@article {pmid40469738,
year = {2025},
author = {Amen, R and Ganzert, L and Friedl, T and Rybalka, N and Wagner, D},
title = {From single pioneers to complex pro- and eukaryotic microbial networks in soils along a glacier forefield chronosequence in continental Antarctica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1576898},
pmid = {40469738},
issn = {1664-302X},
abstract = {INTRODUCTION: In the extremely dry and oligotrophic soils of East Antarctica, where low temperatures and humidity result in minimal biological turnover rates, extracellular DNA (eDNA) can persist over extended timescales. Differentiating between sequences from living, potentially active cells (intracellular DNA, or iDNA) and those from ancient, non-living organisms (eDNA) is crucial for accurately assessing the current microbial community and understanding historical microbial dynamics.

METHODS: This study was conducted along a chronosequence in the Larsemann Hills, East Antarctica, where soil samples were collected from sites at varying distances from the glacier. By employing DNA separation methods, we distinguished iDNA, which represents living cells, from eDNA derived from dead organisms. High-throughput sequencing was used to characterize bacterial and eukaryotic communities across different successional stages.

RESULTS: The DNA separation approach revealed distinct bacterial and eukaryotic community structures along the glacier transect. Actinobacteria were consistently abundant across all sites, while other phyla such as Chloroflexi, Gemmatimonadetes, and Proteobacteria thrived in extreme, nutrient-poor environments. Early successional stages were characterized by the simultaneous colonization of green algae Trebouxiophyceae and cryophilic fungi, alongside nitrogen-fixing bacteria, which contributed to initial soil development. The study also identified three distinct modes of microbial distribution, reflecting varying degrees of activity and adaptability.

DISCUSSION: Our findings provide new insights into microbial dynamics in extreme habitats and propose new hypotheses for microbial colonization in newly exposed soils. Moreover, they contribute to the ongoing debate in microbial ecology regarding the viability of dormant or dead cells and emphasize the need for refining DNA-based methods and exploring functional pathways to deepen our understanding of microbial succession in polar regions.},
}

@article {pmid40469504,
year = {2025},
author = {Van Den Bossche, T and Armengaud, J and Benndorf, D and Blakeley-Ruiz, JA and Brauer, M and Cheng, K and Creskey, M and Figeys, D and Grenga, L and Griffin, TJ and Henry, C and Hettich, RL and Holstein, T and Jagtap, PD and Jehmlich, N and Kim, J and Kleiner, M and Kunath, BJ and Malliet, X and Martens, L and Mehta, S and Mesuere, B and Ning, Z and Tanca, A and Uzzau, S and Verschaffelt, P and Wang, J and Wilmes, P and Zhang, X and Zhang, X and Li, L and , },
title = {The microbiologist's guide to metaproteomics.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70031},
pmid = {40469504},
issn = {2770-596X},
abstract = {Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems. As the primary catalytic and structural components of microbiomes, proteins provide unique insights into the active processes and ecological roles of microbial communities. By integrating metaproteomics with other omics disciplines, researchers can gain a comprehensive understanding of microbial ecology, interactions, and functional dynamics. This review, developed by the Metaproteomics Initiative (www.metaproteomics.org), serves as a practical guide for both microbiome and proteomics researchers, presenting key principles, state-of-the-art methodologies, and analytical workflows essential to metaproteomics. Topics covered include experimental design, sample preparation, mass spectrometry techniques, data analysis strategies, and statistical approaches.},
}

@article {pmid40468430,
year = {2025},
author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE},
title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {60},
pmid = {40468430},
issn = {2524-6372},
support = {#2014/21772-4 and #2014/14935-4//São Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Fundação Agrisus/ ; },
abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.

RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.

CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.},
}

@article {pmid40467851,
year = {2025},
author = {Rakotonindrina, V and Andriamananjara, A and Razafimbelo, T and Okamoto, T and Sarr, PS},
title = {Land Cover and Seasonal Variations Shape Soil Microbial Communities and Nutrient Cycling in Madagascar Tropical Forests.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {60},
pmid = {40467851},
issn = {1432-184X},
mesh = {*Soil Microbiology ; Seasons ; Madagascar ; *Forests ; Soil/chemistry ; Tropical Climate ; Nitrogen/analysis/metabolism ; Carbon/analysis ; *Microbiota ; Bacteria/classification/genetics/isolation & purification/metabolism ; Fungi/genetics/classification/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Phosphorus/analysis/metabolism ; Trees ; Ecosystem ; },
abstract = {Understanding how land cover and seasonal variations influence soil microbial communities and nutrient cycling is crucial for sustainable land management in tropical forests. However, such investigations are limited in Madagascar's tropical ecosystems. This study investigated the impacts of land cover types and seasonal variations on soil properties and microbial communities in the tropical forest region of Andasibe, Madagascar. Soil samples were collected from four land cover types-tree fallow (TSA), shrub fallow (SSA), eucalyptus forest (EUC), and degraded land (TM)-across three seasonal periods: the dry season, the start of the rainy season, and the end of the rainy season. Both land cover and sampling season affected soil pH and available P, whereas total nitrogen, soil organic carbon, and the C/N ratio were affected only by land cover. The soil organic carbon and total nitrogen concentrations were greater in TM. NextSeq sequencing of the 16S rRNA gene and ITS regions of the nuclear rRNA operon revealed distinct microbial community compositions across land covers, with greater diversity in the TSA and SSA. Bacteria are more sensitive to seasonal changes than are fungi, with phosphate-solubilizing (gcd) and phosphate-mineralizing (phoD) genes being more abundant in the rainy season, emphasizing the role of microbes in nutrient availability under different climatic conditions. Principal component analysis highlighted SSA as a hotspot for microbial activity, reinforcing the potential of shrub ecosystems in soil restoration. These findings reveal strong land cover and seasonal effects on soil microbial functions, with implications for nutrient cycling, ecosystem resilience, and sustainable land management in tropical forest landscapes.},
}

*Soil Microbiology
Seasons
Madagascar
*Forests
Soil/chemistry
Tropical Climate
Nitrogen/analysis/metabolism
Carbon/analysis
*Microbiota
Bacteria/classification/genetics/isolation & purification/metabolism
Fungi/genetics/classification/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Phosphorus/analysis/metabolism
Trees
Ecosystem

@article {pmid40467767,
year = {2025},
author = {Yan, Z and Yao, Y and Xu, Q and He, X and Zhou, X and Wang, H},
title = {Dietary microbiota-mediated shifts in gut microbial ecology and pathogen interactions in giant pandas (Ailuropoda melanoleuca).},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {864},
pmid = {40467767},
issn = {2399-3642},
mesh = {Animals ; *Ursidae/microbiology ; *Gastrointestinal Microbiome ; *Diet/veterinary ; Feces/microbiology ; *Bacteria/genetics/classification ; },
abstract = {The impact of dietary microorganisms on host microbiota is recognized, but the underlying mechanisms remain unclear. This study examined the effects of bamboo surface microbiota, including virulence factors, antibiotic resistance genes (ARGs), and mobile genetic elements from different bamboo parts (leaves, shoots, and culms), on giant panda gut microbiota using three pairs of twins. Results showed that bamboo and fecal samples shared 1670 microbial species, with shoot surface microbiota contributing the highest proportion (21%, Bayesian source tracking) of contemporaneous gut microbiota, primarily by increasing abundances of Escherichia coli and ARGs. Klebsiella pneumoniae and Salmonella enterica also showed high co-occurrence in both bamboo and fecal samples, indicating potential colonization. Additionally, Streptococcus suis, Acinetobacter, and Mycobacterium progressively declined in fecal samples as bamboo shoot intake increased, suggesting these microbes are likely transient. The findings emphasize the impact of foodborne microorganisms on the host and the importance of conservation management.},
}

Animals
*Ursidae/microbiology
*Gastrointestinal Microbiome
*Diet/veterinary
Feces/microbiology
*Bacteria/genetics/classification

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40467261,
year = {2025},
author = {Cabezas-Terán, K and Grootaert, C and Van Camp, J and Ortiz, J and Ruales, J and Donoso, S and Van de Wiele, T},
title = {Bioaccessibility of β-carotene during in vitro co-digestion of encapsulated mango peel carotenoids with milk.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116576},
doi = {10.1016/j.foodres.2025.116576},
pmid = {40467261},
issn = {1873-7145},
mesh = {*Mangifera/chemistry ; *beta Carotene/pharmacokinetics/metabolism ; *Milk/chemistry/metabolism ; *Digestion ; Animals ; Biological Availability ; *Fruit/chemistry ; *Carotenoids ; Particle Size ; },
abstract = {β-carotene is a carotenoid with provitamin A activity whose digestive stability and bioaccessibility prior to intestinal absorption are important to fully exploit its health benefits. Microencapsulation protects carotenoids, but there is a lack of information on the extent to which its characteristics and interactions with complex food matrices could impact the carotenoid micellization during digestion. We evaluated the effect of milk fat content on the in vitro bioaccessibility of β-carotene from microparticles containing carotenoids from mango peel. The microparticles tested contained solvent-extracted carotenoids and supercritical fluid-extracted carotenoids, and were separately co-digested with whole, semi-skimmed and skimmed milks. Bioaccessibility was assessed using an in vitro digestion method adapted to carotenoids. β-carotene recoveries after in vitro digestions ranged from 79.6 to 102.2 %, with the highest values corresponding mainly to microparticles with the lowest initial β-carotene concentration. β-carotene bioaccessibilities ranged from 8.8 to 75.5 %, the highest values being obtained mainly when the microparticles were co-digested with whole milk, especially when those containing supercritical fluid-extracted carotenoids were used. The bioaccessibility-enhancing effect of the milk fat was explained by the higher concentration of free fatty acids in the micellar phase, while the better results in the microparticles containing supercritical-fluid-extract was attributed to the lower initial concentration of β-carotene. In conclusion, increasing the milk fat content increased the bioaccessibility of encapsulated β-carotene from mango peel, further determining that, a lower initial concentration of β-carotene in the microparticles resulted in higher bioaccessibility.},
}

*Mangifera/chemistry
*beta Carotene/pharmacokinetics/metabolism
*Milk/chemistry/metabolism
*Digestion
Animals
Biological Availability
*Fruit/chemistry
*Carotenoids
Particle Size

@article {pmid40467013,
year = {2025},
author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S},
title = {Targeted analysis of metagenomes: divide and conquer.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108619},
doi = {10.1016/j.biotechadv.2025.108619},
pmid = {40467013},
issn = {1873-1899},
abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targete methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.},
}

@article {pmid40465274,
year = {2025},
author = {Hassen, B and Hammami, S},
title = {Environmental Phages: Ecosystem Dynamics, Biotechnological Applications and their limits, and Future Directions.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf136},
pmid = {40465274},
issn = {1365-2672},
abstract = {Phages, the most abundant biological entities on Earth, play a crucial role in various microbial ecosystems, significantly impacting biogeochemical cycles and bacterial evolution. They inhabit diverse environments, including soil, water, and extreme conditions, where they contribute to the contribute to regulating microbial populations, facilitate genetic exchange and aid in nutrient cycling. Recent research has highlighted their potential in addressing antibiotic resistance, enhancing wastewater treatment, promoting agricultural sustainability, and tackling environmental issues. However, their ability to disseminate antibiotic resistance genes through horizontal gene transfer raises important concerns, warranting a thorough assessment of their ecological and biotechnological applications. This review synthesizes current knowledge on the diversity, ecological roles, and practical uses of environmental phages, emphasizing both their benefits and limitations. By analyzing recent findings and real-world applications, it provides insights into the challenges encountered and future directions for leveraging phages in environmental management, biotechnology, and healthcare.},
}

@article {pmid40464990,
year = {2025},
author = {Peng, Z and Kang, C and Xu, Y and Zhang, C and Zhang, Y and Yan, B and Wang, S and Guo, X and Wan, X and Lv, C and Huang, L and Guo, L and Wang, H},
title = {Effects of Wild and Domesticated Seeds on the Colonization of Rhizosphere Microorganisms in Atractylodes lancea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {59},
pmid = {40464990},
issn = {1432-184X},
support = {2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; 2023YFC3503804//National Key Research and Development Program of China/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ18-YO-051, ZZ13-YQ-096//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; CI2021A03903, CI2021A03905, CI2021B013//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; No: ZYYCXTD-D-202005//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; },
mesh = {*Rhizosphere ; *Seeds/microbiology/growth & development ; *Soil Microbiology ; *Atractylodes/microbiology/growth & development ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Seedlings/microbiology/growth & development ; Plant Roots/microbiology ; Domestication ; Endophytes/classification/isolation & purification/genetics ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The domestication of plant species has played a pivotal role in shaping human civilization, yet it has also contributed to a significant reduction in the genetic diversity of crop varieties. This reduction may have profound implications for the formation and establishment of rhizosphere microbial communities in plants. This study systematically investigates microbiome dynamics during seed development in wild and domesticated Atractylodes lancea. The seeds from both wild and domesticated A. lancea exhibited shared microbial genera, while their communities were changed significantly. However, when A. lancea seeds from wild and domesticated germinated into seedlings under identical microbiological conditions, the leaves and root endophytic microbial and rhizosphere microbiome displayed similar genus. Remarkably, the rhizosphere microbial communities of the seedlings consistently enriched Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Paenibacillus, Variovorax, Conexibacter, and norank_f__Micropepsaceae. And this convergence likely arises from the shared chemotype of A. lancea and exposure to identical environmental microbiomes. In summary, this study delineates the transmission processes of A. lancea seed endophytes and identifies the dynamic patterns of microbial shifts during its development from seed to seedling. These findings contribute to a broader understanding of plant-microbe interactions and the role of microbial ecology in crop improvement.},
}

*Rhizosphere
*Seeds/microbiology/growth & development
*Soil Microbiology
*Atractylodes/microbiology/growth & development
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Seedlings/microbiology/growth & development
Plant Roots/microbiology
Domestication
Endophytes/classification/isolation & purification/genetics
Plant Leaves/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40463892,
year = {2025},
author = {Shepherd, RM and Oliverio, AM},
title = {The Biogeography of Apicomplexan Parasites in Tropical Soils.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71478},
pmid = {40463892},
issn = {2045-7758},
abstract = {Parasitic protists such as Apicomplexa, an abundant group of soil protists, contribute to ecosystem processes and nutrient cycling in belowground soil systems through their obligate symbioses with soil Metazoa. Yet despite the importance of soil parasites, the biodiversity and biogeography of Apicomplexa in belowground systems remain poorly characterized. Leveraging 205 soils collected across a rainfall gradient spanning the isthmus of Panama, we sought to understand the distribution of soil Apicomplexa lineages and how abiotic (e.g., soil and climatic) and biotic (e.g., soil Metazoa) factors relate to their diversity and structure. Apicomplexa were highly heterogeneous across the samples and comprised 30% of the soil protist community on average. Soil pH, along with phosphorus and magnesium, best explained the overall distribution of Apicomplexa. Soil Metazoa distributions also corresponded to Apicomplexa distributions, and many Metazoan taxa co-occurred with particular Apicomplexa, which may reflect ecological interactions (such as parasitism) or shared habitat preferences. These results highlight the potential roles of both soil and climatic variables and putative hosts in structuring parasite distributions in belowground tropical systems. Our work builds a broader understanding of Apicomplexa biodiversity in tropical soils and sheds light on environmental factors that may contribute to shaping their distribution in belowground systems. These results help inform our understanding of the importance of parasites in tropical forest soils.},
}

@article {pmid40463148,
year = {2025},
author = {Usman, H and Molaei, M and House, S and Haase, MF and Dennis, CL and Niepa, THR},
title = {Magnetically Responsive Nanocultures for Direct Microbial Assessment in Soil Environments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.17.654660},
pmid = {40463148},
issn = {2692-8205},
abstract = {UNLABELLED: Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing currently unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover novel biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semi-permeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for discovering previously uncultured or unknown microbial species.

TEASER: Engineered magnetic nanocultures support microbial growth and magnetic separation from complex environments.},
}

@article {pmid40462960,
year = {2025},
author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and Oliveira, A and Rahme, LG},
title = {MvfR shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum Sensing Inhibition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.16.654325},
pmid = {40462960},
issn = {2692-8205},
abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the in-creasing awareness, there is a fundamental gap in understanding which interactions govern mi-crobial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobi-al and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competi-tion within cocultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum sensing (QS) systems in these interac-tions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coex- istence of P. aeruginosa with ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously atten-uating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.},
}

@article {pmid40462143,
year = {2025},
author = {Kindtler, NL and Sheikh, S and Zervas, A and Ellegaard-Jensen, L and Feld, L and Scheel, M and Jiménez, FC and da Fonseca, RR and Laursen, KH and Jacobsen, CS and Ekelund, F},
title = {Small sample amounts from rhizosphere of barley maintain microbial community structure and diversity revealed by total RNA sequencing.},
journal = {Plant methods},
volume = {21},
number = {1},
pages = {79},
pmid = {40462143},
issn = {1746-4811},
abstract = {Total RNA sequencing is a crucial technique in microbial ecology for profiling active microbial communities in various environments, including the rhizosphere. Since total RNA sequencing yields both 16 S and 18 S ribosomal RNA (rRNA), it is effective for taxonomic profiling of the full microbial community in a sample. However, the effectiveness of this approach with limited initial sample amounts remains unclear. In this study, we grew barley in a growth system designed for highly controlled plant experiments using an inert growth medium inoculated with a soil microbiome. Our objectives were two-fold: firstly, to test the feasibility of extracting total RNA from the rhizosphere of barley grown in an inert growth medium consisting of sand and perlite. Secondly, we aimed to address the challenge of extracting comprehensive taxonomic information from minimal amounts of rhizosphere samples from barley plants, using three different amounts of freeze-dried rhizosphere material: 10, 40, and 200 mg. We showed that although smaller sample amounts yielded lower concentrations of extracted RNA, this did not significantly influence the diversity or composition of the rhizosphere microbiome as indicated by SSU rRNA. Our results demonstrate that total RNA sequencing, focusing on SSU rRNA, robustly captures the taxonomic diversity of active rhizosphere microbial communities, even in small initial sample amounts. Effective use of smaller samples opens new possibilities for detailed studies in environments where sample quantity is limited. We also conclude that the growth system applied in this experiment is suitable for highly controlled plant experiments focusing on total RNA extraction from the rhizosphere.},
}

@article {pmid40461733,
year = {2025},
author = {Ruiz-Blas, F and Friese, A and Bartholomäus, A and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A},
title = {The Deep Subsurface Biosphere and its Substrates Along a One-Million-Year Ferruginous Lake Archive.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {58},
pmid = {40461733},
issn = {1432-184X},
support = {KA 2293/8-1//Deutsche Forschungsgemeinschaft/ ; VU 94/1-1//Deutsche Forschungsgemeinschaft/ ; P2GEP2_148621//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Indonesia ; *Archaea/genetics/classification/isolation & purification ; Phylogeny ; Iron/analysis/metabolism ; Biodiversity ; },
abstract = {Lake Towuti, Indonesia, is an ancient stratified lake with ferruginous (iron-rich, sulfate-poor) anoxic bottom water conditions and a long depositional record affected by redox changes in the water column and sediments. As modern analogue of Earth's early ferruginous oceans, it enables the study of an active microbial subsurface biosphere and its role in organic matter and iron mineralization. Combining 16S rRNA genes, cell counts, pore water geochemistry, and bulk sediment profiles from a 100-m-long core, we present the first comprehensive characterization of the deep subsurface biosphere along a one-million-year lacustrine archive. Electron acceptors in the pore water became depleted at shallow depths, resulting in a drastic decrease in cell densities in the fermentative zone, where Bathyarchaeia dominate the microbial community composition. Although alpha and beta diversity reflected initial depletion of substrates during burial, they also varied across successive lithologies, indicating that sediment composition subsequent to deposition also affects diversity. The upper sediments (0-20 mblf) sheltered a dense and diverse microbial community involved in organic matter remineralization, actively producing and converting volatile fatty acids into carbon dioxide and methane. Deeper sediments (20-70 mblf) contained low-diversity microbial communities adapted to nutrient scarcity. In contrast, deepest lacustrine sediments (70-100 mblf) contained an increased microbial diversity reflecting greater availability of organic matter of terrestrial origin. Despite Bathyarchaeia being prime constituents of the deep subsurface biosphere, increased diversity in 16S rRNA gene composition was observed in discrete sediment layers (tephra, diatom ooze, peat). This demonstrated that depositional conditions remained traceable, while stratified microbial communities drove reductive diagenesis.},
}

*Lakes/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
Indonesia
*Archaea/genetics/classification/isolation & purification
Phylogeny
Iron/analysis/metabolism
Biodiversity

@article {pmid40461630,
year = {2025},
author = {Koch, M and Lado, S and Bodner-Adler, B and Carlin, G and Pacífico, C and Bauer, C and Cartwright, R and Seki, D and Steininger, C and Makristathis, A and Umek, W},
title = {Women suffering from overactive bladder syndrome exhibit a higher urethral viral abundance compared to healthy controls: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19484},
pmid = {40461630},
issn = {2045-2322},
support = {1815//OeNB Jubiläumsfonds/ ; },
mesh = {Humans ; Female ; *Urinary Bladder, Overactive/virology/microbiology ; Pilot Projects ; Middle Aged ; *Urethra/virology/microbiology ; Microbiota ; Case-Control Studies ; Prospective Studies ; Adult ; Phylogeny ; Aged ; Bacteria/genetics ; Virome ; *Viruses/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {The interactions between the human bacterial microbiome and essential bodily functions are well established for organ systems such as the oral cavity, gut, and female reproductive tract. However, the urinary microbiome, particularly its viral component, remains largely unexplored. Emerging evidence suggests that the urinary microbiome may play a significant role in the development of overactive bladder syndrome (OAB). This study aims to fill this knowledge gap by investigating the potential link between the urethral virome and female overactive bladder syndrome, and by aligning these findings with the bacterial microbiome. Prospective pilot study including 15 patients with overactive bladder syndrome and five controls. Current urinary tract infection and antibiotic therapy within the last two months were ruled out and controls were matched to cases by age and body mass index. Urethral swabs (Copan eSwab[®] urethra) were taken from each participant at one single time point. Subsequent viral isolation, purification, and enrichment were conducted using the ViPEP method. Next-generation sequencing was performed on pooled samples, followed by bioinformatic analysis to identify and classify viral contigs. Phylogenetic analysis was conducted to assess genetic relationships among identified viral sequences. The bacterial microbiome was analyzed by sequencing of the variable V3-4 region of the eubacterial 16 S rDNA gene on the Illumina MiSeq platform. We identified twenty-one viruses and bacteriophages only in pooled urethral swab samples of the OAB group, but no valid detections were retained in the control group after analysis. The most abundant human virus in urethral swab samples was human papilloma virus, whereas the most abundant bacteriophages belong to the family of Siphoviridae. In the bacterial microbiome analysis, we identified statistically higher levels of Veillonella and Bacteroides in OAB samples. Results of this pilot study suggest a difference in the urethral virome between women with OAB and healthy controls. When looking deeper into the detected virus families and species, we might postulate a unique microbial pattern of OAB patients. This pattern suggests an interplay of immunosuppression, autoimmune processes and a larger diversity of bacterial and viral microbes. Current evidence strongly suggests a disturbance of the healthy microbiome of the urogenital tract in patients with OAB, leading to subclinical chronic inflammation and thus typical OAB symptoms. Further research should focus on interventions aimed at restoring a healthy microbiome in OAB patients to mitigate inflammation and improve symptom control.},
}

Humans
Female
*Urinary Bladder, Overactive/virology/microbiology
Pilot Projects
Middle Aged
*Urethra/virology/microbiology
Microbiota
Case-Control Studies
Prospective Studies
Adult
Phylogeny
Aged
Bacteria/genetics
Virome
*Viruses/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing

@article {pmid40459550,
year = {2025},
author = {Wu, Y and Zhang, F and Zhang, S and Zhang, J and Zhao, S and Qiu, Z and Zhu 朱, M墨},
title = {Curvularia spicifera causing black rot on Ipomoea batatas in China.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-03-25-0477-PDN},
pmid = {40459550},
issn = {0191-2917},
abstract = {Ipomoea batatas (sweet potato) is an annual herb originating from South America and the large and small Antilles. It is widely cultivated in tropical and subtropical regions around the world and is widely grown in most parts of China. As an edible plant with rich nutrition, I. batatas has high economic and medicinal value (Suhendy et al. 2023). In September 2023, black rot-like disease signs and symptoms were observed on the roots of I. batatas in a farmland (about 6667 m2) located in Kaifeng city, Henan Province, China. The roots showed irregular brown or dark spots on the surface, extending to the internal center, and brown to black necrosis. Additionally, above-ground parts of infected plants showed symptoms such as yellowing and wilting of leaves, brown spots on stems, and stunted growth. Around 80 % of monitored plant roots (n = 200) exhibited the symptoms. Infected roots were cut into pieces and then placed on potato dextrose agar (PDA) (light/dark, 16 h/8 h; temperature, 18°C). After a period of 3-10 days, single hyphal tips of each fungal colony were placed on PDA and incubated for another 5-10 days (Paul et al. 2021). Colonies of the fungal pathogen on PDA reached 50 mm in diameter within 7 days, dark gray on the inner side, dark brown extending to the edge, irregular round edge, with abundant aerial mycelium, cotton-like, irregularly convex upward, undulating. The conidia were brown, ellipsoid to oval, 8 to 19 × 3 to 6 μm (n = 50). Morphologically similar isolates with characteristics consistent with those of Curvularia spicifera (Cui et al. 2020) were recovered from 87% of symptomatic root tissues (n=100). The internal transcribed spacer (ITS) region and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene from three independent isolates (CSZM202101, CSZM202102, and CSZM202103) of the fungus were amplified and sequenced with primers ITS1/ITS4 (Seliger et al. 1990) and GAPDH1/GAPDH3R (Bradshaw et al. 2022) according to a previously reported method (Zhu et al. 2022). The resulting sequences were deposited in GenBank (Accession No. OR885691, PV056889, PV056568, PQ839726, PV072835 and PV02836). BLASTn analysis showed that the ITS and GAPDH sequences had 100% (ITS, 516/516; GAPDH, 508/508) identity with C. spicifera (OQ845826 and CBS 274.52 JN192387) from maize (Ram et al. 2024) and pearl millet (S. et al. 2024), respectively. The phylogenetic analysis clearly illustrated that these isolates clustered with the sequences of a representative reference strain of C. spicifera(CBS 274.52, GenBank accession number JN192387). Therefore, the morphological, molecular and phylogenetic analysis indicated that the pathogen was C. spicifera. To complete Koch's postulates, pathogenicity experiments were carried out by inoculating spore suspension (106 spores mL-1) into the wounded roots (n=10) of I. batatas plants. Sterile distilled water treated wounded roots (n=10) served as control. One to two days after inoculation, visible mycelia were produced at the inoculation sites of I. batatas. Inoculated roots showed black rot signs 21 days post-inoculation; controls were unaffected. This was confirmed in three repeated pathogenicity tests. To our knowledge, this is the first report of black rot caused by C. spicifera on I. batatas in China. The emergence of the black rot pathogen could harm valuable food crops and reduce agricultural productivity in China. Accurate identification of the black rot fungus is essential for devising effective disease management strategies and supporting future control of C. spicifera in China.},
}

@article {pmid40459301,
year = {2025},
author = {Zhang, J and Guo, Z and Liu, J and Pan, X and Huang, Y and Cui, X and Wang, Y and Jin, Y and Sheng, J},
title = {Capabilities and Limitations of Air-Dried Soils in Microbial Biogeography: A Regional-Scale Comparative Analysis.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70111},
doi = {10.1111/1462-2920.70111},
pmid = {40459301},
issn = {1462-2920},
support = {KFJ-SW-YW043-2//Field Station Basic Research Project of the Chinese Academy of Sciences/ ; 42107145//National Natural Science Foundation of China/ ; 42407410//National Natural Science Foundation of China/ ; 0270756100ZX//Jiangsu Agricultural Biodiversity Cultivation and Utilization Research Center/ ; CX (22) 2002//Jiangsu Agricultural Science and Technology Innovation Fund/ ; CX (23) 3105//Jiangsu Agricultural Science and Technology Innovation Fund/ ; 3220220039//Pilot Project for Mineral-Land Integration of Jiangsu Province/ ; //Jiangsu Provincial Territorial Ecological Monitoring/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; China ; *Bacteria/classification/genetics/isolation & purification ; *Desiccation ; Biodiversity ; *Microbiota ; },
abstract = {Air-dried soil archives offer valuable potential for studying long-term microbial dynamics, yet systematic evaluations across large spatial scales with paired fresh-soil comparisons remain limited. Here, we systematically evaluated the effects of 1-month air-drying on microbial biogeography across 244 paddy fields in eastern China. Results showed that air-drying significantly altered communities by reducing diversity through the elimination of rare taxa while enriching desiccation-resistant phyla like Firmicutes, Chloroflexi and Actinobacteria. These compositional shifts further triggered functional bias, enhancing fermentation/methanogenesis pathways while suppressing nitrogen cycling processes. Despite these alterations, air-dried samples maintained remarkable fidelity to key ecological patterns observed in fresh soils. Multivariate analyses demonstrated strong structural concordance between paired samples, with soil pH consistently emerging as the primary environmental driver in both data sets. This preservation of biogeographical relationships occurred despite significant changes in underlying ecological mechanisms. Air-dried soil communities exhibited increased stochastic assembly, reduced niche breadth and simplified co-occurrence networks with altered keystone taxa, indicative of a two-phase process: deterministic filtering of drought-sensitive taxa followed by stochastic reorganisation among survivors. Overall, our findings provide a framework for utilising soil archives in microbial ecology, showing that while air-drying introduces predictable distortions, samples retain essential ecological information for reconstructing historical microbial-environmental relationships at large scales.},
}

*Soil Microbiology
*Soil/chemistry
China
*Bacteria/classification/genetics/isolation & purification
*Desiccation
Biodiversity
*Microbiota

@article {pmid40456365,
year = {2025},
author = {Zhao, X and Overbeek, LV and Burgess, CM and Holden, N and Brennan, F and Johannessen, GS and Allende, A and Höfte, M and Cottyn, B and Pothier, JF and Schikora, A and Uyttendaele, M},
title = {Human Pathogenic Microorganisms in Fresh Produce Production: Lessons Learned When Plant Science Meets Food Safety.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100551},
doi = {10.1016/j.jfp.2025.100551},
pmid = {40456365},
issn = {1944-9097},
abstract = {To enhance control of human pathogenic microorganisms in plant production systems, an EU COST Action (HUPLANTcontrol CA16110) was initiated, bringing together microbiologists in food, environmental and plant microbial ecology. This article summarizes the outcomes of multiple workshops and the four main lessons learned: (i) many terminologies need further explanation to facilitate multidisciplinary communication on the behavior of human pathogens from pre-harvest plant production to post-harvest food storage, (ii) the complexity of bacterial taxonomy pushes microbial hazard identification for greater resolution of characterisation (to subspecies, or even strain level) needing a multi-method approach, (iii) hazard characterisation should consider a range of factors to evaluate the weight of evidence for adverse health effects in humans, including strain pathogenicity, host susceptibility, and the impact of the plant, food, or human gut microbiome, (iv) a wide diversity of microorganisms in varying numbers and behaviours co-exist in the plant microbiome, including good (beneficial for plant or human health), bad (established human or plant pathogens) or ugly (causing spoilage or opportunistic disease). In conclusion, active listening in communication and a multi-perspective approach are the foundation for every successful conversation when plant science meets food safety.},
}

@article {pmid40456197,
year = {2025},
author = {Song, W and Lin, L and Oh, S and Grossart, HP and Yang, Y},
title = {Tire wear particles in aquatic environments: From biota to ecosystem impacts.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126059},
doi = {10.1016/j.jenvman.2025.126059},
pmid = {40456197},
issn = {1095-8630},
abstract = {Tire wear particles (TWPs), mainly generated through friction between tires and road surfaces, represent a major source of traffic-related microplastic pollution, posing threats to biota and ecosystem functions. These particles are a complex mixture of toxic compounds, including heavy metals (e.g., zinc) and organic compounds (e.g., 6-PPD), and their diverse leachates exacerbate their ecological impacts. This review collates current knowledge on the occurrence of TWPs and their leachates in aquatic systems, emphasizing their toxicological effects on species and cascading ecological consequences at the community and ecosystem levels. TWP concentrations in aquatic environments span several orders of magnitude, ranging from 10[-5] to 10[4] mg/L in water via pyrolysis-GC/MS. TWPs and their leachates induce oxidative stress, DNA damage, and alter immune responses of aquatic biota, while disrupting feeding behavior, reproduction, and survival. At the ecosystem level, TWPs and their leachates cause shifts in species composition, reduce biodiversity, and alter trophic interactions, destabilizing natural food web dynamics through selective pressure that promotes tolerant taxa and triggers cascading ecological effects. Their presence significantly influences carbon and nitrogen cycling, with environmentally relevant concentrations could promote primary producers, while higher concentrations inhibit photosynthetic nitrogen-fixing biota, disrupt microbial communities, and impair processes such as denitrification and carbon mineralization. Their toxicological and ecological impacts are likely to be intensified by global environmental change, highlighting the need for long-term studies under realistic environmental conditions to better understand underlying mechanisms and develop effective mitigation strategies.},
}

@article {pmid40453667,
year = {2025},
author = {Yang, H and Shao, C and Liu, Z and Zhang, X and Liu, Y and Xiao, J and Tang, L},
title = {Cold- and hot-classified botanical drugs differentially modulate gut microbiota: linking TCM emic classification to microbial ecology.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1545619},
pmid = {40453667},
issn = {1663-9812},
abstract = {INTRODUCTION: Traditional Chinese Medicine (TCM) classifies botanical drugs based on their thermal properties (an emic classification system), categorizing them as "cold" (e.g., "clearing heat" for anti-inflammatory effects) or "hot" (e.g., "warming the middle" for metabolic enhancement). However, the specific roles of these botanical drugs in restoring gut microbiota dysbiosis remain unclear. This study aimed to explore whether TCM-classified cold and hot botanical drugs differentially restore gut microbiota dysbiosis and host physiology in antibiotic-treated mice.

METHODS: Mice with antibiotic-induced dysbiosis were treated with eight TCM-classified botanical drugs (four cold: Rheum palmatum L., Scutellaria baicalensis Georgi, Senna alexandrina Mill., Coptis chinensis Franch.; four hot: Codonopsis pilosula (Franch.) Nannf., Astragalus membranaceus (Fisch.) Bunge, Angelica sinensis (Oliv.) Diels, Panax ginseng C.A.Mey.) for 20 days. Gut microbiota were analyzed via 16S rRNA sequencing on days 5, 10, 15, and 20, alongside physiological parameters including blood glucose, serum lipids, TNF-α, adiponectin, and intestinal histomorphology.

RESULTS: By day 20, all botanical drugs restored the diversity and ranking of dominant genera (those with >10% abundance, such as Lactobacillus and unclassified Muribaculaceae). However, cold-classified drugs, traditionally associated with anti-inflammatory effects, selectively enriched anti-inflammatory taxa, including Akkermansia and Bifidobacterium. In contrast, hot-classified drugs, linked to metabolic enhancement, promoted metabolic-modulating genera such as Clostridia and Eubacterium coprostanoligenes. These differential enrichments corresponded with the therapeutic principles defined by TCM: cold-classified drugs reduced serum TNF-α levels (P < 0.01), demonstrating anti-inflammatory effects, whereas hot-classified drugs improved lipid profiles (TG: P < 0.001), thereby promoting metabolic modulation.

DISCUSSION: TCM-classified cold and hot botanical drugs universally stabilize dominant microbiota while differentially modulating low-abundance taxa. The enrichment of Akkermansia (cold) and Clostridia (hot) offers a microbiota-driven validation of TCM's empirical classification framework. These findings connect traditional knowledge with microbial ecology, underscoring the potential of TCM-guided microbiota modulation for precision therapies.},
}

@article {pmid40450024,
year = {2025},
author = {Masigol, H and Solbach, MD and Pourmoghaddam, MJ and Ahadi, R and Mostowfizadeh-Ghalamfarsa, R and Taheri, SR and Tobias-Hünefeldt, SP and Bonkowski, M and Grossart, HP},
title = {A glimpse into Oomycota diversity in freshwater lakes and adjacent forests using a metabarcoding approach.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19124},
pmid = {40450024},
issn = {2045-2322},
mesh = {*Lakes/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Forests ; *Oomycetes/genetics/classification/isolation & purification ; Ecosystem ; Germany ; Phylogeny ; Fresh Water/microbiology ; },
abstract = {Oomycota, a diverse group of fungus-like protists, play key ecological roles in aquatic and terrestrial ecosystems, yet their habitat-specific diversity and distribution remain poorly understood. This study investigates the diversity of two major Oomycota classes, Saprolegniomycetes and Peronosporomycetes, in two freshwater lakes and their adjacent forests in northeastern Germany. Using a combination of targeted metabarcoding and traditional isolation techniques, we analyzed samples from six habitats, including soil (forest), rotten leaves (forest and shoreline), sediments (shoreline), and surface waters (littoral and pelagic zones). Metabarcoding revealed 401 Oomycota OTUs, with Pythium, Globisporangium, and Saprolegnia as dominant genera. Culture-based methods identified 110 strains, predominantly from surface water and sediment, with Pythium sensu lato and Saprolegnia as the most frequent taxa. Alpha and beta diversity analyses highlighted distinct community structures influenced by lake and habitat type, with significant co-occurrence of Saprolegniomycetes and Peronosporomycetes across habitats. This study provides the first comprehensive metabarcoding-based exploration of Oomycota biodiversity in interconnected freshwater and terrestrial ecotones, uncovering previously unrecognized patterns of habitat-specific diversity.},
}

*Lakes/microbiology
*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Forests
*Oomycetes/genetics/classification/isolation & purification
Ecosystem
Germany
Phylogeny
Fresh Water/microbiology

@article {pmid40448709,
year = {2025},
author = {Samaniego, T and La Torre, R and Orjeda, G and Ramirez, JL},
title = {Lima Megacity's Influence on Aquatic Microbial Communities in the Rímac River: Dominance Over Spatial and Seasonal Variations.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {57},
pmid = {40448709},
issn = {1432-184X},
support = {B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; B2110006i//Universidad Nacional Mayor de San Marcos/ ; },
mesh = {*Rivers/microbiology ; Seasons ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Peru ; *Microbiota ; *Water Microbiology ; Environmental Monitoring ; DNA, Bacterial/genetics ; Biodiversity ; },
abstract = {The Rímac River, a vital watershed on the Peruvian coast, is confronted with substantial environmental challenges stemming from intensive exploitation and widespread contamination. As the primary source of water for Lima, supplying approximately 80% of the city's needs, the river is heavily impacted by pollutants from domestic, hospital, industrial, and mining effluents. These contaminants introduce microbiota that pose significant public health risks. This study utilizes 16S rRNA gene metabarcoding to characterize the bacterial communities along the Rímac River, examining both spatial (upper, middle, and lower basins) and temporal (dry and rainy seasons) variations. Over a year-long sampling period, DNA sequencing revealed pronounced microbiological differences between the Metropolitan and Regional zones, primarily driven by anthropogenic activities. Key findings include a significant reduction in microbial diversity and an increase in pathogenic bacteria within the Metropolitan zone, while the influence of seasonal variations and altitudinal gradients was comparatively minor. Betaproteobacteria emerged as the most abundant class across most samples. Notably, Aliarcobacter cryaerophilus, an indicator of fecal contamination and a potential public health hazard, was predominantly detected in the Metropolitan zone. These results underscore the necessity for comprehensive monitoring of the Rímac River's microbiota, incorporating advanced molecular techniques to effectively track and mitigate pollution. The study emphasizes the urgent need for robust water quality management strategies to protect this critical resource, ensuring the health and sustainability of Lima and its surrounding regions.},
}

*Rivers/microbiology
Seasons
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Peru
*Microbiota
*Water Microbiology
Environmental Monitoring
DNA, Bacterial/genetics
Biodiversity

@article {pmid40446899,
year = {2025},
author = {Fang, P and Ye, S and Luo, Z and Guo, R and Jiang, Y and Liu, L and Li, S and Xiao, F},
title = {Nanoplastics under the charge effect: Unveiling the potential threats to amphibian (Rana nigromaculata) growth, intestinal damage, and microbial ecology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126566},
doi = {10.1016/j.envpol.2025.126566},
pmid = {40446899},
issn = {1873-6424},
abstract = {Nanoplastics (NPs) are a contaminant that may be found in charged forms in the environment, capable of accumulating in aquatic organisms and affecting their health. This study compared the effects of positively charged NPs (PS-NH2, 30nm) and negatively charged NPs (PS-COOH, 30nm) at 6 and 60 mg/L on the growth and development of black-spotted frog tadpoles (Rana nigromaculata), as well as on intestinal damage, and microbial ecology. The results indicated that exposure to both types of NPs significantly reduced the survival rate of tadpoles, while significantly increasing their body weight and body length (p <0.05). Compared to PS-COOH, exposure to PS-NH2 resulted in more adverse intestinal tissue damage and induced more severe intestinal oxidative stress. Furthermore, exposure to PS-NH2 significantly reduced the abundance and diversity of the microbiome associated with gut function and nutrient absorption, indirectly leading to more severe intestinal damage and growth changes. In addition, functional prediction and gene transcription analysis showed that exposure to charged PS-NPs caused changes in genes associated with glycolysis and lipid metabolism, indicating that the glucose-lipid metabolism of tadpoles is impacted. This study demonstrated the growth differences and intestinal toxicity of NPs exposure in tadpoles, explores the potential connections between gut microbiota and glucose-lipid metabolism, and provides new perspectives on the health risks of NPs in amphibians.},
}

@article {pmid40446767,
year = {2025},
author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A},
title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.},
journal = {Water research},
volume = {284},
number = {},
pages = {123887},
doi = {10.1016/j.watres.2025.123887},
pmid = {40446767},
issn = {1879-2448},
abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.},
}

@article {pmid40446743,
year = {2025},
author = {Jansriphibul, K and Krohn, C and Ball, AS},
title = {Sources of variability for viability PCR using propidium monoazide.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128224},
doi = {10.1016/j.micres.2025.128224},
pmid = {40446743},
issn = {1618-0623},
abstract = {The molecular detection of microorganisms in environmental samples relies on PCR-associated molecular workflows that typically cannot differentiate live from dead microbes. Understanding the microbial functions of complex communities can be significantly hindered by presence of the dead microbes. Using propidium monoazide (PMA), PMA-based viability PCR, is arguably the most convenient method to differentiate viability status apart. Errors from variabilities of non-standardized practices and a lack of understanding of the PMA mechanism deter the viability PCR approach. This review discusses the sources of variability in each of four key sequential steps: pre-analysis, PMA activation, DNA extraction and PCR. An analysis of previous literature on optimization of PMA-based viability PCR indicates that often only one source of variability is considered. However, all steps are interrelated and should be considered together when understanding and mitigating unwanted variability, especially in the PMA activation and PCR steps. Research gaps in PMA are addressed, such as the chemical mechanisms of PMA and possible by-products interferences, internal standard spiking and recommendations for future research.},
}

@article {pmid40446651,
year = {2025},
author = {O'Connor, L and Minogue, E and Carolan, S and Darcy, G and Chueiri, A and Faherty, M and Morton, J and Mc Donagh, F and Singh, NK and Venkateswaran, K and Miliotis, G and Smith, TJ},
title = {Rapid detection of the novel human pathogen Pantoea piersonii: advancements in methodology.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116905},
doi = {10.1016/j.diagmicrobio.2025.116905},
pmid = {40446651},
issn = {1879-0070},
abstract = {Pantoea piersonii a novel bacterium isolated from the International Space Station (ISS) presents a unique challenge for microbial monitoring in spaceflight and more recently in clinical environments. Identification of the organism currently involves culture, followed by whole genome sequencing and analysis of generated sequences. Since the MALDI-TOF profile of this pathogen is absent from the database and 16S rRNA sequencing fails to resolve its identity to the nearest neighbour, a definitive genetic marker is required for unambiguous identification of the organism. Given the increase in the number of reported clinical cases, there exists a need for a rapid method for identification of the organism which could be utilised in a range of environments including the clinical setting. This study describes the design, development and validation of a specific and sensitive real-time PCR assay for the specific detection of P. piersonii. The assay targets a unique region of the malate dehydrogenase gene, confirmed through comparative genomic analysis. We demonstrate the performance of the assay in terms of analytical specificity, sensitivity, and robustness, ensuring its suitability for both space microbiology applications and clinical use.},
}

@article {pmid40445193,
year = {2025},
author = {Cisneros, M and Blanco-Fuertes, M and Lluansí, A and Brotons, P and Henares, D and Pérez-Argüello, A and González-Comino, G and Ciruela, P and Mira, A and Muñoz-Almagro, C},
title = {Synergistic inhibition of pneumococcal growth by Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum: insights into nasopharyngeal microbial interactions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0013825},
doi = {10.1128/spectrum.00138-25},
pmid = {40445193},
issn = {2165-0497},
abstract = {Streptococcus pneumoniae is a nasopharynx colonizer that can invade sterile tissues, causing invasive pneumococcal disease (IPD). Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum are commensal bacteria commonly isolated from the nasopharynx of healthy children, potentially playing a protective role. This study aims to analyze the effects of D. pigrum and C. pseudodiphtheriticum on S. pneumoniae in vitro growth. Pneumococcal strains were collected from IPD patients and healthy carriers in Catalonia (2016-2023). D. pigrum and C. pseudodiphtheriticum strains were isolated from a healthy child's nasopharynx. S. pneumoniae was co-cultured with each commensal bacterium in triplicate experiments. Pneumococcal growth was quantified using a real-time PCR assay targeting the lytA gene. The effect of commensal bacteria on pneumococcal growth was evaluated using a linear mixed-effect regression model. Twenty-eight pneumococcal strains expressing 24 different serotypes and 27 clonal types were analyzed (18 isolated in blood and 10 in nasopharyngeal aspirate). Pneumococcal growth was decreased by D. pigrum (β = -0.763, 95% confidence interval [CI]: -0.94 to -0.59, P < 0.0001) and C. pseudodiphtheriticum (β = -0.583, 95% CI: -0.76 to -0.41, P < 0.0001). The combined presence of both had a stronger inhibitory effect (β = -0.971, 95% CI: -1.15 to -0.79, P < 0.0001). No association was found between isolation site or serotype with pneumococcal growth. D. pigrum and C. pseudodiphtheriticum significantly reduced pneumococcal growth, with a synergistic effect when combined. This antagonistic effect supports the potential protective factor of healthy nasopharyngeal microbiota against IPD and the development of these microorganisms as probiotics.IMPORTANCEInvasive pneumococcal disease (IPD) is a significant worldwide health challenge. The present study highlights the significant inhibitory effect of two commensal bacteria, Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum, on pneumococcal growth, with a stronger effect observed when both bacteria are present together. Through testing different strains of S. pneumoniae and the implementation of a robust statistical model, this research advances in the knowledge of microbial ecology and provides evidence to support the development of the use of these commensal bacteria as probiotics. These results emphasize the possibility of using the nasopharyngeal microbiota's natural interactions to mitigate the risk of IPD.},
}

@article {pmid40444437,
year = {2025},
author = {Pan, Y and Tao, Y and Yang, X and Du, S and Ding, H and Li, J and Jia, H and Chen, H},
title = {Underlying mechanisms of spatial distribution of prokaryotic community in surface seawater from Arctic Ocean to the Sea of Japan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0051725},
doi = {10.1128/spectrum.00517-25},
pmid = {40444437},
issn = {2165-0497},
abstract = {Microorganisms play critical roles in marine ecosystems, so understanding the factors shaping microbial communities across various oceanic regions is essential for predicting ecosystem resilience and biogeochemical cycles. This study investigated the marine prokaryotic communities across 22 stations spanning the Arctic Ocean, the Chukchi Sea, the Bering Sea, and the Sea of Japan, with an emphasis on how environmental factors shape these communities. Results showed that the microbial alpha diversity generally declines with increasing latitude, though Arctic Ocean stations exhibited higher Chao 1 indices compared to the Bering Sea. Beta diversity analyses revealed that temperature and salinity were key factors associated with community composition variation across latitudes. Proteobacteria and Cyanobacteria were the dominant phyla showing opposite distribution trends across sampling stations. Cold-adapted oligotrophs such as Planktomarina and the SAR11 clade thrived in Arctic waters, while Sphingomonas, known for pollutant degradation, was more abundant in the Sea of Japan. Temperature was positively correlated to the relative abundance of Sphingomonas. At broad spatial scales, stochastic processes dominated community assembly of microbial phylogenetic diversity, while in specific regions like the Arctic Ocean, deterministic homogeneous selection appeared to shape microbial communities; and temperature showed a pronounced influence on phylogenetic turnover across all samples. Co-occurrence networks identified several key taxa, such as Polaribacter_1, Candidatus_Aquiluna, and NS5_marine_group. Overall, the study underscores temperature's role in shaping microbial community diversity, composition, and assembly processes across latitudinal gradients, highlighting unique community adaptations to extreme environments.IMPORTANCEMicrobes are the invisible engines of ocean health, recycling nutrients and sustaining marine life. This research helps us understand how climate factors like temperature shape these microscopic communities, which differ starkly between icy Arctic waters and warmer seas. As oceans warm due to climate change, microbial populations and their critical roles in cleaning pollutants or supporting food webs could shift dramatically. The study suggests Arctic microbes are uniquely adapted to cold, low-nutrient conditions, making them vulnerable to warming. By linking temperature to microbial diversity, this work provides clues to predict how marine ecosystems might respond to climate shifts, informing efforts to protect ocean biodiversity and processes vital to Earth's carbon and nutrient cycles.},
}

@article {pmid40442489,
year = {2025},
author = {Ostap-Chec, M and Antoł, W and Bajorek, D and Berbeć, E and Moroń, D and Rapacz, M and Miler, K},
title = {Meta-Analysis and Experimental Evidence Reveal No Impact of Nosema ceranae Infection on Honeybee Carbohydrate Consumption.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {56},
pmid = {40442489},
issn = {1432-184X},
support = {Preludium 2021/41/N/NZ8/02917//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Bees/microbiology/physiology/metabolism ; *Nosema/physiology ; Hemolymph/chemistry/metabolism ; Feeding Behavior ; Trehalose/metabolism/analysis ; *Carbohydrate Metabolism ; },
abstract = {Honeybees (Apis mellifera) are indispensable pollinators for ecosystem stability and agricultural productivity. However, they face numerous challenges, including pathogens threatening their survival and ecosystem services. Among these pathogens, Nosema ceranae, a microsporidian parasite, causes significant damage to the intestinal tract and induces energetic imbalances in the organism, posing a major threat to both individual bees and entire colonies. In response to infections, bees often engage in behavioral defenses, such as self-medicating with antimicrobial substances available in their environment. We hypothesized that bees infected with N. ceranae might compensate behaviorally by increasing their carbohydrate consumption. To test this hypothesis, we conducted a meta-analysis of existing studies comparing sugar consumption in healthy and infected bees, complemented by an experimental study. In our experiment, we measured sugar intake and quantified trehalose levels in the hemolymph, a key indicator of energy reserves. Both the meta-analysis and experimental results consistently showed no significant differences in sugar consumption between healthy and infected bees. Similarly, trehalose levels in the hemolymph remained comparable between the two groups. Our findings suggest that the infection caused by N. ceranae does not elicit compensatory feeding behavior in honeybees. Moreover, the meta-analysis revealed significant gaps in current research, particularly a lack of studies focusing on forager bees, which face the highest energetic demands among colony members. Our findings call for future studies on the energetic effects of nosemosis and studies conducted under natural or semi-natural conditions.},
}

Animals
Bees/microbiology/physiology/metabolism
*Nosema/physiology
Hemolymph/chemistry/metabolism
Feeding Behavior
Trehalose/metabolism/analysis
*Carbohydrate Metabolism

@article {pmid40440849,
year = {2025},
author = {Ramadoss, R and Nishad, AK and Moovarkumudalvan, B and Shomar, B},
title = {Bacterial composition of dust deposited in Qatar: A seasonal study.},
journal = {The Science of the total environment},
volume = {985},
number = {},
pages = {179766},
doi = {10.1016/j.scitotenv.2025.179766},
pmid = {40440849},
issn = {1879-1026},
abstract = {Dust storms in the Middle East threaten public health by deteriorating air quality and transporting microorganisms over vast distances. This study analyzes seasonal variations in dust-borne bacterial diversity on photovoltaic (PV) panels using 16S rRNA gene sequencing and bioinformatics to assess community composition and metabolic potential. Our findings suggest that seasonal ecological factors have potential effects on the composition of the airborne bacterial community. In Qatar, the high atmospheric CO2 levels associated with hydrocarbon refining had promoted the growth of hydrocarbon-degrading bacteria belonging to the phyla Campilobacterota, Proteobacteria, and Bacteroidota. High temperatures and photothermal reactions of summer conditions have favored sulfur-metabolizing bacteria. Conversely, milder temperatures, increased humidity, reduced wind speed, and a decline in summer-favoring bacteria had contributed to the increased abundance of the phyla Patescibacteria, Firmicutes, and Actinobacteriota during other seasons. This study had also identified dust borne pathogenic bacteria associated with human and plant diseases, highlighting the need for environmental surveillance to monitor microbial diversity and its shifts driven by ecological factors. This knowledge is crucial for public health, environmental protection, sustainable farming and advancing our understanding of microbial ecology.},
}

@article {pmid40439420,
year = {2025},
author = {Park, J and Kohn, E and Schenk, S and Davis, KM and Clark, JS and Parfrey, LW},
title = {An experimental test of the influence of microbial manipulation on sugar kelp (Saccharina latissima) supports the core influences host function hypothesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030125},
doi = {10.1128/aem.00301-25},
pmid = {40439420},
issn = {1098-5336},
abstract = {UNLABELLED: Kelp are valued for a wide range of commercial products and their role in kelp forest ecosystems, making kelp cultivation a rapidly expanding economic sector. Microbes associated with kelp and other macroalgae play a critical role in processes such as nutrient exchange, chemical signaling, and defense against pathogens. Thus, manipulating the microbiome to enhance macroalgal growth and resilience is a promising yet underexplored approach for sustainable kelp cultivation. The core microbiome hypothesis suggests that the bacteria that are consistently found on a host (the core microbes) are likely to have a disproportionate impact on host biology, making them an attractive target for microbiome manipulation. In this study, we surveyed wild Saccharina latissima and their surrounding environment to identify core bacterial taxa, compared them to cultivated kelp, and experimentally tested how cultured bacterial isolates affect kelp development. We found that core bacteria are nearly absent in cultivated juvenile sporophytes in nurseries, but eventually colonize them after outplanting to ocean farm sites. Bacterial inoculants had both positive and negative effects on kelp development. Notably, the strength of association of a bacterial genus with kelp in the wild positively correlated with its impact on gametophyte settlement and sporophyte development in kelp co-culture experiments, aligning with predictions from the core microbiome influences host function hypothesis. These findings affirm the feasibility of using microbial manipulations to improve current kelp aquaculture practices and provide a framework for developing these techniques.

IMPORTANCE: Microorganisms consistently associated with hosts are widely thought to be more likely to impact host biology and health. However, this intuitive concept has not been experimentally evaluated. This study formalizes this concept as the Core Microbiome Influences Host Function hypothesis and experimentally tests this hypothesis in sugar kelp (Saccharina). The distribution of bacteria on wild kelp and core microbes was first identified by compiling a broad dataset of the kelp microbiome sampled across space and time. Bacterial cultures were isolated from the surface of sugar kelp and individually grown in laboratory co-culture with sugar kelp spores to assess the ability of bacterial isolates to influence kelp growth and development. In support of the core influences host function hypothesis, isolates belonging to bacterial genera that are more strongly associated with wild sugar kelp are more likely to influence development in laboratory experiments.},
}

@article {pmid40437905,
year = {2025},
author = {Ni, J and Yang, Z and Sun, X and Cui, Q and Zhang, R and Lu, H and Wu, Z and Zhu, J and Mao, H and Liu, K and Tang, C and Wang, C and Xing, C and Zhu, J},
title = {Probiotic Akkermansia muciniphila alleviates acute kidney injury by protecting the intestinal barrier and modulating gut microbiota and metabolites.},
journal = {Journal of biomedical research},
volume = {},
number = {},
pages = {1-12},
doi = {10.7555/JBR.39.20250162},
pmid = {40437905},
issn = {1674-8301},
abstract = {Acute kidney injury (AKI) is a critical condition with limited effective therapies. Akkermansia muciniphila (A. muciniphila) is a probiotic with multiple beneficial effects, including epithelial cell tight junctions regulation. Since renal pathophysiology is associated with gut barrier integrity, we hypothesized that A. muciniphila may have potential preventive effects on AKI. We established a lipopolysaccharide (LPS)-induced AKI mouse model to evaluate the effects of A. muciniphila. Our findings showed that pretreatment with A. muciniphila significantly attenuated kidney injury, as evidenced by reduced serum creatinine and urea nitrogen levels, alongside diminished tubular necrosis and apoptosis. A. muciniphila preserved the intestinal barrier integrity and induced marked shifts in gut microbial ecology and the metabolome. A. muciniphila induced notably an increase in the relative abundance of phylum Proteobacteria while a decrease of Bacteroidetes. At the genus level, Prevotella, Faecalibaculum, Moraxella and Lactobacillus were more abundant in A. muciniphila-pretreated mice. Metabolomic analysis revealed that A. muciniphila altered the gut metabolome affecting modulation of pathways, including tyrosine metabolism, alanine/aspartate/glutamate homeostasis, cancer-related carbon flux, and GABAergic synaptic signaling. In conclusion, our findings demonstrate A. muciniphila's renoprotective effects through gut-kidney axis modulation, laying the foundation for subsequent studies to verify the connection between gut microbiota and AKI.},
}

@article {pmid40436193,
year = {2025},
author = {Lacerda, AL and Casotti, R and Briand, JF and Lenoble, V and Muniategui-Lorenzo, S and Kessler, F and Barre, A and Moscoso-Pérez, CM and Fernández-González, V and Andrade-Garda, JM and Murano, C and Donnarumma, V and Oreste, E and Joyce, H and Hannon, C and Nash, R and Orange, F and Frias, J and Pedrotti, ML},
title = {The plastisphere: a comprehensive description of geographic and temporal community patterns across the Mediterranean Sea and the Atlantic Ocean.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121929},
doi = {10.1016/j.envres.2025.121929},
pmid = {40436193},
issn = {1096-0953},
abstract = {Plastic pollution is a global ecological threat, not only as physical debris but also as a novel substrate hosting microbial communities, known as "plastisphere". Polymer type (virgin vs. recycled), combined with environmental variations, may influence both early and mature colonisation stages. While biogeography has been identified as a key driver of the plastisphere community structure, prior research often relied on isolated studies with no methodological standardization or on opportunistic sampling. Here, this study stands out by conducting a simultaneous and harmonized investigation across environmentally distinct sites in the Mediterranean Sea and the Atlantic Ocean. Three polymers (LDPE, PP-PC, PLA) were incubated in situ, across six locations. Using standardized protocols and eDNA metabarcoding (16S and 18S rRNA), we assessed how biogeography, environmental variables, polymer type, and exposure time shape the diversity and composition of prokaryotic and eukaryotic communities colonizing plastics. Incubations lasted up to one year, with sampling at 7, 30 and 90 days, covering all four seasons. Microbial colonization in all plastics occurred within 7 days, but community richness and maturity fluctuated across sites and seasons. Proteobacteria, Bacteroidia and Planctomycetes were the dominant prokaryotes, while Ciliates, Cercozoa and Dinoflagellata dominated eukaryotes. Taxa with potential for plastic biodegradation (e.g., Oleibacter, Alcanivorax) and pathogenicity (e.g., Pseudomonas, Candida), were identified, highlighting the plastisphere's ecological role. This dataset represents the most comprehensive assessment of marine plastisphere diversity to date, allowing the understanding of species occurrence and their interaction, influence on ecological processes and the emerging health risks, which should be considered when developing global strategies to mitigate ocean plastic pollution.},
}

@article {pmid40435560,
year = {2025},
author = {Fazio, NA and Albertin, W and Masneuf-Pomarede, I and Randazzo, CL and Caggia, C},
title = {Structure of culturable indigenous yeast population and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts during spontaneous fermentation of Etna vineyards grapes.},
journal = {International journal of food microbiology},
volume = {440},
number = {},
pages = {111282},
doi = {10.1016/j.ijfoodmicro.2025.111282},
pmid = {40435560},
issn = {1879-3460},
abstract = {The microbial diversity of indigenous yeasts plays a fundamental role in the spontaneous fermentation of wines, contributing to the concept of microbial terroir and potentially influencing the sensory profile of the final product. This study explores the yeast ecology and genetic diversity of Saccharomyces cerevisiae and non-Saccharomyces yeasts in four wineries located on two different sides of Mount Etna, a region of unique viticultural significance due to its volcanic soils and diverse microclimatic conditions. A total of 454 yeast isolates were obtained from spontaneous fermentations of different grape varieties, and identified as belonging to 18 distinct species. The spontaneous fermentation was characterized by an initial dominance of non-Saccharomyces yeasts, especially Hanseniaspora uvarum and Metschnikowia pulcherrima, followed by a gradual dominance of S. cerevisiae at later stages. Microsatellite genotyping revealed significant genetic diversity among S. cerevisiae strains, with some distinct genetic patterns associated with Italian winery environments. Additionally, H. uvarum exhibited significant genetic variation but lacked clear geographic clustering, suggesting complex ecological and enological interactions. Statistical analyses of microbial diversity indices indicated that vineyard-specific factors, including altitude, soil composition, and agronomic practices, may influence yeast community structure among the four wineries. These findings provide new insights into the microbial ecology of Etna wines and highlight the potential of indigenous yeast populations for maintaining and enhancing regional wine identity.},
}

@article {pmid40432969,
year = {2025},
author = {Wang, JQ and Yu, T and Qiu, HY and Ji, SW and Xu, ZQ and Cui, QC and Li, HF and Liang, WF and Feng, S and Fu, CT and Gao, X and Han, ZZ and Tian, WN and Li, JX and Xue, SJ},
title = {Differential impact of spotted fever group rickettsia and anaplasmosis on tick microbial ecology: evidence from multi-species comparative microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589263},
pmid = {40432969},
issn = {1664-302X},
abstract = {Tick-borne diseases (TBDs) pose a significant public health challenge, as their incidence is increasing due to the effects of climate change and ecological shifts. The interplay between tick-borne pathogens and the host microbiome is an emerging area of research that may elucidate the mechanisms underlying disease susceptibility and severity. To investigate the diversity of microbial communities in ticks infected with vertebrate pathogens, we analyzed the microbiomes of 142 tick specimens. The presence of Rickettsia and Anaplasma pathogens in individual samples was detected through PCR. Our study aimed to elucidate the composition and variation of microbial communities associated with three tick species, which are known vectors for various pathogens affecting both wildlife and humans. We employed high-throughput sequencing techniques to characterize the microbial diversity and conducted statistical analyses to assess the correlation between the presence of specific pathogens and the overall microbial community structure. Pathogen screening revealed an overall positivity rate of 51.9% for Anaplasma and 44.6% for spotted fever group rickettsia (SFGR). Among the three tick species (Dermacentor silvarum, Haemaphysalis concinna, and Haemaphysalis japonica) analyzed, D. silvarum (the predominant species) exhibited the highest pathogen prevalence. The results indicate significant variation in microbial diversity between tick samples, with the presence of Anaplasma and SFGR associated with distinct changes in the microbial community composition. These findings underscore the complex interactions between ticks and their microbial inhabitants, enriching our understanding of tick-borne diseases.},
}

@article {pmid40431577,
year = {2025},
author = {Jia, J and Bao, P and Yu, Q and Li, N and Ren, H and Chen, Q and Yan, P},
title = {Lactobacillus Re-Engineers Gut Microbiota to Overcome E. coli Colonization Resistance in Mice.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050484},
pmid = {40431577},
issn = {2306-7381},
support = {KCXF20201221173205015//the Shenzhen Science and Technology Program/ ; TCYC-TP2023//Xinjiang Tianchi introduction of talent research Program/ ; },
abstract = {The intestinal health and functionality of animals play pivotal roles in nutrient digestion and absorption, as well as in maintaining defense against pathogenic invasions. These biological processes are modulated by various determinants, including husbandry conditions, dietary composition, and gut microbial ecology. The excessive use of anthropogenic antibiotics may disrupt intestinal microbiota composition, potentially leading to dysbiosis that directly compromises host homeostasis. While Lactobacillus species are recognized for their immunomodulatory properties, their precise mechanisms in regulating host anti-inflammatory gene expression and influencing mucosal layer maturation, particularly regarding E. coli colonization resistance, require further elucidation. To investigate the regulatory mechanisms of Lactobacillus in relation to intestinal architecture and function during E. coli infection, we established a colonic infection model using Bal b/c mice, conducting systematic analyses of intestinal morphology, inflammatory mediator profiles, and microbial community dynamics. Our results demonstrate that Lactobacillus supplementation (Pediococcus acidilactici) effectively mitigated E. coli O78-induced enteritis, with co-administration during infection facilitating the restoration of physiological parameters, including body mass, intestinal histoarchitecture, and microbial metabolic functions. Microbiome profiling revealed that the Lactobacillus intervention significantly elevated Lactococcus abundance while reducing Weissella populations (p < 0.05), concurrently enhancing metabolic pathways related to nutrient assimilation and environmental signal processing (including translation mechanisms, ribosomal biogenesis, amino acid transport metabolism, and energy transduction systems; p < 0.05). Mechanistically, Lactobacillus administration attenuated E. coli-induced intestinal pathology through multiple pathways: downregulating pro-inflammatory cytokine expression (IL-1β, IL-1α, and TNF-α), upregulating epithelial junctional complexes (Occludin, Claudin-1, and ZO-1), and stimulating mucin biosynthesis (MUC1 and MUC2; p < 0.05). These modifications collectively enhanced mucosal barrier integrity and promoted epithelial maturation. This investigation advances our comprehension of microbiota-host crosstalk during enteropathogenic infections under probiotic intervention, offering valuable insights for developing novel nutritional strategies and microbial management protocols in animal husbandry.},
}

@article {pmid40431542,
year = {2025},
author = {Karukayil Gopalakrishnan, N and Pappuswamy, M and Meganathan, G and Shanmugam, S and Pushparaj, K and Balasubramanian, B and Kim, IH},
title = {Influence of Probiotic Administration in Canine Feed: A Comprehensive Review.},
journal = {Veterinary sciences},
volume = {12},
number = {5},
pages = {},
doi = {10.3390/vetsci12050449},
pmid = {40431542},
issn = {2306-7381},
abstract = {Dogs are cherished companions, and in today's world, pets are increasingly regarded as family members. Pet owners are placing growing emphasis on their animals' health, particularly for dogs. Probiotics, which are living bacteria that benefit the host when given in sufficient quantities, have drawn a lot of interest in the veterinary nutrition community due to their beneficial effects on companion animals, including dogs. This study emphasizes the advantages of adding probiotics to canine diets in order to enhance the health of the gut flora and the technologies used to incorporate probiotics into canine feed. It looks at the best ways to deal with common dog health problems, highlighting probiotics as a helpful substitute for antibiotics, which can have serious adverse effects, encourage bacterial resistance, and disturb the gut's microbial ecology, which is necessary for digesting. Such disruptions are linked to chronic inflammatory enteropathy and obesity in dogs. This paper also examines biotechnological advancements in probiotic incorporation methods in dog feed, aiming to optimize their health benefits. Probiotic feed supplements may thus represent a promising approach to advancing canine health care, providing a natural adjunct to conventional treatments and preventive measures.},
}

@article {pmid40431287,
year = {2025},
author = {Zhong, J and Ran, Q and Han, Y and Gan, L and Dong, C},
title = {Biosynthetic Mechanisms of Plant Chlorogenic Acid from a Microbiological Perspective.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051114},
pmid = {40431287},
issn = {2076-2607},
support = {32360029//the National Science Foundation of China/ ; 32400111//the National Science Foundation of China/ ; Qiankehe Foundation-ZK (2024) General 091//he Guizhou Provincial Basic Research Program (Natural Science)/ ; },
abstract = {Chlorogenic acid (CGA), a phenolic compound with diverse bioactivities, plays a crucial role in plant defense mechanisms and has significant therapeutic potential in human inflammatory and cardiovascular diseases. The biosynthesis and accumulation of CGA in plants result from a complex interplay between internal factors (e.g., hormones, enzymes, and genes) and external factors (e.g., microbial interactions, drought, and temperature fluctuations). This review systematically investigates the influence of microbes on internal regulatory factors governing CGA biosynthesis in plants. CGA is synthesized through four distinct metabolic pathways, with hormones, enzymes, and genes as key regulators. Notably, microbes enhance CGA biosynthesis by improving plant nutrient uptake, supplying essential hormones, regulating the expression of related enzymes and genes, and the interaction between bacteria and fungi. In addition, our review summarizes the challenges currently present in the research and proposes a series of innovative strategies. These include in-depth investigations into the molecular mechanisms of microbial regulation of plant gene expression, gene editing, development of microbial inoculants, construction of synthetic microbial communities, and exogenous application of plant hormones.},
}

@article {pmid40431158,
year = {2025},
author = {Mirete, S and Sánchez-Costa, M and Díaz-Rullo, J and González de Figueras, C and Martínez-Rodríguez, P and González-Pastor, JE},
title = {Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13050985},
pmid = {40431158},
issn = {2076-2607},
support = {PID2021-126114NB-C43//Spanish Ministry of Science and Innovation which also included European Regional Development Fund (FEDER)/ ; },
abstract = {Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations. MAG-based studies have identified microbial lineages form Archaea and Bacteria responsible for methane oxidation, carbon sequestration in marine sediments, ammonia oxidation, and sulfur metabolism, highlighting their critical roles in ecosystem stability. From a sustainability perspective, MAGs provide essential insights for climate change mitigation, sustainable agriculture, and bioremediation. The ability to characterize microbial communities in diverse environments, including soil, aquatic ecosystems, and extreme habitats, enhances biodiversity conservation and supports the development of microbial-based environmental management strategies. Despite these advancements, challenges such as assembly biases, incomplete metabolic reconstructions, and taxonomic uncertainties persist. Continued improvements in sequencing technologies, hybrid assembly approaches, and multi-omics integration will further refine MAG-based analyses. As methodologies advance, MAGs will remain a cornerstone for understanding microbial contributions to global biogeochemical processes and developing sustainable interventions for environmental resilience.},
}

@article {pmid40427685,
year = {2025},
author = {Chen, Z and Zhong, Y and Chen, L and Liu, W and Lin, C and Chen, Y and Wang, X},
title = {HGF Aggravated Periodontitis-Associated Gut Barrier and Microbial Dysfunction: Implications for Oral-Gut Axis Regulation.},
journal = {Biology},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/biology14050496},
pmid = {40427685},
issn = {2079-7737},
support = {81700985//National Natural Science Foundation of China/ ; 2024A03J0138//Guangzhou Municipal Science and Technology Bureau/ ; 02-408-2304-05037XM and 02-408-240603131063//Plan on Enhancing Scientific Research in Guangzhou Medical University/ ; 202201020203//Guangzhou Science and Technology Program/ ; },
abstract = {While periodontitis is increasingly linked to systemic disorders through the oral-gut axis, the molecular mediators driving gut microbiota dysbiosis and barrier disruption remain elusive. Hepatocyte growth factor (HGF), a novel regulator of inflammatory bone loss in periodontitis, may serve as a critical communicator between oral infection and distal intestinal pathology. This study investigates how HGF overexpression modulates the gut microbial ecosystem and intestinal barrier integrity in a transgenic periodontitis model. In this study, we combined 16S rRNA sequencing of fecal microbiota with comprehensive gut barrier assessments, including systemic markers (D-lactate, LPS, and DAO ELISA), structural integrity (villous morphology), and molecular analysis (ZO-1, occludin, and NOD2 immunohistochemistry), using HGF-overexpressing transgenic (HGF-Tg) mice with periodontitis. The results demonstrated that HGF increased gut permeability in the context of periodontitis, as evidenced by elevated serum levels of D-lactate and LPS compared to wild type (WT) mice. In addition, gut villous morphology disorder was observed in HGF-Tg mice with periodontitis. HGF also diminished the protein level of occludin and upregulated NOD2 expression in mice with periodontitis. Moreover, HGF-Tg mice with periodontitis exhibited significant dysbiosis of gut microbiota, with reduced levels of probiotics (e.g., Faecalibaculum). Notably, HGF also increased the enrichment of the periodontitis-associated pathogens (e.g., Desulfovibrio and Streptococcus) in the gut. Microbial functions, particularly metabolic pathways, were significantly altered by HGF when periodontitis occurred. Some microorganisms like g_Desulfovibrio may play a role in gut barrier disorder in HGF-Tg mice with periodontitis. Overall, our findings position HGF as a novel orchestrator of oral-gut crosstalk, where its overexpression reshapes gut microbial ecology toward a "leaky gut" phenotype to compromise intestinal barrier integrity, further deepening our understanding of the oral-gut axis.},
}

@article {pmid40427319,
year = {2025},
author = {Xu, C and Guo, X and Li, L},
title = {Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/ani15101442},
pmid = {40427319},
issn = {2076-2615},
abstract = {In order to protect endangered species, many zoos adopt diverse rearing models to achieve optimal conservation outcomes. This study employed metagenomic approaches to assess differences in the fecal microbiome of captive and semi-free-ranging ring-tailed lemurs (Lemur catta). The results show that captivity significantly altered the microbial community structure. The inter-individual variability in the microbial community within the captive-bred (CB) group was lower than that in the semi-free-ranging (FR) group, yet these individuals harbored a higher abundance of potential pathogens (Treponema_D). In contrast, microbial genera associated with fiber degradation and short-chain fatty acid production in the FR group were significantly elevated (Faecalibacterium, Roseburia, and Megamonas) as compared to the CB group. Environmental variations between the two rearing systems led to distinct profiles in microbial functions and carbohydrate-active enzyme gene composition. Notably, the FR group of lemurs exhibited an increased abundance of enzyme genes associated with the degradation of complex polysaccharides (cellulose, hemicellulose, and pectin), suggesting that their diet, rich in natural plant fibers, enhances the capacity of their gut microbiota to extract essential energy and nutrients. Conversely, the CB group displayed a more homogeneous microbial community with a higher prevalence of potential pathogens, implying that a captive lifestyle may negatively impact gastrointestinal health. These findings offer valuable insights into the influence of rearing conditions on gut microbial ecology and its potential implications for the health management of ring-tailed lemurs.},
}

@article {pmid40426572,
year = {2025},
author = {Touati, A and Ibrahim, NA and Mairi, A and Kirat, H and Basher, NS and Idres, T},
title = {One Health at Risk: Plasmid-Mediated Spread of mcr-1 Across Clinical, Agricultural, and Environmental Ecosystems.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {5},
pages = {},
doi = {10.3390/antibiotics14050506},
pmid = {40426572},
issn = {2079-6382},
support = {IMSIU-DDRSP2501//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {The global dissemination of plasmid-mediated mcr genes, which confer resistance to the last-resort antibiotic colistin, represents a critical public health challenge driven by the interplay of clinical, agricultural, and environmental factors. This review examines the genetic and ecological dynamics of mcr-bearing plasmids, focusing on their role in disseminating colistin resistance across diverse bacterial hosts and ecosystems. Key plasmid families demonstrate distinct evolutionary strategies, including IncI2, IncHI2, and IncX4. IncI2 plasmids favor stability in livestock and clinical settings. IncHI2 plasmids, on the other hand, leverage transposons to co-select for multidrug resistance, while IncX4 plasmids achieve global dissemination through streamlined, conjugation-efficient architectures. The pervasive spread of mcr genes is exacerbated by their integration into chromosomes via mobile genetic elements and co-selection with resistance to other antibiotic classes, amplifying multidrug-resistant phenotypes. Environmental reservoirs, food chains, and anthropogenic practices further facilitate cross-niche transmission, underscoring the interconnectedness of resistance under the One Health framework. Addressing this crisis requires coordinated strategies, including reducing colistin misuse in agriculture, enhancing surveillance of high-risk plasmid types, and fostering international collaboration to preserve antimicrobial efficacy and mitigate the threat of untreatable infections.},
}

@article {pmid40423845,
year = {2025},
author = {Pérez-Gómez, O and Domínguez-Maqueda, M and García-Márquez, J and Moriñigo, MÁ and Tapia-Paniagua, ST},
title = {Metabolite-Driven Modulation of Biofilm Formation in Shewanella: Insights from Shewanella sp. Pdp11 Extracellular Products.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {55},
pmid = {40423845},
issn = {1432-184X},
support = {PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; PID2020-113637RB-C21//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Shewanella/metabolism/physiology/genetics ; *Biofilms/growth & development/drug effects ; Glycogen/metabolism ; },
abstract = {Biofilm formation is a survival strategy for bacteria, contributing to their persistence in natural and industrial environments. In this study, we investigated the ability of extracellular products (ECPs) produced by the probiotic strain Shewanella sp. Pdp11 under different culture conditions to inhibit biofilm formation in pathogenic and environmental Shewanella strains. ECPs from specific culture conditions altered biofilm formation in several Shewanella strains, with Shewanella hafniensis P14 displaying the highest sensitivity. Metabolomic analysis of the ECPs identified glycogen as a key metabolite associated with biofilm inhibition. Further genomic analysis of S. hafniensis P14 revealed an interruption in its glycogen synthesis pathway, suggesting a dependency on external glycogen-related metabolites for biofilm development. These findings demonstrate that Shewanella sp. Pdp11 ECPs can modify biofilm formation across multiple Shewanella strains, particularly in S. hafniensis P14 through glycogen-associated mechanisms.},
}

*Shewanella/metabolism/physiology/genetics
*Biofilms/growth & development/drug effects
Glycogen/metabolism

@article {pmid40423805,
year = {2025},
author = {Meehan, DE and O'Toole, PW},
title = {A Review of Diet and Foraged Pollen Interactions with the Honeybee Gut Microbiome.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {54},
pmid = {40423805},
issn = {1432-184X},
support = {GOIPG/2024/5035//Taighde Éireann/ ; 12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Pollen/metabolism ; *Diet ; },
abstract = {The honeybee Apis mellifera is a globally vital pollinator for flowering plants and crops, but it is currently facing mounting threats to survival due to habitat anthropization, emerging pathogens, and climate change. Over the past decade, increasing research efforts to understand and combat these challenges have led to an exploration of the honeybee gut microbiome-a relatively simple and highly conserved community of commensals which has a range of effects on the host. Researchers have now unravelled the main functional roles of this microbiome which include innate immune system stimulation, metabolism of dietary compounds, and mediation of host development and behaviour. Key amongst these is its role in aiding nutrition through the metabolism of complex carbohydrates and by degradation of otherwise indigestible pollen compounds. Increasingly, research is indicating that a diverse and high-quality pollen diet is key to maintaining healthy colonies and a stable microbiome. However, colonies can struggle to meet these dietary needs, particularly if they are located in anthropized ecosystems. Disruptions to honeybee diets or a reduction in the availability of diverse foraging options can significantly alter the composition of the microbiome, shifting it towards an abnormal state that leaves the honeybee more vulnerable to infection. Seasonal changes, primarily the overwintering period, also induce shifts in microbiome composition and are periods of time when a colony is particularly vulnerable to pathogenic infection. A comprehensive understanding of the effect these variables have on both microbiome composition and colony health is key to tackling the unprecedented environmental challenges that honeybees now face. This review summarises recent research which has elucidated the functional role of the gut microbiome in metabolism and how the composition of this bacterial community can alter due to seasonal change, anthropized landscapes, and dietary shifts. Finally, we also discuss recent studies investigating the effect that dietary supplementation has on the gut microbiome and the application of probiotic candidates for improving colony resilience and strength.},
}

Bees/microbiology/physiology
Animals
*Gastrointestinal Microbiome
*Pollen/metabolism
*Diet

@article {pmid40423261,
year = {2025},
author = {Rotsaert, C and Minnebo, Y and Duysburgh, C and Liu, LS and Mahalak, KK and Firman, J and Mattei, LM and Moustafa, AM and Bittinger, K and Hu, W and Marzorati, M and Michiels, J and Van de Wiele, T},
title = {Digestive parameters and gut microbiota load and composition along the in vivo piglet gastrointestinal tract.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf107},
pmid = {40423261},
issn = {1525-3163},
abstract = {The increased attention towards the role of the gut microbiome in health and disease for both animals and humans has fuelled the demand for more relevant and accurate research models. In this study, we present an overview of biochemical and microbial parameters measured throughout the digestive tract of ten TopigsNorsvin x German Piétrain piglets to better understand the in vivo dynamics of digestive and fermentative processes in different gastrointestinal segments, as pigs are suggested to be a representative animal model for the human gastrointestinal tract. Our key findings include region-specific and significantly differing (P < 0.001) pH profiles, with the stomach having the lowest pH (3.36 ± 0.72) and the ileum the highest (7.24 ± 0.18). Dry matter content also varied significantly (P < 0.001), with the stomach having the highest (27.8 ± 2.4%) and the duodenum the lowest (10.6 ± 0.7%). The average total transit time was 12 hours and 45 minutes ± 1 hour and 42 minutes. Enzyme activities (pepsin, trypsin, amylase) showed interindividual differences. Amino acid levels varied among piglets, with total concentrations averaging 7.04 x 102 ± 2.29 x 102 µg mL-1 in the duodenum, 1.19 x 103 ± 2.69 x 102 µg mL-1 in the jejunum and 9.39 x 102 ± 2.54 x 102 µg mL-1 in the ileum. Bile acid concentrations varied strongly between piglets, with high levels in the gall bladder and varying levels throughout the digestive tract. Short-chain fatty acid concentrations increased significantly (P < 0.001) along the digestive tract, with the highest levels in the large intestine. The microbial load increased consistently (P < 0.001) along the digestive tract, with the highest loads in the rectum (6.82 x 1010 ± 2.88 x 1010 cells mL-1). The highest microbial diversity was observed in the lower intestine (i.e. caecum, colon and rectum), with significant shifts in microbial community composition, especially from the ileum to the caecum. This study provides valuable insights into the digestive and microbiological parameters of the porcine gut, confirming the pig's relevance as a model for gastrointestinal research. The findings can inform the development of in vitro or ex vivo models, reducing ethical constraints of animal studies and aiding in the assessment of dietary interventions on gut health.},
}

@article {pmid40422247,
year = {2025},
author = {Wheeler, KM and Oh, MW and Fusco, J and Mershon, A and Kim, E and De Oliveira, A and Rahme, LG},
title = {MvfR Shapes Pseudomonas aeruginosa Interactions in Polymicrobial Contexts: Implications for Targeted Quorum-Sensing Inhibition.},
journal = {Cells},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/cells14100744},
pmid = {40422247},
issn = {2073-4409},
support = {5R01AI177555-02/GF/NIH HHS/United States ; N/A//Massachusetts General Hospital Research Scholar Award/ ; },
mesh = {*Quorum Sensing/genetics ; *Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism ; Humans ; *Bacterial Proteins/metabolism/genetics ; Biofilms/growth & development ; Virulence ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Pseudomonas Infections/microbiology ; },
abstract = {Infections often occur in complex niches consisting of multiple bacteria. Despite the increasing awareness, there is a fundamental gap in understanding which interactions govern microbial community composition. Pseudomonas aeruginosa is frequently isolated from monomicrobial and polymicrobial human infections. This pathogen forms polymicrobial infections with other ESKAPEE pathogens and defies eradication by conventional therapies. By analyzing the competition within co-cultures of P. aeruginosa and representative secondary pathogens that commonly co-infect patients, we demonstrate the antagonism of P. aeruginosa against other ESKAPEE pathogens and the contribution of this pathogen's multiple quorum-sensing (QS) systems in these interactions. QS is a highly conserved bacterial cell-to-cell communication mechanism that coordinates collective gene expressions at the population level, and it is also involved in P. aeruginosa virulence. Using a collection of P. aeruginosa QS mutants of the three major systems, LasR/LasI, MvfR/PqsABCDE, and RhlR/RhlI, and mutants of several QS-regulated functions, we reveal that MvfR and, to a lesser extent, LasR and RhlR, control competition between P. aeruginosa and other microbes, possibly through their positive impact on pyoverdine, pyochelin, and phenazine genes. We show that MvfR inhibition alters competitive interspecies interactions and preserves the coexistence of P. aeruginosa with the ESKAPEE pathogens tested while disarming the pathogens' ability to form biofilm and adhere to lung epithelial cells. Our results highlight the role of MvfR inhibition in modulating microbial competitive interactions across multiple species, while simultaneously attenuating virulence traits. These findings reveal the complexity and importance of QS in interspecies interactions and underscore the impact of the anti-virulence approach in microbial ecology and its importance for treating polymicrobial infections.},
}

*Quorum Sensing/genetics
*Pseudomonas aeruginosa/pathogenicity/physiology/genetics/metabolism
Humans
*Bacterial Proteins/metabolism/genetics
Biofilms/growth & development
Virulence
Gene Expression Regulation, Bacterial
Microbial Interactions
Pseudomonas Infections/microbiology

@article {pmid40421462,
year = {2025},
author = {Liu, RZ and Zhao, XY and Feng, B and Zhao, WS and Li, MY and Yu, XF and Hu, SP and Li, RP and Gao, JL and Borjigin, Q},
title = {Research on soil bacterial community assembly and function under different straw returning practices in arid and semi-arid agricultural ecosystems over multiple years.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1590686},
pmid = {40421462},
issn = {1664-302X},
abstract = {INTRODUCTION: Straw return has gained attention for its potential to improve soil quality and crop yields, particularly in semi-arid regions like the Tumu Chuan Plain Irrigation Area. Soil bacteria play a crucial role in regulating soil biological processes, and understanding how straw return affects bacterial populations can guide better agricultural management practices.

METHODS: We investigated the impact of continuous straw return on soil bacterial communities using 16S rRNA gene sequencing. Four treatments were applied: Farmers' shallow rotation (CK), straw incorporated with deep tillage (DPR), straw incorporated with subsoiling (SSR), and no-tillage mulching straw return (NTR). Bacterial community structure, metabolic pathways, and assembly mechanisms were analyzed using Bugbase and PICRUSt2 for phenotypic and metabolic pathway predictions.

RESULTS: The study found that straw return practices significantly altered the relative abundance and life history strategies of bacterial phyla, mainly influenced by soil organic matter (SOM) and enzyme activity. The K-strategist to r-strategist ratio was highest in CK (2.06) and lowest in SSR (1.89). DPR and NTR treatments significantly changed bacterial community structure compared to CK (p < 0.05), resembling SSR. Predictions showed that DPR and NTR enhanced carbohydrate and amino acid metabolism and promoted more stable bacterial networks, with homogenous selection and drift effects. Bacterial aggregation in all treatments was driven by random processes, with varying aggregation levels: CK (20%), DPR (38.6%), SSR (16.5%), and NTR (30.7%).

DISCUSSION: The study demonstrates that continuous straw return practices significantly impact soil bacterial communities. DPR and NTR notably improved microbial diversity, bacterial cooperation, and ecosystem stability. These findings provide valuable insights for sustainable agricultural practices in semi-arid regions, enhancing soil microbial ecology and soil health through strategic straw return.},
}

@article {pmid40419814,
year = {2025},
author = {Srivastava, AK and Riaz, A and Jiang, J and Li, X and Uzair, M and Mishra, P and Zeb, A and Zhang, J and Singh, RP and Luo, L and Chen, S and Yang, S and Zhao, Y and Xie, X},
title = {Advancing Climate-Resilient Sorghum: the Synergistic Role of Plant Biotechnology and Microbial Interactions.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {41},
pmid = {40419814},
issn = {1939-8425},
support = {[2022]091//Guizhou Provincial Youth Science and Technology Talents Growth Project/ ; },
abstract = {Climate-related problems such as drought stress, extreme temperature, erratic rainfall patterns, soil degradation, heatwaves, flooding, water logging, pests and diseases afflict the production and sustainability of sorghum. These challenges may be addressed by adopting climate-resilient practices and using advanced agronomic techniques. These challenges are being addressed through innovative applications of plant biotechnology and microbiology, which offer targeted solutions to enhance sorghum's resilience. For instance, biotechnological tools like CRISPR/Cas9 enable precise genetic modifications to improve drought and heat tolerance, while microbial inoculants, such as plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), enhance nutrient uptake and stress tolerance through symbiotic interactions. However, biotechnological tools lead to the development of sorghum varieties with heat, drought and salinity tolerance, while marker-assisted selection significantly accelerates breeding for stress-resilient traits. When genetic engineering is introduced, genes encoding heat shock proteins, Osmo protectants and antioxidant pathways are introduced to increase plant resistance to abiotic stress. These compounds stabilise cellular structures, protect enzymes, and maintain osmotic balance, enhancing the plant's ability to survive and function in adverse environmental conditions. At the same time, it is reported that microbiology offers beneficial microbes, nitrogen-fixing bacteria, phosphate-solubilizing microorganisms, and arbuscular mycorrhizal fungi that help enhance nutrient availability, soil health and water uptake. Combinations of endophytes and microbial inoculants enhance plant immunity to pests and diseases while increasing tolerance to stress. Biocontrol agents such as Bacillus and Trichoderma contain suppression of pathogens and need less dependence on the use of chemical pesticides. On top of that, genetic modification increases the nutritional quality of sorghum biofortified. This is where biotechnology and microbiology work together to deliver sustainable farming systems reducing environmental impacts, boosting yields and securing food supply under environmental stresses. This review aims to examine the synergistic integration of plant biotechnology and microbial interactions as a strategy to enhance sorghum's resilience to climate-induced stresses, including drought, elevated temperatures, and nutrient-deficient soils. It highlights recent advancements in biotechnological tools such as gene editing, marker-assisted selection, and tissue culture, alongside the emerging role of plant-beneficial microbes in promoting stress tolerance and improving soil health. By synthesizing current knowledge across these disciplines, this review seeks to outline a framework for future research that harnesses the intersection of biotechnology and microbial ecology to support the sustainable improvement of sorghum resilience.},
}

@article {pmid40419768,
year = {2025},
author = {Keegstra, JM and Landry, ZC and Zweifel, ST and Roller, BRK and Baumgartner, DA and Carrara, F and Martínez-Pérez, C and Clerc, EE and Ackermann, M and Stocker, R},
title = {Risk-reward trade-off during carbon starvation generates dichotomy in motility endurance among marine bacteria.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40419768},
issn = {2058-5276},
support = {542395FY22//Simons Foundation/ ; 542379FY22//Simons Foundation/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 205321 207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40 225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Copiotrophic marine bacteria contribute to the control of carbon storage in the ocean by remineralizing organic matter. Motility presents copiotrophs with a risk-reward trade-off: it is highly beneficial in seeking out sparse nutrient hotspots, but energetically costly. Here we studied the motility endurance of 26 marine isolates, representing 18 species, using video microscopy and cell tracking over 2 days of carbon starvation. We found that the trade-off results in a dichotomy among marine bacteria, in which risk-averse copiotrophs ceased motility within hours ('limostatic'), whereas risk-prone copiotrophs converted ~9% of their biomass per day into energy to retain motility for the 2 days of observation ('limokinetic'). Using machine learning classifiers, we identified a genomic component associated with both strategies, sufficiently robust to predict the response of additional species with 86% accuracy. This dichotomy can help predict the prevalence of foraging strategies in marine microbes and inform models of ocean carbon cycles.},
}

@article {pmid40417422,
year = {2025},
author = {Roothans, N and Pabst, M and van Diemen, M and Herrera Mexicano, C and Zandvoort, M and Abeel, T and van Loosdrecht, MCM and Laureni, M},
title = {Long-term multi-meta-omics resolves the ecophysiological controls of seasonal N2O emissions during wastewater treatment.},
journal = {Nature water},
volume = {3},
number = {5},
pages = {590-604},
pmid = {40417422},
issn = {2731-6084},
abstract = {Nitrous oxide (N2O) is the third most important greenhouse gas and originates primarily from natural and engineered microbiomes. Effective emission mitigations are currently hindered by the largely unresolved ecophysiological controls of coexisting N2O-converting metabolisms in complex communities. To address this, we used biological wastewater treatment as a model ecosystem and combined long-term metagenome-resolved metaproteomics with ex situ kinetic and full-scale operational characterization over nearly 2 years. By leveraging the evidence independently obtained at multiple ecophysiological levels, from individual genetic potential to actual metabolism and emergent community phenotype, the cascade of environmental and operational triggers driving seasonal N2O emissions has ultimately been resolved. We identified nitrifier denitrification as the dominant N2O-producing pathway and dissolved O2 as the prime operational parameter, paving the way to the design and fostering of robust emission control strategies. This work exemplifies the untapped potential of multi-meta-omics in the mechanistic understanding and ecological engineering of microbiomes towards reducing anthropogenic impacts and advancing sustainable biotechnological developments.},
}

@article {pmid40413948,
year = {2025},
author = {Pholtaisong, J and Kongsinkaew, C and On-Mee, T and Chittapun, S and Pornpukdeewattana, S and Todhanakasem, T and Kunyanee, K and Panya, A and Phonsatta, N and Yingcharoen, P and Charoenrat, T},
title = {Natural versus Saccharomyces boulardii self-induced anaerobic coffee fermentation: Effects on physicochemical properties and microbial ecology, and their influence on volatile profiles and sensory attributes across roast levels.},
journal = {Food chemistry},
volume = {488},
number = {},
pages = {144871},
doi = {10.1016/j.foodchem.2025.144871},
pmid = {40413948},
issn = {1873-7072},
abstract = {This study investigates the effects of natural self-induced anaerobic fermentation (NSIAF) and Saccharomyces boulardii self-induced anaerobic fermentation (SSIAF) on Arabica coffee during wet processing. Over 24 h of fermentation, NSIAF exhibited greater microbial diversity, higher titratable acidity, and increased reducing sugar consumption, while SSIAF provided a more controlled microbial environment dominated by S. boulardii. Volatile compound analysis identified 207 compounds, with lighter roasts showing the greatest number of significantly different compounds between NSIAF and SSIAF treatments. Sensory evaluation revealed a higher cupping score for NSIAF at a light roast (82.08 ± 0.14) compared to SSIAF (81.58 ± 0.14), reflecting distinct flavor characteristics imparted by each fermentation process. Both methods achieved specialty coffee standards (≥80 points), highlighting the potential of NSIAF for complex and diverse profiles and the suitability of SSIAF for consistency and controlled fermentation.},
}

@article {pmid40413198,
year = {2025},
author = {Brandão Gontijo, J and Huang, L and Levintal, E and Prieto García, C and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL},
title = {Depth-dependent Metagenome-Assembled Genomes of Agricultural Soils under Managed Aquifer Recharge.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {858},
pmid = {40413198},
issn = {2052-4463},
support = {7975//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 2021-38420-34070//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
mesh = {*Soil Microbiology ; *Groundwater ; Agriculture ; *Metagenome ; Microbiota ; Bacteria/genetics/classification ; Metagenomics ; California ; Archaea/genetics ; Soil ; },
abstract = {Managed Aquifer Recharge (MAR) systems, which intentionally replenish groundwater aquifers with excess water, are critical for addressing water scarcity exacerbated by demographic shifts and climate variability. To date, little is known about the functional diversity of the soil microbiome at different soil depth inhabiting agricultural soils used for MAR. Knowing the functional diversity is pivotal in regulating nutrient cycling and maintaining soil health. Metagenomics, particularly Metagenome-Assembled Genomes (MAGs), provide a powerful tool to explore the diversity of uncultivated soil microbes, facilitating in-depth investigations into microbial functions. In a field experiment conducted in a California vineyard, we sequenced soil DNA before and after water application of MAR. Through this process, we assembled 146 medium and 14 high-quality MAGs, uncovering a wide array of archaeal and bacterial taxa across different soil depths. These findings advance our understanding of the microbial ecology and functional diversity of soils used for MAR, contributing to the development of more informed and sustainable land management strategies.},
}

*Soil Microbiology
*Groundwater
Agriculture
*Metagenome
Microbiota
Bacteria/genetics/classification
Metagenomics
California
Archaea/genetics
Soil

@article {pmid40412969,
year = {2025},
author = {Yan, W and Gu, L and Yue, X and Zhong, H and Wang, D},
title = {Vertical distribution of intracellular protoporphyrin IX in coastal sediment cores: Implications for sedimentology and microbial community composition.},
journal = {Journal of environmental sciences (China)},
volume = {156},
number = {},
pages = {712-724},
doi = {10.1016/j.jes.2024.11.014},
pmid = {40412969},
issn = {1001-0742},
mesh = {*Geologic Sediments/chemistry/microbiology ; *Protoporphyrins/analysis ; *Microbiota ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; },
abstract = {Protoporphyrin IX (PPIX), a basic porphyrin system found in nature, all "porphyrin-type" tetrapyrroles with a biological function are biosynthetically derived thereof. PPIX is a metalloprosthetic group of numerous proteins involved in diverse metabolic and respiratory processes across all domains of life, and is thus considered essential for respiring organisms. Determining the biotic and abiotic factors that influence marine microbial growth and community structure is critical for understanding global biogeochemical cycles. Here, we present vertical profiles of intracellular PPIX and four derivative products (Chlorophyll-a/b and Pheophytin-a/b) from two coastal sediment cores, alongside ancillary geochemical and 16S rRNA microbial community data. Our findings indicated that PPIX is present in the natural sediment environment and displays a decreasing trend with depth, revealing a significant positive correlation with both organic matter and microbial abundance. Co-occurrence networks revealed that the environmental distribution of PPIX was positively correlated with the microbial porphyrin producer (high genetic completeness), but negatively correlated with auxotrophs (absence or low genetic completeness). It emphasized the critical role of PPIX as a biological molecule involved in key physiological processes. These results suggest that PPIX is a prominent component of the shared extracellular metabolite pool, especially in anoxic marine sediments where it exists at physiologically relevant concentrations for microbial metabolism. This study highlighted the significance of PPIX in microbial ecology and its potential impact on biogeochemical cycles in marine sedimentary environments.},
}

*Geologic Sediments/chemistry/microbiology
*Protoporphyrins/analysis
*Microbiota
RNA, Ribosomal, 16S
*Environmental Monitoring

@article {pmid40412391,
year = {2025},
author = {Breyer, E and Stix, C and Kilker, S and Roller, BRK and Panagou, F and Doebke, C and Amano, C and Saavedra, DEM and Coll-García, G and Steger-Mähnert, B and Dachs, J and Berrojalbiz, N and Vila-Costa, M and Sobrino, C and Fuentes-Lema, A and Berthiller, F and Polz, MF and Baltar, F},
title = {The contribution of pelagic fungi to ocean biomass.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.004},
pmid = {40412391},
issn = {1097-4172},
abstract = {Metagenomic analysis has recently unveiled the widespread presence of pelagic fungi in the global ocean, yet their quantitative contribution to carbon stocks remains elusive, hindering their incorporation into biogeochemical models. Here, we revealed the biomass of pelagic fungi in the open-ocean water column by combining ergosterol extraction, Calcofluor-White staining, catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and microfluidic mass sensor techniques. We compared fungal biomass with the biomass of other more studied microbial groups in the ocean such as archaea and bacteria. Globally, fungi contributed 0.32 Gt C (CI: 0.19-0.46), refining previous uncertainty estimates from two orders of magnitude to less than one. While fungal biomass was lower than that of bacteria, it exceeded that of the archaea (archaea:fungi:bacteria biomass ratio of 1:9:44). Collectively, our findings reveal the important contribution of fungi to open-ocean biomass and, consequently, the marine carbon cycle, emphasizing the need for their inclusion in biogeochemical models.},
}

@article {pmid40411587,
year = {2025},
author = {Kelleher, LA and Anderson, Z and Stratford, JA and Fortunato, CS},
title = {Deciphering Soil Microbial Dynamics in Northeastern American Grasslands with Goldenrods (Solidago sp.).},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {53},
pmid = {40411587},
issn = {1432-184X},
mesh = {*Soil Microbiology ; *Grassland ; Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Pennsylvania ; *Solidago/microbiology ; Plant Roots/microbiology ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {Grasslands are important centers of biodiversity; however, these ecosystems have been in decline. Although many methods for grassland restoration have been developed, the abundant microbial communities in these regions are understudied and could be used to assist in these efforts. In this study, we aimed to understand how microbial communities varied by soil type, grassland site, and environmental conditions. Samples were taken from rhizosphere soil (attached to plant roots), proximal soil (close to the plant roots), and from bulk cores at Ricketts Glen State Park and Nescopeck State Park in northeastern Pennsylvania, USA, during June and August of 2021 and 2022. Rhizosphere soil samples were taken from the native common grassland plant, Solidago rugosa. 16S rRNA gene sequencing revealed that pH as well as soil type (bulk, proximal, or rhizosphere) significantly influenced the microbial community composition of each soil. Each soil type had its own distinct microbial communities, and proximal soil was identified as a transition zone between rhizosphere and bulk microbial communities. We also observed that the rhizosphere communities were dependent upon geography, as these communities were significantly different between grasslands even though the plant species remained the same. Our results highlight the complex nature of soil microbial communities and how many factors, including pH, soil type, and geography, can be overlayed to impact soil microbes. Results suggest future avenues of conservation research through modification and regulation of specific soil microbial communities in order to aid in the rehabilitation of these diminished regions.},
}

*Soil Microbiology
*Grassland
Rhizosphere
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
RNA, Ribosomal, 16S/genetics
*Microbiota
Pennsylvania
*Solidago/microbiology
Plant Roots/microbiology
Biodiversity
Hydrogen-Ion Concentration

@article {pmid40410028,
year = {2025},
author = {Vareschi, S and Jaut, V and Vijay, S and Allen, RJ and Schreiber, F},
title = {Antimicrobial efflux and biofilms: an interplay leading to emergent resistance evolution.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.012},
pmid = {40410028},
issn = {1878-4380},
abstract = {The biofilm mode of growth and drug efflux are both important factors that impede the treatment of bacterial infections with antimicrobials. Decades of work have uncovered the mechanisms involved in both efflux and biofilm-mediated antimicrobial tolerance, but links between these phenomena have only recently been discovered. Novel findings show how efflux impacts global cellular physiology and antibiotic tolerance, underpinned by phenotypic heterogeneity. In addition efflux can mediate cell-to-cell interactions, relevant in biofilms, via mechanisms including efflux of signaling molecules and metabolites, signaling using pump components and the establishment of local antibiotic gradients via pumping. These recent findings suggest that biofilm antibiotic tolerance and efflux are closely coupled, with synergistic effects leading to the evolution of antimicrobial resistance in the biofilm environment.},
}

@article {pmid40408931,
year = {2025},
author = {Conall Holohan, B and Trego, A and Keating, C and Bressani-Ribeiro, T and Chernicharo, CL and Daigger, G and Galdi, SM and Knörle, U and Paissoni, E and Robles, A and Rogalla, F and Shin, C and Soares, A and Smith, AL and Szczuka, A and Hughes, D and O'Flaherty, V},
title = {Anaerobic microbial core for municipal wastewater treatment - the sustainable platform for resource recovery.},
journal = {Current opinion in biotechnology},
volume = {94},
number = {},
pages = {103317},
doi = {10.1016/j.copbio.2025.103317},
pmid = {40408931},
issn = {1879-0429},
abstract = {The requirement for carbon neutrality and bioresource recovery has shifted our views on water treatment from health and pollution avoidance to one of sustainability with water and nutrient circularity. Despite progress, the current process of wastewater treatment is linear, based on core aerobic microbiology, which is unlikely to be carbon neutral due to its large use of energy and production of waste sludge. Here, we outline a shift from aerobic to anaerobic microbiology at the core of wastewater treatment and resource recovery, illustrating the state-of-the-art technologies available for this paradigm shift. Anaerobic metabolism primarily offers the benefit of minimal energy input (up to 50% reduction) and minimal biomass production, resulting in up to 95% less waste sludge compared with aerobic treatment, which is increasingly attractive, given dialogue surrounding emerging contaminants in biosolids. Recent innovative research solutions have made ambient (mainstream) anaerobic treatment a ready substitute for the aerobic processes for municipal wastewater in temperate regions. Moreover, utilising anaerobic treatment as the core carbon removal step allows for more biological downstream resource recovery with several opportunities to couple the process with (anaerobic) nitrogen and phosphorus recovery, namely, potential mainstream anaerobic ammonium oxidation (anammox) and methane oxidation (N-DAMO). Furthermore, these technologies can be mixed and matched with membranes and ion-exchange systems, high-value biochemical production, and/or water reuse installations. As such, we propose the reconfiguration of the wastewater treatment plant of the futurewith anaerobic microbiology. Mainstream anaerobic treatment at the core of a truly sustainable platform for modern municipal wastewater treatment, facilitating circular economy and net-zero carbon goals.},
}

@article {pmid40408805,
year = {2025},
author = {Bi, W and Butardo, V and Sha, G and Zhang, H and Wu, X and Wang, L},
title = {Microbial degradation and pollutant control in aerobic composting and anaerobic digestion of organic wastes: A review.},
journal = {Waste management (New York, N.Y.)},
volume = {204},
number = {},
pages = {114894},
doi = {10.1016/j.wasman.2025.114894},
pmid = {40408805},
issn = {1879-2456},
abstract = {Aerobic composting (AC) and anaerobic digestion (AD) are promising technologies for organic waste treatment, but their efficiency and safety are influenced by complex waste composition and persistent contaminants. This review identifies the advances in understanding microbial community dynamics, enzymatic degradation pathways, and the fate of contaminants during AC and AD processes. The findings indicate that substrate composition shapes dominant microbial populations and their degradative enzymes, with this correlation potentially useful for predicting functional microbial communities. Additionally, AC shows advantages in antibiotic elimination while AD excels in heavy metal immobilization, with both contributing to removing certain antibiotic resistance genes (ARGs). The strategic manipulation of environmental conditions, particularly temperature and oxygen levels, can drive microbial succession to optimize organic matter decomposition while minimizing ARG proliferation. Economic analyses reveal that AC offers lower operational costs and AD generates valuable by-products with potential energy recovery from organic waste. Case studies indicate that integrating both technologies can overcome individual limitations and enhance degradation efficiency compared to conventional single-technology approaches. This work proposes a comprehensive framework for developing coupled AC-AD systems to achieve more efficient and safer organic waste valorization than conventional single-technology approaches. This review has important implications for advancing sustainable waste management practices and mitigating the spread of antibiotic resistance in the environment.},
}

@article {pmid40408146,
year = {2025},
author = {Fontanarrosa, P and Clare, C and Fedorec, AJH and Barnes, CP},
title = {MIMIC: A Python Package for Simulating, Inferring, and Predicting Microbial Community Interactions and Dynamics.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf174},
pmid = {40408146},
issn = {1367-4811},
abstract = {SUMMARY: The study of microbial communities is vital for understanding their impact on environmental, health, and technological domains. The Modelling and Inference of MICrobiomes Project (MIMIC) introduces a Python package designed to advance the simulation, inference, and prediction of microbial community interactions and dynamics. Addressing the complex nature of microbial ecosystems, MIMIC integrates a suite of mathematical models, including previously used approaches such as Generalized Lotka-Volterra (gLV), Gaussian Processes (GP), and Vector Autoregression (VAR) plus newly developed models for integrating multi-omic data, to offer a versatile framework for analysing microbial dynamics. By leveraging Bayesian inference and machine learning techniques, MIMIC provides the ability to infer the dynamics of microbial communities from empirical data, facilitating a deeper understanding of their complex biological processes, unveiling possible unknown ecological interactions, and enabling the design of microbial communities. Such insights could help to advance microbial ecology research, optimizing biotechnological applications, and contribute to environmental sustainability and public health strategies. MIMIC is designed for flexibility and ease of use, aiming to support researchers and practitioners in microbial ecology and microbiome research.

MIMIC is freely available under the MIT License at https://github.com/ucl-cssb/MIMIC. It is implemented in Python (version 3.7 or higher) and is compatible with Windows, macOS, and Linux operating systems. MIMIC depends on standard Python libraries including NumPy, SciPy, and PyMC. Comprehensive examples and tutorials (including the main text demonstrations) are provided as Jupyter notebooks in the examples/directory and at the MIMIC Docs website, along with detailed installation instructions and real-world data use cases. The software will remain freely available for at least two years following publication. A code snapshot for this publication is also available at Zenodo: https://doi.org/10.5281/zenodo.15149003.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40407874,
year = {2025},
author = {Velthuis, M and Zoccarato, L and Veraart, AJ and Monaghan, MT and Funke, E and Verdonschot, P and Grossart, HP and Hilt, S},
title = {Light-Driven Changes in Macrophyte Tissue Quality Affect the Composition of Associated Microbial Communities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {52},
pmid = {40407874},
issn = {1432-184X},
support = {Veni.202.053//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Biofilms/growth & development/radiation effects ; *Fungi/classification/genetics/radiation effects/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota/radiation effects ; *Light ; *Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism ; Nitrogen/metabolism/analysis ; Carbon/metabolism/analysis ; Phosphorus/metabolism/analysis ; Biodiversity ; Plant Leaves/microbiology ; Phenols/analysis/metabolism ; },
abstract = {Microbial biofilms are important components in macrophyte decomposition, and their composition depends on the decomposition stage and host plant quality. Here, we investigated how macrophyte tissue quality (i.e., C:N:P stoichiometry and phenolic contents) influences epiphytic microbial biofilms during litter decomposition. Consecutive experiments were conducted to (1) modify the C:N:P stoichiometry and phenolic content of the freshwater macrophyte Elodea nuttallii by manipulating light and nutrient availability and (2) test how the modified tissue quality affected epiphytic microbial biofilm diversity and community composition before and during macrophyte decomposition. Our results showed that shading led to lower C:N ratios (28.6 to 12.6) and higher phenolic content (10.8 to 19.2 µg/mg dry weight). Simultaneously, shading affected the epiphytic bacterial and fungal community composition, and these shifts correlated with the macrophyte C:N ratio. While no effects of macrophyte tissue quality on decomposition rates were observed, the epiphytic bacterial community composition on the litter was significantly affected by light treatment, time, and their interaction. Bacterial community composition shifted from a high abundance of Comamonadaceae to a more diverse community over time. Overall bacterial diversity was lower on the litter grown in the shaded mesocosms. Fungal diversity and community composition during litter decomposition were not affected by litter quality. Overall, our results reveal a structuring role of macrophyte tissue quality on its associated microbial biofilm and uniquely show a continuation of light-driven changes in epiphytic bacterial community composition after exposure. We conclude that light-driven changes in C:N stoichiometry are a crucial factor in shaping epiphytic microbial communities during macrophyte decomposition.},
}

Biofilms/growth & development/radiation effects
*Fungi/classification/genetics/radiation effects/isolation & purification
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota/radiation effects
*Light
*Hydrocharitaceae/microbiology/radiation effects/chemistry/metabolism
Nitrogen/metabolism/analysis
Carbon/metabolism/analysis
Phosphorus/metabolism/analysis
Biodiversity
Plant Leaves/microbiology
Phenols/analysis/metabolism

@article {pmid40407873,
year = {2025},
author = {Van Heurck, B and Cardenas, DV and Hylén, A and Jankowska, E and Cole, DB and Montserrat, F and Kreuzburg, M and Romaniello, SJ and Meysman, FJR},
title = {Microbial Community Structure in Contrasting Hawaiian Coastal Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {51},
pmid = {40407873},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology/chemistry ; Hawaii ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Seawater/microbiology/chemistry ; Bays/microbiology/chemistry ; Biodiversity ; },
abstract = {Microbe-mineral interactions play a fundamental role in marine sediments and global biogeochemical cycles. Here, we investigated the sediment microbial communities in two contrasting field sites on Big Island, Hawaii (USA), that differ in their bay morphology and sediment grain size distributions: Papakōlea Beach (exposed, finer sediment) and Richardson Ocean Park (sheltered, coarser sediment). We selected three stations within each bay and characterized the mineral and chemical composition of the sediment and porewater, and used 16S rRNA amplicon sequencing of the V4V5 hypervariable region to investigate the naturally occurring microbial communities. Microbial community structure differed significantly between the two bays, rather than within each bay, whereby microbial diversity was markedly lower at Papakōlea compared to Richardson. We correlated environmental variables to microbial community structure in order to identify the key drivers of community differences between and within the two bays. Our study suggests that differing physico-chemical properties of the sediment and porewater, resulting from the contrasting bay morphologies and geophysical drivers, are the main factors influencing microbial community structure in these two bays. Papakōlea Beach is a naturally occurring "green sand" beach, due to its high olivine content. This site was selected in the broader context of a field campaign investigating olivine as a source mineral for ocean alkalinity enhancement (OAE), a carbon dioxide removal technology. Our results highlight the complexity of marine sediment environments, with implications for the monitoring, reporting and verification of future field trials involving olivine addition for ocean alkalinity enhancement.},
}

*Geologic Sediments/microbiology/chemistry
Hawaii
*Microbiota
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Seawater/microbiology/chemistry
Bays/microbiology/chemistry
Biodiversity

@article {pmid40406230,
year = {2025},
author = {Li, M and Meng, Z and Li, J and Zhang, X and Wang, Y and Li, X and Yang, Y and Li, Y and Yang, X and Chen, X and Fan, Y},
title = {Stochastic processes dominate the community assembly of ectomycorrhizal fungi associated with Betula platyphylla in Inner Mongolia, China.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19364},
pmid = {40406230},
issn = {2167-8359},
mesh = {*Mycorrhizae/genetics/classification/isolation & purification ; China ; *Soil Microbiology ; *Betula/microbiology ; Stochastic Processes ; Biodiversity ; Rhizosphere ; DNA, Fungal/genetics ; Mycobiome ; },
abstract = {The maintenance and driving mechanisms of microbial community structure have become important research focuses in microbial ecology. Therefore, clarifying the assembly of ectomycorrhizal (EM) fungal communities can provide a relevant basis for studying forest diversity, ecological diversity, and ecological evolution. Betula platyphylla is a typical EM dependent tree species with characteristics such as renewal ability and strong competitive adaptability, and it plays a crucial ecological function in Inner Mongolia. However, the research on EM fungi's diversity and community assembly is very limited. We investigated EM fungal communities associated with B. platyphylla from 15 rhizosphere soil samples across five sites in Inner Mongolia. The fungal rDNA ITS2 region was sequenced using Illumina Miseq sequencing. A total of 295 EM fungal OTUs belonging to two phyla, three classes, nine orders, 20 families, and 31 genera were identified, of which Russula, Cortinarius, and Sebacina were the most dominant taxa. Significant differences existed in the composition of dominant genera of EM fungi across the five sites, and the relative abundances of dominant genera also showed significant differences among the sites. The β NTI and NCM fitting analyses suggest that stochastic processes mainly determine the EM fungal community assembly. Our study indicates that B. platyphylla harbors a high EM fungal diversity and highlights the important role of the stochastic process in driving community assembly of mutualistic fungi associated with B. platyphylla in north China.},
}

*Mycorrhizae/genetics/classification/isolation & purification
China
*Soil Microbiology
*Betula/microbiology
Stochastic Processes
Biodiversity
Rhizosphere
DNA, Fungal/genetics
Mycobiome

@article {pmid40405772,
year = {2025},
author = {Onghena, L and Heldens, A and De Paepe, K and Antwi, M and Van Vlierberghe, H and Raevens, S and Verhelst, X and Hoorens, A and Devisscher, L and van Nieuwenhove, Y and Van de Wiele, T and Geerts, A and Lefere, S},
title = {The double-edged sword of metabolic and bariatric surgery: extending the biliary limb can trigger bacterial translocation, sepsis, and liver inflammation - an experimental study.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000002502},
pmid = {40405772},
issn = {1743-9159},
abstract = {BACKGROUND: Metabolic and bariatric surgery (MBS) procedures with extended biliary limb length are gaining popularity to expedite weight loss but can induce liver failure. We aimed to investigate the underlying pathophysiology for this potentially fatal complication.

MATERIALS AND METHODS: We compared mouse models of vertical sleeve plication, sleeve gastrectomy, Roux-en-Y gastric bypass (RYGB), and one-anastomosis gastric bypass with three biliary limb lengths (25% = Ω1, 50% = Ω2, 75% = Ω3) by analyzing mortality, weight loss, metabolic and liver health, bacterial translocation, inflammation, and biliary and fecal microbiome. Gut decontamination with oral antibiotics (amoxicillin, vancomycin, neomycin, and metronidazole) was performed in a subset of Ω3 mice. Liver histology from mice with different biliary limb lengths was compared to samples from human patients who developed liver failure following biliopancreatic diversion or RYGB.

RESULTS: RYGB and Ω1&2 significantly improved glucose intolerance and liver steatosis compared to sham surgery. However, extending the biliary limb (Ω3) resulted in 100% mortality. The Ω3 procedure induced bacterial translocation of enterococcus genus to the spleen and biliary fluid, consistent with increased serum lipopolysaccharide levels and terminal ileum, biliary limb, and hepatic inflammation. Liver histology in Ω3 mice was characterized by mediovesicular steatosis, closely resembling the histological picture observed in patients with liver failure after MBS. Oral gut decontamination significantly improved Ω3 one-week-survival from 31.3% to 80.0%, prevented bacterial overgrowth in biliary fluid and spleen, and decreased liver damage.

CONCLUSION: Mortality in longer biliary limb MBS surgery is caused by bacterial overgrowth, translocation, and gut-liver axis inflammation, which were reversed by oral gut decontamination with antibiotics.},
}

@article {pmid40405300,
year = {2025},
author = {He, T and Moukarzel, R and Fu, M and Yang, M and Du, R and Zhao, J and Liu, J and Wu, J and Deng, W and Zhu, Y and Yang, M and Zhu, S and Du, F},
title = {Rain-shelter cultivation promotes grapevine health by altering phyllosphere microecology in rainy areas.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {56},
pmid = {40405300},
issn = {2524-6372},
support = {32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 32360712//National Natural Science Foundation of China/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 202101BD070001-125//Yunnan Province Agricultural Joint Special Project/ ; 2018HA009//Yunnan Provincial Academician Exploration Funding Project/ ; },
abstract = {Grapes are a globally significant fruit crop, but their cultivation is often challenged by leaf diseases, which limit industrial productivity. Rain-shelter cultivation has emerged as a sustainable agricultural strategy to mitigate these challenges. This study examines the effects of rain-shelter cultivation, compared to open-air cultivation, on the microclimate within the grape canopy and the microbial ecology of the grape phyllosphere. The research focused on two cultivation methods: rain-shelter and open-air cultivation. Key environmental factors such as temperature, relative humidity, and light intensity within the grape canopy were measured during the growing season. The study also explored how these conditions influence the biodiversity, stability, and functional roles of phyllosphere microbiota, particularly focusing on the community assembly processes of bacteria and oomycetes, and the efficacy of culturable microorganisms in combating grape leaf diseases. The results showed that rain-shelter cultivation signifcantly reduced leaf humidity, increased canopy temperature, and decreased light intensity, regardless of weather conditions. This approach led to a significant decrease in the incidence of grape downy mildew without affecting the overall Shannon diversity index of phyllosphere microbes. At the Class level, there was a reduction in Cystobasidiomycetes, Bacteroidia, Brocadiae, and Phycisphaerae, while Oligoflexia levels are significantly increased under rain-shelter conditions. Genus-level analysis revealed significant reductions in plant pathogens such as Erysiphe, Alternaria, and Cercospora. The study found that rain-shelter cultivation shifts fungal community assembly from stochastic to deterministic processes, while bacterial networks showed increased stability. Additionally, the beneficial microorganism Pseudomonas aeruginosa exhibited a preventive effect against grape leaf diseases, enhancing grape berry quality by increasing puncture resistance and leaf internode length. These findings provide understanding of the complex relationship between grape canopy microclimate, disease management, and microbial dynamics suggesting rain-shelter cultivation as a viable strategy for sustainable grape production, it offers insights into the research and development of future biological control agents.},
}

@article {pmid40404904,
year = {2025},
author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Pondering Ponds: Exploring Correlations Between Cloacal Microbiota and Blood Metabolome in Freshwater Turtles.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {50},
pmid = {40404904},
issn = {1432-184X},
mesh = {Animals ; *Turtles/microbiology/blood ; *Metabolome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; *Cloaca/microbiology ; *Ponds/microbiology ; *Microbiota ; Gastrointestinal Microbiome ; Fresh Water ; },
abstract = {The gut microbiota of vertebrates significantly influences host physiology, yet little is known about how habitat factors shape microbiotas in non-human species, especially freshwater turtles. This study explores the relationship between cloacal microbiota and serum metabolome in eastern longneck turtles (Chelodina longicollis), marking the first such investigation in chelonians. By comparing microbiotas from two distinct pond environments, we applied a multi-omics approach combining 16S rRNA sequencing and metabolomic profiling. Results showed that location influenced microbial composition and metabolic profiles, with dominant bacterial phyla Pseudomonadota, Actinomycetota, and Bacillota, and distinct families linked to differences in microbial diversity. Notably, turtles from one pond displayed an unusually high proportion of Actinomycetota. We also found a clear connection between microbiota diversity and metabolome, suggesting certain bacterial combinations impact host physiology. These findings offer important insights into the complex interaction between microbial communities and metabolism in freshwater turtles, a highly threatened group. This research emphasises the value of integrating microbiota and metabolomic data in conservation strategies and highlights the need for further longitudinal studies to explore the dynamic host-microbiota relationship in these understudied species.},
}

Animals
*Turtles/microbiology/blood
*Metabolome
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
*Cloaca/microbiology
*Ponds/microbiology
*Microbiota
Gastrointestinal Microbiome
Fresh Water

@article {pmid40402470,
year = {2025},
author = {Moukarzel, R and Waller, LP and Jones, EE and Ridgway, HJ},
title = {Arbuscular mycorrhizal fungal symbiosis in New Zealand ecosystems: challenges and opportunities.},
journal = {Letters in applied microbiology},
volume = {78},
number = {5},
pages = {},
doi = {10.1093/lambio/ovaf070},
pmid = {40402470},
issn = {1472-765X},
mesh = {*Mycorrhizae/physiology/genetics/classification ; New Zealand ; *Symbiosis ; *Ecosystem ; *Plants/microbiology ; Soil Microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are obligate biotrophs that form a symbiotic and mutualistic relationship with most terrestrial plants, playing an important role in plant growth, nutrient acquisition, and ecosystem stability. This review synthesizes current knowledge on AMF colonization in plants within New Zealand ecosystems, including the challenges and opportunities of molecular identification techniques used in characterizing AMF communities in natural and managed systems. The ecosystem services provided by AMF, such as improved growth parameters, enhanced nutrition, and disease control, are discussed in detail, highlighting their significance in sustainable agriculture and natural ecosystems. Additionally, the role of AMF in invasion ecology was examined, revealing their dual potential to either facilitate or hinder invasive plant species. Despite significant advances in understanding AMF biology, future research is needed to explore the underlying mechanisms of AMF-plant interactions and to address the challenges caused by changing environmental conditions. This review focused on the importance of AMF in promoting ecosystem resilience and suggests avenues for future research to harness their full potential in agricultural and ecological contexts.},
}

*Mycorrhizae/physiology/genetics/classification
New Zealand
*Symbiosis
*Ecosystem
*Plants/microbiology
Soil Microbiology

@article {pmid40402324,
year = {2025},
author = {Mizeriene, G and Lygis, V and Prospero, S},
title = {Oomycete Diversity and Ecology in Declining Alder Stands in Switzerland.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {49},
pmid = {40402324},
issn = {1432-184X},
support = {Project Code 14.035//Sciex-NMSch Fellowship/ ; },
mesh = {Switzerland ; *Alnus/microbiology/parasitology ; *Oomycetes/classification/isolation & purification/genetics ; *Biodiversity ; *Soil Microbiology ; Plant Diseases/microbiology ; Rhizosphere ; Phytophthora/isolation & purification/classification/genetics ; Phylogeny ; Pythium/isolation & purification/genetics/classification ; },
abstract = {In this study, we assessed the occurrence and diversity of four oomycete genera (Phytophthora, Phytopythium, Pythium, and Globisporangium) in 13 declining alder (Alnus glutinosa and A. incana) stands in Switzerland. For this, we sampled and analyzed soil from tree rhizosphere, water from streams and rivers along which the stands were located, and symptomatic alder bark. The overall isolation rate was 47.2%, with a total of 400 oomycete isolates recovered at all 13 sites. The highest incidence of oomycete isolates was in soil samples (baiting, 82.5% isolation rate), followed by water (baiting, 14.7%), and bark (direct isolation, 2.7%). Of all recovered oomycete isolates, 90.3% could be successfully assigned to a known species, for a total of 23 species identified, including both preferential saprotrophs and pathogens. Among all genera, Phytophthora was the most abundant with 273 isolates (75.6%), followed by Phytopythium, Pythium, and Globisporangium. Oomycete species diversity showed a significant variation among substrates. Only one species-Phytophthora lacustris-was abundant in all substrates, while 16 species were restricted to a specific substrate, mainly soil. The rhizosphere of symptomatic alder trees harbored the most diverse oomycete community, highlighting once again the importance of soil as a reservoir for these microorganisms. Only two Phytophthora species were isolated from alder bark lesions, namely, P. × alni, the known causal agent of alder decline, and P. lacustris. The low recovery rate of P. × alni might be due to attempts to isolate it from old, inactive lesions, but may also suggest that alder decline might be caused by other oomycetes infecting the root system of the trees.},
}

Switzerland
*Alnus/microbiology/parasitology
*Oomycetes/classification/isolation & purification/genetics
*Biodiversity
*Soil Microbiology
Plant Diseases/microbiology
Rhizosphere
Phytophthora/isolation & purification/classification/genetics
Phylogeny
Pythium/isolation & purification/genetics/classification

@article {pmid40402315,
year = {2025},
author = {Mitchell, JK and Matthee, S and Ndhlovu, A and Miller, M and Buss, P and Matthee, CA},
title = {The Microbiome and Coxiella Diversity Found in Amblyomma hebraeum and Dermacentor rhinocerinus Ticks Sampled from White Rhinoceros.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {48},
pmid = {40402315},
issn = {1432-184X},
mesh = {Animals ; *Microbiota ; *Perissodactyla/parasitology/microbiology ; *Amblyomma/microbiology ; *Coxiella/genetics/classification/isolation & purification ; *Dermacentor/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; South Africa ; Coxiella burnetii/genetics/isolation & purification ; DNA, Bacterial/genetics ; Bacteria/classification/genetics/isolation & purification ; Female ; Male ; },
abstract = {The microbiome and the prevalence of the pathogenic bacterium Coxiella burnetii in ticks associated with white rhinoceros, Ceratotherium simum, is unknown. Targeted Illumina 16S rRNA amplicon sequencing was used to characterize the bacterial microbiome diversity found within 40 Amblyomma hebraeum and 40 Dermacentor rhinocerinus ticks collected from 40 white rhinoceros individuals in the Kruger National Park, South Africa. Specific emphasis was also given to further investigate the prevalence of the pathogenic C. burnetti in these tick species. At the phylum level, Proteobacteria dominated both tick microbiomes, followed by Actinobacteria and Firmicutes; Coxiella was the most abundant genus within A. hebraeum and Rickettsia within D. rhinocerinus. While alpha diversity did not differ significantly between the two tick species, beta diversity revealed significant species-specific differences in bacterial community composition. Additionally, there was no correlation between sampling region and microbiome diversity or composition for either tick species. Twenty-five Coxiella amplicon sequence variants (ASVs) were identified, forming three distinct monophyletic Coxiella clades and a fourth single ASV lineage. The Coxiella clades showed a correlation to tick species identity with D. rhinocerinus harboring significantly greater Coxiella diversity than A. hebraeum-potentially indicative of different coevolutionary pathways between the bacteria and their respective hosts. PCR of the IS1111 transposase gene for 238 ticks detected a 66.1% (56.7-74.4%) prevalence for C. burnetii in D. rhinocerinus compared to 55.8% in A. hebraeum (46.5-64.8%). These findings support a notion that each tick species is characterized by its own microbiome community composition and that both A. hebraeum and D. rhinocerinus may act as reservoirs and potential vectors of C. burnetii to white rhinoceros.},
}

Animals
*Microbiota
*Perissodactyla/parasitology/microbiology
*Amblyomma/microbiology
*Coxiella/genetics/classification/isolation & purification
*Dermacentor/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
South Africa
Coxiella burnetii/genetics/isolation & purification
DNA, Bacterial/genetics
Bacteria/classification/genetics/isolation & purification
Female
Male

@article {pmid40402178,
year = {2025},
author = {Salazar, J and González, J and Riofrío, R and Siavichay, F and Carrera, M and Mogrovejo, A and Barrera-Galicia, G and Valdez-Tenezaca, A},
title = {MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {47},
pmid = {40402178},
issn = {1432-184X},
support = {PICCIITT19-11//Universidad Católica de Cuenca/ ; PICCIITT19-11//Universidad Católica de Cuenca/ ; PICCIITT19-11//Universidad Católica de Cuenca/ ; },
mesh = {Ecuador ; Animals ; *Skin/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Microbiota ; *Bacteria/classification/isolation & purification/genetics ; *Fungi/classification/isolation & purification/genetics ; *Anura/microbiology ; Biodiversity ; },
abstract = {Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.},
}

Ecuador
Animals
*Skin/microbiology
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Microbiota
*Bacteria/classification/isolation & purification/genetics
*Fungi/classification/isolation & purification/genetics
*Anura/microbiology
Biodiversity

@article {pmid40401940,
year = {2025},
author = {Nieves-Morales, R and Paez-Diaz, JA and Rivera-Lopez, EO and Pérez-Santos, N and Borrero-Villabol, SJ and Rodríguez-Ramos, J and Nieves-Rivera, AM and Rios-Velazquez, C},
title = {Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0002225},
doi = {10.1128/mra.00022-25},
pmid = {40401940},
issn = {2576-098X},
abstract = {Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.},
}

@article {pmid40401939,
year = {2025},
author = {Darden, B and Johnson, G and Busch, G and Sharma, I},
title = {Draft genome sequence of Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0088224},
doi = {10.1128/mra.00882-24},
pmid = {40401939},
issn = {2576-098X},
abstract = {We report a draft genome sequence for Vreelandella neptunia strain 04GJ23 isolated from the underwater Hawaii seamounts. The whole-genome sequence will help understand the ecology and evolution of various ecotypes that are physiologically distinct from the surrounding environments.},
}

@article {pmid40401933,
year = {2025},
author = {Das, J and Pal, S and Negi, A and Sundharam, SS and Yadav, A and Subramanian, S and Sinha, SK and Samanta, J and Krishnamurthi, S},
title = {Genomic insights into novel predatory myxobacteria isolated from human feces.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0214724},
doi = {10.1128/spectrum.02147-24},
pmid = {40401933},
issn = {2165-0497},
abstract = {Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35[T] and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35[T]. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.},
}

@article {pmid40400674,
year = {2025},
author = {Kokociński, M and Graco-Roza, C and Jasser, I and Karosienė, J and Kasperovičienė, J and Kobos, J and Koreivienė, J and Mankiewicz-Boczek, J and Soininen, J and Szczurowska, A},
title = {Environmental factors determining the distribution patterns of invasive Raphidiopsis raciborskii and R. mediterranea in central east Europe.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1533716},
pmid = {40400674},
issn = {1664-302X},
abstract = {OBJECTIVE: In recent decades, the invasive cyanobacteria Raphidiopsis raciborskii and Raphidiopsis mediterranea have expanded their distribution globally, particularly in temperate regions. Understanding the ecological drivers of Raphidiopsis distribution is imperative to addressing the challenges associated with these species. Here, we aimed to characterize the distribution and biomass of R. raciborskii and R. mediterranea across 112 lakes in Poland and Lithuania in relation to local and regional factors.

RESEARCH DESIGN AND METHODS: Integrated water samples were collected from 102 Polish and 10 Lithuanian lakes from different regions for phytoplankton and chemical analyses. The lakes varied in surface area, and exhibited diverse mixing regimes, trophic states, and morphometries. Phytoplankton was identified and quantified using a Fuchs-Rosenthal or Nageotte chamber. Additionally, we characterized the degree of human pressures the climatic constraints experienced by each lake.

RESULTS: R. raciborskii occurrence has increased in eastern regions of Poland but biomass is relatively low compared to western Poland, likely due to lower air temperatures and nutrient concentrations, especially phosphorus. In contrast, R. mediterranea only occurred in a small number of lakes in Poland, and in a single lake in Lithuania, with no relation to measured local and regional variables.

CONCLUSIONS: Our study shows contrasting patterns in the distribution of two invasive cyanobacteria species in Europe, highlighting the importance of climate and nutrients to the distribution of R. raciborskii, the most widespread species, and providing relevant information for decision making and conservation strategies.},
}

@article {pmid40399330,
year = {2025},
author = {Liang, X and Yang, S and Radosevich, M and Wang, Y and Duan, N and Jia, Y},
title = {Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {82},
pmid = {40399330},
issn = {2055-5008},
support = {42377306//National Natural Science Foundation of China/ ; 2023JH3/10200009//Natural Science Foundation of Liaoning Province/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; No.KLFES-2027//CAS Key Laboratory of Forest Ecology and Silviculture, Institute of Applied Ecology, Chinese Academy of Sciences/ ; },
mesh = {*Bacteriophages/physiology ; Phenotype ; *Bacteria/virology/metabolism/genetics ; Ecosystem ; *Host Microbial Interactions ; *Microbiota ; },
abstract = {Bacteriophages (phages) reprogram host metabolism and generate phenotypic heterogeneity, yet the mechanisms and ecological implications remain poorly understood representing a major knowledge gap in microbial ecology. This review explores how phage infection alters microbial physiology, contributes to single-cell variation, and influences population dynamics. We highlight the potential consequences of phage-driven heterogeneity for microbial community structure and biogeochemical cycling, underscoring the importance of integrating phage-host interactions into ecological and ecosystem models.},
}

*Bacteriophages/physiology
Phenotype
*Bacteria/virology/metabolism/genetics
Ecosystem
*Host Microbial Interactions
*Microbiota

@article {pmid40398824,
year = {2025},
author = {Massaro, A and Peruzzo, A and Zacometti, C and Zancato, M and Piro, R and Losasso, C and Tata, A and Peron, G},
title = {Exploring the crosstalk between gut microbiota and stool metabolome in omnivorous, vegetarian, and vegan diets: a pilot study.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109965},
doi = {10.1016/j.jnutbio.2025.109965},
pmid = {40398824},
issn = {1873-4847},
abstract = {Gut microbiota (GM) and fecal metabolome are shaped by different dietary regimens. Nevertheless, outlining generalized patterns is challenging, due to the intrinsic heterogeneity of individual dietary choices. In this work, the fecal metabolome of adult volunteers consuming omnivorous (n = 44), vegetarian (n = 29), and vegan diets (n = 25) for at least 12 months was characterized. The crosstalk among diet, GM and fecal metabolome was also investigated correlating metabolomics and metataxonomics data. Untargeted metabolomic profiles were correlated with metataxonomics data previously acquired on the same stool samples. The sphingomyelin SM(d18:2/18:1-2OH) and phosphoethanolamines from animal-based food were associated to the omnivorous diet and were negatively correlated to beneficial Bacteroides ovatus and Odoribacter genus. Plant glycerides, sterols, triterpenes, and oleic-linoleic acid were associated with the vegan diet. Oleic-linoleic acid was positively correlated with Alistipes putredinis. Chenodeoxycholic acid, a primary bile acid, was identified as a marker of vegan diet, while ketolithocholic acid, a secondary bile acid, was associated to the omnivorous diet. This latter was also negatively correlated to B.ovatus. Overall, results confirm that assessing markers of dietary regimens instead of specific food categories is challenging, especially if volunteers' diet is not strictly monitored. However, the integration of metabolomics and metataxonomic data allows to better understand the effects of specific food components on the GM and represents a suitable approach for further molecular investigation in nutrition.},
}

@article {pmid40394467,
year = {2025},
author = {Van Hee, S and Segurado Luchsinger, AE and Cusumano, A and Masschelein, J and Jacquemyn, H and Lievens, B},
title = {Correction: The plant-beneficial fungus Trichoderma harzianum T22 modulates plant metabolism and negatively affects Nezara viridula.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {671},
pmid = {40394467},
issn = {1471-2229},
}

@article {pmid40394206,
year = {2025},
author = {Khurshid, H and Jamshaid, MB and Salahuudin, Z and Sibtain, K and Fayyaz, I and Ameer, A and Kerbiriou, C and Mckirdy, S and Malik, SN and Gerasimidis, K and Noreen, Z and Javed, S and Tariq, A and Ijaz, UZ and Tariq, A},
title = {Gut microbial ecology and function of a Pakistani cohort with Iron deficiency Anemia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17532},
pmid = {40394206},
issn = {2045-2322},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; MR/Z50628X/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Anemia, Iron-Deficiency/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Humans ; Pakistan/epidemiology ; Female ; Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Iron/metabolism ; Bacteria/genetics/classification ; Diet ; },
abstract = {Iron deficiency anemia (IDA) is a major public health concern among women of reproductive age leading to high maternal mortality. Pakistan being one of the Lower -Middle income countries (LMIC) is facing this challenge tremendously. The objective of this study is to determine the impact of IDA on gut microbial diversity as well as its relationship with microbial metabolites.16 S rRNA gene profiling of healthy and IDA affected meconium samples was performed with additional meta-data collected through questionnaire. The anemia was linked to different dietary parameters through chi-square test of independence and Generalized Linear Latent Variable Model (GLLVM). Anaerobic bacterial genera such as Coprococcus, Anaerovoracaceae, strongly associated with anemia and negatively correlated with red meat and fish consumption. Moreover, these microbes positively correlated with branched short chain fatty acids (BSCFAs) production. BSCFAs have strong implications in metabolic disorders. This study provides a snapshot of how anemia modulates gut microbial diversity and microbial metabolites production which may have an impact on iron metabolism.},
}

*Anemia, Iron-Deficiency/microbiology/epidemiology
*Gastrointestinal Microbiome
Humans
Pakistan/epidemiology
Female
Adult
RNA, Ribosomal, 16S/genetics
Cohort Studies
Iron/metabolism
Bacteria/genetics/classification
Diet

@article {pmid40393817,
year = {2025},
author = {Pantigoso, HA and Ossowicki, A and Stringlis, IA and Carrión, VJ},
title = {Hub metabolites at the root-microbiome interface: unlocking plant drought resilience.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.007},
pmid = {40393817},
issn = {1878-4372},
abstract = {Drought is one of the most devastating environmental challenges, severely affecting agriculture, ecosystems, and global food security. Effective strategies to predict and mitigate drought are limited. The root-soil-microbiome interface is pivotal in mediating plant resilience to drought. Recent studies highlight dynamics between plant root exudates and microbial communities, influencing stress tolerance through chemical signaling under drought. By integrating plant molecular biology, root chemistry, and microbiome research, we discuss insights into how these mechanisms can be harnessed to enhance crop resilience. Here, we focus on the interplay between plants and their microbiomes with metabolites as a central point of interactions. We synthesize recent developments, identify critical knowledge gaps, and propose future directions to leverage plant-microbe interactions to improve plant drought tolerance.},
}

@article {pmid40393246,
year = {2025},
author = {Liu, X and Li, Y and Yuan, C and Zhao, Y and Zhou, L and Yan, Y and Ren, J and Liu, Q},
title = {Sophocarpine suppresses MAPK-mediated inflammation by restoring gut microbiota in colorectal cancer.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {143},
number = {},
pages = {156833},
doi = {10.1016/j.phymed.2025.156833},
pmid = {40393246},
issn = {1618-095X},
abstract = {BACKGROUND: Colorectal cancer (CRC), as one of the most common cancers globally, poses a significant challenge to public health due to its high incidence and mortality rates. This underscores the need for continuous exploration of new therapeutic targets and effective drugs. Sophocarpine (SC), a natural compound derived from traditional Chinese medicine, holds considerable therapeutic potential in the treatment of CRC, however, the relevant mechanisms remains unclear.

PURPOSE: This study aims to explore the anti-tumor effects of SC against CRC by modulating gut microbiota, and uncover potential mechanisms linking SC's therapeutic effects to gut microbiota regulation by analyzing the impact of SC on microbiota composition and CRC progression.

MATERIAL: This study explores the impact of SC on the gut microbiota in CRC by constructing subcutaneous xenograft tumors of CRC and integrating 16S rRNA sequencing and RNA transcriptomic sequencing. The fecal microbiota transplantation (FMT) mouse model was used to validate the biological function of SC in correcting gut microbiota dysbiosis to treat CRC. Subsequently, we conducted in vitro studies on the molecular mechanisms by which SC regulates the gut microbiota as an effective hallmark of CRC treatment, using lipopolysaccharide (LPS) to simulate an inflammatory gut microbiota environment and P38 MAPK knockdown cell line.

RESULTS: SC significantly inhibited CRC cell proliferation with IC50 values of 2.547±0.256 μM for HCT116 and 2.851±0.332 μM for LoVo cells. In vivo experiments demonstrated that SC effectively suppressed tumor growth in xenograft models. 16S rRNA sequencing revealed that SC modulated gut microbiota composition, particularly affecting Bacteroides and Alistipes populations. SC significantly reduced the levels of inflammatory factors and inhibited the MAPK signaling pathway, as evidenced by decreased p-JNK, p-p38 MAPK, and p-NF-κB p65 expression.

CONCLUSIONS: Current clinical practice still lacks effective therapeutic agents targeting CRC through gut microbiota modulation. This study presents the first evidence that SC, a natural compound, exhibits dual-action therapeutic efficacy against CRC progression by simultaneously modulating gut microbial composition and suppressing MAPK pathway-mediated inflammatory responses. These findings highlight SC's novel therapeutic potential as a promising microbiota-regulating candidate for CRC intervention, offering an innovative approach that bridges microbial ecology with cancer signaling pathways.},
}

@article {pmid40387954,
year = {2025},
author = {Warren, ML and Tsuji, K and Decker, LE and Kishi, M and Yang, J and Howe, AC and Fukami, T},
title = {Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {46},
pmid = {40387954},
issn = {1432-184X},
support = {1656518//National Science Foundation Graduate Research Fellowship Program/ ; },
mesh = {Bees/microbiology ; Animals ; *Plant Nectar ; *Bacteria/classification/isolation & purification/genetics ; *Flowers/microbiology ; Japan ; *Mouth/microbiology ; Seasons ; Gastrointestinal Microbiome ; },
abstract = {Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.},
}

Bees/microbiology
Animals
*Plant Nectar
*Bacteria/classification/isolation & purification/genetics
*Flowers/microbiology
Japan
*Mouth/microbiology
Seasons
Gastrointestinal Microbiome

@article {pmid40387916,
year = {2025},
author = {González-Villalobos, E and de Almeida Kumlien, ACM and Sànchez-Melsió, A and Balcázar, JL},
title = {Bacteriophages as Vehicles for Antibiotic Resistance Genes in the Onyar River, Spain.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {41},
pmid = {40387916},
issn = {1432-184X},
support = {CVU: 441304//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 792686//European Union's Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie/ ; SGR 01282//Generalitat de Catalunya/ ; },
mesh = {Spain ; *Rivers/microbiology/virology ; *Bacteriophages/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/virology/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Geologic Sediments/microbiology/virology ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; DNA, Viral/genetics ; },
abstract = {This study aimed to investigate the presence and abundance of antibiotic resistance genes (ARGs) in bacterial and phage DNA fractions from sediment samples collected from the Onyar River, both before and after its passage through the urban area of Girona (northeast Spain). Genes conferring resistance to β-lactams, fluoroquinolones, macrolides, sulfonamides, and tetracyclines were quantified using quantitative PCR. Our findings showed that ARGs are present in both bacterial and phage DNA fractions, with a higher abundance in the bacterial fraction. Notably, our analysis revealed an increased abundance of the sulfonamide resistance gene sulI in the phage DNA fraction when comparing samples collected before and after the river's passage through the city. Although similar trends were observed for other ARGs (e.g., qnrS and sulII), these differences were not statistically significant (p > 0.05). These findings emphasize the importance of phages as potential reservoirs or vehicles for ARGs in environmental settings. Further research is needed to elucidate the factors that influence gene transfer dynamics and the persistence of ARGs within phages.},
}

Spain
*Rivers/microbiology/virology
*Bacteriophages/genetics
*Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/virology/isolation & purification
*Drug Resistance, Bacterial/genetics
Geologic Sediments/microbiology/virology
*Genes, Bacterial
*Drug Resistance, Microbial/genetics
DNA, Viral/genetics

@article {pmid40385475,
year = {2025},
author = {Li, J and Zhou, L and Xiao, Z},
title = {Advances in the study of Ophiopogon japonicus polysaccharides: structural characterization, bioactivity and gut microbiota modulation regulation.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1583711},
pmid = {40385475},
issn = {1663-9812},
abstract = {Ophiopogon japonicus polysaccharides (OJPS), the principal bioactive constituents isolated from Ophiopogon japonicus, demonstrate substantial physiological efficacy. OJPS is characterized by a high molecular weight, typically ranging from 2.48 to 324.7 kDa. Emerging evidence indicates that OJPS modulates the composition and structural organization of the gut microbiota, thereby maintaining intestinal barrier integrity and enhancing both gastrointestinal and systemic homeostasis. Moreover, OJPS and its metabolic derivatives engage in dynamic interactions with microbial communities, mediating cellular signaling cascades and endocrine regulation to elicit hypoglycemic effects. Despite these findings, comprehensive analyses of OJPS extraction and purification methodologies, structural elucidation, biological functionalities, and mechanistic insights into its crosstalk with the gut microbiota remain scarce. This review systematically synthesizes contemporary knowledge pertaining to the preparation, structural attributes, bioactivity, and mechanistic underpinnings of OJPS, with particular emphasis on its dual regulatory role in host physiology and gut microbial ecology.},
}

@article {pmid40384051,
year = {2025},
author = {Khafagy, ES and Saqr, AA and Almutairy, BK and Aldawsari, MF and Lila, ASA and Ibrahim, TS and Hegazy, WAH and Salem, IM},
title = {Repurposing Nitroimidazoles: A New Frontier in Combatting Bacterial Virulence and Quorum Sensing via In Silico, In Vitro, and In Vivo Insights.},
journal = {Drug development research},
volume = {86},
number = {3},
pages = {e70101},
doi = {10.1002/ddr.70101},
pmid = {40384051},
issn = {1098-2299},
support = {//The authors extend their appreciation to Prince Sattam bin Abdulaziz University for funding this research work through the project number (PSAU/2024/03/29653)./ ; },
mesh = {*Quorum Sensing/drug effects ; Animals ; Biofilms/drug effects ; *Drug Repositioning ; Humans ; Molecular Docking Simulation ; Virulence/drug effects ; *Nitroimidazoles/pharmacology ; Mice ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; HeLa Cells ; Chromobacterium/drug effects ; Molecular Dynamics Simulation ; Pseudomonas aeruginosa/drug effects ; Female ; Indoles/metabolism ; },
abstract = {The global antibiotic resistance crisis demands innovative strategies targeting bacterial virulence rather than survival. Quorum sensing (QS), a key regulator of virulence and biofilm formation, offers a promising avenue to mitigate resistance by disarming pathogens without bactericidal pressure. This study investigates the repurposing of nitroimidazoles as anti-QS and anti-virulence agents at subminimum inhibitory concentrations (sub-MICs). In Silico analyses, including molecular docking and molecular dynamics (MD) simulations, were performed to investigate ligand-receptor interactions with structurally distinct Lux-type QS receptors and assess binding stability and conformational dynamics over time. In Vitro assays evaluated the effects of representative nitroimidazoles, metronidazole (MET) and secnidazole (SEC), on QS-controlled phenotypes, including violacein production in Chromobacterium violaceum and biofilm formation and protease activity in Pseudomonas aeruginosa, Acinetobacter baumannii, Salmonella enterica, and Proteus mirabilis. In Vivo efficacy was assessed using a murine infection model and HeLa cell invasion assays. Molecular docking revealed high-affinity binding to QS receptors, corroborating their mechanistic interference. Sub-MIC MET/SEC significantly suppressed violacein synthesis, biofilm biomass, and protease secretion in Gram-negative pathogens. Both compounds reduced bacterial invasiveness in HeLa cells and In Vivo protected mice from lethal P. aeruginosa infections. Crucially, nitroimidazoles attenuated virulence without affecting bacterial viability, preserving microbial ecology. These findings position nitroimidazoles as dual-function agents; antimicrobial at bactericidal doses and anti-virulence at sub-MICs. Their validated efficacy across In Silico, In Vitro, and In Vivo models underscores their potential as adjunctive therapies, bridging the gap between drug repurposing and next-generation anti-infective development.},
}

*Quorum Sensing/drug effects
Animals
Biofilms/drug effects
*Drug Repositioning
Humans
Molecular Docking Simulation
Virulence/drug effects
*Nitroimidazoles/pharmacology
Mice
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
HeLa Cells
Chromobacterium/drug effects
Molecular Dynamics Simulation
Pseudomonas aeruginosa/drug effects
Female
Indoles/metabolism

@article {pmid40383311,
year = {2025},
author = {Zhu, L and Huang, K and Bai, T and Xia, H},
title = {Bacteriophages enhance the transformation of dissolved organic matter during vermicomposting of sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132694},
doi = {10.1016/j.biortech.2025.132694},
pmid = {40383311},
issn = {1873-2976},
abstract = {Vermicomposting is an eco-friendly technology for treating sewage sludge, however its efficiency in transforming biological material is often constrained. This study investigates the potential of bacteriophages to enhance the transformation of dissolved organic matter (DOM) during sludge vermicomposting. Fresh dewatered sludge treated with bacteriophages (VP) were compared to untreated controls (CK) over a 30 days' vermicomposting. The results showed that bacteriophage inoculation led to a 58.17 % reduction in dissolved organic carbon (DOC), significantly higher than the 10.67 % reduction in the CK group (P < 0.05). Additionally, the DOM stability indices in the VP treatment were significantly decreased by 30.95 % (P < 0.05), alongside an increased humification rate. Partial least squares path modeling (PLS-PM) revealed that bacteriophages played a pivotal role in accelerating DOM degradation by selectively lysing specific bacterial populations and altering DOM transformation pathways.},
}

@article {pmid40382531,
year = {2025},
author = {Hasegawa, R and Poulin, R and Salloum, PM},
title = {Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {45},
pmid = {40382531},
issn = {1432-184X},
support = {202460294//Japan Society for the Promotion of Science/ ; UOO2113//Marsden Fund/ ; UOO2113//Marsden Fund/ ; },
mesh = {Animals ; *Trematoda/microbiology/classification ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Snails/parasitology/microbiology ; Phylogeny ; },
abstract = {Elucidating the specific processes and drivers of community assembly in the host microbiome is essential to fully understand host biology. Toward this goal, an important first step is to describe co-occurrence patterns among different microbial taxa, which can be driven by numerous factors, such as host identity. While host identity can be an important influential factor on co-occurrence patterns, a limited number of studies have explored the relative importance of host identity after controlling for other environmental factors. Here, we examined microbial co-occurrence patterns in four phylogenetically distinct trematode species living within the same snail species, collected concomitantly from the same habitat. Our previous study determined that all these trematodes shared some bacterial taxa, and the relative abundance of microbial taxa differed among trematodes, possibly due to differences in their eco-physiological traits. Here, we specifically predict that pairwise microbial co-occurrence patterns also vary among trematode host species. Our results showed that co-occurrence patterns among eight microbial families varied greatly among the four trematode hosts, with some microbial families co-occurring in some trematode species, whereas no such patterns were observed in other trematodes. Our study suggests that the habitat identity (trematode species) and its associated biotic characteristics, such as physiological and ecological traits, can determine co-occurrence patterns among microbial taxa, with substantial effects on local community composition.},
}

Animals
*Trematoda/microbiology/classification
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Snails/parasitology/microbiology
Phylogeny

@article {pmid40382475,
year = {2025},
author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG},
title = {The Microbial Ecology of Antarctic Sponges.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {44},
pmid = {40382475},
issn = {1432-184X},
mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Ecosystem ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.},
}

*Porifera/microbiology
Animals
Antarctic Regions
*Microbiota
Symbiosis
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Ecosystem
Fungi/classification/genetics/isolation & purification

@article {pmid40379949,
year = {2025},
author = {Onaka, H},
title = {Unlocking hidden bioactive compounds: from indolocarbazole and RiPP biosynthesis to the activation of cryptic secondary metabolism via microbial interactions.},
journal = {The Journal of antibiotics},
volume = {},
number = {},
pages = {},
pmid = {40379949},
issn = {1881-1469},
abstract = {Actinomycetes, particularly Streptomyces, are soil microorganisms that produce diverse secondary metabolites with pharmaceutical applications, such as antibiotics and anticancer drugs. These metabolites play important roles in microbial competition and survival. This review highlights three major aspects of actinomycete secondary metabolism: (1) the biosynthesis of indolocarbazoles, (2) the biosynthesis of RiPPs (ribosomally synthesized and post-translationally modified peptides), and (3) the activation of secondary metabolism through microbial interactions. Indolocarbazoles, including staurosporine and rebeccamycin, are potent inhibitors of kinases and DNA topoisomerase I, with potential as anticancer agents. Their biosynthetic pathways involve multiple enzymatic steps, notably carbon-carbon bond formation catalyzed by cytochrome P450 enzymes. RiPPs such as goadsporin and lactazole are highly modular peptide natural products; structural gene modification enables the generation of diverse analogs. A cell-free one-pot synthesis platform has been developed for efficient analog production. To activate cryptic biosynthetic pathways, we employed a combined-culture strategy using actinomycetes and mycolic acid-containing bacteria, resulting in the discovery of 42 novel compounds. Genetic and physiological data indicate that physical contact, rather than diffusible signaling, is essential for induction. These insights emphasize the importance of microbial interactions in natural product biosynthesis and offer new directions for drug discovery through synthetic biology and microbial ecology.},
}

@article {pmid40376461,
year = {2025},
author = {Davis, RA and Mafune, KK and Winkler, MKH},
title = {Biodegradable hydrogels and microbial consortia as a treatment for soil dysbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1565940},
pmid = {40376461},
issn = {1664-302X},
abstract = {Terrestrial microbial communities drive many soil processes and can be pushed into a state of dysbiosis upon disturbance. This dysregulation negatively impacts soil biogeochemical cycles, which threatens plant and soil health. Effective treatment of soil dysbiosis requires simultaneous restoration of multiple system components, addressing both the physical structure of soil and its microbial communities. Hydrogels with microbial consortia simultaneously remedy soil hydrodynamics while promoting microbial reestablishment. The purpose of this review is to shed light on soil management practices through the lens of soil dysbiosis. This is important to address not only for soil health and crop productivity, but also to mitigate climate change through improved soil carbon sequestration and reduced greenhouse gas emissions. This review positions hydrogels and microbes as tools for the treatment of soil dysbiosis, contributing to agricultural and climate resilience.},
}

@article {pmid40194740,
year = {2025},
author = {Nieman, DC and Sakaguchi, CA and Williams, JC and Lawson, J and Lambirth, KC and Omar, AM and Mulani, FA and Zhang, Q},
title = {Gut Prevotella copri abundance linked to elevated post-exercise inflammation.},
journal = {Journal of sport and health science},
volume = {14},
number = {},
pages = {101039},
doi = {10.1016/j.jshs.2025.101039},
pmid = {40194740},
issn = {2213-2961},
abstract = {PURPOSE: This study aimed to examine the linkage between gut microbiome taxa and exercise-induced inflammation.

METHODS: Twenty-five cyclists provided 4 stool samples during a 10-week period and cycled vigorously for 2.25 h at 67% maximal oxygen uptake (VO2max) in a laboratory setting. Blood samples were collected pre- and post-exercise, with additional samples collected at 1.5-h, 3-h, and 24-h post exercise. Primary outcomes included stool microbiome composition and alpha diversity via whole genome shotgun (WGS) sequencing (averaged from 4 stool samples) and a targeted panel of 75 plasma oxylipins. A total of 5719 taxa were identified, and the 339 that were present in more than 20% of stool samples were used in the analysis. Alpha diversity was calculated by evenness, and the Analysis of Composition of Microbiomes (ANCOM) differential abundance analysis was performed using Quantitative Insights Into Microbial Ecology-2 (QIIME2). A composite variable was calculated from 8 pro-inflammatory oxylipins generated from arachidonic acid (ARA) and cytochrome P-450 (CYP).

RESULTS: ARA-CYP oxylipins were significantly elevated for at least 3-h post-exercise (p < 0.001); they were strongly and positively related to Prevotella copri (P. copri) abundance (R[2] = 0.676, p < 0.001) and negatively related to gut microbiome alpha diversity (R[2] = 0.771, p < 0.001).

CONCLUSION: This analysis revealed for the first time a novel, positive relationship between gut microbiome P. copri abundance in cyclists and post-exercise pro-inflammatory oxylipins. These data demonstrate that about two-thirds of the wide variance in inflammation following prolonged and intensive exercise is largely explained by the abundance of a single gut bacterial species: P. copri.},
}

@article {pmid40373669,
year = {2025},
author = {Rescan, M and Gros, M and Borrego, CM},
title = {Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria.},
journal = {Water research},
volume = {282},
number = {},
pages = {123720},
doi = {10.1016/j.watres.2025.123720},
pmid = {40373669},
issn = {1879-2448},
abstract = {City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.},
}

@article {pmid40373649,
year = {2025},
author = {Rosa-Masegosa, A and Vilchez-Vargas, R and Gorrasi, S and Monteoliva-García, A and Gonzalez-Martinez, A and Gonzalez-Lopez, J and Muñoz-Palazon, B},
title = {Unraveling the composition and succession of the microbial community in aerobic granular sludge treating urban wastewater with high load from hospital effluent.},
journal = {Chemosphere},
volume = {381},
number = {},
pages = {144483},
doi = {10.1016/j.chemosphere.2025.144483},
pmid = {40373649},
issn = {1879-1298},
abstract = {The treatment of wastewater containing high concentrations of pharmaceutical compounds is a challenge that has not yet been fully resolved. In this study, the occurrence of pharmaceutical and the bacterial and fungal communities were investigated during the treatment of urban wastewater including the hospital effluents using aerobic granular sludge technology. The physic-chemical results pointed out the capability of this technology to remove high rates of organic matter (97 %), total suspended solids (90 %), and nitrogen (85 %) without compromising the granular integrity and properties. The obtained data of pharmaceuticals remarked that the influent concentration had a strong effect on the removal ratio. The better average pharmaceutical removal performances were for carbamazepine (60-85 %), ketoprofen(50-60 %), cyclophosphamide(∼70 %), and trimethoprim(70 %), while the most recalcitrant compound was diclofenac. The molecular analysis exposed the relevance of endogenous microbial loads in the raw wastewater, especially in the start-up period. The mature granules demonstrated the strong selection of granules-forming bacteria, whereas the fungal populations took a longer period to be stable in granular biomass. Once the reactor was stable, the system was able to compete successfully with the influent microorganisms and avoid the spreading of pathogen microorganisms in the effluent, achieving excellent macro-pollutant and micro-pollutant removal ratios.},
}

@article {pmid40373419,
year = {2025},
author = {Orsi, AS and Lemos Junior, WJF and Alegbeleye, OO and Muniz, DC and Horita, CN and Sant'Ana, AS},
title = {Sodium chloride reduction in meat processing: Microbial shifts, spoilage risks, and metagenomic insights.},
journal = {Meat science},
volume = {226},
number = {},
pages = {109848},
doi = {10.1016/j.meatsci.2025.109848},
pmid = {40373419},
issn = {1873-4138},
abstract = {This review evaluated the impact of sodium chloride (NaCl) reduction or substitution on the microbial ecology of meat products, with a focus on how these changes affect shelf life and safety. Reducing NaCl in fresh meat products promotes the growth of psychrotrophic spoilage bacteria, such as Pseudomonas sp., which thrive at low temperatures, and mesophilic pathogens like Escherichia coli and Staphylococcus aureus, particularly under inadequate storage conditions. In cured and fermented meats, such as salami, lowering NaCl levels disrupts the balance of salt-tolerant microorganisms, notably lactic acid bacteria (LAB) and coagulase-negative staphylococci, potentially leading to increased spoilage and pathogen proliferation. In smoked meats, the combination of reduced NaCl and altered microbial ecology, including a shift toward LAB dominance, may weaken the inhibitory effects on spore-forming bacteria like Clostridium botulinum. Additionally, using metagenomics, we explore the shifts in microbial communities observed in studies involving meat, revealing critical insights into the composition and diversity of bacteria in meat products, as well as the gaps in research on the impact of NaCl reduction and/or substitution on the microbiota. This review provides a comprehensive understanding of these microbial shifts, highlighting the distinct responses of psychrotrophic, mesophilic, and LAB groups to NaCl modification and the need to understand the effects of these alternatives on the meat product microbiome, as well as the neglected microorganisms that can affect the quality and safety of these products.},
}

@article {pmid40372110,
year = {2025},
author = {Rohrhofer, J and Wolflehner, V and Schweighardt, J and Koidl, L and Stingl, M and Zehetmayer, S and Séneca, J and Pjevac, P and Untersmayr, E},
title = {Gastrointestinal Barrier Disruption in Post-COVID Syndrome Fatigue Patients.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16593},
pmid = {40372110},
issn = {1398-9995},
support = {//WE&ME Foundation/ ; //Medizinisch-Wissenschaftlicher Fond des Buergermeisters der Bundeshauptstadt Wien/ ; },
abstract = {BACKGROUND: Post-COVID Syndrome (PCS) is the term for a condition with persistent symptoms in a proportion of COVID-19 patients after asymptomatic, mild, or severe disease courses. Numbers vary, but the current estimate is that after COVID-19 approximately 10% develop PCS. The aim of our study was to evaluate the impact of SARS-CoV-2 infection on the gastrointestinal (GI) tract and associations with the development of PCS with fatigue, post-exertional malaise (PEM), orthostatic dysregulation, autonomous dysregulation, and/or neurocognitive dysregulation.

METHODS: By combining medical record data from a prospective observational study with symptom analysis before, during, and after SARS-CoV-2 infection, we aimed to identify potential risk factors and predictive markers for PCS. Additionally, we analyzed blood, saliva, and stool samples from this well-characterized PCS patient cohort to biologically validate our findings.

RESULTS: We identified significant associations between pre-existing GI complaints and the development of PCS Fatigue. PCS patients showed higher LBP/sCD14 ratios, lower IL-33 levels, and higher IL-6 levels compared to control groups. Our results highlight the critical role of the GI tract in PCS development of post-viral Fatigue.

CONCLUSION: We propose that the viral infection disrupts pathways related to the innate immune response and GI barrier function, evidenced by intestinal low-grade inflammation and GI barrier leakage. Monitoring GI symptoms and markers before, during, and after SARS-CoV-2 infection is crucial for identifying predictive clinical phenotypes in PCS. Understanding the interaction between viral infections, immune responses, and gut integrity could lead to more effective diagnostic and treatment strategies, ultimately reducing the burden on PCS patients.},
}

@article {pmid40367785,
year = {2025},
author = {Wang, Y and Huang, S and He, J and Feng, Z and Wu, W and Guo, C and He, J},
title = {Unveiling the dynamic viral landscape across developmental stages of cold seep ecosystems: Implications for global marine biogeochemistry.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138594},
doi = {10.1016/j.jhazmat.2025.138594},
pmid = {40367785},
issn = {1873-3336},
abstract = {Cold seeps are methane-rich ecosystems playing pivotal roles in global biogeochemical cycling, yet their viral communities remain underexplored. We present the first comprehensive viral metagenomic analysis across developmental stages of the Haima Cold Seep. Characterizing viral assemblages from chemoautotrophic, mature, and extinct seep sediments revealed 4272 viral operational taxonomic units, with 77 % representing novel lineages, highlighting cold seeps' unique viral diversity. Viral community structure and diversity varied significantly by seep stage, with highest diversity in the chemoautotrophic stage. While Siphoviridae and Microviridae dominated, their relative abundances shifted with maturity. Gammaproteobacteria emerged as predominant viral hosts, exhibiting distinct interaction patterns across stages. Notably, the chemoautotrophic stage harbored the highest abundance and diversity of virus-encoded auxiliary metabolic genes (AMGs; ∼450 AMGs), with significantly enriched carbohydrate metabolism and central carbon pathway genes (2.2-fold and 1.8-fold higher respectively, p < 0.005), amino acid metabolism (1.9-fold, p = 0.003), and sulfur relay system genes (2.0-fold, p = 0.002). In contrast, the mature stage exhibited distinct enrichment in energy metabolism genes (up to 3.9-fold difference between sites, p < 0.001) and xenobiotics degradation pathways, suggesting stage-specific viral impacts on biogeochemical cycling. Lytic lifestyles prevailed across stages, indicating dynamic virus-host interactions during seep development. These findings unveil complex viral ecology in cold seeps, with potential influences on microbial community structure and biogeochemical processes. Providing a foundation for understanding viral roles in cold seep ecosystem functioning and biogeochemical cycles, this study has implications for marine microbial ecology and environmental biotechnology.},
}

@article {pmid40366158,
year = {2025},
author = {Geonczy, SE and Hillary, LS and Santos-Medellín, C and Sorensen, JW and Emerson, JB},
title = {Patchy burn severity explains heterogeneous soil viral and prokaryotic responses to fire in a mixed conifer forest.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0174924},
doi = {10.1128/msystems.01749-24},
pmid = {40366158},
issn = {2379-5077},
abstract = {UNLABELLED: Effects of fire on soil viruses and virus-host dynamics are largely unexplored, despite known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we assessed how viral and prokaryotic communities responded to a prescribed burn in a mixed conifer forest. We sequenced 91 viral-size fraction metagenomes (viromes) and 115 16S rRNA gene amplicon libraries from 120 samples: four samples at five timepoints (two before fire and three after fire) at six sites (four treatment, two control). We hypothesized that compositional differences would be most significant between burned and unburned soils, but instead, plot location best distinguished viral communities, more than treatment (burned or not), depth (0-3 or 3-6 cm), or timepoint. For both viruses and prokaryotes, some burned communities resembled unburned controls, while others were significantly different, revealing heterogeneous responses to fire. These patterns were explained by burn severity, here defined by soil chemistry. Viral but not prokaryotic richness decreased significantly with burn severity, and low viromic DNA yields indicated substantial loss of viral biomass at higher severity. The relative abundances of Firmicutes, Actinobacteriota, and the viruses predicted to infect them increased significantly with burn severity, suggesting survival and viral infection of these fire-responsive and potentially spore-forming taxa. The degree of burn severity experienced by each patch of soil, rather than burn status alone, differed over mere meters in the same fire. Therefore, our analyses highlight the importance of high-resolution, paired biogeochemical data to explain soil community responses to fire.

IMPORTANCE: The impact of fire on the soil microbiome, particularly on understudied soil viral communities, warrants investigation, given known microbial contributions to biogeochemical processes and ecosystem recovery. Here, we collected 120 soil samples before and after a prescribed burn in a mixed conifer forest to assess the impacts of this disturbance on soil viral and prokaryotic communities. We show that simple categorical comparisons of burned and unburned areas were insufficient to reveal the underlying community response patterns. The patchy nature of the fire (indicated by soil chemistry data) led to significant changes in viral and prokaryotic community composition in areas of high burn severity, while communities that experienced lower burn severity were indistinguishable from those in unburned controls. Our results highlight the importance of considering highly resolved burn severity and biogeochemical measurements, even in nearby soils after the same fire, in order to understand soil microbial responses to prescribed burns.},
}

@article {pmid40366134,
year = {2025},
author = {Gilbert, NE and Kimbrel, JA and Samo, TJ and Siccardi, AJ and Stuart, RK and Mayali, X},
title = {A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/msystems.00375-25},
pmid = {40366134},
issn = {2379-5077},
abstract = {Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.},
}

@article {pmid40366070,
year = {2025},
author = {Herz, CT and Kulterer, OC and Prager, M and Marculescu, R and Prager, G and Kautzky-Willer, A and Hacker, M and Trajanoski, S and Köfeler, HC and Gallé, B and Haug, AR and Berry, D and Kiefer, FW},
title = {Bariatric surgery promotes recruitment of brown fat linked to alterations in the gut microbiota.},
journal = {European journal of endocrinology},
volume = {192},
number = {5},
pages = {603-611},
doi = {10.1093/ejendo/lvaf081},
pmid = {40366070},
issn = {1479-683X},
support = {P 27391//Austrian Science Fund/ ; 17094//Medical Scientific Fund of the Mayor of the City of Vienna/ ; //Austrian Diabetes Association Research Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Adipose Tissue, Brown/metabolism/diagnostic imaging ; Female ; *Bariatric Surgery ; Male ; Middle Aged ; Adult ; *Obesity, Morbid/surgery/metabolism/microbiology ; Fatty Acids, Volatile/metabolism/blood ; Positron Emission Tomography Computed Tomography ; Energy Metabolism/physiology ; Weight Loss/physiology ; },
abstract = {OBJECTIVE: The mechanisms of bariatric surgery-induced weight loss and metabolic improvements are still incompletely understood and reach beyond malabsorption or calorie restriction. We sought to investigate the effect of bariatric surgery on brown adipose tissue (BAT) activity and a potential connection with changes in energy metabolism, the gut microbiota, and short-chain fatty acid (SCFA) composition.

METHODS: We included 32 subjects (25 females) with morbid obesity and analyzed their metabolic profile, gut microbiota composition, circulating SCFAs, energy expenditure, and cold-induced BAT activity using [18F]Fluorodeoxyglucose-positron emission tomography-computed tomography before and up to 1 year after bariatric surgery.

RESULTS: Twelve months after surgery, the percentage of individuals with active BAT had increased from 28% to 53%. The BAT-negative (BATneg) individuals who had an adverse metabolic profile at baseline compared with subjects with active BAT (BATpos) showed a greater metabolic benefit after surgery. While no changes in overall gut bacterial diversity were observed between BATpos and BATneg, the abundance of 3 specific bacterial families, including Akkermansiaceae, Pasteurellaceae, and Carnobacteriaceae, was distinctly regulated between BAT groups. The bacterial genera most strongly increased in BATpos vs BATneg subjects were all positively correlated with BAT volume and BAT activity. Finally, circulating concentrations of the SCFAs acetate, butyrate, and propionate rose after bariatric surgery and were related to bacterial genera such as Akkermansia, Dialister, and Lachnospiraceae FCS020 group, all known SCFA producers.

CONCLUSIONS: Bariatric surgery helps recruit active BAT in individuals with obesity and is linked to distinct alterations in the gut microbiome and SCFA composition.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (NCT03168009).},
}

Humans
*Gastrointestinal Microbiome/physiology
*Adipose Tissue, Brown/metabolism/diagnostic imaging
Female
*Bariatric Surgery
Male
Middle Aged
Adult
*Obesity, Morbid/surgery/metabolism/microbiology
Fatty Acids, Volatile/metabolism/blood
Positron Emission Tomography Computed Tomography
Energy Metabolism/physiology
Weight Loss/physiology

@article {pmid40361280,
year = {2025},
author = {Wan, SH and Xu, Y and Xu, W and Leung, SKK and Yu, EYN and Yung, CCM},
title = {Environmental Heterogeneity Drives Ecological Differentiation in Vibrio Populations Across Subtropical Marine Habitats.},
journal = {Environmental microbiology},
volume = {27},
number = {5},
pages = {e70107},
doi = {10.1111/1462-2920.70107},
pmid = {40361280},
issn = {1462-2920},
support = {AoE/P-601/23-N//Research Grants Council of Hong Kong/ ; },
mesh = {*Vibrio/genetics/classification/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ecosystem ; Hong Kong ; Temperature ; Salinity ; Chaperonin 60/genetics ; Bays/microbiology ; },
abstract = {Elucidating how environmental gradients structure bacterial communities remains fundamental to microbial ecology. We investigated Vibrio population dynamics across contrasting subtropical marine environments in Hong Kong over a year period. Using an integrated approach combining cultivation techniques with molecular analyses of Hsp60 and 16S rRNA genes, we characterised the population structure between a coastal site (Clear Water Bay) and an estuarine site (Deep Bay). The estuarine environment consistently harboured higher Vibrio abundances (10[4]-10[7] copies/mL) compared to coastal waters (10[2]-10[4] copies/mL), with significantly greater phylogenetic diversity. Multivariate analyses revealed salinity as the primary driver of community differentiation between sites, while temperature governed seasonal succession patterns. Phylogenetic analysis of 1521 Vibrio isolates identified three distinct ecological groups corresponding to specific temperature-salinity niches, with evidence of habitat-specific thermal adaptations among closely related strains. Experimental characterisation of thermal performance curves confirmed physiological differentiation between warm- and cool-temperature adapted strains despite high genetic similarity (> 97% Hsp60 gene sequence identity). Several abundant species detected via amplicon sequencing (including V. navarrensis and V. mimicus) displayed site-specific ecotypes but remained uncultivated, highlighting methodological constraints in community characterisation. Our findings demonstrate how environmental heterogeneity drives fine-scale ecological differentiation in Vibrio populations, providing insights into mechanisms of bacterial adaptation in dynamic marine environments.},
}

*Vibrio/genetics/classification/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
*Seawater/microbiology
*Ecosystem
Hong Kong
Temperature
Salinity
Chaperonin 60/genetics
Bays/microbiology

@article {pmid40359204,
year = {2025},
author = {Ghyselinck, J and Verstrepen, L and Rakebrandt, M and Marynissen, S and Daminet, S and Marzorati, M},
title = {In vitro fermentation of yeast cell walls (mannan-oligosaccharide) and purified β-glucans modulates the colonic microbiota of dogs with inflammatory bowel disease and demonstrates protective effects on barrier integrity and anti-inflammatory properties.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0322877},
doi = {10.1371/journal.pone.0322877},
pmid = {40359204},
issn = {1932-6203},
mesh = {Animals ; Dogs ; *Inflammatory Bowel Diseases/microbiology/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Mannans/metabolism/pharmacology ; *beta-Glucans/pharmacology/metabolism ; Prebiotics ; *Saccharomyces cerevisiae/metabolism/chemistry ; *Cell Wall/metabolism/chemistry ; Humans ; Fermentation ; *Colon/microbiology ; Caco-2 Cells ; *Anti-Inflammatory Agents/pharmacology ; *Oligosaccharides/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa ; },
abstract = {Inflammatory bowel disease (IBD) is characterized by a disruption of intestinal homeostasis, chronic inflammation, and dysbiosis. Prebiotic supplementation may be useful for managing IBD in dogs. The aim of the study is to investigate the effects of two prebiotics, Biolex MB40 or Leiber Beta-S, on the gut microbiota isolated from three dogs with IBD, using the Colon-on-a-plate technology. Biolex MB40 and Leiber Beta-S contain concentrated 1,3-1,6- β-D-glucan isolated from the Saccharomyces cerevisiae cell walls. Biolex MB40 also contains mannan-oligosaccharide (MOS). Wells of the Colon-on-a-plate set up were inoculated with fecal suspensions and supplemented with either Biolex MB40 and Leiber Beta-S, or no test product (blank). Following 48h incubation, bacterial metabolites were measured and 16S rRNA targeted gene sequencing was performed. Colonic supernatants were added to a Caco-2/THP1 co-culture model to evaluate their effects on barrier integrity upon inflammation-induced barrier disruption and interleukin (IL)-10 production. Acetate and propionate concentrations were significantly increased versus blank with Biolex MB40, and biologically relevant numerical increases were observed with Leiber Beta-S supplementation. A donor-dependent, biologically relevant increase in butyrate was observed with both test products versus blank. Alpha diversity and microbiota biomass were increased, as well as the abundance of the five predominant phyla with both test products relative to blank. The greatest increases in abundance were observed for the Bacteroidetes and Firmicutes phyla. Fermentation of both test products had a protective effect on the gut epithelial barrier (measured by transepithelial electrical resistance) that was donor dependent. IL-10 production was significantly increased with Biolex MB40 supplementation for all donors, and with Leiber Beta-S supplementation for one donor. These in vitro findings confirm a prebiotic effect for both products and suggest that supplementation with either Biolex MB40 or Leiber Beta-S may have beneficial effects on the gut microbiota of dogs with IBD.},
}

Animals
Dogs
*Inflammatory Bowel Diseases/microbiology/veterinary
*Gastrointestinal Microbiome/drug effects
*Mannans/metabolism/pharmacology
*beta-Glucans/pharmacology/metabolism
Prebiotics
*Saccharomyces cerevisiae/metabolism/chemistry
*Cell Wall/metabolism/chemistry
Humans
Fermentation
*Colon/microbiology
Caco-2 Cells
*Anti-Inflammatory Agents/pharmacology
*Oligosaccharides/metabolism
RNA, Ribosomal, 16S/genetics
Intestinal Mucosa