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…
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.
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 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…
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…
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…
“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.
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.
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…
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…
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…
