Exploring the Goat Rumen Microbiome from Seven Days to Two Years - Fig 1

<p>The compositions of all microbiome at Kingdom level (a), bacteria (b) and archaea (c) at Phylum level of goat’s rumen in different age groups.</p

Principal coordinate analysis (PCoA) of the community structure using Bray-Curtis, Jclass and ThetaYC distances in Bacteria and Archaea of goats’ rumen.

<p>Different shapes represent different age groups and colors represent different diets.</p

Exploring the Goat Rumen Microbiome from Seven Days to Two Years

<div><p>Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. We found that the bacterial communities were mainly composed of Bacteroidetes, Firmicutes, and Proteobacteria across all age groups. The relative abundance of Firmicutes was stable across all age groups. While changes in relative abundance were observed in Bacteroidetes and Proteobacteria, these two phyla reached a stable stage after weaning (day 90). Euryarchaeota (82%) and Thaumarchaeota (15%) were the dominant phyla of Archaea. Crenarchaeota was also observed, although at a very low relative abundance (0.68% at most). A clear age-related pattern was observed in the diversity of bacterial community with 59 OTUs associated with age. In contrast, no age-related OTU was observed in archaea. In conclusion, our results suggested that from 7 days to 2 years, the ruminal microbial community of our experimental goats underwent significant changes in response to the shift in age and diet.</p></div

Relative abundance of the main Bacterial phyla: Bacteroidetes, Proteobacteria and Firmicutes.

<p>The top and bottom boundaries of each box indicate the 75th and 25th quartile values, respectively. The horizontal lines within each box represent the mean values.</p

Alpha diversities within each age group in bacteria and Archaea respectively.

<p>Diversity was measured by Shannon index; Richness and evenness were measured by the Chao 1 and Simpson evenness index, respectively. The top and bottom boundaries of each box indicate the 75th and 25th quartile values, respectively. The horizontal lines within each box represent the median values.</p

Characterization of the Gut Microbiota in the Red Panda (<i>Ailurus fulgens</i>)

<div><p>The red panda is the only living species of the genus <i>Ailurus</i>. Like giant pandas, red pandas are also highly specialized to feed mainly on highly fibrous bamboo. Although several studies have focused on the gut microbiota in the giant panda, little is known about the gut microbiota of the red panda. In this study, we characterized the fecal microbiota from both wild (n = 16) and captive (n = 6) red pandas using a pyrosequecing based approach targeting the V1-V3 hypervariable regions of the 16S rRNA gene. Distinct bacterial communities were observed between the two groups based on both membership and structure. Wild red pandas maintained significantly higher community diversity, richness and evenness than captive red pandas, the communities of which were skewed and dominated by taxa associated with Firmicutes. Phylogenetic analysis of the top 50 OTUs revealed that 10 of them were related to known cellulose degraders. To the best of our knowledge, this is the first study of the gut microbiota of the red panda. Our data suggest that, similar to the giant panda, the gut microbiota in the red panda might also play important roles in the digestion of bamboo.</p></div

Relative abundance of OTUs at the phylum (A) and genus (B) level in the fecal microbiota from wild and captive red pandas.

<p>Relative abundance of OTUs at the phylum (A) and genus (B) level in the fecal microbiota from wild and captive red pandas.</p

Principal coordinate analysis of the community membership (A) and structure (B) using Jaccard and Theta YC distances, respectively.

<p>Green squares and yellow circles represent captive and wild red panda bacterial communities, respectively. Distances between symbols on the ordination plot reflect relative dissimilarities in community memberships or structures.</p

Comparison of community alpha diversities between the wild and captive red pandas.

<p>Diversity was measured by inverse Simpson (A) and Shannon index (B); Richness (C) and evenness (D) were measured by the number of observed OTUs and Shannon Evenness index, respectively. The top and bottom boundaries of each box indicate the 75^th and 25^th quartile valudes, respectively. The black lines within each box represent the median values. Different lowercase letters above the boxplots indicate significant differences in alpha diversities between wild and captive pandas (P<0.001, Mann Whitney test).</p

Neighbor-joining tree showing the phylogenetic relationship among the top 50 OTUs in this study (red) with known cellulose degraders (blue) and OTUs identified in the giant panda (green).

<p>Different phyla were shaded by different colors: green, Firmicutes; purple, Actinobacteria; orange, Bacteroidetes; blue, Proteobacteria. All bootstrap values > 50% were shown on the tree.</p