Covariation of the gut microbiome with diet in Aves

Abstract

Background:Research over the past few decades has revealed a vital role for the gut microbiome in the health of various animals including birds. Multiple factors can influence the gut microbiome. Opportunistic feeding and multiple other environment factors can influence the results, and bias the conclusions, when wild animals are used to study the influence of phylogeny and diet on their gut microbiomes. Therefore, to study this question in this study, we collected fecal samples from 43 species of Aves at one time to avoid influences such as geography, weather, and season. Results:Approaches based on both 16S rRNA gene sequencing (135 samples) and whole metagenome shotgun sequencing (17 samples) were used. Our data show that diets containing native starch will increase the abundance of Lactobacillus in gut microbiome, while those containing plant-derived fiber will mainly enrich the levels of Clostridium. Greater numbers of Fusobacteria and Proteobacteria are detected in carnivorous birds, while in birds fed a commercial corn-soybean basal diet, a stronger inner-connected microbial community containing Clostridia and Bacteroidia was enriched. Furthermore, a microbial functional analysis based on the metagenomic sequences showed that the function of microbes was adapted to different food types to achieve the most beneficial state for the hosts. Conclusions:The covariation of diet and gut microbiome identified in our study demonstrates modulation of the gut microbiome by dietary diversity and expands our knowledge of diet-microbiome-host interactions in birds.

Genome-Resolved Metagenomics of the Chicken Gut Microbiome

“…However, its central role in the network suggests that further studies are required. Recently, Xiao et al (2020) compared the gut microbiome in different bird species and found that birds fed a corn-soybean basal diet showed a strongly interconnected microbial community with species from the classes Clostridia and Bacteroidia. In line with these findings, although the 155 genomes presented in this study constitute only a small sample of the GIT microorganisms, there was also a strong representation of bacteria in these classes in the network, with bacteria genera Alistipes, Ruminococcus, Fournierella, and Faecalicatena.…”