Microorganisms

18 pages, 2869 KiB

Open AccessArticle

Immunoinformatics Predictions on Variable Mycobacterium tuberculosis Lineage 6 T Cell Epitopes and HLA Interactions in West Africa

by Marta L. Silva, Nuno S. Osório and Margarida Saraiva

Microorganisms 2025, 13(5), 1032; https://doi.org/10.3390/microorganisms13051032 (registering DOI) - 29 Apr 2025

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health challenge. The human-adapted TB-causing bacteria are distributed into ten lineages with distinct global distributions and clinical outcomes. Mtb lineages 4 (L4) and L6 are good prototypes of these differences, because L4 is [...] Read more.

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a global health challenge. The human-adapted TB-causing bacteria are distributed into ten lineages with distinct global distributions and clinical outcomes. Mtb lineages 4 (L4) and L6 are good prototypes of these differences, because L4 is globally prevalent, whereas L6 is geographically restricted to West Africa and associated with slower disease progression. Given the fundamental role of T cells for the control of TB, we questioned whether Mtb L4 or L6 antigens and HLA interactions would be disrupted in West African hosts. Here, we selected variable and validated antigens and demonstrate their expression during in vivo Mtb L4 or L6 infections. We then compared the predicted number of IFN-γ-inducing and HLA high-binding-affinity peptides in Mtb ancestral, L4, or L6 proteins, considering HLA alleles of high or low frequency in West Africa. Our immunoinformatics approach predicts that non-synonymous substitutions of high variance in Mtb L6 strains diminish binding affinities to HLA alleles prevalent in West African populations, suggesting specific adaptations of these strains to their preferred hosts. Future functional studies will advance our knowledge on lineage-specific evolution and inform strategies to enhance TB control in endemic regions. Full article

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

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19 pages, 6271 KiB

Open AccessArticle

Acclimation Time Enhances Adaptation of Heterotrophic Nitrifying-Aerobic Denitrifying Microflora to Linear Anionic Surfactant Stress

by Huihui Han, Peizhen Chen, Wenjie Zhao, Shaopeng Li and Keyu Zhang

Microorganisms 2025, 13(5), 1031; https://doi.org/10.3390/microorganisms13051031 (registering DOI) - 29 Apr 2025

Abstract

Linear anionic surfactants (LAS) pose significant stress to microbial denitrification in wastewater treatment. This study investigated the performance and adaptation mechanisms of heterotrophic nitrification-aerobic denitrification (HN-AD) microbial consortia under LAS exposure after short-term (SCM, 2 months) and long-term (LCM, 6 months) acclimation. Results [...] Read more.

Linear anionic surfactants (LAS) pose significant stress to microbial denitrification in wastewater treatment. This study investigated the performance and adaptation mechanisms of heterotrophic nitrification-aerobic denitrification (HN-AD) microbial consortia under LAS exposure after short-term (SCM, 2 months) and long-term (LCM, 6 months) acclimation. Results showed a dose-dependent inhibition of total nitrogen (TN) removal, with LCM achieving 97.40% TN removal under 300 mg/L LAS, which was 16.89% higher than SCM. Biochemical assays indicated that LCM exhibited lower reactive oxygen species (ROS) levels, a higher ATP content, and reduced LDH release, suggesting enhanced oxidative stress resistance and membrane stability. EPS secretion also increased in LCM, contributing to environmental tolerance. Metagenomic analysis revealed that long-term acclimation enriched key genera including Pseudomonas, Aeromonas, and Stutzerimonas, which maintained higher expression of denitrification (e.g., nosZ, nirS) and ammonium assimilation genes (glnA, gltB). Although high LAS concentrations reduced overall community diversity and led to convergence between SCM and LCM structures, LCM retained greater functional capacity and stress resistance. These findings underscore the importance of acclimation in sustaining denitrification performance under surfactant pressure and offer valuable insights for engineering robust microbial consortia in complex wastewater environments. Full article

(This article belongs to the Section Microbiomes)

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15 pages, 329 KiB

Open AccessReview

Metallic Shipwrecks and Bacteria: A Love-Hate Relationship

by Laurent Urios

Microorganisms 2025, 13(5), 1030; https://doi.org/10.3390/microorganisms13051030 (registering DOI) - 29 Apr 2025

Abstract

For two centuries, metallic shipwrecks have been relics of the history of navigation, trade, and wars. They are also hotspots of marine biodiversity. The degradation of these shipwrecks not only threatens their environment through the release of polluting compounds, but also the reef [...] Read more.

For two centuries, metallic shipwrecks have been relics of the history of navigation, trade, and wars. They are also hotspots of marine biodiversity. The degradation of these shipwrecks not only threatens their environment through the release of polluting compounds, but also the reef ecosystems that have developed. Microorganisms are at the root of both degradation and reef-building, and their roles are still more hypothetical than validated. The aim of this review is to focus on the known or suggested relationships between bacteria and metallic shipwrecks and to identify issues that highlight the need for multidisciplinary studies to better understand the mechanisms at play in these ecosystems with the aim of protecting both the environment and these sites of underwater cultural and natural heritage. Full article

(This article belongs to the Special Issue Microbial Colonization in Marine Environments)

26 pages, 619 KiB

Open AccessReview

The Role of Beneficial Microbiota in COVID-19: Insights from Key Bacterial Genera

by Pabulo Henrique Rampelotto, Clarissa Reginato Taufer and Juliana da Silva

Microorganisms 2025, 13(5), 1029; https://doi.org/10.3390/microorganisms13051029 (registering DOI) - 29 Apr 2025

Abstract

The COVID-19 pandemic has highlighted the need for a comprehensive understanding of the factors influencing disease severity and progression. Emerging research indicates that the human microbiota, particularly beneficial bacteria, significantly impacts immune responses and health outcomes in COVID-19 patients. While existing studies provide [...] Read more.

The COVID-19 pandemic has highlighted the need for a comprehensive understanding of the factors influencing disease severity and progression. Emerging research indicates that the human microbiota, particularly beneficial bacteria, significantly impacts immune responses and health outcomes in COVID-19 patients. While existing studies provide general insights into the relationship between the microbiota and probiotics with COVID-19, they often lack a detailed exploration of how specific bacterial taxa might be used as adjunctive treatments. This review aims to address this gap by focusing on ten key genera of beneficial bacteria, discussing their roles in COVID-19 and evaluating their potential as probiotics for prevention and treatment. The review covers the impact of these microbes on human health, their population alterations in COVID-19 patients, and their interactions with other viral infections. Among these microbes, several exhibit distinct patterns of abundance in COVID-19 patients, influencing disease outcomes and highlighting their potential roles in infection dynamics. In COVID-19 patients, populations of Akkermansia, Ruminococcus, and Roseburia are consistently reduced, while those of Faecalibacterium show a significant decline in more severe cases. Bacteroides presents varying effects depending on the species involved. Alterations in the abundance of Blautia and Lachnospiraceae are associated with increased inflammation and disease severity. Likewise, the depletion of Lachnospira and Coprococcus populations, both linked to anti-inflammatory effects, may exacerbate symptom severity. Oscillospira, though less studied, is connected to overall health and could have implications for viral infections. This review synthesizes the current understanding of these beneficial microbes to highlight the importance of maintaining a healthy microbiota to alleviate the impact of COVID-19 and contribute to the development of novel therapeutic strategies involving microbiota modulation. Full article

(This article belongs to the Special Issue Advances in Human Microbiomes)

20 pages, 2955 KiB

Open AccessArticle

Deep-Sea Cold Seep Campylobacterota: Diversity, Growth, Metabolic Characteristics, and Nutrient Production

by Xiaoman Yan, Qinglei Sun, Ke Xu, Jintao Zhuo, Yuanyuan Sun, Guowei Qian, Xin Zhang and Li Sun

Microorganisms 2025, 13(5), 1028; https://doi.org/10.3390/microorganisms13051028 - 29 Apr 2025

Abstract

Deep-sea chemosynthetic ecosystems, including cold seeps and hydrothermal vents, are widely spread in global oceans. Campylobacterota are important primary producers in deep-sea hydrothermal vents and serve as a vital food source for local invertebrates. However, the nutrients that these bacteria can provide to [...] Read more.

Deep-sea chemosynthetic ecosystems, including cold seeps and hydrothermal vents, are widely spread in global oceans. Campylobacterota are important primary producers in deep-sea hydrothermal vents and serve as a vital food source for local invertebrates. However, the nutrients that these bacteria can provide to their hosts are unclear. To date, research on Campylobacterota in cold seeps is very limited. Consequently, little is known about the biological features and ecological potential of Campylobacterota in cold seeps. In the present work, we examined the diversity, growth, metabolic characteristics, and nutrient production of Campylobacterota in a deep-sea cold seep. Over 1000 Campylobacterota ASVs, especially autotrophic Sulfurovum and Sulfurimonas, were identified. By optimizing the culture medium, 9 Sulfurovum and Sulfurimonas strains were isolated, including three potentially novel species. Two novel species were characterized and found to exhibit unique morphological features. These two novel strains possessed complete reverse tricarboxylic acid pathways. One novel strain, FCS5, was a psychrotolerant autotroph with denitrification and phosphorus-removing capacity. FCS5 could grow in the absence of vitamins. Consistently, metabolomics and transcriptome analyses indicated that FCS5 produced multiple vitamins, which regulated the expressions of a large number of genes associated with carbon fixation and multiple-nutrient synthesis. Besides vitamins, autotrophic Campylobacterota also produced abundant free amino acids, fatty acids (short-chain, medium, and long-chain), and proteins. This study indicates that the cold seep abounds with Campylobacterota, which are capable of providing various nutrients for the chemosynthetic ecosystem. In addition, these bacteria may have wide applications, such as in wastewater treatment and carbon emission reduction. Full article

(This article belongs to the Special Issue Chemolithotrophic Microorganisms)

19 pages, 1580 KiB

Open AccessArticle

Fungistatic and Bactericidal Activity of Hydroalcoholic Extracts of Root of Jatropha dioica Sessé

by Lizeth Aguilar-Galaviz, Jorge Cadena-Iñiguez, Dalia Abigail García-Flores, Gerardo Loera-Alvarado, Diego Rivera-Escareño and María Azucena Ortega-Amaro

Microorganisms 2025, 13(5), 1027; https://doi.org/10.3390/microorganisms13051027 - 29 Apr 2025

Abstract

Jatropha dioica Sessé (JD) is a plant from arid and semiarid zones of Mexico related to local therapeutic uses and possible use in food and agriculture as a control agent of pest organisms that helps to reduce impacts on the environment, human health [...] Read more.

Jatropha dioica Sessé (JD) is a plant from arid and semiarid zones of Mexico related to local therapeutic uses and possible use in food and agriculture as a control agent of pest organisms that helps to reduce impacts on the environment, human health and resistance by phytopathogens. In vitro bactericidal activity was evaluated with the well diffusion method in doses of 1000, 2500, 5000, 7500, 10,000 and 20,000 µg mL⁻¹, and fungistatic activity was evaluated with the agar dilution method (500, 1000, 1500, 2000 and 4000 µg mL⁻¹) in Pseudomonas syringae, Botrytis cinerea and Fusarium oxysporum using hydroalcoholic extracts of J. dioica root in a completely randomized design with five replications. Total phenol and flavonoid contents were recorded by the Folin–Ciocalteu and aluminum chloride methods. Ethanol and methanol extracts showed fungistatic activity on B. cinerea, inhibiting from 42.27 ± 1.09 to 46.68 ± 0.98 mg mL⁻¹, with an IC₅₀ of 5.04 mg mL⁻¹, with no differences by solvent type. In F. oxysporum, inhibition ranged from 14.77 ± 1.08 to 29.19 ± 0.89 mg mL⁻¹, and the methanol extract was more efficient, generating a stress response to the ethanol extract. The bactericidal activity on P. syringae recorded inhibition zones of 17.66 ± 0.33 and 16.66 ± 0.33 mg mL⁻¹, with ethanol being more efficient. The phenol content ranged from 8.92 ± 0.25 to 12.10 ± 0.34 mg EAG g⁻¹ and flavonoid content ranged from 20.49 ± 0.33 to 28.21 ± 0.73 mg QE g⁻¹ of sample dry weight. The results highlight the biological activity of J. dioica as an alternative to biopesticides that minimize agrochemical applications and generate pathogen resistance. These advances contribute to the revaluation and conservation of the species. Full article

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

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13 pages, 231 KiB

Open AccessArticle

The Effect of Silage Microbial Inoculants on the Silage Quality of WL358HQ Alfalfa

by Siyi Wang, Zhennan He, Yuanyuan Jing, Le Sun, Guolin Yang, Bin Liu and Fengqin Gao

Microorganisms 2025, 13(5), 1026; https://doi.org/10.3390/microorganisms13051026 - 29 Apr 2025

Abstract

In order to explore the effect of different silage microbial inoculants on the silage quality of WL358HQ Alfalfa (Medicago sativa L.), the test consists of the following six treatments: Xinlaiwang I—straw silage inoculant (A), Xinlaiwang I—alfalfa silage inoculant (B), Zhuang Le Mei silage [...] Read more.

In order to explore the effect of different silage microbial inoculants on the silage quality of WL358HQ Alfalfa (Medicago sativa L.), the test consists of the following six treatments: Xinlaiwang I—straw silage inoculant (A), Xinlaiwang I—alfalfa silage inoculant (B), Zhuang Le Mei silage inoculant (C), Baoshiqing (D), KOFASIL S lactic acid bacteria silage inoculant (E) and distilled water (F). Nutritional and fermentation indexes were determined after 60 days of natural fermentation at room temperature. The results showed that the contents of crude protein (CP) and water-soluble carbohydrate (WSC) of the B treatment were higher than other treatments. The Relative Feed Value (RFV) of the B treatment was high, the lactic acid (LA) content of the B treatment was significantly increased (p < 0.05) and the contents of neutral detergent fiber (NDF), acid detergent fiber (ADF), pH and ammoniacal nitrogen/total nitrogen (AN/TN) of the B treatment were low. The results showed that treatment B has the best ensilage effect and the highest ensilage membership function, which can effectively improve the quality of WL358 alfalfa silage. Full article

(This article belongs to the Section Microbial Biotechnology)

14 pages, 1985 KiB

Open AccessArticle

Comparative Analysis of Vectorial Capacity Among Triatoma brasiliensis brasiliensis, Triatoma juazeirensis, and Their Experimental Hybrids

by Nathália Cordeiro Correia, Carlos José de Carvalho Moreira, Fernanda Oliveira Firmino, Dayse da Silva Rocha, João Paulo Sales Oliveira-Correia, Cleber Galvão and Jane Costa

Microorganisms 2025, 13(5), 1025; https://doi.org/10.3390/microorganisms13051025 - 29 Apr 2025

Abstract

The existence of a natural hybridization zone of members of the Triatoma brasiliensis complex in Pernambuco, a Brazilian state with areas highly infested by Trypanosoma cruzi vectors, raised questions to be studied about the vectorial capacity of these hybrids. Recently, it was demonstrated [...] Read more.

The existence of a natural hybridization zone of members of the Triatoma brasiliensis complex in Pernambuco, a Brazilian state with areas highly infested by Trypanosoma cruzi vectors, raised questions to be studied about the vectorial capacity of these hybrids. Recently, it was demonstrated that experimental hybrids of T. brasiliensis brasiliensis and Triatoma juazeirensis present vectorial competence superior to that of the parental species. The objective of the present study was to compare bionomic aspects related to the vectorial capacity of T. b. brasiliensis, T. juazeirensis, and their experimental hybrids. Feeding and defecation behavior patterns in fifth instar nymphs were comparatively analyzed between four groups, two parental and two hybrids, respectively: T. b. brasiliensis, T. juazeirensis, Hjb (♀ T. juazeirensis × ♂ T. b. brasiliensis), and Hbj (♀ T. b. brasiliensis × ♂ T. juazeirensis). Fifteen newly molted fifth instar nymphs from each of the mentioned groups were previously subjected to a period of fasting for 10 days and individually kept in identified bottles. In the experiment, the insects were placed in a jar containing a mouse immobilized in nylon mesh, in accordance with the guidelines of the animal ethics committee. The following variables were observed: 1-total number of feedings carried out; 2-time to start feeding; 3-duration of feeding and weight acquired; 4-defecations during feeding; 5-defecation within one minute after cessation of feeding; 6-defecation within ten minutes after cessation of feeding; 7-defecation behavior. Specimens from all groups demonstrated voracity, starting their meal immediately after contact with the mouse, and most of the insects defecated immediately after feeding, with 78% of the insects defecating within 30 s. The results obtained suggest that T. brasiliensis, T. juazeirensis, and their experimental hybrids presented bionomic characteristics compatible with the species considered good vectors in the literature. However, T. b. brasiliensis and T. juazeirensis demonstrated even more effective characteristics for T. cruzi transmission regarding their feeding and defecation patterns when compared to their hybrids. Full article

(This article belongs to the Special Issue Parasites and Parasitic Infections: Strategies to Control, Diagnose, and Treat Parasitic Diseases)

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18 pages, 6598 KiB

Open AccessArticle

Characterization of a Capsule-Deficient Pasteurella multocida Isolated from Cygnus melancoryphus: Genomic, Phenotypic, and Virulence Insights

by Nansong Jiang, Hongmei Chen, Weiwei Wang, Qizhang Liang, Qiuling Fu, Rongchang Liu, Guanghua Fu, Chunhe Wan, Yu Huang and Longfei Cheng

Microorganisms 2025, 13(5), 1024; https://doi.org/10.3390/microorganisms13051024 - 29 Apr 2025

Abstract

Pasteurella multocida is a zoonotic pathogen responsible for severe diseases in domestic and wild animals, posing threats to public health and causing substantial economic losses. Here, we describe a naturally attenuated P. multocida strain, FCF147, isolated from a mortality event involving black-necked swans [...] Read more.

Pasteurella multocida is a zoonotic pathogen responsible for severe diseases in domestic and wild animals, posing threats to public health and causing substantial economic losses. Here, we describe a naturally attenuated P. multocida strain, FCF147, isolated from a mortality event involving black-necked swans (Cygnus melancoryphus) in a wildlife habitat in Fujian, China. Genomic and phylogenetic analyses revealed that FCF147 is evolutionarily distant from other P. multocida lineages and lacks the entire capsule gene cluster. Morphological observations revealed that the loss of the capsule exposed proteins on the bacterial surface. Phenotypic characterization demonstrated reduced capsule production, enhanced biofilm formation, and increased tolerance to heat stress. In vivo infection models confirmed that FCF147 exhibits markedly attenuated virulence in both mice and poultry. However, immunization with FCF147 did not provide effective protection against the challenge of a virulent capsular type A strain. These findings suggest that while FCF147 is poorly virulent, its ability to form robust biofilms and survive thermal stress may facilitate persistence in wild bird reservoirs and potential transmission routes. These findings offer novel insights into the ecological adaptation and pathogenic potential of naturally capsule-deficient P. multocida in wildlife, highlighting their relevance to wildlife surveillance and disease ecology. Full article

(This article belongs to the Section Veterinary Microbiology)

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22 pages, 4320 KiB

Open AccessArticle

Characterization of Sex-Based Differences in Gut Microbiota That Correlate with Suppression of Lupus in Female BWF1 Mice

by James W. Harder, Jing Ma, James Collins, Pascale Alard, Venkatakrishna R. Jala, Haribabu Bodduluri and Michele M. Kosiewicz

Microorganisms 2025, 13(5), 1023; https://doi.org/10.3390/microorganisms13051023 - 29 Apr 2025

Abstract

Systemic lupus erythematosus (SLE) is more prevalent in female mice and humans and is associated with microbiota dysbiosis. We analyzed the fecal microbiota composition in female and male NZBxNZWF1 (BWF1) mice, a model of SLE, using 16S RNA gene sequencing. Composition of gut [...] Read more.

Systemic lupus erythematosus (SLE) is more prevalent in female mice and humans and is associated with microbiota dysbiosis. We analyzed the fecal microbiota composition in female and male NZBxNZWF1 (BWF1) mice, a model of SLE, using 16S RNA gene sequencing. Composition of gut microbiota differed between adult disease-prone female (pre-disease) and disease-resistant male mice. Transfer of male cecal contents by gavage into female mice suppressed kidney disease (decreased proteinuria) and improved survival. After our mouse colony was moved to a new barrier facility with similar housing, male cecal transplants failed to suppress disease in female recipients. After two years, the protective phenotype reemerged: male cecal transplants once again suppressed disease in female mice. We compared the gut microbiota composition in female and male BWF1 mice for the three different periods, during which the male microbiota either protected or failed to protect female recipients. In female vs. male mice and in female mice receiving male cecal transplants, we found Bacteroides was high, Clostridium was low (high Bacteroides/Clostridium ratio), and Alistipes was present during periods when male cecal transplants suppressed disease. These data suggest that specific bacterial populations may have opposing effects on disease suppression in a model of microbiota transplantation. Full article

(This article belongs to the Special Issue The Gut Microbiota and Autoimmune Disease)

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8 pages, 776 KiB

Open AccessCase Report

Primary Cutaneous Nocardiosis (Lymphangitic Type) in an Immunocompetent Patient: A Case Report

by Hilayali Aguilar-Molina, Sonia Toussaint-Caire, Roberto Arenas, Juan Xicohtencatl-Cortes, Luary C. Martínez-Chavarría, Rigoberto Hernández-Castro and Carmen Rodriguez-Cerdeira

Microorganisms 2025, 13(5), 1022; https://doi.org/10.3390/microorganisms13051022 - 29 Apr 2025

Abstract

Cutaneous nocardiosis is an uncommon bacterial infection caused by Nocardia spp.; Nocardia brasiliensis is the agent involved in most cases. This infection is acquired through the direct traumatic inoculation of soil, plants, or other substrates where the bacteria are found. Clinically, it usually [...] Read more.

Cutaneous nocardiosis is an uncommon bacterial infection caused by Nocardia spp.; Nocardia brasiliensis is the agent involved in most cases. This infection is acquired through the direct traumatic inoculation of soil, plants, or other substrates where the bacteria are found. Clinically, it usually manifests as an erythematous ulcerated nodule. In one-third of cases, nodules or gummas are distributed over the lymphatic pathways that resemble lymphocutaneous sporotrichosis. Its manifestations vary and can present acutely or more frequently with a latent clinical picture over time. Diagnosis is established mainly by Gram staining, biopsy, exudate culture, and molecular biology. Nocardia infections can recur, implying that antimicrobial therapy must be prolonged (between 6 and 12 months) and involve monitoring patients for at least 6 months after the end of treatment. Early diagnosis and targeted treatment may reduce patient mortality rates. We report the case of an 82-year-old woman who presented with four nodules with a lymphangitic spread on her left hand and forearm, one week after the trauma. Molecular identification was performed using 16S rDNA gene sequencing, and Nocardia brasiliensis was identified. Full article

(This article belongs to the Special Issue Current Pattern in Epidemiology and Antifungal Resistance)

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19 pages, 2558 KiB

Open AccessArticle

Quorum Sensing in Chromobacterium subtsugae ATCC 31532 (Formerly Chromobacterium violaceum ATCC 31532): Transcriptomic and Genomic Analyses

by Dmitry G. Deryabin, Ksenia S. Inchagova, Eugenia R. Nikonorova, Ilshat F. Karimov and Galimzhan K. Duskaev

Microorganisms 2025, 13(5), 1021; https://doi.org/10.3390/microorganisms13051021 - 29 Apr 2025

Abstract

Chromobacterium spp. use a density-dependent cell-to-cell communication mechanism (quorum sensing, QS) to control various traits, including the pigment violacein biosynthesis. Recently, one of the type strains of this genus, previously deposited in the American Type Culture Collection under accession number C. violaceum 31532, [...] Read more.

Chromobacterium spp. use a density-dependent cell-to-cell communication mechanism (quorum sensing, QS) to control various traits, including the pigment violacein biosynthesis. Recently, one of the type strains of this genus, previously deposited in the American Type Culture Collection under accession number C. violaceum 31532, was reclassified as C. subtsugae, making the QS data obtained for the first species irrelevant to the second. The goal of this study is to conduct transcriptomic and genomic analyses of the C. subtsugae ATCC 31532 (formerly C. violaceum ATCC 31532) strain to identify density-dependent regulated genes and the mechanisms of their QS control. Whole transcriptome dataset analysis comparing QS-negative mid-log phase and QS-positive early stationary phase samples revealed 35 down-regulated and 261 up-regulated genes, including 44 genes that increased transcription activity the most (log2 (fold change) > 4.0). In addition to the violacein biosynthesis, QS-controlled traits in C. subtsugae ATCC 31532 included the following: (i) cdeAB-oprM efflux pump; (ii) RND efflux transporter; (iii) chuPRSTUV iron acquisition system; (iv) polyamine transport system; (v) carbohydrate (semialdehydes) metabolic pathways; (vi) SAM/SPASM maturase system XYE (predicted); (vii) prophage proteins; and (viii) fucose-binding lectin II. Subsequent screening of the promoter regions of the up-regulated genes and operons in most cases showed the presence of CsuR AHL-receptor/transcriptional regulator binding sites with 56.25–68.75% similarity to the ideal 16-base-pair palindrome 5′-CTGTCCGATAGGACAG-3′ sequence, supporting the concept of QS control in C. subtsugae ATCC 31532 by the csuI-csuR gene pair. Notably, several transcriptional regulators (MarR, TetR/AcrR, HU family DNA-binding protein, helix-turn-helix domain-containing protein) were found to be under QS control. Based on these data, a hierarchical QS regulatory network in C. subtsugae ATCC 31532 was hypothesized that provides direct control of the target genes via a canonical autoinduction mechanism and further dissemination of the effect via the activity of QS-controlled transcriptional regulators. Full article

(This article belongs to the Special Issue Bacterial Communication: The Quorum Sensing Paradigm)

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18 pages, 3010 KiB

Open AccessReview

Probiotic Fermentation of Defatted Cottonseed Meal for Sustainable Foods and Non-Food Applications

by Zhanqiang Yan, Tian Li, Gen Zou, Xiaoling Zhang, Lingbo Qu and Yongjun Wei

Microorganisms 2025, 13(5), 1020; https://doi.org/10.3390/microorganisms13051020 - 29 Apr 2025

Abstract

Cottonseed is a valuable source of high-quality proteins and oils. Defatted cottonseed meal (DCSM), a by-product of cottonseed oil extraction, holds significant potential as a sustainable protein resource. This review outlines the chemical composition, structural features, and unique properties of cottonseed, with a [...] Read more.

Cottonseed is a valuable source of high-quality proteins and oils. Defatted cottonseed meal (DCSM), a by-product of cottonseed oil extraction, holds significant potential as a sustainable protein resource. This review outlines the chemical composition, structural features, and unique properties of cottonseed, with a focus on its inherent antinutritional factors, such as gossypol. Strategies for enhancing the utilization of DCSM as a protein source are systematically evaluated, including physical, chemical, and biological methods used to eliminate or reduce antinutritional components. Among these, microbial fermentation, particularly solid-state fermentation, is highlighted as a promising, eco-friendly approach for detoxification and nutritional improvement. This review further discusses critical factors influencing the removal of anti-nutritional compounds, such as pretreatment methods, fermentation parameters, and microbial strains. The efficacy of probiotic strains (e.g., Bacillus and yeasts) in enhancing the protein digestibility, amino acid profiles, and functional properties of DCSM is discussed. Additionally, recent advances in the application of fermented cottonseed protein in foods (e.g., animal feed, functional peptides, and food additives) and non-food sectors (e.g., biofuels and bioplastic) are explored. The integration of probiotic-driven fermentation processes is proposed as a strategy to exploit the full nutritional and economic potential of DCSM, paving the way for its broader and sustainable use in foods and non-food applications. Full article

(This article belongs to the Section Microbial Biotechnology)

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8 pages, 2629 KiB

Open AccessCase Report

A Case of Granulomatous Interstitial Nephritis Associated with Mycobacterium chimaera Disseminated Infection

by Martina Cacciapuoti, Maria Mazzitelli, Elena Naso, Maria Loreta De Giorgi, Giovanni Samassa, Valentina Di Vico, Serena Marinello, Lucia Federica Stefanelli, Lorenzo Calò, Annamaria Cattelan and Federico Nalesso

Microorganisms 2025, 13(5), 1019; https://doi.org/10.3390/microorganisms13051019 - 29 Apr 2025

Abstract

Mycobacterium chimaera infections are becoming increasingly frequent in patients with a history of cardiac surgery. We herein report a case of a patient admitted to the Nephrology Unit of Padua University Hospital with deteriorating kidney function, pancytopenia, hypercalcemia, and respiratory symptoms that emerged [...] Read more.

Mycobacterium chimaera infections are becoming increasingly frequent in patients with a history of cardiac surgery. We herein report a case of a patient admitted to the Nephrology Unit of Padua University Hospital with deteriorating kidney function, pancytopenia, hypercalcemia, and respiratory symptoms that emerged seven years after they underwent heart surgery for prosthetic aortic valve replacement. A kidney biopsy revealed non-caseating necrotizing granulomatous interstitial nephritis, which was initially diagnosed as idiopathic granulomatous interstitial nephritis. The patient was treated with intravenous corticosteroids since no active infections, including mycobacterial infections, were detected. The negativity of the Mycobacterium molecular test following the kidney biopsy delayed the diagnosis of a Mycobacterium chimaera disseminated infection with endocarditis, myositis, cerebral, and kidney involvement, as blood cultures were available only after six weeks. The patient was started on antimicrobial therapy with azithromycin, moxifloxacin, rifampicin, and ethambutol while prednisone was tapered down, leading to an improvement in kidney function, blood count, and blood calcium level. Our case suggests that a Mycobacterium chimaera infection should be considered for patients with a history of cardiac surgery and granulomatous interstitial nephritis even in the absence of mycobacteria in a kidney biopsy. Full article

(This article belongs to the Section Medical Microbiology)

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42 pages, 1615 KiB

Open AccessReview

Treatment of Leishmania infantum Infections in Dogs

by Melanie Kaempfle, Katrin Hartmann and Michèle Bergmann

Microorganisms 2025, 13(5), 1018; https://doi.org/10.3390/microorganisms13051018 - 29 Apr 2025

Abstract

Dogs are reservoir hosts of the zoonotic parasite Leishmania infantum, the causative agent of canine leishmaniosis. Antiparasitic drugs that are commonly used in dogs include allopurinol, miltefosine, and meglumine antimoniate. Treatment success is characterized by an improvement of disease signs, reduction in [...] Read more.

Dogs are reservoir hosts of the zoonotic parasite Leishmania infantum, the causative agent of canine leishmaniosis. Antiparasitic drugs that are commonly used in dogs include allopurinol, miltefosine, and meglumine antimoniate. Treatment success is characterized by an improvement of disease signs, reduction in parasite load, as well as prevention of relapse. However, despite treatment, infections in dogs can usually not be cleared and often lead to (recurrent) signs of disease. Since most of the drugs used in dogs are also applied in human medicine, the prevention of treatment-induced drug-resistant Leishmania strains is a major one-health concern. This review article provides an overview of current treatment options for Leishmania-infected dogs with allopurinol, meglumine antimoniate, and miltefosine, related adverse effects, and drug resistance potential. Full article

(This article belongs to the Special Issue New Advancements in the Field of Leishmaniasis)

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20 pages, 3689 KiB

Open AccessArticle

Molecular Characterization, Antibiotic Resistance, and Biofilm Formation of Escherichia coli Isolated from Commercial Broilers from Four Chinese Provinces

by Saqib Nawaz, Muhammad Shoaib, Cuiqin Huang, Wei Jiang, Yinli Bao, Xiuyi Wu, Lianhua Nie, Wenyan Fan, Zhihao Wang, Zhaoguo Chen, Huifang Yin and Xiangan Han

Microorganisms 2025, 13(5), 1017; https://doi.org/10.3390/microorganisms13051017 - 28 Apr 2025

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Abstract

Escherichia coli (E. coli) represents a significant etiological agent of colibacillosis in poultry, resulting in considerable economic losses for the global poultry sector. The present study aimed to determine molecular characterization, antibiotic resistance, and biofilm formation of E. coli strains isolated [...] Read more.

Escherichia coli (E. coli) represents a significant etiological agent of colibacillosis in poultry, resulting in considerable economic losses for the global poultry sector. The present study aimed to determine molecular characterization, antibiotic resistance, and biofilm formation of E. coli strains isolated from diseased broilers from four provinces of China. A total of 200 tissue samples were collected from the intestine, liver, crop, heart, and spleen and processed for microbiological examination. Molecular detection of E. coli strains, virulence genes, and serotypes was performed using polymerase chain reaction (PCR). Antibiotic susceptibility testing and biofilm formation were assessed using disk diffusion and 96-well microtiter plate assays. The study retrieved 68% (136/200) of E. coli strains from collected samples. Most of the E. coli strains were resistant to enrofloxacin (56%), followed by cefepime (54%), amoxicillin/clavulanate (52%), streptomycin (50%), ampicillin (48%), clindamycin (47%), kanamycin (41%), polymyxin B (37%), tetracycline (35%), sulfamethoxazole/trimethoprim (33%), ceftazidime (31%), meropenem (4.7%), and florfenicol (2.9%). Similarly, the E. coli strains tested positive for at least one virulence gene and specific serotypes. Among these, O145 was the most prevalent serotype, identified in 22 isolates (16.2%), followed by O8 (12.5%), O102 (11.8%), and O9 (11.0%). The tsh gene (10.2%) was the most prevalent virulence gene. This study found that 47.1% of E. coli strains were biofilm-producing, with 62.5% exhibiting weak biofilm production, 29.7% mild biofilm production, and 7.8% strong biofilm production. Similarly, 24.2% of the E. coli strains were avian pathogenic E. coli strains due to the presence of five or more virulence genes, specifically tsh, ompA, fimC, iss, fyuA, and astA, in a single strain by multiplex PCR. The present study recommends continuous surveillance and effective control measures to reduce the burden of avian pathogenic E. coli-related infections in poultry. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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22 pages, 7115 KiB

Open AccessArticle

Identification and Feeding Characterization of Sterkiella histriomuscorum (Protozoa, Ciliophora, Hypotrichia) Isolated from Outdoor Mass Culture of Scenedesmus dimorphus

by Mengyun Wang, Pei Chen, Hongxia Wang, Qiong Deng, Xiaonan Zhang, Guoqing Yuan, Mixue Jiang, Lingling Zheng, Zixuan Hu, Zemao Gu, Denis V. Tikhonenkov and Yingchun Gong

Microorganisms 2025, 13(5), 1016; https://doi.org/10.3390/microorganisms13051016 - 28 Apr 2025

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Abstract

Herbivorous protistan grazers are ubiquitous and abundant in marine and temperate freshwater environments. However, little is known about the algivorous ciliates and their feeding habits in outdoor mass algal cultures. In this study, we report on one hypotrich ciliate, identified as Sterkiella histriomuscorum [...] Read more.

Herbivorous protistan grazers are ubiquitous and abundant in marine and temperate freshwater environments. However, little is known about the algivorous ciliates and their feeding habits in outdoor mass algal cultures. In this study, we report on one hypotrich ciliate, identified as Sterkiella histriomuscorum, from the outdoor mass culture of Scenedesmus in Arizona, USA. A long-term field survey revealed that this species often occurs in Scenedesmus culture in spring and summer, and can graze very heavily on Scenedesmus cells. By isolating Sterkiella cells and then observing them via light microscopy and electron microscopy, detailed information about the morphology, ultrastructure, excystment process, and feeding characteristics of the ciliate was obtained. Specifically, it seems that S. histriomuscorum has a range of different strategies for excystment, and the sharp change in the ion concentration in the environment around the cyst results in osmotic shock, which likely facilitates the excystment. Feeding experiments revealed that S. histriomuscorum preferred to graze on chlorophytes as well as the diatom Phaeodactylum tricornutum and had no interaction with chrysophytes or cyanobacteria. Molecular phylogenetic analysis based on the SSU rRNA gene sequence indicated that both the genus Sterkiella and the species S. histriomuscorum are non-monophyletic. The information obtained from this study will help advance our understanding of the biodiversity and ecological function of S. histriomuscorum, and will also be very useful in the development of early warning systems and control measures for preventing or treating this contaminant in microalgal mass cultures. Full article

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

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13 pages, 3161 KiB

Open AccessArticle

Comparison of Two DNA Labeling Dyes Commonly Used to Detect Metabolically Active Bacteria

by Leena Malayil, Suhana Chattopadhyay, Neha Sripathi, Emmanuel F. Mongodin and Amy R. Sapkota

Microorganisms 2025, 13(5), 1015; https://doi.org/10.3390/microorganisms13051015 - 28 Apr 2025

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Abstract

Bacteria are ubiquitous in the environment and critical to human health and disease, yet only a small fraction can be identified through standard culture methods. Advances in next-generation sequencing techniques have improved bacterial identification, but these DNA-based methods cannot distinguish live bacteria from [...] Read more.

Bacteria are ubiquitous in the environment and critical to human health and disease, yet only a small fraction can be identified through standard culture methods. Advances in next-generation sequencing techniques have improved bacterial identification, but these DNA-based methods cannot distinguish live bacteria from relic DNA. Recently, DNA-labeling dyes (e.g., 5-bromo-2′-deoxyuridine [BrdU] and propidium monoazide [PMA]) have been used to detect metabolically active bacteria in different sample types. Here, we compare BrdU and PMA in combination with 16SrRNA gene sequencing to characterize metabolically active bacteria in two different sample types: (1) manufactured products (n = 78; cigarettes, hookah, and little cigar) and (2) natural samples (n = 186; rainwater, soil, and produce). Metabolically active bacterial communities identified in BrdU-labeled samples had lower alpha diversity than that of PMA-treated and non-treated samples. Pseudomonas, Sphingomonas, Enterobacter, and Acinetobacter were observed in all the samples tested. Irrespective of sample type, Pseudomonas was predominant in BrdU-treated samples, while Acinetobacter was more abundant in non-treated samples compared to PMA-treated samples. We also observed that PMA-treated samples tend to overestimate the metabolically active bacterial fraction compared to BrdU-treated samples. Overall, our study highlights how different labeling techniques influence bacterial community analysis findings, underscoring the need for careful selection of labeling approaches when assessing environmental samples. Full article

(This article belongs to the Section Environmental Microbiology)

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16 pages, 2314 KiB

Open AccessArticle

Indole Acetic Acid: A Key Metabolite That Protects Marine Sulfitobacter mediterraneus Against Oxidative Stress

by Yongliang Gan, Runlin Cai, Guanjing Cai, Jude Juventus Aweya, Jianmin Xie, Ziming Chen and Hui Wang

Microorganisms 2025, 13(5), 1014; https://doi.org/10.3390/microorganisms13051014 - 28 Apr 2025

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Abstract

For marine bacteria, the phycosphere is attractive as a major source of labile nutrients, but it also presents challenges due to the accumulation of stressors, such as reactive oxygen species (ROS) from algal metabolisms. Therefore, successful colonization of bacteria in the phycosphere requires [...] Read more.

For marine bacteria, the phycosphere is attractive as a major source of labile nutrients, but it also presents challenges due to the accumulation of stressors, such as reactive oxygen species (ROS) from algal metabolisms. Therefore, successful colonization of bacteria in the phycosphere requires an efficient mechanism to fight against oxidative stress, which is still a missing piece in studying bacteria–algae interactions. Here, we demonstrate that a common metabolite, indole acetic acid (IAA), enables the Roseobacter clade Sulfitobacter mediterraneus SC1-11, an IAA-producer, to resist hydrogen peroxide (H₂O₂) stress and that IAA biosynthesis can be activated by low concentrations of H₂O₂. Proteomics and metabolomics analyses revealed that bacteria consume high amino acid levels when exposed to H₂O₂ stress, while exogenous supplementation with IAA effectively protects bacteria from ROS damage and alleviates amino acid starvation by upregulating several proteins responsible for replication, recombination, and repair, as well as two proteins involved in amino acid transport and metabolism. Furthermore, the supplementation of some amino acids, such as arginine, also showed a significant protective effect on bacteria under H₂O₂ stress. This study highlights an unprecedented role of IAA in regulating amino acid metabolisms for resisting oxidative stress, which may be a specific strategy for adapting to the phycosphere. Full article

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

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14 pages, 1500 KiB

Open AccessArticle

A Decade of Pediatric CA-MRSA Surveillance in Northern Taiwan: Retrospective Resistance Analysis and Recent Genotypic Characterization

by Chia-Ning Chang, Chia-Hsiang Yu and Chih-Chien Wang

Microorganisms 2025, 13(5), 1013; https://doi.org/10.3390/microorganisms13051013 - 28 Apr 2025

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Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of pediatric infections and has shown evolving molecular characteristics over time. This study aimed to investigate the phenotypic and genotypic features of MRSA isolates collected from pediatric patients at a tertiary medical center in northern [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of pediatric infections and has shown evolving molecular characteristics over time. This study aimed to investigate the phenotypic and genotypic features of MRSA isolates collected from pediatric patients at a tertiary medical center in northern Taiwan between 2011 and 2020. A total of 182 MRSA strains were analyzed for SCCmec types, PVL gene presence, antimicrobial susceptibility, multilocus sequence typing (MLST), and clonal relatedness using pulsed-field gel electrophoresis (PFGE). ST59/SCCmec Vt was the most prevalent genotype, followed by ST59/SCCmec IV and ST8/SCCmec IV. Most ST59/SCCmec Vt and ST8/SCCmec IV isolates clustered genetically. Clindamycin and erythromycin resistance remained high, whereas co-trimoxazole susceptibility ranged from 76% to 100%. These findings confirm ST59 as the dominant clone and highlight the emergence of ST8 and ST45 in community-associated MRSA (CA-MRSA) infections. Oral co-trimoxazole remains the most effective empirical option, while clindamycin and erythromycin should be avoided. Continuous molecular surveillance is warranted to monitor trends and guide treatment strategies in pediatric MRSA infections. Full article

(This article belongs to the Special Issue Advances in Antimicrobial Treatment)

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21 pages, 3747 KiB

Open AccessArticle

Analysis of the Changes in Diversity of Culturable Bacteria in Different Niches of Mulberry Fields and Assessment of Their Plant Growth-Promoting Potential

by Weifu Liu, Ting Yuan, Mengya Wang and Jiping Liu

Microorganisms 2025, 13(5), 1012; https://doi.org/10.3390/microorganisms13051012 - 28 Apr 2025

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Abstract

Microorganisms play a crucial role in agricultural systems. The use of plant growth-promoting bacteria (PGPB) to enhance agricultural production in a sustainable and environmentally friendly manner has been widely recognized as a key technology for the future. In this study, we analyzed the [...] Read more.

Microorganisms play a crucial role in agricultural systems. The use of plant growth-promoting bacteria (PGPB) to enhance agricultural production in a sustainable and environmentally friendly manner has been widely recognized as a key technology for the future. In this study, we analyzed the diversity changes of bacteria in different ecological niches of mulberry fields based on culture-dependent methods, and we further evaluated their antibacterial and plant growth-promoting (PGP) activities. A total of 346 cultivable bacteria belonging to 30 genera were isolated from mulberry rhizosphere soil, mulberry plants and silkworm intestines, among which the dominant genera were Bacillus, Pseudomonas, and Enterobacter. The bacterial communities in the mulberry rhizosphere soil were more diverse than those in the mulberry endophytes and in the silkworm intestines. The antibacterial test showed that 30 bacteria exhibited antibacterial activity against the plant pathogen Ralstonia solanacearum. PGP trait assays indicated that 58 bacteria were capable of nitrogen fixation, phosphate solubilization, potassium release and siderophore production simultaneously. The screened functional strains promoted the growth of mulberry saplings. The results of this study highlight new findings on the application of silkworm intestinal bacteria in PGPB. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 2927 KiB

Open AccessArticle

Multitrophic and Multidimensional Insights into Biodiversity and Functional Trait Responses to Precipitation Changes in Alpine Grasslands

by Yu Liu, Chengxiang Ding and Zhanjun Quan

Microorganisms 2025, 13(5), 1011; https://doi.org/10.3390/microorganisms13051011 - 28 Apr 2025

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Abstract

Biodiversity and functional traits are increasingly recognized as pivotal factors in regulating ecosystem functioning and stability. However, the patterns and processes of multidimensional biodiversity and functional traits along environmental gradients remain insufficiently understood. In this study, we examined taxonomic, phylogenetic, and functional diversity [...] Read more.

Biodiversity and functional traits are increasingly recognized as pivotal factors in regulating ecosystem functioning and stability. However, the patterns and processes of multidimensional biodiversity and functional traits along environmental gradients remain insufficiently understood. In this study, we examined taxonomic, phylogenetic, and functional diversity across multiple trophic levels in 38 alpine grassland sites along a precipitation gradient on the Qinghai–Tibet Plateau. Our findings reveal asynchronous responses of taxonomic, phylogenetic, and functional diversity metrics, as well as functional traits across trophic levels, to variations in precipitation. Soil microbial diversity and functional traits exhibited stronger responses to precipitation changes compared to plant communities, with a tighter coupling observed between microbial diversity and microbial functional traits. Climate and soil properties jointly regulated diversity and functional trait metrics, with the climate exerting greater influence on functional traits and soil properties playing a dominant role in shaping diversity patterns. This study highlights the distinct responses of biodiversity and functional trait attributes to environmental shifts, emphasizing the importance of integrating multidimensional and multitrophic perspectives to advance our understanding of community assembly processes. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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18 pages, 5886 KiB

Open AccessArticle

Effects of Compound Microecological Preparation Supplementation on Production Performance and Nutrient Apparent Digestibility in Hu Sheep from the Rumen Perspective

by Mu-Long Lu, Long Pan, Chen Zheng, Ruo-Yu Mao, Guo-Hong Yuan, Chen-Yang Shi, Zhe-Huan Pu, Hui-Xin Su, Qi-Yu Diao, Halidai Rehemujiang and Gui-Shan Xu

Microorganisms 2025, 13(5), 999; https://doi.org/10.3390/microorganisms13050999 (registering DOI) - 27 Apr 2025

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Abstract

This study evaluates the effects of a compound microecological preparation named ATABG, which is composed of antimicrobial peptide ID13 and Saccharomyces boulardii, on Hu sheep’s growth performance, feed digestibility, and rumen parameters. A total of 40 three-month-old Hu sheep (21.65 ± 0.33 [...] Read more.

This study evaluates the effects of a compound microecological preparation named ATABG, which is composed of antimicrobial peptide ID13 and Saccharomyces boulardii, on Hu sheep’s growth performance, feed digestibility, and rumen parameters. A total of 40 three-month-old Hu sheep (21.65 ± 0.33 kg) were randomly assigned to two groups: the control group (Con), which received a basal diet, and the experimental group (ATABG), which received the same diet supplemented with 1 g/kg ATABG on a dry matter basis. After a 10-day pre-feeding period to adapt the animals to the experimental diet, dry matter intake and weight gain were recorded during the subsequent 63-day trial period. Body weight was measured on days 1, 21, 42, and 63 of the trial, and animals were slaughtered on day 63 to collect rumen fluid and tissue. Results indicated that ATABG supplementation significantly increased the apparent digestibility of crude protein, neutral detergent fiber, acid detergent fiber, and organic matter (p < 0.05). Rumen fluid analysis revealed increased microbial protein concentration and cellulase activity (p < 0.05) in the ATABG group. Microbiota analysis indicated that ATABG increased the relative abundance of Ruminococcus and Proteobacteria, elevated Firmicutes, and reduced Bacteroidota (p < 0.05). Correlation analysis showed Ruminococcus was positively associated with crude protein digestibility, while Quinella correlated with growth-related indices (r > 0.4, p < 0.05). In conclusion, ATABG supplementation improves protein digestibility and rumen microbial protein synthesis by enriching Ruminococcus and enhancing cellulase activity, potentially optimizing nitrogen utilization in Hu sheep. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 3937 KiB

Open AccessArticle

Alteration of the Rhizosphere Microbiota and Growth Performance of Barley Infected with Fusarium graminearum and Screening of an Antagonistic Bacterial Strain (Bacillus amyloliquefaciens)

by Yang Fu, Jing Luan, Jialei Shi, Wenzhu Tang, Xianzhen Li, Zhimin Yu and Fan Yang

Microorganisms 2025, 13(5), 1010; https://doi.org/10.3390/microorganisms13051010 - 27 Apr 2025

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Abstract

Fusarium graminearum is one of the most important pathogenic fungi with a wide range of plant and animal hosts. This study investigated the effects of F. graminearum infection on the rhizosphere microbiota and growth of two barley (Hordeum vulgare L.) cultivars, Baudin [...] Read more.

Fusarium graminearum is one of the most important pathogenic fungi with a wide range of plant and animal hosts. This study investigated the effects of F. graminearum infection on the rhizosphere microbiota and growth of two barley (Hordeum vulgare L.) cultivars, Baudin and Kenpi 7, and explored microbiota transplantation as a strategy to enhance disease resistance. By exchanging surface microbiotas between varieties and analyzing rhizosphere bacterial communities using 16S rRNA sequencing, researchers observed that F. graminearum infection increased bacterial diversity and abundance, especially in Baudin barley. Growth indicators (root length, plant height, fresh/dry mass) also exhibited that Baudin barley showed stronger resistance. Functional analysis underscored that the microbial community composition of Baudin barley promoted metabolic pathways related to plant resilience and was associated with improved seedling health. In contrast, Kenpi 7 barley showed weaker resistance, emphasizing the role of seed-specific microbiotas in pathogen defense. An effective antagonistic strain, Bacillus amyloliquefaciens B1, was isolated from Baudin barley, and its inhibition rate against F. graminearum was 80%. The results showed that microbiota transplantation enhanced the disease resistance of low-diversity seeds, and identified B. amyloliquefaciens B1 as a promising biocontrol agent, providing a potential application for sustainable agriculture and reducing dependence on chemical fungicides. This study highlights the importance of seed-associated microbial communities in plant–pathogen interactions and provides a basis for the development of microbiota-based strategies to mitigate crop diseases. Full article

(This article belongs to the Section Plant Microbe Interactions)

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18 pages, 3781 KiB

Open AccessArticle

Fecal Microbiota Transplantation Using Donor Stool Obtained from Exercised Mice Suppresses Colonic Tumor Development Induced by Azoxymethane in High-Fat Diet-Induced Obese Mice

by Hiroshi Matsumoto, Tingting Gu, Shogen Yo, Momoyo Sasahira, Shuzo Monden, Takehiro Ninomiya, Motoyasu Osawa, Osamu Handa, Eiji Umegaki and Akiko Shiotani

Microorganisms 2025, 13(5), 1009; https://doi.org/10.3390/microorganisms13051009 - 27 Apr 2025

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Abstract

The gut microbiota plays an important role in the development of colorectal tumors. However, the underlying mechanisms remain unclear. In this study, we examined the effects of fecal microbiota transplantation (FMT) on azoxymethane (AOM)-induced colorectal tumors in obese mice. We divided the study [...] Read more.

The gut microbiota plays an important role in the development of colorectal tumors. However, the underlying mechanisms remain unclear. In this study, we examined the effects of fecal microbiota transplantation (FMT) on azoxymethane (AOM)-induced colorectal tumors in obese mice. We divided the study subjects into the following five groups: high-fat diet (HFD), normal diet (ND), ND+exercise (Ex), HFD+FMT from ND-alone donor (HFD+FMT(ND alone)), and HFD+FMT from ND+Ex donor (HFD+FMT(ND+Ex)). The Ex group performed treadmill exercise for 15 weeks. Thereafter, fecal and colonic mucus samples were extracted for microbiome analysis. The deoxyribonucleic acid sample was collected from the feces and colonic mucosa, and V3–V4 amplicon sequencing analysis of the 16S rRNA gene was performed using MiSeq. The number of polyps was significantly lower in the ND (6.0 ± 1.6) and ND+Ex (1.8 ± 1.3) groups than in the HFD group (11.4 ± 1.5). The ND+Ex group had significantly fewer polyps than the ND group. The HFD+FMT(ND alone) (5.2 ± 0.8) and HFD+FMT(ND+Ex) (2.8 ± 2.6) groups also had significantly fewer polyps than the HFD group. The IL-15 mRNA levels in the colonic tissues were significantly higher in the HFD+FMT(ND alone) group than in the ND group. Fecal ω-muricholic acid concentrations were significantly higher in the HFD+FMT(ND alone) group than in the ND group and in the HFD+FMT(ND+Ex) group than in the ND+Ex group. The ND, ND+Ex, HFD+FMT(ND alone), and HFD+FMT(ND+Ex) groups had a significantly higher abundance of Lacyobacillaceae than the HFD group. In the FMT group, Erysipelotrichaceae and Tannerellaceae were significantly less abundant. Compared with the HFD group, the ND, ND+Ex, HFD+FMT(ND alone), and HFD+FMT(ND+Ex) groups had a significantly higher abundance of Muribaculaceae and a significantly higher abundance of Lactobacillaceae and Rikenellaceae in common among the ND and ND+Ex groups. The common and significantly less common species were Bacteroidaceae in the FMT group and Lactobacillaceae and Rikenellaceae in the ND alone and ND+Ex groups. Bacteroidaceae and Lachnospiraceae were significantly less common in the FMT group. We found that FMT inhibited AOM-induced colorectal tumorigenesis in obese mice. Furthermore, the fecal concentrations of short-chain fatty acids, bile acids, microbiota, and mucosa-associated microbiota differed between the FMT and diet/EX groups, suggesting that the inhibitory effect of FMT on colorectal tumorigenesis may be due to mechanisms different from those of ND alone and ND+Ex. Full article

(This article belongs to the Special Issue Fecal Microbiota Transplantation in Animals)

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14 pages, 992 KiB

Open AccessArticle

Increased Measured GFR and Proteinuria in Children with Previous Infection by SARS-CoV-2: Should We Be Concerned?

by Alessia Marcellino, Silvia Bloise, Carmelo Pirone, Giulia Brandino, Antonio Barberi, Emanuela Del Giudice, Vanessa Martucci, Mariateresa Sanseviero, Flavia Ventriglia and Riccardo Lubrano

Microorganisms 2025, 13(5), 1008; https://doi.org/10.3390/microorganisms13051008 - 27 Apr 2025

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Abstract

Over the past 3 years, several kidney complications in children with severe involvement by SARS-CoV-2 have been described. However, literature data are still lacking regarding possible kidney injury in children with paucisymptomatic SARS-CoV-2 infection. Thus, we retrospectively evaluated renal function in those patients. [...] Read more.

Over the past 3 years, several kidney complications in children with severe involvement by SARS-CoV-2 have been described. However, literature data are still lacking regarding possible kidney injury in children with paucisymptomatic SARS-CoV-2 infection. Thus, we retrospectively evaluated renal function in those patients. Children between 3 and 18 years, without any renal disease, with previous paucisymptomatic SARS-CoV-2 infection from May 2020 to March 2022, were recruited at our post-COVID-19 outpatient clinic. We retrospectively collected: Glomerular filtration rate, Fractional-excretion-of-sodium (FENa), tubular-reabsorption-of-phosphate (TRP), calcium-creatinine-urine ratio (CaU/CrU); proteinuria/m²/day and microhematuria by urine cytofluorometry. A total of 148 children were enrolled after a median period of 3 (IQR 6) months after infection. Twenty-six patients (17.6%) had reduced GFR, fifty (33.9%) had hyperfiltration, eleven (7.4%) had abnormal FENa and/or TRP, twenty-two (14.9%) had hypercalciuria, seventy-eight (52.7%) had pathological daily proteinuria. Microhematuria was found in sixteen (10.9%) subjects. Hyperfiltration was more prevalent among males (38.9% vs. 22.4%, p = 0.027); CaU/CrU [median 0.08 (IQR 0.09) vs. 0.13 (IQR 0.13) p = 0.003] was significantly higher in females. Our data suggest that SARS-CoV-2 could determine, in a significant proportion of children, kidney damage characterized by hyperfiltration, proteinuria, and hematuria, warranting strict follow-up in these patients. Full article

(This article belongs to the Special Issue Focus on Pediatric Infectious Diseases)

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23 pages, 9041 KiB

Open AccessArticle

Microbial Community Responses and Nitrogen Cycling in the Nitrogen-Polluted Urban Shi River Revealed by Metagenomics

by Ran Wang, Shang Yang and Wei Zhao

Microorganisms 2025, 13(5), 1007; https://doi.org/10.3390/microorganisms13051007 - 27 Apr 2025

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Abstract

Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021–2023) water quality monitoring with metagenomic sequencing to investigate [...] Read more.

Nitrogen pollution in urban rivers, exacerbated by rapid urbanization, poses a growing threat to water quality. Microbial communities are essential in mediating nitrogen cycling and mitigating pollution in these ecosystems. This study integrated three-year (2021–2023) water quality monitoring with metagenomic sequencing to investigate microbial community dynamics, nitrogen cycling processes, and their responses to nitrogen pollution in the Shi River, Qinhuangdao, China. Nitrogen pollution was predominantly derived from industrial discharges from enterprises in the Shi River Reservoir upstream (e.g., coolant and chemical effluents), agricultural runoff, untreated domestic sewage (particularly from catering and waste in Pantao Valley), and livestock farming effluents. Total nitrogen (TN) concentrations ranged from 2.22 to 6.44 mg/L, exceeding China’s Class V water standard (2.0 mg/L, GB 3838-2002), with the highest level at the urbanized W4 site (6.44 mg/L). Nitrate nitrogen (NO₃-N) accounted for 60–80% of TN. Metagenomic analysis revealed Fragilaria, Microcystis, and Flavobacterium thriving (up to 15% relative abundance) under nitrogen stress, with nitrogen metabolism genes (narG, nifH, nirK) enriched at polluted sites (W2, W4), narG reaching 26% at W1. Dissolved oxygen positively correlated with nitrate reductase gene abundance, while ammonia nitrogen inhibited it. Burkholderiales and Limnohabitans dominated denitrification, offering insights into sustainable urban river management. Full article

(This article belongs to the Special Issue Microbial Communities and Nitrogen Cycling)

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12 pages, 1751 KiB

Open AccessArticle

Transcriptomic Insights into the Degradation Mechanisms of Fomitopsis pinicola and Its Host Preference for Coniferous over Broadleaf Deadwood

by Jianbin Xue, Yulian Wei, Liting Chen and Haisheng Yuan

Microorganisms 2025, 13(5), 1006; https://doi.org/10.3390/microorganisms13051006 - 27 Apr 2025

Viewed by 112

Abstract

The degradation of deadwood is a vital ecological process for geochemical cycling and biodiversity conservation, with two main routes of fungal degradation: brown and white rot. Brown rot fungi cause severe destruction of wood cellulose and lead to brown and modified lignin residue. [...] Read more.

The degradation of deadwood is a vital ecological process for geochemical cycling and biodiversity conservation, with two main routes of fungal degradation: brown and white rot. Brown rot fungi cause severe destruction of wood cellulose and lead to brown and modified lignin residue. Fomitopsis pinicola is a typical brown rot fungus with a distinct host preference for coniferous trees. The mechanisms through which this fungus degrades coniferous and broadleaf wood remain poorly understood. Therefore, in this study, a 60-day cultivation experiment involving F. pinicola growing on deadwood strips of Pinus koraiensis and Betula platyphylla separately was performed. A comparative transcriptome analysis was carried out to explore the mechanisms underlying the differences in degradation, in terms of both physicochemical properties and transcriptomic data. The findings revealed that the host preference of F. pinicola resulted in the more efficient degradation of coniferous wood than broadleaf wood, accompanied by higher gene expression levels. GO enrichment analysis indicated that this preference was primarily associated with the hydrolytic enzyme family and processes related to the Fenton reaction, which is characteristic of brown rot fungi. Furthermore, the KEGG pathways showed that the DEGs were enriched in mainly included histidine metabolism, fatty acid degradation, and so on, indicating underlying carbohydrate and lipid metabolism processes. These results support P. pinicola’s strong ability to degrade the deadwood lignin of P. koraiensis, reflecting its adaptive evolution in host selection and choice of different ecological niches. Full article

(This article belongs to the Section Environmental Microbiology)

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29 pages, 3813 KiB

Open AccessArticle

A Quaternary Sedimentary Ancient DNA (sedaDNA) Record of Fungal–Terrestrial Ecosystem Dynamics in a Tropical Biodiversity Hotspot (Lake Towuti, Sulawesi, Indonesia)

by Md Akhtar-E Ekram, Cornelia Wuchter, Satria Bijaksana, Kliti Grice, James Russell, Janelle Stevenson, Hendrik Vogel and Marco J. L. Coolen

Microorganisms 2025, 13(5), 1005; https://doi.org/10.3390/microorganisms13051005 - 27 Apr 2025

Viewed by 145

Abstract

Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi–soil–plant interactions, [...] Read more.

Short-term observations suggest that environmental changes affect the diversity and composition of soil fungi, significantly influencing forest resilience, plant diversity, and soil processes. However, time-series experiments should be supplemented with geobiological archives to capture the long-term effects of environmental changes on fungi–soil–plant interactions, particularly in undersampled, floristically diverse tropical forests. We recently conducted trnL-P6 amplicon sequencing to generate a sedimentary ancient DNA (sedaDNA) record of the regional catchment vegetation of the tropical waterbody Lake Towuti (Sulawesi, Indonesia), spanning over one million years (Myr) of the lake’s developmental history. In this study, we performed 18SV9 amplicon sequencing to create a parallel paleofungal record to (a) infer the composition, origins, and functional guilds of paleofungal community members and (b) determine the extent to which downcore changes in fungal community composition reflect the late Pleistocene evolution of the Lake Towuti catchment. We identified at least 52 members of Ascomycota (predominantly Dothiodeomycetes, Eurotiomycetes, and Leotiomycetes) and 12 members of Basidiomycota (primarily Agaricales and Polyporales). Spearman correlation analysis of the relative changes in fungal community composition, geochemical parameters, and paleovegetation assemblages revealed that the overwhelming majority consisted of soil organic matter and wood-decaying saprobes, except for a necrotrophic phytopathogenic association between Mycosphaerellaceae (Cadophora) and wetland herbs (Alocasia) in more-than-1-Myr-old silts and peats deposited in a pre-lake landscape, dominated by small rivers, wetlands, and peat swamps. During the lacustrine stage, vegetation that used to grow on ultramafic catchment soils during extended periods of inferred drying showed associations with dark septate endophytes (Ploettnerulaceae and Didymellaceae) that can produce large quantities of siderophores to solubilize mineral-bound ferrous iron, releasing bioavailable ferrous iron needed for several processes in plants, including photosynthesis. Our study showed that sedaDNA metabarcoding paired with the analysis of geochemical parameters yielded plausible insights into fungal-plant-soil interactions, and inferred changes in the paleohydrology and catchment evolution of tropical Lake Towuti, spanning more than one Myr of deposition. Full article

(This article belongs to the Special Issue Ancient Microbiomes in the Environment)

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Open AccessArticle

Hypericin Suppresses SARS-CoV-2 Replication and Synergizes with Antivirals via Dual Targeting of RdRp and 3CLpro

by Helena da Silva Souza, Jéssica Santa Cruz Carvalho Martins, Thiagos das Chagas Sousa, Saiqa Sardar, Natalia Fintelman-Rodrigues, Lina Silva-Trujillo, Thiago Moreno Lopes e Souza, Marilda Mendonça Siqueira, Jorge Hernandes Fernandes and Aline da Rocha Matos

Microorganisms 2025, 13(5), 1004; https://doi.org/10.3390/microorganisms13051004 - 27 Apr 2025

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Abstract

The continuous emergence of SARS-CoV-2 variants underscores the need for novel antiviral candidates. Hypericin (HY), a compound derived from Hypericum perforatum, exhibited potent in vitro activity against SARS-CoV-2 in Vero E6 cells, with low cytotoxicity (CC₅₀ > 200 nM). HY showed [...] Read more.

The continuous emergence of SARS-CoV-2 variants underscores the need for novel antiviral candidates. Hypericin (HY), a compound derived from Hypericum perforatum, exhibited potent in vitro activity against SARS-CoV-2 in Vero E6 cells, with low cytotoxicity (CC₅₀ > 200 nM). HY showed no significant activity against Influenza A (H1N1) or dengue virus serotype 2, supporting its selective action. Antiviral effects were most evident when HY was administered post-infection, in a concentration-dependent manner, while cellular pretreatment or viral pre-incubation produced limited effects. Notably, HY also displayed virucidal activity, significantly reducing viral titers at 4 °C, 22 °C, and 37 °C. Combination treatments with remdesivir or nirmatrelvir enhanced antiviral efficacy by 50–70% relative to monotherapy, depending on compound concentration. Molecular simulations revealed stable interactions with conserved residues in RdRp and 3CLpro, suggesting a low risk of resistance. Together, these findings highlight the potential of HY as a selective antiviral and virucidal agent against SARS-CoV-2, particularly in combination regimens. Full article

(This article belongs to the Special Issue Viral Infection and The Discovery and Mode of Action of Novel Antivirals)

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Microorganisms, Volume 13, Issue 5 (May 2025) – 77 articles

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