MicrobiologyOpen[JOURNAL]
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200 papers
Characterization of Multitrait Plant Growth-Promoting Rhizobacteria From Opuntia ficus-indica in Different Moroccan Climates.
Zouitane I, Campana DC, Cesaro P … +9 more , Massa N, Novello G, Gamalero E, Todeschini V, Ferioun M, Derraz K, Koraichi SI, El Ghachtouli N, Lingua G
Microbiologyopen · 2026 Jun · PMID 42337972 · Full text
Plant growth-promoting rhizobacteria (PGPR) enhance plant fitness through nutrient mobilization, hormone modulation, and improved tolerance to abiotic stresses. Despite the ecological and agricultural importance of Opunt...
Plant growth-promoting rhizobacteria (PGPR) enhance plant fitness through nutrient mobilization, hormone modulation, and improved tolerance to abiotic stresses. Despite the ecological and agricultural importance of Opuntia ficus-indica, a drought-adapted cactus widely cultivated in arid and semiarid regions, little is known about its rhizosphere microbiota. This study aimed to select culturable rhizobacteria associated with O. ficus-indica, assessing their plant growth-promoting (PGP) traits and identifying strains with potential for improving crop performance under challenging environmental conditions. Bacterial strains from the rhizosphere of O. ficus-indica were isolated across three Moroccan regions with distinct rainfall regimes: Tafrant (humid), Fez (semiarid), and Chichaoua (arid). Seventy-seven strains were isolated and screened for their PGP traits, including phosphate solubilization, indole-3-acetic acid, siderophore, ammonia and HCN production, exopolysaccharide synthesis, in vitro nitrogen fixation, and antagonistic activity against Fusarium solani. Twenty-two high-performing isolates displaying superior PGP traits were selected. Molecular identification revealed taxonomic diversity across three bacterial groups: Gammaproteobacteria (Pseudomonas, Acinetobacter, Enterobacter, and Stenotrophomonas), Actinobacteria (Streptomyces, Arthrobacter, Kocuria, and Citricoccus), and Firmicutes (Bacillus, Peribacillus, Virgibacillus, Terribacillus, and Priestia). Isolates from semiarid and arid regions exhibited higher tolerance to drought-mimicking stress. Several isolates enhanced seed germination and seedling growth parameters in wheat, with the highest germination percentage induced by Peribacillus frigotolerans ZFSp2 and Pseudomonas moraviensis ZN17. Sorghum germination rate was highest in the presence of ZFSp2. These results highlight the rhizosphere of O. ficus-indica as a valuable reservoir of PGPR with strong potential for applications in sustainable agriculture, particularly in arid and semiarid regions.
Tryptophan Metabolism and Aryl-Hydrocarbon Receptor Agonists in the Gut Microbiome of People With Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.
Esteban DJ, Conrad B, Cullinan A … +3 more , Luong S, Albaum J, Wilk V
Microbiologyopen · 2026 Jun · PMID 42325052 · Full text
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic disease with unknown biological basis and no cure. Microbiome dysbiosis has been reported in people with ME/CFS but its relevance to p...
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating chronic disease with unknown biological basis and no cure. Microbiome dysbiosis has been reported in people with ME/CFS but its relevance to pathophysiology is unknown. Gut microbes are an important source of tryptophan metabolites that activate the aryl hydrocarbon receptor (AHR), a regulator of homeostatic and inflammatory genes. Dysregulated activation of AHR contributes to pathophysiology of several neuroimmune and chronic diseases but its role in ME/CFS has not been investigated. The purpose of this study was to investigate the production of tryptophan metabolites and AHR agonists by gut microbes of people with ME/CFS. We found lower diversity and altered microbiome community structure in people with ME/CFS and changes in the subcommunity of microbes that correlated with tryptophan metabolites. Using targeted metabolomics we identified nine metabolites elevated in the stool of people with ME/CFS, including three AHR agonists. Stool ex vivo cultures were tested for their capacity to activate AHR in a reporter cell line and by qPCR. AHR activation did not differ between people with ME/CFS and controls, however, we detected elevated agonist activity in people with neurocognitive symptoms, regardless of underlying disease. These findings are consistent with previous work revealing changes in the gut microbiome of people with ME/CFS and adds further support to alterations in tryptophan metabolism associated with the disease. Altered AHR activity by gut microbial metabolites may be a common mechanism contributing to neurocognitive symptoms in diseases including ME/CFS.
Pathogenic Mechanisms of V. vulnificus and Its Role in the Development of Sepsis.
Yu Z, Zhu X, Tang S … +5 more , Yang S, Li J, Luo L, Tan Y, Yin J
Microbiologyopen · 2026 Jun · PMID 42324908 · Full text
Vibrio vulnificus (V. vulnificus) is a highly virulent marine pathogen responsible for severe infections, including necrotizing fasciitis and life-threatening sepsis, particularly in immunocompromised individuals. This r...
Vibrio vulnificus (V. vulnificus) is a highly virulent marine pathogen responsible for severe infections, including necrotizing fasciitis and life-threatening sepsis, particularly in immunocompromised individuals. This review synthesizes current knowledge on V. vulnificus pathogenesis, focusing on key virulence factors such as cytolysins (VvhA and MARTX), iron acquisition systems, and immune evasion strategies. The bacterium's ability to induce rapid tissue damage, endothelial dysfunction, and systemic inflammation-mediated through cytokine storms and necroptosis-underpins V. vulnificus high mortality rates. Risk factors include chronic liver disease, diabetes, and environmental exposure to seafood harboring V. vulnificus or brackish water. Clinical management hinges on early diagnosis, prompt antibiotic therapy (e.g., doxycycline combined with third-generation cephalosporins), and surgical intervention for necrotizing infections. Despite advances, challenges persist, including antibiotic resistance and delayed diagnosis. Future directions emphasize novel therapeutics targeting virulence mechanisms, rapid diagnostics, and climate-adaptive public health strategies to curb the rising incidence of V. vulnificus infections in warming coastal ecosystems. This review underscores the urgent need for multidisciplinary approaches to mitigate the global burden of this formidable pathogen.
Gut Microbiota Alterations Associated With Colonization by Multidrug-Resistant Organisms in ICU Patients: First Systematic Review and Meta-Analysis.
Goicea AE, Leucuța DC, Bodolea C
Microbiologyopen · 2026 Jun · PMID 42324777 · Full text
Colonization by multidrug-resistant organisms (MDROs) is a risk factor for infection and mortality in critically ill patients, yet current strategies to prevent or control dissemination show variable effectiveness. Wheth...
Colonization by multidrug-resistant organisms (MDROs) is a risk factor for infection and mortality in critically ill patients, yet current strategies to prevent or control dissemination show variable effectiveness. Whether alterations in microbiota structure and composition (dysbiosis) are associated with MDRO colonization in critically ill patients is an open question this study aims to address. We conducted the first systematic review and meta-analysis comparing intestinal microbiota structure (diversity) and composition (relative abundance of bacteria) between colonized critically ill patients and noncolonized/control patients. PubMed, Web of Science, and Scopus were systematically searched from inception to September 2025. The study protocol was preregistered on Open Science Framework, under embargo. Of 3003 records identified, 11 studies (n = 2823 patients) published between 2019 and 2025 met the inclusion criteria. The most frequently reported colonizing strains in MDROs-colonized patients were vancomycin-resistant Enterococci (58.2%), carbapenem-resistant Enterobacterales (21.6%), extended-spectrum β-lactamase-producing Enterobacterales (13.4%). All studies employed 16S ribosomal RNA sequencing to assess intestinal microbiota. Colonized critically ill patients had lower values of dominance/evenness and richness, reaching significantly lower values of information when compared with controls (mean difference in Shannon index = -1.18; 95% CI, -1.84 to -0.52; p < 0.001). Composition investigation revealed a significant increase in the Pseudomonadota phylum and the Enterobacteriaceae family in MDROs-colonized patients. Current evidence is limited and largely associational. Nevertheless, altered intestinal microbiota consistently characterize colonized critically ill patients. Further studies are warranted to determine whether early detection of dysbiosis can enhance early prediction/diagnosis of MDROs-colonization and guide the targeted microbiota-based strategies to prevent infections.
Dermatomycosis Caused by Non-Dermatophyte Agents; Diagnosis Based on Molecular Identification.
Ranjbar Golafshani FZ, Akhondzadeh A, Dastbaz Momtaz A … +4 more , Aryanian Z, Kermani F, Ghaffari Lashkenari E, Mahdavi Omran S
Microbiologyopen · 2026 Jun · PMID 42324737 · Full text
Dermatomycoses are a superficial fungal infections affecting of the skin, hair and nails. While dermatophytes are recognized as the primary causative agents of fungal skin infections, the significance of yeasts and molds...
Dermatomycoses are a superficial fungal infections affecting of the skin, hair and nails. While dermatophytes are recognized as the primary causative agents of fungal skin infections, the significance of yeasts and molds in this context warrants greater attention. The present study analyzed samples from patients suspected of non-dermatophyte superficial infections who were referred to dermatology clinics in Babol. The collected samples underwent direct microscopic examination and culture. Identification of the isolates was performed using standard mycological laboratory techniques, including morphological assessments and slide culture. Molecular identification was achieved through DNA extraction and subsequent sequence analysis of the ITS1-5.8S rDNA-ITS4 region. Demographic analysis of 25 patients indicated a predominance of females (72%). The average age of the patients was 52.2 years. Clinical manifestations exhibited considerable variability, with the most prevalent symptoms including pruritus, erythema and scaling. The most frequently affected sites included the feet, nails and groin. Although Candida albicans was the predominant isolate identified, a diverse array of other fungal species was also recognized. The variability seen in patients' demographics, clinical signs and fungal causes highlights the complexity of these infections. Correctly identifying fungal species is essential for proper patient treatment.
Human Gut Phageome Analysis Uncovers Thousands of Highly Modular Endolysins.
Niloy RK, Jewel NA, Karim D … +4 more , Rolin MH, Khan T, Akter A, Mondal SI
Microbiologyopen · 2026 Jun · PMID 42324716 · Full text
The escalating threat of antimicrobial resistance has renewed global interest in bacteriophages as precise and powerful tools for controlling bacterial populations in the human gut. These viruses owe much of their antiba...
The escalating threat of antimicrobial resistance has renewed global interest in bacteriophages as precise and powerful tools for controlling bacterial populations in the human gut. These viruses owe much of their antibacterial potential to phage-encoded endolysins, enzymes capable of rapidly degrading bacterial cell walls with high specificity and low potential for resistance development. Despite their therapeutic promise, the overall composition of the gut phageome and the structural modularity of its endolysins remain poorly understood. In this study, we performed a large-scale analysis of 9141 human gut metagenomic samples from 34 independent studies. Using standardized workflows for assembly, genome clustering, host prediction, and protein domain annotation, we reconstructed 15,267 phage genomes and identified 3794 corresponding endolysins. The recovered genomes showed substantial variation in size and coding density, with an average GC content of 43%. Host prediction indicated that most phages targeted bacterial members of the phyla Bacillota (41%) and Bacteroidota (23%). Endolysin sequences grouped into 296 protein families and displayed striking domain modularity. Catalytic domains such as Amidase_2 and Glyco_hydro_25 frequently co-occurred with cell wall-binding motifs including LysM and CW_7. Remarkably, one endolysin contained 15 distinct domains, the highest natural domain diversity reported to date. Collectively, this study represents the most comprehensive characterization of the human gut phageome and its encoded endolysins to date. The exceptional modular diversity uncovered highlights the gut phageome as a rich reservoir of endolysin variants, providing a strong foundation for developing next-generation therapeutics against multidrug-resistant bacterial pathogens.
Molecular Characterization and Antifungal Profiling of Nine Phenotypic Aspergillus nidulans Isolates: A Case Series From North India.
Nikhil A, Tiwari AK, Parashar P … +6 more , Bhatia M, Tilak R, Kumar D, Singh SK, Narayan RJ, Gupta MK
Microbiologyopen · 2026 Jun · PMID 42324700 · Full text
Aspergillus nidulans is a fungal pathogen that causes respiratory issues in individuals with compromised immune systems. It is identified through culture characteristics and microscopic features such as Cleistothecia and...
Aspergillus nidulans is a fungal pathogen that causes respiratory issues in individuals with compromised immune systems. It is identified through culture characteristics and microscopic features such as Cleistothecia and Hülle Cells. However, similar traits are found in cryptic Aspergillus species, such as stellatus, cristatus, and oryzae. In a case series from a hospital in North India, A. nidulans strains isolated from patients with pulmonary aspergillosis were phenotypically identified and then underwent molecular characterization through sequencing of the amplified ITS1-5.8S rDNA-ITS2 region and antifungal susceptibility testing (AST) according to the CLSI M38A3 guidelines. The molecular characteristics and antifungal profiles of the nine phenotypic A. nidulans were as follows: A. stellatus (n = 5), A. nidulans (n = 2), A. cristatus (n = 1), and A. oryzae (n = 1). Phylogenetic analysis revealed a close relationship between A. stellatus, A. nidulans, and A. cristatus, while A. oryzae showed significant divergence. Furthermore, the minimum inhibitory concentration (MIC) of antifungals was the lowest for caspofungin, followed by voriconazole. However, a higher amphotericin B MIC (2 µg/mL) was observed for A. stellatus. Thus, sequencing the ITS1-5.8S rDNA-ITS2 region can accurately identify cryptic species with superior taxonomic resolution. Additionally, the MIC of amphotericin B against A. stellatus underscores the importance of precise molecular identification and antifungal MIC profiling in each case of pulmonary aspergillosis.
The Role of Neonatal Ward Environment as a Reservoir for the Dissemination of Multidrug-Resistant Klebsiella pneumoniae in Algeria.
Derkaoui M, Fischer MA, Sebaihia M … +5 more , Namoune R, Bouheudjeur F, Beloukarif M, Madaoui B, Lopes BS
Microbiologyopen · 2026 Jun · PMID 42324692 · Full text
Klebsiella pneumoniae is a major cause of hospital-acquired infections and contributes to high mortality. We examined the molecular epidemiology, antibiotic resistance, and virulence features of K. pneumoniae from the ne...
Klebsiella pneumoniae is a major cause of hospital-acquired infections and contributes to high mortality. We examined the molecular epidemiology, antibiotic resistance, and virulence features of K. pneumoniae from the neonatal ward environment of a hospital in Chlef, Algeria, using whole-genome sequencing (WGS). Antibiotic susceptibility was assessed with the Vitek 2 automated system (AST-N365 card). Genomic DNA was extracted with the GF-1 kit, and WGS was performed by GENEWIZ Europe using the NEBNext Ultra II DNA Library Prep Kit. Species identification and virulence genes were determined using Kleborate, antimicrobial resistance genes were detected with AMRfinder Plus. From 9790 publicly available K. pneumoniae genomes, the 112 closest matches were selected, and core-genome MLST and a minimum-spanning tree were generated in SeqSphere + v10.5.04 using a MLST and cgMLST scheme. All isolates were multidrug-resistant, and WGS identified 22 resistance genes. Core genes detected across all samples included the bla, bla, oqxA, oqxB, aph(6)-Id, aph(3")-Ib, sul2, fosA5, emrD and kdeA. Other genes, including bla, bla, bla, bla, qnrB4, qnrS1 and aac(6')-Ib-cr5 were also observed. Yersiniabactin-associated virulence genes ybt and irp were detected in KP32, KP37 and KP57 (high risk clone ST13) while qacE was present only in KP55 (novel strain ST8932). This study highlights the persistence of bla, qnr, and bla in K. pneumoniae from the neonatal ward environment. The presence of the high-risk strain ST13 is particularly concerning, as its identical allelic profiles indicate likely clonal spread within the hospital. These results suggest the hospital environment may act as a reservoir for multidrug-resistant K. pneumoniae.
Hospital-Associated Antimicrobial Resistant Bacteria on 95 Mobile Phones: An International Metagenomic "Phonome" Analysis.
Goldsworthy A, Olsen M, Obonyo NG … +10 more , Jones P, McKirdy S, Senok A, Alghafri R, Ghemrawi R, Almheiri R, Tronstad O, Suen JY, Fraser JF, Tajouri L
Microbiologyopen · 2026 Jun · PMID 42316926 · Full text
Antimicrobial resistant healthcare-associated infections present an increasing threat to public safety and the sustainability of healthcare systems around the world. Mobile phones have been highlighted as a fomite that n...
Antimicrobial resistant healthcare-associated infections present an increasing threat to public safety and the sustainability of healthcare systems around the world. Mobile phones have been highlighted as a fomite that negates hand hygiene and contributes to the dissemination of pathogenic microorganisms in healthcare settings. The objective of the current stidy was to investigate the presence of bacteria, antimicrobial resistance and virulence genes associated with high morbidity on 95 mobile phones within healthcare settings. Next-Generation Metagenomic Sequencing was undertaken and FastQ files were subsequently analyzed within COSMOSid to enable taxonomic identification. Antibiotic resistant genes, virulence genes and bacteriophages were co-located with bacteria associated with the highest global mortality. Antibiotic resistant genes were manually annotated and cross referenced with the Comprehensive Antibiotic Resistance Database (CARD) to identify gene-drug interactions. On average, mobile phones were identified to be contaminated with 3.62 of the top 10 highest mortality-causing bacteria and 2.49 ESKAPE pathogens. A total of 262 unique ARGs, 448 unique VFGs, and 314 bacteriophages were identified. Mobile phones within healthcare settings harbor pathogens alongside genes associated with increased virulence and antimicrobial resistance. Additionally, mobile phones, known to be infrequently sanitized, may increase antimicrobial resistance by providing a contaminated platform which facilitates continued horizontal genetic transfer.
Discordance Between 16S rRNA Similarity and Genome-Based Species Boundaries in Gluconobacter.
Maeno S, Kataoka N, Matsutani M … +1 more , Yakushi T
Microbiologyopen · 2026 Jun · PMID 42316512 · Full text
The 16S rRNA gene is widely used for bacterial identification, but its resolving power is limited in several taxa. In the genus Gluconobacter, species boundaries remain unclear despite reliance on 16S-based classificatio...
The 16S rRNA gene is widely used for bacterial identification, but its resolving power is limited in several taxa. In the genus Gluconobacter, species boundaries remain unclear despite reliance on 16S-based classification. To examine these limitations, we analyzed all publicly available complete genomes (n = 12) together with curated 16S rRNA sequences and compared 16S rRNA sequences similarity with genome-based relatedness. Within the sampled complete genomes, 16S rRNA sequences were highly conserved and showed substantial overlap between intra- and interspecific similarities. In contrast, average nucleotide identity (ANI)-based divergence was pronounced: ANI values ranged from 79.7% to 100%, and G. oxydans included more than one genomic lineage. Notably, two strains (H24 and 1.637) showed higher ANI values (97.2%-97.4%) to G. thailandicus than to other G. oxydans strains. Even the hypervariable V4, V6, and V8 regions lacked clade-specific signatures, indicating limited species-level resolution within this group. Furthermore, type-strain 16S rRNA sequences of G. oxydans, G. frateurii, and G. japonicus show ≥ 99% similarity and are grouped within the same non-redundant representative in the SILVA NR99 database, indicating limited species-level resolution. These results demonstrate a clear mismatch between 16S rRNA sequences similarity and genomic structure in Gluconobacter. Genome-based criteria, supported by refined reference databases and validated gene markers, are essential for accurate taxonomy and microbiome-based analyses.
Antibiotic Resistance and Biofilm Gene Distribution in Colistin-Resistant Acinetobacter baumannii.
Hatem ZA, Kafe FN, Musa FH … +5 more , Al-Taie SF, Ateya NH, Aziz LM, Rajabi E, Hasan RN
Microbiologyopen · 2026 Jun · PMID 42313510 · Full text
Acinetobacter baumannii, a multidrug-resistant opportunistic bacterium, poses a substantial hazard in hospital settings. The emergence of colistin- and tigecycline-resistant strains further limits treatment options and n...
Acinetobacter baumannii, a multidrug-resistant opportunistic bacterium, poses a substantial hazard in hospital settings. The emergence of colistin- and tigecycline-resistant strains further limits treatment options and necessitates detailed investigation of resistance mechanisms. A total of 144 clinical A. baumannii isolates from multiple hospitals in Iran were identified using standard microbiological and molecular techniques. Antimicrobial susceptibility was assessed using both disk diffusion and broth microdilution techniques. Biofilm formation was quantified by crystal violet staining. Resistance and biofilm-related genes were detected by conventional polymerase chain reaction (PCR). The expression of key resistance genes (pmrA, pmrB, adeB, adeJ, and adeG) was evaluated by quantitative PCR (qPCR) in resistant isolates, and MLST was performed to determine the genetic relatedness among tigecycline- and colistin-resistant isolates. Resistance to colistin and tigecycline was observed in 3 (2.08%) and 2 (1.4%) isolates, respectively, and 90.9% of the isolates were biofilm producers, with higher odds of strong biofilm formation significantly correlating with the presence of bla. All isolates carried pmrA and pmrB, but only colistin-resistant isolates showed overexpression of these genes compared to susceptible ones. MLST revealed diverse sequence types among resistant isolates, including ST188, ST138, ST387, ST2288, and ST3337. This study highlights the complex interplay between the presence of genes, their expression, and the resistance phenotype in A. baumannii and underscores the importance of monitoring chromosomal resistance determinants for effective control and treatment strategies.
Interplay Between Virulence Genes, Antimicrobial Resistance Profiles, and Biofilm Formation in Klebsiella pneumoniae Causing Urinary Tract Infections in North Lebanon.
Zaylaa M, Farha R, Taleb J … +6 more , Saad A, Gharbawy OE, Sarraf R, Kassam I, Hamdach C, Bissar N
Microbiologyopen · 2026 Jun · PMID 42310482 · Full text
Klebsiella pneumoniae (K. pneumoniae) is a major cause of urinary tract infections (UTIs) and poses a growing public health concern due to multidrug resistance and virulence potential. This study aimed to characterize an...
Klebsiella pneumoniae (K. pneumoniae) is a major cause of urinary tract infections (UTIs) and poses a growing public health concern due to multidrug resistance and virulence potential. This study aimed to characterize antimicrobial resistance, biofilm formation, and virulence gene distribution among urinary K. pneumoniae isolates from North Lebanon and to explore correlations between these factors. A total of 153 non-duplicate isolates from hospital and community settings were analyzed for antibiotic susceptibility, hypermucoviscosity, biofilm formation, and presence of key virulence (fimH, mrkD, magA, rmpA, entB, iucA, iroN, kfu) and β-lactamase (blaTEM, blaSHV, blaCTX-M) genes. Adhesion-associated genes fimH and mrkD were highly prevalent, particularly in hospital-acquired and strong biofilm-producing isolates. Capsular and regulatory genes (magA) was more frequent in putative hypervirulent and community-acquired strains, while siderophore genes entB and iucA were strongly associated with biofilm formation and hospital-acquired infections. A significantly higher resistance to cephalosporins, along with an increased frequency of multidrug-resistant phenotypes, was detected in hospital-acquired, classical, and strong biofilm-forming isolates. ESBL production was significantly more common in hospital-acquired and biofilm-forming isolates. Strong biofilm formation was largely associated with classical K. pneumoniae and hospital-acquired infections, whereas putative hypervirulent strains were primarily weak biofilm producers and community-acquired. These findings highlight the interplay between virulence determinants, biofilm formation, and antibiotic resistance, emphasizing the need for targeted infection control and treatment strategies in North Lebanon.
Fecal Microbiome Alterations in Colorectal Cancer: A Systematic Review of Compositional Changes and Microbial Biomarkers.
Askari P, Dashtbin S, Navidifar T … +8 more , Dadgar-Zankbar L, Asadi A, Ghamari M, Najafi P, Alamdary SZ, Afifirad R, Ghanavati R, Darbandi A
Microbiologyopen · 2026 Jun · PMID 42310475 · Full text
Colorectal cancer (CRC) is one of the most common types of cancer worldwide, and the gut microbiome plays a crucial role in its development. In the study, we examine the variation in gut microbial community composition a...
Colorectal cancer (CRC) is one of the most common types of cancer worldwide, and the gut microbiome plays a crucial role in its development. In the study, we examine the variation in gut microbial community composition among individuals diagnosed with CRC based on human fecal samples. A systematic search of online databases, including MEDLINE (PubMed), Web of Science, Embase, and Scopus up to March 2026, following the requirements outlined in the PRISMA guideline. The search strategy was based on a combination of keywords, including "colorectal cancer," "gut microbiome", and "feces." The study analyzed 43 research articles on colorectal cancer microbiome. Most investigations utilized culture-independent techniques, revealing variations in microbial profiles between colorectal cancer cases and healthy controls. Fusobacterium and Porphyromonas emerged as potential colorectal cancer biomarkers, while multi-bacteria predictive models showed promise in enhancing colorectal cancer detection sensitivity and specificity. In this review, we will explore how advanced sequencing techniques have the potential to complement current non-invasive methods for early diagnosis and prevention of colorectal cancer. This includes conducting studies with robust statistical power and consistent, replicable methodologies, taking into consideration host factors, and performing external validation of predictive models.
Prevalence, Antimicrobial Resistance, and Resistance Gene Profiles of Extended-Spectrum β-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Isolated From Quails in Sylhet, Bangladesh.
Mamun MA, Hossain H, Chowdhury MSR … +8 more , Nargis SB, Das MR, Hasan R, Liza NA, Mitra S, Uddin MB, Hossain MM, Rahman MM
Microbiologyopen · 2026 Jun · PMID 42304824 · Full text
The rapid emergence of multidrug resistant Enterobacterales, especially extended-spectrum β-lactamase (ESBL)-producing strains, poses a significant One Health challenge in low- and middle-income countries, including Bang...
The rapid emergence of multidrug resistant Enterobacterales, especially extended-spectrum β-lactamase (ESBL)-producing strains, poses a significant One Health challenge in low- and middle-income countries, including Bangladesh. This study aimed to investigate the prevalence, antimicrobial resistance patterns, and resistant genes profile of Escherichia coli and Klebsiella pneumoniae isolated from quails in the Sylhet district of Bangladesh. A cross-sectional study was conducted with 404 cloacal swabs were collected from quails across multiple retail locations. Isolates were identified using culture, biochemical tests, and PCR. Antimicrobial susceptibility was assessed by the Kirby-Bauer disk diffusion method against 12 antibiotics. Resistance and virulence genes, including stx1, tetA, strA, AAC(3)-iv, sul1, and β-lactamase genes, were detected using multiplex and monoplex PCR. Multiple antibiotic resistance index (MARI) and MDR status were determined. E. coli was detected in 63.37% (256/404) of samples, of which 53.91% were Shiga toxin-producing (stx1). K. pneumoniae was confirmed in 11.14% (45) of isolates. Both organisms showed 100% resistance to ampicillin and amoxicillin-clavulanic acid. Nearly all isolates were multidrug resistant, with mean MARI values of 0.58 for E. coli and 0.48 for K. pneumoniae. High frequencies of resistance genes were observed, with strong phenotype-genotype alignment. In K. pneumoniae, the bla (65.96%), Multicase (44.68%) and Multicase (10.63%) genes predominated. Overall, the findings highlight quails in Bangladesh as an important and previously under recognized reservoir of multidrug resistant E. coli and K. pneumoniae, underscoring the urgent need for strengthened antimicrobial stewardship and One Health based surveillance strategies.
A Complete Genome Resource and Bio-Control Activity of Soil-Isolated Pseudomonas citronellolis Strain M03 Against Onion-Pathogenic Burkholderia Species.
Mphande K, MacLellan MP, Malik AA … +1 more , Dutta B
Microbiologyopen · 2026 Jun · PMID 42290189 · Full text
Pseudomonas citronellolis M03 was isolated from the soil of a field, which has been under continuous onion production for approximately 20 years. The soil was naturally infested with onion-pathogenic Burkholderia spp. bu...
Pseudomonas citronellolis M03 was isolated from the soil of a field, which has been under continuous onion production for approximately 20 years. The soil was naturally infested with onion-pathogenic Burkholderia spp. but over the last 2 years bacterial populations had declined. The genome of the bacterial isolate was sequenced. The average nucleotide identity (ANIm) analysis showed > 97% identity and > 84% alignment coverage with the type strain P. citronellolis DSM50332. Digital DNA-DNA hybridization (dDDH) values were 73.6% (formula d4) and 77.8% (formula d0), exceeding the 70% species delineation threshold. The genome comprised of a single 6.73 Mb circular chromosome encoding 5802 coding sequences, including 10 pseudogenes, 428 hypothetical genes, and 81 RNA genes (15 rRNAs, 66 tRNAs). We also identified two NRP-metallophore/NRPS biosynthetic gene clusters showing high similarity to the pyoverdine and enantio-pyochelin clusters of Pseudomonas protegens Pf-5, suggesting the presence of uncharacterized metabolites with potential ecological or biocontrol functions. Phenotypic assays demonstrated strong antagonistic activity of P. citronellolis M03 against Burkholderia cepacia and Burkholderia gladioli in vitro, reducing their populations by > 10-fold and approximately 50%, respectively, after 48 h of co-inoculation. Assessment of onion bulb rot showed significant reductions in both disease incidence and severity when P. citronellolis M03 was co-inoculated with B. cepacia. The ability of P. citronellolis M03 to persist and exert antagonistic effects in complex soil microflora highlights its ecological fitness and adaptability in natural environments. This study provides a valuable genomic resource and experimental evidence for the biocontrol capability of this potentially beneficial bacterium.
Acetate-Linked Energy Metabolism as a Determinant of Early Haemophilus influenzae Infection Fitness.
Nasreen M, Hosmer J, Munshi SK … +6 more , Joshi R, Yamamoto A, Schirra HJ, Sly P, McEwan AG, Kappler U
Microbiologyopen · 2026 Jun · PMID 42289824 · Full text
Acetate is a major metabolic end-product of Haemophilus influenzae and is produced via the phosphotransacetylase-acetate kinase (Pta-AckA) pathway, which also generates adenosine triphosphate (ATP). Despite its importanc...
Acetate is a major metabolic end-product of Haemophilus influenzae and is produced via the phosphotransacetylase-acetate kinase (Pta-AckA) pathway, which also generates adenosine triphosphate (ATP). Despite its importance, the contribution of this pathway to H. influenzae physiology and virulence remains poorly understood. Here, we have investigated the individual roles of AckA and Pta for these processes by generating nonpolar single-gene knockouts in a chronic obstructive pulmonary disease (COPD)-isolate strain (Hi2019) and characterized their metabolic and infection phenotypes. Both mutants exhibited significant growth impairments under microaerobic and anaerobic conditions, with reductions in growth rate of up to 50% compared with the wild type. Loss of AckA or Pta decreased ATP levels to ~ 50% of wild-type values and caused marked overoxidation of the NAD/NADH pool. Metabolomic analyses revealed distinct perturbations at the pyruvate node: the pta mutant produced minimal acetate but accumulated pyruvate and d-lactate, while the ackA mutant continued to produce acetate, likely via nonenzymatic breakdown of acetyl-phosphate. Both mutations also increased sensitivity to oxidative stress and enhanced biofilm formation. In infection models, including bronchial epithelial cells, primary human nasal epithelia, and murine macrophages, intracellular survival of both mutants was significantly reduced during early infection stages, although attenuation diminished over time. These findings demonstrate that the Pta-AckA pathway is critical for metabolic homeostasis, stress resistance, and early intracellular colonization, highlighting its potential as a target for management of early-stage H. influenzae infections.
The Contribution of Chemistry to the Detection and Enumeration of Legionella pneumophila in Environmental Water Samples: Experience With the MICA Method.
Ditommaso S, Garlasco J, Streva C … +4 more , Memoli G, Zotti CM, Bert F, Giacomuzzi M
Microbiologyopen · 2026 Jun · PMID 42284066 · Full text
Legionella is widespread in natural aquatic habitats and can contaminate man-made water systems. Due to public-health risks, measuring microbial load in water samples is essential. This study compared a new lipopolysacch...
Legionella is widespread in natural aquatic habitats and can contaminate man-made water systems. Due to public-health risks, measuring microbial load in water samples is essential. This study compared a new lipopolysaccharide bioprobe method (Microcolony Counter Analysis-MICA), which detects and counts Legionella pneumophila in 2 days, with the standard culture method (ISO 11731:2017), which may take up to 10 days. Our results on 108 water samples showed 82.4% agreement. Fifteen were ISO+/MICA- and four ISO-/MICA+; MICA sensitivity was 67.4%. Analysis of culture-media factors (Legionella inhibition by contaminating flora; culture on Glycine Vancomycin Polymyxin Cycloheximide agar (GVPC) and MICA factors (possible killing/growth inhibition due to acid treatment) showed that (a) ISO counts tended to be higher than MICA, with little difference whether GVPC results or the maximum yield between Buffered Charcoal Yeast Extract agar (BCYE) and GVPC were used. (b) Acid-treated MICA samples tended to yield higher counts than untreated ones, especially at high MICA counts. Considering what has been disclosed, a short 48-h incubation may reduce MICA recovery for some wild L. pneumophila strains, affecting click-based detection. With refinement, MICA could be a practical, user-friendly diagnostic tool, simpler sample prep, no large-volume filtration, no colony isolation or extra confirmation and provides confirmed results in 2 days versus ≥ 10 days for ISO culture.
Integrative Modular, Network-Based, and Machine Learning Framework for Predicting Accessory Genome Functions and Virulence in Escherichia coli O157:H7.
Gambushe SM, Zishiri OT
Microbiologyopen · 2026 Jun · PMID 42272257 · Full text
The pathogenicity of Escherichia coli O157:H7 is shaped not only by chromosomal toxins such as Stx and eae but also by virulence and resistance genes carried on plasmids. To explore the modular structure and predictive p...
The pathogenicity of Escherichia coli O157:H7 is shaped not only by chromosomal toxins such as Stx and eae but also by virulence and resistance genes carried on plasmids. To explore the modular structure and predictive potential of these accessory elements, presence/absence data from 77 strains (70 accessory features) were analyzed. Methods included clustering using Euclidean and Jaccard distances, gene-to-gene network construction with community detection, Fisher's exact tests for associations between plasmid and virulence or antimicrobial resistance genes (AMR), random forest modeling to predict virulence labels and toxin presence (excluding direct toxin markers), and PCA for visualization. Both clustering approaches revealed broad groupings, though Jaccard clustering better captured co-occurring gene patterns. The co-occurrence network identified 12 modules, including a prominent plasmid-virulence module centered on IncF replicons, stx2, ehxA, toxB, and espP. Fisher's tests showed significant associations, notably between IncFIA and stx2c (p = 5.3 × 10). The Random Forest classifier achieved a cross-validated AUC of 0.853 ± 0.067, with gad, espF, IncFIA, and ehxA as key predictors. PCA explained 31.1%, 12.9%, and 10.0% of the variance across the first three components, separating plasmid-virulence module carriers from others. These findings indicate that a modular accessory genome structure contributes to the diversity of O157:H7. IncF plasmids and associated effectors form a highly interconnected subnetwork, and accessory markers independent of direct toxin genes can effectively predict virulence status, offering potential for rapid genomic surveillance of Shiga toxin-producing E. coli (STEC).
Exploring the Mechanism of Alyteserin-1c in Gram-Positive and Gram-Negative Bacterial Membrane Models Using a Computational Approach.
Sasidharan A, Ramalingam R
Microbiologyopen · 2026 Jun · PMID 42271549 · Full text
Alyteserin-1c is a 23-amino-acid cationic antimicrobial peptide exhibiting greater activity against Gram-negative than Gram-positive bacteria (Conlon et al. 2009), yet the molecular basis of this differential membrane se...
Alyteserin-1c is a 23-amino-acid cationic antimicrobial peptide exhibiting greater activity against Gram-negative than Gram-positive bacteria (Conlon et al. 2009), yet the molecular basis of this differential membrane selectivity remains incompletely understood. Using all-atom molecular dynamics simulations (200 ns × 3 independent replicates per system), we examined the interactions of a pre-assembled Alyteserin-1c hexamer with simplified bilayer models representing Gram-positive (75% PG/25% PE) and Gram-negative (75% PE/25% PG) bacterial inner membranes. The hexameric assembly maintained structural stability and substantial α-helical content throughout all simulations, with oligomeric cohesion associated primarily with hydrophobic packing of residues L10, L13, V14, I17, and F6. Cationic residues K7 and K15 remained lipid-exposed with near-permanent headgroup contact occupancy, suggesting their role as principal membrane-anchoring sites. Comparative membrane analyses indicated greater lateral lipid mobility, lower bilayer density, and stronger local acyl chain perturbation in the Gram-negative membrane model, consistent with greater membrane susceptibility at lower peptide concentrations. Helix orientation and pore geometry analyses were inconsistent with stable barrel-stave transmembrane pore formation and instead supported interfacial or transient toroidal-like membrane perturbations. Transient single-file water threading was observed in the Gram-positive system, while perturbations in the Gram-negative membrane remained predominantly surface-localized. These findings provide a computationally derived mechanistic framework for the membrane selectivity of Alyteserin-1c and may inform rational design of membrane-targeting antimicrobial peptides. Given the simplified bilayer models, pre-assembled oligomeric assumption, and accessible simulation timescales, the proposed mechanisms should be interpreted as hypothesis-generating rather than definitive.
Phylogenetic Profiling of the Diabetic Foot Ulcer Microbiome of an Afro-Caribbean Population.
Ojeh N, Mohapatra BR, O'Shea M … +7 more , Springer D, Ward J, Sallu M, Paquette N, Gooding K, Springer A, Peter Adams O
Microbiologyopen · 2026 Jun · PMID 42271189 · Full text
Diabetic foot ulcers (DFUs) are associated with high morbidity, amputation rates, and healthcare costs in Barbados. This pilot study compares the microbiome diversity of chronic DFUs and paired normal skin (controls) fro...
Diabetic foot ulcers (DFUs) are associated with high morbidity, amputation rates, and healthcare costs in Barbados. This pilot study compares the microbiome diversity of chronic DFUs and paired normal skin (controls) from biopsies in Afro-Caribbean patients with type 2 diabetes using Illumina amplicon sequencing targeting the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer 2 (ITS2) region. Both DFUs and controls harbored diverse bacterial and fungal communities, with differences in taxonomic composition and relative abundance profiles. The dominant bacterial genera were Corynebacterium (18.3% in DFUs, 24.3% in controls) and Staphylococcus (14.9% in DFUs, 14.1% in controls). The dominant bacterial species was Corynebacterium striatum (17.3% in DFUs, 23.8% in controls) followed by Pseudomonas aeruginosa in DFUs (8.9%) and Staphylococcus aureus in controls (13.3%). The dominant fungal genera was Densospora (12% in DFUs, 12.6% in controls). The dominant fungal species was Rhodotorula graminis in DFUs (6.18%) and Paracamarosporium leucadendri in controls (3.85%). Candida duobushaemulonii, with intrinsic resistance to antifungal agents, was detected with higher relative abundance in DFUs than in controls (4.44% vs. 2.36%). Fungal Shannon alpha diversity was significantly reduced in DFUs (p = 0.039), while beta diversity did not differ between groups for bacteria (p = 0.982) or fungi (p = 0.975). The differences in taxonomic composition and relative abundance profiles, and co-occurrence of clinically relevant bacterial and fungal taxa, highlight the potential role of polymicrobial communities in DFU chronicity in the Afro-Caribbean cohort studied, and supports future studies to evaluate implications for antimicrobial stewardship.
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