Next Issue
Volume 14, May
Previous Issue
Volume 14, March
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.2
4.7
Journals
Microorganisms
Volume 14
Issue 4
share announcement

Microorganisms, Volume 14, Issue 4 (April 2026) – 215 articles

Cover Story (view full-size image): Weizmannia coagulans is valued for industrial lactic acid production and probiotic properties, but the basis for its growth and division under acidic fermentation conditions is not fully understood. Here, transcriptome and physiological analysis have determined that pH 4.20 is the key threshold for inhibiting cell division while maintaining survival rate. Acid stress triggered reprogramming of central carbon flux, repression of the FtsZ divisome, and PhoPR-mediated inhibition of septal and ribosomal functions. These coordinated adjustments reflect an energy-conservation strategy that prioritizes survival over proliferation. This study provides molecular insights into how W. coagulans preserves viability under acid stress, offering a theoretical basis for optimizing its performance in industrial applications. View this paper
  • Issues are regarded as officially published after their release is announced to the table of contents alert mailing list.
  • You may sign up for e-mail alerts to receive table of contents of newly released issues.
  • PDF is the official format for papers published in both, html and pdf forms. To view the papers in pdf format, click on the "PDF Full-text" link, and use the free Adobe Reader to open them.
Order results
Result details
Section
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
18 pages, 2754 KB  
Article
Genomic and Pathogenicity Diversity of Six Avian Reovirus Strains with Different Genotypes
by Xuemei Lu, Guowei He, Jinyang Huang, Ping Liu and Yijian Wu
Microorganisms 2026, 14(4), 942; https://doi.org/10.3390/microorganisms14040942 - 21 Apr 2026
Viewed by 542
Abstract
Avian reovirus (ARV) causes viral arthritis and leads to considerable economic losses in the poultry industry. In this study, six ARV strains of distinct genotypes (FJNP01–FJNP06) were isolated from commercial broiler farms. Through gene sequencing and pathogenicity assessment, we analyzed the genetic evolution [...] Read more.
Avian reovirus (ARV) causes viral arthritis and leads to considerable economic losses in the poultry industry. In this study, six ARV strains of distinct genotypes (FJNP01–FJNP06) were isolated from commercial broiler farms. Through gene sequencing and pathogenicity assessment, we analyzed the genetic evolution and pathogenic characteristics of the σC, P10, σB, μB, and λC genes. Pathogenicity tests revealed that inoculation with FJNP01–FJNP06 by footpad or oral gavage induced symptoms in specific-pathogen-free (SPF) chickens, including mortality and growth retardation. Among the isolates, FJNP04 (genotype IV) showed the highest pathogenicity, causing increased mortality, weight loss, and severe lesions in the footpads and bursa of Fabricius, followed by FJNP05 and FJNP02. The pathogenicity of FJNP06 varied by inoculation route, with enhanced pathogenicity observed following oral gavage. In contrast, FJNP01 and FJNP03 demonstrated relatively low pathogenicity. Identity analysis indicated that σC and P10 were highly variable, σB was relatively conserved, while μB and λC displayed considerable divergence. Phylogenetic analysis placed FJNP01–FJNP06 into genotypes I to VI, respectively, forming six distinct branches on the σC and P10 phylogenetic trees, yet clustering more closely on the σB, μB, and λC trees. The pathogenicity of different genotypes of ARV varies, among which FJNP04 (genotype IV) exhibits the strongest pathogenicity. Genetic sequence analysis revealed that σC and P10 are highly variable, σB is relatively conserved, while μB and λC display a wide range of variation. This study provides insights into the genetic variation and pathogenic characteristics of ARV and serves as a reference for future research. Full article
(This article belongs to the Topic Advances in Infectious and Parasitic Diseases of Animals)
►▼ Show Figures

Figure 1

21 pages, 3206 KB  
Article
Spatial Distributions of Active Pico- and Nano-Haptophytes (Eukaryota, Hacrobia) in the Tropical and Subtropical Western Pacific Ocean
by Wenlu Li, Yuyu Liao, Nianzhi Jiao and Dapeng Xu
Microorganisms 2026, 14(4), 941; https://doi.org/10.3390/microorganisms14040941 - 21 Apr 2026
Viewed by 631
Abstract
Haptophytes are ubiquitous single-celled eukaryotic plankton in coastal and open oceans that play a key role in marine biogeochemical cycling. Understanding the size structure and community composition of active haptophytes is crucial for elucidating their diversity and ecological functions. This study investigated the [...] Read more.
Haptophytes are ubiquitous single-celled eukaryotic plankton in coastal and open oceans that play a key role in marine biogeochemical cycling. Understanding the size structure and community composition of active haptophytes is crucial for elucidating their diversity and ecological functions. This study investigated the diversity and community structure of pico- (0.2–3 μm) and nano-sized (3–20 μm) haptophytes in the surface waters of the western Pacific Ocean using high-throughput sequencing targeting the hypervariable V4 region of the 18S rRNA. The pico-sized community exhibited significantly higher diversity than the nano-sized community. Community composition varied significantly between size fractions, driven primarily by the genera Chrysochromulina and Syracosphaera. Furthermore, the nano-sized community was more strongly influenced by environmental variables than the pico-sized community, although neither size fraction displayed a clear coastal-to-open-ocean distribution pattern. Null and neutral community model analyses indicated that both size-fractionated communities were primarily regulated by stochastic processes, while deterministic processes exerted a greater influence on the nano-sized community. Co-occurrence network analysis revealed stronger interconnections and a higher number of keystone species within the nano-sized community. In both networks, intermediate taxa (relative abundances of 0.01% to 0.1%) exhibited the highest diversity and abundance among keystone species, highlighting their pivotal role in shaping the network structure and stability. Additionally, phylogenetic analyses revealed that while the majority of ZOTUs clustered with known taxa, multiple deep-branching, uncultured lineages were identified across both size fractions, indicating substantial uncharacterized genetic diversity. This study underscores the variability and hidden diversity of size-fractionated haptophyte community structures in oligotrophic open oceans, providing valuable insights into their functional significance in global biogeochemical cycles. Full article
(This article belongs to the Section Environmental Microbiology)
►▼ Show Figures

Graphical abstract

29 pages, 4186 KB  
Article
Cognitive Improvement and Microbiota–Gut–Brain Axis Regulation by Lycium barbarum Polysaccharides and Glycopeptide in Laboratory-Kenneled Poodles
by Haoran Yan, Miaomiao Zhang, Chuchen Gui, Huiwen Huang, Wenhao Wu, Zhaokun Chen, Yuansheng Wu, Shaohao Chen, Hongcan Huang, Huixian Lin, Yan Guo, Baichuan Deng and Lingna Zhang
Microorganisms 2026, 14(4), 940; https://doi.org/10.3390/microorganisms14040940 - 21 Apr 2026
Viewed by 1120
Abstract
Kennel-housed dogs may experience chronic stress affecting cognition. This study compared the effects of Lycium barbarum polysaccharides (LBP) and glycopeptide (LbGP) on cognitive function in laboratory-kenneled poodles. Eighteen dogs were assigned to CON, LBP, or LbGP groups for 42 days. Cognitive tests were [...] Read more.
Kennel-housed dogs may experience chronic stress affecting cognition. This study compared the effects of Lycium barbarum polysaccharides (LBP) and glycopeptide (LbGP) on cognitive function in laboratory-kenneled poodles. Eighteen dogs were assigned to CON, LBP, or LbGP groups for 42 days. Cognitive tests were performed and serum, saliva, and feces were collected for subsequent analysis. Both supplements improved cognitive performance (e.g., increased the correct rate in the cylinder test by approximately 40.0%, both p < 0.001). LBP enriched beneficial bacteria (Faecalibacterium and Bacteroides, p < 0.05), reduced pathogens (Romboutsia and Terrisporobacter, p < 0.05), and predominantly influenced the indole pathway of tryptophan metabolism. LbGP specifically decreased Escherichia-Shigella and Corynebacterium, increased fecal SCFAs, and mainly targeted the 5-HT pathway. Both treatments regulated immune function (i.e., elevated IL-6 and IL-10) and antioxidant capacity; LBP significantly increased serum superoxide dismutase (SOD) levels by 6.8% (p < 0.01) and BDNF levels by 13.5% (p < 0.05), while LbGP elevated (p < 0.01) glutathione peroxidase (GSH-Px) levels by 20.9% and reduced salivary cortisol levels by 14.2% (p < 0.01). Overall, LBP and LbGP support canine cognition through distinct microbiota-related mechanisms, likely via the microbiota–gut–brain axis, suggesting their potential as functional feed additives for cognitive health. Full article
(This article belongs to the Special Issue Functional Foods from Microbes)
►▼ Show Figures

Figure 1

33 pages, 8476 KB  
Review
Progress of Rapid Detection Technology for Aquatic Microorganisms: A Comprehensive Review
by Qin Liu, Zhuangzhuang Qiu, Mengli Yao, Boyan Jiao, Yu Zhou, Chenghua Li, Haipeng Liu and Lusheng Xin
Microorganisms 2026, 14(4), 939; https://doi.org/10.3390/microorganisms14040939 - 21 Apr 2026
Cited by 1 | Viewed by 1770
Abstract
Microbial contamination in aquatic environments poses severe threats to aquaculture sustainability, ecological balance and public health. Traditional culture-based detection methods, while standardized, are time-consuming and labor-intensive, often failing to meet the urgent need for rapid on-site monitoring required to prevent disease outbreaks and [...] Read more.
Microbial contamination in aquatic environments poses severe threats to aquaculture sustainability, ecological balance and public health. Traditional culture-based detection methods, while standardized, are time-consuming and labor-intensive, often failing to meet the urgent need for rapid on-site monitoring required to prevent disease outbreaks and manage water quality effectively. By integrating latest research advances (2020–2025), this study reviews advances in rapid detection technologies for aquatic microorganisms, including the evolution of nucleic acid amplification strategies, with a focused comparison of the analytical sensitivity and field deployability of quantitative polymerase chain reaction (qPCR) and mainstream isothermal amplification techniques (loop-mediated isothermal amplification, LAMP; recombinase polymerase amplification, RPA). Furthermore, this study reports on the emergence of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated protein (Cas) systems as next-generation diagnostic tools, highlighting their integration with microfluidic Lab-on-a-Chip (LOC) platforms to achieve attomolar sensitivity. We also consider the application of portable nanopore sequencing for real-time pathogen identification and the growing role of Artificial Intelligence (AI) in analyzing complex diagnostic datasets. Advanced molecular methods have achieved significant reductions in time consumption—from days to less than one hour—while challenges regarding sample preparation and environmental matrix inhibition remain. The future of aquatic monitoring lies in integrated, automated systems that combine the specificity of CRISPR-Cas diagnostics with the connectivity of IoT-enabled biosensors. Comparative analysis indicates that isothermal amplification methods (LAMP, RPA) coupled with CRISPR-Cas systems offer the optimal balance of sensitivity, speed, and field deployability for point-of-care aquaculture diagnostics, while qPCR/dPCR remain indispensable for quantitative regulatory applications. We propose a structured technology selection framework to guide researchers and practitioners in choosing appropriate detection modalities based on specific sensitivity, cost, throughput, and deployment requirements. Full article
(This article belongs to the Special Issue Pathogen Infections in Aquatic Animals—Advanced Detection Technologies, Precision Identification, and Pathogenic Mechanisms)
►▼ Show Figures

Figure 1

29 pages, 9458 KB  
Article
Pangenome Architecture and Accessory Gene-Driven Population Structure of Staphylococcus aureus Revealed by a Hospital-Adjacent Environmental Isolate
by Wellington Francisco Rodrigues, Laise Mazurek, Renata Botelho Miguel, Geovana Pina Vilela, Amanda Bertinetti Tres, Sabrina Martins Calegari, Ferdinando Agostinho, Jamil Miguel-Neto, Melissa Carvalho Martins-de-Abreu, Karen M. Wagner, Christophe Morisseau, Carlos Ueira-Vieira, Mariana Santos Cardoso, Aristóteles Góes-Neto, Carlo José Freire Oliveira, Siomar de Castro Soares and Camila Botelho Miguel
Microorganisms 2026, 14(4), 938; https://doi.org/10.3390/microorganisms14040938 - 21 Apr 2026
Viewed by 745
Abstract
Staphylococcus aureus is a globally distributed bacterium that spans interconnected human, animal, and environmental niches and is a major driver of antimicrobial resistance. Environmental and wildlife-associated isolates from hospital-surrounding settings remain underrepresented in comparative genomic studies. To address this gap, we integrated a [...] Read more.
Staphylococcus aureus is a globally distributed bacterium that spans interconnected human, animal, and environmental niches and is a major driver of antimicrobial resistance. Environmental and wildlife-associated isolates from hospital-surrounding settings remain underrepresented in comparative genomic studies. To address this gap, we integrated a newly sequenced environmental isolate recovered from pigeon fecal samples collected around a hospital into a standardized pangenome framework composed of 99 reproducibly selected RefSeq genomes plus the environmental isolate S_S3. Using uniform genome annotation and orthologous gene family clustering, we identified an open pangenome of 8366 gene families (Heaps’ law γ = 0.275), consistent with the high genomic plasticity previously reported for S. aureus. The core genome stabilized at approximately 1757 genes, including 1651 genes conserved across all genomes. Gene frequency spectra showed a dominant cloud genome and a structured shell fraction contributing to interstrain differentiation. Jaccard-based gene content similarity resolved clusters shaped mainly by accessory gene composition. The environmental isolate retained the complete core genome, carried only 15 isolate-specific gene families (0.18% of the pangenome), and clustered within an established lineage. Its unique content included a lincosamide resistance-associated locus and efeB, a gene potentially related to heme or iron metabolism and oxidative stress response. These findings highlight a conserved genomic backbone over a dynamic accessory reservoir and support One Health genomic surveillance that includes wildlife-associated niches, while indicating that the environmental isolate fits within the broader gene content diversity observed in the analyzed dataset. Full article
(This article belongs to the Special Issue Advancements in Pathogenic Bacteria: Detection, Genomic Analysis, and Antibiotic Resistance—2nd Edition)
►▼ Show Figures

Figure 1

23 pages, 7818 KB  
Article
Enhanced Barley Growth in Petroleum-Contaminated Soil Mediated by Xanthan-like Exopolysaccharide of Xanthomonas translucens TRK8
by Ramza Berzhanova, Aisulu Zhuniszhan, Gulnur Tatykhanova, Sarkyt Kudaibergenov, Gulshara Abai, Alibek Kudabayev and Togzhan Mukasheva
Microorganisms 2026, 14(4), 937; https://doi.org/10.3390/microorganisms14040937 - 21 Apr 2026
Viewed by 621
Abstract
Exopolysaccharides (EPS) represent an important tool for application in bio- and phytoremediation technologies due to their ability to enhance water and nutrient retention, support microclimate stability, and protect plants from environmental stress. In the present study, xanthan-like EPS produced by Xanthomonas translucens TRK8 [...] Read more.
Exopolysaccharides (EPS) represent an important tool for application in bio- and phytoremediation technologies due to their ability to enhance water and nutrient retention, support microclimate stability, and protect plants from environmental stress. In the present study, xanthan-like EPS produced by Xanthomonas translucens TRK8 was precipitated by ethanol and isopropanol, with the former yielding 9.2 g L−1 compared with 6.7 g L−1 obtained with the latter. The monosaccharide profile of the TRK8-derived EPS indicated a branched structure composed of rhamnose, mannose, glucose, and galactose residues, containing both α- and β-type pyranose units. The rheological properties of the studied EPS were compared with those of commercial xanthan at concentrations of 1–3 wt.%. Fitting the obtained data to the Ostwald–de Waele power-law model revealed that the flow behaviour index (n) values were below 1 (−0.338, −0.499, and −0.647, respectively), indicating shear-thinning behaviour (i.e., pseudoplasticity). The potential of the TRK8-derived EPS as a plant protection agent was validated by coating barley seeds with 2 wt.% EPS, resulting in a 28.6% increase in shoot length and a 64.7% increase in root length relative to the oil-stressed control. Full article
(This article belongs to the Section Biofilm)
►▼ Show Figures

Figure 1

17 pages, 7482 KB  
Article
Andrographolide Alleviates Liver Damage Caused by Salmonella in Mice by Inhibiting the PANoptosis Pathway
by Quanying Li, Limin Hou, Luna Su, Xiaoyu Wang, Yifan Zhu and Binghu Fang
Microorganisms 2026, 14(4), 936; https://doi.org/10.3390/microorganisms14040936 - 21 Apr 2026
Viewed by 1322
Abstract
The emergence of antibiotic resistance in pathogens, including Salmonella typhimurium, poses a major challenge to animal health and safety. Andrographolide is well known for its antibacterial properties and therefore offers potential as an antimicrobial treatment to lessen the damage caused by Salmonella [...] Read more.
The emergence of antibiotic resistance in pathogens, including Salmonella typhimurium, poses a major challenge to animal health and safety. Andrographolide is well known for its antibacterial properties and therefore offers potential as an antimicrobial treatment to lessen the damage caused by Salmonella. PANoptosis is defined as an inflammatory coordinated cell death pathway encompassing apoptosis, pyroptosis, and necroptosis. To reduce the organ and tissue damage caused by bacterial infection and reduce antibiotic resistance, this study investigated the effect of andrographolide on liver damage in Salmonella-infected mice. We used a mouse model infected with Salmonella typhimurium for in vivo experiments, which involved the detection of the bacterial load in the liver, liver injury indicators, and expression of related PANoptosis-related genes and proteins. Here, our finding indicated that andrographolide effectively inhibited markers associated with apoptosis, pyroptosis, and necroptosis in mouse hepatocytes, alleviated liver injury and clinical symptoms caused by Salmonella typhimurium in mice, and thus exerted therapeutic effects. In this study, we observed that andrographolide modulated the markers associated with these three pathways, indicating their involvement in PANoptosis. These results suggest that andrographolide significantly relieve Salmonella-induced liver injury by inhibiting PANoptosis, highlighting the potential significance of andrographolide as an effective drug for the treatment of Salmonella. Full article
(This article belongs to the Section Medical Microbiology)
►▼ Show Figures

Figure 1

16 pages, 1024 KB  
Article
Characteristics of Legionnaires’ Disease Cases Hospitalized at a Specialized Infectious Disease Hospital, 2023–2024, with a Focus on Clusters Associated with Travel to a Spa Resort
by Constanța-Angelica Vișan, Gina Filip, Carmen-Cristina Vasile, Anca Cristina Drăgănescu, Gheorghiță Jugulete, Anca Streinu-Cercel, Andreea Tudor, Laurențiu Mihăiță Stratan, Daniela Pițigoi and Ana Maria Tudor
Microorganisms 2026, 14(4), 935; https://doi.org/10.3390/microorganisms14040935 - 21 Apr 2026
Viewed by 707
Abstract
Legionnaires’ disease is a rare cause of atypical pneumonia associated with a high mortality rate among untreated patients. In Romania, the disease has historically been underreported due to insufficient surveillance and limited diagnostic capacity. The aim of this study was to describe the [...] Read more.
Legionnaires’ disease is a rare cause of atypical pneumonia associated with a high mortality rate among untreated patients. In Romania, the disease has historically been underreported due to insufficient surveillance and limited diagnostic capacity. The aim of this study was to describe the characteristics of Legionnaires’ disease cases admitted to a specialized infectious disease hospital between 2023 and 2024, with a particular focus on a cluster associated with travel to a spa resort. Most cases included in our study (31/36) were confirmed by urinary antigen testing, while one case was confirmed by a significant increase in the level of specific antibodies against Legionella pneumophila serogroup 1 in paired serum samples. The most frequently reported symptom was fever (28/32), followed by chills (24/32). Among the 32 confirmed cases, 3 patients died. Two cases were identified as part of a family cluster involving a father and son who had undergone physiotherapy at a balneary resort. Both patients presented with fever and gastrointestinal symptoms, and radiological investigations confirmed mixed pneumonia associated with an intense inflammatory syndrome. In the father’s case, hepatic involvement and interstitial nephritis were also identified. Early diagnosis based on epidemiological data, clinical predictive scores, and laboratory investigations would allow timely administration of targeted antibiotic therapy and may contribute to reduced mortality. Full article
(This article belongs to the Special Issue Infectious Disease Surveillance in Romania: Second Edition)
►▼ Show Figures

Figure 1

23 pages, 11726 KB  
Article
Effects of Continuous Electric/Magnetic Field Treatment on Nutrient, Enzyme Activity, and Bacterial Community Structure in Rocky Desertification Soils
by Jun Hu, Yungen Liu, Yan Wang, Wenjiao Gao, Jiaxu Zhang, Silin Yang, Feifeng Deng, Bo Yang and Caishuang Huang
Microorganisms 2026, 14(4), 934; https://doi.org/10.3390/microorganisms14040934 - 21 Apr 2026
Viewed by 836
Abstract
Soil nutrient loss and infertility in rocky desertification areas severely constrain ecological restoration. Exploring the impacts of external field remediation technologies on soil quality in these regions may offer novel strategies for soil enhancement and ecosystem recovery. This study conducted a three-month experiment [...] Read more.
Soil nutrient loss and infertility in rocky desertification areas severely constrain ecological restoration. Exploring the impacts of external field remediation technologies on soil quality in these regions may offer novel strategies for soil enhancement and ecosystem recovery. This study conducted a three-month experiment to investigate the impact of continuous electric (ET, 20 V) and magnetic (MT, 200 mT) field treatments on soil nutrients, enzyme activities, and bacterial communities in simulated moderate and severe rocky desertification soils. Results showed that although an overall declining trends in total contents of key soil nutrients (Total nitrogen, total phosphorus, and total potassium), both electric and magnetic field treatments effectively mitigated the decreases of total nitrogen and potassium content (with the exception of total phosphorus) in rocky desertification soils, while improving their available contents compared to the control (CK). Electric field application significantly reduced the pH of moderate and severe rocky desertification soils through electrolysis, shifting the soil from alkaline (pH 7.69 and 7.73, respectively) to slightly acidic (pH 6.71 and 6.37, respectively); Both electric and magnetic field treatments enhanced urease and sucrase activities in moderately and severely rocky desertified soils. Compared to the CK, the increases were 21.92%, 4.46%, 5.70%, and 66.43% in moderately rocky desertified soil, and 10.06%, 42.15%, 20.66%, and 0.93% in severely rocky desertified soil, respectively. Their effects on phosphatase and catalase activities varied with the degree of rocky desertification. However, in severely rocky desertified soil, both treatments significantly increased phosphatase and catalase activities by 19.55%, 24.63%, 61.07%, and 38.05% compared to the CK, respectively. Furthermore, both electric and magnetic treatments significantly reduced bacterial α-diversity (chao1, ACE, Shannon, Simpson, and Pielou J indices) but optimized community structure by enriching dominant phyla with specific ecological functions, such as Pseudomonadota (7.63–41.10%), Bacteroidota (13.52–69.29%), and Verrucomicrobiota (38.26–104.81%). Functional prediction revealed that the abundances of dominant pathways (such as chemoheterotrophy, aerobic chemoheterotrophy, and nitrogen fixation) was enhanced following both treatments. Mantel analysis further indicated strengthened correlations among soil nutrients, enzyme activities, and bacterial communities, particularly under magnetic field treatment. These findings demonstrate that electric and magnetic field applications effectively facilitate nutrient cycling, stimulate enzyme activities, and optimize microbial community structure, thereby improving soil ecological functions and overall quality in rocky desertification regions, highlighting their potential for ecological restoration in karst areas. Full article
(This article belongs to the Section Environmental Microbiology)
►▼ Show Figures

Figure 1

28 pages, 2835 KB  
Review
Unlocking Microbial Dark Matter: A Comprehensive Review of Isolation Technologies from Traditional Culturing to Single-Cell Technologies
by Xi Sun, Xiaoxuan Zhang and Jia Zhang
Microorganisms 2026, 14(4), 933; https://doi.org/10.3390/microorganisms14040933 - 21 Apr 2026
Viewed by 1871
Abstract
Microorganisms represent the Earth’s most abundant biomass and a vast reservoir of genetic diversity. However, traditional agar plate methods fail to recover the vast majority of these species, leaving a “microbial dark matter” that holds immense potential for the discovery of novel antibiotics [...] Read more.
Microorganisms represent the Earth’s most abundant biomass and a vast reservoir of genetic diversity. However, traditional agar plate methods fail to recover the vast majority of these species, leaving a “microbial dark matter” that holds immense potential for the discovery of novel antibiotics and bioactive compounds. While conventional techniques such as selective media and enrichment culture remain foundational, they are inherently limited by community biases and the inability to support low-abundance, oligotrophic species. To address these bottlenecks, a diverse array of innovative isolation strategies has emerged. This review systematically categorizes and evaluates these methodologies, ranging from in situ cultivation to high-resolution single-cell manipulation. We first examine membrane diffusion-based cultivation (e.g., iChip), which mimics natural microenvironments to resuscitate recalcitrant microbes. Subsequently, we explore high-throughput single-cell technologies, including microfluidics for physicochemical separation, optical tweezers for precise manipulation, and fluorescence-activated cell sorting (FACS). Special attention is given to Raman-activated cell sorting (RACS) as a label-free functional screening tool and reverse genomics for targeted capture. By synthesizing the strengths and limitations of these approaches, we propose integrated workflows designed to accelerate the mining of untapped microbial resources. Full article
(This article belongs to the Section Microbial Biotechnology)
►▼ Show Figures

Figure 1

11 pages, 1007 KB  
Article
Genomic Evolution of Siccibacter colletis: Comparative Analysis and First Clinical Isolate Report
by Wentao Zhu, Qian Liu, Xi Chen, Chunxia Yang, Ming Wei, Li Gu, Hui Yuan and Hong Shen
Microorganisms 2026, 14(4), 932; https://doi.org/10.3390/microorganisms14040932 - 20 Apr 2026
Viewed by 607
Abstract
The genus Siccibacter consists primarily of environmental bacteria, with strains of Siccibacter colletis previously isolated only from plant materials and related environments. This study aims to characterize the first clinical isolate of S. colletis and explore its genomic evolution and clinical relevance. Strain [...] Read more.
The genus Siccibacter consists primarily of environmental bacteria, with strains of Siccibacter colletis previously isolated only from plant materials and related environments. This study aims to characterize the first clinical isolate of S. colletis and explore its genomic evolution and clinical relevance. Strain S25242 was isolated from the urine of a 64-year-old male with a severe urinary tract infection. The genome of S25242 is 4.19 Mb, containing 4012 coding sequences, 73 tRNAs, 10 rRNAs, and 38 snRNAs. Phylogenetic and phylogenomic analyses indicated that strain S25242 is closely related to S. colletis type strain 1383T. The strain shared >70% of digital DNA-DNA hybridization (dDDH) values and >96% of average nucleotide identity (ANI) values with the type strain of S. colletis 1383T, thereby confirming its taxonomic status. The isolate was susceptible to all 11 tested antimicrobials. Comparative genomics identified 1942 S. colletis-specific genes (including multidrug efflux systems) and 13 unique genes in S25242 related to transposition and DNA integration. This study reports the first clinical isolate of S. colletis, providing evidence that genomic plasticity facilitates its transition from an environmental inhabitant to an opportunistic pathogen. The findings highlight the need for enhanced clinical surveillance of the Siccibacter genus and offer insights into its genomic evolution and clinical adaptation. Full article
(This article belongs to the Special Issue New Crucial Pathogens and Antimicrobial Resistance in Animals, Communities, Hospitals and the Environment in the One Health Context)
►▼ Show Figures

Figure 1

12 pages, 5368 KB  
Article
New Postbiotic Derived from Sequential Fermentation of Two Lacticaseibacillus Strains Exerts Beneficial Effects on Epithelial Gut Barrier and Innate Immunity in Human Enterocytes
by Franca Oglio, Alessia Cadavere, Monia De Aloe, Anna Lintura, Marco Michelini, Chiara Luongo, Serena Coppola, Alessandra Agizza, Erika Caldaria and Laura Carucci
Microorganisms 2026, 14(4), 931; https://doi.org/10.3390/microorganisms14040931 - 20 Apr 2026
Cited by 1 | Viewed by 754
Abstract
The efficacy of postbiotics varies significantly between different strains and preparation processes. We aimed at evaluating the effect of an innovative postbiotic product (iPB) generated through the sequential fermentation of Lacticaseibacillus rhamnosus GG and Lacticaseibacillus paracasei NPB-01, compared to single-strain postbiotics, on epithelial [...] Read more.
The efficacy of postbiotics varies significantly between different strains and preparation processes. We aimed at evaluating the effect of an innovative postbiotic product (iPB) generated through the sequential fermentation of Lacticaseibacillus rhamnosus GG and Lacticaseibacillus paracasei NPB-01, compared to single-strain postbiotics, on epithelial barrier integrity and innate immunity in human enterocytes using a Caco-2-cell-based experimental model by measuring human enterocyte proliferation and differentiation (lactase expression), tight junction proteins (occludin and zonula occludens 1, ZO-1), and mucus protein Mucin-2 (Muc-2) expression. The modulatory action on the major innate immunity peptide, Human Beta-Defensin 2 (HBD-2), production was also assessed. The iPB exposure resulted in a higher up-regulation of human enterocyte proliferation and differentiation, as suggested by higher lactase expression, and of occludin, ZO-1, and MUC2 expression compared with the single-strain postbiotics, suggesting a beneficial synergistic action in modulating the epithelial gut barrier. Furthermore, iPB induced a higher production of HBD-2, suggesting a synergistic enhancement of innate immune response. Our findings suggested that the sequential fermentation process could act as a biotechnological catalyst, optimizing the gut-barrier-protective properties and the immunomodulatory action of Lacticaseibacillus strains. This study introduces iPB as a high-performance postbiotic candidate for the prevention and management of conditions characterized by alterations in epithelial gut barrier and innate immunity. Full article
(This article belongs to the Special Issue Interactions Between Probiotics and Host)
►▼ Show Figures

Figure 1

13 pages, 1276 KB  
Review
Autochthonous Leishmaniosis in Dogs, Cats, Horses, and Wildlife in the United States of America
by Chaoqun Yao, Yi Yang and Aifang Du
Microorganisms 2026, 14(4), 930; https://doi.org/10.3390/microorganisms14040930 - 20 Apr 2026
Viewed by 546
Abstract
Leishmaniasis is endemic in 99 countries worldwide, including the United States of America (USA). Its causative pathogens, Leishmania spp. have been detected in both humans and animals within the USA. Lately, we have comprehensively reviewed autochthonous leishmaniasis in humans in this region. Animals [...] Read more.
Leishmaniasis is endemic in 99 countries worldwide, including the United States of America (USA). Its causative pathogens, Leishmania spp. have been detected in both humans and animals within the USA. Lately, we have comprehensively reviewed autochthonous leishmaniasis in humans in this region. Animals play a pivotal role in maintaining its endemicity in some endemic areas and regions, for example, dogs in Brazil and the Mediterranean. In this review, we thoroughly examine autochthonous leishmaniosis in dogs, cats, horses, and wildlife in the USA, and we synthesize integration across species, transmission pathways, the crucial roles the animals play, and the potential risk they pose to humans. The information is essential for public health and for the effective control and management of leishmaniasis through expanding reservoir and vector surveillance using One-Health approaches in the USA. Full article
(This article belongs to the Section Veterinary Microbiology)
►▼ Show Figures

Figure 1

18 pages, 1875 KB  
Article
Anti-Hair Loss Activity of Healthy Human Scalp-Derived Staphylococcus capitis KMH304 Ferment Filtrate in Human Hair-Follicle Dermal Papilla and Keratinocyte Cells
by Hye-Young Yoo, Tae Geun Gil, Na-Rin Kim, Hye-Won Lee, Seoyoung Choi, Sung-Jun Choi, Sung-Ha Park and Byoung-Jun Park
Microorganisms 2026, 14(4), 929; https://doi.org/10.3390/microorganisms14040929 - 20 Apr 2026
Viewed by 996
Abstract
Scalp microbes are recognized as contributors to hair loss by influencing scalp homeostasis and hair growth. However, the in vitro anti-hair loss activity of microbial culture media derived from healthy scalps remains unclear. In this study, resident microbes from 20 Korean participants with [...] Read more.
Scalp microbes are recognized as contributors to hair loss by influencing scalp homeostasis and hair growth. However, the in vitro anti-hair loss activity of microbial culture media derived from healthy scalps remains unclear. In this study, resident microbes from 20 Korean participants with healthy scalps and hair were isolated, and Staphylococcus capitis was used to produce S. capitis ferment filtrate (SCFF). SCFF anti-hair loss activity was evaluated in human follicle dermal papilla cells (HFDPCs) and human adult low-Calcium High-Temperature (HaCaT) keratinocytes via proliferation assays, qPCR, immunocytochemistry, and SA-β-gal staining at 250–1000 μg/mL. SCFF increased cell density after 48 h in a concentration-dependent manner. In HFDPCs, SCFF controlled growth (KGF, IGF-1, and HGF) and androgen (AR and TGF-β2) factors, regulating key mRNAs for hair growth. SCFF mitigated scalp and hair aging by promoting sirtuins 1 and 7 and collagen type 13, while suppressing p21 and X-Gal staining. In HaCaT cells, SCFF exhibited a scalp barrier-strengthening effect by significantly increasing filaggrin and involucrin levels. It suppressed reactive oxidative stress and exhibited DPPH and ABTS radical scavenging activity. These results suggest that SCFF may modulate key pathways associated with hair loss by promoting scalp and hair anti-aging, barrier strengthening, enhancing antioxidant activity, and supporting hair growth. Full article
(This article belongs to the Section Medical Microbiology)
►▼ Show Figures

Figure 1

23 pages, 11448 KB  
Article
Soil Bacterial and Fungal Community Structure and Its Driving Factors Under Small-Scale Altitude Gradient on the Southern Slope of the Qilian Mountains
by Yue Zhang, Huichun Xie, Shuang Ji, Wenfang Chen, Xunxun Qiu, Zhiqiang Dong and Xukai Yang
Microorganisms 2026, 14(4), 928; https://doi.org/10.3390/microorganisms14040928 - 20 Apr 2026
Viewed by 489
Abstract
Aiming to clarify the spatial distribution characteristics of soil microbial assemblages and the environmental factors shaping them across a narrow altitudinal transect, this investigation concentrated on the surface soil layer within naturally occurring mixed forests of Picea crassifolia and Betula platyphylla, situated [...] Read more.
Aiming to clarify the spatial distribution characteristics of soil microbial assemblages and the environmental factors shaping them across a narrow altitudinal transect, this investigation concentrated on the surface soil layer within naturally occurring mixed forests of Picea crassifolia and Betula platyphylla, situated in the elevation band from 2400 to 2800 m along the southern flank of the Qilian Mountains. Leveraging the Illumina NextSeq 2000 high-throughput sequencing platform, integrated with α- and β-diversity analyses and redundancy analysis (RDA), we systematically characterized the composition and diversity traits of soil bacterial and fungal communities, as well as their associations with environmental factors. Notably, the bacterial communities were dominated by Pseudomonadota, Actinomycetota, and Acidobacteria with the abundance of Pseudomonadota decreasing with increasing altitude and that of Acidobacteria increasing with increasing altitude. Furthermore, Ascomycota and Basidiomycota were the dominant phyla in the fungal community. In contrast, bacterial α-diversity—as estimated by the Ace index—showed no significant variation across altitudes. Yet, the fungal alpha diversity metrics—namely Ace and Chao1—were markedly elevated at the 2800 m elevation relative to those observed at both intermediate and lower-altitude locations. Importantly, fungal diversity and community composition showed stronger altitudinal differentiation than bacterial communities in this dataset. Moreover, soil pH, total phosphorus, organic carbon, litter C:N:P stoichiometric ratios, and microbial biomass C:N:P stoichiometric ratios were strongly associated with soil microbial community variation along the altitude gradient, suggesting that they may act as important environmental filters. In conclusion, altitude-driven variations in litter characteristics and soil physicochemical properties jointly shape the assembly processes and spatial distribution patterns of soil microbial communities in this region. Full article
(This article belongs to the Special Issue Research of Soil Microbial Communities)
►▼ Show Figures

Figure 1

11 pages, 535 KB  
Article
Development of a PCR Assay for the Identification of Salmonella Thompson
by Dele Ogunremi, Naana Duah, Tianbi Tan, Bei Zhang and Lawrence Goodridge
Microorganisms 2026, 14(4), 927; https://doi.org/10.3390/microorganisms14040927 - 20 Apr 2026
Viewed by 636
Abstract
The effective control of foodborne salmonellosis relies on the rapid and reliable detection and identification of the pathogen. Reliable detection tools for identifying the most common Salmonella serovars should translate to a considerable alleviation of the health burden attributed to Salmonella. We [...] Read more.
The effective control of foodborne salmonellosis relies on the rapid and reliable detection and identification of the pathogen. Reliable detection tools for identifying the most common Salmonella serovars should translate to a considerable alleviation of the health burden attributed to Salmonella. We have developed a PCR assay for the rapid identification of colonies of Salmonella enterica serovar Thompson, a common serovar. Genomic analyses of publicly available sequences of Salmonella Thompson revealed the presence of a unique, Thompson-specific fragment, which we have used to design a pair of oligonucleotides, STho-F and STho-R, for the PCR amplification of an 808 bp DNA fragment. Using crude DNA extracts, the 808 bp fragment was detected in 77 out of 78 isolates of S. Thompson (sensitivity = 98.7% n = 78 isolates) but not in any of the non-Salmonella organisms tested (n = 100; 100% specificity) nor in non-Thompson Salmonella serovars (n = 100; 100% specificity). The sensitivity (inclusivity) and specificity (exclusivity) indices of the PCR assay for S. Thompson met the standard regulatory requirements. The Thompson primer pair was compatible with other primers pairs in a multiplex PCR designed for three other common Salmonella serovars. Colonies belonging to the Enteritidis serovar (n = 100), Heidelberg serovar (n = 100), Typhimurium serovar (n = 100), and Thompson serovar (n = 77) were correctly designated, indicating excellent inclusivity and exclusivity scores for all four Salmonella serovars tested in a single multiplex PCR. Full article
(This article belongs to the Special Issue Salmonella and Food Safety)
►▼ Show Figures

Figure 1

18 pages, 6630 KB  
Article
First Lysine Lactylation Profiling in Vibrio alginolyticus and Initial Characterization of VaCobQ as a Candidate Delactylase
by Yujia Zhang, Zhiqing Wei, Jiaxin Fan, Weijie Zhang, Shuai Yang, Jichang Jian, Na Wang, Jianyi Wei and Huanying Pang
Microorganisms 2026, 14(4), 926; https://doi.org/10.3390/microorganisms14040926 - 20 Apr 2026
Viewed by 748
Abstract
Vibrio alginolyticus is a common pathogenic bacterium and can cause diseases in aquaculture animals. Lysine lactylation (Kla) is a novel post-translational modification (PTM) that has been confirmed to play critical roles in key biological processes. However, the modification landscape and functions of Kla [...] Read more.
Vibrio alginolyticus is a common pathogenic bacterium and can cause diseases in aquaculture animals. Lysine lactylation (Kla) is a novel post-translational modification (PTM) that has been confirmed to play critical roles in key biological processes. However, the modification landscape and functions of Kla in V. alginolyticus remain unclear. In this study, lactylation modification profiles of the bacterial pathogen V. alginolyticus were first systematically characterized; a total of 9308 lactylation sites on 2155 proteins were successfully identified. The lactylation of cAMP receptor protein (CRP) and triosephosphate isomerase (TPI) was verified by Co-immunoprecipitation (Co-IP) and Western blot to validate the lactylome data. Bioinformatic analysis of the Kla sites revealed 32 conserved sequence motifs surrounding the modified residues. Kla proteins were mainly involved in central metabolic pathways, including glycolysis/gluconeogenesis and ribosome biogen regulators were found to contain Kla modification sites. To investigate crosstalk among lysine acylations in V. alginolyticus, we integrated Kla, lysine acetylation (Kac), and lysine succinylation (Ksuc) profiles and identified 337 co-modified proteins and 5 co-modified sites. Additionally, phylogenetic analysis of Vibrio alginolyticus CobQ based on protein sequence alignment revealed no homology to the known delactylase CobB. Combined in vitro and in vivo functional validation identified VaCobQ as a candidate delactylase with potential NAD+-independent activity. This study establishes a lysine lactylation landscape in V. alginolyticus, providing a resource for exploring Kla functions in bacterial metabolism and its possible connections to virulence. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
►▼ Show Figures

Figure 1

18 pages, 2013 KB  
Article
Environmental Regulation of Gut Microbial Networks Links to Growth Variation in Schizopygopsis younghusbandi Across Contrasting Aquaculture Systems
by Wanliang Wang, Zhuangzhuang Wang, Peng Zhang and Jifeng Zhang
Microorganisms 2026, 14(4), 925; https://doi.org/10.3390/microorganisms14040925 - 20 Apr 2026
Viewed by 542
Abstract
Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host–microbiome–environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial [...] Read more.
Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host–microbiome–environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development. Full article
(This article belongs to the Section Veterinary Microbiology)
►▼ Show Figures

Figure 1

37 pages, 1390 KB  
Systematic Review
Unveiling Lichen’s Hidden Arsenal Against Multidrug Resistance: A Systematic Review of Their Essential Oils, Volatile Compounds and Extracts with Antimicrobial Applications
by Yasser Essadki, Soukaina El Amrani Zerrifi, Maria de Fátima Carvalho, Lillian Barros, Vitor Vasconcelos, Alexandre Campos, Fatima El Khalloufi, Brahim Oudra and Rosário Martins
Microorganisms 2026, 14(4), 924; https://doi.org/10.3390/microorganisms14040924 - 20 Apr 2026
Viewed by 908
Abstract
The increase in multidrug resistance in microorganisms and the rise of emergent infectious diseases worldwide is a threat to human and animal health. Therefore, research on new molecules with antibiotic potential is a priority. Lichens have a unique secondary metabolism with relatively untapped [...] Read more.
The increase in multidrug resistance in microorganisms and the rise of emergent infectious diseases worldwide is a threat to human and animal health. Therefore, research on new molecules with antibiotic potential is a priority. Lichens have a unique secondary metabolism with relatively untapped potential, yet their essential oils (EOs) and volatile organic compounds (VOCs) remain a relatively untapped resource. This systematic review was conducted following PRISMA 2020 guidelines, with a comprehensive search performed in the Web of Science database for studies published up to 2023. From 254 identified records, six studies involving nine lichen species (Evernia prunastri, Evernia divaricata, Cladonia rangiformis, Cladonia furcata, Parmotrema perlatum, Lichina pygmaea, Parmelia perlata, Hypogymnia physodes, and Parmelia sulcata) met the eligibility criteria. The synthesized data show that these volatile fractions possess significant antimicrobial potential, with minimum inhibitory concentrations (MICs) generally lower than 1 mg/mL. Major bioactive constituents identified include atraric acid, orsellinates, and various sesquiterpenes. While the current evidence highlights a strong potential of lichen volatiles against pathogens, research is limited to a small fraction of known species. This review identifies a critical gap in testing these compounds directly against MDR clinical isolates and suggests that future research should focus on high-biomass species and the heterologous expression of lichen biosynthetic genes to develop sustainable antimicrobial applications. Full article
(This article belongs to the Special Issue Research on Antimicrobial Activity of Natural Products, Third Edition)
►▼ Show Figures

Graphical abstract

18 pages, 3014 KB  
Article
Characteristics, Assembly Processes and Stability of Bacterial Communities in Aquatic–Terrestrial Ecotone: A Case Study of Danjiangkou Reservoir, China
by Xucong Lyu, Junjun Mei, Haiyan Chen, Huatao Yuan, Jing Dong, Xiaofei Gao, Jingxiao Zhang, Yunni Gao and Xuejun Li
Microorganisms 2026, 14(4), 923; https://doi.org/10.3390/microorganisms14040923 - 19 Apr 2026
Viewed by 645
Abstract
Aquatic–terrestrial ecotones are highly dynamic biogeochemical hotspots where hydrological fluctuations profoundly influence microbial community structure and ecosystem functioning. However, the mechanisms underlying microbial community responses across hydrological gradients remain insufficiently understood. In this study, 16S rRNA gene sequencing was used to comparatively analyze [...] Read more.
Aquatic–terrestrial ecotones are highly dynamic biogeochemical hotspots where hydrological fluctuations profoundly influence microbial community structure and ecosystem functioning. However, the mechanisms underlying microbial community responses across hydrological gradients remain insufficiently understood. In this study, 16S rRNA gene sequencing was used to comparatively analyze bacterial communities in the waterward and landward zones of the drawdown area of the Danjiangkou Reservoir. The results showed that bacterial community composition differed significantly between the two zones, and waterlogging markedly increased bacterial α-diversity. Community variation was primarily associated with key environmental factors, including total phosphorus (TP), soil moisture content (SMC), and nitrate nitrogen (NO3−-N). Compared with the landward zone, stochastic processes contributed more to community assembly in the waterward zone, which also exhibited higher network complexity and topological stability. In addition, several keystone taxa were identified, suggesting their potential roles in maintaining network structure and ecological stability. Functional prediction further revealed distinct metabolic potentials between zones, with enhanced anaerobic and redox-related functions in the waterward zone and predominantly aerobic metabolism in the landward zone. These findings suggest that hydrological fluctuations reshape bacterial community structure and potential ecological functions by jointly regulating water availability and nutrient dynamics. This study provides new insights into microbial ecological processes in reservoir riparian zones and offers a scientific basis for the management of aquatic–terrestrial ecotone ecosystems. Full article
(This article belongs to the Section Environmental Microbiology)
►▼ Show Figures

Graphical abstract

16 pages, 2154 KB  
Article
Nitrate Nitrogen Addition Promotes Soil Aggregate Stability in Larix olgensis Forest
by Tongbao Qu, Yushan Liu, Shilong Xie, Yihao Zhang, Yinglun Sun and Lei Zhao
Microorganisms 2026, 14(4), 922; https://doi.org/10.3390/microorganisms14040922 - 19 Apr 2026
Viewed by 542
Abstract
Nitrogen addition significantly affects soil aggregate stability by altering the aggregate microenvironment. Although the ecological effects of nitrogen addition on soil aggregates have been extensively investigated, studies specifically focusing on the responses of soil aggregate stability in Larix olgensis forest understories remain scarce. [...] Read more.
Nitrogen addition significantly affects soil aggregate stability by altering the aggregate microenvironment. Although the ecological effects of nitrogen addition on soil aggregates have been extensively investigated, studies specifically focusing on the responses of soil aggregate stability in Larix olgensis forest understories remain scarce. The effects of different forms of nitrogen addition (urea (CO(NH2)2), ammonium chloride (NH4Cl), and sodium nitrate (NaNO3)) were investigated at 20 kg N·ha−1·yr−1 across all treatments, and the physicochemical properties, stability, and microbial community composition of soil aggregates were determined to analyze soil aggregate stability. NaNO3 significantly increased soil nutrient contents, promoted the formation of macroaggregates, and significantly enhanced soil aggregate stability. NH4Cl significantly decreased bacterial diversity in microaggregates, while NaNO3 significantly elevated fungal diversity in macroaggregates. CO(NH2)2 and NH4Cl increased the relative abundances of Ascomycota and Proteobacteria in microaggregates, whereas NaNO3 elevated the relative abundances of Mortierellomycota and Gemmatimonadetes in soil aggregates of all particle sizes. These results indicated that NaNO3 was more effective in improving soil aggregate stability and exerted regulatory effects on microbial community structure compared to the other nitrogen forms. These findings can provide a theoretical basis for an in-depth understanding of the microecological processes of forest soil aggregates under the context of nitrogen deposition. Full article
(This article belongs to the Topic Interactions between Plants and Soil Microbes in Natural Ecosystem)
►▼ Show Figures

Figure 1

15 pages, 551 KB  
Article
Candidate Genomic Features Associated with Persistence in Enterococcus spp.
by Catarina Geraldes, Carolina Silva, Filipa Vale, Eva Cunha, Catarina Araújo, Mónica Nunes, Ricardo Dias, Luís Tavares, Joana Fernandes Guerreiro and Manuela Oliveira
Microorganisms 2026, 14(4), 921; https://doi.org/10.3390/microorganisms14040921 - 19 Apr 2026
Viewed by 600
Abstract
Bacterial persistence has been extensively studied as a possible explanation for strain survival under stress; however, in Enterococcus spp., this ability is still an understudied phenomenon. In this study, 40 Enterococcus spp. isolates of human clinical (n = 10), veterinary commensal (n = [...] Read more.
Bacterial persistence has been extensively studied as a possible explanation for strain survival under stress; however, in Enterococcus spp., this ability is still an understudied phenomenon. In this study, 40 Enterococcus spp. isolates of human clinical (n = 10), veterinary commensal (n = 10), veterinary clinical (n = 10) and veterinary environmental (hospital surfaces) (n = 10) origins, were exposed to a high concentration of ciprofloxacin. Time–kill curves were established, after which antimicrobial susceptibility profiles were reassessed. Subsequently, the only presumptive persister was selected for Whole-Genome Sequencing, together with one isolate showing no evidence of persister formation. Comparative genomic analyses were conducted to identify genetic variations between exposed and non-exposed isolates and to explore potential genetic determinants associated with persistence. Observed genetic features present in the persister isolate included toxin–antitoxin systems, a cold-shock protein and the tyrosine-type recombinase/integrase XerC, which may represent putative candidates for further investigation. Interestingly, the majority of toxin–antitoxin system-associated genes were found in plasmids. This study represents an important step towards a better understanding of persistence development in Enterococcus spp.; however, validation using other methodologies such as RNA-sequencing is an important next step. Full article
(This article belongs to the Collection Feature Papers in Antimicrobial Agents and Resistance)
►▼ Show Figures

Graphical abstract

18 pages, 2828 KB  
Article
Functional Identification of AcsR, a MarR Family Transcriptional Regulator Involved in the Regulation of Aromatic Compound-Degrading Genes in Corynebacterium glutamicum
by Qimiao Shi, Runge Xu, Meng Shao, Shuli Wang, Ruixue Wang, Jinshuo Liu, Xiaona Li, Ruobing Wang, Ting Zou, Mingfei Yang, Meiru Si and Can Chen
Microorganisms 2026, 14(4), 920; https://doi.org/10.3390/microorganisms14040920 - 18 Apr 2026
Viewed by 608
Abstract
The MarR (multiple antibiotic resistance regulator) family regulators, which are widely conserved across various organisms, play pivotal roles in metabolism, stress response mechanisms, and virulence factor production. However, the regulatory functions of these factors in the degradation of aromatic compounds within Corynebacterium glutamicum [...] Read more.
The MarR (multiple antibiotic resistance regulator) family regulators, which are widely conserved across various organisms, play pivotal roles in metabolism, stress response mechanisms, and virulence factor production. However, the regulatory functions of these factors in the degradation of aromatic compounds within Corynebacterium glutamicum remain largely uncharacterized. In this study, we identified a MarR-type regulator, designated AcsR (encoded by ncgl2425), which directly represses the expression of the catechol 2,3-dioxygenase gene ncgl2007 (c23o) and the heavy metal (nickel) transport system permease gene ncgl2351, while activating the expression of ncgl2258 encoding an ABC-type C4-dicarboxylate-binding periplasmic protein. AcsR binds specifically as a dimer to a 6 bp inverted repeat sequence, and this binding is disrupted by catechol in vitro. Correspondingly, catechol induces the expression of c23o in vivo. Phenotypic analysis revealed that the ΔacsR mutant exhibited enhanced resistance to multiple aromatic compounds but increased sensitivity to antibiotics, heavy metals, and oxidants. Collectively, these findings demonstrate that AcsR is an important regulator of stress adaptation in C. glutamicum and provide new insights into the regulatory mechanisms of aromatic compound degradation in this industrially important bacterium. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
►▼ Show Figures

Figure 1

18 pages, 7801 KB  
Article
The Role of the RGD Motif of the IdeC Protein in Streptococcus canis in Adhesion and Invasion
by Saoirse Walsh, Alba Garay-Álvarez, Manfred Rohde, Markus Keller, Juan Hermoso, Simone Bergmann and Marcus Fulde
Microorganisms 2026, 14(4), 919; https://doi.org/10.3390/microorganisms14040919 - 18 Apr 2026
Viewed by 695
Abstract
Streptococcus canis is an opportunistic pathogen that colonises the mucosal surfaces and skin of its host. Though predominantly a veterinary pathogen affecting cats and dogs, S. canis has also been identified as the causative agent in severe human disease. IdeC is a secreted [...] Read more.
Streptococcus canis is an opportunistic pathogen that colonises the mucosal surfaces and skin of its host. Though predominantly a veterinary pathogen affecting cats and dogs, S. canis has also been identified as the causative agent in severe human disease. IdeC is a secreted cysteine protease of S. canis that has a high specificity for IgG, cleaving at the hinge region. We show here that the protein binds back to the surface of the bacteria. Additionally, the protein contains a conserved Arg-Gly-Asp (RGD) motif, the minimal peptide sequence required for integrin binding. Several bacterial proteins containing RGD motifs have been implicated in adhesion and invasion of host cells. This RGD motif along with the ability of IdeC to bind back to the bacterial surface after secretion is the basis for this study into a potential secondary function of IdeC in adhesion and/or invasion. We used protein-coated latex beads to investigate the interaction of IdeC with epithelial and endothelial cells and, further, the extent to which the RGD motif is involved in this interaction by utilising an RGD->RGE recombinant protein. We also report here that the deletion of IdeC in S. canis results in a significant reduction in invasion into epithelial cells. Full article
(This article belongs to the Collection Epidemiology and Pathogenicity of Animal-Adapted Streptococci)
►▼ Show Figures

Figure 1

27 pages, 586 KB  
Systematic Review
Endophytic Fungi as a Promising Source of Bioactive Compounds for Wound Healing: A Systematic Review
by Marina Borges Guimarães, Carolina Castello Branco Rangel Helbourn, Gustavo Oliveira Gonçalves, Maria Beatriz Macedo Gonçalves, Damaris Silviera, Yris Maria Fonseca Bazzo, Paula Elaine Diniz do Reis and Pérola Oliveira Magalhães
Microorganisms 2026, 14(4), 918; https://doi.org/10.3390/microorganisms14040918 - 18 Apr 2026
Viewed by 782
Abstract
Endophytic fungi (EF) inhabit internal plant tissue in a mutually beneficial symbiotic relationship with their host plant. EF synthesizes metabolites that are structurally similar or identical to those found in their host plants, which include alkaloids, flavonoids, terpenoids, phenolic compounds, polysaccharides, proteins, lipids, [...] Read more.
Endophytic fungi (EF) inhabit internal plant tissue in a mutually beneficial symbiotic relationship with their host plant. EF synthesizes metabolites that are structurally similar or identical to those found in their host plants, which include alkaloids, flavonoids, terpenoids, phenolic compounds, polysaccharides, proteins, lipids, and organic acids. These molecules have promising therapeutic effects, such as antimicrobial, antioxidant, anti-inflammatory, and antitumor activities. Wound healing has earned attention in recent years because of its relation to chronic pathological diseases. This systematic review scanned the available scientific literature database about the wound-healing properties of EF biomolecules. Amongst 994 works, 24 were screened after abstract and full-text reading. The studies were published between 2014 and 2026, in twelve countries. In total, 16 studies presented in vivo assays, 11 studies presented in vitro assays, and 3 studies presented both assays. Most studies identified molecules, which include melanin, benzoic acid, terpenes, sesquiterpenes (purpurolide), extracellular polysaccharides, exopolysaccharides, carotenoids, fatty acids, proteins, pyrones, quinones, and hydrocarbon acids, among others. A meta-analysis was not conducted due to high heterogeneity across extracts, methodologies, and outcomes. All studies showed wound-healing properties from EF extracts. The findings suggest a positive effect of EF extracts on wound-healing properties and the need for standardized in vitro and in vivo protocols. Full article
(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances, Second Edition)
►▼ Show Figures

Figure 1

20 pages, 2081 KB  
Review
Penicillin-Binding Protein-4 (PBP4) of Staphylococcus aureus and Its Role in β-Lactam Resistance: An Update
by Nidhi Satishkumar and Som S. Chatterjee
Microorganisms 2026, 14(4), 917; https://doi.org/10.3390/microorganisms14040917 - 18 Apr 2026
Viewed by 982
Abstract
Staphylococcus aureus remains to be one of the leading causes of global mortality. The most common class of antibiotics used to treat S. aureus infections are next-generation β-lactams (NGBs), as they are highly efficacious and have low adverse effects. NGB resistance in S. [...] Read more.
Staphylococcus aureus remains to be one of the leading causes of global mortality. The most common class of antibiotics used to treat S. aureus infections are next-generation β-lactams (NGBs), as they are highly efficacious and have low adverse effects. NGB resistance in S. aureus is classically attributed to penicillin-binding protein-2a (PBP2a), but previous studies from our group have also implicated an altered expression of penicillin-binding protein-4 (PBP4) with NGB resistance. PBP4 is the sole low-molecular-mass (LMM) PBP present in S. aureus; it is also the only known LMM PBP with transpeptidase activity, giving it the unique ability to bring about peptidoglycan cross-linking. In this article, we review some of the recent findings from our group, which reveal that mutations associated with PBP4 lead to altered protein expression and NGB resistance in both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) backgrounds. We discuss the clinical relevance of PBP4-associated mutations, particularly in methicillin-resistant lacking mec (MRLM) isolates, as well as the synergistic effect of altered PBP4 and GdpP functions. Finally, this review summarizes the potential role played by PBP4 in S. aureus virulence. Together, we highlight the increasing relevance of PBP4 as a mediator of NGB resistance and discuss its potential as an important factor during infection diagnosis and therapy. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
►▼ Show Figures

Figure 1

16 pages, 1036 KB  
Article
Clinical Predictors and Pathogen Resistance Dynamics in Hospitalized Patients with Urinary Tract Infections: A 2025 Institutional Study
by Ruxandra Laza, Ioana-Melinda Luput-Andrica, Adelina-Raluca Marinescu, Talida-Georgiana Cut, Alexandra Herlo, Andra-Elena Saizu, Andreea-Cristina Floruncut, Narcisa Nicolescu, Romanita Jumanca, Daniela-Ica Rosoha, Voichita Elena Lazureanu and Romosan Ana-Maria
Microorganisms 2026, 14(4), 916; https://doi.org/10.3390/microorganisms14040916 - 18 Apr 2026
Cited by 1 | Viewed by 691
Abstract
The escalating prevalence of antimicrobial resistance (AMR) in Gram-negative uropathogens represents a critical bottleneck in global clinical management. This study evaluated shifting resistance phenotypes and patient risk profiles to identify independent predictors of multidrug resistance (MDR). A comprehensive retrospective analysis was conducted on [...] Read more.
The escalating prevalence of antimicrobial resistance (AMR) in Gram-negative uropathogens represents a critical bottleneck in global clinical management. This study evaluated shifting resistance phenotypes and patient risk profiles to identify independent predictors of multidrug resistance (MDR). A comprehensive retrospective analysis was conducted on a cohort of 318 patients, utilizing statistical modeling to evaluate the impact of demographics, prolonged hospitalization, and comorbidities on MDR. Findings revealed a significant longitudinal exacerbation of resistance since 2012. A majority of Klebsiella pneumoniae strains and nearly all Myroides and Providencia species exhibited high-level resistance to cephalosporin/beta-lactamase inhibitor combinations. While high-dose piperacillin-tazobactam remains a therapeutic alternative, its utility is increasingly constrained by escalating Minimum Inhibitory Concentrations (MICs) for Klebsiella and Escherichia coli (E. coli). Statistical modeling identified advanced age as the primary independent driver, with MDR risk increasing linearly with every additional year of age. Furthermore, indwelling catheterization was strongly associated with resistant infections, while human immunodeficiency virus (HIV) status emerged as a significant cofactor in the selection of highly resistant strains. These findings underscore the need for a critical recalibration of therapeutic frameworks, prioritizing precision-guided stewardship. Pharmacodynamic optimization, through extended or continuous infusion regimens and individualized loading doses, is essential to mitigate the clinical burden of resistant pathogens within vulnerable geriatric cohorts. Full article
(This article belongs to the Special Issue Infectious Disease Surveillance in Romania: Third Edition)
►▼ Show Figures

Figure 1

17 pages, 1666 KB  
Article
Shotgun Metagenomic Characterization of Acne Microbiota Before and After Treatment with a Topical Biotechnological Phytocomplex: Understanding Skin Dysbiosis
by Adrià Cruells, Cristina Eguren, Aymée Robainas Barcia, Helena Martínez, Mohammed Sharaf, Carlos Ruiz, Antonio Sánchez-Baos, Nerea Carrón, Lola Bou, Montse Pérez, Raúl De Lucas and Aurora Guerra-Tapia
Microorganisms 2026, 14(4), 915; https://doi.org/10.3390/microorganisms14040915 - 18 Apr 2026
Viewed by 850
Abstract
This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, [...] Read more.
This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris. Full article
(This article belongs to the Special Issue Skin Microbiome)
►▼ Show Figures

Figure 1

22 pages, 6017 KB  
Article
RdDM-Dependent Epigenetic Regulation Coordinates Systemic Immunity and Compatibility with Trichoderma atroviride in Arabidopsis thaliana
by Maria Montserrat Rosendo-Vargas, Valeria Ávila-Castillo, Kumari Rashmi and Sergio Casas-Flores
Microorganisms 2026, 14(4), 914; https://doi.org/10.3390/microorganisms14040914 - 18 Apr 2026
Cited by 1 | Viewed by 731
Abstract
Epigenetic regulation plays a central role in modulating plant immune responses and interactions with beneficial microbes. In this study, we investigated the contribution of RNA-directed DNA methylation (RdDM) components—DCL3; AGO9; DCL1; and the de novo DNA methyltransferases CMT3, DRM1, and DRM2—to the interaction [...] Read more.
Epigenetic regulation plays a central role in modulating plant immune responses and interactions with beneficial microbes. In this study, we investigated the contribution of RNA-directed DNA methylation (RdDM) components—DCL3; AGO9; DCL1; and the de novo DNA methyltransferases CMT3, DRM1, and DRM2—to the interaction between Arabidopsis thaliana, Trichoderma atroviride, and foliar pathogens. We show that DCL3 and AGO9 differentially regulate basal and inducible immunity, negatively affecting resistance to the necrotrophic fungus Botrytis cinerea, while promoting defense against the hemibiotrophic bacterium Pseudomonas syringae pv. tomato DC3000. Transcriptional analyses revealed that RdDM components modulate the balance between jasmonic acid/ethylene (JA/ET) and salicylic acid (SA) signaling pathways, influencing the amplitude and coordination of defense responses. In addition, DCL3 and DCL1 appear to be required for the full expression of T. atroviride-mediated systemic resistance, whereas AGO9 and DNA methyltransferases contribute to efficient root colonization. Notably, mutants in these pathways displayed enhanced basal resistance but impaired responsiveness to beneficial microbial signals, revealing a trade-off between constitutive defense activation and inducible systemic protection. Consistent with this, alterations in RdDM components were also associated with changes in plant growth dynamics under specific conditions, supporting a role for epigenetic regulation in coordinating growth–defense trade-offs. Together, our findings support a model in which epigenetic regulation controls defense responsiveness, enabling plants to balance immune activation, growth and compatibility toward beneficial microbes. Full article
(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances, Second Edition)
►▼ Show Figures

Figure 1

21 pages, 2518 KB  
Article
Schleiferilactobacillus harbinensis JNDM Postbiotics Alleviate Atopic Dermatitis with Concurrent Changes in Gut Microbiota and Fecal SCFAs
by Zhijie Shi, Ke Li, Jiaqian Liang, Laifa Yan, Yuzhen Guo, Zhenming Lu, Xiaojuan Zhang, Hongyu Xu and Jinsong Shi
Microorganisms 2026, 14(4), 913; https://doi.org/10.3390/microorganisms14040913 - 17 Apr 2026
Viewed by 974
Abstract
Atopic dermatitis (AD) is a chronic inflammatory dermatosis driven by skin barrier dysfunction, immune dysregulation, and gut–skin axis imbalance. While probiotics show promise, the therapeutic potential and mechanisms of topical postbiotics in modulating the gut–skin axis remain understudied. Here, we investigated the efficacy [...] Read more.
Atopic dermatitis (AD) is a chronic inflammatory dermatosis driven by skin barrier dysfunction, immune dysregulation, and gut–skin axis imbalance. While probiotics show promise, the therapeutic potential and mechanisms of topical postbiotics in modulating the gut–skin axis remain understudied. Here, we investigated the efficacy of Schleiferilactobacillus harbinensis JNDM-derived cell-free supernatant (CFS) and lysate (ShL) in a DNFB-induced AD mouse model. Topical application of both CFS and ShL significantly attenuated AD-like symptoms, reduced epidermal thickening, and restored the expression of the barrier protein filaggrin. Immunologically, treatment suppressed the Th2-dominant inflammatory cascade (IL-4, IL-5, IL-13, IL-33, TSLP) and reduced serum IgE and IFN-γ levels. Notably, ShL exhibited superior systemic efficacy, significantly inhibiting mast cell infiltration and reducing the spleen index. 16S rRNA sequencing revealed that topical intervention remotely remodeled the gut microbiota, specifically reversing the depletion of the beneficial genus Alistipes and suppressing the compensatory increase in Odoribacter. This microbial restructuring was accompanied by distinct metabolic changes: ShL treatment resulted in an approximately 4-fold elevation in fecal butyrate concentrations compared with the model group. Correlation analysis further validated a strong positive axis linking Alistipes abundance and butyrate levels to skin barrier integrity. Collectively, our findings demonstrate that S. harbinensis postbiotics—particularly the lysate—ameliorate AD through a dual mechanism of local barrier repair and systemic metabolic modulation via the gut–skin axis, presenting a promising non-steroidal therapeutic strategy. Full article
(This article belongs to the Section Medical Microbiology)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-215
Previous Issue
Next Issue
Back to TopTop