Dataset Information

Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification.

ABSTRACT: Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia for the synthesis of microbial protein. However, little is known about the diversity and distribution of rumen ureolytic microorganisms. The urease gene (ureC) has been the target gene of choice for analysis of the urea-degrading microorganisms in various environments. In this study, we investigated the predominant ureC genes of the ureolytic bacteria in the rumen of dairy cows using high-throughput sequencing. Six dairy cows with rumen fistulas were assigned to a two-period cross-over trial. A control group (n = 3) were fed a total mixed ration without urea and the treatment group (n = 3) were fed rations plus 180 g urea per cow per day at three separate times. Rumen bacterial samples from liquid and solid digesta and rumen wall fractions were collected for ureC gene amplification and sequencing using Miseq. The wall-adherent bacteria (WAB) had a distinct ureolytic bacterial profile compared to the solid-adherent bacteria (SAB) and liquid-associated bacteria (LAB) but more than 55% of the ureC sequences did not affiliate with any known taxonomically assigned urease genes. Diversity analysis of the ureC genes showed that the Shannon and Chao1 indices for the rumen WAB was lower than those observed for the SAB and LAB (P < 0.01). The most abundant ureC genes were affiliated with Methylococcaceae, Clostridiaceae, Paenibacillaceae, Helicobacteraceae, and Methylophilaceae families. Compared with the rumen LAB and SAB, relative abundance of the OTUs affiliated with Methylophilus and Marinobacter genera were significantly higher (P < 0.05) in the WAB. Supplementation with urea did not alter the composition of the detected ureolytic bacteria. This study has identified significant populations of ureolytic WAB representing genera that have not been recognized or studied previously in the rumen. The taxonomic classification of rumen ureC genes in the dairy cow indicates that the majority of ureolytic bacteria are yet to be identified. This survey has expanded our knowledge of ureC gene information relating to the rumen ureolytic microbial community, and provides a basis for obtaining regulatory targets of ureolytic bacteria to moderate urea hydrolysis in the rumen.

SUBMITTER: Jin D

PROVIDER: S-EPMC5339240 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification.

Jin Di D Zhao Shengguo S Zheng Nan N Bu Dengpan D Beckers Yves Y Denman Stuart E SE McSweeney Christopher S CS Wang Jiaqi J

Frontiers in microbiology 20170307

Ureolytic bacteria are key organisms in the rumen producing urease enzymes to catalyze the breakdown of urea to ammonia for the synthesis of microbial protein. However, little is known about the diversity and distribution of rumen ureolytic microorganisms. The urease gene (ureC) has been the target gene of choice for analysis of the urea-degrading microorganisms in various environments. In this study, we investigated the predominant ureC genes of the ureolytic bacteria in the rumen ...[more]

PMID: 28326079

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Project description:Changes in dietary composition affect the rumen microbiota in ruminants. However, information on the effects of dietary concentrate-to-forage ratio changes on yak rumen bacteria and metabolites is limited. This study characterized the effect of three different dietary concentrate-to-forage ratios (50:50, C50 group; 65:35, C65 group; 80:20, C80 group) on yak rumen fluid microbiota and metabolites using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS) analyses. Rumen fermentation parameters and the abundance of rumen bacteria were affected by changes in the dietary concentrate-to-forage ratio, and there was a strong correlation between them. At the genus level, higher relative abundances of norank_f__F082, NK4A214_group, Lachnospiraceae_NK3A20_group, Acetitomaculum, and norank_f__norank_o__Clostridia_UCG-014 were observed with a high dietary concentrate-to-forage ratio (P < 0.05). Combined metabolomic and enrichment analyses showed that changes in the dietary concentrate-to-forage ratio significantly affected rumen metabolites related to amino acid metabolism, protein digestion and absorption, carbohydrate metabolism, lipid metabolism, and purine metabolism. Compared with the C50 group, 3-methylindole, pantothenic acid, D-pantothenic acid, and 20-hydroxy-leukotriene E4 were downregulated in the C65 group, while spermine and ribose 1-phosphate were upregulated. Compared to the C50 group, Xanthurenic acid, tyramine, ascorbic acid, D-glucuronic acid, 6-keto-prostaglandin F1a, lipoxin B4, and deoxyadenosine monophosphate were upregulated in the C80 group, while 3-methylindole and 20-hydroxy-leukotriene E4 were downregulated. All metabolites (Xanthurenic acid, L-Valine, N-Acetyl-L-glutamate 5-semialdehyde, N-Acetyl-L-glutamic acid, Tyramine, 6-Keto-prostaglandin F1a, Lipoxin B4, Xanthosine, Thymine, Deoxyinosine, and Uric acid) were upregulated in the C80 group compared with the C65 group. Correlation analysis of microorganisms and metabolites provided new insights into the function of rumen bacteria, as well as a theoretical basis for formulating more scientifically appropriate feeding strategies for yak.

Dataset Information

Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on ureC Gene Classification.

Publications

Differences in Ureolytic Bacterial Composition between the Rumen Digesta and Rumen Wall Based on <i>ureC</i> Gene Classification.

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