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Cospeciation of gut microbiota with hominids

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Science  22 Jul 2016:
Vol. 353, Issue 6297, pp. 380-382
DOI: 10.1126/science.aaf3951
  • Fig. 1 Cospeciation between gut bacteria and hominids.

    Inset contains a phylogeny showing the relationships among humans and the African apes. (A) Maximum-likelihood phylogeny of a clade of Bacteroidaceae lineages that codiversified with the African apes but that was lost from the lineage leading to humans. In (A) and subsequent panels, black dots denote nodes supported in >50% of bootstrap replicates, colors correspond to the inset and denote the host species from which each bacterial lineage was recovered, and percentages indicate the percent of host individuals from which each clade was recovered. (B) Maximum-likelihood phylogeny of a clade of Bacteroidaceae lineages that codiversified with the African apes but that was lost from the lineage leading to humans. Note that this Bacteroidaceae lineage bifurcated in an ancestor of chimpanzees and bonobos, giving rise to two, paralogous cospeciating bacterial lineages. (C) Maximum-likelihood phylogeny of a Bacteroidaceae clade that cospeciated with humans, chimpanzees, and bonobos. No gorilla-derived representatives of this clade were recovered. (D) Inferred relationships among Bifidobacteriaceae gyrB sequences recovered from humans and African apes. Black asterisk indicates the transfer of a Bifidobacterium adolescentis relative from bonobos into gorillas.

  • Fig. 2 Bacterial time scale for hominid evolution.

    (A) Divergence times of Hominidae species estimated from Bacteroidaceae and Bifidobacteriaceae gyrB sequences in BEAST. Error bars represent SDs of the mean divergence times estimated from each clade that cospeciated with Hominids. (B) Color-coded trend lines indicate rates of synonymous site divergence of gyrB in each bacterial clade displaying evidence of cospeciation, the host mitochondrial NADH1 (mtNADH1) gene, and the host nuclear topoisomerase I gene (TOPO1). Trend lines correspond to bacterial clades depicted in Figs. 1 and 2, and named bacterial species for each clade are shown when available.

Supplementary Materials

  • Cospeciation of gut microbiota with hominids

    Andrew H. Moeller, Alejandro Caro-Quintero, Deus Mjungu, Alexander V. Georgiev, Elizabeth V. Lonsdorf, Martin N. Muller, Anne E. Pusey, Martine Peeters, Beatrice H. Hahn, Howard Ochman

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S7
    • Captions for tables S1 to S4
    • Captions for Data files S1 to S11

    Additional Data

    Tables S1

    Table S1. Unique identifiers of the fecal samples analyzed, their corresponding metadata, and their barcode sequences used for Illumina multiplexing.

    Table S2. Read counts of Bacteroidaceae strains recovered from each fecal sample. Each row represents a unique gyrB strain and each column represents a fecal sample listed in Table S1.

    Table S3. Read counts of Bifidobacteriaceae strains recovered from each fecal sample. Each row represents a unique gyrB strain and each column represents a fecal sample listed in Table S1.

    Table S4. Read counts of Lachnospiraceae strains recovered from each fecal sample. Each row represents a unique gyrB strain and each column represents a fecal sample listed in Table S1.

    Data S1

    Supplementary File 1. FASTA file of the quality- and abundance-filtered Bacteroidaceae sequences recovered from humans, chimpanzees, bonobos, and gorillas.

    Supplementary File 2. FASTA file of the quality- and abundance-filtered Bifidobacteriaceae sequences recovered from humans, chimpanzees, bonobos, and gorillas.

    Supplementary File 3. FASTA file of the quality- and abundance-filtered Lachnospiraceae sequences recovered from humans, chimpanzees, bonobos, and gorillas.

    Supplementary File 4. Newick file containing the phylogeny of Bacteroidaceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate bootstrap support. Maximum Likelihood phylogeny was constructed in MEGA employing a GTR+I model of nucleotide substitution and 500 bootstrap replicates.

    Supplementary File 5. Newick file containing the phylogeny of Bifidobacteriaceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate bootstrap support. Maximum Likelihood phylogeny was constructed in MEGA employing a GTR+I model of nucleotide substitution and 500 bootstrap replicates.

    Supplementary File 6. Newick file containing the phylogeny of Lachnospiraceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate bootstrap support. Maximum Likelihood phylogeny was constructed in MEGA employing a GTR+I model of nucleotide substitution and 500 bootstrap replicates.

    Supplementary File 7. Newick file containing the chronogram of Bacteroidaceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate 95% posterior intervals of divergence estimates calculated in BEAST. For the dating analysis, topology of the chronogram was constrained to that of the Maximum Likelihood phylogeny.

    Supplementary File 8. Newick file containing the chronogram of Bifidobacteriaceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate 95% posterior intervals of divergence estimates calculated in BEAST. For the dating analysis, topology of the chronogram was constrained to that of the Maximum Likelihood phylogeny.

    Supplementary File 9. Newick file containing the phylogeny of Bacteroidaceae strains recovered from humans from the USA and Malawi, chimpanzees, bonobos, and gorillas. Node labels indicate bootstrap support. In contrast to Supplementary File 1, this file contains sequences extracted from 23 previously reported Malawi-human metagenomes. Maximum Likelihood phylogeny was constructed in MEGA employing a GTR+I model of nucleotide substitution and 500 bootstrap replicates.

    Supplementary File 10. Newick file containing the phylogeny of Bifidobacteriaceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate bootstrap support. In contrast to Supplementary File 1, this file contains sequences extracted from 23 previously reported Malawi-human metagenomes. Maximum Likelihood phylogeny was constructed in MEGA employing a GTR+I model of nucleotide substitution and 500 bootstrap replicates.

    Supplementary File 11. Newick file containing the phylogeny of Lachnospiraceae strains recovered from humans, chimpanzees, bonobos, and gorillas. Node labels indicate bootstrap support. In contrast to Supplementary File 1, this file contains sequences extracted from 23 previously reported Malawi-human metagenomes. Maximum Likelihood phylogeny was constructed in MEGA employing a GTR+I model of nucleotide substitution and 500 bootstrap replicates.

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