Comparison of the diversity of gut microbiomes of individuals across subsistence (a) Alpha diversity based on the phylogenetic metric, phylogenetic distance (PD) whole tree.

<p>(b) Beta diversity within each subsistence group based on unweighted UniFrac distances. (c) Beta diversity for pairs of subsistence groups based on unweighted UniFrac distances. For pairwise comparisons, all are significant (p < 0.05 unless specified (n.s.); Welch’s t-test). All p-values are based on Welch’s t-tests. Fis = Fishing population; Far(S) = Farmers from the South; Far(N) = Farmers from the North; HG = Hunter-gatherers.</p

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by <i>Entamoeba</i> and Subsistence

<div><p>The human gut microbiota is impacted by host nutrition and health status and therefore represents a potentially adaptive phenotype influenced by metabolic and immune constraints. Previous studies contrasting rural populations in developing countries to urban industrialized ones have shown that industrialization is strongly correlated with patterns in human gut microbiota; however, we know little about the relative contribution of factors such as climate, diet, medicine, hygiene practices, host genetics, and parasitism. Here, we focus on fine-scale comparisons of African rural populations in order to (i) contrast the gut microbiota of populations inhabiting similar environments but having different traditional subsistence modes and either shared or distinct genetic ancestry, and (ii) examine the relationship between gut parasites and bacterial communities. Characterizing the fecal microbiota of Pygmy hunter-gatherers as well as Bantu individuals from both farming and fishing populations in Southwest Cameroon, we found that the gut parasite <i>Entamoeba</i> is significantly correlated with microbiome composition and diversity. We show that across populations, colonization by this protozoa can be predicted with 79% accuracy based on the composition of an individual's gut microbiota, and that several of the taxa most important for distinguishing <i>Entamoeba</i> absence or presence are signature taxa for autoimmune disorders. We also found gut communities to vary significantly with subsistence mode, notably with some taxa previously shown to be enriched in other hunter-gatherers groups (in Tanzania and Peru) also discriminating hunter-gatherers from neighboring farming or fishing populations in Cameroon.</p></div

(a) Comparison of alpha diversity for <i>Entamoeba</i> negative (<i>Ent</i>-) and positive (<i>Ent</i>+) individuals using the phylogenetic distance whole tree metric.

<p>(b) Comparison of beta diversity within <i>Ent</i>-, within <i>Ent</i>+, and between <i>Ent</i>- and <i>Ent</i>+ individuals based on unweighted UniFrac distances. P-values are based on Welch’s t-test.</p

(a) Map showing the geographic locations of the villages sampled in Southwest Cameroon, the number of samples (N) collected for each subsistence group (the fishing population, farmers from the South, farmers from the North, and hunter-gatherers), and their genetic ancestry (Bantu or Pygmy).

<p>(b) Principle Components Analysis based on dietary questionnaires for all 64 individuals. The first two principal components (PC1 and PC2) are shown, with the amount of variation explained reported for each axis. Image of Africa is courtesy of NASA/JPL-Caltech.</p

Normalized relative abundance of KEGG metabolic pathways significantly associated with <i>Entamoeba</i> status in an ANOVA (q < 0.05 using the most abundant; ≤ 0.4% in at least one group) (left panel) and the relative contributions of each taxon for each pathway (right panel).

<p>Normalized relative abundance of KEGG metabolic pathways significantly associated with <i>Entamoeba</i> status in an ANOVA (q < 0.05 using the most abundant; ≤ 0.4% in at least one group) (left panel) and the relative contributions of each taxon for each pathway (right panel).</p

Relationship between subsistence modes and fecal microbiome composition.

<p>(a) Summary of the relative abundance of taxa (occurring at > = 0.1% in at least 4 individuals) for individuals across subsistence. Taxa are colored by phylum (Actinobacteria (Act.) = red, Bacteroidetes (Bact.) = green, Cyanobacteria (Cyan.) = black, Elusimicrobia (Elus.) = gold, Firmicutes (Firm.) = blue, Fusobacteria (Fus.) = pink, Lentisphaerae (Lent.) = yellow, Proteobacteria (Prot.) = purple, Spirochaetes (Spir.) = orange, and Tenericutes (Ten.) = gray). The number of individuals (N) in each population is indicated below the bars. (b) Relative abundance of four taxa significantly associated with subsistence based on an ANOVA, q < 0.05. Fis = Fishing population; Far(S) = Farmers from the South; Far(N) = Farmers from the North; HG = Hunter-gatherers.</p

Autosomal nucleotide diversity levels across species, grouped by phylum.

<p>Diversity estimates for each species are the same as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001388#pbio-1001388-g001" target="_blank">Figure 1</a>; here they are ordered within phylum, and phyla are presented in order of their median diversity levels. Within Chordata, open circles indicate mammals, and within Arthropoda, they denote <i>Drosophila</i> species. We note that the three most diverse chordates are all invertebrate sea squirts. In panel (A), estimates are colored by the phylum to which each species belongs and horizontal bars mark the median estimate for each phylum; for Magnoliophyta, a dashed line marks the median for selfing species (open circles) and a solid line marks the median for outcrossing species. (We do not provide <i>p</i> values for comparisons because of the lack of phylogenetic independence.) Crosses denote estimates for individual populations and are shown when population structure was reported in the original study. In panel (B), estimates are colored according to whether the species lives in a terrestrial, freshwater, or marine environment (not all species are categorized). Horizontal bars indicate the median for each category within each phylum (only shown when more than two species fall in the category). The number of species in each habitat is given in parentheses in the legend.</p

Autosomal nucleotide diversity levels across species.

<p>Autosomal genetic diversity is given as the average number of pairwise differences per base pair, in percent, and is shown on a log10 scale. Each estimate represents the mean of at least three loci and in most cases is based on only non-coding or synonymous sites. The estimates are ordered by diversity level, labeled by species name, and colored by the phylum to which each species belongs. The number of species in each phylum is given in parentheses in the legend.</p

Comparison of autosome and sex chromosome nucleotide diversity.

<p>The ratio of sex chromosome to autosome diversity is plotted for the 29 species in which both estimates were available from the same population(s). Colors indicate the phylum to which the species belong. Within Chordata, open circles denote mammals and open triangles birds; within Arthropoda, open circles denote <i>Drosophila</i> species. The number of species in each group is given in parentheses in the legend. Within species, crosses represent the ratio estimated from different populations, with the median of the estimates shown as a triangle (birds) or circle (all other species). Solid horizontal lines indicate the median sex chromosome to autosome ratio for arthropods and chordates, colored as in the key. The black dashed line indicates where sex chromosome diversity equals three-fourths of autosomal diversity.</p

Diagram representing the relative values of expected genetic differentiation for autosomal markers and for X-linked markers .

<p>In the red upper right triangle, the <i>F</i>_ST estimates for autosomal markers are higher than for X-linked markers. In this case, <i>N</i>_f/<i>N</i> is necessarily larger than 0.5. In the blue region of the figure, the <i>F</i>_ST estimates for autosomal markers are lower than for X-linked markers. The white plain line, at which , represents the set of (<i>N</i>_f/<i>N</i>, <i>m</i>_f/<i>m</i>) values where the autosomal and X-linked <i>F</i>_ST estimates are equal. In this case , if <i>N</i>_f = <i>N</i>_m, then the lower effective size of X-linked markers (which would be three-quarters that of autosomal markers) can only be balanced by a complete female-bias in dispersal (<i>m</i>_f/<i>m</i> = 1). Conversely, if <i>m</i>_f = <i>m</i>_m, the large female fraction of effective numbers compensates exactly the low effective size of X-linked markers only for <i>N</i>_f = 7<i>N</i>_m. Last, if <i>m</i>_f = <i>m</i>_m/2, then the autosomal and X-linked <i>F</i>_ST estimates can only be equal as the number of males tends towards zero.</p