To determine the functionality and safety of lactic acid bacteria (LAB), the study using model animals was performed frequently. However, with ambiguous study settings, there is a possibility of overlooking the efficacy of LAB. In this review, I mentioned important information about the small intestine that was one of the main functional organs by LAB administration. Small intestine was not responded universally by LAB administration, whereas it was responded region-specific. It is well known that LAB administration induced villous elongation in the weaning piglets, however this elongation was only detected at middle and ileo-cecal junction of the small intestine. Peyer’s patch (PP) is a main gut immune site in the small intestine. When mice with LAB administration were sacrificed and collected the PP around the duodenum (jPP) and PP around the ileo-cecal junction (iPP), cytokine expressions were differed between the jPP and iPP. Furthermore, cytokine expression was differed among the time after administration of LAB
{"title":"Response is differed among the regions of the small intestine by lactic acid bacteria administration","authors":"T. Tsukahara","doi":"10.4109/jslab.30.32","DOIUrl":"https://doi.org/10.4109/jslab.30.32","url":null,"abstract":"To determine the functionality and safety of lactic acid bacteria (LAB), the study using model animals was performed frequently. However, with ambiguous study settings, there is a possibility of overlooking the efficacy of LAB. In this review, I mentioned important information about the small intestine that was one of the main functional organs by LAB administration. Small intestine was not responded universally by LAB administration, whereas it was responded region-specific. It is well known that LAB administration induced villous elongation in the weaning piglets, however this elongation was only detected at middle and ileo-cecal junction of the small intestine. Peyer’s patch (PP) is a main gut immune site in the small intestine. When mice with LAB administration were sacrificed and collected the PP around the duodenum (jPP) and PP around the ileo-cecal junction (iPP), cytokine expressions were differed between the jPP and iPP. Furthermore, cytokine expression was differed among the time after administration of LAB","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131173654","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}
Among bacteriocins, ribosomally synthesized bacterial antimicrobial peptides, those produced by lactic acid bacteria, in particular, are expected to be used as safe antimicrobial agents for food preservation. Novel bacteriocins with excellent properties have been extensively explored, and functional analysis of the biosynthetic genes has been conducted to elucidate its structure, biosynthesis mechanism and action mechanism. The biosynthetic proteins are encoded on the vicinity of the bacteriocin precursor gene, and the biosynthetic gene cluster includes the genes encoding proteins responsible for self-immunity against their own bacteriocins, secretion of bacteriocins, posttranslational modification and production regulation. The functions of these biosynthetic genes are expected to be applied to secretory production of peptides and introduction of modified structures to various peptides. In this review, we will introduce our novel bacteriocins produced by lactic acid bacteria, focusing on determination of biosynthetic genes and their
{"title":"Functional analysis of biosynthetic genes for bacteriocins","authors":"T. Zendo, Shun Iwatani, K. Sonomoto","doi":"10.4109/jslab.30.18","DOIUrl":"https://doi.org/10.4109/jslab.30.18","url":null,"abstract":"Among bacteriocins, ribosomally synthesized bacterial antimicrobial peptides, those produced by lactic acid bacteria, in particular, are expected to be used as safe antimicrobial agents for food preservation. Novel bacteriocins with excellent properties have been extensively explored, and functional analysis of the biosynthetic genes has been conducted to elucidate its structure, biosynthesis mechanism and action mechanism. The biosynthetic proteins are encoded on the vicinity of the bacteriocin precursor gene, and the biosynthetic gene cluster includes the genes encoding proteins responsible for self-immunity against their own bacteriocins, secretion of bacteriocins, posttranslational modification and production regulation. The functions of these biosynthetic genes are expected to be applied to secretory production of peptides and introduction of modified structures to various peptides. In this review, we will introduce our novel bacteriocins produced by lactic acid bacteria, focusing on determination of biosynthetic genes and their","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129884244","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":"ABCs for analysis of gut microbiota","authors":"R. Inoue","doi":"10.4109/jslab.30.27","DOIUrl":"https://doi.org/10.4109/jslab.30.27","url":null,"abstract":"","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123944622","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":"Methodology of the isolation of lactic acid bacteria strains","authors":"N. Tanaka","doi":"10.4109/jslab.30.3","DOIUrl":"https://doi.org/10.4109/jslab.30.3","url":null,"abstract":"","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115251590","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}
Genetic engineering of lactic acid bacteria is a difficult task for the beginners due to large difference in strains of interest and poor access for genetic tools. In this review, based on the author’ s experiences, experimental directions and methods for selecting the host strain and vectors; transformation of lactic acid bacteria; optimization of expression system; gene disruption/insertion; cultivation of recombinants
{"title":"The directions and methods of genetic engineering and cultivation of lactic acid bacteria for the beginners","authors":"K. Okano","doi":"10.4109/jslab.30.8","DOIUrl":"https://doi.org/10.4109/jslab.30.8","url":null,"abstract":"Genetic engineering of lactic acid bacteria is a difficult task for the beginners due to large difference in strains of interest and poor access for genetic tools. In this review, based on the author’ s experiences, experimental directions and methods for selecting the host strain and vectors; transformation of lactic acid bacteria; optimization of expression system; gene disruption/insertion; cultivation of recombinants","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124943768","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}
Yoshihisa Wakita, H. Kanda, Koji Takazumi, Y. Tsuchiya
Saccharomyces cerevisiae is a representative yeast used for alcohol production. Production of alcohol from milk using S. cerevisiae is not easy, as this species is unable to hydrolyse lactose. Lactobacillus delbrueckii subsp. bulgaricus (LDB) is able to hydrolyse lactose into galactose and glucose, and is widely used in yogurt production. In this study, production of alcohol from milk was attempted by multiple fermentation using S. cerevisiae and LDB. Firstly, strain LDB48A-12, released from catabolite repression, was obtained from LDB48P by N-methyl-N ’-nitro-N-nitrosoguanidine mutagenesis. LDB48A-12 showed high ability of lactose degradation. Surprisingly, growth speed and lactate production of LDB48A-12 were found to be lower than those of LDB48P. Fermentation of 10% skim milk solution using LDB48A-12 and S. cerevisiae SBC3207 for 4 days at 30℃ or 37℃ produced approximately 1~1.5% of alcohol, which was 1.5 times that produced using LDB48P. In addition, decrease in pH was inhibited. These results were thought to demonstrate novel alcoholic milk fermentation. Comparison of genome sequences revealed mutations in RpoA and DnaA in LDB48A-12. These genes are related to catabolite repression and replication of genome DNA, respectively, suggesting that combined mutation of these genes leads to the preferable phenotype for alcoholic milk fermentation.
{"title":"Alcohol fermentation of milk by multiple fermentation","authors":"Yoshihisa Wakita, H. Kanda, Koji Takazumi, Y. Tsuchiya","doi":"10.4109/jslab.29.145","DOIUrl":"https://doi.org/10.4109/jslab.29.145","url":null,"abstract":"Saccharomyces cerevisiae is a representative yeast used for alcohol production. Production of alcohol from milk using S. cerevisiae is not easy, as this species is unable to hydrolyse lactose. Lactobacillus delbrueckii subsp. bulgaricus (LDB) is able to hydrolyse lactose into galactose and glucose, and is widely used in yogurt production. In this study, production of alcohol from milk was attempted by multiple fermentation using S. cerevisiae and LDB. Firstly, strain LDB48A-12, released from catabolite repression, was obtained from LDB48P by N-methyl-N ’-nitro-N-nitrosoguanidine mutagenesis. LDB48A-12 showed high ability of lactose degradation. Surprisingly, growth speed and lactate production of LDB48A-12 were found to be lower than those of LDB48P. Fermentation of 10% skim milk solution using LDB48A-12 and S. cerevisiae SBC3207 for 4 days at 30℃ or 37℃ produced approximately 1~1.5% of alcohol, which was 1.5 times that produced using LDB48P. In addition, decrease in pH was inhibited. These results were thought to demonstrate novel alcoholic milk fermentation. Comparison of genome sequences revealed mutations in RpoA and DnaA in LDB48A-12. These genes are related to catabolite repression and replication of genome DNA, respectively, suggesting that combined mutation of these genes leads to the preferable phenotype for alcoholic milk fermentation.","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114183306","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}
Yuh Shiwa, Satomi Ito, Y. Matsumoto, Tsukasa Suzuki, T. Ishige, T. Kumagai, N. Fujita, Yuji Yamamoto, N. Tanaka
We investigated the effects of heat-killed Lactobacillus paracasei K71 (K71）on lipid metabolism and gut microbiota in an ob/ob mouse model of obesity. Wild-type and ob/ob (ob-AIN group) mice were fed an AIN-93G diet or an AIN-93G diet containing K71 (ob-K71 group) for 90 d. Serum lipids, hepatic gene expression, and gut microbial populations were evaluated. K71 intake had no significant effect on body weight or lipid metabolism in the liver, while serum non-esterified fatty acids (NEFA) were lower in the ob-K71 group than in the ob-AIN group. In addition, the expression of serine palmitoyl transferase (SPT)-1, a key enzyme in the formation of ceramides associated with insulin resistance, was also lower in the livers of the ob-K71 group than in those of the ob-AIN group. Sequencing of the 16S ribosomal RNA gene revealed that K71 intake suppressed the changes in gut microbiota related to type 2 diabetes and nonalcoholic steatohepatitis. Our results suggest that K71 ingestion alters gut microbiota composition and improves insulin resistance via the ceramide
{"title":"Effects of Lactobacillus paracasei K71 on gut microbiota composition and lipid metabolism in ob/ob mice.","authors":"Yuh Shiwa, Satomi Ito, Y. Matsumoto, Tsukasa Suzuki, T. Ishige, T. Kumagai, N. Fujita, Yuji Yamamoto, N. Tanaka","doi":"10.4109/jslab.29.152","DOIUrl":"https://doi.org/10.4109/jslab.29.152","url":null,"abstract":"We investigated the effects of heat-killed Lactobacillus paracasei K71 (K71）on lipid metabolism and gut microbiota in an ob/ob mouse model of obesity. Wild-type and ob/ob (ob-AIN group) mice were fed an AIN-93G diet or an AIN-93G diet containing K71 (ob-K71 group) for 90 d. Serum lipids, hepatic gene expression, and gut microbial populations were evaluated. K71 intake had no significant effect on body weight or lipid metabolism in the liver, while serum non-esterified fatty acids (NEFA) were lower in the ob-K71 group than in the ob-AIN group. In addition, the expression of serine palmitoyl transferase (SPT)-1, a key enzyme in the formation of ceramides associated with insulin resistance, was also lower in the livers of the ob-K71 group than in those of the ob-AIN group. Sequencing of the 16S ribosomal RNA gene revealed that K71 intake suppressed the changes in gut microbiota related to type 2 diabetes and nonalcoholic steatohepatitis. Our results suggest that K71 ingestion alters gut microbiota composition and improves insulin resistance via the ceramide","PeriodicalId":117947,"journal":{"name":"Japanese Journal of Lactic Acid Bacteria","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122342412","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}
Galaxy is an integrative data analysis environment run on the web browser which users can use without using Linux command line. The previous article showed an introduction to the Galaxy system and the basic usage of the public Galaxy server “Galaxy Main.” In this article, using the last article’s results, we present the features to share the analysis results (history) with the other users, or ones to apply the analysis procedures (workflow) to the other data. We also show the useful Galaxy’s features such as copying data across histories, or the direct data import from remote servers. We found a compatibility issue on Internet Explorer with the Galaxy system. Thus we recommend using Google Chrome or Firefox to try the procedures we show in this article. Supplementary materials are available online at: http://www.iu.a.u-tokyo.ac.jp/~kadota/r_seq.html#about_book_JSLAB.
{"title":"Methods for analyzing next-generation sequencing data XII.Galaxy - Sharing histories and workflows","authors":"Tomoko Terada, Tazro Ohta, K. Shimizu, K. Kadota","doi":"10.4109/jslab.29.79","DOIUrl":"https://doi.org/10.4109/jslab.29.79","url":null,"abstract":"Galaxy is an integrative data analysis environment run on the web browser which users can use without using Linux command line. The previous article showed an introduction to the Galaxy system and the basic usage of the public Galaxy server “Galaxy Main.” In this article, using the last article’s results, we present the features to share the analysis results (history) with the other users, or ones to apply the analysis procedures (workflow) to the other data. We also show the useful Galaxy’s features such as copying data across histories, or the direct data import from remote servers. We found a compatibility issue on Internet Explorer with the Galaxy system. Thus we recommend using Google Chrome or Firefox to try the procedures we show in this article. Supplementary materials are available online at: 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":"13 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121005362","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}
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