Microorganisms

17 pages, 4342 KB

Open AccessArticle

Metagenomic Signatures of Colorectal Cancer in the Jordanian Population: A Regional Case-Control Analysis Using 16S rRNA Profiling

by Lo’ai Alanagreh, Minas A. Mustafa, Mohammad Borhan Al-Zghoul, Muhannad I. Massadeh, Osamah Batiha, Maher Sughayer, Rashed Taiseer Almashakbeh, Haya Bader Abu Suilike, Faten S. Tout and Foad Alzoughool

Microorganisms 2025, 13(8), 1963; https://doi.org/10.3390/microorganisms13081963 - 21 Aug 2025

Viewed by 840

Abstract

The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize [...] Read more.

The gut microbiota plays a pivotal role in developing colorectal cancer (CRC) through interactions with host immunity, metabolism, and inflammation. However, microbiome-based studies remain scarce in Middle Eastern populations, limiting regional insights into microbial signatures associated with CRC. This study aimed to characterize the gut microbiota profiles of Jordanian CRC patients using 16S rRNA gene sequencing and compare them to those of healthy controls from the GutFeeling KnowledgeBase (GutFeelingKB). Stool samples from 50 CRC patients were analyzed using Illumina iSeq targeting the V3–V4 region. Taxonomic profiling was conducted with a standardized 16S metagenomics pipeline and compared with GutFeelingKB reference data. CRC samples were enriched in Streptococcus, Enterococcus, Klebsiella, Escherichia, Citrobacter, Veillonella, Megamonas, and Eggerthella, while beneficial butyrate-producing genera such as Roseburia, Ruminococcus, Akkermansia, Faecalibacterium, and Bacteroides were significantly depleted. The absence of Fusobacterium nucleatum and Bacteroides fragilis—commonly seen in global studies—suggests region-specific microbial patterns. This study is the first metagenomic study profiling CRC-associated microbiota in Jordan. The findings reveal a dysbiotic microbial signature that reflects both global changes associated with CRC and local ecological influences. This research emphasizes the importance of population-specific microbiome studies and highlights the need to include appropriately matched controls in future investigations. Full article

(This article belongs to the Section Gut Microbiota)

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13 pages, 1677 KB

Open AccessArticle

A Single Tertiary-Care Center Case Series Using Vertical Rectus Abdominis Myocutaneous Flap in the Management of Complex Periprosthetic Joint Infection of the Hip

by Omar Salem, Jing Zhang, George Grammatopoulos, Simon Garceau and Hesham Abdelbary

Microorganisms 2025, 13(8), 1962; https://doi.org/10.3390/microorganisms13081962 - 21 Aug 2025

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Abstract

Prosthetic joint infections (PJIs) pose significant challenges, often requiring multiple surgeries that lead to soft tissue loss, dead space, and fibrosis. Wound breakdown increases the risk of polymicrobial infection and treatment failure. The vertical rectus abdominis myocutaneous (VRAM) flap is a proven method [...] Read more.

Prosthetic joint infections (PJIs) pose significant challenges, often requiring multiple surgeries that lead to soft tissue loss, dead space, and fibrosis. Wound breakdown increases the risk of polymicrobial infection and treatment failure. The vertical rectus abdominis myocutaneous (VRAM) flap is a proven method for complex wound coverage, but its role in managing hip PJI is underexplored. This study evaluates outcomes of VRAM flap reconstruction in polymicrobial hip PJI. We retrospectively reviewed five patients who underwent VRAM flap reconstruction for polymicrobial hip PJI between December 2020 and December 2023. Primary outcomes included flap survival, infection control, and wound healing. Secondary outcomes were implant retention, postoperative complications, and functional status. At a mean follow-up of 28 months, four patients achieved wound healing and remained infection-free, while one had persistent sinus drainage but retained the implant. Flap survival was 100%, with no necrosis or failure. No major complications requiring reoperation occurred. Two patients developed deep collections, managed with ultrasound-guided drainage (Clavien-Dindo IIIa). Minor complications included donor-site dehiscence (three), flap dehiscence (one), edge necrosis (two), and hernias (two), all managed non-surgically (Clavien-Dindo I/II). All patients retained implants and remained ambulatory. VRAM flap reconstruction is a reliable option for managing complex polymicrobial hip PJI. Flap survival was excellent, and most patients achieved infection control. However, persistent infection and the need for suppressive antibiotics highlight the ongoing challenges in these cases. Full article

(This article belongs to the Special Issue Challenges of Biofilm-Associated Bone and Joint Infections)

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16 pages, 1800 KB

Open AccessArticle

Extracellular Cr(VI) Reduction by the Salt-Tolerant Strain Bacillus safensis BSF-4

by Yilan Liu, Weiping Yu, Tianying Nie, Lu Wang and Yusheng Niu

Microorganisms 2025, 13(8), 1961; https://doi.org/10.3390/microorganisms13081961 - 21 Aug 2025

Viewed by 367

Abstract

Microbial reduction in hexavalent chromium (Cr(VI)) is a well characterized bioremediation strategy, yet the mechanistic diversity among bacterial taxa necessitates detailed investigations into strain-specific pathways. Here, we report the isolation and characterization of Bacillus safensis BSF-4, a halophilic bacterium derived from saline-alkali [...] Read more.

Microbial reduction in hexavalent chromium (Cr(VI)) is a well characterized bioremediation strategy, yet the mechanistic diversity among bacterial taxa necessitates detailed investigations into strain-specific pathways. Here, we report the isolation and characterization of Bacillus safensis BSF-4, a halophilic bacterium derived from saline-alkali soil, which demonstrates efficient Cr(VI) reduction capacity. Physiological assays showed that BSF-4 achieved 89.15% reduction of 20 mg/L Cr(VI) within 72 h, with Cr(III) identified as the primary extracellular end product. Resting cell assays and subcellular fractionation analyses confirmed that Cr(VI) reduction predominantly occurs in the extracellular milieu. X-ray photoelectron spectroscopy (XPS) further revealed soluble Cr(III) complexed with extracellular polymeric substances (EPS). Transcriptomic profiling indicated upregulation of membrane-associated transport systems (facilitating Cr(VI) exclusion) and quorum sensing (QS) pathways (mediating adaptive stress responses). These findings highlight a dual mechanism: (1) extracellular enzymatic reduction mediated by EPS-bound redox proteins, and (2) intracellular detoxification via QS-regulated defense pathways. Collectively, Bacillus safensis BSF-4 exhibits robust Cr(VI) reduction capacity under saline conditions, positioning it as a promising candidate for bioremediation of Cr(VI)-contaminated saline soils and aquatic ecosystems. Full article

(This article belongs to the Section Environmental Microbiology)

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21 pages, 1055 KB

Open AccessReview

Advanced Strategies in Phage Research: Innovations, Applications, and Challenges

by Pengfei Wu, Wanwu Li, Wenlu Zhang, Shasha Li, Bo Deng, Shanghui Xu and Zhongjie Li

Microorganisms 2025, 13(8), 1960; https://doi.org/10.3390/microorganisms13081960 - 21 Aug 2025

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Abstract

The escalating global threat of antimicrobial resistance (AMR) underscores the urgent need for innovative therapeutics. Bacteriophages (phages), natural bacterial predators, offer promising solutions, especially when harnessed through advances in artificial intelligence (AI). This review explores how AI-driven innovations are transforming phage biology, with [...] Read more.

The escalating global threat of antimicrobial resistance (AMR) underscores the urgent need for innovative therapeutics. Bacteriophages (phages), natural bacterial predators, offer promising solutions, especially when harnessed through advances in artificial intelligence (AI). This review explores how AI-driven innovations are transforming phage biology, with an emphasis on three pivotal areas: (1) AI-enhanced structural prediction (e.g., AlphaFold); (2) deep learning functional annotation; (3) bioengineering strategies, including CRISPR-Cas. We further discuss applications extending to medical therapy, biosensing, agricultural biocontrol, and environmental remediation. Despite progress, critical challenges persist—including high false-positive rates, difficulties in modeling disordered protein regions, and biosafety concerns remain. Overcoming these requires experimental validation, robust computational frameworks, and global regulatory oversight. AI integration in phage research is accelerating the development of next-generation therapeutics to combat AMR and advance engineered living therapeutics. Full article

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

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25 pages, 7381 KB

Open AccessArticle

Noctiluca scintillans Bloom Reshapes Microbial Community Structure, Interaction Networks, and Metabolism Patterns in Qinhuangdao Coastal Waters, China

by Yibo Wang, Min Zhou, Xinru Yue, Yang Chen, Du Su and Zhiliang Liu

Microorganisms 2025, 13(8), 1959; https://doi.org/10.3390/microorganisms13081959 - 21 Aug 2025

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Abstract

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses [...] Read more.

The coastal waters of Qinhuangdao are a major hotspot for harmful algal blooms (HABs) in the Bohai Sea, with Noctiluca scintillans being one of the primary algal species responsible for these events. A comprehensive understanding of the microbial community structure and functional responses to N. scintillans bloom events is crucial for elucidating their underlying mechanisms and ecological impacts. This study investigated the microbial community dynamics, metabolic shifts, and the environmental drivers associated with a N. scintillans bloom in the coastal waters of Qinhuangdao, China, using high-throughput sequencing of 16S and 18S rRNA genes, co-occurrence network analysis, and metabolic pathway prediction. The results revealed that the proliferation of autotrophic phytoplankton, such as Minutocellus spp., likely provided a nutritional foundation and favorable conditions for the N. scintillans bloom. The bloom significantly altered the community structures of prokaryotes and microeukaryotes, resulting in significantly lower α-diversity indices in the blooming region (BR) compared to the non-blooming region (NR). Co-occurrence network analyses demonstrated reduced network complexity and stability in the BR, with keystone taxa primarily belonging to Flavobacteriaceae and Rhodobacteraceae. Furthermore, the community structures of both prokaryotes and microeukaryotes correlated with multiple environmental factors, particularly elevated levels of NH₄⁺-N and PO₄³⁻-P. Metabolic predictions indicated enhanced anaerobic respiration, fatty acid degradation, and nitrogen assimilation pathways, suggesting microbial adaptation to bloom-induced localized hypoxia and high organic matter. Notably, ammonia assimilation was upregulated, likely as a detoxification strategy. Additionally, carbon flux was redirected through the methylmalonyl-CoA pathway and pyruvate-malate shuttle to compensate for partial TCA cycle downregulation, maintaining energy balance under oxygen-limited conditions. This study elucidates the interplay between N. scintillans blooms, microbial interactions, and functional adaptations, providing insights for HAB prediction and management in coastal ecosystems. Full article

(This article belongs to the Section Environmental Microbiology)

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25 pages, 14023 KB

Open AccessArticle

Seasonal Variation in In Hospite but Not Free-Living, Symbiodiniaceae Communities Around Hainan Island, China

by Tinghan Yang, Zhao Qi, Haihua Wang, Pengfei Zheng, Shuh-Ji Kao and Xiaoping Diao

Microorganisms 2025, 13(8), 1958; https://doi.org/10.3390/microorganisms13081958 - 21 Aug 2025

Viewed by 316

Abstract

Coral reefs are increasingly threatened by global climate change, and mass bleaching and mortality events caused by elevated seawater temperature have led to coral loss worldwide. Hainan Island hosts extensive coral reef ecosystems in China, yet seasonal variation in Symbiodiniaceae communities within this [...] Read more.

Coral reefs are increasingly threatened by global climate change, and mass bleaching and mortality events caused by elevated seawater temperature have led to coral loss worldwide. Hainan Island hosts extensive coral reef ecosystems in China, yet seasonal variation in Symbiodiniaceae communities within this region remains insufficiently understood. We aimed to investigate the temperature-driven adaptability regulation of the symbiotic Symbiodiniaceae community in reef-building corals, focusing on the environmental adaptive changes in its community structure in coral reefs between cold (23.6–24.6 °C) and warm (28.2–30.6 °C) months. Symbiodiniaceae shuffling and rare genotype turnover were discovered in adaptability variations in the symbiotic Symbiodiniaceae community between two months. Symbiodiniaceae genetic diversity increased during warm months, primarily due to temporal turnover of rare genotypes within the Cladocopium and Durusdinium genera. Coral Favites, Galaxea, and Porites exhibited the shuffling of Symbiodiniaceae between tolerant Durusdinium and sensitive Cladocopium. Symbiodiniaceae interactions in G. fascicularis and P. lutea exhibited the highest levels of stability with the increase in temperature, whereas the interactions in A. digitifera and P. damicornis showed the lowest levels of stability. Rare genotypes functioned as central hubs and important roles within Symbiodiniaceae communities, exhibiting minimal responsiveness to temperature fluctuations while maintaining community structural stability. The temperature-driven adaptability regulation of symbiotic Symbiodiniaceae could be achieved by Symbiodiniaceae shuffling and rare genotype turnover. The process might be aggravated by concurrent adverse factors, including elevated salinity, pollution, and anthropogenic disturbance. These findings provide insights into how the Symbiodiniaceae community influences the adaptation and resilience of coral hosts to temperature fluctuations in coral reefs. Furthermore, they may contribute to assessing the reef-building coral’s capacity to withstand environmental stressors associated with global climate change. Full article

(This article belongs to the Special Issue Microbes in Aquaculture)

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21 pages, 7223 KB

Open AccessArticle

Microbial and Geochemical Diversity of Laguna Timone, an Extreme Hypersaline Crater Lake in Patagonia (52° S)

by Carolina Henríquez, José M. Pérez-Donoso, Nicolás Bruna, Mauricio Calderón, Leonardo Fadel Cury, Paulo Quezada, Gustavo Athayde, Poldie Oyarzún and Anelize Bahniuk

Microorganisms 2025, 13(8), 1957; https://doi.org/10.3390/microorganisms13081957 - 21 Aug 2025

Viewed by 381

Abstract

Extreme environments, such as hypersaline habitats, hot springs, deep-sea hydrothermal vents, glaciers, and permafrost, provide diverse ecological niches for studying microbial evolution. However, knowledge of microbial communities in extreme environments at high southern latitudes remains limited, aside from Antarctica. Laguna Timone is a [...] Read more.

Extreme environments, such as hypersaline habitats, hot springs, deep-sea hydrothermal vents, glaciers, and permafrost, provide diverse ecological niches for studying microbial evolution. However, knowledge of microbial communities in extreme environments at high southern latitudes remains limited, aside from Antarctica. Laguna Timone is a hypersaline crater lake located in a Pleistocene maar of the Pali Aike Volcanic Field, southern Patagonia; the lake was formed during basaltic eruptions in a periglacial setting. Here, we report the first integrative characterization of microbial communities from biofilms and microbial mats in this lake using high-throughput 16S rRNA and ITS gene sequencing, along with mineralogical and hydrochemical analyses of water, sediments, and carbonates. Bacterial communities were dominated by the genera Enterobacterales ASV1, Pseudomonas, Oscillatoria, Nodularia, and Belliella, with site-specific assemblages. Fungal communities included Laetinaevia, Ilyonectria, Thelebolus, Plectosphaerella, and Acrostalagmus, each showing distinct distribution patterns. These baseline data contribute to understanding microbial dynamics in hypersaline maar environments and support future investigations. This integrative approach highlights key microbe–mineral relationships and underscores the potential of Laguna Timone as a natural laboratory for exploring biosignature formation and microbial adaptation in chemically extreme environments, both on early Earth and potentially beyond. Full article

(This article belongs to the Section Environmental Microbiology)

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29 pages, 2219 KB

Open AccessReview

Fecal Microbiota Transplantation in Alzheimer’s Disease: Mechanistic Insights Through the Microbiota–Gut–Brain Axis and Therapeutic Prospects

by Jiayu Ren, Qinwen Wang, Hang Hong and Chunlan Tang

Microorganisms 2025, 13(8), 1956; https://doi.org/10.3390/microorganisms13081956 - 21 Aug 2025

Viewed by 647

Abstract

Alzheimer’s disease (AD), a prevalent neurodegenerative disorder in the aging population, remains without definitive therapeutic solutions. Emerging insights into the gut microbiota (GM) and its bidirectional communication with the central nervous system(CNS) through the microbiota–gut–brain axis (MGBA) have unveiled potential correlative mechanisms that [...] Read more.

Alzheimer’s disease (AD), a prevalent neurodegenerative disorder in the aging population, remains without definitive therapeutic solutions. Emerging insights into the gut microbiota (GM) and its bidirectional communication with the central nervous system(CNS) through the microbiota–gut–brain axis (MGBA) have unveiled potential correlative mechanisms that may contribute to AD pathogenesis, though causal evidence remains limited. Dysregulation of GM composition (dysbiosis) exacerbates AD progression via neuroinflammation, amyloid-β (Aβ) deposition, and tau hyperphosphorylation (p-tau), while restoring microbial homeostasis presents a promising therapeutic strategy. Fecal microbiota transplantation (FMT), a technique to reconstitute gut ecology by transferring processed fecal matter from healthy donors, has demonstrated efficacy in ameliorating cognitive deficits and neuropathology in AD animal models. Preclinical studies reveal that FMT reduces Aβ plaques, normalizes tau phosphorylation, suppresses inflammasome activation, and restores microglial homeostasis through modulation of microbial metabolites and immune pathways. Although clinical evidence remains limited to case reports and small-scale trials showing potential therapeutic effect, safety concerns regarding long-term effects and protocol standardization necessitate further investigation. This review synthesizes current knowledge on GM–AD interactions, evaluates FMT’s mechanistic potential, and discusses challenges in translating this ancient practice into a cutting-edge AD therapy. Rigorous randomized controlled trials and personalized microbiota-based interventions are imperative to advance FMT from bench to bedside. Full article

(This article belongs to the Special Issue Effects of Gut Microbiota on Human Health and Disease, 2nd Edition)

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15 pages, 601 KB

Open AccessSystematic Review

Association of Helicobacter pylori as an Extragastric Reservoir in the Oral Cavity with Oral Diseases in Patients with and Without Gastritis—A Systematic Review

by Eber Cuba, María C. Sánchez, María J. Ciudad and Luis Collado

Microorganisms 2025, 13(8), 1955; https://doi.org/10.3390/microorganisms13081955 - 21 Aug 2025

Viewed by 485

Abstract

This systematic review aimed to evaluate the association between Helicobacter pylori in the oral cavity as an extragastric reservoir and oral diseases in patients with or without gastritis. Following the PRISMA guidelines, a comprehensive search was conducted on the PubMed, Scopus, Cochrane Central, [...] Read more.

This systematic review aimed to evaluate the association between Helicobacter pylori in the oral cavity as an extragastric reservoir and oral diseases in patients with or without gastritis. Following the PRISMA guidelines, a comprehensive search was conducted on the PubMed, Scopus, Cochrane Central, and Embase databases (2010–2025) using MeSH terms and keywords related to H. pylori, the oral cavity, and oral diseases. Inclusion criteria included observational studies, clinical trials, and case–control studies. Data extraction and quality assessment were performed using the Newcastle–Ottawa Scale (NOS). Of the 298 records initially identified, 22 studies met the inclusion criteria. The presence of H. pylori in the oral cavity (plaque, saliva) was variably associated with gastritis, periodontitis, dental caries, and halitosis. Detection rates varied widely (0–100%), influenced by methodological differences (PCR, culture, antigen tests). Some studies reported an improvement in oral health after eradication therapy, while others found no significant association. The oral cavity may serve as a reservoir for H. pylori, with implications for oral and systemic health. Standardized diagnostic methods and integrated treatment approaches (combining gastric eradication and oral hygiene) are needed to clarify their role and optimize clinical outcomes. Further research is warranted to establish causal relationships and therapeutic strategies. Full article

(This article belongs to the Section Medical Microbiology)

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14 pages, 1191 KB

Open AccessArticle

Biodegradation of Zearalenone by a Novel Bacillus Strain X13 Isolated from Volcanic Rock Soil Using the Mycotoxin as the Sole Carbon Source

by Di Meng, Kaizhong Xu, Jinbin Liu and Xiangru Liao

Microorganisms 2025, 13(8), 1954; https://doi.org/10.3390/microorganisms13081954 - 21 Aug 2025

Viewed by 306

Abstract

Zearalenone (ZEN) is a widespread estrogenic mycotoxin that poses serious health risks to both humans and animals through the contamination of cereals and feeds. In this study, a novel Bacillus strain X13 was isolated from volcanic rock soil and demonstrated the unique ability [...] Read more.

Zearalenone (ZEN) is a widespread estrogenic mycotoxin that poses serious health risks to both humans and animals through the contamination of cereals and feeds. In this study, a novel Bacillus strain X13 was isolated from volcanic rock soil and demonstrated the unique ability to utilize ZEN as the sole carbon source for growth and metabolism. Under optimized conditions (37 °C, pH 8.0, and 5% inoculum in M9 minimal medium), strain X13 achieved a ZEN degradation efficiency of 98.57%. LC-MS analysis identified 1-(3,5-dihydroxyphenyl)-6′-hydroxy-1′-undecen-10′-one as the primary degradation product, indicating enzymatic hydrolysis of the lactone ring. Enzymatic assays revealed that the active components were extracellular, proteinaceous, and metal ion-dependent. Furthermore, the strain reduced ZEN content in mold-contaminated corn flour by 74.6%, effectively lowering toxin levels below regulatory limits. These findings suggest that Bacillus sp. X13 is a promising candidate for the bioremediation of ZEN-contaminated agricultural products, with significant potential for application in food and feed detoxification strategies. The robust degradation performance of strain X13 under simulated environmental conditions, combined with its adaptability to agricultural substrates, positions it as a viable solution for large-scale mycotoxin mitigation in the food industry chain, from pre-harvest field management to post-harvest storage processing. Full article

(This article belongs to the Section Environmental Microbiology)

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16 pages, 6730 KB

Open AccessArticle

Insights into the Genomic Architecture and Improvement of the Capabilities of Acinetobacter calcoaceticus for the Biodegradation of Petroleum Hydrocarbons

by Yaning Zeng, Mutian Wang, Xiaoyu Chang, Leilei Wang, Xiaowen Fu, Yujie Huang, Fanyong Song, Lei Ji and Jianing Wang

Microorganisms 2025, 13(8), 1953; https://doi.org/10.3390/microorganisms13081953 - 21 Aug 2025

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Abstract

Petroleum-contaminated terrestrial ecosystems require effective bioremediation strategies. In this study, genomic analysis revealed key biodegradation genes on the Acinetobacter calcoaceticus 21# chromosome: alkane hydroxylases (alkB, almA, LadA) and aromatic ortho-cleavage pathway genes (catABC). Phylogenetic and multiple sequence [...] Read more.

Petroleum-contaminated terrestrial ecosystems require effective bioremediation strategies. In this study, genomic analysis revealed key biodegradation genes on the Acinetobacter calcoaceticus 21# chromosome: alkane hydroxylases (alkB, almA, LadA) and aromatic ortho-cleavage pathway genes (catABC). Phylogenetic and multiple sequence alignment analyses of the almA gene in strain 21# revealed the presence of signature motifs characteristic of Baeyer–Villiger monooxygenase. Functional annotation analysis demonstrated stronger phylogenetic affinity of this protein to previously characterized BVMOs than to hydroxylases. Therefore, it is suggested that the AlmA protein in 21# exhibits BVMO activity and participates in the subterminal oxidation pathway of alkane degradation. Wild-type 21# degraded both n-Octacosane (24.47%) and pyrene (34.03%). Engineered 21#-A3 showed significantly enhanced n-Octacosane degradation (28.68%). To validate AlmA function and assess impacts of exogenous gene integration, we expressed the almA gene from A. vivianii KJ-1 via pET-28a(+)-av-almA-BH vector. Enzymatic assays demonstrated no activity toward long-chain alkanes but high activity for 2-decanone (0.39 U/mg) and 2-dodecanone (0.37 U/mg). Metabolite analysis confirmed recombinant AlmA functions through subterminal oxidation. This study establishes a foundational framework for advancing the optimization of petroleum-degrading bacteria. To engineer more efficient hydrocarbon-degrading strains, future research should integrate meta-cleavage pathways to expand their substrate utilization range for polycyclic aromatic hydrocarbons. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 2710 KB

Open AccessArticle

vapD Mutation Shows Impairment in the Persistence of Helicobacter pylori Within AGS Cells

by Rosario Morales-Espinosa, Gabriela Delgado, Carlos A. Santiago, Alejandro Flores-Alanis, Rafael Diaz-Mendez, Alberto Gonzalez-Pedraza, José L. Méndez and Alejandro Cravioto

Microorganisms 2025, 13(8), 1952; https://doi.org/10.3390/microorganisms13081952 - 21 Aug 2025

Viewed by 309

Abstract

The Helicobacter pylori vapD gene is transcribed and expressed when the bacteria are within the gastric cell. In this current study, we investigated how vapD knockout affects the survival of H. pylori inside human gastric adenocarcinoma cells. We constructed an H. pylori 26695 [...] Read more.

The Helicobacter pylori vapD gene is transcribed and expressed when the bacteria are within the gastric cell. In this current study, we investigated how vapD knockout affects the survival of H. pylori inside human gastric adenocarcinoma cells. We constructed an H. pylori 26695 vapD (Hp ΔvapD) mutant strain. H. pylori 26695 wt and Hp ΔvapD strains were grown in synthetic media and were co-cultured with AGS cells. From the start, the growth curve, total protein concentration and colony-forming units (CFUs) of each strain were measured. From each co-culture, CFUs and total RNA were obtained, and transcript levels of GAPDH, vapD, vacA, ureA, and 16s Hp were measured by qRT-PCR. Hp ΔvapD did not affect the growth rate of the strain in synthetic media, showing that the vapD gene is not necessary when the bacteria grow outside eukaryote cells. However, in the intracellular environment, the number of CFUs recovered from the Hp ΔvapD strain from AGS cells decreased after 36 h. Transcription levels of the vacA gene from the Hp ΔvapD strain were 10,000-fold lower than those of H. pylori wt, to the point of being undetectable. The results suggest that the vapD gene contributed to maintaining H. pylori inside gastric cells. Full article

(This article belongs to the Special Issue Bacterial Pathogenesis and Host Immune Responses)

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15 pages, 3465 KB

Open AccessArticle

Identification of Bioactive Peptides from Caenorhabditis elegans Secretions That Promote Indole-3-Acetic Acid Production in Arthrobacter pascens ZZ21

by Shan Sun, Mengsha Li, Luchen Tao, Xiran Liu, Lei Ouyang, Gen Li, Feng Hu and Huixin Li

Microorganisms 2025, 13(8), 1951; https://doi.org/10.3390/microorganisms13081951 - 21 Aug 2025

Viewed by 285

Abstract

Caenorhabditis elegans, a free-living nematode model, secretes neuropeptides, but the ecological roles of its peptide exudates in regulating rhizosphere microbial activity remain largely unexplored. We identified six short peptides (P1, P9, P19, P20, P25, and P26) from C. elegans exudates that significantly [...] Read more.

Caenorhabditis elegans, a free-living nematode model, secretes neuropeptides, but the ecological roles of its peptide exudates in regulating rhizosphere microbial activity remain largely unexplored. We identified six short peptides (P1, P9, P19, P20, P25, and P26) from C. elegans exudates that significantly enhanced indole-3-acetic acid (IAA) production by the plant growth-promoting bacterium Arthrobacter pascens ZZ21. These peptides were heat-labile and proteinase K-sensitive but unaffected by DNase I or RNase A, confirming their proteinaceous (peptide) nature rather than nucleic acid origin. The retention of bioactivity in n-butanol extracts further supported their hydrophilic, peptide-like properties. LC-MS/MS identified 30 linear peptides, including the six bioactive ones, which exhibited distinct dose-dependent effects, suggesting diverse regulatory mechanisms. Despite their relatively low abundance, these peptides strongly promoted IAA production in the bacterial culture system across multiple concentrations. These findings reveal an unrecognized mechanism whereby free-living nematodes regulate rhizobacterial metabolism via secreted peptides, offering new insights into nematode-mediated chemical signaling. Therefore, this study advances understanding of plant–microbe–nematode interactions and highlights strategies for manipulating rhizosphere microbiota in sustainable agriculture. Full article

(This article belongs to the Section Plant Microbe Interactions)

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16 pages, 2731 KB

Open AccessArticle

BCL-2 Multi-Strain Probiotics for Immunomodulation In Vitro and In Vivo Alleviation of Atopic Dermatitis

by MinKyung Sung, Seongrok Sim, Ahyoung Lim, Jin Seok Moon, JongIk Jeon, Keon Heo, Woongkwon Kwak, Myeong Soo Park, Jungki Kwak, EunYoung Park and Seokmin Yoon

Microorganisms 2025, 13(8), 1950; https://doi.org/10.3390/microorganisms13081950 - 21 Aug 2025

Viewed by 500

Abstract

Atopic dermatitis (AD) is a chronic inflammatory disorder with immune imbalance, including elevated IgE levels and mast cell activation mediated by Th2 cytokines, leading to allergic inflammation and impaired skin barrier function. Current treatment limitations highlight the need for safer and more effective [...] Read more.

Atopic dermatitis (AD) is a chronic inflammatory disorder with immune imbalance, including elevated IgE levels and mast cell activation mediated by Th2 cytokines, leading to allergic inflammation and impaired skin barrier function. Current treatment limitations highlight the need for safer and more effective AD alternatives. We aimed to evaluate the therapeutic effects of multi-strain probiotics, BCL-2 (comprising Lactiplantibacillus plantarum LRCC5264 and Bifidobacterium longum RAPO), in alleviating AD clinical signs and elucidate its underlying immunomodulatory mechanisms. In vitro, BCL-2 treatment significantly reduced IL-4 secretion in RBL-2H3 cells, with higher inhibitory effects than single-strain treatment. In vivo, BCL-2 (10⁶–10⁸ CFU/day) was orally administered for 28 days to AD-induced Nc/Nga mice. BCL-2 treatment improved the clinical signs and histopathological features of AD, including epidermal hypertrophy, hyperkeratosis, and mast cell infiltration (p < 0.05). It also reduced neutrophil and eosinophil counts and modulated cytokine and chemokine profiles, notably decreasing IL-17, IL-5, IL-6, TNF-α, IL-1β, TARC, and eotaxin, while increasing IL-10, IFN-γ, and IL-12 (p < 0.05). Among the tested concentrations, 10⁷ CFU exhibited the most effective immune modulation with no adverse effects on body weight. These findings demonstrate the therapeutic potential of BCL-2 in AD; however, further studies are required to validate its clinical relevance. Full article

(This article belongs to the Section Microbial Biotechnology)

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21 pages, 1531 KB

Open AccessArticle

Diet Quality Modulates Gut Microbiota Structure in Blastocystis-Colonised Individuals from Two Distinct Cohorts with Contrasting Sociodemographic Profiles

by Claudia Muñoz-Yáñez, Alejandra Méndez-Hernández, Faviel Francisco González-Galarza, Adria Imelda Prieto-Hinojosa and Janeth Oliva Guangorena-Gómez

Microorganisms 2025, 13(8), 1949; https://doi.org/10.3390/microorganisms13081949 - 21 Aug 2025

Viewed by 532

Abstract

Diet and gut microbiota are significant determinants of host health, but how dietary quality modulates gut microbiota in Blastocystis-colonised individuals remains underexplored. We studied two contrasting cohorts: university students (FACSA, n = 46) and institutionalised children with their caregivers (PAVILA, n = [...] Read more.

Diet and gut microbiota are significant determinants of host health, but how dietary quality modulates gut microbiota in Blastocystis-colonised individuals remains underexplored. We studied two contrasting cohorts: university students (FACSA, n = 46) and institutionalised children with their caregivers (PAVILA, n = 37), representing distinct dietary and sociodemographic contexts. Eight participants from each cohort tested positive for Blastocystis; however, two PAVILA samples could not be sequenced, resulting in a final microbiota subcohort of 14 individuals (FACSA n = 8, PAVILA n = 6). Dietary quality was assessed using the Healthy Eating Index-2020 (HEI-2020), and faecal microbiota was characterised through 16S rRNA sequencing. Alpha and beta diversity were analysed, and genus-level transformed data were further evaluated using permutational multivariate analysis of variance (PERMANOVA), principal coordinates analysis (PCoA), and distance-based redundancy analysis (db-RDA). The FACSA cohort exhibited higher microbial richness and diversity (Shannon and Simpson indexes, p < 0.01) compared to PAVILA, with marked differences in microbial composition (PERMANOVA R² = 0.39, p = 0.002). Total diet quality correlated with microbial structure (R² = 0.26, p = 0.016), with protein (R² = 0.23, p = 0.017) and vegetable components (R² = 0.17, p = 0.044) as primary contributors. Multivariate analysis showed that higher protein and vegetable intakes were associated with genera such as Sellimonas, Murimonas, Alistipes, and Desulfovibrio (FACSA group). In contrast, Hydrogenoanaerobacterium, V9D2013_group, and Haemophilus were linked to lower-quality diets (PAVILA group). Our results indicate that diet quality significantly influences gut microbiota composition in individuals colonised by Blastocystis, underscoring its potential as a target for nutritional interventions in vulnerable populations. Full article

(This article belongs to the Section Gut Microbiota)

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15 pages, 1438 KB

Open AccessArticle

Broad Host Range Peptide Nucleic Acids Prevent Gram-Negative Biofilms Implicated in Catheter-Associated Urinary Tract Infections

by Hannah Q. Karp, Elizabeth S. Nowak, Gillian A. Kropp, Nihan A. Col, Michael D. Schulz, Nammalwar Sriranganathan and Jayasimha Rao

Microorganisms 2025, 13(8), 1948; https://doi.org/10.3390/microorganisms13081948 - 20 Aug 2025

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Abstract

Biofilms develop in sequential steps resulting in the formation of three-dimensional communities of microorganisms that are encased in self-produced extracellular polymeric substances. Biofilms play a key role in device-associated infections, such as catheter-associated urinary tract infections (CAUTIs), because they protect microorganisms from standard [...] Read more.

Biofilms develop in sequential steps resulting in the formation of three-dimensional communities of microorganisms that are encased in self-produced extracellular polymeric substances. Biofilms play a key role in device-associated infections, such as catheter-associated urinary tract infections (CAUTIs), because they protect microorganisms from standard antimicrobial therapies. Current strategies to prevent biofilm formation in catheter-related infections, including prophylactic antibiotics and antibiotic-coated catheters, have been unsuccessful. This finding highlights a need for novel approaches to address this clinical problem. In this study, biofilm-forming phenotypes of common Gram-negative bacteria associated with CAUTIs were treated with antisense peptide nucleic acids (PNAs), and biofilm biomass and bacterial viability were quantified after 24 h of treatment. A cocktail of PNAs targeting the global regulator genes rsmA, amrZ, and rpoS in Pseudomonas aeruginosa significantly reduced viability and thus appropriately eliminated biofilm biomass. Antisense-PNAs against these same gene targets and the motility regulator gene motA inhibited biofilm formation among isolates of Klebsiella pneumoniae, Enterobacter cloacae, and Escherichia coli but did not reduce bacterial viability. These results suggest that antisense-PNAs are a promising new technology in preventing biofilm formation in urinary catheters, especially as a potential complement to conventional antimicrobials. Full article

(This article belongs to the Special Issue Advanced Research on Microbial Biofilms—a Themed Issue in Honor of Professor Gianfranco Donelli)

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17 pages, 1657 KB

Open AccessArticle

Macrolide-Resistant Bordetella pertussis in Hong Kong: Evidence for Post-COVID-19 Emergence of ptxP3-Lineage MT28 Clone from a Hospital-Based Surveillance Study

by Tsz-Yung Hui, Hayes Kam-Hei Luk, Garnet Kwan-Yue Choi, Sandy Ka-Yee Chau, Lok-Man Tsang, Cindy Wing-Sze Tse, Ka-Kin Fung, Jimmy Yiu-Wing Lam, Ho-Leung Ng, Tommy Hing-Cheung Tang, Edmond Siu-Keung Ma, Herman Tse, Sally Cheuk-Ying Wong, Vivien Wai-Man Chuang and David Christopher Lung

Microorganisms 2025, 13(8), 1947; https://doi.org/10.3390/microorganisms13081947 - 20 Aug 2025

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Abstract

A post-COVID surge of Bordetella pertussis was observed globally. China has reported a high level of macrolide-resistant Bordetella pertussis (MRBP) in recent years; however, the epidemiology of MRBP in Hong Kong remains unknown. We retrieved archived B. pertussis isolates from respiratory samples collected [...] Read more.

A post-COVID surge of Bordetella pertussis was observed globally. China has reported a high level of macrolide-resistant Bordetella pertussis (MRBP) in recent years; however, the epidemiology of MRBP in Hong Kong remains unknown. We retrieved archived B. pertussis isolates from respiratory samples collected at five regional public hospitals in Hong Kong between 2015 and 2024 and tested their minimum inhibitory concentration (MIC) for macrolides and other non-macrolide antibiotics using the Etest method. All isolates were also subjected to whole genome sequencing for genotypic resistance, Multi-locus Antigen Sequence Typing (MLST) and Multi-locus Variable Number of Tandem Repeat Analysis (MLVA) typing. Twenty-nine isolates of B. pertussis were included in the study. All isolates demonstrating phenotypic macrolide resistance harbored the A2047G mutation while showing low MIC to trimethoprim-sulfamethoxazole, doxycycline, levofloxacin, piperacillin-tazobactam and meropenem. In 2023 and 2024, 100% were MRBP and all belonged to the MT28 clone with the ptxP3 antigenic type. The MRBP isolates in Hong Kong were phylogenetically related to those from mainland China during the same period. There was no obvious correlation between macrolide resistance and clinical presentation, laboratory findings, management and outcome. Phylogenetic analysis suggests that MRBP isolates in Hong Kong and mainland China are closely related. Full article

(This article belongs to the Special Issue Challenges in Combating Antimicrobial Resistance in the Vulnerable Population)

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26 pages, 1819 KB

Open AccessArticle

Uropathogenic Escherichia coli in a Diabetic Dog with Recurrent UTIs: Genomic Insights and the Impact of Glucose and Antibiotics on Biofilm Formation

by Inês C. Rodrigues, Marisa Ribeiro-Almeida, Joana Campos, Leonor Silveira, Liliana Leite-Martins, Jorge Ribeiro, Paula Martins da Costa, Joana C. Prata, Ângela Pista and Paulo Martins da Costa

Microorganisms 2025, 13(8), 1946; https://doi.org/10.3390/microorganisms13081946 - 20 Aug 2025

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Abstract

Recurrent urinary tract infections (UTIs) pose a significant clinical challenge in both human and veterinary medicine, due to antibiotic-resistant and biofilm-forming bacteria. We hypothesized that high glucose levels in diabetic animals enhance biofilm formation and reduce antibiotic efficacy, promoting infection persistence. This study [...] Read more.

Recurrent urinary tract infections (UTIs) pose a significant clinical challenge in both human and veterinary medicine, due to antibiotic-resistant and biofilm-forming bacteria. We hypothesized that high glucose levels in diabetic animals enhance biofilm formation and reduce antibiotic efficacy, promoting infection persistence. This study analyzed Escherichia coli from a diabetic female Labrador Retriever with recurrent UTIs over 18 months, focusing on antimicrobial resistance, biofilm-forming capacity, and genomic characterization. Most isolates (9/11) were resistant to ampicillin and fluoroquinolones. Whole genome sequencing of six selected isolates revealed that they belonged to the multidrug-resistant ST1193 lineage, a globally emerging clone associated with persistent infections. Phylogenetic analysis revealed clonal continuity across six UTI episodes, with two distinct clones identified: one during a coinfection in the second episode and another in the last episode. High-glucose conditions significantly enhanced biofilm production and dramatically reduced antibiotic susceptibility, as evidenced by a marked increase in minimum biofilm inhibitory concentrations (MBICs), which were at least 256-fold higher than the corresponding minimum inhibitory concentration (MIC). Sulfamethoxazole–trimethoprim demonstrated the strongest antibiofilm activity, though this was attenuated in glucose-supplemented environments. This research highlights the clinical relevance of glucosuria in diabetic patients and emphasizes the need for therapeutic strategies targeting biofilm-mediated antibiotic tolerance to improve the management of recurrent UTIs. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and the Use of Antibiotics in Animals)

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22 pages, 4008 KB

Open AccessArticle

Dissolved Oxygen Decline in Northern Beibu Gulf Summer Bottom Waters: Reserve Management Insights from Microbiome Analysis

by Chunyan Peng, Ying Liu, Yuyue Qin, Dan Sun, Jixin Jia, Zongsheng Xie and Bin Gong

Microorganisms 2025, 13(8), 1945; https://doi.org/10.3390/microorganisms13081945 - 20 Aug 2025

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Abstract

The Sanniang Bay (SNB) and Dafeng River Estuary (DFR) in the Northern Beibu Gulf, China, are critical habitats for the Indo-Pacific humpback dolphin (Sousa chinensis). However, whether and how the decreased dissolved oxygen (DO) has happened in bottom seawater remains poorly [...] Read more.

The Sanniang Bay (SNB) and Dafeng River Estuary (DFR) in the Northern Beibu Gulf, China, are critical habitats for the Indo-Pacific humpback dolphin (Sousa chinensis). However, whether and how the decreased dissolved oxygen (DO) has happened in bottom seawater remains poorly understood. This study investigated DO depletion and microbial community responses using a multidisciplinary approach. High-resolution spatiotemporal sampling (16 stations across four seasons) was combined with functional annotation of prokaryotic taxa (FAPROTAX) to characterize anaerobic metabolic pathways and quantitative PCR (qPCR) targeting dsrA and dsrB genes to quantify sulfate-reducing bacteria. Partial least-squares path modeling (PLS-PM) was employed to statistically link environmental variables (seawater properties and nutrients) to microbial community structure. Results revealed pronounced bottom DO declining to 5.44 and 7.09 mg L⁻¹, a level approaching sub-optimal state (4.0–4.8 mg L⁻¹) in September. Elevated chlorophyll-a (Chl-a) near the SDH coincided with anaerobic microbial enrichment, including sulfate reducers (dsrA/dsrB abundance: SNB > DFR). PLS-PM identified seawater properties (turbidity, DO, pH) and nitrogen as key drivers of anaerobic taxa distribution. Co-occurrence network analysis further demonstrated distinct microbial modules in SNB (phytoplankton-associated denitrifiers) and DFR (autotrophic sulfur oxidizers, nitrogen fixation, and denitrification). These findings highlight how environmental factors drive decreased DO, reshaping microbial networks and threatening coastal ecosystems. This work underscores the need for regulating aquaculture/agricultural runoff to limit eutrophication-driven hypoxia and temporarily restrict human activities in SNB during peak hypoxia (September–October). Full article

(This article belongs to the Special Issue Microbial Ecology and Assembly Dynamics in the Aquaculture Environment)

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17 pages, 1757 KB

Open AccessArticle

Isolation and Characterization of the Trimethylamine (TMA)-Degrading Microbacterium lacticum Strain PM-1

by Pai Feng, Lei Zhang, Yihao Wu, Yuxuan Hu, Wenda Chen, Yuan Liu and Jiayuan Yang

Microorganisms 2025, 13(8), 1944; https://doi.org/10.3390/microorganisms13081944 - 20 Aug 2025

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Abstract

Trimethylamine (TMA) is a common malodorous pollutant known for its detrimental effects on both the natural environment and human health. In this study, strain PM-1 was successfully isolated from activated sludge in a sewage treatment plant and identified as the first Microbacterium lacticum [...] Read more.

Trimethylamine (TMA) is a common malodorous pollutant known for its detrimental effects on both the natural environment and human health. In this study, strain PM-1 was successfully isolated from activated sludge in a sewage treatment plant and identified as the first Microbacterium lacticum capable of degrading TMA. Strain PM-1 is characterized as a mesophilic and mild halotolerant bacterium, thriving within a temperature range of 20–40 °C and a salinity range of 10–80 g/L NaCl. The optimal initial TMA concentrations for strain PM-1 were determined to be 0.1 wt% under aerobic conditions and 0.05 wt% under anaerobic conditions. The strain demonstrated efficient TMA degradation rates of 98.02 mg/L/h aerobically and 4.44 mg/L/h anaerobically. Additionally, beef extract and peptone significantly enhanced TMA degradation and bacterial growth by 293% and 688%, respectively, under aerobic conditions. Microbacterium lacticum strain PM-1 is the first isolated Microbacterium lacticum with the ability to convert TMA. Further research will focus on its TMA degradation pathway through the identification of key enzymes and application in TMA-containing wastewater and exhaust gas. Full article

(This article belongs to the Topic The Role of Microorganisms in Waste Treatment)

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18 pages, 3684 KB

Open AccessArticle

Enhancement of Mycelial Growth and Antifungal Activity by Combining Fermentation Optimization and Genetic Engineering in Streptomyces pratensis S10

by Lifang Hu, Yan Sun, Ruimin Jia, Xiaomin Dong, Xihui Shen and Yang Wang

Microorganisms 2025, 13(8), 1943; https://doi.org/10.3390/microorganisms13081943 - 20 Aug 2025

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Abstract

The biocontrol strain Streptomyces pratensis S10 was isolated from tomato leaf mold. The fermentation broth of strain S10 can effectively control Fusarium head blight (FHB), caused by Fusarium graminearum. Enhancing antifungal activity is essential in advancing its commercialization. In this study, we [...] Read more.

The biocontrol strain Streptomyces pratensis S10 was isolated from tomato leaf mold. The fermentation broth of strain S10 can effectively control Fusarium head blight (FHB), caused by Fusarium graminearum. Enhancing antifungal activity is essential in advancing its commercialization. In this study, we aimed to improve the antifungal activity of S10 by integrating fermentation optimization and genetic engineering. Single-factor experiments revealed that seven parameters, namely corn flour, yeast extract, NaNO₃, CaCO₃, K₂HPO₄, KCl, ZnSO₄·7H₂O, and MnCl₂·4H₂O, were identified as significant components. A Plackett–Burman design (PDB) indicated that corn flour, yeast extract, and ZnSO₄·7H₂O were the most critical variables affecting its inhibitory activity and mycelial biomass. The fermentation medium was further determined based on the steepest climbing experiment and a Box–Behnken design (BBD), and the mycelial dry weight of S. pratensis S10 was improved from 2.13 g/L in Gauze’s synthetic No. 1 medium to 8.12 g/L in the optimized medium, closely aligning with the predicted value of 7.98 g/L. Under the optimized medium, the antifungal rate of F. graminearum increased from 67.36 to 82.2%. The spore suspension of strain S10 cultured in the optimized medium substantially improved its biocontrol efficacy against FHB. Moreover, disruption of the key gene tetR led to increased antifungal activity of strain S10 against F. graminearum. Importantly, the antifungal activity of ΔtetR was greatly increased under the optimized fermentation medium. This study suggests that the gene tetR negatively regulates bioactive compound biosynthesis, and the optimized medium provides favorable conditions for the growth of S10. These observations establish an extended basis for the large-scale bioactive metabolite secretion of S. pratensis S10, providing a strong foundation for sustainable FHB management in agriculture. Full article

(This article belongs to the Section Microbial Biotechnology)

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19 pages, 3354 KB

Open AccessArticle

Microbial Assembly and Stress-Tolerance Mechanisms in Salt-Adapted Plants Along the Shore of a Salt Lake: Implications for Saline–Alkaline Soil Remediation

by Xiaodong Wang, Liu Xu, Xinyu Qi, Jianrong Huang, Mingxian Han, Chuanxu Wang, Xin Li and Hongchen Jiang

Microorganisms 2025, 13(8), 1942; https://doi.org/10.3390/microorganisms13081942 - 20 Aug 2025

Viewed by 464

Abstract

Investigating the microbial community structure and stress-tolerance mechanisms in the rhizospheres of salt-adapted plants along saline lakes is critical for understanding plant–microbe interactions in extreme environments and developing effective strategies for saline–alkaline soil remediation. This study explored the rhizosphere microbiomes of four salt-adapted [...] Read more.

Investigating the microbial community structure and stress-tolerance mechanisms in the rhizospheres of salt-adapted plants along saline lakes is critical for understanding plant–microbe interactions in extreme environments and developing effective strategies for saline–alkaline soil remediation. This study explored the rhizosphere microbiomes of four salt-adapted species (Suaeda glauca, Artemisia carvifolia, Chloris virgata, and Limonium bicolor) from the Yuncheng Salt Lake region in China using high-throughput sequencing. Cultivable salt-tolerant plant growth-promoting rhizobacteria (PGPR) were isolated and characterized to identify functional genes related to stress resistance. Results revealed that plant identity and soil physicochemical properties jointly shaped the microbial community composition, with total organic carbon being a dominant driver explaining 17.6% of the variation. Cyanobacteria dominated low-salinity environments, while Firmicutes thrived in high-salinity niches. Isolated PGPR strains exhibited tolerance up to 15% salinity and harbored genes associated with heat (htpX), osmotic stress (otsA), oxidative stress (katE), and UV radiation (uvrA). Notably, Peribacillus and Isoptericola strains demonstrated broad functional versatility and robust halotolerance. Our findings highlight that TOC (total organic carbon) plays a pivotal role in microbial assembly under extreme salinity, surpassing host genetic influences. The identified PGPR strains, with their stress-resistance traits and functional gene repertoires, hold significant promise for biotechnological applications in saline–alkaline soil remediation and sustainable agriculture. Full article

(This article belongs to the Section Plant Microbe Interactions)

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22 pages, 1987 KB

Open AccessArticle

Predictive Microbial Markers Distinguish Responders and Non-Responders to Adalimumab: A Step Toward Precision Medicine in Ulcerative Colitis

by Shaghayegh Baradaran Ghavami, Arfa Moshiri, Carola Bonaretti, Maryam Farmani, Margherita Squillario, Eddi Di Marco, Shabnam Shahrokh, Hedieh Balaii, Maria Valeria Corrias, Mirco Ponzoni, Amir Sadeghi and Roberto Biassoni

Microorganisms 2025, 13(8), 1941; https://doi.org/10.3390/microorganisms13081941 - 20 Aug 2025

Viewed by 367

Abstract

Ulcerative colitis (UC) is a chronic, relapsing inflammatory disease of the colon, often associated with gut microbial dysbiosis. Although anti-TNF-α agents, such as Adalimumab (Cinnora^®), are used to treat moderate-to-severe UC, the treatment response is highly variable. Identifying early microbial biomarkers [...] Read more.

Ulcerative colitis (UC) is a chronic, relapsing inflammatory disease of the colon, often associated with gut microbial dysbiosis. Although anti-TNF-α agents, such as Adalimumab (Cinnora^®), are used to treat moderate-to-severe UC, the treatment response is highly variable. Identifying early microbial biomarkers of response could help support personalized therapeutic strategies and prevent unnecessary exposure to ineffective treatments. However, the long-term effects of anti-TNF therapy on both stool and mucosal microbiota remain poorly understood. This prospective longitudinal study included 23 corticosteroid-refractory or -dependent UC patients who started Adalimumab after endoscopy-confirmed flare-ups. Stool samples and inflamed colonic biopsies were collected at baseline, and 3 and 6 months. Microbiota profiling was performed using 16S rRNA sequencing. Microbial changes were analyzed over time and compared between responders (Mayo score 0–1) and non-responders (Mayo score ≥ 2). Sixty percent of patients achieved clinical remission. In responders, stool microbiota showed increased Bacteroidetes and decreased Proteobacteria abundances, along with an enrichment of beneficial taxa including Faecalibacterium prausnitzii, Bifidobacterium, and Akkermansia muciniphila. Mucosal microbiota exhibited persistent dysbiosis, characterized by an increase in Proteobacteria and a reduced Firmicutes/Proteobacteria ratio. Notably, responders showed distinct compartment-specific microbial changes, with a decrease in Gammaproteobacteria in stool and an increase in Corynebacterium in tissue. Adalimumab induces divergent microbial changes in stool and mucosa. While stool microbiota trends toward eubiosis in responders, persistent mucosal dysbiosis may reflect asymptomatic inflammation. These findings underscore the importance of niche-specific microbiome profiling in UC and support its integration into personalized treatment monitoring. Full article

(This article belongs to the Section Microbiomes)

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26 pages, 8002 KB

Open AccessArticle

Functional Genomic Characteristics of Marine Sponge-Associated Microbulbifer spongiae MI-G^T

by Nabila Ishaq, Qianqian Song, Micha Ilan and Zhiyong Li

Microorganisms 2025, 13(8), 1940; https://doi.org/10.3390/microorganisms13081940 - 20 Aug 2025

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Abstract

The genus Microbulbifer comprises a group of marine, gram-negative bacteria known for their remarkable ability to adapt to a variety of environments. Therefore, this study aimed to investigate the genetic diversity and metabolic characteristics of M. spongiae MI-G^T and three Microbulbifer reference [...] Read more.

The genus Microbulbifer comprises a group of marine, gram-negative bacteria known for their remarkable ability to adapt to a variety of environments. Therefore, this study aimed to investigate the genetic diversity and metabolic characteristics of M. spongiae MI-G^T and three Microbulbifer reference strains by genomic and comparative genomic analysis. Compared to free-living reference strains, the lower GC content, higher number of strain-specific genes, pseudogenes, unique paralogs, dispensable genes, and mobile gene elements (MGEs) such as genomic islands (GIs) and insertion sequence (IS) elements, while the least number of CAZymes, indicates that M. spongiae MI-G^T may be a facultative sponge-symbiont. Comparative genomic analysis indicates that M. spongiae MI-G^T possesses a plasmid and a higher number of strain-specific genes than Microbulbifer reference strains, showing that M. spongiae MI-G^T may have acquired unique genes to adapt sponge-host environment. Moreover, there are differences in the functional distribution of genes belonging to different COG-classes in four Microbulbifer strains. COG-functional analysis reveals a lower number of strain-specific genes associated with metabolism, energy production, and motility in M. spongiae MI-G^T compared to Microbulbifer reference strains, suggesting that sponge-associated lifestyle may force this bacterium to acquire nutrients from the sponge host and loss motility genes. Finally, we found that several proteins associated with oxidative stress response (sodC, katA, catA, bcp, trmH, cspA), osmotic stress response (dsbG, ampG, amiD_2, czcA, czcB, and corA), and tolerance to biotoxic metal proteins (dsbG, ampG, amiD_2, czcA, czcB, and corA) are absent in M. spongiae MI-G^T but present in Microbulbifer reference strains, indicating that M. spongiae MI-G^T live in a stable and less stress environment provided by the sponge host than free-living Microbulbifer strains. Our results suggest M. spongiae MI-G^T exhibits gene characteristics related to its adaptation to the sponge host habitat, meanwhile reflecting its evolution towards a sponge-associated lifestyle. Full article

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

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17 pages, 918 KB

Open AccessReview

PapB Family Regulators as Master Switches of Fimbrial Expression

by Fariba Akrami, Hossein Jamali, Mansoor Kodori and Charles M. Dozois

Microorganisms 2025, 13(8), 1939; https://doi.org/10.3390/microorganisms13081939 - 20 Aug 2025

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Abstract

Some bacterial species within the Enterobacteriaceae family possess different types of fimbrial (pili) adhesins that promote adherence to cells and colonization of host tissues. One of the well-characterized fimbrial systems is the pap operon, which encodes P fimbriae, a key virulence factor in [...] Read more.

Some bacterial species within the Enterobacteriaceae family possess different types of fimbrial (pili) adhesins that promote adherence to cells and colonization of host tissues. One of the well-characterized fimbrial systems is the pap operon, which encodes P fimbriae, a key virulence factor in urinary and systemic infections. One of the key regulators of P fimbriae is the transcriptional regulator PapB which plays a pivotal role as a master switch, not only by directing phase-variable expression of its own operon but also by influencing expression of heterologous fimbrial systems. This review explores the structural organization, biogenesis, and multi-tiered regulatory control of P fimbriae, with emphasis on PapB and homologous regulatory proteins such as SfaB, FocB, PixB, and PefB. Comparative genomics and phylogenetic analyses reveal that regulators belonging to the PapB family are evolutionarily conserved across π-fimbrial systems and also regulate other types of fimbriae. These regulators respond to epigenetic changes, host-derived signals, and global transcriptional cues to control levels of production of specific fimbriae in a bacterial population to dynamically modulate bacterial adhesion in different environmental niches. Optimally, understanding these mechanisms could lead to novel approaches to perturb PapB-family proteins and abrogate production of some types of fimbriae as a targeted strategy to prevent bacterial infections dependent on adherence mediated by PapB family regulators. Full article

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

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16 pages, 2105 KB

Open AccessArticle

Enhancing Electron Transfer Efficiency in Microbial Fuel Cells Through Gold Nanoparticle Modification of Saccharomyces cerevisiae

by Teresė Kondrotaitė-Intė, Antanas Zinovičius, Domas Pirštelis and Inga Morkvėnaitė

Microorganisms 2025, 13(8), 1938; https://doi.org/10.3390/microorganisms13081938 - 20 Aug 2025

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Abstract

This study investigates microbial fuel cell (MFC) performance through the modification of Saccharomyces cerevisiae with gold nanoparticles (AuNPs) and polypyrrole (PPy). The yeast/AuNP-modified electrodes generated the highest median current of 2.57 nA, significantly outperforming the yeast/PPy-modified (0.82 nA) electrodes. Power density measurements further [...] Read more.

This study investigates microbial fuel cell (MFC) performance through the modification of Saccharomyces cerevisiae with gold nanoparticles (AuNPs) and polypyrrole (PPy). The yeast/AuNP-modified electrodes generated the highest median current of 2.57 nA, significantly outperforming the yeast/PPy-modified (0.82 nA) electrodes. Power density measurements further confirmed the superior performance of the yeast/AuNP-modified electrodes, showcasing a notable improvement in current densities and power outputs. Yeast/AuNP-modified graphite electrodes produced a higher power density of 22.8 mW/m², while exhibiting a lower current density compared to electrodes modified solely with yeast, which achieved a power density of 5.7 mW/m². These findings highlight the potential of AuNPs in significantly enhancing the electrochemical performance of yeast-based MFCs, providing a promising approach for the development of more efficient bioelectrochemical systems. Full article

(This article belongs to the Section Microbial Biotechnology)

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25 pages, 2958 KB

Open AccessArticle

Brazilian Red Propolis and Its Active Constituent 7-O-methylvestitol Impair Early and Late Stages of Toxoplasma gondii Infection in Human Placental Models

by Samuel Cota Teixeira, Guilherme de Souza, Natalia Carine Lima dos Santos, Rafael Martins de Oliveira, Nagela Bernadelli Sousa Silva, Joed Pires de Lima Junior, Alessandra Monteiro Rosini, Luana Carvalho Luz, Aryani Felixa Fajardo Martínez, Marcos Paulo Oliveira Almeida, Guilherme Vieira Faria, Rosiane Nascimento Alves, Angelica Oliveira Gomes, Maria Anita Lemos Vasconcelos Ambrosio, Rodrigo Cassio Sola Veneziani, Jairo Kenupp Bastos, José Roberto Mineo, Carlos Henrique Gomes Martins, Eloisa Amália Vieira Ferro and Bellisa Freitas Barbosa

Microorganisms 2025, 13(8), 1937; https://doi.org/10.3390/microorganisms13081937 - 20 Aug 2025

Viewed by 417

Abstract

Toxoplasma gondii is a globally distributed protozoan parasite and a major cause of congenital infections, particularly in South America. Current therapies for congenital toxoplasmosis are limited by toxicity, long treatment regimens, and suboptimal efficacy, highlighting the urgent need for safer and more effective [...] Read more.

Toxoplasma gondii is a globally distributed protozoan parasite and a major cause of congenital infections, particularly in South America. Current therapies for congenital toxoplasmosis are limited by toxicity, long treatment regimens, and suboptimal efficacy, highlighting the urgent need for safer and more effective alternatives. In this study, we evaluated the antiparasitic effects of crude ethanolic extract of Brazilian Red Propolis (BRP) and its isolated compounds, focusing on 7-O-methylvestitol, in human trophoblast (BeWo) cells and third-trimester placental explants. Both BRP and 7-O-methylvestitol significantly reduced T. gondii adhesion, invasion, and intracellular replication, without compromising host cell viability. Ultrastructural analyses revealed irreversible parasite damage, and cytokine profiling demonstrated immunomodulatory effects, with enhanced production of interleukin (IL)-6, IL-8, and macrophage migration inhibitory factor (MIF) in BeWo cells and downregulation of IL-6, MIF, and tumor Necrosis Factor (TNF) in infected placental villi. Notably, 7-O-methylvestitol reproduced and, in some assays, surpassed the antiparasitic activity of BRP, suggesting it as a key bioactive constituent responsible for the therapeutic potential of the extract. These findings support the identification of 7-O-methylvestitol as a promising lead compound for structure-based drug design and repositioning strategies, advancing the development of novel, safe, and targeted therapies against congenital toxoplasmosis. Full article

(This article belongs to the Special Issue Advances in Toxoplasma gondii and Toxoplasmosis)

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12 pages, 1067 KB

Open AccessArticle

The Impact of Sugar Beet Seed Pelletization on the Proliferation of Nematophagous Fungi

by Miroslava Soukupová and David Novotný

Microorganisms 2025, 13(8), 1936; https://doi.org/10.3390/microorganisms13081936 - 19 Aug 2025

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Abstract

Pelleting seeds to enhance sowing conditions through the incorporation of pesticides or fertilizers has become a prevalent agricultural practice. This study sought to evaluate the effect of pelletized seeds and the substances they release in the form of an extract on four species [...] Read more.

Pelleting seeds to enhance sowing conditions through the incorporation of pesticides or fertilizers has become a prevalent agricultural practice. This study sought to evaluate the effect of pelletized seeds and the substances they release in the form of an extract on four species of nematophagous fungi. The fungus Pleurotus ostreatus was the most sensitive to the presence of pelletized seeds; the growth of all three evaluated strains of P. ostreatus was inhibited from 42.84 to 94.33% compared to the control. In the case of the fungi Stropharia rugosoannulata and Orbilia oligospora, a statistically significant inhibition of the growth of all three evaluated strains was observed, though this inhibition was less pronounced than in the case of P. ostreatus. In contrast, the inhibitory effect on the fungus Clonostachys rosea exhibited a lower inhibition of mycelial growth (0.65–20.41%) compared to the control. The selection of suitable strains of nematophagous fungi tolerant to substances used for seed pelletization could assist in the management of nematodes. The inoculum of nematophagous fungi can be used in sugar beet sowing as a supplement, but fungi should not be used as part of the seed coatings because their viability is most inhibited in direct contact with fungicides. Full article

(This article belongs to the Section Plant Microbe Interactions)

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25 pages, 2284 KB

Open AccessArticle

Blood Microbiome Analysis Reveals Biomarkers of Treatment Response in Drug-Naïve Patients with First-Episode Psychosis: A Pilot Study

by Marianthi Logotheti, Thomas Gkekas, Panagiotis C. Agioutantis, Alex Hatzimanolis, Stefania Foteli, Diomi Mamma, Nikolaos C. Stefanis, Fragiskos N. Kolisis and Heleni Loutrari

Microorganisms 2025, 13(8), 1935; https://doi.org/10.3390/microorganisms13081935 - 19 Aug 2025

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Abstract

Patients with First-Episode Psychosis (FEP) exhibit variable responses to antipsychotic treatment. Emerging evidence suggests that disease-related dysbiosis of gut and oropharyngeal microbiota may lead to the abnormal translocation of microorganisms via the bloodstream. This study aims to explore the blood microbiome to identify [...] Read more.

Patients with First-Episode Psychosis (FEP) exhibit variable responses to antipsychotic treatment. Emerging evidence suggests that disease-related dysbiosis of gut and oropharyngeal microbiota may lead to the abnormal translocation of microorganisms via the bloodstream. This study aims to explore the blood microbiome to identify candidate biomarkers associated with treatment outcomes in FEP. To address this, blood samples were collected from twenty drug-naïve individuals with FEP, both before and after four weeks of antipsychotic medication. DNA extracted from these samples underwent 16S rRNA gene sequencing and comprehensive bioinformatics analysis. Clinical assessments were based on the Positive and Negative Syndrome Scale and standard remission criteria. Peripheral cytokines (IL1β, TNF-α, IL10) were quantified by immunoassays. Baseline comparisons showed a significantly greater microbiome alpha diversity in remitters, along with differential prevalence in five taxa and 217 metabolic pathways. Post-treatment assessments uncovered a significantly distinct impact of antipsychotics on blood bacterial composition between remission groups, while initial differences on metabolic profiles persisted. Additionally, strong correlations were observed, linking specific taxa abundances to cytokine levels. Conclusively, this pilot study suggests that blood microbiome profiling could provide novel biomarkers for predicting therapeutic response in early psychosis, paving the way for precision medicine interventions. Full article

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

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Open AccessArticle

Environmental Effects on Bacterial Community Assembly in Arid and Semi-Arid Grasslands

by Shenggang Chen, Yaqi Zhang, Jun Ma, Mingyue Bai, Yinglong Chen, Jianbin Guo and Lin Chen

Microorganisms 2025, 13(8), 1934; https://doi.org/10.3390/microorganisms13081934 - 19 Aug 2025

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Abstract

Studying the effects of environmental factors on microbial community assemblies is crucial for understanding microbial biodiversity and ecosystem processes. Although numerous studies have explored the spatial patterns of microbial communities in surface soils, bacterial community distributions in subsurface layers remain poorly understood. We [...] Read more.

Studying the effects of environmental factors on microbial community assemblies is crucial for understanding microbial biodiversity and ecosystem processes. Although numerous studies have explored the spatial patterns of microbial communities in surface soils, bacterial community distributions in subsurface layers remain poorly understood. We investigated multiple community metrics of soil bacteria in arid and semi-arid grasslands in China, and the V4 region of 16S rDNA was analyzed using soil property measurements, fluorescent PCR, and high-throughput sequencing techniques. Specifically, copiotrophic taxa dominate the topsoil, whereas oligotrophic taxa are prevalent in nutrient-limited subsoil. Bacterial diversity decreases from the topsoil to subsoil, and bacterial distribution and ecological community composition exhibit a strong dependence on environmental factors. Moreover, microbial interaction networks demonstrated a progressive simplification with increasing soil depth: topsoil communities displayed higher modularity and a greater prevalence of positive interactions, whereas subsoil networks were significantly less complex. Null model analyses evidenced assembly mechanisms: deterministic processes (particularly homogeneous selection) dominated the bacterial community assembly, but their influence weakened with depth, whereas stochastic processes (e.g., dispersal limitation) increased progressively from the topsoil to subsoil. The PLS-PM analysis demonstrated that the relative influence of abiotic factors (e.g., climatic conditions and nutrient availability), biotic factors (interspecific interactions), along with drift and dispersal limitations on fungal community assembly exhibited depth-dependent patterns. This study provides novel insights into the vertical stratification of bacterial community in arid and semi-arid grasslands, and advances our understanding of pedogenic process under climate change and microbial adaptive strategies in heterogeneous soil environments. Full article

(This article belongs to the Special Issue Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes)

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Microorganisms, Volume 13, Issue 8 (August 2025) – 252 articles

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