The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch

Abstract

BackgroundDarwin’s finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices—ranging from seeds to blood—make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored.ResultsWe characterized the microbial community associated with 12 species of Darwin’s finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin’s finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception—the vampire finch—which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia—bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons.ConclusionsThis study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0555-8) contains supplementary material, which is available to authorized users.

Host-associated microbiomes are predicted by immune system complexity and climate

“…This finding is also supported by studies in other taxa including larval amphibians and aquatic invertebrates [71]. Previous studies found a more prominent role of host diet in shaping the gut microbiome [72,73], particularly within clades such as lizards [74], fish [32,67,75], birds [76,77], or mammals [78]. Captivity may produce bottom-up effects on microbiomes by altering environmental conditions and diets from field conditions [41].…”

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

“…However, the only indication of this function that we detected was a higher abundance in vampire finches of ASV20, taxonomically identified as C. somerae (family Fusobacteriaceae, phylum Fusobacteria) (figure 3; electronic supplementary material, table S2). A separate sequence analysis of these vampire finch faecal samples confirmed this finding [39]. C. somerae is known to produce cobalamin (vitamin B12), a vitamin that has recently been found to serve important roles in the microbial metabolism of other essential compounds such as folate, ubiquinone and methionine [40].…”

The effect of pyridine-alkaloid secondary metabolites on sunbirds gut microbiome

“…5a). This pattern bears high resemblance to the microbiota composition of other neotropical birds [42]and also to that of Darwin's finch [43]. Proteobacteria and Firmicutes were the dominant phyla in the sunbirds treated with nicotine and anabasine after four weeks.…”