The avian gut microbiota: community, physiology and function in wild birds

Abstract

Gastrointestinal microbiota play a vital role in maintaining organismal health, through facilitating nutrient uptake, detoxification and interactions with the immune system. The gastrointestinal microbiota of birds has been poorly studied, especially in wild species under natural conditions. Studies of avian gut microbiota are outnumbered ten to one by studies of mammals, and are dominated by research on domestic poultry. Unlike domestic poultry, wild birds vary widely in environmental preferences, physiology, and life‐history traits, such as migratory behavior and mating systems. Species characteristics result in a vast diversity in gut microbiota and its composition and function. Avian life‐history characteristics pose selection pressures on the gut microbiota, and ultimately affect host health. Here, we review current knowledge of the gut microbiota of wild birds, including: partitioning of digestive function and microbiota among different gastrointestinal compartments, microbial diversity and function in the context of host diet, energetics and behavior, and the intrinsic and extrinsic factors impacting gut microbiota in free‐living birds. The shared core microbiota of wild bird species is dominated by members of four major phyla: Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. However, microbial communities varies inter‐ and intra‐specifically, and among gastrointestinal tract sections. To conclude, we identify three key research areas that warrant further investigation: 1) expanding the range of avian host taxa investigated, 2) identifying the function of avian gut microbiota in physiology and immunology, and 3) transitioning from observational studies to experimental manipulations to identify key determinants of wild bird gut microbiota composition.

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].…”

A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes

“…In terms of similarities, we found that the crane gut microbiota, regardless of host species, was primarily composed of taxa in the phylum Firmicutes (76%). The dominance of Firmicutes is consistent with previous descriptions of crane gut microbiota [46,47] and the avian gut microbiome in general [11]. However, cranes in our study harboured a higher relative abundance of Firmicutes compared with the previous studies of crane gut microbiota [46,47] and was similar to that reported in mammals [48,49].…”

“…Despite widespread evidence of phylosymbiosis across most major taxonomic groups, this phenomenon has yet to be observed in birds (class Aves). Birds are a diverse group of organisms that provide numerous ecological services [10], yet studies into their gut microbial ecology are extremely limited [11]. To date, there have been several attempts to link gut microbial community composition © 2020 The Author(s) Published by the Royal Society.…”

“…While this lack of support for avian phylosymbiosis could be a product of avian evolutionary history (e.g. weight-saving digestive adaptations) [18], it may also be a product of their sensitivity to extrinsic environmental factors or species-specific differences in natural feeding strategies across several avian orders [11,19]. Therefore, studies that reduce the influence of these variables using captive birds on identical diets may increase the chances of detecting subtle phylosymbiotic signatures [7], thereby enabling the identification of the mechanisms and host factors driving this phenomenon [20,21].…”

Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

“…Unsurprisingly, they also exhibit diversity in their microbiomes. Bird microbiomes appear to be dominated by a small number of bacterial phyla, namely Proteobacteria, Firmicutes, and Bacteroidetes (Grond, Sandercock, Jumpponen, & Zeglin, ; Hird et al, ; Waite & Taylor, ) and are influenced by environment (Wienemann et al, ), geographic location (Hird, Carstens, Cardiff, Dittmann, & Brumfield, ), diet (Rubio et al, ), age (Grond, Lanctot, Jumpponen, & Sandercock, ; Teyssier et al, ; Van Dongen et al, ), and host genetics (Kropáčková et al, ). Despite this, little is known about the role of the microbiome in avian evolution.…”