Pub Date : 2025-11-25DOI: 10.1016/j.crmicr.2025.100520
Junhao Wang , Ali Asif , Fangtong Gu , Shuaifeng Gu , Yakun Ding , Yufeng Gu , Muhammad Shahzad Rafiq , Haihong Hao
Multidrug-resistant Campylobacter jejuni (MDR C. jejuni), the leading cause of food-borne gastroenteritis worldwide, poses a significant threat to public health and food safety. The intestinal microbiota prevents MDR C. jejuni colonization, but the specific mechanisms remain poorly understood. In this study, we performed a multi-omics analysis of the gut microbiota in C57BL/6 mice, combined with in vitro experiments, to investigate the role of gut microbiota in C. jejuni colonization. Treatment with tylvalosin, a new macrolide, altered the gut microbiota composition, reducing Bifidobacterium longum communities and decreasing levels of short-chain fatty acids (acetic acid, propionic acid, n-butyric acid, i-butyric acid, and i-valeric acid). This disruption of intestinal homeostasis facilitated C. jejuni colonization. Through metagenomic sequencing, we identified and isolated Lactobacillus murinus (L. murinus) from the mice’s intestinal flora, which exhibited inhibitory activity against C. jejuni in vitro. Metabolomic analysis and in vitro validation further revealed the significance of L. murinus-derived metabolites. Our results indicate that L. murinus inhibits and kills C. jejuni in a co-culture system by secreting acids that synergistically induce apoptosis, leading to cell membrane disruption and the release of cellular contents.
耐多药空肠弯曲杆菌（MDR C. jejuni）是全球食源性胃肠炎的主要病因，对公共卫生和食品安全构成重大威胁。肠道菌群可阻止耐多药空肠梭菌定植，但具体机制尚不清楚。本研究通过对C57BL/6小鼠肠道菌群进行多组学分析，并结合体外实验，探讨肠道菌群在空肠梭菌定植中的作用。用一种新的大环内酯类药物tylvalosin治疗，改变了肠道菌群组成，减少了长双歧杆菌群落，降低了短链脂肪酸（乙酸、丙酸、正丁酸、i-丁酸和i-戊酸）的水平。这种肠道稳态的破坏促进了空肠梭菌的定植。通过元基因组测序，我们从小鼠肠道菌群中鉴定并分离出对空肠杆菌具有体外抑制活性的鼠乳杆菌（Lactobacillus murinus）。代谢组学分析和体外验证进一步揭示了鼠乳杆菌衍生代谢物的意义。我们的研究结果表明，在共培养系统中，L. murinus通过分泌酸抑制和杀死空肠梭菌，这些酸协同诱导细胞凋亡，导致细胞膜破坏和细胞内容物的释放。
{"title":"A naturally isolated symbiotic Lactobacillus murinus suppresses multidrug-resistant Campylobacter jejuni via microbial metabolites","authors":"Junhao Wang , Ali Asif , Fangtong Gu , Shuaifeng Gu , Yakun Ding , Yufeng Gu , Muhammad Shahzad Rafiq , Haihong Hao","doi":"10.1016/j.crmicr.2025.100520","DOIUrl":"10.1016/j.crmicr.2025.100520","url":null,"abstract":"<div><div>Multidrug-resistant <em>Campylobacter jejuni</em> (MDR <em>C. jejuni</em>), the leading cause of food-borne gastroenteritis worldwide, poses a significant threat to public health and food safety. The intestinal microbiota prevents MDR <em>C. jejuni</em> colonization, but the specific mechanisms remain poorly understood. In this study, we performed a multi-omics analysis of the gut microbiota in C57BL/6 mice, combined with <em>in vitro</em> experiments, to investigate the role of gut microbiota in <em>C. jejuni</em> colonization. Treatment with tylvalosin, a new macrolide, altered the gut microbiota composition, reducing <em>Bifidobacterium longum</em> communities and decreasing levels of short-chain fatty acids (acetic acid, propionic acid, <em>n</em>-butyric acid, <em>i</em>-butyric acid, and <em>i</em>-valeric acid). This disruption of intestinal homeostasis facilitated <em>C. jejuni</em> colonization. Through metagenomic sequencing, we identified and isolated <em>Lactobacillus murinus</em> (<em>L. murinus</em>) from the mice’s intestinal flora, which exhibited inhibitory activity against <em>C. jejuni in vitro</em>. Metabolomic analysis and <em>in vitro</em> validation further revealed the significance of <em>L. murinus</em>-derived metabolites. Our results indicate that <em>L. murinus</em> inhibits and kills <em>C. jejuni</em> in a co-culture system by secreting acids that synergistically induce apoptosis, leading to cell membrane disruption and the release of cellular contents.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100520"},"PeriodicalIF":5.8,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145683974","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}
Chemical pesticides considered as one of the emerging environmental contaminants that severally affect the human health and soil and water ecosystem. Despite their well-documented adverse effects on fruit quality, soil structure, the emergence of pesticide-resistant pests, and human well-being, chemical pesticides are still widely used for crop protection, particularly in developing countries. Although to manage the chemical pesticides, various traditional approaches have been employed, however the higher cost, and the generation of toxic residues have shifted research attention toward eco-friendly and sustainable bioremediation strategies. Microorganisms including the bacteria, fungi, and algae play a crucial role in pesticide degradation by transforming toxic compounds into less toxic forms. However, to optimize microbial bioremediation, a comprehensive understanding of microbial metabolism and physiology is essential. In this context, omics technologies such as genomics, metagenomics, transcriptomics, proteomics, and metabolomics, offer powerful tools for elucidating the molecular mechanisms involved in pesticide degradation. These approaches facilitate the identification of microorganism, key genes, enzymes, and metabolic pathways responsible for the breakdown of pesticide compounds and their by-products. Furthermore, advanced technology like the gene editing can enhance the efficacy of pesticides biodegradation by knocking out undesirable genes or introducing beneficial ones in the microorganisms. The Artificial intelligence also plays a significant role in analysing big data, understanding microbial communities’ structure, identifying nature of pesticides and selecting or predicting the microbial species with enhanced pesticides degrading efficacy.
{"title":"The microbial strategies for the management of chemical pesticides: A comprehensive review","authors":"Ajay Kumar , Manoj Kumar Solanki , Manish Kumar , Amit Kaushik , Aditi Arya , Mahaswetta Saikia , Vivek Kumar Gaur , Rahul Prashad Singh , Sandeep Kumar Singh , Vipin Kumar Singh , Laurent Dufossé","doi":"10.1016/j.crmicr.2025.100519","DOIUrl":"10.1016/j.crmicr.2025.100519","url":null,"abstract":"<div><div>Chemical pesticides considered as one of the emerging environmental contaminants that severally affect the human health and soil and water ecosystem. Despite their well-documented adverse effects on fruit quality, soil structure, the emergence of pesticide-resistant pests, and human well-being, chemical pesticides are still widely used for crop protection, particularly in developing countries. Although to manage the chemical pesticides, various traditional approaches have been employed, however the higher cost, and the generation of toxic residues have shifted research attention toward eco-friendly and sustainable bioremediation strategies. Microorganisms including the bacteria, fungi, and algae play a crucial role in pesticide degradation by transforming toxic compounds into less toxic forms. However, to optimize microbial bioremediation, a comprehensive understanding of microbial metabolism and physiology is essential. In this context, omics technologies such as genomics, metagenomics, transcriptomics, proteomics, and metabolomics, offer powerful tools for elucidating the molecular mechanisms involved in pesticide degradation. These approaches facilitate the identification of microorganism, key genes, enzymes, and metabolic pathways responsible for the breakdown of pesticide compounds and their by-products. Furthermore, advanced technology like the gene editing can enhance the efficacy of pesticides biodegradation by knocking out undesirable genes or introducing beneficial ones in the microorganisms. The Artificial intelligence also plays a significant role in analysing big data, understanding microbial communities’ structure, identifying nature of pesticides and selecting or predicting the microbial species with enhanced pesticides degrading efficacy.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100519"},"PeriodicalIF":5.8,"publicationDate":"2025-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145645852","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}
Pub Date : 2025-11-20DOI: 10.1016/j.crmicr.2025.100512
Biao Zou , Qian’er Huo , Xianfeng Zhou , Yongling Lv , Guolong Li , Guang Fu , Hexiao Shen , Sainan Shu
Fecal microbiota transplantation (FMT) efficacy relies on donor microbiome composition and temporal stability, yet the influence of donor age remains inadequately investigated. This longitudinal analysis addressed this gap by examining 81 healthy individuals (3–30 years), stratified into four age groups, who provided monthly fecal samples over 12 months (n = 972 samples). Gut microbiota composition (16S rDNA sequencing) and temporal stability were assessed using Bray–Curtis dissimilarity, intraclass correlation coefficient (ICC), and genus-level co-occurrence network analysis. Results demonstrated a strong age-dependency in microbiota stability. The teenage cohort (13–17 years) exhibited the highest stability, characterized by minimal fluctuations in α- and β-diversity and significantly stronger network centrality. Furthermore, specific genera, notably Faecalibacterium and Bifidobacterium, displayed exceptionally high ICC values (>0.90), identifying them as core taxa associated with temporal consistency. These findings underscore the critical role of donor age in microbial stability and highlight teenagers as possessing optimal microbiota characteristics for FMT. They strongly support the development of an ICC-based screening framework to enhance donor selection protocols.
{"title":"Characteristics and longitudinal stability of Gut Microbiota in healthy individuals across different age groups","authors":"Biao Zou , Qian’er Huo , Xianfeng Zhou , Yongling Lv , Guolong Li , Guang Fu , Hexiao Shen , Sainan Shu","doi":"10.1016/j.crmicr.2025.100512","DOIUrl":"10.1016/j.crmicr.2025.100512","url":null,"abstract":"<div><div>Fecal microbiota transplantation (FMT) efficacy relies on donor microbiome composition and temporal stability, yet the influence of donor age remains inadequately investigated. This longitudinal analysis addressed this gap by examining 81 healthy individuals (3–30 years), stratified into four age groups, who provided monthly fecal samples over 12 months (<em>n</em> = 972 samples). Gut microbiota composition (16S rDNA sequencing) and temporal stability were assessed using Bray–Curtis dissimilarity, intraclass correlation coefficient (ICC), and genus-level co-occurrence network analysis. Results demonstrated a strong age-dependency in microbiota stability. The teenage cohort (13–17 years) exhibited the highest stability, characterized by minimal fluctuations in α- and β-diversity and significantly stronger network centrality. Furthermore, specific genera, notably <em>Faecalibacterium</em> and <em>Bifidobacterium</em>, displayed exceptionally high ICC values (>0.90), identifying them as core taxa associated with temporal consistency. These findings underscore the critical role of donor age in microbial stability and highlight teenagers as possessing optimal microbiota characteristics for FMT. They strongly support the development of an ICC-based screening framework to enhance donor selection protocols.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100512"},"PeriodicalIF":5.8,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145645848","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}
Pub Date : 2025-07-24eCollection Date: 2025-01-01DOI: 10.1016/j.crmicr.2025.100449
Charlotte Mejlstrup Hymøller, Trine S Jensen, Pernille Vigsø Rasmussen, Ditte Bech, Gunna Christiansen, Svend Birkelund
Klebsiella pneumoniae is an opportunistic, gram-negative pathogen causing life-threatening sepsis in patients with co-morbidity. In contrast, in healthy persons, K. pneumoniae rarely causes sepsis. To elucidate how K. pneumoniae is eliminated from normal human blood, eleven K. pneumoniae sepsis isolates were analysed. Most of the isolates were serum-resistant. They solely activated the alternative pathway (AP), and only iC3b was present on their surface due to a rapid cleavage of C3b. Despite serum resistance, all isolates were killed in normal blood. To analyse the mechanism of uptake, two isolates (serum-resistant HA391 and partially resistant HA569) were transfected with a plasmid encoding red fluorescent protein, added to whole blood, analysed by flow cytometry and uptake in neutrophil granulocytes. HA391 was not phagocytosed in 50% heat-inactivated serum (HIHS), but in normal human serum (NHS), it was phagocytosed and subsequently killed. The iC3b deposited on the bacterial surface, colocalised with complement receptor 3 (CR3) and myeloperoxidase (MPO), confirming opsonophagocytosis. HA569 was rapidly phagocytosed by granulocytes in NHS but more slowly in HIHS. Thus, the complement system is essential for the elimination of serum-resistant K. pneumoniae isolates, as neutrophil granulocytes phagocytose HA391 through opsonophagocytosis, while HA569 is also phagocytosed independently of complement. AP lacks specific pattern recognition; however, it plays an essential role in the elimination of serum-resistant K. pneumoniae, as AP is activated by these bacteria, which, nonetheless, escape complement lysis by cleaving C3b to iC3b. Hereby, the bacteria are susceptible to opsonophagocytosis, an ancient function of AP that is crucial for eliminating bacteria.
{"title":"The role of opsonophagocytosis in killing of <i>Klebsiella pneumoniae</i> in human blood.","authors":"Charlotte Mejlstrup Hymøller, Trine S Jensen, Pernille Vigsø Rasmussen, Ditte Bech, Gunna Christiansen, Svend Birkelund","doi":"10.1016/j.crmicr.2025.100449","DOIUrl":"10.1016/j.crmicr.2025.100449","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is an opportunistic, gram-negative pathogen causing life-threatening sepsis in patients with co-morbidity. In contrast, in healthy persons, <i>K. pneumoniae</i> rarely causes sepsis. To elucidate how <i>K. pneumoniae</i> is eliminated from normal human blood, eleven <i>K. pneumoniae</i> sepsis isolates were analysed. Most of the isolates were serum-resistant. They solely activated the alternative pathway (AP), and only iC3b was present on their surface due to a rapid cleavage of C3b. Despite serum resistance, all isolates were killed in normal blood. To analyse the mechanism of uptake, two isolates (serum-resistant HA391 and partially resistant HA569) were transfected with a plasmid encoding red fluorescent protein, added to whole blood, analysed by flow cytometry and uptake in neutrophil granulocytes. HA391 was not phagocytosed in 50% heat-inactivated serum (HIHS), but in normal human serum (NHS), it was phagocytosed and subsequently killed. The iC3b deposited on the bacterial surface, colocalised with complement receptor 3 (CR3) and myeloperoxidase (MPO), confirming opsonophagocytosis. HA569 was rapidly phagocytosed by granulocytes in NHS but more slowly in HIHS. Thus, the complement system is essential for the elimination of serum-resistant <i>K. pneumoniae</i> isolates, as neutrophil granulocytes phagocytose HA391 through opsonophagocytosis, while HA569 is also phagocytosed independently of complement. AP lacks specific pattern recognition; however, it plays an essential role in the elimination of serum-resistant <i>K. pneumoniae</i>, as AP is activated by these bacteria, which, nonetheless, escape complement lysis by cleaving C3b to iC3b. Hereby, the bacteria are susceptible to opsonophagocytosis, an ancient function of AP that is crucial for eliminating bacteria.</p>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"100449"},"PeriodicalIF":5.8,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12356408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.crmicr.2025.100347
Yi-Ni Ma , Xun Xu , Lai-Feng Chen , Jin-Ping Zhou , Zhen-Hui Cao , Qiu-Ye Lin
The present study aimed to optimize the processing technology of natto fermented with Bacillus subtilis natto and Limosilactobacillus fermentum 2–2 and its effect on quality characteristics as well as volatile compounds. The results of single-factor tests and response surface methodology (RSM) showed that the optimal fermentation conditions of natto were L. fermentum inoculation amount of 0.3 %, fermentation temperature at 39 °C, fermentation time of 48 h, and after-ripening time of 24 h. Compared with natto control with B. subtilis natto only, natto co-cultured with B. subtilis natto and L. fermentum 2–2 showed higher scavenging ability of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and greater nattokinase activity. Volatomics analysis revealed that 71 differential volatile compounds were identified with 23 up-regulated and 48 down-regulated. Especially, co-fermentation of B. subtilis natto and L. fermentum 2–2 increased generation of alcohols, ketones and esters while reduced pyrazines formation. The above results indicate that co-culture of B. subtilis natto and L. fermentum can enhance the antioxidant and nattokinase activity and modify the volatile profile in natto and have the potential for application as the mixed starter in natto production.
{"title":"Process optimization and evaluation of quality properties of natto with co-culture of Bacillus subtilis natto and Limosilactobacillus fermentum","authors":"Yi-Ni Ma , Xun Xu , Lai-Feng Chen , Jin-Ping Zhou , Zhen-Hui Cao , Qiu-Ye Lin","doi":"10.1016/j.crmicr.2025.100347","DOIUrl":"10.1016/j.crmicr.2025.100347","url":null,"abstract":"<div><div>The present study aimed to optimize the processing technology of natto fermented with <em>Bacillus subtilis</em> natto and <em>Limosilactobacillus fermentum</em> 2–2 and its effect on quality characteristics as well as volatile compounds. The results of single-factor tests and response surface methodology (RSM) showed that the optimal fermentation conditions of natto were L. <em>fermentum</em> inoculation amount of 0.3 %, fermentation temperature at 39 °C, fermentation time of 48 h, and after-ripening time of 24 h. Compared with natto control with <em>B. subtilis</em> natto only, natto co-cultured with <em>B. subtilis</em> natto and L. <em>fermentum</em> 2–2 showed higher scavenging ability of 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and greater nattokinase activity. Volatomics analysis revealed that 71 differential volatile compounds were identified with 23 up-regulated and 48 down-regulated. Especially, co-fermentation of <em>B. subtilis</em> natto and L. <em>fermentum</em> 2–2 increased generation of alcohols, ketones and esters while reduced pyrazines formation. The above results indicate that co-culture of <em>B. subtilis</em> natto and L. <em>fermentum</em> can enhance the antioxidant and nattokinase activity and modify the volatile profile in natto and have the potential for application as the mixed starter in natto production.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100347"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mangrovibacter phragmitis is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of M. phragmitis strain PSU-3885–11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the Enterobacter cloacae complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as M. phragmitis. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to M. phragmitis MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885–11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885–11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including ompA, hcp/tssD, and rpoS, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of M. phragmitis PSU-3885–11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.
{"title":"First whole genome report of Mangrovibacter phragmitis PSU-3885–11 isolated from a patient in Thailand","authors":"Nattarika Chaichana , Thunchanok Yaikhan , Mingkwan Yingkajorn , Nonthawat Thepsimanon , Sirikan Suwannasin , Kamonnut Singkhamanan , Sarunyou Chusri , Rattanaruji Pomwised , Monwadee Wonglapsuwan , Komwit Surachat","doi":"10.1016/j.crmicr.2025.100350","DOIUrl":"10.1016/j.crmicr.2025.100350","url":null,"abstract":"<div><div><em>Mangrovibacter phragmitis</em> is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of <em>M. phragmitis</em> strain PSU-3885–11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the <em>Enterobacter cloacae</em> complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as <em>M. phragmitis</em>. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to <em>M. phragmitis</em> MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885–11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885–11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including <em>ompA, hcp/tssD,</em> and <em>rpoS</em>, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of <em>M. phragmitis</em> PSU-3885–11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100350"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.crmicr.2025.100391
Clélia Duran , Christine Dupuy , Hélène Agogué , Robert Duran , Cristiana Cravo-Laureau
Benthic prokaryotic communities, utmost important for wetlands and marine environments functioning, are influenced by physical-chemical parameters and interactions with other communities, especially micro-eukaryotes and meiofauna. Thus, a holistic view of the benthic community is necessary to fully understand their organization and functioning. This study assesses the implementation of a comprehensive view, using mock communities and environmental samples. A DNA extraction strategy combining two procedures is proposed: one to obtain DNA from micro-organisms, using 0.25 g of sediment, and the other from meiofauna, using 0.25 g of sieving refluxes from 5 g of sediment. Three conditions were considered to create mock communities: (i) varying eukaryotes’ abundance, (ii) adding meiofauna from salted or freshwater wetlands, and (iii) including or not a sediment matrix. Most organisms composing the mock communities were detected, except a filamentous cyanobacteria. All mock communities showed similar composition indicating that sediment did not affect the DNA extraction. This result also demonstrated that sieving, necessary to enrich meiofauna from sediment, does not significantly affect any of the communities. For the environmental samples investigated, most of the taxa usually described in the literature were retrieved in the salted, brackish and freshwater marshes sediment. The proposed approach was successful in analysing organisms from the three domains of life in a unique environmental sample, providing a holistic view of the benthic community. Furthermore, the significant differences observed between samples from the three different marshes, indicated that our approach can be used for conducting successful ecological studies, especially useful for understanding benthic communities’ interactions.
{"title":"Towards a comprehensive view of wetland benthic communities","authors":"Clélia Duran , Christine Dupuy , Hélène Agogué , Robert Duran , Cristiana Cravo-Laureau","doi":"10.1016/j.crmicr.2025.100391","DOIUrl":"10.1016/j.crmicr.2025.100391","url":null,"abstract":"<div><div>Benthic prokaryotic communities, utmost important for wetlands and marine environments functioning, are influenced by physical-chemical parameters and interactions with other communities, especially micro-eukaryotes and meiofauna. Thus, a holistic view of the benthic community is necessary to fully understand their organization and functioning. This study assesses the implementation of a comprehensive view, using mock communities and environmental samples. A DNA extraction strategy combining two procedures is proposed: one to obtain DNA from micro-organisms, using 0.25 g of sediment, and the other from meiofauna, using 0.25 g of sieving refluxes from 5 g of sediment. Three conditions were considered to create mock communities: (i) varying eukaryotes’ abundance, (ii) adding meiofauna from salted or freshwater wetlands, and (iii) including or not a sediment matrix. Most organisms composing the mock communities were detected, except a filamentous cyanobacteria. All mock communities showed similar composition indicating that sediment did not affect the DNA extraction. This result also demonstrated that sieving, necessary to enrich meiofauna from sediment, does not significantly affect any of the communities. For the environmental samples investigated, most of the taxa usually described in the literature were retrieved in the salted, brackish and freshwater marshes sediment. The proposed approach was successful in analysing organisms from the three domains of life in a unique environmental sample, providing a holistic view of the benthic community. Furthermore, the significant differences observed between samples from the three different marshes, indicated that our approach can be used for conducting successful ecological studies, especially useful for understanding benthic communities’ interactions.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100391"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143864753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The objective of this study was to investigate the link between gut microbiota (GM) dysbiosis, gut inflammation, and bacterial translocation (BT) in recently diagnosed rheumatoid arthritis (RA). This case-control, observational study prospectively recruited recently diagnosed (<12 months) RA patients and age-matched healthy controls (HC) from two French hospitals between July 2014 to March 2018. The primary objective was to investigate GM composition in each group using 16S rRNA sequencing and metaproteomics approaches. Three plasmatic BT markers (sCD14, LPS-binding protein, and number of 16S rRNA gene copies) and one intestinal permeability marker (I-FABP) were quantified in blood samples.
Twenty-five were included in each group, and 50 stools and blood samples were analyzed. 16S rRNA gene analysis showed an decrease in Coprococcus in RA patients after Body Mass Index and HLA status. Circulating bacterial DNA (number of copies of the 16S rRNA gene) and plasmatic I-FABP were higher in RA patients compared to HCs (p < 0.01), indicating increased BT and intestinal permeability in these patients. Metaproteomics from stool samples highlighted an increased host humoral immune response in RA, with elevated levels of inflammatory proteins (azurocidin, cathepsin G, neutrophil defensing 1). Gut inflammation may contribute to increased intestinal permeability, leading to BT into the systemic circulation and thus chronic inflammation.
{"title":"Participation of gut microbiota and bacterial translocation in chronic systemic inflammation in recently diagnosed rheumatoid arthritis patients","authors":"Catherine Dunyach-Remy , Cassandra Pouget , Yves-Marie Pers , Cécile Gaujoux-Viala , Christophe Demattei , Florian Salipante , Lucia Grenga , Jean Armengaud , Jean-Philippe Lavigne , Christian Jorgensen","doi":"10.1016/j.crmicr.2025.100366","DOIUrl":"10.1016/j.crmicr.2025.100366","url":null,"abstract":"<div><div>The objective of this study was to investigate the link between gut microbiota (GM) dysbiosis, gut inflammation, and bacterial translocation (BT) in recently diagnosed rheumatoid arthritis (RA). This case-control, observational study prospectively recruited recently diagnosed (<12 months) RA patients and age-matched healthy controls (HC) from two French hospitals between July 2014 to March 2018. The primary objective was to investigate GM composition in each group using 16S rRNA sequencing and metaproteomics approaches. Three plasmatic BT markers (sCD14, LPS-binding protein, and number of 16S rRNA gene copies) and one intestinal permeability marker (I-FABP) were quantified in blood samples.</div><div>Twenty-five were included in each group, and 50 stools and blood samples were analyzed. 16S rRNA gene analysis showed an decrease in <em>Coprococcus</em> in RA patients after Body Mass Index and HLA status. Circulating bacterial DNA (number of copies of the 16S rRNA gene) and plasmatic I-FABP were higher in RA patients compared to HCs (<em>p</em> < 0.01), indicating increased BT and intestinal permeability in these patients. Metaproteomics from stool samples highlighted an increased host humoral immune response in RA, with elevated levels of inflammatory proteins (azurocidin, cathepsin G, neutrophil defensing 1). Gut inflammation may contribute to increased intestinal permeability, leading to BT into the systemic circulation and thus chronic inflammation.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100366"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.crmicr.2025.100362
Heng Ke, Hongbing Yao, Ping Wei
Epidemiological studies indicate a rising prevalence of allergic diseases, now recognized as a major global public health concern. In children, the progression of these diseases often follows the "atopic march," beginning with eczema, followed by food allergies, allergic rhinitis, and asthma. Recent research has linked gut microbiota dysbiosis to the development of allergic diseases in children. The gut microbiota, a crucial component of human health, plays a vital role in maintaining overall well-being, highlighting its potential in preventing and modifying the course of allergic diseases. This review examines the relationship between childhood allergic diseases and gut microbiota, drawing on the latest evidence. We first elaborated the concepts of allergic diseases and gut microbiota, followed by a discussion of the developmental trajectory of the gut microbiota in healthy children. This review further explored the richness, diversity, and composition of the gut microbiota, as well as specific microbial taxa associated with allergic disease. Lastly, we discussed the current status and future potential of probiotic interventions in managing pediatric allergic diseases.
{"title":"Advances in research on gut microbiota and allergic diseases in children","authors":"Heng Ke, Hongbing Yao, Ping Wei","doi":"10.1016/j.crmicr.2025.100362","DOIUrl":"10.1016/j.crmicr.2025.100362","url":null,"abstract":"<div><div>Epidemiological studies indicate a rising prevalence of allergic diseases, now recognized as a major global public health concern. In children, the progression of these diseases often follows the \"atopic march,\" beginning with eczema, followed by food allergies, allergic rhinitis, and asthma. Recent research has linked gut microbiota dysbiosis to the development of allergic diseases in children. The gut microbiota, a crucial component of human health, plays a vital role in maintaining overall well-being, highlighting its potential in preventing and modifying the course of allergic diseases. This review examines the relationship between childhood allergic diseases and gut microbiota, drawing on the latest evidence. We first elaborated the concepts of allergic diseases and gut microbiota, followed by a discussion of the developmental trajectory of the gut microbiota in healthy children. This review further explored the richness, diversity, and composition of the gut microbiota, as well as specific microbial taxa associated with allergic disease. Lastly, we discussed the current status and future potential of probiotic interventions in managing pediatric allergic diseases.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100362"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01DOI: 10.1016/j.crmicr.2024.100331
Hridesh Mukhopadhyay , Arnab Bairagi , Anushka Mukherjee , Aman Kumar Prasad , Arjama Dhar Roy , Aditi Nayak
The overuse of antibiotics has led to the global dissemination of Acinetobacter baumannii, an increasingly challenging nosocomial pathogen. This review explores the medical significance along with the diverse resistance ability of A. baumannii. Intensive care units (ICUs) serve as a breeding ground for A. baumannii, as these settings harbour vulnerable patients and facilitate the spread of opportunistic microorganisms. A. baumannii belongs to the ESKAPE group of bacterial pathogens that are major contributors to antibiotic-resistant infections. The pathogenic nature of A. baumannii is particularly evident in seriously ill patients, causing pneumonia, wound infections, and other healthcare-associated infections. Historically considered benign, A. baumannii is a global threat due to its propensity for rapid acquisition of multidrug resistance phenotypes. The genus Acinetobacter was formally recognized in 1968 following a comprehensive survey by Baumann et al., highlighting the relationship between previously identified species and consolidating them under the name Acinetobacter. A. baumannii is characterized by its Gram-negative nature, dependence on oxygen, positive catalase activity, lack of oxidase activity, inability to ferment sugars, and non-motility. The DNA G+C content of Acinetobacter species falls within a specific range. For diagnostic purposes, A. baumannii can be cultured on specific agar media, producing distinct colonies. The genus Acinetobacter comprises numerous species those are associated with bloodstream infections with high mortality rates. Therefore, A. baumannii poses a significant challenge to global healthcare due to its multidrug resistance and ability to cause various infections. A comprehensive understanding of the mechanisms underlying its resistance acquisition and pathogenicity is essential for combating this healthcare-associated pathogen effectively.
{"title":"Multidrug resistant Acinetobacter baumannii: A study on its pathogenesis and therapeutics","authors":"Hridesh Mukhopadhyay , Arnab Bairagi , Anushka Mukherjee , Aman Kumar Prasad , Arjama Dhar Roy , Aditi Nayak","doi":"10.1016/j.crmicr.2024.100331","DOIUrl":"10.1016/j.crmicr.2024.100331","url":null,"abstract":"<div><div>The overuse of antibiotics has led to the global dissemination of <em>Acinetobacter baumannii</em>, an increasingly challenging nosocomial pathogen. This review explores the medical significance along with the diverse resistance ability of <em>A. baumannii</em>. Intensive care units (ICUs) serve as a breeding ground for <em>A. baumannii</em>, as these settings harbour vulnerable patients and facilitate the spread of opportunistic microorganisms. <em>A. baumannii</em> belongs to the ESKAPE group of bacterial pathogens that are major contributors to antibiotic-resistant infections. The pathogenic nature of <em>A. baumannii</em> is particularly evident in seriously ill patients, causing pneumonia, wound infections, and other healthcare-associated infections. Historically considered benign, <em>A. baumannii</em> is a global threat due to its propensity for rapid acquisition of multidrug resistance phenotypes. The genus <em>Acinetobacter</em> was formally recognized in 1968 following a comprehensive survey by Baumann <em>et al</em>., highlighting the relationship between previously identified species and consolidating them under the name <em>Acinetobacter. A. baumannii</em> is characterized by its Gram-negative nature, dependence on oxygen, positive catalase activity, lack of oxidase activity, inability to ferment sugars, and non-motility. The DNA G+C content of <em>Acinetobacter</em> species falls within a specific range. For diagnostic purposes, <em>A. baumannii</em> can be cultured on specific agar media, producing distinct colonies. The genus <em>Acinetobacter</em> comprises numerous species those are associated with bloodstream infections with high mortality rates. Therefore, <em>A. baumannii</em> poses a significant challenge to global healthcare due to its multidrug resistance and ability to cause various infections. A comprehensive understanding of the mechanisms underlying its resistance acquisition and pathogenicity is essential for combating this healthcare-associated pathogen effectively.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100331"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142972467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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