An exclusive metabolic niche enables strain engraftment in the gut microbiota

Nature

Volumn 557, Issue 7705, 2018, Pages 434-438

  Shepherd, Elizabeth Stanley ^a,b   Deloache, William C ^b   Pruss, Kali M ^a   Whitaker, Weston R ^b   Sonnenburg, Justin L ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Novome Biotechnologies   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYSACCHARIDE; PORPHYRAN; SEPHAROSE; UNCLASSIFIED DRUG;

ABUNDANCE; BACTERIUM; DIGESTIVE SYSTEM; MARINE ENVIRONMENT; METABOLISM; MICROBIAL ECOLOGY; MICROORGANISM; NICHE; NUTRIENT AVAILABILITY; POLYSACCHARIDE; PROBIOTICS;

ANIMAL TISSUE; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM CULTURE; BACTERIUM ISOLATION; BACTEROIDES; COISOGENIC STRAIN; COMMUNITY STRUCTURE; ECOLOGICAL NICHE; FEMALE; GENE CLUSTER; GENE LOCUS; INTESTINE FLORA; MALE; MOUSE; NONHUMAN; NUTRIENT AVAILABILITY; POPULATION ABUNDANCE; PRIORITY JOURNAL; ANALOGS AND DERIVATIVES; ANIMAL; COLON; FECAL MICROBIOTA TRANSPLANTATION; GROWTH, DEVELOPMENT AND AGING; HUMAN; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; ADULT; ANIMAL EXPERIMENT; CELL THERAPY; CONTROLLED STUDY; ENGRAFTMENT; LETTER; METABOLIC PARAMETERS; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NUTRIENT; PREDICTION;

BACTERIA (MICROORGANISMS); BACTEROIDES; MUS;

ANIMALS; BACTEROIDES; COLON; FECAL MICROBIOTA TRANSPLANTATION; FEMALE; GASTROINTESTINAL MICROBIOME; HUMANS; MALE; MICE; SEPHAROSE;

EID: 85047558885     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/s41586-018-0092-4     Document Type: Article

References (27)

1. Faith, J. J. et al. The long-term stability of the human gut microbiota. Science 341, 1237439 (2013).
2. Frese, S. A., Hutkins, R. W. & Walter, J. Comparison of the colonization ability of autochthonous and allochthonous strains of lactobacilli in the human gastrointestinal tract. Adv. Microbiol. 2, 399-409 (2012).
3. Maldonado-Gómez, M. X. et al. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe 20, 515-526 (2016).
4. Lee, S. M. et al. Bacterial colonization factors control specificity and stability of the gut microbiota. Nature 501, 426-429 (2013).
5. Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485-498 (2009).
6. Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337-341 (2011).
7. Lawley, T. D. et al. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog. 8, e1002995 (2012).
8. Stecher, B. et al. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog. 6, e1000711 (2010).
9. Ratner, M. Seres's pioneering microbiome drug fails mid-stage trial. Nat. Biotechnol. 34, 1004-1005 (2016).
10. Ericsson, A. C., Personett, A. R., Turner, G., Dorfmeyer, R. A. & Franklin, C. L. Variable colonization after reciprocal fecal microbiota transfer between mice with low and high richness microbiota. Front. Microbiol. 8, 196 (2017).
11. Landy, J. et al. Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis. Sci. Rep. 5, 12955 (2015).
12. Whitaker, W. R., Shepherd, E. S. & Sonnenburg, J. L. Tunable expression tools enable single-cell strain distinction in the gut microbiome. Cell 169, 538-546 (2017).
13. Sonnenburg, E. D. et al. Diet-induced extinctions in the gut microbiota compound over generations. Nature 529, 212-215 (2016).
14. Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).
15. Hehemann, J. H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908-912 (2010).
16. David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563 (2014).
17. Sonnenburg, J. L. et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307, 1955-1959 (2005).
18. Xu, J. et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol. 5, e156 (2007).
19. Sonnenburg, E. D. et al. Specificity of polysaccharide use in intestinal Bacteroides species determines diet-induced microbiota alterations. Cell 141, 1241-1252 (2010).
20. Hehemann, J. H., Kelly, A. G., Pudlo, N. A., Martens, E. C. & Boraston, A. B. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. Proc. Natl Acad. Sci. USA 109, 19786-19791 (2012).
21. Drake, J. A. Community-assembly mechanics and the structure of an experimental species ensemble. Am. Nat. 137, 1-26 (1991).
22. Fukami, T. historical contingency in community assembly: integrating niches, species pools, and priority effects. Annu. Rev. Ecol. Evol. Syst. 46, 1-23 (2015).
23. Chandran, S. & Shapland, E. in Synthetic DNA Vol. 1472 (ed. Hughes, R. A.) 187-192 (Humana, New York, 2017).
24. Martens, E. C., Chiang, H. C. & Gordon, J. I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4, 447-457 (2008).
25. Simon, R., Priefer, U. & Pühler, A. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. Nat. Biotechnol. 1, 784-791 (1983).
26. Ostrov, N. et al. Design, synthesis, and testing toward a 57-codon genome. Science 353, 819-822 (2016).
27. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).