News

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…

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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…

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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. 

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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…

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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.

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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…

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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…

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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…

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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…

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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.

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Dr. Sean Gibbons joins ISB faculty as WRF Distinguished Investigator

Dr. Sean Gibbons has joined ISB as our newest faculty member. Gibbons’ new position brings a number of changes, including relocating to the Pacific Northwest from the Northeast. Read on for a Q&A with Gibbons that sheds light on his research career to date, areas of study and even a hidden talent.

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Microbiome Stress Project

The Gibbons Group Joins the Microbiome Stress Project The lab will join researchers at Duke University, the University of New Hampshire, and Montana State University to conduct a large-scale meta-analysis of how environmental stressors impact microbial communities. Prior surveys, like the Earth and Human Microbiome Projects, have established a baseline for healthy ecosystems across the planet. The Microbiome Stress Project will focus on ecological resistance and resilience of natural microbial…

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Christian Diener Joins the Lab

Christian Diener will join the Institute for Systems Biology as the Washington Research Foundation Distinguished Postdoctoral Fellow in the Gibbons Lab. Christian is a computational biologist who has worked extensively on yeast systems biology and has recently moved into studying the human microbiome. He completed his PhD in systems biology at the Max Plank Institute for Molecular Genetics and is currently working at the National Institute for Genome Medicine in…

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Correcting Batch Effects in Microbiome Data

Batch Effects in 16S Datasets Complicate Cross-Study Comparisons High-throughput data generation platforms, like mass-spectrometry, microarrays, and second-generation sequencing are susceptible to batch effects due to run-to-run variation in reagents, equipment, protocols, or personnel. Currently, batch correction methods are not commonly applied to microbiome sequencing datasets. In this paper, we compare different batch-correction methods applied to microbiome case-control studies. We introduce a model-free normalization procedure where features (i.e. bacterial taxa) in…

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