@article {pmid40818553,
year = {2025},
author = {Galinytė, D and Aroffu, M and Manconi, M and Žilius, M and Rysevaitė-Kyguolienė, K and Karosienė, J and Koreivienė, J and Briedis, V and Pauža, DH and Savickas, A and Ferrer, EE and Manca, ML and Savickienė, N},
title = {Cyano-phycocyanin loaded enriched transfersomes for enhanced topical skin delivery and antioxidant protection.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {126079},
doi = {10.1016/j.ijpharm.2025.126079},
pmid = {40818553},
issn = {1873-3476},
abstract = {This study aimed to develop and evaluate cyano-phycocyanin (C-PC)-loaded enriched transfersomes for topical application, improved skin delivery, and antioxidant protection. The main objective was to overcome the limitations associated with C-PC's instability and poor skin permeability due to its high molecular weight and hydrophilicity. Six formulations were prepared using an organic solvent-free two-step method: glycerol-enriched transfersomes (Gly-transfersomes),glycerol and cholesterol-enriched transfersomes (Gly-chol-transfersomes),hyaluronate-enriched transfersomes (Hyal-transfersomes),hyaluronate and cholesterol-enriched transfersomes (Hyal-chol-transfersomes),glycerol and hyaluronate-enriched transfersomes (Hyal-gly-transfersomes), anda combination of all three (Hyal-gly-chol-transfersomes). Empty vesicles were prepared via direct sonication, then C-PC was gently loaded using mild sonication in a temperature-controlled ultrasonic bath. All formulations demonstrated properties suitable for skin delivery, with mean diameters <115 nm, polydispersity indexes <0.2, and zeta potential below -30 mV. Cryo- transmission electron microscopy confirmed spherical, unilamellar or oligolamellar morphology. Gly- and Gly-chol-transfersomes exhibited the highest encapsulation efficiency (∼52 %) and remained stable for up to 8 months at 4 °C. Antioxidant activity of C-PC (∼23-27 μmol TE/g of dry C-PC) was confirmed via DPPH assay. Biological tests on HaCaT cells exposed to H2O2-induced oxidative stress showed ∼80 % cell viability after treatment with C-PC formulations, compared to ∼60 % in untreated cells, indicating cytoprotective activity. Ex vivo skin penetration studies revealed significantly higher C-PC accumulation in the epidermis especially for Gly- and Gly-chol-transfersomes versus aqueous C-PC. These findings confirm the potential of enriched transfersomes as effective carriers to improve the skin delivery and bioactivity of C-PC in antioxidant skin care formulations.},
}

@article {pmid40815942,
year = {2025},
author = {McDonagh, F and Ryan, K and Kovářová, A and Tumeo, A and Clarke, C and Cormican, M and Miliotis, G},
title = {Identification of blaESBL- and blaCARBA- Positive Multi-Drug Resistant Mixta calida Isolates from Distinct Human Hosts.},
journal = {International journal of medical microbiology : IJMM},
volume = {320},
number = {},
pages = {151669},
doi = {10.1016/j.ijmm.2025.151669},
pmid = {40815942},
issn = {1618-0607},
abstract = {OBJECTIVE: This study aimed to investigate the identification of blaCARBA-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.

METHODS: Two carbapenemase-producing M. calida isolates were received by the Galway Reference Laboratory Service in Ireland between June and July 2024. One isolate originated from a sputum sample, while the other was recovered from a routine screening rectal swab. Initial identification was performed using MALDI-ToF mass spectrometry, with genomic confirmation via 16S rRNA sequencing, digital DNA-DNA hybridization, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing was conducted using a MicroScan panel, following EUCAST and CLSI guidelines. Whole-genome sequencing, plasmid replicon typing, and antibiotic-resistance-gene and virulence-factor profiling were employed. Comparative analysis included all additional canonical M. calida genomes from NCBI database.

RESULTS: Both Irish isolates were taxonomically placed as M. calida and exhibited multidrug resistance against penicillins, cephalosporins, monobactams and ertapenem. The acquired genes blaKPC-3, blaOXA-9, and blaTEM-122 were detected on plasmid-borne contigs, indicating horizontal acquisition. Seven plasmid replicon types were shared between the two isolates. Both plasmid replicons and acquired antimicrobial-resistance-genes (ARGs) were seldomly identified across the species. Phylogenetic inference based on core genome analysis identified a monophyletic cluster, suggesting a single introductory event.

CONCLUSION: This study documents a dual occurrence of blaCARBA-positive M. calida in human colonisation and infection. The findings highlight the potential for horizontal-gene-transfer to drive the emergence of multidrug-resistant profiles in the species, underscoring the need for enhanced surveillance, diagnostic precision, and targeted infection control strategies to mitigate public health risks.

IMPACT STATEMENT: This study reports blaESBL and blaCARBA-positive multi-drug resistant Mixta calida isolates from distinct human hosts. Genomic analysis revealed the co-occurrence of plasmid-borne resistance genes blaKPC-3, blaOXA-9, and blaTEM-122. Species-wide phylogenetic analysis grouped the two isolates into a monophyletic cluster, suggesting a single introductory event.},
}

@article {pmid40815475,
year = {2025},
author = {Kondrotaite, Z and Petersen, J and Singleton, C and Peces, M and Petriglieri, F and Jensen, TBN and Sereika, M and Daugberg, AOH and Wagner, M and Dueholm, MKD and Nielsen, PH},
title = {Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0032225},
doi = {10.1128/msystems.00322-25},
pmid = {40815475},
issn = {2379-5077},
abstract = {Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera Candidatus Accumulibacter, Azonexus (formerly Dechloromonas), and Candidatus Phosphoribacter (formerly Tetrasphaera), with most studies focusing on Ca. Accumulibacter, primarily using lab-scale enrichment cultures. Although members from the three genera often co-exist in full-scale WWTPs, the metabolic capabilities and traits that determine the niche differentiation of the specific species are still unknown. We retrieved 214 high-quality metagenome-assembled genomes from a full-scale plant with phosphorus removal and examined the polyphosphate-related metabolic pathways using genome-resolved metatranscriptomics in the different process tanks in situ and by using short-term incubations ex situ. We observed the co-existence of nine uncultured PAO species from the three genera with clear niche differentiation in the utilization of different carbon sources and involvement in the denitrification process. Additionally, we observed several physiological differences among species of the same genus, indicating variations in niche specialization. This suggests that biological P removal and other processes in full-scale WWTPs are carried out by a complex and diverse PAO community that together ensures stable plant performance.IMPORTANCEThe current understanding of the ecology and physiology of polyphosphate-accumulating organisms (PAOs) is mostly based on Candidatus Accumulibacter, primarily studied in enriched lab-scale studies. Recent taxonomic reclassification revealed that the most studied Ca. Accumulibacter species are either not present or present in low abundance in full-scale wastewater treatment plants (WWTPs). This raises concerns that knowledge from lab-scale studies may not apply to species in full-scale plants. Additionally, the indication of a distinct PAO physiology in Candidatus Phosphoribacter compared to Ca. Accumulibacter and the other abundant PAO Ca. Azonexus poses further questions about the accuracy of the current PAO model. Here, we show that in full-scale plant species from Ca. Accumulibacter, Ca. Azonexus, and Ca. Phosphoribacter always co-exist, and they have distinct niche separations in terms of carbon source utilization and the use of electron acceptors. This co-existence and metabolic diversity indicate that a complex microbial community is crucial for efficient phosphorus removal in full-scale WWTPs.},
}

@article {pmid40815158,
year = {2025},
author = {Berman, HL and McKenney, EA and Roche, CE and Michalski, S and Kwon, SH and Weichel, E and Matson, A and Nichols, LM and Alvarado, S and Horvath, JE and Dunn, RR},
title = {Cooking-class style fermentation as a context for co-created science and engagement.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0266024},
doi = {10.1128/spectrum.02660-24},
pmid = {40815158},
issn = {2165-0497},
abstract = {Fermented foods have been consumed for thousands of years and have been used as a model system to study community succession and other ecological questions. Additionally, cooking classes offer opportunities to learn about food preparation and history. In the present study, scientists and chefs delivered cooking-class style workshops in which participants learned the recipes of one of three fermented foods and the microbial ecology within these foods. Participants prepared jars of chow chow, kimchi, or kombucha to set up experiments to study microbial community succession and pH changes. The fermented foods were also used to test the following hypotheses: that increasing the number of substrates results in increased alpha diversity, and that phylogenetically diverse substrates will lead to greater beta diversity among microbial communities. Microbial communities contained lactic and acetic acid bacteria described previously in fermented foods, and indicator species were identified for cabbage and radish substrates in kimchi. Finally, we qualitatively comment on the experience of developing workshops with chefs and the use of participatory science in these experiments.IMPORTANCEThe present study demonstrates the utility of using fermented foods as an inexpensive and effective tool to investigate ecological phenomena and engage the public in microbiology and ecology through cooking-class style workshops. We also model a creative, interdisciplinary collaboration between scientists and chefs.},
}

@article {pmid40812274,
year = {2025},
author = {Bermúdez, JR and Metian, M and Swarzenski, PW and Bank, MS and Bjorøy, Ø and Cajas, J and Bucheli, R and González-Muñoz, R and Lynch, J and Piguave, E and Vargas, N and Vilela, K and Calle, L and Borbor-Cordova, MJ and Gaibor, N},
title = {Marine microplastics on the rise in the Eastern Tropical Pacific: Abundance doubles in 11 years and a ten-fold increase is projected by 2100.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118437},
doi = {10.1016/j.marpolbul.2025.118437},
pmid = {40812274},
issn = {1879-3363},
abstract = {Plastic abundance in the ocean has increased systematically since the mid-20th century. Here we present a time-series dataset of microplastic abundance collected at several stations located in the Eastern Tropical Pacific Ocean off Ecuador from 2008 to 2018. The data reveals a significant and sustained increase in the abundance of microplastics over time across all sampling sites; this implies a homogeneous and sustained input, which likely also occurs at other coastal and marine ecosystems. Fiber strands were the most common microplastic observed, while polyethylene and polypropylene were the principal polymers identified by μFTIR analysis. A forecast model of the time-series data predicted that microplastics will be 3.2, 5.1 and 9.7 times more abundant in 2030, 2050 and 2100, respectively, relative to 2008 observations. These results provide insights into the decade-plus trend in microplastic abundance observed in coastal waters, which have important implications for future marine plastic pollution projections and associated ecosystem impacts.},
}

@article {pmid40812185,
year = {2025},
author = {Common, JE and Payne, RP},
title = {Microbial Makeover: Skin microbiome reset after stem cell transplantation.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1318-1320},
doi = {10.1016/j.chom.2025.07.014},
pmid = {40812185},
issn = {1934-6069},
abstract = {Inborn errors of immunity disrupt host-microbe interactions. In this issue of Cell Host & Microbe, Che et al.[1] examine DOCK8-deficient individuals undergoing stem cell transplantation and show that immune reconstitution rebalances the skin microbiome, underscoring the central role of immunity in shaping cutaneous microbial ecology.},
}

@article {pmid40812176,
year = {2025},
author = {Ramirez-Villacis, DX and Leon-Reyes, A and Pieterse, CMJ and Raaijmakers, JM},
title = {Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1241-1255},
doi = {10.1016/j.chom.2025.06.017},
pmid = {40812176},
issn = {1934-6069},
abstract = {Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced genetic diversity and fixed alleles for desirable traits, coinciding with changes in agricultural practices, particularly soil tilling, crop monocultures, and the (over)use of fertilizers and pesticides. The combined effects-collectively termed "domestication syndrome"-have contributed to the homogenization of soil and plant-associated microbial communities, reducing diversity and disrupting beneficial plant-microbiome alliances. Microbiome rewilding has uncovered ecological, genetic, and molecular principles underlying these depleted plant-microbiome partnerships. Studies have revealed ancestral microbial taxa enriched in wild crop relatives, plant genes, and metabolites critical for microbial recruitment, as well as the potential of reintroducing microbes to enhance nutrient uptake, pathogen resistance, and stress tolerance. These findings offer models for restoring such interactions in modern crops. We review the current state of crop microbiome rewilding and highlight how these discoveries are instrumental for designing resilient crop systems.},
}

@article {pmid40812095,
year = {2025},
author = {Rodríguez-González, L and Santás-Miguel, V and Alexandropoulou, S and Rousk, J},
title = {Effects of salinisation on Cu-contaminated vineyard soils: Assessment of changes in microbial communities and resistance to salt, Cu, and antibiotics.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118838},
doi = {10.1016/j.ecoenv.2025.118838},
pmid = {40812095},
issn = {1090-2414},
abstract = {Climate change increases the risk of soil salinisation in Southern European vineyards. In this study, six of those soils were experimentally salinised, half of which were contaminated with Cu, a widely used fungicide. Changes in soil microbiota were assessed, including bacterial and fungal growth, respiration, carbon use efficiency calculation, and microbial community phospholipid fatty acids composition. The study also investigated whether salinisation induced a shift in the bacterial community toward increased tolerance to salt, Cu, and the antibiotics tetracycline and vancomycin. Results showed that experimental salinisation decreased bacterial growth and respiration, increased fungal growth, and limited fungal, bacterial, and microbial biomass. These effects were strongest in soils with high initial Cu content. In such soils, tolerance to salt stress was more pronounced, and salt-induced tolerance to vancomycin was observed. In contrast, tolerances to Cu and tetracycline antibiotic were not significantly increased by either Cu or salt. Subsequently, the soils underwent leaching, and analyses were repeated. Most changes in microbial parameters and tolerances were reversed, with soil texture being a particularly influential factor. However, leaching caused Cu tolerance in soils that had been salinised and had high Cu content to be greater than in soils that had not been salinised, regardless of whether they had high or low Cu content. After leaching, vancomycin tolerance also became positively correlated with soil Cu content in soils with low Cu levels. This preliminary study explored salinisation effects on soils, revealing possible bacterial resistance linked to past conditions and microbial shifts. Further research is needed to broaden the dataset and explore the underlying mechanisms and microbial species involved.},
}

@article {pmid40811531,
year = {2025},
author = {Guo, D and Liu, Z and Raaijmakers, JM and Xu, Y and Yang, J and Erb, M and Zhang, J and Zhu, YG and Xu, J and Hu, L},
title = {Linalool-triggered plant-soil feedback drives defense adaptation in dense maize plantings.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6761},
pages = {eadv6675},
doi = {10.1126/science.adv6675},
pmid = {40811531},
issn = {1095-9203},
abstract = {High planting density boosts crop yields but also heightens pest and pathogen risks. How plants adapt their defenses under these conditions remains unclear. In this study, we reveal that maize enhances its defense in high-density conditions through a plant-soil feedback mechanism triggered by the leaf volatile linalool. Linalool activates jasmonate signaling in neighboring plants and promotes root exudation of benzoxazinoids, especially 2-(2-hydroxy-4,7-dimethoxy-1,4-benzoxazin-3-one)-β-d-glucopyranose (HDMBOA-Glc). These exudates in turn reshape the rhizosphere microbiome composition to favor growth of specific bacterial taxa that trigger broad-spectrum resistance, albeit at the cost of maize growth. This microbiome-driven feedback loop is governed by salicylic acid signaling. Our findings uncover intricate chemical signaling in high-density cropping, which is instrumental for improving soil health and designing sustainable strategies that balance the trade-off between plant growth and defense.},
}

@article {pmid40810014,
year = {2025},
author = {Fischer, MH and Rzepczynska, A and Kjøller, R},
title = {Taxonomic diversity in the global wheat phyllosphere mycobiome - a meta analysis.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1597807},
pmid = {40810014},
issn = {1664-462X},
abstract = {Wheat (Triticum aestivum L.) is a major crop grown on all continents. Due to environmental concerns, it is desirable to reduce the inputs of both chemical pesticides and inorganic fertilizers. However, yield reduction must be expected when switching to low-input systems. To mitigate such losses, the use of natural or introduced microbiomes may provide the key to maintaining sustainable yield. Phyllosphere fungi, both endophytic and phylloplane-associated, colonize aboveground plant structures, some of which have the potential to mitigate biotic and abiotic stressors. A first step toward realizing the potential of the wheat microbiome is to map the current knowledge on wheat phyllosphere fungi. This meta-analysis aims to map the diversity and abundance of fungal taxa associated with the wheat phyllosphere across global wheat-producing areas. To this end, we searched previous published literature and retrieved fungal community data from relevant studies. Retrieved studies included both culturing-based and metabarcoding amplicon sequence-based studies. We retrieved and analyzed 33 studies from five regions across the world, which differed greatly in their taxonomic composition. Across all regions, we found that while the majority of identified genera were unique to individual studies, some genera occurred across all five wheat growing regions, specifically Alternaria, Aspergillus, Bipolaris, Candida, Chaetomium, Cladosporium, Epicoccum, Fusarium, Nigrospora, Penicillium, Pyrenophora, Stemphylium and Trichoderma. Furthermore, we identified that while community composition differed between wheat growing regions, the identification method used was the most significant factor determining the depiction of community composition. We also highlight a lack of research in important wheat growing regions that are important for global wheat production. These considerations and other knowledge gaps are used to pinpoint future research.},
}

@article {pmid40809124,
year = {2024},
author = {Trego, A and Palmeiro-Sánchez, T and Graham, A and Ijaz, UZ and O'Flaherty, V},
title = {First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities.},
journal = {Frontiers in systems biology},
volume = {4},
number = {},
pages = {1375472},
pmid = {40809124},
issn = {2674-0702},
abstract = {Polyhydroxyalkanoates (PHA) are popular biopolymers due to their potential use as biodegradable thermoplastics. In this study, three aerobic sequencing batch reactors were operated identically except for their temperatures, which were set at 15 °C, 35 °C, and 48 °C. The reactors were subjected to a feast-famine feeding regime, where carbon sources are supplied intermittently, to enrich PHA-accumulating microbial consortia. The biomass was sampled for 16S rRNA gene amplicon sequencing of both DNA (during the enrichment phase) and cDNA (during the enrichment and accumulation phases). All temperatures yielded highly enriched PHA-accumulating consortia. Thermophilic communities were significantly less diverse than those at low or mesophilic temperatures. In particular, Thauera was highly adaptable, abundant, and active at all temperatures. Low temperatures resulted in reduced PHA production rates and yields. Analysis of the microbial community revealed a collapse of community diversity during low-temperature PHA accumulation, suggesting that the substrate dosing strategy was unsuccessful at low temperatures. This points to future possibilities for optimizing low-temperature PHA accumulation.},
}

@article {pmid40804956,
year = {2025},
author = {Idres, T and Ibrahim, NA and Lamara, A and Boudjellaba, S and Derguini, A and Basher, NS and Temim, S and Aleissa, MS and Chebloune, Y},
title = {Epidemiological Insights into Maedi-Visna Virus in Algeria: First National Seroprevalence Survey and Risk Factor Profiling in Sheep Herds.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {15},
pages = {},
pmid = {40804956},
issn = {2076-2615},
support = {IMSIU- DDRSP2502//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Maedi-visna virus (MVV), a small ruminant lentivirus causing chronic multisystemic disease in sheep, poses significant economic burdens due to reduced productivity and a lack of effective treatments. Despite its worldwide prevalence, epidemiological data from Algeria remain absent. This first national seroprevalence study aimed to elucidate MVV distribution, risk factors, and transmission dynamics in Algerian sheep herds. A cross-sectional survey of 1400 sheep across four regions (East, Center, West, South) was conducted, with sera analyzed via indirect ELISA (IDvet). Risk factors (geography, age, sex, breed, farming system) were evaluated using chi-square tests and Cramer's V. Overall seroprevalence was 9.07% (95% CI: 7.57-10.57), with significant variation by sex (females: 20.44% vs. males: 3.68%; p < 0.05), age (1-5 years: 6.86% vs. <1 year: 0.29%; p = 0.01), and region (Central: 3.36% vs. Eastern: 0.86%; p < 0.05). Notably, no association was found with breed or farming system (p ≥ 0.08), contrasting prior studies and suggesting region-specific transmission dynamics. Females exhibited heightened seropositivity, implicating prolonged herd retention and vertical transmission risks. Geographic disparities highlighted industrialized farming in central Algeria as a potential transmission amplifier. Strikingly, seronegative animals in high-prevalence herds hinted at genetic resistance, warranting further investigation. This study provides foundational insights into MVV epidemiology in North Africa, underscoring the need for targeted surveillance, ewe-focused control measures, and genetic research to mitigate transmission. The absence of prior national data elevates its significance, offering actionable frameworks for resource-limited settings and enriching the global understanding of SRLV heterogeneity.},
}

@article {pmid40803134,
year = {2025},
author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC},
title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128299},
doi = {10.1016/j.micres.2025.128299},
pmid = {40803134},
issn = {1618-0623},
abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.},
}

@article {pmid40802392,
year = {2025},
author = {Shaikenova, K and Issabekova, S and Sadenova, M and Omarova, K and Uskenov, R},
title = {Synergistic impact of integrated mechanical, physical, and chemical disinfection on microbial ecology and morphophysiological development in dairy calves.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e295880},
doi = {10.1590/1519-6984.295880},
pmid = {40802392},
issn = {1678-4375},
abstract = {The article presents the results of studies of the influence of the complex process of cleaning and disinfection of the dispensary using mechanical, physical and chemical methods on the growth and development of calves of the dairy period. The dispensary for calves is divided into two rooms, where there were animals of the control and experimental groups selected by the method of pairs of analogues in the same feeding and maintenance conditions. Studies before the treatment of rooms for calves showed a massive growth of bacilli and bacteria - 100%, mold fungi - 80%, yeast - 20%, actinomycetes - 80%. After processing the room for calves of the experimental group, the number of microorganisms during mechanical treatment, microbial contamination decreased by 31%, during physical treatment by 62%, and during chemical treatment by 95%. Monitoring of live weight, exterior features of calves showed that the live weight of calves of the experimental group of monthly calves averaged 58.9 kg, and the control group 58.6 kg, respectively. In the second month, the live weight of the experimental was 7.5 kg or 9.1% more than the control. And also for all body measurements, the experimental group exceeded the control group by an average of 10%. The results of the study of hematological parameters showed that in the experimental group they are all within the normal range, whereas in the control group the content of leukocytes is 13.2 * 109 liters, lymphocytes are 7.7 * 109 liters higher than normal, which indicates inflammatory processes in the body of calves.},
}

@article {pmid40800619,
year = {2025},
author = {van Eijnatten, AL and van Zon, L and Manousou, E and Bikineeva, M and Wubs, ERJ and van der Putten, WH and Morriën, E and Dutilh, BE and Snoek, LB},
title = {SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf036},
pmid = {40800619},
issn = {2730-6151},
abstract = {Correlation networks are commonly used to explore microbiome data. In these networks, nodes are microbial taxa and edges represent correlations between their abundances. As clusters of correlating taxa (co-abundance clusters) often indicate a shared response to environmental drivers, network visualization contributes to the system understanding. Currently, most tools for creating and visualizing co-abundance networks from microbiome data either require the researcher to have coding skills or are not user-friendly, with high time expenditure and limited customizability. Furthermore, existing tools lack a focus on the association between environmental drivers and the structure of the microbiome, even though many edges in correlation networks can be understood through a shared association of two taxa with the environment. For these reasons, we developed SpeSpeNet (Species-Species Network, https://tbb.bio.uu.nl/SpeSpeNet), a practical and user-friendly R-shiny tool to construct and visualize correlation networks from taxonomic abundance tables. The details of data preprocessing, network construction, and visualization are automated, require no programming ability for the web version, and are highly customizable, including associations with user-provided environmental data. Here, we present the details of SpeSpeNet and demonstrate its utility using three case studies.},
}

@article {pmid40800617,
year = {2025},
author = {Fuschi, A and Merlotti, A and Remondini, D},
title = {Microbiome data: tell me which metrics and I will tell you which communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf125},
pmid = {40800617},
issn = {2730-6151},
abstract = {In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Next-gen sequencing data challenge the use of Euclidean metrics for estimating proximity and correlation. Consequently, a variety of distance measures have been developed within ecological frameworks. In this study, we compare several of these metrics-including Bray-Curtis, Canberra, Jensen-Shannon, Hellinger, Euclidean, and Aitchison distances-demonstrating how the choice of metric can significantly influence the interpretation of microbial community structures. Among these, Aitchison distance specifically defined for compositional data shows markedly different behavior from the others, highlighting different features related to the data. We consider two real-world examples: the human gut microbiome sampled using 16S rRNA sequencing with multiple measurements for different patients (G-HMP2) and urban sewage environmental metagenomes collected over time at different sites through shotgun sequencing (E-WADES). We show that, for the same dataset-independently on the sequencing technique or on the sampling context-the community structure depends strongly on the choice of specific metrics. This can be explained by the mathematical properties of the chosen metrics and the specific characteristics of microbiome data, namely their high heterogeneity in species abundance. This provides clear insights into how distance metrics influence interpretation and assists in choosing the most appropriate one for the study objectives.},
}

@article {pmid40799503,
year = {2025},
author = {Parret, L and Simoens, K and De Vrieze, J and Smets, I},
title = {BIO-SPEC: An open-source bench-top parallel bioreactor system.},
journal = {HardwareX},
volume = {23},
number = {},
pages = {e00670},
pmid = {40799503},
issn = {2468-0672},
abstract = {The BIO-SPEC is an open-source, cost-effective, and modular bench-top bioreactor system designed for batch, sequencing batch, and chemostat cultivation. Featuring thermoelectric condensers to eliminate the need for a chiller, it ensures stable long-term operation. Controlled by a Raspberry Pi, the BIO-SPEC offers flexibility in headplate design, gas supply, and feeding strategies, making it a versatile alternative to high-cost commercial systems. This paper details the design, construction, and validation of the BIO-SPEC system, demonstrating its potential to advance microbiology and bioprocessing research through accessible and reliable hardware at a fraction of the cost of commercial systems.},
}

@article {pmid40797302,
year = {2025},
author = {Baborski, A and Barth, SA and Jung, EM and Bloos, F and Rödel, J and Löffler, B and Bauer, M and Busch, A},
title = {Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {56},
pmid = {40797302},
issn = {2730-6844},
abstract = {Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well. This leads to an imbalance of the gut microbiome. However, some bacteria can survive such treatment due to certain survival and resistance mechanisms. Not only antibiotic resistance mechanisms but also forming strong communities via biofilm formation promotes cell survival. Here, we investigated the properties of the isolate AT70PIP076 from a sepsis patient treated with piperacillin and tazobactam. After biochemical analysis and MALDI-TOF analysis, the strain was found to be Enterobacter cloacae. In addition to in vitro, antimicrobial susceptibility testing the genome was further investigated in situ regarding antibiotic resistance. Further live/dead staining was performed, and the biofilm formation was investigated using confocal laser microscopy (cLSM). The genome shows the presence of biofilm-associated genes EU554560, bcsABZC_AP010953, ehaB, KF662843, and crl. The understanding of the underlying mechanism of survival of potential pathogens might contribute to elucidate potential treatment options.ObjectivesGenomic analysis of a bacterium that can survive antibiotic treatment within the gut of an antibiotictreated patient to elucidate survival and resistance mechanisms.Data descriptionThe isolate AT70PIP076 was isolated in 2021 from feces collected from a patient treated with Piperacillin and tazobactam. Whole genome DNA was isolated using the Nextera DNA Flex microbial colony extraction protocol and the Nextera Flex DNA preparation kit according to the manufacturer's instructions. Following paired-end sequencing was performed on the MiSeq platform (Illumina, Inc., San Diego, CA, USA) using a 300-cycle MiSeq reagent kit and a read length of 151 bp. Contamination check and identification of 16 S RNA sequences was done by using ContESt16S. The genomic sequence contained 4,988,237 bp and the G + C content is represented at 54.80%. This genome and its associated data set will serve as a useful resource for further analyses.},
}

@article {pmid40797046,
year = {2025},
author = {Wei, L and Chen, S and Qin, Z and Pan, N and Lan, M and Zhang, T and He, R and Liang, H and Deng, W and Mo, C and Yu, K},
title = {Responses of the Coral Symbiont Cladocopium goreaui to Extreme Temperature Stress in Relatively High-Latitude Reefs, South China Sea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {88},
pmid = {40797046},
issn = {1432-184X},
abstract = {Global climate change has led to frequent extreme temperature events in oceans. Corals are susceptible to extreme high-temperature stress in summer and extreme low-temperature stress in winter in the relatively high-latitude reef areas of the South China Sea (SCS). The most abundant symbiotic coral Symbiodiniaceae in the higher-latitude reefs of the SCS is Cladocopium goreaui, predominantly associating with dominant coral hosts such as Acropora and Porites. However, to date, relatively few studies have focused on the response and mechanism of C. goreaui to the extreme high- and low-temperature stress. In this study, the responses and regulatory mechanisms of the dominant C. goreaui to extreme high- and low-temperature stress were investigated based on physiological indexes, transmission electron microscopy (TEM), and transcriptome analysis. The results showed that (1) under 34 °C heat stress, the disintegration of thylakoids triggered photosynthetic collapse in C. goreaui; survival is enabled through metabolic reprogramming that upregulates five protective pathways and redirects energy via pentose/glucuronate shunting to sustain ATP homeostasis, revealing a trade-off between damage containment and precision energy governance under thermal extremes. (2) Low temperature exposure induced suppression of maximum quantum yield (Fv/Fm), compounded by glutathione pathway inhibition, crippling ROS scavenging. The transcriptome results revealed that C. goreaui prioritizes gene fidelity maintenance under low temperature stress. These findings reveal that energy allocation trade-offs constitute the core strategy of C. goreaui temperature response: prioritizing energy maintenance under high-temperature stress, while safeguarding genetic fidelity at the expense of antioxidant defense under low-temperature stress.},
}

@article {pmid40796291,
year = {2025},
author = {Mohr, AE and Mach, N and Pugh, J and Grosicki, GJ and Allen, JM and Karl, JP and Whisner, CM},
title = {Mechanisms underlying alterations of the gut microbiota by exercise and their role in shaping ecological resilience.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf037},
pmid = {40796291},
issn = {1574-6976},
abstract = {The gut microbiota (GM) is a dynamic ecosystem intricately linked to human health, including metabolic, immune, endocrine, and gastrointestinal functions. Exercise is recognized as a significant modifier of this microbial ecosystem, yet the complexities of this relationship are underexplored. Here, we delve into the multifaceted interactions between structured physical activity and the GM, emphasizing the role of exercise-induced stressors in shaping microbial composition and function. Unique to our review, we discuss the acute effects of different forms of exercise-induced stress on the GM and explore how these responses may influence long-term adaptability, stability, and resilience. Furthermore, we address critical junctures in microbial dynamics leading to shifts between different stable states. Finally, we explore the implications of host-controlled factors such as diet, exercise training, and nutritional supplementation in modulating the microbial community in the gut to optimize athletic performance. We conclude that while the potential to harness the synergistic effects of exercise-induced stressors, dietary interventions, and microbial adaptations appears promising, current evidence remains preliminary, highlighting the need for additional targeted research to guide future strategies that manipulate the GM for optimal health and athletic performance.},
}

@article {pmid40795952,
year = {2025},
author = {Pluer, BD and Travis, J},
title = {The Digestive Microbiome Diversity of the Least Killifish, Heterandria formosa, and Its Implications for Host Adaptability to Varying Trophic Levels.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70164},
pmid = {40795952},
issn = {1758-2229},
support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; },
abstract = {Symbiotic microbes, in associations with aquatic hosts, aid in the acquisition of nutrients, breakdown xenobiotics, and contribute to immune system function. If associations with microbial communities facilitate host adaptation to different ecosystems, understanding the important ecological factors that act as drivers of differences among conspecific populations' microbiomes can help conservation efforts to promote beneficial interactions between fish and their microbiome for freshwater fish species facing rapid environmental changes. Here we describe the microbial communities in the gut of a freshwater fish, Heterandria formosa, in spring habitats using 16S rRNA sequencing. We quantified microbiota composition and diversity among springs ranging from oligotrophic to near eutrophic to determine the extent to which the microbiota are associated with different environmental conditions. We found higher microbial richness at sites with lower nutrient load stress. At more eutrophic sites, we detected the potential for increased metabolic capacity for pollutant degradation in the associated microbiota. We noted greater phylogenetic similarity between more environmentally similar sites, supporting previous evidence that the microbiota of freshwater fish is influenced by site water chemistry. Our findings bring to light microbial taxa and pathways that might play critical roles in the bioremediation of stressful environmental conditions.},
}

@article {pmid40795673,
year = {2025},
author = {Cano, NO and Borrego, CM and Radjenovic, J},
title = {Irreversible inactivation of multidrug-resistant Gram-positive bacteria using S-functionalized graphene sponge anode.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124300},
doi = {10.1016/j.watres.2025.124300},
pmid = {40795673},
issn = {1879-2448},
abstract = {Graphene sponges functionalized with sulfur were employed as anodes and coupled with N-doped graphene sponge cathodes for electrochemical inactivation of a Gram-positive multidrug-resistant bacterium Enterococcus gallinarum in drinking water. The application of 43.5 A m[-2] resulted in 2.3 log removal of E. gallinarum in one-pass, flow-through mode, at 2.7 kWh m[-3] of energy demand. In the case of non-functionalized graphene sponge electrode, 1.8 log removal of E. gallinarum required 3.8 kWh m[-3]. Moreover, no bacterial regrowth was measured in any of the experiments conducted during storage of the treated samples for 16 h. Indeed, the storage of samples led to an additional 1 log removal for the S-functionalized graphene sponge anode, somewhat higher compared with the 0.7 log removal observed for the non-functionalized electrode. To further decrease the energy consumption and exploit the capacitance of graphene, the flow-through system was operated with intermittent current. Application of 43.5 A m[-2] in an intermittent mode, led to a similar, 2.4 log removal of E. gallinarum but with a significantly reduced energy consumption, from 2.7 with continuous current to 1.8 kWh m[-3]. Scanning electron microscopy analyses of the inactivated bacteria confirmed the irreversible damage to the cell walls due to low-voltage electroporation that co-occurred with the presence of abundant cellular debris resulting from the leakage of intracellular material. Using two sequential reactors equipped with the S-doped graphene sponge anode and N-doped graphene sponge cathode operated at 43.5 A m[-2] of anodic current density resulted in an overall 5.8 log removal of E. gallinarum (including storage) from drinking water, and at the energy consumption of 5.4 kWh m[-3] (i.e., electric energy per order of 0.94 kWh m[-3]). Overall, this study demonstrated the feasibility of using an S-functionalized graphene sponge anode for chlorine-free electrochemical inactivation of a multidrug resistant Gram-positive bacterium from low conductivity drinking water.},
}

@article {pmid40795332,
year = {2025},
author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW},
title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf171},
pmid = {40795332},
issn = {1751-7370},
abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.},
}

@article {pmid40795028,
year = {2025},
author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf078},
pmid = {40795028},
issn = {1574-6968},
abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.},
}

@article {pmid40793771,
year = {2025},
author = {Bhandari, R and Wong, AC-N and Lee, JC and Boyd, A and Shelby, K and Ringbauer, J and Kang, DS},
title = {Microbiome composition and co-occurrence dynamics in wild Drosophila suzukii are influenced by host crop, fly sex, and sampling location.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0260824},
doi = {10.1128/spectrum.02608-24},
pmid = {40793771},
issn = {2165-0497},
abstract = {Microbial control of insect pests offers promising alternatives to traditional pesticides. However, the microbial communities and factors influencing these communities within insect hosts remain poorly understood. This study examined the whole-body bacterial communities in wild Drosophila suzukii, commonly known as spotted wing Drosophila (SWD). Fly samples were collected from two farms growing wild Himalayan blackberries near blueberry crops, one blackberry farm, and one elderberry farm across four locations in the United States. Our analyses showed significant differences in microbial communities in flies across various host crops and sampling locations. We identified co-occurring bacterial genera, dominated by Gluconobacter and Morganella, and the overall microbiome was distinct from those found in laboratory-grown flies. Our findings suggest that the host crop, sex of the fly, sampling location, and their interactions play a crucial role in shaping microbial communities in SWD, indicating the influence of various ecological interactions. While no significant differences in microbiome composition were observed between male and female flies, network analysis revealed distinct sex-specific microbial co-occurrence patterns. Female flies displayed a more stable and interconnected microbial network than male flies, suggesting that sex-specific factors might influence bacterial interactions. Interestingly, the most abundant microbial taxa were not necessarily the most connected in the networks, showing that less abundant taxa may also play a significant role in shaping the fly microbiome. This study underscores the complexity of microbial ecology in SWD and highlights the necessity of considering these dynamics when developing pest management strategies in agriculture.IMPORTANCEStudies on the microbiome of spotted wing Drosophila (SWD) have primarily focused on laboratory-reared flies in controlled environments and fed artificial diets. In contrast, we examined microbial communities in wild flies from various host crops across four locations in the United States. Our findings show that these communities are distinct from those of laboratory-grown flies and are influenced by the fly's sex, host crop, geographical location, and their interactions. Our study identifies several dominant bacterial genera across samples, suggesting that these may represent the core microbial communities in wild SWD. Given that microbial communities influence physiological activities in SWD, manipulating the microbiome may have either a positive or negative impact on insect fitness. This study enhances our understanding of microbial dynamics in understudied wild SWD populations, emphasizing the importance of these dynamics in effective integrated pest management strategies.},
}

@article {pmid40791242,
year = {2025},
author = {Song, HC and Elsheikha, H and Yang, T and Cong, W},
title = {Global spillover of land-derived microbes to Ocean hosts: Sources, transmission pathways, and one health threats.},
journal = {Environmental science and ecotechnology},
volume = {27},
number = {},
pages = {100603},
pmid = {40791242},
issn = {2666-4984},
abstract = {Terrestrial pathogens are increasingly being detected in marine organisms, raising concerns about ecosystem sustainability, biodiversity loss, and threats to human health. Over the past two decades, reports of microbial contaminants crossing from land to sea have increased, suggesting shifts in pathogen ecology driven by environmental changes and human activities. Pathogens originating on land can spread, adapt, and persist in marine environments, infecting a wide range of hosts and potentially re-entering terrestrial environments. Despite growing recognition of this issue, a comprehensive understanding of the distribution, diversity, and transmission pathways of these pathogens in marine ecosystems remains limited. In this Review, we provide a global analysis of terrestrial pathogen contamination in marine animal populations. Drawing from pathogen detection data across 66 countries, we used phylogenetic methods to infer land-to-sea transmission routes. We identified 179 terrestrial pathogen species, including 38 bacterial, 39 viral, 80 parasitic, and 22 fungal species, in 20 marine host species. Terrestrial pathogens are not only widespread but also highly diverse in marine ecosystems, highlighting the frequency and ecological significance of cross-system microbial exchange. By revealing the scale and complexity of land-to-sea pathogen flow, we show that climate change, pollution, and other anthropogenic pressures may intensify pathogen spillover events, with potential feedback effects on terrestrial systems. This highlights the urgent need for integrated surveillance and policy frameworks acknowledging the interconnectedness of terrestrial and marine health. Our work advocates a One Health approach to microbial ecology, stressing the need to safeguard marine and human populations from emerging cross-system threats.},
}

@article {pmid40790855,
year = {2025},
author = {Xie, R and Yu, H and Wang, Y and Leung, KY and Habimana, O},
title = {Synergistic effects of sodium acetate and calcium on structure and function in multispecies biofilms.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2025.2545940},
pmid = {40790855},
issn = {1029-2454},
abstract = {This investigation scrutinizes the manner in which sodium acetate (SA) and calcium cations (Ca[2+]) independently and collaboratively affect biofilm development. Confocal microscopy revealed that SA (1 mM) increased biofilm biovolume (5.5-fold) and thickness by enhancing microbial growth, while Ca[2+] (1.5 mM) stabilized the matrix via EPS crosslinking. Combined, SA and Ca[2+] synergistically boosted biovolume (1.5-fold) and thickness (21.3 µm) compared to SA alone. 16S rRNA sequencing showed SA-enriched Actinobacteriota (11%) and exopolysaccharide-producing Brevifollis, whereas Ca[2+] improved surface coverage (22.3%). Functional predictions linked SA to purine degradation and Ca[2+] to fatty acid oxidation, aligning with EPS modifications. These findings highlight how carbon sources and divalent cations collaboratively shape biofilm resilience, offering insights for biofilm management in environmental, industrial, and medical settings where SA and Ca[2+] gradients exist.},
}

@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples-such as soil, water, air, and the human body-metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the wide-ranging applications of metagenomics in environmental monitoring, including sample collection, high-throughput sequencing, and data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will be crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}

@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}

Swine
*Wastewater/microbiology
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Metagenome/genetics
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40788124,
year = {2025},
author = {Ferreira, J and Rediers, H},
title = {Draft genome sequences of 25 candidate biocontrol bacteria against Phytophthora cactorum.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0050225},
doi = {10.1128/mra.00502-25},
pmid = {40788124},
issn = {2576-098X},
abstract = {To provide a biocontrol solution for managing the phytopathogen Phytophthora cactorum, bacteria were tested for antagonistic activity in vitro and in planta. This paper presents the draft genomes of 25 candidate biocontrol organisms, providing a solid foundation to decipher the underlying mechanisms of their antagonistic activity.},
}

@article {pmid40787310,
year = {2025},
author = {S, S and Nayak, P and Pal, K},
title = {Exploring the Microbial Peptides Derived from the Human Gut Microbiota to Regulate Class B GPCRS Using an In Silico Approach.},
journal = {ACS omega},
volume = {10},
number = {30},
pages = {33270-33287},
pmid = {40787310},
issn = {2470-1343},
abstract = {Class B G-protein coupled receptors (GPCRs) are significant therapeutic recipients in cardiovascular, neurological, and metabolic diseases. The human gut microbiome is a complex microbial ecology recently identified as a possible source of bioactive peptides that control host physiological functions. Candidate peptides were found using advanced bioinformatics tools including sequence homology analysis, structure modeling, and molecular docking. These peptides were then evaluated for their binding affinity and potential functional regulation of the GPCR activity. Molecular dynamics simulations offered additional insights regarding the stability and interaction diversity of peptide-receptor complexes, highlighting receptor conformational state of G-protein interaction. The findings identify unique microbial peptides capable of influencing class B GPCR function, providing important insights into microbiome-host interactions and therapeutic potential. This study emphasizes the gut microbiome's previously untapped potential as a source of GPCR modulators, opening up new avenues for microbiome-driven therapy approaches for metabolic and endocrine disorders.},
}

@article {pmid40783766,
year = {2025},
author = {Son, SJ and Wu, X and Roh, HW and Cho, YH and Hong, S and Nam, YJ and Hong, CH and Park, S},
title = {Distinct gut microbiota profiles and network properties in older Korean individuals with subjective cognitive decline, mild cognitive impairment, and Alzheimer's disease.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {187},
pmid = {40783766},
issn = {1758-9193},
support = {HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; HR21C1003//the Ministry of Health and Welfare, Republic of Korea/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2019-NR040055//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; RS-2023-00208567//National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT/ ; },
abstract = {BACKGROUND: The gut microbiota may influence cognitive function via the gut-brain axis. This study aimed to investigate the gut microbiota profiles of 346 older Korean individuals with subjective cognitive decline but no symptoms (SCD), mild cognitive impairment (MCI), or Alzheimer’s disease (AD).

METHODS: Participants aged an average of 72.3 years underwent the profiling of cognitive function, amyloid-β (Aβ) deposition, apolipoprotein E (APOE) genetic variants, depression status, nutrition, and lifestyles. Human fecal bacterial FASTA/Q data (SCD, n = 24; MCI, n = 246; AD, n = 76) were processed using Quantitative Insights Into Microbial Ecology 2 (QIIME2) tools. Operational taxonomic units (OTUs) and their counts were assigned with the National Center for Biotechnology Information Basic Local Alignment Search Tool (BLAST). Machine learning models (random forest and XGBoost) identified key bacterial taxa differentiating groups.

RESULTS: Redundancy analysis revealed associations between gut microbiota composition and cognitive function, age, gender, nutritional status, and body mass index. All three groups shared 71 common bacterial genera with distinct taxonomic profiles across cognitive states. The AD group uniquely harbored Hominisplanchenecus and Lentihominibacter, while the SCD group exclusively contained Anaerosacchariphilus and Anaerobutyricum. Phascolarctobacterium was shared between the AD and MCI groups, and Anaerostipes between the MCI and SCD groups. The SCD group showed significantly elevated Bifidobacterium catenulatum, Anaerobutyricum hallii, and Anaerostipes hadrus. Network analysis demonstrated greater microbial community complexity in the SCD group compared to the MCI and AD groups. Gut bacteria correlated with depression, Aβ deposition, APOE status, and cognitive scores.

CONCLUSIONS: This study identified distinct gut microbiota profiles associated with different stages of cognitive impairment in older Korean adults. The observed associations between gut bacterial composition and cognitive function, neurodegeneration biomarkers, and related clinical factors suggest potential relationships that warrant further investigation. These findings contribute to the growing understanding of gut-brain interactions in cognitive aging.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13195-025-01820-9.},
}

@article {pmid40781093,
year = {2025},
author = {Kojima, CY and Henson, MW and Coelho, JT and Lanclos, VC and Bañuelas, D and Thrash, JC},
title = {Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1388},
pmid = {40781093},
issn = {2052-4463},
support = {OCE-1931113//National Science Foundation (NSF)/ ; Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Faculty Innovation Research Award//USC | Wrigley Institute for Environmental Studies, University of Southern California (USC Wrigley Institute for Environmental Studies)/ ; },
mesh = {Gulf of Mexico ; *Metagenome ; *Water Microbiology ; },
abstract = {Coastal and estuarine systems are hotspots of microbial diversity, activity, and biogeochemical cycling. Despite their importance, we have few comprehensive datasets of microbial populations across space and time from these ecosystems. To improve our understanding of these systems, we generated metagenomes averaging 46 M reads per sample (nearly 389 Gbp total) from four coastal/estuarine locations in the northern Gulf of Mexico across seven timepoints spanning nine months. Using standard methodology combined with a unique assembly and binning approach called subtractive iterative assembly (SIA), we generated 1,313 non-redundant metagenome-assembled genomes (MAGs) with 5% contamination or less and at least 75% completeness. We produced approximately a third of the MAGs through SIA. Actinobacteria and Proteobacteria were represented most. We recovered MAGs of great ecological significance including SAR11, Marine Group I (Thaumarcheaota), Marine Group II Euryarchaeota, SAR324, and Asgardarchaeota. We describe both our methodology using the SIA approach as well as the 28 metagenomes and 1,313 MAGs that provide a rich spatiotemporal dataset with which to study coastal and estuarine microbiology.},
}

Gulf of Mexico
*Metagenome
*Water Microbiology

@article {pmid40780001,
year = {2025},
author = {Grimard-Conea, M and Reyes, EV and Marchand-Senécal, X and Faucher, SP and Prévost, M},
title = {In situ dosing of monochloramine in a hospital hot water system results in drastic microbial communities changes.},
journal = {The Science of the total environment},
volume = {997},
number = {},
pages = {180204},
doi = {10.1016/j.scitotenv.2025.180204},
pmid = {40780001},
issn = {1879-1026},
abstract = {Understanding changes in microbial composition under selective pressures is crucial to assess the emergence of resistant taxa and the survival of drinking water-associated pathogens. This study evaluated the impact of in situ monochloramine disinfection in a hospital hot water system on bacterial (16S rRNA gene amplicon sequencing, 112 samples) and eukaryotic communities (18S rRNA gene amplicon sequencing, 103 samples), and on general microbial measurements (180 samples), including adenosine triphosphate (ATP) and flow cytometry counts. After the onset of treatment, ATP decreased by 1.2- and 3.5-fold, and total cell counts (TCC) dropped by 1- and 2-log at distal and system sites, respectively. During the dosage interruption (27-day), TCC rebounded to pre-treatment levels, but viability percentage decreased, indicating that cells were predominantly damaged. Low-use sites (e.g., showerheads) showed elevated ATP (>15 pg/mL) and TCC (10[5]-10[6] cells/L). Monochloramine drastically altered bacterial and eukaryotic communities. Alpha-diversity showed increased amplicon sequence variant richness during treatment, driven by new, low-abundant taxa, while Beta-diversity revealed distinct shifts in community composition over time, with tight or looser clusters corresponding to each treatment phase. Post-treatment, temporal and spatial heterogeneity was evident across distal sites, while elevated temperatures, consistent flow, and higher monochloramine concentrations in the hot water system resulted in more uniform communities at system sites. Additionally, the persistence of potential pathogenic strains belonging to Legionella and Mycobacterium genera highlights the value of comprehensive risk assessments. These findings emphasize the need to understand microbial shifts under disinfection stress and their public health implications, offering new insights into how treatment interventions shape microbial ecology and pathogen dynamics.},
}

@article {pmid40779244,
year = {2025},
author = {Sung, J and Choi, DH and Lee, Y and Kim, JH and Shin, HH and Kim, YE and Choi, JH and Noh, JH and Gobler, CJ and Park, BS},
title = {Temperature-Driven Intraspecific Diversity in Paralytic Shellfish Toxin Profiles of the Dinoflagellate Alexandrium pacificum and Intragenic Variation in the Saxitoxin Biosynthetic Gene, sxtA4.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {87},
pmid = {40779244},
issn = {1432-184X},
support = {20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20163MFDS641//Ministry of Food and Drug Safety/ ; 20210469//Ministry of Oceans and Fisheries/ ; 20210469//Ministry of Oceans and Fisheries/ ; RS-2021-KS211530//Ministry of Oceans and Fisheries/ ; RS-2023-00209356//Ministry of Science and ICT, South Korea/ ; },
mesh = {*Dinoflagellida/genetics/metabolism/growth & development ; *Saxitoxin/biosynthesis/genetics ; *Genetic Variation ; Temperature ; Harmful Algal Bloom ; Phylogeny ; },
abstract = {Alexandrium pacificum, a globally distributed dinoflagellate, is well-known for causing harmful algal blooms and producing Paralytic Shellfish Toxins (PSTs), a threat to marine life and human health. The frequency and intensity of Alexandrium blooms have increased in recent decades, driven, in some cases, by increasing temperatures. Here, we investigated the temperature-dependent (15 °C, 20 °C, 25 °C, and 30 °C) growth rates and paralytic shellfish toxin profiles of eight A. pacificum strains while concurrently examining differences in sequences of the saxitoxin biosynthetic gene, sxtA4. While maximum cell densities were lowest at 30 °C, toxin production per cell was highest at higher temperatures that inhibited growth, with greater diversity of toxin analogs peaking at 30 °C, as confirmed by the higher Shannon's diversity index obtained for the toxin profiles with the increasing temperatures. Furthermore, genetic analysis of the sxtA4 gene showed that greater genetic diversity-quantified by nucleotide diversity (π) ranging from 9.91 to 30.21 across strains-was positively correlated with this wider array of toxin analogs (Shannon's diversity index; p < 0.0001). Conserved regions within the gene were identified, suggesting that these regions may play important structural or functional roles in the saxitoxin biosynthetic pathway. These findings highlight the role of temperature, genetic diversity, and sxtA4 conserved regions in influencing toxin production and profiles in Alexandrium. Further research into the genetic mechanisms underlying saxitoxin biosynthesis will improve our understanding of Alexandrium's adaptability to changing temperatures. Such insights are essential for effective ecosystem management and safeguarding public health.},
}

*Dinoflagellida/genetics/metabolism/growth & development
*Saxitoxin/biosynthesis/genetics
*Genetic Variation
Temperature
Harmful Algal Bloom
Phylogeny

@article {pmid40778431,
year = {2025},
author = {Maillard, F and Beatty, BH and Geisen, S and Lara, E and Kennedy, PG},
title = {Secondary Decomposers Meet Their Predators: Decomposition Stage and Substrate Quality Jointly Structure Microbial Brown Food Webs During Fungal Necromass Decay.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70060},
doi = {10.1111/mec.70060},
pmid = {40778431},
issn = {1365-294X},
support = {DEB #2038293//National Science Foundation/ ; },
abstract = {Mycelial residues, also known as fungal necromass, represent a substantial fraction of soil organic matter (SOM) pools in terrestrial ecosystems worldwide. Although microbial decomposers are increasingly recognised as key drivers of fungal necromass carbon stock formation, the diversity and composition of their microbial predators-and the roles these predators play in mediating fungal necromass decomposition-have not been explored to date. To address this gap, we produced fungal necromass of varying biochemical quality from Hyaloscypha bicolor and decomposed it in forest topsoil in Minnesota, USA, to investigate how microbial decomposer (bacteria and fungi) and predator (protists and nematodes) communities differ between soil and necromass. We also examined whether microbial predators influence the abundance of fungal necromass decomposers and affect necromass decomposition rates. Over two sampling times (4 and 12 weeks), necromass exhibited rapid early mass loss followed by reduced decay, with a higher stabilised mass in high melanin necromass. Microbial abundances were higher in necromass than in surrounding soil, especially in low melanin necromass. Community composition of both decomposers and their predators differed between soil and necromass and shifted markedly with necromass quality and decomposition stage. Predator community composition was linked to bacterial and fungal abundances at both early and late stages of decay and was marginally associated with decomposition rates. We conclude that fungal necromass acts as a microbial 'hotspot' not only for decomposers but also for their predators. These findings highlight the importance of microbial predator-decomposer interactions to better understand the formation of fungal-derived SOM.},
}

@article {pmid40775374,
year = {2025},
author = {Krasenbrink, J and Hanson, BT and Weiss, AS and Borusak, S and Tanabe, TS and Lang, M and Aichinger, G and Hausmann, B and Berry, D and Richter, A and Marko, D and Mussmann, M and Schleheck, D and Stecher, B and Loy, A},
title = {Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {184},
pmid = {40775374},
issn = {2049-2618},
support = {10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.55776/COE7//Austrian Science Fund/ ; 10.55776/DOC69//Austrian Science Fund/ ; 10.3030/101205556//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 395357507 "SFB1371"//Deutsche Forschungsgemeinschaft/ ; EvoGutHealth, 865615/ERC_/European Research Council/International ; 503-5-7-06.712_00 and 503-5-7-06.709_00//Germany Centre for Infection Research/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; Mice, Inbred C57BL ; Feces/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Male ; Hydrogen Sulfide/metabolism ; Female ; },
abstract = {BACKGROUND: Sulfoquinovose (SQ) is a green-diet-derived sulfonated glucose and a selective substrate for a limited number of human gut bacteria. Complete anaerobic SQ degradation via interspecies metabolite transfer to sulfonate-respiring bacteria produces hydrogen sulfide, which has dose- and context-dependent health effects. Here, we studied potential SQ degradation by the mammalian host and the impact of SQ supplementation on human and murine gut microbiota diversity and metabolism.

RESULTS: [13]CO2 breath tests with germ-free C57BL/6 mice gavaged with [13]C-SQ were negative. Also, SQ was not degraded by human intestinal cells in vitro, indicating that SQ is not directly metabolized by mice and humans. Addition of increasing SQ concentrations to human fecal microcosms revealed dose-dependent responses of the microbiota and corroborated the relevance of Agathobacter rectalis and Bilophila wadsworthia in cooperative degradation of SQ to hydrogen sulfide via interspecies transfer of 2,3-dihydroxy-1-propanesulfonate (DHPS). Similar to the human gut microbiome, the genetic capacity for SQ or DHPS degradation is sparsely distributed among bacterial species in the gut of conventional laboratory mice. Escherichia coli and Enterocloster clostridioformis were identified as primary SQ degraders in the mouse gut. SQ and DHPS supplementation experiments with conventional laboratory mice and their intestinal contents showed that SQ was incompletely catabolized to DHPS. Although some E. clostridioformis genomes encode an extended sulfoglycolytic pathway for both SQ and DHPS fermentation, SQ was only degraded to DHPS by a mouse-derived E. clostridioformis strain.

CONCLUSIONS: Our findings suggest that SQ is solely a nutrient for the gut microbiota and not for mice and humans, emphasizing its potential as a prebiotic. SQ degradation by the microbiota of conventional laboratory mice differs from the human gut microbiota by absence of DHPS degradation activity. Hence, the microbiota of conventional laboratory mice does not fully represent the SQ metabolism in humans, indicating the need for alternative model systems to assess the impact of SQ on human health. This study advances our understanding of how individual dietary compounds shape the microbial community structure and metabolism in the gut and thereby potentially influence host health. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Humans
Mice
Mice, Inbred C57BL
Feces/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Male
Hydrogen Sulfide/metabolism
Female

@article {pmid40774531,
year = {2025},
author = {Morales, MLP and Capurro, L and Bordert, F and Chenia, H and Alonso, C and Bentos, FR and Boccardi, L and Brugnoli, E and They, NH and Agostini, VO and Leães Pinho, GL},
title = {Evaluating macrophyte extracts as eco-friendly antifouling additives for freshwater made-man structures: a field assessment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126952},
doi = {10.1016/j.envpol.2025.126952},
pmid = {40774531},
issn = {1873-6424},
abstract = {Biofouling on artificial aquatic surfaces yields substantial economic losses and operational challenges. Traditional antifouling strategies often rely on synthetic chemical coatings, which have harmful environmental impacts, thus environmentally sustainable solutions, such as natural antifouling compounds are increasingly being sought. Extracts derived from the aquatic macrophytes Pontederia crassipes and Typha domingensis have demonstrated potential antifouling properties in preliminary studies; however, their efficacy under natural field conditions remains unverified. This study is the first to evaluate the antifouling potential of these macrophyte extracts when incorporated with epoxy coatings in a natural freshwater environment (Salto Grande Reservoir, Uruguay River). Stainless steel substrates were treated with 2.5, 5, and 10 g L[-1] of lyophilized macrophyte extracts combined with epoxy and compared to uncoated and epoxy-coated controls. Over a 165-hour period, biofouling was assessed via chlorophyll levels, bacterial counts, macro-organism presence and attachment and taxonomic diversity. Analytical techniques, including gas and liquid chromatography, along with Fourier transform infrared spectroscopy, were employed to identify active compounds in extracts. The P. crassipes extract at 5 and 10 g L[-1] exhibited superior antifouling efficacy compared to T. domingensis. Coatings with P. crassipes significantly reduced bacterial colonization (37%), algae growth (for different photosynthetic pigments), fungal presence, and macro-organism attachment (not found), while promoting the occurrence of opportunistic taxa less conducive to fouling. The observed antifouling activity may be attributed to specific chemical compounds, including long-chain hydrocarbons and phenolic derivatives, identified in the extracts. The study findings demonstrate the field antifouling efficacy of macrophyte extracts incorporated with epoxy coatings, highlighting P. crassipes as a particularly promising, sustainable antifouling candidate. Its high biomass availability and ease of cultivation enhance its potential for industrial-scale development as natural antifouling agents. This work provides critical insights into developing eco-friendly antifouling coatings that minimize environmental impact while maintaining efficacy in biofouling control being the first study to prove in a natural environment the antifouling potential of these macrophytes.},
}

@article {pmid40771314,
year = {2025},
author = {Wang, L and Wang, H and Wu, J and Ji, C and Wang, Y and Gu, M and Li, M and Yang, H},
title = {Gut microbiota and metabolomics in metabolic dysfunction-associated fatty liver disease: interaction, mechanism, and therapeutic value.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1635638},
pmid = {40771314},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolomics ; Dysbiosis ; Liver/metabolism/pathology ; Animals ; *Fatty Liver/metabolism/therapy/microbiology ; *Non-alcoholic Fatty Liver Disease/metabolism/therapy/microbiology ; Biomarkers ; Precision Medicine ; },
abstract = {The global epidemic of Metabolic dysfunction-associated fatty liver disease (MAFLD) urgently demands breakthroughs in precision medicine strategies. Its pathogenesis centers on the cascade dysregulation of the gut microbiota-metabolite-liver axis: microbial dysbiosis drives hepatic lipid accumulation and fibrosis by suppressing short-chain fatty acid synthesis, activating the TLR4/NF-κB inflammatory pathway, and disrupting bile acid signaling. Metabolomics further reveals characteristic disturbances including free fatty acid accumulation, aberrantly elevated branched-chain amino acids (independently predictive of hepatic steatosis), and mitochondrial dysfunction, providing a molecular basis for disease stratification. The field of precision diagnosis is undergoing transformative innovation-multi-omics integration combined with AI-driven analysis of liver enzymes and metabolic biomarkers enables non-invasive, ultra-high-accuracy staging of fibrosis. Therapeutic strategies are shifting towards personalization: microbial interventions require matching to patient-specific microbial ecology, drug selection necessitates efficacy and safety prediction, and synthetically engineered "artificial microbial ecosystems" represent a cutting-edge direction. Future efforts must establish a "multi-omics profiling-AI-powered dynamic modeling-clinical validation" closed-loop framework to precisely halt MAFLD progression to cirrhosis and hepatocellular carcinoma by deciphering patient-specific mechanisms.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Metabolomics
Dysbiosis
Liver/metabolism/pathology
Animals
*Fatty Liver/metabolism/therapy/microbiology
*Non-alcoholic Fatty Liver Disease/metabolism/therapy/microbiology
Biomarkers
Precision Medicine

@article {pmid40770074,
year = {2025},
author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A},
title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1159},
pmid = {40770074},
issn = {2399-3642},
mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; },
abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.},
}

Humans
*Aging
*Biometry/methods
*Deep Learning
*Gastrointestinal Microbiome
*Principal Component Analysis/methods
*Skin Microbiome
Software Validation

@article {pmid40768991,
year = {2025},
author = {Li, J and Sun, Q and Wang, S and Lei, K},
title = {Environmental gradients drive the ecological dynamics of bacterioplankton in the East China Sea based on eDNA metabarcoding.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118539},
doi = {10.1016/j.marpolbul.2025.118539},
pmid = {40768991},
issn = {1879-3363},
abstract = {Understanding the interactions between environmental factors and ecological processes that shape bacterioplankton is a fundamental goal of microbial ecology. With increasing urbanization and environmental stress, marine coastal ecosystems necessitate careful evaluation of microbial dynamics. Environmental DNA was utilized to investigate bacterioplankton in the coastal waters of the East China Sea, revealing distinct environmental gradients that significantly shape bacterioplankton community composition. Distinct spatial differentiation of microbial assemblages was observed along these gradients, primarily driven by nitrogen-related nutrient dynamics. Furthermore, shifts in coastal habitats have driven a transition in community assembly processes from predominantly stochastic to deterministic mechanisms. Changes in environmental conditions also increase the vulnerability of offshore bacterioplankton networks, compromising their stability. These findings emphasize the critical role of environmental gradients in forming coastal microbial community composition, offering valuable insights for advancing marine ecosystem management, biodiversity conservation, and sustainable environmental policies.},
}

@article {pmid40767881,
year = {2025},
author = {Fowler, AE and McFrederick, QS and Adler, LS},
title = {Correction to: Pollen Diet Diversity does not Affect Gut Bacterial Communities or Melanization in a Social and Solitary Bee Species.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {86},
doi = {10.1007/s00248-025-02573-6},
pmid = {40767881},
issn = {1432-184X},
}

@article {pmid40767488,
year = {2025},
author = {Harris, JE and Bledsoe, RB and Guha, S and Omari, H and Crandall, SG and Burghardt, LT and Couradeau, E},
title = {The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0045825},
doi = {10.1128/msystems.00458-25},
pmid = {40767488},
issn = {2379-5077},
abstract = {UNLABELLED: Plant-beneficial microbes have great potential to improve sustainability in agriculture. Still, managing beneficial microbes is challenging because the impact of microbial dormancy on community assembly across the soil, rhizosphere, and endosphere is poorly understood. We address this gap with the first documented use of Biorthogonal Non-Canonical Amino Acid Tagging (BONCAT) to probe active microbes in the soil-to-root gradient. Using nodule-forming legume Trifolium incarnatum, we confirmed that BONCAT is suitable for labeling endospheric microbes with microscopy. Next, we coupled BONCAT to Flow Cytometer Activated Cell Sorting (FACS) and 16S rRNA amplicon sequencing to probe patterns of microbial activity and the structure of the active microbial community across the soil, rhizosphere, root, and nodule with a native soil microbial community. As expected, we found 10 times higher microbial activity in the endosphere than in the rhizosphere or bulk soil, likely due to increased plant resources. Finally, we revealed that microbial activity in the rhizosphere was significantly associated with successful endosphere colonization, more so than microbial abundance alone. This last finding has implications for the development of microbial inoculants, suggesting colonizing plant roots is linked to a microbe's ability to overcome dormancy once deployed in the soil.

IMPORTANCE: Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important for successful plant colonization. We use a novel microbial activity probing technique for the first time on and in plant roots, and with it, we observe microbes increased in activity 10× inside plant tissues compared to the soil, likely in response to plant-produced resources. In complex, native microbial communities, we observe that microbes that are active and abundant are more likely to colonize plant roots successfully than just abundant microbes. Our research shows that plants could be leveraged to promote a distinct active microbial community from the native soil, a discovery that has the potential to improve sustainability in agriculture.},
}

@article {pmid40766845,
year = {2025},
author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS},
title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562965},
pmid = {40766845},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation & purification ; *Virus Diseases/virology ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.

METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.

RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.

CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Bronchoalveolar Lavage Fluid/virology
*Virome/genetics
*Viruses/genetics/classification/isolation & purification
Female
Male
Middle Aged
Adult
Aged
*Lung/virology
*Blood/virology
Bacteria/classification/genetics/isolation & purification
*Virus Diseases/virology

@article {pmid40766442,
year = {2025},
author = {Rathod, D and Silverman, JD},
title = {PCR Bias Impacts Microbiome Ecological Analyses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40766442},
issn = {2692-8205},
support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; },
abstract = {Polymerase Chain Reaction (PCR) is a critical step in amplicon-based microbial community profiling, allowing the selective amplification of marker genes such as 16S rRNA from environmental or host-associated samples. Despite its widespread use, PCR is known to introduce amplification bias, where some DNA sequences are preferentially amplified over others due to factors such as primer-template mismatches, sequence GC content, and secondary structures. Although these biases are known to affect transcript abundance, their implications for ecological metrics remain poorly understood. In this study, we conduct a comprehensive evaluation of how PCR-bias influences both within-samples (α -diversity) and between-sample (β -diversity) analyses. We show that perturbation-invariant diversity measures remain unaffected by PCR bias, but widely used metrics such as Shannon diversity and Weighted-Unifrac are sensitive, with their values varying according to the true community composition. To address this, we provide theoretical and empirical insight into how PCR-induced bias varies across ecological analyses and community structures, and we offer practical guidance on when bias-correction methods should be applied. Our findings highlight the importance of selecting appropriate diversity metrics for PCR-based microbial ecology workflows and offer guidance for improving the reliability of diversity analyses.},
}

@article {pmid40765478,
year = {2025},
author = {Stevens-Green, R and Chénard, C and Mordret, S and MacKinnon, J and Robicheau, BM and LaRoche, J},
title = {Organellar Genomes of Three Globally Important Nanoplanktonic Diatoms Refine Their Taxon-Specific Distribution and Succession Patterns in the Northwest Atlantic.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {5},
pages = {e70033},
pmid = {40765478},
issn = {1550-7408},
support = {A1-019982//NRC-ACRD Internal Project/ ; OCN-500//NRC Ocean Program Grant and Contribution/ ; (RGPIN/04060-2021)//NSERC Discovery Grant awarded to JLR/ ; //CFREF (NWA BCP) awarded to JLR/ ; },
mesh = {*Diatoms/genetics/classification ; Atlantic Ocean ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Chloroplast ; *Phytoplankton/genetics/classification ; DNA Barcoding, Taxonomic ; },
abstract = {Nanoplanktonic diatoms (2-20 μm) are a significant yet historically understudied component of marine ecosystems. We investigated three recently isolated nanoplanktonic diatoms from the Northwest Atlantic Ocean (NWA): Minidiscus spinulatus, Mediolabrus comicus, and Minidiscus trioculatus. Using Oxford Nanopore sequencing, we assembled and annotated their complete chloroplast and mitochondrial genomes. Pangenome analyses revealed that Minidiscus species consistently clustered more closely with select Thalassiosira species, whereas M. comicus formed a sister clade with Skeletonema. Circularized chloroplast genomes allowed us to characterize the full-length 16S ribosomal RNAs for each isolate, thereby leading to higher resolution of these taxa in preexisting 16S metabarcoding data. During our study, M. spinulatus was primarily restricted to the Bedford Basin. In contrast, both M. trioculatus and M. comicus had larger geographic ranges extending to the Labrador Sea, and in the case of M. comicus, to the Canadian Arctic Gateway. Weekly metabarcoding from the coastal Bedford Basin, N.S., Canada (2014-2022), revealed a seasonal succession of nanoplanktonic taxa, with Minidiscus trioculatus dominating in the early months, followed by M. comicus and M. spinulatus. Our results highlight the critical value of phytoplankton isolations and organelle genomics for expanding our understanding of the diversity and biogeography of nanoplanktonic diatoms.},
}

*Diatoms/genetics/classification
Atlantic Ocean
*Genome, Mitochondrial
Phylogeny
RNA, Ribosomal, 16S/genetics
*Genome, Chloroplast
*Phytoplankton/genetics/classification
DNA Barcoding, Taxonomic

@article {pmid40765283,
year = {2025},
author = {Zhang, Y and Wu, H and Wu, X and Grossart, HP and Lorke, A},
title = {Revisiting Cyanobacteria-Temperature Dynamics: Intraspecific Competition and Trait Diversity as Keys to Predicting Harmful Algal Blooms under Climate Change.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04849},
pmid = {40765283},
issn = {1520-5851},
abstract = {Cyanobacterial harmful algal blooms are expanding spatiotemporally, with an increasing occurrence of cold-water cyanobacterial blooms (CWCBs), intensifying ecological and water quality challenges. While abiotic drivers have been identified as contributors to CWCBs, the role of biotic factors─particularly the adaptation induced by the shifts in intraspecific trait distributions─in this process remains largely unexplored. Here, we tested the hypothesis that the thermal history of cyanobacteria affects their thermal adaptations by reshaping the distribution of optimum growth temperature (Topt). Using a trait-based phytoplankton model coupled with a one-dimensional lake model, we simulated cyanobacteria dynamics over 364 days in a large, eutrophic, shallow lake recently experiencing CWCBs. The model demonstrated that Topt diversification promotes cold-adapted strains, leading to CWCBs while mitigating summer blooms. This occurs because the thermal response of Topt-diverse populations depends on their Topt distribution, which is determined by past temperature sequence, allowing Topt-diverse populations to retain a 'memory' of temperatures preceding summer. Consequently, increased summer temperatures inhibit these cold-adapted populations, challenging the prevailing cyanobacteria-temperature paradigm, which suggests that high temperatures universally favor cyanobacteria. These findings reveal that models assuming fixed traits may misrepresent cyanobacterial dynamics under climate change, highlighting the necessity of incorporating trait diversity into predictive frameworks for improved forecasting and to support adaptive lake management strategies.},
}

@article {pmid40762371,
year = {2025},
author = {Li, X and Chen, Y and Gao, Z and Liu, X and Song, Z and Gao, F and Wang, S and Yu, C and Sun, L and Huang, Y and Zheng, L and Wang, G and Sun, Y and Li, J and Yang, X and Bao, Y},
title = {TSP50 in Neural Stem Cells Regulates Aging-Related Cognitive Decline and Neuroinflammation by Altering the Gut Microbiota.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70188},
doi = {10.1111/acel.70188},
pmid = {40762371},
issn = {1474-9726},
support = {GZC20240236//Postdoctoral Fellowship Program of CPSF/ ; 20230204067YY//the Science and Technology Development Program of Jilin Province/ ; 135131002//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Aging is a process of gradual decline in physical and cognitive function and is a major risk factor for mortality. Despite the increasing number of relevant studies, the mechanisms regulating the aging process have not been fully elucidated. Genetic factors have long been recognized as key factors in controlling the rate of aging. Testes-specific protease 50 (TSP50) has been shown to be involved in the regulation of embryonic development and intestinal homeostasis, but its role in the regulation of aging remains unclear. Here, we showed that TSP50 expression was reduced in the hippocampus of both aged humans and mice. TSP50 deficiency in neural stem cells (NSCs) drove accelerated aging in mice, characterized by exacerbated age-related cognitive impairments and significantly elevated neuroinflammation. Notably, aged mice with NSCs-specific knockout of TSP50 exhibited impaired intestinal mucosal barriers, dysbiosis of gut microbiota, and a marked reduction in the production of short-chain fatty acids (SCFAs). Restoring gut microbial ecology using fecal microbiota transplantation (FMT) and overexpressing TSP50 successfully alleviated aging-associated cognitive decline and neuroinflammation. Taken together, our study suggests that TSP50 plays a critical role in the aging process and identifies gut microbiota as a pivotal mediator of TSP50's influence on age-related cognitive decline and neuroinflammation. These findings highlight the potential therapeutic value of targeting TSP50 and gut microbiota for aging, offering insights into aging mechanisms and interventions for aging-related neurodegenerative diseases.},
}

@article {pmid40761850,
year = {2025},
author = {Cai, S and Lin, L and Cai, Y and Wang, C and Lin, Y and Zhou, J and Zhou, F and Chen, M},
title = {Phase angle associates with severity and mortality in acute-on-chronic liver failure.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1541795},
pmid = {40761850},
issn = {2296-858X},
abstract = {BACKGROUND: Acute-on-chronic liver failure is characterized by acute hepatic decompensation and high short-term mortality, thereby necessitating prompt prognostic assessment. Although phase angle (PhA) has been established as a biomarker in chronic diseases, its prognostic significance in ACLF remains unclear.

METHODS: In this study, we evaluated PhA in 78 ACLF patients and compared the results with those of two control groups: 45 patients with chronic hepatitis B infection but normal liver function, and 51 patients with abnormal liver function who did not meet the ACLF criteria. Upon hospital admission, comprehensive laboratory parameters were obtained, and PhA measurements were conducted to explore the associations among PhA, organ dysfunction indices, and established prognostic scoring systems for predicting 90-days outcomes in ACLF patients.

RESULTS: Our analysis demonstrated that ACLF patients exhibited significantly lower PhA values compared with both control groups. Notably, non-survivors within 90 days had substantially lower PhA levels than survivors. Additionally, patients with complications, including hepatic encephalopathy, ascites, gastrointestinal bleeding, and infection, showed markedly lower PhA values than those without such complications. Moreover, the combination of PhA with the Chronic Liver Failure - Sequential Organ Failure Assessment (CLIF-SOFA) score enhanced the predictive accuracy of 90-days mortality in ACLF patients.

CONCLUSION: Phase angle serves as a valuable biomarker for evaluating ACLF severity and predicting short-term mortality, potentially offering a novel approach to risk stratification in ACLF management.},
}

@article {pmid40761338,
year = {2025},
author = {Zhao, Y and Chen, J and Qin, Y and Yuan, J and Yu, Z and Ma, R and Liu, F and Zhao, J},
title = {Linking Short-Chain Fatty Acids to Systemic Homeostasis: Mechanisms, Therapeutic Potential, and Future Directions.},
journal = {Journal of nutrition and metabolism},
volume = {2025},
number = {},
pages = {8870958},
pmid = {40761338},
issn = {2090-0724},
abstract = {Short-chain fatty acids (SCFAs), pivotal metabolites derived from microbial fermentation of dietary fiber, serve as critical modulators of glucose and lipid metabolism. Dysregulation of SCFA levels, often stemming from inadequate fiber intake or dysbiosis of SCFA-producing microbiota, correlates with heightened susceptibility to diverse pathologies, including autoimmune disorders, metabolic syndromes, and malignancies. Emerging evidence underscores the pleiotropic roles of SCFAs in orchestrating gut and systemic homeostasis, positioning them as novel therapeutic candidates for immune dysregulation, inflammatory conditions, and transplant rejection. This review synthesizes current knowledge on SCFA biosynthesis, absorption dynamics, and their multifaceted regulatory mechanisms, spanning epigenetic modulation, G protein-coupled receptor (GPR) signaling, and immune cell crosstalk. We further elucidate their therapeutic potential in clinical contexts, emphasizing their capacity to recalibrate immune responses, suppress chronic inflammation, and mitigate oncogenesis. By integrating recent advances in microbiome research and translational applications, this work highlights the imperative for precision interventions targeting SCFA pathways to bridge the gap between microbial ecology and clinical innovation.},
}

@article {pmid40760940,
year = {2025},
author = {Petrullo, L and Webber, Q and Raulo, A and Boutin, S and Lane, JE and McAdam, AG and Dantzer, B},
title = {Social Microbial Transmission in a Solitary Mammal.},
journal = {Ecology letters},
volume = {28},
number = {8},
pages = {e70186},
pmid = {40760940},
issn = {1461-0248},
support = {//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; 0515849//Division of Environmental Biology/ ; 2010726//Division of Environmental Biology/ ; 2338394//Division of Environmental Biology/ ; },
mesh = {Animals ; *Sciuridae/microbiology/physiology ; *Social Behavior ; *Gastrointestinal Microbiome ; Territoriality ; Population Density ; Behavior, Animal ; Male ; Female ; },
abstract = {Microbial transmission is hypothesised to be a major benefit of sociality, facilitated by affiliative behaviours such as grooming and communal nesting in group-living animals. Whether microbial transmission is also present in animals that do not form groups because territoriality limits interactions and prevents group formation remains unknown. Here, we investigate relationships among gut microbiota, population density and dynamic behavioural and spatial measures of territoriality in wild North American red squirrels (Tamiasciurus hudsonicus). Periods of high population density predicted population-level gut microbial homogeneity but individual-level diversification, alongside changes in obligately anaerobic, non-sporulating taxa indicative of social transmission. Microbial alpha-diversity increased with more frequent territorial intrusions, and pairs with stronger intrusion-based social associations had more similar gut microbiota. As some of the first evidence for social microbial transmission in a solitary system, our findings suggest that fluctuations in density and territorial behaviours can homogenise and diversify host microbiomes among otherwise non-interacting animals.},
}

Animals
*Sciuridae/microbiology/physiology
*Social Behavior
*Gastrointestinal Microbiome
Territoriality
Population Density
Behavior, Animal
Male
Female

@article {pmid40760525,
year = {2025},
author = {Deng, M and Chen, W and Wang, X},
title = {Characteristics of gut microbiota in longevity populations in China and its relationship with healthy aging.},
journal = {Medicine},
volume = {104},
number = {31},
pages = {e43633},
pmid = {40760525},
issn = {1536-5964},
support = {He Technology 202217//Hezhou Science and Technology Bureau/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; China ; *Longevity/physiology ; Male ; Middle Aged ; Female ; Aged ; Adult ; *Healthy Aging/physiology ; Feces/microbiology ; Aged, 80 and over ; Child ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; },
abstract = {This study aimed to investigate the differences in gut microbiota diversity and compositional characteristics between long-lived individuals (≥90 years) and individuals at different life stages (children, young and middle-aged adults, and elderly), in order to provide a foundational basis for microbial interventions in healthy aging. An observational cohort design was adopted, recruiting healthy participants divided into 4 age groups: children, young and middle-aged adults, elderly, and long-lived individuals. Fecal samples were collected and subjected to high-throughput 16S rRNA gene sequencing. The alpha diversity, beta diversity, and community structural differences of the gut microbiota were assessed, and representative microbial taxa were identified using LEfSe analysis. The long-lived group exhibited significantly higher species richness and diversity (Chao1 and Shannon indices, P < .05), with a more balanced and stable microbial structure. At the phylum level, the long-lived group had the highest relative abundance of Firmicutes and the lowest of Bacteroidetes. At the genus level, lactic acid bacteria such as Lactobacillus were significantly enriched. LEfSe analysis indicated that lactic acid bacteria-related taxa may serve as characteristic markers of this population. The gut microbiota of long-lived individuals exhibits higher ecological stability and a distinctive composition, which may be associated with healthy aging. These findings provide preliminary evidence for the relationship between longevity and gut microbial ecology and suggest that structural characteristics of these microbial communities may be involved in the process of healthy aging, offering a basis for future exploration of microbial intervention strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
China
*Longevity/physiology
Male
Middle Aged
Female
Aged
Adult
*Healthy Aging/physiology
Feces/microbiology
Aged, 80 and over
Child
Young Adult
RNA, Ribosomal, 16S/genetics
Cohort Studies

@article {pmid40759677,
year = {2025},
author = {Huang, J and Wu, F and Xiao, Y and Ye, M and Wu, X and Chen, H and Xu, Q},
title = {Deciphering nitrogen-driven microbial succession in an anaerobic membrane bioreactor-coupled A[2]/O ecological system for the remediation of industrial swine wastewater.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28422},
pmid = {40759677},
issn = {2045-2322},
support = {2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2024R1031001, 2024R1031003 and 2022R1032003//Basic Public Welfare Research Program of Fujian Province of China/ ; 2023S0003//Fuzhou Science and Technology Bureau spark project/ ; Q20194303//Scientific Research Items Foundation of Hubei Educational Committee/ ; YY202446//Jingchu University of Technology Ph.D. Startup Fund/ ; },
mesh = {*Bioreactors/microbiology ; Animals ; *Wastewater/microbiology/chemistry ; Swine ; *Nitrogen/metabolism ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; Biological Oxygen Demand Analysis ; Water Purification/methods ; Membranes, Artificial ; Phosphorus ; Industrial Waste ; Biodegradation, Environmental ; },
abstract = {Rapid expansion of industrial pig farming has intensified existing challenges in the management of nutrient-rich wastewater, characterized by high organic loads (chemical oxygen demand (COD): 15,000-30,000 mg/L) and ammonium nitrogen (NH4[+]-N): 800-2,500 mg/L) concentrations. In this study, an integrated treatment system with a combination of a high-density polyethylene (HDPE) membrane-based anaerobic membrane bioreactor and an anoxic/aerobic/oxidation pond (A[2]/O) was developed for swine wastewater remediation. The system achieved exceptional remediation efficiency, removing 99.4, 99.5, 95.4, 92.8, and 97.9% of COD, biochemical oxygen demand (BOD), NH4[+]-N, total phosphorus (TP), and suspended solids (SS), respectively, with the anoxic and aerobic (A[2]) phases contributing to removal of 62.5, 60.9, 80.9, 94.6% of COD, BOD, TP, and SS, respectively. Microbial community analysis revealed process-specific dynamics, including Firmicutes enrichment (8.52 ± 3.33 to 10.81 ± 0.39%) in anaerobic stages and Nitrosomonas dominance (2.38 ± 0.21%) during nitrification. The HDPE membrane-based bioreactor performed effectively under high organic loading rates (5-8 kg COD·m[-3]·day[-1]), whereas the A[2]/O system optimized nutrient cycling through synchronized nitrification-denitrification (dissolved oxygen: 2.0-3.5 mg/L). In this study, we establish a scalable framework for the treatment of industrial swine wastewater by combining engineered infrastructure with the principles of microbial ecology to address conventional pollutants.},
}

*Bioreactors/microbiology
Animals
*Wastewater/microbiology/chemistry
Swine
*Nitrogen/metabolism
Anaerobiosis
*Waste Disposal, Fluid/methods
Biological Oxygen Demand Analysis
Water Purification/methods
Membranes, Artificial
Phosphorus
Industrial Waste
Biodegradation, Environmental

@article {pmid40757865,
year = {2025},
author = {Södergren, J and Noguera, PM and Petersen, MA and Jørgensen, NOG and Podduturi, R and Nicolaisen, MH},
title = {Myxobacteria isolated from recirculating aquaculture systems (RAS): ecology and significance as off-flavor producers.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075725},
doi = {10.1128/aem.00757-25},
pmid = {40757865},
issn = {1098-5336},
abstract = {Despite advances in the operation of recirculating aquaculture systems (RAS), accumulation of earthy-muddy off-flavors in the fish remains a potential risk. Myxobacteria (Myxococcota) are reported to be among the most abundant geosmin synthase-harboring groups in RAS, but previous isolation attempts have been unsuccessful, limiting the knowledge of their role in off-flavor production. For the first time, we successfully isolated two geosmin-producing myxobacteria from RAS: Myxococcus virescens AT3 and Corallococcus exiguus AT4. Cell-specific geosmin production varied with the nutrient content in different media but was highest in a low-nutrient medium and when cultivated in water from RAS. Cultivation in RAS water also stimulated the production of other volatile organic compounds (VOCs). Newly identified potential off-flavor compounds included 4-methyl-2-heptanone ("forest" odor), 3-methyl-1-butanol ("medicinal" and "chemical"), and a presumptive sesquiterpenoid described as "musty," "earthy," and "flowery." The previously known off-flavor compound dimethyl sulfide was also detected. Myxobacteria have previously been proposed as keystone bacteria in the environment due to their predatory lifestyle. In predation assays using isolated bacteria from RAS, M. virescens AT3 and C. exiguus AT4 could successfully feed on 15 of 16 tested strains, suggesting a large influence on the biology of RAS microbiomes. The combination of predatory behavior and potent production of geosmin and other VOCs underscores the ecological and sensory impact of these bacteria in RAS. Understanding their behavior and metabolic outputs is critical to developing strategies for mitigating off-flavors in RAS.IMPORTANCEIssues with off-flavored fish in recirculating aquaculture systems (RAS) due to the presence of the earthy-musty smelling compounds geosmin and 2-MIB are considered as one of the industry's most economically significant challenges. Knowledge of conditions that affect off-flavor production is essential information in the development of viable solutions for its mitigation. Little is known about the function of these microbially produced compounds or the conditions that trigger their production, especially in the underexplored myxobacteria. Investigation of natural isolates is crucial to determine the function of the genes involved and their differential expression in response to environmental cues. While myxobacteria in RAS have been previously shown to harbor the geosmin synthase gene in molecular studies, the present study is the first attempt to isolate these bacteria from RAS and quantify their geosmin production under various nutrient conditions. Through cultivation-based methods, we demonstrate their production of both known and novel compounds with earthy attributes.},
}

@article {pmid40757859,
year = {2025},
author = {Adekoya, AE and West, SR and Arriaga, SK and Ibberson, CB},
title = {Infections as ecosystems: community metabolic interactions in microbial pathogenesis.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0053024},
doi = {10.1128/iai.00530-24},
pmid = {40757859},
issn = {1098-5522},
abstract = {Microbes rarely exist alone; instead, they live in dynamic multi-species communities with a range of metabolic capacities. To establish within a polymicrobial community, an organism must compete with the other members of the community for space and nutrients. In addition, microbes form complex metabolic interdependencies in polymicrobial environments, and these nutrient exchanges are central to overall community function. Interactions between microbial community members dictate key processes, including nutrient cycling, tolerance to disturbances, and disease progression, and these interactions are known to depend on the environment in which they are measured. Therefore, understanding these ecological interactions is fundamental to our understanding of community composition, function, and impacts on disease. In this mini-review, we will describe the mechanisms microbes use to exchange nutrients in host-associated environments, with a focus on the oral and respiratory tracts. We will particularly emphasize the environmental factors that influence community composition and how interactions between organisms, ranging from cooperation to competition, impact nutrient bioavailability and overall community function during infection.},
}

@article {pmid40756216,
year = {2025},
author = {Li, M and Liu, J and Cao, D and Chen, X and Shi, J and Hu, W and Xiao, C and Fang, Y},
title = {Heavy metal pollution simplifies microbial networks and enhances modularity during tailings primary succession: divergent assembly dynamics for bacterial and fungal communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1566627},
pmid = {40756216},
issn = {1664-302X},
abstract = {Microbial community play a fundamental role in primary succession of tailings ecosystems. However, the influence of heavy metal pollution on microbial interactions and assembly dynamics during this process remains poorly understood. In this study, we investigated bacterial and fungal communities in tailing soil and biological soil crusts (BSCs) undergoing primary succession under varying heavy metal pollution. By integrating microbial community profiling with measurements of soil nutrients and heavy metal concentrations, we aimed to elucidate how pollution levels shape microbial composition, co-occurrence networks, and assembly processes. Our results revealed clear differences in soil physicochemical properties, microbial diversity, community structure, and ecological interactions between low and high pollution conditions. Under high contamination, Burkholderiales dominated the bacterial communities, while Saccharomycetales and Pleosporales were representative among fungi. Microbial diversity decreased with increasing pollution, accompanied by simplified co-occurrence networks and increased modularity. In highly polluted environments, both bacterial and fungal communities exhibited stronger correlations with environmental factors. Interestingly, bacterial communities were more strongly associated with soil nutrient parameters, whereas fungal communities responded more closely to heavy metal concentrations. Community assembly analysis further showed a shift toward deterministic processes in bacterial communities under high pollution, while fungal assembly remained largely stochastic. These findings highlight the differential responses of bacterial and fungal communities to heavy metal stress and underscore the critical role of pollution in shaping microbial succession in tailing ecosystems. This study provides important insights into microbial ecology under environmental stress and may inform strategies for the bioremediation and management of contaminated mine lands.},
}

@article {pmid40756212,
year = {2025},
author = {Cortez-Lázaro, AA and Vázquez-Medina, PJ and Caro-Degollar, EM and García Evangelista, JV and Cortez-Lázaro, RA and Rojas-Paz, JL and Legua-Cardenas, JA and Fernandez-Herrera, F and Pesantes-Rojas, CR and Ocrospoma-Dueñas, RW and Oliva-Cruz, SM and Manes-Cangana, GA and Romero Bozzetta, JL and Leiva Espinoza, ST},
title = {Global trends in Trichoderma secondary metabolites in sustainable agricultural bioprotection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595946},
pmid = {40756212},
issn = {1664-302X},
abstract = {The use of Trichoderma spp. constitutes a promising biotechnological strategy for sustainable agriculture, owing to its capacity to control phytopathogens and to produce bioactive secondary metabolites. This study, one of the first of its kind, addresses the absence of a comprehensive bibliometric assessment in this field. A systematic bibliometric analysis was conducted on 235 publications indexed in Scopus (2000-2025). Advanced tools such as VOSviewer and Bibliometrix were employed to track publication trends, identify key research themes, map collaborative networks, and assess the influence of leading authors and institutions. An exponential increase in scientific output was observed, peaking in 2023. Four principal research clusters were identified: antifungal activity, gene regulation, secondary metabolite production, and biosynthesis. India and China accounted for the highest publication volume, while Italy, represented by authors such as Francesco Vinale, accounted for the greatest scientific impact. International collaboration was extensive, particularly between Asia and Europe. The analysis indicates a progression from applied biocontrol studies to research focusing on molecular and genetic mechanisms, highlighting the need for multidisciplinary approaches that integrate biotechnology, agronomy, and microbial ecology. This bibliometric study provides an overview of Trichoderma secondary metabolites in agricultural biocontrol and outlines a research agenda emphasizing field validation, interdisciplinary collaboration, and the adoption of innovative technologies to bridge the gap between research and on-farm application in sustainable agriculture.},
}

@article {pmid40755785,
year = {2025},
author = {Abuassaf, RA and Al-Jamal, FF and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD},
title = {Evaluating the antibacterial properties of deep-sea sponges Dactylospongia elegants, Stelletta fibrosa, and Haliclona manglaris from the Jordanian Gulf of Aqaba.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19735},
pmid = {40755785},
issn = {2167-8359},
mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Porifera/chemistry/genetics ; *Gram-Positive Bacteria/drug effects ; *Haliclona/chemistry ; *Gram-Negative Bacteria/drug effects ; Tandem Mass Spectrometry ; },
abstract = {Marine sponges are known for their rich variety of secondary metabolites, many of which show potential for pharmaceutical applications. In this study, three deep-sea sponge species-Stelletta fibrosa, Dactylospongia elegans, and Haliclona manglaris-were identified using DNA barcoding, and their ethanolic extracts were tested for antibacterial activity. The extracts were evaluated against Gram-positive (e.g., Bacillus pumilus, Staphylococcus aureus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus, MRSA) and Gram-negative bacteria (e.g., Escherichia coli and Klebsiella aerogenes) using the agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined. Among the extracts, D. elegans exhibited the most potent antibacterial activity, with inhibition zones ranging from six to 21 mm against gram-positive bacteria and low MIC/MBC values from 0.25 to three mg/ml. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis of D. elegans revealed the presence of bioactive compounds such as gallic acid, caffeic acid, bolinaquinone, dactyloquinone, and others, which are known for their antimicrobial properties. These findings suggest that D. elegans has promising antibacterial properties that could be valuable in combating antimicrobial resistance.},
}

Animals
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Porifera/chemistry/genetics
*Gram-Positive Bacteria/drug effects
*Haliclona/chemistry
*Gram-Negative Bacteria/drug effects
Tandem Mass Spectrometry

@article {pmid40751837,
year = {2025},
author = {Cruz-Cano, R and Bretón-Deval, L and Martínez-García, M and Díaz-Jaimes, P and Kolb, M},
title = {Changes in Microbial Community Assemblages Due To Urban Pollution, Detected via rRNA Gene Amplicon Sequencing in the Magdalena River, Mexico City.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {85},
pmid = {40751837},
issn = {1432-184X},
support = {516486//Secretaria de Ciencia, Humanidades, Tecnología e Innovación/ ; IN211921//UNAM-PAPIIT/ ; IN211921//UNAM-PAPIIT/ ; IN211921//UNAM-PAPIIT/ ; },
mesh = {Mexico ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; Cities ; Environmental Monitoring ; RNA, Ribosomal, 16S/genetics ; Water Quality ; *Water Pollution/analysis ; Water Microbiology ; Water Pollutants, Chemical/analysis ; },
abstract = {As freshwater sources become increasingly polluted and depleted, the delicate balance of aquatic environments is disrupted, leading to cascading effects throughout entire ecosystems. This disruption manifests in various ways, including changes in water chemistry, temperature fluctuations, and the introduction of contaminants, all of which contribute to alterations in microbial communities. We applied eDNA metabarcoding to characterize microbial communities along an anthropogenic pollution gradient in the Magdalena River, a tropical river in Mexico City. Sampling was conducted at four sites representing different levels of human influence. Results revealed differences in both bacterial and microeukaryotic community compositions between sites. In areas with low to moderate disturbance, bacterial genera associated with nitrogen cycling and plant-microbe interactions (e.g., Rhizobacter, Rhodoferax, and Flavobacterium) were predominant, whereas in more heavily impacted sites, genera linked to enteric, nosocomial, or fecal sources (e.g., Arcobacter, Acinetobacter, and Aeromonas) dominated. Peri-urban sites exhibited higher alpha diversity at the phylum level for bacteria, and microeukaryotic communities; two phyla account for over 75% of the relative abundance throughout the year (Ciliophora & Chlorophyta). Statistical analysis showed that water quality influences microbial composition in the sites. These findings demonstrate that urban influence alter microbial community composition, showing similar patterns to other studies. Our study, however, also discovered certain taxa that had not been previously recorded in tropical urban rivers, thereby broadening the existing knowledge, which has primarily been based on temperate systems. This research offers one of the initial thorough evaluations of microbial communities in urban rivers in Mexico and highlights the potential of eDNA metabarcoding as a valuable tool for environmental monitoring.},
}

Mexico
*Rivers/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
Cities
Environmental Monitoring
RNA, Ribosomal, 16S/genetics
Water Quality
*Water Pollution/analysis
Water Microbiology
Water Pollutants, Chemical/analysis

@article {pmid40750488,
year = {2025},
author = {Lopes, ACA and Martins, LV and Ferreira, GNC and Trivedi, P and Araujo, ASF},
title = {Do plants remember their microbial partners?.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.07.005},
pmid = {40750488},
issn = {1878-4372},
abstract = {Plants host dynamic microbiomes that are critical for stress resilience and productivity. Emerging evidence suggests that 'microbiome memory' enables plants to retain beneficial microbes via epigenetic mechanisms and vertical transmission. Understanding how 'microbiome memory' forms, persists, and influences plant adaptation is crucial for advancing resilient crop systems and sustainable agriculture.},
}

@article {pmid40749586,
year = {2025},
author = {Li, H and Hong, L and Wang, Y and Chai, S and Huang, P and Chen, H and Liu, W and Zhu, W and Marzorati, M and Wang, H and Tian, J and Zhang, X},
title = {Origin-dependent metabolic variations: How Atractylodes macrocephalae Rhizoma extract's chemical diversity leads to stage-specific changes in simulated digestion.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {266},
number = {},
pages = {117082},
doi = {10.1016/j.jpba.2025.117082},
pmid = {40749586},
issn = {1873-264X},
abstract = {Atractylodes macrocephalae Rhizoma (AMR), a traditional Chinese medicine, is extensively utilized in clinical practice for its pharmacological properties, including anti-inflammatory, anti-tumor, and gastrointestinal regulatory effects. Nonetheless, the intricate nature of traditional Chinese medicine extracts has resulted in few studies into the effects of compositional variations in Atractylodes macrocephalae Rhizoma extracts (AMRE) from diverse sources on gastrointestinal metabolic processes. This study developed an integrated in vitro and in vivo compound analysis strategy utilizing Ultrahigh-performance liquid chromatography Quadrupole-Orbitrap tandem mass spectrometry (UHPLC-Q-Orbitrap-MS/MS) and the Simulator of Human Intestinal Microbial Ecosystem (SHIME) to examine the metabolic alterations caused by variations in the chemical constituents of AMRE from diverse sources. A total of 117 chemical constituents were found, primarily classified as terpenoids, organic acids, alkaloids, coumarins, and phenylpropanoids. 51 prototype components and 79 metabolites were identified. The metabolic processes were predominantly observed among terpenoids, with reaction types encompassing hydroxylation, oxidation, hydrogenation, methylation, glucuronidation, and sulfonation. Analysis of dynamic changes revealed that the majority of the prototype components underwent a considerable reduction in the colon, while the metabolites were markedly enriched in both the small intestine and colon. Differential analysis showed that AMRE3 contained the highest number of terpenoid compounds, AMRE1 exhibited the highest average content of chemical constituents, and AMRE2 had the lowest. These disparities were consistently observed in both prototype components and metabolic behaviors, thereby affirming the robust correlation between metabolite distribution and chemical constituents. This study elucidates, for the first time, the variations in the chemical constituents of AMRE from diverse sources and the metabolic characteristics and discrepancies they elicit in the human gastrointestinal tract (GI tract), offering a viable strategy for further clarifying the material basis of its pharmacological effects and clinical applications.},
}

@article {pmid40748243,
year = {2025},
author = {Portal-Gonzalez, N and Wang, W and He, W and Santos-Bermudez, R},
title = {Engineering Plant Holobionts for Climate-Resilient Agriculture.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf158},
pmid = {40748243},
issn = {1751-7370},
abstract = {The plant holobiont-an integrated unit of the host and its microbiome-has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles-priority effects, keystone taxa, and functional redundancy-that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling-including genome-scale metabolic models, dynamic flux balance analysis, and machine learning-to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.},
}

@article {pmid40743118,
year = {2025},
author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS},
title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326358},
pmid = {40743118},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; },
abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.},
}

*Soil Microbiology
*Archaeology
*Bacteria/genetics/classification/drug effects
*Caves/microbiology
RNA, Ribosomal, 16S/genetics
Humans
*Drug Resistance, Microbial/genetics
Microbiota/genetics
Turkey

@article {pmid40742751,
year = {2025},
author = {Fischer, MT and Xue, KS and Costello, EK and Dvorak, M and Raboisson, G and Robaczewska, A and Caty, SN and Relman, DA and O'Connell, LA},
title = {Effects of parental care on skin microbial community composition in poison frogs.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40742751},
issn = {2050-084X},
support = {DP2 HD102042/HD/NICHD NIH HHS/United States ; DP2HD102042/NH/NIH HHS/United States ; Erwin Schroedinger Stipend J-4526B//Austrian Science Fund/ ; },
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Anura/microbiology/physiology ; Larva/microbiology ; Female ; Male ; *Bacteria/classification/isolation & purification/genetics ; Poison Frogs ; },
abstract = {Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects and shaping host health and disease. Microbe acquisition during parental care is well studied in humans and agriculturally relevant species but remains poorly understood in other vertebrate groups, such as amphibians. Here, we investigate vertical transmission of skin microbiota in poison frogs (Dendrobatidae), where fathers transport tadpoles piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of embryos begins after hatching, suggesting that the vitelline envelope acts as a microbial barrier. A cross-foster experiment demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts skin communities of tadpoles in an ecologically relevant setting, we sampled sympatric species that do or do not exhibit tadpole transport in their natural habitat. We did not find a higher degree of similarity between microbial communities of tadpoles and adults in species that transport their offspring compared to those that do not. Similarly, communities of tadpoles were no more similar to their caregiver than to unrelated adults, indicating that most caregiver-associated microbes do not remain in tadpole communities long-term. Nonetheless, some taxa persisted on tadpoles over development. This study is the first to demonstrate that offspring transport facilitates transmission of parental skin microbes in anurans.},
}

Animals
*Skin/microbiology
*Microbiota
*Anura/microbiology/physiology
Larva/microbiology
Female
Male
*Bacteria/classification/isolation & purification/genetics
Poison Frogs

@article {pmid40742667,
year = {2025},
author = {Liang, M and Wu, WJ and Li, L and Qin, H and Li, SN and Zheng, GL and Hou, DM and Huang, Q and Cheng, L and Jie, HQ and Lu, JR and He, JC and Yang, J and Wei, W},
title = {Characteristics of the microbiota in the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic.},
journal = {World journal of pediatrics : WJP},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12519-025-00953-z},
pmid = {40742667},
issn = {1867-0687},
support = {81800903//National Natural Science Foundation of China/ ; 82171135//National Natural Science Foundation of China/ ; 82371140//National Natural Science Foundation of China/ ; 81970881//National Natural Science Foundation of China/ ; 82271160//National Natural Science Foundation of China/ ; 21Y31900504//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 2024YFC2511100//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Microbial colonization in the nasopharynx and nasal cavity plays a defensive role in children. The coronavirus disease 2019 (COVID-19) pandemic may have an influence on the nasopharynx and nasal cavity microbiota. This study aimed to identify and compare the microbiota in the nasopharynx and nasal cavity before and during the COVID-19 pandemic in a healthy pediatric population.

METHODS: Separate mucosal swabs were collected from the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic. A 16S ribosomal RNA-based metagenomic approach was employed to characterize and analyze alterations in the nasopharyngeal and nasal microbiota to determine whether isolation measures, such as mask wearing, influence microbial ecology.

RESULTS: The richness and diversity of the nasopharyngeal and nasal microbiota decreased during the COVID-19 pandemic compared with before the pandemic. Firmicutes and Proteobacteria were the most abundant phyla in the nasopharyngeal and nasal microbiota, respectively, both before and during the pandemic. Corynebacterium and Moraxella were the dominant genera in the nasopharyngeal and nasal microbiota during the COVID-19 pandemic, whereas Pseudomonas and Corynebacterium were dominant before the pandemic. Compared with pre-pandemic conditions, microbial colonization differed significantly for Cyanobacteria/Chloroplast and Bacteroidetes in the nasopharynx and for Planctomycetes in the nasal cavity during the COVID-19 pandemic.

CONCLUSIONS: This study revealed a lower microbiota diversity during COVID-19, possibly accompanied by microbiota dysbiosis, increased risk of respiratory infections and inflammatory responses in healthy children. This study underscores the importance of reestablishing microbiota balance and highlights the need for personalized treatment and prophylactic strategies in routine public health practice. Supplementary file3 (MP4 150533 KB).},
}

@article {pmid40742453,
year = {2025},
author = {Lezcano, MÁ and Carrizo, D and Lominchar, MÁ and Sánchez-García, L and Quesada, A and Parro, V},
title = {Temperature-Sensitive Lipids Reveal Intraspecific Diversity in Bacteria Isolated from an Ancient Antarctic Microbial Mat.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {84},
pmid = {40742453},
issn = {1432-184X},
support = {FJC2018-037246-I//Ministerio de Ciencia e Innovación/ ; PID2022-140180OB-C21//Ministerio de Ciencia e Innovación/ ; RYC2018-023943-I//Ministerio de Ciencia e Innovación/ ; PID2021-126746NB-I00//Ministerio de Ciencia e Innovación/ ; },
mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation & purification/chemistry/metabolism ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/analysis ; *Lipids/analysis/chemistry ; Temperature ; Phylogeny ; *Geologic Sediments/microbiology ; },
abstract = {Ancient Antarctic microbial mats harbour viable bacteria that have been exposed to extreme cold and arid conditions for hundreds of years. To delve into the molecular mechanisms underlaying their survival, we isolated 12 bacterial strains from a 1,000-year-old desiccated microbial mat from the McMurdo Ice Shelf and studied their lipid composition as a function of temperature. Six of the bacterial strains were classified as Paenisporosarcina macmurdoensis, and the other six as Arthrobacter sp., according to 16S rRNA gene analyses. Two strains of each taxon were incubated at their minimum and maximum growth temperatures, and the changes in their lipid profiles were analyzed. The proportion of major fatty acids (saturated, unsaturated, and iso- and anteiso-) remained relatively constant across temperature in the four strains, but the composition of hydrocarbons and alcohols differed between taxa (e.g., presence of unsaturated alkenes in Arthrobacter sp., or unidentified isoprenoid alcohols in P. macmurdoensis). This highlights the diagnostic value of non-fatty acid lipids and revealed a taxon-dependent lipid composition. Despite the taxon-associated lipid profile, incubation temperature also influenced lipid composition in both taxa, with higher temperature correlating with greater lipid richness. Interestingly, the two P. macmurdoensis strains showed distinct lipid profiles at 20°C, suggesting that intraspecific lipid diversity reflects within-species physiological variability with potential relevance for adaptation to temperature fluctuations in the mat. Therefore, assessing the influence of temperature on bacterial lipids is crucial for understanding their adaptation and survival in extreme environments, as well as for expanding species lipid inventories for biological interpretations of ancient samples.},
}

Antarctic Regions
*Bacteria/genetics/classification/isolation & purification/chemistry/metabolism
RNA, Ribosomal, 16S/genetics
Fatty Acids/analysis
*Lipids/analysis/chemistry
Temperature
Phylogeny
*Geologic Sediments/microbiology

@article {pmid40742287,
year = {2025},
author = {Zhang, Y and Sun, H and Huang, Q and Zhang, L and Zou, X and Liu, Y},
title = {Anaerobic Digestion Performance and Microbial Community Structures in a Pilot-Scale Up-Flow Anaerobic Sludge Blanket (UASB) Treating Distillery Wastewater.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {97},
number = {8},
pages = {e70153},
pmid = {40742287},
issn = {1554-7531},
support = {//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant/ ; //NSERC Alliance/ ; //Alberta Distillers Limited/ ; //Alberta Innovates/ ; //City of Calgary/ ; //Canada Research Chair (CRC) in Future Water Services/ ; //China Scholarship Council (CSC) PhD Scholarship/ ; },
mesh = {Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Bioreactors/microbiology ; Pilot Projects ; *Sewage/microbiology ; *Wastewater/microbiology ; *Industrial Waste ; Bacteria/metabolism ; Methane ; },
abstract = {Anaerobic digestion (AD) is a promising technology for treating high-strength industrial wastewater while recovering biogas as a renewable energy source. In this study, a pilot-scale up-flow anaerobic sludge blanket (UASB) reactor, with a working volume of 225 L, was operated for 130 days to treat raw distillery wastewater. Three different types of distillery wastewater, including centrate, spent caustic, and other low-strength process wastewater generated during operations (e.g., condensation water), were mixed to balance extreme pH levels and create conditions more suitable for AD. The UASB reactor demonstrated stable performance at an organic loading rate (OLR) of 10.0 kg COD/m[3]/day, achieving a COD removal efficiency of 86%. Average methane yield was more than 71% throughout the operation. Microbial community analysis revealed a significant increase in key syntrophic bacteria and methanogens, with Methanobacterium accounting for 55.8% of the archaeal population. Network and Mantel analyses indicated that syntrophic partnerships play a crucial role in enhancing AD of distillery wastewater under high OLR conditions. Overall, the UASB reactor exhibited high process stability, highlighting its potential for large-scale application in distillery wastewater treatment.},
}

Anaerobiosis
*Waste Disposal, Fluid/methods
*Bioreactors/microbiology
Pilot Projects
*Sewage/microbiology
*Wastewater/microbiology
*Industrial Waste
Bacteria/metabolism
Methane

@article {pmid40742109,
year = {2025},
author = {Jones, KR and Song, Y and Rinaldi, SS and Moran, NA},
title = {Effects of priority on strain-level composition of the honey bee gut community.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0082825},
doi = {10.1128/aem.00828-25},
pmid = {40742109},
issn = {1098-5336},
abstract = {Host-associated microbiomes are complex communities shaped by interactions between members. The type VI secretion system (T6SS), among other bacterial weapons, allows gram-negative bacteria to deliver toxic effectors into competitors. In this study, we investigated the impact of differential colonization timing on the competitive advantage associated with T6SS possession using Snodgrassella alvi, a core symbiont of the honey bee gut microbiome. Following a timeline based on the natural establishment window of the gut microbiome, we sequentially inoculated newly emerged bees with fluorescently labeled strains that differed in presence of the T6SS-1. When inoculated simultaneously, the T6SS-1-possessing strain (wkB2) consistently excluded the T6SS-1-lacking strain (wkB332); however, when given a 5-day advantage, the second strain was consistently excluded regardless of strain identities. With a 1-day advantage, the effect of priority was weakened, but wkB332 was able to persist following introduction of wkB2. Utilizing a wkB2 T6SS-1 knockout strain, we repeated our 24 hour priority experiments and found that the T6SS-1 contributes to invasion outcomes along with other mechanisms of competition. Through fluorescent microscopy, we explored how coexisting strains in these experimental scenarios organize spatially within the bee ileum. Our results demonstrate that colonization timing can have lasting consequences for strain composition of the established microbiome. These findings illustrate the influence of stochastic processes in microbial community assembly and emphasize that differences in colonization timing may alter competitive outcomes between taxa, impacting taxon coexistence.IMPORTANCEThe bacterial gut communities of honey bees possess considerable strain-level diversity between hives, between individual bees, and within individual bees. However, the factors underlying strain coexistence are unclear. Here, we provide support for timing of colonization, or priority effects, as one factor driving this strain-level diversity. Our results show that priority inoculation can prevent colonization by subsequent competing bacterial strains and mitigate advantages conferred through bacterial weaponry. Further, a brief window of priority can facilitate the coexistence of strongly and weakly competitive strains within single bees. These results add to our understanding of the impacts of priority effects in host-associated microbial communities. Such an understanding can aid the development of future probiotic strategies aimed at improving honey bee health.},
}

@article {pmid40740319,
year = {2025},
author = {Siceloff, AT and Waltman, D and Gunning, CE and Nolan, SP and Rohani, P and Shariat, NW},
title = {Longitudinal study highlights patterns of Salmonella serovar co-occurrence and exclusion in commercial poultry production.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570593},
pmid = {40740319},
issn = {1664-302X},
abstract = {Recent advances in next-generation sequencing approaches have revealed that Salmonella often exists in multiserovar populations, with important implications for public health as time and resource constraints limit serovar characterization by colony-based isolation methods. It is important to characterize Salmonella population dynamics to then understand how the microbial ecology influences serovar evolution and thus, animal and human health outcomes. Chicken remains the leading source of foodborne Salmonella outbreaks in the U. S., despite reductions in contamination at the product level, underscoring the need for targeted control strategies. This study aimed to survey multiserovar Salmonella populations in broiler breeder flocks and monitor fluctuations throughout production. Deep serotyping was performed on environmental breeder samples collected over 2 years as part of a surveillance program. About 18% (104/568) of samples contained multiple serovars, with serovar Kentucky negatively associated with other serovars, often excluding them. Longitudinal sampling across two commercial complexes over 65 weeks included pullet and breeder farms. Environmental samples were collected via pre-moistened boot socks and rodent bait boxes, with on-farm rodents captured. Salmonella prevalence in pullet flocks was 17% (11/64), while 41% (135/330) of breeder samples were positive, peaking at 38 weeks of age. Rodents showed 35% (17/49) positivity in gastrointestinal samples and 9% (3/33) in bait station swabs, with six serovars identified, three of which were shared with flocks. Our cross-sectional and longitudinal Salmonella surveillance highlights the complexity of serovar interactions with further work required to elucidate the mechanisms of competitive exclusion.},
}

@article {pmid40739711,
year = {2025},
author = {Xu, Y and Zhu, Y and Wu, X and Peng, W and Zhong, Y and Cai, Y and Chen, W and Liu, L and Tan, B and Chen, T},
title = {Gut Microbiota-Derived Acetate Ameliorates Endometriosis via JAK1/STAT3-Mediated M1 Macrophage Polarisation.},
journal = {Microbial biotechnology},
volume = {18},
number = {8},
pages = {e70202},
pmid = {40739711},
issn = {1751-7915},
support = {8216140922//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Endometriosis/therapy/microbiology/metabolism ; Mice ; Humans ; Fecal Microbiota Transplantation ; *STAT3 Transcription Factor/metabolism ; *Janus Kinase 1/metabolism ; *Macrophages/metabolism/immunology ; Disease Models, Animal ; *Acetates/metabolism ; Signal Transduction ; Feces/microbiology/chemistry ; },
abstract = {Endometriosis (EMs) is a common inflammatory disorder in women of reproductive age, severely impacting patients' quality of life and fertility. Current hormonal therapies offer limited efficacy, and surgical interventions often fail to prevent recurrence. Recent studies suggest a close association between gut microbiota and the pathophysiology of EMs, though the precise mechanisms remain unclear. To investigate the influence of gut microbiota on EMs, this study established an EMs mouse model and performed faecal microbiota transplantation (FMT) using samples from healthy donors (AH group) and EMs patients (AE group) into the model mice. Results demonstrated that compared to the model group (M group), FMT from healthy donors (AH group) significantly reduced ectopic lesion volume (658.3 ± 116.1 vs. 167.2 ± 112.8 mm[3], p < 0.01) and weight (0.7420 ± 0.1233 vs. 0.1885 ± 0.1239 mg, p < 0.01). Conversely, FMT from EMs patients exacerbated disease progression. Mechanistic studies revealed that healthy donor FMT attenuated EMs by remodelling the gut microbial composition (enhancing α-diversity and Lactobacillus abundance while suppressing Bacteroidetes), significantly elevating acetate levels in faeces and ectopic lesions, activating the JAK1/STAT3 signalling pathway within lesions, and thereby driving macrophage polarisation toward the M1 phenotype (by increased iNOS/CD86 expression and decreased Arg1/CD206 expression). Simultaneously, healthy donor FMT enhanced intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1/5) and reducing levels of intestinal permeability markers (DAO, IFABP). In contrast, AE group FMT disrupted gut microbial ecology, reduced acetate production, failed to activate the JAK1/STAT3 pathway, promoted M2 macrophage polarisation and impaired intestinal barrier function. Collectively, this study elucidates for the first time that acetate, as a key gut microbiota metabolite, exerts anti-EMs effects by activating the JAK1/STAT3 signalling pathway to drive macrophage reprogramming toward the M1 phenotype, thereby positioning gut microbiota reconstruction as a novel therapeutic strategy for endometriosis.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Endometriosis/therapy/microbiology/metabolism
Mice
Humans
Fecal Microbiota Transplantation
*STAT3 Transcription Factor/metabolism
*Janus Kinase 1/metabolism
*Macrophages/metabolism/immunology
Disease Models, Animal
*Acetates/metabolism
Signal Transduction
Feces/microbiology/chemistry

@article {pmid40736560,
year = {2025},
author = {Braglia, C and Cutajar, S and Magagnoli, S and Asciano, D and Burgio, G and Di Gioia, D and Baffoni, L and Alberoni, D},
title = {The Ground Beetle Poecilus (Carabidae) Gut Microbiome and Its Functionality.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {83},
pmid = {40736560},
issn = {1432-184X},
support = {ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Nosema/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Solanum lycopersicum ; },
abstract = {Ground beetles of the genus Poecilus (Carabidae) play key ecological roles in pest control and soil health. However, their gut microbiome remains largely unexplored despite increasing interest in insect-associated microbiota and its environmental implications. This study used next-generation sequencing and qPCR to characterise the gut microbiome of Poecilus beetles collected from organic and conventional tomato fields. Core microbiota were identified through prevalence-abundance filtering, revealing dominant genera including Gilliamella, Weissella, Enterobacter, and Enterococcus, alongside several low-abundance but consistently present taxa. Notably, Carnobacterium was detected for the first time in an insect host, and Nosema ceranae was identified for the first time in Carabidae, expanding the known host range of this microsporidian pathogen. Functional predictions based on 16S rRNA data and comparative genomic analysis showed enrichment in pathways related to amino acid synthesis, protein degradation, and monosaccharide metabolism. Significant inter-individual variation in microbial diversity and predicted functionality was observed, with lowest diversity and metabolic potential in beetles from conventionally managed fields, potentially indicating dysbiosis and environmental stress. The detection of Nosema and Serratia pathogens in some individuals adds new insights into pathogen dynamics within carabid beetles. Our findings reveal that the gut microbiome of Poecilus may be shaped by environmental factors and agricultural practices, influencing host health and ecological performance. These insights support the use of Poecilus as a bioindicator for soil ecosystem health and highlight the potential of microbiome-based metrics in agroecological monitoring.},
}

Animals
*Coleoptera/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Nosema/isolation & purification/genetics
High-Throughput Nucleotide Sequencing
DNA, Bacterial/genetics
Solanum lycopersicum

@article {pmid40732998,
year = {2025},
author = {Herrera, M and Byerley, LO},
title = {Dietary Nitrogen and Its Role in the Gut Microbiome and Inflammatory Bowel Disease: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
pmid = {40732998},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Nitrogen/metabolism ; *Diet ; Dysbiosis ; Animals ; },
abstract = {In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)-including Crohn's disease and ulcerative colitis-being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen's role in gut health and identify novel therapeutic targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Inflammatory Bowel Diseases/microbiology/metabolism
*Nitrogen/metabolism
*Diet
Dysbiosis
Animals

@article {pmid40732683,
year = {2025},
author = {Lin, H and Zeng, Z and Zhang, H and Jia, Y and Pang, J and Chen, J and Zhang, H},
title = {Gut-Vaginal Microbiome Crosstalk in Ovarian Cancer: Implications for Early Diagnosis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40732683},
issn = {2076-0817},
support = {2021YFH0189//Sichuan International Science and Technology Innovation Cooperation/HongKong/Macao/Taiwan Science and Technology Innovation Cooperation Project/ ; 2022NSFSC1363//the Sichuan International Science Foundation Project/ ; 2021HXFH065//the project for disciplines of excellence-Clinical Research Incubation Project, West China Hospital, Sichuan University/ ; },
mesh = {Humans ; Female ; *Ovarian Neoplasms/diagnosis/microbiology ; *Vagina/microbiology ; *Gastrointestinal Microbiome ; Early Detection of Cancer/methods ; Dysbiosis/microbiology ; },
abstract = {Ovarian cancer remains a formidable global health burden, characterized by frequent late-stage diagnosis and elevated mortality rates attributable to its elusive pathogenesis and the critical lack of reliable early-detection biomarkers. Emerging investigations into the gut-vaginal microbiome axis have unveiled novel pathogenic mechanisms and potential diagnostic targets in ovarian carcinogenesis. This comprehensive review systematically examines the compositional alterations in and functional interplay between vaginal and intestinal microbial communities in ovarian cancer patients. We elucidate three principal mechanistic pathways through which microbial dysbiosis may drive oncogenesis: (1) estrogen-mediated metabolic reprogramming via β-glucuronidase activity; (2) chronic activation of pro-inflammatory cascades (particularly NF-κB and STAT3 signaling); (3) epigenetic silencing of tumor suppressor genes through DNA methyltransferase modulation. We propose an integrative diagnostic framework synthesizing multi-omics data-incorporating microbial profiles, metabolic signatures, pathway-specific molecular alterations, established clinical biomarkers, and imaging findings-within a multifactorial etiological paradigm. This innovative approach aims to enhance early-detection accuracy through machine learning-enabled multidimensional pattern recognition. By bridging microbial ecology with tumor biology, this review provides novel perspectives for understanding ovarian cancer etiology and advancing precision oncology strategies through microbiome-targeted diagnostic innovations.},
}

Humans
Female
*Ovarian Neoplasms/diagnosis/microbiology
*Vagina/microbiology
*Gastrointestinal Microbiome
Early Detection of Cancer/methods
Dysbiosis/microbiology

@article {pmid40732215,
year = {2025},
author = {Bodkhe, GA and Kumar, V and Li, X and Pei, S and Ma, L and Kim, M},
title = {Biosensors in Microbial Ecology: Revolutionizing Food Safety and Quality.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40732215},
issn = {2076-2607},
support = {RS-2025-00515546//National Research Foundation (NRF) of Korea grant funded by the Korea Government (MIST)/ ; RS-2020-NR049591//National Research Foundation of Korea/ ; },
abstract = {Microorganisms play a crucial role in food processes, safety, and quality through their dynamic interactions with other organisms. In recent years, biosensors have become essential tools for monitoring these processes in the dairy, meat, and fresh produce industries. This review highlights how microbial diversity, starter cultures, and interactions, such as competition and quorum sensing, shape food ecosystems. Diverse biosensor platforms, including electrochemical, optical, piezoelectric, thermal, field-effect transistor-based, and lateral flow assays, offer distinct advantages tailored to specific food matrices and microbial targets, enabling rapid and sensitive detection. Biosensors have been developed for detecting pathogens in real-time monitoring of fermentation and tracking spoilage. Control strategies, including bacteriocins, probiotics, and biofilm management, support food safety, while decontamination methods provide an additional layer of protection. The integration of new techniques, such as nanotechnology, CRISPR, and artificial intelligence, into Internet of Things systems is enhancing precision, particularly in addressing regional food safety challenges. However, their adoption is still hindered by complex food matrices, high costs, and the growing challenge of antimicrobial resistance. Looking ahead, intelligent systems and wearable sensors may help overcome these barriers. Although gaps in standardization and accessibility remain, biosensors are well-positioned to revolutionize food microbiology, linking ecological insights to practical solutions and paving the way for safer, high-quality food worldwide.},
}

@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}

@article {pmid40731225,
year = {2025},
author = {Sharma, P and Muehe, EM},
title = {Metal-tainted soils: a hidden threat to agriculture and health.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.07.004},
pmid = {40731225},
issn = {1878-4372},
abstract = {Hou et al. have revealed widespread metal contamination in agricultural soils, threatening food security, food quality, and human health. We propose climate-informed risk mapping of the mobile metal pool aligned with crop production mapping, followed by risk management strategies through engineered crops, metal-remediating plants, and targeted organic and microbial amendments.},
}

@article {pmid40730873,
year = {2025},
author = {Roegiers, I and Gheysens, T and Minsart, M and De Clercq, P and Vanbeversluys, K and Rać, N and Stroka, G and de Croock, J and Van de Wiele, T and Dubruel, P and Arroyo, MC},
title = {Author Correction: GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27634},
doi = {10.1038/s41598-025-13398-1},
pmid = {40730873},
issn = {2045-2322},
}

@article {pmid40728944,
year = {2025},
author = {Lange-Enyedi, NT and Tóth, E and Abbaszade, G and Németh, P and Garvie, LAJ and Wolf, J and Neumann-Schaal, M and Khayer, B and Sipos, G and Makk, J},
title = {Pseudogemmobacter sonorensis sp. nov., a new alphaproteobacterium isolated from the slime flux of a tree (Populus fremontii) in the Sonoran Desert (Arizona, USA).},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.006859},
pmid = {40728944},
issn = {1466-5034},
mesh = {RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Bacterial Typing Techniques ; Fatty Acids/chemistry/analysis ; Base Composition ; DNA, Bacterial/genetics ; Desert Climate ; Sequence Analysis, DNA ; Ubiquinone/chemistry/analogs & derivatives/analysis ; *Populus/microbiology ; Phospholipids/analysis ; Nucleic Acid Hybridization ; *Methylobacteriaceae/classification/isolation & purification/genetics ; *Soil Microbiology ; Trees/microbiology ; },
abstract = {The bacterial strain PA1-206B[T] is a Gram-stain-negative, aerobic, non-motile and non-spore-forming bacterium with an irregular rod shape. It was isolated from a tree wound exudate of the Populus fremontii trunk in the Sonoran Desert (USA), and its taxonomic position was investigated by a polyphasic approach. Strain PA1-206B[T] grew optimally at 28-30 °C and from pH 6 to 10 without NaCl. Based on 16S rRNA gene sequence analysis, this isolate showed only 96.0% sequence similarity to the type strain of Pseudogemmobacter hezensis and similarity of 94.4-95.7% to other species of the genus. Phylogenetic analysis based on whole-proteome comparisons placed strain PA1-206B[T] within the genus Pseudogemmobacter but, on a distinct branch, clearly separated from its closest relatives. The major isoprenoid quinone of the strain was ubiquinone Q-10. The predominant fatty acids (>5%) were C18:1 ω7c, C16:0 and 11-methyl-C18:1 ω7c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and two unidentified phospholipids were present. The assembled draft genome of strain PA1-206B[T] had 115 contigs with a total length of 4.5 Mb and a G+C content of 67.4 mol%. The overall genome-related indices (average nucleotide identity <80.4%, average amino acid identity <70.6%, digital DNA-DNA hybridization <21.6%) with respect to close relatives were below the corresponding threshold to demarcate bacterial species. Strain PA1-206B[T] (=DSM 115559[T]=NCAIM B.02680[T]) is suggested as the type strain of a novel Pseudogemmobacter species, for which the name Pseudogemmobacter sonorensis sp. nov. is proposed.},
}

RNA, Ribosomal, 16S/genetics
*Phylogeny
Bacterial Typing Techniques
Fatty Acids/chemistry/analysis
Base Composition
DNA, Bacterial/genetics
Desert Climate
Sequence Analysis, DNA
Ubiquinone/chemistry/analogs & derivatives/analysis
*Populus/microbiology
Phospholipids/analysis
Nucleic Acid Hybridization
*Methylobacteriaceae/classification/isolation & purification/genetics
*Soil Microbiology
Trees/microbiology

@article {pmid40727685,
year = {2025},
author = {Webb, H and Fuchs, M and Abbott, BW and Douglas, TA and Elder, CD and Ernakovich, JG and Euskirchen, ES and Göckede, M and Grosse, G and Hugelius, G and Jones, MC and Koven, C and Kropp, H and Lathrop, E and Li, W and Loranty, MM and Natali, SM and Olefeldt, D and Schädel, C and Schuur, EAG and Sonnentag, O and Strauss, J and Virkkala, AM and Turetsky, MR},
title = {A Review of Abrupt Permafrost Thaw: Definitions, Usage, and a Proposed Conceptual Framework.},
journal = {Current climate change reports},
volume = {11},
number = {1},
pages = {7},
pmid = {40727685},
issn = {2198-6061},
abstract = {PURPOSE OF REVIEW: We review how 'abrupt thaw' has been used in published studies, compare these definitions to abrupt processes in other Earth science disciplines, and provide a definitive framework for how abrupt thaw should be used in the context of permafrost science.

RECENT FINDINGS: We address several aspects of permafrost systems necessary for abrupt thaw to occur and propose a framework for classifying permafrost processes as abrupt thaw in the future. Based on a literature review and our collective expertise, we propose that abrupt thaw refers to thaw processes that lead to a substantial persistent environmental change within a few decades. Abrupt thaw typically occurs in ice-rich permafrost but may be initiated in ice-poor permafrost by external factors such as hydrologic change (i.e., increased streamflow, soil moisture fluctuations, altered groundwater recharge) or wildfire.

SUMMARY: Permafrost thaw alters greenhouse gas emissions, soil and vegetation properties, and hydrologic flow, threatening infrastructure and the cultures and livelihoods of northern communities. The term 'abrupt thaw' has emerged in scientific discourse over the past two decades to differentiate processes that rapidly impact large depths of permafrost, such as thermokarst, from more gradual, top-down thaw processes that impact centimeters of near-surface permafrost over years to decades. However, there has been no formal definition for abrupt thaw and its use in the scientific literature has varied considerably. Our standardized definition of abrupt thaw offers a path forward to better understand drivers and patterns of abrupt thaw and its consequences for global greenhouse gas budgets, impacts to infrastructure and land-use, and Arctic policy- and decision-making.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40641-025-00204-3.},
}

@article {pmid40725499,
year = {2025},
author = {Saint-Jean, M and Claisse, O and Marrec, CL and Samot, J},
title = {Structural and Genetic Diversity of Lysis Modules in Bacteriophages Infecting the Genus Streptococcus.},
journal = {Genes},
volume = {16},
number = {7},
pages = {},
pmid = {40725499},
issn = {2073-4425},
mesh = {*Streptococcus/virology/genetics ; *Genetic Variation ; *Genome, Viral ; *Streptococcus Phages/genetics ; *Bacteriophages/genetics ; Endopeptidases/genetics ; Phylogeny ; Viral Proteins/genetics ; *Bacteriolysis/genetics ; },
abstract = {Background/Objectives: Bacteriophages infecting the genus Streptococcus play a crucial role in microbial ecology and have potential applications in biotechnology and medicine. Despite their importance, significant gaps remain in our understanding of their lysis modules. This study aims to address these deficiencies by analyzing the genomic diversity and lysis module organization in Streptococcus phages. Methods: A search was conducted in the NCBI RefSeq database to identify phage genomes infecting Streptococcus. A representative panel was selected based on taxonomic diversity. Lysis modules were annotated and visualized, functional domains in endolysins were identified, and holins were characterized. Results: A total of 205 phage genomes were retrieved from the NCBI RefSeq database, of which 185 complete genomes were analyzed. A subset of 34 phages was selected for in-depth analysis, ensuring the representation of taxonomic diversity. The lysis modules were annotated and visualized, revealing five distinct organizations. Among the 256 identified endolysins, 25 distinct architectural organizations were observed, with amidase activity being the most prevalent. Holins were classified into 9 of the 74 families listed in the Transporter Classification Database, exhibiting one to three transmembrane domains. Conclusions: This study provides insights into the structural diversity of lysis modules in Streptococcus phages, paving the way for future research and potential biotechnological applications.},
}

*Streptococcus/virology/genetics
*Genetic Variation
*Genome, Viral
*Streptococcus Phages/genetics
*Bacteriophages/genetics
Endopeptidases/genetics
Phylogeny
Viral Proteins/genetics
*Bacteriolysis/genetics

@article {pmid40725462,
year = {2025},
author = {Ait Zenati, F and Baldi, S and Di Gloria, L and Djoudi, F and Bertorello, S and Ramazzotti, M and Niccolai, E and Amedei, A},
title = {Compositional and Functional Disparities in the Breast Oncobiome Between Patients Living in Urban or Rural Areas.},
journal = {Genes},
volume = {16},
number = {7},
pages = {},
pmid = {40725462},
issn = {2073-4425},
support = {2020-WIDE SPREAD-05-2020-Twinning Grant Agreement, No. 952583//European Commission/ ; },
mesh = {Humans ; *Breast Neoplasms/microbiology/genetics/epidemiology/pathology ; Female ; *Microbiota/genetics ; Rural Population ; Middle Aged ; Urban Population ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Adult ; Aged ; },
abstract = {Background/Objectives: Breast cancer (BC) is the leading cause of cancer incidence and mortality among women and the recent identification of a resident mammary microbiota has highlighted its potential role in breast carcinogenesis. Given that environmental and socioeconomic factors influence both BC prevalence and tumor-associated bacterial composition, this study aimed to evaluate the compositional and functional features of the mammary microbiota in cancerous (oncobiome) and adjacent healthy BC tissues from patients living in urban and rural areas. Methods: Microbiota composition in both the oncobiome and adjacent healthy BC tissues was analyzed using 16S rRNA sequencing. Results: Significant variations in breast oncobiome composition were observed among BC patients from urban and rural areas. A statistically significant β dispersion among breast oncobiome of patients from urban or rural areas was highlighted. Specifically, the genera Selenomonas, Centipeda, Leptotrichia, Neisseria and Porphyromonas were found exclusively in BC tissues of patients from rural areas. Additionally, bacteria from the Neisseriaceae, Porphyromonadaceae, and Selenomonadaceae families, as well as the Selenomonas genus, were significantly enriched in the oncobiome of rural BC patients. Furthermore, the results of the PICRUSt2 (phylogenetic investigation of communities by reconstruction of unobserved states) revealed a significant increase in phospholipid biosynthesis pathways in breast oncobiome of patients from rural areas compared to those from urban areas. Conclusions: This study provides evidence of distinct compositional and functional differences in the breast oncobiome between BC patients from rural and urban areas. These findings suggest that environmental factors influence local microbiome composition, potentially contributing to BC development and/or progression.},
}

Humans
*Breast Neoplasms/microbiology/genetics/epidemiology/pathology
Female
*Microbiota/genetics
Rural Population
Middle Aged
Urban Population
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Adult
Aged

@article {pmid40724585,
year = {2025},
author = {Liu, W and Zhang, C and Kuang, X and Zeng, X and Zhang, J and Wang, Q and Yang, H},
title = {Effects of Dietary Calcium and Phosphorus Levels on Growth Performance, Calcium-Phosphorus Homeostasis, and Gut Microbiota in Ningxiang Pigs.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {40724585},
issn = {2075-1729},
support = {2021YFD1300402//Key National Research and Development Program projects/ ; 24A0044//Hunan Provincial Department of Education key project/ ; },
abstract = {Optimal dietary calcium (Ca) and phosphorus (P) requirements remain undetermined for Ningxiang pigs, a valuable indigenous Chinese breed. This study conducted a continuous feeding trial with two growth phases (grower: 30-50 kg; finisher: 50-80 kg) using fixed Ca/P ratios to systematically evaluate the effects of Ca/P levels on growth performance and mineral metabolism. A total of 180 pigs per phase were allocated to four Ca/P levels. During the grower phase, a dietary regimen of 0.83% Ca/0.67% P significantly increased the average daily feed intake (ADFI), average daily gain (ADG), and apparent total tract digestibility (ATTD) of energy and P. In the finisher phase, 0.60/0.48% Ca/P showed optimal growth performance, upregulated jejunal mineral transporters (CaSR and SLC34A2), enhanced bone mineralization (metatarsal ash content), and improved intestinal morphology (duodenal and jejunal villus height, jejunal villus surface area). This regimen also selectively enriched Peptostreptococcaceae abundance, indicating improved host-microbe interactions. Based on these findings, stage-specific nutritional strategies were recommended: 0.83% Ca/0.67% P during the grower phase and 0.60% Ca/0.48% P during the finisher phase. These protocols synergistically improve microbial ecology, intestinal function, and bone metabolism, thereby maximizing the growth potential of Ningxiang pigs.},
}

@article {pmid40723916,
year = {2025},
author = {Wei, M and Liu, H and Hu, Z and Wen, P and Ye, Y and Chamba, Y and Zhang, H and Shang, P},
title = {A Mechanistic Approach to Replacing Antibiotics with Natural Products in the Treatment of Bacterial Diarrhea.},
journal = {Biomolecules},
volume = {15},
number = {7},
pages = {},
pmid = {40723916},
issn = {2218-273X},
support = {533325001//Xizang agriculture and Aninal Husbandry University Doctoral Progran in forestry (Fhase I) funded by Grant/ ; XZ202501ZY0147//Sxpported by Science and Technology Projects of Xizang Axtonomoxs Region, China/ ; 2023YFD1801304//National Key Research and Development Program/ ; },
mesh = {*Biological Products/therapeutic use/pharmacology ; *Diarrhea/drug therapy/microbiology ; Humans ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Animals ; Bacteria/drug effects ; *Bacterial Infections/drug therapy/microbiology ; },
abstract = {Natural products have emerged as potential alternatives to antibiotics in the treatment of bacterial diarrhea, due to their multi-targeting effects, low potential for inducing resistance, and favorable safety profiles. Currently, the search for natural product-based therapies has become an emerging focus in medical research. This growing interest is driven by the increasing awareness that the widespread and irrational use of antibiotics has contributed to the alarming rise in antibiotic-resistant bacterial strains, which in turn diminishes the efficacy of conventional drugs. Among these concerns, the limitations of antibiotics in managing bacterial diarrhea and the potential mechanisms by which natural products exert therapeutic effects are the main focus of this paper. Natural products, containing a wide array of bioactive compounds, can not only directly inhibit the growth of pathogenic bacteria, disrupt bacterial membrane synthesis, and reduce toxin production, but also modulate inflammatory responses, enhance immune function, repair intestinal barriers, and restore gut microbial ecology-highlighting their systemic and multi-targeted therapeutic potential. Therefore, this paper will elaborate on how natural products combat bacterial diarrhea from three aspects: the pathogen and pathogenesis of bacterial diarrhea, natural product-based therapeutic studies, and the underlying mechanisms of action, thereby proposing natural products as viable alternatives to antibiotics.},
}

*Biological Products/therapeutic use/pharmacology
*Diarrhea/drug therapy/microbiology
Humans
*Anti-Bacterial Agents/therapeutic use/pharmacology
Gastrointestinal Microbiome/drug effects
Animals
Bacteria/drug effects
*Bacterial Infections/drug therapy/microbiology

@article {pmid40723361,
year = {2025},
author = {Jiang, J and Zhang, H and Hussain, M and Abdullah, and Feng, F and Guan, R and Zhong, H},
title = {Novel Approaches in Glucose and Lipid Metabolism Disorder Therapy: Targeting the Gut Microbiota-Bile Acid Axis.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723361},
issn = {2079-7737},
support = {32402088//National Natural Science Foundation of China/ ; 2024C04012//"Pioneer" and "Leading Goose" R&D Program of Zhejiang Province/ ; LQ23C200011//Zhejiang Provincial Natural Science Foundation of China/ ; KYY-HX-20230084, KYY-HX-20240810//Zhejiang University of Technology - Company Crosswise Project/ ; },
abstract = {Metabolic dysregulation involving glucose and lipids is closely associated with chronic diseases such as type 2 diabetes mellitus. Emerging evidence highlights the regulatory role of bile acid (BA)-gut microbiota interactions in these metabolic disorders. The gut microbiota orchestrates the biotransformation of primary BAs into bioactive secondary BAs, which function as endocrine signaling molecules by activating the nuclear farnesoid X receptor (FXR) and G protein-coupled membrane receptor (TGR5), forming a communication network essential for metabolic homeostasis. BAs also reciprocally modulate gut microbiota composition. This BA-gut microbiota co-metabolism has emerged as a promising therapeutic target for lipid metabolism disorders. This comprehensive review examines the bidirectional interplay between gut microbiota and BA metabolism, focusing on microbial transformation of BAs, host-microbial co-regulatory pathways and mechanisms of BA metabolism, and the therapeutic implications of modulating the gut microbiota-BA axis in addressing glucose and lipid metabolism disorders. The synthesis of current evidence aims to elucidate the intricate crosstalk between microbial ecology and host metabolism mediated by BA signaling pathways, thereby exploring novel therapeutic intervention strategies.},
}

@article {pmid40722002,
year = {2025},
author = {Jordan, S and Pothier, JF and de Maayer, P and Broders, K and Kvitko, BH and Coutinho, TA and Smits, THM},
title = {Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {456},
pmid = {40722002},
issn = {1471-2180},
support = {310030L_204333//Swiss National Science Foundation (SNSF)- South-African National Research Foundation (NRF) Lead Agency project/ ; 2019-51181-30013//USDA NIFA SCRI/ ; },
mesh = {*Enterobacter/genetics/classification/isolation & purification ; *Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.

RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.

CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.},
}

*Enterobacter/genetics/classification/isolation & purification
*Polymerase Chain Reaction/methods
*DNA Primers/genetics
DNA, Bacterial/genetics
Phylogeny

@article {pmid40721486,
year = {2025},
author = {de Aviz, RO and Campos, JR and Silva, DEO and Barbosa, LMP and Costa, RM and Borges, JF and Leite, MRL and Rocha, SMB and Morais, PGC and Dauala, GA and Pereira, APA and de Medeiros, EV and Araujo, ASF},
title = {Microbial biomass and enzymatic activity in the rhizosphere of prickly-pear cactus genotypes inoculated with Bacillus subtilis and Paenibacillus Sp.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27415},
pmid = {40721486},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Paenibacillus/physiology ; *Bacillus subtilis/physiology ; Biomass ; Genotype ; Soil Microbiology ; *Cactaceae/microbiology/genetics ; },
abstract = {Some bacterial taxa, such as Bacillus and Paenibacillus, are known to colonize the rhizosphere and promote plant growth. However, little is known about their effect on microbial biomass and enzymatic activity in the rhizosphere of plants under semi-arid conditions. This field study assessed the effects of B. subtilis and Paenibacillus sp. in the rhizosphere of two prickly-pear cactus genotypes on microbial biomass of C, N, and P, and on enzymatic activity during early and late growth stages. The analysis of variance showed that microbial biomass and enzymatic activity were significantly influenced by the interaction between PGPB taxa (B. subtilis and Paenibacillus sp.), prickly-pear cactus genotypes ('Baiana' and 'Doce'), and plant growth stage (90 and 270 days). Specifically, PGPB inoculation increased microbial biomass P, β-glucosidase, and acid phosphatase, while microbial biomass of C and N were primarily driven by differences between cactus genotypes 'Baiana' and 'Doce'. At the early growth stage (90 days), the highest values of microbial biomass C, P, and acid phosphatase were observed, whereas N biomass was higher at the later stage (270 days). B. subtilis increased microbial biomass P in the 'Doce' genotype and acid phosphatase in 'Baiana,' while Paenibacillus sp. increased β-glucosidase in 'Baiana.' The combination of the 'Doce' genotype with B. subtilis enhanced phosphorus availability, suggesting that specific plant-microbe interactions may benefit nutrient acquisition in arid, nutrient-poor soils; however, further research is needed to confirm whether this effect extends to other genotypes.},
}

*Rhizosphere
*Paenibacillus/physiology
*Bacillus subtilis/physiology
Biomass
Genotype
Soil Microbiology
*Cactaceae/microbiology/genetics

@article {pmid40719475,
year = {2025},
author = {Fan, X and Guo, X and Qi, Q and Gui, H and Li, Y and Yang, Y and He, J-S and Wu, L},
title = {Long-term elevated precipitation promotes an acid metabolic preference in soil microbial communities in a Tibetan alpine grassland.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0047025},
doi = {10.1128/msystems.00470-25},
pmid = {40719475},
issn = {2379-5077},
abstract = {Alpine ecosystems store vast amounts of soil organic carbon but are highly sensitive to climate change. Despite this, the response of in situ soil microbial metabolic processes, especially carbon substrate utilization, to climatic shifts remains underexplored. Here, we assessed microbial activity by metatranscriptomics in a Tibetan alpine grassland after a decade of experimental warming (+2°C) and altered precipitation (+50% and -50% of ambient precipitation). The experiment revealed that altered precipitation, rather than warming, shaped the active microbial community. Altered precipitation and warming had significant interactions: warming combined with increased precipitation generally suppressed microbial carbohydrate metabolism and methane oxidation, while warming with decreased precipitation enhanced these processes. Notably, increased precipitation induced a shift in microbial communities towards acid metabolism over sugar metabolism, predominantly driven by taxa such as Betaproteobacteria. This metabolic shift corresponded with an increased emission ratio of methane (CH4) to carbon dioxide (CO2), a change primarily driven by CH4, underscoring the critical role of microbial carbon metabolic preferences in regulating greenhouse gas emissions. Our findings highlight the necessity of integrating microbial carbon metabolic preferences and their interactions with climatic factors into models to accurately predict carbon-climate feedbacks.IMPORTANCEMicrobes have specific preferences for different carbon substrates, but their responses to climate change remain unclear. Our study, conducted through a long-term climate manipulation experiment in a Tibetan alpine grassland, reveals that increased precipitation leads soil microbial communities to favor acid metabolism over sugar metabolism. This shift significantly affects greenhouse gas emissions by increasing the CH4/CO2 ratio, which has important implications for global warming. These findings are crucial for accurately forecasting carbon-climate feedbacks and managing alpine ecosystems as climate change progresses.},
}

@article {pmid40715283,
year = {2025},
author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM},
title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27297},
pmid = {40715283},
issn = {2045-2322},
mesh = {*Biofilms/growth & development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; },
abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.},
}

*Biofilms/growth & development
*Hot Springs/microbiology
*Metagenome
Hot Temperature
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Biodiversity
Genome, Bacterial
Metagenomics/methods
Malaysia

@article {pmid40711892,
year = {2025},
author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and , },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002111},
pmid = {40711892},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; },
abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.},
}

*Viruses/classification/genetics
*Bacteria/virology
Phylogeny
*Classification/methods

@article {pmid40711674,
year = {2025},
author = {Xiong, Q and Wang, R and Lai, D and Cai, S and Wang, H and Zhou, N},
title = {Metagenomic Insights into the Root‒Soil Response Mechanisms of Indica and Japonica Rice Under Nitrogen Deficiency and High-Efficiency Nitrogen Compensation.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {72},
pmid = {40711674},
issn = {1939-8425},
support = {32101816//National Natural Science Foundation of China/ ; 2021M702768//China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; 2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; 202425YBKT17//Jiangxi Provincial Water Resources Department Science and Technology Project/ ; 20242BAB20263//Natural Science Foundation of Jiangxi Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Nitrogen (N) dynamics critically regulate rice productivity through root-mediated absorption and assimilation processes. This study investigates the differential responses of japonica (Suxiu 867) and indica (Yangxianyou 918) rice to N deficiency and subsequent high-efficiency compensation, integrating metagenomic analysis with physiological assessments of N metabolism. Building on an established high-efficiency N compensation period (18 days after tillering for japonica and 12 days for indica), we demonstrate that optimized N compensation significantly enhances dry matter accumulation and yield in both subspecies through distinct biological mechanisms. Compensation treatment elevated key metabolic indicators including soluble protein content (Cpr), glutamine synthetase (GDH) activity, soil urease (S-UE) activity, glutamate synthase (GOGAT) activity, and glutamine synthetase (GS) activity, collectively enhancing N assimilation efficiency. Rhizosphere microbiome restructuring showed subspecies-specific patterns, with Chloroflexi and Betaproteobacteria abundance positively correlating with N metabolic enzymes in indica, versus Actinomycetia, Deltaproteobacteria associations in japonica. Functional microbial analysis revealed divergent keystone taxa, with Noviherbaspirillum (indica) and Bacillus (japonica) driving N conversion efficiencies through niche-specific community synergies. Notably, indica rice presented a relatively high N absorption capacity and conversion efficiency, while japonica rice presented relatively stable N absorption and distribution mechanisms, and relatively high N fertilizer application significantly increased the abundance of specific microbial communities in japonica rice. These findings elucidate how subspecies-specific root physiology coordinates with rhizosphere microbial ecology to optimize N utilization, providing actionable insights for precision N management strategies tailored to rice genetic types.},
}

@article {pmid40711470,
year = {2025},
author = {Lera-Lozano, D and Ruiz-Toquica, JS and Kratman, SA and Holt, MW and McIntyre, CA and Jones, EK and Lopez-Victoria, M and Ritchie, KB and Medina, M and González-Pech, RA},
title = {Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001456},
pmid = {40711470},
issn = {2057-5858},
mesh = {*Bacteria/genetics/metabolism/isolation & purification/classification ; *Rhodophyta/microbiology ; Biosynthetic Pathways/genetics ; *Anti-Bacterial Agents/biosynthesis ; Multigene Family ; *Anti-Infective Agents/metabolism ; Genome, Bacterial ; Animals ; *Anthozoa/microbiology ; Genomics ; Microbiota/genetics ; Phylogeny ; },
abstract = {The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA.},
}

*Bacteria/genetics/metabolism/isolation & purification/classification
*Rhodophyta/microbiology
Biosynthetic Pathways/genetics
*Anti-Bacterial Agents/biosynthesis
Multigene Family
*Anti-Infective Agents/metabolism
Genome, Bacterial
Animals
*Anthozoa/microbiology
Genomics
Microbiota/genetics
Phylogeny

@article {pmid40709922,
year = {2025},
author = {Li, H and Li, W and Liu, X and Zhang, J and Lin, C and Ji, S and Jiang, H and Wang, T and Su, Z},
title = {The gut microbiota features and the application value in predicting recurrent risks for gallstone patients who underwent laparoscopic cholecystectomy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0176024},
doi = {10.1128/msystems.01760-24},
pmid = {40709922},
issn = {2379-5077},
abstract = {Gut microbiota is associated with gallstone occurrence and recurrence. But whether they can predict post-cholecystectomy choledocholithiasis recurrence needs to be investigated. From September 2020 to June 2021, a total of 100 symptomatic gallstone patients scheduled for laparoscopic cholecystectomy were enrolled in the Disease group in the Department of Hepatobiliary Surgery at Quanzhou First Hospital. Meanwhile, a total of 50 age- and sex-matched healthy controls were included in the Control group. Fecal specimens were collected from both groups and subjected to 16S rDNA sequencing (V3V4 region) for microbiologic analysis. After laparoscopic cholecystectomy, patients were followed up, and recurrent cases were recorded. Finally, a nomogram for predicting recurrent risks was built. The gut microbial diversity in the Disease group was significantly lower than that of the Control group (all P < 0.05). The Chao1 index of the recurrent group was remarkably lower than the control group (P < 0.05). Linear discriminant analysis (LDA) effect size (LEfSe) analysis showed that Phocaeicola dorei (LDA score = 4.2, P < 0.05) was the feature microbiota in the recurrent group. Logistic regression analysis showed that the composition of stones, the high abundances of P. dorei and Fusobacterium necrogenes were potential risk factors for recurrent choledocholithiasis, and a nomogram based on these factors demonstrated high accuracy and excellent calibration. This study has identified potential risk factors for recurrent choledocholithiasis and built a nomogram that can well predict recurrent risks for patients who undergo cholecystectomy, which might serve as a useful tool for patients' stratification and post-surgery management.IMPORTANCEThis study identifies specific gut microbiome signatures of gallstone patients and indicates that reduced diversity and high abundances of Phocaeicola dorei and Fusobacterium necrogenes might be potential predictors for choledocholithiasis recurrence after cholecystectomy. By demonstrating a link between gut microbiota composition and post-surgical recurrence risk, it advances our understanding beyond simple association with predictive capability. The development of a nomogram incorporating these microbial markers provides a novel, clinically applicable tool for accurate risk stratification of patients undergoing cholecystectomy, therefore bridging the gap between microbial ecology and clinical practice. The significance of this study lies in that it aims to address a critical unmet need in gallstone disease management by offering a more cost-effective and non-invasive tool to improve long-term patient outcomes and pave the way for microbiome-targeted interventions.CLINICAL TRIALSThis study is registered with Chinese Clinical Trial Registry Center as ChiCTR2400090232.},
}

@article {pmid40708948,
year = {2025},
author = {Zai, X and Zhu, F and Zhao, M and Diao, X and Zhang, F and Dini-Andreote, F and Melkonian, C and Medema, MH and Raaijmakers, JM and Cordovez, V and Song, C},
title = {Harnessing the phyllosphere microbiota of wild foxtail millet for designing beneficial cross-kingdom synthetic communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf066},
pmid = {40708948},
issn = {2730-6151},
abstract = {Understanding the interplay between mechanisms in plant microbiome assembly and functioning of wild ancestors has led to the proposal of a novel strategy to enhance resilience to the (a)biotic stresses of domesticated crops. The challenge is determining how to harness the diverse microbiota of wild crop ancestors in their natural habitats in order to design effective synthetic microbial communities (SynComs) that reconstitute specific microbiome-associated plant phenotypes. In this study, we profiled the phyllosphere microbiota of wild green foxtail collected from seven geographically diverse natural ecosystems and showed that variations in soil parameters and climatic conditions as well as plant genetic distance significantly correlated with bacterial and fungal community compositions. Environmental selection and dispersal limitation differently governed the assembly of bacterial and fungal communities with distinct habitat niche breadth. Specific bacterial and yeast genera were identified as core phyllosphere taxa of wild green foxtail millet on the basis of their abundance and prevalence across the seven sampling sites. Moreover, several genera of bacteria (Bacillus, Pantoea, Methylobacterium) and yeast (Vishniacozyma, Filobasidium, Sporobolomyces) displayed significant correlations with the abundances of one or more foliar pathogenic fungi, in particular fungi of the genus Alternaria. Subsequent isolation and characterization of these bacterial and yeast genera allowed the design of cross-kingdom SynComs that protected domesticated foxtail millet from leaf infections by Alternaria alternata. These results provide fundamental insight into the mechanisms governing the phyllosphere microbiota assembly of a wild crop ancestor across large geographic scales and a practical framework to leverage this fundamental knowledge for the design of SynComs that mitigate the biotic stress of the domesticated crop.},
}

@article {pmid40708946,
year = {2025},
author = {Liu, ZQ and Yang, XY and Chen, JH and Ge, SC and Dai, SX and Zhu, SH and Xian, ZY},
title = {From dysbiosis to precision therapy: decoding the gut-bladder axis in bladder carcinogenesis.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1630726},
pmid = {40708946},
issn = {2234-943X},
abstract = {The gut-bladder axis (GBA), a bidirectional network connecting gastrointestinal and urinary systems, has recently emerged as a pivotal focus in bladder cancer research. Beyond conventional risk factors, gut dysbiosis, aberrant microbial metabolites, and neuro-immune pathway disruptions have been implicated in tumorigenesis and progression. Short-chain fatty acids (SCFAs), microbial-derived metabolites, are shown to indirectly modulate tumor behavior through immune microenvironment regulation and inflammatory response attenuation. Cross-organ crosstalk is further mediated by neural pathways (e.g., vagal signaling) and shared receptors, including the Farnesoid X Receptor (FXR) and Toll-like Receptor 4 (TLR4). Novel therapies leveraging microbial ecology principles demonstrate potential, including immune checkpoint inhibitors combined with microbiota modulation (e.g., Parabacteroides distasonis-enhanced PD-1 efficacy), probiotics to reverse chemoresistance, and microbiota reprogramming for SCFA-targeted strategies. However, molecular mechanisms underlying GBA-host interactions remain poorly characterized. Clinical translation is hindered by limited cohort sizes and interindividual heterogeneity. Current studies, while revealing partial pathways, face methodological inconsistencies, particularly in urinary microbiome profiling, and a lack of longitudinal human data. Future breakthroughs will require multi-omics integration, organoid-based models, and interdisciplinary collaboration to address these gaps.},
}

@article {pmid40708752,
year = {2025},
author = {Zhang, Y},
title = {Fucoidan as a therapeutic agent for ulcerative colitis: mechanisms of action and modulation of the gut microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1626614},
pmid = {40708752},
issn = {2235-2988},
mesh = {*Polysaccharides/pharmacology/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Animals ; Cytokines/metabolism ; *Anti-Inflammatory Agents/pharmacology/therapeutic use ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; },
abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease driven by gut dysbiosis, immune dysregulation, and oxidative stress, lacks universally effective therapies. Fucoidan (FCD), a sulfated polysaccharide derived from brown algae, has emerged as a multifaceted therapeutic candidate due to its anti-inflammatory, antioxidant, and immunomodulatory properties. This review synthesizes FCD's mechanisms in UC pathogenesis, emphasizing its suppression of NF-κB and MAPK signaling pathways to reduce proinflammatory cytokines (e.g., IL-6, TNF-α) and regulate TLR-mediated macrophage polarization. FCD enhances intestinal barrier integrity via upregulation of tight junction proteins (Claudin-1, ZO-1) and mucin MUC2 expression, while remodeling gut microbial ecology through enrichment of SCFAs-producing bacteria (e.g., Ruminococcaceae) and suppression of pathogens (Escherichia coli, Candida albicans). Preclinical studies highlight LMWF as a superior candidate, demonstrating enhanced bioavailability and efficacy in mitigating DSS-induced colitis. Despite its promise, challenges persist in structural heterogeneity (source- and extraction-dependent), scalable production of LMWF, and insufficient pharmacokinetic data. Emerging strategies-including nanoparticle-based delivery systems and structural modifications (cross-linking, covalent bonding)-aim to overcome bioavailability limitations. This review underscores FCD's potential as a functional food or adjuvant therapy for UC, while advocating for rigorous clinical validation to bridge translational gaps, Enrichment of SCFAs-producing taxa and suppression of pathobionts (Escherichia coli, Candida albicans), mediated through prebiotic fermentation. Suppression of NF-κB activation via IκBα stabilization and inhibition of p65 nuclear translocation, and downregulation of MAPK phosphorylation (ERK1/2, JNK, p38), reducing proinflammatory cytokines (IL-6, TNF-α, IL-1β). FCD can be used as a potential treatment for UC.},
}

*Polysaccharides/pharmacology/therapeutic use
Humans
*Gastrointestinal Microbiome/drug effects
*Colitis, Ulcerative/drug therapy/microbiology
Animals
Cytokines/metabolism
*Anti-Inflammatory Agents/pharmacology/therapeutic use
NF-kappa B/metabolism
Signal Transduction/drug effects

@article {pmid40708120,
year = {2025},
author = {Perkins, AK and Grossart, HP and Rojas-Jimenez, K and Retter, A and Oakes, JM},
title = {The Functional Role of Fungi and Bacteria in Sulfur Cycling During Kelp (Ecklonia Radiata) Degradation: Unconventional Use of PiCrust2.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70140},
pmid = {40708120},
issn = {1758-2229},
support = {RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security, HUN-REN Balaton Limnological Research Institute/ ; DFG GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Sulfur/metabolism ; *Bacteria/metabolism/genetics/classification ; *Fungi/metabolism/genetics/classification ; *Kelp/microbiology/metabolism ; Metabolic Networks and Pathways ; Ecosystem ; High-Throughput Nucleotide Sequencing ; },
abstract = {Macroalgae is a major source of detritus in coastal ecosystems, contributing approximately 1521 ± 732 Tg C year[-1] to global net primary production. Fungal remineralisation of Ecklonia radiata detritus produces substantial amounts of dimethylsulfoniopropionate, total alkalinity, and dissolved inorganic carbon, supporting coastal biogeochemical cycles. To expand on the role of fungi during E. radiata degradation, we examined changes in fungal and bacterial communities at the start and after 21 days in a mesocosm, comparing microbial functional roles between blades and stipes. We employed next-generation sequencing to evaluate the potential contributions of fungi and bacteria, and additionally utilized FUNGuild, FungalTraits, and PiCrust2 databases. We cross-referenced the metabolic pathways predicted by PiCrust2 with the literature to determine whether these pathways have been documented in fungi. Of the 423 metabolic pathways identified, 342 have also been reported in fungi, including 281 redox-related pathways, 220 associated with nicotinamide adenine dinucleotide, and 194 linked to sulfur metabolism. These overlaps suggest that bacteria and fungi could play complementary roles in kelp degradation, contributing distinct yet interconnected functions. Our results highlight that these metabolic pathways cannot be attributed to bacteria alone and fungi are essential to kelp remineralisation.},
}

*Sulfur/metabolism
*Bacteria/metabolism/genetics/classification
*Fungi/metabolism/genetics/classification
*Kelp/microbiology/metabolism
Metabolic Networks and Pathways
Ecosystem
High-Throughput Nucleotide Sequencing

@article {pmid40707845,
year = {2025},
author = {Jürisoo, L and Agan, A and Tedersoo, L and Witzell, J and Selikhovkin, A and Drenkhan, R},
title = {Fungal Assemblages in Northern Elms-Impacts of Host Identity and Health, Growth Environment, and Presence of Dutch Elm Disease.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {82},
pmid = {40707845},
issn = {1432-184X},
support = {PRG1615//Estonian Research Competency Council/ ; TEMTA22//the European Union and Ministry of Education and Research/ ; },
mesh = {*Plant Diseases/microbiology ; *Ulmus/microbiology/growth & development/genetics ; Estonia ; Endophytes/genetics/classification/isolation & purification ; *Mycobiome ; *Ophiostoma/genetics/isolation & purification ; Russia ; *Fungi/classification/genetics/isolation & purification ; },
abstract = {Dutch elm disease (DED), caused by the pathogenic ascomycete Ophiostoma novo-ulmi, has devastated natural elm (Ulmus spp.) populations in Europe and North America. Elm species vary in their susceptibility to this vascular disease, which may partly reflect differences in their associated mycobiomes. To investigate the diversity and composition of fungal endophyte communities in relation to host genotype, health status, and environment, we analyzed twig-associated fungi in symptomatic and asymptomatic individuals of highly susceptible U. glabra, less susceptible U. laevis, and hybrid elms growing in Estonia and Russia. Fungal communities were analyzed using PacBio long-read amplicon sequencing of the ITS1-5.8S-ITS2 gene region. Tree species exhibited distinct fungal community profiles. Ophiostoma novo-ulmi was detected exclusively in symptomatic trees and was dominant in U. glabra; it was absent in symptomatic hybrid elms. In contrast, the canker-associated pathogen Sphaeropsis ulmicola occurred in both symptomatic and asymptomatic trees, was dominant in symptomatic U. laevis, and common in symptomatic and healthy U. glabra, though less prevalent in symptomatic hybrid elms. Remarkably, S. ulmicola was associated with the highest level of damage in U. laevis while being present also in hybrid elms. While O. novo-ulmi's presence did not affect overall fungal richness, S. ulmicola was linked to higher fungal diversity. Additionally, fungal species richness was significantly greater in urban compared to rural environments. This was the first comparable analysis of fungal diversity and composition on three different Ulmus species shoots.},
}

*Plant Diseases/microbiology
*Ulmus/microbiology/growth & development/genetics
Estonia
Endophytes/genetics/classification/isolation & purification
*Mycobiome
*Ophiostoma/genetics/isolation & purification
Russia
*Fungi/classification/genetics/isolation & purification

@article {pmid40707215,
year = {2025},
author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE},
title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.},
journal = {Microbes and environments},
volume = {40},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME24067},
pmid = {40707215},
issn = {1347-4405},
mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Archaea/classification/metabolism/genetics/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; },
abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.},
}

*Hot Springs/microbiology/chemistry
Japan
*Bacteria/classification/metabolism/genetics/isolation & purification
*Archaea/classification/metabolism/genetics/isolation & purification
Oxidation-Reduction
Phylogeny
Nitrogen Fixation
Oceans and Seas
Iron/metabolism
*Biodiversity
Carbon Cycle
RNA, Ribosomal, 16S/genetics
Nitrogen Cycle
Hydrogen/metabolism

@article {pmid40705368,
year = {2025},
author = {Duff, AM and Giles, M and Ganasamurthy, S and Santos, A and Morales, SE and Brennan, F},
title = {Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {8},
pages = {},
doi = {10.1093/femsec/fiaf073},
pmid = {40705368},
issn = {1574-6941},
support = {696356//European Union/ ; },
mesh = {*Soil Microbiology ; *Real-Time Polymerase Chain Reaction/methods/standards ; *Microbiota/genetics ; *Bacteria/genetics/isolation & purification ; },
abstract = {Quantitative polymerase chain reaction (qPCR) is widely used in soil microbial ecology to quantify microbial communities, but its accuracy can be compromised by coextracted inhibitors. Furthermore, large-scale international studies involving multiple laboratories or meta-analyses studies can introduce variation in qPCR results when data generated from different sources are compared. This study evaluated the performance of four commercial mastermixes across different soil types, a mock community, and a positive template control against three targets on three widely used platforms. Sensitivity to inhibitors was tested, with one mastermix affected, although this was mitigated by adding 1 mg/ml bovine serum albumin. Amplification success varied by mastermix, platform, gene, and sample matrix. Most mastermix-platform combinations showed low accuracy emphasizing the need for careful pairing. Precision was primarily influenced by gene target, followed by platform, sample matrix, and mastermix, and was reduced at lower template concentrations. Only 64.67% of intraassay (within an assay) measurements meet accepted thresholds. Interassay (between platforms) quantification was unreliable due to significant variability, which increased the risk of inaccurate data interpretation. The study highlights the necessity of considering inter- and intraassay variation, assay accuracy, and inhibitors that may impact sample amplification when utilizing qPCR for quantification of microbial communities in environmental samples.},
}

*Soil Microbiology
*Real-Time Polymerase Chain Reaction/methods/standards
*Microbiota/genetics
*Bacteria/genetics/isolation & purification

@article {pmid40705167,
year = {2025},
author = {Gdanetz, K and Noel, ZA and Saville, K and Marsh, T and Scribner, KT and Trail, F},
title = {Eukaryotic Microbiome of Lake Sturgeon Eggs, and Identification of Chemical Thresholds for Infection Control.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {80},
pmid = {40705167},
issn = {1432-184X},
mesh = {Animals ; *Fishes/microbiology ; *Microbiota/drug effects ; Lakes/microbiology ; *Fish Diseases/microbiology/prevention & control/parasitology ; *Ovum/microbiology ; *Fungi/isolation & purification/classification/drug effects/genetics ; Oomycetes/drug effects/isolation & purification ; Aquaculture ; *Eukaryota/isolation & purification/classification/drug effects/genetics ; },
abstract = {Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.},
}

Animals
*Fishes/microbiology
*Microbiota/drug effects
Lakes/microbiology
*Fish Diseases/microbiology/prevention & control/parasitology
*Ovum/microbiology
*Fungi/isolation & purification/classification/drug effects/genetics
Oomycetes/drug effects/isolation & purification
Aquaculture
*Eukaryota/isolation & purification/classification/drug effects/genetics