BackgroundThe rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach.ResultsTaxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples.ConclusionsResults reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2340-4) contains supplementary material, which is available to authorized users.

Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (P<0.01) compared to the liquid fraction, whereas bacteria considered to be utilizers of the degraded product (i.e. Prevotella, Bacteroides, Parabacteroides, Paludibacter and Victivallis) were dominant in the liquid fraction (P<0.05). Likewise, expression of fibre degrading enzymes and related carbohydrate binding modules (CBMs) occurred in the solid fraction. When metagenomic and metatranscriptomic data were compared, it was found that some genera and species were transcriptionally more active, although they were in low abundance, making an important contribution to fibre degradation and its further metabolism in the rumen. This study also identified some of the transcriptionally active genera, such as Caldicellulosiruptor and Paludibacter, whose potential has been less-explored in rumen. Overall, the comparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis.

A study was carried out on infertile (acyclic and endometriotic) crossbred cows under field and normal cyclic (all 4 phases of cycle) as well as pregnant (3, 6, 9 month) crossbred cows of University farm to evaluate the plasma progesterone (P4) and estradiol (E2) hormones by RIA, and plasma total protein, cholesterol, calcium and phosphorus concentrations by using assay kits on chemistry analyzer. The mean progesterone levels in cows during the diestrus phase and in pregnancy were significantly (p less than 0.05) higher than those during proestrus, estrus, metestrus, anestrus, and endometritis status. At six month of gestation, the mean P4 level was significantly (p less than 0.05) higher than at early or late gestation. The mean E2 values at estrus and 9th month of gestation were highest (p less than 0.01) as compared to another status. The mean plasma total protein and cholesterol levels were significantly (p less than 0.05) lower during six and nine months of pregnancy than during cyclic and acyclic stages. The cholesterol profile of all three stages of pregnancy and endometriotic cows were statistically similar, though distinctly low at 9 month of pregnancy. Plasma levels of P4 and E2 thus correlated with the physiological and clinical status of cows, while cholesterol levels reflected steroidogenic status. The mean plasma calcium and inorganic phosphorus concentrations of cyclic, acyclic, pregnant and endometriotic cows, however, did not differ significantly.

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An experiment was conducted to study the effect of different feeding regimes on hematological profile of crossbred cows. Study was conducted on 18 crossbred cows which were distributed into three treatment groups comprising of 6 animals in each group. Animals of T 1 (Farmers' feeding) group were maintained as per the feeding regime followed by small and marginal farmers. Animals of T 2 (Modified feeding) group comprised of feeding with scientific interventions with resources available with farmers. Animals of T 3 (Farm feeding) group were fed as per feeding followed at Livestock Research Station. Average WBC count (10 3 /µL) was significantly (p<0.05) more in T 3 (7.98±0.12) as compared to T 1 (7.43±0.17) and T 2 (7.52±0.17) groups. Lymphocyte (10 3 /µL) was maximum in T 3 (3.32±0.07), followed by T 1 (3.24±0.10) and T 2 (3.12±0.09) group but there was no significant difference among treatment groups. Average monocyte (10 3 /µL) level was significantly higher in T 3 (0.61±0.01) when compared with T 1 (0.57±0.01) and T 2 (0.56±0.01) groups. Granulocyte (10 3 /µL) was significantly (p<0.05) higher in T 3 (4.05±0.10) as compared to T 1 (3.62±0.11) group. However, the value of T 2 (3.85±0.12) group was at par with T 1 and T 3 groups. Average RBC (10 6 /µL) was significantly (p<0.05) more in T 3 (6.69±0.08) in comparison to T 2 (6.35±0.07) group, whereas, the value of T 1 (6.50±0.07) group was at par with T 2 and T 3 groups. Hb (g/dL) was significantly (p<0.05) higher in T 3 (10.54±0.10) as compared to T 1 (9.50±0.08) and T 2 (9.62±0.10) groups. Average PCV (%) was significantly (p<0.05) higher in T 3 (33.71±0.32) when compared with T 1 (30.04±0.27) and T 2 (30.56±0.35) groups. MCV was 46.73±0.42, 48.32±0.38 and 50.77±0.32 fL in T 1 , T 2 and T 3 groups, respectively which differed significantly (p<0.05) among each other. Average of MCH was 14.80±0.17, 15.30±0.13 and 15.77±0.08 pg in T 1 , T 2 and T 3 groups, respectively which also differed significantly (p<0.05) among each other. MCHC was 31.63±0.15, 31.52±0.12 and 31.22±0.11 g/dL in T 1 , T 2 and T 3 groups, respectively which did not differ significantly among each other. It may be concluded from the present study that WBC, Monocyte, Hb, PCV, MCH and MCHC were significantly (p<0.05) more in T 3 as compared to T 1 and T 2 groups, whereas all the parameters except MCV and MCH in T 1 and T 2 group were at par which shows that modified feeding did not influence hematological profile. Although the health of animals was at par in all treatment groups, production and reproduction performance was different among the treatment groups.