Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ?75% of the genus-level bacterial and archaeal taxa present in the rumen.publishersversionPeer reviewe

Localization of Ruminal Cellulolytic Bacteria on Plant Fibrous Materials as Determined by Fluorescence In Situ Hybridization and Real-Time PCR

To visualize and localize specific bacteria associated with plant materials, a new fluorescence in situ hybridization (FISH) protocol was established. By using this protocol, we successfully minimized the autofluorescence of orchard grass hay and detected rumen bacteria attached to the hay under a fluorescence microscope. Real-time PCR assays were also employed to quantitatively monitor the representative fibrolytic species Fibrobacter succinogenes and Ruminococcus flavefaciens and also total bacteria attached to the hay. F. succinogenes was found firmly attached to not only the cut edges but also undamaged inner surfaces of the hay. Cells of phylogenetic group 1 of F. succinogenes were detected on many stem and leaf sheath fragments of the hay, even on fragments on which few other bacteria were seen. Cells of phylogenetic group 2 of F. succinogenes were often detected on hay fragments coexisting with many other bacteria. On the basis of 16S rRNA gene copy number analysis, the numbers of bacteria attached to the leaf sheaths were higher than those attached to the stems (P < 0.05). In addition, R. flavefaciens had a greater tendency than F. succinogenes to be found on the leaf sheath (P < 0.01) with formation of many pits. F. succinogenes, particularly phylogenetic group 1, is suggested to possibly play an important role in fiber digestion, because it is clearly detectable by FISH and is the bacterium with the largest population size in the less easily degradable hay stem

Fibrobacter succinogenesを中心とするルーメン内繊維分解コンソーシャム構成細菌の検出および同定

A fibrolytic consortium, dominated by the rumen cellulolytic bacterium Fibrobacter succinogenes, was artificially constructed on hay stems to detect and identify rumen bacteria that can potentially interact with F. succinogenes. Consortium-bacterial members were determined by DGGE and sequencing analysis targeted bacterial 16S rDNA. An artificial consortium was formed in a 2-step incubation of hay stems; the first step with group 1, 2 or 3 F. succinogenes strains, the second step with rumen fluid. After consortium formation, morphologically different bacteria were observed in association with F. succinogenes. DGGE exhibited more than 30 bands, the pattern of which depended on the F. succinogenes group. Sequencing suggested that Butyrivibrio fibrisolvens, Pseudobutyrivibrio ruminis, Clostridium sp., F. succinogenes group 2, Prevotella ruminicola and unclassified Bacteroides were prominent in the group 1 consortium and that Treponema bryantii, B. fibrisolvens, Acinetobacter sp, and Wolinella succinogenes were prominent in the group 2 consortium. However, in the group 3 consortium, F. succinogenes-like bacteria were microscopically undetectable, whereas cellulolytic Ruminococcus albus and F. succinogenes group 1 were prominent, suggesting that the group 3 cannot be a core member of this consortium. This study is the first attempt to identify bacterial members of a fibrolytic consortium dominated by a specific bacterium.ルーメン内繊維分解性細菌Fibrobacter succinogenesと相互作用をもつ細菌種を検出・同定するため、本菌系統グループ1から3の菌株を中心とする繊維分解コンソーシャムをオーチャードグラス乾草上に人為的に作成した（作成コンソーシャム）。作成コンソーシャムにおいてはF. succinogenes様細胞に異なる形態の細菌が付着する様子が電顕観察された。作成コンソーシャムのDGGE解析では30以上のバンドが検出され、そのバンドパターンは主構成員である系統グループの違いを反映していた。グループ1の作成コンソーシャムからはButyrivibrio fibrisolvens, Pseudobutyrivibrio ruminis, Clostridium属細菌, F. succinogenesグループ2, Prevotella ruminicolaおよび未培養のBacteroides属細菌が、グループ2のそれからはTreponema bryantii, B. fibrisolvens, Acinetobacter属細菌およびWolinella succinogenesが構成細菌として同定された。一方、グループ3のコンソーシャムでは主構成員であるはずのF. succinogenesの観察頻度は下がり、他の繊維分解菌に置き換わっていたため、グループ3のF. succinogenesはコンソーシャムで主導的な役割を担い得ないと考えられた。本研究は特定の細菌を中心として構成される繊維分解コンソーシャムに対し、その構成細菌を明らかにしようとした初めての報告である

Microbial community structure of the bovine rumen as affected by feeding cashew nut shell liquid, a methane-inhibiting and propionate-enhancing agent

The effect of cashew nut shell liquid (CNSL) feeding on bacterial and archaeal community of the bovine rumen was investigated by analyzing clone libraries targeting 16S rRNA genes, methyl-coenzyme reductase A-encoding genes (mcrA), and their respective transcripts. Rumen samples were collected from three non-lactating cows fed on a hay and concentrate diet with or without CNSL supplementation. DNA and complementary DNA (cDNA) libraries were generated for investigating rumen microbial communities. MiSeq analysis also was performed to understand more comprehensively the changes in the microbial community structures. Following CNSL supplementation, the number of operational taxonomical unit (OTU) and diversity indices of bacterial and archaeal community were decreased. Bacterial OTUs belonging to Proteobacteria, including Succinivibrio, occurred at a higher frequency with CNSL feeding, especially in cDNA libraries. The methanogenic archaeal community became dominated by Methanomicrobium. A bacterial community shift also was observed in the MiSeq data, indicating that CNSL increased the proportion of Succinivibrio and other genera known to be involved in propionate production. Methanogenic archaeal community shifts to increase Methanoplanus and to decrease Met hanobrevibacter also were observed. Together, these results imply the occurrence of significant changes in rumen communities, not only for bacteria but also for methanogens, following CNSL feeding

Association between Experience of Pet Ownership and Psychological Health among Socially Isolated and Non-Isolated Older Adults

The psychological health effects of pet ownership have been widely studied, but only a few studies investigated its impact among socially isolated older adults. The present study aims to investigate the psychological health of older adults with or without the experience of pet (i.e., dog or cat) ownership who are socially isolated or not socially isolated. This study used cross-sectional data from 9856 community-dwelling older adults in a metropolitan area of Japan. Social and non-social isolation and type of pet ownership (i.e., dog or cat) were stratified to examine the psychological health. Logistic regression models indicated that, after adjusting for demographic and potential confounders, socially isolated older adults who never owned a dog were 1.22 times more likely to report lower psychological health in comparison to socially isolated current or past dog owners. No such difference was observed among cat owners. The results suggest that the experience of dog ownership may be effective to improve the psychological health among socially isolated older adult

Transportation modes and social participation in older drivers and non-drivers: Results from urbanised Japanese cities

Age-related changes contribute to shifting transportation modes, which affects participation in social activities. Driving status has been highlighted in this context, but there is less evidence on the differences in transportation modes regarding how conducive they are to social participation between drivers and non-drivers. This study examined the relationship between transportation modes and social participation among older adults. The participants were 17,364 older adults aged 65–84 years living in Tokyo and Yokohama, Japan, which are urbanised cities with well-developed public transportation systems. We obtained data on transportation modes used at least once per week, including walking, cycling, car use as a driver, car use as a passenger, train use, and bus use. Social participation was defined as participation in the following social groups at least once per month: public social activities (i.e. neighbourhood associations and senior clubs) and private social activities (i.e. volunteering, sports, and hobbies). We performed a logistic regression analysis and included product terms between driving status (drivers or non-drivers) and other modes of transportation. Subgroup analyses were conducted regardless of the significance of the product term, as they would yield valuable information. There was a significant relationship of the product term between driving status and cycling with participation in private social activities; cycling was associated with 30% (95% CI: 1.12, 1.51) higher odds in drivers and 68% (1.52, 1.85) higher odds of participation in those activities in non-drivers. For both driving statuses, cycling was associated with higher odds of participation in public social activities, and train and bus use showed higher odds of participation in private social activities. These results suggest that cycling and public transportation use are crucial for participation in social activities among both older drivers and non-drivers living in urbanised cities, and the importance of cycling may be emphasised in nondrivers. Our findings would help the transportation, urban planning, and public health sectors develop plans to encourage older adults to participate in social activities