Microorganisms

15 pages, 5904 KiB

Open AccessArticle

The Vaginally Exposed Extracellular Vesicle of Gardnerella vaginalis Induces RANK/RANKL-Involved Systemic Inflammation in Mice

by Yoon-Jung Shin, Xiaoyang Ma, Ji-Su Baek and Dong-Hyun Kim

Microorganisms 2025, 13(4), 955; https://doi.org/10.3390/microorganisms13040955 - 21 Apr 2025

Viewed by 187

Abstract

Gardnerella vaginalis (GV), an opportunistic pathogen excessively proliferated in vaginal dysbiosis, causes systemic inflammation including vaginitis, neuroinflammation, and osteitis. To understand its systemic inflammation-triggering factor, we purified extracellular vesicles isolated from GV (gEVs) and examined their effect on the occurrence of vaginitis, osteitis, [...] Read more.

Gardnerella vaginalis (GV), an opportunistic pathogen excessively proliferated in vaginal dysbiosis, causes systemic inflammation including vaginitis, neuroinflammation, and osteitis. To understand its systemic inflammation-triggering factor, we purified extracellular vesicles isolated from GV (gEVs) and examined their effect on the occurrence of vaginitis, osteitis, and neuroinflammation in mice with and without ovariectomy (Ov). The gEVs consisted of lipopolysaccharide, proteins, and nucleic acid and induced TNF-α and RANKL expression in macrophage cells. When the gEVs were vaginally exposed in mice without Ov, they significantly induced RANK, RANKL, and TNF-α expression and NF-κB⁺ cell numbers in the vagina, femur, hypothalamus, and hippocampus, as observed in GV infection. The gEVs decreased time spent in the open field (OT) in the elevated plus maze test by 47.3%, as well as the distance traveled in the central area (DC) by 28.6%. In the open field test, they also decreased the time spent in the central area (TC) by 39.3%. Additionally, gEVs decreased spontaneous alteration (SA) in the Y-maze test by 33.8% and the recognition index (RI) in the novel object recognition test by 26.5%, while increasing the immobility time (IT) in the tail suspension test by 36.7%. In mice with OV (Ov), the gEVs also induced RANK, RANKL, and TNF-α expression and increased NF-κB⁺ cell numbers in the vagina, femur, hypothalamus, and hippocampus compared to vehicle-treated mice. When gEVs were exposed to mice with Ov, gEVs also reduced the DC, TC, OT, SA, and RI to 62.1%, 62.7%, 28.2%, 90.7%, and 85.4% of mice with Ov, respectively, and increased IT to 122.9% of mice with Ov. Vaginally exposed fluorescein-isothiocyanate-tagged gEVs were detected in the blood, femur, and hippocampus. These findings indicate that GV-derived gEVs may induce systemic inflammation through the activation of RANK/RANKL-involved NF-κB signaling, leading to systemic disorders including vaginitis, osteoporosis, depression, and cognitive impairment. Therefore, gEVs may be an important risk factor for vaginitis, osteoporosis, depression, and cognitive impairment in women. Full article

(This article belongs to the Special Issue Insights into Microbial Infections, Co-Infections, and Comorbidities)

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16 pages, 5397 KiB

Open AccessArticle

Genetic Evolution of Antibiotic Resistance and Virulence Genes in Escherichia coli Isolates from a Chinese Hospital over a 12-Year Period

by Chengjie Feng, Hongbing Jia, Qian Yang and Qinghua Zou

Microorganisms 2025, 13(4), 954; https://doi.org/10.3390/microorganisms13040954 - 21 Apr 2025

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Abstract

Escherichia coli is a significant pathogen capable of inducing a variety of infections in both human and animal hosts. Despite its clinical significance, there is a lack of longitudinal research aimed at elucidating the genomic attributes that facilitate antimicrobial resistance and clonal dissemination [...] Read more.

Escherichia coli is a significant pathogen capable of inducing a variety of infections in both human and animal hosts. Despite its clinical significance, there is a lack of longitudinal research aimed at elucidating the genomic attributes that facilitate antimicrobial resistance and clonal dissemination in this bacterium. In this study, we investigated the genetic dynamics of antibiotic resistance and virulence factors within a collection of 137 E. coli isolates retrieved from a Chinese hospital over a 12-year period. Notably, a substantial increase in resistance to various antibiotics, including broad-spectrum β-lactams, aminoglycosides, and quinolones, was observed. Additionally, our study revealed the acquisition of diverse antibiotic resistance and virulence genes across different sequence types (STs). Among the STs, ST131 emerged as the most prevalent, exhibiting a high level of multidrug resistance. In contrast, ST73 and ST12 demonstrated a higher prevalence of virulence genes, suggestive of a potential trade-off between antibiotic resistance and virulence. What’s more, we identified significant intra-clonal diversification and convergence of antibiotic resistance and virulence traits within the dominant ST131 group. These findings underscore the importance of longitudinal studies in understanding the evolution of bacterial pathogens and the necessity for ongoing research to inform public health strategies. Full article

(This article belongs to the Special Issue Omics Research in Microbial Ecology)

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19 pages, 2340 KiB

Open AccessArticle

Antibacterial Effect and Mechanism of Chelerythrine on Xanthomonas oryzae pv. oryzae

by Yi Yan, Jueyu Wang, Na Zhao, Daizong Cui and Min Zhao

Microorganisms 2025, 13(4), 953; https://doi.org/10.3390/microorganisms13040953 - 21 Apr 2025

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Abstract

Xanthomonas oryzae pv. oryzae (Xoo) is a biotrophic bacterial pathogen, which causes devastating bacterial blight disease worldwide. In this study, we thoroughly investigated the antimicrobial effect of the plant-derived extract chelerythrine against Xanthomonas oryzae pv. oryzae (Xoo) and elucidated [...] Read more.

Xanthomonas oryzae pv. oryzae (Xoo) is a biotrophic bacterial pathogen, which causes devastating bacterial blight disease worldwide. In this study, we thoroughly investigated the antimicrobial effect of the plant-derived extract chelerythrine against Xanthomonas oryzae pv. oryzae (Xoo) and elucidated its mechanism. Chelerythrine is a quaternary ammonium alkaloid with a 2,3,7,8-tetrasubstituted phenanthridine structure, extracted from plants, such as the whole plant of Chelidonium majus, and the roots, stems, and leaves of Macleaya cordata. We found that chelerythrine significantly inhibited the growth of Xoo at a concentration of 1.25 μg/mL. Further experiments revealed that chelerythrine interfered with the division and reproduction of the bacterium, leading to its filamentous growth. Additionally, it increased the permeability of Xoo cell membranes and effectively decreased the pathogenicity of Xoo, including the inhibition of extracellular polysaccharide production, cellulase secretion, and biofilm formation. Chelerythrine induced the accumulation of reactive oxygen species in the bacterium, triggering oxidative stress. The result showed that chelerythrine inhibited the formation of the Z-ring of Xoo, interfered with the synthesis of pyrimidine and purine nucleotides, inhibited DNA damage repair, and inhibited the formation of peptidoglycan and lipid-like A, thus interfering with cell membrane permeability, inhibiting carbohydrate metabolism and phosphorylation of sugars, reducing pathogenicity, and ultimately inhibiting bacterial growth and leading to the destruction or lysis of bacterial cells. Altogether, our results suggest that the antimicrobial effect of chelerythrine on Xoo exhibits multi-target properties. Additionally, its effective inhibitory concentration is low. These findings provide a crucial theoretical basis and guidance for the development of novel and efficient plant-derived antimicrobial compounds. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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18 pages, 1673 KiB

Open AccessReview

Silver Nanoparticles and Antibiotics: A Promising Synergistic Approach to Multidrug-Resistant Infections

by Eudald Casals, Muriel F. Gusta, Neus Bastus, Jordi Rello and Victor Puntes

Microorganisms 2025, 13(4), 952; https://doi.org/10.3390/microorganisms13040952 - 21 Apr 2025

Viewed by 282

Abstract

The escalating threat of antibiotic resistance demands innovative strategies against multidrug-resistant (MDR) microorganisms, particularly in hospital settings where such infections represent a major global health challenge. Since the rapid growth of nanotechnology interdisciplinary research and funding programs in the 2000s, silver ions have [...] Read more.

The escalating threat of antibiotic resistance demands innovative strategies against multidrug-resistant (MDR) microorganisms, particularly in hospital settings where such infections represent a major global health challenge. Since the rapid growth of nanotechnology interdisciplinary research and funding programs in the 2000s, silver ions have re-emerged as potent antimicrobial agents, offering a promising complement to conventional therapies. This therapeutic potential is nowadays explored through the use of silver nanoparticles (AgNPs) as sources for silver ions release. Recent studies have shown that controlled silver ion release enhances the efficacy of common antibiotics. This can be attributed to the energetically demanding nature of the bacterial response to silver, which weakens bacterial metabolism and, in turn, overwhelms bacterial defenses and increases antibiotic effectiveness. Herein, historical insights into the use of colloidal silver and AgNPs are combined with a review of recent research on the exploitation of the synergistic effect between AgNPs and antibiotics as a promising strategy against MDR pathogens. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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24 pages, 2116 KiB

Open AccessReview

Environmental Risk Factors Contributing to the Spread of Antibiotic Resistance in West Africa

by Adenike Adenaya, Adedapo Adedayo Adeniran, Chidera Linus Ugwuoke, Kaosara Saliu, Mariam Adewumi Raji, Amartya Rakshit, Mariana Ribas-Ribas and Martin Könneke

Microorganisms 2025, 13(4), 951; https://doi.org/10.3390/microorganisms13040951 - 21 Apr 2025

Viewed by 347

Abstract

Antibiotic resistance is a well-documented global health challenge that disproportionately impacts low- and middle-income countries. In 2019, the number of deaths attributed to and associated with antibiotic resistance in Western Sub-Saharan Africa was approximately 27 and 115 per 100,000, respectively, higher than in [...] Read more.

Antibiotic resistance is a well-documented global health challenge that disproportionately impacts low- and middle-income countries. In 2019, the number of deaths attributed to and associated with antibiotic resistance in Western Sub-Saharan Africa was approximately 27 and 115 per 100,000, respectively, higher than in other regions worldwide. Extensive research has consistently confirmed the persistent presence and spread of antibiotic resistance in hospitals, among livestock, within food supply chains, and across various environmental contexts. This review documents the environmental risk factors contributing to the spread of antibiotic resistance in West Africa. We collected studies from multiple West African countries using the Web of Science and PubMed databases. We screened them for factors associated with antibiotic-resistant bacteria and resistance genes between 2018 and 2024. Our findings indicate that antibiotic resistance remains a significant concern in West Africa, with environmental pollution and waste management identified as major factors in the proliferation of antibiotic-resistant bacteria and resistance genes between 2018 and 2024. Additional contributing factors include poor hygiene, the use of antibiotics in agriculture, aquaculture, and animal farming, and the transmission of antibiotic resistance within hospital settings. Unfortunately, the lack of comprehensive genetic characterization of antibiotic-resistant bacteria and resistance genes hinders a thorough understanding of this critical issue in the region. Since antibiotic resistance transcends national borders and can spread within and between countries, it is essential to understand the environmental risk factors driving its dissemination in West African countries. Such understanding will be instrumental in developing and recommending effective strategies nationally and internationally to combat antibiotic resistance. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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23 pages, 3094 KiB

Open AccessSystematic Review

How the Built Environment Shapes Children’s Microbiome: A Systematic Review

by Rozalynne Samira, Muntazar Monsur and Nazia Afrin Trina

Microorganisms 2025, 13(4), 950; https://doi.org/10.3390/microorganisms13040950 - 20 Apr 2025

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Abstract

This systematic review aims to synthesize key empirical findings to understand how various elements of the built environment influence the microbiome concerning children’s health and well-being. A comprehensive literature search was conducted across multiple databases, focusing on studies that examined the relationship between [...] Read more.

This systematic review aims to synthesize key empirical findings to understand how various elements of the built environment influence the microbiome concerning children’s health and well-being. A comprehensive literature search was conducted across multiple databases, focusing on studies that examined the relationship between built environment factors and the microbiome aspects of childhood. A total of 42 studies were included in the final systematic review. We analyzed these studies from a range of different lenses, starting with basic research questions and variables to types of built environments, age groups of children, sampling strategy, bioinformatics, and the biological methods utilized. This review highlights a growing emphasis on children’s exposure to nature within built environments and its potential to beneficially alter the microbiome, with 38% of studies addressing this link. It also identifies a significant research gap in connecting built environment design features (landscape and/or architectural) to microbiome outcomes and associated health, behavioral, and mental health impacts on children. The findings indicate that interventions aimed at improving the built environment quality via design could foster healthier microbiomes in children’s environments. This review underscores the need for interdisciplinary research and policy initiatives that integrate microbiome science with built environment design to promote children’s health and well-being. Full article

(This article belongs to the Special Issue Microbiota: From the Environment to Humans, 2nd Edition)

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22 pages, 1961 KiB

Open AccessArticle

The Clinical Validity and Utility of PCR Compared to Conventional Culture and Sensitivity Testing for the Management of Complicated Urinary Tract Infections in Adults: A Secondary (Ad Hoc) Analysis of Pathogen Detection, Resistance Profiles, and Impact on Clinical Outcomes

by Moustafa Kardjadj, Tara W. Chang, Roel Chavez, DeAndre Derrick, Frank L. Spangler, Itoe P. Priestly, Lauren Y. Park and Thomas K. Huard

Microorganisms 2025, 13(4), 949; https://doi.org/10.3390/microorganisms13040949 - 20 Apr 2025

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Abstract

Clinical success in treating complicated urinary tract infections (cUTIs) depends on accurate pathogen detection, given the common occurrence of polymicrobial infections and antimicrobial resistance. This multicenter, randomized, investigator-blinded study compared polymerase chain reaction (PCR)-based diagnostics to conventional culture and sensitivity (C&S) testing in [...] Read more.

Clinical success in treating complicated urinary tract infections (cUTIs) depends on accurate pathogen detection, given the common occurrence of polymicrobial infections and antimicrobial resistance. This multicenter, randomized, investigator-blinded study compared polymerase chain reaction (PCR)-based diagnostics to conventional culture and sensitivity (C&S) testing in guiding the treatment of cUTIs. PCR identified polymicrobial infections in 43.52% of cases, a significantly higher rate than that observed with C&S (31.95%, p = 0.033). Patients in the C&S arms with undetected polymicrobial infections had a significantly higher clinical failure rate (33.33%, 14/42, p = 0.041) compared to those with concordant polymicrobial infection identification by both methods (22.22%, 12/54). PCR also detected additional pathogens in 54.44% (92/169) of cases in the C&S arm, where clinical failure was significantly higher when C&S missed pathogens (28.26% vs. 14.29%, p = 0.015). Similarly, when C&S failed to detect phenotypic resistance (compared to PCR), clinical failure occurred in 50% (16/42) of cases, compared to 13.22% (21/121, p = 0.001) when resistance detection was concordant (PCR and C&S). To further illustrate the clinical impact, patient-level case analyses are included to demonstrate how PCR-guided therapy improved pathogen detection and enabled more appropriate antimicrobial selection compared to C&S. These findings highlight the limitations of C&S in detecting polymicrobial infections, antimicrobial resistance, and hetero-resistance due to its limited clonal analysis, supporting the integration of PCR for more accurate diagnostics and optimized cUTI management. Full article

(This article belongs to the Special Issue New Advancements in Clinical Microbiology: Surveillance, Diagnosis, and Treatment)

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24 pages, 1057 KiB

Open AccessReview

The Microbiota–Human Health Axis

by Harrie Toms John, Treesa Clare Thomas, Ezenwa Collins Chukwuebuka, Ali Bacar Ali, Reggani Anass, Yididiya Yilma Tefera, Bency Babu, Nicoleta Negrut, Anca Ferician and Paula Marian

Microorganisms 2025, 13(4), 948; https://doi.org/10.3390/microorganisms13040948 - 20 Apr 2025

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Abstract

Trillions of microorganisms play a pivotal role in maintaining health and preventing disease in humans. Their presence influences daily life, habits, energy levels, and pathologies. The present narrative review synthesized recent studies of microbial diversity across organ systems. The composition of the microbiota [...] Read more.

Trillions of microorganisms play a pivotal role in maintaining health and preventing disease in humans. Their presence influences daily life, habits, energy levels, and pathologies. The present narrative review synthesized recent studies of microbial diversity across organ systems. The composition of the microbiota regulates the intestinal barrier, modulates the immune response, influences metabolism, and produces essential compounds such as short-chain fatty acids and neurotransmitters. Dysbiosis is associated with numerous pathologies, including metabolic, autoimmune, neurodegenerative, and cardiovascular diseases. The microbiota is key to maintaining physiological balance and reducing disease risk. Therapeutic interventions, such as probiotics, prebiotics, postbiotics, and microbiome transplantation, offer promising perspectives in restoring microbial homeostasis and preventing chronic diseases. Full article

(This article belongs to the Section Medical Microbiology)

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Graphical abstract

22 pages, 4223 KiB

Open AccessArticle

Microbiome Migration from Soil to Leaves in Maize and Rice

by Jiejia Ma, Qianze Peng, Silu Chen, Zhuoxin Liu, Weixing Zhang, Chi Zhang, Xiaohua Du, Shue Sun, Weiye Peng, Ziling Lei, Limei Zhang, Pin Su, Deyong Zhang and Yong Liu

Microorganisms 2025, 13(4), 947; https://doi.org/10.3390/microorganisms13040947 - 20 Apr 2025

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Abstract

The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize ( [...] Read more.

The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize (Zea mays) was analyzed through 16S rRNA sequencing and phenotypic assessments. When we used the same soil microbiome source to grow rice and maize, microbiota and functional traits were specifically enriched by maize in its phyllosphere and rhizosphere. This indicated that plants can selectively assemble microbiomes from a shared microbiota source. Therefore, 22 strains were isolated from the phyllospheres of rice and maize and used to construct a synthetic microbial community (SynCom). When the soil for rice and maize growth was inoculated with the SynCom, strains belonging to Bacillus were enriched in the maize phyllosphere compared to the rice phyllosphere. Additionally, a strain belonging to Rhizobium was enriched in the maize rhizosphere compared to the rice rhizosphere. These results suggest that plant species influence the migration of microbiota within their respective compartments. Compared with mock inoculation, SynCom inoculation significantly enhanced plant growth. When we compared the microbiomes, strains belonging to Achromobacter, which were assembled by both rice and maize, played a role in enhancing plant growth. Our findings underscore the importance of microbial migration dynamics and functional assembly in leveraging plant–microbe interactions for sustainable agriculture. Full article

(This article belongs to the Section Microbiomes)

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12 pages, 1894 KiB

Open AccessArticle

New Findings on the Survival of Durusdinium glynnii Under Different Acclimation Methods to Low Salinities

by Barbara de Cassia S. Brandão, Jéssika L. de Abreu, Deyvid Willame S. Oliveira, Clarissa Vilela F. da Silva Campos, Ingrid M. Thó de Aguiar, Pedro R. de Sena, Alfredo O. Gálvez and Carlos Yure B. Oliveira

Microorganisms 2025, 13(4), 946; https://doi.org/10.3390/microorganisms13040946 - 20 Apr 2025

Viewed by 122

Abstract

This study investigated the effects of salinity on the growth and cell morphotype of the coral-associated dinoflagellate Durusdinium glynnii under two acclimation strategies: abrupt saline shock (S5) and gradual reduction (S2). Results revealed optimal growth rates (µ = 0.22–0.35 day⁻¹) at [...] Read more.

This study investigated the effects of salinity on the growth and cell morphotype of the coral-associated dinoflagellate Durusdinium glynnii under two acclimation strategies: abrupt saline shock (S5) and gradual reduction (S2). Results revealed optimal growth rates (µ = 0.22–0.35 day⁻¹) at salinities of 20–30 g L⁻¹, while extreme conditions (10 and 40 g L⁻¹) significantly inhibited development. The S2 strategy enabled adaptation to salinities as low as 16 g L⁻¹, maintaining higher cell densities compared to the S5 method. Gradual salinity reduction also influenced cellular morphology: below 12 g L⁻¹, a predominant shift occurred from motile forms (mastigotes) to non-motile spherical structures (coccoid), suggesting an adaptive response to osmotic stress, gradually reducing the growth rate due to the lower reproductive rate of coccoid cells, as previously reported in studies. The findings conclude that D. glynnii is a euryhaline species, tolerant of moderate salinity variations (16–30 g L⁻¹) but limited under extreme conditions. Its morphological plasticity and gradual acclimation capacity highlight its potential for cultivation in brackish environments and biomass production for biotechnological applications, such as antioxidants and antimicrobials. The data provide a foundation for future studies on molecular mechanisms of salinity tolerance, essential for coral conservation strategies and bioprospecting efforts. Full article

(This article belongs to the Special Issue New Advances in Microalgae Biotechnology—Increasing Productivity Towards Achieving a More Profitable Production Chain)

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17 pages, 19135 KiB

Open AccessArticle

Carbonate Buffer Mixture Alleviates Subacute Rumen Acidosis Induced by Long-Term High-Concentrate Feeding in Dairy Goats by Regulating Rumen Microbiota

by Guyue Fan, Nier Su, Yuhong He, Chongshan Yuan, Caijun Zhao, Xiaoyu Hu, Yunhe Fu and Naisheng Zhang

Microorganisms 2025, 13(4), 945; https://doi.org/10.3390/microorganisms13040945 - 19 Apr 2025

Viewed by 153

Abstract

This study aimed to elucidate the therapeutic mechanisms of carbonate buffer mixture (CBM) in mitigating subacute rumen acidosis (SARA) by examining its effects on rumen pH, systemic inflammation, and rumen microbiota in a dairy goat model. Using a controlled experimental design, SARA was [...] Read more.

This study aimed to elucidate the therapeutic mechanisms of carbonate buffer mixture (CBM) in mitigating subacute rumen acidosis (SARA) by examining its effects on rumen pH, systemic inflammation, and rumen microbiota in a dairy goat model. Using a controlled experimental design, SARA was induced through 8-week high-concentrate diet feeding (70% concentrate, 30% forage), followed by 2-day CBM treatment. Comprehensive analyses included rumen pH monitoring, serum inflammatory marker quantification (IL-1β, TNF-α) by ELISA, rumen barrier integrity assessment through tight junction proteins (TJs) ZO-1, Occludin, and Claudin-3 by western blot analysis, and 16S rRNA sequencing of rumen microbiota. The results demonstrated that CBM administration rapidly elevated depressed rumen pH within 6 h post-treatment while concurrently reducing circulating LPS levels. The analysis of rumen 16S rRNA showed that CBM significantly increased the rumen microbial diversity and abundance of SARA dairy goats. Butyric acid generation groups such as Rikenellaceae_RC9_gut_group, NK4A214_group, and Prevotellaceae UCG-001 were selectively enriched, and corresponding functional predictions showed that the butyric acid synthesis pathway (PICRUSt2) was enhanced. These findings suggest that CBM has a multidimensional therapeutic effect by simultaneously correcting rumen acidosis, alleviating systemic inflammation, and restoring microbial balance through pH-dependent and pH-independent mechanisms, providing a scientifically validated nutritional strategy for SARA management in intensive ruminant production systems. Full article

(This article belongs to the Section Veterinary Microbiology)

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13 pages, 423 KiB

Open AccessSystematic Review

The Mystery of Certain Lactobacillus acidophilus Strains in the Treatment of Gastrointestinal Symptoms of COVID-19: A Review

by Belén Bertola, Amparo Cotolí-Crespo, Nadia San Onofre and Jose M. Soriano

Microorganisms 2025, 13(4), 944; https://doi.org/10.3390/microorganisms13040944 - 19 Apr 2025

Viewed by 231

Abstract

COVID-19 presents a wide range of symptoms, including gastrointestinal manifestations such as diarrhea, nausea, and abdominal pain. Lactobacillus acidophilus has been proposed as a potential adjunct therapy to alleviate these symptoms due to its probiotic properties, which help restore gut microbiota balance and [...] Read more.

COVID-19 presents a wide range of symptoms, including gastrointestinal manifestations such as diarrhea, nausea, and abdominal pain. Lactobacillus acidophilus has been proposed as a potential adjunct therapy to alleviate these symptoms due to its probiotic properties, which help restore gut microbiota balance and modulate immune responses. This review systematically analyzed studies assessing the effects of L. acidophilus in COVID-19 patients with gastrointestinal symptoms. The literature search was conducted through PubMed and the WHO COVID-19 database using keywords such as “Lactobacillus acidophilus”, “COVID-19”, “gastrointestinal symptoms”, and “inflammation markers”. The search covered studies published until February 2025. Inclusion criteria: observational and clinical trials with L. acidophilus for symptom relief. Exclusion: animal studies and non-ethical approvals. The findings suggest that L. acidophilus supplementation may contribute to faster resolution of diarrhea, improved gut microbiota balance, and reduced inflammatory markers. However, some studies have found no significant impact on hospitalization rates or disease progression. The probiotic’s mechanisms of action appear to involve microbiota modulation, intestinal barrier reinforcement, and anti-inflammatory effects rather than direct viral inhibition in COVID-19 after progression. Some L. acidophilus strains show promise, and clinical validation should follow careful preclinical studies (in vitro, cell lines, and animal models), especially in vulnerable populations such as immunocompromised individuals. Understanding the gut–lung axis and its role in immune response regulation, together with the need for a thorough characterization of the specific strains, including biochemical, genomic, and functional properties, before testing in humans, may provide deeper insights into the therapeutic potential of probiotics in viral infections. Full article

(This article belongs to the Section Gut Microbiota)

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30 pages, 13959 KiB

Open AccessArticle

A Comparison Between High- and Low-Performing Lambs and Their Impact on the Meat Quality and Development Level Using a Multi-Omics Analysis of Rumen Microbe–Muscle–Liver Interactions

by Haibo Wang, Jinshun Zhan, Shengguo Zhao, Haoyun Jiang, Haobin Jia, Yue Pan, Xiaojun Zhong and Junhong Huo

Microorganisms 2025, 13(4), 943; https://doi.org/10.3390/microorganisms13040943 - 19 Apr 2025

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Abstract

Through an integrated multi-omics analysis of rumen microbial communities, muscle transcriptomes, metabolic profiles, and liver metabolic profiles, this study systematically compared high- and low-performing lambs to elucidate their divergent effects on meat quality attributes and growth development. A total of 100 male lambs [...] Read more.

Through an integrated multi-omics analysis of rumen microbial communities, muscle transcriptomes, metabolic profiles, and liver metabolic profiles, this study systematically compared high- and low-performing lambs to elucidate their divergent effects on meat quality attributes and growth development. A total of 100 male lambs with similar birth weight (3.07 ± 0.06 kg) were selected within 72 h. All test lambs were synchronized weaning at 45 days of age and uniformly fed the same diet (total mixed ration) in the same pen until 180 days of age, with ad libitum access to food and water throughout this period. Subsequently, the eight lambs with the highest (HADG) and lowest (LADG) average daily gains were slaughtered for performance evaluation and multi-omics analysis. This study found that HADG lambs increased body weight, muscle fiber diameter, eye muscle area, improved amino acid (histidine, arginine, valine, isoleucine, essential amino acid/total amino acid, and essential amino acid/nonessential amino acid), and fatty acid (linoleic acid, behenic acid, and arachidonic acid) composition enhanced rumen enzymes (pepsase, lipase, xylanase, amylase, and carboxymethyl cellulose) and promoted efficient fermentation (p < 0.05). Analysis of microbial populations indicated a notable increase in Prevotella levels within the rumen of HADG lambs. Furthermore, the rumen markers Schwartzia and Streptococcus exhibited significant correlations with differential meat quality traits. Analysis of the muscle transcriptome indicated a significant correlation between the turquoise module and host phenotypes, particularly body weight. Additionally, muscle metabolism is primarily concentrated within the black module; however, it exhibits a significant correlation with the host body phenotype in the yellow module (p < 0.05). Moreover, liver metabolites, rumen microbes, host phenotype, and muscle transcripts were significantly correlated (p < 0.05). In conclusion, the interactions among rumen microbes, muscle, and liver in lambs promote rumen fermentation, which in turn regulate muscle transcriptional activity and modify metabolic profiles in both the liver and muscle. Moreover, PCK1, SPP1, FGF7, NR4A1, DUSP5, GADD45B, etc., can be candidate genes for muscle growth and development. This finding provides a theoretical basis for further exploiting the production potential of Hu lambs. Full article

(This article belongs to the Section Veterinary Microbiology)

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21 pages, 646 KiB

Open AccessSystematic Review

Evaluation of the Disinfection Efficacy of Er-YAG Laser Light on Single-Species Candida Biofilms: Systematic Review

by Diana Dembicka-Mączka, Magdalena Gryka-Deszczyńska, Jacek Sitkiewicz, Aleksander Makara, Jakub Fiegler-Rudol and Rafał Wiench

Microorganisms 2025, 13(4), 942; https://doi.org/10.3390/microorganisms13040942 - 19 Apr 2025

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Abstract

The relevance of the current study is to increase the resistance of fungal biofilms to traditional disinfection methods. The aim of the study was to determine how effectively Er:YAG laser light inhibits single-species Candida biofilms. The study involved a systematic review of 57 [...] Read more.

The relevance of the current study is to increase the resistance of fungal biofilms to traditional disinfection methods. The aim of the study was to determine how effectively Er:YAG laser light inhibits single-species Candida biofilms. The study involved a systematic review of 57 scientific publications (2015–2024) selected according to specific criteria, followed by an assessment of quantitative and qualitative indicators of colony-forming unit reduction. The results show that under optimal parameters (power 1.5–3.9 W and duration 60–90 s), the Er:YAG laser can reduce the number of viable Candida albicans cells by an average of 70–90%, and when combined with sodium hypochlorite or chlorhexidine solutions, this figure can exceed 90%. Separate in vitro tests show that Candida glabrata and Candida tropicalis require higher power or longer exposure to achieve a similar effect, while the use of the Er:YAG laser on titanium and dental surfaces minimizes damage to the substrate and effectively removes the biofilm matrix. In addition, laser treatment accelerates tissue regeneration and helps reduce the number of cases of reinfection, which is confirmed by the positive dynamics in clinical practice. Data analysis using confocal microscopy and microbiological seeding indicates a significant disruption of the biofilm structure and increased permeability to antimycotics after laser exposure. Er:YAG laser disinfection method is promising in counteracting fungal biofilms, especially for surfaces with a high risk of microbial colonization. The practical value lies in the possibility of developing standard protocols for the clinical use of the laser, which will increase the effectiveness of treatment and prevention of Candidal lesions. Full article

(This article belongs to the Special Issue Research on Fungal Pathogen Candida spp. and Alternative Therapy)

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16 pages, 2829 KiB

Open AccessArticle

Analysis of Fecal Microbiome and Metabolome Changes in Goats When Consuming a Lower-Protein Diet with Varying Energy Levels

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

Microorganisms 2025, 13(4), 941; https://doi.org/10.3390/microorganisms13040941 - 18 Apr 2025

Viewed by 169

Abstract

The objective of this study was to evaluate the effect of fecal bacterial community and metabolomics in goats when consuming a lower-protein diet with different energy levels. Eight healthy Leizhou goats, with 11 ± 0.78 kg of body weight, were selected and housed [...] Read more.

The objective of this study was to evaluate the effect of fecal bacterial community and metabolomics in goats when consuming a lower-protein diet with different energy levels. Eight healthy Leizhou goats, with 11 ± 0.78 kg of body weight, were selected and housed individually in cages. The animals were randomly allocated to a lower-protein diet that varied with four metabolites energy levels (7.01, 8.33, 9.66, and 10.98 MJ/kg DM) in a replicated 4 × 4 Latin square design. Notably, energy-dependent microbial restructuring was observed at both phylum and genus levels. At the phylum level, the relative abundances of Firmicutes and Spirochaetote increased linearly, whereas the Bacteroidota and Patescibacteria decreased linearly with increasing dietary energy levels (p < 0.05). The relative abundances of Verrucomicrobiota increased quadratically, whereas others decreased quadratically with increasing dietary energy levels (p < 0.05). At the genus level, a total of 316 bacteria were identified in the 32 fecal samples. The relative abundances of Christensenellaceae_R-7_group, unclassified_f__Lachnospiraceae, Ruminococcus, norank_o__Clostridia_UCG-014, Treponema, [Eubacterium]_siraeum_group, and [Eubacterium]_ruminantium_group increased linearly, whereas the Oscillospiraceae_UCG-005, norank_f__[Eubacterium]_coprostanoligenes_group, Prevotellaceae_UCG-004, unclassified_c__Clostridia, norank_f__Ruminococcaceae, unclassified_f__ Oscillospiraceae, and others decreased linearly with an increasing dietary energy levels (p < 0.05). In addition, the metabolomic analysis of feces showed that there are many differential metabolites in goats when consuming a lower-protein diet with different energy levels; for example, lipid metabolism and amino acid metabolic pathways were increased in MLE, MHE, and HE groups compared to the LE group. In conclusion, this study provides further information regarding the effects on fecal bacterial community composition and metabolites in goats when consuming a lower-protein diet with different energy levels. Full article

(This article belongs to the Section Gut Microbiota)

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13 pages, 2308 KiB

Open AccessArticle

Bioprospecting of Marine Organisms: Exploring Antibacterial Activities in Aqueous and Organic Extracts

by Vinícius Paulino Pinto Menezes, Aldeni Moreira da Silva Filho, Aline Jeferson Costa, Elielton Nascimento, Ulisses Santos Pinheiro, Renata Pinheiro Chaves, Alexandre Lopes Andrade, Mayron Alves de Vasconcelos, Edson Holanda Teixeira, Alexandre Holanda Sampaio, Celso Shiniti Nagano and Rômulo Farias Carneiro

Microorganisms 2025, 13(4), 940; https://doi.org/10.3390/microorganisms13040940 - 18 Apr 2025

Viewed by 121

Abstract

This study evaluated the antibacterial activity of aqueous and organic extracts from 78 marine organisms, including seaweeds and sponges, collected along the coast of Ceará, Brazil. Extracts were obtained by maceration using distilled water and 50% acetonitrile and tested against Staphylococcus aureus, [...] Read more.

This study evaluated the antibacterial activity of aqueous and organic extracts from 78 marine organisms, including seaweeds and sponges, collected along the coast of Ceará, Brazil. Extracts were obtained by maceration using distilled water and 50% acetonitrile and tested against Staphylococcus aureus, Staphylococcus epidermidis (Gram-positive), and Escherichia coli (Gram-negative) using the disk diffusion method, and inhibition zone diameters were measured. Antibacterial activity was observed in 30.7% of the extracts, with organic extracts showing higher efficacy. Several sponge species, particularly those from the genus Aplysina, as well as Amphimedon compressa, Amphimedon viridis, Mycale sp., and Pseudosuberites sp., demonstrated notable inhibitory effects. While seaweed aqueous extracts showed no activity, some organic extracts—especially from Amansia multifida—were effective against Gram-positive strains. In general, Gram-positive bacteria were more susceptible than Gram-negative bacteria. These findings underscore the biotechnological potential of marine organisms from the Brazilian coast as promising sources of antibacterial compounds and support future efforts focused on the isolation, characterization, and toxicological evaluation of active metabolites for pharmaceutical and industrial applications. Full article

(This article belongs to the Special Issue BioWarriors Unleashed: Exploring Nature's Arsenal Against Pathogenic Microorganisms)

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14 pages, 3435 KiB

Open AccessArticle

Germination and Outgrowth of Bacillus subtilis Spores Deficient in BER and DisA Unveil Alternative Genetic Checkpoints

by Alejandra Rangel-Mendoza, Luz I. Valenzuela-García, Eduardo A. Robleto and Mario Pedraza-Reyes

Microorganisms 2025, 13(4), 939; https://doi.org/10.3390/microorganisms13040939 - 18 Apr 2025

Viewed by 257

Abstract

During Bacillus subtilis spore germination/outgrowth, the rehydration of the spore core and activation of aerobic metabolism can generate reactive oxygen species (ROS)-promoted DNA lesions that are repaired via the base excision repair pathway (BER). Accordingly, spores deficient in the AP-endonucleases (APEs) Nfo and [...] Read more.

During Bacillus subtilis spore germination/outgrowth, the rehydration of the spore core and activation of aerobic metabolism can generate reactive oxygen species (ROS)-promoted DNA lesions that are repaired via the base excision repair pathway (BER). Accordingly, spores deficient in the AP-endonucleases (APEs) Nfo and ExoA exhibit a delayed outgrowth that is suppressed following disruption of the checkpoint protein DisA. Here, we report that DisA-independent DNA damage checkpoints operate during B. subtilis spore outgrowth. Consistent with this notion, spores lacking Nfo, ExoA, and Nth, which functions as an APE, did not suppress delayed outgrowth following disA disruption. Furthermore, in reference to the ∆nfo ∆exoA ∆nth spores, spores deficient for these APEs and DisA displayed a significantly higher number of oxidative genetic lesions and failed to properly segregate its chromosome during the first round of replication in the outgrowth stage. Finally, we found that DisA promotes low-fidelity repair and replication events, as revealed by DNA-alkaline gel electrophoresis (AGE) as well as spontaneous and H₂O₂-promoted Rif^R mutagenesis. Overall, our results unveil the existence of DisA-independent DNA damage checkpoint(s) that are activated by genomic lesions of an oxidative nature during spore germination and outgrowth, ensuring a proper transition to vegetative growth. Full article

(This article belongs to the Special Issue Microbial Biotechnological Application for Metabolite Bioprocesses)

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15 pages, 2692 KiB

Open AccessArticle

Isolation, Antimicrobial Susceptibility, and Genotypes of Three Pasteurellaeae Species Prevalent on Pig Farms in China Between 2021 and 2023

by Fangxin Li, Xin Zong, Guosheng Chen, Yu Zhang, Qi Cao, Lu Li, Huanchun Chen, Zhong Peng and Chen Tan

Microorganisms 2025, 13(4), 938; https://doi.org/10.3390/microorganisms13040938 - 18 Apr 2025

Viewed by 154

Abstract

Pasteurella multocida (PM), Glaesserella parasuis (GPS), and Actinobacillus pleuropneumoniae (APP) are among the species with the top five isolation rates on Chinese pig farms annually. To understand the antimicrobial susceptibility and genotypes of these three pathogens that are currently prevalent on pig farms, [...] Read more.

Pasteurella multocida (PM), Glaesserella parasuis (GPS), and Actinobacillus pleuropneumoniae (APP) are among the species with the top five isolation rates on Chinese pig farms annually. To understand the antimicrobial susceptibility and genotypes of these three pathogens that are currently prevalent on pig farms, we investigated 151 bacterial strains (64 PM, 48 GPS, and 39 APP) isolated from 4190 samples from farms in 12 Chinese provinces between 2021 and 2023. The prevalent serotypes were PM type D (50.0%), GPS type 5/12 (47.92%), and APP type 7 (35.90%). A relatively high proportion of PM and APP were resistant to ampicillin (PM, 93.75%; APP, 71.79%), tilmicosin (PM, 64.06%; APP, 58.97%), tetracycline (PM, 43.75%; APP, 61.54%), and enrofloxacin (PM, 34.38%; APP, 10.26%). Ampicillin, tetracycline, and enrofloxacin exhibited low MIC₉₀ values against GPS (8 µg/mL), while sulfamethoxazole-trimethoprim had a high MIC₉₀ value (512 µg/mL). A total of 18 genes conferring resistance to various antimicrobial classes were identified, and tet(L), tet(M), tet(A), bla_TEM, sul2, aph(3′)-Ia, dfrA12, qnrS1, strA, sul3, and mef(B) exhibited a high frequency of identification (≥70%). The analysis of regular virulence factor genes showed that several genes, including fimB, fimA, fimD, fimF, and fepG, were found in all PM, GPS, and APP strains. However, certain genes exhibited species-specific preferences, even if they belonged to the same category. Full article

(This article belongs to the Special Issue Bacterial Infections and Antibiotic Resistance in Veterinary Medicine, 2nd Edition)

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30 pages, 1100 KiB

Open AccessReview

Antibiotic Abuse in Ornamental Fish: An Overlooked Reservoir for Antibiotic Resistance

by Chun Au-Yeung, Yat-Lai Tsui, Man-Hay Choi, Ka-Wai Chan, Sze-Nga Wong, Yuk-Ki Ling, Cheuk-Ming Lam, Kit-Ling Lam and Wing-Yin Mo

Microorganisms 2025, 13(4), 937; https://doi.org/10.3390/microorganisms13040937 - 18 Apr 2025

Viewed by 165

Abstract

Ornamental fish represent a significant aquaculture sector with notable economic value, yet their contribution to antibiotic residues and resistance remains underrecognized. This review synthesizes evidence on widespread and often unregulated antibiotic use—including tetracyclines and fluoroquinolones—in ornamental fish production, transportation, and retail, primarily targeting [...] Read more.

Ornamental fish represent a significant aquaculture sector with notable economic value, yet their contribution to antibiotic residues and resistance remains underrecognized. This review synthesizes evidence on widespread and often unregulated antibiotic use—including tetracyclines and fluoroquinolones—in ornamental fish production, transportation, and retail, primarily targeting bacterial diseases such as aeromonosis and vibriosis. Pathogenic microorganisms including Edwardsiella, Flavobacterium, and Shewanella spp. cause diseases like hemorrhagic septicemia, fin rot, skin ulcers, and exophthalmia, impairing fish health and marketability. Prophylactic and therapeutic antibiotic applications elevate antibiotic residues in fish tissues and carriage water, thereby selecting for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). These resistant elements pose significant risks to fish health, human exposure via direct contact and bioaerosols, and environmental health through contamination pathways. We emphasize the urgent need for a holistic One Health approach, involving enhanced surveillance, stringent regulatory oversight, and adoption of alternative antimicrobial strategies, such as probiotics and advanced water treatments. Coordinated global actions are crucial to effectively mitigate antibiotic resistance within the ornamental fish industry, ensuring sustainable production, safeguarding public health, and protecting environmental integrity. Full article

(This article belongs to the Special Issue Emerging Diseases in Aquatic Animals)

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15 pages, 801 KiB

Open AccessCommunication

Metataxonomics Characterization of Soil Microbiome Extraction Method Using Different Dispersant Solutions

by David Madariaga-Troncoso, Isaac Vargas, Dorian Rojas-Villalta, Michel Abanto and Kattia Núñez-Montero

Microorganisms 2025, 13(4), 936; https://doi.org/10.3390/microorganisms13040936 - 18 Apr 2025

Viewed by 128

Abstract

Soil health is essential for maintaining ecosystem balance, food security, and human well-being. Anthropogenic activities, such as climate change and excessive agrochemical use, have led to the degradation of soil ecosystems worldwide. Microbiome transplantation has emerged as a promising approach for restoring perturbed [...] Read more.

Soil health is essential for maintaining ecosystem balance, food security, and human well-being. Anthropogenic activities, such as climate change and excessive agrochemical use, have led to the degradation of soil ecosystems worldwide. Microbiome transplantation has emerged as a promising approach for restoring perturbed soils; however, direct soil transfer presents practical limitations for large-scale applications. An alternative strategy involves extracting microbial communities through soil washing processes, but its success highly depends on proper microbiota characterization and efficient extraction methods. This study evaluated a soil wash method using four different dispersant solutions (Tween-80, NaCl, sodium citrate, and sodium pyrophosphate) for their ability to extract the majority of microbial cells from Antarctic and Crop soils. The extracted microbiomes were analyzed using 16S rRNA gene metataxonomics to assess their diversity and abundance. We found that some treatments extracted a greater proportion of specific taxa, and, on the other hand, some extracted a lower proportion than the control treatment. In addition, these dispersant solutions showed the extraction of the relevant microbial community profile in soil samples, composed of multiple taxa, including beneficial bacteria for soil health. Our study aims to optimize DNA extraction methods for microbiome analyses and to explore the use of this technique in various biotechnological applications. The results provide insights into the effect of dispersant solutions on microbiome extractions. In this regard, sodium chloride could be optimal for Antarctic soils, while sodium citrate is suggested for the Crop soils. Full article

(This article belongs to the Section Environmental Microbiology)

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25 pages, 2388 KiB

Open AccessReview

Lignin-Degrading Enzymes and the Potential of Pseudomonas putida as a Cell Factory for Lignin Degradation and Valorization

by Qing Zhou, Annabel Fransen and Han de Winde

Microorganisms 2025, 13(4), 935; https://doi.org/10.3390/microorganisms13040935 - 18 Apr 2025

Viewed by 391

Abstract

Efficient utilization of lignin, a complex polymer in plant cell walls, is one of the key strategies for developing a green and sustainable bioeconomy. However, bioconversion of lignin poses a significant challenge due to its recalcitrant nature. Microorganisms, particularly fungi and bacteria, play [...] Read more.

Efficient utilization of lignin, a complex polymer in plant cell walls, is one of the key strategies for developing a green and sustainable bioeconomy. However, bioconversion of lignin poses a significant challenge due to its recalcitrant nature. Microorganisms, particularly fungi and bacteria, play a crucial role in lignin biodegradation, using various enzymatic pathways. Among bacteria, Pseudomonas putida is considered a promising host for lignin degradation and valorization, due to its robust and flexible metabolism and its tolerance to many noxious and toxic compounds. This review explores the various mechanisms of lignin breakdown by microorganisms, with a focus on P. putida’s metabolic versatility and genetic engineering potential. By leveraging advanced genetic tools and metabolic pathway optimization, P. putida can be engineered to efficiently convert lignin into valuable bioproducts, offering sustainable solutions for lignin valorization in industrial applications. Full article

(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)

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16 pages, 6507 KiB

Open AccessArticle

The Effects of Varying Concentrations of Didecyl Methylpropyl Ammonium Iodide (DMPAI) on the Structure and Function of Soil Bacterial Communities in the Lake–Terrestrial Ecotone

by Qi Zhu, Lingquan Zeng, Chunhua Li and Chun Ye

Microorganisms 2025, 13(4), 934; https://doi.org/10.3390/microorganisms13040934 - 18 Apr 2025

Viewed by 160

Abstract

To address freshwater lake blooms resulting from eutrophication, the application of quaternary ammonium compounds as algaecides serves as an effective emergency remediation strategy. Didecyl methylpropyl ammonium iodide (DMPAI) is a novel quaternary ammonium algaecide; however, its bacteriostatic properties may significantly disrupt the microbial [...] Read more.

To address freshwater lake blooms resulting from eutrophication, the application of quaternary ammonium compounds as algaecides serves as an effective emergency remediation strategy. Didecyl methylpropyl ammonium iodide (DMPAI) is a novel quaternary ammonium algaecide; however, its bacteriostatic properties may significantly disrupt the microbial activity in lakes, particularly within the lake–terrestrial ecotone. To investigate the degradation process of DMPAI in the lake–terrestrial ecotone and its impact on the microbial community, experiments were conducted using a large-scale indoor simulation device to analyze DMPAI concentrations, the composition of the lake microbial community, and associated gene functions. The results showed that (1) DMPAI was completely removed from the lake water body in approximately 36 h; (2) The addition of DMPAI altered the microbial community structure in the lake–terrestrial ecotone, as evidenced by an increase in the diversity index and the proliferation of microorganisms capable of tolerating and degrading DMPAI, such as Pseudomonas and Flavobacterium, within a short period. These changes were typically observed after 10 d and generally recovered, not persisting for extended periods. (3) Functional genes involved in carbon, nitrogen, and sulfur cycling are more significantly impaired in the lake–terrestrial ecotone with DMPAI addition. The destabilization of the microbial community may lead to a short-term increase in pathogenic bacteria during the recovery process. This phenomenon was more pronounced in environments with higher concentrations of DMPAI. Therefore, the concentration of DMPAI should be controlled within the range of 0.5 to 2.0 mg L⁻¹. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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18 pages, 2831 KiB

Open AccessArticle

Microbiomic and Metabolomic Insights into the Roles of Hydrolysable Versus Condensed Tannins on the Growth Performance, Nutrient Digestion, and Rumen Fermentation in Liaoning Cashmere Goats

by Xin Zhu, Xingtang Dou, Tingting Su, Lisha Ye, Lu Zhang, Haiying Liu and Di Han

Microorganisms 2025, 13(4), 933; https://doi.org/10.3390/microorganisms13040933 - 17 Apr 2025

Viewed by 270

Abstract

This study was conducted to compare the effects of hydrolysable versus condensed tannins on growth performance, nutrient digestion, and rumen fermentation in goats. A total of 27 Liaoning cashmere goats with similar initial body weights were randomly distributed into three groups: a basal [...] Read more.

This study was conducted to compare the effects of hydrolysable versus condensed tannins on growth performance, nutrient digestion, and rumen fermentation in goats. A total of 27 Liaoning cashmere goats with similar initial body weights were randomly distributed into three groups: a basal diet, a basal diet +0.5% tannic acid (hydrolysable tannin, HT), or a basal diet +0.5% quebracho tannin (condensed tannin, CT), respectively. Compared to the control group, HT showed a decreased (p < 0.05) feed intake, while CT showed an increased (p < 0.05) feed intake and body weight gain. Digestibility of dry matter, crude protein, neutral detergent fiber, and acid detergent fiber did not differ (p > 0.05) among groups. The HT group showed lower pH and acetic acid concentration in the rumen (p < 0.05), while the CT group showed a decrease (p < 0.05) in the abundances of Verrucomicrobia and Methanobrevibacter. Supplementation of CT decreased (p < 0.05) the levels of dihydrouracil, xanthosine, alpha-D-mannose, and L-tryptophan, while HT increased (p < 0.05) these metabolites. In conclusion, this study suggested that responses of ruminal microbiota and metabolite profiles to the type of tannins varied, and CT displayed a more positive effect on the growth performance of goats than HT when supplemented at the same level in the diets. Full article

(This article belongs to the Section Gut Microbiota)

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17 pages, 2442 KiB

Open AccessArticle

Effects of Spent Mushroom Substrate Treated with Plant Growth-Promoting Rhizobacteria on Blueberry Growth and Soil Quality

by Mengjiao Wang, Desheng Sun and Zhimin Xu

Microorganisms 2025, 13(4), 932; https://doi.org/10.3390/microorganisms13040932 - 17 Apr 2025

Viewed by 209

Abstract

Spent mushroom substrate (SMS) is the residual biomass generated after harvesting the fruitbodies of edible fungi. It is produced in large quantities and contains abundant nutrients. Plant growth-promoting rhizobacteria (PGPR) are a group of plant-associated microorganisms known for their ability to enhance plant [...] Read more.

Spent mushroom substrate (SMS) is the residual biomass generated after harvesting the fruitbodies of edible fungi. It is produced in large quantities and contains abundant nutrients. Plant growth-promoting rhizobacteria (PGPR) are a group of plant-associated microorganisms known for their ability to enhance plant growth, improve disease resistance, and boost soil quality. In this study, three PGPR strains with the highest plant growth-promoting potential were selected based on their ability to grow effectively in SMS extract. The SMS substrates were mixed with PGPR solutions and sterile water to establish a batch culture system. The mixture was initially incubated at 28 °C for 3 days, followed by continuous aerobic decomposition in a ventilated environment for 180 days. Based on the quality analysis of the PGPR-treated SMS, the 54-day treatment for transplanting blueberry seedlings was selected. The PGPR-treated substrates showed significantly higher TN, HN, and AP than controls (p < 0.05), suggesting a potential role of PGPR in enhancing nutrient availability. Alpha diversity index analysis revealed significant differences in microbial diversity between the PGPR-treated substrates and the control. Furthermore, the PGPR-treated substrates significantly influenced plant growth characteristics, soil nutrient content, and rhizosphere microbial diversity. Enhanced plant growth characteristics were strongly correlated with increased soil nutrient levels, suggesting a potential link between rhizospheric microbial communities and plant growth performance. This study provides a novel approach and experimental framework for the utilization of SMS and the development of PGPR-based biofertilizers, offering valuable insights into sustainable agricultural practices. Full article

(This article belongs to the Section Environmental Microbiology)

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15 pages, 949 KiB

Open AccessArticle

First Detection of Cryptosporidium Canis and Occurrence of Cryptosporidium spp. in Hospitalized Patients in Romania

by Rodica Georgiana Dărăbuș, Mirela Imre, Gheorghe Dărăbuș, Marius Stelian Ilie, Alexander Tudor Olariu, Diana Maria Dărăbuș, Voichița Lăzureanu, Ovidiu Roșca and Tudor Rareș Olariu

Microorganisms 2025, 13(4), 931; https://doi.org/10.3390/microorganisms13040931 - 17 Apr 2025

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Abstract

The study aimed to identify Cryptosporidium infection in hospitalized patients in Western Romania. Stool samples were collected from 175 patients, both male and female, aged between 2 months and 88 years, residing in urban and rural areas. The identification of Cryptosporidium was performed [...] Read more.

The study aimed to identify Cryptosporidium infection in hospitalized patients in Western Romania. Stool samples were collected from 175 patients, both male and female, aged between 2 months and 88 years, residing in urban and rural areas. The identification of Cryptosporidium was performed using a qualitative chromatographic rapid test, supplemented by the modified Ziehl–Neelsen method described by Henricksen and Pohlenz. Cryptosporidium spp. were identified through PCR analysis and Sanger sequencing. To assess potential risk factors for cryptosporidiosis, a questionnaire was administered to the study participants. Laboratory test results revealed a cryptosporidiosis occurrence of 7.42%, with a significantly higher occurrence observed in urban areas (p < 0.05). Two species were identified, C. parvum and C. canis, the latter being reported for the first time in humans in Romania. Among the assessed risk factors, only the area of residence significantly influenced the occurrence of Cryptosporidium infection. The other evaluated risk factors—age, sex, concomitant microbial infections, contact with animals, use of public transport, international travel, frequenting children’s playgrounds, and swimming pools—although potentially involved in Cryptosporidium infection, did not have a significant contribution. This study represents the first report of C. canis identified in humans in Romania. Our results indicate a high occurrence of human cryptosporidiosis in hospitalized patients, with a significantly higher rate observed in individuals residing in urban areas. Full article

(This article belongs to the Special Issue Epidemiology of Zoonotic Pathogens)

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13 pages, 6136 KiB

Open AccessArticle

The Subgingival Microbial Composition in Health and Periodontitis with Different Probing Depths

by Jingyan Wang, Yiran Geng, Jing Guo, Jiahan Peng, He Xu, Bingqian Zhao, Shiyan Huang, Man Qin, Wenbin Du and Jing Tian

Microorganisms 2025, 13(4), 930; https://doi.org/10.3390/microorganisms13040930 - 17 Apr 2025

Viewed by 201

Abstract

The differences in microbiota between periodontitis and health have been extensively studied; however, knowledge about how the microbiota shifts from shallow to deep periodontal pockets remains limited despite its clinical importance in disease progres-sion and management. Patients diagnosed with stage III periodontitis commonly [...] Read more.

The differences in microbiota between periodontitis and health have been extensively studied; however, knowledge about how the microbiota shifts from shallow to deep periodontal pockets remains limited despite its clinical importance in disease progres-sion and management. Patients diagnosed with stage III periodontitis commonly pre-sent varied probing depths (PD) within the same oral cavity, reflecting localized disease severity. This study aims to analyze the microbiome of subgingival plaques at various PDs in periodontitis patients. Subgingival plaques were collected from sixteen healthy subjects (health group) and periodontal pockets of sixteen stage III periodontitis pa-tients (PD 0–3 mm, PD 4–5 mm and PD 6–9 mm groups). A total of 64 subgingival plaque samples underwent 16S rRNA gene sequencing. The PD 6–9 mm group exhib-ited significantly higher alpha diversity than the health group, and distinct subgingival microbial community structures were observed in periodontitis patients, regardless of probing depth. The relative abundance of specific genera differed notably between health and periodontitis states; Corynebacterium and Cardiobacterium decreased, whereas Schaalia increased in shallow pockets (PD 0–3 mm) of periodontitis relative to the health group. Co-occurrence network analysis on the species level revealed that the PD 4–5 mm group had the most complex interspecies interactions, followed by the PD 6–9 mm and PD 0–3 mm groups. These findings indicate significant variations in mi-crobial diversity, composition, and interspecies interactions associated with periodon-tal health and periodontitis severity, highlighting their potential relevance for clinical diagnosis and targeted therapeutic strategies. Full article

(This article belongs to the Section Medical Microbiology)

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20 pages, 950 KiB

Open AccessArticle

Genome-Informed Real-Time PCR Assay for Detection of ‘Candidatus Phytoplasma Prunorum,’ Which Is Associated with European Stone Fruit Yellows

by Jarred Yasuhara-Bell and Yazmín Rivera

Microorganisms 2025, 13(4), 929; https://doi.org/10.3390/microorganisms13040929 - 17 Apr 2025

Viewed by 245

Abstract

‘Candidatus Phytoplasma prunorum’ has been associated with severe disease in Prunus spp., which are commodities of economic importance in the USA. The introduction and establishment of ‘Ca. P. prunorum’ in the USA could result in huge economic losses, thus creating a [...] Read more.

‘Candidatus Phytoplasma prunorum’ has been associated with severe disease in Prunus spp., which are commodities of economic importance in the USA. The introduction and establishment of ‘Ca. P. prunorum’ in the USA could result in huge economic losses, thus creating a need for validated diagnostic tools, which are the cornerstone of successful surveillance, quarantine, and eradication measures. Whole-genome comparisons led to the identification of a diagnostic marker gene specific to ‘Ca. P. prunorum’ (PE639). The PE639 assay was duplexed with an 18S rDNA plant internal control and compared to modified 23S (phytoplasmas) and imp (‘Ca. P. mali’) assays. The PE639 assay produced congruent results to 23S and imp assays for all metrics, demonstrating high linearity, repeatability, intermediate precision, and reproducibility. The limit of detection was comparable for all assays tested, and all demonstrated 100% analytical specificity, selectivity, and diagnostic specificity for their respective target species. Assays metrics were consistent across two platforms, the ABI QuantStudio™ 5 and Bio-Rad CFX96™ OPUS. A synthetic gBlocks™ control was designed and validated to work with all assays, as well as conventional PCR assays targeting 16S rDNA and tuf genes. These validated assays and synthetic control represent beneficial tools that support efforts to protect USA agriculture and facilitate safe trade. Full article

(This article belongs to the Special Issue Phloem Localized Insect Transmitted Bacteria Associated with Plant Diseases)

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13 pages, 1513 KiB

Open AccessArticle

Intra- and Post-Operative Bacteriological Surveys of Surgical Site in Horses: A Single-Centre Study

by Anna Cerullo, Matteo Riccardo Di Nicola, Nicola Scilimati, Alice Bertoletti, Giuseppe Pollicino, Barbara Moroni, Marco Pepe, Sara Nannarone, Rodolfo Gialletti and Fabrizio Passamonti

Microorganisms 2025, 13(4), 928; https://doi.org/10.3390/microorganisms13040928 - 17 Apr 2025

Viewed by 245

Abstract

Bacterial contamination of the surgical site in horses is a major risk factor for the development of surgical site infections (SSIs), which increase morbidity, mortality, the hospitalisation period, antibiotic use, and management costs. While contamination is a prerequisite for infection, its progression to [...] Read more.

Bacterial contamination of the surgical site in horses is a major risk factor for the development of surgical site infections (SSIs), which increase morbidity, mortality, the hospitalisation period, antibiotic use, and management costs. While contamination is a prerequisite for infection, its progression to clinical infection depends on additional factors that compromise host defences. The present study, conducted at the Veterinary Teaching Hospital of the University of Perugia over an 11-month period, investigated bacterial contamination in 70 surgeries (53 clean and 17 clean-contaminated) at the end of the procedure. To exclude pre-existing contamination, a sterile swab was collected after surgical scrub, and only cases that entered surgery with a sterile operative field were considered. A swab, biopsy, and fine-needle aspiration from the wound margins were then performed at the end of the surgery to conduct a qualitative assessment of the bacterial contamination of the surgical sites. Risk factors for surgical field contamination were analysed separately for clean and clean-contaminated procedures. Specifically, for clean-contaminated surgeries, the presence of emergency conditions, surgery duration, and intra-operative complications were evaluated. For clean surgeries, risk factors included the type of operating room, surgical duration, tissue involved, use of local anaesthetics, and placement of surgical drapes. The results revealed bacterial contamination rates of 49.1% in clean surgeries and 41.2% in clean-contaminated surgeries. Coagulase-negative staphylococci were the most frequently isolated bacteria, followed by Burkholderia cepacia, Bacillus sp., and Stenotrophomonas maltophilia. A statistical analysis showed no significant results on the predictive factors of the contamination evaluated. However, the observed trends suggest the importance of further investigating these risk factors in a larger sample size. These results emphasise the importance of effective prophylactic measures to limit surgical site contamination. Future research will focus on optimising pre-operative and intra-operative prophylaxis strategies to reduce bacterial contamination to sub-pathogenic levels, thereby enhancing post-operative outcomes. Full article

(This article belongs to the Section Veterinary Microbiology)

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22 pages, 1266 KiB

Open AccessReview

The Strategy and Application of Gene Attenuation in Metabolic Engineering

by Yahui Zhang, Zhaoxia Jin, Linxia Liu and Dawei Zhang

Microorganisms 2025, 13(4), 927; https://doi.org/10.3390/microorganisms13040927 - 17 Apr 2025

Viewed by 288

Abstract

Metabolic engineering has a wide range of applications, spanning key sectors such as energy, pharmaceuticals, agriculture, chemicals, and environmental sustainability. Its core focus is on precisely modulating metabolic pathways to achieve efficient, sustainable, and environmentally friendly biomanufacturing processes, offering new possibilities for societal [...] Read more.

Metabolic engineering has a wide range of applications, spanning key sectors such as energy, pharmaceuticals, agriculture, chemicals, and environmental sustainability. Its core focus is on precisely modulating metabolic pathways to achieve efficient, sustainable, and environmentally friendly biomanufacturing processes, offering new possibilities for societal sustainable development. Gene attenuation is a critical technique within metabolic engineering, pivotal in optimizing metabolic fluxes and improving target metabolite yields. This review article discusses gene attenuation mechanisms, the applications across various biological systems, and implementation strategies. Additionally, we address potential future challenges and explore its potential to drive further advancements in the field. Full article

(This article belongs to the Section Microbial Biotechnology)

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19 pages, 1874 KiB

Open AccessArticle

The Effect of Climate Variables, Soil Characteristics, and Peanut Cultivars on the Rhizobial Bacteria Community

by Juan Li, Zhong-De Yang, En-Tao Wang, Li-Qin Sun and Yan Li

Microorganisms 2025, 13(4), 926; https://doi.org/10.3390/microorganisms13040926 - 17 Apr 2025

Viewed by 195

Abstract

Peanuts are widely cultivated across the world; however, peanut’s rhizobial community and the determinant factors of their composition are still to be elucidated. This study investigates the biogeography and determinant soil environmental factors for peanut rhizobia. A total of 1001 rhizobial isolates were [...] Read more.

Peanuts are widely cultivated across the world; however, peanut’s rhizobial community and the determinant factors of their composition are still to be elucidated. This study investigates the biogeography and determinant soil environmental factors for peanut rhizobia. A total of 1001 rhizobial isolates were obtained from the peanut root nodules, mainly belonging to two cultivars (X9 and M6) cultivated in 20 sampling sites across China. According to recA sequence analysis, all the isolates were classified as 84 haplotypes, and a representative strain for each haplotype was randomly selected to perform subsequent analyses. Based on multilocus sequence analysis (MLSA) of housekeeping genes dnaK, glnII, gyrB, recA, and rpoB, all the representative strains were classified as 42 genospecies in the genus Bradyrhizobium, including 12 effectively published and 30 undefined genospecies. Strains belonging to six genospecies were predominant (>5%), including B. ottawaense, B. liaoningense, B. yuanmingense, Bradyrhizobium sp. XXIX, B. guangdongense, and B. nanningense. However, only a single isolate was obtained for 15 genospecies. The diversity indices of peanut rhizobia distributed in South China are obviously higher than those in North China, but no obvious peanut cultivar selection for rhizobial genospecies was found. Correlation analyses indicated that the community composition of peanut rhizobia was mainly affected by MAP, MAT, soil AP, and pH. Nodulation tests indicated that the 79 representative strains belonging to 37 genospecies with both nodC and nifH could perform nitrogen-fixing symbiosis with peanuts. This study revealed the great diversity and varied composition of communities of peanut rhizobia in different geographic regions across China. Full article

(This article belongs to the Special Issue Nitrogen-Fixing Bacteria and Plant–Microbe Interaction)

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Microorganisms, Volume 13, Issue 4 (April 2025) – 257 articles

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