@article {pmid40312547,
year = {2025},
author = {Hu, L and Zhang, K and Xu, Y and Zheng, X and Waterman, JM and Ouyang, X and Wu, Z and Shen, Z and He, Y and Ma, B and Robert, CAM and Raaijmakers, JM and Ye, M and Erb, M and Xu, J},
title = {Herbivory-induced green leaf volatiles increase plant performance through jasmonate-dependent plant-soil feedbacks.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40312547},
issn = {2055-0278},
support = {32372775//National Natural Science Foundation of China (National Science Foundation of China)/ ; 200355//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {Plants influence each other chemically by releasing leaf volatiles and root exudates, but whether and how these two phenomena interact remains unknown. Here we demonstrate that volatiles that are released by herbivore-attacked leaves trigger plant-soil feedbacks, resulting in increased performance of different plant species. We show that this phenomenon is due to green leaf volatiles that induce jasmonate-dependent systemic defence signalling in receiver plants, which results in the accumulation of beneficial soil bacteria in the rhizosphere. These soil bacteria then increase plant growth and enhance plant defences. In maize, a cysteine-rich receptor-like protein kinase, ZmCRK25, is required for this effect. In four successive year-field experiments, we demonstrate that this phenomenon can suppress leaf herbivore abundance and enhance maize growth and yield. Thus, volatile-mediated plant-plant interactions trigger plant-soil feedbacks that shape plant performance across different plant species through broadly conserved defence signalling mechanisms and changes in soil microbiota. This phenomenon expands the repertoire of biologically relevant plant-plant interactions in space and time and holds promise for the sustainable intensification of agriculture.},
}

@article {pmid40310547,
year = {2025},
author = {Calcagnile, M and Quarta, E and Sicuro, A and Pecoraro, L and Schiavone, R and Tredici, SM and Talà, A and Corallo, A and Verri, T and Stabili, L and Alifano, P},
title = {Effect of Bacillus velezensis MT9 on Nile Tilapia (Oreochromis Niloticus) Intestinal Microbiota.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {37},
pmid = {40310547},
issn = {1432-184X},
support = {ARS01_01053//Ministero dell'Istruzione e del Merito/ ; ARS01_01053//Ministero dell'Istruzione e del Merito/ ; CUP B83C22002930006//European Union Next Generation EU (PNRR)/ ; },
mesh = {Animals ; *Bacillus/physiology/genetics ; *Cichlids/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; RNA, Ribosomal, 16S/genetics ; Aquaculture ; Bacteria/classification/genetics/isolation & purification ; Animal Feed/analysis ; },
abstract = {In recent years, there has been a growing interest in the use of probiotics in aquaculture, due to their effectiveness on production, safety, and environmental friendliness. Probiotics, used as feed additives and as an alternative to antibiotics for disease prevention, have been shown to be active as growth promoters, improving survival and health of farmed fish. In this study, we have investigated the ability of the strain Bacillus velezensis MT9, as potential probiotic, to modulate the intestinal microbiota of the Nile tilapia (Oreochromis niloticus) fed with the Bacillus velezensis-supplemented feed in an experimental aquaculture plant. The analysis of the microbial community of the Nile tilapia by culture-based and 16S rRNA gene metabarcoding approaches demonstrated that B. velezensis MT9 reshapes the fish intestinal microbiota by reducing the amounts of opportunistic Gram-negative bacterial pathogens belonging to the phylum of Proteobacterium (Pseudomonadota) and increasing the amounts of beneficial bacteria belonging to the phyla Firmicutes (Bacillota) and Actinobacteria (Actinomycetota). Specifically, dietary supplementation of Nile tilapia with B. velezensis MT9 resulted in an increase in the relative abundance of bacteria of the genus Romboutsia, which has a well-documented probiotic activity, and a decrease in the relative abundance of Gammaproteobacteria of the genera Aeromonas and Vibrio, which include opportunistic pathogens for fish, and Escherichia/Shigella, which may pose a risk to consumers. The whole genome sequence of B. velezensis MT9 was then determined. Genome analysis revealed several peculiarities of B. velezensis MT9 compared to other B. velezensis reference strains including specific metabolic traits, differences in two-component and quorum sensing systems as well as the potential ability to produce a distinct array of secondary metabolites, which could explain the strong ability of this strain to modulate the intestinal microbiota of the Nile tilapia.},
}

Animals
*Bacillus/physiology/genetics
*Cichlids/microbiology
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/pharmacology
RNA, Ribosomal, 16S/genetics
Aquaculture
Bacteria/classification/genetics/isolation & purification
Animal Feed/analysis

@article {pmid40309103,
year = {2025},
author = {Cong, X and Liu, X and Zhou, D and Xu, Y and Liu, J and Tong, F},
title = {Characterization and comparison of the fecal bacterial microbiota in Red Back Pine Root Snake (Oligodon formosanus) and Chinese Slug-Eating Snake (Pareas chinensis).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1575405},
pmid = {40309103},
issn = {1664-302X},
abstract = {INTRODUCTION: The gastrointestinal tracts and oral cavities of animals harbor complex microbial communities that assist hosts in nutrient absorption and immune responses, thereby influencing behavior, development, reproduction, and overall health.

METHODS: We utilized metagenomic sequencing technology to conduct a detailed analysis of the fecal bacterial communities of six Red Back Pine Root Snakes (Oligodon formosanus, XT) and three Chinese Slug-Eating Snakes (Pareas chinensis, Z) individuals. The microbial composition was assessed through taxonomic profiling, alpha diversity analysis, and functional annotation using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

RESULTS: The results indicated that Proteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in XT samples, while Z samples additionally contained Patescibacteria. Alpha diversity analysis revealed significant differences in species abundance at the family level, with Z samples exhibiting higher microbial richness than XT. Furthermore, KEGG analysis showed that XT had higher functional gene abundance in pathways related to transcription, translation, environmental adaptation, membrane transport, cellular communities (prokaryotes), motility, and replication/repair compared to Z.

DISCUSSION: This study provides a comparative analysis of their gut microbiomes, offering valuable insights for future research on zoonotic diseases, host-microbe interactions, and ecological, evolutionary, behavioral, and seasonal influences on snake microbiota. These findings contribute to a broader understanding of microbial ecology in reptiles and its implications for conservation and disease dynamics.},
}

@article {pmid40307095,
year = {2025},
author = {Zhang, D and Gao, JT and Zhou, SG},
title = {Microbial electrotaxis: rewiring environmental microbiomes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.04.005},
pmid = {40307095},
issn = {1878-4380},
abstract = {Electric fields in sediments and soils are critical yet overlooked drivers of microbial ecology. This review examines the importance of electrotaxis in shaping microbial community dynamics and ecology models, surpassing traditional frameworks centered on chemotaxis. We analyze evidence that electric field gradients influence microbial community structure, function, and biogeochemical cycles in natural environments. Current mechanistic models, primarily based on eukaryotic systems, insufficiently explain bacterial electrotactic responses, necessitating new conceptual frameworks that integrate electrochemical and biological perspectives. We also evaluate its applications in environmental and microbiome engineering, with future research recommendations and methodologies in electrotaxis research. This synthesis aims to establish electrotaxis as an essential consideration in microbial ecology, presenting both challenges and opportunities for advancing our understanding of microbial ecosystems.},
}

@article {pmid40305681,
year = {2025},
author = {Bennett, BD and Meier, DAO and Lanclos, VC and Asrari, H and Coates, JD and Thrash, JC},
title = {Polyhydroxybutyrate production by freshwater SAR11 (LD12).},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf087},
pmid = {40305681},
issn = {1751-7370},
abstract = {SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate polymers. Here, we investigated the relevance of polyhydroxyalkanoate production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that many LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate, a common form of polyhydroxyalkanoate, and estimated the total polyhydroxybutyrate content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the polyhydroxybutyrate. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated polyhydroxybutyrate granules and expression of the phaCAB locus remained constant. We suggest that polyhydroxybutyrate synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This work characterizes polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism.},
}

@article {pmid40304437,
year = {2025},
author = {Kardish, MR and Stachowicz, JJ},
title = {More Than a Stick in the Mud: Eelgrass Leaf and Root Bacterial Communities Are Distinct From Those on Physical Mimics.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70086},
doi = {10.1111/1758-2229.70086},
pmid = {40304437},
issn = {1758-2229},
support = {//UC Davis Center for Population Biology/ ; OCE 1829992//National Science Foundation/ ; //National Science Foundation GRFP/ ; TG-DEB160008//Extreme Science and Engineering Discovery Environment (XSEDE)/ ; //Gordon and Betty Moore Foundation/ ; },
mesh = {*Zosteraceae/microbiology ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {We examine the role of physical structure versus biotic interactions in structuring host-associated microbial communities on a marine angiosperm, Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant-microalgal-pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.},
}

*Zosteraceae/microbiology
*Plant Roots/microbiology
*Plant Leaves/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid40303429,
year = {2025},
author = {Zhao, C and Zhang, J and Chen, Y and Yang, L and Chen, H and Liang, Y and Wang, W and He, S and Luo, Y and Zhang, J and Zhang, H and Yang, S and Guo, G and Dai, W and Yang, Z and Chen, J and Zhou, Y and Khan, WU and Liu, G and Jiang, Y and Zhu, T and Xu, Y and García-Caparros, P and Van de Peer, Y and Xue, JY and Chen, C and Zhang, L and Chen, F},
title = {Water lily pond: a multiomics database for water lilies.},
journal = {Horticulture research},
volume = {12},
number = {6},
pages = {uhaf076},
pmid = {40303429},
issn = {2662-6810},
}

@article {pmid40302853,
year = {2025},
author = {Gharbi, D and Neumann, FH and Podile, K and McDonald, M and Linde, JH and Frampton, M and Liebenberg, JL and Cilliers, S and Mmatladi, T and Nkosi, P and Paledi, K and Piketh, S and Staats, J and Burger, RP and Havenga, H and Garland, RM and Bester, P and Lebre, PH and Ricci, C},
title = {Exposure to outdoor aerospora and associated respiratory health risks among adults in Potchefstroom, North-West province, South Africa.},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1568669},
pmid = {40302853},
issn = {2673-6101},
abstract = {BACKGROUND: Data on allergic rhinitis and respiratory health metrics are limited for South Africa, with grass pollen as a key outdoor aeroallergen. Exotic trees such as plane trees and ragweed produce highly allergenic pollen, dominating indigenous trees and weeds. Pollen allergy prevalence data is lacking in cities of North-West province such as Potchefstroom.

OBJECTIVES: This study aimed to (i) assess the prevalence of allergies to major aeroallergens, including Poaceae (grasses), Cupressus/Hesperocyparis (cypresses), Platanus (plane tree), Ulmus (elm), Quercus (oak), Betula (birch), Olea (olive), Artemisia (sagebrush), Amaranthus (amaranth), Plantago (plantain), Morus (mulberry), and Ambrosia (ragweed), along with fungal spores such as Alternaria, Cladosporium, and Penicillium/Aspergillus, and (ii) investigate the monthly incidence of major aeroallergens and reactivity levels in sensitized adults in Potchefstroom.

METHODS: Skin prick tests (SPTs) were performed on 202 adults aged 18-64 years with confirmed allergic symptoms during a field campaign at North-West University (NWU)'s Potchefstroom campus. A test panel of grass, weed, tree, and fungal spore extracts previously identified via aerobiological monitoring was used. Symptom scores were recorded using ISAAC questionnaires; Spearman's statistical correlation between symptom frequency and monthly aeroallergen concentrations were analyzed.

RESULTS: Among the participants, 184 (91%) exhibited positive SPT reactions: 104 (57%) are monosensitized to pollen, 45 (24%) to fungal spores, and 35 (19%) are polysensitized. Aeroallergen prevalence was higher in females (73%) than in males (27%). The most common pollen allergens were Cynodon dactylon (Bermuda grass) (85%), Zea mays (maize) (46%), Platanus spp. (plane tree) (35%), and Ulmus campestris (field elm) (33%). Among fungal spores, Alternaria was the most common (93%), followed by Cladosporium (27%). A significant and positive statistical correlation was found between allergic rhinitis symptoms and monthly pollen concentrations of Betula, Morus, Platanus, and Quercus.

DISCUSSION & CONCLUSION: This pilot study linked aeroallergens detected in Potchefstroom with allergy profiles of local residents. The findings highlight the need for more comprehensive regional studies that integrate allergen testing with aerobiological data. Raising awareness and implementing health strategies are essential for managing allergic rhinitis in South Africa. More affordable and available SPTs kits, adapted to allergy prevalence in South Africa, are strongly suggested.},
}

@article {pmid40301344,
year = {2025},
author = {Zhu, C and Wu, L and Ning, D and Tian, R and Gao, S and Zhang, B and Zhao, J and Zhang, Y and Xiao, N and Wang, Y and Brown, MR and Tu, Q and , and Ju, F and Wells, GF and Guo, J and He, Z and Nielsen, PH and Wang, A and Zhang, Y and Chen, T and He, Q and Criddle, CS and Wagner, M and Tiedje, JM and Curtis, TP and Wen, X and Yang, Y and Alvarez-Cohen, L and Stahl, DA and Alvarez, PJJ and Rittmann, BE and Zhou, J},
title = {Global diversity and distribution of antibiotic resistance genes in human wastewater treatment systems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4006},
pmid = {40301344},
issn = {2041-1723},
support = {EF-2025558//National Science Foundation (NSF)/ ; 32371724//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82202299//National Natural Science Foundation of China (National Science Foundation of China)/ ; 61872218//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Wastewater/microbiology ; Humans ; Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Water Purification ; *Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Antibiotic resistance poses a significant threat to human health, and wastewater treatment plants (WWTPs) are important reservoirs of antibiotic resistance genes (ARGs). Here, we analyze the antibiotic resistomes of 226 activated sludge samples from 142 WWTPs across six continents, using a consistent pipeline for sample collection, DNA sequencing and analysis. We find that ARGs are diverse and similarly abundant, with a core set of 20 ARGs present in all WWTPs. ARG composition differs across continents and is distinct from that of the human gut and the oceans. ARG composition strongly correlates with bacterial taxonomic composition, with Chloroflexi, Acidobacteria and Deltaproteobacteria being the major carriers. ARG abundance positively correlates with the presence of mobile genetic elements, and 57% of the 1112 recovered high-quality genomes possess putatively mobile ARGs. Resistome variations appear to be driven by a complex combination of stochastic processes and deterministic abiotic factors.},
}

*Wastewater/microbiology
Humans
Sewage/microbiology
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/drug effects/classification/isolation & purification
*Genes, Bacterial
Anti-Bacterial Agents/pharmacology
Water Purification
*Drug Resistance, Bacterial/genetics
Interspersed Repetitive Sequences/genetics

@article {pmid40301151,
year = {2025},
author = {Kaufmann, H and Salvador, C and Salazar, VW and Cruz, N and Dias, GM and Tschoeke, D and Campos, L and Sawabe, T and Miyazaki, M and Maruyama, F and Thompson, F and Thompson, C},
title = {Genomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {36},
pmid = {40301151},
issn = {1432-184X},
mesh = {*Geologic Sediments/microbiology ; *Vibrionaceae/genetics/classification/isolation & purification ; *Genome, Bacterial ; Phylogeny ; Japan ; *Seawater/microbiology ; Genetic Variation ; },
abstract = {The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1). Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.},
}

*Geologic Sediments/microbiology
*Vibrionaceae/genetics/classification/isolation & purification
*Genome, Bacterial
Phylogeny
Japan
*Seawater/microbiology
Genetic Variation

@article {pmid40301143,
year = {2025},
author = {Weitzman, CL and Day, K and Brown, GP and Gibb, K and Christian, K},
title = {Differential Temporal Shifts in Skin Bacteria on Wild and Captive Toads.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {35},
pmid = {40301143},
issn = {1432-184X},
support = {DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; DP210102176//Australian Research Council/ ; },
abstract = {Skin bacteria on amphibian hosts play an important role in host health, but those communities are also constantly shifting based on environmental and host-related feedback. On some hosts, stability of skin communities depends on relatively abundant taxa, with less abundant taxa more readily entering and exiting the system. Cane toads (Rhinella marina) have invaded widespread, diverse tropical ecosystems, with varying ecology, physiology, and behaviour in different environments. In this study, we described temporal patterns of skin bacterial communities on cane toads at a site in northern Australia through the wet and dry seasons over two years. Toads in the wild population were paired with a captive-held population, housed in a semi-natural environment, to detect effects of time and season on wild toads, explore bacterial transience and volatility in skin taxa, and determine the extent to which skin communities on captive toads represent those on the wild population. We found community differences by captivity status, sampling timepoint, and season, with increased richness in the wet season on wild toads. Bacterial communities also became more similar among individuals (lower dispersion) in the wet season. Captive toads harboured more stable communities over time, likely owing to the reduced bacterial reservoirs experienced while in captivity. We propose that cane toads, with varied movement patterns among their diverse invaded habitats, provide an interesting direction for future work understanding the influences of habitat and movement on skin microbes, and the flexibility of microbial symbiotic interactions in invasive hosts.},
}

@article {pmid40300605,
year = {2025},
author = {Lopez, JA and McKeithen-Mead, S and Shi, H and Nguyen, TH and Huang, KC and Good, BH},
title = {Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.03.073},
pmid = {40300605},
issn = {1879-0445},
abstract = {The human gut contains diverse communities of bacteriophage, whose interactions with the broader microbiome and potential roles in human health are only beginning to be uncovered. Here, we combine multiple types of data to quantitatively estimate gut phage population dynamics and lifestyle characteristics in human subjects. Unifying results from previous studies, we show that an average human gut contains a low ratio of phage particles to bacterial cells (∼1:100) but a much larger ratio of phage genomes to bacterial genomes (∼4:1), implying that most gut phage are effectively temperate (e.g., integrated prophage and phage-plasmids). By integrating imaging and sequencing data with a generalized model of temperate phage dynamics, we estimate that phage induction and lysis occur at a low average rate (∼0.001-0.01 per bacterium per day), imposing only a modest fitness burden on their bacterial hosts. Consistent with these estimates, we find that the phage composition of a diverse synthetic community in gnotobiotic mice can be quantitatively predicted from bacterial abundances alone while still exhibiting phage diversity comparable to native human microbiomes. These results provide a foundation for interpreting existing and future studies on links between the gut virome and human health.},
}

@article {pmid40299544,
year = {2025},
author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA},
title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70018},
pmid = {40299544},
issn = {1529-8817},
support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; },
abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.},
}

@article {pmid40298441,
year = {2025},
author = {Peng, S-X and Gao, S-M and Lin, Z-L and Luo, Z-H and Zhang, S-Y and Shu, W-S and Meng, F and Huang, L-N},
title = {Biogeography and ecological functions of underestimated CPR and DPANN in acid mine drainage sediments.},
journal = {mBio},
volume = {},
number = {},
pages = {e0070525},
doi = {10.1128/mbio.00705-25},
pmid = {40298441},
issn = {2150-7511},
abstract = {Recent genomic surveys have uncovered candidate phyla radiation (CPR) bacteria and DPANN archaea as major microbial dark matter lineages in various anoxic habitats. Despite their extraordinary diversity, the biogeographic patterns and ecological implications of these ultra-small and putatively symbiotic microorganisms have remained elusive. Here, we performed metagenomic sequencing on 90 geochemically diverse acid mine drainage sediments sampled across southeast China and recovered 282 CPR and 189 DPANN nonredundant metagenome-assembled genomes, which collectively account for up to 28.6% and 31.2% of the indigenous prokaryotic communities, respectively. We found that, remarkably, geographic distance represents the primary factor driving the large-scale ecological distribution of both CPR and DPANN organisms, followed by pH and Fe. Although both groups might be capable of iron reduction through a flavin-based extracellular electron transfer mechanism, significant differences are found in their metabolic capabilities (with complex carbon degradation and chitin degradation being more prevalent in CPR whereas fermentation and acetate production being enriched in DPANN), indicating potential niche differentiation. Predicted hosts are mainly Acidobacteriota, Bacteroidota, and Proteobacteria for CPR and Thermoplasmatota for DPANN, and extensive, unbalanced metabolic exchanges between these symbionts and putative hosts are displayed. Together, our results provide initial insights into the complex interplays between the two lineages and their physicochemical environments and host populations at a large geographic scale.IMPORTANCECandidate phyla radiation (CPR) bacteria and DPANN archaea constitute a significant fraction of Earth's prokaryotic diversity. Despite their ubiquity and abundance, especially in anoxic habitats, we know little about the community patterns and ecological drivers of these ultra-small, putatively episymbiotic microorganisms across geographic ranges. This study is facilitated by a large collection of CPR and DPANN metagenome-assembled genomes recovered from the metagenomes of 90 sediments sampled from geochemically diverse acid mine drainage (AMD) environments across southeast China. Our comprehensive analyses have allowed first insights into the biogeographic patterns and functional differentiation of these major enigmatic prokaryotic groups in the AMD model system.},
}

@article {pmid40297467,
year = {2025},
author = {Deep, A and Sieber, G and Boden, L and David, GM and Baikova, D and Buchner, D and Starke, J and Stach, TL and Reinders, T and Hadžiomerović, U and Beszteri, S and Probst, AJ and Boenigk, J and Beisser, D},
title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19120},
pmid = {40297467},
issn = {2167-8359},
mesh = {*Plant Leaves/metabolism/microbiology ; *Bacteria/genetics/metabolism ; *Fungi/genetics/metabolism ; *Rivers/microbiology ; Ecosystem ; Alnus ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.},
}

*Plant Leaves/metabolism/microbiology
*Bacteria/genetics/metabolism
*Fungi/genetics/metabolism
*Rivers/microbiology
Ecosystem
Alnus
Transcriptome
RNA, Ribosomal, 16S/genetics

@article {pmid40294427,
year = {2025},
author = {Ran, X and Wang, T and Zhou, M and Li, Z and Wang, H and Tsybekmitova, GT and Guo, J and Wang, Y},
title = {A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01214},
pmid = {40294427},
issn = {1520-5851},
abstract = {Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.},
}

@article {pmid40294268,
year = {2025},
author = {Sun, W and Wang, J and Wang, G and Jiang, L and Feng, W and Dang, S and Li, M and Jiao, S and Wei, G and Gu, J and Tiedje, JM and Qian, X},
title = {Exposure and health risks of livestock air resistomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {18},
pages = {e2403866122},
doi = {10.1073/pnas.2403866122},
pmid = {40294268},
issn = {1091-6490},
support = {42277412 and 42207463//NSF of China/ ; 2024RS-CXTD-68//Shaanxi Innovation Support Program/ ; },
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Air Microbiology ; Anti-Bacterial Agents/pharmacology ; Farms ; Swine ; China ; Chickens ; *Drug Resistance, Microbial/genetics ; *Occupational Exposure ; *Drug Resistance, Bacterial/genetics ; Europe ; },
abstract = {Most of the global antibiotic consumption is by the livestock industry, making livestock farms a hotspot of antibiotic resistance genes (ARGs). Farm air poses direct ARG exposure to workers, but the health risks of air resistomes remain unclear. We evaluated the human exposure and health risks of air resistomes in pig and chicken farms and compared air resistomes in Chinese farms to those in European farms given their long-term restrictions on use of antibiotics in livestock. We found that livestock air was highly enriched in ARGs, with each cell harboring seven times more ARGs than urban air. The daily ARG inhalation of farm workers was equivalent to several years of ARG inhalation by urban residents. ARGs encoding resistance to last-resort antibiotics such as mcr-1 and tetX were detected in farm air, and tetX variants were prevalent in both Chinese and European farms. ARGs in livestock air were highly associated with mobile genetic elements, and conjugation experiments confirmed their cross-phyla transferability. The projected resistome risk of farm air was significantly higher than well-recognized ARG hotspots like air from hospitals, sewage treatment plants, and from animal manures. The diversity, abundance, and risk score of air resistomes in Chinese farms were significantly higher than those in European farms, suggesting that long-term restriction of antibiotic use mitigates antibiotic resistance in the livestock environment. Our results underscore the high exposure of farm workers to ARGs via farm air and highlight its role in ARG dissemination, supporting the importance of antibiotic stewardship practices in combating antibiotic resistance.},
}

Animals
*Livestock/microbiology
Humans
*Air Microbiology
Anti-Bacterial Agents/pharmacology
Farms
Swine
China
Chickens
*Drug Resistance, Microbial/genetics
*Occupational Exposure
*Drug Resistance, Bacterial/genetics
Europe

@article {pmid40293502,
year = {2025},
author = {Cao, X and Liu, H and Zhang, R and Wen, Y and Ma, L and Xu, Z and Wen, L and Zhuo, Y and Liu, D and Wang, L},
title = {Composition, Predicted Functions, and Co-occurrence Networks of Bacteria and Fungi in Hummock Wetlands of Northeastern Inner Mongolia, China.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {34},
pmid = {40293502},
issn = {1432-184X},
support = {YSS2021007//the Funds of Yinshanbeilu Grassland Eco-hydrology National Observation and Research Station/ ; 32160279, 32161143025, 31960249//the National Natural Science Funds, P.R. China/ ; 2022YFHH0017//Science and Technology Major Project of Inner Mongolia/ ; 2022EEDSKJZDZX010, 2022EEDSKJXM005//Ordos Science and Technology Plan/ ; },
mesh = {*Wetlands ; China ; *Fungi/classification/genetics/isolation & purification ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; Ecosystem ; Microbiota ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {Wetland microhabitats, varying in water table position, pH, and biochemical properties, have been understudied in terms of their influence on soil microbial community structure. This study employed amplicon-based gene sequencing to investigate the responses of both fungal and bacterial communities to habitat changes in northeastern Inner Mongolia, China. The results showed that while α-diversity indices (Shannon and Chao1) did not significantly differ between hummocks and hollows, β-diversity analyses revealed distinct microbial community structures in these habitats. Bacterial communities were primarily influenced by soil pH, EC, and AP, whereas fungal communities were affected by pH, AKP, MBC, MBN, and AP. Bacterial interactions were predominant in hollows, whereas fungal interactions were predominant in hummocks. Hummocks significantly enhanced amino acid metabolism function, whereas hollows significantly increased the abundance of endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. This study underscores the importance of habitats in regulating microbial networks and functions, thereby enhancing our understanding of the influence of microhabitats, such as hummocks, on wetland ecosystem structure and function.},
}

*Wetlands
China
*Fungi/classification/genetics/isolation & purification
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
Ecosystem
Microbiota
Biodiversity
Hydrogen-Ion Concentration

@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}

Phylogeny
*Genome, Bacterial
*Software
*Bacteria/genetics/classification
*Amino Acids/genetics
*Computational Biology/methods

@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Glycine max/microbiology/growth & development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}

*Rhizosphere
*Metagenomics/methods
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Glycine max/microbiology/growth & development
*Microbiota/genetics
China
Fungi/classification/genetics/isolation & purification
Plant Roots/microbiology
Archaea/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid40287657,
year = {2025},
author = {De Maayer, P and Green, T and Jordan, S and Smits, THM and Coutinho, TA},
title = {Pan-genome analysis of the Enterobacter hormaechei complex highlights its genomic flexibility and pertinence as a multidrug resistant pathogen.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {408},
pmid = {40287657},
issn = {1471-2164},
support = {310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030L_204333//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Enterobacter/genetics/classification/drug effects/pathogenicity ; *Genome, Bacterial ; Phylogeny ; *Drug Resistance, Multiple, Bacterial/genetics ; *Genomics/methods ; Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Plasmids/genetics ; },
abstract = {BACKGROUND: Enterobacter hormaechei is of increasing concern as both an opportunistic and nosocomial pathogen, exacerbated by its evolving multidrug resistance. However, its taxonomy remains contentious, and little is known about its pathogenesis and the broader context of its resistome. In this study, a comprehensive comparative genomic analysis was undertaken to address these issues.

RESULTS: Phylogenomic analysis revealed that E. hormaechei represents a complex, comprising three predicted species, E. hormaechei, E. hoffmannii and E. xiangfangensis, with the latter putatively comprising three distinct subspecies, namely oharae, steigerwaltii and xiangfangensis. The species and subspecies all display open and distinct pan-genomes, with diversification driven by an array of mobile genetic elements including numerous plasmid replicons and prophages, integrative conjugative elements (ICE) and transposable elements. These elements have given rise to a broad, relatively conserved set of pathogenicity determinants, but also a variable set of secretion systems. The E. hormaechei complex displays a highly mutable resistome, with most taxa being multidrug resistant.

CONCLUSIONS: This study addressed key issues pertaining to the taxonomy of the E. hormaechei complex, which may contribute towards more accurate identification of strains belonging to this species complex in the clinical setting. The pathogenicity determinants identified in this study could serve as a basis for a deeper understanding of E. hormaechei complex pathogenesis and virulence. The extensive nature of multidrug resistance among E. hormaechei complex strains highlights the need for responsible antibiotic stewardship to ensure effective treatment of these emerging pathogens.},
}

*Enterobacter/genetics/classification/drug effects/pathogenicity
*Genome, Bacterial
Phylogeny
*Drug Resistance, Multiple, Bacterial/genetics
*Genomics/methods
Anti-Bacterial Agents/pharmacology
DNA Transposable Elements
Plasmids/genetics

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

@article {pmid40287414,
year = {2025},
author = {Bull, F and Tavaddod, S and Bommer, N and Perry, M and Brackley, CA and Allen, RJ},
title = {Different factors control long-term versus short-term outcomes for bacterial colonisation of a urinary catheter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3940},
pmid = {40287414},
issn = {2041-1723},
support = {682237 EVOSTRUC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council(H2020 Excellent Science - European Research Council)/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft(German Research Foundation)/ ; EP/L015110/1//RCUK | Engineering and Physical Sciences Research Council(EPSRC)/ ; },
abstract = {Urinary catheters are used extensively in hospitals and long-term care and they are highly prone to infection. Understanding the pathways by which bacteria colonise a urinary catheter could guide strategies to mitigate infection, but quantitative models for this colonisation process are lacking. Here we present a mathematical model for bacterial colonisation of a urinary catheter that integrates population dynamics and fluid dynamics. The model describes bacteria migrating up the outside surface of the catheter, spreading into the bladder and being swept through the catheter lumen. Computer simulations of the model reveal that clinical outcomes for long-term versus short-term catheterisation are controlled by different factors: the rate of urine production by the kidneys as opposed to urethral length, catheter surface properties and bacterial motility. Our work may help explain variable susceptibility to catheter-associated urinary tract infection (CAUTI) among individuals and the mixed success of antimicrobial surface coatings. Our model suggests that for long-term catheterised patients, increasing fluid intake or reducing residual urine volume in the bladder may help prevent infection, while antimicrobial surface coatings are predicted to be effective only for short-term catheterised patients. Therefore, different catheter management strategies could be rationally targeted to long-term vs short-term catheterised patients.},
}

@article {pmid40286617,
year = {2025},
author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS},
title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.},
journal = {The Science of the total environment},
volume = {979},
number = {},
pages = {179495},
doi = {10.1016/j.scitotenv.2025.179495},
pmid = {40286617},
issn = {1879-1026},
abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.},
}

@article {pmid40285533,
year = {2025},
author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A},
title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70211},
doi = {10.1111/gcb.70211},
pmid = {40285533},
issn = {1365-2486},
support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; },
mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; },
abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.},
}

*Microbiota
*Plankton
China
*Rivers/microbiology
Bacteria/genetics/drug effects
Urbanization

@article {pmid40284744,
year = {2025},
author = {Yahya, R and Albaqami, A and Alzahrani, A and Althubaiti, SM and Alhariri, M and Alrashidi, ET and Alhazmi, N and Al-Matary, MA and Alharbi, N},
title = {Comprehensive Genomic Analysis of Klebsiella pneumoniae and Its Temperate N-15-like Phage: From Isolation to Functional Annotation.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040908},
pmid = {40284744},
issn = {2076-2607},
support = {NRC21R/053/02//King Abdullah International Medical Research Center/ ; },
abstract = {Antibiotic resistance to Klebsiella pneumoniae poses a major public health threat, particularly in intensive care unit (ICU) settings. The emergence of extensively drug-resistant (XDR) strains complicates treatment options, requiring a deeper understanding of their genetic makeup and potential therapeutic targets. This research delineated an extensively drug-resistant (XDR) Klebsiella pneumoniae strain obtained from an ICU patient and telomeric temperate phage derived from hospital effluent. The bacteria showed strong resistance to multiple antibiotics, including penicillin (≥16 μg/mL), ceftriaxone (≥32 μg/mL), and meropenem (≥8 μg/mL), which was caused by SHV-11 beta-lactamase, NDM-1 carbapenemase, and porin mutations (OmpK37, MdtQ). The strain was categorized as K46 and O2a types and carried virulence genes involved in iron acquisition, adhesion, and immune evasion, as well as plasmids (IncHI1B_1_pNDM-MAR, IncFIB) and eleven prophage regions, reflecting its genetic adaptability and resistance dissemination. The 172,025 bp linear genome and 46.3% GC content of the N-15-like phage showed strong genomic similarities to phages of the Sugarlandvirus genus, especially those that infect K. pneumoniae. There were structural proteins (11.8%), DNA replication and repair enzymes (9.3%), and a toxin-antitoxin system (0.4%) encoded by the phage genome. A protelomerase and ParA/B partitioning proteins indicate that the phage is replicating and maintaining itself in a manner similar to the N15 phage, which is renowned for maintaining a linear plasmid prophage throughout lysogeny. Understanding the dynamics of antibiotic resistance and pathogen development requires knowledge of phages like this one, which are known for their temperate nature and their function in altering bacterial virulence and resistance profiles. The regulatory and structural proteins of the phage also provide a model for research into the biology of temperate phages and their effects on microbial communities. The importance of temperate phages in bacterial genomes and their function in the larger framework of microbial ecology and evolution is emphasized in this research.},
}

@article {pmid40284675,
year = {2025},
author = {Li, M and Liu, X and Chen, W and Xu, H and Huang, F and Yao, Q and Jia, X and Huang, Y},
title = {Alleviating Effect of Lactiplantibacillus plantarum HYY-S10 on Colitis in Mice Based on an Analysis of the Immune Axis in the Intestine.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040840},
pmid = {40284675},
issn = {2076-2607},
support = {32302242//the National Natural Science Foundation of China/ ; 2022A1515110426//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023B0202040002//Guangdong Provincial Key Research and Development Program/ ; 2022B1212010015//Key Laboratory Project of Guangdong Province/ ; },
abstract = {The pathogenesis of ulcerative colitis (UC) has been fundamentally associated with intestinal microbiota dysbiosis and disruption of immune homeostasis. This study systematically investigates the therapeutic potential of Lactiplantibacillus plantarum HYY-S10 (HYY-S10), a novel strain isolated from De'ang sour tea in Yun an, China, with a focus on its mechanisms for alleviating colitis through the modulation of gut microbiota. Using a dextran sulfate sodium (DSS)-induced colitis model in C57BL/6J mice, our findings demonstrated that seven days of oral supplementation with HYY-S10 (1 × 10[8] CFU/mL, 0.2 mL/10 g body weight) significantly improved Disease Activity Index (DAI) scores and attenuated characteristic colitis symptoms, including progressive weight loss, rectal bleeding, and abnormal stool consistency. Administration of HYY-S10 exhibited significant immunomodulatory effects characterized by the downregulation of pro-inflammatory mediators (such as IL-1β, IL-6, IFN-γ, and LPS) while concomitantly upregulating anti-inflammatory IL-10 expression. Additionally, the strain enhanced intestinal antioxidant capacity by increasing GSH-Px activity, which collectively contributed to the reduction in intestinal inflammation. Furthermore, HYY-S10 demonstrated multifaceted protective effects by ameliorating oxidative stress through the restoration of redox homeostasis and modulation of gut microbial ecology. Probiotic intervention significantly increased short-chain fatty acids (SCFAs) production and notably enhanced the relative abundance of beneficial taxa, including Akkermansia and Ruminococcus_B, while restoring microbial diversity and ecological stability. Collectively, our results demonstrate that HYY-S10 alleviates experimental colitis by modulating the intestinal immune axis and microbiota composition, providing mechanistic insights to support its potential as a probiotic-based therapeutic strategy for UC.},
}

@article {pmid40284595,
year = {2025},
author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA},
title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040758},
pmid = {40284595},
issn = {2076-2607},
support = {3090-31630-006//USDA-ARS CRIS/ ; },
abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.},
}

@article {pmid40280843,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Plant-microbe interactions: plants modulating their defenses.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.001},
pmid = {40280843},
issn = {1878-4372},
abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.},
}

@article {pmid40280003,
year = {2025},
author = {Cholet, F and Vignola, M and Quinn, D and Ijaz, UZ and Sloan, WT and Smith, CJ},
title = {Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: A meta-analysis.},
journal = {Water research},
volume = {281},
number = {},
pages = {123684},
doi = {10.1016/j.watres.2025.123684},
pmid = {40280003},
issn = {1879-2448},
abstract = {Biofiltration, a sustainable water treatment technology relying on microbial processes to remove contaminants, offers a promising approach to achieving the United Nations Sustainable Goal 6 of universal access to clean water and sanitation by 2030. However, a key barrier to optimising biofiltration is the incomplete understanding of the biological mechanisms governing its performance. Despite numerous studies examining how engineering decisions impact biofilter performance and the associated microbiome, the significant influence of geographical location on microbial communities raises the question of whether these findings are universally applicable or location-specific. To address this, we conducted a meta-analysis of 15 biofilter microbiomes using 16S rRNA high-throughput sequencing (HTS) data, mainly originating from rapid gravity and/or granular activated carbon (GAC) filters. Despite different types and scales, results highlight geographical location as the major contributor to microbiome dissimilarity in biofilter samples (Top and Bottom) (R[2]∼ 0.5; p-value<0.001). The same was observed for influent waters (PERMANOVA R[2]= 0.76; p-value<0.001), indicating location-specific microbiomes as opposed to differences driven by different biofilter operating parameters. Irrespective of location, the higher percentage of the microbiome was assembled through deterministic processes (∼55 %) compared to stochastic processes (∼45 %). Finally, our findings suggest that the depth stratification of biofilter microbiomes may be associated with the enrichment of taxa capable of metabolising more complex organic carbon in deeper filter layers (10 enriched pathways in biofilter Bottom layers compared to 3 at the Top). These insights provide a broader understanding of biofiltration microbiomes and offer possible research avenues for targeted and effective biofilter design strategies.},
}

@article {pmid40279085,
year = {2025},
author = {Zheng, F and Zhao, J and Yuan, Z and Gao, Y and Li, Y and Li, Y and Geng, Y and Qiang, Y},
title = {Interpretable drug-target affinity prediction based on pre-trained models' output as embeddings and based on structure-aware cross-attention for feature fusion.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {40279085},
issn = {1573-501X},
support = {U21A20469//National Natural Science Foundation of China/ ; 82170716//National Natural Science Foundation of China/ ; 62376183//National Natural Science Foundation of China/ ; 202304051001009//the special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2020-PT320-005//National Health Commission Key Laboratory of Pneumoconiosis/ ; },
abstract = {The characteristics of protein pockets can better capture the interaction information between proteins and small molecules, thereby improving the performance of drug-target interaction (DTI) prediction tasks. However, pocket data typically need to be predicted using software such as AlphaFold, which would entail a massive workload for datasets ranging from tens of thousands to hundreds of thousands of samples. Moreover, feature representation networks for 3D pocket data are computationally intensive. To address this, we propose simulating 3D pocket data using sequence data through feature fusion of two different objects based on structure cross-attention (CASD). Additionally, precise feature representation is a prerequisite for accurately identifying pocket information. We introduce a method that leverages the output of the last layer of a pre-trained model as an embedding layer for training a new model from scratch. This approach not only incorporates prior knowledge from the pre-trained model but also expands model capacity, enabling more accurate feature representation. Furthermore, we enhance the multimodal representation of small molecule compounds using feature fusion based on structure cross-attention for the same object (CASS), further improving feature representation capabilities. Our cross-attention mechanisms operate at the token-level or node-level, allowing fine-grained capture of interactions between amino acids and atoms. This enables the identification of the contribution score of each atom or amino acid to the task, making our model interpretable for drug-target prediction. Experimental validation demonstrates that our model achieves state-of-the-art predictive performance.},
}

@article {pmid40277367,
year = {2025},
author = {Thapa, BS and Flynn, TM and Jensvold, ZD and Kemner, KM and Sladek, MF and O'Loughlin, EJ and Marshall, CW},
title = {Effects of soluble electron shuttles on microbial iron reduction and methanogenesis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0222224},
doi = {10.1128/aem.02222-24},
pmid = {40277367},
issn = {1098-5336},
abstract = {In many aquatic and terrestrial ecosystems, iron (Fe) reduction by microorganisms is a key part of biogeochemical cycling and energy flux. The presence of redox-active electron shuttles in the environment potentially enables a phylogenetically diverse group of microbes to use insoluble iron as a terminal electron acceptor. We investigated the impact that different electron shuttles had on respiration, microbial physiology, and microbial ecology. We tested eight different electron shuttles, seven quinones and riboflavin, with redox potentials between 0.217 and -0.340 V. Fe(III) reduction coupled with acetate oxidation was observed with all shuttles. Once Fe(III) reduction began to plateau, a rapid increase in acetate consumption was observed and coincided with the onset of methane production, except in the incubations with the shuttle 9,10-anthraquinone-2-carboxylic acid (AQC). The rates of iron reduction, acetate consumption, methanogenesis, and the microbial communities varied significantly across the different shuttles independent of redox potential. In general, shuttles appeared to reduce the overall diversity of the community compared to no shuttle controls, but certain shuttles were exceptions to this trend. Geobacteraceae were the predominant taxonomic family in all enrichments except in the presence of AQC or 1,2-dihydroxyanthraquinone (AQZ), but each shuttle enriched a unique community significantly different from the no shuttle control conditions. This suggests that the presence of different redox-active electron shuttles can have a large influence on the microbial ecology and total carbon flux in the environment.IMPORTANCEIron is the fourth most abundant element in the Earth's crust, and the reduction of iron by microbes is an important component of global biogeochemical cycles. A phylogenetically diverse group of microbes is capable of conserving energy with oxidized iron as a terminal electron acceptor, but the environmental conditions favoring certain taxonomic clades in iron-reducing environments are unclear. One complicating factor often overlooked in small-scale enrichments is the influence of soluble, redox-active electron shuttles on the rate and microbial ecology of iron reduction. We tested the effects of eight different electron shuttles on microbial physiology and ecology in iron-reducing enrichments derived from a local wetland. Each electron shuttle varied the microbial activity and enriched for a microbial community distinct from the no shuttle control condition. Therefore, in complex subsurface environments with many redox-active compounds present, we propose electron shuttles as a reason for the coexistence of multiple clades of iron-reducing bacteria.},
}

@article {pmid40277363,
year = {2025},
author = {Wang, Y and Yang, L and Wu, W and Feng, Z and He, J and Guo, C and He, J},
title = {Bacillus haimaensis sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0245624},
doi = {10.1128/aem.02456-24},
pmid = {40277363},
issn = {1098-5336},
abstract = {Deep-sea cold seeps harbor unique microbial communities that play crucial roles in biogeochemical cycles and possess potential biotechnological applications. Herein, we report the isolation, characterization, and genomic analysis of a novel Bacillus species, Bacillus haimaensis sp. nov. (type strain CSS-39[T], CCTCC M20241382), obtained from sediments collected at a depth of 1,350 m in the Haima cold seep, South China Sea. Phylogenomic analysis, revealing an average nucleotide identity of 87.78% and a digital DNA-DNA hybridization value of 34.0% with its closest relative B. tianshenii DSM 25879[T], confirms the taxonomic novelty of the genus Bacillus. The complete 4.54 Mb genome of B. haimaensis reveals adaptations to the cold seep environment, including enhanced nutrient acquisition capabilities and stress response mechanisms. Comparative genomic analysis identifies 27 unique gene clusters related to spore germination and sulfate assimilation, suggesting specialized metabolic strategies for this extreme habitat. Furthermore, six biosynthetic gene clusters, including a novel lassopeptide cluster, indicate a potential for secondary metabolite production. Phenotypic characterization demonstrates the strain's ability to utilize diverse carbon sources and tolerate a wide range of environmental conditions. Our findings provide insights into microbial adaptations to deep-sea cold seeps and highlight the potential of B. haimaensis for biotechnological applications in bioremediation and natural product discovery. This study expands our understanding of microbial diversity in extreme marine environments and offers a new model bacterium for investigating bacterial adaptations to deep-sea ecosystems.IMPORTANCEThe discovery of Bacillus haimaensis sp. nov. in the Haima cold seep of the South China Sea represents a significant advancement in our understanding of microbial adaptations to extreme marine environments. This novel species exhibits remarkable metabolic versatility and unique genomic features, providing insights into bacterial survival strategies in nutrient-variable, high-pressure deep-sea ecosystems. Comprehensive genomic analysis reveals distinctive biosynthetic gene clusters, suggesting untapped potential for discovering novel natural product. Furthermore, B. haimaensis exhibits promising capabilities for aromatic compound degradation, indicating potential applications in marine bioremediation. This work not only expands our knowledge of microbial diversity in understudied deep-sea habitats but also highlights the biotechnological promise of extremophiles. The adaptive mechanisms elucidated in B. haimaensis, particularly those related to sporulation and sulfate assimilation, contribute to our broader understanding of microbial ecology in cold seeps and may inform future research on climate change impacts on deep-sea ecosystems.},
}

@article {pmid40276016,
year = {2025},
author = {Papazlatani, C and Wagner, A and Chen, Z and Zweers, H and de Boer, W and Garbeva, P},
title = {Enhancement of production of pathogen-suppressing volatiles using amino acids.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100385},
pmid = {40276016},
issn = {2666-5174},
abstract = {Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.},
}

@article {pmid40275504,
year = {2025},
author = {Ekemezie, SC and Davis, CC and Russo, MV and Carpenter, LP and Russell, AL},
title = {Pollen-microbe interactions in nectar weakly influence bee foraging behavior.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf017},
pmid = {40275504},
issn = {1557-7023},
abstract = {Plant-pollinator interactions are frequently affected by microbes that grow on flowers. Bacteria and yeast commonly grow within floral nectar, which is a sugar-rich floral reward often sought out by pollinators. Nectar is also commonly contaminated with protein-rich pollen. Microbes can induce this pollen to germinate or burst within the nectar, which potentially results in pollen nutrients being made available to nectar foraging pollinators. Yet whether pollen-microbe interactions in nectar impact pollinator behavior remains unknown. We therefore investigated how a common nectar yeast (Metschnikowia reukaufii) and bacteria (Acinetobacter nectaris) affected pollen germination and bursting within artificial nectar and effects on bumble bee (Bombus impatiens) foraging behavior. We found that both bacteria and yeast reduced the proportion of intact pollen in nectar, with bacteria inducing the most germination and bursting. Although microbes may thus potentially increase the quality of the nectar reward via increased access to pollen nutrients, we did not observe effects on bee flower preference. Similarly, bees did not show increased constancy (i.e., fidelity to one flower type across flower visits) to nectar contaminated with pollen and microbes. In contrast, bees were much more likely to reject flowers with nectar contaminated with pollen and yeast alone or together, relative to flowers that offered uncontaminated nectar. Altogether, our work suggests pollen-microbe interactions within nectar may have relatively minor influences on pollinator foraging behavior. We discuss possible explanations and implications of these results for plant and pollinator ecology.},
}

@article {pmid40273553,
year = {2025},
author = {Ballan, D and Picot, A and Rolland, N and Bovo, C and Prévost, C and Coton, E and Mounier, J},
title = {Diversity of spoilage microorganisms associated with fresh fruits and vegetables in French households.},
journal = {International journal of food microbiology},
volume = {437},
number = {},
pages = {111204},
doi = {10.1016/j.ijfoodmicro.2025.111204},
pmid = {40273553},
issn = {1879-3460},
abstract = {Food loss and waste generated throughout the food chain are major concerns in today's society. A high level of food waste occurs at the household's level and fresh fruit and vegetable (FFV) spoilage caused by microbial growth accounts for a large part of these losses. While numerous studies focused on spoilage microorganism diversity from primary production to distribution, little is known about those involved at the household level. In this context, this study aimed at investigating which FFV are usually wasted depending on the season and storage conditions at households, and identifying the microorganisms associated with spoiled FFV. During two periods (summer and autumn), 346 spoiled FFV samples were collected using a citizen science approach in 49 households in the Brest area (Finistère, Brittany, France). About three quarters of spoiled FFV collected originated from room temperature storage and 75 % were collected during summer. Among the studied samples, 75 % showed microbial growth after plating onto agar-based medium, and therefore, were likely spoiled because of microbial spoilage. Overall, 183 molds, 31 yeasts and 96 bacteria were isolated and identified using MALDI-TOF MS and sequencing. Among the 42 different mold species identified, Penicillium spp. were the most common representing more than 50 % of mold isolates followed by Botrytis (12.4 %), Mucor (8.6 %) and Cladosporium (7.6 %) spp. Hanseniaspora uvarum and Aureobasidium pullulans were the most prevalent yeast species while bacterial isolates showed the highest diversity of all identified organisms (49 species) with Pseudomonas spp., enterobacteria and lactic acid bacteria representing the most frequently isolated taxa. This study shows for the first time the microbial diversity associated with spoiled FFV of which a large proportion were stored at room temperature, suggesting that a better usage of FFV refrigeration could help reduce FFV waste in households.},
}

@article {pmid40270585,
year = {2025},
author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L},
title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf057},
pmid = {40270585},
issn = {2730-6151},
abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.},
}

@article {pmid40270532,
year = {2025},
author = {Ma, J and Wang, M and Sun, Y and Zheng, Y and Lai, S and Zhang, Y and Wu, Y and Jiang, C and Shen, F},
title = {Cockroach Microbiome Disrupts Indoor Environmental Microbial Ecology with Potential Public Health Implications.},
journal = {Environment & health (Washington, D.C.)},
volume = {3},
number = {4},
pages = {380-391},
doi = {10.1021/envhealth.4c00216},
pmid = {40270532},
issn = {2833-8278},
abstract = {Cockroaches pose a significant global public health concern. However, besides the well-recognized cockroach-induced allergy, the potential impact of the cockroach microbiome on human health through various means is not yet fully elucidated. This study aimed to clarify the health impacts of cockroaches by investigating the microbial interactions among cockroaches, the indoor environment, and humans. We simultaneously collected cockroach, indoor environment (indoor air and floor dust), and human (exhaled breath condensate and skin) samples from residential areas in five cities representing distinct climate zones in China. The 16S rDNA sequencing results revealed that cockroaches harbor diverse bacterial populations that vary across different cities. The prevalence of potential pathogenic bacteria (PPB) in cockroaches ranged from 1.1% to 58.9%, with dominant resistance genes conferring resistance to tetracycline, macrolide, and beta-lactam. The relationships between the cockroach microbiome and the associated environmental and human microbiomes were explored by using fast expectation-maximization microbial source tracking (FEAST). The potential contribution of cockroach bacteria to the floor dust-borne microbiome and indoor airborne microbiome was estimated to be 5.6% and 1.3%, respectively. Similarly, the potential contribution of cockroach PPB to the floor dust-borne microbiome and indoor airborne microbiome was calculated to be 4.0% and 1.2%, respectively. In residences with cockroach infestations, the contribution of other sources to the indoor environment was slightly increased. Collectively, the role of cockroaches in the transmission of microorganisms, particularly pathogenic bacteria and antibiotic resistance genes, cannot be overlooked.},
}

@article {pmid40268300,
year = {2025},
author = {Goyal, A and Chure, G},
title = {Paradox of the Sub-Plankton: Plausible Mechanisms and Open Problems Underlying Strain-Level Diversity in Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70094},
doi = {10.1111/1462-2920.70094},
pmid = {40268300},
issn = {1462-2920},
mesh = {*Biodiversity ; *Microbiota ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genetic Variation ; Ecosystem ; Biological Evolution ; },
abstract = {Microbial communities are often complex and highly diverse, typically with dozens of species sharing spatially-restricted environments. Within these species, genetic and ecological variation often exists at a much finer scale, with closely related strains coexisting and competing. While the coexistence of strains in communities has been heavily explored over the past two decades, we have no self-consistent theory of how this diversity is maintained. This question challenges our conventional understanding of ecological coexistence, typically framed around species with clear phenotypic and ecological differences. In this review, we synthesise plausible mechanisms underlying strain-level diversity (termed microdiversity), focusing on niche-based mechanisms such as nutrient competition, neutral mechanisms such as migration, and evolutionary mechanisms such as horizontal gene transfer. We critically assess the strengths and caveats of these mechanisms, acknowledging key gaps that persist in linking genetic similarity to ecological divergence. Finally, we highlight how the origin and maintenance of microdiversity could pose a major challenge to conventional ecological thinking. We articulate a call-to-arms for a dialogue between well-designed experiments and new theoretical frameworks to address this grand conceptual challenge in understanding microbial biodiversity.},
}

*Biodiversity
*Microbiota
*Bacteria/genetics/classification
Gene Transfer, Horizontal
Genetic Variation
Ecosystem
Biological Evolution

@article {pmid40267173,
year = {2025},
author = {Bull, CT and Salgado-Salazar, C and Romberg, MK and Allen, C and Kantor, M and Handoo, Z and Aboughanem-Sabanadzovic, N and Sabanadzovic, S and Coutinho, T},
title = {Plant Pathogen Name Game: Cross Kingdom Review for the Naming of Biotic Agents Associated with Plants.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-111424-090412},
pmid = {40267173},
issn = {1545-2107},
abstract = {To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.},
}

@article {pmid40196585,
year = {2025},
author = {Dellicour, S and Gámbaro, F and Jacquot, M and Lequime, S and Baele, G and Gilbert, M and Pybus, OG and Suchard, MA and Lemey, P},
title = {Comparative performance of novel viral landscape phylogeography approaches.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40196585},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; },
abstract = {The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.},
}

@article {pmid40266732,
year = {2025},
author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX},
title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030269},
pmid = {40266732},
issn = {2075-4450},
support = {Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.},
}

@article {pmid40266381,
year = {2025},
author = {Cuny, MAC and Gloder, G and Bourne, ME and Kalisvaart, SN and Verreth, C and Crauwels, S and Cusumano, A and Lievens, B and Poelman, EH},
title = {Parasitoid Calyx Fluid and Venom Affect Bacterial Communities in Their Lepidopteran Host Labial Salivary Glands.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {33},
pmid = {40266381},
issn = {1432-184X},
support = {ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; ALWOP.368//Netherlands Organization for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; G.0961.19 N//Flemish Fund for Scientific Research/ ; },
mesh = {Animals ; *Salivary Glands/microbiology ; *Wasps/physiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota ; Larva/parasitology/microbiology ; Host-Parasite Interactions ; *Butterflies/microbiology/parasitology ; Hemolymph/microbiology ; Polydnaviridae/physiology ; *Wasp Venoms/pharmacology ; *Moths/microbiology/parasitology ; },
abstract = {The influence of gut and gonad bacterial communities on insect physiology, behaviour, and ecology is increasingly recognised. Parasitism by parasitoid wasps alters many physiological processes in their hosts, including gut bacterial communities. However, it remains unclear whether these changes are restricted to the gut or also occur in other tissues and fluids, and the mechanisms underlying such changes are unknown. We hypothesise that host microbiome changes result from the injection of calyx fluid (that contain symbiotic viruses known as polydnaviruses) and venom during parasitoid oviposition and that these effects vary by host tissue. To test this, we microinjected Pieris brassicae caterpillars with calyx fluid and venom from Cotesia glomerata, using saline solution and natural parasitism by C. glomerata as controls. We analysed changes in the bacterial community composition in the gut, regurgitate, haemolymph, and labial salivary glands of the host insects. Multivariate analysis revealed distinct bacterial communities across tissues and fluids, with high diversity in the salivary glands and haemolymph. Parasitism and injection of calyx fluid and venom significantly altered bacterial communities in the salivary glands. Differential abundance analysis showed that parasitism affected bacterial relative abundance in the haemolymph, and that Wolbachia was only found in the haemolymph of parasitized caterpillars. Altogether, our findings reveal that parasitism influences the host haemolymph microbiome, and both parasitism and injection of calyx fluid and venom drive changes in the bacterial community composition within the host salivary glands. Given that the composition of salivary glands can influence plant response to herbivory, we discuss these results in the broader context of plant-parasitoid interactions.},
}

Animals
*Salivary Glands/microbiology
*Wasps/physiology
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota
Larva/parasitology/microbiology
Host-Parasite Interactions
*Butterflies/microbiology/parasitology
Hemolymph/microbiology
Polydnaviridae/physiology
*Wasp Venoms/pharmacology
*Moths/microbiology/parasitology

@article {pmid40262702,
year = {2025},
author = {Zhang, S and Sun, C},
title = {Ecological divergence of marine bacteria Alteromonas mediterranea.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108359},
doi = {10.1016/j.ympev.2025.108359},
pmid = {40262702},
issn = {1095-9513},
abstract = {Alteromonas mediterranea, originally designated as A. macleodii, is a deep-sea ecotype that plays an important ecological role in the ocean. However, a comprehensive understanding of their biogeographic distribution and evolutionary histories remains limited. In this study, our analysis indicated that A. mediterranea members could adapt contrasting marine ecosystems and flourish in nutrient-rich habitats such as feces and coral reefs. No significant correlations between the relative abundance of A. mediterranea members and the environmental variables were identified. Phylogenetic analysis and geographic patterns of A. mediterranea strains suggested that they could be clustered into two clades (clade Ⅰ and clade Ⅱ). In contrast, many distinct genomic traits exist between these clades, such as the complete genes encoding cytochrome o ubiquinol oxidase only involved in clade Ⅱ. Genes were more likely to be lost in the evolutionary history of A. mediterranea relatives. Gene loss might be a major force in all phylogenetic groups driving the distinct clades. Adaptation to different biotopes resulted in the functional differentiation of A. mediterranea members, with the loss of genes encoding carbohydrate-active enzymes. Genes acquired horizontally from unclassified bacteria, and Proteobacteria represented by Gammaproteobacteria played key roles in the functional diversification of A. mediterranea in marine habitats. Given these data, these results are useful for information supplementation of A. mediterranea strains, particularly for making significant advances in understanding marine microbial ecology within different clonal frames using genome-wide recruitments.},
}

@article {pmid40262432,
year = {2025},
author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z},
title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.},
journal = {Water research},
volume = {282},
number = {},
pages = {123626},
doi = {10.1016/j.watres.2025.123626},
pmid = {40262432},
issn = {1879-2448},
abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.},
}

@article {pmid40261360,
year = {2025},
author = {Cho, KH and Kwon, Y and Kasani, PH and Lee, SG and Jeong, SJ},
title = {Influence of Maternal Weight Dynamics Prior to and Throughout Gestation on Early Infant Gut Microbiome Colonization.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {32},
pmid = {40261360},
issn = {1432-184X},
support = {HR22C1605//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bacteria/classification/genetics/isolation & purification ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Adult ; Body Mass Index ; Feces/microbiology ; *Gestational Weight Gain ; Male ; Meconium/microbiology ; Infant ; *Body Weight ; },
abstract = {This study is aimed at exploring the relationship between maternal weight categories, including pre-pregnancy body mass index (P-BMI) and gestational weight gain (GWG), and the composition of the infant gut microbiome in the early days of life. We recruited 71 mother-infant pairs from Kangwon National University Hospital and Bundang CHA Hospital, collecting meconium samples from the infants within the first 5 days postpartum. Using 16S ribosomal RNA gene sequencing (V3-V4 region), this study assessed microbial diversity and the relative abundance of specific bacterial taxa in these initial stool samples. Participants were categorized into groups based on maternal P-BMI and GWG, enabling a comprehensive comparison of the microbiota composition in the infants' meconium across different maternal weight metrics. Our analysis identified significant variations in the infant gut microbiome correlated with maternal weight categories. Key findings include a differential abundance of genera such as Sphingobacteriaceae, Bacillaceae, Cytophagaceae, and Alteromonadaceae across maternal P-BMI groups, whereas Moraxellaceae and Rhodospirillaceae varied across GWG groups. In the P-BMI category, infants born to overweight mothers demonstrated a higher abundance of Pseudopedobacter, and a lower abundance of Citrobacter and Lachnospira, while infants in the underweight group showed a higher abundance of Lachnospira and Weissella. In the normal weight group, Citrobacter and Pseudopedobacter were more abundant. Within the GWG category, infants in the inadequate group showed a higher abundance of Klebsiella, whereas the normal group showed a higher abundance of Holdemania. The composition of the infant gut microbiome in the early postnatal period is significantly influenced by maternal weight categories. Understanding the role of maternal weight in shaping early microbial colonization may provide insights into developing strategies to optimize infant health outcomes through targeted interventions before and during pregnancy.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
*Bacteria/classification/genetics/isolation & purification
Infant, Newborn
RNA, Ribosomal, 16S/genetics
Adult
Body Mass Index
Feces/microbiology
*Gestational Weight Gain
Male
Meconium/microbiology
Infant
*Body Weight

@article {pmid40261136,
year = {2025},
author = {Elias Masiques, N and De Vrieze, J and Hemeryck, LY and Vanhaecke, L and De Smet, S and Van Hecke, T},
title = {Dietary fiber mitigates the differential impact of beef and chicken meat consumption on rat intestinal health.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo00900f},
pmid = {40261136},
issn = {2042-650X},
abstract = {In this rat feeding study, it was hypothesized that the impact of red (vs. white) meat consumption on gut health is more pronounced in fiber-deprived diets, whereas fiber-rich diets may attenuate meat-related differences. For this purpose, rats were fed a red (beef) or white (chicken) meat diet with and without fructo-oligosaccharides (FOS) for three weeks. Gut health was assessed through colonic microbiota, fermentation metabolites, oxidative stress, inflammation, DNA adducts and histology. In rats on the fiber-deprived diets, beef consumption resulted in higher abundance of mucin-degrading bacteria Akkermansia and lower blood glutathione levels compared to chicken-fed rats. Adding FOS to the meat diets modulated the gut microbiota and fermentation metabolites, affected oxidative stress and inflammation markers in tissues and blood, increased colon length, and reduced fat deposition and liver weight. Thus, results showed that the dietary context should be considered when evaluating the impact of red meat consumption on gut health.},
}

@article {pmid40260087,
year = {2025},
author = {Matsumura, E and Kato, H and Hara, S and Ohbayashi, T and Ito, K and Shingubara, R and Kawakami, T and Mitsunobu, S and Saeki, T and Tsuda, S and Minamisawa, K and Wagai, R},
title = {Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1557188},
pmid = {40260087},
issn = {1664-302X},
abstract = {Soil particles in plant rooting zones are largely clustered to form porous structural units called aggregates where highly diverse microorganisms inhabit and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microorganisms exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. However, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus, adequate cell extraction methods from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) from the topsoil of cultivated Acrisol. We postulated that the extraction of microorganisms with distinct taxonomy and functions could be achieved depending on the degree of soil aggregate dispersion. To test this idea, we used six individual aggregates and performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion techniques improved the extractability of bacterial cells compared to previous ones, the sonication technique led to more efficient dispersion and yielded a higher number and more diverse microorganisms than the bead technique. Furthermore, the analyses of nitrogen cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to the greater recovery of microorganisms strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microorganisms holding the genes (potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. Overall, all six aggregates studied showed similarities in pore characteristics, phylum-level composition, and microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggests that conventional methods employed for the extraction of cells and DNA may not be optimal. The findings of this study emphasize the necessity of advancing extraction methodologies to facilitate a more comprehensive understanding of microbial diversity and function in soil environments.},
}

@article {pmid40259028,
year = {2025},
author = {Hsieh, YE and Yang, SY and Liu, SL and Wang, SW and Wang, WL and Tang, SL and Yang, SH},
title = {Microbial Community Shifts and Nitrogen Utilization in Peritidal Microbialites: The Role of Salinity and pH in Microbially Induced Carbonate Precipitation.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {31},
pmid = {40259028},
issn = {1432-184X},
support = {MOST 111-2621-B-029 -002 -MY3//National Science and Technology Council, Taiwan/ ; MOST 110-2611-M-002-024//National Science and Technology Council/ ; },
mesh = {*Carbonates/metabolism/chemistry ; Hydrogen-Ion Concentration ; Salinity ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Microbiota ; *Seawater/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Chemical Precipitation ; },
abstract = {Microbialites have the potential to record environmental changes and act as biosignatures of past geochemical conditions. As such, they could be used as indicators to decipher ancient rock records. Modern microbialites are primarily found in environments where competitors and destructors are absent or where biogeochemical conditions favor their continuous formation. Many previous studies have essentially focused on the role of photosynthetic microbes in controlling pH and carbonate speciation and potentially overlooked alternative non-photosynthetic pathways of carbonate precipitation. Given that microbial activity induces subtle geochemical changes, microbially induced carbonate precipitation (MICP) can involve several mechanisms, from extracellular polymeric substances (EPS), sulfate reduction, anaerobic oxidation of methane, to nitrogen cycling processes, such as ammonification, ureolysis, and denitrification. Moreover, the peritidal zone where temperate microbialites are mostly found today, is under the influence of both freshwater and seawater, arguing for successive biogeochemical processes leading to mineral saturation, and questioning interpretations of fossil records. This study investigates microbialites in three tide pools from the peritidal zone of Fongchueisha, Hengchun, Taiwan, to address the influence of salinity on microbial community composition and carbonate precipitation mechanisms. Microbial samples were collected across varying salinity gradients at multiple time points and analyzed using next-generation sequencing (NGS) of bacterial 16S and eukaryotic 18S rRNA genes. Our results indicate that dominant bacterial groups, including Cyanobacteria and Alphaproteobacteria, were largely influenced by salinity variations, albeit pH exhibited stronger correlation with community composition. Combining our results on geochemistry and taxonomic diversity over time, we inferred a shift in the trophic mode under high salinity conditions, during which the use of urea and amino acids as a nitrogen source outcompetes diazotrophy, ureolysis and ammonification of amino acids reinforcing carbonate precipitation dynamics by triggering an increase in both pH and dissolved inorganic carbon.},
}

*Carbonates/metabolism/chemistry
Hydrogen-Ion Concentration
Salinity
*Nitrogen/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
*Microbiota
*Seawater/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
Chemical Precipitation

@article {pmid40258091,
year = {2025},
author = {Hashem, I and Wang, J and Van Impe, JFM},
title = {A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012974},
doi = {10.1371/journal.pcbi.1012974},
pmid = {40258091},
issn = {1553-7358},
abstract = {Individual-based modeling (IbM) is an instrumental tool for simulating spatial microbial growth, with applications in both microbial ecology and biochemical engineering. Unlike Cellular Automata (CA), which use a fixed grid of cells with predefined rules for interactions, IbMs model the individual behaviors of cells, allowing complex population dynamics to emerge. IbMs require more detailed modeling of individual interactions, which introduces significant computational challenges, particularly in resolving spatial overlaps between cells. Traditionally, this is managed using arrays or kd-trees, which require numerous pairwise comparisons and become inefficient as population size increases. To address this bottleneck, we introduce the Discretized Overlap Resolution Algorithm (DORA), which employs a grid-based framework to efficiently manage overlaps. By discretizing the simulation space further and assigning circular cells to specific grid units, DORA transforms the computationally intensive pairwise comparison process into a more efficient grid-based operation. This approach significantly reduces the computational load, particularly in simulations with large cell populations. Our evaluation of DORA, through simulations of microbial colonies and biofilms under varied nutrient conditions, demonstrates its superior computational efficiency and ability to accurately capture microbial growth dynamics compared to conventional methods. DORA's grid-based strategy enables the modeling of densely populated microbial communities within practical computational timeframes, thereby expanding the scope and applicability of individual-based modeling.},
}

@article {pmid40257249,
year = {2025},
author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS},
title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0133524},
doi = {10.1128/mra.01335-24},
pmid = {40257249},
issn = {2576-098X},
abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.},
}

@article {pmid40253969,
year = {2025},
author = {Achouri, H and Derguini, A and Idres, T and Selamoglu, Z and Hamadi, NB and Jalouli, M and Elfalleh, W and Bendif, H and Badraoui, R and Boufahja, F and Dellali, M},
title = {Impact of climate change on the toxicity of bisphenol A in Mytilus galloprovincialis and assessment of phycoremediation using Nannochloropsis salina via a multi-biomarker strategy and modeling.},
journal = {Marine pollution bulletin},
volume = {216},
number = {},
pages = {118010},
doi = {10.1016/j.marpolbul.2025.118010},
pmid = {40253969},
issn = {1879-3363},
abstract = {In the current study, the mussels Mytilus galloprovincialis, exposed to four varying temperatures (17, 20, 23, and 26 °C), were contaminated with 50 μg/L of bisphenol A both with and without Nannochloropsis salina. The toxicity evaluation is determined by quantifying various biomarkers related to oxidative stress, neurotoxicity, and cellular damage. The key findings indicate that the toxicity of bisphenol A is heightened by rising temperature. The impact of bisphenol A is most evident at 26 °C, leading to excessive production of reactive oxygen species, depletion of non-enzymatic antioxidants, and activation of antioxidant enzymes (catalase and glutathione-S-transferase). The rise in malondialdehyde levels confirms lipid peroxidation caused by bisphenol A and intensified by thermal stress. These findings have been supported by strong molecular interactions between bisphenol A and lectin mytilec apo-form and proximal thread matrix protein 1 from M. galloprovincialis following the computational modeling assay. The incorporation of N. salina as a food additive helped, firstly, to mitigate the stress effects and, secondly, resulted in a noticeable enhancement of oxidative balance and filtration ability, along with decreased lipid peroxidation.},
}

@article {pmid40252751,
year = {2025},
author = {Tuts, L and Heyndrickx, M and Becue, I and Boon, N and De Maesschalck, P and Rasschaert, G},
title = {Tracking antibiotics and antibiotic resistant E. coli in the aquatic environment linked to agriculture.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126265},
doi = {10.1016/j.envpol.2025.126265},
pmid = {40252751},
issn = {1873-6424},
abstract = {The application of manure to fertilize agricultural land is associated with the introduction of antibiotic residues and bacteria, including antibiotic resistant bacteria, which can reach surface water through runoff and drainage and groundwater through leaching from the soil. This was investigated by sampling 50 surface water locations (before and after fertilization) and 50 groundwater wells for the presence of antibiotic residues and the presence of antibiotic-resistant bacteria. For the latter, Escherichia coli and extended-spectrum β-lactamase (ESBL) producing E. coli were used as indicators and profiled for antibiotic resistance. The presence of a wide range of antibiotic residues, though at low concentrations (0.01 - 10 μg/L), in freshwater ecosystems highlights the extensive spread of these substances. Only 16% of the samples were consistently free of antibiotic residues throughout both sampling periods. Notably, the frequent occurrence of sulfonamides and lincomycin in surface waters raises concerns as their concentrations occasionally exceed the predicted no-effect levels for antimicrobial resistance selection. Maximum concentrations were reported at 8.83 μg/L and 1.60 μg/L for sulfamethoxazole and lincomycin, respectively. Additionally, resistance patterns in E. coli indicate increased resistance to sulfamethoxazole following the fertilization period, suggesting that the application of manure on fields contributes to a rise in antibiotic resistance from 20% to 48%. Although antibiotic contamination in groundwater is less prevalent, antibiotic resistance remains widespread. In particular, ESBL-producing E. coli exhibit heightened resistance levels, not limited to β-lactam antibiotics. The detection of resistance to critical last-resort antibiotics such as carbapenems and colistin further emphasizes the urgency of addressing antibiotic resistance in environmental contexts. This study highlights the need for continued monitoring and the implementation of legislation to reduce antibiotic pollution and tackle resistance in aquatic ecosystems.},
}

@article {pmid40251008,
year = {2025},
author = {Rizaludin, MS and Diaz, ASL and Zweers, H and Raaijmakers, JM and Garbeva, P},
title = {Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf042},
pmid = {40251008},
issn = {1574-6941},
abstract = {The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root volatilome compounds. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root volatilome and microbiome composition, highlighting its systemic effects on plant-root chemistry and microbiome composition.},
}

@article {pmid40250533,
year = {2025},
author = {Rosario Rodero, MD and Steyer, JP and Pérez-Bernal, MF and Verstraete, W and Escudié, R and Capson-Tojo, G},
title = {Dinitrogen fixation by open purple non-sulfur bacteria cultures for protein production: Diazotrophy boosts photoheterotrophic uptake rates.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132554},
doi = {10.1016/j.biortech.2025.132554},
pmid = {40250533},
issn = {1873-2976},
abstract = {Purple non-sulfur bacteria (PNSB) offer a sustainable alternative to current inefficient protein production systems thanks to their high yields. This study explored the potential of specialized diazotrophic PNSB open cultures for protein production, benchmarking their performance against ammonium-grown PNSB and other diazotrophs. While diazotrophic yields (0.85-0.93 gCODbiomass·gCODsubstrate[-1]; COD being chemical oxygen demand) were slightly lower than non-diazotrophic (∼1.0), they were over double those of heterotrophic-diazotrophic rhizobacteria, with full N recovery as biomass (∼1.0 gNbiomass·gNfixed[-1]). Photoheterotrophic-diazotrophic uptake rates were the fastest ever reported for PNSB and any other diazotroph (e.g., 5.20 ± 0.83 vs. 2.64 ± 0.34 gCODsubstrate·gCODbiomass[-1]·d[-1] for PNSB on NH4[+]). Optimal rates required high light intensities, aligning with diazotrophic energy demands. Photoheterotrophic-diazotrophic conditions were highly selective, enriching a specialized Rhodopseudomonas palustris strain. Biomass protein contents and essential amino acid metrics confirmed nutritional suitability for humans. This work lays the background to exploit PNSB's potential to address global protein demands through sustainable nitrogen fixation.},
}

@article {pmid40248914,
year = {2025},
author = {Zhang, RG and Shang, HY and Milne, RI and Almeida-Silva, F and Chen, H and Zhou, MJ and Shu, H and Jia, KH and Van de Peer, Y and Ma, YP},
title = {SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.},
journal = {Nucleic acids research},
volume = {53},
number = {7},
pages = {},
doi = {10.1093/nar/gkaf320},
pmid = {40248914},
issn = {1362-4962},
support = {2022YFF1301700//National Key Research and Development Program/ ; KIBXD202401//Kunming Institute of Botany, Chinese Academy of Sciences/ ; //Light of West China/ ; 202101BC070003//Key Basic Research Programs of Yunnan Province/ ; 2022SJ07X-03//PSESP/ ; },
mesh = {*Synteny/genetics ; *Genomics/methods ; *Evolution, Molecular ; *Genome, Plant ; Phylogeny ; Polyploidy ; Algorithms ; Plants/genetics ; },
abstract = {With the explosive growth of whole-genome datasets, accurate detection of orthologous synteny has become crucial for reconstructing evolutionary history. However, current methods for identifying orthologous synteny face great limitations, particularly in scaling with varied polyploidy histories and accurately removing out-paralogous synteny. In this study, we developed a scalable and robust approach, based on the Orthology Index (OI), to effectively identify orthologous synteny. Our evaluation across a large-scale empirical dataset with diverse polyploidization events demonstrated the high reliability and robustness of the OI method. Simulation-based benchmarks further validated the accuracy of our method, showing its superior performance against existing methods across a wide range of scenarios. Additionally, we explored its broad applications in reconstructing the evolutionary histories of plant genomes, including the inference of polyploidy, identification of reticulation, and phylogenomics. In conclusion, OI offers a robust, interpretable, and scalable approach for identifying orthologous synteny, facilitating more accurate and efficient analyses in plant evolutionary genomics.},
}

*Synteny/genetics
*Genomics/methods
*Evolution, Molecular
*Genome, Plant
Phylogeny
Polyploidy
Algorithms
Plants/genetics

@article {pmid40248762,
year = {2025},
author = {Flores, C and Millard, S and Seekatz, AM},
title = {Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems.},
journal = {Current clinical microbiology reports},
volume = {12},
number = {1},
pages = {9},
pmid = {40248762},
issn = {2196-5471},
abstract = {PURPOSE OF REVIEW: This review explores the application of classical ecological theory to host-associated microbiomes during initial colonization, maintenance, and recovery. We discuss unique challenges of applying these theories to host-associated microbiomes and host factors to consider going forward.

RECENT FINDINGS: Recent studies applying community ecology principles to host microbiomes continue to demonstrate a role for both selective and stochastic processes in shaping host-associated microbiomes. However, ecological frameworks developed to describe dynamics during homeostasis do not necessarily apply during diseased or highly perturbed states, where large variations can potentially lead to alternate stable states.

SUMMARY: Despite providing valuable insights, the application of ecological theories to host-associated microbiomes has some unique challenges. The integration of host-specific factors, such as genotype or immune dynamics in ecological models or frameworks is crucial for understanding host microbiome assembly and stability, which could improve our ability to predict microbiome outcomes and improve host health.},
}

@article {pmid40247944,
year = {2025},
author = {Sun, Y and Sun, S and Zahid, MS and Qiu, Q and Wang, L and Wang, S},
title = {Root-applied brassinosteroid and salicylic acid enhance thermotolerance and fruit quality in heat-stressed 'Kyoho' grapevines.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1563270},
pmid = {40247944},
issn = {1664-462X},
abstract = {INTRODUCTION: The increasingly severe global greenhouse effect has become an irreversible trend, significantly impacting viticulture regions through heat stress during various grape growth stages, especially under protected cultivation conditions where high temperatures frequently occur. Therefore, studying the impact of heat stress on grapevine growth and fruit quality across the entire growth and development period, along with effective mitigation measures, is crucial.

METHODS: In this study, three-year-old 'Kyoho' grapevines were used as experimental materials, with four treatment groups: a control group, a hightemperature group (heat stress, HT), a high-temperature + brassinolide group (BR), and a high-temperature + salicylic acid group (SA). During the flowering, young berry swelling, and veraison stages, BR and SA were applied via nutrient solutions every seven days.

RESULTS: The results demonstrated that BR restored the maximum photosynthetic rate (Amax) to 96.14% of CK by the 18th day of flowering, significantly outperforming SA's recovery rate of 86.64%. Both treatments maintained light saturation points (1200 μmol•m[⁻²]•s[⁻¹]) and CO2 saturation thresholds equivalent to CK. The decline in PSII photochemical efficiency (Fv/Fm) was reduced from 18% in HT to 5-8% in BR/SA-treated groups, with BR showing minimal deviation (2.3%) from CK during veraison, effectively mitigating PSII photoinhibition caused by heat stress. Furthermore, both treatments reduced leaf malondialdehyde (MDA) content, minimizing membrane lipid peroxidation, while increasing soluble protein (SP) content to protect leaves. Under heat stress, BR notably improved the fruit set rate by 22.67% compared to HT (SA: 13%), promoted berry expansion, and enhanced the accumulation of sugars and anthocyanins in the fruit skin, with SA showing similar, though slightly less pronounced, effects.

DISCUSSION: These findings provide valuable theoretical insights into the use of exogenous hormones in root nutrient solutions as a strategy to mitigate the adverse effects of heat stress in grape production.},
}

@article {pmid40247820,
year = {2025},
author = {Liu, M and Yao, X and Wang, H and Xu, X and Kong, J and Wang, Y and Chen, W and Bai, H and Wang, Z and Setati, ME and Crauwels, S and Blancquaert, E and Fan, P and Liang, Z and Dai, Z},
title = {Carposphere microbiota alters grape volatiles and shapes the wine grape typicality.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70152},
pmid = {40247820},
issn = {1469-8137},
support = {NXNYYZ202101//Agricultural Breeding Project of Ningxia Hui Autonomous Region/ ; U20A2041//National Natural Science Foundation of China/ ; JCTD-2022-06//CAS Youth Interdisciplinary Team/ ; 2021YFE0109500//National Key Research and Development Program of China/ ; YSBR-093//CAS Project for Young Scientists in Basic Research/ ; },
abstract = {While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.},
}

@article {pmid40247656,
year = {2025},
author = {Bonazzi, E and De Barba, C and Lorenzon, G and Maniero, D and Bertin, L and Barberio, B and Facciotti, F and Caprioli, F and Scaldaferri, F and Zingone, F and Savarino, EV},
title = {Recent developments in managing luminal microbial ecology in patients with inflammatory bowel disease: from evidence to microbiome-based diagnostic and personalized therapy.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2495087},
pmid = {40247656},
issn = {1747-4132},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition characterized by abnormal immune responses and intestinal inflammation. Emerging evidence highlights the vital role of gut microbiota in IBD's onset and progression. Recent advances have shaped diagnostic and therapeutic strategies, increasingly focusing on microbiome-based personalized care. Methodology: this review covers studies from 2004 to 2024, reflecting the surge in research on luminal microbial ecology in IBD. Human studies were prioritized, with select animal studies included for mechanistic insights. Only English-language, peer-reviewed articles - clinical trials, systematic reviews, and meta-analyses - were considered. Studies without clinical validation were excluded unless offering essential insights. Searches were conducted using PubMed, Scopus, and Web of Science.

AREAS COVERED: we explore mechanisms for managing IBD-related microbiota, including microbial markers for diagnosis and novel therapies such as fecal microbiota transplantation, metabolite-based treatments, and precision microbiome modulation. Additionally, we review technologies and diagnostic tools used to analyze gut microbiota composition and function in clinical settings. Emerging data supporting personalized therapeutic strategies based on individual microbial profiles are discussed.

EXPERT OPINION: Standardized microbiome research integration into clinical practice will enhance precision in IBD care, signaling a shift toward microbiota-based personalized medicine.},
}

@article {pmid40246153,
year = {2025},
author = {Bharathan, A and Arafath, Y and Fathima, A and Hassan, S and Singh, P and Kiran, GS and Selvin, J},
title = {Affection of Environmental Factors on the Pathogenicity of Vibrio vulnificus: Insights into Gene Activation and Disease.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107591},
doi = {10.1016/j.micpath.2025.107591},
pmid = {40246153},
issn = {1096-1208},
abstract = {Climate change, particularly rising sea surface temperatures and altered salinity levels has contributed to the increased prevalence of Vibrio vulnificus infections in humans and marine life. This opportunistic pathogen thrives in warm, estuarine environments, and its virulence is influenced by temperature-dependent gene expression, such as the activation of pVvBt2. Elevated temperatures and iron availability enhance pathogenicity by upregulating key virulence factors, including hemolysin, exotoxins, and biofilm-associated genes. Climate-driven shifts in microbial ecology have also facilitated the global expansion of V. vulnificus, leading to more frequent outbreaks and an increasing threat to public health. The unregulated use of antibiotics has also contributed to the emergence of resistant strains, complicating treatment strategies. This review explores the complex interplay between climate change and the molecular mechanisms driving V. vulnificus pathogenicity, global gene expression responses, and the implications for disease outbreaks. We also discuss current and emerging therapeutic approaches, including antibiotic stewardship and vaccine development, to mitigate the rising health risks posed by this climate-sensitive pathogen.},
}

@article {pmid40244660,
year = {2025},
author = {Narla, AV and Hwa, T and Murugan, A},
title = {Dynamic coexistence driven by physiological transitions in microbial communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {16},
pages = {e2405527122},
doi = {10.1073/pnas.2405527122},
pmid = {40244660},
issn = {1091-6490},
support = {542387//Simons Foundation (SF)/ ; 2029480//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; R35GM151211//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 2317138//NSF | MPS | Division of Physics (PHY)/ ; },
mesh = {*Ecosystem ; *Models, Biological ; Biomass ; *Microbiota/physiology ; *Microbial Interactions/physiology ; Bacteria/growth & development ; },
abstract = {Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, "community states," in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom-up studies based on fixed, idealized interspecies interaction to top-down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics.},
}

*Ecosystem
*Models, Biological
Biomass
*Microbiota/physiology
*Microbial Interactions/physiology
Bacteria/growth & development

@article {pmid40243315,
year = {2025},
author = {Weng, L and Cui, Y and Jian, W and Zhang, Y and Pang, L and Cao, Y and Zhou, Y and Liu, W and Lin, H and Tao, Y},
title = {Inter-kingdom interactions and environmental influences on the oral microbiome in severe early childhood caries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0251824},
doi = {10.1128/spectrum.02518-24},
pmid = {40243315},
issn = {2165-0497},
abstract = {UNLABELLED: Dental caries arise from intricate interactions among oral microorganisms, impacting ecological stability and disease progression. In this study, we aimed to investigate the microbial diversity and inter-kingdom interactions in severe early childhood caries (S-ECC) and assess the influence of environmental factors such as salivary pH and trace elements. We analyzed 61 children aged 3-4 years with complete deciduous dentition, evaluating salivary pH, buffering capacity, and trace elements (iron, fluoride). We examined the performance of 16S rRNA V1-V9 regions gene and internal transcribed spacer (ITS) primers for bacteria and fungi from plaque and saliva to characterize community compositions and diversity. Findings revealed significant shifts in bacterial diversity in S-ECC saliva samples, marked by decreased diversity and elevated abundance of cariogenic species, particularly Streptococcus mutans. Candida albicans was notably more prevalent in the S-ECC group, implicating its potential role in pathogenesis. Iron and fluoride concentrations showed no significant correlation with microbial community structure. Network analyses uncovered complex intra- and inter-kingdom interactions, underscoring cooperative and competitive dynamics. S-ECC children exhibited higher abundances of bacteria (Streptococcus mutans, Granulicatella, Actinomyces) and fungi (Candida albicans), with specific microbial taxa associated with reduced salivary pH.

IMPORTANCE: This study illuminates the intricate relationship between bacteria and fungi within the oral microbial community of children, specifically highlighting differences between those with S-ECC and those without caries. Through an extensive analysis of the microbial composition in both saliva and dental plaque, we identified a significant increase in the abundance of specific bacterial taxa (e.g., S. mutans, Granulicatella, Actinomyces) and fungal species (e.g., C. albicans) in the oral cavities of children with S-ECC. This finding underscores the potential role of these microorganisms in the development of caries. Contrary to previous studies that emphasize the importance of iron and fluoride in oral health, our research found no significant correlation between the concentrations of these elements and the composition of oral microbial communities. This result challenges conventional understanding and opens new avenues for future research. Additionally, our findings revealed an association between Veillonella sp., Propionibacterium sp., and Candida sp. and reduced salivary pH. This provides novel insights into the relationship between the oral microenvironment and caries development. The implications of our findings are substantial for the development of prevention and intervention strategies targeting childhood caries. They also underscore the critical need for a deeper exploration of oral microbial interactions and their environmental influences.},
}

@article {pmid40241747,
year = {2025},
author = {Takahashi, M and Hiraoka, S and Matsumoto, Y and Shibagaki, R and Ujihara, T and Maeda, H and Seo, S and Nagasaki, K and Takeuchi, H and Matsuzaki, S},
title = {Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112264},
pmid = {40241747},
issn = {2589-0042},
abstract = {Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.},
}

@article {pmid40240613,
year = {2025},
author = {Dhungana, I and Nguyen, NH},
title = {Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {30},
pmid = {40240613},
issn = {1432-184X},
support = {HAW08042-H//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/growth & development ; *Fungi/classification/growth & development/genetics/isolation & purification ; Soil/chemistry ; Agriculture/methods ; Zea mays/growth & development/microbiology ; *Archaea/classification/growth & development/genetics/isolation & purification ; *Microbiota ; Tropical Climate ; Crops, Agricultural/growth & development/microbiology ; Lactuca/growth & development/microbiology ; Mustard Plant/growth & development/microbiology ; },
abstract = {Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.},
}

*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/growth & development
*Fungi/classification/growth & development/genetics/isolation & purification
Soil/chemistry
Agriculture/methods
Zea mays/growth & development/microbiology
*Archaea/classification/growth & development/genetics/isolation & purification
*Microbiota
Tropical Climate
Crops, Agricultural/growth & development/microbiology
Lactuca/growth & development/microbiology
Mustard Plant/growth & development/microbiology

@article {pmid40239902,
year = {2025},
author = {Ma, H and Chen, S and Lv, L and Ye, Z and Yang, J and Wang, B and Zou, J and Li, J and Ganigué, R},
title = {Large-sized aerobic granular biofilm: stable biotechnology to improve nitrogen removal and reduce sludge yield.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132543},
doi = {10.1016/j.biortech.2025.132543},
pmid = {40239902},
issn = {1873-2976},
abstract = {Three parallel sequencing batch reactors (control, small-sized polyurethane sponge (PUS) (3.0 mm), and large-sized PUS (10.0 mm)) were used to investigate aerobic granular biofilm (AGB) characteristics. Results show that 10.0 mm PUS facilitated rapid formation of large-sized AGB (AGBL), which exhibited higher biomass concentration (8.5 g/L) and faster settling velocity (69.2-159.3 m/h) than aerobic granular sludge (AGS) (3.2 g/L and 38.6-80.0 m/h). The AGBL system also maintained long-term structural stability with a lower instability coefficient (0.004-0.018 min[-1]) than AGS (0.053-0.090 min[-1]). Additionally, during long-term operation, the AGBL system achieved excellent removal efficiencies for NH4[+]-N (99.6 ± 0.4 %) and total nitrogen (92.3 ± 2.6 %), and exhibited a lower sludge yield (0.05 gVSS/gCOD) than AGS (0.14 gVSS/gCOD). The larger size and compact structure of AGBL increased anoxic/anaerobic zones, enriching denitrifying and hydrolytic/fermentative bacteria. These findings highlight AGBL with large PUS as a more promising biotechnology for practical applications than conventional AGS.},
}

@article {pmid40238873,
year = {2025},
author = {Bukhdruker, S and Gushchin, I and Shevchenko, V and Kovalev, K and Polovinkin, V and Tsybrov, F and Astashkin, R and Alekseev, A and Mikhaylov, A and Bukhalovich, S and Bratanov, D and Ryzhykau, Y and Kuklina, D and Caramello, N and Rokitskaya, T and Antonenko, Y and Rulev, M and Stoev, C and Zabelskii, D and Round, E and Rogachev, A and Borshchevskiy, V and Ghai, R and Bourenkov, G and Zeghouf, M and Cherfils, J and Engelhard, M and Chizhov, I and Rodriguez-Valera, F and Bamberg, E and Gordeliy, V},
title = {Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.},
journal = {Science advances},
volume = {11},
number = {16},
pages = {eadu5303},
doi = {10.1126/sciadv.adu5303},
pmid = {40238873},
issn = {2375-2548},
mesh = {*Protons ; *Rhodopsins, Microbial/chemistry/metabolism ; Hydrogen Bonding ; Models, Molecular ; Proton Pumps/chemistry/metabolism ; Protein Conformation ; },
abstract = {Bacterial proton pumps, proteorhodopsins (PRs), are a major group of light-driven membrane proteins found in marine bacteria. They are functionally and structurally distinct from archaeal and eukaryotic proton pumps. To elucidate the proton transfer mechanism by PRs and understand the differences to nonbacterial pumps on a molecular level, high-resolution structures of PRs' functional states are needed. In this work, we have determined atomic-resolution structures of MAR, a PR from marine actinobacteria, in various functional states, notably the challenging late O intermediate state. These data and information from recent atomic-resolution structures on an archaeal outward proton pump bacteriorhodopsin and bacterial inward proton pump xenorhodopsin allow for deducing key universal elements for light-driven proton pumping. First, long hydrogen-bonded chains characterize proton pathways. Second, short hydrogen bonds allow proton storage and inhibit their backflow. Last, the retinal Schiff base is the active proton donor and acceptor to and from hydrogen-bonded chains.},
}

*Protons
*Rhodopsins, Microbial/chemistry/metabolism
Hydrogen Bonding
Models, Molecular
Proton Pumps/chemistry/metabolism
Protein Conformation

@article {pmid40238292,
year = {2025},
author = {Zhang, Y and Lin, H and Xiong, Y and Zhang, Z and Zeng, L and Liu, Z},
title = {Fu Brick Tea Protects the Intestinal Barrier and Ameliorates Colitis in Mice by Regulating Gut Microbiota.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071122},
pmid = {40238292},
issn = {2304-8158},
support = {2024HX118//Horizontal project of Shaoyang University/ ; 2024JJ7497//Foundation regional joint fund of Hunan Province natural Science/ ; 202401001313//The teaching reform research project of Hunan Province in 2024/ ; 2022YFE0111200//Innovation and transformation of key technologies for efficient preparation of catechin oxidation polymerization products/ ; },
abstract = {Ulcerative colitis (UC) pathogenesis is strongly linked to gut microbiota dysbiosis and compromised intestinal barrier integrity. Emerging evidence suggests that targeted dietary interventions may restore microbial homeostasis and ameliorate colitis progression. In this study, we evaluated the therapeutic potential of Fu Brick tea (FBT) using a dextran sulfate sodium (DSS)-induced murine colitis model. The results indicated that oral administration of FBT extract significantly improved the disease index, reduced inflammatory response, protected intestinal barrier protein (e.g., ZO-1), and maintained intestinal structure integrity. Furthermore, FBT intake increased the diversity of gut microbiota, promoted the growth of beneficial bacteria (e.g., Akkermansia), inhibited the proliferation of harmful bacteria (e.g., Desulfovibrioceae, Escherichia, and Helicobacter), restored intestinal homeostasis, and alleviated colitis symptoms including diarrhea. These findings position FBT as a promising nutraceutical candidate for UC management via multi-target modulation of mucosal immunity and microbial ecology.},
}

@article {pmid40238218,
year = {2025},
author = {Zhadyra, S and Tao, F and Xu, P},
title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071102},
pmid = {40238218},
issn = {2304-8158},
abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.},
}

@article {pmid40237447,
year = {2025},
author = {Choudoir, MJ and Ishaq, SL and Beiko, RG and Silva, DS and Allen-Vercoe, E and O'Doherty, KC},
title = {The case for microbiome stewardship: what it is and how to get there.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0006225},
doi = {10.1128/msystems.00062-25},
pmid = {40237447},
issn = {2379-5077},
abstract = {Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.},
}

@article {pmid40235320,
year = {2025},
author = {Bahram Wlia, A and Majedi, S},
title = {Optimizing hygiene and microbial aspect of paper recycling: a sustainable approach for environmental conservation.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {71},
number = {3},
pages = {151-157},
doi = {10.14715/cmb/2025.71.3.18},
pmid = {40235320},
issn = {1165-158X},
mesh = {*Recycling/methods ; *Paper ; *Hygiene ; *Bacteria/isolation & purification/classification/genetics ; *Conservation of Natural Resources/methods ; Iraq ; Waste Management/methods ; },
abstract = {This study explores microbial dynamics in paper recycling, emphasizing the significance of sustainable practices for environmental preservation. Samples were collected from various urban waste sources in Erbil city, Kurdistan Region, Iraq, including materials such as pizza boxes, cigarette packets, and coffee cups. Pure bacterial colonies were isolated using standard methods, and their morphological and physiological traits were characterized through biochemical tests. Identification of bacterial species followed established protocols. The study identified diverse bacterial species associated with paper waste, highlighting potential hygiene concerns in the recycling process. The findings of this study contribute to understanding the microbial ecology associated with paper waste and recycling processes. By optimizing hygiene measures and gaining insights into the microbial communities present, this research underscores the importance of sustainable practices in paper recycling to mitigate environmental impacts and promote a healthier ecosystem. Policies for future waste management and reduction of environmental risks have been proposed.},
}

*Recycling/methods
*Paper
*Hygiene
*Bacteria/isolation & purification/classification/genetics
*Conservation of Natural Resources/methods
Iraq
Waste Management/methods

@article {pmid40234253,
year = {2025},
author = {Yao, B and Mou, X and Li, Y and Lian, J and Niu, Y and Liu, J and Lu, J and Li, Y and Li, Y and Wang, X},
title = {Distinct Assembly Patterns of Soil Bacterial and Fungal Communities along Altitudinal Gradients in the Loess Plateau's Highest Mountain.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {29},
pmid = {40234253},
issn = {1432-184X},
support = {23JRRA672//Youth Science and Technology Fund Program of Gansu Province/ ; 2023449//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 22JR5RA076//Gansu Province Natural Science Foundation Program/ ; },
mesh = {*Soil Microbiology ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; Soil/chemistry ; Ecosystem ; *Microbiota ; Biodiversity ; *Mycobiome ; China ; High-Throughput Nucleotide Sequencing ; },
abstract = {A critical issue in microbial ecology is quantifying the relative contributions of deterministic and stochastic processes to microbial community assembly, and predicting ecosystem function by understanding the ecological processes of community composition is an integral part. However, the mechanisms driving microbial community assembly along altitudinal gradients in mountain ecosystems remain largely unexplored. Here, we used high-throughput sequencing to examine the structural characteristics and diversity maintenance mechanisms of soil bacterial and fungal communities along an altitudinal gradient (2632-3661 m) in Mahan Mountain, the highest peak of the Loess Plateau. Proteobacteria, Acidobacteriota and Actinobacteriota dominated the bacterial communities, while Ascomycota, Basidiomycota and Mortierellomycota were the predominant fungal groups. Although elevation did not significantly affect bacterial and fungal alpha diversity, notable shifts in community structure were observed along the altitudinal gradients. Bacterial communities were predominantly shaped by deterministic processes, leading to pronounced structural and compositional differentiation across altitudes. In contrast, fungal community assembly was primarily determined by a combination of deterministic and stochastic processes, leading to small pronounced structural divergence. The interplay of topography, climate, and soil conditions influenced the altitudinal distribution and community structure of soil bacteria in this mountain ecosystem.},
}

*Soil Microbiology
*Altitude
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
Soil/chemistry
Ecosystem
*Microbiota
Biodiversity
*Mycobiome
China
High-Throughput Nucleotide Sequencing

@article {pmid40230839,
year = {2025},
author = {Zhao, T and Wang, C and Liu, Y and Li, B and Shao, M and Zhao, W and Zhou, C},
title = {The role of polysaccharides in immune regulation through gut microbiota: mechanisms and implications.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555414},
pmid = {40230839},
issn = {1664-3224},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Polysaccharides/immunology/metabolism ; Animals ; Fatty Acids, Volatile/metabolism ; *Immunomodulation ; Cytokines/metabolism ; },
abstract = {Polysaccharides, as complex carbohydrates, play a pivotal role in immune modulation and interactions with the gut microbiota. The diverse array of dietary polysaccharides influences gut microbial ecology, impacting immune responses, metabolism, and overall well-being. Despite their recognized benefits, there is limited understanding of the precise mechanisms by which polysaccharides modulate the immune system through the gut microbiota. A comprehensive search of Web of Science, PubMed, Google Scholar, and Embase up to May 2024 was conducted to identify relevant studies. This study employs a systematic approach to explore the interplay between polysaccharides and the gut microbiota, focusing on cytokine-mediated and short-chain fatty acid (SCFA)-mediated pathways. The findings underscore the significant role of polysaccharides in shaping the composition and function of the gut microbiota, thereby influencing immune regulation and metabolic processes. However, further research is necessary to elucidate the detailed molecular mechanisms and translate these findings into clinical applications.},
}

*Gastrointestinal Microbiome/immunology
Humans
*Polysaccharides/immunology/metabolism
Animals
Fatty Acids, Volatile/metabolism
*Immunomodulation
Cytokines/metabolism

@article {pmid40229524,
year = {2025},
author = {Sakae, K and Kitagami, Y and Matsuda, Y},
title = {Rhizosphere Bacterial Communities Alter in Process to Mycorrhizal Developments of a Mixotrophic Pyrola japonica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {28},
pmid = {40229524},
issn = {1432-184X},
support = {2023-4099//Japan Science Society/ ; JRMJSP2137//Japan Science and Technology Agency/ ; 24K01796//Japan Society for the Promotion of Science/ ; },
mesh = {*Mycorrhizae/growth & development/physiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; *Ericaceae/microbiology/growth & development ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; },
abstract = {Rhizosphere bacteria work in synergy with mycorrhizal fungi to promote plant growth. The community structure of rhizosphere bacteria may be influenced by continuous changes in fungal associations with host plants. Asiatic herbaceous plant Pyrola japonica (Ericaceae) forms arbutoid mycorrhizas without fungal mantles, with its mycorrhizal development being visually distinguishable at the cellular level. This study aimed to investigate roles of rhizosphere bacteria and their community shifts along with mycorrhizal developments. We examined bacterial communities at three different developmental stages of mycorrhizal roots-limited, full, and digested-via a partial 16S rRNA amplicon sequencing. Both α- and β-diversities in the full condition were significantly lower than those in the limited and digested conditions. Significant clusters of bacterial compositions were found among all treatments. In terms of ecological processes of community assembly, communities in limited conditions and bulk soil were influenced by both deterministic and stochastic processes, whereas those in full and digested conditions were regulated only by stochastic ways. Furthermore, the order Rhizobiales and Actinomycetales known as mycorrhizal helper bacteria were characterized in the full and digested conditions through phylogenetic analysis and detection of indicator taxa. These results suggest that mycorrhizal fungi may play ecologically important roles not only as temporal drivers initiating the formation rhizosphere bacterial communities but also as key founders exerting continuous influences to establish priority effects. Moreover, the rhizosphere bacterial community remains after mycorrhizal degeneration and their historical continuity may contribute to maintaining plant-mycorrhizal fungi-bacterial associations.},
}

*Mycorrhizae/growth & development/physiology
*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
Plant Roots/microbiology
*Ericaceae/microbiology/growth & development
*Microbiota
Biodiversity
DNA, Bacterial/genetics

@article {pmid40228732,
year = {2025},
author = {Zhang, R and Gong, C and Gao, Y and Chen, Y and Zhou, L and Lou, Q and Zhao, Y and Zhuang, H and Zhang, J and Shan, S and Wang, X and Qian, X and Lei, L and Wong, MH},
title = {Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126245},
doi = {10.1016/j.envpol.2025.126245},
pmid = {40228732},
issn = {1873-6424},
abstract = {Increasing attention has been given to the role of reductive soil disinfestation (RSD) on antibiotic resistance genes (ARGs) in soil. The selection of organic materials in RSD is crucial to the effectiveness of the RSD method. However, the effects of distinct organic materials on ARGs remains unclear. In this study, we selected straw and rapeseed meal as the organic materials in RSD and explored their effects on ARGs. The results showed that using straw significantly reduced the abundance of ARGs, high-risk ARGs, and mobile genetic elements (MGEs) by 31.5%-65.8%, while using rapeseed meal led to ARGs enrichment. Structural equation modeling (SEM) analysis identified MGEs and microbial communities as the primary drivers of ARGS changes under different organic materials. The abundance of MGEs was effectively controlled in straw treatments, reducing the potential for horizontal gene transfer of ARGs. Bacterial diversity was significantly lower in the straw treatments compared to the rapeseed meal treatments, potentially leading to a reduced abundance of ARGs host bacteria. Network co-occurrence analysis further revealed that Symbiobacteraceae and Bacillus were potential bacterial hosts of ARGs. In straw treatments, these genera' abundance decreased by 12%-100% compared to the control (CK) and rapeseed meal groups, further inhibiting the spread of ARGs. These findings demonstrate that RSD with straw as the organic material is more effective in mitigating ARGs compared to rapeseed meal, providing insights into controlling soil antibiotic resistance risks and utilizing agricultural waste resources.},
}

@article {pmid40227232,
year = {2025},
author = {Prochera, A and Muppirala, AN and Kuziel, GA and Soualhi, S and Shepherd, A and Sun, L and Issac, B and Rosenberg, HJ and Karim, F and Perez, K and Smith, KH and Archibald, TH and Rakoff-Nahoum, S and Hagen, SJ and Rao, M},
title = {Enteric glia regulate Paneth cell secretion and intestinal microbial ecology.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.97144},
pmid = {40227232},
issn = {2050-084X},
support = {R01DK130836/NH/NIH HHS/United States ; K08DK110532/NH/NIH HHS/United States ; R01DK135707/NH/NIH HHS/United States ; Fellowship//Schmidt Family Foundation/ ; Graduate Research Fellowship Program//National Science Foundation/ ; Fellowship//National Defense Science and Engineering Graduate/ ; Odyssey Award//Smith Family Foundation/ ; },
mesh = {Animals ; *Paneth Cells/metabolism/physiology ; Mice ; *Neuroglia/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Myelin Proteolipid Protein/metabolism/genetics ; *Intestinal Mucosa/metabolism/microbiology ; *Enteric Nervous System/physiology ; Mice, Inbred C57BL ; Male ; Female ; },
abstract = {Glial cells of the enteric nervous system (ENS) interact closely with the intestinal epithelium and secrete signals that influence epithelial cell proliferation and barrier formation in vitro. Whether these interactions are important in vivo, however, is unclear because previous studies reached conflicting conclusions (Prochera and Rao, 2023). To better define the roles of enteric glia in steady state regulation of the intestinal epithelium, we characterized the glia in closest proximity to epithelial cells and found that the majority express the gene Proteolipid protein 1 (PLP1) in both mice and humans. To test their functions using an unbiased approach, we genetically depleted PLP1[+] cells in mice and transcriptionally profiled the small and large intestines. Surprisingly, glial loss had minimal effects on transcriptional programs and the few identified changes varied along the gastrointestinal tract. In the ileum, where enteric glia had been considered most essential for epithelial integrity, glial depletion did not drastically alter epithelial gene expression but caused a modest enrichment in signatures of Paneth cells, a secretory cell type important for innate immunity. In the absence of PLP1[+] glia, Paneth cell number was intact, but a subset appeared abnormal with irregular and heterogenous cytoplasmic granules, suggesting a secretory deficit. Consistent with this possibility, ileal explants from glial-depleted mice secreted less functional lysozyme than controls with corresponding effects on fecal microbial composition. Collectively, these data suggest that enteric glia do not exert broad effects on the intestinal epithelium but have an essential role in regulating Paneth cell function and gut microbial ecology.},
}

Animals
*Paneth Cells/metabolism/physiology
Mice
*Neuroglia/physiology/metabolism
*Gastrointestinal Microbiome/physiology
Humans
Myelin Proteolipid Protein/metabolism/genetics
*Intestinal Mucosa/metabolism/microbiology
*Enteric Nervous System/physiology
Mice, Inbred C57BL
Male
Female

@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods/trends
*Metabolomics/methods
*Genomics/methods
Proteomics/methods
Precision Medicine
Host Microbial Interactions
Multiomics

@article {pmid40222749,
year = {2025},
author = {Belda, I and Izquierdo-Gea, S and Benitez-Dominguez, B and Ruiz, J and Vila, JCC},
title = {Wine Fermentation as a Model System for Microbial Ecology and Evolution.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70092},
doi = {10.1111/1462-2920.70092},
pmid = {40222749},
issn = {1462-2920},
support = {//Center for Computational, Evolutionary and Human Genomics, Stanford University. Postdoc Fellowship to Jean CC VIla/ ; FPU21/06830//Spanish Ministry of Science, Innovation and Universities/ ; PID2019-105834GA-I00//Agencia Estatal de Investigación/ ; PID2022-138343NB-I00//Agencia Estatal de Investigación/ ; PRE2022-103063//Agencia Estatal de Investigación/ ; },
mesh = {*Wine/microbiology ; *Fermentation ; *Biological Evolution ; Microbiota ; *Bacteria/metabolism/genetics ; Ecosystem ; Models, Biological ; Ecology ; },
abstract = {In vitro microbial communities have proven to be invaluable model systems for studying ecological and evolutionary processes experimentally. However, it remains unclear whether quantitative insights obtained from these laboratory systems can be applied to complex communities assembling and evolving in their natural ecological context. To bridge the gap between the lab and the 'real-world', there is a need for laboratory model systems that better approximate natural and semi-natural ecosystems. Wine fermentation presents an ideal system for this purpose, balancing experimental tractability with rich ecological and evolutionary dynamics. In this perspective piece we outline the key features that make wine fermentation a fruitful model system for ecologists and evolutionary biologists. We highlight the diversity of environmentally mediated interactions that shape community dynamics during fermentation, the complex evolutionary history of wine microbial populations, and the opportunity to study the impact of complex ecologies on evolutionary dynamics. By integrating knowledge from both wine research and microbial ecology and evolution we aim to enhance understanding and foster collaboration between these fields.},
}

*Wine/microbiology
*Fermentation
*Biological Evolution
Microbiota
*Bacteria/metabolism/genetics
Ecosystem
Models, Biological
Ecology

@article {pmid40220383,
year = {2025},
author = {Li, C and Zhu, L and Axe, L and Li, M},
title = {Acclimation of sludge-derived biofilms for effective removal of emerging contaminants: Impacts of inoculum source and carbon supplementation.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138235},
doi = {10.1016/j.jhazmat.2025.138235},
pmid = {40220383},
issn = {1873-3336},
abstract = {Contaminants of emerging concern (CECs) have gathered significant public attention due to their widespread occurrence, high persistence, and increasing exposure potential. In this study, we used polyethylene biocarriers for acclimating biofilms from singular or combined activated sludges collected from three wastewater treatment plants (R, P, and L) over 5 month-long cycles. The acclimated biofilms achieved an average removal rate at 0.333, 0.313, and 0.185 week[-1] for N, N-diethyl-meta-toluamide (DEET), sulfamethoxazole (SMX), and carbamazepine (CBZ), respectively, when external carbon was supplemented, which were significantly higher (p < 0.05) than biofilms that did not receive external carbons. Metabolite screening revealed SMX transformation through ipso-hydroxylation and acetyl conjugation, while CBZ degradation could be initiated by epoxidation. Significant but slower degradation rates (0.024∼0.031 week[-1]) were observed for aminotriazole (AMT), lidocaine (LDC), and trimethoprim (TMP), whereas atrazine (ATZ) exhibited minimal removal, highlighting its high recalcitrance. Biofilms acclimated from individual R and P sludges, with external carbon supplementation, attained the greatest removal efficiencies for 7 CECs. Multivariate statistical correlations (p < 0.05) identified potential degraders, including Sphingomonas and Zoogolea for AMT, Labrys and Koazkia for CBZ, and Asprobacter, unclassified Cyclobacteriaceae (ELB16-189) and Bryobacteraceae (Fen-178) for LDC. Abundance distribution of potential degraders among biofilms revealed that Sludge R favored the enrichment of key degraders for AMT, CBZ and LDC, while Sludge P was more conducive to acclimating CBZ degraders. This study advances our understanding of strategies in biofilm acclimation to improve CEC removal and provides insights into degradation pathways and associated microbial communities for future research.},
}

@article {pmid40220189,
year = {2025},
author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A},
title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {27},
pmid = {40220189},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; },
abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.},
}

Animals
*Gastrointestinal Microbiome
*Eucalyptus/parasitology/chemistry
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Diet
South Africa
*Coleoptera/microbiology/physiology
Gas Chromatography-Mass Spectrometry
Introduced Species
Biodiversity

@article {pmid40216640,
year = {2025},
author = {Huttunen, KL and Malazarte, J and Jyväsjärvi, J and Lehosmaa, K and Muotka, T},
title = {Temporal Beta Diversity of Bacteria in Streams: Network Position Matters But Differently for Bacterioplankton and Biofilm Communities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {26},
pmid = {40216640},
issn = {1432-184X},
support = {356403//Research Council of Finland/ ; 318230//Research Council of Finland/ ; 318230//Research Council of Finland/ ; },
mesh = {*Biofilms/growth & development ; *Rivers/microbiology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; *Biodiversity ; *Plankton/classification/genetics ; Soil Microbiology ; Ecosystem ; Seasons ; },
abstract = {Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land-water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.},
}

*Biofilms/growth & development
*Rivers/microbiology/chemistry
*Bacteria/classification/genetics/isolation & purification
*Biodiversity
*Plankton/classification/genetics
Soil Microbiology
Ecosystem
Seasons

@article {pmid40214404,
year = {2025},
author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, MØ and Rudi, K},
title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12464},
pmid = {40214404},
issn = {1520-5851},
abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.},
}

@article {pmid40209676,
year = {2025},
author = {Schell, LD and Carmody, RN},
title = {An energetic framework for gut microbiome-mediated obesity induced by early-life exposure to antibiotics.},
journal = {Cell host & microbe},
volume = {33},
number = {4},
pages = {470-483},
doi = {10.1016/j.chom.2025.03.009},
pmid = {40209676},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; *Obesity/chemically induced/microbiology/etiology/metabolism ; Animals ; Humans ; *Energy Metabolism/drug effects ; Female ; Mice ; Male ; },
abstract = {Early-life antibiotic (ELA) exposure has garnered attention for its potential role in modulating obesity risk, although outcomes from mouse experiments and human epidemiological studies often vary based on dosage and sex. Low-dose (subtherapeutic) antibiotics can enhance energy availability through moderate alterations in gut microbiome profile, while high-dose (therapeutic) antibiotics substantially deplete the gut microbiota, thereby contributing to short-term negative energy balance. In this perspective, we propose a framework to understand how these distinct impacts of antibiotics on the gut microbiome during critical developmental windows shape long-term obesity risk through their influence on host energy balance. Using this framework, we then propose several hypotheses to explain variation in ELA-induced obesity outcomes across males and females. We conclude by discussing the evolutionary implications of ELAs, positing that the response of the gut microbiome to ELAs may signal energy availability and environmental volatility, influencing metabolic programming and adaptive traits across generations.},
}

*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/adverse effects/pharmacology
*Obesity/chemically induced/microbiology/etiology/metabolism
Animals
Humans
*Energy Metabolism/drug effects
Female
Mice
Male

@article {pmid40208324,
year = {2025},
author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN},
title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {25},
pmid = {40208324},
issn = {1432-184X},
support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; },
mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation & purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; },
abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.},
}

Animals
*Porifera/microbiology
*Fungi/classification/genetics/isolation & purification
Mediterranean Sea
*Mycobiome
*Seawater/microbiology
Phylogeny
Biodiversity
DNA Barcoding, Taxonomic
DNA, Fungal/genetics
Ecosystem

@article {pmid40208265,
year = {2025},
author = {DiPietri, VT and Grady, ZS and Frost, AN and Stitzel, SE and Sivey, JD},
title = {Toilet Bowl Cleaning Tablets as Sources of Chlorine, Bromine, and Disinfection Byproducts in Wastewater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12026},
pmid = {40208265},
issn = {1520-5851},
abstract = {Commercial toilet bowl cleaning tablets were examined in laboratory systems to characterize their release of active halogens and their potential to form trihalomethanes (THMs) when combined with synthetic sewage. Active halogens (e.g., HOCl, HOBr, and reactive halamines) were quantified via derivatization with 1,3,5-trimethoxybenzene prior to analysis by liquid chromatography. The effects of several variables on halogen release profiles were examined, including pH, ionic strength, temperature, tank solution volume, flushing frequency, and tablet brand. Changes in pH resulted in modest or no appreciable changes in halogen release profiles. Release of active halogens increased as ionic strength decreased and as temperature increased. Tank volume, flushing frequency, and tablet brand had pronounced impacts on halogen release profiles. Maximum measured active chlorine and bromine concentrations in toilet tank water were 189 mg/L as Cl2 and 164 mg/L as Cl2, respectively. Active halogens persisted in toilet bowl water for >24 h. When toilet-tablet-treated water was combined with synthetic sewage, THMs formed at up to 219 ppb with bromine incorporation factors up to 2.86. Active halogens and highly brominated THMs released into wastewater from toilet tablets could have implications for downstream microbial ecology, septic system performance, and overall water quality.},
}

@article {pmid40206699,
year = {2025},
author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS},
title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.},
journal = {Polar biology},
volume = {48},
number = {2},
pages = {62},
pmid = {40206699},
issn = {0722-4060},
abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.},
}

@article {pmid40205489,
year = {2025},
author = {Soares, A and Rassner, SME and Edwards, A and Farr, G and Blackwell, N and Sass, H and Guglielmo, P and Schofield, D and Mitchell, AC},
title = {Hydrogeological and geological partitioning of iron and sulfur cycling bacterial consortia in subsurface coal-based mine waters.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf039},
pmid = {40205489},
issn = {1574-6941},
abstract = {Pyrite oxidation drives iron and sulfur availability across Earth's subsurface and is partly microbially mediated. Subsurface microbial communities accelerate this process at circumneutral pH directly by weathering pyritic surfaces and indirectly by causing changes to the surrounding microenvironment thereby further accelerating pyrite weathering. However, our understanding of community structure dynamics and associated biogeochemistry in Fe- and S-rich lithologies, e.g. pyritic coal, is limited. Here we present the first comprehensive regional and seasonal genus-level survey of bacterial groundwater communities in a pyritic coal-based aquifer in the South Wales Coalfield (SWC), using 16S rRNA gene amplicon sequencing. Seasonal changes in community structure were limited, suggesting limited influence of surface processes on subsurface communities. Instead, hydrogeologically distinct mine water blocks (MWB) and coal rank largely explained bacterial community structure variation across sites. Fe(II)-oxidising Betaproteobacteriales genera Gallionella and Sideroxydans dominated the bacterial communities across nine sites and seven MWBs, while three sites within a single MWB, were dominated by S-oxidising Epsilonbacteraeota genera Sulfuricurvum and Sulfurovum. The co-occurrence of pairs of Fe(II)- and S-oxidising bacterial genera suggests functional redundancy, which coupled with genus-specific morphologies and life strategies, indicates the importance of distinct environmental and ecological niches within the SWC groundwater at seasonal and regional scales.},
}

@article {pmid40205473,
year = {2025},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V},
title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf033},
pmid = {40205473},
issn = {1574-6941},
abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.},
}

@article {pmid40205253,
year = {2025},
author = {Dasgupta, M and Paul, R and Chowdhury, P and Mondal, S and Ahmed, J and Mukherjee, C and Das, S and Tribedi, P},
title = {Management of Enterococcus faecalis biofilms: a combinatorial approach with phytochemical.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40205253},
issn = {1678-4405},
support = {TNU/R&D/MP/2021/010//The Neotia University/ ; },
abstract = {The rapid emergence of antimicrobial resistance in Enterococcus faecalis infections was primarily due to their robust biofilm formation, highlighting the urgent need for meaningful strategies. Since combinatorial application of natural phytochemical often offer promising outcomes in dealing with microbial infections, present study indicated the pharmacological, antimicrobial and antibiofilm potential of combinatorial strategies of natural phytochemical involving cuminaldehyde and thymoquinone against E. faecalis. Towards this direction, in silico analysis suggested that both compounds could show favourable oral bioavailability and high GI absorption, with a considerable solubility and drug-likeness profiles. Furthermore, in vitro antimicrobial assay indicated that the minimum inhibitory concentrations (MIC) of cuminaldehyde and thymoquinone were found to be 500 µg/mL and 30 µg/mL, respectively against E. faecalis. Thereafter, the fractional inhibitory concentration (FIC) index score of 0.73 indicated an additive effect prevailed between cuminaldehyde and thymoquinone, enhancing their antimicrobial potential. Thereafter, sub-MIC doses of cuminaldehyde (40 µg/mL) and thymoquinone (8 µg/mL) were selected to assess their antibiofilm potential. Though the compounds were able to show antibiofilm activity separately, their combination was significantly more effective, reduced biofilm formation by approximately 80%, and decreased production of extracellular polymeric substance (EPS) and protein content by ~ 76% and ~ 70%, respectively. Further studies revealed that the antibiofilm activity of the test compounds could likely to be attributed to the accumulation of reactive oxygen species (ROS) and enhancement of membrane permeability. Taken together, all this experimental observation revealed that combination of these natural compounds could potentially improve the treatment outcomes of biofilm-borne infections of E. faecalis.},
}

@article {pmid40203032,
year = {2025},
author = {Timilsina, S and Iruegas-Bocardo, F and Jibrin, MO and Sharma, A and Subedi, A and Kaur, A and Minsavage, GV and Huguet-Tapia, JC and Klein-Gordon, J and Adhikari, P and Adhikari, TB and Cirvilleri, G and de la Barrera, LBT and Bernal, E and Creswell, TC and Doan, TTK and Coutinho, TA and Egel, DS and Félix-Gastélum, R and Francis, DM and Kebede, M and Ivey, ML and Louws, FJ and Luo, L and Maynard, ET and Miller, SA and Nguyen, NTT and Osdaghi, E and Quezado-Duval, AM and Roach, R and Rotondo, F and Ruhl, GE and Shutt, VM and Thummabenjapone, P and Trueman, C and Roberts, PD and Jones, JB and Vallad, GE and Goss, EM},
title = {Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013036},
doi = {10.1371/journal.ppat.1013036},
pmid = {40203032},
issn = {1553-7374},
abstract = {Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.},
}

@article {pmid40202691,
year = {2025},
author = {Pimentel, AC and Cesar, CS and Martins, AHB and Martins, M and Cogni, R},
title = {Wolbachia Offers Protection Against Two Common Natural Viruses of Drosophila.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {24},
pmid = {40202691},
issn = {1432-184X},
mesh = {Animals ; *Wolbachia/physiology ; *Drosophila melanogaster/virology/microbiology ; *Drosophila/virology/microbiology ; Symbiosis ; Female ; },
abstract = {Wolbachia pipientis is a maternally transmitted endosymbiont infecting more than half of terrestrial arthropod species. Wolbachia can express parasitic phenotypes such as manipulation of host reproduction and mutualist phenotypes such as protection against RNA virus infections. Because Wolbachia can invade populations by reproductive manipulation and block virus infection, it is used to modify natural insect populations. However, the ecological importance of virus protection is not yet clear, especially due to scarce information on Wolbachia protection against viruses that are common in nature. We used systemic infection to investigate whether Wolbachia protects its host by suppressing the titer of DMELDAV and DMelNora virus, two viruses that commonly infect Drosophila melanogaster flies in natural populations. Antiviral protection was tested in three systems to assess the impact of Wolbachia strains across species: (1) a panel of Wolbachia strains transfected into Drosophila simulans, (2) two Wolbachia strains introgressed into the natural host D. melanogaster, and (3) two native Wolbachia strains in their natural hosts Drosophila baimaii and Drosophila tropicalis. We showed that certain Wolbachia strains provide protection against DMelNora virus and DMELDAV, and this protection is correlated with Wolbachia density, which is consistent with what has been observed in protection against other RNA viruses. Additionally, we found that Wolbachia does not protect its original host, D. melanogaster, from DMELDAV infection. While native Wolbachia can reduce DMELDAV titers in D. baimaii, this effect was not detected in D. tropicalis. Although the Wolbachia protection-induced phenotype seems to depend on the virus, the specific Wolbachia strain, and the host species, our findings suggest that antiviral protection may be one of the mutualistic effects that helps explain why Wolbachia is so widespread in arthropod populations.},
}

Animals
*Wolbachia/physiology
*Drosophila melanogaster/virology/microbiology
*Drosophila/virology/microbiology
Symbiosis
Female

@article {pmid40201423,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J},
title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf049},
pmid = {40201423},
issn = {2730-6151},
abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.},
}

@article {pmid40200306,
year = {2025},
author = {Bindels, LB and Watts, JEM and Theis, KR and Carrion, VJ and Ossowicki, A and Seifert, J and Oh, J and Shao, Y and Hilty, M and Kumar, P and Hildebrand, F and Lovejoy, C and Wigley, P and Yu, K and Zhang, M and Zhang, T and Walter, J and Desai, MS and Huws, SA and Schriml, LM and Ravel, J and Fricke, WF and Eloe-Fadrosh, EA and Lee, CK and Clavel, T},
title = {A blueprint for contemporary studies of microbiomes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {95},
pmid = {40200306},
issn = {2049-2618},
mesh = {*Microbiota ; Humans ; },
abstract = {This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.},
}

*Microbiota
Humans

@article {pmid40197060,
year = {2025},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0327524},
doi = {10.1128/spectrum.03275-24},
pmid = {40197060},
issn = {2165-0497},
abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.},
}

@article {pmid40197052,
year = {2025},
author = {Liu, S and Ru, J and Guo, X and Gao, Q and Deng, S and Lei, J and Song, J and Zhai, C and Wan, S and Yang, Y},
title = {Altered precipitation and nighttime warming reshape the vertical distribution of soil microbial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124824},
doi = {10.1128/msystems.01248-24},
pmid = {40197052},
issn = {2379-5077},
abstract = {Soil depth determines microbial community composition. Yet, it remains largely unexplored how climate changes affect the vertical distribution of soil microbial communities. Here, we investigated the effects of altered precipitation and nighttime warming on microbial communities in the topsoils (0-20 cm) and subsoils (20-50 cm) of a temperate grassland in Inner Mongolia, China. As commonly observed under nutrient scarcity conditions, bacterial and fungal α-diversity and network complexity decreased with soil depth. However, protistan α-diversity and network complexity increased, which was attributed to less niche overlap and smaller body size. Strikingly, the slopes of linear regressions of microbial α-diversity/network complexity and soil depth were all reduced by altered precipitation. Microbial community composition was significantly influenced by both depth and reduced precipitation, and to a lesser extent by nighttime warming and elevated precipitation. The ribosomal RNA gene operon (rrn) copy number, a genomic proxy of bacterial nutrient demand, decreased with soil depth, and the percentages of positive network links were higher in the subsoil, supporting the "hunger game" hypothesis. Both reduced precipitation and nighttime warming decreased the rrn copy number in the subsoils while increasing the percentages of positive links, enhancing potential niche sharing among bacterial species. The stochasticity level of bacterial and fungal community assemblies decreased with soil depth, showing that depth acted as a selection force. Altered precipitation increased stochasticity, attenuating the depth's filtering effect and diminishing its linear relationship with microbial diversity. Collectively, we unveiled the predominant influence of altered precipitation in affecting the vertical distribution of soil microbial communities.IMPORTANCEUnderstanding how climate change impacts the vertical distribution of soil microbial communities is critical for predicting ecosystem responses to global environmental shifts. Soil microbial communities exhibit strong depth-related stratification, yet the effects of climate change variables, such as altered precipitation and nighttime warming, on these vertical patterns have been inadequately studied. Our research uncovers that altered precipitation disrupts the previously observed relationships between soil depth and microbial diversity, a finding that challenges traditional models of soil microbial ecology. Furthermore, our study provides experimental support for the hunger game hypothesis, highlighting that oligotrophic microbes, characterized by lower ribosomal RNA gene operon (rrn) copy numbers, are selectively favored in nutrient-poor subsoils, fostering increased microbial cooperation for resource exchange. By unraveling these complexities in soil microbial communities, our findings offer crucial insights for predicting ecosystem responses to climate change and for developing strategies to mitigate its adverse impacts.},
}

@article {pmid40195174,
year = {2025},
author = {Burazerović, J and Jovanović, M and Savković, Ž and Breka, K and Stupar, M},
title = {Finding the Right Host in the Darkness of the Cave-New Insights into the Ecology and Spatio-temporal Dynamics of Hyperparasitic Fungi (Arthrorhynchus nycteribiae, Laboulbeniales).},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {23},
pmid = {40195174},
issn = {1432-184X},
support = {451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; 451- 03- 66/2024- 03/200178; 451- 03- 65/2024- 03/ 200178//Ministry of Science, Technological Development and Innovation of the Republic of Serbia/ ; },
mesh = {Animals ; *Chiroptera/parasitology/microbiology ; *Caves/microbiology ; *Ascomycota/genetics/isolation & purification/physiology/classification ; *Diptera/microbiology ; Serbia ; Male ; Female ; Phylogeny ; },
abstract = {The aim of this study was to determine the presence of the hyperparasitic fungus Arthrorhynchus nycteribiae and to analyze its spatio-temporal pattern in the two bat flies (Penicillidia conspicua and P. dufourii) parasitizing on bats. We collected 612 samples of bat flies from 400 bats in 20 caves in the Central Balkans. Hyperparasite was identified based on morphological and molecular analyses of rDNA genes (LSU and SSU). A. nycteribiae was reported for the first time in Bosnia and Herzegovina and Montenegro, and confirmed in Serbia. Of the 20 sites examined, we found A. nycteribiae at 11 sites. The prevalence of A. nycteribiae infection in the bats examined was approximately 17%. Miniopterus schreibersii harbored the highest number of bat flies and was the only bat species hosting the infected bat flies of the species P. conspicua. Our results showed significant differences in infection patterns during the different seasons: the highest prevalence of bat flies with hyperparasitic fungi was found in the summer season (23%) and the lowest in spring (2%). Female bat fly hosts showed a significantly higher prevalence of infection than male bat flies. This study makes an important contribution to the knowledge of the distribution of A. nycteribiae and to the understanding of complex parasite-host relationships in the poorly studied areas of the Central Balkans.},
}

Animals
*Chiroptera/parasitology/microbiology
*Caves/microbiology
*Ascomycota/genetics/isolation & purification/physiology/classification
*Diptera/microbiology
Serbia
Male
Female
Phylogeny

@article {pmid40186763,
year = {2025},
author = {Huang, YD and Zhao, XL and Lin, Y and Ouyang, XM and Cheng, XS and Liang, LY and Huo, YN and Xie, GJ and Lin, JH and Jazag, A and Guleng, B},
title = {Mindin orchestrates the macrophage-mediated resolution of liver fibrosis in mice.},
journal = {Hepatology international},
volume = {},
number = {},
pages = {},
pmid = {40186763},
issn = {1936-0541},
support = {No. 81970460//National Natural Science Foundation of China/ ; No. 2023J011598//Natural Science Foundation of Fujian Province/ ; },
abstract = {BACKGROUND & AIMS: Liver disease that progresses to cirrhosis is an enormous health problem worldwide. The extracellular matrix protein Mindin is known to have immune functions, but its role in liver homeostasis remains largely unexplored. We aimed to characterize the role of Mindin in the regulation of liver fibrosis.

APPROACH & RESULTS: Mindin was upregulated in mice with carbon tetrachloride (CCl4) or thioacetamide (TAA)-induced liver fibrosis, and was primarily expressed in hepatocytes. Global Mindin knockout mice were generated, which were susceptible to liver fibrosis. Notably, Mindin failed to activate hepatic stellate cells directly; however, it played a role in promoting the recruitment and phagocytosis of macrophages, and caused a phenotypic switch toward restorative macrophages during liver fibrosis. Furthermore, Mindin was found to bind to the αM-I domain of CD11b/CD18 heterodimeric receptors. To further explore this mechanism, we created Mindin and CD11b double-knockout (DKO) mice. In DKO mice, phagocytosis was further reduced, and liver fibrosis was markedly exacerbated.

CONCLUSIONS: Mindin promotes the resolution of liver fibrosis and the Mindin/CD11b axis might represent a novel target for the macrophage-mediated regression of liver fibrosis.},
}

@article {pmid40186595,
year = {2025},
author = {Pérez, J and Boyero, L and Pearson, RG and Gessner, MO and Tonin, A and López-Rojo, N and Rubio-Ríos, J and Correa-Araneda, F and Alonso, A and Cornejo, A and Albariño, RJ and Anbalagan, S and Barmuta, LA and Boulton, AJ and Burdon, FJ and Caliman, A and Callisto, M and Campbell, IC and Cardinale, BJ and Carneiro, LS and Casas, JJ and Chará-Serna, AM and Chauvet, E and Colón-Gaud, C and Davis, AM and de Eyto, E and Degebrodt, M and Díaz, ME and Douglas, MM and Encalada, AC and Figueroa, R and Flecker, AS and Fleituch, T and Frainer, A and García, EA and García, G and García, PE and Giller, PS and Gómez, JE and Gonçalves, JF and Graça, MAS and Hall, RO and Hamada, N and Hepp, LU and Hui, C and Imazawa, D and Iwata, T and Junior, ESA and Landeira-Dabarca, A and Leal, M and Lehosmaa, K and M'Erimba, CM and Marchant, R and Martins, RT and Masese, FO and Maul, M and McKie, BG and Medeiros, AO and Middleton, JA and Muotka, T and Negishi, JN and Ramírez, A and Rezende, RS and Richardson, JS and Rincón, J and Serrano, C and Shaffer, AR and Sheldon, F and Swan, CM and Tenkiano, NSD and Tiegs, SD and Tolod, JR and Vernasky, M and Wanderi, EW and Watson, A and Yule, CM},
title = {Positive Feedback on Climate Warming by Stream Microbial Decomposers Indicated by a Global Space-For-Time Substitution Study.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70171},
doi = {10.1111/gcb.70171},
pmid = {40186595},
issn = {1365-2486},
support = {UAL18-RNM-B006-B//2014-2020 Operational Programme FEDER Andalusia/ ; IT951-16//Eusko Jaurlaritza/ ; IT1471-22//Eusko Jaurlaritza/ ; UIDB/04292/2020//Funda ç ão para a Ci ência e a Tecnologia, Portugal/ ; //UAL-HIPATIA/ ; },
mesh = {*Rivers/microbiology ; *Climate Change ; Temperature ; *Global Warming ; Plants/metabolism ; Carbon Cycle ; },
abstract = {Decomposition of plant litter is a key ecological process in streams, whose contribution to the global carbon cycle is large relative to their extent on Earth. We examined the mechanisms underlying the temperature sensitivity (TS) of instream decomposition and forecast effects of climate warming on this process. Comparing data from 41 globally distributed sites, we assessed the TS of microbial and total decomposition using litter of nine plant species combined in six mixtures. Microbial decomposition conformed to the metabolic theory of ecology and its TS was consistently higher than that of total decomposition, which was higher than found previously. Litter quality influenced the difference between microbial and total decomposition, with total decomposition of more recalcitrant litter being more sensitive to temperature. Our projections suggest that (i) warming will enhance the microbial contribution to decomposition, increasing CO2 outgassing and intensifying the warming trend, especially in colder regions; and (ii) riparian species composition will have a major influence on this process.},
}

*Rivers/microbiology
*Climate Change
Temperature
*Global Warming
Plants/metabolism
Carbon Cycle

@article {pmid40185870,
year = {2025},
author = {Ripoll, J and Stenger, PL and Nuñez, NF and Demenois, J and Stokes, A and Gourmelon, V and Dinh, K and Robert, N and Drouin, J and Mournet, P and Léopold, A and Read, J and Gardes, M and Maggia, L and Carriconde, F},
title = {Unexpected microbial diversity in new Caledonia's ultramafic ecosystems with conservation implications in a biodiversity hotspot.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11564},
pmid = {40185870},
issn = {2045-2322},
support = {IAC-SLN Research Collaboration N°DE2013-041//Société Le Nickel (SLN-Eramet Group)/ ; agreement CSF N°1PS2013-CNRT.IAC/BIOINDIC//CNRT "Nickel & son Environnement"/ ; },
mesh = {New Caledonia ; *Biodiversity ; *Soil Microbiology ; *Ecosystem ; Mycorrhizae/genetics/classification ; Conservation of Natural Resources ; Fungi/genetics/classification ; *Bacteria/genetics/classification ; },
abstract = {Soils harbour an incredible diversity of microorganisms that play crucial roles in ecosystem functioning. However, this biodiversity remains largely overlooked, with a poor understanding of how patterns form across landscapes. An eDNA metabarcoding approach was used to identify potential overarching patterns in fungal and bacterial communities from ultramafic ecosystems in New Caledonia, a renowned biodiversity hotspot. Our comprehensive analysis revealed several key findings, notably an important microbial diversity in the extreme environments of iron crust soils. Clear tendencies in phyla composition were also observed, with the fungal groups Ascomycota and Mucoromycota acting as potential indicators of land degradation (only in lateritic soils for Mucoromycota). For bacteria, Chloroflexi was characteristic of open vegetation, while Proteobacteria and Cyanobacteria were observed in higher relative abundances in the closed vegetation. The ectomycorrhizal fungal functional group was also found to be rich and unique, with a hypothetical endemism rate of 87%, and over-represented by the Cortinarius genus in rainforests and maquis (shrublands) dominated by ectomycorrhizal plants. Finally, each ultramafic Massif demonstrated a unique microbial community. Thus, our findings provide valuable insights into microbial ecology and emphasize the need for tailored conservation strategies for this biodiversity hotspot.},
}

New Caledonia
*Biodiversity
*Soil Microbiology
*Ecosystem
Mycorrhizae/genetics/classification
Conservation of Natural Resources
Fungi/genetics/classification
*Bacteria/genetics/classification

@article {pmid40184706,
year = {2025},
author = {He, L and Li, J and Tang, L and Wang, Y and Zhao, X and Ding, K and Xu, L and Gu, L and Cheng, S and Wei, YY},
title = {Applying side-stream gas recirculation to promote anaerobic digestion of food waste under ammonia stress: Overlooked impact of gaseous atmospheres on microorganisms.},
journal = {Water research},
volume = {281},
number = {},
pages = {123571},
doi = {10.1016/j.watres.2025.123571},
pmid = {40184706},
issn = {1879-2448},
abstract = {High ammonia concentrations can be toxic to microorganisms, leading to the accumulation of hydrogen (H2) and acids in anaerobic digestion (AD) system. In this study, a side gas recycling strategy (SGR), coupled with a primary reactor and a small side-stream reactor, which recirculates biogas between primary reactor and side reactor was employed to mitigate ammonia inhibition. This approach enabled the mesophilic side-stream gas recirculation system (SMGR) and the thermophilic side-stream gas recirculation system (STGR) to ultimately withstand ammonia stress levels of 2.5 g/L and 3.5 g/L, respectively, while maintaining lower hydrogen partial pressures. In contrast, the control group experienced system failure at an ammonia concentration of 2 g/L. Enzyme activity, microbial community, and metaproteomic analysis indicated that the side reactor enriched microorganisms with strong hydrogen-utilizing capacity, while the primary reactor was enriched with Methanosaeta. Furthermore, key pathways related to propionate metabolism, ABC transporters, and methane production were enhanced in the primary reactor, along with increased ATPase activity. The activity of key enzymes involved in AD was also significantly enhanced. This study enhances the understanding of the impact of gas atmosphere control on the microbial ecology and metabolic characteristics of AD system, providing valuable insights and practical guidance for the development of Engineering applications in this field.},
}