| Yunnan is rich in chicken genetic resources with varieties of native chicken breeds.The gut microbial community in these birds results from the long-term co-evolution which has an important exploitation value for the enhancement of healthy breeding and the development of poultry industry in Yunnan.In order to understand the composition and potential function of the gut microbial community of Yunnan native chickens,analyze the differences in the composition and function of the gut microbial community of Yunnan native chickens,and explore how the factors such as geographical location and breeding mode affect the gut microbes of Yunnan native chickens,this research will employ metagenomics sequencing techniques to determine the composition and interpret the function of gut microbiomes of Yunnan native chickens,to compare the differences in composition and function of the gut microbiome between different Yunnan native chicken breeds,and to probe the effects of altitude on the composition and function of gut microbiomes in Yunnan native chickens,and the effects of breeding mode on the gut microbe diversity and metabolic phenotype in these birds.The results of this research are as followed:(1)Study on the composition and potential function of gut microbial community in Yunnan native chickenWe sequenced the gut metagenomes of 3 kinds of Yunnan native chicken using next-generation sequencing technology to obtain a better understanding of the microbial diversity and functional capacity of Yunnan native chicken gut microbiome.Taxonomic analysis of the metagenomic reads indicated that the gut microbiome of the Nixi Chicken was dominated by Bacteroidetes and Fusobacteria.Moreover,at the genus level,Bacteroides,Alistipes,Clostridium and Prevotella were most abundant in the Nixi chicken gut metagenome.At the species level,Alistipes sp.CAG:831,Bacteroides fragilis,Faecalibacterium prausnitzii and Bacteroides salanitronis were the species with highest abundances in the Nixi chicken gut microbiome.The primary functional categories were associated mainly with Carbohydrate metabolism and amino acid metabolism.Taxonomic analysis of the metagenomic reads indicated that the gut microbiome of the Wuding Chicken was dominated by Bacteroidetes,Firmicutes and Proteobacteria.Moreover,at the genus level,Bacteroides,Alistipes and Prevotella were most abundant in the Wuding chicken gut metagenome.At the species level,Alistipes sp.CAG:831,Bacteroides fragilis,Faecalibacterium prausnitzii and Bacteroides salanitronis were the species with highest abundances in the Wuding chicken gut microbiome.The primary functional categories were associated mainly with Carbohydrate metabolism and amino acid metabolism.Taxonomic analysis of the metagenomic reads indicated that the gut microbiome of the Chahua Chicken were dominated by Bacteroidetes,Firmicutes and Proteobacteria.Moreover,at the genus level,Bacteroides,Alternaria,Clostridium,Prevotella,and Faecalibacterium were most abundant in the Chahua chicken gut metagenome.At the species level,Clostridium prazines,Bacteroides CAG :598,Bacteroides Pasteurella and Bacteroides fragilis were the species with highest abundances in the Chahua chicken gut microbiome.The primary functional categories were associated mainly with Carbohydrate metabolism and Amino acid metabolism.(2)A comparative metagenomics study on gut microbes among different chickensBy studying the gut microbial community of 3 Yunnan native chickens,we deeply analyze the differences in gut microbiome structure and function between Nixi chicken,Wuding chicken and Chahua chicken.The results showed that there were significant differences between the gut microbiome of the Nixi chicken and Wuding chicken in 29 phyla,555 genera and 1607 species.The abundance of Verrucomicrobia,Spirochaeles and Deferribacteres in the gut microbiome of Nixi chicken is higher than that of Wuding chicken,and the abundance of Actinobacleria is lower than that of Wuding chicken.At the genus level,the abundance of Treponema,Sutterella,Para Prevotella,Mucispirillum and Brachyspira in Nixi chicken is higher than that of Wuding chicken.At the species level,the abundance of Mucispirillum schaedleri and Bacteroides barnesiae in Nixi chicken is higher than that of Wuding chicken.In its function,there are significant differences found in a total of 31 pathway.The results showed that there are significant differences between the gut microbiome of the Nixi chicken and Chahua chicken in 23 phyla,420 genera and 1431 species.The abundance of Verrucomicrobia,Spirochaeles in the gut microbiome of Nixi chicken was higher than that of Chahua chicken,and the abundance of Euryarchaeota and Actinobacteria is lower than that of Chahua chicken.At the genus level,the abundance of Para Prevotella,Sphaerochaeta and Oscillibacter in Nixi chicken is higher than that of Chahua chicken.At the species level,the abundance of Prevotella sp.CAG:755 and Prevotella sp.CAG:279 in Nixi chicken is higher than that of Chahua chicken.In its function,there are significant differences found in a total of 36 pathways.The results showed that there were significant differences between the gut microbiome of the Wuding chicken and Chahua chicken in 35 phyla,287 genera and1082 species.The abundance of Verrucomicrobia,Fusobacteria and Euryarchaeota in the gut microbiome of Wuding chicken is lower than that of Chahua chicken.At the genus level,the abundance of Megasphaera,Lachnoclostridium,Dorea and Desulfovibrio in Wuding chicken is higher than that of Chahua chicken.At the species level,the abundance of Prevotella sp.CAG:755,Prevotella sp.CAG:279,Eubacterium sp.ER2 and Bacteroides fragilis in Nixi chicken is higher than that of Chahua chicken.In its function,there were significant differences found in a total of 33 pathways.(3)A comparative metagenomics study on gut microbes among chickens with different sexes and ways of captivityBy comparatively analyzing the difference in gut microbiome structure and function between male chicken and female chicken,it showed that there were significant differences between the gut microbiome of the male chicken and female chicken in 2phyla,77 genera and 338 species.The abundance of Tenericutes in the gut microbiome of male chicken is lower than that of female chicken.At the genus level,the abundance of Paludibacter in male chicken is higher than that of female chicken,the abundance of Mycoplasma,Faecalitalea and Atopobium in male chicken is lower than that of female chicken.At the species level,the abundance of Para Bacteroides sp.CAG:409,Paludibacter propionicigenes,Bacteroides sp.CAG:633 and Bacteroides plebeius CAG:211 in male chicken is higher than that of female chicken.In its function,there are significant differences found in a total of 26 pathways.By comparatively analyzing the difference in gut microbiome structure and function between free-range chicken and caged chicken,the results showed that there were significant differences between the gut microbiome of the free-range chicken and caged chicken in 18 phyla,77 genera and 1373 species.The abundance of Bacteroidetes in the gut microbiome of free-range chicken is higher than that of caged chicken.At the genus level,the abundance of Prevotella,Para Prevotella,Bacteroides in free-range chicken is higher than that of caged chicken,the abundance of Ruminococcus,Faecalibacterium and Blautia in free-range chicken is lower than that of caged chicken.At the species level,the abundance of Prevotella sp.CAG:1320,Bacteroides salanitronis and Bacteroides fragilis in free-range chicken is higher than that of caged chicken,the abundance of Ruminococcus torques,Faecalibacterium prausnitzii and Bacteroides sp.CAG:598 in free-range chicken is lower than that of caged chicken.In its function,there are significant differences found in a total of 33 pathways.In conclusion,Nixi chicken,Wuding chicken and Chahua chicken have similar but independent composition and potential function of the gut microbial community.There were significant differences in the composition structure and potential function of gut microbial among Nixi chickens,Wuding chickens and Chahua chicken.Gender and different feeding patterns affected the composition and function of gut microbial in Yunnan native chickens. |
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