Journal of Microbiology最新文献_第3页

Corrigendum: Transcription Factors Tec1 and Tec2 Play Key Roles in the Hyphal Growth and Virulence of Mucor lusitanicus Through Increased Mitochondrial Oxidative Metabolism. 更正：转录因子Tec1和Tec2通过增加线粒体氧化代谢在lusitanicus的菌丝生长和毒力中发挥关键作用。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-29 DOI: 10.71150/jm.2504100

Viridiana Alejandre-Castaneda, J Alberto Patino-Medina, Marco I Valle-Maldonado, Alexis Garcia, Rafael Ortiz-Alvarado, Leon F Ruiz-Herrera, Karla Viridiana Castro-Cerritos, Joel Ramirez-Emiliano, Martha I Ramirez-Diaz, Victoriano Garre, Soo Chan Lee, Victor Meza-Carmen

引用次数: 0

Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter. 浮膜过滤器富集土壤硝化微生物的基因组图谱。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-29 DOI: 10.71150/jm.2502002

Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Aderonke Odunayo Adigun, Sung-Keun Rhee

{"title":"Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.","authors":"Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Aderonke Odunayo Adigun, Sung-Keun Rhee","doi":"10.71150/jm.2502002","DOIUrl":"https://doi.org/10.71150/jm.2502002","url":null,"abstract":"Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera \"Candidatus Nitrosocosmicus\" and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 4","pages":"e2502002"},"PeriodicalIF":3.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007558","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

Arctic lichen Cladonia borealis-induced cell death is mediated by p53-independent activation of Caspase-9 and PARP-1 signaling in human colorectal cancer cell lines. 北极地衣Cladonia borealis诱导的人类结直肠癌细胞系细胞死亡是由p53独立激活Caspase-9和PARP-1信号介导的。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-29 DOI: 10.71150/jm.2412012

Ju-Mi Hong, Seul Ki Min, Kyung Hee Kim, Se Jong Han, Joung Han Yim, Sojin Kim, Youn-Jung Kim, Il-Chan Kim

{"title":"Arctic lichen Cladonia borealis-induced cell death is mediated by p53-independent activation of Caspase-9 and PARP-1 signaling in human colorectal cancer cell lines.","authors":"Ju-Mi Hong, Seul Ki Min, Kyung Hee Kim, Se Jong Han, Joung Han Yim, Sojin Kim, Youn-Jung Kim, Il-Chan Kim","doi":"10.71150/jm.2412012","DOIUrl":"https://doi.org/10.71150/jm.2412012","url":null,"abstract":"The anti-cancer effects of Cladonia borealis (an Arctic lichen) methanol extract (CBME) on human colon carcinoma HCT116 cells were investigated for the first time. The proliferation of the HCT116 cells treated with CBME significantly decreased in a dose- and time-dependent manner. Flow cytometry results indicated that treatment with CBME resulted in significant apoptosis in the HCT116 cells. Furthermore, immunoblotting and qRT-PCR results revealed the expression of apoptosis-related marker genes and indicated a significant downregulation of the apoptosis regulator B-cell lymphoma expression and upregulation of the cleaved form of poly (ADP-ribose) polymerase as DNA repair and apoptosis regulators and central tumor suppressor p53. Therefore, CBME significantly inhibited cell proliferation by inducing apoptosis via the mitochondrial apoptotic pathway in colon carcinoma cells. Collectively, these data suggested that CBME contained one or more compounds with anti-cancer effects and could be a potential therapeutic agent. Further studies are required to identify candidate compounds and understand the mechanism of action of CBME.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 4","pages":"e2412012"},"PeriodicalIF":3.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040545","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

A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces. 链霉菌生物合成基因簇的基因组挖掘和遗传操作指南。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-29 DOI: 10.71150/jm.2409026

Heonjun Jeong, YeonU Choe, Jiyoon Nam, Yeon Hee Ban

{"title":"A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces.","authors":"Heonjun Jeong, YeonU Choe, Jiyoon Nam, Yeon Hee Ban","doi":"10.71150/jm.2409026","DOIUrl":"https://doi.org/10.71150/jm.2409026","url":null,"abstract":"Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 4","pages":"e2409026"},"PeriodicalIF":3.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030303","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

FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis. FunVIP：基于系统发育分析的真菌验证和鉴定管道。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-29 DOI: 10.71150/jm.2411017

Chang Wan Seo, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Martin Steinegger, Young Woon Lim

{"title":"FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis.","authors":"Chang Wan Seo, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Martin Steinegger, Young Woon Lim","doi":"10.71150/jm.2411017","DOIUrl":"https://doi.org/10.71150/jm.2411017","url":null,"abstract":"The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 4","pages":"e2411017"},"PeriodicalIF":3.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022594","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

Genetic insights into novel lysis suppression by phage CSP1 in Escherichia coli. 大肠杆菌中噬菌体CSP1新型裂解抑制的遗传学见解。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-29 DOI: 10.71150/jm.2501013

Moosung Kim, Sangryeol Ryu

{"title":"Genetic insights into novel lysis suppression by phage CSP1 in Escherichia coli.","authors":"Moosung Kim, Sangryeol Ryu","doi":"10.71150/jm.2501013","DOIUrl":"https://doi.org/10.71150/jm.2501013","url":null,"abstract":"Lysis inhibition (LIN) in bacteriophage is a strategy to maximize progeny production. A clear plaque-forming mutant, CSP1C, was isolated from the turbid plaque-forming CSP1 phage. CSP1C exhibited an adsorption rate and replication dynamics similar to CSP1. Approximately 90% of the phages were adsorbed to the host cell within 12 min, and both phages had a latent period of 25 min. Burst sizes were 171.42 ± 31.75 plaque-forming units (PFU) per infected cell for CSP1 and 168.94 ± 51.67 PFU per infected cell for CSP1C. Both phages caused comparable reductions in viable E. coli cell counts at a low multiplicity of infection (MOI). However, CSP1 infection did not reduce turbidity, suggesting a form of LIN distinct from the well-characterized LIN of T4 phage. Genomic analysis revealed that a 4,672-base pairs (bp) DNA region, encompassing part of the tail fiber gene, CSP1_020, along with three hypothetical genes, CSP1_021, CSP1_022, and part of CSP1_023, was deleted from CSP1 to make CSP1C. Complementation analysis in CSP1C identified CSP1_020, CSP1_021, and CSP1_022 as a minimal gene set required for the lysis suppression in CSP1. Co-expression of these genes in E. coli with holin (CSP1_092) and endolysin (CSP1_091) resulted in lysis suppression. Lysis suppression was abolished by disrupting the proton motive force (PMF), supporting their potential role as antiholin. Additionally, CSP1_021 directly interacts with holin, suggesting that it may function as an antiholin. These findings identify new genetic factors involved in lysis suppression in CSP1, providing broader insights into phage strategies for modulating host cell lysis.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 4","pages":"e2501013"},"PeriodicalIF":3.3,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143972002","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

Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria. 小调控rna作为病原菌抗生素耐药性的关键调节剂。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.71150/jm.2501027

Yubin Yang, Hana Hyeon, Minju Joo, Kangseok Lee, Eunkyoung Shin

引用次数: 0

Advancements in the production of value-added products via methane biotransformation by methanotrophs: Current status and future perspectives. 甲烷氧化菌甲烷生物转化生产增值产品的进展：现状和未来展望。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2412024

Ok Kyung Lee, Jong Seok Lee, Yoonyong Yang, Moonsuk Hur, Kyung Jin Lee, Eun Yeol Lee

引用次数: 0

Progress and challenges in CRISPR/Cas applications in microalgae. CRISPR/Cas在微藻中的应用进展与挑战

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2501028

Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee

{"title":"Progress and challenges in CRISPR/Cas applications in microalgae.","authors":"Quynh-Giao Tran, Trang Thi Le, Dong-Yun Choi, Dae-Hyun Cho, Jin-Ho Yun, Hong Il Choi, Hee-Sik Kim, Yong Jae Lee","doi":"10.71150/jm.2501028","DOIUrl":"10.71150/jm.2501028","url":null,"abstract":"Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have emerged as powerful tools for precise genome editing, leading to a revolution in genetic research and biotechnology across diverse organisms including microalgae. Since the 1950s, microalgal production has evolved from initial cultivation under controlled conditions to advanced metabolic engineering to meet industrial demands. However, effective genetic modification in microalgae has faced significant challenges, including issues with transformation efficiency, limited target selection, and genetic differences between species, as interspecies genetic variation limits the use of genetic tools from one species to another. This review summarized recent advancements in CRISPR systems applied to microalgae, with a focus on improving gene editing precision and efficiency, while addressing organism-specific challenges. We also discuss notable successes in utilizing the class 2 CRISPR-associated (Cas) proteins, including Cas9 and Cas12a, as well as emerging CRISPR-based approaches tailored to overcome microalgal cellular barriers. Additionally, we propose future perspectives for utilizing CRISPR/Cas strategies in microalgal biotechnology.","PeriodicalId":16546,"journal":{"name":"Journal of Microbiology","volume":"63 3","pages":"e2501028"},"PeriodicalIF":3.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803599","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

Advancing microbial engineering through synthetic biology. 通过合成生物学推进微生物工程。

IF 3.3 4区生物学

Journal of Microbiology Pub Date : 2025-03-01 Epub Date: 2025-03-28 DOI: 10.71150/jm.2503100

Ki Jun Jeong

引用次数: 0