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Representative Publications

Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL. Infection leaves a genetic and functional mark on the gut population of a commensal bacterium. Cell Host Microbe. 2023 May 10;31(5):811-826.e6. doi: 10.1016/j.chom.2023.04.005. Epub 2023 Apr 28. PubMed PMID: 37119822; PubMed Central PMCID: PMC10197903.

Bao Y, Verdegaal AA, Anderson BW, Barry NA, He J, Gao X, Goodman AL. A Common Pathway for Activation of Host-Targeting and Bacteria-Targeting Toxins in Human Intestinal Bacteria. mBio. 2021 Aug 31;12(4):e0065621. doi: 10.1128/mBio.00656-21. Epub 2021 Aug 31. PubMed PMID: 34465018; PubMed Central PMCID: PMC8406203.

Zimmermann M*, Zimmermann-Kogadeeva M*, Wegmann R, Goodman AL: Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature. 2019 Jun 3. doi: 10.1038/s41586-019-1291-3. PMID: 31158845 (* equal contribution)

Zimmermann M*, Zimmermann-Kogadeeva M*, Wegmann R, Goodman AL: Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science. 2019 Feb 8;363(6427). pii: eaat9931. doi: 10.1126/science.aat9931. Epub 2019 Feb 7. PMID: 30733391 (* equal contribution)

Wexler AG, Schofield WB, Degnan PH, Folta-Stogniew E, Barry NA, Goodman AL: Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins. ELife. 2018 Sep 18;7. pii: e37138. doi: 10.7554/eLife.37138. PMID: 30226189

Schofield WB*, Zimmermann-Kogadeeva M*, Zimmermann M, Barry NA, Goodman AL: The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut. Cell Host Microbe. 24(1) p120-132 (2018). PMID: 30008292 (* equal contribution)

Lim B, Zimmermann M, Barry NA, Goodman AL: Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. Cell. 169(3) p547-558 (2017). PMID: 28431252

Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL: Human symbionts inject and neutralize antibacterial toxins to persist in the gut. PNAS. 133(13) p3638-44 (2016). PMID: 26957597

Cullen TW, Schofield WB, Barry NA, Putnam EE, Rundell EA, Trent MS, Degnan PH, Booth CJ, Yu H, Goodman AL: Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation. Science. 347(6218) p170-175 (2015). PMID: 25574022

Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, Gordon JI: Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. PNAS. 108(15) p6252-6257 (2011). PMID: 21436049

Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI: Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe. 6(3) p279-289 (2009). PMID: 19748469

Goodman AL, Kulasekara B, Rietsch A, Boyd D, Smith RS, Lory S: A signaling network reciprocally regulates genes associated with acute infection and chronic persistence in Pseudomonas aeruginosa. Dev Cell. 7(5) p745-754 (2004). PMID: 15525535

Recent Reviews

Wexler AG, Goodman AL: An insider's perspective: Bacteroides as a window into the microbiome. Nat Microbiol. 2:17026 p1-11 (2017). PMID: 28440278

Culp EJ, Goodman AL. Cross-feeding in the gut microbiome: Ecology and mechanisms. Cell Host Microbe 12;31(4):485-499 (2023). PMID: 37054671.

Verdegaal AA, Goodman AL. Integrating the gut microbiome and pharmacology. Science Translational Medicine 16(732):eadg8357 (2024). PMID: 38295186