Microorganisms

19 pages, 4158 KB

Open AccessArticle

2′-Fucosyllactose Attenuates Fusobacterium nucleatum Virulence and Modulates the Oral Microbiota

by Xinyu Wu, Shuangshuang Han, Yifeng Wang, Xintong Chen, Sijia Liu, Mengxiang Li, Shan Lin, Liying Feng, Xiaoya Guo, Zhengang Li, Huilin Hao, Xin Wang, Di Huang, Lu Feng, Bin Liu and Lei Wang

Microorganisms 2026, 14(7), 1603; https://doi.org/10.3390/microorganisms14071603 - 22 Jul 2026

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Abstract

Fusobacterium nucleatum (F. nucleatum) is a key periodontal pathobiont associated with oral inflammation. This bacterium forms biofilms and expresses adhesins that facilitate its adhesion to and invasion of gingival epithelial cells. These processes disrupt the epithelial barrier and trigger oral inflammation, [...] Read more.

Fusobacterium nucleatum (F. nucleatum) is a key periodontal pathobiont associated with oral inflammation. This bacterium forms biofilms and expresses adhesins that facilitate its adhesion to and invasion of gingival epithelial cells. These processes disrupt the epithelial barrier and trigger oral inflammation, and in some cases, systemic inflammation. Conventional antimicrobial strategies predominantly depend on the utilization of antibiotics. Nevertheless, this can result in the proliferation of drug-resistant strains and the disruption of the oral microbiome equilibrium. As the predominant human milk oligosaccharide, 2′-Fucosyllactose (2′-FL) demonstrates considerable promise in inhibiting pathogenic bacterial adhesion and fortifying epithelial barrier function, mediated by its characteristic structural and bioactive attributes. In this study, we showed that 2′-FL attenuates the expression of virulence genes in F. nucleatum, reduces biofilm formation, and suppresses the bacterium’s ability to adhere to human gingival epithelial cells (HGECs). Furthermore, at the transcriptional level, 2′-FL suppressed F. nucleatum-induced inflammatory cytokine overexpression in both HGECs and RAW 264.7 macrophages, and upregulated barrier-related proteins (ZO-1, Occludin) and MUC-1 gene expression in HGECs. In vivo studies demonstrated the inhibitory effect of 2′-FL on F. nucleatum-induced periodontal injury in Balb/c mice. Furthermore, 16S rRNA sequencing analysis demonstrated that 2′-FL modulated oral microbiota composition of healthy volunteers and significantly reduced the abundance of Fusobacterium. Full article

(This article belongs to the Section Microbiomes)

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28 pages, 18729 KB

Open AccessArticle

Patterns of Soil Microbial Diversity, Assembly, and Co-Occurrence Along a Natural Salinity Gradient in an Inland Saline–Alkali Wetland

by Jie Wei, Fan Chang, Haomin Yang, Yan Sun, Zhi Li, Jun Li, Nannan Liu and Zhuan Hao

Microorganisms 2026, 14(7), 1602; https://doi.org/10.3390/microorganisms14071602 - 22 Jul 2026

Cited by 1 | Viewed by 426

Abstract

Natural inland saline–alkaline wetlands offer opportunities for evaluating microbial responses to long-term salinity stress. This study examined surface soils from non-saline, moderately saline, and hypersaline sites in the Luyang Lake wetland, measuring comprehensive edaphic variables (including SAR, ESP, carbonate/bicarbonate chemistry, moisture, DOC, and [...] Read more.

Natural inland saline–alkaline wetlands offer opportunities for evaluating microbial responses to long-term salinity stress. This study examined surface soils from non-saline, moderately saline, and hypersaline sites in the Luyang Lake wetland, measuring comprehensive edaphic variables (including SAR, ESP, carbonate/bicarbonate chemistry, moisture, DOC, and inorganic N) alongside bacterial and fungal communities via 16S rRNA and ITS sequencing. A coupled salinity–ion and nutrient gradient was identified, with hypersaline soils characterized by high Na⁺, Cl⁻, SAR, and ESP alongside depleted organic carbon and nitrogen. Bacterial α-diversity exhibited a significant unimodal response along the salinity gradient (quadratic regression: p < 0.001), peaking at moderate salinity. Fungal Shannon diversity declined with increasing salinity, but fungal Chao1 richness showed a U-shaped response, highlighting domain-specific and metric-dependent patterns along the gradient. Community assembly analyses revealed contrasting dynamics: deterministic processes were more prevalent in bacterial assembly in hypersaline soils, while fungal assembly remained predominantly stochastic. Co-occurrence networks showed sparser topological structure in high-salinity soils. These patterns are consistent with domain-specific microbial variation along the gradient to coupled edaphic stressors in inland saline–alkaline wetlands. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 5541 KB

Open AccessArticle

Caffeic Acid Phenethyl Ester Suppresses Adhesion to Mediate Its Antibiofilm Activity Against Methicillin-Resistant Staphylococcus aureus

by Kaiyue Feng, Haoni Luan, He Sang, Wenhan Qiu, Rui Yang, Jie Cheng, Wei Feng, Wei Xu, Peng Song and Fei Wang

Microorganisms 2026, 14(7), 1601; https://doi.org/10.3390/microorganisms14071601 - 22 Jul 2026

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Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious threat to public health and can form biofilms to enhance its drug resistance. Caffeic acid phenethyl ester (CAPE), which is primarily extracted from propolis, possesses diverse biological activities. However, its effect on anti-MRSA biofilms and the [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious threat to public health and can form biofilms to enhance its drug resistance. Caffeic acid phenethyl ester (CAPE), which is primarily extracted from propolis, possesses diverse biological activities. However, its effect on anti-MRSA biofilms and the relevant mechanisms have not been fully clarified. Therefore, this study explored the ability of CAPE to combat MRSA biofilms. The results showed that CAPE has significant antibiofilm activities against MRSA. The minimum inhibitory concentration (MIC) values of CAPE were 256 µg/mL for the MRSA strains ATCC 33591, CI2, and CI3. Crystal violet (CV) assay and XTT assays demonstrated that CAPE could inhibit the formation and consolidation of MRSA CI2 biofilms. Experiments on scanning electron microscopy (SEM), bacterial adhesion assays, and the levels of extracellular polysaccharides confirmed that CAPE can inhibit bacterial adhesion, as well as the synthesis of extracellular polysaccharides in MRSA CI2. Real-time quantitative PCR (RT-qPCR) experiments confirmed that CAPE can affect the expression of MRSA icaADBC, sarA, fnbAB, and clfAB genes. Therefore, the proposed antibiofilm mechanism of CAPE involves the downregulation of aforementioned genes, leading to reduced production of extracellular polysaccharides and adhesion-related proteins, thereby weakening MRSA adhesion and ultimately exerting an antibiofilm effect. In conclusion, these findings suggest CAPE is a promising candidate drug as an antimicrobial agent for managing and preventing biofilm-associated infections caused by MRSA. Full article

(This article belongs to the Special Issue Research on Antimicrobial Activity of Natural Products, Third Edition)

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19 pages, 9128 KB

Open AccessArticle

Colonization of Endophytic Bacillus velezensis BHZ-29 in Cotton and Its Induction of Resistance to Cotton Verticillium Wilt

by Yingwu Shi, Xinxiang Niu, Ablimit Nuraliya, Yue Sheng, Hongmei Yang, Min Chu, Ning Wang, Huifang Bao and Kai Lou

Microorganisms 2026, 14(7), 1600; https://doi.org/10.3390/microorganisms14071600 - 22 Jul 2026

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Abstract

Cotton Verticillium wilt is a devastating fungal disease caused by Verticillium dahliae, and biological control has become a safe and efficient strategy for its green prevention and control. In this study, the endophytic strain Bacillus velezensis BHZ-29 was used as the biocontrol [...] Read more.

Cotton Verticillium wilt is a devastating fungal disease caused by Verticillium dahliae, and biological control has become a safe and efficient strategy for its green prevention and control. In this study, the endophytic strain Bacillus velezensis BHZ-29 was used as the biocontrol material, and rifampicin labeling and greenhouse pot assays were performed to clarify its colonization characteristics and induced disease resistance mechanism in cotton. The results showed that the rifampicin-resistant mutant strain maintained consistent morphological traits, antagonistic activity and biocontrol performance with the wild-type strain, ensuring the reliability of colonization tracing. Strain BHZ-29 could stably colonize the roots, stems and leaves of different cotton varieties, with roots serving as the dominant colonization tissue. Physiological analysis indicated that BHZ-29 inoculation significantly activated the antioxidant and defense enzyme system of cotton, including POD, CAT, SOD, PPO and PAL. The defense enzyme activities of cotton leaves showed a trend of first increasing and then decreasing, and the combined inoculation of BHZ-29 and V. dahliae exhibited the highest enzyme activity. Meanwhile, BHZ-29 treatment significantly increased vitamin C content and reduced malondialdehyde accumulation in cotton, alleviating pathogen-induced oxidative damage. Field pot verification confirmed that BHZ-29 possessed excellent and broad-spectrum biocontrol effects on cotton Verticillium wilt with stable control efficacy across different cotton varieties. This study clarifies the colonization and induced resistance mechanism of strain BHZ-29 against Verticillium wilt, providing a promising microbial resource and theoretical basis for the green biological control of cotton soil-borne diseases. Full article

(This article belongs to the Section Plant Microbe Interactions)

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22 pages, 9014 KB

Open AccessArticle

Comparative Gene Expression Patterns of Two EcobNPV Strains in Ectropis grisescens Revealed by Transcriptome Analysis

by Xinxin Zhang, Yang Mei, Guoqing Chen, Qiang Xiao, Meijun Tang and Guozhong Feng

Microorganisms 2026, 14(7), 1599; https://doi.org/10.3390/microorganisms14071599 - 22 Jul 2026

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Abstract

Ectropis obliqua nucleopolyhedrovirus (EcobNPV) is an important biocontrol agent against Ectropis obliqua and E. grisescens. A previously isolated strain, EcobNPV-QF4, exhibits significantly higher virulence than the original strain EcobNPV-QV, yet the molecular basis for this difference remains unclear. Leaf-dipping bioassays demonstrated that [...] Read more.

Ectropis obliqua nucleopolyhedrovirus (EcobNPV) is an important biocontrol agent against Ectropis obliqua and E. grisescens. A previously isolated strain, EcobNPV-QF4, exhibits significantly higher virulence than the original strain EcobNPV-QV, yet the molecular basis for this difference remains unclear. Leaf-dipping bioassays demonstrated that EcobNPV-QF4 caused significantly higher larval mortality than EcobNPV-QV from 10 dpi onward, reaching 97.9% versus 33.8% at 16 dpi, and higher pupal mortality (100% versus 47.3%), confirming its superior virulence across both larval and pupal stages. To investigate the transcriptional dynamics underlying virulence variation, we performed a comparative time-course transcriptomic analysis of E. grisescens infected with either strain at 0, 2, 6, 12, 24, 36, and 48 h post-infection. The reliability of the RNA-seq data was validated by qRT-PCR for selected expressed genes. The results showed that, relative to EcobNPV-QV, the EcobNPV-QF4 strain exhibits a transcriptional strategy characterized by comprehensive and accelerated activation: the transcriptional initiation of its functional modules is globally advanced by approximately 6 h compared with EcobNPV-QV, and genes associated with midgut escape, virion assembly, and viral DNA replication are preferentially and coordinately expressed, resulting in a more synchronized transcriptional profile. Based on these findings, we hypothesize that the enhanced virulence of EcobNPV-QF4 is not attributable to a single factor but rather reflects a synergistic, multitiered acceleration of transcriptional progression that may compress the infection cycle and enhance viral dissemination efficiency. These findings provide critical insights into the molecular mechanisms that may underlie baculovirus virulence and provide a basis for future mechanistic studies. Full article

(This article belongs to the Section Virology)

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17 pages, 1414 KB

Open AccessArticle

A Fusarium Isolate from a Salt Marsh Improves the Salinity Tolerance of a Commercial Cultivar of Festuca rubra via Enhanced Root K⁺ Homeostasis

by Liping Wang, Sasirekha Munikumar, Junjie Yi, Marten Staal, Jan Henk Venema and Theo Elzenga

Microorganisms 2026, 14(7), 1598; https://doi.org/10.3390/microorganisms14071598 - 22 Jul 2026

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Abstract

Salinity poses a major threat to sustainable agriculture and coastal ecosystems, resulting in a substantial loss of plant productivity and biodiversity. Although some coastal grass species exhibit natural adaptation to saline conditions, the physiological mechanisms underlying salt tolerance remain incompletely understood, particularly regarding [...] Read more.

Salinity poses a major threat to sustainable agriculture and coastal ecosystems, resulting in a substantial loss of plant productivity and biodiversity. Although some coastal grass species exhibit natural adaptation to saline conditions, the physiological mechanisms underlying salt tolerance remain incompletely understood, particularly regarding the contribution of plant-associated microorganisms. In a previous study, a commercial cultivar of red fescue (Festuca rubra ssp. rubra cv. Rafael) was shown to be salt sensitive when grown hydroponically, whereas wild populations of F. rubra commonly occur in coastal salt marshes (possibly ssp. litoralis). We hypothesized that this difference in salt tolerance is partly associated with beneficial fungal plant interactions. To test this hypothesis, we investigated whether inoculation with a fungal isolate designated Fusarium sp. 1 and isolated from F. rubra growing on a salt marsh along the Dutch Wadden Sea coast could improve the salinity tolerance of the commercial cultivar. The results showed that inoculation with Fusarium sp. 1 alleviated the salt-induced growth inhibition. At 100 mM NaCl, shoot and root biomass were partially restored relative to non-inoculated controls, accompanied by a significant increase in the shoot-to-root ratio. To investigate the physiological basis of this response, we applied the Microelectrode Ion Flux Estimation (MIFE) technique to quantify Na⁺ -induced K⁺ efflux in roots. Inoculated plants exhibited improved K⁺ homeostasis, characterized by a reduced instantaneous Na⁺-induced K⁺ efflux and a faster recovery of root fluxes. Moreover, inoculated plants grown at 50 and 100 mM NaCl displayed 333% and 397% greater net K⁺ influx, respectively, compared with non-inoculated controls. Our results indicated that inoculation with Fusarium sp. 1 improves the salinity tolerance of F. rubra, likely through enhanced root K⁺ retention. These findings suggest that commercial F. rubra cultivars remain responsive to beneficial microbial associations and highlight the potential of exploring plant–microbe interactions from naturally salt-adapted environments to improve salinity resilience in grasses and potentially other crops. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture, 2nd Edition)

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25 pages, 10901 KB

Open AccessArticle

Lineage Diversification and Evolutionary Dynamics of the Hemagglutinin–Neuraminidase Gene in Mumps Virus Genotype G

by Fuminori Mizukoshi, Miu Takada, Ryusuke Kimura, Wei Liu, Yasuyoshi Hatayama, Mayuko Nishi, Yuka Sato-Fujimoto, Akira Kimura, Fumihiro Kato, Kei Miyakawa, Hirokazu Kimura and Akihide Ryo

Microorganisms 2026, 14(7), 1597; https://doi.org/10.3390/microorganisms14071597 - 22 Jul 2026

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Abstract

Mumps virus (MuV) genotype G is widely represented among circulating strains, but the evolutionary patterns of the hemagglutinin–neuraminidase (HN) gene remain incompletely understood. In this study, we analyzed publicly available full-length genotype G HN sequences using phylogenetic, phylodynamic, codon-based selection, and [...] Read more.

Mumps virus (MuV) genotype G is widely represented among circulating strains, but the evolutionary patterns of the hemagglutinin–neuraminidase (HN) gene remain incompletely understood. In this study, we analyzed publicly available full-length genotype G HN sequences using phylogenetic, phylodynamic, codon-based selection, and structure-guided epitope prediction approaches. The genotype G HN sequences were categorized into Clade 1, an operationally defined Diverse group, and Clade 2. Clade 1, which was composed mainly of Japanese strains, showed a relatively structured pattern over time. In contrast, Clade 2 showed more recent diversification and an overall increase in relative genetic diversity, although this phylodynamic pattern was sensitive to sampling structure. The Diverse group was phylogenetically heterogeneous, and its Bayesian skyline estimates were not used for biological interpretation because repeated analyses showed unstable posterior behavior. Root-to-tip regression supported temporal structure in the complete dataset, with the strongest signal in Clade 2. Bayesian molecular dating estimated the time to the most recent common ancestor of the sampled genotype G HN sequences at approximately 1932, and the mean evolutionary rate was 4.925 × 10⁻⁴ substitutions/site/year. Although the HN protein is a major surface antigen and a target of neutralizing antibodies, codon-based analyses showed no robust evidence of positive selection using multiple methods. Instead, many codon sites were inferred to be under purifying selection, suggesting that genotype G HN evolution is largely constrained by the need to maintain protein function. Predicted B-cell epitope regions were broadly similar among representative genotype G strains. Overall, these findings indicate that genotype G HN lineages have followed distinct evolutionary patterns, while the HN gene remains mainly shaped by purifying selection. These findings may help improve our understanding of MuV genotype G HN gene evolution and support future molecular surveillance. Full article

(This article belongs to the Special Issue Feature Papers on Respiratory Virus Infections)

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10 pages, 3498 KB

Open AccessCase Report

Diagnostic Discordance During MDR-TB Treatment: Retrospective Identification of Mycobacterium avium Complex-Associated Nontuberculous Mycobacterium by Whole-Genome Sequencing

by Ivy Rukasha, Kabelo Gabriel Kaapu, Nakamozi Francine Nemaguvhuni, Felicia Wells-Hunter, Abhinav Sharma, Jody Emile Phelan, Mutlisi Jacqueline Kolobe, Molebogeng Ruth Lekalakala-Mokaba, Robin Mark Warren and Emilyn Costa Conceição

Microorganisms 2026, 14(7), 1596; https://doi.org/10.3390/microorganisms14071596 - 22 Jul 2026

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Abstract

Nontuberculous mycobacteria (NTM) pose significant diagnostic challenges in high tuberculosis (TB)-burden settings, particularly when routine molecular assays suggest multidrug-resistant TB (MDR-TB). Current diagnostic algorithms in high TB-burden settings are primarily designed to detect members of the Mycobacterium tuberculosiscomplex (MTBC) and may inadequately [...] Read more.

Nontuberculous mycobacteria (NTM) pose significant diagnostic challenges in high tuberculosis (TB)-burden settings, particularly when routine molecular assays suggest multidrug-resistant TB (MDR-TB). Current diagnostic algorithms in high TB-burden settings are primarily designed to detect members of the Mycobacterium tuberculosiscomplex (MTBC) and may inadequately distinguish NTM when discordant laboratory findings are encountered. The value of this case lies not in demonstrating that whole-genome sequencing (WGS) should guide real-time treatment, but in illustrating how diagnostic uncertainty can arise when routine MTBC-focused tests fail to identify NTM and how genomic surveillance can contribute to species-level characterization in such settings. We report a complex case which was initially diagnosed as rifampicin- and isoniazid-resistant MTBC and subsequently managed according to programmatic MDR-TB guidelines. Persistent acid-fast bacilli positivity in the presence of negative MTBC antigen testing during follow-up raised suspicion of NTM involvement. Whole-genome sequencing (WGS), performed retrospectively on a follow-up isolate, identified an NTM belonging to the Mycobacterium avium complex (MAC) which was phylogenetically closest to genomes provisionally designated Mycobacterium europaeum_A and distinct from Mycobacterium europaeum sensu stricto, a member of the Mycobacterium simiae complex. The identification of a MAC-associated NTM provided an explanation for the observed diagnostic discordance but could not determine whether the organism represented colonization, sequential infection, or concurrent infection. Although WGS did not inform clinical management, it provided high-resolution species identification and highlighted important limitations of MTBC-focused diagnostic workflows when discordant microbiological findings are encountered. This case underscores the need for the targeted investigation of NTM in patients with acid-fast bacilli-positive cultures and negative MTBC antigen testing and supports the use of genomic surveillance to improve species-level identification and understanding of NTM epidemiology in high TB-burden settings such as Limpopo Province, South Africa. Full article

(This article belongs to the Special Issue New Trends in Medical Bacteriology: Diagnosis, Treatment and Prevention—Second Edition)

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20 pages, 21587 KB

Open AccessArticle

Taxonomic and Functional Comparative Metagenomics of Peruvian Salterns: Insights into Microbial Communities and Aminotransferase Potential

by Carol N. Flores-Fernández, Thomas K. Hiron, Dragana Dobrijevic, Amparo I. Zavaleta, Jack W. E. Jeffries, Chris A. O’Callaghan, Gary J. Lye, John M. Ward and Max Cárdenas-Fernández

Microorganisms 2026, 14(7), 1595; https://doi.org/10.3390/microorganisms14071595 - 22 Jul 2026

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Abstract

Metagenomic analysis of extreme environments is essential in biotechnological research. This work aimed to determine and compare the microbial diversity of two Peruvian saline environments and characterise their functional profiles. Soil metagenomic DNA (mDNA) was analysed from Maras and Pilluana salterns, both with [...] Read more.

Metagenomic analysis of extreme environments is essential in biotechnological research. This work aimed to determine and compare the microbial diversity of two Peruvian saline environments and characterise their functional profiles. Soil metagenomic DNA (mDNA) was analysed from Maras and Pilluana salterns, both with a thalassohaline origin but with different geographical and environmental conditions. Maras samples exhibited more diversity and a remarkably higher abundance of archaea (phylum Euryarchaeota). The most dominant bacterial phyla across all the samples were Pseudomonadota and Actinomycetota. Multiple pathways specific to archaea were more abundant in Maras, as were pathway-related synthesis and degradation of compatible osmolytes such as glycine betaine and ectoine. The most abundant pathways in Pilluana were associated with fatty acid biosynthesis and oxidation. A total of 49 and 47 metagenomic-assembled genomes (MAGs) were retrieved from Maras and Pilluana samples, respectively. Bacterial MAGs were mainly classified within the phyla Psudomonadota, Actinomycetota, Planctomycetota, and Gemmatimonadota. Additionally, a total of 20 putative aminotransferases class III (ATs, PF00202) from Maras3 were cloned and expressed in E. coli Rosetta, and their substrate scoping was assayed against several aldehyde and ketone substrates; AT pQR3082 and pQR3090 showed unique broad substrate acceptance for aromatic and aliphatic substrates. Our study provides new insights into the microorganisms and metabolic pathways of these unique extreme environments, highlighting the promising biotechnological potential of metagenomic ATs. Full article

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22 pages, 1390 KB

Open AccessArticle

Computational Identification of Novel Transcriptional Regulators and Functional Gene Clusters in Lactococcus lactis Using Integrated Bioinformatics Approaches

by Ekaterina Wolf, Tatiana Sokolova, Ilya Akberdin and Aleksey Sazonov

Microorganisms 2026, 14(7), 1594; https://doi.org/10.3390/microorganisms14071594 - 22 Jul 2026

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Abstract

Lactococcus lactis is an essential industrial “cell factory” used extensively in food fermentation and biotechnology. However, a critical biological question regarding the regulatory mechanisms of the microorganism’s adaptation process remains unresolved: how does the bacterium transcriptionally coordinate the trade-off between primary metabolism and [...] Read more.

Lactococcus lactis is an essential industrial “cell factory” used extensively in food fermentation and biotechnology. However, a critical biological question regarding the regulatory mechanisms of the microorganism’s adaptation process remains unresolved: how does the bacterium transcriptionally coordinate the trade-off between primary metabolism and cell-surface remodeling during environmental stress and competence? To date, a unified, global model of its gene regulatory networks (GRNs) that accounts for this transition remains lacking. To address this fragmentation and eliminate selection bias, we integrated the complete compendium of publicly available transcriptomic datasets for L. lactis deposited in the NCBI database as of the summer of 2025. This exhaustive dataset encompasses a wide range of conditions, including thermal, acid, and phage-induced stress, as well as natural competence, providing the necessary transcriptional variance for robust network inference. We implemented an integrated bioinformatics pipeline using the GENIE3 algorithm to infer a core regulatory network common to all tested conditions, complemented by an ensemble of DeepTFactor, Entraf, and p2TF tools to predict strain-specific potential transcription factors (TFs) for L. lactis. The co-expression network partitioned into 50 functional clusters, notably highlighting putative regulators for a unique WxL operon potentially involved in cell-surface modifications. Furthermore, we proposed candidate regulatory targets for the master competence regulator, ComX, and computationally predicted CpsY as a potential LysR-family regulator of branched-chain amino acid metabolism. These findings provide a transcriptomics-based computational model of L. lactis regulation. By clearly distinguishing between established regulatory pathways and purely computational predictions, we suggest several uncharacterized proteins as putative key nodes in the bacterial response to environmental challenges. While requiring direct experimental validation to establish physical interactions, this computational approach generates high-confidence hypotheses and offers a curated resource of candidates for targeted metabolic engineering. Full article

(This article belongs to the Special Issue Microbial Metabolism Regulation in Engineered Production Strains)

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18 pages, 3609 KB

Open AccessArticle

Modulatory Role of ATG5 Protein in Immune Modulation During Experimental Tularemia

by Mirna Mihelčić, Ina Viduka, Maša Antonić, Andreja Zubković, Valentina Marečić, Mateja Ožanič, Kjell Eneslätt, Maja Abram, Anders Sjöstedt and Marina Šantić

Microorganisms 2026, 14(7), 1593; https://doi.org/10.3390/microorganisms14071593 - 21 Jul 2026

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Abstract

Autophagy is a crucial mechanism in the host response to intracellular bacterial pathogens during which microorganisms may undergo direct degradation in autophagolysosomes. As a highly virulent intracellular pathogen, Francisella tularensis has developed survival strategies to escape from the phagosome, replicate in the cytosol [...] Read more.

Autophagy is a crucial mechanism in the host response to intracellular bacterial pathogens during which microorganisms may undergo direct degradation in autophagolysosomes. As a highly virulent intracellular pathogen, Francisella tularensis has developed survival strategies to escape from the phagosome, replicate in the cytosol of mononuclear cells, and avoid degradation within the double-membrane vacuole during the autophagy-mediated response. The aim of this study was to investigate the role of the ATG5 autophagy protein in the host immune response to Francisella tularensis subsp. holarctica, live vaccine strain (LVS), since ATG5 plays an important role in autophagosome formation during canonical autophagy. In vitro experiments were conducted on immortalized bone marrow macrophages subjected to starvation-induced autophagy. Transgenic mice deficient in ATG5 of cells of the myeloid lineage (monocytes/macrophages and granulocytes) were used to analyze the immunological responses after intradermal infection. Cytokine levels were analyzed using Luminex, RT-qPCR, and ELISA, while inflammatory cell infiltration in the lung was analyzed by immunohistochemistry. Our results demonstrate that induced autophagy decreased bacterial replication in vitro. However, ATG5 deficiency in myeloid cells in vivo significantly diminished levels of pro-inflammatory cytokine IFN-γ in the sera, spleen, liver, and lung during Francisella infection. The attenuated pro-inflammatory response also led to significantly reduced macrophage and T cell infiltration in the lung tissue. Our findings also reveal that neutralization of IL-1β in myeloid ATG5ΔMye mice increased susceptibility to tularemia by increasing bacterial burden in organs. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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12 pages, 481 KB

Open AccessArticle

Characterization of CRISPR Loci and Antimicrobial Resistance in Foodborne Listeria monocytogenes Isolates

by Yufan Wu, Xiaoqiang Huang, Qiang Gu, Yun Li, Yuan Zhou, Lu Sun and Xiang Wang

Microorganisms 2026, 14(7), 1592; https://doi.org/10.3390/microorganisms14071592 - 21 Jul 2026

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Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) are widespread in bacterial and archaeal genomes as an adaptive immune system against invading mobile genetic elements. This study investigated the distribution of CRISPR loci and their potential association with antimicrobial resistance (AMR) in 40 foodborne [...] Read more.

Clustered regularly interspaced short palindromic repeats (CRISPR) are widespread in bacterial and archaeal genomes as an adaptive immune system against invading mobile genetic elements. This study investigated the distribution of CRISPR loci and their potential association with antimicrobial resistance (AMR) in 40 foodborne Listeria monocytogenes isolates. CRISPR analysis showed that 18 isolates harbored CRISPR Locus 1, five carried Locus 2, and five possessed both loci. Antimicrobial susceptibility testing against seven antimicrobial agents indicated that most isolates were highly susceptible to the tested agents. Specifically, all isolates were susceptible to gentamicin, ampicillin, penicillin, and tetracycline, whereas resistance was observed in a small subset of isolates: four were resistant to chloramphenicol, five to levofloxacin, and four to ciprofloxacin. Statistical analysis showed no statistically significant association between the presence of CRISPR loci and antimicrobial susceptibility phenotypes. These findings provide baseline information on CRISPR locus distribution and antimicrobial susceptibility profiles in foodborne L. monocytogenes isolates. Further studies based on larger isolate collections, whole-genome sequencing, and characterization of associated cas genes are needed to clarify the potential role of CRISPR-Cas systems in AMR evolution in this species. Full article

(This article belongs to the Special Issue Advanced Antimicrobial Susceptibility Testing and Detection)

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20 pages, 1591 KB

Open AccessReview

Metabolomic Approaches in Fermented Meat Products: Focus on Lactic Acid Bacteria and Starter Cultures

by Marianthi Sidira, Grigorios Nelios and Theodoros Varzakas

Microorganisms 2026, 14(7), 1591; https://doi.org/10.3390/microorganisms14071591 - 21 Jul 2026

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Abstract

Lactic Acid Bacteria (LAB) and other starter cultures play key roles in fermented meat products by influencing fermentation, safety, sensory properties, and metabolite formation. Metabolomic approaches based mainly on mass spectrometry, including GC-MS, LC-MS, and CE-MS, as well as nuclear magnetic resonance (NMR), [...] Read more.

Lactic Acid Bacteria (LAB) and other starter cultures play key roles in fermented meat products by influencing fermentation, safety, sensory properties, and metabolite formation. Metabolomic approaches based mainly on mass spectrometry, including GC-MS, LC-MS, and CE-MS, as well as nuclear magnetic resonance (NMR), provide useful tools for characterizing volatile and non-volatile metabolites, monitoring quality, and identifying candidate biomarkers. This narrative review summarizes recent studies from the past seven years on metabolomic approaches applied to fermented meat products, with emphasis on LAB, starter cultures, and metabolites related to quality, safety, and fermentation. Overall, metabolomics can support the holistic characterization of fermented meat products and improve understanding of microbial activity during fermentation and ripening. Full article

(This article belongs to the Special Issue Microbial Safety and Beneficial Microorganisms in Foods, 2nd Edition)

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19 pages, 4693 KB

Open AccessArticle

Molecular Docking and Energetic Analysis of Deferoxamine in Uropathogenic Escherichia coli in an Experimental Model

by Mayane Cristina Pereira Marques, Flávia Danyelle Oliveira Nunes, Camila Evangelista Carnib Nascimento, José Lima Pereira-Filho, Israel Viegas Moreira, Ana Beatriz Santos Sousa, Aline Santana Figueredo, Roseane Lustosa de Santana Lima, Gabriel Moreira Pereira, Raysa Lins Caldas, Antônio Silva Machado, Rosilda Silva Dias, Jaiza Sousa Penha, Bruna Caroline Silva Falcão, Phelipe Austríaco Teixeira, Marliete Carvalho da Costa, Joicy Cortez de Sá Sousa, Caio Pavão Tavares, Valério Monteiro-Neto, Eduardo Martins de Sousa and Rafael Cardoso Carvalho Show full author list Hide full author list

Microorganisms 2026, 14(7), 1590; https://doi.org/10.3390/microorganisms14071590 - 21 Jul 2026

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Abstract

Neurogenic bladder is a condition associated with impaired voiding, leading to urinary stasis and increased susceptibility to urinary tract infections, predominantly caused by Escherichia coli. In this context, bacterial iron acquisition systems represent attractive targets for alternative antimicrobial strategies. This study aimed [...] Read more.

Neurogenic bladder is a condition associated with impaired voiding, leading to urinary stasis and increased susceptibility to urinary tract infections, predominantly caused by Escherichia coli. In this context, bacterial iron acquisition systems represent attractive targets for alternative antimicrobial strategies. This study aimed to investigate the interactions of deferoxamine with E. coli iron acquisition proteins, combining an experimental model of neurogenic bladder with molecular analyses. The experimental model of neurogenic bladder was induced by complete spinal cord transection in rats, followed by urine collection by cystocentesis and microbiological characterization of uropathogens. Subsequently, molecular docking and energetic analyses were performed to evaluate the binding of deferoxamine and its Fe-DFO complex to the FhuE receptor of the ferric hydroxamate uptake pathway, with FhuA and FhuD prepared as correlated targets of the same pathway for structural context. The animals presented urinary retention and bacterial colonization, with E. coli identified as the pathogen. The results of the molecular docking revealed geometrically plausible accommodation of Fe-DFO within siderophore recognition pockets, involving residues associated with siderophore recognition and transport, as well as binding affinity scores consistent with weak-to-moderate structural complementarity compared to reference ligands. It is concluded that the neurogenic bladder model provides a biologically relevant framework for the study of urinary tract infections and that deferoxamine exhibits molecular interactions consistent with the ferric hydroxamate uptake system of E. coli. Because the present analysis was restricted to the Fhu pathway, these findings cannot be extrapolated to overall bacterial iron homeostasis, which involves multiple parallel acquisition systems. The current work is explicitly positioned as a proof-of-concept investigation; in vivo administration of DFO in the neurogenic bladder model, functional assays of iron uptake, transporter specificity experiments, and molecular dynamics analyses are identified as priority directions for future work. Full article

(This article belongs to the Section Medical Microbiology)

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13 pages, 564 KB

Open AccessArticle

Bacillus subtilis M2-Fermented Soybean Meal Improves Growth Performance and Modulates Cecal Microbiota in Dongxiang Green-Shell Laying-Type Chicken

by Huifang Lu, Lidan Zhou, Enchao Yu, Xinru Cai, Jinhua Zhang, Qiufen Li and Baosheng Liu

Microorganisms 2026, 14(7), 1589; https://doi.org/10.3390/microorganisms14071589 - 21 Jul 2026

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Abstract

Feeding animals with soybean meal (SBM) fermented by probiotics normally confers benefits. This study evaluated the growth-promoting effects of SBM fermented with Bacillus subtilis M2 (M2-FSBM), a probiotic strain with antimicrobial activity, as a replacement for conventional SBM in chicken diets. A total [...] Read more.

Feeding animals with soybean meal (SBM) fermented by probiotics normally confers benefits. This study evaluated the growth-promoting effects of SBM fermented with Bacillus subtilis M2 (M2-FSBM), a probiotic strain with antimicrobial activity, as a replacement for conventional SBM in chicken diets. A total of 264 one-day-old Dongxiang green-shell laying-type chickens were randomly assigned to four groups (six replicates/group, 11 birds/replicate) and fed a basal diet with 0% (control, with 35% SBM), 25%, 50%, or 75% of SBM replaced by M2-FSBM for 45 days. Growth performance, feed consumption, serum insulin-like growth factor and epidermal growth factor, small intestinal morphology, and cecal microbiota diversity were evaluated. Compared with the control, M2-FSBM replacement significantly increased body weight at day 15 (all replacement levels) and day 30 (50% and 75% groups), and at day 45 (75% group) (p < 0.05). The improved growth was attributed to increased average daily feed intake rather than improved feed conversion ratio. The 75% M2-FSBM group showed significantly increased villus height in the duodenum, jejunum, and ileum, and elevated jejunal villus height-to-crypt depth ratio (p < 0.05). Cecal microbiota analysis revealed increased abundances of Faecalibacterium and Negativibacillus and decreased abundances of Mediterraneibacter, Blautia, and unclassified_f_Lachnospiraceae, while Lactobacillus and Limosilactobacillus remained stable. Replacing SBM with M2-FSBM improves growth performance in young chickens, likely through increased feed intake and improved intestinal morphology, accompanied by beneficial modulation of cecal microbiota. M2-FSBM shows promise as a growth-promoting alternative feed material for poultry. Full article

(This article belongs to the Special Issue Dietary and Animal Gut Microbiota, 2nd Edition)

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14 pages, 3847 KB

Open AccessArticle

rs1051838 Promotes Intracellular Survival of Mycobacterium tuberculosis H37Ra by Regulating DUSP14 Expression

by Jiao Feng, Yan Meng, Jinyu Liang, Yuming Zhang, Runru Wang, Yanran Li, Xiaogang Cui, Zhiqiang Yang, Li Xing and Changxin Wu

Microorganisms 2026, 14(7), 1588; https://doi.org/10.3390/microorganisms14071588 - 21 Jul 2026

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Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a major global health burden. Host genetic factors play a critical role in TB susceptibility, but the underlying mechanisms are not fully understood. Genome-wide association studies have identified DUSP14 as a TB susceptibility [...] Read more.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a major global health burden. Host genetic factors play a critical role in TB susceptibility, but the underlying mechanisms are not fully understood. Genome-wide association studies have identified DUSP14 as a TB susceptibility gene, and the single nucleotide polymorphism (SNP) rs1051838 in DUSP14 seems to be associated with TB risk. Using in vitro models including THP-1-derived macrophages, A549 cells, and HEK293T cells, we investigated how rs1051838 regulates DUSP14 expression and modulates macrophage responses to Mtb infection. We found that the G allele of rs1051838 exhibits higher transcriptional activity than the A allele in reporter assays. The G allele creates a CpG dinucleotide that is subject to methylation-mediated repression. Mtb infection reduced CpG methylation across this region to upregulate DUSP14, leading to suppressed JNK phosphorylation via its phosphatase activity, reduced pro-inflammatory cytokine production, and promoted intracellular bacterial survival. Knockdown of DUSP14 decreases bacterial burden and increases cytokine secretion. These findings reveal a functional link between genetic variation and immune response in TB and point to DUSP14 as a potential target for host directed therapy, although further validation in primary cells or using virulent strains and in vivo models is needed. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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21 pages, 1063 KB

Open AccessArticle

Strain-Specific Loci in Bacterial Genomes: Whole-Genome Discovery, Genomic Context, and Application for Multi-Strain qPCR Monitoring

by Emil Elmirovich Valiakhmetov, Mikhail Frolov, Artemiy Yurievich Sukhanov, Aynur Kamilevich Miftakhov and Shamil Zavdatovich Validov

Microorganisms 2026, 14(7), 1587; https://doi.org/10.3390/microorganisms14071587 - 21 Jul 2026

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Abstract

Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, [...] Read more.

Monitoring individual strains in complex microbial communities remains a fundamental challenge in microbial ecology and biotechnology. Here, we present an integrated pipeline for identifying and validating strain-specific loci (SSL) in four biotechnologically relevant plant growth promoting strains from three genera (Stenotrophomonas, Bacillus, and Pseudomonas). The pipeline applies a two-round specificity-filtering strategy combining whole-genome comparison and high-sensitivity BLASTn validation of revealed strain-specific loci (SSL) against the NCBI nucleotide database. SSL count decreased with increasing Average nucleotide identity (ANIb) of the strains used for the analysis, ranging from one locus in B. halotolerans (ANIb = 98.91%) to 15 loci in S. rhizophila (ANIb = 86.49%). All 25 SSL were universally AT-rich, mainly accessory-genome-associated, with flanking regions enriched in genes of unknown function (34.6%) and mobile genetic elements (19.2%). TaqMan qPCR assays targeting SSL demonstrated high specificity—no target sequences were detected across ten geographically distinct soil samples, nor in a native rhizosphere metagenome—and sensitivity, with limits of detection of 0.01–0.1 pg of genomic DNA. Spike-in experiments in soil yielded method detection limits (MDL) of 850–15,000 CFU/g. All four strains were detected in the wheat rhizosphere seven days after consortium application in a field experiment, validating the pipeline for multi-strain field monitoring. Full article

(This article belongs to the Section Microbial Biotechnology)

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16 pages, 8284 KB

Open AccessArticle

High-Risk ExPEC from Commensal Phylogroup A: Genomic Characterization of a Bovine Meningoencephalitis Isolate, BN01

by Jingjing Ren, He Qin, Wenliang Yan, Yayin Qi, Dongdong Du, Pengyan Wang, Wenli Yan and Jianjun Jiang

Microorganisms 2026, 14(7), 1586; https://doi.org/10.3390/microorganisms14071586 - 21 Jul 2026

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Abstract

Extraintestinal pathogenic Escherichia coli (ExPEC) causes severe infections in humans and animals, yet bovine isolates remain poorly characterized. Here, we report the first complete genome of a bovine ExPEC strain, BN01 (serotype O101:H9-ST10-phylogroup A), isolated from calf meningoencephalitis. Unlike classical ExPEC that typically [...] Read more.

Extraintestinal pathogenic Escherichia coli (ExPEC) causes severe infections in humans and animals, yet bovine isolates remain poorly characterized. Here, we report the first complete genome of a bovine ExPEC strain, BN01 (serotype O101:H9-ST10-phylogroup A), isolated from calf meningoencephalitis. Unlike classical ExPEC that typically belong to B2/D phylogroups and O1/O2/O18 serotypes, BN01 represents the A-ST10-O101 sublineage that has emerged as predominant among bovine ExPEC populations. The genome comprises a chromosome encoding 197 virulence factors, with cdiA uniquely identified in BN01 compared to six other representative ExPEC genomes—a contact-dependent growth inhibition system, and three distinct plasmids: a conjugative ESBL carrier (blaCTX-M-164, IncI1), a bovine-associated multidrug resistance island (IncY), and a mobilization-ready vector (IncFII). Animal virulence assays demonstrated that intraperitoneal challenge with E. coli BN01 caused 80% mortality (8/10 mice) within the observation period and yielded an LD₅₀ of 10^6.3 CFU/mouse. These findings demonstrate that high-risk ExPEC can occur in phylogroups typically associated with commensal strains, expanding the conventional understanding of phylogroup–virulence associations. They highlight the need to assess the zoonotic potential of livestock-associated atypical lineages and support integrated genomic surveillance under the One Health framework. Full article

(This article belongs to the Section Veterinary Microbiology)

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11 pages, 675 KB

Open AccessArticle

Short-Term Bacteriophage Exposure Is Associated with Shifts in Antibiotic Susceptibility Profiles of Clinical Pseudomonas aeruginosa

by Nurullah Çiftçi, Özkan Şeşen, Güray Kor, Zeynep Özer, Uğur Vural, Zeynep Çelik, Mustafa Çilkız and İbrahim Halil Kılıç

Microorganisms 2026, 14(7), 1585; https://doi.org/10.3390/microorganisms14071585 - 21 Jul 2026

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Abstract

Bacteriophage exposure can impose strong selective pressure on bacterial populations and may alter antimicrobial susceptibility beyond direct lytic effects. However, the persistence of such changes after the removal of phage pressure remains insufficiently characterized in clinical P. aeruginosa isolates. This study evaluated whether [...] Read more.

Bacteriophage exposure can impose strong selective pressure on bacterial populations and may alter antimicrobial susceptibility beyond direct lytic effects. However, the persistence of such changes after the removal of phage pressure remains insufficiently characterized in clinical P. aeruginosa isolates. This study evaluated whether short-term exposure to the lytic bacteriophage KPP10 was associated with changes in antimicrobial susceptibility categories and whether these changes remained detectable after serial passage in phage-free medium. Five non-duplicate clinical P. aeruginosa isolates were exposed to KPP10 for 24 h at a multiplicity of infection of 10. Antimicrobial susceptibility testing was performed by disk diffusion at baseline, immediately after exposure (F24) and after four serial passages in phage-free medium. Categories were interpreted according to the EUCAST 2024 clinical breakpoints. Nine categorical susceptibility shifts were detected across six antibiotics: four toward increased susceptibility and five toward decreased susceptibility. Six shifts (66.7%) remained detectable after four serial passages, whereas three shifts (33.3%), involving ciprofloxacin, cefepime, and aztreonam in LBK20, reverted to their baseline categories. Eight of the nine shifts involved β-lactam antibiotics, and cefepime was the most frequently affected agent. These exploratory findings show that short-term KPP10 exposure was associated with isolate-specific and bidirectional changes in categorical antimicrobial susceptibility and support repeated susceptibility monitoring in future phage–antibiotic studies. Full article

(This article belongs to the Special Issue The Epidemiology, Clinical Aspects, Treatment and Preventive Strategies for Infectious Diseases in the Era of Antimicrobial Resistance (AMR))

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17 pages, 1858 KB

Open AccessArticle

Prevalence of Biofilm-Forming Non-Typhoidal Salmonella Across the Farm-to-Fork Continuum: A Systematic Review and Meta-Analysis

by Asmita Shrestha, Smriti Shringi, Babafela Awosile and Devendra H. Shah

Microorganisms 2026, 14(7), 1584; https://doi.org/10.3390/microorganisms14071584 - 20 Jul 2026

Viewed by 719

Abstract

Non-typhoidal Salmonella (NTS) remains a major cause of foodborne illness worldwide, and its persistence along the food-production continuum poses a significant public health challenge. Biofilm formation is an adaptive mechanism that enhances NTS survival and persistence outside the primary animal reservoir, particularly under [...] Read more.

Non-typhoidal Salmonella (NTS) remains a major cause of foodborne illness worldwide, and its persistence along the food-production continuum poses a significant public health challenge. Biofilm formation is an adaptive mechanism that enhances NTS survival and persistence outside the primary animal reservoir, particularly under extra-host stress conditions in food and environmental settings. We hypothesized that true biofilm-positive NTS are less prevalent in animal reservoirs and relatively enriched in food-, environmental-, and human-associated sources along the farm-to-fork continuum, reflecting their increased likelihood of persisting in foods and contributing to human exposure. Systematic review and meta-analysis were conducted following PRISMA guidelines, identifying 88 eligible studies; 57 qualified for systematic review, and 47 and 35 qualified for source- and serogroup-based meta-analyses, respectively. Descriptive synthesis revealed substantial biological and methodological heterogeneity across studies. Proportion-based analysis showed that true biofilm-positive (TBP) prevalence was lowest among animal isolates (58.4%), increased in food (67.7%) and human isolates (73.1%), and was highest among environmental isolates (88.1%) (χ² test, p < 0.001). In the source-based meta-analysis, the pooled TBP prevalence was 73.9% (95% CI: 58.4–85.06%). Meta-regression demonstrated that the predicted proportion of TBP NTS among food and human sources was significantly higher compared with the animal reservoir (food: p = 0.0002; human: p = 0.0005), whereas the difference between the environmental and animal reservoirs was not statistically significant (p = 0.075). These findings suggest that biofilm-forming NTS are enriched outside the primary animal reservoir under extra-host stress conditions. The results raise testable hypotheses regarding biofilm-mediated persistence and enrichment across the food-production continuum and support future longitudinal studies to evaluate its role in transmission and targeted sanitation strategies. Full article

(This article belongs to the Special Issue Foodborne Pathogens in Complex Food Systems: Ecology, Surface Interactions, and Sustainable Control Strategies)

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30 pages, 6275 KB

Open AccessReview

Wastewater Metagenomics for Antimicrobial Resistance and Pathogen Surveillance: A Bibliometric Analysis

by Yiran Zheng, Ningxuan Ma, Bingxuan Zhao, Yuhe Li, Yuxin Tian, Jinpu Liu and Yue Quan

Microorganisms 2026, 14(7), 1583; https://doi.org/10.3390/microorganisms14071583 - 20 Jul 2026

Viewed by 405

Abstract

Wastewater systems are critical reservoirs where antibiotic resistance genes, antibiotic-resistant bacteria, and pathogens converge and disseminate into receiving waters, posing risks to ecosystems and public health. Metagenomics enables culture-independent surveillance of resistome and pathogens in wastewater. After the COVID-19 pandemic, the rapid expansion [...] Read more.

Wastewater systems are critical reservoirs where antibiotic resistance genes, antibiotic-resistant bacteria, and pathogens converge and disseminate into receiving waters, posing risks to ecosystems and public health. Metagenomics enables culture-independent surveillance of resistome and pathogens in wastewater. After the COVID-19 pandemic, the rapid expansion of wastewater-based epidemiological surveillance, together with growing emphasis on the One Health framework, has further promoted the integration of wastewater metagenomic monitoring with public-health surveillance strategies. However, no bibliometric study has systematically mapped the global research landscape at the intersection of metagenomics, wastewater systems, antimicrobial resistance, and pathogen surveillance. This study retrieved 1161 publications from the Web of Science Core Collection and used CiteSpace to conduct bibliometric analyses. From 2010 to 2025, annual publications increased from 1 to 219, with 72.7% of the total output concentrated between 2021 and 2025. China led in publication output but showed low betweenness centrality, whereas Australia and Sweden served as key intermediaries. Keyword analysis revealed a gradual thematic evolution from the basic detection of antibiotic resistance genes in activated sludge, through studies of dissemination mechanisms, to recent work on One Health and wastewater surveillance. Literature co-citation analysis showed that integration between environmental monitoring and public health literature remains limited, suggesting that the translation of metagenomic surveillance data into health risk assessment frameworks is still at an early stage. By mapping the field’s knowledge structure and gaps, this review highlights priorities for advancing wastewater-based Antimicrobial Resistance surveillance, including standardizing analytical methods, developing artificial intelligence-assisted resistome analysis, promoting equitable participation from underrepresented regions, and operationalizing One Health surveillance, thereby supporting the translation of wastewater monitoring into actionable public-health solutions. Full article

(This article belongs to the Special Issue From Sewers to Solutions: Wastewater Surveillance in the Fight Against Antimicrobial Resistance)

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17 pages, 137992 KB

Open AccessArticle

Mechanism of Pasteurella multocida Lysis by Virulent Phage vB_PmuP_Pa7: Insights from a Strand-Specific Transcriptome Analysis

by Hongjian Zhang, Jinlin Ma, Wei Zhang, Wenliang Li, Jing Zhao, Xin Wei, Chunhui Feng, Yaqiong Fang and Fei Yang

Microorganisms 2026, 14(7), 1582; https://doi.org/10.3390/microorganisms14071582 - 20 Jul 2026

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Abstract

Virulent phage vB_PmuP_Pa7 is a promising candidate for controlling Pasteurella multocida infection, yet the molecular basis of its lytic process remains poorly understood. Here, we performed strand-specific RNA sequencing on P. multocida S34 infected with Pa7 at 0, 20, 30, and 120 min [...] Read more.

Virulent phage vB_PmuP_Pa7 is a promising candidate for controlling Pasteurella multocida infection, yet the molecular basis of its lytic process remains poorly understood. Here, we performed strand-specific RNA sequencing on P. multocida S34 infected with Pa7 at 0, 20, 30, and 120 min to characterize phage–host transcriptional dynamics. A total of 234, 433, and 558 differentially expressed genes (DEGs) were detected at 20, 30, and 120 min, respectively, indicating progressive host reprogramming during infection. PCA, expression distribution analysis, and sample correlation analysis confirmed clear stage-specific transcriptional shifts. GO and KEGG enrichment analyses indicated that Pa7 infection was associated with changes in translation, ribosome function, ABC transporters, amino sugar and nucleotide sugar metabolism, bacterial chemotaxis, and the TCA cycle. Four representative differentially expressed genes involved in transport, carbohydrate metabolism, and translation-related functions were selected for RT-qPCR analysis. The RT-qPCR results showed partial, gene- and time-point-dependent agreement with the RNA-seq-derived expression patterns. Together, these findings provide a time-resolved transcriptional profile of Pa7 infection and identify host pathways potentially associated with the infection process and bacterial cell lysis. However, the direct functional contributions of these genes and pathways remain to be experimentally determined. Full article

(This article belongs to the Section Veterinary Microbiology)

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29 pages, 15908 KB

Open AccessArticle

Stage-Specific Differences in Fungal Community Structure and Functional Potential During Litter Decomposition in a Lava Plateau

by Yan Zhu, Jiaxing Huang, Yingjun Ye, Zhichao Tian, Jianhui Jia, Yueyu Sui and Yanli Zhang

Microorganisms 2026, 14(7), 1581; https://doi.org/10.3390/microorganisms14071581 - 20 Jul 2026

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Abstract

Litter-inhabiting fungi drive organic matter mineralization, regulate nutrient cycling, and support ecosystem stability. Understanding their dynamics in unique geological habitats is essential for predicting ecological recovery on volcanic landforms. Using high-throughput ITS sequencing and physicochemical analyses, we investigated litter-inhabiting fungal communities across four [...] Read more.

Litter-inhabiting fungi drive organic matter mineralization, regulate nutrient cycling, and support ecosystem stability. Understanding their dynamics in unique geological habitats is essential for predicting ecological recovery on volcanic landforms. Using high-throughput ITS sequencing and physicochemical analyses, we investigated litter-inhabiting fungal communities across four stand types on the Jingpo Lake lava plateau—shrub forest (SF), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—at the early (t₁) and late (t₂) stages of decomposition. The results showed significant differences in litter physical and chemical properties among forest stand types (p < 0.05). Regarding community composition, Ascomycota and Basidiomycota dominated throughout, and the core genera were primarily unclassified_o__Helotiales, Mortierella, and unclassified_k__Fungi. Alpha diversity analysis showed that DB had the highest Shannon and Pielou-e indices at stage t₁, while CB exhibited higher OTUs and Chao1 indices at stage t₂. Beta diversity showed that SF communities were significantly separated between the two stages. Co-occurrence networks showed the highest connectivity in CF with pronounced modularity. Notably, LEfSe analysis revealed that DB had the fewest biomarkers, suggesting matrix heterogeneity suppresses single-taxon dominance. Functionally, saprotrophs dominated initially but transitioned toward complex soil saprotroph and endophyte assemblages over time. Redundancy analysis (RDA) identified litter moisture content (LMC) and carbon (C) content as primary drivers, orchestrating a systematic shift in community assembly from “moisture-driven colonization” at t₁ to “carbon quality screening” at t₂. These findings provide a microecological basis for understanding plant-litter-microorganism coupling mechanisms and guiding ecological restoration in lava plateau ecosystems. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 4267 KB

Open AccessArticle

Trade-Offs and Driving Factors of Microbial Carbon and Nitrogen Use Efficiency in Typical Forest Ecosystems of Funiu Mountain

by Yadong Xu, Yiran Lai, Luotong Zhao, Shujuan Guo and Tianfu Han

Microorganisms 2026, 14(7), 1580; https://doi.org/10.3390/microorganisms14071580 - 20 Jul 2026

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Abstract

Soil microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are fundamental parameters governing organic matter turnover in terrestrial ecosystems, yet how forest type-driven variation in litter quality propagates through the litter–soil–microbe continuum to regulate these efficiencies remains poorly resolved. Across three [...] Read more.

Soil microbial carbon use efficiency (CUE) and nitrogen use efficiency (NUE) are fundamental parameters governing organic matter turnover in terrestrial ecosystems, yet how forest type-driven variation in litter quality propagates through the litter–soil–microbe continuum to regulate these efficiencies remains poorly resolved. Across three forest types in the Funiu Mountains, central China—a Larix gmelinii (LG) plantation, a Quercus aliena var. acuteserrata (QA) secondary forest, and a mixed Quercus aliena var. acutiserrata and Pinus armandii (QP) forest—we quantified litter chemistry, soil physicochemical properties, microbial biomass, extracellular enzyme activities, and microbial nutrient use efficiencies (MUE: NUE, and phosphorus use efficiency, PUE) derived from a modified saturation kinetics model. Principal coordinate analysis revealed significant multivariate differentiation among forest types across litter, soil, microbial biomass, and enzyme modules (Adonis R² = 0.198–0.427; all p < 0.05). Compared with LG and QA, QP exhibited a pronounced stoichiometric imbalance: it supported the highest litter organic carbon and total nitrogen, the lowest lignin-to-cellulose ratio, the largest soil C and N pools (SOC and STN), and the greatest microbial biomass carbon (MBC). However, despite this resource-rich environment, microbial biomass C:N:P ratios exhibited constrained variation, while soil C:P (SCP) and N:P ratios (SNP) in QP reached extreme values (112.3 and 7.25, respectively), generating severe stoichiometric imbalance. Vector analysis indicated that all forests were under relative nitrogen limitation (vector angle < 45°), with QP showing the strongest limitation (41.6 ± 0.4°). Critically, QP exhibited the highest NUE (0.47 ± 0.03) but the lowest CUE (0.95 ± 0.01), and CUE and NUE were nearly perfectly negatively correlated across all sites (R = −0.98, p < 0.001). Random forest analysis identified extracellular enzyme stoichiometry as the dominant proximate predictor of MUE. Partial least squares structural equation modeling (GOF = 0.673–0.674; R² = 0.592–0.603) revealed that litter and soil properties had no significant direct effects on CUE or NUE; instead, soil nutrients exerted strong indirect association through a cascade—soil → microbial biomass → enzyme activity—with opposite total effects on CUE (−0.731, p < 0.001) versus NUE (+0.755, p < 0.001). These findings reveal that the same soil nutrient enrichment that accompanies mixed-species afforestation drives divergent microbial metabolic responses—suppressing CUE while promoting NUE—through a shared cascading structure, with implications for predicting soil carbon and nutrient retention under shifting forest compositions. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)

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18 pages, 3553 KB

Open AccessArticle

The Cyclic Di-GMP Receptor HpoR Modulates Mycobacterial Multidrug Susceptibility by Regulating IniBAC-Mediated Envelope Permeability

by Xiao Liu, Xiaocui Ling, Kun Wang, Jiachen Zheng, Hao Li, Minhao Guo, Yanzhe Ou, Jie Lu and Weihui Li

Microorganisms 2026, 14(7), 1579; https://doi.org/10.3390/microorganisms14071579 - 20 Jul 2026

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Abstract

Isoniazid (INH) targets cell wall biosynthesis and is a potent antimycobacterial agent. Elucidating the regulatory networks that govern drug susceptibility in mycobacterial models is fundamental to understanding intrinsic resistance in pathogenic species. The iniBAC operon plays a crucial role in INH tolerance and [...] Read more.

Isoniazid (INH) targets cell wall biosynthesis and is a potent antimycobacterial agent. Elucidating the regulatory networks that govern drug susceptibility in mycobacterial models is fundamental to understanding intrinsic resistance in pathogenic species. The iniBAC operon plays a crucial role in INH tolerance and envelope permeability, yet the transcriptional regulatory mechanisms controlling its expression in response to INH-induced stress remain incompletely understood. The second messenger cyclic di-GMP (c-di-GMP) regulates drug susceptibility in several bacteria, but its downstream receptors and regulatory pathways in mycobacteria have not been explored. Here, we demonstrate that c-di-GMP reduces INH susceptibility via the receptor HpoR. Mechanistically, c-di-GMP alleviates HpoR-mediated repression of the iniBAC operon in a concentration-dependent manner, which decreases envelope permeability and consequently modulates multidrug susceptibility in both M. bovis BCG and M. smegmatis. This regulatory paradigm is likely conserved in pathogenic mycobacteria. Full article

(This article belongs to the Special Issue Bacterial Infections and Antimicrobial Resistance)

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3 pages, 148 KB

Open AccessEditorial

Editorial for the Special Issue “Advances in Microbial Cell Factories”—Pioneering the Circular Bioeconomy

by Thomas Brück and Dania Awad

Microorganisms 2026, 14(7), 1578; https://doi.org/10.3390/microorganisms14071578 - 20 Jul 2026

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Abstract

The need to transition from a fossil resource-based economy to a sustainable, circular bioeconomy has never been more urgent [...] Full article

(This article belongs to the Special Issue Advances in Microbial Cell Factories)

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15 pages, 3409 KB

Open AccessArticle

Salt–Alkali Gradient Correlates with Distinct Bacterial Communities of Salicornia europaea L. Across Soil–Root–Leaf Compartments in Guhya Salt Lake

by Chaobing Luo, Xiu Zhang, Chenbo Tan, Yueting Lang, Hongyan Ma and Zhaojun Liu

Microorganisms 2026, 14(7), 1577; https://doi.org/10.3390/microorganisms14071577 - 20 Jul 2026

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Abstract

Bacteria play a vital role in enhancing host resistance to salt–alkali stress. However, the composition and structure of bacterial communities associated with halophytes under natural high salt–alkali conditions remain poorly understood. Here, a transect comprising six sampling points (0, 9, 18, 27, 36, [...] Read more.

Bacteria play a vital role in enhancing host resistance to salt–alkali stress. However, the composition and structure of bacterial communities associated with halophytes under natural high salt–alkali conditions remain poorly understood. Here, a transect comprising six sampling points (0, 9, 18, 27, 36, and 45 m) was established across a natural population of Salicornia europaea L. in Guhya Salt Lake salt–alkali soils. At each sampling site, bulk soil, rhizosphere soil, root, and leaf samples were collected for 16S rRNA gene amplicon sequencing. The pH and soil electrical conductivity (EC) significantly increased along the sampling sites establishing a distinct salt–alkali gradient. This gradient provides an ideal model for studying the ecological adaptation mechanisms of halophytes and their related microorganisms. The results showed that alpha diversity (Shannon index) of bacterial communities significantly decreased across sampling sites in bulk soil, rhizosphere soil and root, but not in leaf. Beta diversity varied significantly across sampling points in all sample types examined. Linear Discriminant Analysis Effect Size (LEfSe) identified specific microbial biomarkers (such as Halomonas spp.) for each sampling point and sample type, many of which are known salt–alkali-tolerant lineages. Random forest and correlation analysis indicated that soil chemical properties had a clear impact on these identified biomarkers. Overall, salt–alkali gradient was associated with habitat-specific microbial communities across plant compartments and certain bacterial taxa were found to be enriched in specific niches. These taxa include known salt–alkali-tolerant lineages, and may putatively contribute to host adaptation to extreme environments, which provides deeper insights into plant–microbe interactions in natural ecosystems and offers potential microbial resources for improving crop salt–alkali tolerance. Full article

(This article belongs to the Section Microbiomes)

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4 pages, 2157 KB

Open AccessCorrection

Correction: Zou et al. Two-Component MprAB System Regulates the Expression of Genes Involved in Cell Envelope Biosynthesis in Corynebacterium glutamicum. Microorganisms 2025, 13, 1120

by Yu Zou, Danni Huang, Xiuxia Liu, Yankun Yang, Chunli Liu, Ye Li and Zhonghu Bai

Microorganisms 2026, 14(7), 1576; https://doi.org/10.3390/microorganisms14071576 - 20 Jul 2026

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Abstract

In the original publication [...] Full article

(This article belongs to the Section Microbial Biotechnology)

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19 pages, 10150 KB

Open AccessArticle

Cold Exposure Shifts Gut Microbial Butyrate Synthesis Toward the Lysine-Dependent and But-Mediated Terminal Pathways to Enhance Cold Tolerance in Min Pigs

by Yang Chang, Xinlei Liu, Lujing Song, Fei Xu, Ziwen Zhang, Miao Yu, Guandong Wu, Dongjie Zhang and Chunzhu Xu

Microorganisms 2026, 14(7), 1575; https://doi.org/10.3390/microorganisms14071575 - 19 Jul 2026

Viewed by 347

Abstract

This study combined seasonal observation in Min pigs and acute cold challenge experiments in Min pigs and Large White pigs to analyze changes in gut butyrate synthesis under cold exposure and its association with thermogenesis. Compared with summer, Min pigs in winter showed [...] Read more.

This study combined seasonal observation in Min pigs and acute cold challenge experiments in Min pigs and Large White pigs to analyze changes in gut butyrate synthesis under cold exposure and its association with thermogenesis. Compared with summer, Min pigs in winter showed significantly higher Bacteroidota abundance (p = 0.006), lysine-pathway genes (p < 0.05), and relative gene abundance of the but terminal pathway (p < 0.05). Fecal (47.96 vs. 40.24 µmol/L, p = 0.020) and serum (4.64 vs. 2.17 µmol/L, p = 0.046) butyrate were also elevated and correlated with 10 thermogenesis-related genes (p < 0.05). Acute cold challenge increased serum butyrate (p = 0.017) and SLC16A1 expression (adjusted p = 0.027) only in Min pigs. Min pigs exhibited higher lysine pathway abundance and greater but terminal contribution than Large White pigs. Metagenomic binning recovered 40 lysine-pathway MAGs (27 unique to Min pigs) and 15 dual-pathway MAGs (11 unique to Min pigs), with Bacteroidota MAGs harboring complete lysine and dual terminal pathways. Collectively, cold exposure correlates with enrichment of lysine-dependent and but terminal butyrate synthesis pathways, highlighting butyrate-producing bacteria as candidate taxa for further investigation of cold-induced gut metabolic remodeling in pigs. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 1544 KB

Open AccessArticle

Twenty-Two Months of Syndromic Multiplex-PCR Testing for Acute Infections in a Southern Italian Hospital: Pathogen Epidemiology, Diagnostic Appropriateness and the Cost of Negative Results

by Daniela Chirizzi, Angela Spedicato, Gabriele Bianco, Laura Lupo, Ilaria Serafini, Daniele Pisanò, Maria Rita Orsi, Giovanni Moschettini, Angelo Sorge, Rosanna Bruno, Camilla Panico, Silvana Arnesano, Antonella Simone, Luciana Corciulo, Antonella Pico, Claudia Pagano, Letizia Fulceri, Giulia Apruzzi, Anna De Filippis, Massimiliano Galdiero and Francesco Broccolo Show full author list Hide full author list

Microorganisms 2026, 14(7), 1574; https://doi.org/10.3390/microorganisms14071574 - 19 Jul 2026

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Abstract

Syndromic multiplex-PCR panels deliver rapid, comprehensive detection of pathogens and resistance determinants in acute infections, but their unrestricted use can generate a high proportion of negative results with substantial economic and stewardship implications. We retrospectively analysed all BioFire FilmArray meningitis/encephalitis (ME), upper-respiratory (RP2.1), [...] Read more.

Syndromic multiplex-PCR panels deliver rapid, comprehensive detection of pathogens and resistance determinants in acute infections, but their unrestricted use can generate a high proportion of negative results with substantial economic and stewardship implications. We retrospectively analysed all BioFire FilmArray meningitis/encephalitis (ME), upper-respiratory (RP2.1), pneumonia (PN) and gastrointestinal (GI) determinations performed at the UOSD Microbiology and Virology of P.O. “Vito Fazzi”, ASL Lecce (Apulia, Italy) between 1 July 2024 and 30 April 2026. Repeat determinations from the same patient with the same panel were identified in the laboratory information system and removed before any analysis, so that each determination analysed corresponds to a distinct diagnostic episode. Across 5381 determinations (CNS, n = 761; upper respiratory, n = 2601; lower respiratory, n = 399; gastrointestinal, n = 1620), 59.3% were negative for every target, with a steep appropriateness gradient: 90.0% negativity for the ME panel and 77.1% for the gastrointestinal panel versus 44.2% for the upper-respiratory and 26.6% for the pneumonia panel. CNS positives were predominantly viral (75%), led by enterovirus; Streptococcus pneumoniae was the only consistent bacterial agent. Human rhinovirus/enterovirus dominated the respiratory ecology; influenza A was almost entirely H3 and H1N1pdm09, but 8.1% of influenza-A–positive specimens were equivocal or non-subtypeable and were never referred for sequencing, an avoidable surveillance blind spot for novel/zoonotic (avian) influenza. Pneumonia-panel resistance markers (mecA/C–MREJ, CTX-M, KPC, NDM) clustered in Enterobacterales co-infections. The gastrointestinal panel was dominated by diarrhoeagenic Escherichia coli pathotypes (chiefly EPEC and EAEC) and Clostridioides difficile toxin, its 77% negativity identifying a second over-utilised stream. We argue for CSF-pleocytosis gating, tiered/reflex respiratory algorithms, gastrointestinal-panel gating to community-onset diarrhoea, and mandatory reflex sequencing of unsubtypeable influenza A. Full article

(This article belongs to the Section Virology)

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Microorganisms, Volume 14, Issue 7 (July 2026) – 217 articles

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