MicrobiologyOpen[JOURNAL]
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200 papers
Expression OF Concern: Eggerthella timonensis sp. nov, A New Species Isolated from the Stool Sample of a Pygmy Female.
Microbiologyopen · 2026 Feb · PMID 41711407 · Full text
M. Bilen, M.D.M. Fonkou, E. Tomei, N. Armstrong, F. Bittar, J.-C. Lagier, Z. Daoud, P.-E. Fournier, D. Raoult, and F. Cadoret, "Eggerthella timonensis sp. nov, A New Species Isolated from the Stool Sample of a Pygmy Fema...
M. Bilen, M.D.M. Fonkou, E. Tomei, N. Armstrong, F. Bittar, J.-C. Lagier, Z. Daoud, P.-E. Fournier, D. Raoult, and F. Cadoret, "Eggerthella timonensis sp. nov, A New Species Isolated from the Stool Sample of a Pygmy Female," Microbiology Open 7, no. 5 (2018): e00575, https://doi.org/10.1002/mbo3.575. This Expression of Concern is for the above article, published online on 13 June 2018 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. A concern has also been raised by a third party about a potential conflict of interest for co-author for Didier Raoult. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.
EXPRESSION OF CONCERN: Genome Sequence and Description of Gracilibacillus timonensis sp. nov. Strain Marseille-P2481, A Moderate Halophilic Bacterium Isolated from the Human Gut Microflora.
Microbiologyopen · 2026 Feb · PMID 41711406 · Full text
A. Diop, E. Seck, G. Dubourg, N. Armstrong, C. Blanc-Tailleur, D. Raoult, and P.-E. Fournier, "Genome Sequence and Description of Gracilibacillus timonensis sp. nov. Strain Marseille-P2481, A Moderate Halophilic Bacteriu...
A. Diop, E. Seck, G. Dubourg, N. Armstrong, C. Blanc-Tailleur, D. Raoult, and P.-E. Fournier, "Genome Sequence and Description of Gracilibacillus timonensis sp. nov. Strain Marseille-P2481, A Moderate Halophilic Bacterium Isolated from the Human Gut Microflora," MicrobiologyOpen 8, no. 2 (2019): e00638, https://doi.org/10.1002/mbo3.638. This Expression of Concern is for the above article, published online on 19 April 2018 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. In addition, a third party has reported that Figure 4a in this article has strong similarities with a figure published in an earlier article by the same authors. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.
EXPRESSION OF CONCERN: Bacillus kwashiorkori sp. nov., A New Bacterial Species Isolated from a Malnourished Child Using Culturomics.
Microbiologyopen · 2026 Feb · PMID 41711402 · Full text
E. Seck, M. Beye, S.I. Traore, S. Khelaifia, C. Michelle, C. Couderc, S. Brah, P.-E. Fournier, D. Raoult, and F. Bittar, "Bacillus kwashiorkori sp. nov., A New Bacterial Species Isolated from a Malnourished Child Using C...
E. Seck, M. Beye, S.I. Traore, S. Khelaifia, C. Michelle, C. Couderc, S. Brah, P.-E. Fournier, D. Raoult, and F. Bittar, "Bacillus kwashiorkori sp. nov., A New Bacterial Species Isolated from a Malnourished Child Using Culturomics," Microbiology Open 7, no. 1 (2018): e00535, https://doi.org/10.1002/mbo3.535. This Expression of Concern is for the above article, published online on 27 October 2017 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.
EXPRESSION OF CONCERN: Taxonogenomics Description of Parabacteroides timonensis sp. nov. Isolated from a Human Stool Sample.
Microbiologyopen · 2026 Feb · PMID 41711401 · Full text
M. Bilen, M.D.M. Fonkou, S. Khelaifia, E. Tomei, F. Cadoret, Z. Daoud, N. Armstrong, F. Bittar, P.-E. Fournier, D. Raoult, and G. Dubourg, "Taxonogenomics Description of Parabacteroides timonensis sp. nov. Isolated from...
M. Bilen, M.D.M. Fonkou, S. Khelaifia, E. Tomei, F. Cadoret, Z. Daoud, N. Armstrong, F. Bittar, P.-E. Fournier, D. Raoult, and G. Dubourg, "Taxonogenomics Description of Parabacteroides timonensis sp. nov. Isolated from a Human Stool Sample," Microbiology Open 8, no. 4 (2019): e00702, https://doi.org/10.1002/mbo3.702. This Expression of Concern is for the above article, published online on 11 October 2018 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert the readers.
EXPRESSION OF CONCERN: Noncontiguous Finished Genome Sequence and Description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, Two New Bacterial Species Isolated from the Human Gut.
Microbiologyopen · 2026 Feb · PMID 41711400 · Full text
S.I. Traore, M. Bilen, M. Beye, A. Diop, M.D.M. Fonkou, M.L. Tall, C. Michelle, M. Yasir, E.I. Azhar, F. Bibi, F. Bittar, A.A. Jiman-Fatani, Z. Daoud, F. Cadoret, P.-E. Fournier, and S. Edouard, "Noncontiguous Finished G...
S.I. Traore, M. Bilen, M. Beye, A. Diop, M.D.M. Fonkou, M.L. Tall, C. Michelle, M. Yasir, E.I. Azhar, F. Bibi, F. Bittar, A.A. Jiman-Fatani, Z. Daoud, F. Cadoret, P.-E. Fournier, and S. Edouard, "Noncontiguous Finished Genome Sequence and Description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, Two New Bacterial Species Isolated from the Human Gut," Microbiology Open 8, no. 6 (2019): e00758, https://doi.org/10.1002/mbo3.758. This Expression of Concern is for the above article, published online on 30 January 2019 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. Additionally, a third party noted that the two bacterial strains reported in this article may have been previously reported by some of the same authors in different publications. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.
EXPRESSION OF CONCERN: Microvirga massiliensis sp. nov., the Human Commensal with the Largest Genome.
Microbiologyopen · 2026 Feb · PMID 41711396 · Full text
A. Caputo, J.-C. Lagier, S. Azza, C. Robert, D. Mouelhi, P.-E. Fournier, and D. Raoult, "Microvirga massiliensis sp. nov., the Human Commensal with the Largest Genome," Microbiology Open 5, no. 2 (2016): 307-322, https:/...
A. Caputo, J.-C. Lagier, S. Azza, C. Robert, D. Mouelhi, P.-E. Fournier, and D. Raoult, "Microvirga massiliensis sp. nov., the Human Commensal with the Largest Genome," Microbiology Open 5, no. 2 (2016): 307-322, https://doi.org/10.1002/mbo3.329. This Expression of Concern is for the above article, published online on 8 January 2016 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.
EXPRESSION OF CONCERN: Miniphocibacter massiliensis gen. nov., sp. nov., A New Species Isolated from the Human Gut and Its Taxono-Genomics Description.
Microbiologyopen · 2026 Feb · PMID 41711185 · Full text
M. Bilen, M.D.M. Fonkou, T.T. Nguyen, M. Richez, Z. Daoud, P-E. Fournier, D. Raoult, and F. Cadoret, "Miniphocibacter massiliensis gen. nov., sp. nov., A New Species Isolated from the Human Gut and Its Taxono-Genomics De...
M. Bilen, M.D.M. Fonkou, T.T. Nguyen, M. Richez, Z. Daoud, P-E. Fournier, D. Raoult, and F. Cadoret, "Miniphocibacter massiliensis gen. nov., sp. nov., A New Species Isolated from the Human Gut and Its Taxono-Genomics Description," Microbiology Open 8, no. 5 (2019): e00735, https://doi.org/10.1002/mbo3.735. This Expression of Concern is for the above article, published online on 2 October 2018 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by John Wiley & Sons Ltd. The Expression of Concern has been agreed due to questions raised about the study's adherence to French legal and ethical requirements for research involving human subjects, including questions regarding proper informed consent for research involving vulnerable populations. A concern has also been raised by a third party about a potential conflict of interest for co-author for Didier Raoult. The investigation into these concerns is ongoing. Therefore, the journal has decided to issue an Expression of Concern to inform and alert readers.
Genome Analysis Reveals Diversity and Functional Potential of Novel Janthinobacterium Species From Subarctic Soils.
Kumar A, Männistö MK, Kerkhof LJ … +1 more , Häggblom MM
Microbiologyopen · 2026 Feb · PMID 41711050 · Full text
The Arctic tundra and boreal forest regions are affected by ongoing climate change, leading to increased warming, increased plant production, and heightened microbial activity. Microbes play a key role in carbon release...
The Arctic tundra and boreal forest regions are affected by ongoing climate change, leading to increased warming, increased plant production, and heightened microbial activity. Microbes play a key role in carbon release from stored soil organic matter, and characterizing their diversity and function in high-latitude soils is thus of significant interest. The Pseudomonadota are abundant and diverse members of high-latitude soils. Here, we describe two novel species of the genus Janthinobacterium, of the order Burkholderiales, isolated from tundra heath and northern boreal forest soils. The isolates are aerobic, chemoorganotrophic psychrophiles and are well-adapted to the subarctic climate conditions. Phylogenomic analyses and ANI values confirmed the novelty of the strains, designated as Janthinobacterium silvisoli sp. nov. K2Li3 and Janthinobacterium saanense sp. nov. S3T4. Genome analysis revealed that the new species have the metabolic potential for degradation of complex carbon and polyphenols, which are abundant in tundra heath and lichen-dominated, nutrient-poor forest soils. The strains are well-adapted to nitrogen-limited soil ecosystems and can scavenge nitrogen from both organic and inorganic sources. Additionally, the strains harbor secondary metabolite gene clusters that encode antimicrobial compound production, potentially enhancing their competitiveness in the subarctic environment. The comparative pangenome analysis indicated that the strains have unique gene clusters for carbohydrate transport and metabolism, and energy generation and conservation. The genome-based functional exploration enhances our understanding of this genus and how environmental conditions may shape the functionality and interactions of Janthinobacterium species in subarctic soil ecosystems.
Antibody-Antibiotic Conjugates: Mechanisms, Clinical Progress, and Next-Generation Strategies Against Multidrug-Resistant Bacterial Infections.
Askari P, Eshaghi S, Omidvar L … +1 more , Mahi-Birjand M
Microbiologyopen · 2026 Feb · PMID 41709436 · Full text
The rise of multidrug-resistant (MDR) bacterial pathogens presents a critical challenge to global health, highlighting the need for innovative therapeutic strategies beyond conventional antibiotics. Antibody-antibiotic c...
The rise of multidrug-resistant (MDR) bacterial pathogens presents a critical challenge to global health, highlighting the need for innovative therapeutic strategies beyond conventional antibiotics. Antibody-antibiotic conjugates (AACs) combine the high specificity of monoclonal antibodies with the potent bactericidal activity of antibiotics, offering targeted delivery to extracellular and intracellular bacteria while minimizing off-target toxicity. The present review provides a comprehensive analysis of AAC development, including key components, such as antigen selection, antibody engineering, linker chemistry, antibiotic payload optimization, and bioconjugation strategies. We summarize the mechanistic principles underlying AAC-mediated bacterial clearance, emphasizing targeted payload release, fragment crystallizable region of the antibody (Fc)-mediated immune engagement, and intracellular delivery. The temporal evolution of AACs is examined, highlighting milestones from early proof-of-concept studies to modern site-specific, humanized constructs and emerging bispecific or dual-payload designs. Furthermore, clinical development is discussed, focusing on pharmacokinetics, pharmacodynamics, safety, efficacy, and regulatory considerations, for example, intracellular infections and biofilm-associated infectious agents. Current challenges, including antigen heterogeneity, immunogenicity, linker-payload optimization, and manufacturing scalability, are critically analyzed, alongside strategies for next-generation AACs. Collectively, AACs represent a transformative platform for precision-targeted antimicrobial therapy, bridging gaps left by conventional antibiotics and offering a promising approach to combating MDR bacterial infections and associated clinical complications.
Reversing Antibiotic Resistance: Strategies From Adjuvants to Innovative Therapeutics.
Li T, Zeng F, Zhang J … +2 more , Zhang Y, Yin W
Microbiologyopen · 2026 Feb · PMID 41691452 · Full text
The escalating prevalence of antibiotic resistance has become a major threat to the effectiveness of conventional antibiotics. Meanwhile, the development of novel antibiotics faces substantial challenges, including lengt...
The escalating prevalence of antibiotic resistance has become a major threat to the effectiveness of conventional antibiotics. Meanwhile, the development of novel antibiotics faces substantial challenges, including lengthy research cycles, high costs, and the rapid emergence of bacterial tolerance, making it difficult for new drugs to keep pace with bacterial evolution. In this context, molecular reversal strategies targeting antibiotic resistance genes have emerged as a promising avenue to overcome this impasse. Among them, the use of antibiotic adjuvants, agents that enhance the efficacy of existing antibiotics by inhibiting resistance gene function, preventing their horizontal transfer or modulating host defense has gained considerable attention. Furthermore, innovative approaches such as CRISPR-Cas gene editing, photodynamic therapy, nanotechnology, and ecological competition strategies have shown great potential in reversing antimicrobial resistance. Collectively, these strategies offer novel insights into addressing the global crisis of antibiotic resistance, paving the way for more effective clinical interventions and ensuring the sustained efficacy of current antibiotic therapies.
Microbial Diversity Across Chemolithotrophic and Phototrophic Biofilms in Cold Sulfur Springs.
Frings DM, Mellinger JM, Drace KM
Microbiologyopen · 2026 Feb · PMID 41668299 · Full text
Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are wel...
Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are well studied, microbial communities in cold terrestrial sulfur springs remain less understood. In this study, we used 16S rRNA gene sequencing to examine how sulfur availability and environmental conditions shape microbial assemblages across different biofilm types in a cold sulfur spring system at Blount Springs, Alabama (33.9301° N, 86.7928° W). Sulfur-oxidizing chemolithotrophs, including Sulfurovum and Halothiobacillus, represented the majority of the recovered reads in sulfur-rich white biofilms, while purple phototrophic biofilms were enriched with anoxygenic sulfur-oxidizing bacteria, such as Chromatium and Chlorobium. Nonsulfur biofilms from adjacent environments displayed greater microbial diversity, including a high abundance of photosynthetic diatoms, like, Melosira. Notably, Sulfurovum was abundant across both sulfur-rich and phototrophic niches, suggesting ecological flexibility and a central role in sulfur metabolism. These findings highlight the influence of sulfur chemistry and light availability in structuring microbial communities and contribute to a broader understanding of microbial adaptation and sulfur cycling in cold sulfur spring ecosystems.
Computational Validation of Multi-Epitope mRNA Vaccine Targeting Streptococcus anginosus Surface Protein (TMPC) as an Effective Alternative Treatment to Reduce Gastric Cancer.
Zhu F, Luo Y, Zhou Z … +5 more , Qin R, Ma S, Xu Y, Chen J, Pan P
Microbiologyopen · 2026 Feb · PMID 41668164 · Full text
Streptococcus anginosus is a Gram-positive coccus that can increase gastric cancer risk through interaction with the TMPC-ANXA2-MAPK axis in gastric epithelial cells. There is currently no commercially available vaccine,...
Streptococcus anginosus is a Gram-positive coccus that can increase gastric cancer risk through interaction with the TMPC-ANXA2-MAPK axis in gastric epithelial cells. There is currently no commercially available vaccine, and prolonged antibiotic treatment may increase drug resistance. We developed a Treponema pallidum membrane protein C (TMPC)-based multi-epitope vaccine targeting nine TMPC-positive streptococcal species dominated by S. anginosus. B-cell and T-cell epitopes were chosen based on their binding affinity, antigenicity, immunogenicity, and safety, with adjuvants and linker sequences improving construct stability and immune response. Immune simulations predicted robust humoral and cellular responses, such as cytokine production and memory cell activation. Molecular docking and molecular dynamics analysis further confirmed stable interactions between the vaccine construct and key immune receptors (HLA-A*02:01, HLA-DRB1*01:01, TLR2, and TLR4). The antigen was further modified as a messenger RNA vaccine to enhance cytotoxic T-cell induction; however, animal research is needed to confirm its immunogenicity and protective effectiveness.
Revisiting Hyaluronan Catabolism in Bacteroides: Pathway Conservation, Overlooked Proteins, and Predictive Accuracy.
Sindelar M, Kocurkova A, Simek M … +4 more , Roudnicky P, Ambrozova G, Kubala L, Turkova K
Microbiologyopen · 2026 Feb · PMID 41645592 · Full text
The ability of gut microbes to degrade host- and diet-derived glycans is central to microbiome ecology and host interactions, yet predicting these functions in silico remains challenging. Hyaluronan (HA), a glycosaminogl...
The ability of gut microbes to degrade host- and diet-derived glycans is central to microbiome ecology and host interactions, yet predicting these functions in silico remains challenging. Hyaluronan (HA), a glycosaminoglycan (GAG) abundant in host tissues and dietary supplements, is depolymerized by specialized polysaccharide utilization loci (PULs) in Bacteroides. Here, we combined comparative protein analysis, functional assays, and quantitative proteomics to evaluate the reliability of sequence-based predictions of HA utilization. Clustering of more than 3900 PL8 and GH88 protein sequences from 54 Bacteroides species did not distinguish known HA degraders from nondegraders, underscoring the limited predictive power of these enzymes alone. Experimental validation in Bacteroides acidifaciens DSM 111135 and Bacteroides thetaiotaomicron DSM 2079 confirmed HA degradation, as HA-derived fragments were identified by liquid chromatography-mass spectrometry. Proteomic profiling revealed coordinated induction of both canonical GAG-specific PULs-encoded proteins and noncanonical accessory proteins (BT4410/BT4411) in response to HA in both species. Incorporating such noncanonical components into comparative frameworks may improve prediction of glycan utilization potential and help link microbial genomic content to ecological function in the gut.
Characterization and Functional Evaluation of Carotenoids From Haloarcula rubripromontorii BS2.
Nagar DN, Das D, Aduri R … +1 more , Braganca JM
Microbiologyopen · 2026 Feb · PMID 41645574 · Full text
Haloarcula rubripromontorii BS2, an extremely halophilic archaeon was obtained from the solar salt pans of Goa, India. It grew luxuriantly on EHM medium with 25% NaCl with a bright orange pigmentation. This study aimed t...
Haloarcula rubripromontorii BS2, an extremely halophilic archaeon was obtained from the solar salt pans of Goa, India. It grew luxuriantly on EHM medium with 25% NaCl with a bright orange pigmentation. This study aimed to extract and characterize the carotenoids from Haloarcula rubripromontorii BS2 and evaluate their antioxidant properties, biocompatibility and provide insight into their potential therapeutic applications. Preparative high-performance liquid chromatography (HPLC) was employed to fractionate and separate the haloarchaeal carotenoids. Further detailed characterization using liquid chromatography-mass spectrometry (LC-MS), Raman spectroscopy and nuclear magnetic resonance (NMR) spectroscopy for each fraction confirmed the presence of C50 carotenoids primarily bacterioruberin, monoanhydrobacterioruberin, and their different isomeric forms. Our results indicate that these carotenoids are more stable in oil compared to solvents. 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3 ethylbenzothiazoline-6-sulfonic acid (ABTS) assays resulted in an IC of 4.31 ± 0.07 µgmL and 2.04 ± 0.02 µgmL respectively, indicating their potential as excellent antioxidants. Haloarchaeal carotenoids were found to be biocompatible with human keratinocyte skin cells (HaCaT). C50 carotenoids from Har. rubripromontorii BS2 represent promising, eco-friendly alternatives to synthetic antioxidants for use in high-value cosmetic and dermatological applications.
Harnessing the Gut Microbes of Low Abundance With a Bent-Capillary-Centrifugal-Driven (BCCD) Microdroplet Method.
Jiang MZ, Zhang ZW, Wang Z … +8 more , Zhu XY, Abdugheni R, Jiang H, Wang Y, Wang ZJ, Zhang L, Cheng YQ, Liu SJ
Microbiologyopen · 2026 Feb · PMID 41630194 · Full text
Gut microbe cultivation is essential for studying host-microbiota interactions. Traditional cultivation methods often fail to recover microbial species at low abundance (< 0.1%). To overcome this limitation, we employed...
Gut microbe cultivation is essential for studying host-microbiota interactions. Traditional cultivation methods often fail to recover microbial species at low abundance (< 0.1%). To overcome this limitation, we employed the bent-capillary-centrifugal-driven (BCCD) method to encapsulate and cultivate fecal microbes in microdroplets. Fecal bacterial cells were distributed into ~50 nL microdroplets via the BCCD generator, and the microdroplets were dispersed in the oil phase and further incubated under controlled conditions. The BCCD method significantly increased the frequency of microbes at low abundance. Compared to the plate-based method, BCCD-based cultivation produced distinct microbial community structures and exhibited significantly lower temporal variation during cultivation (p < 0.05). Lineage-specific effect size (LEfSe) analysis revealed that BCCD-based cultivation enriched 29 low-abundant bacterial genera, whereas the plate-based method enriched 26. Using this method, we isolated 1,049 bacterial strains representing 123 species and 58 genera, including 8 novel species. Among the isolated and cultivated genera, 62.1% (36/58) were microbes of low abundance in the original fecal sample, and 41.4% (12/29) of the BCCD-specific enriched genera were successfully obtained. Notably, comparison with four major gut microbial culture studies revealed 45 species were exclusively recovered in this work. Taken together, the results demonstrated that our BCCD-based cultivation method effectively enriched and facilitated the isolation and cultivation of microbes at low abundance and novel gut bacterial species.
Rapid Typing of Extended-Spectrum β-Lactamase (ESBL)- and Metallo-β-Lactamase (MBL)-Producing Enterobacterales Using Fourier Transform Infrared (FT-IR) Spectroscopy.
Kawamoto Y, Kosai K, Murata M … +7 more , Ota K, Mitsumoto-Kaseida F, Kaku N, Hasegawa H, Izumikawa K, Mukae H, Yanagihara K
Microbiologyopen · 2026 Feb · PMID 41627971 · Full text
This study investigated the usefulness of the IR Biotyper, which types bacterial strains using Fourier transform infrared (FT-IR) spectroscopy, against extended-spectrum β-lactamase (ESBL)- and metallo-β-lactamase (MBL)-...
This study investigated the usefulness of the IR Biotyper, which types bacterial strains using Fourier transform infrared (FT-IR) spectroscopy, against extended-spectrum β-lactamase (ESBL)- and metallo-β-lactamase (MBL)-producing Enterobacterales. Sixty-six clinical isolates (20 ESBL-producing Klebsiella pneumoniae, 15 IMP-producing K. pneumoniae, and 31 IMP-producing Enterobacter cloacae complex isolates) were analyzed using the IR Biotyper, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome single-nucleotide polymorphism (wgSNP) analyses and the results were compared. Of the 20 ESBL-producing K. pneumoniae strains analyzed, the IR Biotyper detected three clusters. Of these clusters, two were determined as respective clusters by PFGE and wgSNP analyses, and the strains included in each cluster showed the same STs. The IR Biotyper detected three clusters in the analysis of 15 IMP-producing K. pneumoniae strains. Of these clusters, strains in the two clusters showed high concordance with PFGE, MLST, and wgSNP analyses. The IR Biotyper identified six clusters among the IMP-producing E. cloacae complex isolates. These results were fully concordant with those of PFGE, MLST, and wgSNP analyses in the two clusters. The range of adjusted Rand index was 0.734-0.967 between the IR Biotyper and PFGE and 0.658-0.857 between the IR Biotyper and MLST or wgSNP analyses. This study demonstrated the performance of IR Biotyper for the detection of clonal similarities in ESBL- and IMP-producing Enterobacterales and it might be useful for outbreak investigation.
Alterations in Gut Microbiota and Metabolic Profiles in Relapsed or Refractory Lymphoma.
Guo YY, Xue KJ, Wang L … +3 more , Wang GG, Zhang TT, Hou SL
Microbiologyopen · 2026 Feb · PMID 41626654 · Full text
To identify potential therapeutic strategies for relapsed or refractory lymphoma (R/RL) by examining differences in gut microbiota composition and metabolic profiles between patients with R/RL and those with primary, tre...
To identify potential therapeutic strategies for relapsed or refractory lymphoma (R/RL) by examining differences in gut microbiota composition and metabolic profiles between patients with R/RL and those with primary, treatment-naïve lymphoma (PL), using fecal microbiota analysis and metabolomics. A total of 21 patients with lymphoma were enrolled at the Department of Lymphoma and Oncology, Shanxi Bethune Hospital, between November 2023 and December 2024. The cohort included 14 patients with R/RL and 7 with PL, who served as the control group. Pretreatment fecal samples and clinical data were collected from all participants. Gut microbiota profiling was conducted using 16S rDNA sequencing, including alpha diversity, beta diversity, species composition, and differential abundance. Untargeted metabolomics was employed to identify and analyze differentially expressed metabolites between the groups. Patients with R/RL exhibited increased relative abundances of Actinobacteriota and Alphaproteobacteria and decreased levels of Erysipelotrichales, Morganellaceae, Faecalibacterium, Clostridium, Klebsiella, and Ruminococcus. Seven metabolites were significantly upregulated in the R/RL group (p < 0.05): 3-amino-4-methylpentanoic acid (p = 0.028), 2-hydroxybutyric acid (p = 0.020), UDP-N-acetylglucosamine (UDP-N-AG) (p = 0.011), pantothenic acid (p = 0.037), isoleucine (p = 0.028), glycine (p = 0.044), and alanine (p = 0.025). Literature review and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated enhanced central carbon metabolism and amino acid metabolism in cancer. Alterations in gut microbiota and metabolic activity may contribute to the pathophysiology of R/RL. Therapeutic modulation of the gut microbiota, including the use of fecal microbiota transplantation, may improve the intestinal immune microenvironment in this patient population. The present work is hypothesis-generating and requires large-scale validation.
The Burden of Antimicrobial-Resistant Pseudomonas aeruginosa Isolates in Children With Cystic Fibrosis: Molecular Characterization and Genotyping Analysis.
Jafari E, Pourakbari B, Asadi Karam MR … +3 more , Azizian R, Modaresi MR, Mamishi S
Microbiologyopen · 2026 Feb · PMID 41606674 · Full text
Pseudomonas aeruginosa poses a significant therapeutic challenge in pediatric patients with cystic fibrosis (CF) due to increasing multidrug resistance (MDR) and carbapenem resistance, underscoring the need for surveilla...
Pseudomonas aeruginosa poses a significant therapeutic challenge in pediatric patients with cystic fibrosis (CF) due to increasing multidrug resistance (MDR) and carbapenem resistance, underscoring the need for surveillance to guide treatment strategies. In this study, sputum and throat swab samples were collected from inpatient and outpatient CF children with pulmonary infection at the Children's Medical Center in Tehran, Iran. Isolates were identified using standard culture and biochemical methods, followed by antimicrobial susceptibility testing. Carbapenemase production was assessed phenotypically and by molecular detection of resistance genes, and genetic diversity was also evaluated using Random Amplified Polymorphic DNA (RAPD)-polymerase chain reaction (PCR). A total of 117 P. aeruginosa isolates were recovered (prevalence 17.41%), of which 94.9% were nonsusceptible to at least one antimicrobial agent. Carbapenem-resistant P. aeruginosa (CRPA) and MDR isolates accounted for 24.8% and 23.1% of isolates, respectively. Carbapenemase gene coexistence was significantly associated with MDR (ρ = 0.227, p = 0.014) and CRPA (ρ = 0.314, p = 0.001). Metallo-β-lactamase production was detected in 13.7% of isolates, while blaVIM was the most frequently identified carbapenemase gene (59%). RAPD-PCR demonstrated marked genetic heterogeneity, grouping isolates into 24 distinct clusters. Overall, the substantial burden of MDR and CRPA identified at this tertiary pediatric center highlights an urgent need for stricter antimicrobial stewardship, enhanced infection control measures, and ongoing surveillance to mitigate resistance spread and preserve therapeutic effectiveness in this vulnerable population. These findings warrant multicenter investigation to determine whether similar patterns exist across other Iranian pediatric CF facilities.
Construction of Reverse Genetics System for Feline Calicivirus FCV-BJ616 and Proteomic Analysis.
Xu C, Zhao J, Liu H … +7 more , Gu H, Tang X, Liang L, Ding J, Hou S, Zhao X, Liang R
Microbiologyopen · 2026 Feb · PMID 41603492 · Full text
Feline calicivirus (FCV) is a primary cause of upper respiratory tract infections and oral ulcerative disease in cats and exhibits substantial genetic diversity that complicates prevention and control. In this study, we...
Feline calicivirus (FCV) is a primary cause of upper respiratory tract infections and oral ulcerative disease in cats and exhibits substantial genetic diversity that complicates prevention and control. In this study, we isolated the FCV-BJ616 strain, established a reverse-genetics system, and investigated its pathogenic mechanisms, thereby providing a foundation for antibody-based therapies and broad-spectrum vaccine development. The virus was purified by three rounds of plaque cloning, and its morphology was examined by electron microscopy. VP1 expression was confirmed by immunofluorescence and Western blotting. Using integrated systems-biology and reverse-genetics approaches, an infectious clone of rFCV-BJ616 was successfully assembled and rescued, exhibiting genetic stability comparable to that of the parental strain. In vivo infection experiments showed that rFCV-BJ616 retained wild-type virulence, causing persistent high fever, weight loss, and multiorgan pathology in infected cats. Proteomic analysis indicated that infection with FCV-BJ616 or rFCV-BJ616 markedly activated cytokine-mediated inflammatory signaling pathways. Both FCV-BJ616 and rFCV-BJ616 significantly upregulated the expression of IL-8, S100A8/A9, and TLR3, which are associated with acute inflammation and tissue damage. Furthermore, elevated IFN-β levels concomitant with STAT1 downregulation suggested a transient attenuation of antiviral signaling during early immune activation. These findings were corroborated by ELISA-based validation of serum cytokine profiles. Collectively, this study provides new insights into the molecular pathogenesis and evolution of FCV-BJ616 and establishes a robust reverse-genetics platform for precise genome manipulation and future vaccine development.
Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.
Petraro S, Tarracchini C, Mancabelli L … +4 more , Lugli GA, Turroni F, Ventura M, Milani C
Microbiologyopen · 2026 Feb · PMID 41591867 · Publisher ↗
Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfa...
Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.
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