Opportunistic feeding and multiple other environment factors can modulate the gut microbiome, and bias conclusions, when wild animals are used for studying the influence of phylogeny and diet on their gut microbiomes. Here, we controlled for these other confounding factors in our investigation of the magnitude of the effect of diet on the gut microbiome assemblies of nonpasserine birds. We collected fecal samples, at one point in time, from 35 species of birds in a single zoo as well as 6 species of domestic poultry from farms in Guangzhou city to minimize the influences from interfering factors. Specifically, we describe 16S rRNA amplicon data from 129 fecal samples obtained from 41 species of birds, with additional shotgun metagenomic sequencing data generated from 16 of these individuals. Our data show that diets containing native starch increase the abundance of Lactobacillus in the gut microbiome, while those containing plant-derived fiber mainly enrich the level 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, the metagenome functions of the microbes (such as lipid metabolism and amino acid synthesis) were adapted to the different food types to achieve a beneficial state for the host. In conclusion, the covariation of diet and gut microbiome identified in our study demonstrates a modulation of the gut microbiome by dietary diversity and helps us better understand how birds live based on diet-microbiome-host interactions. IMPORTANCE Our study identified food source, rather than host phylogeny, as the main factor modulating the gut microbiome diversity of nonpasserine birds, after minimizing the effects of other complex interfering factors such as weather, season, and geography. Adaptive evolution of microbes to food types formed a dietary-microbiome-host interaction reciprocal state. The covariation of diet and gut microbiome, including the response of microbiota assembly to diet in structure and function, is important for health and nutrition in animals. Our findings help resolve the major modulators of gut microbiome diversity in nonpasserine birds, which had not previously been well studied. The diet-microbe interactions and cooccurrence patterns identified in our study may be of special interest for future health assessment and conservation in birds.
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.
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