The avian gut microbiota: Diversity, influencing factors, and future directions

Abstract

The gut microbiota is viewed as the “second genome” of animals, sharing intricate relationships with their respective hosts. Because the gut microbial community and its diversity are affected by many intrinsic and extrinsic factors, studying intestinal microbes has become an important research topic. However, publications are dominated by studies on domestic or captive birds, while research on the composition and response mechanism of environmental changes in the gut microbiota of wild birds remains scarce. Therefore, it is important to understand the co-evolution of host and intestinal bacteria under natural conditions to elucidate the diversity, maintenance mechanisms, and functions of gut microbes in wild birds. Here, the existing knowledge of gut microbiota in captive and wild birds is summarized, along with previous studies on the composition and function, research methods employed, and factors influencing the avian gut microbial communities. Furthermore, research hotspots and directions were also discussed to identify the dynamics of the avian gut microbiota, aiming to contribute to studies of avian microbiology in the future.

Falcon gut microbiome is shaped by diet and enriched inSalmonella

“…Despite its importance, the potential contribution of avian microbiome in bird evolution, conservation, and public health remains understudied because of several limitations. First, most bird microbiome studies have primarily focused on domesticated birds of economic value (17). Although microbiome studies of wild and captive birds using 16S rDNA sequencing are emerging, each study consists of limited samples– potentially reflecting difficulties in collecting samples from non-commercial birds (52) –which may lead to inconsistent findings across studies.…”

“…Consequently, the bird gut microbiota harbors hundreds of bacterial species belonging to diverse phyla that are associated with body size, flight, and dietary adaptations (15), indicating these bacteria play an important role in regulating physiological functions in birds (16). However, bird microbiome studies have predominantly focused on birds of commercial importance (17). Uber-carnivorous raptors whose diet almost exclusively consists of animal flesh, are highly underrepresented in the microbiome literature (18), with the exception of a few studies that include a handful of hawks, eagles, vultures, and falcons (15,(18)(19)(20)(21).…”

Impacts of coprophagic foraging behaviour on the avian gut microbiome

“…In these species, some nutrients and short-chain fatty acids may be absorbed by the caecum (McWhorter et al, 2009), but primary absorption by the small intestine is missed. In such cases, coprophagy has been suggested to be a critical foraging behaviour that facilitates the uptake of lost or missing nutrients (Soave & Brand, 1991;Starks & Peter, 1991;Gallant, 2004;McWhorter et al, 2009). In some mammalian species, thiamine, K and B vitamins, and proteins are primarily excreted in faeces without absorption, but uptake can be increased via faeces reingestion (Soave & Brand, 1991).…”

Nearly (?) sterile avian egg in a passerine bird

“…Is a bird egg also initially sterile or do females deposit any bacteria into the egg to direct the initial embryonic and chick microbiome development? Although with the advent of NGS, our understanding of avian microbiota composition exponentially increased over the last decade (Sun et al . 2022), this improvement concerns mostly avian adults, with little being known about the bacterial colonization of the bird egg and microbial communities formed during embryonic development.…”

“…Is a bird egg also initially sterile or do females deposit any bacteria into the egg to direct the initial embryonic and chick microbiome development? Although with the advent of NGS, our understanding of avian microbiota composition exponentially increased over the last decade (Sun et al 2022), this improvement concerns mostly avian adults, with little being known about the bacterial colonization of the bird egg and microbial communities formed during embryonic development. Early bacterial colonisers may shape GIT and the immune system of developing embryos and also influence their survival and the composition of chick microbial communities after hatching (Hansen et al 2015;Roto, Kwon and Ricke 2016).…”