Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail

Abstract

Background: Japanese quail (Coturnix japonica) are important and widely distributed poultry in China. Researchers continue to pursue genetic selection for heavier quail. The intestinal microbiota plays a substantial role in growth promotion; however, the mechanisms involved in growth promotion remain unclear.Results: We generated 107.3 Gb of cecal microbiome data from ten Japanese quail, providing a series of quail gut microbial gene catalogs (1.25 million genes). We identified a total of 606 main microbial species from 1,033,311 annotated genes distributed among the ten quail. Seventeen microbial species from the genera Anaerobiospirillum, Alistipes, Barnesiella, and Butyricimonas differed significantly in their abundances between the female and male gut microbiotas. Most of the functional gut microbial genes were involved in metabolism, primarily in carbohydrate transport and metabolism, as well as some active carbohydrate-degrading enzymes. We also identified 308 antibiotic-resistance genes (ARGs) from the phyla Bacteroidetes, Firmicutes and Euryarchaeota. Studies of the differential gene functions between sexes indicated that abundances of the gut microbes that produce carbohydrate-active enzymes varied between female and male quail. Bacteroidetes was the predominant ARG-containing phylum in female quail; Euryarchaeota was the predominant ARG-containing phylum in male quail.Conclusion: This article provides the first description of the gene catalog of the cecal bacteria in Japanese quail as well as insights into the bacterial taxa and predictive metagenomic functions between male and female quail to provide a better understanding of the microbial genes in the quail ceca.

Gut microbiome and serum metabolome analyses identify biomarkers associated with sexual maturity in quails

“…In accordance with previous studies ( Liu et al, 2015 ; Wilkinson et al, 2016 ; Vollmar et al, 2020 ; Ma et al, 2021 ), Bacteroidetes and Firmicutes were the 2 most dominant phyla in quail gut microbiota. In the current study, the gut microbiota from the d 20 group was substantially different form that from the d 70 group, particularly with regard to the higher proportion of Firmicutes detected.…”

A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome

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Figure 1 Categories and relative abundance of the gut microbiome at the species level based on the shotgun metagenomic sequencing data for all the tested samples. Sample name beginning with B (e.g., B20.11 and B70.1M) was Hengyan white quail, beginning with C (e.g., C20.1F and C70.3F) was Japanese quail, beginning with H (e.g., H70.1M) was Chinese yellow quail, and others 10 were Japanese quails and obtained in our previous study ( Ma et al, 2021 ).

Figure 2 A co-occurrence network constructed with 235 core species.

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“…A total of 40 quail samples were used in this study for metagenomic sequencing, including 30 samples that were sequenced in this study and 10 cecum luminal content samples that were obtained in our previous study ( Ma et al, 2021 ). The 30 samples sequenced in this study included 22 feces and 8 cecum luminal content samples from 3 different breeds on the same farm ( Supplementary Table S1 ).…”

“…We collected the 22 feces and 8 cecum lumen contents samples from a Chinese yellow quail population, Hengyan white quail population and Japanese quail population. We performed shotgun metagenomic sequencing and established a catalog of the quail gut microbial genes by processing 30 newly sequenced samples and 10 published samples from our previous study ( Ma et al, 2021 ). Then, we recovered the MAGs of the quail gut microbiome, which were clustered to the species-level genome bins ( SGBs ).…”

Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal

“…Notably, these species are responsible for the fermentation of carbohydrates and production of butyrate in chickens ( Stanley et al, 2013 ). Given that Bacteroides contributes to disease resistance in chickens ( Ma et al, 2021 ), high number population of this genus suggests that MBM may indirectly prevents enteric diseases in chickens. Furthermore, Ruminococcus is capable of producing butyrate and other SCFA, such as acetic and succinic acids, through glucose metabolism and cellulose digestion, while Alistipes genus can produce acetic acid through the synthesis of fibrinolyisin, digestion of gelatin and fermentation of carbohydrates ( Biasato et al, 2019 ).…”