Is there convergence of gut microbes in blood-feeding vertebrates?

Abstract

Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

Keywords: convergence; haematophagy; microbiome.

Figure 1.

Conceptual diagram of alternative hypotheses of microbiome convergence. Hypothesis 1 (No convergence, H1): no evidence of either compositional or functional convergence of the microbiome. Support for this hypothesis may indicate that the microbiome does not play an important role in the host convergent trait in question. Hypothesis 2 (Taxonomic convergence, H2): the microbiomes of convergent hosts share similar bacterial taxonomic composition. Support for this hypothesis would indicate that the microbes have an important role in the functional trait of the host and that the identity of those microbes is key (or that the trait selects for microbes with specific identities). Hypothesis 3 (Functional convergence): the microbiomes of convergent hosts differ in their taxonomic composition but share key gene functions related to the convergent trait of the host. Support for this hypothesis would indicate that compositionally different microbial communities can converge on the same functional trait to aid the host in achieving a specific function. (Online version in colour.)

Figure 2.

Principal coordinate analysis (PCoA) plots of the unweighted UniFrac distance among samples from haematophagous (red) and non-haematophagous (blue) species. PCoA ordination of distances among all bat and bird samples are shown in (a), with axes 1 and 3 in the larger image showing stratification between haematophagous and non-haematophagous animals, and axes 1 and 2 in the smaller inset. Separate ordinations for bats and birds are shown in (b,c), respectively. In bats, the different sample types collected are also indicated.

Figure 3.

Boxplots show the eight most abundant exact sequence variants (ASVs) identified as being differentially abundant between haematophagous (shown in red) and non-haematophagous (shown in cross-hatched blue) bats (top two rows) and birds (bottom two rows). Stars above the paired boxplots indicate the level of significance when means are compared using a Wilcoxon test (***p < 0.0005, ****p < 0.00005, n.s.: not significant). Except for ASV25, which is lower in the vampire finch, blue bars are not visible because these ASVs were not detected or detected at very low levels in non-haematophagous animals. (Online version in colour.)

Figure 4.

Predicted orthologous gene families (based on the KEGG database) (KOs) of interest from those detected as differentially abundant between at least one pair of haematophagous versus non-haematophagous species. KOs are separated into broad groups based on whether they are associated with metabolic pathways involving amino acids, haeme/iron, short-chain fatty acids, urea or sodium transport, and bar graphs show the mean difference in abundance between haematophagous and non-haematophagous individuals (all are higher in haematophagous individuals). (Online version in colour.)

Figure 5.

Mean relative abundance of OTUs (≥1% mean relative abundance) contributing to KEGG Ortholog groups (KOs) associated with elevated functions of interest. Abundances in bats (Phyllostomidae) are shown in the upper row and birds (Thraupidae) in the lower row. Bar size represents the average relative abundance of OTUs in the samples from a given bacterial group, collapsed to the family taxonomic level. Colours represent different bacterial families.

Figure 6.

Boxplots show the KEGG pathways detected as differentially abundant between both pairs of haematophagous (red) and non-haematophagous (blue) species. Stars above the paired boxplots indicate the level of significance when means are compared using a Wilcoxon test (****p < 0.00005; ***p < 0.0005).