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Culture-enriched community profiling improves resolution of the vertebrate gut microbiota.

Publication ,  Journal Article
Goldman, SL; Sanders, JG; Yan, W; Denice, A; Cornwall, M; Ivey, KN; Taylor, EN; Gunderson, AR; Sheehan, MJ; Mjungu, D; Lonsdorf, EV; Pusey, AE ...
Published in: Molecular ecology resources
January 2022

Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.

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Published In

Molecular ecology resources

DOI

EISSN

1755-0998

ISSN

1755-098X

Publication Date

January 2022

Volume

22

Issue

1

Start / End Page

122 / 136

Related Subject Headings

  • Pan troglodytes
  • Mice
  • Lizards
  • Gastrointestinal Microbiome
  • Evolutionary Biology
  • Bacteria
  • Animals
  • 06 Biological Sciences
 

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Goldman, S. L., Sanders, J. G., Yan, W., Denice, A., Cornwall, M., Ivey, K. N., … Moeller, A. H. (2022). Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. Molecular Ecology Resources, 22(1), 122–136. https://doi.org/10.1111/1755-0998.13456
Goldman, Samantha L., Jon G. Sanders, Weiwei Yan, Anthony Denice, Margaret Cornwall, Kathleen N. Ivey, Emily N. Taylor, et al. “Culture-enriched community profiling improves resolution of the vertebrate gut microbiota.Molecular Ecology Resources 22, no. 1 (January 2022): 122–36. https://doi.org/10.1111/1755-0998.13456.
Goldman SL, Sanders JG, Yan W, Denice A, Cornwall M, Ivey KN, et al. Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. Molecular ecology resources. 2022 Jan;22(1):122–36.
Goldman, Samantha L., et al. “Culture-enriched community profiling improves resolution of the vertebrate gut microbiota.Molecular Ecology Resources, vol. 22, no. 1, Jan. 2022, pp. 122–36. Epmc, doi:10.1111/1755-0998.13456.
Goldman SL, Sanders JG, Yan W, Denice A, Cornwall M, Ivey KN, Taylor EN, Gunderson AR, Sheehan MJ, Mjungu D, Lonsdorf EV, Pusey AE, Hahn BH, Moeller AH. Culture-enriched community profiling improves resolution of the vertebrate gut microbiota. Molecular ecology resources. 2022 Jan;22(1):122–136.
Journal cover image

Published In

Molecular ecology resources

DOI

EISSN

1755-0998

ISSN

1755-098X

Publication Date

January 2022

Volume

22

Issue

1

Start / End Page

122 / 136

Related Subject Headings

  • Pan troglodytes
  • Mice
  • Lizards
  • Gastrointestinal Microbiome
  • Evolutionary Biology
  • Bacteria
  • Animals
  • 06 Biological Sciences