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Kerala Veterinary and Animal Sciences University, Wayanad

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2018 - 20192
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Subject: Animal Genetics and Breeding × Author: TINA SADAN × End date: 2019 ×
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    ThesisItemOpen Access
    RUMEN METAGENOME PROFILES AND METHANE EMISSION LEVELS IN VECHUR AND CROSSBRED CATTLE UNDER DIFFERENT DIETARY REGIMENS
    (Kerala Veterinary and Animal Sciences Mannuthy, Thrissur, 2019-09-30) TINA SADAN; T. V. Aravindakshan
    A 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.
  • Thumbnail Image
    ThesisItemOpen Access
    RUMEN METAGENOME PROFILES AND METHANE EMISSION LEVELS IN VECHUR AND CROSSBRED CATTLE UNDER DIFFERENT DIETARY REGIMENS
    (COLLEGE OF VETERINARY AND ANIMAL SCIENCES-MANNUTHY,THRISSUR, 2018) TINA SADAN; T. V. Aravindakshan
    A study was conducted to assess the rumen metagenome profiles and methane emission levels in Vechur and crossbred cattle under different dietary regimens. 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.