{"title":"Bifidobacterial key genetic factors for development of infant gut ecosystems","authors":"H. Matsumoto, T. Matsuki","doi":"10.4109/JSLAB.29.19","DOIUrl":"https://doi.org/10.4109/JSLAB.29.19","url":null,"abstract":"","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128116935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The human gut microbiome includes commensal bacteria from genus Bifidobacterium, which primarily colonizes the region from the small intestine to the colon. This region has a mucus layer composed mainly of mucin glycoproteins. In addition to providing a habitat for the microbiota, the mucus is also a potential glycan source. Therefore, interaction with mucus could provide a competitive advantage for Bifidobacterium within the gut ecosystem. In this review, we first outline the role of Bifidobacterium extracellular proteins in bacterium-mucus interactions, and then we focus on extracellular glycoside hydrolases and a recently discovered pilus-mediated colonization process unique
{"title":"Factors involved in the interaction between Bifidobacterium and the host mucosal surface","authors":"Keita Nishiyama, T. Mukai","doi":"10.4109/JSLAB.29.13","DOIUrl":"https://doi.org/10.4109/JSLAB.29.13","url":null,"abstract":"The human gut microbiome includes commensal bacteria from genus Bifidobacterium, which primarily colonizes the region from the small intestine to the colon. This region has a mucus layer composed mainly of mucin glycoproteins. In addition to providing a habitat for the microbiota, the mucus is also a potential glycan source. Therefore, interaction with mucus could provide a competitive advantage for Bifidobacterium within the gut ecosystem. In this review, we first outline the role of Bifidobacterium extracellular proteins in bacterium-mucus interactions, and then we focus on extracellular glycoside hydrolases and a recently discovered pilus-mediated colonization process unique","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117305876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Isolation and application of lactic acid bacteria and yeasts from coastal “ Satoumi ” environments","authors":"T. Kuda","doi":"10.4109/JSLAB.28.51","DOIUrl":"https://doi.org/10.4109/JSLAB.28.51","url":null,"abstract":"","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129328240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Novel fatty acid metabolism in lactic acid bacteria and the physiological function of metabolites","authors":"S. Kishino, J. Ogawa","doi":"10.4109/JSLAB.28.58","DOIUrl":"https://doi.org/10.4109/JSLAB.28.58","url":null,"abstract":"","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121883130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Dynamism and diversity of human gut microbial community","authors":"Ayaka Uchikawa, Masaru Tanaka, J. Nakayama","doi":"10.4109/JSLAB.28.74","DOIUrl":"https://doi.org/10.4109/JSLAB.28.74","url":null,"abstract":"","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128838070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Many fermented foods are produced in Japan, and the preparation conditions are set very carefully so that strict microbial control can be carried out. Even the manufacturing methods of them have been developed empirically, specific microorganism is established to be reproduced well in the fermentation medium of each food from ancient times. Although the history of bacterial flora research of fermented foods is old, it has become possible to obtain more detailed information by development of high-throughput 16S rRNA gene analysis using next-generation sequencing. Analysis of the bacterial flora of the fermented food of Ishikawa prefecture, Japan, showed that various bacterial species are intermingled among the fermented products, and that sometimes different kinds of bacteria became dominant even for the same type of food. Lactobacillus sakei, which is known as the predominant lactic acid bacterium in Japanese sake starter, prominently proliferated in “kaburazushi” that contains rice koji, which is a shared ingredient among the both foods. Six “narezushi” products obtained from Noto peninsula were found to be dominated by various Lactobacillus and Pediococcus species. In “yamahai-moto”, nitrate-reducing bacteria normally found in the early stage of fermentation was hardly detected, while Lactobacillus acidipiscis was present at the stage. This review illustrates, through introducing several case studies, how the bacterial flora of fermented foods are robustly and/or variably controlled to achieve the final dominance of lactic
{"title":"Transition and diversity of bacterial flora found in traditional fermented foods","authors":"T. Koyanagi","doi":"10.4109/JSLAB.28.84","DOIUrl":"https://doi.org/10.4109/JSLAB.28.84","url":null,"abstract":"Many fermented foods are produced in Japan, and the preparation conditions are set very carefully so that strict microbial control can be carried out. Even the manufacturing methods of them have been developed empirically, specific microorganism is established to be reproduced well in the fermentation medium of each food from ancient times. Although the history of bacterial flora research of fermented foods is old, it has become possible to obtain more detailed information by development of high-throughput 16S rRNA gene analysis using next-generation sequencing. Analysis of the bacterial flora of the fermented food of Ishikawa prefecture, Japan, showed that various bacterial species are intermingled among the fermented products, and that sometimes different kinds of bacteria became dominant even for the same type of food. Lactobacillus sakei, which is known as the predominant lactic acid bacterium in Japanese sake starter, prominently proliferated in “kaburazushi” that contains rice koji, which is a shared ingredient among the both foods. Six “narezushi” products obtained from Noto peninsula were found to be dominated by various Lactobacillus and Pediococcus species. In “yamahai-moto”, nitrate-reducing bacteria normally found in the early stage of fermentation was hardly detected, while Lactobacillus acidipiscis was present at the stage. This review illustrates, through introducing several case studies, how the bacterial flora of fermented foods are robustly and/or variably controlled to achieve the final dominance of lactic","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124908403","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yasuhiro Tanizawa, T. Fujisawa, J. Mashima, Kyungbum Lee, M. Tohno, M. Sakamoto, M. Ohkuma, Yasukazu Nakamura, K. Shimizu, K. Kadota
The International Nucleotide Sequence Database Collaboration (INSDC) has maintained a primary sequence database that collects experimentally-determined nucleotide sequence data directly from researchers. Now data deposition to the INSDC is mandatory for research publication at most of the scientific journals. However, the procedure to deposit data to the INSDC is a big burden, especially for those who are not familiar with computer skills. Recently, we have developed a genome annotation pipeline DFAST, which also assists data deposition to the INSDC. In this article, we show the instruction to deposit annotated genome sequence data using the DFAST web service. Supplementary materials are available at our web site, http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html#about_book_ JSLAB.
{"title":"Methods for analyzing next-generation sequencing data X. Registration to DDBJ through Mass Submission System","authors":"Yasuhiro Tanizawa, T. Fujisawa, J. Mashima, Kyungbum Lee, M. Tohno, M. Sakamoto, M. Ohkuma, Yasukazu Nakamura, K. Shimizu, K. Kadota","doi":"10.4109/JSLAB.28.94","DOIUrl":"https://doi.org/10.4109/JSLAB.28.94","url":null,"abstract":"The International Nucleotide Sequence Database Collaboration (INSDC) has maintained a primary sequence database that collects experimentally-determined nucleotide sequence data directly from researchers. Now data deposition to the INSDC is mandatory for research publication at most of the scientific journals. However, the procedure to deposit data to the INSDC is a big burden, especially for those who are not familiar with computer skills. Recently, we have developed a genome annotation pipeline DFAST, which also assists data deposition to the INSDC. In this article, we show the instruction to deposit annotated genome sequence data using the DFAST web service. Supplementary materials are available at our web site, http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html#about_book_ JSLAB.","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124769833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：