The Bacterial Microbiome in the Small Intestine of Hooded Seals (Cystophora cristata).

Arctic hooded seals (Cystophora cristata) are monogastric carnivores that go through extreme fasting and re-feeding in early life. They are born isolated on sea ice; suckle high-fat milk for four days and may then fast for up to one month before they start hunting and feeding on small prey (fish and crustaceans). Previous studies of the gut microbiota in pinnipeds have focused on the large intestine, while little data exist on the small intestinal microbiota. In this study, the bacterial microbiome in the proximal and distal small intestine of four captive two-year old seals (two males and two females) fed herring (Clupea harengus) was sampled post-mortem and characterized using 16S rRNA metabarcoding from the V1-V3 hypervariable region of the 16S ribosomal RNA (rRNA) genes. The seals were originally born in the wild and taken into human care at the end of the suckling period. Molecular-based analysis using Illumina Hiseq resulted in 569,910 16S rRNA sequences from the four seals (both sampling sites together). Taxonomical classification applying a naive Bayesian algorithm gave 412 Operational Taxonomic Units (OTUs). Firmicutes was the major phylum across samples (Proximal (P): 90.5% of total sequences, on average; Distal (D): 94.5%), followed by Actinobacteria (P: 7%; D: 0.3%) and Proteobacteria (P: 1.7%; D: 1.9%). Bacterial spp. belonging to the Clostridium (P: 54.1%; D: 41.6%) and SMB53 (P: 15.3%; D: 21.5%) constituted the major genera in both the proximal and distal small intestine. Furthermore, comparison with hindgut and fecal samples from geographically diverse marine mammals highlighted similarities in the microbiome between our seals and those sharing similar aquatic environments. This study has provided a first reliable glimpse of the bacterial microbiota in the small intestine microbiome of hooded seals.

Characterization of the cecum microbiome from wild and captive rock ptarmigans indigenous to Arctic Norway.

Rock ptarmigans (Lagopus muta) are gallinaceous birds inhabiting arctic and sub-arctic environments. Their diet varies by season, including plants or plant parts of high nutritional value, but also toxic plant secondary metabolites (PSMs). Little is known about the microbes driving organic matter decomposition in the cecum of ptarmigans, especially the last steps leading to methanogenesis. The cecum microbiome in wild rock ptarmigans from Arctic Norway was characterized to unveil their functional potential for PSM detoxification, methanogenesis and polysaccharides degradation. Cecal samples were collected from wild ptarmigans from Svalbard (L. m. hyperborea) and northern Norway (L. m. muta) during autumn/winter (Sept-Dec). Samples from captive Svalbard ptarmigans fed commercial pelleted feed were included to investigate the effect of diet on microbial composition and function. Abundances of methanogens and bacteria were determined by qRT-PCR, while microbial community composition and functional potential were studied using 16S rRNA gene sequencing and shotgun metagenomics. Abundances of bacteria and methanogenic Archaea were higher in wild ptarmigans compared to captive birds. The ceca of wild ptarmigans housed bacterial groups involved in PSM-degradation, and genes mediating the conversion of phenol compounds to pyruvate. Methanomassiliicoccaceae was the major archaeal family in wild ptarmigans, carrying the genes for methanogenesis from methanol. It might be related to increased methanol production from pectin degradation in wild birds due to a diet consisting of primarily fresh pectin-rich plants. Both wild and captive ptarmigans possessed a broad suite of genes for the depolymerization of hemicellulose and non-cellulosic polysaccharides (e.g. starch). In conclusion, there were no physiological and phenotypical dissimilarities in the microbiota found in the cecum of wild ptarmigans on mainland Norway and Svalbard. While substantial differences in the functional potential for PSM degradation and methanogenesis in wild and captive birds seem to be a direct consequence of their dissimilar diets.

A Comparative Study on the Faecal Bacterial Community and Potential Zoonotic Bacteria of Muskoxen (Ovibos moschatus) in Northeast Greenland, Northwest Greenland and Norway.

Muskoxen (Ovibos moschatus) are ruminants adapted to a high-fibre diet. There is increasing interest in the role that gut microbes play in the digestion and utilization of these specialized diets but only limited data available on the gut microbiome of high-Arctic animals. In this study, we metabarcoded the 16S rRNA region of faecal samples from muskoxen of Northeast Greenland, Northwest Greenland and Norway, and quantified the effects of physiological and temporal factors on bacterial composition. We found significant effects of body mass, year of sampling and location on the gut bacterial communities of North East Greenland muskoxen. These effects were however dwarfed by the effects of location, emphasizing the importance of the local ecology on the gut bacterial community. Habitat alterations and rising temperatures may therefore have a considerable impact on muskoxen health and reproductive success. Moreover, muskoxen are hunted and consumed in Greenland, Canada and Alaska; therefore, this study also screened for potential zoonoses of food safety interest. A total of 13 potentially zoonotic genera were identified, including the genera Erysipelothrix and Yersinia implicated in recent mass die-offs of the muskoxen themselves.

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions.

Reindeer (Rangifer tarandus tarandus) are large Holarctic herbivores whose heterogeneous diet has led to the development of a unique gastrointestinal microbiota, essential for the digestion of arctic flora, which may include a large proportion of lichens during winter. Lichens are rich in plant secondary metabolites, which may affect members of the gut microbial consortium, such as the methane-producing methanogenic archaea. Little is known about the effect of lichen consumption on the rumen and cecum microbiotas and how this may affect methanogenesis in reindeer. Here, we examined the effects of dietary lichens on the reindeer gut microbiota, especially methanogens. Samples from the rumen and cecum were collected from two groups of reindeer, fed either lichens (Ld: n = 4), or a standard pelleted feed (Pd: n = 3). Microbial densities (methanogens, bacteria and protozoa) were quantified using quantitative real-time PCR and methanogen and bacterial diversities were determined by 454 pyrosequencing of the 16S rRNA genes. In general, the density of methanogens were not significantly affected (p>0.05) by the intake of lichens. Methanobrevibacter constituted the main archaeal genus (>95% of reads), with Mbr. thaueri CW as the dominant species in both groups of reindeer. Bacteria belonging to the uncharacterized Ruminococcaceae and the genus Prevotella were the dominant phylotypes in the rumen and cecum, in both diets (ranging between 16-38% total sequences). Bacteria belonging to the genus Ruminococcus (3.5% to 0.6%; p = 0.001) and uncharacterized phylotypes within the order Bacteroidales (8.4% to 1.3%; p = 0.027), were significantly decreased in the rumen of lichen-fed reindeer, but not in the cecum (p = 0.2 and p = 0.087, respectively). UniFrac-based analyses showed archaeal and bacterial libraries were significantly different between diets, in both the cecum and the rumen (vegan::Adonis: pseudo-F<0.05). Based upon previous literature, we suggest that the altered methanogen and bacterial profiles may account for expected lower methane emissions from lichen-fed reindeer.

First insight into the faecal microbiota of the high Arctic muskoxen (Ovibos moschatus).

The faecal microbiota of muskoxen (n=3) pasturing on Ryøya (69° 33' N 18° 43' E), Norway, in late September was characterized using high-throughput sequencing of partial 16S rRNA gene regions. A total of 16 209 high-quality sequence reads from bacterial domains and 19 462 from archaea were generated. Preliminary taxonomic classifications of 806 bacterial operational taxonomic units (OTUs) resulted in 53.7-59.3 % of the total sequences being without designations beyond the family level. Firmicutes (70.7-81.1 % of the total sequences) and Bacteroidetes (16.8-25.3 %) constituted the two major bacterial phyla, with uncharacterized members within the family Ruminococcaceae (28.9-40.9 %) as the major phylotype. Multiple-library comparisons between muskoxen and other ruminants indicated a higher similarity for muskoxen faeces and reindeer caecum (P>0.05) and some samples from cattle faeces. The archaeal sequences clustered into 37 OTUs, with dominating phylotypes affiliated to the methane-producing genus Methanobrevibacter (80-92 % of the total sequences). UniFrac analysis demonstrated heterogeneity between muskoxen archaeal libraries and those from reindeer and roe deer (P=1.0e-02, Bonferroni corrected), but not with foregut fermenters. The high proportion of cellulose-degrading Ruminococcus-affiliated bacteria agrees with the ingestion of a highly fibrous diet. Further experiments are required to elucidate the role played by these novel bacteria in the digestion of this fibrous Artic diet eaten by muskoxen.