Andrew Goodman, PhD


Research Departments & Organizations

Microbial Pathogenesis: Goodman Lab

Diabetes Research Center

Yale Cancer Center: Virus and Other Infection-associated Cancers

Yale Microbial Sciences Institute

Office of Cooperative Research

Research Interests

Bacteria; Genomics; Germ-Free Life; Microbial Consortia; Microbiota; Symbiosis

Research Summary

Each of us harbors an enormous microbial community. In the gut, these microbes form a metabolic organ whose genes outnumber those in the human genome by over 100-fold, and whose composition can change overnight. It is becoming increasingly clear that variation in these communities has important consequences for health. The overall goal of the lab is to dissect the mechanisms that commensal gut microbes use to compete, cooperate, and antagonize each other in the gut and to explore how microbiome variation impacts our response to external perturbations, including pathogenic infection and medical drugs.

Specialized Terms: Microbiota; Microbiome; Genomics; Gnotobiotic; Germfree; Symbiosis; Gut; Flora; Bacteria; Pathogen

Extensive Research Description

My laboratory works to create new approaches for understanding the contributions of the human gut microbiome to health.

New strategies for mechanistic study of the microbiome (Lim, Cell 2017; Goodman, PNAS 2011; Goodman, Cell Host & Microbe 2009). We have created new approaches for microbiome manipulation, including insertion sequencing (INSeq), personalized culture collections, and systems for tuning microbiome gene expression in the gut. INSeq combines transposon mutagenesis with high-throughput sequencing, enabling the first largescale screen for fitness determinants of a human symbiont in a mammalian host. These approaches have been extended to symbionts and pathogens of plants, insects, humans, and other animals. Together these tools open the door to measuring fundamental aspects of host-microbiome interactions, such as dose-response and time. 

Cooperation and competition in the microbiome (Wexler, PNAS 2016; Degnan, Cell Host & Microbe 2014; Faith, Science 2013). We’ve applied these tools to uncover new interactions between gut microbes. In one example (Degnan), we identify a class of small molecules that commensals exchange in the gut and how this molecular currency determines commensal fitness. These tools also revealed how gut commensals kill each other on contact (Wexler).

Mechanisms of host-microbiome interaction (Perry, Nature 2016; Cullen, Science 2015; Palm, Cell 2014). We’ve also used these approaches to understand host-microbiome interaction. For example, we discovered the mechanisms that determine commensal stability during inflammation (Cullen).

Clinical Trials

Conditions Study Title
Children's Health, Diseases of the Respiratory Systems Microbiome Acquisition and Progression of Inflammation and Airway Disease in Infants and Children With Cystic Fibrosis

Selected Publications

See list of PubMed publications

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Contact Info

Andrew Goodman, PhD
Mailing Address
Microbial PathogenesisYale West Campus
PO Box 27388

West Haven, CT 06516

Goodman lab