@article {pmid41703847,
year = {2026},
author = {Gil, MI and Tudela, JA and Illán, G and Hernández, N and Andújar, S and Sabater, D and Allende, A and Truchado, P},
title = {Industrial-scale application of bacteriophages on baby spinach: One-year study of Listeria control, quality and microbial community shifts.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118384},
doi = {10.1016/j.foodres.2026.118384},
pmid = {41703847},
issn = {1873-7145},
mesh = {*Spinacia oleracea/microbiology ; *Bacteriophages ; *Food Microbiology/methods ; *Listeria/virology ; Listeria monocytogenes/virology ; Microbiota ; *Food Preservation/methods ; Food Handling/methods ; Food Contamination/prevention & control ; },
abstract = {Bacteriophages have emerged as promising biocontrol agents against pathogenic bacteria due to their strong antimicrobial activity and host specificity. In this study, we evaluated a previously validated industrial bacteriophage cocktail (PhageGuard Listex™) for its performance on baby spinach, focusing on product quality and microbial community dynamics. Twenty industrial trials conducted over one year compared non-treated and phage-treated baby spinach samples after processing (day 0) and after 10 days of storage under commercial (3 d at 4 °C followed by 7 d at 7 °C) and abusive (continuous 10 °C) temperature conditions. Phage stability was confirmed in the application solution and persistence on the product surface after storage. Although Listeria monocytogenes was not detected in any sample (0/600), the proportion of samples positive for Listeria spp. was significantly lower in the phage-treated group (6%) than in the non-treated group (12%). The preventive phage application did not affect headspace gas composition, sensory attributes, or objective color parameters. Quality deterioration was observed only at 10 °C, regardless of phage treatment. Despite the reduction in Listeria spp. prevalence, microbial diversity and community structure were unaffected by phage application, consistent with the low relative abundance of Listeria spp. in the microbiota and the narrow host range of the phage cocktail; storage conditions, particularly temperature, were the most influential factor affecting bacterial taxonomic composition. The relative abundance of Pseudomonas and Flavobacterium increased during storage, while Bacillus and Exiguobacterium decreased. These findings support the feasibility of using this bacteriophage-based treatment as a preventive intervention that does not affect product quality and preserves the natural microbial ecology of baby spinach during storage.},
}

*Spinacia oleracea/microbiology
*Bacteriophages
*Food Microbiology/methods
*Listeria/virology
Listeria monocytogenes/virology
Microbiota
*Food Preservation/methods
Food Handling/methods
Food Contamination/prevention & control

@article {pmid41703844,
year = {2026},
author = {Fang, X and Pu, Q and Qu, A and Wang, C and Shen, T and Wu, S and Li, M and Sui, M and Ji, Z and Huang, Y},
title = {Mechanisms of phenolic conversion in anaerobic fermentation of tea leaves revealed by integrating microbiome and metabolome analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118381},
doi = {10.1016/j.foodres.2026.118381},
pmid = {41703844},
issn = {1873-7145},
mesh = {*Fermentation ; *Phenols/metabolism/analysis ; *Plant Leaves/microbiology/metabolism/chemistry ; *Microbiota ; *Tea/microbiology/chemistry/metabolism ; *Metabolome ; Anaerobiosis ; Metabolomics/methods ; Bacteria/metabolism ; *Camellia sinensis/microbiology ; Flavonoids/metabolism ; },
abstract = {To systematically investigate the phenolic transformation mechanisms during tea anaerobic fermentation, the changes in phenolics and microbial communities of pickled teas under varying extrusion degrees were analyzed by combining metabolomics and microbiomics. The changes in 118 differential phenolics (p < 0.05, variable importance in projection >1.0, and fold change >1.2 or < 1/1.2) revealed that anaerobic fermentation drives the bioconversion of bound phenolics into free phenolics and their derivatives in tea leaves. Additionally, the potential metabolic pathways of tea phenolics in anaerobic fermentation were comprehensively proposed, mainly including hydrolysis of polymerized/galloylated catechins, hydrolysis of flavonoid glycosides, and hydrolysis of galloylated phenolics to release gallic acid and its further derivatization. The degree of extrusion significantly influenced microbial community succession: high-extrusion enriched Enterobacter, Cladosporium, Setophoma, and Vishniacozyma, enhancing the hydrolysis of flavonoid glycosides and depsides, while light-extrusion promoted Candida, Cyberlindnera, Lactobacillus, and Pantoea, favoring the accumulation of free phenolics and their derivatives. These findings establish a mechanistic link between microbial ecology and phenolic biotransformation, providing a foundation for precision fermentation in tea processing.},
}

*Fermentation
*Phenols/metabolism/analysis
*Plant Leaves/microbiology/metabolism/chemistry
*Microbiota
*Tea/microbiology/chemistry/metabolism
*Metabolome
Anaerobiosis
Metabolomics/methods
Bacteria/metabolism
*Camellia sinensis/microbiology
Flavonoids/metabolism

@article {pmid41700860,
year = {2026},
author = {Machushynets, NV and Elsayed, SS and Du, C and Lysenko, V and de la Cruz, M and Sanchez, P and Genilloud, O and Martin, NI and Liles, MR and van Wezel, GP},
title = {Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0149625},
doi = {10.1128/msystems.01496-25},
pmid = {41700860},
issn = {2379-5077},
abstract = {The growing threat of antimicrobial resistance necessitates the discovery of novel antibiotics with activity against drug-resistant pathogens. Members of the genus Paenibacillus are a rich source of nonribosomal peptides (NRPs), including well-known antibiotics such as polymyxins, paenibacterin, and tridecaptins. Here, we use a targeted mass spectrometry query language (MassQL)-based approach to identify the NRPs produced by a collection of 227 taxonomically diverse plant-associated Paenibacillus strains, providing detailed insights into their NRP-producing potential. Using MassQL to zoom in specifically on NRPs containing basic amino acids, we discovered a novel family of bacitracins, which we designated paenitracins. The paenitracins are the first bacitracin-type peptides reported in Paenibacillus and are distinguished from canonical bacitracins by three previously unseen amino acid substitutions. The paenitracins exhibit potent activity against gram-positive pathogens, including vancomycin-resistant Enterococcus faecium E155. Our work provides a novel metabolomics-guided and genomics-guided workflow for the discovery of bioactive NRPs as a strategy to prioritize natural product chemical space and accelerate antibiotic discovery.IMPORTANCEMembers of the genus Paenibacillus play an important role in soil ecology, producing a range of important nonribosomal peptides (NRPs). A collection of plant-associated Paenibacillus spp. were analyzed for their phylogenetic and metabolic diversity. We developed a novel discovery pipeline that combines feature-based molecular networking with mass spectrometry query language queries to systematically prioritize bioactive NRPs containing basic amino acids. Thus, we provide a comprehensive genus-wide inventory of NRPs produced by Paenibacillus spp. We thereby identified the paenitracins, a new sub-family of bacitracins active against multidrug-resistant gram-positive pathogens. Our pipeline enables the discovery of novel peptidic natural products to accelerate the prioritization of chemical space for antibiotics.},
}

@article {pmid41700805,
year = {2026},
author = {Zhou, S and Bai, X and Xue, B and Chu, W},
title = {A Vaginal Microbiota-Ovary Axis in Chemotherapy-Accelerated Ovarian Aging: Single-Cell Insights into Cellular Dysregulation.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioag042},
pmid = {41700805},
issn = {1529-7268},
abstract = {BACKGROUND: Chemotherapy-induced premature ovarian failure (POF) represents a major challenge to female reproductive health, yet the potential regulatory role of vaginal microbiota in this process remains largely unexplored.

RESULTS: Using a well-established model of chemotherapy-induced ovarian aging, we observed significant disruptions in vaginal microbial ecology characterized by depletion of Lactobacillus species and concomitant enrichment of pathogenic bacteria. Microbiota transplantation effectively reversed these dysbiosis patterns and restored ovarian function. Single-cell transcriptomic analysis revealed that microbial intervention promoted the recovery of granulosa and luteal cell populations while simultaneously suppressing inflammatory activation in ovarian stromal cells, demonstrating the vaginal microbiota's capacity to maintain follicular integrity. Further mechanistic insights showed that microbiota transplantation upregulated key antioxidant defense systems and ribosomal protein networks within ovarian cells, suggesting coordinated actions to mitigate oxidative stress and enhance cellular repair capacity, although the specific microbial metabolites mediating these effects require further elucidation.

CONCLUSIONS: Our findings establish for the first time the existence of a functional vaginal microbiota-ovary axis and delineate its critical role in protecting against chemotherapy-induced ovarian damage. This work not only advances our fundamental understanding of microbial-endocrine crosstalk but also identifies concrete microbial targets for developing innovative strategies to preserve fertility in cancer patients.},
}

@article {pmid41697449,
year = {2026},
author = {Zavřel, T and Pohland, AC and Pfennig, T and Matuszyńska, AB and Tóth, SZ and Bernát, G and Červený, J},
title = {Correction to: Estimating the redox state of the plastoquinone pool in algae and cyanobacteria via OJIP fluorescence: perspectives and limitations.},
journal = {Photosynthesis research},
volume = {164},
number = {2},
pages = {14},
doi = {10.1007/s11120-026-01203-7},
pmid = {41697449},
issn = {1573-5079},
}

@article {pmid41697388,
year = {2026},
author = {Ding, Z and Guo, Y and Guo, L and Ren, B and Yang, J and Li, J and Bai, L},
title = {Reintroduction of Grassland Plant Species Shapes Soil Bacterial Ecological Groups and Contributes Differently To Bacterial Diversity.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02718-1},
pmid = {41697388},
issn = {1432-184X},
support = {LJKMZ20221053//Foundation of Liaoning Province Education Administration/ ; X2021012//Shenyang Agricultural University/ ; },
}

@article {pmid41696024,
year = {2026},
author = {Pendleton, A and Schmidt, ML},
title = {Interpreting UniFrac with absolute abundance: a conceptual and practical guide.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf250},
pmid = {41696024},
issn = {2730-6151},
abstract = {[Formula: see text]-diversity is central to microbial ecology, yet commonly used metrics overlook changes in microbial load (or "absolute abundance"), limiting their ability to detect ecologically meaningful shifts. Popular for incorporating phylogenetic relationships, UniFrac distances currently default to relative abundance and therefore omit important variation in microbial abundances. As quantifying absolute abundance becomes more accessible, integrating this information into [Formula: see text]-diversity analyses is essential. Here, we introduce "Absolute UniFrac" ([Formula: see text]), a variant of Weighted UniFrac that incorporates absolute abundances. Using simulations and a reanalysis of four 16S rRNA metabarcoding datasets (from a nuclear reactor cooling tank, the mouse gut, a freshwater lake, and the peanut rhizospere), we demonstrate that Absolute UniFrac captures microbial load, composition, and phylogenetic relationships. While this can improve statistical power to detect ecological shifts, we also find Absolute Unifrac can be strongly correlated to differences in cell abundances alone. To balance these effects, we also incorporate absolute abundance into the generalized extension ([Formula: see text]) that has a tunable, continuous ecological parameter ([Formula: see text]) that modulates the relative contribution of rare versus abundant lineages to [Formula: see text]-diversity calculations. Finally, we benchmark GU[A] and show that although computationally slower than conventional alternatives, GU[A] is comparably sensitive to noise in load estimates compared to conventional alternatives like Bray-Curtis dissimilarities, particularly at lower [Formula: see text]. By coupling phylogeny, composition, and microbial load, Absolute Unifrac integrates three dimensions of ecological change, better equipping microbial ecologists to quantitatively compare microbial communities.},
}

@article {pmid41695957,
year = {2026},
author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H},
title = {Chloroflexota in agricultural soils: current knowledge and future research directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705889},
pmid = {41695957},
issn = {1664-302X},
abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.},
}

@article {pmid41695945,
year = {2026},
author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD},
title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759987},
pmid = {41695945},
issn = {1664-302X},
abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.},
}

@article {pmid41695141,
year = {2025},
author = {Uh, YR and Park, SN and Song, MJ},
title = {Characterization of the gut micro biota in Koreans and investigation of its association with probiotic consumption: implications for microbial ecology and host health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745533},
pmid = {41695141},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut micro biota is reportedly closely related to human health, and its composition and diversity are determined by a variety of factors, including age, diet, and probiotic intake. Although many studies on the gut micro biota have been conducted, most have focused on Western populations or have been limited by small sample sizes, making it difficult to understand micro biota differences across populations and lifestyles. In this study, we analyzed a large Korean cohort of 3,450 individuals, focusing on gut micro biome differences according to age and host-related markers, as well as the impact of probiotic supplementation.

METHODS: Fecal samples from 3,450 Koreans were analyzed using 16S rRNA gene sequencing (V3-V4 region). Bioinformatics and taxonomic analyses were performed to compare microbial composition and diversity according to age and probiotic intake.

RESULTS: The data revealed a significant increase in microbial diversity with age and distinct shifts in taxonomic composition between younger and older participants. In addition, probiotic intake did not alter overall community diversity but increased the detection of probiotics, suggesting that they serve as moderators rather than direct drivers of diversity.

CONCLUSION: These findings emphasize the importance of population-specific micro biome research and suggest that diverse host-related and lifestyle factors jointly contribute to shaping gut microbial ecology in Koreans. Probiotic supplementation primarily increased the detection of specific lactic acid bacteria and bifidobacterial species without substantially altering overall alpha diversity, consistent with a modulatory role on targeted taxa rather than broad community restructuring. Together, these results provide a useful framework for future studies linking probiotic-responsive microbial features to human health outcomes and for developing precision nutrition and probiotic strategies in Korean and similar populations.},
}

@article {pmid41695122,
year = {2026},
author = {Yash, and Ghosh, A and Dey, A and Sinha, M and Bera, N and Chakraborty, S and Bhadury, P},
title = {Genomic insights into Brevibacterium sediminis strain IMA_C3 isolated from an integrated mangrove aquaculture pond.},
journal = {Access microbiology},
volume = {8},
number = {2},
pages = {},
pmid = {41695122},
issn = {2516-8290},
abstract = {Brevibacterium sediminis strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond near the Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium at a salinity of 20. Phylogenetic analysis based on 16S rRNA sequencing showed a 99.67% identity with Brevibacterium linens AE038-8 from the International Nucleotide Sequence Database Collaboration DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing on the Oxford Nanopore MinION platform, with genome annotation performed against the NCBI Reference Sequence Database and The Genome Taxonomy Database databases. The genome is ~4.1 Mb in size, with a G+C content of 64.59 mol%. Functional analysis of the genome revealed genes related to complex carbon utilization, nitrogen and phosphate metabolism and metal transport. Additionally, the genome encodes secondary metabolites, including ε-poly-l-lysine, ectoine, terpene and phenazine, which could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.},
}

@article {pmid41695029,
year = {2026},
author = {Qin, H and Zhang, L and Rao, Z and Wei, X and Táncsics, A and Sheng, R and Liu, Y and Chen, A and Fang, C and Huang, F and Long, P and Zhu, B},
title = {Decoding endophytic microbiome dynamics: engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes.},
journal = {Horticulture research},
volume = {13},
number = {2},
pages = {uhaf286},
pmid = {41695029},
issn = {2662-6810},
abstract = {Biological control leveraging endophytic microbes represents a promising eco-friendly strategy to mitigate soil-borne diseases, yet the efficacy and mechanistic underpinnings of synthetic microbial communities (SynComs) derived from plant endophytes remain poorly understood. This study employed a holistic approach-integrating field sampling, microbial profiling, and functional validation-to investigate the dynamics of edible lily (Lilium) microbiomes under continuous cropping and develop targeted SynComs against Fusarium oxysporum. Metacommunity analysis revealed that prolonged monoculture co-enriched both potentially beneficial taxa (e.g. Pseudomonas, Bacillus) and pathogenic Fusarium, reflecting a dynamic equilibrium where naturally recruited antagonists were insufficient to prevent pathogen dominance, while increasing the complexity of endophytic co-occurrence networks. Keystone bacterial lineages, including Burkholderiaceae and Pseudomonas, emerged as critical stabilizers of the endosphere microbiome. Notably, 50% of endogenous bacterial taxa exhibited rhizospheric origins, contrasting with fungal communities where <10% derived from soil-a finding underscoring host-specific filtering mechanisms. Through systematic isolation and combinatorial testing, we engineered SynComs combining core antagonistic strains (Rhizobium, Methylobacterium, Talaromyces) with auxiliary microbes. Fungal-integrated SynComs outperformed bacteria-only consortia in plant growth promotion and pathogen suppression. By bridging fundamental microbial ecology with translational agriculture, our findings establish SynComs as scalable tools for sustainable soil health management, reducing reliance on synthetic fungicides while addressing the yield-limiting challenges in continuous cropping systems.},
}

@article {pmid41694331,
year = {2026},
author = {Mourot, R and Lebert, S and Martinez-Rabert, E and Barani, A and Grégori, G and Nunige, S and Dufour, A and Guasco, S and Larose, C and Bradley, JA},
title = {SIESTA Project: Svalbard summer 2025 expedition report.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {23},
pmid = {41694331},
issn = {2732-5121},
abstract = {Microbial dormancy plays an important role in the persistence, dispersal, and functioning of microbial communities in moderate to extreme environments. The activity or inactivity of microbial communities also has implications for rates of biogeochemical transformations and thus elemental stocks and redox conditions. Microbial communities inhabiting glacier surface environments encounter harsh and variable environmental conditions including nutrient limitation, low temperatures, and light availability across various micro-habitats including cryoconite and the bare ice surface. The metabolic states of cells within these microhabitats and in relation to their environment is fundamental to the functioning of the ecosystem and has implications for ecosystem resilience, responses to environmental change, and biogeochemical cycling. This report describes an expedition to Brøggerhalvøya, north-west Svalbard, carried out in July 2025, within the framework of the ERC SIESTA project. A major objective of the project is to resolve microbial activity and dormancy on an individual cell basis, to characterise the adaptive and functional traits of active and dormant fractions of the native glacier microbial population, and to link microbial metabolic states to broader ecological and biogeochemical dynamics. Here we report the site characteristics, the samples collected, the analyses undertaken, and the future analyses planned. Two small valley glaciers near to Ny-Ålesund were selected for investigation during this summer campaign: Midtre Lovénbreen and Austre Brøggerbreen. The data collected in the field, combined with subsequent laboratory analyses, will provide insights into the spectrum of dormancy and activity in situ among glacier microbial communities, and the taxa and functions associated with active and inactive fractions of the communities. These findings will contribute to a deeper understanding of the impacts and role of both short- and long-term microbial dormancy in glacial environments.},
}

@article {pmid41692701,
year = {2026},
author = {Keneally, C and Gaget, V and Chilton, D and Dornan, TN and Hensel, J and Keneally, AE and Kidd, SP and Brookes, JD},
title = {Extreme Salinity Change Governs Microbial Community Assembly and Interactions.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70301},
doi = {10.1111/1758-2229.70301},
pmid = {41692701},
issn = {1758-2229},
support = {2024316//Medical Research Future Fund/ ; },
mesh = {*Salinity ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; *Archaea/genetics/classification/metabolism/isolation & purification ; South Australia ; Ecosystem ; Seawater/microbiology/chemistry ; Wetlands ; Sulfur/metabolism ; },
abstract = {Coastal wetlands are highly vulnerable to climate-driven salinisation, which reshapes critical microbial processes underpinning nutrient cycling and energy flow. We examined how sediment microbial communities vary with salinity across the Coorong Lagoon (South Australia), spanning estuarine (0-40 g L[-1]), intermediate (40-100 g L[-1]) and hypersaline (100-150 g L[-1]) waters. Salinity was found to be the dominant driver of sediment microbial community composition, diversity and assembly. High salinity favoured specialists and homogenous community structures, with generalist bacteria persisting across intermediate salinities and supporting ecosystem resilience. Sulfur and carbon cycling is likely dependent on salinity, as bacterial sulfur-oxidisers were abundant estuarine specialists, whereas methane producers (Archaeal methanogens) and sulfate-reducers were enriched at high salinity. Deterministic microbial community assembly (homogeneous selection) was dominant, increasing at extreme salinity, which acted as a strong environmental filter. Community complexity increased at both high and low salinity ranges, with intermediate salinity exhibiting less complexity, suggesting community reorganisation under osmotic stress. The varied roles of specialists and generalists at different salinities support ecosystem function, where increased heterogeneity and specialisation in hypersaline conditions suggest vulnerability of the community to disturbance. These findings provide insight into how microbially underpinned ecosystems may respond to future climate-driven salinisation, important for making predictions and informing mitigation strategies.},
}

*Salinity
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota
*Geologic Sediments/microbiology/chemistry
*Archaea/genetics/classification/metabolism/isolation & purification
South Australia
Ecosystem
Seawater/microbiology/chemistry
Wetlands
Sulfur/metabolism

@article {pmid41691943,
year = {2026},
author = {Huang, J and Tan, Z and Sun, R and Dai, Z and He, L and Li, C},
title = {Vertical and spatial variations of microbial communities in sediment cores from the mangrove of Gaoqiao National Nature Reserve.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119416},
doi = {10.1016/j.marpolbul.2026.119416},
pmid = {41691943},
issn = {1879-3363},
abstract = {Sediment microbial communities act as key regulators of mangrove ecosystem functions. However, systematic studies on the spatial distribution characteristics, potential functions, and environmental driving mechanisms of microbial communities within sediment cores in mangrove ecosystems remain scarce. In this study, fifteen sediment cores were obtained from the mangrove within the Gaoqiao National Nature Reserve. The microbial community composition within the sediment cores was investigated using 16S rRNA high-throughput sequencing. Significant differences in microbial community structure were observed among the three designated zones (Nearshore, Mangrove, and Offshore) and across different sediment depths ranging from 0 to 80 cm. The dominant bacterial phyla identified comprised Pseudomonadota, Actinomycetota, and Chloroflexota, along with the archaeal phylum Thermoplasmatota. Their distributions demonstrated clear biogeographic and vertical stratification patterns. Functional prediction revealed that microbial communities extensively involved in carbon, nitrogen, and sulfur cycles exhibited higher richness, as these communities demonstrated stronger expression of metabolic functional genes. Furthermore, the abundance of metabolic functional genes was found to be higher in the mid-depth sediments at depths of 30 to 45 cm. Redundancy analysis (RDA) and variation partitioning analysis (VPA)demonstrated that sediment pH, electrical conductivity (EC), and total organic carbon (TOC) content were identified as the primary environmental factors governing the succession of both microbial community structure and function. This study advances our understanding of mangrove sediment microbial ecology and provides a scientific basis for targeted conservation and restoration of the Gaoqiao mangrove ecosystem.},
}

@article {pmid41691853,
year = {2026},
author = {Wei, Y and Chen, Y and Lv, S and Ou, D and Tao, Y and Zhou, Y and Yang, J and Song, X},
title = {Persistence of the coccidiostat robenidine in soil and its impacts on the soil microbiome and enzyme functions.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119858},
doi = {10.1016/j.ecoenv.2026.119858},
pmid = {41691853},
issn = {1090-2414},
abstract = {Robenidine is a synthetic coccidiostat that is excreted from animals in its prototype form, leading to soil contamination. Despite its widespread use, comprehensive environmental risk assessments remain limited. Consequently, we initially constructed a manure-soil microcosm and investigated the degradation pattern of robenidine using a highly efficient HPLC-dSPE method. The degradation half-lives of robenidine in soil were 14.74 days at 0.8 mg/kg and 21.26 days at 8 mg/kg. Exposure to 8 mg/kg of robenidine significantly altered the soil microbial community, leading to a 140.0 % increase in the abundance of Proteobacteria. However, the Shannon index indicated that soil microbial diversity decreased by 32.4 % from 1 d to 60 d. Compared to the control check group, 8 mg/kg of robenidine significantly increased the abundance of harmful bacteria (e.g., unclassified_Intrasporangiaceae increased by 33.5 %) in the soil at 60 d, while simultaneously reducing the populations of beneficial bacteria such as Bacillaceae (decreased by 23.8 %), Pseudograilibacillus (decreased by 39.6 %), and Massilia (decreased by 31.7 %). Network correlation and FAPROTAX analyses indicated that long-term exposure to robenidine inhibited chitinolysis and aromatic compound degradation pathways. Furthermore, low-dose robenidine increased the activities of dehydrogenase, acid phosphatase, and β-glucosidase by 34.0 %, 24.7 %, and 21.6 % at 1 d, respectively, while these enzymes returned to control levels over time. These findings provide critical insights into the biological and metabolic impacts of robenidine exposure on soil microbial communities, which is crucial for clarifying the ecological concerns associated with robenidine.},
}

@article {pmid41691349,
year = {2026},
author = {Fan, S and Liu, H and Yan, Y and Xu, M and Wan, X and Hao, Y and Gong, C and Wang, C and Zhang, Y and Liu, D and Zheng, J and Chen, J},
title = {Metatranscriptomic analyses of gut bacterial and viral communities in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) under distinct environments.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00528-x},
pmid = {41691349},
issn = {2524-4671},
}

@article {pmid41690572,
year = {2026},
author = {Koffel, T and Grimaud, G and Litchman, E and Klausmeier, CA},
title = {Metabolically structured population models: a unifying framework for microbial ecology and evolution.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {112410},
doi = {10.1016/j.jtbi.2026.112410},
pmid = {41690572},
issn = {1095-8541},
abstract = {Cells grow by acquiring external resources and transforming them internally, forming new cells as they divide. Metabolic networks focus on the flow of such resources within the cell as they undergo series of biochemical reactions. How population growth emerges from these complex dynamical networks remains unclear. Modeling the emergence of population growth, a central ecological concept, is thus essential to understand the forces shaping microbial communities. Here we present a novel theoretical framework that builds on structured population theory to model the growth of cell populations whose intracellular dynamics are driven by arbitrarily complex metabolic networks. Population growth is driven by limitation regimes, which capture how reaction-level limitations combine in the network to determine growth rate. Resource availability changes trigger switches between limitation regimes, capturing resource interaction and colimitation. We also discovered alternative metabolic states, where different regimes are reached depending on initial metabolite concentrations. We first use a minimal metabolic network of limitation by two essential resources to illustrate our framework, then apply it to E. coli's glycolysis pathway to showcase its capabilities on a more realistic, albeit still simplistic, network. By integrating metabolic networks into ecological theories, our work provides a mechanistic foundation for understanding the structure and evolution of microbial communities.},
}

@article {pmid41646430,
year = {2026},
author = {Thompson, AW and Lamberson, K and Sutherland, KR},
title = {Coexisting salps exhibit distinct feeding selectivity on microorganisms in the North Pacific Subtropical Gyre.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {41646430},
issn = {2693-5015},
abstract = {Mortality mechanisms play an important role in how oceanic microorganisms contribute to global biogeochemical cycles. Salps are widespread pelagic tunicates known to remove phytoplankton from coastal and high-latitude waters, but their interaction with microorganisms in the vast tropical and subtropical gyres is not well quantified. Using quantitative measurements of six major marine microorganisms in the guts of six distinct but co-occurring salp species from the North Pacific Subtropical Gyre, we examined the impact and dynamics of salp feeding on marine microorganisms in a vast open ocean region. All salps preferentially removed prey greater than 1 μm in diameter, including marine Synechococcus, diatoms, Crocosphaera, and Chrysochromulina, while the smaller Prochlorococcus and SAR11 were not a major source of prey biomass. We also found that salp feeding varied between salp taxa with some salp guts dominated by both Crocosphaera and Chrysochromulina while others were dominated by Crocosphaera alone. Together, these results suggest that salp impacts are not uniform across taxa and their patterns of selective feeding among marine microbes requires consideration of species-specific feeding strategies and environmental context. Further, this work suggests that the mortality pressure of salp feeding on marine microorganisms may shape microbial community structure and that this pressure varies with the diversity and dynamics of macrozooplankton predators.},
}

@article {pmid41690245,
year = {2026},
author = {Hu, J and Zhou, Y and Ishii, S and Ahmed, W and Sadowsky, MJ and Xia, X and Du, Z and Cytryn, E and Mwakalapa, EB and Rivera, WL and Zhou, Y and Rensing, C and Zhang, Q},
title = {Sources, contamination pathways, and monitoring of pathogens in urban estuaries.},
journal = {Marine pollution bulletin},
volume = {226},
number = {},
pages = {119415},
doi = {10.1016/j.marpolbul.2026.119415},
pmid = {41690245},
issn = {1879-3363},
abstract = {Urban estuaries are critical ecological and socio-economic interfaces but are increasingly impacted by microbial pathogen contamination driven by anthropogenic activities such as wastewater discharge, stormwater runoff, agriculture, and wildlife inputs. Despite extensive documentation of estuarine pathogens, effective risk assessment and management remain constrained by key knowledge gaps related to source apportionment, environmental fate, and monitoring relevance. This review synthesizes current understanding of pathogen sources and transmission pathways in urban estuaries and critically examines the physicochemical, hydrodynamic, and sediment-mediated processes that regulate pathogen persistence, redistribution, and exposure risk. We identify three interconnected challenges: (i) limited resolution in differentiating human and non-human contamination sources due to overlapping microbial signatures; (ii) inadequate incorporation of estuarine hydrodynamics and sediment reservoirs into fate-and-transport frameworks; and (iii) misalignment between conventional monitoring indicators and actual pathogen and antimicrobial resistance risks. Emerging approaches, including microbial source tracking, sequencing-based surveillance, biosensors, and hybrid predictive modelling, are evaluated for their capacity to support risk-relevant decision-making. Framed within a One Health perspective, this review integrates microbial ecology, environmental processes, and surveillance technologies to support evidence-based management and sustainable mitigation of pathogen risks in urban estuaries.},
}

@article {pmid41689629,
year = {2026},
author = {Mohammadzadeh, MH and Asadollahpour, M and Sharbatdar, HR and Darbouy, MS and Fekrirad, Z},
title = {Voices of Eukaryotic Microbes: Chemical Communication Via Quorum Sensing.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02716-3},
pmid = {41689629},
issn = {1432-184X},
abstract = {Quorum sensing (QS) is a cell-cell communication mechanism mediated by secreted hormone-like signaling molecules that operates in both Gram-positive and Gram-negative bacteria, driving coordinated alterations in gene expression once a critical cell density is reached. In these prokaryotic systems, bacteria produce, release, detect, and respond to small autoinducers, such as acyl-homoserine lactones in Gram-negative bacteria, oligopeptides in Gram-positive bacteria, and the universal autoinducer-2, to regulate community behaviors including biofilm formation, virulence factor production, and stress adaptation. The concept of QS in eukaryotic microbes emerged decades ago, and later investigations confirmed that unicellular fungi and protozoa similarly measure population density to regulate collective activities. In Saccharomyces cerevisiae, aromatic alcohols (2-phenylethanol, tryptophol, tyrosol) serve as QS signals to control filamentous growth, biofilm assembly, and environmental stress responses. Candida albicans employs farnesol to suppress hyphal development while utilizing tyrosol to accelerate germ tube emergence and biofilm maturation. African trypanosomes, including Trypanosoma brucei and related species, generate oligopeptides via secreted peptidases that accumulate as stumpy induction factors (SIFs), triggering a density-dependent shift from proliferative slender forms to transmission-competent stumpy forms essential for tsetse fly infection. QS-based mechanisms influence virulence factors in fungal and protozoan pathogens, affecting their ability to colonize hosts. Exploring QS in eukaryotic organisms opens new possibilities for antifungal treatments and parasite management. By interfering with QS signaling, researchers can disrupt fungal biofilm formation and regulate protozoan development, paving the way for innovative disease control methods.},
}

@article {pmid41687498,
year = {2026},
author = {Liao, B and Wang, Q and Zhang, T and Lu, X and Fang, N},
title = {Optimizing carbon source strategy for denitrification using food waste fermentation liquid: Synergistic mechanisms of butyrate and sucrose.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128950},
doi = {10.1016/j.jenvman.2026.128950},
pmid = {41687498},
issn = {1095-8630},
abstract = {Food waste fermentation liquid, rich in volatile fatty acids (VFAs) and carbohydrates, serves as a sustainable electron donor for biological nitrogen removal. However, the compositional fluctuation of fermentation liquid often leads to unstable denitrification, and the mechanistic influence of mixed VFA-saccharide interactions on microbial ecology remains poorly understood. In this study, four carbon-source systems-three simulating typical mixed fermentation products (acetate + sucrose, propionate + sucrose, butyrate + sucrose) and one single-carbon control (acetate alone)-were systematically evaluated in sequencing batch reactors (SBRs). Results indicated that the butyrate-sucrose system (A3) exhibited superior performance, achieving a nitrate removal efficiency of 98.5%, which was 13.5% and 8.2% higher than that of the acetate-sucrose (A1) and propionate-sucrose (A2) systems, respectively. Furthermore, A3 maintained the lowest nitrite accumulation (<0.5 mg/L). Mechanistically, A3 facilitated the selective enrichment of functional genera Ferruginibacter and Terrimonas. PICRUSt2 functional predictions revealed that this specific combination significantly enhanced KEGG pathways related to membrane transport (ABC transporters) and energy metabolism, suggesting a synergistic effect that accelerates electron transfer and metabolic turnover. This study demonstrates that regulating acidogenic fermentation towards a butyrate-dominant composition is a promising strategy to maximize the utility of food waste as a carbon source, ensuring robust nitrogen removal in wastewater treatment.},
}

@article {pmid41687164,
year = {2026},
author = {Kim, D and Yun, N and Du, H and Li, C and Preheim, S and Rossi, R},
title = {Enabling microbial electrolysis cell scale-up via electrochemistry-, hydrodynamic-, and microbial ecology-informed framework.},
journal = {Water research},
volume = {294},
number = {},
pages = {125503},
doi = {10.1016/j.watres.2026.125503},
pmid = {41687164},
issn = {1879-2448},
abstract = {Microbial electrolysis cells (MECs) can produce green hydrogen while removing organic contaminants from liquid waste streams by leveraging the metabolic activity of electroactive microorganisms. Despite their potential in a sustainable, circular economy, large-scale MECs that can treat relevant volumes of wastewater have failed to deliver performance proportional to their lab-scale counterparts. The reason behind this lower performance at scale remains unclear. In this study, we developed a combined electrochemistry-, hydrodynamic-, and microbial ecology-informed framework to analyze and optimize MEC performance during scale-up, enabling accurate quantification of major limitations and the identification of strategies to overcome them, ultimately facilitating equivalent performance at scale. Applying this framework to the scale-up of a zero-gap MEC from 9 cm[2] electrode area to 100 cm[2] electrode area, resulted in similar maximum current densities in a 100 cm[2] MEC (21.7 ± 1.1 A/m[2]) compared to a 9 cm[2] system (25.1 ± 2.7 A/m[2]), as well as equivalent hydrogen production rates of 69.3 L/L-d (100 cm[2]) and 67.7 ± 2.4 L/L-d (9 cm[2]). COMSOL flow dynamics simulations were used to scale up the reactor configuration without negatively affecting electrolyte velocity and distribution in the cell, minimizing the increase in internal resistances during scale-up (11.7 ± 0.5 mΩm[2] at 9 cm[2]; 19.7 ± 1.3 mΩm[2] at 100 cm[2]). Microbial community structures were assessed at both scales using high-throughput sequencing, highlighting the differences of populations across electrode dimensions and operational parameters. The framework presented here accelerates the development of effective strategies toward the scale-up of MECs by furthering the understanding of how electrochemical, hydrodynamic, and microbial ecology parameters change as the reactor dimension is increased. Ultimately, this approach contributes to advancing electrochemical biotechnology toward practical deployment in energy-efficient wastewater treatment systems.},
}

@article {pmid41686264,
year = {2026},
author = {Wu, CY and Cheng, HY and Lin, YC and Wang, YC and Meng, YZ and Hsieh, YE and Liu, AC and Yang, SH},
title = {Role of Core Microbiome Shifts in Octocoral Litophyton Under Diurnal Temperature Fluctuations.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02715-4},
pmid = {41686264},
issn = {1432-184X},
support = {NSTC 112-2611-M-002 -020//National Science and Technology Council/ ; NTUCCP- 115L891306//National Taiwan University/ ; },
abstract = {Climate change is projected to raise sea surface temperatures and intensify diurnal temperature fluctuations (DTF), threatening the survival of both scleractinian corals and octocorals. Litophyton, a common octocoral in Taiwan's shallow reefs, is frequently exposed to large DTF and summer heat stress, making it a suitable model to study thermal resilience. Coral-associated bacterial communities are known to shift under thermal stress, and key bacterial taxa may play crucial roles in host acclimation. This study aimed to address two questions: (1) Can higher DTF mitigate cumulative heat stress in octocorals? (2) If so, what physiological and microbial community changes accompany this effect? To answer these questions, we conducted tank experiments under constant warming and two short-term DTF regimes (± 5 °C and ± 7 °C; baseline 25-27.8 °C), along with a no-fluctuation control. We measured physiological stress indicators, including superoxide dismutase (SOD) and catalase (CAT) activities, and monitored bacterial community dynamics. Our results show that DTF helped maintain stable photosynthetic efficiency (Fv/Fm) compared to constant warming. Notably, significant differences in ROS activity were only observed in the ± 5 °C group, rather than in the larger ± 7 °C group, indicating a measurable alleviation of thermal stress and greater plasticity in Litophyton coping with temperature changes. Moreover, 29.4% more significantly abundant in the ± 7 °C group compared to the control in the core microbiome Endozoicomonas preceded detectable physiological changes in the host, suggesting a potential role in early stress mitigation. These findings deepen our understanding of octocoral holobiont resilience under fluctuating thermal regimes and highlight Endozoicomonas diversity as a potential indicator of Litophyton health.},
}

@article {pmid41685888,
year = {2026},
author = {Gilson, M and Bayon-Vicente, G and Krings, S and Toubeau, L and Wattiez, R and Leroy, B},
title = {Fundamental aspects of sucrose metabolism reveal a trophic link between Rhodospirillum rubrum and Rhodobacter capsulatus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0371725},
doi = {10.1128/mbio.03717-25},
pmid = {41685888},
issn = {2150-7511},
abstract = {Purple non-sulfur bacteria (PNSB) are well known to have an exceptional metabolic versatility. However, while the growth of PNSB on sugar-rich streams has been extensively explored, their ability to metabolize sugars is poorly understood. Here, we explore the metabolic mechanisms of sucrose, glucose, and fructose utilization in two phototrophic PNSB, Rhodospirillum rubrum and Rhodobacter capsulatus. Our findings demonstrate distinct carbohydrate assimilation capacities, as well as the use of different metabolic strategies for each species. Moreover, a trophic link was identified between the two species during co-cultivation, resulting from the production of fermentation by-products by Rh. capsulatus, which are then reassimilated by Rs. rubrum. Finally, we demonstrate that the synergy observed between Rs. rubrum and Rh. capsulatus can be successfully scaled up in a photobioreactor system. Our study highlights how fundamental knowledge of metabolism and the establishment of a trophic link between two PNSB species might be useful for the development of biobased economy and resource recovery strategies.IMPORTANCEThe diverse metabolic capacities found in microbial communities expand the possibilities of microbial biotechnological exploitation. In this study, we demonstrate that Rhodospirillum rubrum and Rhodobacter capsulatus, two purple non-sulfur bacteria, adopt different metabolic strategies for sugar assimilation. These differences allow them to benefit from each other, resulting in enhanced carbon yield and productivity compared to pure cultures. We also showed that the trophic link between both species can be scaled up in a photobioreactor system. Understanding these interactions expands the potential for designing microbial consortia optimized for the valorization of carbohydrate-rich waste streams using purple non-sulfur bacteria.},
}

@article {pmid41683185,
year = {2026},
author = {Song, D and Song, L and Zhong, X and Wu, Y and Zhang, Y and Yang, L},
title = {Integrated Molecular Informatics and Sensory-Omics Study of Core Trace Components and Microbial Communities in Sauce-Aroma High-Temperature Daqu from Chishui River Basin.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683185},
issn = {2304-8158},
support = {MTXYTD202501//Science and Technology Innovation Team of Moutai Institute/ ; QianKeHeJiChu-ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; ZunShiKeHe HZ Zi[2023]112//The Fund of Zunyi Technology and Big data Bureau, Moutai Institute Joint Science and Technology Research and Development Project/ ; mygccrc[2022]011, mygccrc[2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Industry Group Co., Ltd/ ; },
abstract = {Flavor-relevant trace volatiles and microbial communities were examined in six sauce-aroma high-temperature Daqu samples. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS) quantified 210 trace volatile compounds across 14 chemical classes. Orthogonal partial least squares discriminant analysis (OPLS-DA) with variable importance in projection (VIP) screening was integrated with sensory scoring, correlation analysis, and molecular docking to an olfactory receptor model. Volatile profiles showed clear stratification in total abundance. Pyrazines dominated the high-total group. Tetramethylpyrazine served as a major driver. Sensory evaluation indicated that aroma explained overall quality best. (E)-2-pentenal and dimethyl trisulfide showed significant positive associations with aroma and overall scores. In the olfactory receptor, the polar residue module that provides directional constraints for Daqu odor activation was formed by Ser75, Ser92, Ser152, Ser258, Thr74, Thr76, Thr98, Thr200, Gln99, and Glu94. The hydrogen-bond or charge network was further reinforced by Arg150, Arg262, Asn194, His180, His261, Asp182, and Gln181. The core discriminant set comprised acetic acid, hexanoic acid, (E)-2-pentenal, nonanal, decanal, dimethyl trisulfide, trans-3-methyl-2-n-propylthiophane, 2-hexanone oxime, ethyl linoleate, propylene glycol, 2-ethenyl-6-methylpyrazine, 4-methylquinazoline, 5-methyl-2-phenyl-2-hexenal, and 1,2,3,4-tetramethoxybenzene. Sequencing revealed higher bacterial diversity than fungal. Bacillus and Kroppenstedtia were dominant bacterial genera. Aspergillus, Paecilomyces, Monascus, and Penicillium were major fungal genera. Correlation patterns suggested that Bacillus and Monascus were positively linked to acetic acid and 1,2,3,4-tetramethoxybenzene. Together, these results connected chemical fingerprints, sensory performance, receptor-level plausibility, and microbial ecology. Concrete targets are provided for quality control of high-temperature Daqu.},
}

@article {pmid41683077,
year = {2026},
author = {Jiang, X and Li, X and Song, P and Dou, Y and Xue, J and Wu, Z and Ma, S and Wei, W and Zheng, W and Dou, S and Dong, L},
title = {Analysis of Microbial Interactions During the Production of Chinese Ethnic Fermented Foods.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683077},
issn = {2304-8158},
support = {No.2025-MSLH-016//Liaoning Provincial Science and Technology Plan Joint Plan (Natural Science Foundation-General Program)/ ; 2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS20230376//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; },
abstract = {Food fermentation is an ancient bioprocess characterized by complex biochemical transformations driven primarily by microbial communities. Across the diverse regions of China, various ethnic groups have developed a rich array of traditional fermented foods through long-term practical experience. These foods are integral to local culinary heritage and provide valuable systems for studying microbial ecology and function. From the perspective of microbial interactions, this review summarizes key concepts and major interaction types-including mutualism, commensalism, and competition-and describes how bacteria, yeasts, and molds interact via metabolic division of labor to drive substrate conversion, flavor formation, preservation, and biosynthesis of functional compounds. Focusing on four representative ethnic fermented foods-Dong fermented fish, Mongoslian milk curd, Miao sour soup, and Manchurian kombucha-we analyze how microbial interactions contribute to product quality, safety, and sensory attributes. Given current challenges in industrializing traditional fermented foods, such as poor standardization and variable quality, we propose future research directions centered on modern microbiome tools, designed microbial consortia, and process optimization. This work aims to provide a scientific foundation and practical strategies for modernization and quality improvement of traditional fermented foods.},
}

@article {pmid41681446,
year = {2026},
author = {Onbaşılar, EE and Yalçın, S and Batur, B and Yalçın, S and Kılıçlı, İB and Bakıcı, C and Bakır, B and Kartal, YK and Sel, T},
title = {Effects of Xylanase and Protease Supplementation on Growth Performance, Meat Quality, Gut Health, Cecal Fermentation, and Bone Traits in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030465},
pmid = {41681446},
issn = {2076-2615},
abstract = {This study investigated the effects of dietary xylanase and protease supplementation, applied individually or in combination, on growth performance, intestinal characteristics, gut fermentation, meat quality, and skeletal traits in broiler chickens. A total of 540-day-old male broiler chicks were allocated to six experimental groups and fed a control corn-soybean meal-based diet or diets supplemented with xylanase, protease, or a xylanase-protease combination. Enzyme supplementation significantly improved body weight gain and feed efficiency, particularly between days 22 and 42, and reduced intestinal digesta viscosity. Improvements in gut morphology were reflected by increased villus height and villus-to-crypt ratios, accompanied by higher cecal total volatile fatty acid concentrations, increased Lactobacillus populations, and reduced coliform counts. In contrast, breast meat physicochemical composition and antioxidant status were not affected by dietary treatments. Skeletal development was positively influenced, with improvements observed in selected morphometric and structural bone traits. Overall, dietary xylanase and protease supplementation enhanced broiler performance and skeletal development primarily through improved digestive efficiency and favorable modulation of gut morphology, microbial ecology, and intestinal fermentation, without adverse effects on meat quality.},
}

@article {pmid41681371,
year = {2026},
author = {Tang, D and Chen, S and Tang, C and Li, X and Li, M and Li, X and Zhang, K and Ma, J},
title = {The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030390},
pmid = {41681371},
issn = {2076-2615},
support = {2021YFYZ0009//Main livestock and poultry molecular breeding platform (Breeding research project)/ ; CARS-43-A-3//Supported by the earmarked fund for China Agriculture Research System/ ; },
abstract = {This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine.},
}

@article {pmid41680172,
year = {2026},
author = {Lu, Q and Wang, K and Gu, S and Ma, J and Cui, D and Chi, Z and Li, B and Zai, X and Wang, N and Wang, T and Dou, Z and Zhang, F and Geisen, S and Raaijmakers, JM and Song, C and Zuo, Y},
title = {Siderophore-producing Bacillus and free-living nematodes are associated with soil suppressiveness to banana root-knot nematodes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69647-y},
pmid = {41680172},
issn = {2041-1723},
support = {No. 32372810//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32302668//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 42577142//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The control of soil-borne diseases is crucial for ensuring global food security. Here, we investigate the impact of the root-knot nematode (Meloidogyne) on banana continuous cropping over a period of 11 years. The results show significant root infestation initially, but disease incidence declined markedly from the 7th cropping year onwards. Soil community profiling revealed that this intriguing onset of nematode suppressiveness was associated with changes in free-living nematode populations and rhizosphere microbiome composition. Rhizosphere microbiome analyses and strain isolation pinpointed Bacillus velezensis as a keystone taxon in soil suppressiveness to Meloidogyne. Genomics, metabolomics and bioassays validated the suppressive effects of B. velezensis against Meloidogyne and identified the siderophore bacillibactin as key metabolite with repellent and nematicidal activities. By integrating long-term field studies with multi-omics approaches, this study uncovered co-occurring increases in specific rhizobacterial genera and free-living nematodes associated with reduced root-parasitic nematode populations, offering valuable insights for sustainable agriculture.},
}

@article {pmid41679819,
year = {2026},
author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M},
title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124886},
doi = {10.1016/j.carbpol.2026.124886},
pmid = {41679819},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation & purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.},
}

*Gastrointestinal Microbiome/drug effects
*Galactans/chemistry/pharmacology/isolation & purification
Fermentation
*Agaricales/chemistry
Molecular Docking Simulation
Fatty Acids, Volatile/metabolism
Prebiotics

@article {pmid41679575,
year = {2026},
author = {Kovarova, A and Ryan, K and Tumeo, A and McDonagh, F and Clarke, C and Cormican, M and Miliotis, G},
title = {Emergence of dual β-lactam and Colistin resistance via blaFRI-8 and mcr-10.2 co-carriage on an IncFII family plasmid in Enterobacter vonholyi.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105899},
doi = {10.1016/j.meegid.2026.105899},
pmid = {41679575},
issn = {1567-7257},
abstract = {OBJECTIVES: Enterobacter vonholyi isolate E323169 represents a rare case of co-carriage of the antimicrobial resistance genes (ARGs) blaFRI-8, mcr-10.2, isolated from a clinical rectal swab. E323169 represents one of only 11 known E. vonholyi genomes. To date, within the NCBI Pathogen Detection resource, blaFRI-8 was identified in three assemblies and mcr-10.2 in two. In that dataset, blaFRI-8 co-occurred with an mcr-10 hit only once (Enterobacter asburiae). This study analyzes the genomic, phenotypic and epidemiological importance of this rare co-occurrence.

METHODS: Species identification for E323169 was initially assigned by MALDI-TOF and subsequently confirmed using a multifactorial genomic workflow. Antimicrobial susceptibilities were determined by MIC assay. The genome of E323169 was sequenced on an Illumina-NextSeq-1000, assembled, and annotated for ARGs, virulence factors, and plasmid replicons detection. Comparative phylogenomics used all canonical E. vonholyi RefSeq assemblies, and NCBI metadata were analysed for plasmid distributions of blaFRI-8 and mcr-10.2.

RESULTS: E323169 carried six ARGs: four chromosomally encoded (blaACT-91, fosA, oqxA10, oqxB9) and two plasmid-borne (blaFRI-8 and mcr-10.2) co-located on IncFII(p14)_1_p14 replicon. Additional plasmid replicons: Col(MG828)_1 and ColRNAI_1 were also identified. By mining the NCBI Pathogen Detection pipeline, we identified blaFRI-8 on IncFII replicon in E. asburiae JBIWA002, and mcr-10.2 on a multi-replicon (IncFIB/IncFII) plasmid in E. kobei 11,778-yvys.

CONCLUSION: This report, to our knowledge, represents the first E. vonholyi isolate co-harboring blaFRI-8 and mcr-10.2 on a single IncFII family plasmid in a non Enterobacter cloacae complex species, showing the widening host range of plasmid-mediated resistance to carbapenems/colistin. These findings suggest IncFII-family plasmids as recurrent scaffolds for the accumulation of high-impact resistance determinants in Enterobacter and suggest that monitoring IncFII backbones may provide an early warning signal for future convergence events.

IMPACT STATEMENT: The detection of Enterobacter vonholyi across human, animal, plant, and environmental sources underscore its relevance within a One Health framework, highlighting the potential for cross-sectoral circulation of antimicrobial resistance. The convergence of blaFRI-8 and mcr-10.2 on an IncFII plasmid in E. vonholyi exposes an unrecognized reservoir of last-line resistance in a species prone to misidentification. Together, these findings emphasize the importance of integrating genomic surveillance into routine diagnostics to identify hidden reservoirs of carbapenem and colistin resistance and to strengthen infection prevention strategies before wider dissemination occurs.},
}

@article {pmid41677726,
year = {2026},
author = {Zeng, T and Zuo, L and Yu, Q and Wu, Q and Bao, Z and Xiong, H and Luo, M and Li, B},
title = {Role and Mechanisms of Gut Microbiota in Infectious Diseases: Recent Evidence from Animal Models.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677726},
issn = {2079-7737},
support = {XGKJ2024010037//Xiaogan Municipal Bureau of Science and Technology (Hubei Province， China)/ ; 2025K009//Hubei Small Town Development Research Center, Hubei University of Engineering/ ; },
abstract = {Infectious diseases present persistent and complex challenges to global public health, with conventional antibiotic therapies increasingly limited by antimicrobial resistance, microbiota disruption, and adverse effects. There is a critical need to explore complementary strategies that augment host defense mechanisms without exacerbating these limitations. Accumulating evidence underscores the integral role of the gut microbiota-a diverse microbial ecosystem within the gastrointestinal tract-in regulating systemic immunity and pathogen susceptibility. This review synthesizes recent advances from animal models to delineate the multi-faceted mechanisms by which commensal microbes and their metabolites confer protection against enteric and respiratory infections. Key processes include competitive exclusion for nutrients and ecological niches, production of antimicrobial compounds, reinforcement of intestinal barrier integrity, and orchestration of local and systemic immunity via gut-lung axes. We further discuss the potential of microbiota-targeted interventions to enhance treatment efficacy and patient outcomes. By integrating mechanistic insights with translational applications, this review aims to inform the rational design of next-generation anti-infective strategies grounded in microbial ecology and host immunobiology.},
}

@article {pmid41675709,
year = {2025},
author = {Lin, W and Niu, M and Mu, C and Wang, C and Ye, Y},
title = {Key species drive community and functional stability of segment-specific gut microbiomes after the swimming crab molting.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e51},
pmid = {41675709},
issn = {2996-9514},
abstract = {Molting is a crucial process for crab growth and development. However, the impacts of molting on the structure and function of the gut bacterial community in swimming crab Portunus trituberculatus are poorly understood. Then, dynamic changes in the microbiotas of gut segments (foregut, midgut, and hindgut) after molting were investigated using 16S rRNA gene amplicon and shotgun metagenomic sequencing. We highlight the segment-specific responses in bacterial community compositions, alpha-diversity, and co-occurrence patterns, emphasizing the significant impact of hindgut bacteria on the analysis of the whole gut. The identification of enriched and emerged species and their source, coupled with insights into functional stability and multifunctionality, adds granularity to our understanding of postmolt microbial ecology. We offer potential keys to driving microbial community succession. These findings provide essential insights into the stability and dynamics of gut microbiota, which are crucial for both ecological understanding and sustainable management of crab probiotic regulation.},
}

@article {pmid41674154,
year = {2026},
author = {Măgălie, A and Marantos, A and O'Brien, JM and Schwartz, DA and Marchi, J and Lennon, JT and Weitz, JS},
title = {Phage infection fronts trigger early sporulation and viral entrapment in bacterial populations.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag023},
pmid = {41674154},
issn = {1751-7370},
abstract = {Bacteriophage (phage) infect, lyse, and propagate within bacterial populations. However, physiological changes in bacterial cell state can protect against infection even within genetically susceptible populations. One such example is the generation of endospores by Bacillus and its relatives, characterized by a reversible state of reduced metabolic activity that protects cells against stressors including desiccation, energy limitation, antibiotics, and infection by phage. Here we tested how sporulation at the cellular scale impacts phage dynamics at population scales when propagating amongst B. subtilis in spatially structured environments. Plaques resulting from infection and lysis were approximately 3-fold smaller on lawns of spore-forming bacteria vs. non-spore-forming bacteria. Analysis of plaque growth revealed that final plaque size was reduced due to an early termination of expanding phage plaques rather than the reduction of plaque growth speed. Microscopic imaging of the plaques revealed "sporulation rings", i.e., spores enriched around plaque edges relative to phage-free regions. We developed a series of mathematical models of phage, bacteria, spore, and small molecules that recapitulate plaque dynamics. We show evidence that phage infections trigger the formation of sporulation rings that reduce the productivity of phage infections and halt plaque spread even when resources are available for infection and lysis further away from plaque centers. Moreover, sporulation rings are also enriched in viable virospores, suggesting that although dormancy limits phage infections at population scales in the near-term, viruses may co-opt phage-avoidance strategies to re-emerge over the long-term, opening new avenues to explore the entangled fates of phages and their bacterial hosts.},
}

@article {pmid41673345,
year = {2026},
author = {Lafont, A and Violle, C and Ranchou-Peyruse, M and Guignard, M and Mura, J and Fargetton, T and Cézac, P and Ranchou-Peyruse, A},
title = {Successional Trajectories of Deep Subsurface Microbiomes in Response To Experimental Dihydrogen Injection.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02697-3},
pmid = {41673345},
issn = {1432-184X},
support = {ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; ANR-20-CHIN-0001//Agence Nationale de la Recherche/ ; },
abstract = {Converting pre-existing gas storage facilities to dihydrogen storage raises critical questions about storage quality and dihydrogen consumption by prokaryotes. To investigate biologically driven changes during such transitions, we analyzed data from five dihydrogen pulse experiments conducted in pressurized bioreactors that replicate deep aquifer pressure and temperature conditions. Our goal was to determine whether consistent community-level responses to dihydrogen injection could be identified. We found that dihydrogen exposure consistently led to a decline in fermentative ASVs, likely driven by environmental filtering. Hydrogenotrophic sulfate reducers initially dominated in some experiments, with total sulfate depletion observed in certain cases, followed by the emergence of methanogenic archaea. In some instances, a succession pattern involving Thermodesulfovibrio and Methanothermobacter appeared across taxonomically distinct communities, suggesting deterministic ecological processes. Additionally, we observed potential dispersal limitation and selection pressures, possibly linked to pH shifts caused by autotrophy. These findings underscore the importance of considering microbial dynamics in dihydrogen storage strategies in deep aquifers and suggest that, despite initial variability, predictable ecological succession may occur under specific geochemical conditions.},
}

@article {pmid41673333,
year = {2026},
author = {Lu, L and Wang, X and Qin, Y and Xiao, Y and Zhang, Y and Ma, H and Wang, D and Li, Z},
title = {Hydrological Fragmentation Driving Microbial Carbon Necromass Reduction in Columnar Sediments: Evidence from CAZyme Genomic Signatures in Cascade Reservoirs.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02705-6},
pmid = {41673333},
issn = {1432-184X},
support = {52470202//National Natural Science Foundation of China/ ; U2340222//National Natural Science Foundation of China/ ; NBWL202200489 and 202403005//China Three Gorges Corporation/ ; 309GJHZ2024110GC//Chinese Academy of Sciences/ ; },
abstract = {Microbial necromass carbon (MNC), a key component of soil organic carbon, plays a vital role in aquatic carbon sequestration. Its accumulation and transformation are highly sensitive to environmental changes, particularly in reservoir sediments-critical zones for organic matter storage and biogeochemical cycling. This study investigated the vertical distribution and regulatory mechanisms of MNC in cascade reservoir systems through sediment analysis and metagenomic sequencing. Our findings reveal that MNC constitutes 15 ~ 35% of total sediment organic carbon (SeOC) , with fungal-derived necromass consistently dominating over bacterial contributions. Metagenomic data highlight distinct functional potentials in carbon cycling, showing that bacterial necromass exhibits higher lability than fungal necromass, as evidenced by shifts in carbohydrate-active enzyme (CAZyme) gene abundances-particularly those involved in glucan and peptidoglycan degradation. Notably, cascade damming introduced spatial heterogeneity in MNC distribution , with downstream reservoirs experiencing reduced MNC accumulation due to altered hydrological connectivity and nutrient regimes. These results underscore the pivotal role of MNC in aquatic carbon storage while highlighting the complex interplay between environmental factors, microbial metabolic traits, and anthropogenic disturbances in regulated river systems. Therefore, our findings demonstrate that fungal necromass is a dominant and relatively stable component of sediment carbon, and its dynamics must be integrated to accurately assess and predict carbon sequestration in dammed rivers.},
}

@article {pmid41671169,
year = {2026},
author = {Saati-Santamaría, Z and Pérez-Mendoza, D and Khashi U Rahman, M and de Sousa, BFS and Montero-Calasanz, MDC and Rey, L and Roy, S and Sanjuán, J and García-Fraile, P},
title = {Evolutionary mechanisms underlying bacterial adaptation to the plant environment.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuag005},
pmid = {41671169},
issn = {1574-6976},
abstract = {Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that are essential for plant survival and ecosystem function. Bacterial adaptation to plant environments involves dynamic evolutionary mechanisms including horizontal gene transfer, gene regulation, and metabolic specialization, enabling bacteria to persist and specialize within diverse plant-associated niches. Here we review how evolutionary forces such as selection, drift, and gene flow shape bacterial genomes, regulatory networks, and ecological strategies in response to plant-imposed pressures, underpinning both beneficial and pathogenic lifestyles. Understanding these processes provides a unified evolutionary framework for bacterial adaptation to plants and highlights their implications for sustainable agriculture and microbiome-based innovations.},
}

@article {pmid41668299,
year = {2026},
author = {Frings, DM and Mellinger, JM and Drace, KM},
title = {Microbial Diversity Across Chemolithotrophic and Phototrophic Biofilms in Cold Sulfur Springs.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70223},
pmid = {41668299},
issn = {2045-8827},
mesh = {*Biofilms/growth & development ; *Sulfur/metabolism ; RNA, Ribosomal, 16S/genetics ; Alabama ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phototrophic Processes ; *Microbiota ; Phylogeny ; *Biodiversity ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; Chemoautotrophic Growth ; Cold Temperature ; *Natural Springs/microbiology ; Sequence Analysis, DNA ; Oxidation-Reduction ; },
abstract = {Sulfur-rich environments host specialized microbial communities that drive key biogeochemical processes, particularly sulfur cycling. While sulfur-oxidizing microbiota from hydrothermal vents and volcanic systems are well studied, microbial communities in cold terrestrial sulfur springs remain less understood. In this study, we used 16S rRNA gene sequencing to examine how sulfur availability and environmental conditions shape microbial assemblages across different biofilm types in a cold sulfur spring system at Blount Springs, Alabama (33.9301° N, 86.7928° W). Sulfur-oxidizing chemolithotrophs, including Sulfurovum and Halothiobacillus, represented the majority of the recovered reads in sulfur-rich white biofilms, while purple phototrophic biofilms were enriched with anoxygenic sulfur-oxidizing bacteria, such as Chromatium and Chlorobium. Nonsulfur biofilms from adjacent environments displayed greater microbial diversity, including a high abundance of photosynthetic diatoms, like, Melosira. Notably, Sulfurovum was abundant across both sulfur-rich and phototrophic niches, suggesting ecological flexibility and a central role in sulfur metabolism. These findings highlight the influence of sulfur chemistry and light availability in structuring microbial communities and contribute to a broader understanding of microbial adaptation and sulfur cycling in cold sulfur spring ecosystems.},
}

*Biofilms/growth & development
*Sulfur/metabolism
RNA, Ribosomal, 16S/genetics
Alabama
*Bacteria/classification/genetics/metabolism/isolation & purification
Phototrophic Processes
*Microbiota
Phylogeny
*Biodiversity
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
Chemoautotrophic Growth
Cold Temperature
*Natural Springs/microbiology
Sequence Analysis, DNA
Oxidation-Reduction

@article {pmid41668183,
year = {2026},
author = {Zhang, Y and Jing, G and Chen, R and Gong, Y and Li, Y and Wang, Y and Wang, X and Zhang, J and Mao, Y and He, Y and Zheng, X and Wang, M and Yuan, H and Xu, J and Sun, L},
title = {RamEx: an R package for high-throughput microbial ramanome analyses with accurate quality assessment.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02339-3},
pmid = {41668183},
issn = {2049-2618},
abstract = {BACKGROUND: Microbial single-cell Raman spectroscopy (SCRS) has emerged as a powerful tool for label-free phenotyping, enabling rapid characterization of microbial diversity, metabolic states, and functional interactions within complex communities. However, high-throughput SCRS datasets often contain spectral anomalies from noise and fluorescence interference, which obscure microbial signatures and hinder accurate classification. Robust algorithms for outlier detection and microbial ramanome analysis remain underdeveloped.

RESULTS: Here, we introduce RamEx, an R package specifically designed for high-throughput microbial ramanome analyses with robust quality control and phenotypic classification. At the core of RamEx is the Iterative Convolutional Outlier Detection (ICOD) algorithm, which dynamically detects spectral anomalies without requiring predefined thresholds. Benchmarking on both simulated and real microbial datasets-including pathogenic bacteria, probiotic strains, and yeast fermentation populations-demonstrated that ICOD achieves an F1 score of 0.97 on simulated datasets and 0.74 on real datasets, outperforming existing approaches by at least 19.8%. Beyond anomaly detection, RamEx provides a modular and scalable workflow for microbial phenotype differentiation, taxonomic marker identification, metabolic-associated fingerprinting, and intra-population heterogeneity analysis. It integrates Raman-based species-specific biomarkers, enabling precise classification of microbial communities and facilitating functional trait mapping at the single-cell level. To support large-scale studies, RamEx incorporates C++ acceleration, GPU parallelization, and optimized memory management, enabling the rapid processing of over one million microbial spectra within an hour.

CONCLUSIONS: By bridging the gap between high-throughput Raman-based microbial phenotyping and computational analysis, RamEx provides a comprehensive toolkit for exploring microbial ecology, metabolic interactions, and antibiotic susceptibility at the single-cell resolution. RamEx is freely available under the MIT license at https://github.com/qibebt-bioinfo/RamEx. Video Abstract.},
}

@article {pmid41675503,
year = {2025},
author = {Gu, S and Shao, J and He, R and Xiong, G and Qu, Z and Shao, Y and Yu, L and Zhang, D and Wang, F and Xu, R and Guo, P and Xi, N and Li, Y and Wu, Y and Wei, Z and Li, Z},
title = {Forging the iron-net: Towards a quantitative understanding of microbial communities via siderophore-mediated interactions.},
journal = {Quantitative biology (Beijing, China)},
volume = {13},
number = {2},
pages = {e84},
pmid = {41675503},
issn = {2095-4697},
abstract = {Iron is a critical yet limited nutrient for microbial growth. To scavenge iron, most microbes produce siderophores-diverse small molecules with high iron affinities. Different siderophores are specifically recognized and uptaken by corresponding recognizers, enabling targeted interventions and intriguing cheater-producer dynamics. We propose constructing a comprehensive iron interaction network, or "iron-net", across the microbial world. Such a network offers the potential for precise manipulation of the microbiota, with conceivable applications in medicine, agriculture, and industry as well as advancing microbial ecology and evolution theories. Previously, our successful construction of an iron-net in the Pseudomonas genus demonstrated the feasibility of coevolution-inspired digital siderophore-typing. Enhanced by machine learning techniques and expanding sequencing data, forging such an iron-net calls for multidisciplinary collaborations and holds significant promise in addressing critical challenges in microbial communities.},
}

@article {pmid41667848,
year = {2026},
author = {González-Azcona, C and Solano-González, F and Jiménez-Ruiz, S and Santos, N and Marañón-Clemente, I and Álvarez-Gómez, T and Eguizábal, P and Alonso, CA and Benito, D and Zarazaga, M and Torres, C and Lozano, C},
title = {High Nasal Carriage of MRSA-mecC in Wild Rabbits in the Iberian Peninsula: a Wildlife Reservoir?.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02713-6},
pmid = {41667848},
issn = {1432-184X},
}

@article {pmid41666926,
year = {2026},
author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P},
title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.12.051},
pmid = {41666926},
issn = {1097-4172},
abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.},
}

@article {pmid41666603,
year = {2026},
author = {Cristino, S and Caligaris, L and Salaris, S and Derelitto, C and Bonincontro, C and Marino, F and Grottola, A and Girolamini, L},
title = {Legionella petroniana sp. nov., a novel species isolated in Bologna, Italy: taxonomic, genomic and ecological insights in the era of environmental change.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126694},
doi = {10.1016/j.syapm.2026.126694},
pmid = {41666603},
issn = {1618-0984},
abstract = {This study presents the characterization of a novel Legionella species isolated in Italy over three different years from one company and two hospitals. Starting from standard techniques such as culture of water samples, agglutination test, MALDI-TOF MS and gene sequencing analysis used to identify the isolates, genomic and metabarcoding approaches were subsequently employees to further characterize the species. Legionella contamination ranged from 400 to 700 CFU/L. The tiny colonies displayed atypical morphology compared to typical Legionella features, although they grew on BCYE medium supplemented with L-cysteine. Microscopic and phenotypic analyses revealed Gram-stain negative, Ziehl-Neelsen-negative, rod-shaped, motile cells capable of growing at 32-37 °C, including on selective media such as GVPC and MWY. The isolates tested positive for oxidase and gelatinase activity. Fatty acid profiling identified the dominant components as Summed Features 3 (C16:1 ω7c/C16:1 ω6c, 28.9%), C16:0 iso (18.4%), and C15:0 anteiso (15.4%). Ubiquinone Q13 was the major quinone. Sequence analysis of the mip and rpoB genes showed 98.2% and 95.1% similarity, respectively, to L. feeleii (WO-44C ATCC 35072[T]). Whole genome sequencing (WGS) revealed a GC content of 41.5%, a dDDH value of ≤54.9%, and an ANI of 94.06% with L. feeleii (WO-44C ATCC 35072[T]), supporting the classification of a novel species within the genus Legionella. Furthermore, taxonomic resolution of water samples revealed the presence of 168 bacterial genera, including several respiratory, opportunistic, and zoonotic pathogens, as well as seven Legionella species. The name Legionella petroniana sp. nov. is proposed, with strain 31fI33[T] (=DSM 114357[T]=CCUG 76442[T]) designated as type strain.},
}

@article {pmid41663799,
year = {2026},
author = {Gao, S and Zhao, W and Guan, X and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Pan, Y and Sun, H and Jiang, P and Mi, R and Jiang, J and Zhou, Z},
title = {Stronger Adaptability of Eukaryotic Communities than Prokaryotes in Seawater across an Extensive Salinity Gradient.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {28},
number = {1},
pages = {32},
pmid = {41663799},
issn = {1436-2236},
support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//Fundamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; },
mesh = {*Salinity ; *Seawater/microbiology/chemistry ; *Eukaryota/physiology/genetics/classification ; *Prokaryotic Cells/physiology ; *Adaptation, Physiological ; *Microbiota ; Biodiversity ; },
abstract = {Researching microbial ecology in extreme environments is crucial for advancing the basic ecological theory and exploring their potential applications in biotechnology. The salt drying system provides an accessible but harsh environment that covers a maximum salinity gradient. In this study, we conducted a comparative analysis of the salinity adaptation and assembly mechanisms of prokaryotic and eukaryotic communities in several salt drying tanks using high-throughput amplicon sequencing and multiple ecological analyses. The beta diversity analysis, based on the unweighted and weighted Unifrac distances, revealed significant variations in microbial community compositions along the salinity gradient, with stronger influences on prokaryotes. Species turnover was the primary mechanism driving the beta diversity patterns, which was regulated by the local species pool. Further comparisons of multiple niche and adaptation indices indicated that seawater eukaryotic communities exhibited stronger salinity adaptability than prokaryotes. In addition, the beta deviation index suggested that heterogeneous processes shaped the microbial communities. Moreover, the neutral community model showed higher dispersal ability of eukaryotes than prokaryotes. Also, they were stochastic and deterministic dominant communities along the salinity gradient, respectively. Overall, our findings contributed significantly to understanding the microbial ecology in relation to salinity gradients.},
}

*Salinity
*Seawater/microbiology/chemistry
*Eukaryota/physiology/genetics/classification
*Prokaryotic Cells/physiology
*Adaptation, Physiological
*Microbiota
Biodiversity

@article {pmid41661138,
year = {2026},
author = {Bäcker, M and Doekes, HM and Garza, DR and Meijer, J and van Vliet, S and Allen, RJ and Hogeweg, P and Dutilh, BE and van Dijk, B},
title = {Spatial structure: Shaping the ecology and evolution of microbial communities.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf067},
pmid = {41661138},
issn = {1574-6976},
abstract = {Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.},
}

@article {pmid41660022,
year = {2026},
author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R},
title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.},
journal = {Journal of conservative dentistry and endodontics},
volume = {29},
number = {1},
pages = {60-64},
pmid = {41660022},
issn = {2950-4708},
abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.

AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.

MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.

STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).

RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.

CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.},
}

@article {pmid41659429,
year = {2026},
author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT},
title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.27.701854},
pmid = {41659429},
issn = {2692-8205},
abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae . At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella , and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae . By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.},
}

@article {pmid41655393,
year = {2026},
author = {Tao, S and Gao, J and He, B and Zhang, T and Chen, B and Yin, Y and Shi, J and Mao, Y and Hu, L and Jiang, G},
title = {Understanding microbial mercury methylation via metabolic pathways: Processes associated with one-carbon metabolism.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141373},
doi = {10.1016/j.jhazmat.2026.141373},
pmid = {41655393},
issn = {1873-3336},
abstract = {Microbial mercury methylation is the key step responsible for the high toxicity and bioaccumulation potential of mercury. Since metabolic pathways serve as a bridge between mercury methylation and microbial activity, studying mercury methylation from the perspective of metabolic pathways will offer valuable insights into its underlying mechanism and integration into microbial metabolism. This review aims to summarize current understanding of the metabolic pathways that supply methyl groups for mercury methylation and to elucidate the relationships between them. The acetyl-coenzyme A pathway is extensively studied and well recognized for its role in methyl group transfer. The Wolfe cycle, representing the methanogenesis pathway in methanogenic archaea, has recently been identified as a distinct source of methyl groups contributing to mercury methylation. In addition, at the chemical level, S-adenosyl-L-methionine from the methionine biosynthesis pathway has been shown to donate a methyl group to mercury via the HgcAB complex, although this process has not yet been validated in vivo. Finally, the dimethylsulfoniopropionate degradation pathway is proposed as a speculative and potential route for mercury methylation. By integrating these pathways, we provide a comprehensive overview of their interconnections, demonstrating that microbial mercury methylation is embedded within the broader framework of one-carbon metabolism. The close association between methylation and one-carbon flux suggests that mercury methylation may function as an interspecies competition strategy that enhances microbial survival in mercury-rich environments. This pathway-centered perspective advances our understanding of the biochemical basis of microbial mercury methylation and may inform future research into its environmental controls and microbial ecology.},
}

@article {pmid41654744,
year = {2026},
author = {Wünschmann, T and Ghaderiardakani, F and Homeier-Bachmann, T and Quartino, ML and Wichard, T and Busch, A},
title = {Genomic and functional characterization of Pseudosulfitobacter pseudonitzschiae BPC-C4-2: a growth-promoting symbiont in Antarctic Ulva communities.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12626-w},
pmid = {41654744},
issn = {1471-2164},
}

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household Environmental Characteristics Influence House Dust Metagenome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5,821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

@article {pmid41653300,
year = {2026},
author = {Zenelt, W and Hoffmann, A and Sadowska, K and Krawczyk, K},
title = {Insects as a New Source of Plant Growth Promoting Bacteria - Review.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02692-0},
pmid = {41653300},
issn = {1432-184X},
}

@article {pmid41653280,
year = {2026},
author = {Kalatehjari, P and Wolf, R and Jedlitschky, G and Tolksdorf, C and Rauch, BH and Müller, C},
title = {The great diversity: monomeric and oligomeric hirudins, hirudin-like factors and decorsins in the Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis.},
journal = {Parasitology research},
volume = {125},
number = {1},
pages = {18},
pmid = {41653280},
issn = {1432-1955},
mesh = {Animals ; *Hirudins/genetics/chemistry/metabolism ; *Leeches/genetics/classification/metabolism ; Phylogeny ; Platelet Aggregation/drug effects ; Amino Acid Sequence ; },
abstract = {Medicinal leeches express a broad variety of anticoagulants and other bioactive factors that are involved in the blood feeding process. For most of the anticoagulants, several genes exist that may encode isoforms of the respective proteins, including hirudins and decorsins. Decorsins negatively affect platelet aggregation, whereas hirudins are potent thrombin inhibitors. Both factors belong to the hirudin superfamily that also includes the group of hirudin-like factors, and all hematophagous leeches analyzed so far contain several gene copies that encode representatives of at least two of the three groups of these factors. Members of the hirudin superfamily may contain only one central globular domain, but others may contain two or more copies. Here we describe the molecular identification and partial functional characterization of a broad variety of putative mono-, bi and multimeric hirudins, decorsins and hirudin-like factors in two Asian medicinal leech species, namely Hirudo nipponia and H. tianjinensis. Some of the monomeric hirudins and decorsins have already been described before, but they represent only a small part of the overall diversity. For the first time, putative monomeric and one oligomeric decorsins of H. tianjinensis were expressed as recombinant proteins, functionally characterized and successfully verified as platelet aggregation inhibitors. In addition we have conducted phylogenetic analyses based on genomic and mitochondrial markers and found convincing evidence that H. nipponia and H. tianjinensis together with members of the genus Whitmania form a monophyletic clade that is clearly distinct from clades that are formed either by European members of the genus Hirudo or by members of the genus Hirudinaria.},
}

Animals
*Hirudins/genetics/chemistry/metabolism
*Leeches/genetics/classification/metabolism
Phylogeny
Platelet Aggregation/drug effects
Amino Acid Sequence

@article {pmid41652742,
year = {2026},
author = {Van Meulebroek, L and Ghyselinck, J and Van Elst, D and Duysburgh, C and Gessner, A and Thas, O and Marzorati, M},
title = {The impact of Symprove™ multi-strain probiotic on enterotoxigenic Escherichia coli- or antibiotic-induced gut microbiome dysbiosis using high-throughput in vitro screening.},
journal = {Food research international (Ottawa, Ont.)},
volume = {227},
number = {},
pages = {118172},
doi = {10.1016/j.foodres.2025.118172},
pmid = {41652742},
issn = {1873-7145},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; *Dysbiosis/microbiology/chemically induced ; *Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Enterotoxigenic Escherichia coli/drug effects ; Fatty Acids, Volatile/metabolism ; Adult ; Male ; High-Throughput Screening Assays ; Female ; Escherichia coli Infections/microbiology ; Fermentation ; Young Adult ; },
abstract = {The gut microbiome plays a significant role in host physiology, both in health and disease. Assessment of changes in microbial metabolites beyond short-chain fatty acids (SCFAs) following probiotic supplementation may identify additional metabolic pathways that are activated or suppressed in response to probiotics. This study assessed changes in microbial metabolites in healthy and dysbiosed microbiomes following supplementation with Symprove™, a multistrain probiotic, using the Colon-on-a-plate® miniaturized short-term batch fermentation system with a fractional factorial design. The fecal microbiome from 10 healthy human donors was evaluated under healthy and dysbiosed (enterotoxigenic Escherichia coli infection and/or low-, medium-, or high-dose antibiotics) conditions. Samples were supplemented with Symprove™ or water (control) and evaluated for microbial metabolites at 24 h and 48 h using untargeted metabolic fingerprinting, capillary gas chromatography, and targeted metabolic profiling. Favorable impacts were observed with Symprove™ supplementation across the different antibiotic doses. SCFA levels (acetate, propionate, butyrate) were significantly increased and levels of branched SCFAs were significantly decreased with Symprove™ supplementation versus control in both the healthy and dysbiosed populations. Significant increases and decreases in several other microbial metabolites were also observed with Symprove™, many of which could be considered to have beneficial effects on intestinal inflammation, intestinal barrier health, and the gut-brain axis. Symprove™ supplementation significantly affected microbial metabolism, with many of the observed changes being considered positive for human health. Importantly, these benefits were shown not only in healthy fecal microbiomes, but also in fecal microbiomes with in vitro antibiotic-induced dysbiosis, showing therapeutic potential.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Probiotics/pharmacology
*Dysbiosis/microbiology/chemically induced
*Anti-Bacterial Agents/adverse effects
Feces/microbiology
*Enterotoxigenic Escherichia coli/drug effects
Fatty Acids, Volatile/metabolism
Adult
Male
High-Throughput Screening Assays
Female
Escherichia coli Infections/microbiology
Fermentation
Young Adult

@article {pmid41652077,
year = {2026},
author = {Jeong, YS and Jeon, BS and Park, MG},
title = {Dinopallor Comventus n. gen., n. sp., a Novel Parasitoid of Marine Dinoflagellates Representing a Sister Lineage to Seagrass Parasites and Expanding the Host Range of Phytomyxea (Rhizaria, Endomyxa).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02707-4},
pmid = {41652077},
issn = {1432-184X},
support = {RS-2025-00552993//National Research Foundation of Korea/ ; RS-2022-NR068504//National Research Foundation of Korea/ ; RS-2023-00256330//Korea Institute of Marine Science and Technology promotion/ ; },
abstract = {Phytomyxea (SAR: Rhizaria: Endomyxa) is a group of obligate biotrophic parasitic protists comprised of two orders: Plasmodiophorida, found in terrestrial or freshwater environments, and Phagomyxida, found in marine environments. While Plasmodiophorida has been extensively studied due to its economic importance as plant pathogens, Phagomyxida remains poorly investigated despite its ecological significance in marine ecosystems. During intensive sampling along the Korean coast from April to December 2023, novel parasitoids infecting dinoflagellates were discovered in seawater collected at 10 coastal stations. A total of 23 isolates were successfully established in culture, and the morphology of infected host cells resembled that of known Phagomyxa infections. The newly identified parasitoid exhibits a life cycle that includes zoospore penetration, multinucleate plasmodium development, and formation of a sporangiosorus composed of numerous zoosporangia. Each zoosporangium produces three biflagellate zoospores, and no resting spores were observed. A key morphological feature distinguishing this parasitoid from Phagomyxa species is the presence of a sporangiosorus wall enclosing the zoosporangia. Phylogenetic analysis based on small subunit (SSU) ribosomal DNA (rDNA) revealed that this parasitoid forms a distinct clade with Marinomyxa and the environmental sequence TAGIRI-5, suggesting a disparity between its morphological similarity to Phagomyxa and its molecular phylogenetic position. The SSU rRNA gene sequence of the new parasitoid showed 99.87% identity to the TAGIRI-5 sequence obtained from an anoxic sediment in Kagoshima Bay, Japan. Cross-infection experiments demonstrated that infections occurred only in five dinoflagellate genera among the taxa tested. Based on morphological and molecular data obtained in this study, we propose a new genus and species, Dinopallor comventus n. gen., n. sp., for this newly discovered parasitoid.},
}

@article {pmid41648583,
year = {2026},
author = {Bald, S and Zhang, J and Nelson, R and Scott, DC and Dukovski, I and de Raad, M and Northen, TR and Segrè, D},
title = {Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.11.698878},
pmid = {41648583},
issn = {2692-8205},
abstract = {Synthetic microbial ecology aims at designing communities with desired properties based on mathematical models of individual organisms. It is unclear whether simplified models harbor enough detail to predict the composition of synthetic communities in metabolically complex environments. Here, we use longitudinal exometabolite data of monocultures for 15 rhizosphere bacteria to parametrize a consumer-resource model, which we use to predict pairwise co-cultures and higher order communities. The capacity to artificially "switch off" cross-feeding interactions in the model demonstrates their importance in ecosystem structure. Leave-one-out and leave-two-out experiments demonstrate that pairwise co-cultures do not necessarily capture inter-species interactions within larger communities and broadly highlight the nonlinearity of interactions. Finally, we demonstrate that our model can be used to identify new sub-communities of three strains with high likelihood of coexistence. Our results establish hybrid mechanistic and data-driven metabolic models as a promising and extendable framework for predicting and engineering microbial communities.},
}

@article {pmid41646503,
year = {2025},
author = {Abjani, F and Er, YX and Lee, SC and Madhavan, P and Rhodes, A and Lim, YAL and Chong, PP and Chinna, K},
title = {Gut Microbiota of Sarawak's "Orang Ulu" Indigenous Community in East Malaysia Reveals Vanish Microbes: A Comparison With Urban Communities.},
journal = {British journal of biomedical science},
volume = {82},
number = {},
pages = {15378},
pmid = {41646503},
issn = {2474-0896},
mesh = {Humans ; Malaysia ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; Feces/microbiology ; Urban Population ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Middle Aged ; Bacteria/genetics/classification ; Indigenous Peoples ; },
abstract = {INTRODUCTION: Urbanization often correlates with reduced diversity in human gut microbiota, with notable variations observed between the gut microbiota among the Indigenous communities in rural villages and urban citizens residing in modern settings. Although research has been conducted on the gut microbiota of healthy adults in Malaysia, there has been no study characterising the gut microbiota of Sarawak's Indigenous communities to date. This study aims to fill this gap by examining the gut microbiota profile of the Sarawak Indigenous groups (specifically Orang Ulu subethnic groups Kayan and Kenyah), comparing them with semi-urbanized Selangor Indigenous communities from Peninsular Malaysia (represented by Proto Malay subtribe Temuan) and Urban communities from Kuala Lumpur.

METHODS: We conducted a cross-sectional study and collected stool samples from 86 Indigenous participants from Sarawak and compared them with published data from 45 Malaysian Indigenous participants from Selangor and 18 Urban citizens living in Kuala Lumpur City. DNA was extracted from the stool samples, and subsequently, the V4 hypervariable region of the 16S rRNA gene was sequenced. The raw sequence data were analyzed using the Quantitative Insights into Microbial Ecology 2 (QIIME2) bioinformatics platform.

RESULTS AND DISCUSSION: Analysis revealed that the Sarawak Indigenous community exhibited the highest gut microbial diversity, followed by the Peninsular Indigenous and Urban groups. The Prevotella/Bacteroides (P/B) ratio revealed that the Sarawak Indigenous community showed the highest presence of Prevotella at 88.3%, while Kuala Lumpur Urban residents had a predominantly Bacteroides composition at 61%. The Selangor Indigenous community also exhibited a Prevotella-dominant profile at 75.5%. VANISH microbes (Prevotella, Faecalibacterium, and Succinivibrio) were identified as dominant genera in the Sarawak Indigenous gut microbiota, contrasting with the BIoSSUM microbe (Bacteroidaceae) found in the Kuala Lumpur cohort.

CONCLUSION: This study sheds light on the distinct gut microbiota composition of Sarawak's Indigenous community, which has not been previously explored. It highlights the impact of urbanization on gut microbiota composition during lifestyle transitions.},
}

Humans
Malaysia
*Gastrointestinal Microbiome/genetics
Male
Female
Adult
Feces/microbiology
Urban Population
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
Middle Aged
Bacteria/genetics/classification
Indigenous Peoples

@article {pmid41642996,
year = {2026},
author = {Ma, W and Liu, Y and Wei, X and Zhang, X and Li, X and Liu, Z and Yuan, L and Li, G and Zhang, S and Yang, Q and Chang, X and Han, Z and Liang, H and Luan, Z and Wang, Q and Gu, Y and Wang, X and Zhao, X and Liu, Q and Sun, X and Liu, M and Feng, D and Lu, Y and Luo, S and Yang, L and Li, M and Allaby, R and Wang, K and Zhang, T and Shen, S and Van de Peer, Y and Hong, Y and Yuan, Y and Zhao, J},
title = {Gapless pangenome analyses reveal fast Brassica rapa subspeciation.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6785},
pages = {eady7590},
doi = {10.1126/science.ady7590},
pmid = {41642996},
issn = {1095-9203},
mesh = {*Brassica rapa/genetics/classification/anatomy & histology ; *Genome, Plant ; Genes, Plant ; Centromere/genetics ; Plant Leaves/anatomy & histology/genetics/growth & development ; Genome-Wide Association Study ; Plant Proteins/genetics ; Telomere/genetics ; Plant Breeding ; Genetic Variation ; },
abstract = {Brassica rapa (Br) encompasses many morphotypes and subspecies, so it is a good model with which to investigate plant diversification and subspeciation. Here, we resequenced the genomes of 1720 Br accessions and de novo assembled 11 representative telomere-to-telomere gapless genomes for seven elite subspecies that underwent intensive morphotypification and developed distinct agronomic traits valued to agriculture. We identified 6992 unknown genes, 110 complete (peri)centromeres, and five new satellites associated with Br morphotypes and subspecies and Brassica species evolution. The pangenome, built on 11 gapless and 20 published genomes, reveals structural variations and gene diversities among Br subspecies. Pangenome-wide association studies uncovered that the gene BrLH1 controls leaf-head formation. We show that structural changes have occurred in satellites, (peri)centromeres, and genes, contributing to fast subspeciation and morphotypification during the short history of Br cultivation, providing invaluable resources for Brassica breeding.},
}

*Brassica rapa/genetics/classification/anatomy & histology
*Genome, Plant
Genes, Plant
Centromere/genetics
Plant Leaves/anatomy & histology/genetics/growth & development
Genome-Wide Association Study
Plant Proteins/genetics
Telomere/genetics
Plant Breeding
Genetic Variation

@article {pmid41642984,
year = {2026},
author = {Spohn, M and Arnillas, CA and Bakker, JD and Borer, ET and Bråthen, KA and Cadotte, MW and Carbutt, C and Catford, JA and DuPre, ME and Dwyer, C and Eisenhauer, N and Estrada, C and Hagenah, N and Haider, S and Harms, KE and Hautier, Y and Hersch-Green, EI and Knops, JMH and Laanisto, L and Laungani, R and Macek, P and Martinson, H and Millett, J and Pärtel, M and Pennings, SC and Peri, PL and Power, SA and Risch, AC and Roscher, C and Seabloom, EW and Smith, NG and Stevens, C and Virtanen, R and Wardle, GM and Zhang, P},
title = {Intense solar radiation constrains plant species richness in global grasslands.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {6},
pages = {e2527128123},
doi = {10.1073/pnas.2527128123},
pmid = {41642984},
issn = {1091-6490},
mesh = {*Biodiversity ; *Grassland ; *Plants/radiation effects/classification ; Biomass ; *Sunlight ; Poaceae/radiation effects ; Photosynthesis/radiation effects ; },
abstract = {The search for predictors of plant diversity has challenged scientists for decades. Here we identify intense photosynthetically active radiation (PAR) as a major factor constraining plant species richness in global grasslands. We show that the strength of the negative relationship between species richness and PAR increases with increasing elevation and that species richness is more strongly correlated with intense PAR than with UV-B radiation, climate variables, and atmospheric nitrogen deposition. In addition to species richness, plant biomass was also negatively correlated with PAR at higher elevations, indicating that intense PAR also constrains plant biomass in montane grasslands. Furthermore, we show that the decrease in plant species richness with increasing PAR is mainly caused by a decrease in species richness of forbs, sedges, and rushes. In contrast, species richness of grasses was only negatively correlated with PAR at high elevations, and species richness of legumes was not significantly correlated with PAR. Our results suggest that PAR constrains plant species richness in global grasslands and limits the extent to which plant species of specific functional groups can migrate uphill in response to climate warming.},
}

*Biodiversity
*Grassland
*Plants/radiation effects/classification
Biomass
*Sunlight
Poaceae/radiation effects
Photosynthesis/radiation effects

@article {pmid41640738,
year = {2025},
author = {Zöhrer, PA and Unterberger, S and Aschauer, R and Draxler, A and Somloi, S and Kapeller, M and Bauer, T and Heinz, C and Reichstam, S and Franzke, B and Strasser, EM and Hausmann, B and Pjevac, P and Berry, D and Wessner, B and Wagner, KH},
title = {The impact of a high-protein diet with strength training on the gastrointestinal microbiota in community-dwelling older adults: subanalysis of a randomized controlled trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1712451},
pmid = {41640738},
issn = {2296-861X},
abstract = {BACKGROUND: A balanced gastrointestinal (GI) microbiota is essential for healthy aging. Although high-protein diets and strength training are recommended for older adults to maintain muscle mass, their effects on GI microbiota remain unclear.

METHODS: This randomized controlled trial examined the effect of a habitual diet with recommended protein intake or high protein intake combined with strength training on the GI microbiota of 112 community-dwelling adults aged 65-85 years. The participants were divided into three groups: no intervention control (CON), recommended protein intake plus strength training (RP + T), and high protein intake plus strength training (HP + T). Over 17 weeks, protein intake increased significantly from 0.80 (IQR: 0.30-0.50) g/kg body weight at baseline, reaching 1.07 ± 0.25 g/kg in RP + T, and 1.62 ± 0.37 g/kg in HP + T groups. Stool samples collected at baseline, after dietary intervention, and after combined dietary and training intervention were analyzed using 16S rRNA gene amplicon sequencing.

RESULTS: Despite increased protein intake, microbiota richness, diversity, and composition showed no significant changes within or between groups. Residual energy and inflammatory markers indicated that higher protein intake was well tolerated.

CONCLUSION: The findings suggest that increasing protein intake via food sources up to 1.6 g/kg body weight for more than 4 months, with or without strength training, does not adversely affect the GI microbiota composition in older adults.},
}

@article {pmid41640304,
year = {2026},
author = {Hart, DW and Ng, AS and Gazińska, P and Goldin, R and Gopal, P and O'Dell, N and Zargar, A and Pytowski, L and Montazid, S and Bardella, C and East, JE and Tomlinson, IP and Koch, N and Bennett, NC and Irshad, S},
title = {Characterisation of bacteria-induced colitis and its modulation by probiotics in naked mole rats: a new mammalian model for acute inflammatory disease.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.70034},
pmid = {41640304},
issn = {1096-9896},
support = {DST-NRF (GUN 64756)//Department of Science and Technology-National Research Foundation/ ; //The National Institute for Health and Care Research (NIHR) Oxford Biomedical Research Centre (BRC)/ ; },
abstract = {Enteropathogenic bacteria are a major cause of morbidity and mortality globally. While mouse models have been indispensable in advancing our understanding of infectious enteric diseases, key differences in intestinal microbiota and immunobiology between mice and humans underscore the need for alternative mammalian models that better recapitulate human disease states. The naked mole rat (NMR), the longest-lived rodent and a model of healthy ageing, presents a unique opportunity. It possesses an exceptionally robust intestinal barrier, an abundance of goblet cells, a thicker mucin layer, and reduced gut permeability compared to mice. Additionally, the NMR gut microbiome exhibits compositional and functional features shared with human centenarians and traditional-lifestyle populations (e.g. Hadza hunter-gatherers), including an enrichment of health-associated taxa and metabolic pathways. Here, we leverage this model to show that systemic Citrobacter braakii infection is associated with colonic inflammation and epithelial injury that closely mimics human haemorrhagic colitis. Infected NMRs develop mucosal erosions, ulcerations, depletion of goblet cells, expansion of proliferative compartments, and active inflammation in the lamina propria. Without intervention, systemic inflammation associated with sepsis ensues and results in high mortality. Furthermore, we demonstrate the utility of this model for therapeutic testing by showing a strong effect of a probiotic cocktail comprising lactobacilli, bifidobacteria, streptococci, and enterococci. Treatment with this cocktail promoted mucosal healing, restored intestinal homeostasis, and exerted an anti-inflammatory effect. Taken together, we establish the NMR as a translatable model for investigating disease mechanisms in infectious colitis, including disruptions in mucosal barrier permeability, gut microbial ecology, and local and systemic immune regulation, as well as for testing functional probiotic strains as potential therapeutics. © 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.},
}

@article {pmid41637059,
year = {2026},
author = {Xiong, S and Liu, Z and Xiao, N and Hua, Y and Wan, X and Zhao, J},
title = {Vallisneria Invasion into Myriophyllum Community: Differential Responses of Comammox Community in Changing Rhizosphere Environment.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag038},
pmid = {41637059},
issn = {1365-2672},
abstract = {AIMS: Species invasion is one of the key issues in global ecosystems. This study investigated the changes in the rhizosphere community structure of complete ammonia-oxidizing bacteria (Comammox) after the invasion of the long-rooted submerged macrophyte Vallisneria spiralis L. into the community of the short-rooted submerged macrophyte Myriophyllum spicatum L.

METHODS AND RESULTS: Different planting ratios simulated varying invasion intensities. Increasing invasion intensity significantly altered rhizosphere factors, increasing invasion intensity significantly reduced dissolved organic carbon (DOC) and lowered pH, thereby causing distinct alterations in the rhizosphere environment. Comammox Clade A remained dominant with stable abundance, indicating strong adaptability. In contrast, Clade B abundance increased under low-moderate invasion but declined sharply under high intensity, suggesting a preference for mixed roots or low-intensity invasion. Higher pH and dissolved organic carbon provided a stable niche for Clade A. High invasion intensities elevated NH₄⁺-N and NO₃⁻-N concentrations, which coupled with stronger oxidative conditions promoted ammonia-oxidizing bacteria (AOB) and certain Clade A subgroups, thereby suppressing the low-nitrogen-adapted Clade B.

CONCLUSIONS: This study demonstrates that submerged macrophyte invasion reshapes the rhizosphere environment and drives Comammox community differentiation, offering new insights into plant invasion's ecological effects and nitrogen cycling regulation.},
}

@article {pmid41635904,
year = {2025},
author = {Fan, X and Wang, X and Chao, Y and Xu, E},
title = {Probiotic and prebiotic mechanisms in IBD-associated colorectal carcinogenesis: recent advances.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1693875},
pmid = {41635904},
issn = {2296-861X},
abstract = {Inflammatory bowel disease (IBD), a chronic relapsing inflammatory disorder of the gastrointestinal tract, significantly increases the risk of progression to colorectal cancer (CRC). Emerging studies highlight the critical roles of gut microbial dysbiosis and sustained intestinal inflammation in driving this pathological transformation. Probiotics and prebiotics, as modulators of gut microbial ecology, have attracted considerable attention as potential interventions to restore microbial balance, regulate immune responses, and mitigate carcinogenic processes. In this review, we integrate the interplay mechanisms among inflammation, microbiota, and immunity in IBD-associated colorectal carcinogenesis (IBD-CRC), with a focus on the roles of probiotics and prebiotics in microbial remodeling, enhancement of epithelial barrier integrity, inhibition of inflammatory signaling, and activation of antitumor immunity. Furthermore, we discuss preclinical and clinical evidence supporting their efficacy in delaying or preventing IBD-CRC. The review also provides perspectives on future customized synbiotic strategies in microbiota-targeted therapy and cancer prevention.},
}

@article {pmid41635399,
year = {2026},
author = {Morton, SG and Vucelic-Frick, G and Dickey, JR and Rajput, BS and Spiegel, CJ and Loomis, DA and Jackrel, SL and Burkart, MD and Shurin, JB},
title = {Microplastic pollution induces algae blooms in experimental ponds but bioplastics are less harmful.},
journal = {Communications sustainability},
volume = {1},
number = {1},
pages = {16},
pmid = {41635399},
issn = {3059-4308},
abstract = {An ever-growing sea of plastic waste permeates even the most remote ecosystems; however, its ecological impact is unclear. Less persistent bioplastic alternatives are available but also have unknown environmental effects. We conducted a three-month experiment exposing plankton in experimental ponds to 10 concentrations of three different thermoplastic polyurethane microplastics, including two biodegradable bioplastics. Algal blooms with dense chlorophyll occurred consistently at high concentrations of the petroleum-derived thermoplastic polyurethane, but only occasionally with the two bioplastics. Herbivorous zooplankton density was strongly reduced by typical thermoplastic polyurethane and only weakly by bioplastics, therefore the effect on algae is at least partly due to reductions in top-down grazing pressure. Microbial communities exhibited compositional shifts in response to all three plastic types, with petroleum-derived plastic associated with the most pronounced differences across both prokaryotic and eukaryotic domains. Our results show that plastic pollution may contribute to the growing global problems of eutrophication, coastal hypoxia and harmful algae blooms, and that biodegradable plastics may have smaller environmental footprints.},
}

@article {pmid41632325,
year = {2026},
author = {Lyons, R and Chan, CM and Hodal, CME and Parry, AR and Lant, P and Pratt, S and Laycock, B and Dennis, PG},
title = {The Diversity of Plastisphere Bacterial and Fungal Communities Differs between Biodegradable Polymer Types in Soil.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02677-z},
pmid = {41632325},
issn = {1432-184X},
}

@article {pmid41632308,
year = {2026},
author = {Gayithri, M and Singh, S and Pradhan, B and Boorla, V and Chand, S},
title = {Multifunctional Roles of Bacillus spp. in Sustainable Agriculture: Advances in Biocontrol, Omics, and Ecological Applications.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02709-2},
pmid = {41632308},
issn = {1432-184X},
}

@article {pmid41630783,
year = {2026},
author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS},
title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100544},
pmid = {41630783},
issn = {2666-5174},
abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.},
}

@article {pmid41628729,
year = {2026},
author = {Romeiro, K and Siqueira, JF and Rôças, IN and Gominho, LF and Villela, LB and Brisson-Suárez, K and Carmo, FL},
title = {Root Canal Microbiome in Patients Undergoing Antineoplastic Therapy: a Next-Generation Sequencing Study.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.01.020},
pmid = {41628729},
issn = {1878-3554},
abstract = {INTRODUCTION: This study compared the intracanal microbiome of teeth with apical periodontitis in oncological and healthy patients using 16S rRNA gene-based next generation sequencing.

METHODS: Root canal samples were taken from 46 teeth with pulp necrosis and primary apical periodontitis (23 from oncological patients and 23 from healthy controls). DNA was extracted and sequenced using the Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. Bioinformatics processing was conducted using QIIME2 and DADA2. Alpha and beta diversity analyses, genus-level abundance comparisons, and indicator species analyses were performed.

RESULTS: After quality filtering, 3,307,822 sequence reads were retained, averaging 68,912.96 reads/sample, and resulting in 3,241 unique amplicon sequence variants. Oncological patients exhibited significantly higher bacterial richness (p = 0.01), while Shannon diversity showed no significant difference between groups. Beta diversity analysis (Bray-Curtis, MDS stress = 0.14) did not reveal significant differences between groups. Indicator species analysis identified some specific taxa more associated with oncological patients, including the candidate endodontic pathogens Prevotella, Selenomonas, Alloprevotella, Rothia, and Fretibacterium.

CONCLUSIONS: The root canal microbiome of oncologic patients with apical periodontitis was broadly similar to that of healthy controls. The oncologic group showed higher species richness, but no significant differences in the overall bacterial diversity or community structure.},
}

@article {pmid41628277,
year = {2026},
author = {Marrec, L and Lehtinen, S},
title = {Cluster dispersal shapes microbial diversity during community assembly.},
journal = {PLoS computational biology},
volume = {22},
number = {2},
pages = {e1013918},
doi = {10.1371/journal.pcbi.1013918},
pmid = {41628277},
issn = {1553-7358},
abstract = {Identifying the drivers of diversity remains a central challenge in microbial ecology. In microbiota, within-community diversity is often linked to host health, which makes it all the more important to understand. Since many communities assemble de novo, microbial dispersal plays a critical role in shaping community structure during the early stages of assembly. While theoretical models typically assume microbes disperse individually, this overlooks cases where microbes disperse in clusters, such as, for example, during host feeding. Here, we investigate how cluster dispersal impacts species richness, between-community dissimilarity, and species abundance in the initial steps of microbial community assembly. We developed a model in which microbes disperse from a pool into communities as clusters and then replicate locally. Using both analytical and numerical approaches, we show that cluster dispersal promotes community homogenization by increasing within-community richness and reducing dissimilarity across communities, even at low dispersal rates. Moreover, it modulates the influence of local selection on microbial community assembly and, consequently, on species abundance. Our results demonstrate that cluster dispersal has distinct effects from simply increasing the dispersal rate. This work reveals new evidence for the role of cluster dispersal in the early dynamics of microbial community assembly.},
}

@article {pmid41627727,
year = {2026},
author = {Ginger, ML and Karnkowska, A and McCall, LI and Silber, AM and Michels, PAM},
title = {Why Euglenozoans.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {3-22},
pmid = {41627727},
issn = {1940-6029},
mesh = {*Euglenozoa/physiology/genetics/classification ; Animals ; },
abstract = {To accompany a new collection of methods and protocols, we discuss the relevance of the microbial eukaryotes belonging to the protist phylum Euglenozoa. For those interested by Euglena, applied biology is often relevant: as a starting point for useful natural products including biofuels, nutritional supplements, and metabolites with biomedical potential, or as an environmental agent for bioremediation. Arguably the most widely studied euglenozoans are the parasitic trypanosomatids. Collectively, trypanosomatids cause several serious neglected tropical diseases and economically important diseases of animals and plants; since the early 1900s, drug discovery and disease intervention have been prominent research areas. Yet for those interested in evolution, trypanosomatids and Euglena are host to all sorts of extreme biology either not seen or so pronounced in other eukaryotes. Euglenozoans are also relevant in an ecology context: free-living relatives of the trypanosomatids are abundant in freshwater environments. Moreover, the other major euglenozoan group, the diplonemids, are recently recognized as the most abundant heterotrophic protists in the world's oceans, their diversity and abundance at least comparable to major algal groups. Finally, the long history of euglenozoan study illustrates nicely the evolving nature of scientific discovery and reporting since Van Leeuwenhoek first saw Euglena in the pioneering days of microscopy.},
}

*Euglenozoa/physiology/genetics/classification
Animals

@article {pmid41627051,
year = {2026},
author = {Shoemaker, WR and Grilli, J},
title = {The macroecological dynamics of sojourn trajectories in the human gut microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0122125},
doi = {10.1128/msystems.01221-25},
pmid = {41627051},
issn = {2379-5077},
abstract = {The human gut microbiome is a dynamic ecosystem. Host behaviors (e.g., diet) provide a regular source of environmental variation that induces fluctuations in the abundances of resident microbiota. Despite these displacements, microbial community members remain highly resilient. Population abundances tend to fluctuate around a characteristic steady-state over long timescales in healthy human hosts. These temporary excursions from steady-state abundances, known as sojourn trajectories, have the potential to inform our understanding of the fundamental dynamics of the microbiome. However, to our knowledge, the macroecology of sojourn trajectories has yet to be systematically characterized. In this study, we leverage theoretical tools from the study of random walks to characterize the duration of sojourn trajectories, their shape, and the degree that diverse community members exhibit similar qualitative and quantitative dynamics. We apply the stochastic logistic model as a theoretical lens for interpreting our empirical observations. We find that the typical timescale of a sojourn trajectory does not depend on the mean abundance of a community member (i.e., carrying capacity), although it is strongly related to its coefficient of variation (i.e., environmental noise). This work provides fundamental insight into the dynamics, timescales, and fluctuations exhibited by diverse microbial communities.IMPORTANCEMicroorganisms in the human gut often fluctuate around a characteristic abundance in healthy hosts over extended periods of time. These typical abundances can be viewed as steady states, meaning that fluctuating abundances do not continue towards extinction or dominance but rather return to a specific value over a typical timescale. Here, we empirically characterize the (i) length (i.e., number of days), (ii) relationship between length and height, and (iii) typical deviation of a sojourn trajectory. These three patterns can be explained and unified through an established minimal model of ecological dynamics, the stochastic logistic model of growth.},
}

@article {pmid41627043,
year = {2026},
author = {Tan, Y and Liang, J and Yi, Q},
title = {Study on geographic differentiation and environment-host synergistic assembly mechanism of root-associated fungal communities in Paphiopedilum purpuratum.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0257325},
doi = {10.1128/spectrum.02573-25},
pmid = {41627043},
issn = {2165-0497},
abstract = {The orchid-fungus symbiosis is fundamental to orchid survival and reproduction; however, the diversity patterns and assembly mechanisms of the root-associated mycobiota in Paphiopedilum purpuratum remain inadequately characterized. We utilized high-throughput sequencing of the internal transcribed spacer 2 region to investigate the composition, diversity, sources, and assembly processes of the endophytic fungal communities across eight geographically distinct populations, with complementary profiling of rhizosphere soil fungi. Our results indicated that Ascomycota constituted the dominant phylum within the root mycobiota, while core taxonomic groups exhibited pronounced geographic differentiation at both family and genus levels. Significant inter-population disparities in α-diversity metrics reflected underlying community compositional divergence. Environmental variables, particularly longitude, exerted a stronger influence on community structure than biotic factors. Approximately 44.05% of root fungal operational taxonomic units were soil-derived, and the host plant selectively enriched fungal taxa, most of which possessed unknown trophic modes. Community assembly processes were compartment-specific: the root endophytic mycobiota was primarily governed by stochastic ecological drift, whereas the rhizosphere communities were predominantly shaped by deterministic dispersal limitation. This compartment-specific assembly was evidenced by the prevalence of stochastic processes (|βNTI| < 2) in the root endosphere, contrasting with the dominance of deterministic processes (|βNTI| > 2) in the rhizosphere. Co-occurrence network analysis revealed higher connectivity and robustness in the endophytic mycobiota. The interaction network between orchid mycorrhizal fungi and other root-associated soil fungi formed an efficient and stable functional system whose complexity showed population-specific differentiation. Collectively, our findings demonstrate clear geographic divergence in the root fungal communities of P. purpuratum and underscore a synergistic environment-host assembly mechanism, thereby providing critical ecological insights for informing conservation strategies for this endangered orchid.IMPORTANCEThis study investigates the root-associated fungal communities of the endangered orchid Paphiopedilum purpuratum across its geographical distribution. We identified clear geographical differentiation in community composition and diversity, predominantly driven by abiotic factors-particularly longitude-rather than biotic factors. A key finding reveals that 44% of root fungal taxa originate from the soil, indicating active host-mediated selection. A fundamental dichotomy in assembly mechanisms was observed: stochastic ecological drift dominated within roots, whereas deterministic dispersal limitation prevailed in the rhizosphere. Co-occurrence networks demonstrated that the root fungal community is highly connected and robust, suggesting a stable functional system. Our findings elucidate the synergistic roles of environment and host in shaping fungal assembly, providing novel insights into orchid-fungus symbiosis with theoretical implications for mycorrhizal ecology and practical relevance for conservation strategies.},
}

@article {pmid41626752,
year = {2026},
author = {Demeter, K and Savio, D and Kirschner, AKT and Reischer, GH and Kolarevic, S and Parajka, J and Derx, J and Jakwerth, S and Wurzbacher, C and Blaschke, AP and Mach, RL and Blöschl, G and Farnleitner, AH and Eiler, A},
title = {Hydrological regime of a continental river system predicts bacterial macroecological patterns.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag013},
pmid = {41626752},
issn = {1751-7370},
abstract = {Modelling bacterial dynamics in large river systems is crucial for predicting continental-scale ecosystem functioning under anthropogenic pressures. Although the River Continuum and Metacommunity concepts have provided theoretical frameworks, quantitative parameters necessary for microbial macroecological models remain scarce. Here, we present results from two whole-river surveys, conducted six years apart along 2600 km of the Danube River. Using bacterial secondary production, cell counts, and 16S rRNA gene amplicon sequencing, we quantified carbon, cell, phylotype, and diversity turnover along the river. Carbon incorporation per cell declined with water travel time by 6,000 - 21,000 atoms per hour. Bacterial cells multiplied every eight days, resulting in four to six doublings during downstream transport. Growth responses at the level of individual phylotypes differed up to a hundredfold from these bulk community estimates. Bacterial diversity dynamics were dominated by phylotype turnover rather than phylotype loss. Turnover ranged 0.92 to 0.96 across the river, indicating an almost complete replacement of phylotypes with 2-11% of headwater-associated ASVs persisting under base-flow conditions. Richness declined gradually downstream at a rate of approximately 0.13 ASVs per hour. Variations in bacterial secondary production, cell abundance, and observed ASVs were best explained by models combining hydrological and water quality parameters, whereas beta diversity followed a gradual development primarily structured by water travel time. Together, these results identify water travel time as the key integrative parameter governing microbial macroecological dynamics along large rivers, with environmental conditions fine-tuning local responses. These models can help predict changes in microbial diversity and functioning under anthropogenic alterations.},
}

@article {pmid41626630,
year = {2026},
author = {Lin, L and Neves, ALA and Ominski, KH and Guan, LL},
title = {Metatranscriptomics uncovers diet-driven structural, ecological, and functional adaptations in the rumen microbiome linked to feed efficiency.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf251},
pmid = {41626630},
issn = {2730-6151},
abstract = {The rumen microbiome plays a pivotal role in modulating feed efficiency in ruminants, yet the ecological mechanisms mediating the active interactions among microbial adaptations, dietary inputs, and host feed efficiency within the rumen remain poorly understood. To address this gap, we analyzed 120 metatranscriptomic datasets obtained from 30 purebred Angus bulls (each sampled four times) classified as high-feed-efficiency or low-feed-efficiency based on feed conversion ratio, and fed either forage-based (n = 15) or grain-based (n = 15) diets. We constructed a comprehensive active gene catalog comprising 1 744 067 non-redundant genes and compiled a reference set of 25 115 ruminant microbial genomes. Using integrated Neutral Community Model analysis and carbohydrate-active enzyme profiling, we examined how ecological processes and functional capacities differed across host phenotypes and diets. Neutral Community Model fits revealed that stochastic processes broadly governed rumen microbial community structures (R[2] = 0.779 for high-feed-efficiency; R[2] = 0.781 for low-feed-efficiency). Within the predominantly stochastic processes, however, high-feed-efficiency bulls exhibited strong positive selection for diet-responsive microbial lineages: Fibrobacter spp. (positively selected species-level genome bins: 61.3%-76.0%; negatively selected: 0%-1.3%), Butyrivibrio spp. (positively selected: 13.3%-46.0%; negatively selected: 1.0%-11.2%) under forage feeding, and UBA1067 spp. (positively selected: 33.3%-48.5%; negatively selected: 0%-8.3%) under grain feeding. These lineages encoded catalytic domains appended with carbohydrate-binding modules, such as tandem carbohydrate-binding modules linked to glycoside hydrolases, thereby enhancing substrate adhesion and degradation. In contrast, low-feed-efficiency bulls showed more random community structures and reduced functional specialization. Therefore, these suggest that cattle hosts with higher feed efficiency promote microbial populations functionally aligned with dietary inputs, a process we define as efficient host-mediated microbial amplification. These findings offer new insight into how ecological assembly and functional adaptation of the microbiome contribute to feed efficiency and lay the foundation for microbiome-informed strategies to enhance ruminant production sustainability.},
}

@article {pmid41624311,
year = {2026},
author = {Marchal, C and Ballan, D and Azib, S and Innocent, M and Urien, B and Tamaro, A and Gall-Ely, ML and Coton, E and Picot, A and Mounier, J and Coroller, L and Gabriel, P},
title = {Participatory and multi-disciplinary science dataset and surveys for the assessment of the microbiological and behavioural factors influencing fresh fruits and vegetables' waste at home.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112434},
pmid = {41624311},
issn = {2352-3409},
abstract = {Fresh fruits and vegetables (FFV) represent the largest part of food waste at the consumer level. This waste directly results from FFV physiological and microbiological spoilage, itself intricately linked to behavioural factors such as consumer practices, including purchase, storage and hygiene practices, but also consumers' perceptions towards spoilage. Based on a dual approach combining microbiological and behavioural sciences, we examined the link between FFV waste produced by 49 volunteering French households, measured using connected bins, the microbial ecology of their storage compartments, using culture-dependent and -independent approaches, and their consumer behaviour, cleaning and storage practices, through in-depth interviews and a dedicated survey. An exploratory qualitative survey carried out on 17 individuals followed by two quantitative data collections on 1048 and 815 representative French consumers enabled us to identify anti-FFV waste practices and to cluster consumers according to their anti-FFV waste behaviours. Spoilage dynamics of commonly consumed FFV, according to storage temperature, microbial contamination level and the presence or absence of surface wounds, were also performed in controlled conditions. This citizen-science-based dataset covers a wide array of microbiological and behavioural factors related to domestic FFV waste, as well as real measurements of waste volumes thanks to the innovative use of connected bins. Altogether, this data could provide interesting insights into more effective and accessible guidelines for FFV waste reduction at the consumer level, and thus to a potential reduction of global food waste and its related costs.},
}

@article {pmid41624200,
year = {2025},
author = {Xu, H and Liu, X and Sun, W and Dong, X and Liu, X and Xie, Y and He, J and Ali, A and Chen, M and Wu, L and Ma, J and Shao, K},
title = {Multi-omics elucidation of Lactiplantibacillus plantarum NKK20 in preventing PCOS via the gut-ovary axis: SCFAs-mediated microbiota-metabolite-immune crosstalk.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1709581},
pmid = {41624200},
issn = {2296-861X},
abstract = {PURPOSE: Polycystic ovary syndrome (PCOS) is a clinically prevalent endocrine and metabolic disorder characterized by gut microbial disturbances and chronic low-grade inflammatory responses.

METHODS: This study explores the therapeutic potential and mechanistic insights of Lactiplantibacillus plantarum NKK20 (LP) in a PCOS murine model established through high-fat diet (HFD) and letrozole co-induction. By integrating multi-omics profiling (16S rRNA sequencing and untargeted metabolomics) with histopathological evaluation, we systematically assessed LP-mediated modulations of gut microbiota composition, metabolic signatures, ovarian function, and intestinal barrier integrity.

RESULTS: The results demonstrated that LP administration effectively counteracted metabolic dysregulation in PCOS mice, mitigating body weight gain, ameliorating lipid abnormalities (reduced total cholesterol, triglycerides, and LDL-C alongside elevated HDL-C), and lowering fasting glucose levels. Hormonally, LP suppressed hyperandrogenism, as evidenced by decreased testosterone, while rebalancing inflammatory mediators through IL-10 upregulation and concomitant reduction of TNF-α, IL-6, IL-1β, and MCP-1. Ovarian histomorphology revealed attenuated follicular cysts and enhanced luteinization. Critically, LP restored intestinal homeostasis by (i) augmenting short-chain fatty acid (SCFA) production-particularly butyrate-(ii) fortifying the gut barrier via increased ZO-1 and occludin expression, and (iii) diminishing circulating endotoxin. Microbial sequencing identified enrichment of Bacteroidetes and Muribaculum following LP treatment. Serum metabolomics further uncovered LP-induced normalization of steroid hormone biosynthesis and glycerophospholipid metabolism, coinciding with elevated anti-inflammatory mediators such as 6a-prostaglandin I1.

CONCLUSION: Collectively, these findings delineate a novel preventive axis through which LP inhibits PCOS progression - namely, via coordinated "gut microbiota-metabolite-ovarian" crosstalk involving SCFA-mediated barrier restoration, microbial ecology stabilization, and suppression of ovarian inflammatory onset. This work advances the translational rationale for probiotic-based strategies in PCOS prevention.},
}

@article {pmid41624197,
year = {2025},
author = {Govaert, M and Duysburgh, C and Kesler, B and Marzorati, M},
title = {Effects of NatureKnit™ organic, a blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols, on the metabolic activity and community composition of the human gut microbiome using the M-SHIME[®] gastrointestinal model.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1740906},
pmid = {41624197},
issn = {2296-861X},
abstract = {OBJECTIVES: The effects of a proprietary blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols (commercially known as NatureKnit™ Organic) on the human gut microbiome were assessed.

METHODS: Short-term (48 h) in vitro colonic simulations using the validated Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME[®]) platform, with fecal inoculum from nine individual healthy human donors, were performed. Purified organic fibers (inulin and psyllium) were evaluated as comparators and a negative control was included. Primary measures included pH, gas pressure, short-chain fatty acid (SCFA) production, and microbial community composition.

RESULTS: All test products were well fermented with NatureKnit™ Organic showing slower fermentation kinetics than the purified fibers. SCFAs were significantly increased with all test products versus the negative control (p < 0.0001 for all) and NatureKnit™ Organic reached significance versus both purified fibers (p < 0.0001 for both). While relative abundances in the mucosal compartment were similar among all test conditions, luminal bacterial abundance increased with NatureKnit™ Organic and psyllium versus the negative control. The latter was mainly associated with statistically increased abundance (p < 0.05) of the genera Eisenbergiella and Monoglobus, with an additional strong enrichment of Bacteroidaceae. Furthermore, bacterial species richness was significantly increased with NatureKnit™ Organic versus the negative control (p = 0.0495), which was not observed for the purified organic fibers (p = 0.0567 and p = 0.4285 for inulin and psyllium, respectively).

CONCLUSION: Overall, the obtained results indicate that NatureKnit™ Organic may have a greater and gentler prebiotic effect compared with established purified prebiotic fibers.},
}

@article {pmid41621727,
year = {2026},
author = {De Luca, D},
title = {FastqOrienter: A Python utility for the automated orientation and quality diagnostics of paired-end Illumina metabarcoding reads.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107413},
doi = {10.1016/j.mimet.2026.107413},
pmid = {41621727},
issn = {1872-8359},
abstract = {FastqOrienter is a Python tool that corrects inconsistent read orientations in Illumina paired-end metabarcoding reads using a primer-aware logic and IUPAC-compliant matching. In addition, it provides detailed diagnostics and actionable insights for discarded reads. It ensures data integrity for downstream pipelines like DADA2 and QIIME 2.},
}

@article {pmid41620541,
year = {2026},
author = {Wang, Y and Han, S and Zhang, W and Shen, W and Dong, B and Wang, N},
title = {Microbial Mediators of Pine Defense Resistance: Stage-Specific Gut Symbionts Enable Acantholyda posticalis to Overcome Terpenoid Barriers.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02641-x},
pmid = {41620541},
issn = {1432-184X},
support = {SDAIT-24//Modern Agricultural Technology Industry System of Shandong province/ ; ZR2022MC198//Natural Science Foundation of Shandong Province/ ; 2023TSGC0345//Science and Technology of Small and Medium Enterprises Innovation Ability Enhancement in Shandong Province/ ; },
abstract = {Acantholyda posticalis (Matsumura) is a globally significant forest pest that inflicts substantial economic losses through its feeding activity on Pinus species. As an oligophagous insect, A. posticalis relies critically on its gut microbiota to overcome the defensive secondary metabolites of pine needles, particularly α- and β-pinene terpenoids. This study investigated the dynamic compositional changes of gut bacterial communities across different developmental stages of A. posticalis and characterized their functional roles in host adaptation. Through traditional culturing methods, two pinene-degrading bacterial strains-Klebsiella variicola and Enterobacter hormaechei-were isolated from the larval gut. In vitro assays demonstrated their significant capacity to degrade the two pinenes. High-throughput 16S rRNA sequencing revealed stage-specific bacterial enrichment patterns. Functional prediction suggested these microbial communities participate in critical metabolic processes, including phosphotransferase systems, GST activity, and detoxification pathways. This work advances understanding of insect-microbe symbiosis in oligophagous systems and proposes novel strategies for ecologically sustainable A. posticalis control through manipulation of its gut microbiota.},
}

@article {pmid41618023,
year = {2026},
author = {Han, D and Hong, HW and Kim, H and Richter-Heitmann, T and Ryu, JS and Yoo, KC},
title = {Unraveling the Complex Planktonic Microbial Community in the Amundsen Sea, Southern Ocean.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02696-4},
pmid = {41618023},
issn = {1432-184X},
support = {NRF- 2022R1F1A1065719//National Research Foundation of Korea/ ; 2025-RISE-10-004//the Ministry of Education (MOE) and the Gangwon State (G.S.)/ ; KOPRI PE24090//Ministry of Oceans and Fisheries/ ; },
abstract = {Spatial differences in microbial community structure and function were examined across polynyas, sea ice zones (SIZ), and ice-free waters of the Amundsen Sea, Southern Ocean, using 16 S and 18 S rRNA gene-based eDNA metabarcoding and quantitative PCR targeting nitrogen cycling and dimethylsulfoniopropionate (DMSP) degradation genes. The SIZ exhibited enrichment of psychrophilic bacteria (Colwellia spp.) and dominant eukaryotic taxa such as Diatomea and Prymnesiophyceae, likely linked to sea-ice-driven shifts in nutrient stoichiometry (elevated N: P and positive N*). Network analysis revealed interactions among primary producers, bacteria, and zooplankton, highlighting complementary roles in trophic energy transfer and nutrient recycling. Metabolic pathway predictions implied active bacterial processes related to sulfur and nitrogen cycling in the SIZ, particularly dissimilatory nitrate reduction and DMSP demethylation, suggesting coupling between carbon, nitrogen, and sulfur pathways. Quantitative PCR showed higher copy numbers of nitrogen cycling genes and DMSP degradation genes in the SIZ than in other regions, consistent with enhanced microbial denitrification, nitrogen fixation, and sulfur cycling under cold conditions shaped by sea-ice-driven nutrient dynamics. These findings demonstrate that environmental variation in Antarctic waters influences microbial diversity, reshapes ecological interactions, and modulates biogeochemical functions, with implications for nutrient cycling, food web dynamics, and ecosystem resilience in this climate-sensitive region.},
}

@article {pmid41617658,
year = {2026},
author = {Yan, Z and Liu, R and Zhang, ZA and Dai, T and Zhu, D and Zhang, Y},
title = {Intestinal Microplastic Retention Reshapes Gut Microbial Ecology through Surface-Associated Colonization and Additive Leaching.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16988},
pmid = {41617658},
issn = {1520-5851},
abstract = {Microplastics (MPs) have attracted increasing attention due to their potential impacts on the human gut microbiota, yet the mechanisms governing MP-microbiota interactions remain insufficiently resolved. Here, we employed the Simulator of the Human Intestinal Microbial Ecosystem, a dynamic host-free in vitro model, to investigate how intestinally retained poly(ethylene terephthalate) MPs influence gut microbial communities. We show that MP retention is associated with two separable processes: surface-mediated spatial redistribution of microbes and additive-associated perturbations. Compared with additive-eluted MPs and inert SiO2 particles, MPs exhibited greater surface roughness and hydrophobicity, promoting selective colonization by hydrophobic, potentially pathogenic, and organic-degrading taxa. This surface-associated colonization coincided with the displacement of luminal keystone taxa and pronounced restructuring of microbial co-occurrence networks, reflected by reduced negative cohesion and altered community stability. In parallel, leachable MP-associated additives independently shifted microbial composition and predicted functional potential, including enrichment of pathways related to xenobiotic degradation. This work provides mechanistic insight into how retained MPs may condition gut microbial ecosystems and underscores the importance of considering MP-associated microbial perturbations in gut-relevant exposure assessments.},
}

@article {pmid41615200,
year = {2026},
author = {Yang, J and Qin, X and Zhang, D and Dong, C},
title = {Microbial landscape: composition and health associations of environmental microbiome in key functional spaces of premium elderly care facilities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183725},
doi = {10.1128/spectrum.01837-25},
pmid = {41615200},
issn = {2165-0497},
abstract = {The environmental microbiome in elderly care facilities plays a crucial role in the health of aging populations with immunosenescence; however, its composition and health associations remain underexplored. This study characterizes the microbial ecology of premium elderly care facilities, focusing on key functional spaces, environmental drivers, and implications for resident health. We conducted 16S rRNA gene sequencing (V3-V4 regions) on 320 surface and air samples from six functional spaces (dining areas, medical facilities, bedrooms, bathrooms, recreational rooms, and corridors) across four premium elderly care facilities. Environmental parameters (temperature, humidity, CO2, and occupancy) were measured concurrently. Bioinformatics analysis (QIIME 2, DADA2, and Silva database) and statistical modeling (permutational multivariate analysis of variance, distance-based redundancy analysis, and PICRUSt2) were employed to assess microbial diversity, taxonomic composition, functional potential, and environmental correlations. Using 16S rRNA gene sequencing across four facilities in different geographic regions, we identified significant spatial heterogeneity in microbial diversity and composition, with dining areas and recreational rooms exhibiting higher richness (Shannon index: 6.07 ± 0.37) and human-associated taxa (e.g., Firmicutes), while medical facilities and bathrooms harbored lower diversity but elevated opportunistic pathogens (Pseudomonas and Klebsiella). Environmental parameters-particularly relative humidity (explaining 13.8% of community variation) and occupancy-strongly influenced the microbial structure. A core microbiome dominated by Proteobacteria, Firmicutes, and Actinobacteria was conserved across facilities, while functional predictions revealed space-specific traits, including predicted enrichment of antibiotic resistance genes in medical facilities (ARG Shannon diversity: 4.87 ± 0.42) and carbohydrate metabolism pathways in dining areas. Negative correlations between beneficial (Lactobacillus) and pathogenic taxa (Staphylococcus aureus) were consistent with potential ecological strategies for microbial balance, although validation with absolute quantification is needed. This study highlights the need for space-specific microbial management in elderly care environments, emphasizing humidity control, ventilation, and targeted hygiene to mitigate pathogen risks while preserving beneficial communities. Our findings suggest the potential value of ecologically informed stewardship over pathogen-centric approaches. Future research should integrate multi-omics and longitudinal health data to optimize microbiome-resident health interactions.IMPORTANCEAs people age, their immune systems weaken, making the elderly especially vulnerable to germs in their surroundings. This study reveals that the types and amounts of bacteria living on surfaces and in the air within premium elderly care facilities differ significantly depending on the room's purpose-such as dining areas, medical rooms, or bathrooms. We found that humidity and how many people use a space strongly influence these bacterial communities. Crucially, areas like medical rooms had more bacteria linked to infections and antibiotic resistance, while social spaces hosted more diverse and potentially beneficial bacteria. This shows that a "one-size-fits-all" cleaning approach is not ideal. Instead, tailoring hygiene practices and environmental controls (like managing humidity) to specific spaces could better protect residents' health by reducing harmful germs while supporting helpful ones, offering a smarter way to manage these critical living environments for our aging population.},
}

@article {pmid41615027,
year = {2026},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Rodríguez, CAD and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag012},
pmid = {41615027},
issn = {1751-7370},
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence (AI)-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}

@article {pmid41614284,
year = {2026},
author = {Karmakar, R and Paul, P and Malik, M and Maity, A and Mishra, MC and Tribedi, P and Ghosh, MM},
title = {In Silico and In Vitro Investigations of Novel Strategies to Combat Drug-Resistant Comamonas aquatica.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {134},
number = {2},
pages = {e70152},
doi = {10.1111/apm.70152},
pmid = {41614284},
issn = {1600-0463},
support = {BT/INF/22/SP41296/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; IMSXC2022-23/010//St. Xavier's College (Autonomous) Kolkata/ ; },
mesh = {*Biofilms/drug effects ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Tetracycline/pharmacology ; Computer Simulation ; *Benzaldehydes/pharmacology ; Humans ; *Drug Resistance, Bacterial ; Reactive Oxygen Species/metabolism ; },
abstract = {Comamonas aquatica, an emerging nosocomial pathogen, poses significant clinical challenges through biofilm-mediated antimicrobial resistance. This study investigated the efficacy of cuminaldehyde combined with tetracycline against C. aquatica biofilms using an integrated approach. In silico predictions (PASS online, SwissADME, PROTOX 3.0, OSIRIS) indicated that cuminaldehyde exhibited favorable oral bioavailability with acceptable toxicity profiles, while tetracycline showed limited oral absorption due to molecular size and polarity constraints. Experimentally, individual minimum inhibitory concentrations (MICs) were determined as 300 μg/mL for cuminaldehyde and 0.2 μg/mL for tetracycline. The fractional inhibitory concentration index (FICI) of 0.66 demonstrated additive interactions between the compounds (cuminaldehyde and tetracycline). The result indicated that the combinatorial application of compounds exhibited enhanced antimicrobial potential against the test organism. Furthermore, co-application of cuminaldehyde and tetracycline was found to show increased antibiofilm potential against the same organism. The result showed that the biofilm inhibition under the influence of the combinatorial application could be attributed to the enhancement of bacterial cell membrane permeability and accumulation of intracellular reactive oxygen species. In a nutshell, the findings of this study highlight a promising strategy of using combinatorial therapy involving cuminaldehyde-tetracycline for dealing with biofilm-associated infections caused by C. aquatica.},
}

*Biofilms/drug effects
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Tetracycline/pharmacology
Computer Simulation
*Benzaldehydes/pharmacology
Humans
*Drug Resistance, Bacterial
Reactive Oxygen Species/metabolism

@article {pmid41614084,
year = {2026},
author = {Kwarteng, SA and Mensah, JO and Obuam, PK and Odenteh, EA and Foriwaah, PD and Mbelede, AI and Dziwornu, E and Duker, EO and Boakye, JD and Agbotse, GD and Yanney, JN and Aba Aude Koffi, MC and DeWitt, ME and Addo, SO},
title = {Occurrence of Tick-Borne Pathogens in Rhipicephalus sanguineus Sensu Lato From Domestic Dogs in Kumasi, Ghana.},
journal = {Veterinary medicine international},
volume = {2026},
number = {},
pages = {8881048},
pmid = {41614084},
issn = {2090-8113},
abstract = {Tick-borne pathogens, transmitted by ticks, infect humans and animals worldwide. The brown dog tick, Rhipicephalus sanguineus sensu lato, is a significant vector of a number of pathogens, including Ehrlichia canis, Rickettsia and Anaplasma species. In Ghana, there is limited information on the pathogens carried by Rh. sanguineus s.l. As such, Rh. sanguineus ticks taken from domestic dogs in Kumasi were screened for tick-borne pathogens, including Coxiella burnetii, Rickettsia, Babesia, Theileria, Anaplasma, Ehrlichia and Hepatozoon species. A total of 204 ticks collected from 56 infested dogs were morphologically identified as Rh. sanguineus s.l. From the 88 pools screened, 36 (40.9%) were positive for pathogen DNA. The pathogens identified were Rickettsia africae (5 pools), Ehrlichia canis (10 pools) and uncultured Anaplasma sp. (21 pools) with maximum likelihood estimates as 2.48% (95% CI: 0.93, 5.38%), 5.22% (95% CI: 2.69, 9.15%) and 11.20% (95% CI: 7.32, 16.29%), respectively. There was no association between the detection of a pathogen and the tick sex or dog breed, age or sex. This study provides important baseline data on the circulation of tick-borne pathogens in Rh. sanguineus s.l. ticks in Kumasi, with implications for both veterinary and human health. The presence of uncultured Anaplasma sp. suggests a wider diversity of tick-borne bacteria with unknown pathogenicity. There is a need for integrated tick control, improved diagnosis and additional epidemiological studies to mitigate the impact of tick-borne diseases in Ghana.},
}

@article {pmid41613253,
year = {2026},
author = {Samimi, A and Verdon, N and Allen, RJ and Rosenbaum, MA},
title = {Probing Antibiotic Inhibition in Small Bacterial Populations With Combinatorial Droplet Microfluidics.},
journal = {Small science},
volume = {6},
number = {1},
pages = {e202500421},
pmid = {41613253},
issn = {2688-4046},
abstract = {Bacterial infections often involve small, local populations of bacteria, yet antibiotic treatment decisions are generally based on bulk population susceptibility assays. Stochastic variability among local small populations can influence susceptibility, limiting the predictive capability of bulk assays. Therefore there is a need to better understand antibiotic response in small populations. Droplet-based microfluidics enables the high-throughput production of tens of thousands of picolitre droplets, in which small populations of bacteria (e.g., 8 cells) can be encapsulated and their responses to different environmental conditions tracked. Here, we use a combinatorial droplet-generation platform, combined with microscopy and image analysis, to interrogate the responses of small populations of Escherichia coli to different bulk-determined sub-inhibitory concentrations of the antibiotics tetracycline, streptomycin, and ampicillin within a single experiment. We observe qualitatively distinct small-population responses for these antibiotics. For the bacteriostatic ribosome-targeting antibiotic tetracycline, growth varies nonmonotonically at low antibiotic concentrations. For the bactericidal ribosome-targeting antibiotic streptomycin, we observe apparent bistability, some replicate populations growing while others die. For the bactericidal cell-wall targeting antibiotic ampicillin, we observe stochastic bacterial filamentation. Our study shows how distinct phenomena impacting antibiotic susceptibility may emerge in small bacterial populations, laying a foundation for deeper studies into potential treatment implications.},
}

@article {pmid41612472,
year = {2026},
author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y},
title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03892-1},
pmid = {41612472},
issn = {2047-783X},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; },
abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.

METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.

RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.

CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.},
}

@article {pmid41612032,
year = {2026},
author = {Li, Q and Shen, J and Feng, J and Liu, Y and Huang, Z and Wang, X},
title = {Patterns of ARGs and VFs Driven by Short-Term Seasonal Hydro-Environmental Stress Interactions in a Eutrophic Plateau Lake.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02703-8},
pmid = {41612032},
issn = {1432-184X},
support = {No. 202303AC100016//the Key Research and Development Program of Yunnan/ ; Project No. 202301AT070001//the Yunnan Fundamental Research Projects/ ; No. 2024YFD1700100//the National Key Research and Development Program of China/ ; },
abstract = {With the intensification of human activities, large amounts of antibiotics, heavy metals, and disinfectants enter lakes, exerting continuous selective pressure and driving the enrichment and dissemination of ARGs and VFs in aquatic microbial communities. Previous studies have primarily focused on the occurrence and abundance of ARGs in extreme plateau environments. However, the diversity and abundance of ARGs and VFs in eutrophic plateau lakes under different seasons and environmental pressures remain underexplored. In this study, we analyzed the presence of ARGs and VFs in the eutrophic plateau lake Qilu Lake across different seasons. From the perspective of hydrology and water quality, there is no inflow into the lake during the dry season, while the wet season sees an inflow of 28.1724 million cubic meters. Organic matter and metal ions are significantly higher in the dry season, whereas total nitrogen and pH levels rise notably in the wet season. We found 29 types of ARGs and 601 types of VFs in the dry season, compared to 45 types of ARGs and 637 types of VFs in the wet season. In both seasons, glycopeptide antibiotic resistance genes were the most abundant ARGs. LPS was the most abundant VFs in the dry season, while Type IV pili dominated in the wet season. The primary microbial-driven resistance mechanism strategy in both seasons was Antibiotic target alteration. The microorganism with the highest abundance of ARGs and VFs in both seasons was Pseudomonadota. Correlation analysis showed a positive relationship between the abundance of ARGs and VFs in both seasons, with this relationship being more pronounced in the dry season. Our findings indicate that the increased diversity and abundance of ARGs during the wet season may be directly linked to the heightened input of exogenous antibiotic-resistant bacteria and the promotion of plasmid conjugation transfer by hydraulic disturbances. Although VFs diversity was higher in the wet season, the low-water concentration effect and metal ion stress during the dry season significantly elevated the relative abundance of core VFs (e.g., type IV pili), resulting in the abundance of VFs per unit volume surpassing that of the wet season.},
}

@article {pmid41611907,
year = {2026},
author = {Capri, FC and Prazzi, E and Casamento, G and Alduina, R},
title = {Influence of Nest Microbiota on Hatching Success of Caretta Caretta on Lampedusa Island.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02699-1},
pmid = {41611907},
issn = {1432-184X},
abstract = {Egg hatching success in sea turtle nests can be influenced by multiple abiotic and biotic factors. Although interest in nest microbiota as a determinant of embryo development and viability is increasing, its role has not yet been fully elucidated. In this study, we profiled the bacterial communities of four Caretta caretta nests on Lampedusa Island: Cala Pisana (P1 and P2) and Spiaggia dei Conigli (C1 and C2), which showed different hatching success rates (P1 = 85.2%, P2 = 1.1%, C1 = 1.1%, C2 = 0.0%). Using 16S rRNA gene (V3-V4) sequencing, we analyzed different sample types, including sand from inside and outside the nest chamber, eggshells, and inner membranes. Alpha diversity was highest in sand and lower in eggshells and inner membranes. β-diversity clearly separated the only successful nest (P1) from the others (P2, C1, and C2) (PERMANOVA p < 0.001). Across all nests, the dominant phyla were Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota; notably, the Firmicutes/Bacteroidota (F/B) ratio was lowest in P1 compared with P2, C1, and C2. Nests with low hatching success were Firmicutes-dominated, enriched in Bacillus and Pseudomonas, and harbored hydrocarbon-degrading genera (Pseudoxanthomonas and Devosia), suggesting environmental influences. Opportunistic pathogens (Ochrobactrum and Simkaniaceae), likely associated with vertical transmission, were detected exclusively in C1 and C2 nests. Overall, our findings highlight the potentially critical role of nest microbiota in reproductive success. Both vertical (maternal) and horizontal (environmental and anthropogenic) transmission appear to shape microbial composition, potentially affecting hatchling viability and offering useful insights for conservation monitoring.},
}

@article {pmid41611865,
year = {2026},
author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR},
title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36282-y},
pmid = {41611865},
issn = {2045-2322},
abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.},
}

@article {pmid41611114,
year = {2026},
author = {Young, RB and Correia, GDS and MacIntyre, DA},
title = {Host, microbial and environmental drivers of vaginal microbiota composition.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2026.01.020},
pmid = {41611114},
issn = {1556-5653},
abstract = {The human vagina harbours a microbial community that differs markedly in compositional structure from all mammals, including closely related primates. Lactobacilli are the most abundant vaginal species, and their dominance in this niche are associated with protection against adverse health outcomes including preterm birth, sexually transmitted infections and bacterial vaginosis. However, the vaginal environment can also support compositions of diverse anaerobic bacteria, which have been linked to poor reproductive health outcomes. Here, we review current knowledge on host and microbial determinants that influence microbial community structure within the vaginal niche, emphasising the interplay between host physiology, immune and metabolic interactions as well as lifestyle factors. This integrated understanding provides a foundation for linking vaginal microbiome compositions to clinically relevant phenotypes and highlights mechanisms that could be exploited to promote improved reproductive health.},
}

@article {pmid41610262,
year = {2026},
author = {Wrightson, I and Man, M and Castañeda-Gómez, L and Srikanthan, N and Tong, H and Knorr, MA and Frey, SD and Nadelhoffer, KJ and Lajtha, K and Simpson, MJ},
title = {Three Decades of Litter Manipulation Distinctly Shifts Soil Organic Matter Composition and Constrains Soil Carbon Sequestration in Temperate Forest Soils.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11996},
pmid = {41610262},
issn = {1520-5851},
abstract = {The capacity of forest soils to sequester carbon (C) is susceptible to shifts in the litter quantity and chemistry. Using measurements from the third decade of a long-term Detrital Input and Removal Treatment (DIRT) experiment at Harvard Forest (MA, USA), extending previously published work from 20 years, we examined how litter inputs shape soil organic matter (SOM) chemistry. Elemental analysis, targeted compound analysis, solid-state [13]C nuclear magnetic resonance (NMR) spectroscopy, and microbial biomass and community composition measurements were used. Despite doubled litter inputs over 30 years, no net soil C accumulation occurred, and the SOM decomposition stage was similar to the control, suggesting continuous microbial processing of added inputs. The exclusion of litter, roots, or both led to lower soil C and more advanced SOM decomposition in mineral soils. Shifts in microbial community composition, particularly an increase in Gram (+) to Gram (-) bacteria under exclusion treatments, point to microbial reorganization in response to altered substrate availability. This long-term study underscores the limited potential for long-term soil C sequestration due to sustained microbial decomposition and the role of continuous plant inputs in shaping SOM chemisty under changing detrital regimes in a temperate forest.},
}

@article {pmid41610138,
year = {2026},
author = {Dubey, S and Shukla, S and Gupta, N and Dixit, R and Bhadury, P and Kumar, A},
title = {Effect of perchlorate on biocementation capable bacteria and Martian bricks.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340252},
doi = {10.1371/journal.pone.0340252},
pmid = {41610138},
issn = {1932-6203},
mesh = {*Perchlorates/pharmacology ; *Mars ; *Bacteria/drug effects/metabolism/genetics ; Calcium Carbonate/chemistry ; *Construction Materials/microbiology ; Urease/metabolism ; },
abstract = {With the recent discovery of perchlorate (0.5-1%) in Martian regolith, more experiments related to the impact of perchlorate on microbial life are crucial to understanding the possibility of earth life forms that could sustain on the Martian terrain. While we are familiar with the idea of bioconsolidated Martian bricks made via Microbially Induced Calcite Precipitation (MICP), studies on the effect of perchlorate on Martian bricks & biocementation capable microbes have been obscure. In this work, we investigated the effect of perchlorate (MgClO4- salt) on a lab-isolated biocementation capable bacteria & Martian bricks bioconsolidated by the same, with 1% perchlorate in Mars Global Simulant-1 (MGS-1). The screening of biocementation-capable bacteria involved phenol red assay for urease activity followed by Scanning Electron Microscopy (SEM) and X-ray diffraction (XRD) study of the precipitate formed through MICP via ureolytic pathway. The biocementation capable bacterium SI_IISc_isolate was found to be phylogenetically closest to Sporosarcina pasteurii strain S2135 with a draft genome size of 3.69 Mb. To understand the effect of perchlorate on SI_IISc_isolate, we majorly relied on Gram-staining & SEM. The negative effect of perchlorate stress on the isolate was evident by its decreased growth in the presence of varying concentrations of perchlorate through plate assays, growth curve studies in broth & live-dead staining. Gram-staining study and SEM both revealed that perchlorate induces the release of extracellular matrix (ECM) and promotes clustering of cells by the bacteria, which we termed as 'multicellularity-like behavior.' Further, we constructed Martian bricks with Martian Global Simulant (MGS-1) along with 1% perchlorate, utilizing the microbially induced calcite precipitation ability of the Sporosarcina sp. strain SI_IISc_isolate via ureolysis, following an established protocol at our lab. The bioconsolidation experiments showed that in the presence of a natural adhesive - guar gum, perchlorate tends to significantly improve the compressive strength of Martian bricks. However, the end result eventually relies on the overall effect of various additives in the regolith.},
}

*Perchlorates/pharmacology
*Mars
*Bacteria/drug effects/metabolism/genetics
Calcium Carbonate/chemistry
*Construction Materials/microbiology
Urease/metabolism

@article {pmid41609879,
year = {2026},
author = {Sánchez Espinosa, KC and Fernández-González, M and Dias-Lorenzo, DA and Rodríguez-Rajo, FJ},
title = {First Report of Alternaria in the Olive Agroecosystem of NW Spain: Aerobiological Characterization and Relationship with Meteorological Factors.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02700-x},
pmid = {41609879},
issn = {1432-184X},
abstract = {Alternaria spp. is one of the fungal genera affecting olive cultivation, and its temporal dynamics are influenced by climatic variations occurring throughout the crop's vegetative cycle. The aim of this study was to determine the presence of Alternaria spp. in an olive-growing area in northwestern Spain and to examine the relationship between its airborne concentrations and meteorological variables, in order to preliminarily predict its presence in the atmosphere during the olive tree's phenological cycle. To achieve this, a phenological, aeromycological, and meteorological study was conducted from 2021 to 2024. Alternaria spp. conidia were detected in the air throughout all major phenological stages, with peak concentrations occurring mainly during fruit development. The highest percentages of spores were recorded between 11:00 and 22:00, primarily influenced by temperature and sunlight. During the maturity of fruit stages in 2023 and 2024, isolates from the Alternaria section Alternaria were identified as the cause of olive rot. A predictive model was obtained that estimates the atmospheric concentrations of this type of fungus in the study area, based on average temperature values and hours of sunshine. This study constitutes the first report of Alternaria spp. in an olive-growing area of northwestern Spain and provides models that preliminarily predict its presence. These models can inform growers of the pathogen's presence in the air before visible symptoms appear, thereby reducing the likelihood of infection in susceptible plants when environmental conditions favor its development.},
}

@article {pmid41608689,
year = {2025},
author = {Yan, W and Du, N and Zhang, K and Yang, P and Guo, J and Xu, L},
title = {Bilirubin-microbiota interaction: molecular mechanisms and therapeutic strategies in neonatal jaundice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1749152},
pmid = {41608689},
issn = {1664-302X},
abstract = {Recent studies have revealed a complex interplay between bilirubin metabolism and the gut microbiota. Bilirubin functions as a potent antioxidant and signaling molecule in humans, and its concentration-dependent effects on distinct microbial taxa indicate that the compound exerts selective pressure on the gut ecosystem. The gut microbiota modulates bilirubin metabolism by altering intestinal pH, producing and activating Bilirubin metabolic enzyme, and bile acids. Because perturbations in bilirubin handling are especially common-and potentially neurotoxic-in neonates, a concise synthesis of recent progress is warranted. Here we review how microbial communities reshape bilirubin flux, how bilirubin and its conjugates, in turn, sculpt microbial ecology, and how the dynamic equilibrium between conjugated and unconjugated bilirubin in hyperbilirubinaemia is influenced by the microbiome. Regulating gut microbiota to accelerate bilirubin clearance or attenuate its toxicity may therefore offer a tractable therapeutic avenue.},
}

@article {pmid41607130,
year = {2026},
author = {Stewart, JD and Ramirez, DX and Leon-Reyes, A and Barriga, N and Llerena, S and Manley, BF and Carpintero-Salvador, N and Ruiz-Uriguen, M and Raaijmakers, JM and Kiers, ET and Weedon, JT},
title = {Land Use Change Reshapes Climate-Driven Diversity Patterns of Tropical Arbuscular Mycorrhizal Fungi.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70253},
doi = {10.1111/mec.70253},
pmid = {41607130},
issn = {1365-294X},
support = {MICROP 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; //Paul G. Allen Family Foundation/ ; //Schmidt Family Foundation/ ; },
mesh = {*Mycorrhizae/genetics/classification ; *Biodiversity ; *Soil Microbiology ; Agriculture ; Tropical Climate ; Temperature ; Ecosystem ; Soil ; Climate ; *Climate Change ; },
abstract = {Land use change and agricultural expansion threaten biodiversity yet the effects on soil life remain poorly understood, especially for microbes. Arbuscular mycorrhizal (AM) fungi are microbes that form associations with most plant species and are essential for plant nutrient uptake. The diversity of these fungi is also sensitive to both land use change and regional climatic conditions. We therefore asked whether variation in AM fungal diversity is driven by land use change, and whether these effects are further influenced by interactions with temperature and precipitation gradients. To test this, we quantified AM fungal biodiversity in cultivated and adjacent uncultivated soils across a 1700 m elevational gradient (temperature: 7.7°C-16.5°C and precipitation: 1000-3500 mm). We found that conversion of uncultivated soils to agriculture reduced AM fungal richness by 80%, on average. Richness in uncultivated soils increased with the temperature gradient, while richness in farms declined. A similar but inverted trend was found for precipitation, where richness in uncultivated sites declined as precipitation increased. Uncultivated soils contained approximately three-fold more unique AM fungal species compared to cultivated soils. Our findings demonstrate that interactions between climate and land use strongly influence AM fungal biodiversity patterns in tropical mountain ecosystems. Incorporating both factors into conservation and sustainable agriculture strategies will be critical to preserving belowground biodiversity under global change.},
}

*Mycorrhizae/genetics/classification
*Biodiversity
*Soil Microbiology
Agriculture
Tropical Climate
Temperature
Ecosystem
Soil
Climate
*Climate Change

@article {pmid41606790,
year = {2026},
author = {Clutter, CH and Leung, DT},
title = {Tracing MR1 expression across tissues to find the perfect MAIT.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiag014},
pmid = {41606790},
issn = {1938-3673},
abstract = {Mucosal associated invariant T (MAIT) cells are part of a T cell subset that is activated upon presentation of B2 vitamin (riboflavin) metabolites by the major histocompatibility complex, class I related (MR1) protein. Though there is a clear relationship between microbial production of riboflavin and MAIT cell development and persistence, little is known about the cells that primarily communicate with MAIT cells and other MR1-restricted T cells. Elegant work by Deng et al demonstrates that it is macrophages from the lung and peritoneum that express the highest amount of MR1 and are the most efficient at presenting vitamin B antigens to MAIT cells. This landmark study not only definitively identifies and maps the key antigen presenting cell populations involved in MAIT cell activation, it also reveals a bidirectional relationship between MR1 expression and the host microbiome. While further work on how these findings translate to human MAIT cell biology is needed, this study has provided us with unprecedented insights into the mechanistic interplay and microbial ecology of MR1 presentation of riboflavin metabolites.},
}

@article {pmid41606115,
year = {2026},
author = {Hao, YQ and Li, BH and Chen, JY and Shu, WS and Zhao, XF},
title = {Bacterial necromass recycling promotes diversity maintenance in bacterial communities via resource partitioning.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41606115},
issn = {2397-334X},
support = {32371597//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32271600//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Understanding how high species diversity is maintained in natural bacterial communities is a central question in microbial ecology. Due to the versatile heterotrophic capacities of bacteria and the rich nutrients released by deceased bacterial cells, necromass recycling plays an important role in sustaining bacterial growth. Such nutrient cycling within communities can provide additional resource niches for bacteria, but its potential effects on bacterial diversity maintenance have been neglected. Here we conducted two independent experiments and studied the assembly of 276 soil-derived bacterial communities sustained by a wide range of bacterial necromass combinations, from single-species necromass to combinations of up to nearly 1,000 species. Our results highlight the existence of a species-rich bacterial necrobiome in soil. We found that the composition of necromass-decomposing communities was determined by the various organic compounds in the different necromass combinations, and the increases in necromass-producing species constantly promoted species diversity of necromass-decomposing communities. Moreover, the average niche breadth and overlap of coexisting necromass-decomposing species in utilizing distinct single-species necromass decreased with increases in necromass diversity, supporting the hypothesis of resource partitioning in utilizing different single-species necromass. Our study provides insights into diversity maintenance in bacterial communities from a perspective of internal nutrient cycling.},
}

@article {pmid41605992,
year = {2026},
author = {Dickerson, AL and Jechow, A and Nößler, M and Walles, TJW and Berger, SA and Hölker, F and Nejstgaard, JC},
title = {High-resolution in situ imaging reveals size-specific moonlight responses in zooplankton diel vertical migration.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4086},
pmid = {41605992},
issn = {2045-2322},
mesh = {Animals ; *Zooplankton/physiology ; *Moon ; Copepoda/physiology ; Light ; *Animal Migration/physiology ; Body Size ; Germany ; Cladocera/physiology ; Lakes ; },
abstract = {Light is the primary cue driving zooplankton diel vertical migration (DVM), a strategy that balances predation risk with resource access. However, DVM is often oversimplified, with limited consideration of how light-driven risks and resource needs vary across taxa and life stages. This simplification is partly due to constraints on collecting high-resolution, size-resolved data -especially at night, when subtle shifts in illumination reshape nocturnal risk landscapes. To overcome these limitations, we deployed a high-resolution in situ modular Deep-focus Plankton Imager and an image-recognition approach to quantify fine scale DVM and body sizes of Cladocerans and Copepods in Lake Stechlin, Germany. Data was collected from day into night and across moonrise and was compared with environmental data from vertical profiling sondes. Typical DVM patterns emerged, with deeper daytime distributions, however, moonlight introduced additional behavioural complexity: larger individuals avoided illuminated layers, likely managing predation risk, while smaller individuals moved into these layers, possibly exploiting foraging opportunities and reduced risk. These light-mediated shifts were further shaped by ecological conditions; copepods tracked food-rich layers regardless of light levels at night, while cladocerans showed light-dependent responses to both temperature and food, such that light caused them to avoid otherwise favourable (warm, food-rich) layers. Our approach provides new insight into how zooplankton navigate nocturnal lightscapes, revealing size- and taxon-specific strategies. By establishing size-dependent responses to natural moonlight, this work provides a crucial baseline for predicting how artificial light at night may restructure zooplankton communities and destabilize freshwater food webs.},
}

Animals
*Zooplankton/physiology
*Moon
Copepoda/physiology
Light
*Animal Migration/physiology
Body Size
Germany
Cladocera/physiology
Lakes

@article {pmid41605068,
year = {2026},
author = {Truswell, A and Jordan, D and Pang, S and Cherrington, T and Hampson, DJ and Blinco, J and Adsett, S and Abraham, R and Stegger, M and Abraham, S},
title = {Genomic analysis of a porcine exudative epidermitis outbreak caused by Staphylococcus hyicus.},
journal = {Veterinary microbiology},
volume = {314},
number = {},
pages = {110883},
doi = {10.1016/j.vetmic.2026.110883},
pmid = {41605068},
issn = {1873-2542},
abstract = {Exudative epidermitis (EE) causes substantial morbidity and mortality in piglets. This study investigated the microbial ecology, antimicrobial resistance (AMR), and genomic diversity of Staphylococcus hyicus associated with an EE outbreak in an Australian piggery. Lesion swabs from 20 affected piglets yielded 160 bacterial isolates (including S. hyicus and cohabiting species). Isolates underwent species identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) of S. hyicus for AMR/virulence gene profiling and core-genome SNP analysis to assess genomic relatedness. S. hyicus predominated among lesion isolates. Phenotypic testing showed varied AMR, with frequent resistance to erythromycin and tetracycline. WGS of 27 S. hyicus isolates identified five distinct genotypic AMR profiles, including combinations spanning multiple drug classes. All S. hyicus carried the exfoliative toxin gene shetA, and 24 also carried exhD. Core-genome analysis indicated a highly clonal outbreak: 24/27 genomes differed by 0 core SNPs, with the remaining three closely related. Despite this clonality, resistance gene carriage varied across isolates. Consequently, reliance on a single colony to represent an outbreak could understate resistance and overstate treatability. These findings support routine multi-isolate sampling to capture within-clone AMR variability, bolster antimicrobial selection during EE management, and inform consideration of autogenous vaccines targeting dominant outbreak clones.},
}