Space, time and captivity: quantifying the factors influencing the fecal microbiome of an alpine ungulate

Abstract

The community of microorganisms in the gut is affected by host species, diet and environment and is linked to normal functioning of the host organism. Although the microbiome fluctuates in response to host demands and environmental changes, there are core groups of microorganisms that remain relatively constant throughout the hosts lifetime. Ruminants are mammals that rely on highly specialized digestive and metabolic modifications, including microbiome adaptations, to persist in extreme environments. Here, we assayed the fecal microbiome of four mountain goat (Oreamnos americanus) populations in western North America. We quantified fecal microbiome diversity and composition among groups in the wild and captivity, across populations and in a single group over time. There were no differences in community evenness or diversity across groups, although we observed a decreasing diversity trend across summer months. Pairwise sample estimates grouped the captive population distinctly from the wild populations, and moderately grouped the southern wild group distinctly from the two northern wild populations. We identified 33 genera modified by captivity, with major differences in key groups associated with cellulose degradation that likely reflect differences in diet. Our findings are consistent with other ruminant studies and provide baseline microbiome data in this enigmatic species, offering valuable insights into the health of wild alpine ungulates.

Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

“…Although the members of the phyla Bacteroidetes and Firmicutes are generally dominant in the gut of humans ( 17 ) and animals ( 18 ), the proportions of these two phyla change with shifts in environmental and host factors ( 19 ). Firmicutes have been recognized as “obesity bacteria” because of their functions related to energy harvest and fat storage ( 20 – 22 ), and a higher F/B ratio has generally been associated with obesity and elevated body mass index ( 23 , 24 ). The higher Firmicutes abundance and F/B ratio in the free-range sika deer indicated that these animals utilized their gut microbiota to derive more nutrients to support their increased activities, and the results implied better body condition.…”

Effects of supplemental feeding on the fecal bacterial communities of Rocky Mountain elk in the Greater Yellowstone Ecosystem

“…Genus Ruminococcus UCG-009 was enriched in fed elk, whereas Flexilinea and Erysipelatoclostridium were enriched in unfed elk. Ruminococcus UCG-009 has also been shown to be enriched in captive versus wild Pere David's deer [31], and Flexilinea and Erysipelatoclostridium vary temporally in other wild herbivores [54,55], presumably due to fluctuating forage availability. Overall, these findings suggest that elk gut microbiome composition is relatively robust to dietary changes associated with hay supplementation, but changes to a few key taxa are consistent with patterns identified in studies of other wild herbivore species.…”

Gut microbiome composition predicts summer core range size in a generalist and specialist ungulate

“…Following DADA2 strict quality filtering, ~1.16 million paired-end reads (n MG =709,457, n WTD =457,541) were retained for taxonomic and diversity analyses. Losing this many reads to quality filtering is typical (see [39]), as permitted error rates are extremely low in DADA2, resulting in high certainty among retained reads [61]. White-tailed deer had higher averages of both Pielou’s evenness (mean 0.95, min 0.92, max 0.96, SD 0.012) and Firmicutes to Bacteroidetes ratios (mean 8.3, min 1.49, max 21.5, SD 6.22) than mountain goats (Pielou’s evenness mean 0.92, min 0.84, max 0.95, SD 0.028; Firmicutes to Bacteroidetes ratio mean 6.90, min 3.51, max 12.10, SD 2.43).…”

“…In muskoxen ( Ovibos moschatus ), the abundance of Firmicutes stayed similar across seasons, while Bacteroidetes increased in the summer months, meaning the ratio of Firmicutes to Bacteroidetes is lower in the summer [67]. The ability to conserve bacteria necessary for adding fat, namely high levels of Firmicutes , while exhibiting changes in gut composition suggests ungulates can prepare for the winter even though the gut microbiome is shifting (see [39]). This concept is of importance to white-tailed deer, as diet turnover is pronounced in Ontario [68].…”

“…The validated Illumina 16S rRNA Metagenomic Sequencing Library Preparation (#15044223 rev. B) protocol was followed for library preparation using slight modifications [39]. The V3 and V4 regions of the 16S ribosomal ribonucleic acid (16S rRNA) hypervariable region were targeted with four variants of 341F and 805R primers designed by [40].…”