News

Nick Bohmann Joins the Lab

Nick Bohmann joins the lab as a Ph.D. student from the Molecular Engineering and Sciences program at UW. Nick graduated from Virginia Tech in 2019 with B.S. in Biological Systems Engineering. His research interests include genome-scale metabolic modeling and ‘omics based computational biology, specifically related to the human gut microbiome. Nick’s work in the lab will focus on using computational tools to enhance the predictive capability of models of the…

James Johnson Joins the Lab

James Johnson joins the lab as a bioengineering PhD student at the University of Washington (UW). James earned his BS in Chemical Engineering from Texas A&M University. After graduating, he took a job as an R&D Associate Engineer at PepsiCo. After three years of applied science and engineering at PepsiCo, James decided to apply to the Bioengineering PhD program at UW in Seattle so that he could return to working…

Keystone Taxa Indispensable for Microbiome Recovery

How can we harness successional ecology to quickly repair antibiotic-damaged gut microbiota? ISB Assistant Professor Dr. Sean Gibbons wrote this commentary for the journal Nature Microbiology detailing recent research that answers that question. Click the link to read the story (link will open as a new window). Illustration by Allison Kudla, PhD / ISB. 

Harnessing our inner ecology to track and treat disease

ISB’s virtual course and symposium focusing on the microbiome and its future role in precision medicine will take place on October 15 and 16. The event’s website went live earlier this week. The virtual course will be taught by Sean Gibbons, Christian Diener, Tomasz Wilmanski, Noa Rappaport, Alex Carr, Priyanka Baloni and Nathan Price. Symposium speakers are Jason Papin (University of Virginia), Ines Thiele (National University of Ireland, Galway), Thomas…

Reshaping STEM Education Toward a More Equitable Future for Students

ISB Assistant Professor Dr. Sean Gibbons recently participated in a virtual event titled “Reshaping STEM Education Toward Equitable Futures for Washington Students.” Panelists shared their insights about how to leverage this complex moment to reshape STEM education toward equity, sustainability, and prosperity for Washington state’s students — especially those furthest from opportunity.

Bacterial tug of war between prevotella and bacteroides -- gut microbiome

It’s ‘Either/Or’ for Two Common Gut Microbiome Genera, and Switching Teams Is Tougher Than Expected

There is a dichotomy between Bacteroides- and Prevotella-dominated guts — two common gut bacterial genera — and there is a significant barrier when it comes to transitioning from one to the other.

Dr. Christian Diener, postdoc in ISB's Gibbons Lab.

New Modeling Tool Allows Microbiome Researchers to Map Community Ecology to Ecosystem Function

A promising new open-source metabolic modeling tool provides microbiome researchers a path forward in predicting ecosystem function from community structure. News of the software package, called MICOM, was developed in part by researchers in ISB’s Gibbons Lab, and its uses were published in the journal mSystems.

Using Blood to Predict Gut Microbiome Diversity

Predicting the alpha diversity of an individual’s gut microbiome is possible by examining metabolites in the blood. The robust relationship between host metabolome and gut microbiome diversity opens the door for a fast, cheap and reliable blood test to identify individuals with low gut diversity.

Use and abuse of correlations

We recently published a Perspective Article in the ISME Journal on the ‘Use and abuse of correlation analyses in microbial ecology.’ In this piece, we highlight the pitfalls of inferring microbe-microbe interactions from sequencing data. The lead author, Alex Carr, wrote a blog post titled ‘Inferring microbial interactions from relative abundance: not as easy as you would think’ detailing his inspiration for writing this perspective. You can check out the…

Seeing the microbiome through a host lens

Sean recently published a commentary in the journal mSystems that outlines a vision of defining ‘microbiome health’ through a host lens: i.e. determining what exact components of the variation in the microboita influence host phenotypes. Much of the variation in the microbiome likely has nothing to do with the health state of the host, but loss/gain of critical diversity and/or functionality can have a major impact on host health. To…

ISB Microbiome Researcher Dr. Sean Gibbons Featured in TIME Article

Freaked out about a “germy” bathroom? You don’t need to be. ISB Assistant Professor and microbiome researcher Dr. Sean Gibbons was featured prominently in an article, headlined “The Germiest Place in your Bathroom Isn’t Your Toilet,” published online by TIME. 

Microbiome Stress Project’s first publication

Microbial communities are highly sensitive to their environments, which makes studying them under heterogeneous conditions difficult. Environmental perturbations (stressors) generate spatiotemporal heterogeneity in natural systems. While large databases of natural ecosystems exist (e.g. the Earth Microbiome Project or the Human Microbiome Project), there are no databases that catalog microbial ecosystems subjected to applied environmental stress. The Microbiome Stress Project (MSP) was established to build such a database and perform a…

Dr. Sean Gibbons

All About the Human Microbiome

The human microbiome is a relatively new area of research, and there are numerous questions surrounding it. What is the human microbiome? Can we change it? Does it make us sick? Keep us well? ISB Assistant Professor and microbiome researcher Dr. Sean Gibbons answers these questions — and many more.

Sushmita Patwardhan Joins the Lab

Dr. Sushmita Patwardhan joins the Gibbons Lab as a postdoctoral fellow at the Institute for Systems Biology. Dr. Patwardhan recently completed her PhD in marine microbial ecology at Rutgers University, supervised by Prof. Costantino Vetriani. Her work involved the cultivation of bacteria from shallow marine vents and the characterization of these complex communities by integrating multi-omics data, field studies, and lab-based experiments. Dr. Patwardhan will apply her ecological expertise to…

Alex Carr Joins the Lab

Alex Carr will join the Institute for Systems Biology for his PhD work, co-advised by Nitin Baliga and Sean Gibbons. Alex is a graduate student in the Molecular Engineering Program at the University of Washington. Prior to starting graduate school at UW, Alex worked in Adam Arkin’s lab at UC Berkeley, characterizing species-species interactions in synthetic gut bacterial communities. For his dissertation, Alex will pursue novel experimental and computational approaches…

Global Microbiome Conservancy

The Global Microbiome Conservancy is a non-profit collaboration between scientists and communities around the world, unified around a common goal: to collect and preserve the full biodiversity of human gut microbes for future generations. The work of the conservancy is centered on four core goals: Conservation We dedicate our efforts to conserve an invisible, intimate and crucial biodiversity of the human body: the gut microbiome. By culturing, isolating and storing…

Spore-Forming Bacteria Widely Shared Across Humans

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome…

ISB's Dr. Sean Gibbons on the importance of the human microbiome

“This new organ that we’re coming to recognize as the microbiome is part and parcel to the functionality of the whole system, and if it breaks down, if it starts to fall apart, we start to get sick,” said Dr. Sean Gibbons, ISB’s newest faculty member, in a WGBH Forum Network presentation.