Microorganisms

19 pages, 2900 KB

Open AccessArticle

Analysis of Gut Microbial Communities and Functions in Passer ammodendri Under Two Extreme Environments

by Yaqi Liu, Peng He, Dongxin Liu, Yang Song, Chenxi Jia, Duochun Wang, Qinghua Jin, Gang Song and Qiang Wei

Microorganisms 2025, 13(11), 2642; https://doi.org/10.3390/microorganisms13112642 (registering DOI) - 20 Nov 2025

Abstract

The gut microbiome regulates multiple physiological processes of the host and plays a significant role in the adaptation of wild animal hosts to extreme environments. The saxaul sparrow (Passer ammodendri) is a typical bird species found in the northwest of China, [...] Read more.

The gut microbiome regulates multiple physiological processes of the host and plays a significant role in the adaptation of wild animal hosts to extreme environments. The saxaul sparrow (Passer ammodendri) is a typical bird species found in the northwest of China, characterized by its strong adaptability to extreme environments. Studying it can help reveal the microbial adaptation mechanisms of the host to extreme environments. Therefore, we conducted a comparative analysis of the intestinal microbial community characteristics and functions of the saxaul sparrow in high-altitude (Pamir Plateau) and desert (Tazhong Town) habitats in Xinjiang. The results of full-length 16S rRNA sequencing and species annotation indicated that the bacterial species composition (relative abundance > 0.1%) of the intestinal microbiota community of the saxaul sparrow was Candidatus Arthromitus sp. SFB rat Yit, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, and Klebsiella pneumoniae, in sequence. In addition, Lysinibacillus sphaericus is a unique strain specific to the Tazhong group, while Stenotrophomonas maltophilia has a much higher abundance in the Tazhong group than in the Pamir Plateau group. It is worth noting that both groups of samples contain potential opportunistic pathogenic bacteria, such as Escherichia coli and Klebsiella pneumoniae. The Shannon index of the Pamir Plateau group was lower than that of the Tazhong Town group (p = 0.0026), indicating that the intestinal microbial diversity of the Pamir Plateau group was lower than that of the Tazhong Town group. However, there was no significant difference in the ACE index between the two groups and it was not statistically significant (p > 0.05). The Beta diversity analysis revealed that the distance between the two groups of samples was considerable (p = 0.001), indicating a significant separation. The functional annotation results indicated that the Pamir Plateau group exhibited enhanced capabilities in carbohydrate metabolism, energy metabolism, and DNA damage repair, while the Tazhong Town group demonstrated enhanced lipid metabolism and detoxification abilities. These findings will help reveal the possible impact of the living environment on the composition and function of the intestinal microbiota of the saxaul sparrow, fill the gap in comparative studies of the intestinal microbiota characteristics of the saxaul sparrow in two extreme environments, and provide new theoretical support for subsequent related research. Full article

(This article belongs to the Section Gut Microbiota)

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16 pages, 3259 KB

Open AccessArticle

Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms

by Adriana Garzon, Rafael Portillo-Gonzalez, Gregory Habing, Bart C. Weimer, Cory Schlesener, Noelia Silva-del-Rio, Betsy M. Karle, Craig Miramontes and Richard V. Pereira

Microorganisms 2025, 13(11), 2641; https://doi.org/10.3390/microorganisms13112641 (registering DOI) - 20 Nov 2025

Abstract

Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and [...] Read more.

Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems. Full article

(This article belongs to the Section Microbiomes)

18 pages, 3151 KB

Open AccessArticle

Isolation and Identification of Bacteria Bacillus velezensis with Antagonistic Activity Against Major Pathogens of Coconut

by Hui Zhu, Sajid Mehmood and Xiaoqing Niu

Microorganisms 2025, 13(11), 2640; https://doi.org/10.3390/microorganisms13112640 - 20 Nov 2025

Abstract

Coconut (Cocos nucifera L.) cultivation is increasingly threatened by destructive fungal pathogens that reduce yield and compromise tree health, particularly in tropical regions in China. To address this challenge, the present study aimed to isolate and identify antagonistic bacteria with potential biocontrol [...] Read more.

Coconut (Cocos nucifera L.) cultivation is increasingly threatened by destructive fungal pathogens that reduce yield and compromise tree health, particularly in tropical regions in China. To address this challenge, the present study aimed to isolate and identify antagonistic bacteria with potential biocontrol activity against key pathogens of coconut, including Ceratocystis paradoxa (crown rot), Pestalotiopsis menezesiana (leaf blight), and Curvularia oryzae (leaf spot). A total of 65 bacterial strains were isolated from 58 soil samples collected from healthy coconut orchards. Among these, strain X1 exhibited the most vigorous antagonistic activity, with inhibition rates exceeding 70% against multiple pathogens in both plate confrontation and mycelial growth rate assays. Morphological, physiological, biochemical, and molecular (16S rDNA and gyrB gene sequencing) analyses confirmed the identity of strain X1 as Bacillus velezensis. Optimization of fermentation conditions for strain X1 revealed that maximum antimicrobial activity was achieved using a medium containing 2% glucose, 3% peptone, 0.3% NaH₂PO₄·2H₂O, and 0.4% Na₂HPO₄·2H₂O, at 28 °C and pH 7.0–7.5, 5% inoculum, 50–70 mL liquid volume in 250 mL flasks, 72 h fermentation, and agitation at 180–220 rpm. These findings highlight B. velezensis X1 as an up-and-coming biocontrol agent with dual functionalities: effective suppression of coconut fungal pathogens and potential plant growth promotion. Its application could significantly reduce the dependence on synthetic fungicides, offering an eco-friendly alternative for integrated disease management in coconut farming. Full article

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

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17 pages, 1860 KB

Open AccessArticle

Effects of Sea Buckthorn Polysaccharides on Rumen In Vitro Fermentation Characteristics and Microbial Composition of Hu Sheep

by Junlin Lan, Zhenzi Xu, Jiahao Li, Xin Li, Yuanyuan Li and Wenju Zhang

Microorganisms 2025, 13(11), 2639; https://doi.org/10.3390/microorganisms13112639 - 20 Nov 2025

Abstract

This study evaluated the effects of sea buckthorn polysaccharides (SBP) on rumen fermentation in Hu sheep through in vitro fermentation. A single-factor randomized design was employed with four treatment groups in which SBP was added to a basal diet at 0, 1%, 2% [...] Read more.

This study evaluated the effects of sea buckthorn polysaccharides (SBP) on rumen fermentation in Hu sheep through in vitro fermentation. A single-factor randomized design was employed with four treatment groups in which SBP was added to a basal diet at 0, 1%, 2% and 3% of the total ration dry matter (DM). Based on gas production, degradation rates, and fermentation parameters, the control group and the 2% group were selected for 16S rDNA sequencing. The results showed that compared with the control group, the 2% SBP treatment significantly increased gas production rate (p < 0.05). Addition of 2% and 3% SBP significantly increased DM degradability (p < 0.05). SBP supplementation significantly increased fermentation fluid pH (p < 0.05) and altered volatile fatty acid profiles, increasing the acetate/propionate ratio as well as the concentrations of butyrate, isobutyrate and valerate. Compared with the control group, the addition of 2% SBP led to significant changes in the microbial composition of the in vitro rumen fermentation fluid. It significantly increased beneficial bacterial phyla and genera, such as Bacteroidetes, Rikenellaceae_RC9_gut_group and others, while reducing pathogenic bacteria (p < 0.05). Additionally, functional prediction revealed that the SBP group was significantly enriched in pathways related to carbohydrate metabolism, biosynthesis of amino acid, and biosynthesis of secondary metabolites (p < 0.05). In summary, adding 2% SBP to Hu sheep feed can improve the Rumen fermentation and microbial communities. However, higher doses did not yield additional benefits in these measured indicators. Full article

(This article belongs to the Special Issue Rumen Microorganisms)

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24 pages, 767 KB

Open AccessReview

Bacteriophages and Endolysins Used in the Biocontrol of Staphylococcus aureus

by Maryoris E. Soto Lopez, Ana Margarita Otero-Herrera, Fernando Mendoza-Corvis, Jose Jorge Salgado-Behaine, Rocio López-Vergara, Ana M. Hernández-Arteaga, Derrick Cortessi, Pedro M. P. Vidigal and Omar Pérez-Sierra

Microorganisms 2025, 13(11), 2638; https://doi.org/10.3390/microorganisms13112638 - 20 Nov 2025

Abstract

Staphylococcus aureus is a major foodborne pathogen associated with contamination of dairy and meat products, posing a persistent challenge to food safety due to its biofilm formation and resistance to multiple antibiotics. In this review, we summarize recent advances in the use of [...] Read more.

Staphylococcus aureus is a major foodborne pathogen associated with contamination of dairy and meat products, posing a persistent challenge to food safety due to its biofilm formation and resistance to multiple antibiotics. In this review, we summarize recent advances in the use of bacteriophages and phage-derived endolysins as targeted biocontrol agents against S. aureus in food systems. Bacteriophages exhibit host specificity and self-replicating capacity, while endolysins provide rapid lytic activity, minimal resistance development, and effectiveness against biofilm-embedded cells. Studies demonstrate significant microbial reductions in milk, cheese, and meat matrices, although factors such as pH, salt, and fat content can influence their efficacy. The integration of these biocontrol tools into food preservation represents a sustainable and safe alternative to conventional antimicrobials. Finally, we discuss current limitations and the need for optimizing formulations, stability, and regulatory frameworks to facilitate the adoption of phage and endolysin-based products in the food industry. Full article

(This article belongs to the Special Issue Novel Antimicrobial Approaches in Biofilm Control in the Food Industry: Future Perspectives)

14 pages, 2667 KB

Open AccessArticle

Mosquito Exposure Risks in Equine Facilities: An Environmental–Managerial Assessment in Western Romania

by Paula Nistor, Livia Stanga, Andreia Chirila, Vlad Iorgoni, Alexandru Gligor, Alexandru Ciresan, Bogdan Florea, Carina Bota, Vlad Cocioba, Ionela Popa, Gabriel Orghici, Ionica Iancu, Cosmin Horatiu Maris, Janos Degi and Viorel Herman

Microorganisms 2025, 13(11), 2637; https://doi.org/10.3390/microorganisms13112637 - 20 Nov 2025

Abstract

West Nile Virus (WNV) is a mosquito-borne zoonosis with recurrent equine and human cases in Romania. Horses, although dead-end hosts, act as sentinels for local viral circulation. Farm-level risk conditions remain under-characterized. This pilot, exploratory cross-sectional study assessed 42 equine facilities in western [...] Read more.

West Nile Virus (WNV) is a mosquito-borne zoonosis with recurrent equine and human cases in Romania. Horses, although dead-end hosts, act as sentinels for local viral circulation. Farm-level risk conditions remain under-characterized. This pilot, exploratory cross-sectional study assessed 42 equine facilities in western Romania (2024). A standardized 10-item checklist was applied and a Composite Environmental Risk Score (CERS) (0–10, unweighted) was computed per facility. Spatial analysis in QGIS included distances to nearby water bodies. No serological or entomological data were collected; these are recommended for future validation. Stagnant water occurred at 71.4% (30/42) of facilities, uncovered rain-collecting containers at 64.3% (27/42), and outdoor housing of horses at 81.0% (34/42). Insect screens were present at 21.4% (9/42) and chemical/biological control at 33.3% (14/42). By design, the CERS ranged from 0 to 10; in our sample the observed range was 0–8 because not all assessed risk conditions co-occurred across sites. Overall, 42.9% (18/42) were classified as high risk (≥6). Neurological signs were reported anecdotally by some managers but were not analyzed. Mosquito-favorable conditions are widespread in Romanian equine facilities. CERS shows promise as a low-cost, rapid tool for routine facility-level assessment of environmental conditions favoring mosquito presence and prioritization of preventive actions. Integrating environmental risk scoring with entomological and serological surveillance could strengthen One Health early-warning systems. Such integration would support prevention of WNV and other mosquito-borne zoonotic pathogens in endemic European settings. Full article

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

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13 pages, 1159 KB

Open AccessArticle

Microbial Diversity Analysis of Soil in the Rhizosphere of Securidaca longipedunculata (African Violet Tree)

by Sphelele Zondi, Mahloro Hope Serepa-Dlamini and Pfariso Maumela

Microorganisms 2025, 13(11), 2636; https://doi.org/10.3390/microorganisms13112636 - 20 Nov 2025

Abstract

This study explored the microbial diversity within the rhizosphere of Securidaca longipedunculata (African violet tree), a medicinal plant recognized for its ethnobotanical importance. Six rhizospheric bacterial isolates were identified and characterized for their plant growth-promoting abilities and environmental resilience. Growth-promoting assays demonstrated that [...] Read more.

This study explored the microbial diversity within the rhizosphere of Securidaca longipedunculata (African violet tree), a medicinal plant recognized for its ethnobotanical importance. Six rhizospheric bacterial isolates were identified and characterized for their plant growth-promoting abilities and environmental resilience. Growth-promoting assays demonstrated that the isolates could grow in a nitrogen free environment, solubilize phosphate, produce ammonia, and synthesize indole acetic acid (IAA). Morphological and biochemical characterizations differentiated four Gram-positive from two Gram-negative strains. The bacterial isolates demonstrated plant-growth promoting potential, showing an enhanced ability (p-value < 0.05) to promote root elongation and biomass accumulation compared to the control treatments. The strains showed antifungal properties with some isolates recording 100% fungal mycelial growth and spore germination inhibition. Phylogenetic studies linked these isolates to the genera Pseudomonas and Bacillus. These findings highlight the diversity of rhizospheric bacteria associated with S. longipedunculata and emphasize their role in enhancing soil fertility and plant resilience to pathogens. Full article

(This article belongs to the Special Issue Research of Soil Microbial Communities)

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22 pages, 2641 KB

Open AccessArticle

Infection-Mediated Shifts in the Microbial Communities of Deer-Fed Ixodes scapularis Ticks

by Patil Tawidian, Bradley J. Tucker, Tela E. Zembsch, Hon S. Ip and Lyric C. Bartholomay

Microorganisms 2025, 13(11), 2635; https://doi.org/10.3390/microorganisms13112635 - 20 Nov 2025

Abstract

The holobiont of the blacklegged tick (Ixodes scapularis) includes maternally inherited rickettsial endosymbionts and environmentally acquired microbes that may influence tick fitness and vector competence. While previous studies have focused on characterizing the microbiota of I. scapularis ticks, less is known [...] Read more.

The holobiont of the blacklegged tick (Ixodes scapularis) includes maternally inherited rickettsial endosymbionts and environmentally acquired microbes that may influence tick fitness and vector competence. While previous studies have focused on characterizing the microbiota of I. scapularis ticks, less is known about the influence of tick infection status on microbial assemblages. Here, we collected engorged female I. scapularis ticks from hunter-harvested white-tailed deer (Odocoileus virginianus) across 11 counties in Wisconsin during fall 2022. The ticks were maintained in laboratory conditions for oviposition and then frozen for nucleic acid extraction. The infection status of each tick was determined using qPCR, targeting Borrelia spp., Babesia spp., and Powassan virus. Bacterial and fungal communities were characterized through amplicon-based sequencing targeting the 16S rRNA gene and ITS2 region, respectively. Our targeted pathogen testing revealed that 14.1% of the collected ticks were infected with Babesia odocoilei and 23.3% with Borrelia burgdorferi. The microbial community composition of ticks was significantly influenced by infection status and pathogen identity. Notably, Borrelia-infected ticks exhibited distinct microbiota profiles and increased microbial network connectivity. These findings provide new insights into the microbial ecology of deer-fed I. scapularis ticks and highlight the role of infection in shaping both microbiota and mycobiota communities. Full article

(This article belongs to the Special Issue Ticks and Threats: Insights on Tick-Borne Diseases)

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19 pages, 1102 KB

Open AccessArticle

Cultivar-Dependent Differences in Agronomic Characteristics, Nutritional Value, Fermentation Quality, and Bacteriome Profile of Whole-Plant Sorghum Silage

by Yawei Zhang, Danqi Feng, Juanli Huo, Jiabao Xu, Yuehong Wang, Qiang Liu, Wenbin Bai, Qingshan Liu and Yuanqing Zhang

Microorganisms 2025, 13(11), 2634; https://doi.org/10.3390/microorganisms13112634 - 20 Nov 2025

Abstract

Forage scarcity in semi-arid regions necessitates the identification of optimal sorghum cultivars for high-quality silage production. This study systematically evaluated varietal differences in agronomic characteristics, nutritive value, fermentation quality, and bacterial community structure of whole-plant sorghum silage. A completely randomized design was implemented [...] Read more.

Forage scarcity in semi-arid regions necessitates the identification of optimal sorghum cultivars for high-quality silage production. This study systematically evaluated varietal differences in agronomic characteristics, nutritive value, fermentation quality, and bacterial community structure of whole-plant sorghum silage. A completely randomized design was implemented with four sorghum cultivars representative of semi-arid northwestern China: Liaotian1 (LT1), Jinnuo3 (JN3), Jinza2001 (JZ2001), and Jinza1531 (JZ1531). Five quadrats per cultivar in experimental fields were randomly designated as biological replicates for silage production. The plants were harvested at the dough stage, chopped, and ensiled in laboratory-scale silos (n = 20, 4 cultivars × 5 replicates) for 120 days. Analyses included agronomic measurements, chemical composition, fermentation parameters, microbial plate enumeration, and bacterial community profiling via 16S rRNA gene amplicon sequencing of the V3–V4 hypervariable region. The results showed that cultivar significantly influenced (p < 0.01) all agronomic traits and most nutritional parameters. The forage-type cultivar LT1 showed the highest biomass yield but the lowest nutritional quality, with higher neutral detergent fiber (47.77% vs. 29.21–32.35%; p < 0.05) and lower starch (10.94% vs. 18.10–24.30%; p < 0.05) contents as well as higher dry matter losses (1.39% vs. 0.91–1.23%; p < 0.05) than grain-type cultivars. In contrast, the grain-type cultivar JN3 exhibited balanced yield-quality traits with the highest (p < 0.05) starch (24.30%) and crude protein (7.50%) contents. Most fermentation parameters differed significantly (p < 0.01) among cultivars, with JN3 showing elevated ammonia-nitrogen (0.24 g/kg) but within acceptable ranges. Microbial diversity analysis revealed cultivar-driven differences in bacterial communities, with JN3 enriched in Leuconostoc and early-colonizing taxa (p < 0.05 and LDA Score > 4). It is concluded that the grain-type cultivar JN3 is the most suitable cultivar for whole-plant sorghum silage production in water-limited regions due to its optimal yield-quality balance. The findings underscore the importance of integrated cultivar evaluation and suggest the potential of targeted microbial inoculants for enhancing silage quality. Full article

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

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19 pages, 2183 KB

Open AccessArticle

Linking N₂O Emission with AOB and nirK-Denitrifier in Paddy Fields of Karst and Non-Karst Areas

by Zhenjiang Jin, Weijian Chen, Wu Yuan, Yunlong Sun, Xiaoyi Xiao, Heyao Liang, Chengxi Yang and Bin Dong

Microorganisms 2025, 13(11), 2633; https://doi.org/10.3390/microorganisms13112633 - 20 Nov 2025

Abstract

Denitrification and nitrification are two pivotal microbial processes relating to N₂O emissions. However, the difference in N₂O emission fluxes and N₂O-producing bacteria between a karst (KA) and non-karst area (NKA) remains unclear. The objective of this study [...] Read more.

Denitrification and nitrification are two pivotal microbial processes relating to N₂O emissions. However, the difference in N₂O emission fluxes and N₂O-producing bacteria between a karst (KA) and non-karst area (NKA) remains unclear. The objective of this study is to compare the differences in soil N₂O emissions, nitrifying bacteria, and denitrifying bacteria during the growth period of rice in KA and NKA, and to explore the mechanisms by which microorganisms and environmental factors drive N₂O emissions. Here, N₂O emission fluxes of paddy fields were collected using the static dark chamber and measured using gas chromatography at KA and NKA in the Maocun Karst Experimental Site in Guilin, China. The nitrifying bacteria (ammonia-oxidizing bacteria, AOB) and denitrifying bacteria (nirK-denitrifier) were determined using real-time PCR and high-throughput sequencing, respectively. Results showed that during the rice growth period, the N₂O emission fluxes in KA was generally lower than that in NKA, with cumulative N₂O emissions of −0.054 and 0.229 kg·hm⁻² in KA and NKA, respectively. The absolute abundance of AOB in KA (8.91 × 10⁶–2.68 × 10⁷ copies·g⁻¹) was significantly higher than that in NKA (1.57 × 10⁶–6.48 × 10⁶ copies·g⁻¹), while the absolute abundance of nirK-denitrifier had no significant difference between the two areas. The composition and diversity of AOB and nirK-denitrifier differed significantly between KA and NKA. Results from partial least squares structural equation modeling (PLS-SEM) indicated that soil properties, carbon sources, and nitrogen sources had positive effects on AOB and nirK-denitrifier, while nirK-denitrifier had a negative effect on N₂O emissions. Partial least squares regression (PLSR) predictions revealed that NO₃⁻-N, SOC, TN, Mg²⁺, Ca²⁺, and pH were the most important factors influencing N₂O emission fluxes. This study highlights the critical role of the typical characteristics of KA soils in reducing N₂O emissions from paddy fields by driving the evolution of AOB and nirK-denitrifier. Full article

(This article belongs to the Topic Evaluating the Functional Value of Agroecosystems under Different Management Scenarios)

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21 pages, 8603 KB

Open AccessArticle

Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area

by Ping Hu, Andrew N. Carr, Mirjana Parlov, Dionne Swift, Jay P. Tiesman, Nivedita Ramji, Jennifer J. Schoch and Amber G. Teufel

Microorganisms 2025, 13(11), 2632; https://doi.org/10.3390/microorganisms13112632 - 20 Nov 2025

Abstract

Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, [...] Read more.

Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions. Full article

(This article belongs to the Special Issue Skin Microbiome)

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33 pages, 3452 KB

Open AccessReview

History of Shrimp Farming and the Main Viral and Bacterial Diseases in Mexico

by Cesar Marcial Escobedo-Bonilla, Jareli Itzel Colula-Ocampo, Rosa Idalia Hernández-Herrera, Martina Hilda Gracia-Valenzuela and Pablo San Martín del Ángel

Microorganisms 2025, 13(11), 2631; https://doi.org/10.3390/microorganisms13112631 - 20 Nov 2025

Abstract

Shrimp farming is probably the most recent animal production activity generating high-quality animal protein, jobs, and economic revenue for many developing and middle-income countries worldwide. Despite the steady growth over the last two decades, aquaculture production has recently seen a decreased growth rate, [...] Read more.

Shrimp farming is probably the most recent animal production activity generating high-quality animal protein, jobs, and economic revenue for many developing and middle-income countries worldwide. Despite the steady growth over the last two decades, aquaculture production has recently seen a decreased growth rate, with infectious diseases being a culprit. Mexico is a major farmed shrimp producer in the world, with the industry generating about USD 1 billion each year and providing jobs for those in vulnerable social sectors. Nonetheless, various viral and bacterial diseases have affected production and hampered development. This review provides a historic account of shrimp farming in Mexico and the chronology, features, and impact of the main infectious diseases. At present, Penstylhamaparvovirus (formerly known as IHHNV) has decreased in importance as a pathogen and is the only virus that has coexisted with other major pathogens. In Mexico, main pathogens dominate shrimp farming during certain periods, then they become eclipsed by a new emergent pathogen. Exotic pathogens likely entered Mexico through the movement of live broodstock or larvae or through contaminated imported crustacean commodities for human consumption. Stronger biosecurity measures such as quarantine protocols and sensitive diagnostic tools at the borders are required to reduce the risk of other emergent pathogens. Full article

(This article belongs to the Special Issue Infectious Diseases in Aquaculture)

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21 pages, 4209 KB

Open AccessArticle

High-Resolution Wastewater-Based Surveillance of Three Influenza Seasons (2022–2025) Reveals Distinct Seasonal Patterns of Viral Activity in Munich, Germany

by Jessica Neusser, Astrid Zierer, Anna Riedl, Jasmin Javanmardi, Raquel Rubio-Acero, Elisabeth Waldeck, Thomas Kletke, Annemarie Bschorer, Stefanie Huber, Patrick Dudler, Martin Hoch, Merle M. Böhmer, Caroline Herr, Ute Eberle, Andreas Sing, Nikolaus Ackermann, Michael Hoelscher, Katharina Springer and Andreas Wieser

Microorganisms 2025, 13(11), 2630; https://doi.org/10.3390/microorganisms13112630 - 20 Nov 2025

Abstract

In the Northern Hemisphere, annual waves of influenza disease with varying degrees of spread and severity are observed each winter. With wastewater-based surveillance (WBS), including both centralized (one wastewater treatment plant, WWTP) and decentralized (three sewers) sampling, we aimed to detect differences in [...] Read more.

In the Northern Hemisphere, annual waves of influenza disease with varying degrees of spread and severity are observed each winter. With wastewater-based surveillance (WBS), including both centralized (one wastewater treatment plant, WWTP) and decentralized (three sewers) sampling, we aimed to detect differences in influenza viral copy numbers in wastewater over time, to investigate (sub)-community transmission within a city. A total of 313 grab/spot and composite samples were collected in Munich, Germany, during three consecutive influenza seasons (2022/23, 2023/24, and 2024/25) and were analyzed for influenza A virus (IAV) and influenza B virus (IBV) nucleic acids using digital droplet PCR (ddPCR). IAV and IBV wastewater copy numbers and citywide reported influenza cases showed strong correlations in both sampling approaches, suggesting the decentralized approach to be a reliable indicator of infection trends across the city. The three influenza seasons analyzed differed significantly in terms of their seasonal distribution, for example, exhibiting a strong co-circulation of IAV and IBV only in the 2024/25 season. Only with wastewater analysis, we reveal a reporting delay of influenza A cases at the beginning of the 2023/24 season. Higher influenza copy numbers were detected in sewer samples compared to the WWTP influent, likely due to viral decay. The study underscores the potential of influenza WBS to enable detection of seasonal onset early, identify local transmission patterns, and reveal underreporting in routine surveillance systems. Full article

(This article belongs to the Special Issue Surveillance of Health-Relevant Pathogens Employing Wastewater)

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14 pages, 17931 KB

Open AccessArticle

Chemical Inactivation of Bacillus subtilis Endospores Preserves Recombinant Protein Antigenic Properties

by Amalia A. Saperi, Atiqah Hazan, Nurfatihah Zulkifli, Hai Yen Lee and Sazaly AbuBakar

Microorganisms 2025, 13(11), 2629; https://doi.org/10.3390/microorganisms13112629 - 19 Nov 2025

Abstract

Recombinant Bacillus subtilis endospores are promising bacterial expression platforms for oral protein delivery, such as oral vaccines. A simple and effective spore inactivation method that preserves protein functionality, however, is needed to prevent potential shedding into the environment. This study evaluated iron or [...] Read more.

Recombinant Bacillus subtilis endospores are promising bacterial expression platforms for oral protein delivery, such as oral vaccines. A simple and effective spore inactivation method that preserves protein functionality, however, is needed to prevent potential shedding into the environment. This study evaluated iron or copper combined with EDTA and ethanol as sporicidal solutions for the inactivation of recombinant spores expressing the 1PR82 gene. Immunoblot and immunofluorescence (IF) assay confirmed the presence of antigenic proteins post-treatment, while electron microscopy (SEM/TEM) assessed spore morphology. Mice immunization tested immunogenicity, and fecal analysis monitored gastrointestinal persistence. Iron ethanol treatment completely inactivated the spores while maintaining recombinant protein detection using antibody-based assays. SEM/TEM revealed morphological damage, yet antigenicity was preserved, as evidenced by robust IgG responses in immunized mice. Fecal analysis showed no prolonged spore shedding, confirming effective inactivation. These findings demonstrate that iron ethanol efficiently inactivates recombinant B. subtilis spores without compromising protein antigenicity. Despite structural damage, the recombinant protein remained immunogenic, and inactivated spores posed no environmental persistence risk. This inactivation method supports the safe use of Bacillus subtilis recombinant spores for oral delivery applications, balancing inactivation efficacy with functional protein preservation. Further research could optimize this approach for clinical or industrial applications. Full article

(This article belongs to the Section Microbial Biotechnology)

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11 pages, 247 KB

Open AccessArticle

Risk Factors for Severe Outcomes Among Pediatric Cancer Patients with Respiratory Viral Infection

by Alon Kristal, Avi Magid, Nira Arad-Cohen, Moran Szwarcwort-Cohen and Yael Shachor-Meyouhas

Microorganisms 2025, 13(11), 2628; https://doi.org/10.3390/microorganisms13112628 - 19 Nov 2025

Abstract

Background: Viral respiratory infections pose a significant risk for pediatric cancer patients and may lead to a delay in chemotherapy, prolonged hospitalization, and mortality. Limited data exist regarding the contributors to adverse clinical outcomes. The present study aims to describe the associations between [...] Read more.

Background: Viral respiratory infections pose a significant risk for pediatric cancer patients and may lead to a delay in chemotherapy, prolonged hospitalization, and mortality. Limited data exist regarding the contributors to adverse clinical outcomes. The present study aims to describe the associations between clinical, epidemiological, and laboratory factors and severe outcomes of respiratory viral infections among children with cancer. Methods: This was a retrospective cohort study among pediatric cancer patients treated in the Pediatric Hematology–Oncology Department at Rambam Health Care Campus from 2016 to 2022. Patients with a positive rt-qPCR test for one of the following viruses were included: Adenovirus, Respiratory Syncytial Virus (RSV), Human Metapneumovirus (HMPV), SARS-CoV-2, Parainfluenza, or Influenza. Demographic, clinical, and laboratory data were collected for each case. GEE analyses were conducted to assess the associations between independent variables and severe outcomes (admission to the Pediatric Intensive Care Unit (PICU), hospitalizations exceeding seven days, co-bacterial infections, and mortality within 30 days). Results: A total of 366 viral infections episodes were identified among 238 patients. There were 187 (51%) children with hematological malignancies, 113 (31%) with solid tumors, and 66 patients (18%) who had undergone bone marrow transplantation. Influenza was the most frequently detected virus, accounting for 89 events (24%), followed closely by Adenovirus, with 82 events (23%). Among the 38 severe events, prolonged hospitalization was the most prevalent outcome, occurring in 33 cases. Adenovirus infection was significantly associated with severe outcomes (OR = 2.97, p = 0.010), and antibiotic therapy was associated with 3.62 times higher odds of severe outcomes (p = 0.010). Patients presenting with O2 saturation levels below 92% had 5.71 times higher odds of experiencing severe outcomes. Among the subgroup of hematological malignancies, RSV was positively associated with severe outcomes (OR = 4.08, p = 0.048). Conclusions: Adenovirus was associated with severe outcomes in pediatric cancer patients, highlighting its prevalence and potential for treatment. Similarly, RSV was associated with adverse outcomes specifically among hematological cancer patients, emphasizing the importance of vaccination. A very low mortality from viral infection was also notable. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Third Edition)

19 pages, 6303 KB

Open AccessArticle

A Microbial Inoculum (PLC-8) Improves Composting of Spent Mushroom Substrate

by Jiamin Yin, Hairu Yu, Sen Qi, Yufu Hu, Di Chen, Hongyan Zhao and Zongjun Cui

Microorganisms 2025, 13(11), 2627; https://doi.org/10.3390/microorganisms13112627 - 19 Nov 2025

Abstract

Composting is a useful way to reduce and recycle agricultural and forestry waste; however, low-temperature environments can inhibit the microbial processes involved in composting. Spent mushroom substrate has a high lignocellulose content, making it particularly difficult to decompose. There is a need to [...] Read more.

Composting is a useful way to reduce and recycle agricultural and forestry waste; however, low-temperature environments can inhibit the microbial processes involved in composting. Spent mushroom substrate has a high lignocellulose content, making it particularly difficult to decompose. There is a need to explore methods for effectively promoting microbial activity and enhancing composting efficiency under low-temperature conditions. This study explored the use of C/N ratio adjustments and a microbial inoculum (PLC-8; comprising Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Basidiomycota, Ascomycota, and Cryptomonadales) to improve spent mushroom substrate composting in a low-temperature environment. The temperature, lignocellulose content, pH, and gas emissions were measured during composting, and the microbial community structure was determined to explore associations between biotic and abiotic factors. Compost piles with PLC-8 entered the high-temperature period in 25 days, which was 15 days earlier than the control pile. When the C/N ratio was adjusted to 30:1 and PLC-8 was applied, the cellulose and hemicellulose degradation rates after 60 days were 88.04% and 71.95%, whereas the control group only exhibited degradation rates of 25.39% and 35.64%. Moreover, PLC-8 significantly increased CH₄ and CO₂ emissions and reduced nitrous oxide emissions. Microbial community analysis showed that Proteobacteria and Ascomycota were the dominant phyla in the piles with PLC-8, and these phyla were responsible for lignocellulose decomposition and carbon metabolism. Full article

(This article belongs to the Special Issue Microbiota Dynamics in Environmental and Host Systems: From Ecology to Applications)

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21 pages, 5829 KB

Open AccessArticle

The Effects of Feeding ybfQ-Deficient Gut Bacteria on Radio-Tolerance in Symbiotic Caenorhabditis elegans: The Key Role of Isoscoparin

by Liu Ding, Jingjing Zhang, Shanpeng Qiao, Jiyu Xu, Jing Li, Wenjing Zhang, Qiyi Yi, Yuejin Wu, Ting Wang and Po Bian

Microorganisms 2025, 13(11), 2626; https://doi.org/10.3390/microorganisms13112626 - 19 Nov 2025

Abstract

It is inevitable for life on earth to be exposed to various types of ionizing and non-ionizing radiation, underscoring the importance of radioprotection. The symbiotic interaction between gut microbiota and the host provides a strategy for protecting the organism against these stressors. However, [...] Read more.

It is inevitable for life on earth to be exposed to various types of ionizing and non-ionizing radiation, underscoring the importance of radioprotection. The symbiotic interaction between gut microbiota and the host provides a strategy for protecting the organism against these stressors. However, the genetic mechanisms underlying this interaction remain poorly understood due to the complexity and diversity of gut microbiota. In this study, we employed a symbiotic experimental system involving Caenorhabditis elegans and Escherichia coli to systemically investigate the effects of bacterial genetic alterations on host responses to radiation exposure. Our findings revealed that deletion of the bacterial ybfQ gene (ΔybfQ) significantly enhanced worm tolerance to UV-B radiation. Transcriptomic analysis demonstrated an enhanced antioxidant capacity in ΔybfQ-fed worms, as evidenced by reduced levels of reactive oxygen species (ROS) and restored oxidative homeostasis. Notably, ΔybfQ bacteria exhibited overproduction of isoscoparin, and exogenous supplementation with isoscoparin similarly enhanced worm radio-tolerance, underscoring its crucial role in ΔybfQ-mediated antioxidant of host worm. Both interventions retained their protective effects in IIS-deficient worms (daf-16). However, the protective effects of ΔybfQ feeding, but not isoscoparin treatment, were attenuated in daf-2 worms with a constitutively activated IIS pathway, accompanied by reduced bacteria gut colonization. Collectively, our results provide novel insights into the genetic basis of host-microbe interactions and propose a potential pharmacological strategy for radiation protection. Full article

(This article belongs to the Section Gut Microbiota)

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25 pages, 3386 KB

Open AccessArticle

Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts

by Julia E. Paoli, Thanaporn Thongthum, Maclean Bassett, Jakob Beardsley, Massimiliano S. Tagliamonte, Melanie N. Cash, Jason Spertus Newman, Lisa M. Smith, Benjamin D. Anderson, Marco Salemi, Kuttichantran Subramaniam, Michael E. von Fricken, Elizabeth Braun de Torrez, Verity Mathis and Carla N. Mavian

Microorganisms 2025, 13(11), 2625; https://doi.org/10.3390/microorganisms13112625 - 19 Nov 2025

Abstract

Florida’s bat virome remains poorly characterized despite the state’s high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like [...] Read more.

Florida’s bat virome remains poorly characterized despite the state’s high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments. Full article

(This article belongs to the Special Issue Advances in Viral Metagenomics)

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20 pages, 4837 KB

Open AccessArticle

Diversity of Multicellular Magnetotactic Prokaryotes in Sanya Haitang Bay

by Jiangxue Shi, Wenyan Zhang, Yi Dong, Yao Liu, Min Liu, Tian Xiao, Longfei Wu and Hongmiao Pan

Microorganisms 2025, 13(11), 2624; https://doi.org/10.3390/microorganisms13112624 - 19 Nov 2025

Abstract

The intertidal sediments of Sanya Haitang Bay, a tropical coast, harbor abundant multicellular magnetotactic prokaryotes (MMPs). Using light and electron microscopy, micromanipulation sorting, and whole-genome amplification, we examined their diversity from morphological, phylogenetic, and ecological perspectives. Two types of MMPs were identified: ellipsoidal [...] Read more.

The intertidal sediments of Sanya Haitang Bay, a tropical coast, harbor abundant multicellular magnetotactic prokaryotes (MMPs). Using light and electron microscopy, micromanipulation sorting, and whole-genome amplification, we examined their diversity from morphological, phylogenetic, and ecological perspectives. Two types of MMPs were identified: ellipsoidal (eMMPs) and spherical (sMMPs). Their average abundance was 1.37 × 10³ ind./dm³ in autumn and 0.27 × 10³ ind./dm³ in spring, indicating strong seasonal variation. eMMPs averaged 9.74 × 8.15 µm, consisting of 80–100 cells arranged in layers, whereas sMMPs averaged 5.64 µm in diameter with 40–50 cells organized radially or spirally. Electron microscopy revealed bullet-shaped magnetosomes in both types: those in eMMPs averaged 90.1 × 34.0 nm, while those in sMMPs averaged 97.2 × 36.3 nm. Interestingly, Cu was homogenously detected in the magnetosomes of sMMPs. 16S rRNA gene analysis identified nine OTUs, including three potential new species in the Desulfobacteraceae family within Thermodesulfobacteriota phylum. Of these, two may represent a new genus, and one is affiliated with Candidatus Magnetananas. Global distribution analysis suggests that eMMPs prefer stable, nutrient-rich environments, whereas sMMPs occupy broader ecological niches. Together, these findings expand understanding of tropical MMP diversity and distribution, and the discovery of Cu-containing magnetosomes provides new insight into biomineralization mechanisms. Full article

(This article belongs to the Special Issue Advances in Magnetotactic Bacteria)

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