Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

Abstract

We lack a deep understanding of genetic and metabolic attributes specializing in microbial consortia for initial and subsequent waves of colonization of our body habitats. Here we show that phylogenetically interspersed bacteria in Clostridium cluster XIVa, an abundant group of bacteria in the adult human gut also known as the Clostridium coccoides or Eubacterium rectale group, contains species that have evolved distribution patterns consistent with either early successional or stable gut communities. The species that specialize to the infant gut are more likely to associate with systemic infections and can reach high abundances in individuals with Inflammatory Bowel Disease (IBD), indicating that a subset of the microbiota that have adapted to pioneer/opportunistic lifestyles may do well in both early development and with disease. We identified genes likely selected during adaptation to pioneer/opportunistic lifestyles as those for which early succession association and not phylogenetic relationships explain genomic abundance. These genes reveal potential mechanisms by which opportunistic gut bacteria tolerate osmotic and oxidative stress and potentially important aspects of their metabolism. These genes may not only be biomarkers of properties associated with adaptation to early succession and disturbance, but also leads for developing therapies aimed at promoting reestablishment of stable gut communities following physiologic or pathologic disturbances.

Figure 1.

Co-occurrence network of human gut bacteria, based on a relative abundance matrix previously reported in Qin et al. (2010). The nodes represent species whose genomes have been sequenced. The size of the nodes indicates the average relative abundance across the 124 individuals in the MetaHIT cohort, and the color of the node reflects taxonomic information. Species with significantly positive co-occurrence for any of six measures used (Pearson, Spearman, Kendall, Bray-Curtis, Euclidean, and mutual information) are joined with an edge. Co-occurrence modules are defined as a set/collection of species that are connected among each other (directly or via several steps), but not to any other species in the network, and are labeled with Mx. Species' full names are shown in Supplemental Table S1, and phylogenetic relationships among them as determined with 16S rRNA are shown in Supplemental Fig. S1. For further discussion of this network, see the Supplemental Material.

Figure 2.

Phylogenetic relationships between species in Clostridium cluster XIVa. Bootstrap support (based on 1000 replicates) is indicated on the branches of the 16S rRNA NJ tree when >40% (except for Ruminococcus sp. SR1/5, as this was added by parsimony insertion after the initial tree creation, since only a short region of 16S rRNA sequence was available; see Methods). The species names are colored according to their module in the co-occurrence network: M1 (blue), M2 (turquoise), M3 (red), and M4 (green). Species that were evaluated in the network analysis but showed no significant co-occurrence are in black text. Species that were not evaluated for co-occurrence are colored purple. These were added to further support that the species in this group that can cause disease form a clade with expanded genome size. The branches are colored by genome size rank, with the red branches representing the largest genomes and the blue branches the smallest. The genome size in Mb is listed after the species name. Species that have been recovered from clinical samples (e.g., bacteremia) are marked with a red circle, and those reported to be in increased abundance with IBD are marked with a blue circle. Species that contain the genomic machinery for a flagellum are marked with a blue curved line. Note that the network diagram only shows species with significant co-occurrence with at least one other species; thus 36.7% (11/30) of evaluated species in Clostridium cluster XIVa, are not shown. Details about the evaluated species are provided in Table 1.

Figure 3.

Relative abundance of species in M1 and M3 in various gut samples. Sample categories are detailed in Supplemental Table S2. (A) Average relative abundance across samples from individuals with and without gastrointestinal disease. (Blue circles) M1 species; (red squares) M3 species. The SEM for each treatment is plotted. For healthy, estimated using data from (1) stool samples from obese and lean twins and their mothers (Turnbaugh et al. 2009a) (Turnbaugh Feces), (2) samples from three healthy adults from six mucosal sites along the length of the colon (Eckburg et al. 2005) (Eckburg Mucosal), (3) fecal samples from the same three individuals as in Eckburg Mucosal (Eckburg Feces). For diseased, averaged relative abundance across (1) colon (Frank Colon), (2) small intestine (Frank SI), and (3) MLNs (Frank MLN) from individuals with gastrointestinal disease including Crohn's disease, ulcerative colitis, and colon cancer from Frank et al. (2007) (B) Results from humanized gnotobiotic mice (Turnbaugh et al. 2009b). Fecal samples from the healthy human donor (donor, [1]) and from the recipient gnotobiotic mice ([2] stomach, [3] small intestine [SI], [4] cecum, [5] colon, and [6] feces). The points representing R. torques, which was an outlier in this analysis, are marked with a green circle. Error bars represent the median and interquartile range. (C) Age trends in M1 and M3 species in a single infant using data from Koenig et al. ( 2011). The x-axis in each plot is the age in days and the y-axis is the relative abundance in a single sample. The species in M1 have series colored in blue, M3 red, and those with no detected co-occurring microbes are in black. The relative abundance of each OTU in the mother is plotted at day 950 in light green. The period before the introduction of solid food is shaded in blue and between then and the switch from breast milk to formula is shaded in yellow. Ruminococcus sp. SR 1/5 was not evaluated because sequence information for the V2 region of its 16S rRNA is incomplete. Coprococcus comes is not shown because it was absent across the infant timeseries and in the mother.

Figure 4.

Metabolic network. Generated based on the combined metabolic network of M1 and M3 genomes (see Methods). The nodes (circles) are compounds and the edges are reactions. Edges colored blue have more copies or are more likely present in M3 genomes compared with M1. Red edges are reactions known to occur, but no described enzymes that perform them are in any of these genomes. The node color indicates the fraction of M3 genomes in which that compound is found with white being 100% and black being 0%. The thick green edges indicate that branches of the network emanating from that node were eliminated from the figure.