Bacteria; Germ-Free Life; Symbiosis; Genomics; Microbial Consortia; Microbiota
Microbial Pathogenesis: Goodman Lab
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
How do the enormous microbial
populations that accompany us through life influence our health? Much of what
we consume, both beneficial and noxious, is first encountered and processed by
the human gut microbiota, a metabolic organ of 10-100 trillion cells that
encodes an enormous genetic repository strikingly different from our human
genomes in its content, extent of inter-individual variation, and plasticity. A
lifelong course of environmental exposures, selection, and competition shapes
the structure and function of these communities: this is a central issue in
interpreting microbial diversity, a major challenge in human microbiome
projects, and a process that we know almost nothing about.
Due to the availability of massively parallel DNA sequencing and new techniques for high-throughput metabolite profiling, our ability to describe these communities has exploded: this surge of data far outpaces existent strategies to mechanistically dissect the relationship between microbiota composition and function. Consequently, fundamental questions connecting microbial genome content to function remain unexplored. For example, do human symbiotic microbes, like their pathogenic counterparts, possess dedicated mechanisms critical for survival in vivo or is their existence largely passive or based on highly redundant, interchangeable pathways? Does community structure influence this map of genetic requirements? What host or environmental factors play dominant roles in this selective process? These questions are timely because a role for the gut microbiota is an emergent theme in our understanding of many metabolic disorders and infectious diseases.
To this end, we developed a generally applicable, new experimental approach (insertion sequencing, or INSeq) for functional genome-wide analysis of organisms for which a genome sequence (and potentially little else) is known. This approach is based on modification of the broad host-range, randomly integrating transposable element mariner to capture short fragments of adjacent genomic DNA. Massively parallel sequencing of these captured genomic fragments from tens of thousands of mariner insertion strains of a given bacterial species produces a high-resolution map of the precise location and relative abundance of each transposon in the population. Selection changes the representation of transposon mutants, thereby allowing identification of genes and pathways that are key to fitness under the conditions being examined. We first applied this system to the prominent human gut symbiont Bacteroides thetaiotaomicron, in vitro and in vivo in wildtype and genetically manipulated gnotobiotic mice, in the presence or absence of defined communities of other human gut symbionts. The results clearly indicated that symbiont survival in the gut is in no way a ‘passive’ affair; instead, we identified hundreds of genes that are absolutely required for fitness in vivo. These genes (i) include, but extend far beyond, those required for maximal growth in vitro; (ii) are not a random sampling of the genome, but instead are enriched in specific functional categories; and (iii) often display a community context-dependent impact on fitness, such that they are required by B. thetaiotaomicron as a member of some defined microbial communities but not others. These studies also highlighted an unexpected aspect of selection and competition in this system—the vitamin B12 and its analogs (corrinoids), studied for over 50 years for their role in human health, may be key mediators of microbial community structure in the mammalian gut. Future studies are focused on understanding corrinoid exchange in the gut and applying INSeq to other prominent human gut symbionts.
For many microbial communities, the great majority of organisms have not been cultured in the laboratory. We’re developing high-throughput approaches for assembling large human gut culture collections from single healthy or diseased individuals, with the goal of re-uniting discrete components of these communities in germfree mice. These personalized culture collections provide a new platform for studying resource sharing and competition in the gut.
Human symbionts inject and neutralize antibacterial toxins to persist in the gut.
Wexler, A.W., Bao, Y., Whitney, J.C., Bobay, L-M., Xavier, J.B., Schofield, W.B., Barry, N.A., Russell, A.B., Tran, B.Q., Goo, Y., Goodlett, D.R., Ochman, H.O., Mougous, J.D., and Goodman, A.L. Proceedings of the National Academy of Sciences 133(13) p3639-44 (2016).
Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation.
Cullen, T.W., Schofield, W.B., Barry, N.A., Putnam, E.E., Rundell, E.A., Trent, M.S., Degnan, P.H., Booth, C.J., Yu, H., and Goodman, A.L. Science 347(6218) p170-175 (2015).
Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease.
Palm, N.W., de Zoete, M.R., Cullen, T.W., Barry, N.A., Stefanowski, J., Hao, L., Degnan, P.H., Hu, J., Peter, I., Zhang, W., Ruggiero, E., Cho, J.H., Goodman, A.L., and Flavell, R.A. Cell 158(5) p1000-1010 (2014).
Human gut microbes use multiple transporters to distinguish vitamin B12 analogs and compete in the gut.
Degnan, P.H., Barry, N.A., Mok, K.C., Taga, M.E., and Goodman, A.L. Cell Host & Microbe 15 p47-57 (2014).
Experimental approaches for defining functional roles of microbes in the human gut.
Dantas, G., Sommer, M.O.A., Degnan, P.H., and Goodman, A.L. Annual Reviews Microbiology 67 p459-75 (2013).
Full List of PubMed Publications
- Wexler AG, Goodman AL: An insider's perspective: Bacteroides as a window into the microbiome. Nat Microbiol. 2017 Apr 25; 2017 Apr 25. PMID: 28440278
- Lim B, Zimmermann M, Barry NA, Goodman AL: Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. Cell. 2017 Apr 20. PMID: 28431252
- Raymann K, Moeller AH, Goodman AL, Ochman H: Unexplored Archaeal Diversity in the Great Ape Gut Microbiome. mSphere. 2017 Jan-Feb; 2017 Feb 22. PMID: 28251182
- Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, Petersen KF, Kibbey RG, Goodman AL, Shulman GI: Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome. Nature. 2016 Jun 9. PMID: 27279214
- 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. Proc Natl Acad Sci U S A. 2016 Mar 29; 2016 Mar 8. PMID: 26957597
- Amiram M, Haimovich AD, Fan C, Wang YS, Aerni HR, Ntai I, Moonan DW, Ma NJ, Rovner AJ, Hong SH, Kelleher NL, Goodman AL, Jewett MC, Söll D, Rinehart J, Isaacs FJ: Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids. Nat Biotechnol. 2015 Dec; 2015 Nov 16. PMID: 26571098
- Tan Y, Zanoni I, Cullen TW, Goodman AL, Kagan JC: Mechanisms of Toll-like Receptor 4 Endocytosis Reveal a Common Immune-Evasion Strategy Used by Pathogenic and Commensal Bacteria. Immunity. 2015 Nov 17; 2015 Nov 3. PMID: 26546281
- Brooks JF 2nd, Gyllborg MC, Cronin DC, Quillin SJ, Mallama CA, Foxall R, Whistler C, Goodman AL, Mandel MJ: Global discovery of colonization determinants in the squid symbiont Vibrio fischeri. Proc Natl Acad Sci U S A. 2014 Dec 2; 2014 Nov 17. PMID: 25404340
- Degnan PH, Taga ME, Goodman AL: Vitamin B12 as a modulator of gut microbial ecology. Cell Metab. 2014 Nov 4; 2014 Nov 4. PMID: 25440056
- Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, Degnan PH, Hu J, Peter I, Zhang W, Ruggiero E, Cho JH, Goodman AL, Flavell RA: Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell. 2014 Aug 28. PMID: 25171403
- Russell AB, Wexler AG, Harding BN, Whitney JC, Bohn AJ, Goo YA, Tran BQ, Barry NA, Zheng H, Peterson SB, Chou S, Gonen T, Goodlett DR, Goodman AL, Mougous JD: A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. Cell Host Microbe. 2014 Aug 13; 2014 Jul 25. PMID: 25070807
- Gao B, Lara-Tejero M, Lefebre M, Goodman AL, Galán JE: Novel components of the flagellar system in epsilonproteobacteria. MBio. 2014 Jun 24; 2014 Jun 24. PMID: 24961693
- Degnan PH, Barry NA, Mok KC, Taga ME, Goodman AL: Human gut microbes use multiple transporters to distinguish vitamin B₁₂ analogs and compete in the gut. Cell Host Microbe. 2014 Jan 15. PMID: 24439897
- Goodman AL, Wu M, Gordon JI: Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nat Protoc. 2011 Nov 17; 2011 Nov 17. PMID: 22094732
- Kwon HL, Ortiz B, Swaner R, Shoemaker K, Jean-Louis B, Northridge ME, Vaughan RD, Marx T, Goodman A, Borrell LN, Nicholas SW, Harlem Children's Zone Asthma Initiative.: Childhood asthma and extreme values of body mass index: the Harlem Children's Zone Asthma Initiative. J Urban Health. 2006 May. PMID: 16739045