Pub Date : 2024-09-24DOI: 10.1007/s00284-024-03902-7
Si-Tong Song, Chun Yan Li, Chun Tao Gu
A novel lactic acid bacterial strain (designated N163-3-2T), isolated from traditional Chinese pickle ('Suan cai'), was characterized using a polyphasic approach. Strain N163-3-2T was most closely related to the type strains of Lacticaseibacillus baoqingensis, Lacticaseibacillus manihotivorans, and Lacticaseibacillus porcinae, having 97.9-98.4% 16S rRNA gene, 82.0-85.1% pheS, 87.5-87.8% rpoA, and 85.8-86.7% concatenated pheS and rpoA sequence similarities. Strain N163-3-2T had 74.4-81.7% ANI, 22.6-23.9% dDDH, and 74.0-75.1% AAI values with L. baoqingensis 47-3T, L. manihotivorans DSM 13343T and L. porcinae JCM 19617T, less than the threshold for species demarcation (95-96%, 70% and 95-96%, respectively), indicating that strain N163-3-2T represented a novel species of the genus Lacticaseibacillus. Based upon the data obtained in the present study, a novel species, Lacticaseibacillus jixiensis sp. nov., is proposed, and the type strain is N163-3-2T (= CCTCC AB 2024125T = JCM 36999T).
{"title":"Lacticaseibacillus jixiensis sp. nov., Isolated from Traditional Chinese Pickle.","authors":"Si-Tong Song, Chun Yan Li, Chun Tao Gu","doi":"10.1007/s00284-024-03902-7","DOIUrl":"https://doi.org/10.1007/s00284-024-03902-7","url":null,"abstract":"<p><p>A novel lactic acid bacterial strain (designated N163-3-2<sup>T</sup>), isolated from traditional Chinese pickle ('Suan cai'), was characterized using a polyphasic approach. Strain N163-3-2<sup>T</sup> was most closely related to the type strains of Lacticaseibacillus baoqingensis, Lacticaseibacillus manihotivorans, and Lacticaseibacillus porcinae, having 97.9-98.4% 16S rRNA gene, 82.0-85.1% pheS, 87.5-87.8% rpoA, and 85.8-86.7% concatenated pheS and rpoA sequence similarities. Strain N163-3-2<sup>T</sup> had 74.4-81.7% ANI, 22.6-23.9% dDDH, and 74.0-75.1% AAI values with L. baoqingensis 47-3<sup>T</sup>, L. manihotivorans DSM 13343<sup>T</sup> and L. porcinae JCM 19617<sup>T</sup>, less than the threshold for species demarcation (95-96%, 70% and 95-96%, respectively), indicating that strain N163-3-2<sup>T</sup> represented a novel species of the genus Lacticaseibacillus. Based upon the data obtained in the present study, a novel species, Lacticaseibacillus jixiensis sp. nov., is proposed, and the type strain is N163-3-2<sup>T</sup> (= CCTCC AB 2024125<sup>T</sup> = JCM 36999<sup>T</sup>).</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chronic inflammation is the gate of many human illnesses and happens when the immune system is unable to suppress external attacks in the correct form. Nonetheless, the gut microbiome plays a pivotal role in keeping homeostasis in the human body and preventing inflammation. Imbalanced microbiota and many diseases can result in inflammation, which when not taken seriously, can be turned into chronic ones and ultimately lead to serious diseases such as cancer. One approach to maintaining hemostasis in the human body is consumption of probiotics as a supplement. Probiotics impact the immune functions of dendritic cells (DCs), T cells, and B cells in the gut-associated lymphoid tissue by inducing the secretion of an array of cytokines. They activate the innate immune response through their microbial-associated molecular pattern, and this activation is followed by multiple cytokine secretion and adaptive elicitation that mitigates pro-inflammatory expression levels and tumor incidence. Thus, according to several studies showing the benefit of probiotics application, alone or in combination with other agents, to induce potent immune responses in individuals against some inflammatory disorders and distinct types of cancers, this review is devoted to surveying the role of probiotics and the modulation of inflammation in some cancer models.
慢性炎症是许多人类疾病的根源,当免疫系统无法以正确的方式抑制外部攻击时,就会出现慢性炎症。然而,肠道微生物群在保持人体平衡和预防炎症方面发挥着举足轻重的作用。微生物群失衡和许多疾病都会导致炎症,如果不加以重视,炎症就会转变为慢性炎症,最终导致癌症等严重疾病。维持人体止血的一种方法是将益生菌作为补充剂食用。益生菌通过诱导一系列细胞因子的分泌,影响肠道相关淋巴组织中树突状细胞(DC)、T 细胞和 B 细胞的免疫功能。它们通过与微生物相关的分子模式激活先天性免疫反应,激活后分泌多种细胞因子并诱发适应性反应,从而降低促炎症表达水平和肿瘤发病率。因此,有多项研究表明,单独或与其他制剂联合应用益生菌可诱导个体对某些炎症性疾病和不同类型的癌症产生有效的免疫反应,本综述将专门探讨益生菌的作用以及在某些癌症模型中对炎症的调节作用。
{"title":"Inflammatory Modulation Effects of Probiotics: A Safe and Promising Modulator for Cancer Prevention.","authors":"Mehran Mahooti, Elahe Abdolalipour, Samira Sanami, Davood Zare","doi":"10.1007/s00284-024-03901-8","DOIUrl":"https://doi.org/10.1007/s00284-024-03901-8","url":null,"abstract":"<p><p>Chronic inflammation is the gate of many human illnesses and happens when the immune system is unable to suppress external attacks in the correct form. Nonetheless, the gut microbiome plays a pivotal role in keeping homeostasis in the human body and preventing inflammation. Imbalanced microbiota and many diseases can result in inflammation, which when not taken seriously, can be turned into chronic ones and ultimately lead to serious diseases such as cancer. One approach to maintaining hemostasis in the human body is consumption of probiotics as a supplement. Probiotics impact the immune functions of dendritic cells (DCs), T cells, and B cells in the gut-associated lymphoid tissue by inducing the secretion of an array of cytokines. They activate the innate immune response through their microbial-associated molecular pattern, and this activation is followed by multiple cytokine secretion and adaptive elicitation that mitigates pro-inflammatory expression levels and tumor incidence. Thus, according to several studies showing the benefit of probiotics application, alone or in combination with other agents, to induce potent immune responses in individuals against some inflammatory disorders and distinct types of cancers, this review is devoted to surveying the role of probiotics and the modulation of inflammation in some cancer models.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-23DOI: 10.1007/s00284-024-03891-7
M Hemapriya, K N Nataraja, T S Suryanarayanan, R Uma Shaanker
Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.
{"title":"Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition.","authors":"M Hemapriya, K N Nataraja, T S Suryanarayanan, R Uma Shaanker","doi":"10.1007/s00284-024-03891-7","DOIUrl":"https://doi.org/10.1007/s00284-024-03891-7","url":null,"abstract":"<p><p>Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142307303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-22DOI: 10.1007/s00284-024-03897-1
Nathália Abichabki, Gilberto Gambero Gaspar, Luísa Vieira Zacharias, Renata Helena Cândido Pocente, Denissani Aparecida Ferrari Santos Lima, Natália Augusta Barbosa de Freitas, Guilherme Thomaz Pereira Brancini, Natália Columbaro Moreira, Gilberto Úbida Leite Braga, Fernando Bellissimo-Rodrigues, Valdes Roberto Bollela, Ana Lúcia Costa Darini, Leonardo Neves Andrade
We investigated the in vitro antibacterial activity of the combination rifampicin (RIF) + polymyxin B (PB) against extensively drug-resistant (XDR) Klebsiella pneumoniae isolates. We evaluated clinical isolates co-resistant to PB (non-mcr carriers; eptB, mgrB, pmr operon, and ramA mutations) and to carbapenems (KPC, CTX-M, and SHV producers; including KPC + NDM co-producer), belonging to sequence types (ST) ST16, ST11, ST258, ST340, and ST437. We used the standard broth microdilution method to determine RIF and PB minimum inhibitory concentration (MIC) and the checkerboard assay to evaluate the fractional inhibitory concentration index (FICI) of RIF + PB as well as to investigate the lowest concentrations of RIF and PB that combined (RIF + PB) had antibacterial activity. Time-kill assays were performed to evaluate the synergistic effect of the combination against selected isolates. PB MIC (32-256 µg/mL) and RIF MIC (32-1024 µg/mL) were determined. FICI (<0.5) indicated a synergistic effect for all isolates evaluated for the combination RIF + PB. Our results showed that low concentrations of PB (PB minimal effective antibiotic concentration [MEAC], ≤0.25-1 µg/mL) favor RIF (≤0.03-0.125 µg/mL) to reach the bacterial target and exert antibacterial activity against PB-resistant isolates, and the synergistic effect was also observed in time-kill results. The combination of RIF + PB showed in vitro antibacterial activity against XDR, carbapenem-, and PB-resistant K. pneumoniae and could be further studied as a potential combination therapy, with cost-effectiveness and promising efficacy.
{"title":"In Vitro Synergistic Activity of Rifampicin Combined with Minimal Effective Antibiotic Concentration (MEAC) of Polymyxin B Against Extensively Drug-Resistant, Carbapenem-, and Polymyxin B-Resistant Klebsiella pneumoniae Clinical Isolates.","authors":"Nathália Abichabki, Gilberto Gambero Gaspar, Luísa Vieira Zacharias, Renata Helena Cândido Pocente, Denissani Aparecida Ferrari Santos Lima, Natália Augusta Barbosa de Freitas, Guilherme Thomaz Pereira Brancini, Natália Columbaro Moreira, Gilberto Úbida Leite Braga, Fernando Bellissimo-Rodrigues, Valdes Roberto Bollela, Ana Lúcia Costa Darini, Leonardo Neves Andrade","doi":"10.1007/s00284-024-03897-1","DOIUrl":"https://doi.org/10.1007/s00284-024-03897-1","url":null,"abstract":"<p><p>We investigated the in vitro antibacterial activity of the combination rifampicin (RIF) + polymyxin B (PB) against extensively drug-resistant (XDR) Klebsiella pneumoniae isolates. We evaluated clinical isolates co-resistant to PB (non-mcr carriers; eptB, mgrB, pmr operon, and ramA mutations) and to carbapenems (KPC, CTX-M, and SHV producers; including KPC + NDM co-producer), belonging to sequence types (ST) ST16, ST11, ST258, ST340, and ST437. We used the standard broth microdilution method to determine RIF and PB minimum inhibitory concentration (MIC) and the checkerboard assay to evaluate the fractional inhibitory concentration index (FICI) of RIF + PB as well as to investigate the lowest concentrations of RIF and PB that combined (RIF + PB) had antibacterial activity. Time-kill assays were performed to evaluate the synergistic effect of the combination against selected isolates. PB MIC (32-256 µg/mL) and RIF MIC (32-1024 µg/mL) were determined. FICI (<0.5) indicated a synergistic effect for all isolates evaluated for the combination RIF + PB. Our results showed that low concentrations of PB (PB minimal effective antibiotic concentration [MEAC], ≤0.25-1 µg/mL) favor RIF (≤0.03-0.125 µg/mL) to reach the bacterial target and exert antibacterial activity against PB-resistant isolates, and the synergistic effect was also observed in time-kill results. The combination of RIF + PB showed in vitro antibacterial activity against XDR, carbapenem-, and PB-resistant K. pneumoniae and could be further studied as a potential combination therapy, with cost-effectiveness and promising efficacy.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-22DOI: 10.1007/s00284-024-03896-2
Bożena Szermer-Olearnik, Karolina Filik-Matyjaszczyk, Jarosław Ciekot, Anna Czarny
The bacteriophage F8 belongs to the Myoviridae group of phages and is a pathogen of Pseudomonas aeruginosa. Since Pseudomonas aeruginosa is a multidrug-resistant opportunistic bacterium and can cause serious challenges for health services, studying the potential use of phages against them is a promising approach. Pseudomonas aeruginosa can be found on medical devices because bacteria can attach to surfaces and develop biofilms, which are difficult to eradicate because of their high resistance to environmental conditions and antimicrobial therapeutics. Phage therapy is becoming promising as an alternative for the treatment of antibiotic-resistant infections, but there is still a lack of standardized protocols approved by health organizations for possible use in the clinic. In our research, we focused on the potential use of 1-octanol, which was previously used by our team to develop a method for phage purification from bacterial lysate. 1-octanol is a fatty alcohol that is mostly used in the cosmetics industry, and its advantage is that it is approved by the FDA as a food additive. In this paper, we studied the protective properties of the addition of 1-octanol for storing phage liquid preparations. We demonstrated the stabilization effect of 1-octanol addition on F8 bacteriophage preparation during storage under various conditions. Interestingly, more effective biofilm reduction was observed after treatment with the purified bacteriophage and with 1-octanol addition compared to crude lysate.
{"title":"The Hydrophobic Stabilization of Pseudomonas aeruginosa Bacteriophage F8 and the Influence of Modified Bacteriophage Preparation on Biofilm Degradation.","authors":"Bożena Szermer-Olearnik, Karolina Filik-Matyjaszczyk, Jarosław Ciekot, Anna Czarny","doi":"10.1007/s00284-024-03896-2","DOIUrl":"https://doi.org/10.1007/s00284-024-03896-2","url":null,"abstract":"<p><p>The bacteriophage F8 belongs to the Myoviridae group of phages and is a pathogen of Pseudomonas aeruginosa. Since Pseudomonas aeruginosa is a multidrug-resistant opportunistic bacterium and can cause serious challenges for health services, studying the potential use of phages against them is a promising approach. Pseudomonas aeruginosa can be found on medical devices because bacteria can attach to surfaces and develop biofilms, which are difficult to eradicate because of their high resistance to environmental conditions and antimicrobial therapeutics. Phage therapy is becoming promising as an alternative for the treatment of antibiotic-resistant infections, but there is still a lack of standardized protocols approved by health organizations for possible use in the clinic. In our research, we focused on the potential use of 1-octanol, which was previously used by our team to develop a method for phage purification from bacterial lysate. 1-octanol is a fatty alcohol that is mostly used in the cosmetics industry, and its advantage is that it is approved by the FDA as a food additive. In this paper, we studied the protective properties of the addition of 1-octanol for storing phage liquid preparations. We demonstrated the stabilization effect of 1-octanol addition on F8 bacteriophage preparation during storage under various conditions. Interestingly, more effective biofilm reduction was observed after treatment with the purified bacteriophage and with 1-octanol addition compared to crude lysate.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-21DOI: 10.1007/s00284-024-03887-3
Lin Jiang, Zixian Zeng, Zhi Wang, Min Tang, Sai Jiang, Qingxian Ma, Zhong Wang, Dian Peng, Shunxiang Li, Hong Pu
In the present study, using genome mining, Streptomyces sp. JL1001, which possesses a leinamycin-type gene cluster, was identified from 14 strains of Streptomyces originating from the rhizosphere soil of Polygonatum cyrtonema Hua. The complete genome of Streptomyces sp. JL1001 was sequenced and analyzed. The genome of Streptomyces sp. JL1001 consists of a 7,943,495 bp chromosome with a 71.71% G+C content and 7315 protein-coding genes. We also identified 36 biosynthetic gene clusters (BGCs) for secondary metabolites in Streptomyces sp. JL1001. Twenty-seven BGCs had low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. In addition, a comparative analysis was conducted between the leinamycin-type gene cluster in Streptomyces sp. JL1001 and the biosynthetic gene clusters of leinamycin and largimycin. This study aims to provide a comprehensive analysis of the genomic features of rhizosphere Streptomyces sp. JL1001. It establishes the foundation for further investigation into experimental trials involving novel bioactive metabolites such as AT-less type I polyketides that have important potential applications in medicine and agriculture.
{"title":"Genomic Investigation of a Rhizosphere Isolate, Streptomyces sp. JL1001, Associated with Polygonatum cyrtonema Hua.","authors":"Lin Jiang, Zixian Zeng, Zhi Wang, Min Tang, Sai Jiang, Qingxian Ma, Zhong Wang, Dian Peng, Shunxiang Li, Hong Pu","doi":"10.1007/s00284-024-03887-3","DOIUrl":"https://doi.org/10.1007/s00284-024-03887-3","url":null,"abstract":"<p><p>In the present study, using genome mining, Streptomyces sp. JL1001, which possesses a leinamycin-type gene cluster, was identified from 14 strains of Streptomyces originating from the rhizosphere soil of Polygonatum cyrtonema Hua. The complete genome of Streptomyces sp. JL1001 was sequenced and analyzed. The genome of Streptomyces sp. JL1001 consists of a 7,943,495 bp chromosome with a 71.71% G+C content and 7315 protein-coding genes. We also identified 36 biosynthetic gene clusters (BGCs) for secondary metabolites in Streptomyces sp. JL1001. Twenty-seven BGCs had low (< 50%) or moderate (50-80%) similarity to other known secondary metabolite BGCs. In addition, a comparative analysis was conducted between the leinamycin-type gene cluster in Streptomyces sp. JL1001 and the biosynthetic gene clusters of leinamycin and largimycin. This study aims to provide a comprehensive analysis of the genomic features of rhizosphere Streptomyces sp. JL1001. It establishes the foundation for further investigation into experimental trials involving novel bioactive metabolites such as AT-less type I polyketides that have important potential applications in medicine and agriculture.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282050","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-21DOI: 10.1007/s00284-024-03895-3
Venkatesan Dhanalakshmi, Jeyaprakash Rajendhran
Multidrug resistance in clinical pathogens is a significant challenge in healthcare, requiring the development of novel approaches to combat infections. In this study, we report the identification of novel antimicrobial biosynthetic gene clusters from Brevibacillus parabrevis WGTm-23, the bacterial strain isolated from a termitarium. This strain showed an antagonistic effect against drug-resistant clinical pathogens, such as Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella paratyphi, Streptococcus gordonii, and enteropathogenic Escherichia coli. The whole genome of this strain was sequenced using the Illumina platform. The genome mining revealed a total of 17 biosynthetic gene clusters (BGCs) responsible for the synthesis of secondary metabolites. The metabolites produced by this strain were predicted by constructing an identity network of the BGCs and performing a comparative analysis with genetically related strains. The genome contains multiple BGCs coding for ribosomally synthesized and post-translationally modified peptides (RiPPs). In the genome of Br. parabrevis WGTm-23, we identified BGCs that code for ulbactin F, ulbactin G, gramicidin, and bacillopaline with the highest identity. We also identified a few BGCs with less than 50% sequence identity to MC-LR/MC-LHty/MC-HphHty/MC-LHph/MC-HphHph, xenocoumacin 1/xenocoumacin II, and tyrocidine. In addition, we found fourteen BGCs that do not resemble or show identity to any entries within the antiSMASH database. Therefore, Br. parabrevis WGTm-23 has the potential to synthesize new classes of antimicrobial compounds.
{"title":"The Termite Nest-Associated Bacterium Brevibacillus parabrevis WGTm-23 Contains Unique Biosynthetic Gene Clusters Potentially Coding for Novel Antimicrobial Agents.","authors":"Venkatesan Dhanalakshmi, Jeyaprakash Rajendhran","doi":"10.1007/s00284-024-03895-3","DOIUrl":"https://doi.org/10.1007/s00284-024-03895-3","url":null,"abstract":"<p><p>Multidrug resistance in clinical pathogens is a significant challenge in healthcare, requiring the development of novel approaches to combat infections. In this study, we report the identification of novel antimicrobial biosynthetic gene clusters from Brevibacillus parabrevis WGTm-23, the bacterial strain isolated from a termitarium. This strain showed an antagonistic effect against drug-resistant clinical pathogens, such as Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella paratyphi, Streptococcus gordonii, and enteropathogenic Escherichia coli. The whole genome of this strain was sequenced using the Illumina platform. The genome mining revealed a total of 17 biosynthetic gene clusters (BGCs) responsible for the synthesis of secondary metabolites. The metabolites produced by this strain were predicted by constructing an identity network of the BGCs and performing a comparative analysis with genetically related strains. The genome contains multiple BGCs coding for ribosomally synthesized and post-translationally modified peptides (RiPPs). In the genome of Br. parabrevis WGTm-23, we identified BGCs that code for ulbactin F, ulbactin G, gramicidin, and bacillopaline with the highest identity. We also identified a few BGCs with less than 50% sequence identity to MC-LR/MC-LHty/MC-HphHty/MC-LHph/MC-HphHph, xenocoumacin 1/xenocoumacin II, and tyrocidine. In addition, we found fourteen BGCs that do not resemble or show identity to any entries within the antiSMASH database. Therefore, Br. parabrevis WGTm-23 has the potential to synthesize new classes of antimicrobial compounds.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19DOI: 10.1007/s00284-024-03885-5
Natalia Y. Gavrilova, Muslimbek G. Normatov, Lidiya A. Soprun, Vladimir J. Utekhin, Tamara V. Fedotkina, Leonid P. Churilov
In post-COVID-19 syndrome, clinical presentation of the nerve fiber dysfunction plays an important role. The possibility of autoantigen cross-mimicry of human coronaviruses and the peripheral nervous system needs to be investigated. The bioinformatic analysis was applied to search for possible common protein sequences located in the immunoreactive epitopes. Among the autoantigens of the human nervous system, fibroblast growth factor receptor protein 3, myelin protein P0, myelin protein P2, sodium channel protein type 9, alpha protein subunit, plexin-D1 protein and ubiquitin-carboxyl-terminal hydrolase protein of the L1 isoenzyme were selected. The original “Alignmentaj” analytical program was created. The UniProt database, Protein Data Bank, and AlphaFold databases were used. The analysis of protein sequence similarities of spike glycoproteins in human coronaviruses revealed common pentapeptides of the MERS-CoV-2 virus with the fibroblast growth factor receptor 3 and myelin protein P2. Among seasonal coronaviruses, common peptide sequences were identified in HCoV-HKU-1 virus with sodium channel protein type 9 subunit alpha and Plexin-D1, HCoV-OC43 with Plexin-D1, as well as HCoV-NL63 with Plexin-D1 and Ubiquitin carboxyl-terminal hydrolase isozyme L1. Some shared peptides belong to immunoreactive epitopes. The most important targets for the molecular similarities are the sodium channel subunits and fibroblast growth factor receptor 3, both for seasonal and highly pathogenic coronaviruses. The data obtained make it possible to identify new potential targets for the development of autoimmune reactions that may occur against the background of the infections with highly pathogenic as well as seasonal coronaviruses.
{"title":"Autoantigens of Small Nerve Fibers and Human Coronavirus Antigens: Is There a Possibility for Molecular Mimicry?","authors":"Natalia Y. Gavrilova, Muslimbek G. Normatov, Lidiya A. Soprun, Vladimir J. Utekhin, Tamara V. Fedotkina, Leonid P. Churilov","doi":"10.1007/s00284-024-03885-5","DOIUrl":"https://doi.org/10.1007/s00284-024-03885-5","url":null,"abstract":"<p>In post-COVID-19 syndrome, clinical presentation of the nerve fiber dysfunction plays an important role. The possibility of autoantigen cross-mimicry of human coronaviruses and the peripheral nervous system needs to be investigated. The bioinformatic analysis was applied to search for possible common protein sequences located in the immunoreactive epitopes. Among the autoantigens of the human nervous system, fibroblast growth factor receptor protein 3, myelin protein P0, myelin protein P2, sodium channel protein type 9, alpha protein subunit, plexin-D1 protein and ubiquitin-carboxyl-terminal hydrolase protein of the L1 isoenzyme were selected. The original “Alignmentaj” analytical program was created. The UniProt database, Protein Data Bank, and AlphaFold databases were used. The analysis of protein sequence similarities of spike glycoproteins in human coronaviruses revealed common pentapeptides of the MERS-CoV-2 virus with the fibroblast growth factor receptor 3 and myelin protein P2. Among seasonal coronaviruses, common peptide sequences were identified in HCoV-HKU-1 virus with sodium channel protein type 9 subunit alpha and Plexin-D1, HCoV-OC43 with Plexin-D1, as well as HCoV-NL63 with Plexin-D1 and Ubiquitin carboxyl-terminal hydrolase isozyme L1. Some shared peptides belong to immunoreactive epitopes. The most important targets for the molecular similarities are the sodium channel subunits and fibroblast growth factor receptor 3, both for seasonal and highly pathogenic coronaviruses. The data obtained make it possible to identify new potential targets for the development of autoimmune reactions that may occur against the background of the infections with highly pathogenic as well as seasonal coronaviruses.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19DOI: 10.1007/s00284-024-03886-4
Jalal Soltani, Adib Sheikh-Ahmadi
Alternaria species (Deuteromycetes, Ascomycota) as ubiquitous fungi and prolific producers of a variety of toxic compounds are a part of microbiomes of plants, humans, and animals, mainly causing disease, allergic reactions, and toxicosis. However, some species have also been reported as endophytic microorganisms with highly bioactive metabolites. Our previous results indicate that potentially endophytic Alternaria species from Cupressaceae produce bioactive metabolites that possibly contribute to plant holobiont's health. Here, a possible mechanism behind this bioactivity is elucidated. As some endophytic fungi are reported to produce cytotoxic taxane diterpenoids, eight potentially endophytic Alternaria isolates from our collection were analyzed for the presence of the key genes of the paclitaxel (Taxol) biosynthetic pathway, i.e., taxadin synthase (ts), 10-deacetylbaccatin III-10-O-acetyltransferase (dbat), and C-13-phenylpropanoid side-chain CoA acyltransferase (bapt). The presence of all genes, i.e., ts, dbat, and bapt, was detected by PCR in six isolates and dbat and bapt in two isolates. Chemical analyses of the fermentation broths by TLC and HPLC chromatography and IR spectroscopy indicated the synthesis of the final product, i.e., paclitaxel. So, we introduce the synthesis of taxane diterpenoids as a possible mechanism by which Alternaria occupies the plant niches and protects the plant holobiont in the presence of competing microorganisms.
{"title":"Genomic and Chemical Evidence on Biosynthesis of Taxane Diterpenoids in Alternaria Isolates from Cupressaceae.","authors":"Jalal Soltani, Adib Sheikh-Ahmadi","doi":"10.1007/s00284-024-03886-4","DOIUrl":"https://doi.org/10.1007/s00284-024-03886-4","url":null,"abstract":"<p><p>Alternaria species (Deuteromycetes, Ascomycota) as ubiquitous fungi and prolific producers of a variety of toxic compounds are a part of microbiomes of plants, humans, and animals, mainly causing disease, allergic reactions, and toxicosis. However, some species have also been reported as endophytic microorganisms with highly bioactive metabolites. Our previous results indicate that potentially endophytic Alternaria species from Cupressaceae produce bioactive metabolites that possibly contribute to plant holobiont's health. Here, a possible mechanism behind this bioactivity is elucidated. As some endophytic fungi are reported to produce cytotoxic taxane diterpenoids, eight potentially endophytic Alternaria isolates from our collection were analyzed for the presence of the key genes of the paclitaxel (Taxol) biosynthetic pathway, i.e., taxadin synthase (ts), 10-deacetylbaccatin III-10-O-acetyltransferase (dbat), and C-13-phenylpropanoid side-chain CoA acyltransferase (bapt). The presence of all genes, i.e., ts, dbat, and bapt, was detected by PCR in six isolates and dbat and bapt in two isolates. Chemical analyses of the fermentation broths by TLC and HPLC chromatography and IR spectroscopy indicated the synthesis of the final product, i.e., paclitaxel. So, we introduce the synthesis of taxane diterpenoids as a possible mechanism by which Alternaria occupies the plant niches and protects the plant holobiont in the presence of competing microorganisms.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142282049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-18DOI: 10.1007/s00284-024-03869-5
Luis Yndy Ariem Ramirez, Inga Leena Angell, Tonje Nilsen, Knut Rudi
Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus Pseudarchobacter within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus Pseudarchobacter which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.
{"title":"Delayed Shift in Microbiota Composition in a Marine Microcosm Pollution Experiment","authors":"Luis Yndy Ariem Ramirez, Inga Leena Angell, Tonje Nilsen, Knut Rudi","doi":"10.1007/s00284-024-03869-5","DOIUrl":"https://doi.org/10.1007/s00284-024-03869-5","url":null,"abstract":"<p>Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus <i>Pseudarchobacter</i> within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus <i>Pseudarchobacter</i> which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.</p>","PeriodicalId":11360,"journal":{"name":"Current Microbiology","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142261981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}