News

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.

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.

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…

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…

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…