| The yak(Bos grunniens)is a key domestic animal on the Qinghai-Tibet Plateau and plays a vital role in the sustainable development of local animal husbandry.The rumen of the yak is a complex micro-ecosystem,and the rumen microecosystem affects the health and the production performance of host.Previous studies have uncovered bacterial composition and the dominant bacterial communities of yak.According to the characteristics of rumen physiology and nutrient metabolism,four environments can be distinguished for the rumen ecosystem: a solid-adherent fraction,the liquid fraction,the ventral epithelium fraction and dorsal epithelium fraction.However,the changes of bacterial communities in different rumen environment of yak,the diversity of rumen bacterial communities between yak and other ruminants,and the function of microorganisms in different ecological niche of yak rumen is still unclear.Therefore,we selected 5 female yaks(4 years old)as the research object.We used 16S-r RNA gene sequencing analysis to explore the microbial composition and function in different rumen fractions of yak,including the bacterial communities in the solid,liquid,dorsal,and ventral epithelium fractions of yak rumen,comparison of bacterial composition in rumen solid,liquid,ventral epithelium fractions of yak and cattle.Finally,we used the metagenomic analysis to explore the microbial functions in the solid and liquid factions of yak rumen.1.We collected samples of solid,liquid,dorsal,and ventral epithelium fractions from five female yaks.The V4 region of bacterial 16 S r RNA genes in each sample was amplified and sequenced on the Mi Seq illumina platform.There were significant differences in the solid,liquid and epithelial-attached bacteria communities in rumen of yaks,and there were also significant differences between ventral and dorsal epithelium fractions.The abundance of Rikenellaceae RC9,the families Lachnospiraceae and Ruminococcaceae,and Fibrobacter spp.were higher in solid fraction,while the abundance of genera Prevotella and Prevotellaceae UCG 003 were higher in the liquid fraction.Campylobacter spp.,Comamonas spp.,Desulfovibrio spp.,and Solobacterium spp.have significantly higher relative abundance in dorsal epithelium,while the relative abundance of Howardella spp.,Prevotellaceae UCG001,Ruminococcaceae UCG 005,and Treponema 2 were higher in the ventral epithelium.The functional profiles of the four fractions significantly differed.Amino acid metabolism,enzyme families,and energy metabolism pathways were enriched in the solid fraction,relative to the liquid fraction,while xenobiotic biodegradation and metabolism pathways were enhanced in the liquid fraction.Cell motility,and membrane transport were enriched in the dorsal epithelium fraction relative to the ventral epithelium,while carbohydrate metabolism,enzyme families,metabolism of terpenoids and polyketides,and biodegradation of xenobiotics were stronger in the dorsal fraction than the ventral epithelium fraction.These results showed that the composition,predicted function and abundance of bacteria in different rumen fractions of the yak were significantly different.2.We collected the 16 S r RNA gene V4 region sequencing data of cattle in different rumen fractions published by De Mulder et al.,and we combined that with the sequencing data of yak to compare the bacterial communities of yak and cattle.Therefore,these results suggested that there is no significant difference in the diversity of bacteria in ventral fraction of yak and cattle rumen.Comparing the OTUs of yak and cattle,it was found that most bacterial communities were shared between yak and cattle,and the number of OTU unique of each niche in the rumen of cattle was smaller than that of yaks.The phyla with the highest relative abundance of both solid and liquid fractions in cattle rumen were Bacteroidetes,followed by Firmicutes and Fibrobacteres.The phyla with the highest relative abundance in ventral rumen of cattle was Firmicutes,followed by Bacteroidetes and Fibrobacteres.The phylum with the highest relative abundance of bacteria attached to the solid,liquid and ventral epithelium fraction of yak was Firmicutes,followed by Bacteroidetes.Lachnoclostridium 10,Lachnospiraceae FCS020 group and Lachnospiraceae UCG006 had higher relative abundance in yak solid fraction than that in solid fraction of cattle,they were related to cellulose degradation and VFA generation,while the relative abundance of Prevotellaceae UCG-003,Eubacterium coprostanoligenes group and Ruminococcaceae UCG-010 had higher relative abundance in yak liquid fraction,they were related to degradation of cellulose and soluble sugar.Treponema 2,Prevotellaceae UCG-001 and Ruminococcaceae UCG-005 were found to be more abundant in yak ventral epithelium fraction,and they were related with Associated with disease and immune inflammation.There were significant differences in bacterial functions between yak and cattle in different rumen fractions.The relative abundance of P42-PWY,FASYN-ELONG-PWY,PWY-6969,POLYISOPRENSYN-PWY,PWY-5913,PWY-3781,FOLSYN-PWY,PANTO-PWY were more abundance in solid fraction of yak.PWY0-162,FASYN-ELONG-PWY,PWY-3781,PWY-841,DENOVOPURINE2-PWY,PWY-6969,PWY-5913,DENOVOPURINE2 –PWY were more abundance in liquid fraction of yak.There is only one pathway was more abundant in ventral fraction of yak rumen:DENOVOPURINE2 –PWY.These results suggested that the density and diversity of bacteria in solid fraction of yak rumen were lower than those in cattle.And the diversity of bacteria in liquid fraction of yak rumen was also lower than that of cattle rumen.In addition,there was no significant difference in the diversity of bacteria in the ventral epithelium fraction between yak and cattle rumen.The significant difference in the relative abundance of bacteria in solid and liquid fractions of yak and cattle were all related to carbohydrate digestion and volatile fatty acid production.The significant difference in the relative abundance of bacteria in yak and cattle rumen ventral fraction is related to host immunity and health.3.Samples were collected from solid and liquid fractions of yak rumen to extract microbial genomic DNA,and sequenced on the Mi Seq illumina platform.A total of486.29 Gb high-quality clean reads were obtained.Based on the NR database,23576687 non-redundant open reading frames(ORFs)were predicted.Using Kraken for taxonomic assignment,the dominant bacteria in the solid and liquid fractions were Bacteroidetes and Firmicutes.A total of 342 medium quality MAGs were obtained.There are 110 MAGs in the solid fraction and 305 in the liquid fraction.less than 20%of them had classification information at the species level.And 10 nearly complete bacterial genomes were obtained,among which 5 were obtained in solid fraction and10 bacterial genomes were obtained from liquid fraction.More than 80% of these genomes have not been found in existing databases and may be new species.Glycoside hydrolases and glycosyltransferases ranked the top two in the abundance of genome-encoded carbohydrates in the solid fraction and the liquid fraction,accounting for more than 80% in both fractions.In the solid fraction,the genome belonging to Fibrobacterota had the largest amount of carbohydrate digestive enzymes encoded by each genome,followed by the genome of Bacteroidota.In the liquid fraction,the genome with the largest number of carbohydrate digestive enzymes encoded per genome belongs to Firmicutes,followed by Fibrobacterota.Therefore,the main enzymes for digestion of cellulose,lignin and pectin were the same in the solid fraction and the liquid fraction,but the abundance of bacteria encoding carbohydrate-digestion enzymes was different between the solid and liquid fractions.In summary,these results showed that bacteria communities in different rumen fractions of yak have significant differences,the bacteria communities in different fractions of yak and cattle were significantly different.The enzymes that digest cellulose,lignin and pectin enzymes in solid and liquid fraction had no significant different,but the abundance of bacteria which encode carbohydrate digestive enzymes in solid fraction and liquid fraction had significantly diffrent.These results provide a new understanding of rumen microbial community and function,and provide theoretical support for improving the regulation and performance of rumen microbes in yaks. |
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