Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing

<div><p>The ability of rumen microorganisms to use fibrous plant matter plays an important role in ruminant animals; however, little information about rumen colonization by microbial populations after weaning has been reported. In this study, high-throughput sequencing was used to investigate the establishment of this microbial population in 80 to 110-day-old goats. Illumina sequencing of goat rumen samples yielded 101,356,610 nucleotides that were assembled into 256,868 reads with an average read length of 394 nucleotides. Taxonomic analysis of metagenomic reads indicated that the predominant phyla were distinct at different growth stages. The phyla Firmicutes and Synergistetes were predominant in samples taken from 80 to 100-day-old goats, but Bacteroidetes and Firmicutes became the most abundant phyla in samples from 110-day-old animals. There was a remarkable variation in the microbial populations with age; Firmicutes and Synergistetes decreased after weaning, but Bacteroidetes and Proteobacteria increased from 80 to 110 day of age. These findings suggested that colonization of the rumen by microorganisms is related to their function in the rumen digestive system. These results give a better understanding of the role of rumen microbes and the establishment of the microbial population, which help to maintain the host’s health and improve animal performance.</p></div

Rarefaction analysis of the different samples.

<p>Rarefaction curves of OTUs clustered at 97% sequence identity across different samples.</p

Genera-level composition of the rumen microbiome.

<p>A color-coded bar plot showing the average bacterial genera distribution across the different age groups that were sampled.</p

The relative abundance (%) of cellulose-degrading bacteria in different age groups of goats.

<p>The relative abundance (%) of cellulose-degrading bacteria in different age groups of goats.</p

Diversity estimation of the 16S rRNA gene libraries of the rumen of goats from the sequencing analysis^a.

<p>^a The operational taxonomic units (OTUs) were defined with 3% dissimilarity. The richness estimators (ACE and Chao) and diversity indices (Shannon and Simpson) were calculated.</p><p>^b The 80-day-old group samples included goats 21, 22 and 23; the 90-day-old group samples included goats 31, 32 and 33; the 100-day-old group samples included goats 41, 42 and 43; the 110-day-old group samples included goats 51, 52 and 53.</p><p>Diversity estimation of the 16S rRNA gene libraries of the rumen of goats from the sequencing analysis<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117811#t001fn001" target="_blank">^a</a>.</p

A heat map of the rumen microbiome composition at the species level.

<p>The heat map indicates the relative percentage of each genera for the different age groups sampled.</p

Temporal changes in the relative abundance (% reads) of (A) the most dominant phylum and (B) the most dominant genera in the rumen microbial community of goats with age.

<p>Error bars represent the SD of three samples. Boxes with a different letter above the error bars are significantly different at P<0.05 or P<0.1 (Firmicutes) by <i>t</i>-test analyses.</p