Microorganisms

19 pages, 10516 KiB

Open AccessArticle

The Isolation of Lead-Tolerant PGPR from Red Clover Soil and Its Role in Promoting the Growth of Alfalfa

by Wanting Nie, Yuchen Wu, Jingwen Jiang, Zicheng Wang, Meiqi Mu, Siwen Zhao, Minghao Yang, Xi Long, Xiujie Yin and Xiaohua Teng

Microorganisms 2025, 13(1), 210; https://doi.org/10.3390/microorganisms13010210 (registering DOI) - 19 Jan 2025

Abstract

Alfalfa (Medicago sativa L.) is an outstanding species used for the remediation of heavy metal-contaminated soil, and our previous research has shown that PGPR can promote plant growth under high-concentration lead stress. This discovery has forced scientists to search for PGPR strains [...] Read more.

Alfalfa (Medicago sativa L.) is an outstanding species used for the remediation of heavy metal-contaminated soil, and our previous research has shown that PGPR can promote plant growth under high-concentration lead stress. This discovery has forced scientists to search for PGPR strains compatible with alfalfa to develop an innovative bioremediation strategy for the remediation of lead-contaminated soil. This study used lead-tolerant rhizosphere soil of red clover as experimental material; cultured, isolated, and screened 52 excellent lead-tolerant bacteria that promote rhizosphere growth; and then inoculated them into alfalfa. Marked differences existed in the secretion of auxin, protease, and ACC deaminase among these strains. The results indicated that Pseudomonas spp. (strain Y2), Pseudomonas spp. (strain Y22), and Bacillus spp. (strain Y23) exhibited a strong growth-promoting ability in alfalfa, and there was no antagonistic reaction among the three strains, enabling their coexistence. The pot experiment manifested that strains Y2, Y22, Y23, and YH (a mixture of Y2, Y22, and Y23) could increase the plant height, root length, fresh and dry weight above ground, and fresh and dry weight below ground of alfalfa. They could all significantly raise the chlorophyll content and antioxidant enzyme activity in alfalfa (p < 0.05) and the content of malondialdehyde (MDA) in alfalfa. Furthermore, the concurrent inoculation of three distinct types of plant growth-promoting rhizobacteria (PGPR) significantly diminished lead (Pb) concentrations in rhizosphere soil, enhanced the levels of available potassium (AK) and available phosphorus (AP), and augmented the capacity of plants to absorb Pb. The results imply that PGPR can be employed to facilitate plant growth and microbial-assisted remediation of lead and other heavy metal-contaminated soil and establish a basis for further research on the growth-promoting mechanism of PGPR in plants. Full article

(This article belongs to the Section Plant Microbe Interactions)

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13 pages, 1039 KiB

Open AccessArticle

Prevalence and Antibiotic Resistance of Escherichia coli Isolated from Raw Cow’s Milk

by Roxana Ionela Drugea, Mădălina Iulia Siteavu, Elena Pitoiu, Cristina Delcaru, Ecaterina Monica Sârbu, Carmen Postolache and Stelian Bărăităreanu

Microorganisms 2025, 13(1), 209; https://doi.org/10.3390/microorganisms13010209 (registering DOI) - 19 Jan 2025

Abstract

Escherichia coli (E. coli) is one of the most common pathogens in both humans and livestock. This study aimed to investigate the prevalence of E. coli isolated from raw cow milk and evaluate its antimicrobial resistance rates. A total of 1696 milk samples were [...] Read more.

Escherichia coli (E. coli) is one of the most common pathogens in both humans and livestock. This study aimed to investigate the prevalence of E. coli isolated from raw cow milk and evaluate its antimicrobial resistance rates. A total of 1696 milk samples were collected from Romanian dairy farms from 2018 to 2022. E. coli was isolated on various selective agar media, such as Cled agar and Columbia Agar with 5% Sheep Blood. The identification of E. coli was performed by MALDI-TOF MS. E. coli isolates were tested for their susceptibility against 18 commonly used antibiotics in a disk diffusion method. The overall prevalence of E. coli was 22.45% of all isolated pathogens. Antibiogram analysis revealed that 27.51% of E. coli isolates from milk were multidrug-resistant. Resistance was highest for penicillin–novobiocin (87.78%), followed by streptomycin (53.7%). Resistance to six drugs (amoxicillin, streptomycin, kanamycin–cephalexin, marbofloxacin, ampicillin) showed a significant increasing trend over time, while for two drugs (penicillin G-framycetin, doxycycline), a significant decrease was observed. Our results suggest that milk can be a reservoir of bacteria with the potential for infection in humans via the food chain. Furthermore, there is a need for surveillance and monitoring to control the increase in resistance to currently used antimicrobials in dairy farms because the occurrence of multidrug-resistant E. coli isolated from milk poses a health hazard to consumers. Full article

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

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20 pages, 5634 KiB

Open AccessArticle

Association Analysis of the Genomic and Functional Characteristics of Halotolerant Glutamicibacter endophyticus J2-5-19 from the Rhizosphere of Suaeda salsa

by Longhao Sun, Shanshan Sun, Tianyang Liu, Xinmin Lei, Ruiqi Liu, Junyi Zhang, Shanshan Dai, Jing Li and Yanqin Ding

Microorganisms 2025, 13(1), 208; https://doi.org/10.3390/microorganisms13010208 (registering DOI) - 18 Jan 2025

Abstract

Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from [...] Read more.

Halotolerant plant growth-promoting bacteria (HT-PGPB) have attracted considerable attention for their significant potential in mitigating salt stress in crops. However, the current exploration and development of HT-PGPB remain insufficient to meet the increasing demands of agriculture. In this study, an HT-PGPB isolated from coastal saline-alkali soil in the Yellow River Delta was identified as Glutamicibacter endophyticus J2-5-19. The strain was capable of growing in media with up to 13% NaCl and producing proteases, siderophores, and the plant hormone IAA. Under 4‰ salt stress, inoculation with strain J2-5-19 significantly increased the wheat seed germination rate from 37.5% to 95%, enhanced the dry weight of maize seedlings by 41.92%, and notably improved the development of maize root systems. Moreover, this work presented the first whole-genome of Glutamicibacter endophyticus, revealing that G. endophyticus J2-5-19 resisted salt stress by expelling sodium ions and taking up potassium ions through Na⁺/H⁺ antiporters and potassium uptake proteins, while also accumulating compatible solutes such as betaine, proline, and trehalose. Additionally, the genome contained multiple key plant growth-promoting genes, including those involved in IAA biosynthesis, siderophore production, and GABA synthesis. The findings provide a theoretical foundation and microbial resources for the development of specialized microbial inoculants for saline-alkali soils. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

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14 pages, 448 KiB

Open AccessReview

Fungal Infections in Kidney Transplant Recipients: A Comprehensive Narrative Review

by Maria Mazzitelli, Federico Nalesso, Alberto Enrico Maraolo, Vincenzo Scaglione, Lucrezia Furian and Annamaria Cattelan

Microorganisms 2025, 13(1), 207; https://doi.org/10.3390/microorganisms13010207 (registering DOI) - 18 Jan 2025

Abstract

Background: Despite kidney transplantation being a life-saving procedure, patients experience a high risk of developing fungal infections (FIs), with an increased risk of both morbidity and mortality, especially during the first year after transplant. Methods: We herein conducted a narrative review of the [...] Read more.

Background: Despite kidney transplantation being a life-saving procedure, patients experience a high risk of developing fungal infections (FIs), with an increased risk of both morbidity and mortality, especially during the first year after transplant. Methods: We herein conducted a narrative review of the most common FIs in kidney transplant recipients (KTRs), with a focus on prevalence, risk factors, mortality, and prevention strategies. Results: The most common fungal pathogens in KTRs include Candida species (up to 70% of the overall FIs), Aspergillus species, Pneumocystis jiroveci, and Cryptococcus species. Fungal colonization, diabetes mellitus, chronic liver disease, malnutrition, and pre-existing lung conditions should all be acknowledged as possible predisposing risk factors. The mortality rate can vary from 25 to 50% and according to different settings and the types of FIs. Preventive strategies are critical for reducing the incidence of FIs in this population. These include antifungal prophylaxis, environmental precautions, and infection control measures. The use of novel tools (such as PCR-based molecular assays and NGS) for rapid and accurate diagnosis may play an important role. Conclusions: Early recognition, the appropriate use of antifungal therapy, and preventive strategies are essential for improving graft loss and fatal outcomes in this vulnerable population. Future research is needed to optimize diagnostic tools, identify novel antifungal agents, and develop better prophylactic strategies for high-risk transplant recipients. Full article

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

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16 pages, 2259 KiB

Open AccessArticle

Comparative Genomic Analysis of Campylobacter Plasmids Identified in Food Isolates

by Yiping He, Gretchen Elizabeth Dykes, Siddhartha Kanrar, Yanhong Liu, Nereus W. Gunther IV, Katrina L. Counihan, Joe Lee and Joseph A. Capobianco

Microorganisms 2025, 13(1), 206; https://doi.org/10.3390/microorganisms13010206 (registering DOI) - 18 Jan 2025

Abstract

Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, [...] Read more.

Campylobacter is one of the leading bacterial causes of gastroenteritis worldwide. It frequently contaminates poultry and other raw meat products, which are the primary sources of Campylobacter infections in humans. Plasmids, known as important mobile genetic elements, often carry genes for antibiotic resistance, virulence, and self-mobilization. They serve as the main vectors for transferring genetic material and spreading resistance and virulence among bacteria. In this study, we identified 34 new plasmids from 43 C. jejuni and C. coli strains isolated from retail meat using long-read and short-read genome sequencing. Pangenomic analysis of the plasmid assemblies and reference plasmids from GenBank revealed five distinct groups, namely, pTet, pVir, mega plasmids (>80 kb), mid plasmids (~30 kb), and small plasmids (<6 kb). Pangenomic analysis identified the core and accessory genes in each group, indicating a high degree of genetic similarity within groups and substantial diversity between the groups. The pTet plasmids were linked to tetracycline resistance phenotypes in host strains. The mega plasmids carry multiple genes (e.g., aph(3’)-III, type IV and VI secretion systems, and type II toxin–antitoxin systems) important for plasmid mobilization, virulence, antibiotic resistance, and the persistence of Campylobacter. Together, the identification and comprehensive genetic characterization of new plasmids from Campylobacter food isolates contributes to understanding the mechanisms of gene transfer, particularly the spread of genetic determinants of virulence and antibiotic resistance in this important pathogen. Full article

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

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18 pages, 17896 KiB

Open AccessArticle

Biodegradation of Phenol at High Initial Concentration by Rhodococcus opacus 3D Strain: Biochemical and Genetic Aspects

by Tatiana O. Anokhina, Tatiana Z. Esikova, Valentina N. Polivtseva, Nataliya E. Suzina and Inna P. Solyanikova

Microorganisms 2025, 13(1), 205; https://doi.org/10.3390/microorganisms13010205 (registering DOI) - 18 Jan 2025

Abstract

Phenolic compounds are an extensive group of natural and anthropogenic organic substances of the aromatic series containing one or more hydroxyl groups. The main sources of phenols entering the environment are waste from metallurgy and coke plants, enterprises of the leather, furniture, and [...] Read more.

Phenolic compounds are an extensive group of natural and anthropogenic organic substances of the aromatic series containing one or more hydroxyl groups. The main sources of phenols entering the environment are waste from metallurgy and coke plants, enterprises of the leather, furniture, and pulp and paper industries, as well as wastewater from the production of phenol–formaldehyde resins, adhesives, plastics, and pesticides. Among this group of compounds, phenol is the most common environmental pollutant. One of the cheapest and most effective ways to combat phenol pollution is biological purification. However, the inability of bacteria to decompose high concentrations of phenol is a significant limitation. Due to the uncoupling of oxidative phosphorylation, phenol concentrations above 1 g/L are toxic and inhibit cell growth. This article presents data on the biodegradative potential of Rhodococcus opacus strain 3D. This strain is capable of decomposing a wide range of toxicants, including phenol. In the present study, cell growth with phenol, growth after rest, growth of immobilized cells before and after rest, phase contrast, and scanning microscopy of immobilized cells on fiber were studied in detail. The free-living and immobilized cells can decompose phenol concentrations up to 1.5 g/L and 2.5 g/L, respectively. The decomposition of the toxicant was catalyzed by the enzymes catechol 1,2-dioxygenase and cis,cis-muconate cycloisomerase. The role of protocatechuate 3,4-dioxygenase in biodegradative processes is discussed. In this work, it is shown that the immobilized cells can be stored for a long time (up to 2 years) without significant loss of their degradation activity. An assessment of the induction of genes potentially involved in this process was taken. Based on our investigation, we can conclude that this strain can be considered an effective destructor that is capable of degrading phenol at high concentrations, increases its biodegradative potential during immobilization, and retains this ability for a long storage time. Therefore, the strain can be used in biotechnology for the purification of aqueous samples at high concentrations from phenolic contamination. Full article

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

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15 pages, 1375 KiB

Open AccessArticle

Photodynamic Therapy with Protoporphyrin IX Precursors Using Artificial Daylight Improves Skin Antisepsis for Orthopedic Surgeries

by Tiziano A. Schweizer, Julia S. Würmli, Julia Prinz, Maximilian Wölfle, Roger Marti, Hendrik Koliwer-Brandl, Ashley M. Rooney, Vanni Benvenga, Adrian Egli, Laurence Imhof, Philipp P. Bosshard and Yvonne Achermann

Microorganisms 2025, 13(1), 204; https://doi.org/10.3390/microorganisms13010204 (registering DOI) - 18 Jan 2025

Abstract

Classical preoperative skin antisepsis is insufficient in completely eliminating bacterial skin colonization for arthroplasty. In contrast, photodynamic therapy (PDT) with red light and methyl-aminolevulinate (MAL), combined with skin antisepsis, led to the absence of bacterial growth in healthy participants, though with local skin [...] Read more.

Classical preoperative skin antisepsis is insufficient in completely eliminating bacterial skin colonization for arthroplasty. In contrast, photodynamic therapy (PDT) with red light and methyl-aminolevulinate (MAL), combined with skin antisepsis, led to the absence of bacterial growth in healthy participants, though with local skin erythema, posing an obstacle for orthopedic surgery. Therefore, we explored whether artificial daylight PDT (PDT-DL) was superior to red light. Twenty healthy participants were allocated to either 5-aminolevulinic acid-(5-ALA) PDT-DL (n = 10) or MAL-PDT-DL (n = 10) before antisepsis with povidone-iodine/alcohol. Skin swabs from the groin were taken to cultivate bacteria at baseline, after PDT-DL, and after the subsequent antisepsis. Additional swabs were taken on day 4 before and after antisepsis without PDT. The contralateral groin of each participant and of ten additional healthy volunteers served as the control (n = 30). In selected participants, 16S rRNA-based amplicon deep sequencing was performed. All participants showed a baseline bacterial colonization. After a PDT-DL with skin antisepsis, bacterial growth occurred in three (30%) and in one (10%) participants with 5-ALA and MAL, respectively, compared to the sixteen (55%) participants in the control group. On day 4, three (30%) participants per group showed positive cultures post antisepsis. Adverse effects were reported in six (60%) and zero (0%) participants for 5-ALA- and MAL-PDT-DL, respectively. The skin bacteriome changes correlated with the bacterial culture results. The MAL-PDT-DL with skin antisepsis significantly increased bacterial reduction on the skin without adverse effects. This offers an opportunity to prevent infections in arthroplasty patients and reduce antibiotic use, thus contributing to antibiotic stewardship goals emphasized in the One Health approach. Full article

(This article belongs to the Special Issue Photodynamic Inactivation in Bacterial Infections within a One Health Setting)

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19 pages, 3427 KiB

Open AccessArticle

Microbial Composition Change and Heavy Metal Accumulation in Response to Organic Fertilization Reduction in Greenhouse Soil

by Qin Qin, Jun Wang, Lijuan Sun, Shiyan Yang, Yafei Sun and Yong Xue

Microorganisms 2025, 13(1), 203; https://doi.org/10.3390/microorganisms13010203 (registering DOI) - 18 Jan 2025

Abstract

Increased application of organic fertilizer is an effective measure to improve greenhouse soil quality. However, prolonged and intensive application of organic manure has caused nutrient and certain heavy metal accumulation in greenhouse soil. Therefore, the optimal quantity of organic manure required to sustain [...] Read more.

Increased application of organic fertilizer is an effective measure to improve greenhouse soil quality. However, prolonged and intensive application of organic manure has caused nutrient and certain heavy metal accumulation in greenhouse soil. Therefore, the optimal quantity of organic manure required to sustain soil fertility while mitigating the accumulation of heavy metals and other nutrients resulting from continuous application remains unclear. This study evaluated the impacts of sustained and reduced organic manure application on soil physicochemical properties, heavy metal contents, and microbial community through a 9-year greenhouse field experiment. Treatments included a control without any fertilizer (CK), conventional manure (M), and three reduced manure treatments (−25%M, −37.5%MNPK, and −50%MNPK). Compared to CK, either M treatment or manure reduction treatments either maintained or significantly elevated soil pH and soil organic matter, total nitrogen, total phosphorus, and available phosphorus. Notably, −37.5%MNPK exhibited further increases in the available nitrogen and potassium. The M treatment significantly increased in the total concentrations of cadmium, copper, lead, zinc, and the availability of chromium and zinc. However, reduced manure treatments showed no change or a significantly reduced in heavy metal availability. The −25%M and −37.5%MNPK treatments significantly improved bacterial diversity. Reducing organic manure altered microbial taxa abundance. The soil pH emerged as the primary driving factor for variation in the bacterial community structure, whereas available nitrogen, potassium, and lead were the key factors influencing fungal community structural changes. These results indicate that reducing excessive organic manure input is an effective strategy to control heavy metal accumulation, enhance soil fertility, and optimize microbial community structure. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)

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12 pages, 2808 KiB

Open AccessArticle

Efflux Pumps and Porins Enhance Bacterial Tolerance to Phenolic Compounds by Inhibiting Hydroxyl Radical Generation

by Xinyue Sui, Likun Guo, Zixian Bao, Mo Xian and Guang Zhao

Microorganisms 2025, 13(1), 202; https://doi.org/10.3390/microorganisms13010202 (registering DOI) - 18 Jan 2025

Abstract

Phenolic compounds are industrially versatile chemicals that have been successfully produced in microbial cell factories. Unfortunately, most phenolic compounds are highly toxic to cells in specific cellular environments or above a particular concentration because they form a complex with iron and promote hydroxyl [...] Read more.

Phenolic compounds are industrially versatile chemicals that have been successfully produced in microbial cell factories. Unfortunately, most phenolic compounds are highly toxic to cells in specific cellular environments or above a particular concentration because they form a complex with iron and promote hydroxyl radical production in Fenton reactions, resulting in the ferroptosis of cells. Here, we demonstrated that overexpression of efflux pumps and porins, including porins LamB and OmpN, and efflux pumps EmrAB, MdtABC, and SrpB, can enhance Escherichia coli phloroglucinol (PG) tolerance by inhibiting the generation of hydroxyl radicals. In addition, LamB and OmpN overexpression improved the bioproduction of PG. Furthermore, efflux pumps and porins can enhance bacterial tolerance to various phenolic compounds, including phenol, catechol, resorcinol, pyrogallol, and 2-naphthol. LamB and MdtABC confer a generalized tolerance to phenols. However, EmrAB, OmpN, and SrpB showed inconsistent effects of bacterial tolerance to different phenolic compounds. Our results will theoretically support the construction of phenolic compound-tolerant bacteria strains, which should be more efficient in the biosynthesis of phenols. Full article

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

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8 pages, 205 KiB

Open AccessCommunication

Clinical Evaluation of a Rapid Reciprocal-Flow PCR Assay and Real-Time PCR Assay with Quenching Probe for Detection of Mycobacterium tuberculosis Complex

by Kosuke Kosai, Keisuke Matsumoto, Takahisa Ishikawa, Yasuhide Kawamoto, Norihiko Akamatsu, Kenji Ota, Fujiko Mitsumoto-Kaseida, Norihito Kaku, Hiroo Hasegawa, Koichi Izumikawa, Hiroshi Mukae and Katsunori Yanagihara

Microorganisms 2025, 13(1), 201; https://doi.org/10.3390/microorganisms13010201 - 17 Jan 2025

Abstract

This study investigated the diagnostic efficiencies of two assays for the detection of Mycobacterium tuberculosis complex: (1) the reciprocal-flow real-time polymerase chain reaction (PCR)-based GeneSoC assay and (2) the real-time PCR based GENECUBE MTB assay with quenching probe. These assays were performed for [...] Read more.

This study investigated the diagnostic efficiencies of two assays for the detection of Mycobacterium tuberculosis complex: (1) the reciprocal-flow real-time polymerase chain reaction (PCR)-based GeneSoC assay and (2) the real-time PCR based GENECUBE MTB assay with quenching probe. These assays were performed for stored clinical samples and results were compared with the confirmed results based on culture and COBAS TaqMan MTB assay. A total of 53 samples (20 confirmed positives and 33 confirmed negatives) were included in the performance analysis. The GeneSoC assay showed concordance in all 53 samples, regardless of specimen type, while the GENECUBE MTB assay showed concordance in 19 of the 20 confirmed positive samples and all 33 confirmed negative samples. The overall agreement was 100.0% for the GeneSoC assay and 98.1% for the GENECUBE MTB assay. Positive and negative percent agreements were 100.0% each for the GeneSoC assay and 95.0% and 100.0%, respectively, for the GENECUBE MTB assay. Both the GeneSoC and GENECUBE MTB assays exhibited excellent performance in detecting M. tuberculosis complex. The GeneSoC assay is useful for independent assays of individual samples, whereas the GENECUBE MTB assay is suitable for batch assays of multiple samples. Full article

(This article belongs to the Special Issue Detection and Analysis of Clinical Microbial Infections, Second Edition)

16 pages, 1166 KiB

Open AccessArticle

Probiotic Supplementation Alleviates Corticosterone-Induced Fatty Liver Disease by Regulating Hepatic Lipogenesis and Increasing Gut Microbiota Diversity in Broilers

by Yuyan Feng, Wenqing Mei, Qu Chen, Xiaojing Chen, Yingdong Ni, Mingming Lei and Jie Liu

Microorganisms 2025, 13(1), 200; https://doi.org/10.3390/microorganisms13010200 - 17 Jan 2025

Abstract

Emerging evidence indicates a close relationship between gut microbiota and fatty liver disease. It has been suggested that gut microbiota modulation with probiotics ameliorates fatty liver disease in rodents and humans, yet it remains unclear whether the same results will also be obtained [...] Read more.

Emerging evidence indicates a close relationship between gut microbiota and fatty liver disease. It has been suggested that gut microbiota modulation with probiotics ameliorates fatty liver disease in rodents and humans, yet it remains unclear whether the same results will also be obtained in poultry. The aim of this study was to investigate whether a mixture of probiotics supplemented after hatching can prevent CORT-induced fatty liver disease in broilers, and to determine how such effects, if any, are associated with hepatic de novo lipogenesis and gut microbiota composition. Ninety-six one-day-old green-legged chickens were divided into a control group (CON) and probiotic group (PB). At 28 days of age, fatty liver was induced in 16 broilers that were randomly selected from the CON or PB group. At the end of the experiment, broilers from four groups, (i) the control group (CON), (ii) corticosterone group (CORT), (iii) probiotic group (PB), and (iv) PB plus CORT group (CORT&PB), were slaughtered for sampling and analysis. The results showed that probiotic administration significantly prevented CORT-induced body weight loss (p < 0.05) but did not alleviate the weight loss of immune organs caused by CORT. Compared to CON, the broilers in the CORT group exhibited a significant increase in triglyceride (TG) levels in plasma and liver (p < 0.01), as well as severe hepatocytic steatosis and hepatocellular ballooning, which was accompanied by the upregulation of hepatic lipogenesis gene expression. However, probiotic supplementation markedly decreased the intrahepatic lipid accumulation and steatosis histological score, which was associated with the downregulation of sterol regulatory element-binding protein-1 (SREBP1) and acetyl-CoA carboxylase (ACC) mRNA (p < 0.05) and the expression of its protein (p = 0.06). The cecal microbiota composition was determined by 16S rRNA high-throughput sequencing. The results showed that CORT treatment induced distinct gut microbiota alterations with a decrease in microbial diversity and an increase in Proteobacteria abundance (p < 0.05). In contrast, probiotic supplementation increased the beta diversity, the community richness, and the diversity index (p > 0.05), as well as the abundance of Intestinimonas (p < 0.05). Our results indicate that CORT treatment induced severe fatty liver disease and altered the gut microbiota composition in broilers. However, post-hatching probiotic supplementation had a beneficial effect on alleviating fatty liver disease by regulating lipogenic gene expression and increasing gut microbiota diversity and the abundance of beneficial bacteria. We demonstrate for the first time that the supplementation of probiotics to chicks had a beneficial effect on preventing fatty liver disease through regulating lipogenic gene expression and improving the gut microbial balance. Thus, our results indicate that probiotics are a potential nutritional agent for preventing fatty liver disease in chickens. Full article

(This article belongs to the Special Issue Beneficial Microbes: Food, Mood and Beyond, 2nd Edition)

13 pages, 359 KiB

Open AccessArticle

In Vivo and In Vitro Studies Assessing the Antiviral Efficacy of Double Combinations Against Coxsackievirus B Infection

by Adelina Stoyanova, Simeon Galabov, Vadim Makarov and Angel S. Galabov

Microorganisms 2025, 13(1), 199; https://doi.org/10.3390/microorganisms13010199 - 17 Jan 2025

Abstract

Coxsackievirus B (CVB) infections, ranging from mild to severe diseases, lack specific antiviral treatments, underscoring the need for novel therapeutic strategies. Drug therapy is an important tool for controlling enterovirus infections, but clinically effective drugs do not currently exist, mainly due to the [...] Read more.

Coxsackievirus B (CVB) infections, ranging from mild to severe diseases, lack specific antiviral treatments, underscoring the need for novel therapeutic strategies. Drug therapy is an important tool for controlling enterovirus infections, but clinically effective drugs do not currently exist, mainly due to the development of drug resistance. Combination therapy with two or more drugs has the potential to successfully inhibit viral infection more effectively than either drug alone as well as delay the development of resistance. This study explores the consecutive alternating administration (CAA) scheme in mice with CVB1 infection, utilizing double antiviral combinations consisting of pleconaril and MDL-860, with guanidine hydrochloride and oxoglaucine. The CAA combinations of pleconaril achieved a survival rate, in infected mice, of up to 59%, while the combinations of MDL-860 showed no significant effects. CAA reduced mortality, prolonged mean survival time (up to 5 days), and mitigated drug resistance compared to monotherapy or simultaneous administration. Monotherapeutic courses and daily administration of double combinations had no effect. Phenotypic characterization using the IC₅₀ marker of virus isolates from brain tissue of infected and treated mice was of particular importance for the evaluation of the CAA treatment scheme. The results show increased susceptibility of the virus isolates to the partner compounds in double CAA combinations. In contrast, virus isolates from the monotherapeutic groups manifested a diminished susceptibility to their respective compound, which signals the development of drug resistance. All data obtained prove the potential of the CAA scheme for the development of effective chemotherapy of enterovirus infections. Full article

(This article belongs to the Special Issue Epidemiology and Pathogenesis of Human Enteroviruses: 2nd Edition)

21 pages, 2808 KiB

Open AccessArticle

Beyond Microbial Variability: Disclosing the Functional Redundancy of the Core Gut Microbiota of Farmed Gilthead Sea Bream from a Bayesian Network Perspective

by Federico Moroni, Fernando Naya-Català, Ahmed Ibrahem Hafez, Ricardo Domingo-Bretón, Beatriz Soriano, Carlos Llorens and Jaume Pérez-Sánchez

Microorganisms 2025, 13(1), 198; https://doi.org/10.3390/microorganisms13010198 - 17 Jan 2025

Abstract

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core [...] Read more.

The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core microbiota and constructing stochastic Bayesian network (BN) models with SAMBA. We combined three experiments performed with gilthead sea bream juveniles of the same hatchery batch, reared at the same season/location, and fed with diets enriched on processed animal proteins (PAP) and other alternative ingredients (NOPAP-PP, NOPAP-SCP). Microbiota data analysis disclosed a high individual taxonomic variability, a high functional homogeneity within trials and highlighted the importance of the core microbiota, clustering PAP and NOPAP fish microbiota composition. For both NOPAP and PAP BNs, > 99% of the microbiota population were modelled, with a significant proportion of bacteria (55–69%) directly connected with the diet variable. Functional enrichment identified 11 relevant pathways expressed by different taxa across the different BNs, confirming the high metabolic plasticity and taxonomic heterogeneity. Altogether, these results reinforce the comprehension of the functional bacteria–host interactions and in the near future, allow the use of microbiota as a species-specific growth and welfare benchmark of livestock animals, and farmed fish in particular. Full article

(This article belongs to the Special Issue Host–Bacteria Interactions in Aquaculture Systems, 2nd Edition)

13 pages, 577 KiB

Open AccessReview

Chronic Endometritis and Antimicrobial Resistance: Towards a Multidrug-Resistant Endometritis? An Expert Opinion

by Francesco Di Gennaro, Giacomo Guido, Luisa Frallonardo, Laura Pennazzi, Miriana Bevilacqua, Pietro Locantore, Amerigo Vitagliano, Annalisa Saracino and Ettore Cicinelli

Microorganisms 2025, 13(1), 197; https://doi.org/10.3390/microorganisms13010197 - 17 Jan 2025

Abstract

Chronic endometritis (CE) is a persistent inflammatory condition of the endometrium characterized by abnormal infiltration of plasma cells into the endometrial stroma. Frequently associated with repeated implantation failure, recurrent pregnancy loss, and infertility, CE significantly impacts women’s health, contributing to conditions such as [...] Read more.

Chronic endometritis (CE) is a persistent inflammatory condition of the endometrium characterized by abnormal infiltration of plasma cells into the endometrial stroma. Frequently associated with repeated implantation failure, recurrent pregnancy loss, and infertility, CE significantly impacts women’s health, contributing to conditions such as abnormal uterine bleeding and endometriosis. Treatment typically involves antibiotic therapy; however, the efficacy of these treatments is increasingly compromised by the rise of antimicrobial resistance (AMR). This paper examines the critical links between AMR and CE, proposing strategies to enhance clinical management and optimize treatment outcomes. Full article

(This article belongs to the Special Issue New Obstacles in Bacterial, Fungal and Viral Infections: Antimicrobial Resistance and Emerging Pathogens)

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20 pages, 901 KiB

Open AccessArticle

Risk Factors and Circulating Subtypes of Cryptosporidium spp. and Giardia duodenalis in Hospitalized Children in Mozambique

by Ofélia Nhambirre, Maria Luísa Lobo, Idalécia Cossa-Moiane, Adilson Bauhofer, Nilsa de Deus and Olga Matos

Microorganisms 2025, 13(1), 196; https://doi.org/10.3390/microorganisms13010196 - 17 Jan 2025

Abstract

Cryptosporidium spp. and Giardia duodenalis are important diarrheal agents in children in developing countries. Little is known about their molecular epidemiology; as such, the objective of this study was to determine the risk factors and genetic diversity of both parasites in diarrheal samples [...] Read more.

Cryptosporidium spp. and Giardia duodenalis are important diarrheal agents in children in developing countries. Little is known about their molecular epidemiology; as such, the objective of this study was to determine the risk factors and genetic diversity of both parasites in diarrheal samples in Mozambique. In this study, two nested PCRs targeting ssurRNA and gp60 genes were used for genetic diversity of Cryptosporidium spp. and b-giardin for G. duodenalis. Sociodemographic and clinical characteristics were obtained through questionnaires. The location (odds ratio [OR] 3.499), mother’s education level (OR 2.150) and age were significant factors for acquiring infection by Cryptosporidium spp. (p < 0.05). Cryptosporidium hominis was the predominant (77.8%) species. Four families (three C. hominis and one C. parvum) were identified, with the highest for Ib (73.9%), followed by Id (13%), Ia (8.7%) and IIc (4.3%). The location (p-value < 0.001), drinking untreated water (p-value = 0.04) and living in masonry houses (p-value = 0.002) were identified as risks associated with G. duodenalis infection. Assemblage A was the dominant type (65.2%). Among the subassemblages of assemblage A, AII was the most frequent (86.6%), followed by AIII (6.6%). For assemblage B, subassemblages BIII (87.5%) and BIV (12.5%) were identified. The dominance of the subtype IbA9G3 of C. hominis, as well as the AII subassemblage of G. duodenalis, seems to indicate that the transmission of both protozoa occurs mainly through the anthroponotic route. Full article

(This article belongs to the Special Issue The One Health Challenge: Zoonotic Parasites)

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19 pages, 5639 KiB

Open AccessArticle

First Detection and Genomic Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolates in Bulgaria

by Tanya V. Strateva, Preslava Hristova, Temenuga J. Stoeva, Hristina Hitkova and Slavil Peykov

Microorganisms 2025, 13(1), 195; https://doi.org/10.3390/microorganisms13010195 - 17 Jan 2025

Abstract

Linezolid is an oxazolidinone antibiotic and is considered a last-resort treatment option for serious infections caused by problematic Gram-positive pathogens, including vancomycin-resistant enterococci. The present study aimed to explore the linezolid resistance mechanisms and genomic characteristics of two vancomycin-susceptible Enterococcus faecalis isolates from [...] Read more.

Linezolid is an oxazolidinone antibiotic and is considered a last-resort treatment option for serious infections caused by problematic Gram-positive pathogens, including vancomycin-resistant enterococci. The present study aimed to explore the linezolid resistance mechanisms and genomic characteristics of two vancomycin-susceptible Enterococcus faecalis isolates from Bulgaria. The strains designated Efs2503-bg (inpatient from Pleven) and Efs966-bg (outpatient from Varna) were recovered from wounds in 2018 and 2023, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing, and phylogenomic analysis based on 332 linezolid-resistant E. faecalis genomes were performed. Efs2503-bg was high-level resistant to linezolid (MIC > 256 mg/L) and displayed the G2576T mutation affecting three of the four 23S rDNA loci. Efs966-bg (MIC = 8 mg/L) carried a plasmid-located optrA determinant surrounded by fexA and ermA. No mutations in the genes encoding for ribosomal proteins L3, L4, and L22 were detected. The isolates belonged to the sequence types ST6 (Efs2503-bg) and ST1102 (Efs966-bg). Phylogenomic analysis revealed that Efs2503-bg and Efs966-bg are genetically distinct, with a difference of 12,051 single-nucleotide polymorphisms. To our knowledge, this is the first report of linezolid-resistant enterococci in Bulgaria. Although the global incidence of linezolid-resistant enterococci is still low, their emergence is alarming and poses a growing clinical threat to public health. Full article

(This article belongs to the Collection Feature Papers in Medical Microbiology)

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21 pages, 5649 KiB

Open AccessArticle

Bidirectional Mendelian Randomization Analysis to Study the Relationship Between Human Skin Microbiota and Radiation-Induced Skin Toxicity

by Hui Chen, Xiaojie Xia, Kexin Shi, Tianyi Xie, Xinchen Sun, Zhipeng Xu and Xiaolin Ge

Microorganisms 2025, 13(1), 194; https://doi.org/10.3390/microorganisms13010194 - 17 Jan 2025

Abstract

Radiation-induced skin toxicity, resulting from ionizing or nonionizing radiation, is a common skin disorder. However, the underlying relationship between skin microbiota and radiation-induced skin toxicity remains largely unexplored. Herein, we uncover the microbiota–skin interaction based on a genome-wide association study (GWAS) featuring 150 [...] Read more.

Radiation-induced skin toxicity, resulting from ionizing or nonionizing radiation, is a common skin disorder. However, the underlying relationship between skin microbiota and radiation-induced skin toxicity remains largely unexplored. Herein, we uncover the microbiota–skin interaction based on a genome-wide association study (GWAS) featuring 150 skin microbiota and three types of skin microenvironment. Summary datasets of human skin microbiota were extracted from the GWAS catalog database, and summary datasets of radiation-induced skin toxicity from the FinnGen biobank. Mendelian Randomization (MR) analysis was leveraged to sort out the causal link between skin microbiota and radiation-induced skin toxicity. We identified 33 causal connections between human skin microbiota and radiation-induced skin toxicity, including 19 positive and 14 negative causative directions. Among these potential associations, the genus Staphylococcus could serve as a common risk factor for radiation-induced skin toxicity, especially for radiodermatitis. And Streptococcus salivarius was identified as a potential protective factor against radiation-induced skin toxicity. Additional analysis indicated no pleiotropy, heterogeneity, or reverse causal relationship in the results. We comprehensively assessed potential associations of skin microbiota with radiation-induced skin toxicity and identified several suggestive links. Our results provide promising targets for the prevention and treatment of radiation-induced skin toxicity. Full article

(This article belongs to the Special Issue Skin Microbiome)

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19 pages, 3419 KiB

Open AccessArticle

Phenotypic Profiling of Selected Cellulolytic Strains to Develop a Crop Residue-Decomposing Bacterial Consortium

by Arman Shamshitov, Egidija Satkevičiūtė, Francesca Decorosi, Carlo Viti and Skaidrė Supronienė

Microorganisms 2025, 13(1), 193; https://doi.org/10.3390/microorganisms13010193 - 17 Jan 2025

Abstract

Slow decomposition rates of cereal crop residues can lead to agronomic challenges, such as nutrient immobilization, delayed soil warming, and increased pest pressures. In this regard, microbial inoculation with efficient strains offers a viable and eco-friendly solution to accelerating the decomposition process of [...] Read more.

Slow decomposition rates of cereal crop residues can lead to agronomic challenges, such as nutrient immobilization, delayed soil warming, and increased pest pressures. In this regard, microbial inoculation with efficient strains offers a viable and eco-friendly solution to accelerating the decomposition process of crop residues. However, this solution often focuses mostly on selecting microorganisms based on the appropriate enzymic capabilities and neglects the metabolic versatility required to utilize both structural and non-structural components of residues. Therefore, this study aimed to address these limitations by assessing the metabolic profiles of five previously identified cellulolytic bacterial strains, including Bacillus pumilus 1G17, Micromonospora chalcea 1G49, Bacillus mobilis 5G17, Streptomyces canus 1TG5, and Streptomyces achromogenes 3TG21 using Biolog Phenotype Microarray analysis. Moreover, this study evaluated the impact of wheat straw inoculation with single strains and a bacterial consortium on soil organic carbon and nitrogen content in a pot experiment. Results revealed that, beyond the core subset of 12 carbon sources, the strains exhibited diverse metabolic capacities in utilizing 106 carbon sources. All strains demonstrated effective straw biomass degradationcompared to the negative control, with significant differences detected only in oil seed rape straw biodegradation estimations. Furthermore, wheat straw inoculated with a bacterial consortium showed a significant increase in soil organic carbon content after 180 days in the pot experiment. Overall, these findings underscore the critical role of metabolic profiling in gaining a deeper understanding of microbial capabilities and addressing the complexities of residue composition and environmental variability. Full article

(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)

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15 pages, 1951 KiB

Open AccessArticle

Beneficial Effects of In Vitro Reconstructed Human Gut Microbiota by Ginseng Extract Fermentation on Intestinal Cell Lines

by Margherita Finazzi, Federica Bovio, Matilde Forcella, Marina Lasagni, Paola Fusi and Patrizia Di Gennaro

Microorganisms 2025, 13(1), 192; https://doi.org/10.3390/microorganisms13010192 - 17 Jan 2025

Abstract

Oxidative stress caused by reactive oxygen species (ROS) affects the aging process and increases the likelihood of several diseases. A new frontier in its prevention includes bioactive foods and natural extracts that can be introduced by the diet in combination with specific probiotics. [...] Read more.

Oxidative stress caused by reactive oxygen species (ROS) affects the aging process and increases the likelihood of several diseases. A new frontier in its prevention includes bioactive foods and natural extracts that can be introduced by the diet in combination with specific probiotics. Among the natural compounds that we can introduce by the diet, Panax ginseng extract is one of the most utilized since it contains a vast number of bioactive molecules such as phenolic acids, flavonoids, and polysaccharides that have been shown to possess antioxidant, anti-ageing, anti-cancer, and immunomodulatory activity. In this work, the ability of a P. ginseng extract in combination with a probiotic formulation was taken into consideration to evaluate its effects on the modulation of in vitro reconstructed human gut microbiota (HGM). After evaluating the growth of the individual strains on the ginseng extract, we tested the in vitro reconstructed HGM setup (probiotics, minimal core, and whole community) using 2% w/v ginseng as the only carbon and energy source. The probiotic strains reached the highest growth, while the minimal core and the whole community showed almost the same growth. Specifically, the presence of the ginseng extract favors L. plantarum and B. animalis subsp. lactis among the probiotics, while B. cellulosilyticus prevails over the other strains in the minimal core condition. In the presence of both probiotics and minimal core strains, L. plantarum, B. animalis subsp. lactis, and B. cellulosilyticus reach the highest growth values. The bacterial metabolites produced during ginseng extract fermentation in the three conditions were administered to human intestinal epithelial cells (HT-29) to investigate a potential antioxidant effect. Remarkably, our results highlighted a significant reduction in the total ROS and a slightly reduction in the cytosolic superoxide anion content in HT-29 cells treated with bacterial metabolites deriving from ginseng extract fermentation by the whole community. Full article

(This article belongs to the Section Gut Microbiota)

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