Microorganisms

18 pages, 2892 KiB

Open AccessArticle

Risk of Secondary Bacterial Infections Revealed by Changes in Trachinotus ovatus Skin and Gill Microbiota During a Cryptocaryon irritans Infection Cycle

by Naiqi Liang, Li Zhu, Shifeng Wang, Weihao Zhang, Xinlei Lin, Yongcan Zhou, Haizhu Ke, Shanheng Yuan, Meijing Li and Yan Cai

Microorganisms 2025, 13(7), 1660; https://doi.org/10.3390/microorganisms13071660 (registering DOI) - 14 Jul 2025

Abstract

This study aims to investigate the response of surface bacterial communities in Trachinotus ovatus to Cryptocaryon irritans infection at different stages of a single infection cycle (0~168 h). These samples were analyzed using high-throughput 16S rRNA sequencing. Alpha diversity analysis showed a reduction [...] Read more.

This study aims to investigate the response of surface bacterial communities in Trachinotus ovatus to Cryptocaryon irritans infection at different stages of a single infection cycle (0~168 h). These samples were analyzed using high-throughput 16S rRNA sequencing. Alpha diversity analysis showed a reduction in the richness and diversity of skin microbiota during infection, with partial recovery post-detachment. Beta diversity analysis revealed distinct structural shifts in skin microbiota at early (24 h) and post-detachment (168 h) stages compared to other phases, while gill microbiota remained stable except during detachment. At the phylum level, Proteobacteria, Actinobacteriota, Bacteroidetes, and Firmicutes were dominant on the skin at different stages, whereas the gill microbiota was predominantly Proteobacteria (>90%). At the genus level, opportunistic pathogens, such as Vibrio and Nautella, increased in relative abundance on the skin with the infection progression, while gill microbiota composition barely changed. The hepatic bacterial load continued to increase with infection duration. These findings indicate that C. irritans alters microbiota composition on skin, facilitating pathogen invasion, thereby elevating the risk of secondary bacterial infections in T. ovatus. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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15 pages, 809 KiB

Open AccessArticle

Fermentation of Microalgae as a Platform for Naturally Encapsulated Oil Powders: Characterization of a High-Oleic Algal Powder Ingredient

by Walter Rakitsky, Leon Parker, Kevin Ward, Thomas Pilarski, James Price, Mona Correa, Roberta Miller, Veronica Benites, Dino Athanasiadis, Bryce Doherty, Lucy Edy, Jon Wittenberg, Gener Eliares, Daniel Gates, Manuel Oliveira, Frédéric Destaillats and Scott Franklin

Microorganisms 2025, 13(7), 1659; https://doi.org/10.3390/microorganisms13071659 (registering DOI) - 14 Jul 2025

Abstract

Powdered oil ingredients are widely used across food, nutrition, and personal care industries, but they are typically produced through encapsulation technologies that involve multiple additives and stabilizers. These systems can compromise oxidative stability, clean-label compliance, and functional performance. Here, we present the development [...] Read more.

Powdered oil ingredients are widely used across food, nutrition, and personal care industries, but they are typically produced through encapsulation technologies that involve multiple additives and stabilizers. These systems can compromise oxidative stability, clean-label compliance, and functional performance. Here, we present the development and characterization of a novel high-oleic algal powder (HOAP) produced from a heterotrophically fermented microalgae. The production strain was developed through classical mutagenesis to enhance oleic acid and lipid accumulation. Three independent fermentation batches at a 20 L scale demonstrated strong reproducibility in key metrics, including dried-cell weight (210.0 g per L on average, CV% = 0.7), oil content (62.0% of DCW on average, CV% = 2.0), and oleic acid (88.8% of total fatty acids on average, CV% = 0.1). HOAP exhibited a favorable nutritional profile (e.g., high monounsaturated fat and fiber, low sugar and moisture) and good oxidative stability under ambient and accelerated storage conditions. Microbiological analyses confirmed compliance with food-grade standards, and in silico allergenicity screening revealed no clinically relevant homologs. Unlike traditional oil powders, HOAP does not require encapsulation and retains oil within a natural protein–fiber matrix, offering both functional and clean-labeling advantages. Its compositional attributes and stability profile support potential use in food, nutrition, and the delivery of bioactive nutrients. These findings establish HOAP as a next generation of oil powder ingredients with broad application potential. Full article

(This article belongs to the Special Issue Microalgal Biotechnology: Innovations and Applications)

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18 pages, 4199 KiB

Open AccessArticle

Effects of Antibiotic Residues on Fecal Microbiota Composition and Antimicrobial Resistance Gene Profiles in Cattle from Northwestern China

by Wei He, Xiaoming Wang, Yuying Cao, Cong Liu, Zihui Qin, Yang Zuo, Yiming Li, Fang Tang, Jianjun Dai, Shaolin Wang and Feng Xue

Microorganisms 2025, 13(7), 1658; https://doi.org/10.3390/microorganisms13071658 - 14 Jul 2025

Abstract

Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the [...] Read more.

Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (bla_KPC and bla_VIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying bla_CTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments. Full article

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

16 pages, 5800 KiB

Open AccessArticle

Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults

by Lihua Deng, Jun Xu, Qian Xue, Yanan Wei and Jingtong Wang

Microorganisms 2025, 13(7), 1657; https://doi.org/10.3390/microorganisms13071657 - 14 Jul 2025

Abstract

Many studies have focused on ageing and gut microbiota, but the correlation between gut microbiota and physical function in older adults, especially those with longevity, remains obscure and deserves further exploration. In this study we investigated changes in the gut microbiota and the [...] Read more.

Many studies have focused on ageing and gut microbiota, but the correlation between gut microbiota and physical function in older adults, especially those with longevity, remains obscure and deserves further exploration. In this study we investigated changes in the gut microbiota and the association between gut microbiota and physical function in adults with longevity. This is a prospective observational study. Fifty-one older adults aged ≥ 60 years (including 27 participants aged 90 years and above) were enrolled. Information on clinical data, physical function including intrinsic capacity by Integrated Care for Older People (ICOPE) tool, and dietary habits of participants was collected and analysed. Gut microbiota structure and functional pathways were analysed by Metagenomics. Intrinsic capacity (measured as ICOPE scores) of adults’ longevity (aged 90–98, longe group) was significantly lower than older adults aged 60–89 years (CON group) (5.44 ± 2.15 vs. 6.71 ± 1.46, p = 0.017). Gut microbiota of the longe group is enriched in Akkermansia and Bifidobacterium, which may be beneficial to health. Gut microbiota was closely related to daily milk (including plain milk, flavoured milk with a content of cow’s milk or reconstituted milk of ≥80%, or reconstituted milk or fermented milk with a content of cow’s milk or milk powder of ≥80%) consumption, anxiety, and physical function including grip strength by the Short Physical Performance Battery (SPPB). Bacteroides plebeius and Bacteroides eggerthii were increased in long-living adults with better physical function. Escherichia coli was more abundant in frail young-old adults. Grip strength is positively correlated with the abundance of Roseburia hominis, Eubacterium rectale, Eubacterium eligens, and Roseburia intestinalis (p < 0.05). Pathways related to amino acid synthesis that include L-isoleucine, L-valine, and L-threonine were over-presented in long-living adults of better physical function. Adults with longevity showed comparable gut microbiota abundance to younger elderly individuals. The gut microbiota of long-living adults showed higher abundance of potentially beneficial bacteria, and the altered bacteria are closely associated with physical function. Changes in the gut microbiota may precede clinical indicators during the process of ageing. Gut microbiota may be a potential biomarker for longevity and healthy ageing. Nutrition and emotional state can be important influencing factors. Full article

(This article belongs to the Section Gut Microbiota)

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14 pages, 869 KiB

Open AccessArticle

Subgingival Microbiome Profiles in Bulgarian Children Aged 10–14 with Gingival Inflammation and Healthy Periodontium: A Targeted PCR Study

by Hristina Tankova and Nadezhda Mitova

Microorganisms 2025, 13(7), 1656; https://doi.org/10.3390/microorganisms13071656 - 14 Jul 2025

Abstract

The subgingival microbiome is a critical component of the oral microbiota and plays a central role in pediatric periodontology. This study investigated differences in periodontopathogen profiles in children with gingival inflammation compared to healthy controls using real-time PCR, with a focus on the [...] Read more.

The subgingival microbiome is a critical component of the oral microbiota and plays a central role in pediatric periodontology. This study investigated differences in periodontopathogen profiles in children with gingival inflammation compared to healthy controls using real-time PCR, with a focus on the microbial complexes defined by Socransky. A total of 73 children (ages 10–14) underwent comprehensive periodontal assessment, including assessments of general health status, the O’Leary hygiene index (HI), gingival condition, and the papillary bleeding index (PBI). Subgingival plaque samples were analyzed using real-time PCR to identify key bacterial species associated with gingival health and disease. Highly pathogenic periodontopathogens such as Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, and Eubacterium nodatum were absent in healthy subjects. In contrast, Tannerella forsythia was significantly more frequently detected in children with gingival inflammation (p < 0.05). The most abundant species in the inflammation group were Prevotella intermedia and Capnocytophaga gingivalis. Children with gingival inflammation exhibit a distinct subgingival microbiome profile characterized by an increased presence of specific periodontopathogens, including a higher prevalence of red complex species as defined by Socransky. However, the cross-sectional nature of this study limits the ability to establish causal relationships. Full article

(This article belongs to the Section Medical Microbiology)

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16 pages, 1767 KiB

Open AccessArticle

Population Structure, Genomic Features, and Antibiotic Resistance of Avian Pathogenic Escherichia coli in Shandong Province and Adjacent Regions, China (2008–2023)

by Shikai Song, Yao Wang, Zhihai Liu, Rongling Zhang, Kaiyuan Li, Bin Yin, Zunxiang Yan, Shifa Yang, Shuqian Lin and Yunpeng Yi

Microorganisms 2025, 13(7), 1655; https://doi.org/10.3390/microorganisms13071655 - 13 Jul 2025

Abstract

Avian pathogenic Escherichia coli (APEC) poses a global threat to poultry health and public safety due to its high lethality, limited treatment options, and potential for zoonotic transmission via the food chain. However, long-term genomic surveillance remains limited, especially in countries like China [...] Read more.

Avian pathogenic Escherichia coli (APEC) poses a global threat to poultry health and public safety due to its high lethality, limited treatment options, and potential for zoonotic transmission via the food chain. However, long-term genomic surveillance remains limited, especially in countries like China where poultry farming is highly intensive. This study aimed to characterize the population structure, virulence traits, and antimicrobial resistance of 81 APEC isolates from diseased chickens collected over 16 years from Shandong and neighboring provinces in eastern China. The isolates were grouped into seven Clermont phylogroups, with A and B1 being dominant. MLST revealed 27 STs, and serotyping identified 29 O and 16 H antigens, showing high genetic diversity. The minor phylogroups (B2, C, D, E, G) encoded more virulence genes and had higher virulence-plasmid ColV carriage, with enrichment for iron-uptake, protectins, and extraintestinal toxins. In contrast, the dominant phylogroups A and B1 primarily carried adhesin and enterotoxin genes. Antimicrobial resistance was widespread: 76.5% of isolates were multidrug-resistant. The minor phylogroups exhibited higher tetracycline resistance (mediated by tet(A)), whereas the major phylogroups showed increased resistance to third- and fourth-generation cephalosporins (due to bla_CTX-M-type ESBL genes). These findings offer crucial data for APEC prevention and control, safeguarding the poultry industry and public health. Full article

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

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14 pages, 1496 KiB

Open AccessArticle

Tetanus in Romania—Trends and Challenges

by Andreea Marilena Păuna, Ștefan Eduard Mîinea, Bianca Georgiana Enciu, Daniela Pițigoi, Anca Mirela Sîrbu, Rodica Popescu, Carmen Daniela Chivu, Carmen-Cristina Vasile and Maria Dorina Crăciun

Microorganisms 2025, 13(7), 1654; https://doi.org/10.3390/microorganisms13071654 - 12 Jul 2025

Abstract

Tetanus is a life-threatening, vaccine-preventable disease caused by tetanospasmin and tetanolysin, which are potent neurotoxins produced by Clostridium tetani, an anaerobic, spore-forming bacterium. Due to the widespread presence of spores in the environment, the disease cannot be eradicated. However, global tetanus prevention [...] Read more.

Tetanus is a life-threatening, vaccine-preventable disease caused by tetanospasmin and tetanolysin, which are potent neurotoxins produced by Clostridium tetani, an anaerobic, spore-forming bacterium. Due to the widespread presence of spores in the environment, the disease cannot be eradicated. However, global tetanus prevention initiatives have contributed to a significant decline in tetanus incidence worldwide. Aiming to present the tetanus trends in Romania, we conducted a retrospective analysis of the tetanus surveillance data. During the study period (2010–2023), 97 cases of tetanus were reported in Romania (median: 6.5; IQR: 5–7) with an average incidence rate of 0.03 per 100,000 inhabitants (95% CI: 0.02–0.04; range: 0.01–0.09). The highest incidence rates were recorded among people aged 1 to 14 years old (0.09 per 100,000 inhabitants, 95% CI: 0.06–0.13; range: 0.00–0.20), male (0.05 per 100,000 inhabitants; 95% CI: 0.03–0.06; range: 0.03–0.12), and from rural areas (0.05 per 100,000 inhabitants; 95% CI: 0.03–0.08; range: 0.01–0.17). A decline in the number of tetanus cases of 7% by year was observed, which is supported by the statistical analysis showing a p-value of 0.005 (IRR: 0.93; 95% CI: 0.88–0.98). However, the same decline in tetanus incidence was not supported by the statistical analysis (IRR: 0.93; 95% CI: 0.44–1.98; p = 0.9). Forty-seven tetanus deaths were recorded, with an average case fatality ratio of 42% (95% CI: 25.62–57.92; range: 0–100), showing a decreasing trend of 9% by year (IRR: 0.91; 95% CI: 0.89–0.93). Although the annual number of tetanus cases in Romania has shown a slight downwards trend, its situation has remained relatively stable, as shown by the tetanus incidence. Moreover, the case fatality rate continues to be high. Therefore, our study emphasizes the importance of achieving high vaccination uptake among children and adolescents, raising awareness of the importance of booster doses in adults, and improving the management of tetanus-prone wounds. Full article

(This article belongs to the Special Issue Infectious Disease Surveillance in Romania)

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18 pages, 2705 KiB

Open AccessArticle

Irrigation of Suaeda salsa with Saline Wastewater and Microalgae: Improving Saline–Alkali Soil and Revealing the Composition and Function of Rhizosphere Bacteria

by Qiaoyun Yan, Yitong Zhang, Zhenting Xu, Wenying Qu, Junfeng Li, Wenhao Li, Chun Zhao and Hongbo Ling

Microorganisms 2025, 13(7), 1653; https://doi.org/10.3390/microorganisms13071653 - 12 Jul 2025

Abstract

Limited research has been conducted on the potential and mechanisms of irrigating Suaeda salsa with wastewater and microalgae to improve saline–alkali land. This study used three irrigation treatments (freshwater, saline wastewater, and saline wastewater with microalgae) to irrigate S. salsa, and microalgae [...] Read more.

Limited research has been conducted on the potential and mechanisms of irrigating Suaeda salsa with wastewater and microalgae to improve saline–alkali land. This study used three irrigation treatments (freshwater, saline wastewater, and saline wastewater with microalgae) to irrigate S. salsa, and microalgae promoted the growth of S. salsa and increased soil nutrient content, increasing available nitrogen (4.85%), available phosphorus (44.51%), and organic carbon (24.05%) while alleviating salt stress through reduced soil salinity (13.52%) and electrical conductivity (21.62%). These changes promoted eutrophic bacteria while inhibiting oligotrophic bacteria. Bacterial community composition exhibited significant variations, primarily driven by soil pH, total nitrogen, and organic carbon content. Notably, rhizosphere bacteria showed enhanced functional capabilities, with increased abundance of salt stress resistance and nitrogen metabolism-related genes compared to original soil, particularly under saline irrigation conditions. Furthermore, microalgae addition enriched nitrogen metabolism-related gene abundance. These findings revealed the potential role of key bacteria in enhancing plant growth and the soil environment and highlighted the potential of applying S. salsa, wastewater, and microalgae for the synergistic improvement of saline–alkali land. Full article

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

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17 pages, 4334 KiB

Open AccessArticle

Responses of Different Temperature-Acclimated Diatom Species, Smaller Thalassiosira pseudonana and Larger Thalassiosira rotula, to Increased Ambient Temperature

by Wei Zhao, Jihua Liu, Hui Song, Bokun Chen, Hongli Ji, Xue Yang and Gang Li

Microorganisms 2025, 13(7), 1652; https://doi.org/10.3390/microorganisms13071652 - 12 Jul 2025

Abstract

The acute rise in temperature due to marine heatwaves has a strong impact on marine phytoplankton. To determine whether these effects depend on ambient temperature and cell size, we acclimated two diatom species, smaller Thalassiosira pseudonana (Hasle and Heimdal, 1970) and larger Thalassiosira [...] Read more.

The acute rise in temperature due to marine heatwaves has a strong impact on marine phytoplankton. To determine whether these effects depend on ambient temperature and cell size, we acclimated two diatom species, smaller Thalassiosira pseudonana (Hasle and Heimdal, 1970) and larger Thalassiosira rotula (Meunier, 1910), at low (LAT), medium (MAT) and high ambient temperatures (HAT) and examined their physiochemical and transcriptional responses to temperature rise (AT + 6 °C). The specific growth rate (µ) of smaller cells was increased by 32% due to temperature rise at LAT, but decreased by 13% at HAT, with the stimulatory and inhibitory extent being ~50% less than that of larger cells. At LAT, chlorophyll a (Chl a), carotenoid (Car) and carbon (POC) contents were increased in smaller cells due to temperature rise, but were decreased in larger cells; at HAT, Chl a and Car were increased in both smaller and larger cells and POC was increased in only smaller cells. At LAT, temperature rise led to a disproportionate increase in photosynthesis and dark respiration, resulting in an increase in carbon utilization efficiency (CUE) in smaller cells and a decrease in CUE in larger cells; at HAT, there was a decrease in CUE in both the smaller and larger cells, but to a lesser extent in the former than in the latter. Our results also show that smaller cells cope with the acute temperature rise mainly by strengthening their enzyme activity (e.g., the antioxidant system) and conservatively regulating their metabolism, while larger cells mainly regulate their photosynthetic and central carbon metabolism. Moreover, larger cells can outperform their smaller counterparts when the temperature rise occurs at lower ambient temperature. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 3395 KiB

Open AccessArticle

Hybrid Whole Genomes of Brucella melitensis from Tunisian Animal Isolates: Virulence Factors, Antimicrobial Susceptibility, and Phylogeny

by Ibtihel Ben Abdallah, Germán Kopprio, Awatef Béjaoui, Susanne Köhler, Kaouther Guesmi, Sana Kalthoum, Jacob Gatz, Amel Arfaoui, Monia Lachtar, Haikel Hajlaoui, Mohamed Naceur Baccar, Holger Scholz and Abderrazak Maaroufi

Microorganisms 2025, 13(7), 1651; https://doi.org/10.3390/microorganisms13071651 - 12 Jul 2025

Abstract

Brucellosis remains endemic in Tunisia, causing abortions in small ruminants, and represents a public health threat through occupational exposure and the consumption of contaminated animal products. The aims of this study are to assess the antibiotic susceptibility of two Brucella melitensis isolates (TATA [...] Read more.

Brucellosis remains endemic in Tunisia, causing abortions in small ruminants, and represents a public health threat through occupational exposure and the consumption of contaminated animal products. The aims of this study are to assess the antibiotic susceptibility of two Brucella melitensis isolates (TATA and SBZ) from aborted sheep, to analyze their genomes using hybrid whole-genome sequencing, and to investigate their antimicrobial resistance (AMR), potential virulence factors (VFs), and phylogenetic relationships. Both isolates were phenotypically confirmed to be susceptible to doxycycline, gentamicin, rifampicin, streptomycin, and trimethoprim–sulfamethoxazole, and no corresponding classical AMR genes were identified. However, several potential AMR-related genes (mprF, bepCDEFG, qacG, and adeF) and a mutation in the parC gene were detected. The analysis of the genotypes revealed 74 potential virulence genes, primarily involved in lipopolysaccharide synthesis and type IV secretion systems. Genomic comparison showed over 99% nucleotide identity between the Tunisian strains, B. melitensis bv. 1 16M and B. melitensis bv. 3 Ether. Five gene clusters, including three hypothetical proteins with 100% identity, were detected exclusively in the TATA and SBZ strains. Additionally, two unique gene clusters were identified in SBZ: a rhodocoxin reductase and another hypothetical protein. Both isolates were assigned to sequence types ST11 and ST89. Core-genome-based phylogenetic analysis clustered both strains with biovar 3 and ordered the Tunisian strains into two distinct groups: TATA within Tunisian Cluster 1 is closely related to strains from Egypt and Italy, while SBZ near MST Cluster 4 is more related to isolates from Austria and two outliers from Italy and Tunisia. This study provides the first genomic characterization of B. melitensis from aborted sheep in Tunisia and offers valuable insights into AMR, virulence, and phylogenetic distribution. Full article

(This article belongs to the Special Issue Epidemiology and Control Strategies for Brucellosis)

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13 pages, 2979 KiB

Open AccessArticle

Taxon-Dependent Community Assembly of Bacteria and Protists in River Ecosystems: A Case Study from the Yujiang River

by Yusen Li, Wenjian Chen, Yaoquan Han, Jianjun Lei, Bo Huang, Youjie Qin, Feng Lin, Caijin Li, Dapeng Wang and Lei Zhou

Microorganisms 2025, 13(7), 1650; https://doi.org/10.3390/microorganisms13071650 - 12 Jul 2025

Abstract

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan [...] Read more.

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan communities along the Yujiang River using environmental DNA metabarcoding. Bacterial communities exhibited significantly greater alpha diversity and broader habitat niches compared to protists. Additionally, a negative correlation was found between alpha diversity and niche breadth for both groups. Protistan communities exhibited significantly higher beta diversity (Bray–Curtis distance) than bacterial communities, with species turnover being the principal factor driving the variations in both communities. Null model results indicated that heterogeneous selection primarily structured bacterial communities, while stochastic processes (drift) mainly governed protist communities. Redundancy analysis and Mantel tests showed significant associations between environmental factors (e.g., temperature and pH) and bacterial community composition. Moreover, the longitude of sampling sites was linked to spatial variations in both bacterial and protistan communities. Further analyses, including distance-decay patterns, variation partitioning, and multiple regression on distance matrices, demonstrated that bacterial communities were driven by both environmental and spatial factors, while protist communities exhibited a stronger response to spatial factors. These results enhance our understanding of microbial community assembly in river ecosystems and provide valuable insights for the conservation and sustainable management of freshwater systems. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 1764 KiB

Open AccessArticle

Surface Display of Avian H5 and H9 Hemagglutinin Antigens on Non-Genetically Modified Lactobacillus Cells for Bivalent Oral AIV Vaccine Development

by Fuyi Liu, Jingbo Chang, Jingqi Huang, Yuping Liao, Xiaonan Deng, Tingting Guo, Jian Kong and Wentao Kong

Microorganisms 2025, 13(7), 1649; https://doi.org/10.3390/microorganisms13071649 - 11 Jul 2025

Abstract

A novel bivalent oral vaccine candidate against H5N1 and H9N2 avian influenza virus (AIV) was developed using Lactobacillus surface display technology without genetic modification. The hemagglutinin subunit 1 (HA1) antigens from both subtypes were fused to the surface layer-binding domain of Lactobacillus crispatus [...] Read more.

A novel bivalent oral vaccine candidate against H5N1 and H9N2 avian influenza virus (AIV) was developed using Lactobacillus surface display technology without genetic modification. The hemagglutinin subunit 1 (HA1) antigens from both subtypes were fused to the surface layer-binding domain of Lactobacillus crispatus K313, expressed in Escherichia coli, and purified. Wild-type Lactobacillus johnsonii H31, isolated from chicken intestine, served as a delivery vehicle by adsorbing and stably displaying the HA1 proteins on its surface. This approach eliminates the need for bacterial engineering while utilizing lactobacilli’s natural capacity to protect surface-displayed antigens, as evidenced by HA1’s protease resistance. Mouse immunization studies demonstrated induction of strong systemic IgG and mucosal IgA responses against both H5N1 and H9N2 HA1. The system offers several advantages, including safety through non-GMO probiotics, potential for multivalent vaccine expansion, and intrinsic antigen protection by lactobacilli. These findings suggest this platform could enable development of cost-effective, multivalent AIV vaccines. Full article

(This article belongs to the Section Food Microbiology)

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19 pages, 2862 KiB

Open AccessArticle

Characterization of Soil Bacterial Communities in Different Vegetation Types on the Lava Plateau of Jingpo Lake

by Yanli Zhang, Jiaxing Huang, Jiaxin Xue, Kaining Zhang, Xintong Chen, Jianhui Jia and Qingyang Huang

Microorganisms 2025, 13(7), 1648; https://doi.org/10.3390/microorganisms13071648 - 11 Jul 2025

Abstract

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical [...] Read more.

To explore the interactions within the vegetation–soil–microorganism continuum on the Jingpo Lake lava platform, five vegetation types—grassland (GL), shrubland (SL), deciduous broad-leaved forest (DB), coniferous and broad-leaved mixed forest (CB), and coniferous forest (CF)—were examined. Significant differences in the soil physical and chemical properties were identified among these types (p < 0.05). The soil bacterial community structures also varied significantly (p < 0.05), with Actinobacteriota, Proteobacteria, and Acidobacteria as the dominant phyla, exhibiting notable genus-level differences (p < 0.05). The soil organic matter (SOM), available nitrogen (AN), total nitrogen (TN), and soil water content (SWC) were significantly correlated with the bacterial community structure (p < 0.05 or p < 0.01), acting as key determinants of the microbial community structure and function. PICRUSt2 functional predictions revealed significant variations in the metabolic functions of the soil bacterial communities across vegetation types, indicating distinct functional specializations. In conclusion, the Jingpo Lake lava plateau harbors abundant bacterial resources. When devising vegetation adaptation strategies, it is essential to take into account variations in the rhizosphere soil bacteria across different vegetation types. Furthermore, prioritizing the implementation of forest vegetation is crucial in the adaptive management of the lava plateau. This approach holds significant implications for studying the bacterial diversity in the lava plateau and exploring the cultivation and application of functional bacteria in extreme environments. Full article

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

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10 pages, 1272 KiB

Open AccessCommunication

Antibiotic Resistance in Bifidobacterium animalis subsp. lactis and Bifidobacterium longum: Definition of Sensitivity/Resistance Profiles at the Species Level

by Mario Terlizzi, Barbara Speranza, Milena Sinigaglia, Maria Rosaria Corbo and Antonio Bevilacqua

Microorganisms 2025, 13(7), 1647; https://doi.org/10.3390/microorganisms13071647 - 11 Jul 2025

Abstract

Antimicrobial resistance is a threat to probiotic microorganisms due to their potential role in harboring and transmitting resistance genes. This study focuses on two Bifidobacterium species (B. animalis subsp. lactis and B. longum) by analyzing 657 Minimal Inhibitory Concentration (MIC) values [...] Read more.

Antimicrobial resistance is a threat to probiotic microorganisms due to their potential role in harboring and transmitting resistance genes. This study focuses on two Bifidobacterium species (B. animalis subsp. lactis and B. longum) by analyzing 657 Minimal Inhibitory Concentration (MIC) values extracted from research articles indexed in Scopus, PubMed, and Web of Science, published since 2014, and considering 17 different antibiotics. MIC values were used for descriptive statistical analysis (boxplots and violin plots) to evaluate both inter- and intraspecies distributions. The results showed an overall increase in MIC values compared to historical data, with B. longum exhibiting high resistance to tetracyclines and streptomycin—approximately 25% to 50% of the strains had MIC values > EFSA cut-offs. The violin plots revealed the presence of resistant subpopulations, particularly within B. longum. These findings support the relevance of longitudinal MIC analysis as a tool for detecting early shifts in antimicrobial susceptibility and highlight the importance of data-driven approaches for microbiological risk assessment in probiotic applications. Full article

(This article belongs to the Section Food Microbiology)

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19 pages, 1297 KiB

Open AccessReview

Biology and Application of Chaetomium globosum as a Biocontrol Agent: Current Status and Future Prospects

by Shailja Sharma, Saurabh Pandey, Sourabh Kulshreshtha and Mukesh Dubey

Microorganisms 2025, 13(7), 1646; https://doi.org/10.3390/microorganisms13071646 - 11 Jul 2025

Abstract

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum [...] Read more.

Chaetomium globosum is a widely distributed fungal species recognized for its ability to produce a range of secondary metabolites. This fungus plays a significant ecological role by degrading organic matter and contributing to nutrient cycling in diverse ecosystems. In recent years, C. globosum has attracted considerable scientific interest due to its potential as a biocontrol agent [BCA] against a wide array of diseases in numerous plant species. While the precise mechanisms of C. globosum as a BCA remain poorly understood, interference competition through antibiosis is one of the key mechanisms. Moreover, C. globosum can enhance plant health by promoting nutrient availability, manipulating the rhizosphere microbiome, and inducing plant defense responses. The formulation of C. globosum for agricultural applications has been reported, which can significantly improve stability and efficacy under field conditions. However, despite significant advancements in omics and molecular biology technologies, the biology of C. globosum is understudied. Enhanced research into the genetics and functional genomics of C. globosum could pave the way for its applications in sustainable agriculture. This review summarizes the role of C. globosum as a BCA, focusing on its underlying mechanisms such as genomics and transcriptomics, and the effects of C. globosum application on soil health and the rhizosphere microbiome. Full article

(This article belongs to the Section Plant Microbe Interactions)

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14 pages, 13698 KiB

Open AccessArticle

Gut Microbiota Diversity in 16 Stingless Bee Species (Hymenoptera: Apidae: Meliponini)

by María de Lourdes Ramírez-Ahuja, Kenzy I. Peña-Carrillo, Mayra A. Gómez-Govea, Mariana Lizbeth Jiménez-Martínez, Gerardo de Jesús Trujillo-Rodríguez, Marisol Espinoza-Ruiz, Antonio Guzmán Velasco, Adriana E. Flores, José Ignacio González-Rojas, Diana Reséndez-Pérez and Iram Pablo Rodríguez-Sánchez

Microorganisms 2025, 13(7), 1645; https://doi.org/10.3390/microorganisms13071645 - 11 Jul 2025

Abstract

Bacterial symbionts play an important role in insect survival by contributing to key metabolic and defensive functions. While stingless bees are known to harbor diverse microbial communities, their core bacterial symbionts remain poorly characterized. In this study, we analyzed the gut microbiota of [...] Read more.

Bacterial symbionts play an important role in insect survival by contributing to key metabolic and defensive functions. While stingless bees are known to harbor diverse microbial communities, their core bacterial symbionts remain poorly characterized. In this study, we analyzed the gut microbiota of sixteen stingless bee species collected from different regions of Mexico using 16S rRNA gene sequencing on the Illumina^® MiSeq™ platform. Our results revealed that Proteobacteria, Firmicutes, and Actinobacteria are the most abundant bacterial phyla across species. Among the dominant genera, lactic acid bacteria, such as Lactobacillus spp., Bifidobacterium, and Fructobacillus spp., were the most prevalent. These bacteria are responsible for developing biochemical functions in metabolic processes like lactic fermentation and the biotransformation of complex organic compounds into molecules that are more easily assimilated by bees. This study offers a novel perspective on the diversity and predicted composition of gut microbiota in Mexican stingless bees. By highlighting differences in microbial communities among species with different feeding habits, our results emphasize the importance of preserving microbial biodiversity in these pollinators. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 5258 KiB

Open AccessArticle

Fusobacterium nucleatum Is Associated with Tumor Characteristics, Immune Microenvironment, and Survival in Appendiceal Cancer

by Christopher Sherry, Neda Dadgar, Hyun Park, Chelsea Knotts, Erin Grayhack, Rose Blodgett, Kunhong Xiao, Ashten N. Omstead, Albert D. Donnenberg, David L. Bartlett, Vera Donnenberg, Ajay Goel, Ali H. Zaidi and Patrick L. Wagner

Microorganisms 2025, 13(7), 1644; https://doi.org/10.3390/microorganisms13071644 - 11 Jul 2025

Abstract

Emerging evidence highlights the role of the tumor microbiome, including Fusobacterium nucleatum (Fn), in a wide range of gastrointestinal cancers. Fn purportedly contributes to tumorigenesis by activating oncogenic pathways and modulating immune responses. Although the prevalence and impact of Fn has been extensively [...] Read more.

Emerging evidence highlights the role of the tumor microbiome, including Fusobacterium nucleatum (Fn), in a wide range of gastrointestinal cancers. Fn purportedly contributes to tumorigenesis by activating oncogenic pathways and modulating immune responses. Although the prevalence and impact of Fn has been extensively studied in colorectal cancer, no previous systematic or in situ studies have been performed in appendiceal cancer (AC). The aim of this study was to evaluate the prevalence and association of Fn density in AC with clinical factors and oncologic outcomes. Archival tissue from 54 patients with AC was assessed for Fn density using RNA in situ hybridization. Clinicopathological variables were obtained for each case through electronic medical record review, and the immune microenvironment was characterized in each case using immunohistochemistry to quantify CD3+ and CD8+ T lymphocytes and M1-/M2-like tumor-associated macrophages. In AC, Fn density was associated with patient age, tumor grade, and histologic subtype. Fn was negatively associated with CD3+ and CD8+ T lymphocytes and positively associated with M2-like TAMs in low-grade AC. Interestingly, tumor Fn content was associated with better overall and progression-free survival, even when controlling for tumor grade. In this exploratory study, we found that Fn is prevalent in AC. Fn is associated with a number of clinical, pathologic, immunologic, and prognostic variables in AC that are distinct from the corresponding observed associations in colorectal cancer. Further research is warranted to validate these findings and explore the mechanistic contributions of Fn to AC pathogenesis or immune response. Full article

(This article belongs to the Special Issue The Microbiome in Ecosystems)

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20 pages, 2510 KiB

Open AccessArticle

In Vitro Evaluation of the Probiotic Properties and Whole Genome Sequencing of Lacticaseibacillus rhamnosus J3205 Isolated from Home-Made Fermented Sauce

by Yiming Chen, Lingchao Ma, Weiye Chen, Yiwen Chen, Zile Cheng, Yongzhang Zhu, Min Li, Yan Zhang, Xiaokui Guo and Chang Liu

Microorganisms 2025, 13(7), 1643; https://doi.org/10.3390/microorganisms13071643 - 11 Jul 2025

Abstract

Lacticaseibacillus rhamnosus J3205 was isolated from traditional fermented sauces and demonstrated potential probiotic properties. The strain exhibited high tolerance to simulated saliva (93.24% survival) and gastrointestinal conditions (69.95% gastric and 50.44% intestinal survival), along with strong adhesion capacity (58.25%) to intestinal epithelial cells. [...] Read more.

Lacticaseibacillus rhamnosus J3205 was isolated from traditional fermented sauces and demonstrated potential probiotic properties. The strain exhibited high tolerance to simulated saliva (93.24% survival) and gastrointestinal conditions (69.95% gastric and 50.44% intestinal survival), along with strong adhesion capacity (58.25%) to intestinal epithelial cells. Safety assessments confirmed the absence of virulence and antibiotic resistance genes. Genomic analysis revealed stress-response genes and 34 insertion sequence (IS) elements, while proteomic profiling identified Pgk as a key enzyme in lactic acid production and SecY in oxidative stress resistance. Functionally, J3205 significantly reduces pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and enhances antioxidant markers (SOD, GSH) in vitro. These results position L. rhamnosus J3205 as a promising candidate for gut-health foods, anti-inflammatory nutraceuticals, and oxidative-stress therapeutics, warranting further in vivo validation. Full article

(This article belongs to the Section Food Microbiology)

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16 pages, 528 KiB

Open AccessArticle

Elixhauser Comorbidity Measure and Charlson Comorbidity Index in Predicting the Death of Spanish Inpatients with Diabetes and Invasive Pneumococcal Disease

by Enrique Gea-Izquierdo, Rossana Ruiz-Urbaez, Valentín Hernández-Barrera and Ángel Gil-de-Miguel

Microorganisms 2025, 13(7), 1642; https://doi.org/10.3390/microorganisms13071642 - 11 Jul 2025

Abstract

Invasive pneumococcal disease (IPD) is a serious infection caused by the bacterium Streptococcus pneumoniae (pneumococcus) that can produce a wide spectrum of clinical manifestations. The aim of this study was to analyze the comorbidity factors that influenced the mortality in patients with diabetes [...] Read more.

Invasive pneumococcal disease (IPD) is a serious infection caused by the bacterium Streptococcus pneumoniae (pneumococcus) that can produce a wide spectrum of clinical manifestations. The aim of this study was to analyze the comorbidity factors that influenced the mortality in patients with diabetes (D) according to IPD. A retrospective study to analyze patients with D and IPD was carried out. Based on the discharge reports from the Spanish Minimum Basic Data Set (MBDS) from 1997 to 2022, the Elixhauser Comorbidity Index (ECI) and the Charlson Comorbidity Index (CCI) were calculated to predict in-hospital mortality (IHM) in Spain. A total of 12,994,304 patients with D were included, and 84,601 cases of IPD were identified. The average age for men was 70.23 years and for women 73.94 years. In all years, ECI and CCI were larger for type 2 D than for type 1 D, with men having a higher mean than women. An association was found between risk factors ECI, age, type 1 D, COVID-19, IPD (OR = 1.31; 95% CI: 1.29–1.35; p < 0.001); CCI, age, type 1 D, COVID-19, IPD (OR = 1.45; 95% CI: 1.42–1.49; p < 0.001), and increased mortality. The IHM increased steadily with the number of comorbidities and index scores from 1997 to 2022. D remains a relevant cause of hospitalization in Spain. Comorbidities reflected a great impact on patients with D and IPD, which would mean a higher risk of mortality. Predicting mortality events and length of stay by comparing indices showed that CCI outperforms ECI in predicting inpatient death after IPD. Full article

(This article belongs to the Section Public Health Microbiology)

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