Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

The analysis of 16S rDNA sequence of bacteria in feces of Hokkaido native horses and light horses were performed to compare the hindgut microbiota between the two breeds. One hundred and four bacterial 16S rDNA clones (57 clones from four native horses and 47 clones from two light horses) were obtained. Only four sequences (3.8% of total sequences) showed 97% or more similarity to known species. The sequences were mainly affiliated with Cytophaga-Flavobacter-Bacteroides and low GC Gram-positive bacteria (LGCGP). Proportion of LGCGP was higher in light horses. Other phyla including Verrucomicrobia, Spirochaetes and Archaea were detected only for native horses, suggesting high diversity of microbiota in native horses. In LGCGP, clusters related to known cellulolytic species were found only for native horses, while a cluster related to soluble sugar-utilizing species was detected only for light horses. The library composition-comparing software LIBSHUFF showed significant (P < 0.05) difference of fecal microbiota between the horse breeds. The number of Fibrobacter succinogenes-related sequence and the frequency of detection of novel groups were found to be higher in native horses by selective amplification analysis. The results suggest that genetic diversity and population size of the F. succinogenes group are higher in the hindgut of native horses.

A total of 32 wild Hokkaido sika deer ( Cervus nippon yesoensis ) were shot (13 in summer, nine in autumn and 10 in winter) in the Syari district, Shiretoko Peninsula of Hokkaido Island, Japan. The ingested foods, rumen fermentation parameters and microbes were determined to evaluate digestive strategy and food availability in each season. Ingested foods and ruminal characteristics greatly varied by season. Rumen digesta mainly comprised of graminoids in summer, graminoids and agricultural products in autumn, and bark and twigs in winter. Rumen pH showed seasonal differences ( P < 0.05) and was lowest in summer, highest in winter, and intermediate in autumn, reflecting the seasonal differences in ruminal concentration of total volatile fatty acids which were significantly lower ( P < 0.05) in winter than in summer and autumn. Acetate proportions were significantly higher in winter than in other seasons ( P < 0.05), while the opposite trend was seen in proportions of propionate and butyrate. Rumen ammonia levels showed significant seasonal differences ( P < 0.05), decreasing from summer to autumn to winter. Rumen protozoa levels in autumn and winter decreased to 28 and 10% of the levels observed in summer, respectively ( P < 0.05 for both). The rumen bacteria level in winter was lower ( P < 0.05) than that in autumn, but no difference was seen for the other seasonal comparisons. Gram negative cocci were present in significantly higher proportions in winter than in other seasons ( P < 0.05), while Gram negative curved rods were less frequently observed in winter ( P < 0.05). Based on these results, wild sika deer in this area are shown to survive with rumen microbial populations altered with the dietary conditions that vary greatly by season.

Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.

| INTRODUC TI ONWild ruminant animals are excellent models for the functional surveillance of rumen microbes (Kobayashi, 2006), since these animals are expected to harbor specific rumen microbes in response to the dietary conditions to which they are exposed. Changes of rumen microbiota likely depend on the area in which the wild animals inhabit. In particular, harsh dietary conditions might select for rumen microbiota to digest and ferment fibrous materials as a main dietary ingredient in order to maximize nutrient extraction. This is because the rumen is the main digestive organ for degrading fibrous foods by microbes and also acts as a reservoir of ingested foods (Itabashi, 1998).Hokkaido, the northernmost island of Japan, is home to more than a million head of wild sika deer (Hokkaido sika deer, Cervus nippon yesoensis), many of which live in snowy areas with limited access to food. We have elucidated seasonal changes of body size, ingesta, body fat reserve, and rumen fermentation products of sika deer in the Shiretoko Peninsula of Hokkaido, characterized by severe winter conditions (long duration of low temperatures AbstractRumen digesta was obtained from wild Hokkaido sika deer to compare bacterial flora between summer and winter. Bacterial flora was characterized with molecular-based approaches and enrichment cultivation. Bacteroidetes was shown as a major phylum followed by Firmicutes, with similar proportions in both seasons. However, two phylogenetically unique groups in Bacteroidetes were found in each season: unknown group A in winter and unknown group B in summer. The ruminal abundance of unknown group A was the highest followed by Ruminococcus flavefaciens in winter.Moreover, the abundance of these two was higher in winter than in summer. In contrast, the abundance of unknown group B was higher in summer than in winter. In addition, this group showed the highest abundance in summer among the bacteria quantified. Unknown group A was successfully enriched by cultivating with oak bark and sterilized rumen fluid, particularly that from deer. Bacteria of this group were distributed in association with the solid rather than the liquid rumen fraction, and were detected as small cocci. Accordingly, unknown group A is assumed to be involved in degradation of fibrous materials. These results suggest that wild Hokkaido sika deer develop a rumen bacterial flora in response to changes in dietary conditions. K E Y W O R D Secology, fiber digestion, quantitation, rumen bacteria, sika deer