Current Research in Microbial Sciences最新文献

{"title":"Assessment of the efficacy of an antimicrobial peptide in the context of cystic fibrosis airways","authors":"Albane Jouault ,&nbsp;Inès Jeguirim ,&nbsp;Inès Ben Hadj Kaddour ,&nbsp;Lhousseine Touqui","doi":"10.1016/j.crmicr.2025.100367","DOIUrl":"10.1016/j.crmicr.2025.100367","url":null,"abstract":"<div><div>Antimicrobial peptides (AMPs) offer a promising alternative to control airway infections with multi-resistant bacteria, such as methicillin-resistant <em>Staphylococcus aureus</em> (MRSA), which commonly infects patients with cystic fibrosis (CF). However, the behavior of AMPs in the CF context has yet to be fully elucidated. CF airways produce large amounts of proteases and viscous mucus (sputum), which may affect the efficacy of AMPs. The present work aimed to determine whether CF conditions affect the bactericidal efficacy of CAMA, a promising AMP known to kill clinical MRSA strains efficiently. Using a killing assay, we quantified CAMA bactericidal activity on a CF clinical MRSA strain in the presence of several compounds of CF airways, including sputum and bronchial epithelial cells (BECs). Our results indicate that CF sputum impairs the bactericidal efficacy of CAMA. Similar results were observed when CAMA was incubated with an artificial sputum medium (ASM). When used separately, sputum components (DNA, lipids, and mucins) reproduced the inhibitory effects of ASM. Additionally, the bactericidal efficacy of CAMA was also slightly altered when planktonic <em>S. aureus</em> strains were co-cultured with CF BECs. However, CAMA was not active against <em>S. aureus</em> cultured on BEC in biofilm mode, characteristic of chronic infections in CF patients. These findings suggest that although CAMA represents a promising tool to treat MRSA strains, the CF environment may impair the efficacy of this AMP. Identifying strategies to protect AMPs from the deleterious effects of CF sputum is a key priority.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100367"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143580495","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}

{"title":"Salinity tolerance in resting cysts of colpodid ciliates: Comparative transcriptomics analysis and chemical analysis of cyst walls to investigate their tolerance capability","authors":"Ryota Saito ,&nbsp;Hiroki Yamanobe ,&nbsp;Kazuma Yabuki ,&nbsp;Tomohiro Suzuki ,&nbsp;Takeru Saito ,&nbsp;Shuntaro Hakozaki ,&nbsp;Manfred Wanner ,&nbsp;Ryota Koizumi ,&nbsp;Tatsuya Sakai ,&nbsp;Maribet Gamboa ,&nbsp;Toshihiko Tanaka ,&nbsp;Akiko Ono ,&nbsp;Hoa Thanh Nguyen ,&nbsp;Yuta Saito ,&nbsp;Tetsuya Aoyama ,&nbsp;Katsuhiko Kojima ,&nbsp;Futoshi Suizu ,&nbsp;Kozo Watanabe ,&nbsp;Yoichiro Sogame","doi":"10.1016/j.crmicr.2025.100371","DOIUrl":"10.1016/j.crmicr.2025.100371","url":null,"abstract":"<div><div>The formation of resting cysts is a strategy for survival in unfavorable environments by single cell organisms such as protists. Here, we show that <em>Colpoda</em> resting cysts have high salinity tolerance and investigate the changes in gene expression that underpin this effect. <em>Colpoda</em> resting cysts can tolerate saline conditions up to 3.5 % NaCl. A comparative transcriptome analysis of vegetative cells and resting cysts showed that the relative levels of expression of genes associated with membrane function increased in resting cysts. These changes in gene expression suggest that reconstruction of the plasma membrane is associated with salinity tolerance. The resting cyst forms cyst-specific cellular structure known as the cyst wall. The outer shell-like layer, called the ectocyst, while the inner multiple layers, known as the endocyst. The chemical analysis showed ectocyst contains chitin and endocyst contains several proteins. These structures can protect cells by acting as a biological armor or protective materials. The results of this study offer a possible scenario in which salinity tolerance enables the widespread dispersal of protists.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100371"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143619376","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}

{"title":"Flocculation Mechanisms in Brettanomyces bruxellensis: Influence of ethanol and sulfur dioxide on FLO gene expression","authors":"Alessandra Di Canito,&nbsp;Roberto Foschino,&nbsp;Ileana Vigentini","doi":"10.1016/j.crmicr.2025.100372","DOIUrl":"10.1016/j.crmicr.2025.100372","url":null,"abstract":"<div><div>The mechanisms underlying flocculation in <em>Brettanomyces bruxellensis</em>, unlike the well-characterized <em>FLO</em>-family gene regulation in <em>Saccharomyces cerevisiae</em>, remain largely unexplored. This study investigates the flocculant phenotypes of 99 <em>B. bruxellensis</em> strains, revealing that only a minority exhibits this clumping behavior and confirms its strain-dependent attitude. Focusing on two strains, CBS2499 (flocculant) and UMY321 (non-flocculant), genetic analysis uncovered polymorphisms and distinct allelic heterozygosity in the <em>FLO1</em> and <em>FLO11</em> genes, potentially linked to the phenotypic differences. To further examine these traits, Response Surface Methodology (RSM) was used to simulate oenological conditions, testing the impact of pH, ethanol, and sulfur dioxide (SO₂) levels on flocculation and gene expression. The findings revealed that environmental stressors, especially ethanol and SO₂, significantly increase the expression of <em>FLO1</em> and <em>FLO11</em> in CBS2499, indicating a regulatory role in flocculation under stress. These insights broaden our understanding of stress adaptation in <em>B. bruxellensis</em>, especially its survival strategies in wine environments. By elucidating factors influencing flocculation, this study contributes valuable knowledge for managing <em>B. bruxellensis</em> spoilage, potentially aiding in the development of targeted approaches to reduce its impact on wine quality.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100372"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143643070","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}

{"title":"Heptad repeat 1-derived N peptide inhibitors improve broad-spectrum anti-HIV-1 activity","authors":"Chen Yuan ,&nbsp;Jia-Ye Wang ,&nbsp;Bu-Yi Wang ,&nbsp;Yi-Lin Zhao ,&nbsp;Yan Li ,&nbsp;Di Li ,&nbsp;Hong Ling ,&nbsp;Min Zhuang","doi":"10.1016/j.crmicr.2025.100364","DOIUrl":"10.1016/j.crmicr.2025.100364","url":null,"abstract":"<div><h3>Background</h3><div>HIV-1 N-peptide inhibitor (NPI) derived from N-terminal heptad-repeat region (HR1) of gp41 can target C-terminal heptad-repeat region (HR2) or the HR1 to interfere with the formation of endogenous six-helix bundle (6HB). However, the NPI is less active than the C-peptide inhibitor. In this study, we reported three HR1-derived NPIs designed by adding fusion peptide proximal region (FPPR) of gp41 or a trimeric motif MTQ into the N36 peptide and then evaluated their anti-HIV-1 activities.</div></div><div><h3>Methods</h3><div>Molecular modeling was performed using Swiss Model. The inhibitory activity of NPIs on HIV-1 was assessed by Env-pseudovirus infection assays and cell-cell fusion assays. Interaction between NPIs and HR2 peptides was evaluated by circular dichroism and Native PAGE.</div></div><div><h3>Results</h3><div>The three newly designed NPIs, FPPR-N36, MTQ-N36, and MTQ-FPPR-N36, exhibited higher anti-HIV-1 activity than N36. The stability of the coiled-coil core formed by three designed NPIs or the 6HB formed by C34 and these NPIs were significantly higher than those of corresponding monomer N36 or isoleucine zipper-engineered trimeric N36 (IZN36). The 50 % inhibitory concentrations (IC₅₀) of MTQ-N36 against HIV-1 infection were at a nanomolar level, lower than those of other tested NPIs. The FPPR-N36 could also inhibit infection of HIV-1 strains that were resistant to N36 and IZN36.</div></div><div><h3>Conclusions</h3><div>The three newly designed NPIs had inhibitory activity against HIV-1 infection. Among them, MTQ-N36 exhibited a higher potential to inhibit HIV-1 entry than other peptides, and FPPR-N36 might be a promising candidate NPI for suppressing HIV-1 strains that are resistant to conventional NPIs.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100364"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143509202","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}

{"title":"Chronic wounds and adaptive Pseudomonas aeruginosa: A phenotypic and genotypic characterization","authors":"Kasandra Buchholtz ,&nbsp;Rie Jønsson ,&nbsp;Rasmus L. Marvig ,&nbsp;Biljana Mojsoska ,&nbsp;Karen Angeliki Krogfelt","doi":"10.1016/j.crmicr.2025.100348","DOIUrl":"10.1016/j.crmicr.2025.100348","url":null,"abstract":"<div><div>Phenotypic and genetic diversity is found in varying prevalence in clinical populations where beneficial adaptations enable the bacteria to avoid recognition and eradication by the host immune system. This study aimed to investigate the presence of <em>Pseudomonas aeruginosa</em> in chronic venous leg ulcers wounds over an 8-week time course. This was performed using genomic and phenotypic approaches to understand the survival and persistence of <em>Pseudomonas</em> strains. The findings of this study show that the two patients were colonized with a recurring <em>P. aeruginosa</em> genotype with only minor phenotypic differences and few SNP differences, suggesting that the <em>Pseudomonas</em> isolates present in the wound can survive and proliferate in the host's hostile environment. The results provided from this study will allow us to understand <em>P. aeruginosa</em> colonization during a 8 week time period.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100348"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143378991","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}

{"title":"Carbapenemase and extended-spectrum β-lactamase producing bacteria isolated from municipal wastewater treatment plant and urban river in Nepal","authors":"Santosh Khanal ,&nbsp;Deepa Neupane ,&nbsp;Joshna Thapa ,&nbsp;Suman SK ,&nbsp;Sudeep K C ,&nbsp;Tista Prasai Joshi ,&nbsp;Dev Raj Joshi","doi":"10.1016/j.crmicr.2025.100467","DOIUrl":"10.1016/j.crmicr.2025.100467","url":null,"abstract":"<div><div>Municipal wastewater treatment plants (WWTPs) and rivers receiving sewage are known hotspots for antibiotic-resistant bacteria (ARB), harboring a wide variety of antibiotic resistance genes (ARGs) and mobile genetic elements. However, the specific distribution of ARB carrying multiple resistance genes in municipal WWTPs and their receiving rivers in Kathmandu remains unclear. Therefore, this study investigated the proportion of antibiotic-resistant bacterial populations and the presence of various ARGs and integrons in carbapenemase- and extended-spectrum β-lactamase (ESBL)-producing bacteria isolated from municipal wastewater and river water. The improvement in water’s physicochemical characteristics and a significant reduction in ARB and antibiotic resistance determinants were observed in treated municipal wastewater compared to untreated wastewater. Among 232 bacterial isolates from these samples, 34.82 % were identified as carbapenemase producers, while 42.50 % were confirmed as ESBL producers. <em>E. coli</em> and <em>K. pneumoniae</em> were the predominant carbapenemase- and ESBL-producing bacteria, with their highest abundance in untreated municipal wastewater. Among carbapenemase-producing bacteria, <em>bla</em>_NDM and <em>bla</em>_OXA genes were more prevalent, whereas <em>bla</em>_TEM and <em>bla</em>_CTX-M genes were commonly detected in ESBL-producing bacteria. Nearly half of these bacterial isolates carried the <em>intI1</em> gene, indicating its role in the dissemination of ARGs. These findings underscore the critical role of WWTPs in the removal of chemical and biological pollutants, highlighting their significance in urban ecosystem-based adaptation. However, the simultaneous presence of multiple resistance genes and integrons in ARB contributes to the rising antimicrobial resistance in the environment, emphasizing the need for targeted efforts to manage and mitigate the spread of resistance factors.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100467"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144931877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomic insights into the prebiotic and metabolic regulatory properties of ellagic acid and urolithins on probiotic-like bacteria in vitro","authors":"Yang Yang ,&nbsp;Ke Wang ,&nbsp;Jia-Chi Chiou ,&nbsp;Danyue Zhao","doi":"10.1016/j.crmicr.2025.100425","DOIUrl":"10.1016/j.crmicr.2025.100425","url":null,"abstract":"<div><div>Mounting evidence suggests that dietary polyphenols exert health benefits partly through their favorable interactions with gut bacteria. However, little is known about polyphenol’s metabolic regulatory effects towards individual bacteria at the molecular level. Ellagic acid (EA), a polyphenol abundantly present in plant-based foods, was found to exhibit prebiotic properties through differential interactions with probiotic-like bacteria, including the EA-to-urolithin converting species such as <em>Gordonibacter urolithinfaciens</em> (<em>G. uro</em>). This study aimed to investigate the crosstalk between EA and EA-responsive beneficial bacteria, including both conventional and next-generation probiotics originating from the human gut, and to understand the underlying mechanism by which EA exerts prebiotic activities <em>in vitro</em>. The influence of EA and urolithins on probiotic bacteria was investigated at the levels of fecal microbiota and individual strains via anaerobic culturomics and metabolomics approaches. Results indicate that dietary-level EA favorably regulated gut microbial composition through the enrichment of probiotic genera (e.g., <em>Bifidobacterium</em> and <em>Akkermansia</em>) <em>in vitro</em>. Regarding individual bacteria, EA supplementation promoted the growth of <em>Lacticaseibacillus rhamnosus</em> GG and <em>Bifidobacterium infantis</em>. Integrated targeted and untargeted metabolomic analyses of intracellular and extracellular metabolites revealed that EA/urolithins modulated metabolic pathways associated with amino acid metabolism, energy production and oxidative stress. Furthermore, <em>G. uro</em> exhibited strong EA uptake ability, facilitating the urolithin bioconversion and cellular accumulation in a dose-dependent manner. Overall, this study provides in-depth understanding on how dietary polyphenols with prebiotic properties regulate the growth and metabolic functions of probiotic-like bacteria.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100425"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144471867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"First report of a carbapenem-resistant Serratia sarumanii clinical strain co-harboring blaKPC-2 and blaNDM-1 genes in China","authors":"Xiao Liu ,&nbsp;Zhen Liu ,&nbsp;Xuemei Bai ,&nbsp;He Gao ,&nbsp;Zhiwen Sun ,&nbsp;Duochun Wang","doi":"10.1016/j.crmicr.2025.100411","DOIUrl":"10.1016/j.crmicr.2025.100411","url":null,"abstract":"<div><div>Carbapenem-resistant <em>Enterobacteriaceae</em> (CRE), particularly those co-harboring multiple carbapenemase genes, pose a significant global health threat. However, the coexistence of <em>bla</em>_KPC-2 and <em>bla</em>_NDM-1 in <em>Serratia sarumanii</em> has not been previously reported. This study aims to report and characterize the first carbapenem-resistant <em>S. sarumanii</em> (CRSS) clinical strain MAS3954 in China co-harboring <em>bla</em>_KPC-2 and <em>bla</em>_NDM-1, focusing on its genetic characteristics, plasmid stability, and transfer potential. Whole-genome analysis revealed that the <em>bla</em>_KPC-2 and <em>bla</em>_NDM-1 were located on two distinct plasmids. Plasmid pMAS3954-KPC (113,856 bp, IncFII/IncFIB) exhibited low similarity (&lt;66%) to known plasmids, indicating a novel fusion event between pKPC-h2 and <em>S. marcescens</em> chromosome, while pMAS3954-NDM (55,235 bp, IncX3) was highly conserved (100% identity/coverage). Conjugation experiments showed that the <em>bla</em>_NDM-1 was transferable, while <em>bla</em>_KPC-2 was not. During 10 days of continuous passage, the genetic context of <em>bla</em>_NDM-1 was gradually excised from the plasmids after the 8th day, whereas they maintained 100% retention for <em>bla</em>_KPC-2. <em>S. sarumanii</em> MAS3954 was multidrug-resistant (MDR), including carbapenems, β-lactams, β-lactam/β-lactamase inhibitors, trimethoprim-sulfamethoxazole, tetracycline, nitrofurantoin, colistin, and fluoroquinolones, but remained susceptible to certain aminoglycosides and tigecycline. Phylogenomic analysis identified a distinct clade for <em>S. sarumanii</em> MAS3954, diverging notably from other strains. Comparison of resistance genes further highlighted the unique co-harboring of <em>bla</em>_KPC-2 and <em>bla</em>_NDM-1 in MAS3954, absent in other strains. To our knowledge, this study represents the first characterization of clinical <em>S. sarumanii</em> strain co-harboring <em>bla</em>_KPC-2 and <em>bla</em>_NDM-1. The findings highlight the need for enhanced surveillance and infection control to prevent the spread of these MDR strains in healthcare settings.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100411"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144195581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The rise and evolving role of Fusobacterium nucleatum subspecies","authors":"Marietta Wolf ,&nbsp;Thorsten Steinberg ,&nbsp;Konstantin Johannes Scholz ,&nbsp;Anne Kruse ,&nbsp;Sama Rezasoltani ,&nbsp;Georg Conrads ,&nbsp;Ali Al-Ahmad ,&nbsp;Fabian Cieplik","doi":"10.1016/j.crmicr.2025.100414","DOIUrl":"10.1016/j.crmicr.2025.100414","url":null,"abstract":"<div><div>This review examines the classification, distribution, and detection methods of <em>Fusobacterium nucleatum</em> subspecies, focusing on their distinct roles in health and disease. The evolution of <em>F. nucleatum</em> classification is traced from early to modern protein-based and genomic methods, such as 16S rRNA and next generation sequencing and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). The review highlights the importance of distinguishing <em>F. nucleatum</em> subspecies due to their varying pathogenic potentials and ecological niches in both oral and extraoral environments. Different subspecies exhibit distinct prevalence and activity levels in specific clinical conditions, such as periodontitis and oral squamous cell carcinoma (OSCC). This highlights the importance of accurately identifying subspecies to understand their role in disease progression. Moreover, understanding the varying pathogenic potential of <em>F. nucleatum</em> subspecies, which is driven by genetic diversity and virulence factors, is also essential for advancing research and improving patient outcomes.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100414"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144243556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the genetic basis of biochemical pathways of plant growth promotion in Bacillus pumilus and the first genomic insights into B. pseudomycoides as a biostimulant","authors":"Esmeralda Dushku ,&nbsp;Charalampos Kotzamanidis ,&nbsp;Athanasios Kargas ,&nbsp;Maria-Eleni Fanara-Lolou ,&nbsp;Virginia Giantzi ,&nbsp;Evdokia Krystallidou ,&nbsp;Antonios Zdragas ,&nbsp;Andigoni Malousi","doi":"10.1016/j.crmicr.2025.100419","DOIUrl":"10.1016/j.crmicr.2025.100419","url":null,"abstract":"<div><div><em>Bacillus</em> species are among the most promising plant growth-promoting bacteria (PGPB) due to their adaptability to various environmental niches and extensive biosynthetic capabilities. Despite the available data on the PGP-traits (PGPTs) of <em>Bacillus</em>, the genetic basis underlying their beneficial effects remains largely unexplored. In this study, a comparative genomic analysis of three <em>B. pumilus</em> and one <em>B. pseudomycoides</em> strains, isolated from the maize rhizosphere, is presented to elucidate the molecular mechanisms behind their PGP-traits. All strains exhibited multiple PGP-traits, including phosphate solubilization, phytohormone and siderophore production, growth in nitrogen-free medium, stress tolerance, and biofilm formation. Phylogenomic analysis revealed that plant-associated strains have higher genetic similarity, emphasizing niche-specific evolution. Genome analyses revealed strain- and species-specific adaptations, particularly in relation to nutrient acquisition and abiotic stress response mechanisms. <em>B. pumilus</em> strains encoded alternative sigma factors (SigB, SigM, SigW) enabling enhanced salt tolerance, whereas <em>B. pseudomycoides</em> lacked this system and relied on conventional osmoprotective strategies. The strains utilized different tryptophan-dependent (IAN, IAM or IPyA) pathways for auxin biosynthesis and differed in phosphate solubilization ability, which can be attributed to upstream and missense variants in genes affecting acid metabolism (<em>gltA, acnA, acnB, citM</em>, and <em>citS)</em> and phosphatase (<em>phoA</em>) activity. Iron uptake <em>via</em> bacillibactin-siderophores was exclusive to <em>B. pumilus</em>. The inability of the <em>B. pseudomycoides</em> strain to acquire iron was associated with structural variants (absence of <em>bsaA</em> gene) within the bacillibactin biosynthetic gene cluster. This work provides new insights into the molecular basis of PGP traits in <em>Bacillus</em> and supports the development of <em>Bacillus</em>-based bioinoculants for sustainable agriculture.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100419"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279832","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}