The Effects of Selenium on Rumen Fermentation Parameters and Microbial Metagenome in Goats

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Abstract

This study evaluated the effects of selenium yeast (SY) on rumen fermentation parameters, rumen bacterial diversity, and expression pathways in goats. A total of 18 Qianbei-pockmarked weather goats from Guizhou (body weight, 25.75 ± 1.75 kg; mean ± standard deviation) were assigned to three groups according to a completely randomized design. Control group (CON, n = 6) kids were fed a basal diet, while treatment 1 (LS, n = 6) and treatment 2 (HS, n = 6) kids were fed a basal diet with 2.4 and 4.8 mg/kg SY, respectively. The feeding trial lasted for 74 days. The results indicated that the ruminal fluid of LS goats had significantly higher levels of propionic, caproic, isobutyric, and isovaleric acids than that of the CON. The levels of butyric and valeric acids were higher in the HS group than in the CON. The acetate:propionate ratio was significantly higher in the CON than in the two treatments. In addition, the inclusion of 2.4 mg/kg SY can lead to a significant decrease in the relative abundances of Euryarchaeota, and Proteobacteria at the phylum level compared to the CON and the HS groups. At the genus level, the LS group had a significant decrease in the relative abundance of Methanobrevibacter and Sarcina, whereas it could lead to a significant increase in the relative abundance of Clostridium in the ruminal fluid relative of the other two groups. At the species level, the LS group had a significant decrease in the relative abundance of bacterium_P3, bacterium_P201, and Sarcina_sp._DSM_11001 compared to the other groups. Moreover, the CON group had a significant decrease in the relative abundance of bacterium_P201 compared to the other two treatments. Compared to the CON, the addition of 2.4 mg/kg SY significantly enriched carbohydrate metabolism pathways in the ruminal fluid for gene encoding. Additionally, goats receiving SY showed a significant upregulation of glycosyl transferase and carbohydrate binding module pathways. These results suggest that dietary supplementation with SY modulates fermentation parameters, and it affects microbial diversity and microbial metagenome in the rumen of Qianbei-pockmarked goats.

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KEGG: new perspectives on genomes, pathways, diseases and drugs

Minoru Kanehisa, Miho Furumichi, Mao Tanabe … (2016)

KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as a functional ortholog of genes and proteins. Higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules. In the past the KO database was developed for the purpose of defining nodes of molecular networks, but now the content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases. The newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined. Furthermore, the DISEASE and DRUG databases have been improved by systematic analysis of drug labels for better integration of diseases and drugs with the KEGG molecular networks. KEGG is moving towards becoming a comprehensive knowledge base for both functional interpretation and practical application of genomic information.

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Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition.

P.J. van Soest, J.B. Robertson, B.A. Lewis (1991)

There is a need to standardize the NDF procedure. Procedures have varied because of the use of different amylases in attempts to remove starch interference. The original Bacillus subtilis enzyme Type IIIA (XIA) no longer is available and has been replaced by a less effective enzyme. For fiber work, a new enzyme has received AOAC approval and is rapidly displacing other amylases in analytical work. This enzyme is available from Sigma (Number A3306; Sigma Chemical Co., St. Louis, MO). The original publications for NDF and ADF (43, 53) and the Agricultural Handbook 379 (14) are obsolete and of historical interest only. Up to date procedures should be followed. Triethylene glycol has replaced 2-ethoxyethanol because of reported toxicity. Considerable development in regard to fiber methods has occurred over the past 5 yr because of a redefinition of dietary fiber for man and monogastric animals that includes lignin and all polysaccharides resistant to mammalian digestive enzymes. In addition to NDF, new improved methods for total dietary fiber and nonstarch polysaccharides including pectin and beta-glucans now are available. The latter are also of interest in rumen fermentation. Unlike starch, their fermentations are like that of cellulose but faster and yield no lactic acid. Physical and biological properties of carbohydrate fractions are more important than their intrinsic composition.

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Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

Gemma Henderson, Faith Cox, Siva Ganesh … (2015)

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.