RUMEN METAGENOME PROFILES AND METHANE EMISSION LEVELS IN VECHUR AND CROSSBRED CATTLE UNDER DIFFERENT DIETARY REGIMENS

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dc.contributor.advisorT. V. Aravindakshan
dc.contributor.authorTINA SADAN
dc.date.accessioned2022-11-02T10:09:43Z
dc.date.available2022-11-02T10:09:43Z
dc.date.issued2019-09-30
dc.descriptionSubmitted in partial fulfillment of the requirement for the degree of Master of Veterinary Science of Animal Genetics and Breedingen_US
dc.description.abstractA study was conducted to assess the rumen metagenome profiles and methane emission levels in Vechur and crossbred cattle under different dietaryregimens. Feeding patterns were designed to have an increasing proportion of forage and a decreasing proportion of the concentrate mix. A total of ten adult cows comprising five in each genetic group maintained on standard ration (Forage: concentrate ratio of 50:50) formed the material for the whole metagenomic study. Out of twelve adult cows, six adult cows each of Vechur and crossbred cattle fed with forage: concentrate ratio of 75:25 and 100:0 for a period of three weeks were selected as the experimental animals for 16S rRNA based metagenome study. Rumen liquor and rumen gas samples were collected from all the experimental animals. DNA samples isolated from rumen liquor using standard procedure were pooled genetic group wise and subjected to metagenome sequencing using Illumina HiSeq 2500 platform and further bioinformatics analysis. The concentrations of methane (per cent) in the gas samples were determined using a methane analyser. Research findings from whole metagenomic study revealed that bacteria followed by Archaea and Eukaryota dominated in the Vechur as well as the crossbred rumen samples. In Vechur and crossbred cattle rumen, 1086 and 1262 microbial species were observed exclusively and 4731 species were shared between habitats. There was a significant difference in total microbial species abundance between two genetic groups. Diversity indices displayed a higher microbial diversity in Vechur cows compared to crossbred cows and also there was a significant difference in diversity between genetic groups. Functional annotation of contigs carried out by SEED classification revealed sequence reads related to carbohydrate and protein metabolism were the most abundant in rumen of both genetic groups. A significant difference in genes associated with different metabolic pathway as revealed by KEGG pathway analysis was found between two genetic groups. The 16S rRNA based metagenome sequencing study showed that Bacteroidetes and Firmicutes were the predominant phyla in both genetic groups. An increase in the Firmicutes to Bacteroidetes ratio observed with the increase in roughage proportion. There was highly significant difference in bacterial diversity indices and no significant difference in total bacterial phylum abundance between diets and genetic groups. Comparison of methane emission levels in Vechur and crossbred cattle under different diets confirmed the effect of genetic group and diet on methane emission levels. Significantly higher methane emission levels were observed for Vechur cattle and 100 per cent forage dietary regimen in both genetic groups.The 16S rRNA based metagenome sequencing study showed that Bacteroidetes and Firmicutes were the predominant phyla in both genetic groups. An increase in the Firmicutes to Bacteroidetes ratio observed with the increase in roughage proportion. There was highly significant difference in bacterial diversity indices and no significant difference in total bacterial phylum abundance between diets and genetic groups. Comparison of methane emission levels in Vechur and crossbred cattle under different diets confirmed the effect of genetic group and diet on methane emission levels. Significantly higher methane emission levels were observed for Vechur cattle and 100 per cent forage dietary regimen in both genetic groups.en_US
dc.identifier.urihttps://krishikosh.egranth.ac.in/handle/1/5810189529
dc.keywordsRUMEN METAGENOME PROFILES, METHANE EMISSION LEVELS IN VECHUR AND CROSSBRED CATTLE, DIETARY REGIMENS, CATTLE OF KERALA, Vechur cattle, Crossbred cattle of Kerala,RUMEN MICROBIAL COMMUNITY, rumen microbes and physiological parameters, Influence of Diet, Influence of host factors, Culture techniques and limitation, Transition to Molecular techniques, METAGENOMICS,EXTRACTION OF DNA, METAGENOME SEQUENCING, Bioinformatic tools,MetaSPAdes, MetaGeneAnnotator,Diamond,MEGAN,Taxonomic analysis and functional analysis, 6S rRNA AMPLICON SEQUENCING, METHANE PRODUCTION FROM RUMINANTS, Methanogenesis, methanogenic abundance, Rumen liquor collection, Rumen gas collection, DNA ISOLATION, Protocol for total DNA isolation from rumen liquo, Agarose gel electrophoresis, Nanodrop spectrophotometry, Cluster generation, Paired- End sequencing, Sequencing by synthesis, De novo Assembly, ORF prediction,OTUs classification, ESTIMATION OF METHANE, Mann-Whitney test, G-test / Fisher's test, Evenness indices, Shannon-Wiener diversity index,en_US
dc.language.isoEnglishen_US
dc.pages151 p.en_US
dc.publisherKerala Veterinary and Animal Sciences Mannuthy, Thrissuren_US
dc.research.problemGenerate and compare rumen metagenome profiles of Vechur and crossbred cattle under standard feeding and management conditions, Study the effect of dietary regimens on the rumen bacterial communities and their comparison among the two genetic groups, Compare methane emission levels in Vechur and crossbred cattle fed under different dietary regimens.en_US
dc.subAnimal Genetics and Breedingen_US
dc.themeRUMEN METAGENOME PROFILES AND METHANE EMISSION LEVELS IN VECHUR AND CROSSBRED CATTLE UNDER DIFFERENT DIETARY REGIMENSen_US
dc.these.typeM.V.Sc.en_US
dc.titleRUMEN METAGENOME PROFILES AND METHANE EMISSION LEVELS IN VECHUR AND CROSSBRED CATTLE UNDER DIFFERENT DIETARY REGIMENSen_US
dc.typeThesisen_US
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