Widespread extinctions of co-diversified primate gut bacterial symbionts from humans

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Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. / Sanders, Jon G.; Sprockett, Daniel D.; Li, Yingying et al.
In: Nature Microbiology, Vol. 8, No. 6, 06.2023, p. 1039-1050.

Research output: Contribution to journalArticlepeer-review

HarvardHarvard

Sanders, JG, Sprockett, DD, Li, Y, Mjungu, D, Lonsdorf, EV, Ndjango, J-BN, Georgiev, AV, Hart, JA, Sanz, CM, Morgan, DB, Peeters, M, Hahn, BH & Moeller, AH 2023, 'Widespread extinctions of co-diversified primate gut bacterial symbionts from humans', Nature Microbiology, vol. 8, no. 6, pp. 1039-1050. https://doi.org/10.1038/s41564-023-01388-w

APA

Sanders, J. G., Sprockett, D. D., Li, Y., Mjungu, D., Lonsdorf, E. V., Ndjango, J.-B. N., Georgiev, A. V., Hart, J. A., Sanz, C. M., Morgan, D. B., Peeters, M., Hahn, B. H., & Moeller, A. H. (2023). Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nature Microbiology, 8(6), 1039-1050. https://doi.org/10.1038/s41564-023-01388-w

CBE

Sanders JG, Sprockett DD, Li Y, Mjungu D, Lonsdorf EV, Ndjango J-BN, Georgiev AV, Hart JA, Sanz CM, Morgan DB, et al. 2023. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nature Microbiology. 8(6):1039-1050. https://doi.org/10.1038/s41564-023-01388-w

MLA

VancouverVancouver

Sanders JG, Sprockett DD, Li Y, Mjungu D, Lonsdorf EV, Ndjango JBN et al. Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. Nature Microbiology. 2023 Jun;8(6):1039-1050. Epub 2023 May 11. doi: 10.1038/s41564-023-01388-w

Author

Sanders, Jon G. ; Sprockett, Daniel D. ; Li, Yingying et al. / Widespread extinctions of co-diversified primate gut bacterial symbionts from humans. In: Nature Microbiology. 2023 ; Vol. 8, No. 6. pp. 1039-1050.

RIS

TY - JOUR

T1 - Widespread extinctions of co-diversified primate gut bacterial symbionts from humans

AU - Sanders, Jon G.

AU - Sprockett, Daniel D.

AU - Li, Yingying

AU - Mjungu, Deus

AU - Lonsdorf, Elizabeth V.

AU - Ndjango, Jean-Bosco N.

AU - Georgiev, Alexander V.

AU - Hart, John A.

AU - Sanz, Crickette M.

AU - Morgan, David B.

AU - Peeters, Martine

AU - Hahn, Beatrice H.

AU - Moeller, Andrew H.

PY - 2023/6

Y1 - 2023/6

N2 - Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.

AB - Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.

U2 - 10.1038/s41564-023-01388-w

DO - 10.1038/s41564-023-01388-w

M3 - Article

VL - 8

SP - 1039

EP - 1050

JO - Nature Microbiology

JF - Nature Microbiology

SN - 2058-5276

IS - 6

ER -