from

being super startups and commercialization to being straight up hostile to it. And like, you know, and so we want to just talk about it and like, get your opinions. And obviously, if you were super hostile, I wouldn’t have.

Right, right?

So, I’m assuming you’re pro. So, so yeah. So, let’s first off, this episode is about the microbiome. You know, why is it about the microbiome? The microbiome is cool. I work with the microbiome, and I organized the show.

So why do you do so much microbiome work? What’s like? What’s your favorite thing about it? Like what? What draws you to that particular topic?

Yeah, the number of things, actually. And can you hear and see me? Okay, sounds amazing. OK, great. So, a few things. The real inspiration came from two events that happened around the same time as that one. I just became a father and saw a lot of microbial interactions from a new lens, which is just, you know, infants

crawling on the floor, licking things, putting everything in their mouth. I actually talked to our daycare when we first dropped her off and said we should do an experiment. There’s a lot happening here in terms of microbial transfer.

And of course, then I realize I immediately was that creepy, weird scientist. That’s like, why is he planning experiments on our children so we didn’t do that because that would have been a little weird, but the thought never left my head.

The other thing that was happening at the same time is we started doing a lot of whole genome sequencing clinically in 2011 2012, and there are always fragments of DNA, even if you know, especially you get from a skin sample.

But even sometimes blood samples that didn’t match up to the human genome part of it because the human genome is incomplete. But also, you will have microbial sometimes contaminants that are there, but sometimes actually mediating biology. And they’ve recently been found inside of tumors.

They’ve been found, of course, in gut samples and skin samples, but even circulating in blood. We now have a company you one of my companies, Biotia is working on ways to sequence microbes from anywhere, including CSF or from things that normally have blood that you wouldn’t think would have that much unless you’re really sick.

There’s actually trace signal that’s there every time you sequence a sample, that’s you human microbial really in any kingdom of life. So, as I became more and more of a clinical geneticist in practice and also in startups, I just began to realize you have to be really kingdom agnostic to do the best possible science.

So even if you’re a computer empirically, wonderfully, trained human geneticist, if you only look at the human genome as a geneticist, you’re actually really crappy human geneticist because you’re missing a lot of biology. So, to understand health, wellness, disease trajectories of any of them, you have to look at it from a kingdom agnostic or kingdom inclusive view

across all domains of life.

Yeah, no, it’s really, it’s really cool. Like the thing that drew me to it, honestly, was that just the fact that if you think about like, you know, if you think about diminishing returns of discovery, right? Like we’ve done a lot of work on cancer, we’ve got a lot of work on human biology.

But like if I see sequence, if I scoop a little thing of soil right outside my like, it’s all new. Like, it’s like an unknown and it’s not like we invented it. It’s always been right. Like, we just.

Now.

Everything we do, we just have not had the tools to really to really measure it. Yeah. What about like the flashy projects? So, like, what was your favorite thing about the space poop? And like, how long did it take to like, get into that whole thing and become like, then that’s like, are you?

I’m assuming the next stage is going to be terraforming Mars with just sending them like poop and dumping it on there. Yeah.

Matt Damon. Yeah. I mean, it’ll take a while, but it actually did just publish a book called The Next 500 Years, which is a five-year plan to actually get people on to Mars and other planets, which involves a lot of microbial engineering, potentially even human genome modification or engineering to make it feasible.

So, I think there is a lot that we can do that we’ve just learned the tools do some of the genetic manipulation. Most obvious is CRISPR or some of the new Amiga systems that can do gene editing, but also just the catalog of genetic what’s in our DNA toolbox of just functional elements from all microbes.

Other species that we can use and deploy is getting bigger every day. And that’s kind of it’s really exciting as we are. We’re still in in this discovery phase, but it’s ramping at a super exponential pace. So, we can really sort of imagine doing this for, you know, anything from as simple as microbial monitoring on the space

station, which we’ve been doing for a few years. And most recently, I know Jack Gilbert, Robin, I’ve done some sampling up there as well. So, like more and more teams are thinking like, well, what can we learn from the microbes in space when we bring them back down and sequence them or even sequencing in space, which we

published a few years ago? They’re actually different. They evolve quite quickly. It’s a unique selective environment, which, you know, it’s not too surprising when you think about it. But you know, everywhere we look, including the space station, there’s new things to discover.

And I think a lot of the space projects are my favorite because I consider it my life’s work to try and get that goal.

But we’re like, I got hit by a bus tomorrow. At least I would have sequenced poop in space.

That’s right. That’s right. At least I got that. Check that off my list.

And yeah, the first time we sequenced the platypus, that’s what I said to myself. If I die today, I can say we sequenced a platypus one.

Funny you mentioned there is a bus rule in the labs that if you get hit by a bus, the work has to continue to document that. We’re very careful with the lab notebooks. We call it the bus rule in lab.

Which is that’s a that’s a that’s a good one. Yes, testing it might be a little hard, but what do you think will be the next thing? The next? What’s the next big thing in the space?

We just finished the inspiration for mission, and now we’re planning some other missions with Axiom. I going to have its own private space station by 2024. So, I think I think the next big thing is this commercial space sector, which is kind of a new space race.

So, we work with the medical ops team at Space X a lot over the past nine months to set up the first aerospace biobank and set up some of the very first protocols for sampling for private astronauts. What’s kind of amazing now is it’s going to be like Axiom is just space station.

So, if you want to do anything up there, as long as you can afford it, you can fly it up there and do whatever you want. So, it’s in the ranges of tens of millions of dollars, or sometimes hundreds of millions of dollars, depending on how long you want to go up there.

But you know, if you can afford it, you can go do whatever you want up there. So, we’re working. Yeah, we’re working on a bunch of interesting missions where one person wants to go for 500 days and stay in space for the longest time ever to simulate a trip to Mars and back.

Basically, other people want to do manufacturing in space. A lot of people want to do, you know, microbial engineering, even in space or organoid work that’s already happening. So, I think there’s a lot in the space sector is opening up a lot and it really was hard to get up there and difficult before.

But now it’s going to be it’s going to be pretty routine, which is pretty cool. So, if they have any experimental thing to do, it’s possible.

The space. All right, let’s talk about startups. So, as I mentioned, you are super active and super successful. You have a lab. You know, how and why did you get involved with startups?

I got my first startup failed, which is important now. I think a lot of people feel like it was one called Genome Liberty, which is right after the AMP versus myriad decision in 2013. We thought, OK, now genes are no longer patented.

We should make it so anyone can sequence any gene they want. I want to like a run down the streets of Manhattan and say, you get a genome, you get a genome, you everyone get the genome like Oprah.

But I was just so. Saying it because it had really democratized access to people’s own genetic information, and so we started a company that was the beginning of kind of a direct-to-consumer genetic testing company like 23 and me but more focused on actionable genes like pharmacogenomics and cancer genes, which ended up this idea ended

up being something like what color genomics is doing other companies. But at the time, the FDA was really clamping down on DTC genetics companies. And so, we and they even been sending letters to 23 and me. So, I thought at that time with a newborn child and a fairly young professor, do I spend a lot of time

and regulatory back and forth with the FDA, with the company that has very little funding? We did a crowdfunding campaign to get it off the ground and got some money, but at the end it was just some point to do a startup.

You need more than one or two people who are doing it part time to really get off the ground and what’s often called fire in the belly. And some of that’s like, I’m going to leave my job and have this be my job.

You don’t want to get to faculty doing it like 5% of the time. It’s never going to take off, right? So. So but the concept of it I really like is that there are ways where you can’t do it at an academic lab.

And academic labs are great for many things, for a lot of the pure discovery, pure development of new protocols, but to scale them or to get them out to the mat, a large number really have to do in a company setting.

You have to really, you know, like you can’t do, you can’t work with 1,000,000,000 people or get things a vaccine, for example, to 1,000,000,000 people from a small academic lab or even a big academic. That right, it’s just not it’s not worth for.

And so, I really start to think more about how do I really launch some of the things we’re tinkering with in lab and get them into a commercial setting? And that’s actually what led to Biotia was getting all the metagenomics work we were doing.

How do we make it so we can use this as a diagnostic and really get it to market? So, I think it’s a classic pinpoint let it pay pain point. And at what point can we go from a cool concept in the lab?

It’s working. We know it has capacity to change how we treat a certain disease or do diagnostics, but you have to at some point either set up as an LDT in your own CLIA lab or actually start a lab if you really want to go in that direction.

So yes, we’re going to get it be. It’s basically if you look around the world and the thing that you want doesn’t exist at some point you just have to either buy it or build it, and it didn’t exist, so we wanted to build it.

That’s awesome. And I think. There are two points that you made that I think are super important for our audience. one is that Chris Mason had a startup that failed. one of the things that startup founders and just startup people in general deal with all the time is this bias of like, you only hear about the successes

, but actually, failure is super common. And so, anyone who gets anywhere near what doesn’t seem like success starts having all these anxiety issues right? And so, I wanted to highlight that like, you know, like, it’s normal. These are every startup is an experiment, right?

And you don’t know what’s going to happen and you think, you know, you think you’re going to nail it out of the park, but you don’t really know, ever. And so just highlighting it for people in the audience maybe who are considering or thinking about it, like it’s normal, it happens and as part of the ecosystem.

And then the other thing that you mentioned that was interesting to me is this prime mover idea is that like you like you need; you need people who are going to go all in at some point.

I also when I started phase, like I kept one toe in academia for a long time. Eventually, I had to jump. And you know, and the faculty are generally the ones who do the jumping because you guys have good, solid jobs and you’re right.

Because you’re tenured faculty like, well, why would I give up this literally like guaranteed lifetime job? And so, it’s got to be. And also, I have to look for people who left my lab and go to start companies.

I also it’s going to be a good opportunity to look at an actual capitalized company where they’re going to do a real job, not, oh, I think we’ve got some money will go look for more money later. You really have to make sure you launch with a full, full tank when you hit the road.

So, so let’s talk about that a little bit, because I guess I mentioned sort of the relationship between faculty and students who go into industry can be touchy sometimes and sometimes people, they want to, you know, sometimes they want to start a startup, but sometimes they just want to go work for a company like, you know, work

for Agilent or Illumina or something. And how do you like, how do you what sort of. Interaction, do you have how do you relate to students who are doing that kind of stuff? Like what do you do to encourage and discourage them?

You know that kind of stuff.

I think mostly they do. I mean, the interactions depend a lot on the person, of course, it’s a little everyone’s a little unique snowflake in a way, but the one thing I do is I discourage people, feel like a first-year grad student and think, oh, I’ve heard about startups, I want to make my own company.

I think, well, you know, give it a I mean, you can’t like you could be the next Steve Jobs or Bill Gates, but the odds are that you’re not like, you know, you may not need to finish college or grad school and just jump right in, you know, maybe, but you got to play the odds a little

bit. And then also, you can still do some of the tinkering and development and IP development at. I mean, I think most people I encourage them say like file patents when you’re a grad student or postdoc. The university loves it and then you can license that IP to start.

A company in the UK have a good foundation for the company rather than. I have an idea and I need $10 million to get off the ground. If you actually have IP, investors will like that a lot more. Not surprisingly, and so will your customers because of something that they’re using, that’s unique.

So, I think the I encourage them to file patents encouragement to not do their first year of grad school, but that they should, you know, when you’re getting towards the middle years to start to think about if they really want to go that direction.

So, try to be as encouraging as I can. And you know, I actually wish people had told me, hey, if you have an idea, go meet with the tech transfer people out of university because they can help you file patents when you get out to the private market.

Filing patents is bloody expensive right after it’s 20 to $50,000 per patent prosecution. Depending on how complex it is. The university does that for you, of course. Then you have to pay them later to license it.

But at that point, somebody else was paying for it. So that’s another really, really good point. You know, when you’re and maybe this is helpful to someone in the audience. But if you don’t know if you’re a grad student or postdoc, and you invent something the university owns that invention or what that means, is that they

will be the ones paying for patenting it if you convince them that it’s worth it. And so, yeah, it’s hard to imagine a scenario where it’s you shouldn’t patent.

Even for it is like, I don’t know if my idea is that good, but just go pick up the phone and call the patent attorneys who look at this, and you’d be surprised how often things are really straightforward can lead to a patent.

Yes, because no one’s gone for them.

Yeah. And if nothing else, you learn a lot of stuff. Like the other thing about startups is that like when you go through the process, you just like the first six months is like the most learning intensive process period of your life.

Like you’re learning things that you’ve never heard about before or maybe you’ve heard of. Have no idea what they are, you know, and patents is one of those things, at least, you know, it’s something you should be aware of.

It’s part of our ecosystem. What do you think like, what have you seen in terms of the general ecosystem, like for other labs? Like what have you seen in terms of kind of how folks, you know, you know, New York is very high tech, obviously.

Like, what do you how do you see the shift happening like that, like you told your own story about sort of startups and interacting with students? What about everybody else? Like, are more faculty becoming into it? Or like, what?

What do you see?

Yeah, it really is. It’s become much more of a of a sort of startup friendly, entrepreneurial friendly ecosystem in most academic centers that I’ve seen, especially in the past five or six years. You know, there’s even a dean who’s just about biopharma collaboration and entrepreneurship at Cornell, at the med school.

There’s also one at Cornell up in Ithaca. So, there are, you know, now dean level appointments of people who think we should just encourage this, encourage Google to come up with ideas. Also, the NSF and the NIH and DARPA all help support startup companies.

So, NASA even has something like an SBAR fund, which is a small business innovation or research award, but it’s a NASA version, so almost every federal agency really applauds and encourages people in academic sites to come up with an idea, get it capitalized, get it off to market, and we’ll give you grants for it, non-dilutive capital

coming from the government to help get your company going. So, I think that’s always been there. But I think in the past few years, you know, 15, 20 years ago, there was much more of a, you know, academia over here in pharma and industry over there, and they shouldn’t, you know, engage with each other.

But I think we’ve just realized there’s a lot more to be done that can be done faster if you do it together. So, I think there’s a lot more collaboration coordination between academic medical centers and industry and pharma and startups.

And it’s gotten it’s encouraged. You know, people, you know, encourage entrepreneurship in a way that I’ve not seen. I feel that wasn’t really the case seven or eight years ago in New York, in particular, is now a multiple incubator startup hub.

There’s Harlem, Biospace Spaces, Alexandria Labs, there’s cure building that just launches. You know, all these spaces, the bio that’s now the one where there’s a lab space. You can get a startup, get some space, get going and have a startup company.

Yeah. So let me do let me do a couple of questions from the audience. So, I have one. So, following up on the patent question, if the university owns a patent, then how do you build a business on that?

So, I mean, there’s a technical answer, which is you start a company and then you get a license from the university. But sort of. You know, follow up on that, like, what do you guys, how much work and maybe how much resistance have you seen, like if somebody’s getting something via Cornell and then they want to

go find the company? How difficult is it to get a license? That process can also be touchy sometimes between.

Yeah, see this question. And it does depend on the university. Generally, they will. They actually are much happier, more happy to file a patent for someone if they know that you either have an I.D. to make a company or that you’ve already got a partner with the company who’s interested in your invention.

So, I think they encourage that. But then you do have to license it and the university could. It’s like any negotiation for any piece of property, like buying a house or a piece of land. The negotiation could break down.

They can give you a bad deal, or you could be entrenched into the university, and they don’t have to. You know, it’s like any property. They don’t have to give it to you. They could give it to someone.

They could have an exclusive right over here and then no one else can have it. But normally, universities like to have multiple licenses because it gives them more money. At the end of the day, the more money that comes in, the more they can do with other investigators and other patents.

So, it always just depends on what you want to negotiate for. You know, at a certain number of revenue that some things kick in or a certain volume of sales that you can, everything’s negotiable. But the university that is the caveat is that if they own it, they own it, and you have to negotiate with them

. one distinction is Cornell Tech is where the tech school is. It’s and also just in New York City. On Roosevelt Island, they allow fully transferable IP, even though they’ll file it for you. Like, for example, Biotia. We can take a look at it.

We found when we spun the lab out of Cornell Tech, and it’s allowing a fully transferable IP to the company to then be selected. The company got sold and exit, which is very unusual, but it’s very progressive for Cornell Tech to do this to allow you to bring that fully bring IP, not just the license, but actually

take it with you. So that’s the only place I’ve seen that done before. So. But it is possible to do.

That’s cool. And how much? So, the question sort of sort of how much development is needed to get into this market, like, is a patent enough? Do you need a patent to go in? Like is it required? It’s not a question I get sometimes is how much IP protection do you need?

This trade secret.

Off.

Where it’s as various kinds of IP, there’s patents which most people know about, but there’s also just trade secrets. It’s up as a form of intellectual property. It’s obviously less clear what it is when you have a trade secret.

But Coca-Cola has a trade secret like no one actually knows the coke form, except for a few people that originally were sniffing cocaine. But now they just have a lot of sugar water. But you know, it was originally cocaine.

in Coca-Cola. So, there’s ways you can have a, you know, something that’s widely used, but no one knows exactly you have. And you know that that is a form of IP.

And one of the reasons I kind of asked that is because a lot of people don’t realize you don’t have to have a patent to start a company. You can start a company doing PCR for people like you can start a company selling pencils you can say you don’t need, you know, like there’s a lot of things

you buy from companies with Qiagen and like a lot of them, don’t have IP on them. And so, you don’t actually think about it as just like all patents. But it’s really about invention and developing technology and moving the space forward.

OK, let me get one more. OK? This is a good that’s actually will be we’re running off a time. This would be a good closer. How do you educate the public on this space? Like, you know, yeah, microbiome space is full of sort of fact and fiction mixed together, and it’s super tempting to get caught away, caught

in like the just the hype of the microbiome and overselling the microbiome. You know this ball and how do you keep it, keep it grounded in reality, but at the same time, interesting.

I do. Yeah. And you know, I myself, I think everyone, it’s easy to get excited because there’s so much you can discover so quickly for the microbiome and research and clinical approaches. But it’s like any bit of science.

It’s anchored on reproducibility and independent validation of whatever you think you’re seeing. So, you know, the placental microbiome is a great example of what people think. They see some things, but if it’s not replicating how sure that it’s real.

And I think you have to temper your enthusiasm with really good controls, positive negative controls like any experiment and independent validation of it. So, I think, you know, it’s not like you need any magic. It’s the same principles of good science in any field is just replication and independent confirmation.

You know, intra and inter lab validation and that lets you know that it’s real. And so, I think, I guess and using multiple methods to assay whatever your question is, which is also important for way to confirm what you think you’re seeing.

But we’ve published a lot of paper showing that depending on what tool you use, you get very different results for metagenomics processing or how you clean up the sample. How you fragment the sample is well known biases at every stage of collection, analysis, processing and interpretation.

So, you just do it many ways and make sure you keep getting the same answer.

Is there any? Just to close out? Is there anything that you want to tell? The audience like about the space and about startups and whatnot. You know, I can’t see who’s this, but it’s all like. So, is there anything you want to tell people a piece of advice?

Some sage wisdom?

I would say, you know, be pretty, you know, definitely file as many patents you can if you’re in grad school already said that, but I’d say be pretty fearless because you might think, oh, someone else must know the answer to this, but a lot of times no one knows the answer.

So, I would say be a little bit fearless and jump right in because there’s still so much that we don’t know, especially in the microbiome space, that you should jump in, and you can start a company with not with just an idea and a little bit of cash.

And many people did that during COVID. They just sold PCR tests that were already on the market and now they have a ton of money. So, you don’t need, you know, IP or that’s unique for a company that does help long term.

But you know, but the world needs a lot more people innovating on these ideas that bring things to market whenever you can.

Awesome. Yeah, definitely. Startup is very courage dependent and whatnot. So, thank you for coming, Chris. You will also be as a recipient of one of these amazing DNA socks.

They are fabulous. They’re very.

Good. The real prize. And I’m going to give one away right now to somebody in the audience. And that person is that person is Elizabeth Stewart. So, get in touch with Kayla afterwards. Chris, thanks again. We’re now going to go to our panel, and it’s been it’s going to be moderated by Dr. Kiki Sanford from

This Week in Science. And stay tuned and reach out to us if you have any questions and I’m going to give away more stocks at the end.

Thanks. Thanks, Chris.

Thank you. Thanks, Chris.

Next up, we are going to move along to our panel. So, I want to introduce our panel moderator, Dr. Kiki Sanford. Kiki is the vice president of public relations at Science Talk. She is the owner of Broader Impact Productions, and she is the host of the This Week in Science podcast, which I highly recommend and will

link in the messages. So, she’s going to introduce our panelists, and there will be another question-and-answer session at the end. So let me add them. OK, over to you, Kiki.

Thanks, Kayla. Oh, I just want to say thank you to Ivan and Phase Genomics and s2s PR for inviting me to be a moderator for this session. I am excited to be able to talk with all of these CEOs, founders, amazing scientists interested in exploring, launching and growing a startup in the human microbiome space for all

of us today. So, we are joined today by three founders who I will introduce right now. Colleen Cutcliffe is the CEO and co-founder of Pendulum Therapeutics. This is a company developing microbiome targeted medical probiotics. Nick Greenfield is head of microbiome at Invitae, the medical genetic testing company that acquired the company.

Nick founded the microbial genomics and bioinformatics platform one Codex. And finally, but. Not least at all, just the last on the list, Momo Vuyisich, which is the founder and chief science officer for Viome which describes itself as the world’s first and only at home m RNA test for precision nutrition, scanning gene expression to provide health and

nutrition insights. Each of these founders has a fascinating background and has taken different paths to getting where they are today, and hopefully we will be able to dig into what they’ve done, how they got there. And welcome to all of you for joining us today for this conversation and this panel.

first, I want to ask, Colleen, can you give us a little background, what was it that pushed you from what you were doing, a Ph.D. in biochemistry, having moved on to a postdoc and then into research in industry?

What pushed you into starting and founding your own company?

Well, thanks for having me on the panel discussions. Super excited to get to be alongside Momo and Nick. I haven’t seen anybody in years, but good to see you guys, at least on the screen. So, for me, when we decided to start this company, I was working at a DNA sequencing instrument company that had gone public, and

there was just a kind of fundamental new science around the microbiome that was in academia at that time. And it felt like the moment was right to be able to translate all that great academic work into products and at the heart of being able to identify novel products in the microbiome was DNA sequencing technologies and the ability

to analyze them. And of course, that was eight or nine years ago. We’ve come a long way since then and all the additional tools and technologies around understanding the microbiome. But at that time, it felt like me and my two co-founders had a leg up on really understanding how to use DNA sequencing.

And then at a personal level, as I started learning more about the microbiome, I realized that my older daughter had potentially some microbiome deficiencies of her own. So, she was born almost two months premature. And when you have a baby born that early, you get to see them for a couple of seconds, and they get taken away

from you to intensive care, which is where she spent the first month of her life hooked up to all these machines and monitors and receiving multiple doses of antibiotics. Not because she had an infection, but because that’s prophylactic.

They’re so fragile, they want to make sure they don’t get an infection. And around the time that we were starting this company, this publication came out that where they studied 12,000 children and saw that infants who had been systematically exposed to antibiotics below six months of age were also systematically more prone to obesity and diabetes as they

got older. And the Mayo Clinic recently repeated this where they showed that kids who are under two years old and have been systematically exposed to antibiotics were more prone to diseases later in life. Not just obesity and diabetes, but also things like celiac disease, ADHD.

And so, my own daughter was experiencing metabolism issues, and she was in elementary school at that time. And so, for me, I realized we had this technological advantage. We could create products that could help millions of people, including my own daughter.

And the microbiome is a very special opportunity because it allows you to create products that have potentially the efficacy of a drug, but the safety of a probiotic. And that’s really the promise of the microbiome. We’re all trying to realize.

That personal angle, too. There are so many of us who are wondering, you know, how we can, how we can use our personal ecosystem to our benefit and Momo. You also have taken a path from academia to research working at Los Alamos National Labs and into this startup industry.

Can you talk about what led you to make the jump?

I was really driven. I developed some kind of an early onset arthritis, ankylosing spondylitis, autoimmune. No one really knew what it was, but I was suffering for just over a decade, and I was able to cure myself with a diet switch.

It was all science based, and it’s a long story, but I really was entrepreneurial at all times, and I really wanted to use my scientific skills to improve humanity and not just published papers in an academic setting. And so, I switched my career, and I worked really hard with my awesome team to develop some foundational technologies that

we then I basically did. What Ivan and what was discussed earlier, which is we patented the technologies at my previous institution and then I left, and we license those. And so that’s what we’re using today. So that worked really well.

And yeah, so I really want to apply a systems biology approach to all chronic diseases and cancers and find ways to prevent them instead of to treat them. That’s why I was formed.

That prevention through ongoing health and nutrition being a huge aspect of that for sure. And yeah, and nick, from your perspective, you’ve taken a little bit different path to get to where you are getting Master of Arts in environmental based sciences.

And yeah, but environmental.

Studies actually on.

Environmental.

Studies, the.

Science interloper here.

Yeah, please tell that story.

Well, the. I mean, it’s almost a cliche that the story is that I was having a beer on New Year’s Eve with a friend and an M.D., Ph.D., program early like nine. And there was a there was a competition sponsored by an agency called the Defense Threat Reduction Agency, or Vitra, which one of the functions that they

perform as they kind of act as the CDC for the Defense Department. They also run a series of overseas labs, and they’re really interested in weird infections that, you know, military personnel and others get out and they’re also interested in biodefense.

So, they were running this competition for better metagenomics algorithms in 2013. I didn’t know what metagenomics was on New Year’s Eve 2012, but by kind of mid-January, my friend had convinced me to dive in headlong because I knew about software and contests, and he knew about genomics.

And so… really my background is more in thinking about scientific data and data at scale and software, and we approach the problem algorithmically built some cool early technology that we found really intellectually compelling and then put a little demo together that we thought folks would say like, Oh, the algorithms so accurate or oh, the algorithm so

fast. And it was a crummy demo like a really crummy, ugly experience. And we put it on Twitter as one is wanting to do. And folks said, oh, this is so easy to use. And that was kind of that was in maybe March or April of 2014.

And that was kind of the aha moment of we thought we’d built a really cool piece of really cool piece of computational biology software with some data structures and other very low-level details. And then we put a really crude web interface in front of it, and people said that’s really compelling and useful.

And I think at the time, it’s probably still too early. But at the time, you know, there were MySEQ’s landing and state public health laboratories and kind of more and more groups outside of a few of the core kind of early Pioneer Labs were starting to do microbiome.

And so, I think, you know, there was this real need to. Help more applied scientists or folks who aren’t kind of computational, we focused access and make sense of some of this data, and that was kind of the genesis of what became one codex and how we got into the space and obviously dry side perspective

and bias. But yeah, we were a bunch of data weenies, basically.

I like the science, the science for scientists, the data, the bioinformatics side of it. Can you talk a bit about creating a startup that was kind of for scientists that and now it’s been taken up by Invitae and is more public medical facing?

But the startup part of it was it just primarily like, oh, we’re putting it out there for the scientific community to access and use?

Yeah. Well, it’s a good question. So, we did a lot of that. I think if anyone in the audience is thinking about software startups, for scientists, it’s a very hard thing to sell because, you know, unfortunately. Well, I don’t know.

Scientists don’t really like paying for software as a general rule, and there’s a lot of, I guess, under accounted for labor and academic institutions that that can be used in lieu of paying for third party services and science and software in particular.

So, we didn’t really focus on selling to that academic scientific market. We really… our core business was and remains actually, at Invitae be focused on helping biopharma groups, folks doing live biotherapeutics development and otherwise interested in the role of interactions between microbiome and other life, by therapeutics or other therapeutics.

To more systematically understand who’s there in these samples, where the different bugs that are present, as well as what’s going on. So, so we always thought of ourselves as building tools to enable greater velocity of either therapeutic discovery or assay development.

And I think that in Invitae, actually, we’re really supporting both that as well as internally. We’re now obviously at a diagnostics company interested in the microbiome as a source of biomarkers for diagnostics. And the software is really, and data infrastructure is really about supporting that effort at scale and with a certain amount of velocity so that

it can be, you know, so hopefully we can get there and find something interesting and bring something into the world that improves then impacts patients’ lives.

Yeah, thank you. And Momo, your company, you’ve gotten into Nordstrom stores at Bloomingdales, you’re working very highly at the consumer facing interface. So, can you talk about creating a product that is so consumer focused?

I can. So, I do want to intrude with a little bit of an understanding of our company. So, our company recently renamed was renamed to Viome Life Sciences and everything that you can see on Viome dot com. It’s simply one application, just one application of our technology platform, and I am actually on the not on that part

of the company. I’m actually cleaning our Viome health sciences platform. And I want to mention this briefly because I’m really particularly excited about it. The systems biology platform we’ve created. It enables clinical research and large data collection from samples and data analyzes and data science and machine learning.

And this platform has been developed over the last eleven years, both prior at Los Alamos National Lab six years and here at Viome for five years. And the really exciting part about this platform is think of it as the App Store.

So, it’s like a health app store where we provide all the software and the hardware, and anyone can plug into this platform. It’s literally now open to the whole world. So, everything that I have at my disposal, anyone in the whole world can access that 100%.

And so, it’s an open platform where others can build whatever health application is of their interest, whether they want to build a diagnostic device for whatever favorite disease they have or a companion diagnostic device for any drug they’re interested in or look for therapeutic targets.

And so that’s really exciting to me. And then Viacom is just one of the applications we’re building, other applications in cancer diagnostics and vaccines and therapeutics and so on. So, let’s not talk about that one application, Viome dot com. So that is a direct-to-consumer wellness service where consumers provide their stool and blood and soon saliva samples as

well. They actually collect all these at home ship them for our clinical labs, we generate what I call chemistry data. They’re actually metatranscriptomic data, but I call them chemistry and then we overlay mathematical equations. On top of that, those chemistry data to generate personalized food and supplement recommendations for every customer.

And those supplements, they can go purchase them on their own, or they can actually purchase them via subscription from Viome directly. And so, this was basically one of the original ideas as one of the applications of the platform.

And so. Very quickly, we got to work on that, so five months after we started the company, we already offered the stool test and some initial recommendations. And at that time, the recommendations were actually made manually by a large team of people.

So, it was like a team of nutritionists and molecular physiologists and microbial physiologists and some naturopathic doctors. So, it’s really, they would get the data out of the lab, and they would interpret them. But after the initial few months, they actually started teaching all the all our A.I., all the algorithms that they were using for

this. And I started learning from all the data and from our clinical research. And so, about a year and a half later, all everything was replaced by automated algorithms. And then we added the blood test, and now we’re adding the saliva test.

So, we really want to understand it every kind of a chronic disease in sense of systems biology. I’m not sure if you had any specific questions about this.

No, I find it interesting. What I what I was trying to get out was the question of actually producing something that is usable by the consumers and so that the ability of your team, which is multifaceted to be able to interpret your scientific data to create that product, that then is something that, as Ivan asked

earlier, was a question to Chris Mason of, you know, are we not overselling the microbiome to people?

Yeah, I mean, we are just starting. We’re scratching the surface of the tip of the iceberg. So, we’re just starting, but you have to start somewhere. And as long as people don’t make health claims based on, you know, no trials, then that I think it’s OK to start and we are seeing some absolutely phenomenal improvements in some of

our customers and it’s going to get better and better because we’ve created a platform that self-learning. And it’s like a flywheel. And so, for example, one of the fundamental differences between Viome and, let’s say, Quest Laboratories, is that when Quest Laboratories performs 1,000,000th test on a patient, they provide no additional information than from the first test, meaning

they have not learned anything. They simply collect the sample, do the test and report the data. Whereas we use every single additional customer and all the data we get, we use it for machine learning so that every new customer benefits more.

And so, it’s really a self-learning flywheel. So and as we go, we’ll learn more. And right now, you know, I get a I get an email from a customer saying, you know, my psoriasis completely went away, and I’ve been trying to treat it for 40 years.

And they went to Japan, and they went to Bulgaria, and they drink the holy water, and they tried every pharmaceutical and nothing worked. And three months after the Viome diet, their psoriasis went away and they asked me, How the hell did you do this?

And I said, I don’t know. Well, we are not treating psoriasis. We don’t know how to treat psoriasis. But what we’re doing is we’re modulating the microbiome to produce fewer pro-inflammatory signals and to produce more anti-inflammatory signals and just so happens in you.

That was what was the cause of your psoriasis. And we succeeded. But it’s not like a pharmaceutical where you can target a very specific pathway and you can inhibit it, and that was the cause of disease. So, we’re still having to learn a lot and we are only really, we’ve already legally made huge progress in four indications

so far, but we’re going through more.

Great. And, Colleen, your company Pendulum is working in the medical therapeutics industry, but can you talk a bit about how interfacing with the medical community, interfacing with organizations that you need? How do you how do you how do you navigate all of the integrations that need to happen for your company?

Yeah, well, we’re not doing drug development in the way of pharmaceutical would and so we’re selling our products directly to consumers, and I think it’s super important when we’re talking about disease states that the health care community is behind you and you’re continuing to bring them along on the journey because people as much information is available from

Dr. Google. People still do also talk to their actual health care providers. And so, for us, you know, there’s a couple of really important things. The first is that the Mayo Clinic were our first investors and they’ve invested in us at every round.

And I think that that was sort of the beginnings, the foundation of the company and being really clinically and scientifically focused and driven. We have academic partners and clinical partners that we have trials that we’ve been running with, and I think COVID really, really caused us to lose a lot of money on that front.

However, I think it is really important to keep that front and center to Momo’s point. It’s not just about running a trial; it’s continuing to run trials. It’s showing that your product works in different settings and understanding more about where is there a microbiome opportunity and where is there not.

And I think that’s been really important. So, we have educational materials, clinical trial work, medical advisory boards, scientific advisory board, you know, and I always joke that those aren’t just pretty pictures on a website. We actually put all of our advisors to work so.

Chris Mason, who was on earlier, is one of our advisors. We have multiple collaborations together, including through his company, Onegevity. And so, I think those are it’s important to really stick to the science and the medicine so that you aren’t just putting out.

I think somebody wrote earlier shampoo with microbiome in it.

Yeah. Not just sharp shampoo with microbiome, it’s what microbiome, what aspects are you influencing its ecology here we’re talking about? But speaking of systems ecology, as a woman in science and a female CEO, you are. You are a rarity, and I would love it if you could speak to your experiences in in trying to secure funding and

to actually managing a company as a woman and there have been any specific challenges.

Well, I think it’s pretty well established that it’s hard to start a company no matter what. And securing fundraising is hard, I think, and managing teams and growing teams and setting a vision and figuring out when you need a pivot and when you shouldn’t pivot and kind of dig your heels.

And all of those are the challenges of being a founder. And I would say probably for me, the most important thing that I’ve experienced is having co-founders as really important, and I think I don’t know how anybody starts a company by themselves.

But having co-founders that are literally going through the same thing as you or being able to divvy up work or just having someone that you can. Say all the things you’re worried about are nervous about two very openly, it gets harder and harder as the company grows because, you know, there’s not that you don’t want to be

transparent, but there’s just certain fears that you should just keep to yourself. So, I think that having co-founders makes life much easier and much like anything else, just having partnerships and people and a good support network around you helps you be successful.

But I only have an end of one. I’ve never started another company, but I can say, like, it’s ******* hard to raise money. I don’t care who you are.

I think that is just a truism. Put it on a T-shirt and bumper stickers, though. So, we have some questions this half hour. I knew it was going to go by very quickly, but it is just zipping past.

We have some questions from our audience. For those of all of you who have transitioned to industry, McKenzie Lynes is asking How has that transition changed your perspective on science? So, Momo, if you want to start this one.

Well, I kind of had this perspective before I transitioned to industry, I really wanted to do something applied as something that can change people’s lives. So that has remained the same always. I did not, you know, I went to I went to an academic retirement party and the person had published 180 papers and it was

a big To-Do. And it was like, wow, this guy is amazing. He published 180 papers. And I asked, did this that any of these papers impact any humans on this planet in any positive way? And that was a difficult question to answer because they really didn’t.

And so, this is the kind of realization that drove me to exit that academic world where it’s publish proposals, publish proposals, published proposals, just exit that cycle and do something that actually changes people’s lives. And it’s true in industry, you can actually do that.

Yeah, quite true, Colleen.

Yeah, I totally agree, I think being able to point to a population of people and say it changes people’s lives is extremely rewarding and you come in every day. Your goal isn’t around publishing. Your goal is around. How many more people can I help?

And so, if that’s the kind of thing that motivates you, it’s very rewarding to be an industry. I would say the thing that most surprised me when I had my first job in industry coming out of academia because I didn’t work in between my education I just went straight through was that I feel like there was this

perception that if you’re a really good scientist, you’re in academia, you’re a professor. And if you’re like a, you know, second tier scientist or you’re OK, you’re an industry. And I would say that I at my first job, I just kind of walk through the doors thinking that I was going to be a hot shot and

I was definitely not a hot shot. And I think what I. My perspective changed that there are amazing scientists up and down, left and right and industry. And so, if you’re coming out of academia and you only know that one world and you’ve only seen your professors and their colleagues and what that life looks like, I encourage

people to go hang out with some people in industry. See if you can shadow sit in on a lab meeting because I think what you’ll find is that there’s amazing science with just a slightly different perspective that’s going on everywhere.

And I think that was that was important. I just learned it by accident.

Thank you for sharing that. And Nick, did your perspective change?

Well, I don’t I don’t know. I didn’t go through that transition, so yeah.

But you did transition to industries. I mean, you weren’t specifically working in industry.

Yes, I did transition to yes, I transition to microbiome. I mean, I guess I can say a tiny bit about that. But yeah. For me and for the team that we built and now actually the team at Invitae, I think, you know, the reason I got into this space was very much to pursue.

Well, I was in San Francisco, right? There’s a common trope about how there are a lot of brilliant minds being wasted on optimizing ad spend. And I think there’s some truth to that. And, you know, this was a compelling problem through which.

Better software, better data analysis, some of those skills that that I and the team that we built had could, you know, make a difference, whether that’s by accelerating certain therapeutics developments or whether that’s, you know, particular diagnostic opportunities that I think are still a few a little way down the line.

But that we’re actively working towards. And so, I think, you know, finding that was really meaningful for me and really meaningful for the team and kind of that industry transition was really motivated by knowing or having the intuition that that would be there, that kind of meaningful balance of something that was both intellectually engaging but

also had a had a deeper purpose than ads. Not that I worked on ads before or just for the record, but you know, could happen.

If you want more than just clicks, that’s good. And as we get down into the last minute or so, hear from each of you. I’d love to see if you have any words of wisdom for future generations of microbiome startup founders.

If there’s one thing that you could tell yourself before you started, what would you go back and tell yourself? Nick, if you want to start this.

Sure. Well, so I think what Colleen said is true, a lot of things, Colleen said, are true. So, I think it’s very hard to raise money. I think it’s very hard to do. I’m sort of a solo founder and that wasn’t that kind of happened by accident.

And some just like unfortunate context about return to medical school of my co-founder and things like this. I wouldn’t do it that way, like I would strongly recommend not doing it that way. I think having a partner or a couple partners as you get started is really important and really valuable, and I’m particularly stubborn, so I

like managed to get through it. I think being stubborn in general and like not taking no for an answer is an essential quality of a founder and a lot of ways because you’ll go through some valleys or troughs, for sure.

It’s just a question of how deep they are and how regular on the journey. So, I think all those things are true. I think getting great partners is really important. If you can, then if you can’t have those people as co-founders having them as your early team, it’s really important.

And then I guess the other thing I would say is. I think that people often. Think that despite the responsibility and burden of the startup resting on the founders’ shoulders, which it often does a particularly in relationships with investors, I think sometimes there’s an incredible community of folks who’ve built companies or done similarly entrepreneurial things that

I think are there for folks to reach out to and are happy to give back and kind of pay it forward. You know, so I would also say finding folks who’ve been in your shoes or the path that you hope to walk can be hugely helpful.

And, you know, speaking for myself, like if anyone’s doing anything and microbiome on the bio side, I’m always happy to chat and I think a lot of people are.

Momo, would you like to chime in here?

Yeah, I have a couple of actually suggestions. one is that to me, I think while thinking of, say, an academic position or any kind of a position where you have a job and you’re not actually a founder, well, that seems to be less risky.

And people say, 00, founding a company, a company is too risky. I would actually turn that around and say that it’s actually far riskier to have that cushy job because it’s going to prevent you from reaching your maximum potential.

It’s going to slow you down over time. And you’re basically you already know what you’re risking. You’re risking making big progress. You already are setting yourself on a path. Right? Whereas if you become an entrepreneur, you may have failures.

I mean, you guys saw Chris Mason had a failure early on and look at what he’s doing today, right? So, you may have failures. You may have these valleys where you may feel like you made a mistake, but as long as you keep learning and growing, you will eventually come out a winner.

So that to me is a is really the perception that I think is wrong among most people to think that it’s risky to do a startup. I think it’s the opposite. So that’s one thing. And the other thing that I want to mention is it’s the people, it’s the people who you co-found with.

It’s the people who you hire, it’s the partners that you work with. Nothing else matters or everything else to me is just, you know, patents, trade secrets, location, theme. All that stuff is just not important. If you have the right people, you will succeed.

It’s really that simple. And so, pick the right co-founders, the right employees, the right partners, and life is going to be just a blissful success.

You’ll be sitting pretty. And Colin, do you want to finish? Just finish us up here with some advice.

Wow. I really. They took all my ideas. Now I think it’s great advice. I mean, I didn’t get any advice when I started the company. So, it’s kind of like having kids. It’s better to not know what’s about to happen.

I think in addition to all of the awesome ideas here, even though we kind of all very clearly said it’s very hard to fundraise, I think it’s actually really important to try to pick investors that are that are going to be good for you and for the company.

And what that means is like, there’s a tendency to try to alter your pitch to be the thing that you think that investor wants to invest in. And the goal isn’t to get that dollar in the door. That is the immediate goal.

But the goal is to build a company that is going to create the kind of change that you’re envisioning when you start the company. And so, to the point that the moment is all about the people, it’s not just the people in your company, it’s also the investors that you surround yourself with.

And science is hard, and it takes a while to do things. And so having investors that are alongside you for that and aren’t going to pressure you to do things that aren’t really your vision of the company, I think is super important.

It’s hard. It’s a hard thing to do when you’re out trying to get a book to say and also be selective. But I do think it makes a difference to end up with strong investors that are aligned with you.

And the other thing I would say is that expect failure. Failure is just a part of the whole thing. Little failures every day. Larger failures company going under. All of these things are just part of growing and learning.

And if you’re not feeling you’re not really doing something interesting. And so, I think just trying to be not afraid of failure and embracing it, I think is important you’re being courageous if you’re starting a company and failure comes with that.

Yeah, I think scientists, people going through the scientific process are probably well versed in failure, so many experience experiments don’t go anywhere. Your methods don’t work. The protocols are wrong. You have to go back to the drawing board.

So hopefully, you know, this is something that many scientists, graduate students, postdocs are in the process of really getting good at right now to be able to take into their into the world with them. Thank you all of you for this wonderful conversation.

This has been great to get. Get your information. And if anybody in the chat giving comments has questions about specific companies, you can reach out to these individuals separately.

Great. Thank you. Thank you, everyone. I’m just echoing what Kiki said. We really appreciate that as a great panel and yeah, like, thank you for your insights. So, I’m going to go ahead and remove you from the stream.

So, thank you and goodbye. And then we’ll wrap up the event.

Oh, why hello there? Well, thank you guys for staying through all that. That was awesome. Nick, Colleen, Momo, I’ve known you guys for a long time. We worked together, possibly eaten burritos together. But to see you guys all in the panel is like amazing.

I’m very privileged to have you. Dr. Kiki is an awesome moderator. For those of you in the audience. Don’t know. Dr. Typekit runs a podcast called This Week in Science. That is super fun, and I was the guest on it once, and you all should watch it or listen to it.

And they talk about not just genomics. They talk about like space and like fungi that control ants and like that kind of stuff. And so big shout out to that big shout out to our sponsors once again. And the final thing we do at the end is I’m going to give away two more of these babies

and the winners are. McKenzie Lynes and Karl Sabby, you’re going to get an email at the end of this and you’re going to get your very own DNA socks, everybody else. Thank you so much. Follow us on Twitter.

I was about to say smash that subscribe button, but I forgot this is not a Minecraft play video. So, follow us on Twitter. We’re going to have more of these. Send us questions. You know, our goal is to connect you and help you guys do what you need to do.

So, with that, I guess I’ll just sort of stop talking and thank you for coming.

Thank you, everyone. Have a good evening.

Unlock the Virome with ProxiPhage

Posted on July 26, 2021 by - Genomics, Metagenomics, ProxiMeta

viruses moving through a net

 

Metagenomic studies are illuminating the diverse array of microbiomes that exist from the ocean floor to our gastrointestinal tracts. Understanding these microbial communities is essential to understanding modern health and the environment; however, outdated lab techniques are laborious, costly, and fail to create a complete picture of the microbiome. This article, posted by Ivan Liachko, describes how advancements in biotechnology are facilitating exciting discoveries with recent tools developed to capture phage and other mobile genetic element dynamics within microbiome samples.

Continue reading to discover how ProxiPhage, a recent addition to the ProxiMeta platform, is helping scientists answer questions relating to microbiome composition dynamics, prophage prevalence, frequency of transient infections, spread of antibiotic resistance, and more.

https://www.linkedin.com/pulse/unlocking-virome-proximity-guided-metagenomics-new-frontier-liachko/

 

 

Better together: long-range and long-read DNA sequencing methods, combined, reach record heights in microbiome discovery

Posted on May 27, 2021 by - Genomics, Hi-C, Metagenomics, ProxiMeta

Microbiome plate and Phase Genomics logo. Reads "Breaking records in microbiome discovery"

 

Click here for an updated blog post.

 

Since its debut, next-generation sequencing has not rested on its laurels. Improved sequencing platforms have reduced error and lengthened reads into the tens of thousands of bases. The debut of long-range sequencing methods that are based on proximity ligation (aka Hi-C) has brought a new order-of-magnitude into reach by linking DNA strands with their neighbors before sequencing.

 

This progress has birthed high-resolution metagenomics, the sequencing and assembly of genomes from environmental samples to study ecosystem dynamics. But metagenomic experiments often undersample microbial diversity, missing rare residents, overlooking closely related organisms (like bacterial strains), losing rich genetic data (like metabolite gene clusters), and ignoring host-viral or host-plasmid interactions.

 

A revolution within a revolution

 

New sequencing platforms and methods can reform metagenomics from within. Long-read platforms, such as the PacBio® Sequel® IIe system, now yield HiFi reads of up to 15,000 base pairs with error rates below 1%. In addition, Phase Genomics created ProxiMeta™ kits to generate proximity-ligated long-range sequencing libraries, which preserve associations between DNA strands originating in the same cell.

 

In a study posted May 4 to bioRxiv, a team — led by Dr. Timothy Smith and Dr. Derek Bickhart at the U.S. Department of Agriculture and Dr. Pavel Pevzner at the University of California, San Diego — employed both PacBio HiFi sequencing and ProxiMeta in a deep sequencing experiment to uncover record levels of microbial diversity from a fecal sample of a Katahdin lamb. Combined, PacBio HiFi sequencing and ProxiMeta eased assembly, recovered rare microbes, resolved hundreds of strains and haplotypes, and preserved hundreds of plasmid and viral interactions.

 

HiFi family trees

 

The team constructed SMRTbell® libraries to generate HiFi data, and ProxiMeta kits to generate long-range libraries. The two datasets, along with the metaFlye and ProxiMeta algorithms, allowed them to assemble contigs and create draft genomes without manual curation.

 

Researchers compared the breadth and depth of HiFi data-derived metagenome-assembled genomes, or MAGs, to control MAGs from assemblies of the same sample made using long, error-prone reads. HiFi data yielded more complete MAGs — 428 versus 335 — from more bacteria and archaea. HiFi data also generated more low-prevalence MAGs, capturing a larger slice of the community’s diversity by picking up more genomes from less common residents.

 

The HiFi MAGs also contained more than 1,400 complete and 350 partial sets of gene clusters for synthesizing metabolites such as proteasome inhibitors, which likely help some of these microbes colonize the gut. HiFi data picked up about 40% more of such clusters than control MAGs, illustrating just how much data is lost when long reads aren’t also highly accurate reads.

 

The team also used the HiFi MAGs to trace lineages within the community. They computationally resolved 220 MAGs into strain haplotypes, based largely on variations within single-copy genes. One MAG had 25 different haplotypes, which are likely strains of the same genus or species.

 

ProxiMeta’s long-range discoveries

 

The ProxiMeta-generated libraries added flesh to these MAG frames skeletons by unveiling additional rich biological information. Long-range sequencing linked nearly 300 HiFi-assembled plasmids to specific MAGs — revealing the species that hosted them. One plasmid, for example, was found in bacteria from 13 different genera. Long-range data also identified the first plasmids associated with two archaea, Methanobrevibacter and Methanosphaera.

 

Long-range sequencing illuminated the viral burden in this community. The HiFi library included nearly 400 viral contigs, more than half of which came from a single family of viruses that infect both bacteria and archaea. The team identified 424 unique viral-host interactions, including 60 between viruses and archaea, which is a more than 7-fold increase over controls.

 

What’s around the bend?

 

This study has lessons beyond one lamb’s gastrointestinal tract. It shows decisively that the highly accurate long reads generated by HiFi sequencing ideal partners for Hi-C-derived methods like ProxiMeta — together generating increasingly sophisticated metagenome assemblies for biologists to interrogate.

 

Applied to other environmental samples, this platform could illuminate the diversity and complexity of other microbial communities — from the bottom of the sea to mountain peaks, and within the stomach of every human being. It could probe pressing issues of our day, such as antibiotic resistance, soil health, or how microbes can break down pollutants. These endeavors will not just fuel the engines of scientific inquiry. Broader use of this method could generate new insights into pressing problems of our times, including antibiotic resistance.

Choose This Year’s Metagenomics Award Winner

Posted on September 3, 2019 by - ProxiMeta

Congratulations to Dr. Ben Tully on winning this year’s Project ProxiMeta: 2019 Metagenomics Award! Read more about his project, 4. The Complete Hydrothermal Microbial Metal Metabolism

This summer, researchers from across the U.S. sent in short proposals for a chance to win a full-service ProxiMeta™ microbiome workup for a sample of their choice. ProxiMeta combines shotgun metagenomics with in vivo proximity ligation (Hi-C) and necessary bioinformatic tools to help researchers assemble high-quality microbial genomes directly from complex microbiome samples.

 

 

HOW TO VOTE

Each project was assessed by a panel of scientists for scientific merit, novelty, impact, and feasibility, and four finalists were selected. Cast your vote on Twitter for your favorite project.

 

 

THE FINALISTS

1. The Gut Microbiome as a Risk Factor for Arsenic-Induced Cancer

Twitter Name: Gut & As-Induced Cancer

It is estimated that ~200 million people worldwide are exposed to arsenic concentrations exceeding current safety standards. Our collaborators have recently demonstrated that mice and human microbiomes can protect mice from arsenic toxicity. While human stool supplementation fully restores protection to arsenic in germ-free mice, researchers were only able to isolate one microbe, Faecalibacterium prausnitzii, that successfully conferred protection to both parent and infant mice. These results are huge because arsenic poses the highest lifetime risk for developing cancer in humans.We will investigate the role of arsenic-transforming bacteria within the gastrointestinal (GI) microbiome as another possible risk factor.

In nature, arsenic-reducing microorganisms are well known for their ability to generate more toxic arsenic products called arsenites, which are typically formed in anaerobic environments like the gut. Past research indicates that ingested arsenic may also be transformed into the toxic product arsenite by gut microbes thus increasing the risk for the host. On the other hand, arsenite-oxidizing microbes may also provide a benefit to the host by lowering arsenite concentrations. The ability of the microbiome to transform arsenic is determined by its genetic composition, therefore ProxiMeta sequencing technology will allow us to immediately analyze our collaborators rodent stool samples for genetic clues regarding this mysterious protection. Our project goals are to expand on this knowledge by: (1) characterizing the genetic basis for protection to arsenic provided by the microbiome (2) identifying, and then isolating, the bacteria-harboring arsenic transforming genes involved in protection.

We predict that differences in the gut metagenome composition will explain the incidences in arsenic susceptibility within a population or even at the family level. This project will provide important insight regarding how gut microbes contribute to cancer and may lead to novel therapies and probiotics that could target the microbiome of arsenic-exposed individuals.

2. Evaluating Antimicrobial Resistance in Backyard Poultry Environments

Twitter: AMR in Backyard Poultry

Approximately 13 million rural, urban, and suburban US residents reported owning backyard poultry (BYP) in 2014, and interest in BYP ownership is nearly four times that amount. BYP ownership has risen recently due to product quality, public health, ethical, and animal welfare concerns of commercial operations. However, BYP ownership and disease treatment is largely under-regulated, unlike commercial poultry production. Lack of regulation poses public health concerns of transmission of antimicrobial resistant (AMR) bacteria, such as AMR strains of Salmonella, Mycoplasma gallisepticum, and Escherichia coli commonly associated with BYP. BYP owners (2014 survey) were largely uninformed about poultry diseases and treatments but were interested in learning more on disease management.

The combination of a lack of regulation and public information warrants further research into the bacterial communities of BYP and their environments. Cloacal and environmental swabs were collected as part of a 2018 citizen science study where BYP owners reported current and historical poultry antibiotic usage. We propose to conduct shotgun metagenomic sequencing and proximity ligation using the ProxiMeta platform, allowing for increased detection of full-length AMR gene alleles compared to that revealed by short-read sequencing. The combination of PacBio reads with HiC intercontig ligation analysis allows for identification of potential gene transfer events of AMR genes within communities and potential dissemination throughout the environment.

This analysis is especially important considering the public health concerns of AMR persistence in backyard environments. Additionally, investigation of lytic and prophage presence would allow investigation of phage-mediated bacterial regulation that would not be possible with short-read sequencing alone. ProxiMeta analysis of these samples would provide the most comprehensive insight of AMR presences and persistence in BYP environments to date. These findings will be critical for new regulation and disease management for the increasing number of BYP flocks, which currently pose a potential health risk.

3. Unraveling the Metagenomics of Contamination

Twitter: Steel Site Contamination

We propose a metagenome characterization of contaminated Munger Landing sediment located in the St. Louis River, Duluth, MN USA. Seasonal samples are already collected and stored; of which one will be sequenced. Munger landing, is located downstream from the U.S. Steel Superfund site and contaminants include PAHs, dioxins, PCBs, and heavy metals.

Soil condition is integral to high productivity and ecosystem balance at all trophic levels. Human activities erode soil condition through agriculture, mining, sewage outflows and/or chemical/waste disposal into waterways. These practices alter the chemical structure of the soil and break down the microbial community processes responsible for ensuring the balance of biogeochemical cycling patterns in the soil. We hypothesize the activity of these pathways involved in cycling of nitrogen, phosphorus and carbon are altered in contaminated soil systems.

Metagenomic profiling of Munger Landing will provide data to examine microbes, metabolic pathways, and contaminant-processing genes present in the community that can be characterized further using qRTPCR. This project will be presented within a community college microbiology course module. Curriculum utilizing real-world data and the sequencing technology from Phase Genomics will teach students experimental design, troubleshooting, hypothesis testing, data analysis and how to communicate the broader impacts of a study to society, the field of environmental microbiology or conservation.

In the future, this data will assist in designing a longitudinal metagenomic and metatranscriptomic study to assess the ability of remediation to ‘recover’ bacterial community function at the Munger Landing site; slated to start in 2020-2021 as compared to two uncontaminated control sites. Ten sites, slated for remediation, have been identified as having high chemical and heavy metal contamination for the St. Louis River Estuary. The Munger Landing project will establish a workflow that can be applied to other contaminated sites.

4. The Complete Hydrothermal Microbial Metal Metabolism

Twitter: Hydrothermal Microbiome

Hydrothermal vents replenish the oceans with much-needed micronutrients, spewing iron, magnesium, nickel, and other metals from the earth’s crust. These metal micronutrients are used as biological cofactors for organisms throughout the marine food chain. Boiling, sterile hydrothermal fluids quickly cool and are colonized by highly specialized microorganisms that begin to cycle the metal species mixing with the seawater. Though regularly sampled, rarely have hydrothermal plumes been tracked through the water column to establish how microbial colonization occurs through time and space. We lack understanding regarding the replicability of colonization to what extent stochastic processes shape microbial community structure.

While on station at the East Pacific Rise hydrothermal vent field, size-fractionated samples (0.2, 3.0 and 5.0-μm) were collected in the hydrothermal plume emanating from Bio Vent. Samples fluids were collected from the source through the first 1-km of dispersal – the key distance for colonization – and this effort was repeated over the course of 10-days – to determine the replicability of natural colonization events. The application of standard metagenomics sequencing and microbial genome reconstruction through binning would provide novel insight into the cycling of metals within the plume but the use of cross-linked DNA techniques would deliver an unprecedented understanding of how strain diversity impacts colonization and how microbes interact with extrachromosomal elements in the environment.

While some microbes are poised to take advantage of reduced metal species for lithotrophic growth, microbes from the water column that become entrained in the plume will need metal-resistance adaptations to alleviate stress from the elevated metal concentrations present. Metal-resistance genes dispersed through the viral and plasmid pools are essential elements for understanding the functioning of the microbial community in this globally important source of metals to the oceans and effective interpretation of the community can only be achieved through cross-linked DNA metagenomic techniques.

*All finalists projects are owned by verified researchers at U.S. academic institutions.

 

RESOURCES

 

Project ProxiMeta: 2019 Metagenomics Award

Posted on June 3, 2019 by - Metagenomics, ProxiMeta

Win a Free Proximity-Ligation Metagenomics Project

Win a chance to collaborate with Phase Genomics on a metagenomics research project. The grand prize winner will receive a full-service ProxiMeta Metagenome Deconvolution project, including proximity-ligation and shotgun library prep, sequencing, and analysis. Characterize a microbial community of your choice and assemble hundreds of bacterial and eukaryotic genomes, associate plasmids and phage with hosts, and discover novel microbial life.

Submit your proposal by August 8, 2019 The four project finalists will be announced on September 5, 2019 via Twitter based on scientific merit, novelty, and impact. After a week of public voting, the project with the most votes will be named the 2019 Metagenomics Award winner and will receive a full ProxiMeta service project.

With ProxiMeta, you can explore the microbiome with confidence. Only high-quality microbial genomes can provide true insights into the dark matter of the microbiome. Submit your proposal for the 2019 Metagenomics Award today!

KEY DATES

8 August                                      Deadline for Entries

4 September                               Finalists Announced

5-12 September                          Vote for Projects @PhaseGenomics Twitter

12 September                             2019 Metagenomics Award Announcement

 

Help Us Choose the Winner!

We need your help choosing which project to sequence! Below are our four finalists, read through the project proposals and choose your favorite; voting is open to the public and will take place on Twitter September 5, 2019 for one week.

1. The Gut Microbiome as a Risk Factor for Arsenic-Induced Cancer

It is estimated that ~200 million people worldwide are exposed to arsenic concentrations exceeding current safety standards. Our collaborators have recently demonstrated that mice and human microbiomes can protect mice from arsenic toxicity. While human stool supplementation fully restores protection to arsenic in germ-free mice, researchers were only able to isolate one microbe, Faecalibacterium prausnitzii, that successfully conferred protection to both parent and infant mice. These results are huge because arsenic poses the highest lifetime risk for developing cancer in humans.We will investigate the role of arsenic-transforming bacteria within the gastrointestinal (GI) microbiome as another possible risk factor.

In nature, arsenic-reducing microorganisms are well known for their ability to generate more toxic arsenic products called arsenites, which are typically formed in anaerobic environments like the gut. Past research indicates that ingested arsenic may also be transformed into the toxic product arsenite by gut microbes thus increasing the risk for the host. On the other hand, arsenite-oxidizing microbes may also provide a benefit to the host by lowering arsenite concentrations. The ability of the microbiome to transform arsenic is determined by its genetic composition, therefore ProxiMeta sequencing technology will allow us to immediately analyze our collaborators rodent stool samples for genetic clues regarding this mysterious protection. Our project goals are to expand on this knowledge by: (1) characterizing the genetic basis for protection to arsenic provided by the microbiome (2) identifying, and then isolating, the bacteria-harboring arsenic transforming genes involved in protection.

We predict that differences in the gut metagenome composition will explain the incidences in arsenic susceptibility within a population or even at the family level. This project will provide important insight regarding how gut microbes contribute to cancer and may lead to novel therapies and probiotics that could target the microbiome of arsenic-exposed individuals.

2. Evaluating antimicrobial resistance in backyard poultry environments

Approximately 13 million rural, urban, and suburban US residents reported owning backyard poultry (BYP) in 2014, and interest in BYP ownership is nearly four times that amount. BYP ownership has risen recently due to product quality, public health, ethical, and animal welfare concerns of commercial operations. However, BYP ownership and disease treatment is largely under-regulated, unlike commercial poultry production. Lack of regulation poses public health concerns of transmission of antimicrobial resistant (AMR) bacteria, such as AMR strains of Salmonella, Mycoplasma gallisepticum, and Escherichia coli commonly associated with BYP. BYP owners (2014 survey) were largely uninformed about poultry diseases and treatments but were interested in learning more on disease management.

The combination of a lack of regulation and public information warrants further research into the bacterial communities of BYP and their environments. Cloacal and environmental swabs were collected as part of a 2018 citizen science study where BYP owners reported current and historical poultry antibiotic usage. We propose to conduct shotgun metagenomic sequencing and proximity ligation using the ProxiMeta platform, allowing for increased detection of full-length AMR gene alleles compared to that revealed by short-read sequencing. The combination of PacBio reads with HiC intercontig ligation analysis allows for identification of potential gene transfer events of AMR genes within communities and potential dissemination throughout the environment.

This analysis is especially important considering the public health concerns of AMR persistence in backyard environments. Additionally, investigation of lytic and prophage presence would allow investigation of phage-mediated bacterial regulation that would not be possible with short-read sequencing alone. ProxiMeta analysis of these samples would provide the most comprehensive insight of AMR presences and persistence in BYP environments to date. These findings will be critical for new regulation and disease management for the increasing number of BYP flocks, which currently pose a potential health risk.

3. Unraveling the metagenomics of contamination

We propose a metagenome characterization of contaminated Munger Landing sediment located in the St. Louis River, Duluth, MN USA. Seasonal samples are already collected and stored; of which one will be sequenced. Munger landing, is located downstream from the U.S. Steel Superfund site and contaminants include PAHs, dioxins, PCBs, and heavy metals.

Soil condition is integral to high productivity and ecosystem balance at all trophic levels. Human activities erode soil condition through agriculture, mining, sewage outflows and/or chemical/waste disposal into waterways. These practices alter the chemical structure of the soil and break down the microbial community processes responsible for ensuring the balance of biogeochemical cycling patterns in the soil. We hypothesize the activity of these pathways involved in cycling of nitrogen, phosphorus and carbon are altered in contaminated soil systems.

Metagenomic profiling of Munger Landing will provide data to examine microbes, metabolic pathways, and contaminant-processing genes present in the community that can be characterized further using qRTPCR. This project will be presented within a community college microbiology course module. Curriculum utilizing real-world data and the sequencing technology from Phase Genomics will teach students experimental design, troubleshooting, hypothesis testing, data analysis and how to communicate the broader impacts of a study to society, the field of environmental microbiology or conservation.

In the future, this data will assist in designing a longitudinal metagenomic and metatranscriptomic study to assess the ability of remediation to ‘recover’ bacterial community function at the Munger Landing site; slated to start in 2020-2021 as compared to two uncontaminated control sites. Ten sites, slated for remediation, have been identified as having high chemical and heavy metal contamination for the St. Louis River Estuary. The Munger Landing project will establish a workflow that can be applied to other contaminated sites.

4. The Complete Hydrothermal Microbial Metal Metabolism

Hydrothermal vents replenish the oceans with much-needed micronutrients, spewing iron, magnesium, nickel, and other metals from the earth’s crust. These metal micronutrients are used as biological cofactors for organisms throughout the marine food chain. Boiling, sterile hydrothermal fluids quickly cool and are colonized by highly specialized microorganisms that begin to cycle the metal species mixing with the seawater. Though regularly sampled, rarely have hydrothermal plumes been tracked through the water column to establish how microbial colonization occurs through time and space. We lack understanding regarding the replicability of colonization to what extent stochastic processes shape microbial community structure.

While on station at the East Pacific Rise hydrothermal vent field, size-fractionated samples (0.2, 3.0 and 5.0-μm) were collected in the hydrothermal plume emanating from Bio Vent. Samples fluids were collected from the source through the first 1-km of dispersal – the key distance for colonization – and this effort was repeated over the course of 10-days – to determine the replicability of natural colonization events. The application of standard metagenomics sequencing and microbial genome reconstruction through binning would provide novel insight into the cycling of metals within the plume but the use of cross-linked DNA techniques would deliver an unprecedented understanding of how strain diversity impacts colonization and how microbes interact with extrachromosomal elements in the environment.

While some microbes are poised to take advantage of reduced metal species for lithotrophic growth, microbes from the water column that become entrained in the plume will need metal-resistance adaptations to alleviate stress from the elevated metal concentrations present. Metal-resistance genes dispersed through the viral and plasmid pools are essential elements for understanding the functioning of the microbial community in this globally important source of metals to the oceans and effective interpretation of the community can only be achieved through cross-linked DNA metagenomic techniques.

 

 

 

RESOURCES

Hi-C Technology Links Antimicrobial Resistance Genes to the Microbiome

Posted on December 4, 2018 by - Hi-C, Metagenomics, ProxiMeta, Uncategorized

 

Antibiotic resistance is a rapidly growing global health threat as bacteria share and spread resistance genes via plasmids and other mobile genetic elements. Several teams of researchers applied a new method to understand which microorganisms house genes for antibiotic resistance within complex microbiome communities.
Read the paper, Linking the Resistome and Plasmidome to the Microbiome.

 

ANTIMICROBIAL RESISTANCE ON THE RISE

 

According to the World Health Organization, antimicrobial resistance (AMR) in microbial pathogens is expected to take 10 million lives by 2050 if there are no new pharmaceutical or technological advancements dedicated to combating this pressing problem. For almost a century, medicine has made remarkable impact on human life by using antibiotics to treat infections, but this has led to a very concerning overuse problem, stoking an arms race between antibiotics and the pathogens they target. The CDC points out that at least 30% of antibiotic prescriptions are unnecessary and there is a massive contribution to antibiotic overuse in the food and agriculture industry where each year 130,000 tons of antibiotics are given to food animal livestock. Both of these problems correlate with the rise of AMR.

 

Though there are naturally occurring antibiotic-resistant bacteria, there are two mechanisms by which bacteria can acquire antimicrobial resistance genes (ARGs) and become resistant: 1) through spontaneous genetic mutations and/or 2) by acquiring genetic material from other microbes via plasmids, viruses, or other means of horizontal gene transfer. Due to the evolutionary pressure exerted on microbes by antibiotic overuse, pathogens resistant to these antibiotics within our body, hospitals, and the environment become reservoirs of transmittable AMR genes that can rapidly spread and accumulate within a single microbe contributing to the emergence of multidrug-resistant microbes commonly known as superbugs.

 

PROXIMITY-LIGATION (HI-C) LINKS ARG AND PLASMIDS TO THEIR HOSTS

 

One of the biggest obstacles faced by scientists when studying AMR is the inability to determine which microbes are carrying and spreading specific ARGs. Because these genes often travel on mobile elements, they can move dynamically between different species and can therefore be found in numerous organisms without one clear parental host. When attempting to sequence the DNA of a mixed microbial sample, all the DNA is purified from all the cells at the same time and the host-plasmid connection is severed, making it nearly impossible to determine where each mobile element came from or if they were shared among several species. In this newly published paper, researchers highlight a novel method for linking ARGs and other mobile genetic elements to their hosts directly from microbiome samples using the latest version of the proximity-ligation (Hi-C) data analysis tool, ProxiMeta Hi-C.

 

Phase Genomics CEO, Dr. Ivan Liachko, describes how our Hi-C platform solves one of microbiologists’ greatest problems pertaining to the linking of plasmids with their hosts.

 

Hi-C utilizes in vivo proximity-ligation which can assemble complete genomes down to the strain-level directly from mixed-population samples as well as physically links plasmids/ARGs to their host. This method is particularly useful for researchers studying the “dark-matter” of the microbiome because the method does not require culturing nor a priori information about a sample.

 

USING HI-C TO TRACK ARGs IN THE MICROBIOME

 

Lead author Thibault Stalder from the University of Idaho used the ProxiMeta Hi-C kit on a complex microbiome wastewater community, a suspected AMR reservoir, to learn more about which bacteria carry ARGs. After the Hi-C library was sequenced, Phase Genomics used the data to inform contig clustering of hundreds of genomes, most of which are novel, with our cloud-based software – ProxiMeta. Using the genome clusters found by ProxiMeta, the Hi-C linkages of each ARG-, plasmid-, and integron-bearing contigs to each genome were measured to determine which species physically hosted the relevant mobile elements.

 

ProxiMeta was able to cluster contigs into >1000 genome clusters and search for over 30 groups of ARGs, plasmids, and integrons which speed up the adaptive process of newly integrated ARGs (Figure 1, circle plot). For each of these genes, we inferred hosts (Figure 2). Moreover, these organisms generally belonged to families known to host each known gene (marked with an “X” in Figure 2), supporting the accuracy of the analysis. In the future, this information will allow us to track the spread of AMR in complex communities consisting of many diverse organisms.

 

Microbiome Antibiotic Resistance Genes and Plasmids

Figure 1: Hi-C linkage between ARGs, plasmid markers, and integrons among clusters belonging to Alpha, Beta, Gamma and Delta Proteobacteria.

 

Over 200 genome clusters had strong Hi-C links to ARGs, of which 12 had high-quality assemblies. These resultant genomes include both gram positive and gram-negative bacteria and most belonged to species that were previously unsequenced. ARGs were mostly linked to genome clusters belonging to the Gammaproteobacteria, Betaproteobacteria and Bacteroidetes (Figure 2, below).

 

Microbiome Antibiotic Resistance Genes AMR and Plasmids

Figure 2: Normalized Hi-C links between ARGs, plasmids, and families of bacteria.

 

 

FUTURE DIRECTIONS

 

This method can be useful for researchers not only studying the microbiome, but the virome as well. Phages, or viruses, also distribute genetic information amongst bacteria to influence host biology, much like plasmids. Several previous studies showed that in vivo proximity-ligation can be used to link phages with their hosts directly from mixed complex samples, much like was done with plasmids and AMR genes in this study. This information could be crucial to labs and companies that are now engineering phages that could replace the widespread use of antibiotics and combat AMR.

 

This year, antibiotic resistant bugs have infected more than 2 million people globally; 23,000 of those individuals will die because of our inability to fight these superbugs. By using ProxiMeta Hi-C to better understand the genomics of microbial communities suspected to be AMR reservoirs, researchers can identify ARG carriers down to the strain-level and quantify how prevalent these genes are. With further exploration, this tool could one day offer a new solution to limit the spread of these genes and reverse the trend of increasing antibiotic resistance and save lives.

 

BRING A HI-C KIT INTO YOUR LAB TODAY

 

Phase Genomics offers a wide variety of proximity-ligation products and services including Hi-C preparation kits and a range of different cloud-based bioinformatic analysis platforms. Power your microbiome research with ProxiMeta Hi-C and our easy Hi-C kits; assemble hundreds of complete genomes for novel, unculturable microbes, and associate plasmids with hosts directly from raw microbiome samples using ProxiMeta Hi-C.

Earth’s Wine Cellar: Digging into the Microbiome of Vineyards

Posted on September 6, 2018 by - Hi-C, Metagenomics, ProxiMeta, Uncategorized

 

Phase Genomics partnered with Browne Family Vineyards to begin to understand, the microbiome makeup of soils within different vineyards across the state of Washington. The findings were unveiled at the Pacific Science Center’s “STEM: Science Uncorked” winetasting event.

There are many different factors that contribute to soil composition, such as parent material, topography, climate, geological time, and the thousands of different and undiscovered microbes living in the soil—the least understood factor. In April of 2018, Browne Family Vineyards staff visited five of their vineyards, filled a bag with soil from each site, and sent it to Phase Genomics to analyze the microbiome in each of the soil samples.

SYMBIOSIS BETWEEN PLANTS AND MICROBES

Plants rely heavily on their microbiome to live, grow, and protect themselves from pathogens. One example of this symbiotic relationship is that plants release chemicals into the soil in order to attract microbes. These microbes bring nutrients such as nitrogen, iron, potassium, and phosphorus to the plants in exchange for sugar, which the microbes require to survive. Microbes also play an important role in nitrogen fixation, organic decay, and biofilm production to protect the plant roots from drought. It is evident that this symbiotic relationship between microbes and plants is critical to the health and survival of both, but further research into this complex community is inhibited by two main problems: It is impossible to isolate microbes in such a complex mix and most of the microbes have never been discovered before.

THE DARK MATTER OF THE MICROBIOME

Microbes live in communities where they rely on each other. This makes it difficult to isolate or culture (i.e. grow) microbes without killing them or altering their genetic makeup. Moreover, there can be millions of microbes living in a single teaspoon of soil, making these samples extremely complex environments. This causes most of the microbial world to be unknown, sometimes referred to as the “Dark Matter of the Microbiome”.

The most effective way to identify the microbes in the community is to look at the genetic makeup of the microbiome to try to classify microbial genomes present. Standard practices include sequencing of 16S (a hypervariable genomic region) and shotgun sequencing.  By combining these standard practices with Hi-C, researchers are now able to fully reconstruct genomes from a mix because Hi-C captures the DNA within each microbe to exploit key genetic features unique to each individual in the community. The Phase Genomics Hi-C kit and software, ProxiMetaTM, uses this information to capture even novel genomes straight from the sample without culturing—illuminating the dark matter of the microbiome.

THE PROCEDURE

Shotgun Sequencing Procedure and Difficulties

Figure 1: Shotgun Sequencing Procedure and Difficulties

Once the soil samples were collected from the five vineyards, Phase Genomics produced shotgun libraries to obtain DNA from all of the microbes in each sample (Figure 1)—essentially taking the soil sample, breaking open all of the microbial cells then purifying the DNA (1.A). Since DNA is fragile, most of it gets broken into smaller pieces during this process, leaving a mix of many DNA fragments from all of the microbes that were present in the original soil sample. The fragmented DNA is then sequenced and the “sequence reads” are uploaded into a database of known microbial genomes (1.B). This database then searches for matches or “hits” to see if the reads are similar to anything in the database (1.C).

A problem with relying on shotgun data is that it’s unclear which DNA fragments belong to which microbe, thus relying heavily on computational techniques and the accuracy of the reference database for classification. This results in little improvement or clarity on the makeup of the sample, again, leaving the microbiome in the dark. Though shotgun sequencing only provides a glimpse into the microbial community, this data allows scientists to differentiate the taxonomy (phyla, genera, species) of the microorganisms living in the soil.

THE RESULTS

Shotgun sequencing identified over 10,000 different species from each of the vineyard soil samples; however, it is impossible to know if this is the true number of species because only ~ 20% of the reads matched the database, indicating ~80% was either incomplete or undiscovered (see table below).

Table 1: Vineyard Read Classification
Vineyard Total Reads Percent of Reads Classified Number of Organisms Found Percent of Unknown Organisms
Canyon 19,001,222 15.95% 10,726 73.32%
Canoe Ridge 21,214,190 17.66% 11,721 55.55%
Waterbrook 19,469,954 19.6% 10,782 50.58%
Skyfall 63,850,810 16.17% 15,101 80.08%
Willow Crest 43,941,026 17.13% 13,914 71.84%

 

Moreover, of assigned reads, >50% did not match to a genus or species—hinting that many of the organisms found are novel. Without digging too deep into the microbiome analysis, it is evident that the microbial makeup is different for each of the samples. Varying levels of reads from each vineyard were able to be classified (Table 1), and among the classified reads, the vineyards have 3-4 microbes that vary in abundance in common. These microbes, such as Proteobacteria, Rhizobacteria, and Actinobacteria, generally, are very common in soil.

Proteobacteria

Proteobacteria

There are obvious differences in the biodiversity of the soil samples both in number of species and relative abundance. For example, Canoe Ridge and Waterbrook samples were >20%, Delftia, while the microbes in the other vineyards were more evenly distributed, with abundance closer to 1-5%. Interestingly, Delftia, a rod-shaped bacterium, has the ability to break down toxic chemicals and to produce gold.

Actinobacteria

Actinobacteria

There are two main components that influence microbe classification in these samples: the desired taxonomy level, and the statistical threshold, or minimum number of reads, set to define it. Much like zooming in and out, the most “zoomed out” analysis is achieved by a stringent threshold and will reveal phylum, while the most “zoomed in” analysis is achieved by a more lenient threshold and will reveal genus and species

If the data is “zoomed in” further, about 37% of the microbes in each community can be identified by genus. On average, 63% of the communities do not match to a genus at all, hinting that these microbes may have never been sequenced. The most abundant microbe genera present in these samples are Bradyrhizobium, Streptomyces, and Nocardiodes.

As discussed earlier, this data highlights the issues that are present with shotgun data and the corresponding analysis: there is still far too much that is unknown. In order to better understand these samples, we also performed Hi-C on two of the samples which will be discussed in further detail in the next section.

 

HI-C AND FINDING NOVEL GENOMES

One thing all these soil samples have in common is that they are composed of numerous novel species. To obtain more information on the microbes present in these samples, and solve the issue discussed earlier surrounding shotgun data, Hi-C was performed on two of the soil samples, Skyfall and Willow Crest. Essentially, Hi-C assigns DNA fragments from shotgun sequencing to the correct species by connecting DNA while the cells are still intact.

Hi-C enables clustering of shotgun assemblies and subsequently yields complete genomes from a microbiome, even if the genome has never been sequenced before. With complete microbe genomes, it becomes easier to classify organisms down to the strain-level—a step even further than species. By having the genome, we can essentially read a microorganism’s blueprint and learn more about its genes, evolution, and even function once the genome is annotated.

For example, preliminary data from the Willow Crest soil sample yielded 400 different genome clusters. When compared to known bacterial genomes in the RefSeq database, which aggregates all published microbial genomic data, over half of the extracted genomes are unable to be identified at a genus level and thus likely represent newly discovered bacterial organisms.

SCIENCE UNCORKED

When the microbiome data from the vineyards were presented to the public at the Pacific Science Center, two questions consistently arose: How does this influence wine taste, and how can growers select for a healthy microbiome? These very forward-thinking questions unfortunately cannot be answered—yet.

Scientists do know that soil plays a big role in plant health, and this could in part be due to the plants’ symbiotic relationship with microbes, as discussed earlier. It has also been shown that biodiversity can benefit plants because of the diverse functions individual microbes have, i.e. with more microbes, there are more potential functions being served versus 1 microbe serving one function. However, nailing down answers to these questions will take a lot of research. With emerging technologies, like Hi-C, the answers have become much more obtainable.

Though the term “microbiome” may not be household vocabulary, many of the attendees were very aware about the role that microbes play in human health, and how they influence the world around us. It goes to show that the rapid developments in the microbiome field are reaching beyond just research and becoming more tangible for the general public. Relevant stories—like looking into the microbiome of vineyards— are helping them understand the intricate concept of microbial life.

Learn more about ProxiMeta Hi-C and the microbiome by visiting our website www.phasegenomics.com and connect with us on twitter by following @PhaseGenomics

Hi-C solves the problem of linking plasmids to hosts in microbiome samples

Posted on August 8, 2018 by - ProxiMeta

Plasmids are hard!

Plasmids are an important part of microbial biology. Plasmid-borne genes can have serious public health consequences by conferring virulence traits or resistance to antibiotic drugs, and can be readily shared among bacterial cells through cell-cell conjugation or other means. In principle, any gene that gives bacterial cells a selective advantage is likely to be shared via plasmids among related cells. For example, so-called “epidemic resistance plasmids” have been instrumental in the rise of multi-drug resistance in pathogenic E. coli and Klebsiella pneumoniae.

However, determining the bacterial hosts of any given plasmid in a sample can be difficult. The classic approach is to isolate host and plasmid together and culture them in the lab. However, in complex samples with numerous organisms, many of which cannot be cultured readily or even where culturing may alter the selection pressure on the organisms of interest, this approach is often impossible. Alternatives like statistical metagenomic approaches also have difficulty with plasmid-host association, as plasmids do not necessarily resemble their host genomes in either abundance or nucleotide composition and single-cell sequencing approaches are expensive and have a limited range of samples and species they can be used on.

Hi-C to the rescue

Fortunately, recent developments in genomic technology have yielded some novel tools that allow us to circumvent this limitation. Hi-C is a method that allows us to measure 3-dimensional distances between sequences inside intact cells and was originally developed to model 3D folding of genomes inside cells. These structural measurements include a clear signal about which sequences originated inside the same cell simply because the cell membrane generally prevents inter-cellular sequences from coming into contact. Hi-C therefore provides direct physical evidence of DNA sequences originating from the same cell.

Phase Genomics has developed the ProxiMeta™ Hi-C metagenome deconvolution method, which is specifically optimized for metagenomic applications (Figure 1). At Phase Genomics we use ProxiMeta Hi-C to reconstruct whole genomes from a variety of complex samples such as human fecal, wastewater, soil, and co-culture communities (for more information, see our paper about ProxiMeta).

 

Figure 1. Schematic of ProxiMeta Hi-C. (a) Hi-C crosslinking junctions will form only between sequences in the same cell. (b) Proximity-ligation creates chimeric Hi-C junctions between adjacent DNA molecules which can be directly observed by paired-end sequencing. (c) clustering methods can be used to infer the starting genomes based on the Hi-C junction information. Originally published here.

 

As a necessary part of their life cycle, plasmids need to pass through their bacterial host cells to replicate. Therefore, plasmids typically form Hi-C links to their host genomes simply by virtue of being inside the same cell as their host genome. So, to find the hosts of a given plasmid,  one only needs to find these plasmid-genome links. Our analysis of metagenomic Hi-C data bears this conclusion out repeatedly through multiple publications, as described below.

Hi-C links plasmids and hosts

A pair of early publications showed that using this method we could correctly associate several plasmids with their bacterial hosts in an artificial community using and early version of the Hi-C  method.

In our more recent paper, we have demonstrated that Hi-C links between plasmids and hosts in a complex human fecal sample link described plasmids to their known hosts. Excitingly, in a single experiment we can now assemble numerous novel microbial genomes, complete with plasmid content, from a complex sample with hundreds of different species present.

An exciting finding from this complex community is that we can directly visualize how plasmids are shared between bacteria in a community (Figure 2). Recall from above that the sharing and spread of plasmids is a serious problem in the epidemiology of antibiotic resistance and infectious disease. For example, the sequence marked with “*” in Figure 2 shows substantial similarity to a plasmid called pBUN24, in addition to other plasmids with unknown hosts. It is clear that this plasmid shows contacts with a variety of genome clusters corresponding to different organisms, suggesting that all of these organisms can act as hosts for this plasmid.

 

Figure 2. Heatmap representing quantitative Hi-C links between plasmids (columns) and genome clusters (rows) in a human fecal metagenome. For scale see top right key (blue=no contact). Columns where more than one cell shows signal are possible instances of plasmid sharing. All genome cluster rows are near-complete genomes, e.g. have >90% completeness and <10% redundancy according to CheckM analysis.

 

In a more recent collaboration with Mick Watson’s group at the Roslin Institute, we applied ProxiMeta Hi-C to the cow rumen microbiome, a very complex microbial community. In this peer-reviewed paper, we were able to not only discover scores of novel genomes in this community, but also to profile plasmid-genome linkages for these genomes. Thus, Hi-C linkages of plasmids to genomes are robust even to very high complexity of the community.

Looking to the future: Plasmid Biology conference and more.

We have multiple exciting ongoing collaborations using Hi-C to understand the host range and biology of plasmids and other mobile elements; the best is yet to come! To see several examples of our Hi-C technology applied to this problem, you need only read the abstracts for the 2018 Plasmid Biology conference, August 5-10 at the University of Washington in Seattle.

We will be writing more about the uses of ProxiMeta and metagenomic Hi-C on this blog in the future, so stay tuned.

Lil BUB Aids in Discovery of New Bacteria

Posted on August 1, 2018 by - Hi-C, Metagenomics, ProxiMeta, Random, Science

Published author, talk show host, movie star, musician, and philanthropist—Lil BUB has now also helped to discover novel microbial life living in her gut in collaboration with AnimalBiome, KittyBiome, and Phase Genomics. Enter to sequence your cat’s microbiome in our #Meowcrobiome twitter raffle!

 

We live in an era of discovery, especially as it relates to the microbiome and how microbial diversity influences our world, our health—and even our pet’s health. To better understand the microbial life of our feline friends, Lil BUB volunteered to sequence her gut microbiome. Thanks to a recent collaboration with AnimalBiome, KittyBiome, and Phase Genomics, Lil BUB helped discover 22 new microbes living in cats which, in time, could reveal new insights into cat health and happiness.

When KittyBiome started back in 2015 with an intent to understand the cat microbiome,  Lil BUB’s owner Mike “Dude” Bridavsky provided a sample of her poop to be analyzed. Because of Lil BUB and over 1,000 other cats, KittyBiome’s microbial census will help us identify what microbes are associated with healthy cats and work towards helping cats with Inflammatory Bowel Disease (IBD), diabetes and other ailments likely to be associated with the microbiome.

 

USING GENOMICS TO FIND MICROBES

Late last year, Phase Genomics offered to analyze samples from Lil BUB and another cat, Danny (belonging to Jennifer Gardy—a microbiologist at the University of British Columbia and science TV host), using our ProxiMeta™ Hi-C Metagenomic Deconvolution platform to obtain complete microbial genomes from their samples.  This method solves a huge problem in microbiome research—how to tell apart different species when their DNA is all mixed up in one sample (imagine a thousand jigsaw puzzles mixed together).

ProxiMeta Hi-C revealed about two hundred different species of microorganisms living in Lil BUB and Danny’s poop, many of which have never been seen before. The genome sequences of the microorganisms found in these samples were analyzed using our software and other microbiome analysis tools to measure the quality of the different assembled genomes and to see if those genomes matched any known microbes (Lil BUB’s and Danny’s data are available for free on our website). Without using our ProxiMeta Hi-C platform to extract these genomes, many of them would have been undetectable and gone unseen.

Lil BUB and Danny the Cat

Phase Genomics sequenced both Lil BUB (left) and Danny’s (right) poop samples.

 

OVER 20 NEW BACTERIAL GENOMES DISCOVERED

Lil BUB being heldTogether, Lil BUB and her buddy Danny carry 22 previously undescribed bacterial species in their guts.  Lil BUB’s poop sample had 13 species and Danny’s sample had 9 species that have never before been fully sequenced or characterized.

These new bacterial species mostly belong to the order Clostridiales, and the team is currently analyzing the genomes to better characterize them. This discovery will help continue to build a database that contains cat bacteria that are new to science, so we can better identify the contributions of the microbiome to various health conditions.

This cool discovery, made with the help of Lil BUB and Danny, highlights that there’s a  universe of undiscovered microbial life out there. If we found 22 potentially novel species in only two cats, just imagine what else is out there, and what the implications might be for new ways to support and improve the health of our pets.

 

WHO ARE OUR HERO CATS?

Lil BUB is a one of a kind critter, made famous on the Internet due to her adorable genetic anomalies. She is a “perma-kitten”, which means she will stay kitten-sized and maintain kitten-like features her entire life. She has an extreme case of dwarfism, which means her limbs are disproportionately small relative to the rest of her body. Her lower jaw is significantly shorter than her upper jaw, and her teeth never grew in so her tongue is always hanging out. Lil BUB is also a polydactyl cat, meaning she has extra toes – 22 toes total!  Lil BUB and Her Dude travel all over the country raising hundreds of thousands of dollars for animals in need.

Danny, an exotic shorthair with a face much like Grumpy Cat, is equally adorable.  He is the companion cat of one of KittyBiome’s original researchers, Jennifer Gardy, and was one of the very first cats to lend his poop profile to the KittyBiome initiative.  He is a very healthy cat and his microbial profile has helped us learn what a balanced gut in cats looks like.

WHAT’S NEXT?

Phase Genomics and AnimalBiome are eager to learn more about these newly-discovered bacterial species. They hope to work with the scientific community to analyze, identify, characterize and publish these genomes, starting with exploring their identities based on 16S rRNA and other marker genes.

HOW TO GET INVOLVED

  • Help characterize the new bacteria: If you know of a researcher, scientist or cat-lover who would like to help us, we are soliciting input on the analysis that needs to be done to properly characterize and publish these genomes. Participants who contribute in a substantive manner to the project will be co-authors on the publication. All data associated with the project will be deposited into publicly available databases and we will publish the findings in open access journals, so all pet lovers can read them. We will hold a raffle to award one lucky contributor a free Hi-C sample kit from Phase Genomics. If interested, contact us at team@animalbiome.com to learn more.
  • Name the new bacteria: We’re looking for input from the community on what we should name these 22 new bacteria, so if you have any fun ideas, please drop us an email at team@animalbiome.com. The format should follow standard practices of scientific nomenclature, so it should be constructed like this: “Clostridium _________.”
  • Submit your pet’s sample for genomic research: If you don’t win the raffle and still want your pet to contribute to scientific knowledge through the identification of new bacterial species, please contact us at team@animalbiome.com. We can provide you with the details and pricing involved for us to identify new species in your cat or dog through in depth analyses like we did for Lil BUB and Danny using the Hi-C approach pioneered by Phase Genomics, which would also result in a publication.

Improving databases of the microbiome of cats (and dogs) with new bacteria like this could help us learn more about how the gut microbiome helps support the digestive health of all pets.

ENTER YOUR CAT IN OUR TWITTER RAFFLE

Phase Genomics, AnimalBiome and KittyBiome are hosting a twitter raffle where you can enter to sequence your cat’s microbiome! All you have to do is go to either the Phase Genomics’ or AnimalBiome’s original tweet of this blog, retweet it with a picture and introduction of your cat with the hashtag #Meowcrobiome. On August 8th 2018, we will randomly draw one (1) winner whose cat poop will be scientifically analyzed by Phase Genomics with ProxiMeta Hi-C to search for novel microbes, and three (3) additional winners whose cat poop will receive a Kitty Kit to have their cat’s poop analyzed by Animal Biome to compare their cat’s gut to healthy cat guts.  Send in your cat’s poop, and you too can help discover new microbial life!

LIL BUB AND DANNY’S STORY FEATURED ON GEEKWIRE PODCAST

GeekWire discussed Lil BUB, Danny, and the new bacteria found in their poop in their weekly Week in Geek podcast. Check out the full podcast on their website (the segment begins around 22:58), or play just the segment about Lil BUB and Danny below.

 

 

Uncovering the microbiome: What will you do with metagenomics?

Posted on March 1, 2018 by - Hi-C, Metagenomics, ProxiMeta, Science

In this Nature Microbiology blog post, Mick Watson shares his journey into the depths of the rumen microbiome. Read more here to learn how Phase Genomics ProxiMeta Hi-C Metagenomic Deconvolution techniques are helping investigators advance their metagenomic research in complex samples. This study successfully assembled 913 genomes and will help to improve our understanding of the microbial population in cow rumen in an unprecedented way using these new metagenomics techniques. We look forward to seeing what else comes from Microbiome 2.0. and are proud to be a part of this impressive piece of work.

Hundreds of Genomes Isolated from Single Fecal Sample with Hi-C Kit

Posted on October 18, 2017 by - Hi-C, Metagenomics, ProxiMeta, Science

 

Hi-C Kit Microbiome

A Phase Genomics Hi-C kit for any sample type are now available!

Phase Genomics recently launched its ProxiMeta™ Hi-C metagenome deconvolution kit + software
product, enabling researchers to bring this powerful technology (previously only available through the ProxiMeta service) into their own labs. A new paper posted to biorxiv describes the results of employing ProxiMeta technology to deconvolute a human gut microbiome sample.

 

In the paper, ProxiMeta was used on a single human gut microbiome sample and isolated 252 individual microbial genomes or genome fragments, with 50 of these genomes meeting the “near-complete” threshold typically used as the standard according to the CheckM tool (>90% complete, <10% contaminated). Examining the tRNA and rRNA content of the genomes found 10 to meet “high-quality” and 75 to meet “medium-quality” thresholds. Additionally, 14 of the genomes represent near-complete assemblies of novel species or strains not found in RefSeq, showing that even after many years of research, there remain numerous unknown microbes in the human gut that are discoverable with new approaches.

 

ProxiMeta’s results were compared to those achieved with MaxBin, a common tool used to perform metagenomic binning based on heuristics such as shotgun read depth and tetranucleotide profiles. MaxBin was able to create 29 near-complete genomes (cf. 50 for ProxiMeta), with only 5 meeting high-quality (cf. 10) and 44 meeting medium-quality (cf. 75) thresholds based on tRNA and rRNA content. In terms of ability to construct similar sets of near-complete genomes, ProxiMeta and MaxBin constructed 27 of approximately the same genomes, with ProxiMeta constructing an additional 32 genomes that MaxBin did not, and MaxBin constructing 9 genomes that ProxiMeta did not. ProxiMeta’s assembled genomes also exhibited a much lower amount of contamination than MaxBin’s assembled genomes, with 43% of MaxBin’s assemblies exceeding the 10% contamination limit that is the typical standard for genome quality, compared to only 2% of ProxiMeta’s assemblies.

 

Other results unique to ProxiMeta include the discovery of near-complete genomes for 14 novel species or strains and various associations of plasmids with their hosts. Of the 14 novel genomes, 10 appear to be of the class Clostridia, a common group of gut microbes that are poorly characterized due to their difficulty to culture.  ProxiMeta also assigned 137 contigs containing plasmid content to a cluster and identified candidate plasmid sequences as being present across multiple, distantly related bacteria. For example, ProxiMeta placed a known megaplasmid into an assembly for Eubacterium eligens that included homologous plasmid sequences placed into several other genomes, suggesting either the presence of the megaplasmid into other species, or variants of the megaplasmid being found on other mobile elements spread through the metagenome.

 

The depth of the resulting data and results offers the opportunity to learn much more about this microbial niche and research continues to unlock new discoveries about this community. Phase Genomics is thrilled to be able to offer all researchers the same new power to dig deeper into their mixed samples than ever before, especially now with a product that puts the power of discovery in their hands.

 

To learn more about ordering our kits or services, just send us an email at info@phasegenomics.com