Microorganisms

17 pages, 8801 KB

Open AccessArticle

Bioavailability, Ecological Risk, and Microbial Response of Rare Earth Elements in Sediments of the Remediated Yitong River: An Integrated DGT and Multi-Parameter Assessment

by Yu Zhong, Chanchan Wu, Jiayi E, Yangguang Gu, Hai Chi and Xinglin Du

Microorganisms 2025, 13(11), 2443; https://doi.org/10.3390/microorganisms13112443 (registering DOI) - 24 Oct 2025

Abstract

The expanding use of rare earth elements (REEs) in high-tech industrials has increased their environmental release, raising concerns about their ecological risks. This study employed the Diffusive Gradients in Thin Films (DGT) technique to assess REE bioavailability, spatial distribution, and ecological risks of [...] Read more.

The expanding use of rare earth elements (REEs) in high-tech industrials has increased their environmental release, raising concerns about their ecological risks. This study employed the Diffusive Gradients in Thin Films (DGT) technique to assess REE bioavailability, spatial distribution, and ecological risks of REEs in sediments of the Yitong River, a historically polluted urban river in Changchun, China. Sediment characteristics (organic matter, pH, salinity), nutrient dynamics (N, P), and metal concentrations (Fe, Mn, As, etc.) were analyzed alongside REEs to evaluate their interactions and environmental drivers. Results revealed that REE concentrations (0.453–1.687 μg L⁻¹) were dominated by light REEs (50.1%), with levels an order of magnitude lower than heavily industrialized regions. Ecological risk quotients (RQ) for individual REEs were below thresholds (RQ < 1), indicating negligible immediate risks, though spatial trends suggested urban runoff influences. Probabilistic risk assessment integrating DGT data and species sensitivity distributions (SSD) estimated a low combined toxic probability (2.26%) for REEs and nutrients. Microbial community analysis revealed correlations between specific bacterial (e.g., Clostridium, Dechloromonas) and fungal genera (e.g., Pseudeurotium) with metals and REEs, highlighting microbial sensitivity to pollutant shifts. This study provides a multidimensional framework linking REE bioavailability, sediment geochemistry, and microbial ecology, offering insights for managing REE contamination in urban riverine systems. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 1639 KB

Open AccessArticle

Evaluation of the Oral Microbiome in Patients with Alström and Bardet-Biedl Syndromes and Their Heterozygous Family Members

by Ewa Zmysłowska-Polakowska, Tomasz Płoszaj, Sebastian Skoczylas, Julia Grzybowska-Adamowicz, Aleksandra Palatyńska-Ulatowska, Monika Łukomska-Szymańska and Agnieszka Zmysłowska

Microorganisms 2025, 13(11), 2442; https://doi.org/10.3390/microorganisms13112442 (registering DOI) - 24 Oct 2025

Abstract

Alström (ALMS) and Bardet-Biedl syndromes (BBS) are rare ciliopathies characterized by obesity and hyperglycemia that lead to type 2 diabetes, but also other disorders, including neurodegeneration. However, isolated clinical manifestations can be observed in carriers of heterozygous mutations in the ALMS1 and BBS [...] Read more.

Alström (ALMS) and Bardet-Biedl syndromes (BBS) are rare ciliopathies characterized by obesity and hyperglycemia that lead to type 2 diabetes, but also other disorders, including neurodegeneration. However, isolated clinical manifestations can be observed in carriers of heterozygous mutations in the ALMS1 and BBS genes. Recently, the influence of oral bacteria on the presence of obesity, type 2 diabetes, and neurodegenerative processes has been widely discussed. The purpose of the research project was to analyze the profile of the microbiome in the oral cavity by sequencing the 16S rRNA gene in ALMS/BBS patients and carriers of causative variants in these genes. Oral mucosal swabs were taken from 8 ALMS/BBS patients, 24 family members, 20 obese patients, and 29 healthy individuals. Streptococcus (30.7%), Haemophilus (18.9%), and Prevotella (11%) were the most common bacteria in the study group. Comparison between groups showed a higher abundance of Prevotella, Enterococcus, Eikenella, Capnocytophaga, Parvimonas, Selenomonas, and Corynobacterium, and a lower abundance of Lactobacillus in the study group compared to other groups. The specific profile of the oral microbiome found in patients with variants in the ALMS1 and BBS genes may enable the identification of the modulatory role of the oral microbiome in these disorders and point to new directions for additional therapy for these patients and heterozygous family members in the future. Full article

(This article belongs to the Special Issue Oral Bacteria, Viruses, and Fungi: Oral Health, Disease, and Systemic Links)

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20 pages, 3209 KB

Open AccessArticle

Comparative Genomics and Phylogenomics of Novel Radiation-Resistant Bacterium Paracoccus qomolangmaensis sp. nov. S3-43^T, Showing Pyrethroid Degradation

by Yang Liu, Tuo Chen, Yiyang Zhang, Lu Zhang, Xiaowen Cui, Tian Cheng, Guangxiu Liu, Wei Zhang and Gaosen Zhang

Microorganisms 2025, 13(11), 2441; https://doi.org/10.3390/microorganisms13112441 (registering DOI) - 24 Oct 2025

Abstract

This study focused on the multifunctional characteristics and bioremediation potential of Paracoccus spp. A novel Gram-stain-negative, aerobic, non-motile, ellipsoidal bacterium, named Paracoccus qomolangmaensis S3-43^T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of [...] Read more.

This study focused on the multifunctional characteristics and bioremediation potential of Paracoccus spp. A novel Gram-stain-negative, aerobic, non-motile, ellipsoidal bacterium, named Paracoccus qomolangmaensis S3-43^T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 6109 m above sea level (a.s.l.). To clarify the phylogenetic relationship of this strain within the Paracoccus genus and systematically characterize its features, analyses were conducted using polyphasic taxonomy and comparative genomics. Results revealed two distinct functional characteristics of strain S3-43^T: First, strain S3-43^T exhibits exceptional radiation resistance, particularly tolerance to ionizing radiation. Genome annotation indicates abundant DNA repair and antioxidant-related genes (e.g., vsr, mutL, mutS, ruvC, radA, addA, recA, recN, recO). Second, strain S3-43^T contained several pyrethroids degradation related genes, including cytochrome P450, monooxygenase, and aminopeptidase. The results of the genomic comparison of strain S3-43^T with related type strains also revealed differences and distribution of key genes related to stress response, environmental variables, and bioactive metabolites. Based on the results of the polyphasic taxonomic analysis, strain S3-43^T (=KCTC 8297^T = GDMCC 1.3460^T) should be classified as a novel species of the genus Paracoccus, designated as Paracoccus qomolangmaensis sp. nov. Full article

(This article belongs to the Section Environmental Microbiology)

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25 pages, 3231 KB

Open AccessArticle

Unveiling the 2017 Karenia Bloom in NW Chilean Patagonia by Integrating Remote Sensing and Field Data

by Patricio A. Díaz, Raúl Gormaz, Paula Aguayo, Iván Pérez-Santos, Gonzalo S. Saldías, Rosa I. Figueroa, Pamela A. Fernández, Gonzalo Álvarez, Camilo Rodríguez-Villegas, Camila Schwerter, David Cassis, Rodrigo Vera and Carlos Conca

Microorganisms 2025, 13(11), 2440; https://doi.org/10.3390/microorganisms13112440 (registering DOI) - 24 Oct 2025

Abstract

In southern Chile, harmful algal blooms (HABs) pose a threat to public health, artisanal fisheries, and the aquaculture industry (mussels and salmon). However, little is known about the environmental factors contributing to outbreaks of HABs in fjord systems. In summer 2017, an oceanographic [...] Read more.

In southern Chile, harmful algal blooms (HABs) pose a threat to public health, artisanal fisheries, and the aquaculture industry (mussels and salmon). However, little is known about the environmental factors contributing to outbreaks of HABs in fjord systems. In summer 2017, an oceanographic cruise was carried out to study the physical processes associated with a bloom of the dinoflagellate Karenia spp. in the Gulf of Penas and Taitao Peninsula, Chilean Patagonia, causing a massive mortality of salmon (approximately 170,000 fish, worth USD 390,000). Satellite images from Sentinel-3 were utilized to distinguish between areas with high and low densities of Karenia cells. Cell densities were highest in the waters of the northern Taitao Peninsula (70 × 10³ cells L⁻¹), and lowest at the Gulf of Penas. Support vector classification (SVC) based on bands 1 (400 nm), 2 (412.5 nm), and 6 (560 nm) from the Sentinel-3 images and the normalized fluorescence line height (FLH) classified bloom presence/absence with an 83% coincidence rate. The SVC model correctly identified non-bloom areas, with limited false positives, and successfully captured bloom zones where Karenia densities were highest. These results demonstrate the importance of incorporating satellite tools in the design and implementation of monitoring programs for the early detection of HABs, particularly in remote, difficult-to-access areas. Full article

(This article belongs to the Special Issue Climate Warming and Eutrophication on Phytoplankton Ecology: Effects and Restoration)

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18 pages, 1619 KB

Open AccessArticle

Ferulic Acid Esterase-Producing Inoculant Improves Fiber Degradation and Modulates Microbial Diversity in Corn Bran Silage and Whole-Plant Corn Silage

by Yang Yu, Xiaojun Guo, Haoer Li, Chen Yu, Hao Liu and Wei Guo

Microorganisms 2025, 13(11), 2439; https://doi.org/10.3390/microorganisms13112439 (registering DOI) - 24 Oct 2025

Abstract

Ferulic acid esterase (FAE) catalyzes the hydrolysis of the feruloyl ester bond in lignocellulose, exposing cellulose. The objective of this research was to examine the impacts of Bacillus amyloliquefaciens A30 producing FAE on the fermentation quality, fiber degradation, enzyme activity and microbial diversity [...] Read more.

Ferulic acid esterase (FAE) catalyzes the hydrolysis of the feruloyl ester bond in lignocellulose, exposing cellulose. The objective of this research was to examine the impacts of Bacillus amyloliquefaciens A30 producing FAE on the fermentation quality, fiber degradation, enzyme activity and microbial diversity of corn bran silage and whole-plant corn silage. The experimental treatments were as follows: control (CK), cellulase (CEL), strain A30 (A30) and CEL + A30. Corn bran and whole-plant corn were ensiled for 14 d and 60 d, respectively. The results showed that all additive treatments effectively reduced the pH, neutral detergent fiber, acid detergent fiber and cellulose contents of both corn bran silage and whole-plant corn silage in comparison with control, with CEL + A30 group performing the best effects. Meanwhile, higher FAE activity was detected in A30 and CEL + A30 groups during ensiling. Furthermore, the supplementation of A30 increased the degradation ratio of NDF, ADF, ADL, and cellulose of corn bran silage and whole-plant corn silage. Additionally, treatments with A30 and CEL + A30 increased the abundance of Lactobacillus, and reduced the proportion of pathogenic genera, including Acinetobacter, Enterobacter, and Sphingobacterium. In conclusion, the application of A30 may effectively promote fiber degradation and the stability of microecological system for corn silage. Full article

(This article belongs to the Section Microbial Biotechnology)

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25 pages, 8134 KB

Open AccessArticle

Bacterial Community Characteristics of Kengyilia thoroldiana Rhizosphere Soil in Different Topographic Habitats of the Yellow River Source Region and Their Response to Vegetation-Soil Factors

by Liangyu Lyu, Pei Gao, Yunfei Xing, Jun Ma, Yan Liu, Zhijie Yang, Xin Wang and Jianjun Shi

Microorganisms 2025, 13(11), 2438; https://doi.org/10.3390/microorganisms13112438 - 24 Oct 2025

Abstract

This study aims to uncover the structural and functional characteristics of rhizosphere soil bacterial communities of Kengyilia thoroldiana under five types of topographic habitats in the source region of the Yellow River, and to explore the interaction mechanisms between bacterial communities and plant-soil [...] Read more.

This study aims to uncover the structural and functional characteristics of rhizosphere soil bacterial communities of Kengyilia thoroldiana under five types of topographic habitats in the source region of the Yellow River, and to explore the interaction mechanisms between bacterial communities and plant-soil factors, thereby providing microbiological support for the ecological restoration of Kengyilia thoroldiana artificial grasslands in alpine desert grassland. In this study, high-throughput sequencing technology was employed to compare the species composition, diversity, interaction networks, and functional characteristics of rhizosphere bacterial communities of Kengyilia thoroldiana across five topographic habitats in the source region of the Yellow River. Additionally, Mantel tests and redundancy analysis (RDA)) were conducted to explore the key environmental factors driving the structure of bacterial communities. The results showed that habitat differences significantly influenced the community characteristics of Kengyilia thoroldiana and soil physicochemical properties. The plant height, coverage, biomass, and soil carbon, nitrogen, and phosphorus contents were highest in habitats H2 and H5, while they were lowest in habitats H1 and H3. In contrast, soil pH and electrical conductivity exhibited an opposite trend. At the bacterial community level, the number of operational taxonomic units (OTUs) in habitat H5 reached 1917, with α-diversity indices such as Shannon, Ace, and Chao1 being 6.13, 1820.85, and 1844.80, respectively, significantly higher than those in habitat H1. Cluster analysis revealed that habitat H3 formed a distinct group, while the bacterial community structures in the remaining four habitats were similar. Functional prediction indicated that chemoheterotrophy and aerobic chemoheterotrophy were the dominant functions across all habitats, with functional expression values exceeding 9300 in habitats H2, H4, and H5. Redundancy analysis confirmed that soil pH and SOC were the key factors driving the structure of rhizosphere bacterial communities of Kengyilia thoroldiana. In summary, topographic habitats influence the growth of Kengyilia thoroldiana plant communities by shaping soil environmental heterogeneity, thereby regulating the structure and function of rhizosphere bacteria associated with Kengyilia thoroldiana. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 1776 KB

Open AccessArticle

Neobacillus terrisolis sp. nov. and Neobacillus solisequens sp. nov. Isolated from Soil

by Haoyu Wu, Congguo Ran, Nan Zhou, Xize Zhao, Xingyu Liu, Chengying Jiang, Yinghao Zhao and Ying Lv

Microorganisms 2025, 13(11), 2437; https://doi.org/10.3390/microorganisms13112437 (registering DOI) - 24 Oct 2025

Abstract

Two bacterial strains, designated LXY-1^T and LXY-4^T, were isolated from soil samples collected at a heavy metal smelting plant located in Guangxi, China. Phylogenetic analysis indicated that these strains formed two distinct lineages within the genus Neobacillus. Both strains [...] Read more.

Two bacterial strains, designated LXY-1^T and LXY-4^T, were isolated from soil samples collected at a heavy metal smelting plant located in Guangxi, China. Phylogenetic analysis indicated that these strains formed two distinct lineages within the genus Neobacillus. Both strains were characterized as facultative anaerobic, Gram-positive staining, endospore-forming, non-motile, short-rod bacteria. The major cellular fatty acids identified in these strains included C_16:0, iso-C_15:0, antéiso-C_15:0, and antéiso-C_17:0. The predominant polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG). The average nucleotide identity (ANI) values between the newly isolated strains and their closest phylogenetic relatives, the type strains of the genus Neobacillus, were found to be below 95%, with corresponding digital DNA–DNA hybridization (dDDH) values remaining below 70%. Based on a comprehensive polyphasic taxonomic analysis incorporating chemotaxonomic, phenotypic, phylogenetic, and genomic data, we proposed that strains LXY-1^T and LXY-4^T represent two novel species of the genus Neobacillus, for which the names Neobacillus terrisolis sp. nov. and Neobacillus solisequens sp. nov. are designated. The type strains are LXY-1^T (= CGMCC 30313^T = JCM 37671^T) and LXY-4^T (= CGMCC 1.62901^T = JCM 37672^T), respectively. Full article

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

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16 pages, 2312 KB

Open AccessArticle

Association of Diarrheagenic Escherichia coli Virulence Genes and Antimicrobial Resistance Genes in an Interface Model of Swine Colonization and Human Diarrhea in Mexico

by Elsa M. Tamayo-Legorreta, Eduardo Moreno-Vazquez, Jackeline Cerón-López, Fabian Tellez-Figueroa, Rosa M. Medina-Julián, Hugo López-Gatell and Celia M. Alpuche-Aranda

Microorganisms 2025, 13(11), 2436; https://doi.org/10.3390/microorganisms13112436 - 23 Oct 2025

Abstract

The accelerated spread of antimicrobial resistance, driven by the misuse of antibiotics in the context of ‘One Health’, is a public health concern worldwide due to the increasing number of human infections associated with foodborne and/or environmental pathogens, including multidrug-resistant Escherichia coli ( [...] Read more.

The accelerated spread of antimicrobial resistance, driven by the misuse of antibiotics in the context of ‘One Health’, is a public health concern worldwide due to the increasing number of human infections associated with foodborne and/or environmental pathogens, including multidrug-resistant Escherichia coli (E. coli). Monitoring pathogenic and multidrug-resistant E. coli isolates is essential for sustainable disease management in swine and human diarrhea cases. This study was designed to assess the multidrug resistance (MDR) profiles and virulence-associated gene (pathotypes) frequency of pathogenic and commensal E. coli strains by antimicrobial susceptibility testing and endpoint PCR among 983 E. coli isolates from swine fecal material and 425 stool isolates from human diarrhea cases, obtained from a closely monitored population between March 2015 and April 2016. Our results reveal that >50% of E. coli strains isolated from swine were resistant to nalidixic acid (78.94%), tetracycline (72%), ampicillin (55.54%), and co-trimoxazole (53.91%), and that, in humans, the highest resistance was observed in tetracycline (71.77%), nalidixic acid (65.41%), ampicillin (57.88%), and co-trimoxazole (53.88%). A lower frequency of resistance to ciprofloxacin was demonstrated in both swine (23.4%) and humans (15.3%), and minimal resistance to third-generation cephalosporins, ceftazidime (2.54%), and cefotaxime (2.44%) was observed in swine; however, resistance to these cephalosporins is much higher at 14.6% and 11.53% in humans. Among the pathotypes, EPEC was the most predominant (70.97%) in swine and DAEC (40%) in humans. In addition, pulsed-field gel electrophoresis separates the E. coli isolates into 22 patterns. Pathotypes such as EPEC and EHEC in swine highlight the need for surveillance and control in animal production to prevent zoonotic transmission. These results suggest that swine could act as a reservoir in human infection and that antimicrobial resistance could be transferred to humans from swine. Although we did not find clonal dissemination between the human and swine strains, the spread of similar multi-resistance profiles was observed, thus suggesting that multidrug resistance has been widely selected in this closed environment and may pose a public health risk. Full article

(This article belongs to the Special Issue Virulence Factors and Antibiotic Resistance of Enterobacterales: Third Edition)

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31 pages, 1529 KB

Open AccessReview

Presence of Microorganisms in the Environment: One Health Approach

by Helen Haydee Fernanda Ramirez-Plascencia, Ana Gabriela Colima-Fausto, Karel Cesar Licona-Lasteros, Mariana Díaz-Zaragoza, Gerardo Cazarez-Navarro, Jose Guadalupe Macias-Barragan and Sergio Yair Rodriguez-Preciado

Microorganisms 2025, 13(11), 2435; https://doi.org/10.3390/microorganisms13112435 - 23 Oct 2025

Abstract

The One Health approach offers an integrative framework to understand infectious threats, environmental factors, antimicrobial resistance (AMR) and how their interactions affect the human–animal–environment interface. This review examines the epidemiology, transmission pathways, and mechanisms of microorganisms of public health importance (bacteria, fungi, parasites, [...] Read more.

The One Health approach offers an integrative framework to understand infectious threats, environmental factors, antimicrobial resistance (AMR) and how their interactions affect the human–animal–environment interface. This review examines the epidemiology, transmission pathways, and mechanisms of microorganisms of public health importance (bacteria, fungi, parasites, and viruses). It highlights the interconnectedness of ecosystems, where the environment plays a central role in the dissemination of pathogens, driven by climate change, globalization, agricultural intensification, and habitat degradation. AMR is a major concern, driven by the indiscriminate use of pharmaceuticals in human, veterinary, and agricultural settings, horizontal gene transfer through mobile genetic elements, and microbial evolution. The study of different pathogens is of great importance due to their high prevalence in different ecosystems, their virulence, clinical interest, and mortality rates produced. Some of them are ESKAPE bacteria, Candida auris, Plasmodium falciparum, and emerging viruses such as SARS-CoV-2, which present complex transmission dynamics influenced by ecological and health determinants. The review also addresses the effects of climate change on the persistence and geographic spread of pathogens. Successful implementation of the One Health program requires intersectoral policies, integrated surveillance systems, prudent use of antimicrobials and investment in translational science. Coordinating these strategies is essential to limit the spread of pathogens, protect biodiversity, and save global health in the face of the growing threat of infectious diseases. Full article

(This article belongs to the Section Environmental Microbiology)

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21 pages, 4324 KB

Open AccessArticle

Organic and Inorganic Phosphorus Inputs Shape Wheat Productivity and Soil Bioavailability: A Microbial and Enzymatic Perspective from Long-Term Field Trials

by Zhiyi Zhang, Yafen Gan, Fulin Zhang, Xihao Fu, Linhuan Xiong, Ying Xia, Dandan Zhu and Xianpeng Fan

Microorganisms 2025, 13(11), 2434; https://doi.org/10.3390/microorganisms13112434 - 23 Oct 2025

Abstract

Bioavailable phosphorus is essential for sustaining high crop productivity, yet excessive inorganic P fertilization often leads to P accumulation in stable soil forms, reducing utilization efficiency. Straw serves as an organic P source and enhances P availability by stimulating microbial activity. However, systematic [...] Read more.

Bioavailable phosphorus is essential for sustaining high crop productivity, yet excessive inorganic P fertilization often leads to P accumulation in stable soil forms, reducing utilization efficiency. Straw serves as an organic P source and enhances P availability by stimulating microbial activity. However, systematic studies on how organic P inputs (straw returning) and inorganic P fertilizers regulate soil bioavailable P through microbial and enzymatic processes remain limited. A 16-year field experiment was carried out in a rice–wheat rotation system, including five fertilization treatments: no fertilization (CK), optimized fertilization (OPT), increased N (OPTN), increased P (OPTP), and optimized fertilization combined with straw mulching/returning (OPTM). This study evaluates the impacts of long-term organic and inorganic P sources on soil P fractions, extracellular enzyme activities, and the composition of microbial communities, alongside their collective contributions to crop yield. In this study, based on soil samples collected in 2023, we found that fertilization led to significant increases in Citrate-P and HCl-P, enhanced the activities of β-1,4-glucosidase (BG), β-D-cellobiosidase (CBH), and β-1,4-N-acetylglucosaminidase (NAG), and altered both microbial diversity and co-occurrence network complexity. The OPTM treatment showed the highest yield and improved microbial diversity and network complexity, with Enzyme-P, Citrate-P, and HCl-P increasing by 62.64%, 11.24%, and 9.49%, and BG, CBH, and NAG activities rising by 22.74%, 40.90%, and 18.09% compared to OPT. Mantel tests and random forest analyses revealed significant associations between microbial community and biochemical properties, while partial least squares path modeling (PLS-PM) indicated that inorganic P source enhanced yield primarily through altering soil P dynamics and enzymatic processes, while microbial communities under organic P source acted as key mediators to increase crop productivity. These findings deepen insights into how microbial communities and enzymatic stoichiometry synergistically regulate phosphorus bioavailability and wheat yield, providing a theoretical basis for sustainable fertilization practices in rice–wheat rotation systems. Full article

(This article belongs to the Section Microbiomes)

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13 pages, 1514 KB

Open AccessArticle

Effects of Rumen-Protected Methionine and Lysine on the Fecal Microbiota of Leizhou Goats

by Weishi Peng, Hu Liu, Ke Wang, Yuanting Yang, Anmiao Chen, Meng Zeng, Qun Wu, Jiancheng Han, Mao Li and Hanlin Zhou

Microorganisms 2025, 13(11), 2433; https://doi.org/10.3390/microorganisms13112433 - 23 Oct 2025

Abstract

This study investigates the effects of rumen-protected methionine and lysine (RPML) on the fecal microbiota of Leizhou goats, focusing on growth performance and fecal microbial community composition. A total of 10 three-month female Leizhou goats (9.90 ± 0.08 kg) were randomly assigned to [...] Read more.

This study investigates the effects of rumen-protected methionine and lysine (RPML) on the fecal microbiota of Leizhou goats, focusing on growth performance and fecal microbial community composition. A total of 10 three-month female Leizhou goats (9.90 ± 0.08 kg) were randomly assigned to one of two dietary treatments: a CON group fed a basal diet and an RPML group receiving the basal diet supplemented with 1.5 g/d/head of rumen-protected methionine and 4.5 g/d/head of rumen-protected lysine. Results indicated that RPML significantly enhanced average daily gain (ADG) and final body weight (FBW), as well as significantly decreased the ratio of dry matter intake (DMI) to ADG (p < 0.001). Fecal microbiota composition showed a decrease in abundance of UCG-005, Phascolarctobacterium, and norank_f__Bacteroidales_RF16_group and an increase in others like Christensenellaceae R-7 and unclassified_c__Clostridia (p < 0.05). Moreover, the correlations between the abundance of certain bacterial genera and the concentrations of short-chain fatty acids (SCFAs) suggest that the modulation of the gut microbiota is associated with improved growth performance and feed efficiency in Leizhou goats, indicating that RPML supplementation can modulate the gut microbiota to improve growth performance and feed efficiency in Leizhou goats. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 1907 KB

Open AccessArticle

Outer Membrane Vesicles, Lipidome, and Biofilm Formation in the Endophyte Enterobacter Cloacae SEA01 from Agave Tequilana

by Kátia R. Prieto, Hellen P. Valério, Adriano B. Chaves-Filho, Marcos Y. Yoshinaga, Sayuri Miyamoto, Fernanda M. Prado, Itzel Zaizar-Castañeda, Paul Montaño-Silva, América Martinez-Rodriguez, Mario Curiel, Marisa H. G. Medeiros, Flavia V. Winck, Paolo Di Mascio and Miguel J. Beltran-Garcia

Microorganisms 2025, 13(11), 2432; https://doi.org/10.3390/microorganisms13112432 - 23 Oct 2025

Abstract

Bacterial outer-membrane vesicles (OMVs) mediate stress tolerance, biofilm formation, and interkingdom communication, but their role in beneficial endophytes remains underexplored. We isolated 11 non-redundant isolates associated with Bacillus, Enterococcus, Kosakonia and Kocuria from Agave tequilana seeds, identified by MALDI-TOF MS and [...] Read more.

Bacterial outer-membrane vesicles (OMVs) mediate stress tolerance, biofilm formation, and interkingdom communication, but their role in beneficial endophytes remains underexplored. We isolated 11 non-redundant isolates associated with Bacillus, Enterococcus, Kosakonia and Kocuria from Agave tequilana seeds, identified by MALDI-TOF MS and 16S rRNA gene sequencing. We focused on the catalase-negative Enterobacter cloacae SEA01, which exhibits plant-promoting traits and support agave growth under nutrient-poor microcosms. In addition, this endophyte produces OMVs. Time-resolved SEM documented OMV release and cell aggregation within 9 h, followed by mature biofilms at 24 h with continued vesiculation. Purified OMVs (≈80–300 nm) contained extracellular DNA and were characterized by dynamic light scattering and UHPLC–ESI–QTOF-MS lipidomics. The OMV lipidome was dominated by phosphatidylethanolamine (~80%) and was enriched in monounsaturated fatty acids (16:1, 18:1), while the stress-associated cyclopropane fatty acids (17:1, 19:1) were comparatively retained in the whole-cell membranes; OMVs also exhibited reduced ubiquinone-8. SEA01 is catalase-negative, uncommon among plant-associated Enterobacter, suggesting a testable model in which oxidative factors modulate OMV output and biofilm assembly. These may have implications for recognition and redox signaling at the root interface. Future works should combine targeted proteomics/genomics with genetic or chemical disruption of catalase/OMV pathways. Full article

(This article belongs to the Section Plant Microbe Interactions)

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32 pages, 3539 KB

Open AccessArticle

Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China

by Man Guo, Dong Liu, Zhilan Xia, Tao Xie, Luofeng Su, Jesus Pérez-Moreno and Fuqiang Yu

Microorganisms 2025, 13(11), 2431; https://doi.org/10.3390/microorganisms13112431 (registering DOI) - 23 Oct 2025

Abstract

Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. [...] Read more.

Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5–V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R² = 0.46, p < 0.001) was a stronger structuring force than tissue type (R² = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom. Full article

(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health: Second Edition)

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17 pages, 5574 KB

Open AccessArticle

Screening and Genomic Analysis of Bacillus velezensis R12 as a Biocontrol Agent Against Fusarium oxysporum Causing Wilt in Longya Lily (Lilium brownii var. viridulum)

by Huiying Guo, Yushan Huang, Zihan Cheng, Qinyuan Zheng, Qingxiu Li, Mengting Zhan, Hongjie Ji, Kuan Zhao, Du Zhu and Shaofang Liu

Microorganisms 2025, 13(11), 2430; https://doi.org/10.3390/microorganisms13112430 - 23 Oct 2025

Abstract

Longya Lily (Lilium brownii var. viridulum) bulb rot, a devastating soil-borne disease caused by Fusarium oxysporum f. sp. lilii (Fol L1-1), severely compromises yield and quality of this economically significant crop. In this study, strain R12 was isolated from the rhizosphere [...] Read more.

Longya Lily (Lilium brownii var. viridulum) bulb rot, a devastating soil-borne disease caused by Fusarium oxysporum f. sp. lilii (Fol L1-1), severely compromises yield and quality of this economically significant crop. In this study, strain R12 was isolated from the rhizosphere soil of asymptomatic Longya lily plants and identified as Bacillus velezensis. The strain significantly disrupted the spore germination and hyphal morphology of Fol L1-1. In pot experiments, R12 not only effectively suppressed disease development but also promoted plant growth, a trait potentially linked to its indole-3-acetic acid (IAA) production capacity. Genomic analysis revealed a 4,015,523 bp circular chromosome (46.42% GC content) harboring gene clusters for the synthesis of diverse secondary metabolites, including surfactin, fengycin, difficidin, and bacillibactin. These findings highlight the potential of B. velezensis R12 as a biocontrol agent and provide insights into its mechanisms for suppressing phytopathogens and promoting plant growth. Full article

(This article belongs to the Section Microbial Biotechnology)

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21 pages, 2744 KB

Open AccessArticle

Genomic Surveillance and Resistance Profiling of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates: Clonal Diversity and Virulence Insights

by Maria Vittoria Ristori, Ilaria Pirona, Lucia De Florio, Sara Elsa Aita, Gabriele Macari, Silvia Spoto, Raffaele Antonelli Incalzi and Silvia Angeletti

Microorganisms 2025, 13(11), 2429; https://doi.org/10.3390/microorganisms13112429 - 23 Oct 2025

Abstract

Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen that poses critical challenges in hospital settings due to its environmental resilience and high resistance to antibiotics. Genomic surveillance has become essential for identifying transmission patterns, guiding antimicrobial stewardship, and informing infection control policies. We conducted [...] Read more.

Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen that poses critical challenges in hospital settings due to its environmental resilience and high resistance to antibiotics. Genomic surveillance has become essential for identifying transmission patterns, guiding antimicrobial stewardship, and informing infection control policies. We conducted whole-genome sequencing on 44 A. baumannii isolates collected between 2022 and 2023 from diverse wards in an Italian hospital. Illumina-based sequencing was followed by a comprehensive bioinformatics pipeline, including genome assembly, taxonomic validation, MLST, SNP-based phylogeny, pan-genome analysis, antimicrobial resistance (AMR) gene profiling, and virulence factor prediction. Most isolates were classified as ST2; SAMPLE-34 was ST1 and genetically distinct. Phylogenetic analysis revealed four clonal clusters with cluster-specific AMR and accessory gene content. The pan-genome included 5050 genes, with notable variation linked to hospital ward origin. ICU and internal medicine strains carried higher loads of AMR genes, especially against aminoglycosides, β-lactams, and quinolones. Virulence profiling highlighted widespread immune evasion mechanisms; “Acenovactin” was predominant, while some isolates lacked key adhesion or toxin factors. Our findings underscore the clinical relevance of integrating genomic epidemiology into routine hospital surveillance. Identifying clonal clusters and resistance signatures supports real-time outbreak detection, risk stratification, and targeted infection prevention strategies. Full article

(This article belongs to the Collection Feature Papers in Antimicrobial Agents and Resistance)

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14 pages, 4699 KB

Open AccessArticle

Impact of Diet on Gut Microbiota in Diverticular Disease of the Colon: An Exploratory Retrospective Study

by Antonio Tursi, Giorgia Procaccianti, Federica D’Amico, Rudi De Bastiani, Leonardo Allegretta, Natale Antonino, Elisabetta Baldi, Carlo Casamassima, Giovanni Casella, Mario Ciuffi, Marco De Bastiani, Lorenzo Lazzarotto, Claudio Licci, Maurizio Mancuso, Antonio Penna, Giuseppe Pranzo, Guido Sanna, Cesare Tosetti, Maria Zamparella, Marcello Picchio and Silvia Turroni Show full author list Hide full author list

Microorganisms 2025, 13(11), 2428; https://doi.org/10.3390/microorganisms13112428 - 23 Oct 2025

Abstract

Symptomatic uncomplicated diverticular disease (SUDD) is the primary clinical manifestation of diverticular disease (DD). Although gut microbiota (GM) perturbation and dietary habits are considered important factors in the development of the disease, there is currently a lack of data on the potential relationship [...] Read more.

Symptomatic uncomplicated diverticular disease (SUDD) is the primary clinical manifestation of diverticular disease (DD). Although gut microbiota (GM) perturbation and dietary habits are considered important factors in the development of the disease, there is currently a lack of data on the potential relationship between diet, GM profile and SUDD. An exploratory retrospective study was conducted in a SUDD cohort of 47 patients to investigate this relationship; a diverticulosis cohort of 19 patients served as the control group. Patients were stratified by their self-reported dietary habits, i.e., Mediterranean diet, predominantly plant-based diet or omnivorous diet. GM was profiled using 16S rRNA amplicon sequencing of fecal swabs. SUDD patients following a Mediterranean or predominantly plant-based diet showed higher alpha diversity and enrichment of known fibre degraders and short-chain fatty acid producers, such as members of the Lachnospiraceae, Ruminococcaceae, Oscillospiraceae and Prevotellaceae families. This suggests that their gut (and whole-body) health is less impaired. In contrast, those following an omnivorous diet showed an increased presence of pro-inflammatory taxa, including the mucus degrader R. torques, which suggests impaired gut barrier function and potential systemic implications. Similar associations between GM profile and dietary habits were found when considering SUDD patients with moderate abdominal pain severity (according to visual analogue scale, VAS) and those scored as DICA 1 according to the endoscopic severity of the disease. However, no such associations or trends were observed in SUDD patients scored as DICA 2, which suggests that diet may be unable to impact GM dysbiosis as SUDD severity increases. Despite the study’s limitations, primarily its retrospective design and related biases, our findings suggest that other GM modulation tools should be employed in more severe cases of SUDD to reverse dysbiosis while alleviating symptoms. Full article

(This article belongs to the Special Issue Advances in Host-Gut Microbiota)

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19 pages, 5986 KB

Open AccessArticle

Potential Biomarkers and Underlying Pathogenesis of Mycoplasma synoviae Infection: Insights from Metabolomics Analysis

by Xiaona Wei, Mengyao Sun, Kuan Zhang, Jing Wen, Zhuanqiang Yan, Yangxue Liu and Lianxiang Wang

Microorganisms 2025, 13(11), 2427; https://doi.org/10.3390/microorganisms13112427 - 23 Oct 2025

Abstract

Mycoplasma synoviae (MS) is a prominent poultry pathogen that has caused considerable economic pressure on the poultry industry. Although we have a good understanding of MS infection, research is still lacking on the pathogenicity of MS and host-MS interactions, especially the metabolic basis [...] Read more.

Mycoplasma synoviae (MS) is a prominent poultry pathogen that has caused considerable economic pressure on the poultry industry. Although we have a good understanding of MS infection, research is still lacking on the pathogenicity of MS and host-MS interactions, especially the metabolic basis of MS infection. In this study, a lethal MS strain ZX313 was identified. Then, untargeted metabolomic analysis was performed on the plasma of 18 SPF chickens infected with the ZX313 strain and the low-virulence strain SD2. A total of 699 and 720 significantly differentially abundant metabolites (SDMs) were detected after ZX313 and SD2 infection, respectively, among which 95 and 116 SDMs were group-specific. Metabolic pathway enrichment analysis revealed that MS infection significantly disturbed host amino acid, nucleotide and lipid metabolism. Moreover, the differential expression of amino acid metabolism in different virulence groups may be related to the severity of the disease and the pathogenicity of MS. A total of 20 plasma metabolites were identified to exhibit a significant correlation with disease severity, with an area under the curve of 0.986. These findings demonstrate that the host’s systemic metabolism undergoes significant changes following MS infection, providing valuable references for elucidating infection-related metabolic alterations and their association with disease severity. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 784 KB

Open AccessArticle

Quantitative Estimation of Low-Abundance Targets in Engineered Systems and Environmental Samples: Comparative Study Between Droplet Digital PCR and Real-Time PCR

by Alessia Ayala Alban, Barbara Tonanzi, Simona Crognale, Francesca Di Pippo and Simona Rossetti

Microorganisms 2025, 13(11), 2426; https://doi.org/10.3390/microorganisms13112426 - 23 Oct 2025

Abstract

Real-Time PCR (qPCR) is an extensively used biomolecular tool for the detection and quantification of nucleic acids for a variety of applications, spanning from clinical to environmental settings. However, qPCR relies on an external calibration curve and can be susceptible to inhibition caused [...] Read more.

Real-Time PCR (qPCR) is an extensively used biomolecular tool for the detection and quantification of nucleic acids for a variety of applications, spanning from clinical to environmental settings. However, qPCR relies on an external calibration curve and can be susceptible to inhibition caused by pollutants that are commonly found in environmental samples. More recently, droplet digital PCR (ddPCR) was proven to be the method of choice for detection and quantification when a target is present at a low abundance. While it has been extensively utilized in clinical studies, only a small amount of data is available for complex samples, which are often characterized by a low target concentration and high abundances of non-target and PCR inhibitors. In this study, ddPCR and qPCR assays were performed on the same DNA serial dilutions with both Eva/SYBR Green and TaqMan chemistry. The comparative analysis was conducted on seven different samples taken from environmental and engineered settings. Ammonia-oxidizing bacteria (AOB) were chosen as the target, as they are ubiquitous and widespread and responsible for a fundamental environmental process in the global biogeochemical nitrogen cycle and in engineered settings such as wastewater treatment plants (WWPTs). ddPCR produced precise, reproducible, and statistically significant results in all samples, also showing an increased sensitivity to detecting AOB in complex samples characterized by low levels of the target and low target/non-target ratios. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 2194 KB

Open AccessArticle

Driving Effects of Soil Microbial Diversity on Soil Multifunctionality in Carya illinoinensis Agroforestry Systems

by Cheng Huang, Mengyu Zhou, Fasih Ullah Haider, Lin Wu, Jia Xiong, Songling Fu, Zhaocheng Wang, Fan Yang and Xu Li

Microorganisms 2025, 13(11), 2425; https://doi.org/10.3390/microorganisms13112425 - 23 Oct 2025

Abstract

Sustainable soil management requires striking a balance between productivity and soil health. While agroforestry practices are known to improve soil health and ecosystem functions, the contribution of microbial diversity to maintaining multifunctional soil processes in pecan (Carya illinoinensis) cultivation has yet [...] Read more.

Sustainable soil management requires striking a balance between productivity and soil health. While agroforestry practices are known to improve soil health and ecosystem functions, the contribution of microbial diversity to maintaining multifunctional soil processes in pecan (Carya illinoinensis) cultivation has yet to be fully elucidated. This study examined microbial diversity, soil functions, and multifunctionality across different pecan intercropping setups. We compared a monoculture pecan plantation with three agroforestry models: pecan–Paeonia suffruticosa–Hemerocallis citrina (CPH), pecan–P. suffruticosa (CPS), and pecan–P. lactiflora (CPL). We employed high-throughput sequencing (16S and ITS) to determine the soil bacterial and fungal communities and analyzed the species diversity, extracellular enzyme activities, and physicochemical properties. Soil multifunctionality (SMF) was evaluated using 20 indicators for nutrient supply, storage, cycling, and environmental regulation. Agroforestry increased soil fungal diversity and improved multifunctionality when compared to monoculture. The CPS and CPH models were the most beneficial, increasing multifunctionality by 0.74 and 0.55 units, respectively. Structural equation modeling revealed two key pathways: bacterial diversity significantly enhanced nutrient cycling and environmental regulation, whereas fungal diversity primarily promoted nutrient cycling. These pathways together delivered clear gains in multifunctionality. Random forest analysis identified key predictors (total nitrogen, total carbon, available potassium, β-1,4-N-acetylglucosaminidase, and alkaline phosphatase), highlighting the joint importance of nutrients and microbial enzymes. Our results demonstrate that selecting species in pecan agroforestry alters microbial communities and activates key functions that support soil health and long-term resilience. Hence, pecan agroforestry maintains SMF through microbial processes, with CPS showing the strongest effect. These results can inform species selection and encourage broader testing for resilient, biodiversity-based farming practices. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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15 pages, 2389 KB

Open AccessArticle

In Vitro Assessment of Gold Nanoparticles Synthesized by Gamma Irradiation for Antimicrobial and Anticancer Effects

by Doaa E. El-Hadedy, Nesreen A. Safwat, Hoda H. Saleh and Zakaria I. Ali

Microorganisms 2025, 13(11), 2424; https://doi.org/10.3390/microorganisms13112424 - 23 Oct 2025

Abstract

The emergence of multidrug-resistant microbes presents a serious public health threat that requires new antimicrobial methods. A potential solution to combat resistance involves using metal nanoparticles that possess improved biological characteristics. The researchers have synthesized gold nanoparticles (Au-NPs) using gamma irradiation of Polyacrylamide [...] Read more.

The emergence of multidrug-resistant microbes presents a serious public health threat that requires new antimicrobial methods. A potential solution to combat resistance involves using metal nanoparticles that possess improved biological characteristics. The researchers have synthesized gold nanoparticles (Au-NPs) using gamma irradiation of Polyacrylamide (PAM) at 5, 10, and 15 kGy doses and through Au/chitosan nanocomposite production methods. They have also assessed the antimicrobial and anticancer functions of the produced nanomaterials by testing them on various microorganisms and cancer cell lines. Gold nanoparticles exhibited strong antibacterial effects against multiple Gram-positive bacterial strains, including Bacillus subtilis, Micrococcus luteus, Staphylococcus epidermidis, Staphylococcus aureus, and Streptococcus mutans, as well as methicillin-resistant Staphylococcus aureus (MRSA). Escherichia coli showed a significant inhibition zone of 23 mm, and Salmonella spp. showed similar inhibition. The inhibition zone for Klebsiella pneumoniae ATCC 13883 revealed resistance. The Au-NPs/chitosan composite showed moderate antifungal effectiveness against Syncephalis racemosum and Aspergillus niger alongside Candida albicans and several other tested fungi. Au-NPs showed cytotoxicity to breast MCF-7 cells, as well as liver HepG-2 cells and colon HCT-116 cells. The combination of Au-NPs with chitosan demonstrated limited effectiveness in countering hepatitis A virus (HAV-10) and herpes simplex virus type 1 (HSV-1). The combination of gamma-irradiated Au-NPs with biopolymers like chitosan demonstrates significant promise in antimicrobial and anticancer biomedical applications. Full article

(This article belongs to the Section Medical Microbiology)

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16 pages, 3852 KB

Open AccessArticle

Microbial Community Restructuring and Functional Response in Giant Duckweed (Spirodela polyrhiza) Fronds Driven by Cadmium Stress

by Bingliang Liu, Chen Yang, Xin Wan, Suming Chen, Yang Tao, Qiang Li, Hai Zhao and Xinhui Wang

Microorganisms 2025, 13(11), 2423; https://doi.org/10.3390/microorganisms13112423 - 22 Oct 2025

Abstract

As a typical heavy metal pollutant, cadmium (Cd) poses significant threats to ecosystems and human health. Giant duckweed (Spirodela polyrhiza), a small aquatic plant characterized by rapid growth and efficient heavy metal accumulation, holds great promise for phytoremediation. However, the mechanisms [...] Read more.

As a typical heavy metal pollutant, cadmium (Cd) poses significant threats to ecosystems and human health. Giant duckweed (Spirodela polyrhiza), a small aquatic plant characterized by rapid growth and efficient heavy metal accumulation, holds great promise for phytoremediation. However, the mechanisms by which S. polyrhiza enriches Cd—particularly the contributions of its surface-associated microbiota—remain poorly understood. In this study, S. polyrhiza fronds were exposed to 0, 1, and 10 μM Cd, and we observed a concentration-dependent increase in the abundance of epiphytic microorganisms on the frond surfaces. High-throughput 16S rRNA gene sequencing revealed that Cd stress significantly altered the diversity of the frond-epiphytic bacterial community. Notably, the relative abundances of the genera Herbaspirillum, Enterobacter, and Pantoea increased significantly with rising Cd concentrations. Functional prediction using PICRUSt2 indicated enrichment under Cd stress of specific traits—such as the nitrate/nitrite transporter NarK, signal transduction mechanisms, and ion channel proteins—suggesting these taxa may actively participate in Cd uptake and tolerance. Together, our results reveal a synergistic S. polyrhiza–microbiome response to Cd and identify taxa/functions as targets and biomarkers for microbe-augmented remediation. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)

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23 pages, 2825 KB

Open AccessReview

Metabolic Engineering of Yeasts for the Production of the Triterpene Squalene: Current Status and Future Prospective

by Shasha Zuo, Xinjia Tan, Jiwei Mao, Fanglin Hu, Jiaxu Chen, Liusha Fan, Qiyuan Lu, Yifei Zhao, Yongtong Wang, Zhiqiang Xiao, Siqi Zhang, Yang Shan, Juan Liu and Fuhua Fu

Microorganisms 2025, 13(11), 2422; https://doi.org/10.3390/microorganisms13112422 - 22 Oct 2025

Abstract

Squalene, a linear triterpene compound characterized by its distinctive isoprenoid backbone with six transisoprene units, is widely used in the medicinal, nutraceutical, and cosmetic industries. The escalating global demand for squalene, coupled with growing ethical concerns over shark-derived sources and the inherent limitations [...] Read more.

Squalene, a linear triterpene compound characterized by its distinctive isoprenoid backbone with six transisoprene units, is widely used in the medicinal, nutraceutical, and cosmetic industries. The escalating global demand for squalene, coupled with growing ethical concerns over shark-derived sources and the inherent limitations of plant extraction (low yield) and chemical synthesis (environmental burden), has propelled microbial biosynthesis as a sustainable alternative. While substantial progress has been made in elucidating the mevalonate pathway and regulatory mechanisms of squalene biosynthesis, achieving industrially viable titers through microbial platforms remains an unresolved challenge. This review systematically summarizes recent advances in squalene biosynthesis using yeast chassis, with a focus on metabolic engineering strategies implemented in Saccharomyces cerevisiae and Yarrowia lipolytica. Furthermore, we elaborated on how squalene yields a diverse array of downstream derivatives through intricate enzymatic reactions. These derivatives—including triterpenoid saponins, triterpenoid acids, and steroids—exhibit significant applications in the pharmaceutical, nutraceutical, and cosmetic sectors. By integrating systems metabolic engineering with emerging synthetic biology tools, this work provides a roadmap for advancing strain engineering toward economically feasible squalene biomanufacturing. Full article

(This article belongs to the Topic Microbial Cell Factories for Natural Products)

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10 pages, 923 KB

Open AccessArticle

Molecular Epidemiology and Seroepidemiology of Oz Virus Infection in Ticks and Wild Boars in Ibaraki Prefecture, Japan

by Shuichi Osawa, Hirokazu Kimura, Sakurako Abe, Noriko Nagata, Eri Ueno, Hideki Ebihara, Ryusuke Kimura and Tetsuya Furuya

Microorganisms 2025, 13(11), 2421; https://doi.org/10.3390/microorganisms13112421 - 22 Oct 2025

Abstract

Oz virus (OZV), an emerging negative-sense single-stranded RNA virus classified under the family Orthomyxoviridae and genus Thogotovirus, was first isolated from Amblyomma testudinarium ticks in Ehime Prefecture, Japan, in 2013. Moreover, a single fatal case in an elderly individual, suspected to be [...] Read more.

Oz virus (OZV), an emerging negative-sense single-stranded RNA virus classified under the family Orthomyxoviridae and genus Thogotovirus, was first isolated from Amblyomma testudinarium ticks in Ehime Prefecture, Japan, in 2013. Moreover, a single fatal case in an elderly individual, suspected to be associated with OZV infection, was reported in Ibaraki Prefecture in 2023. Given these circumstances, this study was conducted to investigate the molecular epidemiology and seroepidemiology of OZV in Ibaraki Prefecture, Japan. From April to November 2023, a total of 2430 ticks were collected at 19 sites. The OZV RNA was detected in one A. testudinarium nymph. Additionally, among 934 wild boar serum samples collected between 2019 and 2023, one sample tested positive for OZV RNA. Neutralizing antibody assays revealed that 243 samples (26.0%) obtained from wild boars were seropositive, indicating widespread exposure among wild boars. Antibody prevalence and titers were highest in the central–western mountainous region, suggesting an active transmission hotspot. Sequence analysis of the OZV viral RNA detected from one tick sample and one wild boar serum revealed that a 212 bp fragment of segment 4 and a 261 bp fragment of segment 5 were 100% identical to a human-derived strain isolated in the same prefecture, suggesting the circulation of a single viral lineage within the local environment. These findings represent the first report demonstrating the circulation of OZV in the natural environment in Ibaraki Prefecture, implicating A. testudinarium as the principal vector and wild boars as a potential source of OZV infection These results suggest that OZV should be considered a potential emerging zoonotic pathogen. Further seroepidemiological studies among residents are warranted to assess the risk of human infection in the region. Full article

(This article belongs to the Special Issue One Health Research on Zoonotic Tick-Borne Pathogens)

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14 pages, 2092 KB

Open AccessArticle

Community Structure of Labyrinthulomycetes Protists in Zostera marina Seagrass Beds of Northern China

by Yibo Fu, Tianle Chu, Xinlong An, Yike He, Chen Dai, Shibo Li, Yining Gu, Zhaoge Guo, Yingbo Duan and Qiuzhen Wang

Microorganisms 2025, 13(11), 2420; https://doi.org/10.3390/microorganisms13112420 - 22 Oct 2025

Abstract

Labyrinthulomycetes protists play important roles in organic matter decomposition and nutrient cycling in marine ecosystems. To better understand their distribution and potential ecological functions in Caofeidian seagrass beds of the Bohai Sea, we conducted high-throughput sequencing of samples collected from multiple habitats, including [...] Read more.

Labyrinthulomycetes protists play important roles in organic matter decomposition and nutrient cycling in marine ecosystems. To better understand their distribution and potential ecological functions in Caofeidian seagrass beds of the Bohai Sea, we conducted high-throughput sequencing of samples collected from multiple habitats, including leaves (L), rhizosphere (R), sediments (S), and seawater (W). Our results revealed distinct habitat-specific patterns of community composition. Oblongichytrium and Stellarchytrium were dominant in certain samples, exhibiting clear differences across stations. Oblongichytrium showed particularly high abundance in leaf and seawater samples, likely reflecting the availability of particulate and dissolved substrates enriched by seagrass beds. In the rhizosphere, Sicyoidochytrium, Stellarchytrium and Labyrinthula were enriched, whereas unclassified Labyrinthulomycetes and Thraustochytriaceae lineages prevailed in seawater and specific leaf samples. Notably, a substantial proportion of sequences corresponded to unclassified lineages, potentially representing uncultured “seagrass-associated” taxa. Compared with previous reports, our study revealed both a significantly higher abundance of Stellarchytrium and a remarkably greater proportion of unclassified lineages, suggesting unique features of Labyrinthulomycetes communities in the Caofeidian seagrass ecosystem. These findings provide new insights into the ecological roles of Labyrinthulomycetes in seagrass beds and offer an important reference for future taxonomic and functional studies of this group. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 3477 KB

Open AccessArticle

Metagenomic Analysis of Distribution Characteristics and Driving Mechanisms of Antibiotic Resistance Genes, Virulence Factors, and Microbial Communities in Rice Seedling Cultivation Soils

by Yu Zhong, Chanchan Wu, Zhipeng Yao, Xinyang Li, Hai Chi, Tao Wu and Xinglin Du

Microorganisms 2025, 13(11), 2419; https://doi.org/10.3390/microorganisms13112419 - 22 Oct 2025

Abstract

The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil’s pivotal role as [...] Read more.

The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil’s pivotal role as a primary reservoir for ARGs and the inherent potential for these genes to translocate into agricultural produce, this study endeavors to evaluate the distribution patterns of ARGs and virulence factors (VFs) in soils designated for rice seedling cultivation. This study employed metagenomic sequencing to analyze antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial communities in four rice seedling cultivation soils. The results revealed significant variations in microbial alpha diversity, community structure, ARGs, and VFs across soils, with multidrug resistance, glycopeptide resistance, and tetracycline resistance genes predominating. The inclusion of organic matter increased the complexity of the microbial network by increasing the levels of ARGs and VFs. Neutral community model analysis revealed that stochastic processes predominantly governed the assembly of microbial taxa, ARGs, and VFs, though ARGs were subject to stronger deterministic pressures. These communities were shaped by the pH, nitrogen, organic carbon content, electrical conductivity, and salinity of the soil. The core Actinobacteria genera acted as key vectors for ARGs and VFs dissemination. Our findings elucidate the complex interactions between microbes, ARGs, and VFs in cultivation soils and highlight that organic matter amendment, while enhancing fertility, can also increase the potential spread of microbial risk genes, underscoring the need for monitoring and managing ARGs and VFs in agricultural soils to mitigate public health risks. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)

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4 pages, 186 KB

Open AccessEditorial

Borreliosis and Other Tick-Borne Diseases in the Northern and Southern Hemispheres

by Giusto Trevisan, Serena Bonin and Nestor Oscar Stanchi

Microorganisms 2025, 13(11), 2418; https://doi.org/10.3390/microorganisms13112418 - 22 Oct 2025

Abstract

Lyme disease (LD) is an anthropozoonosis caused by the spirochaete Borrelia burgdorferi sensu lato (Bbsl), which is transmitted by ticks belonging to the genus - Ixodes [...] Full article

(This article belongs to the Special Issue Borreliosis and Other Tick-Borne Diseases in the Northern and Southern Hemispheres)

21 pages, 10923 KB

Open AccessArticle

Incidence of Crown and Root Rot in Rhododendron simsii Caused by Phytopythium vexans in China and Screening of Endophytic Bacteria for Biocontrol

by Zhuo Liu, Yang Sun, Zhuoma Yongcuo, Xiaorui Zhang, Guibin Wang, Yuhua Liu and Tingting Dai

Microorganisms 2025, 13(11), 2417; https://doi.org/10.3390/microorganisms13112417 - 22 Oct 2025

Abstract

Azaleas (Ericaceae) are among the most diverse ornamental plants, celebrated for their cultural and economic significance. R. simsii has been extensively utilized in horticulture as a parent species for both “pot azalea” cultivars and various cultivars grown in the warmer regions of China. [...] Read more.

Azaleas (Ericaceae) are among the most diverse ornamental plants, celebrated for their cultural and economic significance. R. simsii has been extensively utilized in horticulture as a parent species for both “pot azalea” cultivars and various cultivars grown in the warmer regions of China. From 2021 to 2023, approximately 15% of R. simsii in nurseries situated in the Xuanwu District, Nanjing, exhibited symptoms of wilting and chlorosis. Investigations revealed that these symptoms were caused by a pathogen responsible for crown and root rot. Strains were isolated from the roots of affected plants. The morphology of the colonies was predominantly radial to stellate, characterized by intercalary and terminal hyphal swelling. The sporangia appeared spherical, pyriform, or ovoid with a single papillae. For accurate identification, the 28S rDNA gene (Large subunit, LSU), cytochrome oxidase subunit I (COXI), and cytochrome oxidase subunit II (COXII) genes were amplified through PCR and then sequenced. The species was identified as P. vexans after completing the phylogenetic analysis. Healthy R. simsii plants were infected with zoospores and developed symptoms similar to those of natural infection. Furthermore, the morphological characteristics of the isolates from the experimentally infected plants were similar to those of the original inoculated strains. This study identified P. vexans as the pathogen causing root rot in R. simsii. During the sampling process, several strains were isolated from the rhizosphere soil of healthy rhododendron plants. Based on this, research was immediately initiated to explore whether there are specific bacterial species in the soil that have the potential to inhibit the occurrence of root rot. Additionally, an endophytic bacterial strain BL1 was isolated from rhizosphere soil and subjected to Whole-Genome Shotgun (WGS) sequencing, thus constructing a bacterial genome framework for this isolate. The strain BL1 was identified as Bacillus licheniformis. To our knowledge, this is the first report of the occurrence of P. vexans causing crown and root rot of R. simsii in China. In this study, we also focused on exploring the potential of biological control agents against P. vexans. The isolation and identification of the endophytic bacterial strain BL1 (Bacillus licheniformis) from the rhizosphere soil of healthy soil show strong in vitro antagonism, identifying it as a promising candidate for future biological control studies of root rot in R. simsii. The genomic component analysis and coding gene annotation of BL1 provide insights into its genetic makeup and potential mechanisms of action against pathogens. However, these findings are based on in vitro assays. Therefore, further research, including in planta experiments, is essential to confirm the efficacy of BL1 in controlling P. vexans infections in R. simsii and to evaluate its potential for practical application. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture, Second Edition)

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26 pages, 7022 KB

Open AccessReview

Microbial Interventions for Inflammatory Skin Diseases: A Systematic Review and Meta-Analysis of Atopic Dermatitis and Psoriasis

by Yamil Liscano, Daniel Muñoz Morales, Fernanda Suarez Daza, Sinthia Vidal Cañas, Darly Martinez Guevara and Esteban Artunduaga Cañas

Microorganisms 2025, 13(11), 2416; https://doi.org/10.3390/microorganisms13112416 - 22 Oct 2025

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Abstract

Inflammatory dermatological diseases represent a significant global health burden, with emerging evidence suggesting that modulation of the gut–skin axis microbial interventions may offer therapeutic benefits. However, current evidence is fragmented, with considerable heterogeneity limiting definitive conclusions. A systematic review and a meta-analysis were [...] Read more.

Inflammatory dermatological diseases represent a significant global health burden, with emerging evidence suggesting that modulation of the gut–skin axis microbial interventions may offer therapeutic benefits. However, current evidence is fragmented, with considerable heterogeneity limiting definitive conclusions. A systematic review and a meta-analysis were conducted following PRISMA guidelines, registered in PROSPERO (CRD42024629809). Seven databases were searched for randomized controlled trials evaluating probiotics, synbiotics, or postbiotics in inflammatory skin conditions. Primary outcomes included disease severity scores (SCORAD for atopic dermatitis, PASI for psoriasis). Statistical analysis employed random-effect models with standardized mean differences (SMDs) and Hedges’ g as effect size measures, using R software. Heterogeneity among studies was assessed using Q statistics and the I² index. Results: In total, 19 studies encompassing 1104 participants met the inclusion criteria. For atopic dermatitis, a meta-analysis of 12 studies (n = 817) demonstrated significant clinical improvement with microbial interventions versus placebo (SMD = −0.72; 95% CI: −1.26 to −0.17; p = 0.015), though substantial heterogeneity in the treatment effects was observed across studies (I² = 85.1%). The psoriasis results were more variable, with five studies (n = 287) showing non-significant pooled effects (SMD = −0.63; 95% CI: −1.74 to 0.48; p = 0.192). Multi-strain formulations and synbiotic combinations appeared to show greater efficacy compared to single-strain preparations. Safety profiles remained consistently favorable across all interventions. Microbial interventions represent a promising adjunctive therapeutic approach for inflammatory dermatological diseases, particularly atopic dermatitis, acting via gut–skin axis mechanisms. The substantial heterogeneity between the included studies emphasizes the need for standardized protocols and personalized medicine approaches integrating microbiome profiling to optimize clinical outcomes. Full article

(This article belongs to the Special Issue Skin Microbiome)

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2 pages, 254 KB

Open AccessCorrection

Correction: Khayat et al. Hiring of the Anti-Quorum Sensing Activities of Hypoglycemic Agent Linagliptin to Alleviate the Pseudomonas aeruginosa Pathogenesis. Microorganisms 2022, 10, 2455

by Maan T. Khayat, Tarek S. Ibrahim, Khaled M. Darwish, Ahdab N. Khayyat, Majed Alharbi, El-Sayed Khafagy, Mohamed A. M. Ali, Wael A. H. Hegazy and Hisham A. Abbas

Microorganisms 2025, 13(11), 2415; https://doi.org/10.3390/microorganisms13112415 - 22 Oct 2025

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(This article belongs to the Special Issue Microbial Quorum Sensing: Advances and Challenges)

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Microorganisms, Volume 13, Issue 11 (November 2025) – 29 articles

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