Additional file 1: Table S1. of Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis)

Detailed composition of the diet fed. (DOCX 11 kb

Additional file 4: Figure S3. of Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis)

Methanogenesis pathway (Abundance of enzymes during three different treatments shown in parentheses). (JPG 320 kb

Effect of dietary treatment, fraction and primer and their interactions on relative abundance of rumen bacterial taxa at the genus level.

<p>P: primer; T: treatment; F: fraction; NS: Non-significant;</p><p>***: P<0.001;</p><p>**: P<0.01;</p><p>*: P<0.05.</p><p>Effect of dietary treatment, fraction and primer and their interactions on relative abundance of rumen bacterial taxa at the genus level.</p

Rarefaction plots for three different primer pairs.

<p>Sequence depths a) 200, b) 5000 and c) 7000 displaying species richness (Chao 1 and Observed species) and phylogenetic relationship (Shannon index); (P1: targeting V1–V3 region; P2: targeting V4–V5 region and P3: targeting V6–V8 region).</p

Bacterial Diversity Dynamics Associated with Different Diets and Different Primer Pairs in the Rumen of Kankrej Cattle

<div><p>The ruminal microbiome in herbivores plays a dominant role in the digestion of lignocellulose and has potential to improve animal productivity. Kankrej cattle, a popular native breed of the Indian subcontinent, were used to investigate the effect of different dietary treatments on the bacterial diversity in ruminal fractions using different primer pairs. Two groups of four cows were assigned to two primary diets of either dry or green forages. Each group was fed one of three dietary treatments for six weeks each. Dietary treatments were; K1 (50% dry/green roughage: 50% concentrate), K2 (75% dry/green roughage: 25% concentrate) and K3 (100% dry/green roughage). Rumen samples were collected using stomach tube at the end of each dietary period and separated into solid and liquid fractions. The DNA was extracted and amplified for V1–V3, V4–V5 and V6–V8 hypervariable regions using P1, P2 and P3 primer pairs, sequenced on a 454 Roche platform and analyzed using QIIME. Community compositions and the abundance of most bacterial lineages were driven by interactions between primer pair, dietary treatment and fraction. The most abundant bacterial phyla identified were <i>Bacteroidetes</i> and <i>Firmicutes</i> however, the abundance of these phyla varied between different primer pairs; in each primer pair the abundance was dependent on the dietary treatment and fraction. The abundance of <i>Bacteroidetes</i> in cattle receiving K1 treatment indicate their diverse functional capabilities in the digestion of both carbohydrate and protein while the predominance of <i>Firmicutes</i> in the K2 and K3 treatments signifies their metabolic role in fibre digestion. It is apparent that both liquid and solid fractions had distinct bacterial community patterns (P<0.001) congruent to changes in the dietary treatments. It can be concluded that the P1 primer pair flanking the V1–V3 hyper-variable region provided greater species richness and diversity of bacterial populations in the rumen of Kankrej cattle.</p></div

PCR primer pair targeting different hyper variable regions of 16S rDNA.

<p>PCR primer pair targeting different hyper variable regions of 16S rDNA.</p

Fold changes in STabundant bacterial lineages at family level.

<p>Bacterial lineages a) loss of lineages in <i>Bacteroidetes</i>; b) gain in lineages in <i>Firmicutes</i>, across both fractions and primers, as the animals transitioned from K1 (50% dry/green forage: 50% concentrate) to K3 (100% dry/green forage).</p

Thermal double dendrogram of the most abundant bacterial operational taxonomic units (OTUs).

<p>Rumen fraction a) liquid; b) solid; Primer pair (P1: targeting V1–V3 region; P2: targeting V4–V5 region and P3: targeting V6–V8 region), treatment: (DK1: 50% dry forage: 50% concentrate; DK2: 75% dry forage: 25% concentrate and DK3: 100% dry forage; GK1: 50% green forage: 50% concentrate; GK2: 75% green forage: 25% concentrate; GK3: 100% green forage).</p

Phylogenetic composition by primer pairs and dietary treatments.

<p>Rumen fraction a) liquid; b) solid; Primer pair (P1: targeting V1–V3 region; P2: targeting V4–V5 region and P3: targeting V6–V8 region), treatment: (DK1: 50% dry forage: 50% concentrate; DK2: 75% dry forage: 25% concentrate and DK3: 100% dry forage; GK1: 50% green forage: 50% concentrate; GK2: 75% green forage: 25% concentrate; GK3: 100% green forage) and fraction: solid (S) and liquid (L).</p

Effect of dietary treatment, fraction and primer and their interactions on relative abundance of rumen bacterial phyla.

<p>P: primer; T: treatment; F: fraction; NS: Non-significant;</p><p>***: P<0.001;</p><p>**: P<0.01;</p><p>*: P<0.05.</p><p>Effect of dietary treatment, fraction and primer and their interactions on relative abundance of rumen bacterial phyla.</p