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Miyake, S.

Publications and source records attributed to Miyake, S..

2 recordsLinked to original sources
bioRxiv2018

Description of Schaedlerella arabinophila gen. nov., sp. nov., a D-arabinose utilizing bacterium isolated from feces of C57BL/6J mice and a close relative of Clostridium sp. ASF 502

The use of gnotobiotics has gained large interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotics mouse model, the Altered Schaedler Flora (ASF) has been used for several decades. ASF comprises eight different bacterial species, which have been characterized to different extent, but only few are available through public strain collections. Here, the isolation of a close relative to one of the less studied ASF strains, Clostridium sp. ASF 502, is reported. Isolate TLL-A1, which shares 99.6% 16S rRNA gene sequence identity with Clostridium sp. ASF 502, was obtained from feces of C57BL/6J mice where is was detectable at a relative abundance of less than one percent. D-arabinose was used as sole carbon source in the anaerobic cultivation medium. Growth experiments with TLL-A1 on different carbon sources and analysis of its ~6.5 gigabase genome indicate that TLL-A1 harbors a large gene repertoire to utilize different carbohydrates for growth. Comparative genome analyses of TLL-A1 and Clostridium sp. ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate activating enzymes. Based on physiology and genomic analysis it is proposed to name TLL-A1 to gen. nov. sp. nov Schaedlerella arabinophila TLL-A1 (DSMZ 106076T; KCTC 15657T). The closely related Clostridium sp. ASF 502 is proposed to be renamed to Schaedlerella arabinophila to reflect its taxonomic standing and to keep ASF 502 as strain designation.\n\nImportanceThe Altered Schaedler Flora (ASF) remains an important tool to mechanistically investigate host-microbe interactions in the mammalian alimentary tract. Extensively characterizing the eight different bacterial strains, which are constituting ASF, has the potential to further increase the definition of this widely used model microbial community and to enhance our understanding of how individual microorganism interact with a host and/or how they may affect its physiology. However, some of the ASF strains have unfortunately been lost or are not easily accessible to the scientific community. The isolation and characterization of the here described species, proposed to be named Schaedlerella arabinophila, which is closely related to Clostridium species ASF502, may therefore be an important corner stone in further improving the value of studies using ASF or other defined synthetic microbial communities that require usage of autochthonous microorganisms in gnotobiotic mice.

microbiology↗
bioRxiv2018

Insights into the microbiota of Asian seabass (Lates calcarifer) with tenacibaculosis symptoms and description of sp. nov. Tenacibaculum singaporense

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the Bacteroidetes genus Tenacibaculum, most notably T. maritimum. The impact of tenacibaculosis on fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissue types of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farm fish. The microbiota of diseased farm fish was dominated by Proteobacteria (relative abundance{+/-}standard deviation, 74.5%{+/-}22.8%) and Bacteroidetes (18.07%{+/-}21.7%), the latter mainly comprised by a high abundance of Tenacibaculum species (17.6%{+/-}20.7%). In healthy seabass Proteobacteria had also highest relative abundance (48.04%{+/-}0.02%), but Firmicutes (34.2%{+/-}0.02%) and Fusobacteria (12.0%{+/-}0.03%) were the next two major constituents. Experimentally infected fish developed lesions characteristic for tenacibaculosis, but the microbiota was primarily dominated by Proteobacteria (90.4%{+/-}0.2%) and Firmicutes (6.2%{+/-}0.1%). The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in the commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One strain was isolated and is described here as sp. nov. Tenacibaculum singaporense TLL-A1T (=DSM 106434T, KCTC 62393T). The genome of T. singaporense was sequenced and compared to those of T. maritimum DSM 17995T and the newly sequenced T. mesophilum DSM 13764T.\n\nImportanceFish production from aquaculture facility has become a major source of protein for human consumption and is expected to further grow to meet the growing demands. Devastating fish diseases, such as tenacibaculosis, can eradicate entire stocks of aquaculture fish in a short time and pose a serious threat to individual fish farmers and overall fish production. Understanding the disease processes and the individual microbial players involved has the potential to develop methods to prevent or mitigate infections on aquaculture farms. This study provides important insights into the microbial ecology of tenacibaculosis from an aquaculture facility in Singapore and highlights the complexity of this fish disease at two different disease stages. Furthermore, the isolation of a novel Tenacibaculum species and comparative genome analysis of three different Tenacibaculum species enhance our view of this economically and environmentally important bacterial genus.

microbiology↗