Journal of General and Applied Microbiology最新文献_第4页

PCR bias in 16S rRNA genes caused by GC content leads to insufficient detection of some abundant species in amplicon sequencing analyses of thermophilic microbial communities. 在嗜热微生物群落扩增子测序分析中，GC含量导致的16S rRNA基因的PCR偏置导致一些丰富的物种检测不足。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-10-24 Epub Date: 2025-05-23 DOI: 10.2323/jgam.2025.04.003

Shigeru Kawai, Katsumi Matsuura, Shawn Erin McGlynn

{"title":"PCR bias in 16S rRNA genes caused by GC content leads to insufficient detection of some abundant species in amplicon sequencing analyses of thermophilic microbial communities.","authors":"Shigeru Kawai, Katsumi Matsuura, Shawn Erin McGlynn","doi":"10.2323/jgam.2025.04.003","DOIUrl":"10.2323/jgam.2025.04.003","url":null,"abstract":"Amplicon sequencing is a widely used method for surveying biological diversity. However, the technique is disturbed by PCR bias leading to errors in community composition analyses. In this study, microbial community composition was evaluated in twenty-eight locations of hot spring water with temperatures between 87-48°C at Nakabusa Hot Springs, Japan, using amplicon sequencing analysis with the V4 region of the 16S rRNA gene. In discrepancy with the greenish color and the absorption spectra of the microbial samples, the relative abundance of amplicon sequence variants (ASVs) in the major photosynthetic organisms, Chloroflexus spp., were scarce in any sample when using the annealing temperature of 50°C in amplicon PCR. Changing the annealing temperature to 68ºC significantly improved the detection efficiency of Chloroflexus ASVs, and the obtained numbers were consistent with the presence of the photosynthetic pigments. The abundance of many other microbial ASVs was also dependent on the annealing temperature. The log ratio in the abundance of major ASVs between two annealing temperatures was correlated with the GC content of the 16S rRNA gene, suggesting that even some other major ASVs in the community are seriously affected by PCR bias due to the GC content. Combined usage of results from two different annealing temperatures, rather than a result using a single annealing temperature, seems to be a better way to obtain community structure information with less PCR bias in thermophilic organisms of high 16S rRNA GC content.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Screening system for MAA-CoA productivity using 2-methylcitrate biosensor. 2-甲基柠檬酸盐生物传感器MAA-CoA产率筛选系统。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-10-24 Epub Date: 2025-06-20 DOI: 10.2323/jgam.2025.05.003

Satoshi Hasegawa, Ryota Kato, Daichi Ishihara, Miyu Tsukada, Takumi Ojima, Takashi Maruyama, Soushi Saito, Shigeko Kawai-Noma, Daisuke Umeno

引用次数: 0

Effects of cloned murE gene for peptidoglycan synthesis on morphology and amino acid composition of peptidoglycan of Escherichia coli. 克隆murE肽聚糖合成基因对大肠杆菌肽聚糖形态及氨基酸组成的影响

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-10-23 DOI: 10.2323/jgam.2025.10.002

Sho Noguchi, Sakura Onoue, Hiroaki Kouzai, Kazuyoshi Kawahara

{"title":"Effects of cloned murE gene for peptidoglycan synthesis on morphology and amino acid composition of peptidoglycan of Escherichia coli.","authors":"Sho Noguchi, Sakura Onoue, Hiroaki Kouzai, Kazuyoshi Kawahara","doi":"10.2323/jgam.2025.10.002","DOIUrl":"https://doi.org/10.2323/jgam.2025.10.002","url":null,"abstract":"In the biosynthesis of peptidoglycan (PG), murE protein (MurE) adds a diamino acid at position 3 of the peptide chain of peptidoglycan. The diamino acid that is added by MurE and makes cross-linkage with adjacent peptide chain differs depending on the bacterial species: Gram-negative bacteria add meso-diaminopimelic acid (DAP), while most Gram-positive bacteria add L-lysine (Lys). In this study, the murE gene of Levilactobacillus brevis that transfers Lys in PG synthesis was cloned into Escherichia coli that has DAP-type PG. The transformant cells harboring L. brevis murE showed reduction of colony forming units during cultivation, and were elongated or burst when murE was expressed. Amino acid analysis of solubilized PG revealed that the Lys/DAP ratio increased in the PG of the transformants. Interestingly, aspartic acid that is responsible for the formation of cross-linkages between Lys and other peptide chain in the PG of L. brevis also increased, suggesting that Lys-type PG with Asp cross-linkage was partially formed by the cloning of murE gene.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145345601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanosensitive channels are versatile exporters in microbial cell factories. 机械敏感通道是微生物细胞工厂中通用的出口通道。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-09-26 DOI: 10.2323/jgam.2025.09.002

Tomoyuki Konishi, Yasuyuki Sawada, Ken-Ichi Hashimoto, Isamu Yabe, Masahiro Sokabe, Hisashi Kawasaki

{"title":"Mechanosensitive channels are versatile exporters in microbial cell factories.","authors":"Tomoyuki Konishi, Yasuyuki Sawada, Ken-Ichi Hashimoto, Isamu Yabe, Masahiro Sokabe, Hisashi Kawasaki","doi":"10.2323/jgam.2025.09.002","DOIUrl":"https://doi.org/10.2323/jgam.2025.09.002","url":null,"abstract":"The extracellular export of target chemicals is essential for achieving the target productivity of microbial cell factories (MCFs). We demonstrated that MscCG, a mechanosensitive channel responsible for glutamate export in glutamate-producing MCF of Corynebaterium glutamicum, can export various intracellular low-molecular-weight chemicals outside the cell. The mechanosensitive channels exporter improved L-Lys productivity and conferred substantial 5'-IMP fermentative production ability to the Escherichia coli MCF, which lacks inherent 5'-IMP exporters, indicating that mechanosensitive channels, which are low selective, functioned effectively as MCF exporters. We also demonstrated the effectiveness of a gain-of-function (GOF) mutation of mechanosensitive channels as MCF exporters; however, the essential mechanism underlying this GOF mutation remains unknown. Therefore, we performed molecular dynamics simulations to identify this mechanism at the atomic level. Consequently, we partially elucidated the underlying mechanism of G46D-induced GOF in MscL, which was effective as a 5'-IMP exporter. Specifically, the kink at A38 in the inner transmembrane helix of MscL forming its pore can affect GOF behavior. Based on these results, we conclude that mechanosensitive channels have potential as innovative and versatile exporters of MCFs, capable of enhancing the production efficiency of target chemicals and enabling their production in the absence of natural exporters.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145185956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of the acylglycerolphosphate acyltransferase in Actinoplanes missouriensis. 密苏里放线虫酰基甘油磷酸酰基转移酶的研究。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-09-12 DOI: 10.2323/jgam.2025.09.001

Shixuan Hu, Takeaki Tezuka, Yasuo Ohnishi

引用次数: 0

Diverse fungal communities in commercial karebushi produced with or without a starter culture. 在有或没有发酵剂的情况下，商业鹿茸中不同的真菌群落。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-08-26 DOI: 10.2323/jgam.2025.08.001

Kazuna Yanagi, Kentaro Hiramatsu, Chihiro Kadooka, Atsushi Nishitani, Kayu Okutsu, Yumiko Yoshizaki, Kazunori Takamine, Hisanori Tamaki, Taiki Futagami

引用次数: 0

Characterization of the Azotobacter vinelandii nitrogenase complex expressed in Escherichia coli toward further activity improvement. 在大肠杆菌中表达的氮化固氮菌氮酶复合体的鉴定，以期进一步提高其活性。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-07-15 Epub Date: 2025-01-10 DOI: 10.2323/jgam.2024.12.001

Yusuke Ito, Daisuke Yoshidome, Makoto Hidaka, Yasuko Araki, Kotaro Ito, Saori Kosono, Makoto Nishiyama

引用次数: 0

CRISPR-Cas9 genome editing of miso and soy source yeast Zygosaccharomyces sp. miso和soy来源酵母Zygosaccharomyces sp.的CRISPR-Cas9基因组编辑

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-07-15 Epub Date: 2025-04-30 DOI: 10.2323/jgam.2025.04.002

Tomoo Ogata, Kotori Koide, Shiori Kudou, Miu Suto, Kotaro Uehara, Teruya Kaneko

{"title":"CRISPR-Cas9 genome editing of miso and soy source yeast Zygosaccharomyces sp.","authors":"Tomoo Ogata, Kotori Koide, Shiori Kudou, Miu Suto, Kotaro Uehara, Teruya Kaneko","doi":"10.2323/jgam.2025.04.002","DOIUrl":"10.2323/jgam.2025.04.002","url":null,"abstract":"Genome modification would be useful for developing breeding techniques for haploid Zygosaccharomyces rouxii and natural hybrid allodiploid Zygosaccharomyces sp. yeast strains used in miso and soy sauce production. In this study, genome editing using CRISPR-Cas9 was attempted in Zygosaccharomyces sp. strains. Based on techniques in Saccharomyces cerevisiae, the Cas9 gene and guide RNA (gRNA) were expressed from the same plasmid. Targeting of the ZygoLEU2 gene of haploid Z. rouxii strain DA2 led to of a single-nucleotide insertion in the ORF, resulting in termination of translation at 10 amino acids. This single-base insertion was 3-bp upstream of the protospacer-associated motif (PAM) sequence, suggesting that it occurred during the repair process following the Cas9-induced double-strand break. The transformant was auxotrophic for leucine, verifying that genome editing using CRISPR-Cas9 had occurred. Application of the CRISPR-Cas9 system to allodiploid Zygosaccharomyces sp. strains, which have T- and P-subgenomes, resulted in transformants with base insertions or deletions upstream of the PAM sequence, or insertions of different subgenome sequences. Leucine-auxotrophic transformants were obtained in which the ORF of the ZygoLEU2 gene in both subgenomes were mutated. In some genome-edited strains, a significant region of one subgenome chromosome was missing. Lastly, we applied CRISPR-Cas9 to the gene encoding Hog1, a protein kinase involved in adaptation to high-salt and high-osmolarity conditions. Mutation of the HOG1 genes of both the T- and P-subgenomes by CRISPR-Cas9 significantly reduced growth in high salt and high osmolarity conditions.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144063999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and characterization of a methyl-accepting chemotaxis protein in Ralstonia pseudosolanacearum using chemically undefined materials. 利用化学性质不明确的材料鉴定和表征假龙葵中一个甲基接受趋化蛋白。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-07-15 Epub Date: 2025-03-17 DOI: 10.2323/jgam.2025.03.001

Asmaa Ali Ahmed, Akiko Hida, Takahisa Tajima, Junichi Kato

{"title":"Identification and characterization of a methyl-accepting chemotaxis protein in Ralstonia pseudosolanacearum using chemically undefined materials.","authors":"Asmaa Ali Ahmed, Akiko Hida, Takahisa Tajima, Junichi Kato","doi":"10.2323/jgam.2025.03.001","DOIUrl":"10.2323/jgam.2025.03.001","url":null,"abstract":"Ralstonia pseudosolanacearum is a plant-pathogenic bacterium that causes bacterial wilt in economically important crops. Chemotaxis is required for full virulence in R. pseudosolanacearum. R. pseudosolanacearum Ps29 possesses 20 methyl-accepting chemotaxis proteins (MCPs) and 2 MCP-like chemoreceptors. To understand the role of chemotaxis in plant infection, we are characterizing the functions of these 20 MCPs. Out of 20 MCPs, 8 MCPs have been characterized. To characterize the remaining MCPs, we deleted the 8 genes encoding characterized MCPs in R. pseudosolanacearum Ps29 to construct R. pseudosolanacearum D8. R. pseudosolanacearum D8 was examined for chemotactic responses to several chemically undefined materials including vegetable juices and tryptic soy broth (TSB) to find attractants. R. pseudosolanacearum D8 showed strong responses to green pepper and carrot juices and TSB. We constructed a mutant library of R. pseudosolanacearum D8 by deleting each of the MCP genes. Chemotaxis assays to TSB revealed that an MCP which we named McpD was responsible for sensing an attractant(s) in TSB. Because amino acids are the major constituents of TSB, we measured chemotactic responses of R. pseudosolanacearum D8 to 20 proteinogenic amino acids and found Asp and Glu as the major attractants of McpD and Cys as the minor attractant. R. pseudosolanacearum Ps29 can utilize Asp and Glu as sole carbon and nitrogen sources, suggesting that the role of McpD-mediated chemotaxis is finding growth substrates.","PeriodicalId":15842,"journal":{"name":"Journal of General and Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":0.8,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Screening to isolate Bacillus subtilis mutants with enhanced NADPH levels. 提高NADPH水平的枯草芽孢杆菌突变体的筛选。

IF 0.8 4区生物学

Journal of General and Applied Microbiology Pub Date : 2025-07-15 Epub Date: 2025-01-16 DOI: 10.2323/jgam.2025.01.001

Yuzheng Wu, Shu Ishikawa, Ken-Ichi Yoshida

引用次数: 0