Microorganisms

18 pages, 2026 KiB

Open AccessArticle

Cooperative Interplay Between PGPR and Trichoderma longibrachiatum Reprograms the Rhizosphere Microecology for Improved Saline Alkaline Stress Resilience in Rice Seedlings

by Junjie Song, Xueting Guan, Lili Chen, Zhouqing Han, Haojun Cui and Shurong Ma

Microorganisms 2025, 13(7), 1562; https://doi.org/10.3390/microorganisms13071562 (registering DOI) - 2 Jul 2025

Abstract

Soil salinization has become a major obstacle to global agricultural sustainability. While microbial inoculants show promise for remediation, the functional coordination between Trichoderma and PGPR in saline alkali rhizospheres requires systematic investigation. Pot studies demonstrated that while individual inoculations of Trichoderma longibrachiatum (M) [...] Read more.

Soil salinization has become a major obstacle to global agricultural sustainability. While microbial inoculants show promise for remediation, the functional coordination between Trichoderma and PGPR in saline alkali rhizospheres requires systematic investigation. Pot studies demonstrated that while individual inoculations of Trichoderma longibrachiatum (M) or Bacillus aryabhattai (A2) moderately improved rice growth and soil properties, their co-inoculation (A2 + M) synergistically enhanced stress tolerance and nutrient availability—increasing available nitrogen (AN +28.02%), phosphorus (AP +11.55%), and potassium (AK +8.26%) more than either strain alone, while more effectively mitigating salinity (EC −5.54%) and alkalinity (pH −0.13 units). High-throughput sequencing further revealed that the A2 + M treatment reshaped the rhizosphere microbiome, uniquely enriching beneficial taxa (e.g., Actinomycetota [+9.68%], Ascomycota [+50.58%], Chytridiomycota [+152.43%]), and plant-growth-promoting genera (e.g., Sphingomonas, Trichoderma), while drastically reducing saline-alkali-adapted Basidiomycota (−87.96%). Further analysis identified soil organic matter (SOM), AN, and AP as key drivers for the enrichment of Chytridiomycota and Actinomycetota, whereas pH and EC showed positive correlations with Mortierellomycota, Aphelidiomycota, unclassified_k__Fungi, and Basidiomycota. Collectively, the co-inoculation of Trichoderma and PGPR strains enhanced soil microbiome structure and mitigated saline alkali stress in rice seedlings. These findings demonstrate the potential of microbial consortia as an effective bio-strategy for saline alkali soil amelioration. Full article

(This article belongs to the Section Plant Microbe Interactions)

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13 pages, 537 KiB

Open AccessArticle

Effects of Blackcurrant Extract and Partially Hydrolyzed Guar Gum Intake on Gut Dysbiosis in Male University Rugby Players

by Hiroto Miura, Machi Oda, Kanako Abe, Hiromi Ikeda, Mami Fujibayashi, Naoko Oda, Tomohiro Segawa, Aya Abe, Natsumi Ueta, Takamitsu Tsukahara, Tomohisa Takagi, Yuji Naito and Ryo Inoue

Microorganisms 2025, 13(7), 1561; https://doi.org/10.3390/microorganisms13071561 (registering DOI) - 2 Jul 2025

Abstract

Our previous study reported that male university rugby players tended to have a gut with a dysbiotic environment, characterized by abundant pathobiont bacteria and an accumulation of succinate, when compared with age-matched, non-rugby playing healthy males. In the present study, we conducted a [...] Read more.

Our previous study reported that male university rugby players tended to have a gut with a dysbiotic environment, characterized by abundant pathobiont bacteria and an accumulation of succinate, when compared with age-matched, non-rugby playing healthy males. In the present study, we conducted a randomized, double-blinded, placebo-controlled experiment to evaluate the potential of blackcurrant extract and/or partially hydrolyzed guar gum (PHGG) to improve the gut environment of university rugby players. Participants were supplemented with blackcurrant extract and/or PHGG or a placebo for 4 weeks. Beneficial gut bacteria such as Megasphaera spp. tended to increase (p < 0.10) and Bifidobacterium spp. increased (p < 0.05) with the intake of blackcurrant extract and/or PHGG. A subgroup analysis further indicated that, unlike in those with a eubiotic gut environment, the dietary supplements also increased the number of beneficial gut bacteria such as Phascolarctobacterium spp. (p < 0.10) and Faecalibacterium spp. (p < 0.10) and fecal SCFA concentrations (p < 0.05) in participants with a possible dysbiotic gut environment. However, a synergistic effect between blackcurrant extract and PHGG was not clearly observed. Although further investigation is recommended, it was concluded that blackcurrant extract and PHGG can at least be used as functional materials to improve gut dysbiosis in university rugby players. Full article

(This article belongs to the Special Issue Nutrition and Gut Microbiome)

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21 pages, 1987 KiB

Open AccessArticle

Dietary Protein-Induced Changes in Archaeal Compositional Dynamics, Methanogenic Pathways, and Antimicrobial Resistance Profiles in Lactating Sheep

by Maida Mushtaq, Xiaojun Ni, Muhammad Khan, Xiaoqi Zhao, Hongyuan Yang, Baiji Danzeng, Sikandar Ali, Muhammad Hammad Zafar and Guobo Quan

Microorganisms 2025, 13(7), 1560; https://doi.org/10.3390/microorganisms13071560 (registering DOI) - 2 Jul 2025

Abstract

Dietary protein levels greatly influence gut microbial ecosystems; however, their effects on gut archaea and associated functions in ruminants require further elucidation. This study evaluated the impact of varying dietary protein levels on gut archaeal composition, antimicrobial resistance (AMR) genes, virulence factors, and [...] Read more.

Dietary protein levels greatly influence gut microbial ecosystems; however, their effects on gut archaea and associated functions in ruminants require further elucidation. This study evaluated the impact of varying dietary protein levels on gut archaeal composition, antimicrobial resistance (AMR) genes, virulence factors, and functional capacities in sheep. Eighteen ewes (Yunnan semi-fine wool breed, uniparous, 2 years old, and averaging 50 ± 2 kg body weight) were randomly assigned to diets containing an 8.5 (low; H_1), 10.3 (medium; H_m), or 13.9% (high; H_h) crude protein level from the 35^th day of pregnancy to the 90^th day postpartum. The total duration of the experiment was approximately 202 days. A total of nine fecal samples (three from each group) were analyzed via 16S rRNA and metagenomics sequencing. Higher archaeal alpha diversity and richness were observed in the H_m and H_h groups compared to the H_l group (p < 0.05). A Beta diversity analysis revealed the archaeal community’s distinct clustering mode based on protein levels. The methanogenic genera Methanobrevibacter and Methanocorpusculum were dominant across the three groups, and their abundance was influenced by protein intake. A functional prediction analysis indicated moderate changes in amino acid and carbohydrate metabolism, which are particularly associated with methane production, an important source of greenhouse gases. AMR genes (e.g., tetA (60), patA, vat, and Erm methyltransferase) and virulence factors (Bacillibactin, LPS) were significantly enriched when animals were fed high-protein diets. Our results demonstrated that dietary protein levels significantly influence gut archaeal composition, AMR gene enrichment, and related functional pathways. Medium-protein diets promoted greater archaeal diversity, whereas high-protein diets favored resistance gene proliferation and enhanced methanogenic activity. Optimizing dietary protein intake may enhance gut health, mitigate antimicrobial resistance risk, and reduce methane emissions, thereby supporting livestock sustainability and environmental protection. Full article

(This article belongs to the Special Issue Gut Microbiota of Food Animal)

17 pages, 2338 KiB

Open AccessArticle

Paenibacillus hubeiensis sp. nov.: A Novel Selenium-Resistant Bacterium Isolated from the Rhizosphere of Galinsoga parviflora in a Selenium-Rich Region of Enshi, Hubei Province

by Jiejie Kong, Ziyue Fu, Yueyang Liu, Can Jin, Xiaobo Peng, Xiaolong Liu, Yang Gao, Qiusheng Xiao, Yuting Su, Zhigang Zhao, Yunqiong Song, Xingjie Li and Daofeng Zhang

Microorganisms 2025, 13(7), 1559; https://doi.org/10.3390/microorganisms13071559 (registering DOI) - 2 Jul 2025

Abstract

ES5-4^T, a Gram-positive, motile, aerobic, and rod-shaped strain, was isolated from the rhizosphere of Galinsoga parviflora growing in the selenium-rich ore area of Enshi, Hubei Province, China. This strain can grow at pH levels of 5.0–10.0 and temperatures of 4–42 °C, [...] Read more.

ES5-4^T, a Gram-positive, motile, aerobic, and rod-shaped strain, was isolated from the rhizosphere of Galinsoga parviflora growing in the selenium-rich ore area of Enshi, Hubei Province, China. This strain can grow at pH levels of 5.0–10.0 and temperatures of 4–42 °C, with optimal growth at pH 7.0 and 28 °C. It was found to resist NaCl up to 5% (w/v), with an optimal growth condition of 0.5–1.0%. The strain exhibited tolerance to selenite (Se⁴⁺) concentrations up to 5000 mg/L. The major fatty acids of the ES5-4^T strain were anteiso-C_15:0 (46.5%) and C_16:0 (21.7%), its predominant respiratory quinone was MK-7, and its polar lipids included diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and an unidentified phospholipid (PL). The presence of the 16S rRNA gene sequence implies that ES5-4^T belongs to a member of the genus Paenibacillus, with the highest sequence similarity of 98.4% to Paenibacillus pabuli NBRC 13638^T. The bac120 tree also confirmed that the strain is within the genus Paenibacillus. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between ES5-4^T and closely related members of the genus Paenibacillus were all below the cutoff levels of 95–96% and 70%, respectively. Based on a polyphasic approach, including phenotypic, chemotaxonomic, and phylogenetic analyses, the ES5-4^T strain is proposed as a novel species of the genus Paenibacillus, for which the name Paenibacillus hubeiensis sp. nov. is proposed. This type strain is designated as ES5-4^T (=GDMCC 1.3540^T = KCTC 43478^T). Full article

(This article belongs to the Section Environmental Microbiology)

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23 pages, 3116 KiB

Open AccessArticle

Short-Chain Fatty Acid Utilization in Cyberlindnera jadinii for Single-Cell Protein and Odd-Chain Fatty Acid Production

by Christian Hermansen, Rowanne Siao, Gi Gi Chua, Mikko Ru Xuan Lee, Aaron Thong, Melanie Weingarten, Nic Lindley and Eric Charles Peterson

Microorganisms 2025, 13(7), 1558; https://doi.org/10.3390/microorganisms13071558 (registering DOI) - 2 Jul 2025

Abstract

In view of the growing global need for sustainable protein sources, this study explores the utilization of short-chain fatty acids into single-cell protein using the non-conventional yeast Cyberlindnera jadinii. Short-chain fatty acids can be sustainably produced via anaerobic digestion of organic waste, [...] Read more.

In view of the growing global need for sustainable protein sources, this study explores the utilization of short-chain fatty acids into single-cell protein using the non-conventional yeast Cyberlindnera jadinii. Short-chain fatty acids can be sustainably produced via anaerobic digestion of organic waste, presenting a promising fermentation substrate for a circular bioeconomy. Cyberlindnera jadinii is demonstrated to be capable of growing on acetate, propionate and butyrate as both a carbon and energy source without strong inhibition. Bioprocess development was conducted in stirred tank bioreactors, where a fed-batch pH-stat bioprocess led to improved efficiency without substrate inhibition. The highest titer of 31.3 ± 1.0 g/L, rate of 0.67 ± 0.02 g/L/h and yield of 0.36 ± 0.01 g/g was achieved with propionate. The resulting biomass contained 41.3% crude protein, and 17.3% crude lipids with 81% unsaturated fatty acids. In contrast to acetate and butyrate, propionate as a substrate led to accumulation of 37% odd-chain fatty acids with titer, rate and yield of 1.74 ± 0.06 g/L, 0.037 ± 0.001 g/L/h and 0.020 ± 0.001 g/g. These findings confirm that short-chain fatty acids are viable fermentation substrates not only for single-cell protein, but also unsaturated and odd-chain fatty acid production with Cyberlindnera jadinii. Full article

(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology, 2nd Edition)

17 pages, 5007 KiB

Open AccessReview

PROTAC-Based Antivirals for Respiratory Viruses: A Novel Approach for Targeted Therapy and Vaccine Development

by Amith Anugu, Pankaj Singh, Dharambir Kashyap, Jillwin Joseph, Sheetal Naik, Subhabrata Sarkar, Kamran Zaman, Manpreet Dhaliwal, Shubham Nagar, Tanishq Gupta and Prasanna Honnavar

Microorganisms 2025, 13(7), 1557; https://doi.org/10.3390/microorganisms13071557 (registering DOI) - 2 Jul 2025

Abstract

The global burden of respiratory viral infections is notable, which is attributed to their higher transmissibility compared to other viral diseases. Respiratory viruses are seen to have evolved resistance to available treatment options. Although vaccines and antiviral drugs control some respiratory viruses, this [...] Read more.

The global burden of respiratory viral infections is notable, which is attributed to their higher transmissibility compared to other viral diseases. Respiratory viruses are seen to have evolved resistance to available treatment options. Although vaccines and antiviral drugs control some respiratory viruses, this control is limited due to unexpected events, such as mutations and the development of antiviral resistance. The technology of proteolysis-targeting chimeras (PROTACs) has been emerging as a novel technology in viral therapeutics. These are small molecules that can selectively degrade target proteins via the ubiquitin–proteasome pathway. PROTACs as a therapy were initially developed against cancer, but they have recently shown promising results in their antiviral mechanisms by targeting viral and/or host proteins involved in the pathogenesis of viral infections. In this review, we elaborate on the antiviral potential of PROTACs as therapeutic agents and their potential as vaccine components against important respiratory viral pathogens, including influenza viruses, coronaviruses (SARS-CoV-2), and respiratory syncytial virus. Advanced applications of PROTAC antiviral strategies, such as hemagglutinin and neuraminidase degraders for influenza and spike proteins of SARS-CoV-2, are detailed in this review. Additionally, the role of PROTACs in targeting cellular mechanisms within the host, thereby preventing viral pathogenesis and eliciting an antiviral effect, is discussed. The potential of PROTACs as vaccines, utilizing proteasome-based virus attenuation to achieve a robust protective immune response, while ensuring safety and enhancing efficient production, is also presented. With the promises exhibited by PROTACs, this technology faces significant challenges, including the emergence of novel viral strains, tissue-specific expression of E3 ligases, and pharmacokinetic constraints. With advanced computational design in molecular platforms, PROTAC-based antiviral development offers an alternative, transformative path in tackling respiratory viruses. Full article

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

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21 pages, 2986 KiB

Open AccessArticle

Bacillus amyloliquefaciens SQ-2 and Biochar: A Promising Combination for Enhancing Rice Growth in Pb/Al-Contaminated Acidic Soils

by Guohui Gao, Xue Li, Jiajun Ma, Yumeng Cui, Ming Ying, Lei Huang and Meitong Li

Microorganisms 2025, 13(7), 1556; https://doi.org/10.3390/microorganisms13071556 (registering DOI) - 2 Jul 2025

Abstract

In this study, Bacillus amyloliquefaciens SQ-2, previously isolated from a commercial watercress paste, was investigated for its potential in promoting rice growth in Pb/Al-contaminated acidic soil, especially when used in conjunction with corn straw biochar. Firstly, the physiological properties of rice were enhanced, [...] Read more.

In this study, Bacillus amyloliquefaciens SQ-2, previously isolated from a commercial watercress paste, was investigated for its potential in promoting rice growth in Pb/Al-contaminated acidic soil, especially when used in conjunction with corn straw biochar. Firstly, the physiological properties of rice were enhanced, with the activities of catalase and superoxide dismutase increasing by 162.5% and 162.9%, respectively. Additionally, the total phenolic and chlorophyll contents of rice increased by 17.6% and 83.7%, respectively. Secondly, the nutrient content of the rice rhizosphere soil was improved. In particular, nitrate nitrogen, available potassium, and sucrase were enhanced by 9.4%, 45.9%, and 466.8%, respectively. Moreover, SQ-2–biochar was demonstrated to have a notable capacity for removing Pb²⁺ and Al³⁺. The mineralization of Pb²⁺ and Al³⁺ was achieved through the use of SQ-2–biochar, as revealed by SEM-EDS, XRD, XPS, and FT-IR analyses, with the main precipitates being Pb₃(PO₄)₂ and AlPO₄. Functional groups such as C-O-C, C=O, N-H, P-O, and -O-H on the microbial surface were found to be involved in the biosorption process of Pb²⁺ and Al³⁺. In summary, SQ-2–biochar can effectively mineralize Pb²⁺ and Al³⁺, enhance the physiological properties of rice, and improve soil nutrients, thereby augmenting the antioxidant capacity, photosynthesis, and stress resistance of rice and ultimately promoting rice growth. Full article

(This article belongs to the Special Issue Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion)

21 pages, 2974 KiB

Open AccessArticle

Maximizing Biomass Production and Carotenoid-like Pigments Yield in Kocuria sediminis As04 Through Culture Optimization

by Daniela Jakeline López-Mora, Andrea Goreti Flores-Dávalos, Miguel Angel Lorenzo-Santiago, Beatriz Genoveva Guardado-Fierros, Jacobo Rodriguez-Campos and Silvia Maribel Contreras-Ramos

Microorganisms 2025, 13(7), 1555; https://doi.org/10.3390/microorganisms13071555 - 2 Jul 2025

Abstract

The global chemical pigment industry faces environmental challenges despite its economic importance. This study investigates the potential of Kocuria sediminis AS04, an airborne isolate, for sustainable pigment and biomass production. Microbial kinetics were evaluated under Taguchi design conditions with temperature (30, 34, and [...] Read more.

The global chemical pigment industry faces environmental challenges despite its economic importance. This study investigates the potential of Kocuria sediminis AS04, an airborne isolate, for sustainable pigment and biomass production. Microbial kinetics were evaluated under Taguchi design conditions with temperature (30, 34, and 38 °C), stirring speed (110, 120, and 130), and pH (6.0, 6.5, and 7.0), measuring biomass through dry weight and viable cells, pigment production, and identification of its pigment using UPLC-MS/MS; structural and chemical characterization of biomass was conducted using SEM and FTIR. Among the tested conditions, the treatment at 30 °C, 130 rpm, and pH 6.5 resulted in the highest CFU count (5.7 × 10⁹ CFU mL⁻¹) and the greatest biomass yield (13.3 g L⁻¹). In contrast, the highest pigment yield (0.0016 mg g⁻¹) was obtained at 38 °C, 130 rpm, and pH 6.0. Cell extracts identified key carotenoid compounds such as β-cryptoxanthin, Rhodovibrin, and other precursors. These findings highlight the potential of Kocuria sediminis AS04 as a sustainable source of pigments and valuable bioproducts, offering promising alternatives for eco-friendly industrial applications. Full article

(This article belongs to the Special Issue Bioactive Molecules from Microbial Sources)

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16 pages, 2462 KiB

Open AccessArticle

Potential of LP as a Biocontrol Agent for Vibriosis in Abalone Farming

by Ling Ke, Chenyu Huang, Song Peng, Mengshi Zhao, Fengqiang Lin and Zhaolong Li

Microorganisms 2025, 13(7), 1554; https://doi.org/10.3390/microorganisms13071554 - 2 Jul 2025

Abstract

Vibrio species are among the primary pathogenic bacteria affecting abalone aquaculture, posing significant threats to farming practices. Current clinical control predominantly relies on antibiotics, which can result in antibiotic residues in both abalone and the surrounding marine environments. Lactobacillus plantarum (LP) [...] Read more.

Vibrio species are among the primary pathogenic bacteria affecting abalone aquaculture, posing significant threats to farming practices. Current clinical control predominantly relies on antibiotics, which can result in antibiotic residues in both abalone and the surrounding marine environments. Lactobacillus plantarum (LP) has been shown to release bioactive antagonistic substances and exhibits potent inhibitory effects against marine pathogenic bacteria. This study aimed to screen and characterize the probiotic properties of LP strains isolated from rice wine lees to develop a novel biocontrol strategy against Vibriosis in abalone. The methods employed included selective media cultivation, streak plate isolation, and single-colony purification for strain screening, followed by Gram staining, 16S rDNA sequencing, and phylogenetic tree construction using MEGA11 for identification. The resilience, antimicrobial activity, and in vivo antagonistic efficacy of the strains were evaluated through stress tolerance assays, agar diffusion tests, and animal experiments. The results demonstrated the successful isolation and purification of four LP strains (NDMJ-1 to NDMJ-4). Phylogenetic analysis revealed closer genetic relationships between NDMJ-3 and NDMJ-4, while NDMJ-1 and NDMJ-2 were found to be more distantly related. All strains exhibited γ-hemolytic activity, bile salt tolerance (0.3–3.0%), and resistance to both acid (pH 2.5) and alkali (pH 8.5), although they were temperature sensitive (inactivated above 45 °C). The strains showed susceptibility to most of the 20 tested antibiotics, with marked variations in hydrophobicity (1.91–93.15%) and auto-aggregation (13.29–60.63%). In vitro antibacterial assays revealed that cell-free supernatants of the strains significantly inhibited Vibrio parahaemolyticus, V. alginolyticus, and V. natriegens, with NDMJ-4 displaying the strongest inhibitory activity. In vivo experiments confirmed that NDMJ-4 significantly reduced mortality in abalone infected with V. parahaemolyticus. In conclusion, the LP strains isolated from rice wine lees (NDMJ-1 to NDMJ-4) possess robust stress resistance, adhesion capabilities, and broad antibiotic susceptibility. Their metabolites exhibit significant inhibition against abalone-pathogenic Vibrios, particularly NDMJ-4, which demonstrates exceptional potential as a candidate strain for developing eco-friendly biocontrol agents against Vibriosis in abalone aquaculture. Full article

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

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20 pages, 3681 KiB

Open AccessArticle

Regime Shifts in Microbial and Water Quality Dynamics in Red Tilapia Ponds

by Ziyan Liu, Jiaqi Li, Lei Luo, Yang Yu, Jianing Yan, Caiyun Sun, Xiangjun Miao and Wensheng Li

Microorganisms 2025, 13(7), 1553; https://doi.org/10.3390/microorganisms13071553 - 2 Jul 2025

Abstract

Changes in the aquatic ecological environment have a significant impact on aquaculture efficiency. In order to understand the changes in water quality and the dynamics of microalgae and bacteria in the process of aquaculture, 16S rRNA and 18S rRNA high-throughput sequencing technologies were [...] Read more.

Changes in the aquatic ecological environment have a significant impact on aquaculture efficiency. In order to understand the changes in water quality and the dynamics of microalgae and bacteria in the process of aquaculture, 16S rRNA and 18S rRNA high-throughput sequencing technologies were used to determine the microorganisms in a red tilapia (Oreochromis sp.) aquaculture pond. During the breeding period (from 6 July 2023 to 13 November 2023), water samples were collected from three ponds, on average once every 20 days. The results of water quality analysis showed that at the end of culture (13 November 2023), the concentrations of NH₄⁺-N and NO₂⁻-N increased significantly, and both the air temperature (36.00 ± 0.00 to 21 ± 0.00 °C) and water temperature (32.83 ± 0.29 to 22.75 ± 0.42 °C) decreased significantly. The NH₄⁺-N and NO₂⁻-N concentrations increased by 597% (0.67 ± 0.17 to 4.67 ± 0.33 mg/L) and 782% (0.34 ± 0.16 to 3.00 ± 1.15 mg/L), respectively, from T1 to T6. Bacterial diversity decreased to T3 and then increased. The relative abundance of hgcI_clade (from 14.91% to 7.18%) and CL500-29_marine_group (from 3.35% to 1.39%) in aquaculture water generally decreased with the extension of aquaculture time. The abundance of Komma increased from T1 (1.44%) to T3 (13.90%) and decreased from T3 to T6 (4.21%). The pH, dissolved oxygen concentration, and temperature were main factors affecting the dynamics of bacteria, while dissolved oxygen, NH₄⁺-N, and NO₂⁻-N concentrations affected that of microalgae. In conclusion, this study revealed regime shift in the water quality and microalgal–bacterial community with increasing culture time in red tilapia aquaculture ponds. Full article

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

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14 pages, 1767 KiB

Open AccessArticle

Antimicrobial Metabolites Isolated from Some Marine Bacteria Associated with Callyspongia crassa Sponge of the Red Sea

by Amal N. Alahmari, Shahira A. Hassoubah, Bothaina A. Alaidaroos, Ahmed M. Al-Hejin, Noor M. Bataweel, Reem M. Farsi, Khloud M. Algothmi, Naheda M. Alshammari and Amal T. K. Ashour

Microorganisms 2025, 13(7), 1552; https://doi.org/10.3390/microorganisms13071552 - 2 Jul 2025

Abstract

The Red Sea is rich in symbiotic microorganisms that have been identified as sources of bioactive compounds with antimicrobial, antifungal, and antioxidant properties. In this study, we aimed to explore the potential of marine sponge-associated bacteria as sources of antibacterial compounds, emphasizing their [...] Read more.

The Red Sea is rich in symbiotic microorganisms that have been identified as sources of bioactive compounds with antimicrobial, antifungal, and antioxidant properties. In this study, we aimed to explore the potential of marine sponge-associated bacteria as sources of antibacterial compounds, emphasizing their significance in combating antibiotic resistance (AMR). The crude extracts of Micrococcus, Bacillus, and Staphylococcus saprophyticus exhibited significant antibacterial activity, with inhibition zones measuring 12 mm and 14 mm against Escherichia coli, Staphylococcus aureus, Candida albicans, and other infectious strains. The DPPH assay showed that the bacterial isolates AN3 and AN6 exhibited notable antioxidant activity at a concentration of 100 mg/mL. To characterize the chemical constituents responsible for the observed bioactivity, a GC–MS analysis was performed on ethyl acetate extracts of the potent strains. The analysis identified a range of antimicrobial compounds, including straight-chain alkanes (e.g., Tetradecane), cyclic structures (e.g., Cyclopropane derivatives), and phenolic compounds, all of which are known to disrupt microbial membranes or interfere with metabolic pathways. The bioprospecting and large-scale production of these compounds are challenging. In conclusion, this study underscores the potential for marine bacteria associated with sponges from the Red Sea to be a source of bioactive compounds with therapeutic relevance. Full article

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

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12 pages, 971 KiB

Open AccessArticle

Detection of Microbial Growth on Indoor Building Materials in Two Countries Using qPCR

by Helena Rintala, Oliver Röhl, Pinja Tegelberg and Teija Meklin

Microorganisms 2025, 13(7), 1551; https://doi.org/10.3390/microorganisms13071551 - 1 Jul 2025

Abstract

According to several reports, 10–50% of buildings in Europe and worldwide suffer from moisture problems, which can lead to microbial growth in building materials. Unrepaired moisture and microbial damage can lead to the degradation of building structures and reduce visual appeal, resulting in [...] Read more.

According to several reports, 10–50% of buildings in Europe and worldwide suffer from moisture problems, which can lead to microbial growth in building materials. Unrepaired moisture and microbial damage can lead to the degradation of building structures and reduce visual appeal, resulting in economic losses; they can also result in adverse health effects for the building’s occupants. Consequently, robust and reliable methods for the detection of abnormal microbiological conditions in buildings are needed, alongside skilled technical investigations, to plan appropriate renovation actions. In this work, 964 building material samples, which were obtained as part of routine building investigations in two countries, were analyzed for their fungal content using the qPCR method. Cultivation analysis was performed using the same samples, according to corresponding national guidelines. In a sample subset, the total cell counts after staining with acridine orange were determined. The microbial concentrations obtained with all three methods correlated well. Threshold values for the qPCR results were determined using cultivation as a reference method for both countries separately, with similar values obtained for both datasets. Hence, qPCR has great potential to become a standard method of detecting microbes in indoor environments. Full article

(This article belongs to the Special Issue Microbiome and Microbiota in Indoor Spaces: Communities, Control and Potential Hazards)

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20 pages, 6718 KiB

Open AccessArticle

Genetic Diversification of Tomato and Agricultural Soil Management Shaped the Rhizospheric Microbiome of Tomato (Solanum lycopersicum)

by Máximo González, Juan Pablo Araya-Angel, Ashlie Muñoz, Adalid Alfaro-Flores, Massimiliano Cardinale and Alexandra Stoll

Microorganisms 2025, 13(7), 1550; https://doi.org/10.3390/microorganisms13071550 - 1 Jul 2025

Abstract

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to [...] Read more.

The domestication process not only reduced the allelic diversity of tomato genotypes but also affected the genetic traits associated to microbial recruitment, their composition, and their diversity in different compartments of the plant host. Additionally, this process included the transition from natural to agricultural soils, which differ in nutrient availability, physicochemical properties, and agricultural practices. Therefore, modern cultivars may fail to recruit microbial taxa beneficial to their wild relatives, potentially losing important ecological functions. In this study, we analyzed the phylogenetic relationship and the rhizosphere microbiota of four tomato genotypes, Solanum chilense (wild species), S. lycopersicum var. cerasiforme (Cherry tomato), and the S. lycopersicum landrace ‘Poncho Negro’ and the modern cultivar ‘Cal Ace’, grown in both natural and agricultural soils. Microbial communities were identified using 16S rRNA (bacteria) and ITS2 (fungi) amplicon sequencing, allowing cross-domain taxonomic characterization. While the soil type was the main driver of overall microbial diversity, the host genotype influenced the recruitment of specific microbial taxa, which exhibited different recruitment patterns according to the genetic diversification of Solanum genotypes and soil types. Additionally, co-occurrence network analysis identified two main clusters: first, taxa did not show any preferential associations to particular genotypes or soil types, while the second cluster revealed specific microbial patterns associated to fungal taxa in natural soil and bacterial taxa in agricultural soil. Finally, the functional analysis suggested the loss of specific functions through tomato domestication independently of soil type. These findings highlight the role of the plant genotype as a fine-tuning factor in microbiome assembly, with implications for breeding strategies aimed at restoring beneficial plant–microbe interactions. Full article

(This article belongs to the Special Issue Plant-Microbe Interactome: The Green Dialogue Within the Plant Holobiont)

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18 pages, 9709 KiB

Open AccessArticle

Waterborne Transmission Driving the Prevalence of Blastocystis sp. in Los Ríos Region, Southern Chile

by Daniel Sanhueza Teneo, Cedric B. Chesnais, Javiera Manzano, María Paz Moll, Analía Téllez and Guillermo Valenzuela-Nieto

Microorganisms 2025, 13(7), 1549; https://doi.org/10.3390/microorganisms13071549 - 1 Jul 2025

Abstract

Waterborne gastrointestinal infections remain a global health concern, with approximately 1.7 billion diarrhea-related illnesses annually attributable to protozoan parasites. These pathogens are transmitted through contaminated water and exhibit high resistance to chlorination, posing substantial challenges to effective water treatment. This study focused on [...] Read more.

Waterborne gastrointestinal infections remain a global health concern, with approximately 1.7 billion diarrhea-related illnesses annually attributable to protozoan parasites. These pathogens are transmitted through contaminated water and exhibit high resistance to chlorination, posing substantial challenges to effective water treatment. This study focused on the most prevalent intestinal parasites in the Los Ríos Region of Chile: Blastocystis sp., Giardia duodenalis, and Entamoeba coli. The objectives were to assess the prevalence of eukaryotic parasites in water samples—covering both drinking and recreational sources—to describe the circulating subtypes of Blastocystis sp. and to identify ecological factors associated with parasite presence. Water samples were analyzed using conventional PCR, next-generation sequencing (NGS) was employed for Blastocystis sp. subtype identification, and the environmental predictors were evaluated using a multivariable logistic regression model. A total of 132 water samples were analyzed, of which 15.2% were positive for Blastocystis sp. and 1.5% for E. coli, while no samples tested positive for G. duodenalis. We identified subtypes ST1–ST4 of Blastocystis sp., along with ST7, ST10, ST14, ST21, and ST23–ST26, the latter being reported for the first time in Chile. Ecological factors significantly associated with Blastocystis sp. presence included higher water temperature and greater rainfall at positive sites. Potable water was associated with significantly lower odds of Blastocystis sp. infection (aOR = 0.04, 95% CI: 0.00–0.87; p = 0.041), while precipitation increased infection odds by 3% per additional millimeter (aOR = 1.03, 95% CI: 1.00–1.06; p = 0.036). Greater distance to the nearest farmhouse was also significantly associated with reduced infection risk, suggesting that proximity to livestock environments may influence Blastocystis sp. transmission. These findings help explain the high prevalence of Blastocystis sp. observed in humans in the Los Ríos Region and highlight the pivotal role of ecological conditions in driving waterborne transmission. To our knowledge, this is the first environmental study in Chile to clearly demonstrate the association between human infection, environmental factors, and the transmission dynamics of Blastocystis sp. Full article

(This article belongs to the Special Issue Water Microorganisms Associated with Human Health, 2nd Edition)

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26 pages, 3317 KiB

Open AccessArticle

Biosurfactant Produced by Bacillus subtilis UCP 1533 Isolated from the Brazilian Semiarid Region: Characterization and Antimicrobial Potential

by Antônio P. da C. Albuquerque, Hozana de S. Ferreira, Yali A. da Silva, Renata R. da Silva, Carlos V. A. de Lima, Leonie A. Sarubbo and Juliana M. Luna

Microorganisms 2025, 13(7), 1548; https://doi.org/10.3390/microorganisms13071548 - 1 Jul 2025

Abstract

The increasing resistance of pathogenic microorganisms to antimicrobials has driven the search for safe and sustainable alternatives. In this context, microbial biosurfactants have gained prominence due to their antimicrobial activity, low toxicity, and high stability under extreme conditions. This study presents the production [...] Read more.

The increasing resistance of pathogenic microorganisms to antimicrobials has driven the search for safe and sustainable alternatives. In this context, microbial biosurfactants have gained prominence due to their antimicrobial activity, low toxicity, and high stability under extreme conditions. This study presents the production and characterization of a biosurfactant with antimicrobial potential, obtained from Bacillus subtilis isolated from soil, for application in the control of resistant strains. Bacterial identification was performed using mass spectrometry (MALDI-TOF), confirming it as Bacillus subtilis. The strain B. subtilis UCP 1533 was cultivated using different carbon sources (glucose, soybean oil, residual frying oil, and molasses) and nitrogen sources (ammonium chloride, sodium nitrate, urea, and peptone), with evaluations at 72, 96, and 120 h. The best condition involved a mineral medium supplemented with 2% soybean oil and 0.12% corn steep liquor, resulting in the production of 16 g·L⁻¹ of biosurfactant, with a critical micelle concentration (CMC) of 0.3 g·L⁻¹ and a reduction in water surface tension to 25 mN·m⁻¹. The biosurfactant showed an emulsification index of 100% for used motor oil and ranged from 50% to 100% for different vegetable oils, maintaining stability across a wide range of pH, salinity, and temperature. FT-IR and NMR analyses confirmed its lipopeptide nature and anionic charge. Toxicity tests with Tenebrio molitor larvae showed 100% survival at all the tested concentrations. In phytotoxicity assays, seed germination rates above 90% were recorded for Solanum lycopersicum and Lactuca sativa. Antimicrobial tests revealed inhibitory activity against resistant strains of Escherichia coli and Pseudomonas aeruginosa, as well as against species of the genus Candida (C. glabrata, C. lipolytica, C. bombicola, and C. guilliermondii), highlighting the biosurfactant as a promising alternative in combating antimicrobial resistance (AMR). These results indicate the potential application of this biosurfactant in the development of antimicrobial agents for pharmaceutical formulations and sustainable strategies for phytopathogen control in agriculture. Full article

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

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Graphical abstract

19 pages, 1767 KiB

Open AccessArticle

The Abundance and Distribution of the acdS Gene in Microbial Communities from the Rhizosphere of Copiapoa solaris, a Native Cactus in the Arid Coastal Region of Antofagasta, Chile

by Mayra Cayo, Francisco Solís-Cornejo, Andrés Santos, Pedro Zamorano and Bernardita Valenzuela

Microorganisms 2025, 13(7), 1547; https://doi.org/10.3390/microorganisms13071547 - 1 Jul 2025

Abstract

Copiapoa solaris is an endemic cactus species from the Antofagasta region, Chile, thriving in arid coastal ecosystems known as “fog oases,” where the rising marine moisture is the primary water source. This study investigates the role of microbial communities associated with the rhizosphere [...] Read more.

Copiapoa solaris is an endemic cactus species from the Antofagasta region, Chile, thriving in arid coastal ecosystems known as “fog oases,” where the rising marine moisture is the primary water source. This study investigates the role of microbial communities associated with the rhizosphere of C. solaris in adapting to extreme environmental conditions, particularly focusing on the acdS gene, which encodes ACC deaminase—an enzyme that reduces ethylene production under stress. This research aims to elucidate the gene’s contribution to the adaptation of C. solaris in these challenging environments. Samples were collected from three sites (El Cobre, Quebrada Botija, and Quebrada Izcuña) that differ in relative humidity, temperature, and topography. Environmental DNA was extracted, phylogenetic diversity was analyzed, and metagenomic annotation of the acdS gene was conducted. The acdS gene was detected in all samples, with the highest relative abundance at Quebrada Izcuña (0.05%), characterized by low relative humidity (<70%) and severe water stress. Phylogenetic analysis revealed conserved sequences across sites, while taxonomic and alpha diversity were similar among them. However, beta diversity indicated that Quebrada Izcuña was the least homogeneous, hosting distinct taxa potentially associated with stress mitigation. The acdS gene was detected on plasmids at El Cobre and Quebrada Izcuña, suggesting its potential mobility within the metagenome. The results of this study highlight the intricate relationships between microbial communities and the resilient cactus species C. solaris in extreme environments. The conservation and abundance of the acdS gene, particularly in low-humidity conditions, suggest its vital role in facilitating stress tolerance through microbial interactions. Understanding these dynamics is crucial for developing strategies to enhance plant resilience in arid ecosystems, with potential applications in sustainable agriculture and ecosystem management under changing climatic conditions. Full article

(This article belongs to the Special Issue Microbial Dynamics in Desert Ecosystems)

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15 pages, 1101 KiB

Open AccessArticle

Impact of Co-Fermentation on the Soluble Pentosan, Total Phenol, Antioxidant Activity, and Flavor Properties of Wheat Bran

by Yan Chen, Li Zhang, Yifan Chen, Hongling Wang, Wenpei Ge, Zhanying Xue, Xinran Cui, Xin Wang, Aimei Liao, Yuansen Hu and Na Liu

Microorganisms 2025, 13(7), 1546; https://doi.org/10.3390/microorganisms13071546 - 1 Jul 2025

Abstract

Most wheat bran in China is used as animal feed due to its coarse taste. However, fermentation can degrade cellulose in wheat bran, improving its taste and flavor. The effects of co-fermentation with Lactiplantibacillus plantarum and Monascus purpureus on wheat bran remain unclear. [...] Read more.

Most wheat bran in China is used as animal feed due to its coarse taste. However, fermentation can degrade cellulose in wheat bran, improving its taste and flavor. The effects of co-fermentation with Lactiplantibacillus plantarum and Monascus purpureus on wheat bran remain unclear. In this study, we evaluated soluble pentosan, total phenol content, and antioxidant activity in co-fermented wheat bran. Following treatment, the soluble pentosan content was 6.03-fold higher than in raw bran. The total phenol content increased by 5.74-fold, and antioxidant activity was enhanced as well. The flavor profile of wheat bran co-fermented with L. plantarum and M. purpureus changed significantly, with alcohols and pyrazines increasing by 3- to 20-fold and aldehydes decreasing by 52.76%, resulting in a fruity, sweet, and nutty aroma. This study supports the comprehensive utilization of wheat bran and provides novel insights into improving its functionality and quality. Full article

(This article belongs to the Section Food Microbiology)

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46 pages, 3719 KiB

Open AccessArticle

Gut Microbiome Modulation and Health Benefits of a Novel Fucoidan Extract from Saccharina latissima: A Double-Blind, Placebo-Controlled Trial

by Gissel Garcia, Josanne Soto, Carmen Valenzuela, Mirka Bernal, Jesús Barreto, María de la C. Luzardo, Raminta Kazlauskaite, Neil Waslidge, Charles Bavington and Raúl de Jesús Cano

Microorganisms 2025, 13(7), 1545; https://doi.org/10.3390/microorganisms13071545 - 30 Jun 2025

Abstract

This randomized, double-blind, placebo-controlled, three-arm clinical trial evaluated the effects of a proprietary bioactive fucoidan-rich extract derived from Saccharina latissima (SLE-F) on gut microbial composition and function in healthy adults. The objective of the study was to assess the potential of SLE-F to [...] Read more.

This randomized, double-blind, placebo-controlled, three-arm clinical trial evaluated the effects of a proprietary bioactive fucoidan-rich extract derived from Saccharina latissima (SLE-F) on gut microbial composition and function in healthy adults. The objective of the study was to assess the potential of SLE-F to beneficially modulate the gut microbiome, with this paper specifically reporting on microbial diversity, taxonomic shifts, and functional pathway outcomes. Ninety-one participants received either a low dose (125 mg), high dose (500 mg), or placebo twice daily for four weeks. The primary endpoint was the microbiome composition assessed via 16S rRNA sequencing (V3–V4 region), with secondary outcomes including surveys, adverse event monitoring, and clinical evaluations. High-dose supplementation resulted in dose-dependent improvements in the microbial diversity; increased abundance of beneficial taxa, including Bifidobacterium, Faecalibacterium, and Lachnospiraceae; and reductions in inflammation-associated taxa, such as Enterobacteriaceae and Pseudomonadota. A functional pathway analysis showed enhancement in short-chain fatty acid biosynthesis and carbohydrate metabolism. The low-dose group showed modest benefits, primarily increasing Bifidobacterium, with limited functional changes. In vitro colonic simulations further demonstrated a dose-dependent increase in short-chain fatty acids and postbiotic metabolite production following SLE-F exposure. SLE-F was well tolerated, with only mild, nonspecific adverse events reported. These findings support the potential of SLE-F as a safe and effective microbiome-modulating agent, warranting further study of the long-term use and synergy with dietary interventions. Full article

(This article belongs to the Special Issue Gut Microbiota in Health and Diseases: The Role of Pro-/Pre-/Syn-/Post-Biotics in the Gut–Liver–Brain Axis)

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20 pages, 2484 KiB

Open AccessArticle

Characterization and Therapeutic Potential of Three Depolymerases Against K54 Capsular-Type Klebsiella pneumoniae

by Yanjun Lu, Chengju Fang, Li Xiang, Ming Yin, Lvxin Qian, Yi Yan, Luhua Zhang and Ying Li

Microorganisms 2025, 13(7), 1544; https://doi.org/10.3390/microorganisms13071544 - 30 Jun 2025

Abstract

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp), a pathogen causing severe nosocomial infections and high mortality rates, is increasingly becoming a serious global public health threat. Capsular polysaccharide (CPS), a major virulence factor of hvKp, can be enzymatically degraded by bacteriophage-derived depolymerases. However, to our [...] Read more.

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp), a pathogen causing severe nosocomial infections and high mortality rates, is increasingly becoming a serious global public health threat. Capsular polysaccharide (CPS), a major virulence factor of hvKp, can be enzymatically degraded by bacteriophage-derived depolymerases. However, to our knowledge, depolymerases targeting K. pneumoniae K54-type strains have rarely been identified. Here, we identified and characterized three novel capsule depolymerases, Dep_C, Dep_Y, and Dep_Z, derived from three different K. pneumoniae phages, which retained robust activity across a broad pH range (pH 3.0–12.0) and demonstrated thermal stability up to 50 °C. These depolymerases could efficiently digest the CPS of K. pneumoniae K54-serotype strains, significantly inhibit biofilm formation, and remove their mature biofilms. Although no bactericidal activity was detected, these depolymerases rendered host bacteria susceptible to serum complement-mediated killing. We further demonstrate that Dep_C, Dep_Y, and Dep_Z can effectively and significantly prolong the survival time of mice in a pneumonia model infected with K54-type K. pneumoniae and reduce the colonization and virulence of the bacteria in the mice. These findings indicate that depolymerases Dep_C, Dep_Y, and Dep_Z could increase bacterial susceptibility to host immune responses of hvKp to the host through their degradation effect on the CPS. In conclusion, our study demonstrates that the three capsule depolymerases are promising antivirulent agents to combat CR-hvKp infections. Full article

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

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