Covariation of the Fecal Microbiome with Diet in Nonpasserine Birds

Abstract

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.

Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation

“…Thus, migratory status (pre‐ vs. postmigration in autumn) and the sampling region (Russia vs. Israel) did not have large effects on the microbial communities compared to the differences observed between autumn and winter or supplemented and nonsupplemented areas. This is in contrast to several bird studies that show a higher association with migratory status and locality than diet (Grond et al, 2019; Turjeman et al 2020), but is in line with other studies that found overall community composition to be similar among co‐occurring migrants and residents (Risely et al, 2018) and influenced by local food availability at stopover sites (Lewis et al, 2017; Xiao et al 2021). Cranes sampled during autumn in Russia and Israel also did not differ in microbiota richness and diversity (Figure 3) despite their different migratory status in these sites.…”

Intestinal Microbiota Regulate Certain Meat Quality Parameters in Chicken

“…Native breeds of livestock have superior meat quality and capacity for fat deposition, compared to commercial breeds ( 33 , 34 ). Recently, numerous studies have demonstrated the important role of gut microbiota in regulating skeletal muscle synthesis and development ( 26 , 35 , 36 ). The gut microbiota-muscle axis has been identified ( 37 , 38 ) and, to the best of our knowledge, this is the first report on the intestinal microbiota profile of the Beijing-You broilers by FMT.…”

“…The Quantitative Insights Into Microbial Ecology (QIIME) process was not directly used for operational taxonomic unit (OTU) clustering and species notes. Instead, we used some targeted software to deal with some pivotal steps ( 25 , 26 ). Specifically, the UCHIME function in Vsearch software (version 2.7.1) was used to compare the sequences of removed chimeras.…”

Gut microbiome composition better reflects host phylogeny than diet in breeding wood-warblers

“…Despite our finding of no relationship between diet diversity and gut microbiome diversity, many studies have shown host diet indeed influences the avian gut microbiome. Broad categorization of natural feeding guild and diet type explain differences in the gut microbiomes of wild passerines in New Guinea and of zoo and farm birds in China, respectively (Bodawatta et al 2021a, Xiao et al 2021). Further, experimental manipulations of passerine diets have been associated with shifts in gut microbiome diversity and composition (Davidson et al 2020, Tyssier et al 2020, Knutie 2020, Perkarsky et al 2021).…”