Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.

BACKGROUND: Sika deer (Cervus nippon) have different dietary preferences to other ruminants and are tolerant to tannin-rich plants. Because the rumen bacteria in domestic Sika deer have not been comprehensively studied, it is important to investigate its rumen bacterial population in order to understand its gut health and to improve the productivity of domestic Sika deer. RESULTS: The rumen bacterial diversity in domestic Sika deer (Cervus nippon) fed oak leaves- (OL group) and corn stalks-based diets (CS group) were elucidated using 16S rRNA gene libraries and denaturing gradient gel electrophoresis (DGGE). Overall, 239 sequences were examined from the two groups, 139 clones from the OL group were assigned to 57 operational taxonomic units (OTUs) and 100 sequences from the CS group were divided into 50 OTUs. Prevotella-like sequences belonging to the phylum Bacteroidetes were the dominant bacteria in both groups (97.2% OL and 77% CS), and sequences related to Prevotella brevis were present in both groups. However, Prevotella shahii-like, Prevotella veroralis-like, Prevotella albensis-like, and Prevotella salivae-like sequences were abundant in the OL group compared to those in the CS group, while Succinivibrio dextrinosolvens-like and Prevotella ruminicola-like sequences were prevalent in the CS group. PCR-DGGE showed that bacterial communities clustered with respect to diets and the genus Prevotella was the dominant bacteria in the rumen of domestic Sika deer. However, the distribution of genus Prevotella from two groups was apparent. In addition, other fibrolytic bacteria, such as Clostridium populeti and Eubacterium cellulosolvens were found in the rumen of domestic Sika deer. CONCLUSIONS: The rumen of domestic Sika deer harbored unique bacteria which may represent novel species. The bacterial composition appeared to be affected by diet, and sequences related to Prevotella spp. may represent new species that may be related to the degradation of fiber biomass or tannins. Moreover, the mechanism and biological functions of Prevotella spp. in the rumen ecosystem, and synergistic interactions with other microorganisms should be noticed.

Differences in the methanogen population exist in sika deer (Cervus nippon) fed different diets in China.

Understanding the methanogen structure from sika deer (Cervus nippon) in China may be beneficial to methane mitigation. In the present preliminary study, we investigated the methanogen community in the rumen of domesticated sika deer fed either tannin-rich plants (oak leaf, OL group) or corn stalk (CS group) using 16S rRNA gene clone libraries. Overall, we obtained 197 clone sequences, revealing 146 unique phylotypes, which were assigned to 36 operational taxonomic units at the species level (98 % identity). Methanogens related to the genus Methanobrevibacter were the predominant phylotypes representing 83.9 % (OL library) and 85.9 % (CS library) of the clones. Methanobrevibacter millerae was the most abundant species in both libraries, but the proportion of M. millerae-related clones in the CS library was higher than in the OL library (69.5 and 51.4 %, respectively). Moreover, Methanobrevibacter wolinii-related clones (32.5 %) were predominant in the OL library. Methanobrevibacter smithii-related clones and Methanobrevibacter ruminantium-related clones accounted for 6.5 and 6.6 % in the CS library, respectively. However, these clones were absent from the OL library. The concentrations of butyrate and total short-chain fatty acids (SCFAs) were significantly higher in the OL group, but the concentrations of acetate, propionate, and valerate and the acetate to propionate ratio in the OL group were not significantly different between the two groups. Tannin-rich plants may have affected the distribution of genus Methanobrevibacter phylotypes at the species level and the concentration and composition of SCFAs.

The complete mitochondrial genome sequence of Alopex lagopus (Caniformia: Canidae).

The phylogenetic and taxonomic positions of the blue fox (Alopex lagopus) have long been unclear. In this study, we determined and described the complete mitogenome sequence of A. lagopus for the first time, which is 16,629 bp in length and contains 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 origin of replication on the light-strand and a putative control region. The overall base composition is A: 31.3%, T: 27.8%, C: 26.1% and G: 14.8%, with a slight AT bias (59.1%). Most of them have TAA as the stop codon, except ND2 uses TAG, ND4 uses AGG, Cytb uses AGA and COX3 and ND3 use an incomplete stop codon TA. This information could not only contribute to provide useful molecular data for the species identification, but also to further taxonomic and phylogenetic studies of Alopex and Canidae.

The complete mitochondrial genome of silver fox (Caniformia: Canidae).

Silver fox is color variant of Vulpes vulpes. At present, there are few studies on phylogeny of Canidae and Caniformia. In this article, we determined and described the complete mitogenome of silver fox for the first time, which is 16,723 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, one origin of replication on the light-strand (OL) and a putative control region (CR). The overall base composition is 31.4% A, 27.9% T, 26.0% C, 14.7% G, respectively, with a AT bias (59.3%). Ten protein-coding genes use the initiation codon ATG while ND2, ND3 and ND5 use ATA. Most of them have TAA as the stop codon, except ND2 uses TAG, Cytb uses AGA, and COX3, ND3, ND4 use an incomplete stop codon TA. The information is expected to provide useful molecular data for further taxonomic and phylogenetic studies of Canidae and Caniformia.

The complete mitochondrial genome sequence of Neovison vison (Carnivora: Mustelidae).

The phylogenetic and taxonomic position of the American mink Neovison vison have long been unclear. In this paper, the complete mitogenome of N. vison was sequenced and characterized. The total length was 16,594 bp and typically consists of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, a large control region (CR) and a light-strand replication origin (OL). Gene contents, locations, and arrangements were identical to those of typical vertebrate. The overall base composition is 33.6%, 25.4%, 27.8% and 13.3% for A, C, T and G, respectively, with a moderate bias on AT content (61.4%). This result is expected to provide useful molecular data and contribute to further taxonomic and phylogenetic studies of Mustelidae and Carnivora.