@article {pmid41135049,
year = {2025},
author = {Zhang, X and Guo, Y and Shi, J and Zang, Q and Li, Y},
title = {Exclusive Effects of Moxibustion on Gut Microbiota: Protocol for a Focused Systematic Review and Meta-Analysis.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e73317},
doi = {10.2196/73317},
pmid = {41135049},
issn = {1929-0748},
mesh = {*Moxibustion/methods ; *Gastrointestinal Microbiome/physiology ; Humans ; Meta-Analysis as Topic ; Systematic Reviews as Topic ; Animals ; Research Design ; },
abstract = {BACKGROUND: The gut microbiota (GM) plays a critical role in systemic health, influencing immune, metabolic, and neurological functions. There is emerging evidence suggesting that moxibustion, a traditional thermal therapy, may modulate the GM to restore microbial homeostasis, yet its exclusive effects remain undifferentiated from those of combined therapies such as acupuncture. Previous meta-analyses lack mechanistic specificity, necessitating a focused evaluation of moxibustion's impact on microbial ecology.

OBJECTIVE: This systematic review and meta-analysis aims to quantify moxibustion-induced changes in GM diversity, taxonomic composition, and functional metabolites (eg, short-chain fatty acids).

METHODS: We will systematically search the PubMed, Web of Science, Cochrane Library, China National Knowledge Infrastructure, Wanfang, and VIP databases from inception to December 31, 2024, using keywords such as "moxibustion," "gut microbiota," and "intestinal flora." Eligible preclinical (animal) and clinical (human) studies evaluating stand-alone moxibustion interventions on the GM will be included. Primary outcomes include microbial α diversity indexes (Shannon and Simpson) and relative abundance of key taxa (eg, Firmicutes and Bacteroidetes). Risk of bias will be assessed using the Systematic Review Center for Laboratory Animal Experimentation risk-of-bias tool for animal studies and the modified Collaborative Approach to Meta-Analysis and Review of Animal Data from Experimental Studies criteria for human trials. Pooled effect estimates for continuous outcomes (eg, diversity indexes and taxa ratios) will be calculated using the ratio of means with 95% CIs. Statistical analyses will be conducted in RevMan (version 5.4) and R (metafor package), with data archived on Figshare for reproducibility.

RESULTS: As of March 2025, the literature search and screening have been completed, and 31 studies meeting the inclusion criteria have been identified. The comprehensive analysis is scheduled to be completed by October 2025, with results anticipated to be published in late 2025. On the basis of previous work, an anticipated result is that moxibustion may reduce pathogenic genera such as Ruminococcus while enhancing beneficial genera, effects that are expected to be associated with improved intestinal barrier integrity and anti-inflammatory responses.

CONCLUSIONS: This protocol provides a rigorous framework to evaluate moxibustion's unique role in GM modulation, bridging traditional medicine with microbiome science. The results will inform optimized, nonpharmacological strategies for managing microbiome-associated chronic diseases and guide future research priorities.},
}

*Moxibustion/methods
*Gastrointestinal Microbiome/physiology
Humans
Meta-Analysis as Topic
Systematic Reviews as Topic
Animals
Research Design

@article {pmid41131424,
year = {2025},
author = {Aidarova, A and Carels, M and Haegman, M and Driege, Y and Timmermans, S and Van Damme, E and Aguilera-Lizarraga, J and Viola, MF and de Cássia Collaço, R and Manils, J and Ley, SC and Bosmans, F and Van de Wiele, T and Boeckxstaens, G and Libert, C and Beyaert, R and Afonina, IS},
title = {CARD14 signaling in intestinal epithelial cells induces intestinal inflammation and intestinal transit delay.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {41131424},
issn = {1757-4684},
support = {G035517N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G0I1422//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G000220N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 12Z3922N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; G0A7T24N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3G086521//Fonds Wetenschappelijk Onderzoek (FWO)/ ; 3S003122//Strategic Basic Research grants from FWO/ ; 3179K5620//Strategic Basic Research grants from FWO/ ; 01G00419//Ghent University grant GOA/ ; 01M00121//Methusalem/ ; 2024/01/511//Universiteit Gent (UGent)/ ; 365C06721//Stichting Tegen Kanker (Fondation Contre le Cancer)/ ; 222487/Z/21/Z//Wellcome Trust Investigator/ ; },
abstract = {CARD14 is an intracellular NF-κB signaling mediator in the skin, and rare CARD14 variants have been associated with psoriasis and atopic dermatitis. CARD14 is also expressed in intestinal epithelial cells (IEC). However, its function in the intestine remains unknown. We demonstrate here that transgenic mice expressing the psoriasis-associated gain-of-function human CARD14(E138A) mutant specifically in IEC show mild intestinal inflammation, without epithelial damage. Moreover, CARD14(E138A)[IEC] mice show a drastic reduction in intestinal motility, often associated with rectal prolapse. Enteric neuronal survival and functionality are unaffected in CARD14(E138A)[IEC] mice. Transcriptome analysis of IEC from CARD14(E138A)[IEC] mice reveals decreased expression of antimicrobial peptides by Paneth cells, accompanied by microbial dysbiosis and increased susceptibility to enteric bacterial infection. Our findings suggest that gain-of-function CARD14 mutations may not only predispose patients to psoriasis but also mild intestinal inflammation, reduced intestinal motility, and increased sensitivity to intestinal infection. CARD14(E138A)[IEC] mice are also a valuable tool for further investigation of IEC-intrinsic molecular processes involved in intestinal inflammation and motility disorders.},
}

@article {pmid41131131,
year = {2025},
author = {Corduneanu, A and Bendjeddou, ML and Sándor, AD and Mihalca, AD and Hornok, S and Péter, Á and Khelfaoui, F and Aželytè, J and Obregon, D and Mateos-Hernández, L and Maitre, A and Abuin-Denis, L and Wu-Chuang, A and Kratou, M and Ben Said, M and Cabezas-Cruz, A},
title = {Microbial network assembly in bat flies with differing host specificity from North Africa.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41131131},
issn = {1618-1905},
support = {14/2022-2024//Ministerul Cercetării şi Inovării/ ; 1500107//Hungarian Research Network/ ; NTP-NFTÖ-20-B-0094//Hungarian Ministry of Human Resources, Hungary/ ; SGCE - RAPPORT No 0300//Collectivité de Corse/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; },
abstract = {The study investigates the microbial composition of bat flies (Diptera: Nycteribiidae) collected from Myotis punicus in Algeria, focusing on the diversity and dynamics of their microbiota through network analysis. The analysis targets two genera, Nycteribia and Penicillidia, comparing oioxenous and stenoxenous species to understand host specificity's influence on microbial communities. Utilizing 16S rRNA sequencing, alpha and beta diversity metrics, and co-occurrence networks, the study assesses microbial diversity, community composition, and the impact of specific bacteria (endosymbionts, commensals, and pathogens) on network stability. Results reveal significant microbial community variations between genera and species, with N. latreillii exhibiting the most complex network. We showed that host specificity and feeding strategies significantly influence microbial diversity and interactions within bat flies. Robustness analysis through node removal simulations identifies the roles of key bacteria, such as Wolbachia, Arsenophonus, and Bartonella, in maintaining network stability. Findings highlight the complex interplay between these microorganisms and their hosts, offering insights into microbial ecology and vector-pathogen dynamics. The research underscores the importance of bat flies in shaping pathogen transmission networks, contributing valuable knowledge to wildlife ecology, disease control, and conservation strategies.},
}

@article {pmid41129402,
year = {2025},
author = {Kovács, E and Szűcs, C and Juhász-Erdélyi, A and Bagi, Z and Kovács, KL},
title = {Anaerobic fungi - effective warriors in lignocellulosic biomass degradation and fermentation.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf108},
pmid = {41129402},
issn = {1574-6941},
abstract = {The significant advancements in understanding the roles of anaerobic fungi within microbial ecology have opened numerous avenues for biotechnological exploitation, particularly in enhancing the productivity of livestock. The efficient, unique, and complex enzyme systems of anaerobic fungi play a determining role in the metabolic conversion of lignocellulosic plant matter into animal products such as milk and meat by mammalian herbivores. Mitigation of methane emissions through microbial or dietary strategies in ruminants is a major environmental climate change issue. In turn, controlled management of the inter-kingdom syntrophic interactions among the eukaryotic anaerobic fungi, prokaryotic bacteria and archaea can lead to the production of valuable biofuels, (biomethane, biohydrogen, bioethanol), and organic acids. These products can also serve as building blocks in numerous processes to generate high value chemicals in circular bioeconomy.},
}

@article {pmid41128906,
year = {2025},
author = {Ma, Z and Wang, J and Huang, C and Cao, Y and Sun, Y and Hu, Y and Basit, MF and Huang, J},
title = {Effects of Facility Cultivation Shaping Soil Microbial Community Structure in Jujube Orchard.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {112},
pmid = {41128906},
issn = {1432-184X},
support = {2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 2019YFD1001605//National Key Research and Development Program of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; 31870584//National Natural Science Foundation of China/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; XJCYTX-01//Xinjiang Jujube Industrial Technology System/ ; },
mesh = {*Soil Microbiology ; *Ziziphus/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; Soil/chemistry ; *Mycorrhizae/classification/genetics/isolation & purification ; *Microbiota ; Nitrogen/analysis ; *Agriculture/methods ; Carbon/analysis ; Hydrogen-Ion Concentration ; Biodiversity ; },
abstract = {Facility cultivation systems provide protection for jujube (Ziziphus jujuba) against rain-induced fruit cracking during the maturation and regulate the fruit ripening process. Prolonged cultivation within these controlled environments may alter the soil microbial community structure, potentially detrimentally affecting plant growth and fruit quality. There is a lack of information regarding the arbuscular mycorrhizal fungi (AMF) and bacterial communities in orchards under facility conditions. This study compared the soil bacterial and AMF communities in jujube orchards under greenhouse and rain shelter conditions. Greenhouse cultivation significantly increased soil organic carbon (SOC), total nitrogen (TN), and electrical conductivity, while it decreased soil pH compared to rain shelters. These changes were associated with reduced α-diversity indices in both bacterial and AMF communities. Non-metric multidimensional scaling analysis demonstrated distinct differences between bacteria and AMF communities under the two cultivation types. The phyla Actinobacteria, Gemmatimonadetes, and Rokubacteria were identified as key contributors to the observed alterations in the bacterial community, while variations in the genus Glomus and Paraglomus were responsible for changes in the AMF communities between the two cultivation types. Redundancy analysis revealed that pH was the primary factor shaping microbial community structure across the two cultivation types. Using a Zi-Pi plot, we identified several keystone ASVs, which showed a positive correlation with pH, SOC, and TN. The findings highlight the significant impact of cultivation type on soil microbial community structure and function, which has important implications for optimizing cultivation practices and ensuring sustainable jujube production.},
}

*Soil Microbiology
*Ziziphus/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
Soil/chemistry
*Mycorrhizae/classification/genetics/isolation & purification
*Microbiota
Nitrogen/analysis
*Agriculture/methods
Carbon/analysis
Hydrogen-Ion Concentration
Biodiversity

@article {pmid41127647,
year = {2025},
author = {von Friesen, LW and Farnelid, H and von Appen, WJ and Benavides, M and Grosso, O and Laber, CP and Schüttler, J and Sundbom, M and Torres-Valdés, S and Bertilsson, S and Peeken, I and Snoeijs-Leijonmalm, P and Riemann, L},
title = {Nitrogen fixation under declining Arctic sea ice.},
journal = {Communications earth & environment},
volume = {6},
number = {1},
pages = {811},
pmid = {41127647},
issn = {2662-4435},
abstract = {With climate change-induced sea ice decline in the Arctic Ocean, nitrogen is expected to become an increasingly important determinant of primary productivity. Nitrogen fixation is the conversion of molecular nitrogen to bioavailable ammonium by microorganisms called diazotrophs. Here, we report nitrogen fixation rates, diazotroph composition, and expression under different stages of declining sea ice in the Central Arctic Ocean (multiyear ice, five stations) and the Eurasian Arctic (marginal ice zone, seven stations). Nitrogen fixation in the Central Arctic Ocean was positively correlated with primary production, ranging from 0.4 ± 0.1 to 2.5 ± 0.87 nmol N L[-1] d[-1]. Along two transects across the marginal ice zone, nitrogen fixation varied between days and ice regime from below detection up to 5.3 ± 3.65 nmol N L[-1] d[-1] associated with an ice-edge phytoplankton bloom. We show nitrogen fixation in sea ice-covered waters of the Arctic Ocean and provide insight into present and active non-cyanobacterial diazotrophs in the region.},
}

@article {pmid41127399,
year = {2025},
author = {Guo, Y and Ouyang, H and Su, J and Zhong, M and Huang, W and Huang, M and Xie, C},
title = {Developing and validating a nomogram for predicting endoscopic hemostasis failure in cirrhotic patients with esophageal variceal bleeding.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1670759},
pmid = {41127399},
issn = {2296-858X},
abstract = {BACKGROUND AND AIMS: This study aimed to create and validate a model to predict the failure of endoscopic hemostasis in Chinese cirrhosis patients with acute esophagogastric variceal bleeding (EGVB), enabling early identification of high-risk individuals.

METHODS: A retrospective study analyzed 296 cirrhotic patients with EGVB who received emergency endoscopic therapy from January 2020 to February 2025. Patients were divided into success (n = 273) and failure (n = 23, defined as bleeding recurrence within 5 days) groups. LASSO regression optimized variable selection, and multivariate logistic regression identified independent predictors to create a nomogram. Internal validation used Bootstrap resampling (500 iterations). Model performance was assessed using ROC curves, calibration plots, and decision curve analysis (DCA), and compared with CTP (Child-Turcotte-Pugh), MELD (Model for End-Stage Liver Disease), and Rockall scores.

RESULTS: The cumulative incidence of endoscopic failure was observed to be 7.8%. Independent predictors identified included a shock index (SI) > 1.2 (OR = 5.447), the presence of a red color (RC) sign (OR = 10.005), active bleeding observed during endoscopy (OR = 5.962), and the CTP (OR = 1.584). The nomogram exhibited superior discriminatory power with an AUC of 0.890 (95% CI: 0.820-0.960), outperforming the CTP (AUC = 0.771, 95% CI: 0.656-0.886; P < 0.001), MELD (AUC = 0.733, 95% CI: 0.616-0.849; P < 0.001), and Rockall (AUC = 0.656, 95% CI: 0.545-0.768; P < 0.001). Calibration was satisfactory as indicated by the Hosmer-Lemeshow test (χ[2] = 10.021, P = 0.263). DCA demonstrated a clinical net benefit across a broad range of thresholds.

CONCLUSION: A validated nomogram that integrates the SI, RC sign, active bleeding, and CTP provides an effective prediction of the risk of endoscopic hemostasis failure in patients with cirrhotic EGVB, thereby facilitating timely intervention.},
}

@article {pmid41126179,
year = {2025},
author = {Heuberger, M and Wehrkamp, CM and Pfammatter, A and Poretti, M and Graf, JP and Herger, A and Isaksson, J and Schlagenhauf, E and Honegger, R and Wicker, T and Sotiropoulos, AG},
title = {A reference metagenome sequence of the lichen Cladonia rangiformis.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {319},
pmid = {41126179},
issn = {1741-7007},
support = {310030_212428//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lichens/genetics/microbiology ; *Metagenome ; Symbiosis/genetics ; *Genome, Fungal ; *Ascomycota/genetics ; Chlorophyta/genetics ; },
abstract = {BACKGROUND: Lichens are an ancient symbiosis comprising the thalli of lichen-forming fungi, their photoautotrophic partners, and their microbiome. So far, they were poorly studied at the genome sequence level. Here, we present a reference metagenome for the holobiont of Cladonia rangiformis, aiming to illuminate the genomic complexity and evolutionary interactions within lichen symbioses.

RESULTS: Using long-read sequences from an entire symbiotic complex, plus short-read libraries from 28 additional diverse European lichen samples, we were able to separate genome sequences of 20 individual species. We constructed chromosome-scale assemblies of the C. rangiformis fungus and its trebouxioid green algal photobiont Asterochloris mediterranea. The genome of the fungus comprises ~ 22% transposable elements and is highly compartmentalized into genic regions and large TE-derived segments which show extensive signatures of repeat-induced point mutations (RIP). We found that A. mediterranea centromeres are predominantly derived from two interacting retrotransposon families. We also identified strong candidates for genes that were horizontally transferred from bacteria to both alga and fungus. Furthermore, we isolated 18 near-complete bacterial genomes, of which 13 are enriched in the lichen compared to surrounding soil. Analysis of gene content in fungus, algae, and bacteria identified 22 distinct biosynthetic gene cluster categories for known secondary metabolites.

CONCLUSIONS: Our findings revealed that the thalli of C. rangiformis have a highly complex microbiome, comprising a mix of species that may include opportunists, ecologically obligate symbionts and possibly even lichen-beneficial bacteria. This study provides the first chromosome-scale genomic framework for a lichen holobiont, offering a foundational resource for future research into metagenomics, symbiosis, and microbial ecology in lichens.},
}

*Lichens/genetics/microbiology
*Metagenome
Symbiosis/genetics
*Genome, Fungal
*Ascomycota/genetics
Chlorophyta/genetics

@article {pmid41124090,
year = {2025},
author = {Ahumada, D and Schwob, G and Osorio, M and Astorga, MS and Lavergne, C and Olgun, N and Thalasso, F and Poulin, E and Orlando, J and Cabrol, L},
title = {Higher variability of bacterial communities across space than over time in Antarctic lakes, and contrasting assembly processes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0107925},
doi = {10.1128/aem.01079-25},
pmid = {41124090},
issn = {1098-5336},
abstract = {As sentinels of environmental changes, Antarctic lakes are ideal systems for studying the temporal and spatial dynamics of microbial communities. However, the relative magnitude and underlying mechanisms driving these variations remain poorly understood. Studying the spatiotemporal variation of microbial communities is crucial to provide a robust baseline for predicting ecosystem responses to global changes. Here, we investigated the spatial and inter-annual variation of bacterial community structure and their underlying assembly processes across sediment and water habitats in 11 lakes on the Fildes Peninsula, Maritime Antarctica, sampled during austral summers from 2017 to 2023, using 16S rRNA gene sequencing. The communities primarily clustered by habitat, with higher diversity in sediment (characterized by Rhodoferax, Intraporangiaceae, and Vicinamibacterales) compared to water (characterized by Polaromonas, Flavovacterium, and Sporichthyaceae). Spatial turnover of communities dominated over inter-annual variation in both habitats. Accordingly, the temporal core microbiome showed greater stability than the spatial core. The conserved bacterial communities (core communities) over time and across space exhibited a strikingly similar taxonomic composition. Community assembly processes differed between habitats, with a stronger contribution of dispersal limitation in sediment, versus ecological drift in water, as expected from the differences in connectivity within each habitat. Spatial and temporal variations in sediment were driven by globally similar assembly processes. In contrast, in water communities, different assembly processes explained the spatial and temporal variation. These insights emphasize the need to consider both spatial and temporal scales and various habitat types when predicting future bacterial dynamics in Antarctic lakes in a changing environment.IMPORTANCEUnderstanding the inherent baseline microbial dynamics in Antarctic lakes is crucial for predicting their responses to environmental changes. Our findings underscore the predominance of spatial (rather than inter-annual) factors in shaping bacterial communities and highlight the slightly higher contribution of stochastic processes in sediment compared to water habitats. The stochastic processes differed considerably among habitats. The greater stability of the temporal core microbiome suggests a certain degree of resilience toward possible seasonal fluctuations between the inter-annual sampling dates. In water, dispersal limitation and homogeneous selection played a greater role in the spatial than in the temporal turnover of communities, whereas environmental filtering exerted a stronger influence over time. Future studies should integrate both spatial and temporal dimensions in evaluating microbial community variability to improve forecasting of ecosystem shifts in response to global change and thus provide a better baseline for Antarctic biodiversity conservation and management.},
}

@article {pmid41124050,
year = {2025},
author = {Zhu, J and Chen, C and Zhang, Y and Li, C},
title = {Impact of ecological restoration on the soil microbial communities during the restoration of damaged Mountain Slope in China's Heilong River Basin.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf262},
pmid = {41124050},
issn = {1365-2672},
abstract = {AIMS: This study aimed to elucidate the dynamics of soil microbial communities during ecological restoration on degraded mountain slopes, specifically comparing the impacts of two common strategies: aggregate spray-seeding and planted forest establishment, against undisturbed natural slopes, and assessing key drivers of microbial recovery.

METHODS AND RESULTS: Soil microbial community composition (bacteria and fungi), diversity, and co-occurrence network structure were analyzed seven years after restoration initiation. Both restoration approaches facilitated microbial community recovery, with restored slope compositions converging towards natural slope baselines. Fungal communities exhibited greater OTU diversity than bacteria, attributed to engineered substrates and rapid vegetation stabilization from spray-seeding. Crucially, restoration successfully increased microbial network complexity. Spray-seeding specifically achieved network stability comparable to natural ecosystems. Significant environmental relationships were identified: soil water content (SWC) showed negative correlations with fungal richness and composition, while below-ground biomass (BGB) positively correlated with bacterial composition.

CONCLUSIONS: Restoration effectively promotes soil microbial community recovery towards natural ecosystem states, albeit with distinct dynamics for bacteria and fungi. Fungal communities are particularly responsive to restoration techniques like spray-seeding. Soil properties (SWC) and plant development (BGB) are pivotal drivers shaping microbial assemblage during restoration.},
}

@article {pmid41123377,
year = {2025},
author = {Piccolo, BD and Chen, M-H and Lan, RS and Moody, B and Yao, T and Huang, T-Y and Pack, L and Adams, SH and Lindemann, SR},
title = {Xenometabolomics reveals metabolic functional guilds unique to specific inulin subtypes in human gut microbiota cultures.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103125},
doi = {10.1128/msystems.01031-25},
pmid = {41123377},
issn = {2379-5077},
abstract = {UNLABELLED: Dietary fibers promote positive health outcomes that are generally attributed to large bowel bacterial fermentation and associated bioactive metabolites. Historically, studies of the latter have focused on short-chain fatty acids such as butyrate. The gastrointestinal microbiota generate thousands of xenometabolites (microbe-derived, "non-host" metabolites). Most remain uncharacterized for composition and potential bioactivity, and little is known about the impact of fiber structure on the xenometabolome. Using LC/MS, we characterized culture supernatant metabolite profiles in human stool lineages derived from three healthy adult donors and six inulins covering a range of degrees of polymerization (DPs): chicory-derived Frutalose L90 (L90; DP ~ 3), Alfa Aesar (AA; DP ~ 5), Frutafit CLR (CLR; DP ~ 8), Frutafit IQ (IQ; DP ~ 12), Frutafit TEX (TEX; DP > 23), and the highly branched Frutafit agave inulin (AGA). Of the 1,219 LC/MS detected metabolites included in the final data analysis, concentrations of 704 were statistically significant (FDR < 0.1; Kruskal-Wallis test). Of these, 15 metabolites had a structural annotation, highlighting the large number of "unknown" xenometabolites associated with inulin substrates. Each fiber type led to distinct metabolite signatures, despite lineages displaying highly disparate microbial community structures within and across donors. This illustrates that fiber-specific metabolic functional guilds manifest despite highly diverse human gut bacteria communities. While speculative, these metabolic functional guilds could help explain why health effects of dietary fibers are prevalent across the population despite highly disparate gut microbiota patterns. The results also reinforce that fiber structures have a profound effect on the xenometabolome.

IMPORTANCE: Dietary fibers can convey positive health effects, but the full suite of mechanisms and fiber type differences remains to be elaborated. Historically, most discussions have focused on the impact of fibers in promoting lower gut bacterial fermentation, leading to the generation of short-chain fatty acids (especially butyrate) and promoting growth of specific microbes. That said, health effects associated with dietary fiber are generally shared across diverse individuals harboring disparate gut microbial species, and it is increasingly appreciated that xenometabolites derived from microbial metabolism number in the thousands. In the current report, we applied metabolomics characterization to human stool cultures incubated with six structurally distinct inulin fibers. The results indicate that distinct, fiber-specific metabolite signatures manifest despite quite diverse bacterial community structures across donors. Such outcomes point to the existence of metabolic functional guilds that shape the metabolite landscape-and likely the unique bioactive characteristics-across dietary fiber types.},
}

@article {pmid41123360,
year = {2025},
author = {Campbell, KD and Bohannan, BJM and Adair, KL},
title = {Assembly of skin microbiomes is more neutral than gut microbiomes in multiple animal species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0222325},
doi = {10.1128/spectrum.02223-25},
pmid = {41123360},
issn = {2165-0497},
abstract = {The gut and external tissues of most animals are colonized by communities of microorganisms that can influence the health, development, and fitness of the host. The composition of these communities can vary greatly between individuals within a host species, and both selective factors (e.g., host immune response) and neutral processes (e.g., random loss of microbial cells) have been shown to contribute to this variation. Although it is known that microbiome composition differs between tissues within an individual host, less is known about the ecological processes that underlie these differences. To address this, we investigated whether the contribution of neutral ecological processes to microbiome assembly differs between external (skin and scale) and internal (gut) host tissues for a diverse panel of animal hosts. To do this, we fit a neutral ecological model to microbial communities from external and internal tissues across a variety of animal hosts. Strikingly, we discovered that the neutral model was equally or a better fit to skin or scale microbial communities across all hosts, suggesting that neutral processes play a larger role in the assembly of skin or scale microbiomes compared with gut microbiomes. Furthermore, we observed that this trend is robust to different definitions of the metacommunity (i.e., the microbial taxa available to colonize a host). Finally, we leveraged a simulation framework to compare the model fits of empirical versus simulated microbial communities. We found that neutral model fits to empirical communities can differ from simulated communities, emphasizing the importance of temporal sampling in profiling animal microbiomes.IMPORTANCEAnimal microbiomes are complex assemblages of microorganisms that influence a wide variety of host phenotypes. Despite their importance, we lack a thorough understanding of the processes that guide the formation of microbiomes (i.e., microbiome assembly). Understanding how microbiomes assemble is essential to managing microbiomes for host health, conservation, and other goals. Our work highlights the relatively underappreciated role of neutral ecological processes (the random loss or gain of microbial cells) in the assembly of animal microbiomes. We document a potentially general trend: the microbiomes of external tissues (i.e., skin or scales) tend to be more neutrally assembled than those of internal tissues (i.e., guts). This observation suggests that the commonly reported differences in microbiome composition of external and internal animal tissues may be due in part to different assembly processes. Our work also highlights the dynamic nature of microbiomes and the importance of longitudinal sampling when studying animal microbiomes.},
}

@article {pmid41123190,
year = {2025},
author = {Dieter, C and Lemos, NE and Girardi, E and Massignam, ET and Kowalski, TW and Recamonde-Mendoza, M and Puñales, M and Assmann, TS and Crispim, D},
title = {Expression of long noncoding RNAs in peripheral blood mononuclear cells of patients with type 1 diabetes mellitus: potential biomarkers for disease onset.},
journal = {Archives of endocrinology and metabolism},
volume = {69},
number = {6},
pages = {e240496},
doi = {10.20945/2359-4292-2024-0496},
pmid = {41123190},
issn = {2359-4292},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/blood/diagnosis ; *RNA, Long Noncoding/genetics/blood/metabolism ; *Leukocytes, Mononuclear/metabolism ; Female ; Male ; Biomarkers/blood ; Adult ; Case-Control Studies ; Young Adult ; Up-Regulation ; Adolescent ; Glycated Hemoglobin/analysis ; },
abstract = {OBJECTIVE: Long non-coding RNAs (lncRNAs) do not encode proteins and are transcripts longer than 200 nucleotides. The precise involvement of lncRNAs in type 1 diabetes mellitus (T1DM) pathogenesis remains unclear. Therefore, this study aimed to analyze the expressions of five lncRNAs in peripheral blood mononuclear cells of individuals with T1DM and without DM.

MATERIALS AND METHODS: This study comprised 27 patients with T1DM (cases) and 13 individuals without DM (controls). The case group was divided into two subgroups based on T1DM duration: < 5 years of diagnosis group and long-term diabetes group (≥5 years). LncRNA expression was evaluated by qPCR.

RESULTS: MALAT1 and TUG1 were upregulated in patients within the first five years of diagnosis of T1DM compared to the other groups. MEG3 was upregulated in the case group of < 5 years of diagnosis compared to controls. TUG1 and MALAT1 levels were negatively correlated with the duration of T1DM, while TUG1 and MEG3 were positively correlated with glycated hemoglobin levels. Bioinformatics analysis revealed that MALAT1, MEG3, and TUG1 regulate and interact with protein-codifying genes and microRNAs involved in T1DM-related pathways.

CONCLUSION: Our study revealed MALAT1, MEG3, and TUG1 upregulation in patients within the first five years of diagnosis of T1DM.},
}

Humans
*Diabetes Mellitus, Type 1/genetics/blood/diagnosis
*RNA, Long Noncoding/genetics/blood/metabolism
*Leukocytes, Mononuclear/metabolism
Female
Male
Biomarkers/blood
Adult
Case-Control Studies
Young Adult
Up-Regulation
Adolescent
Glycated Hemoglobin/analysis

@article {pmid41118732,
year = {2025},
author = {Zahn, G and Amend, A and Gladfelter, A},
title = {Mycology: The rising tide of marine fungal research.},
journal = {Current biology : CB},
volume = {35},
number = {20},
pages = {R946-R948},
doi = {10.1016/j.cub.2025.09.024},
pmid = {41118732},
issn = {1879-0445},
mesh = {*Fungi/physiology ; *Seawater/microbiology ; *Carbon Cycle ; Biomass ; Oceans and Seas ; },
abstract = {A new study provides a robust global estimate of pelagic fungal biomass. Their findings reveal fungi as ecologically significant components of the ocean carbon cycle, marking a turning point for integrating fungi into marine microbial ecology.},
}

*Fungi/physiology
*Seawater/microbiology
*Carbon Cycle
Biomass
Oceans and Seas

@article {pmid41118316,
year = {2025},
author = {Liang, B and Pu, M and Xu, YN and Li, Y and Sun, JN and Zhu, Y and Doraiswamy, C and Dadd, T and Chu, CC},
title = {Dandruff scalp microbiome exhibits flake severity and sex-related differences.},
journal = {The British journal of dermatology},
volume = {193},
number = {Supplement_2},
pages = {ii32-ii39},
doi = {10.1093/bjd/ljaf099},
pmid = {41118316},
issn = {1365-2133},
support = {//Unilever Global R&D/ ; },
mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; *Dandruff/microbiology/pathology ; *Scalp/microbiology ; Adult ; Severity of Illness Index ; Sex Factors ; Middle Aged ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S ; Young Adult ; },
abstract = {BACKGROUND: Dandruff is a prevalent scalp condition characterized by flakiness and itchiness. Its severity can be assessed clinically based on the grade of flakes and coverage area of flakes adhering to the scalp. Dysbiosis of the scalp microbiome is a key factor associated with dandruff, as revealed by studies comparing healthy individuals with those with dandruff.

OBJECTIVES: This study further investigated the interplay between microbiome alterations and dandruff severity, and whether these changes are consistent across different sexes.

METHODS: Dandruff condition was assessed using the Total Weighted Head Score for Adherent Flakes (TWHS AF). Male and female participants with lower dandruff severity (TWHS AF = 32-40 inclusive) and higher dandruff severity (TWHS AF ≥ 44) were recruited following ethical clearance of the study and obtaining informed consent. Scalp bacterial composition was investigated by 16S rRNA amplicon sequencing. The absolute abundance of key scalp microbes was quantified by quantitative polymerase chain reaction.

RESULTS: Notable microbiome compositional differences were observed between scalps with lower and higher dandruff severity. More severe dandruff exhibited a significantly reduced abundance of Cutibacterium acnes and elevated levels of Staphylococcus capitis and Corynebacterium spp. The absolute numbers of Malassezia restricta significantly increased with increased dandruff severity, while M. globosa remained similar. Additionally, distinctive scalp microbial profiles were observed between female and male participants with dandruff, even with the same levels of severity. Interestingly, beta diversity analysis revealed that the microbiomes from male participants with less severe dandruff clustered closely with those of male and female participants with more severe dandruff. Similarly, microbiome metabolic pathway profiles indicated that metabolic alteration in male participants with less severe dandruff was more similar to male and female participants with more severe dandruff.

CONCLUSIONS: Our findings underscored significant severity-associated variations in microbial ecology. For the first time, we unveiled sex-related differences in microbiome profiles among individuals with dandruff, with male profiles resembling a severe dandruff dysbiosis state. These results highlight a progressive development of microbiome dysbiosis with dandruff severity and suggest potential mechanistic differences between male and female dandruff conditions, which may require different intervention strategies.},
}

Humans
Female
Male
*Microbiota/genetics
*Dandruff/microbiology/pathology
*Scalp/microbiology
Adult
Severity of Illness Index
Sex Factors
Middle Aged
*Dysbiosis/microbiology
RNA, Ribosomal, 16S
Young Adult

@article {pmid41117697,
year = {2025},
author = {Li, Z and Kuang, X and Ling, J and Shen, T and Shan, G and Wu, J},
title = {Mouse chymase mast cell protease-4 facilitates blood feeding of Aedes aegypti (Diptera: Culicidae) mosquitoes.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf137},
pmid = {41117697},
issn = {1938-2928},
support = {24 3505 Pj//Swedish Cancer Society/ ; //Guizhou High-level Innovative Talents Training Program (Qiankehe Platform Talents-GCC[2022]033-1)/ ; //Science and Technology Innovation Talent Team of Guizhou Province (Qian Ke He Platform Talent-CXTD [2022]004)/ ; ZK[2021]430]//Guizhou Provincial Basic Research Program (Natural Science)/ ; 21NSFCP29//Incubation Funding of Guizhou Medical University National Natural Science Foundation/ ; },
abstract = {Aedes aegypti (Linnaeus) are rapidly spreading across the globe. Evidence suggests that a Type I hypersensitivity reaction, characterized by IgE-mediated mast cell degranulation, may enhance the blood-feeding behavior of Ae. aegypti. Chymases, the mast cell-specific proteases, may play a critical role in this process. To investigate the role of mouse chymase mast cell protease-4 (mMCP-4) on mosquito blood feeding, we incubated bone marrow-derived mast cells with serum from mice sensitized by female Ae. aegypti bites and subsequently challenged the cells with salivary gland proteins (SGPs) from female mosquito. And the degradation of SGPs by mMCP-4 was assessed. Then, the MCP-4 deficient mice were sensitized twice by Ae. aegypti, the first bite on day 0 and the second on day 3. Throughout these experiments, we recorded the total blood meal duration, probing time, and blood feeding of the mosquitoes and analyzed the cutaneous microbiota. We discovered that serum from sensitized mice enhanced mast cell degranulation and chymase release. And mMCP-4 degraded some SGPs, in particular, potentially cleaving the blood-feeding-related salivary protein D7. Mcpt-4 deficiency resulted in prolonged blood-feeding duration during the second exposure, without affecting initial probing behavior. Moreover, Mcpt-4-deficient mice exhibited a reduced proportion of mosquitoes achieving rapid engorgement. Skin microbiome profiling revealed that Mcpt-4 deficiency attenuated the bite-induced expansion of potentially harmful bacterial taxa, including the dominant genus Corynebacterium (Mycobacteriales: Corynebacteriaceae). These findings identify mMCP-4 as a critical mediator of mosquito blood-feeding behavior and a modulator of skin microbial ecology in response to Ae. aegypti bites.},
}

@article {pmid41117590,
year = {2025},
author = {Guo, X and Yang, C and Fu, Q and Li, H and Fang, J and Zheng, R},
title = {Impact of yak excreta on soil bacterial community in alpine marsh under warming conditions.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0149325},
doi = {10.1128/aem.01493-25},
pmid = {41117590},
issn = {1098-5336},
abstract = {Livestock excreta and climate warming are two main disturbances of wetlands embedded in grazing lands, resulting in long-lasting changes in soil microorganisms. However, the impact of livestock excreta on the soil bacteria community in wetlands with climate warming has not been elucidated. In the current study, a laboratory culture experiment was designed to investigate how yak excreta, temperature, and their interaction regulate the soil bacterial community in an alpine marsh. The results show that yak dung increased soil moisture, pH, total organic carbon (TOC), and available phosphorus (AP), but decreased NO3[-]-N (P < 0.05). Yak urine increased soil moisture, NH4[+]-N, and NO3[-]-N (P < 0.05). Warming decreased soil moisture and pH of marsh soil (P < 0.05). Warming increased the alpha-diversity of the bacterial community in marsh soil; yak dung had an opposite effect, while yak urine exerted almost a negligible effect. In comparison with warming, yak excreta was the main cause of changing the bacterial community in marsh soil. Yak dung altered more bacterial genera of marsh soil than yak urine. Moreover, yak dung obviously strengthened the bacterial association interaction in marsh soil, while yak urine had the opposite trend. Yak excreta and temperature altered the bacterial community by regulating NO3[-]-N, AP, pH, TOC, and moisture of marsh soil. This study confirms the different influences of yak dung and urine on the bacterial community of marsh soil under warming conditions and highlights that the impacts of yak excreta on the bacterial community are sensitive to climate warming.IMPORTANCEInvestigating the response of the bacterial community in marsh soil to external disturbances is an important but poorly elucidated topic in microbial ecology. In this study, we evaluated the impacts of yak excreta, temperature, and their interaction on the bacterial community in alpine marsh soil. Our results showed that yak excreta exhibited a stronger influence on the bacterial community of marsh soil than temperature. The response of the bacterial community of marsh soil to yak dung is more sensitive than to yak urine. Yak excreta and temperature significantly altered the bacterial community by regulating NO3[-]-N, AP, pH, TOC, and moisture of marsh soil. Understanding the impact of yak excreta on soil bacterial community under warming conditions is extremely significant for managing grazing and maintaining a healthy alpine marsh ecosystem.},
}

@article {pmid41117558,
year = {2025},
author = {Maltz, MR and Topacio, TM and Lo, DD and Zaza, M and Freund, L and Botthoff, J and Swenson, M and Cocker, D and Biddle, T and Yisrael, K and Del Castillo, D and Drover, RW and Aronson, E},
title = {Lung microbiomes' variable responses to dust exposure in mouse models of asthma.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0020925},
doi = {10.1128/msphere.00209-25},
pmid = {41117558},
issn = {2379-5042},
abstract = {UNLABELLED: Inhalation of dust is significant and relevant to health effects. As pollution and climate change worsen in dryland regions, wind currents entrain loose sediment and dust. This potentially disperses toxic geochemical and microbial burdens throughout the region. When inhaled environmental dust and host-associated microbiomes mingle, they pose exposure risks to host respiratory health. The Salton Sea, California's largest lake, is shrinking, thus exposing nearby communities to playa dust. Therefore, we analyze the effect of Salton Sea dust exposure in murine models to relate lung microbial communities and respiratory health. We used an environmental chamber to expose mice to dust filtrate or ambient air and examined the effects of those exposures on lung microbiomes. We found that lung microbial composition varied by dust exposure. Furthermore, dust elicited neutrophil recruitment and immune responses more than mice exposed to ambient air. Sources of dust differentially affected the composition of the lung core microbiome. Lung microbial diversity correlated with neutrophil recruitment as lungs associated with inflammatory responses harbored more diverse microbiomes. Although Salton Sea dust influences dust microbiomes and prevalent taxa, these responses are variable. The composition of lungs exposed to dust collected further from the Salton Sea was more similar to lungs from ambient air exposures; in contrast, dust collected near the Salton Sea yielded lung microbiomes that clustered further from lungs exposed to ambient air. As lakes continue to dry out, we expect greater public health risks in proximal dryland regions, which may correlate with dust microbial dispersal-related changes to lung microbiomes.

IMPORTANCE: Dust inhalation can lead to health effects, especially when toxic chemicals and microbes mix in with the dust particles. As California's Salton Sea dries up, it exposes lake bottom sediments to wind, which disperses the dried sediments. To mimic the effect of inhaling Salton Sea dust, we collected and filtered airborne dust to use in exposure experiments with mice in environmental chambers. We predicted that inhaling small dust particles, chemicals, and microbial residues found in this dust would affect mouse respiratory health or change the microbes found inside their lungs. We found that inhaling dust led to lung inflammation, and the dust source influenced the type of microbes found inside mouse lungs. As lakes continue to dry out, we expect greater health risks and changes to lung microbiomes.},
}

@article {pmid41117325,
year = {2025},
author = {Kaundal, R and Parkash, V and Paul, S and Thapa, M},
title = {Heavy metal stress alters soil microbial structure and diversity in the BBN industrial corridor, Himachal Pradesh, India.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/15226514.2025.2572305},
pmid = {41117325},
issn = {1549-7879},
abstract = {Soil microorganisms are essential to ecosystem functioning, yet their communities are highly susceptible to environmental disturbances such as heavy metal contamination from industrial activities. This study investigates the impact of heavy metal pollution on soil bacterial and fungal communities in the Baddi-Barotiwala-Nalagarh (BBN) Industrial Corridor, Himachal Pradesh, India. Soil samples were analyzed for physicochemical properties and heavy metal content, i.e., cadmium (Cd), iron (Fe), copper (Cu), arsenic (As), lead (Pb), chromium (Cr), zinc (Zn), and manganese (Mn), followed by the isolation and characterization of culturable bacterial and fungal communities. Microbial profiling indicated significant variations in community composition, diversity, and abundance across industrial sites. Firmicutes (Bacillota) and Proteobacteria emerged as dominant bacterial phyla, while the fungal communities were predominantly composed of Ascomycota. Although overall microbial richness and diversity declined with increasing heavy metal concentrations, several isolates exhibited key plant growth-promoting (PGP) traits, including phosphate solubilization, siderophore production, indole-3-acetic acid (IAA) synthesis, ammonia production, and nitrate reduction. Pearson correlation analysis demonstrated a relation between microbial community structure and multiple environmental variables, including heavy metals and key soil physicochemical properties. The findings highlight the dual role of soil microbes as indicators of environmental stress and as potential agents for microbe-assisted bioremediation.},
}

@article {pmid41114872,
year = {2025},
author = {Dyczko, D and Hałupka, L and Czyż, B and Czułowska, A and Kiewra, D},
title = {Ticks on migrating birds in southwestern Poland: occurrence of Ixodes ricinus and the first Polish record of Haemaphysalis concinna on birds.},
journal = {Experimental & applied acarology},
volume = {95},
number = {4},
pages = {46},
pmid = {41114872},
issn = {1572-9702},
mesh = {Animals ; Poland/epidemiology ; *Bird Diseases/parasitology/epidemiology ; Nymph/physiology/growth & development/genetics ; *Tick Infestations/veterinary/parasitology/epidemiology ; Larva/growth & development/physiology/genetics/classification ; *Ixodidae/physiology/growth & development/genetics/classification/anatomy & histology ; Animal Migration ; Ixodes/physiology/growth & development ; *Songbirds ; Female ; Male ; Animal Distribution ; },
abstract = {During ornithological research conducted at the Milicz Fishponds Nature Reserve (Barycz Valley Landscape Park, southwestern Poland) from May to July 2024, a total of 245 birds were captured. Four ticks were collected: two Ixodes ricinus larvae and two Haemaphysalis concinna nymphs. We present the first confirmed record of H. concinna parasitising a great reed warbler (Acrocephalus arundinaceus) in Poland. Identification of H. concinna was based on both morphological identification keys and molecular analysis of the COI gene. This finding expands current knowledge on the biodiversity of ticks parasitising birds in Poland and highlights the need for further research on the role of migratory birds in the dispersal of ticks across Central Europe.},
}

Animals
Poland/epidemiology
*Bird Diseases/parasitology/epidemiology
Nymph/physiology/growth & development/genetics
*Tick Infestations/veterinary/parasitology/epidemiology
Larva/growth & development/physiology/genetics/classification
*Ixodidae/physiology/growth & development/genetics/classification/anatomy & histology
Animal Migration
Ixodes/physiology/growth & development
*Songbirds
Female
Male
Animal Distribution

@article {pmid41114853,
year = {2025},
author = {de Scally, SZ and McDonald, MJ},
title = {Evolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {110},
pmid = {41114853},
issn = {1432-184X},
support = {CE230100001//Australian Research Council/ ; },
mesh = {*Escherichia coli/genetics/growth & development/physiology ; *Saccharomyces cerevisiae/genetics/growth & development/physiology ; *Biological Evolution ; Models, Biological ; Ecosystem ; Introduced Species ; },
abstract = {The species that make up a microbial community determine its potential function. A major goal of microbial ecology is to make assemblages of microbes - synthetic communities - with targeted applications. Replacing a dysfunctional community with a synthetic microbial community can have transformative impacts upon a host or ecosystem, yet the introduced community may be outcompeted by local species or communities, resulting in transient effects. Here, we study a simple synthetic community comprised of two species - E. coli and S. cerevisiae - that have coevolved for either 0, 1000 or 4000 generations, and evaluate the potential for 12 bacterial strains, from five species, to invade. We find that the dominant species (E. coli) in the community protects the less dominant species from being outcompeted during an invasion, and that this effect is strengthened by longer periods of coevolution. Using a mathematical model, we show how prolonged co-evolution leads to protective effects for a community member sensitive to displacement.},
}

*Escherichia coli/genetics/growth & development/physiology
*Saccharomyces cerevisiae/genetics/growth & development/physiology
*Biological Evolution
Models, Biological
Ecosystem
Introduced Species

@article {pmid41114740,
year = {2025},
author = {Hopton, CM and Cockell, CS},
title = {Spatiotemporal Impacts of Enceladus- and Earth-relevant Ammonia Gas On Cultivation of Extremophile Halomonas meridiana.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {111},
pmid = {41114740},
issn = {1432-184X},
support = {NE/S007407/1//Natural Environment Research Council/ ; ST/V000586/1//Science and Technology Facilities Council/ ; },
mesh = {*Ammonia/metabolism ; *Halomonas/growth & development/metabolism/drug effects ; Volatilization ; },
abstract = {One underexplored aspect of microbial growth is the impact of toxic gases transported through the atmosphere. Ammonia is a gas that can supply essential nitrogen but also exert cellular toxicity. Ammonia volatilized from a concentrated source into surrounding environments is therefore a crucial consideration when assessing the capacity of environments to support life, such as within terrestrial environments polluted with ammonia, or the ice crusts above ammonia-water oceans of icy moons. We cultivate Halomonas meridiana proximal to an ammonia source and examine the impact of ammonia volatilization on growth. Lower cell densities (OD600 = 0-1) occurred nearest the ammonia source. At 24 h, wells exhibiting an OD600 = 0-0.5 were evident when ammonia concentrations were ≥ 0.5 M. H. meridiana in proximity to 0 M, 0.1 M, 0.25 M, 0.5 M, and 1 M ammonia exhibited OD600 > 2 in 89.86%, 57.97%, 37.32%, 30.07%, and 18.48% of culture wells at 48 h, respectively. Alteration to growth kinetics and viability of H. meridiana cultivated adjacently to an ammonia source ("adjacently exposed") were not as severe compared to direct culture in ammonia ("directly exposed"). Compared to control, adjacent exposure to 0.1 M ammonia exerted no significant detrimental effect on growth kinetics and enhanced cell density, but adjacent exposure to ≥ 0.5 M ammonia greatly extended lag time, doubling time, reduced cell density, and reduced viability. Ammonia volatilized from 0.1 M sources may thus minimally affect, if not improve, habitability, whereas environments exposed to ammonia volatilized from sources at ≥ 0.5 M could constrain habitability.},
}

*Ammonia/metabolism
*Halomonas/growth & development/metabolism/drug effects
Volatilization

@article {pmid41114647,
year = {2025},
author = {Basso, TO and Venturini, AM and Ceccato-Antonini, SR and Gombert, AK},
title = {Microbial Ecology Applied to Fuel Ethanol Production from Sugarcane.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf100},
pmid = {41114647},
issn = {1574-6941},
abstract = {The production of fuel ethanol in sugarcane biorefineries is a non-aseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.},
}

@article {pmid41114112,
year = {2025},
author = {Yang, YQ and Li, N and Liu, S and Yu, YW},
title = {Uridine diphosphate-glucose 6-dehydrogenase-mediated glucuronidation and its emerging role in gut-liver immune regulation.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {10},
pages = {110464},
pmid = {41114112},
issn = {1948-5204},
abstract = {This editorial builds on a recent study by Cao et al, which identified uridine diphosphate-glucose 6-dehydrogenase (UGDH) as a pro-tumorigenic enzyme in hepatocellular carcinoma (HCC). UGDH, a key catalyst in glucuronidation, promotes tumor growth and correlates with immunosuppressive features in the HCC microenvironment. Expanding on these findings, we explore broader implications of UGDH within the gut-liver axis. We propose that UGDH regulates immune tone not only through detoxification of bile acids and microbial products, but also by maintaining intestinal barrier integrity. Its dysregulation may impair glucuronidation, leading to bile acid accumulation, increased gut permeability, and microbial translocation, collectively promoting hepatic immune tolerance. Additionally, emerging evidence suggests that gut microbiota-derived metabolites can modulate hepatic UGDH expression, forming a bidirectional feedback loop between microbial ecology and liver metabolism. In this context, UGDH may act as a metabolic immune checkpoint, linking metabolic dysfunction with immune escape mechanisms such as programmed cell death ligand 1 upregulation and cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes pathway activation. Targeting UGDH could therefore help restore gut-liver immune balance and delay gastrointestinal cancer progression, especially in metabolic HCC. This editorial integrates metabolic, microbial, and immunological perspectives to support a novel translational framework.},
}

@article {pmid41114005,
year = {2025},
author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM},
title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf164},
pmid = {41114005},
issn = {2730-6151},
abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.},
}

@article {pmid41113651,
year = {2025},
author = {Lan, R and De Paula Ramos, L and Chen, Z and Carrouel, F},
title = {Editorial: Exploring the oral-gut microbiome interactions: pathways to therapeutic strategies and implications for systemic health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691238},
pmid = {41113651},
issn = {1664-302X},
}

@article {pmid41112761,
year = {2025},
author = {Lestin, L and Villemur, R},
title = {Modulation of carbon-to-nitrogen ratio shapes the microbial ecology in a methanol-fed recirculating marine denitrifying reactor.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20129},
pmid = {41112761},
issn = {2167-8359},
mesh = {*Denitrification ; *Methanol/metabolism ; *Bioreactors/microbiology ; *Nitrogen/metabolism/analysis ; Biofilms/growth & development ; *Carbon/metabolism/analysis ; Piscirickettsiaceae/metabolism/genetics ; Nitrates/metabolism ; Water Purification/methods ; },
abstract = {BACKGROUND: Nitrate (NO3 [-]) can accumulate in closed-circuit ecosystems to a toxic level. Adding heterotrophic denitrification process to the water treatment is a strategy to reduce this level. This type of process usually requires the addition of a carbon source. Carbon-to-nitrogen ratio (C/N) is a key parameter known to influence both the function and the activity of microbial communities in bioprocesses. Few studies have examined the influence of C/N on denitrification systems operated under methylotrophic and marine conditions. Here we assessed the influence of C/N (methanol and NO3 [-]) on the performance of a laboratory-scale, recirculating denitrifying reactor operated under marine conditions. We monitored the evolution of the bacterial community in the biofilm to assess its stability during the operating conditions. Finally, the relative gene expression profiles of Methylophaga nitratireducenticrescens strain GP59, the main denitrifier in the denitrifying biofilm, were determined during the operating conditions and compared with those of GP59 planktonic pure cultures.

METHODOLOGY: A 500-mL methanol-fed recirculating denitrification reactor operated under marine conditions and colonized by a naturally occurring multispecies denitrifying biofilm was subjected to eight different C/N. We monitored several physico-chemical parameters (denitrifying activities, methanol consumption, CO2 production) throughout the operating conditions. The evolution of the bacterial community in the biofilm during these conditions was determined by 16S rRNA gene amplicon sequencing. Metatranscriptomes were derived from the biofilm to determine (1) the relative gene expression profiles of strain GP59, and (2) the functional diversity of the active microorganisms in the biofilm.

RESULTS: Changes in C/N did not correlate with the denitrification dynamics (NO3 [-] and NO2 [-] reduction rates, NO2 [-] and N2O dynamics), but did correlate with the methanol consumption rates, and the CO2 production rates. Throughout the operating conditions, nitrite and N2O appeared transiently, and ammonium was not observed. The bacterial community in the reactor increased in diversity with biofilm aging, especially among heterotrophic bacteria, at the expense of methylotrophic bacteria. The relative expression profiles of strain GP59 in the biofilm are distinct from those of planktonic pure cultures of strain GP59, and that the expression of several riboswitches and xoxF would be involved in these differences.

CONCLUSIONS: When the biofilm community is well established in the reactor, it can withstand changes in C/N with limited impact on the denitrification performance. The increase in the proportion of heterotrophs would allow the reactor to be more flexible regarding carbon sources. This knowledge can be useful for improving the efficiency of denitrification system treating close circuit systems such as marine recirculating aquaculture wastewater or seawater aquarium.},
}

*Denitrification
*Methanol/metabolism
*Bioreactors/microbiology
*Nitrogen/metabolism/analysis
Biofilms/growth & development
*Carbon/metabolism/analysis
Piscirickettsiaceae/metabolism/genetics
Nitrates/metabolism
Water Purification/methods

@article {pmid41112022,
year = {2025},
author = {Gao, J and Zhang, J and Wang, J and Chang, Y and Qin, Z and Sun, L and Li, M and Yang, Q},
title = {Intraspecific Genetic Diversity Analyses of Yam (Dioscorea polystachya Turcz.) Based on DUS Traits and SSR Molecular Markers.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72295},
pmid = {41112022},
issn = {2045-7758},
abstract = {Yam (Dioscorea polystachya Turcz.) is an asexually reproduced food and traditional Chinese medicinal crop with extensive genomic variability. However, the detailed characterization of genetic diversity among different yam germplasm samples is still insufficient. This study evaluated the genetic divergence and genetic structure of 113 D. polystachya accessions collected from 17 provinces in China based on 50 distinctness, uniformity, and stability (DUS) traits and 19 simple sequence repeat (SSR) markers. All the selected varieties were categorized into three groups based on morphological characteristics and further validated by principal component analysis. Furthermore, 14 core traits, including 6 leaf traits, 4 tuber traits, 3 bulbil traits, and 1 stem trait, were selected to increase field inspection efficiency. SSR fingerprinting, utilizing 19 highly polymorphic markers, successfully distinguished all 113 yam varieties, revealing relatively high levels of genetic variation. Interestingly, the optimal genetic structure defined three groups, whereas a finer-scale model consistently classified the varieties into five groups, corroborating the genotypic cluster analysis. Furthermore, this study preliminarily identified 10 groups of potential heterotypic synonyms and 13 groups of potential homonyms among the yam accessions. These results demonstrate that the 19 selected SSR markers, in conjunction with DUS traits, can effectively discriminate the 113 D. polystachya varieties. Our findings provide critical insights for the conservation of pure breeds and the utilization of Dioscorea germplasm resources.},
}

@article {pmid41109620,
year = {2025},
author = {Rojas Oñate, D and Opazo Capurro, A and González Rocha, G and Zornoza, R and Torres Bustos, C and Hasbún, R and Bucarey, B and Osman, JR and Schoebitz, M},
title = {Plastisphere and the occurrence of antibiotic resistance in a 40-year-old abandoned coastal landfill site in Chile.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127280},
doi = {10.1016/j.envpol.2025.127280},
pmid = {41109620},
issn = {1873-6424},
abstract = {Plastispheres are microbial communities that inhabit plastic surfaces and have been extensively studied in aquatic environments. However, little is known about their occurrence in landfills. We investigated plastisphere communities in a 40-year-old coastal abandoned landfill in Rocuant-Andalién, Chile, and aimed to characterize landfill plastisphere communities and assess their potential role as reservoirs of antibiotic resistance genes (ARGs). High-density polyethylene was the predominant plastic type (56 %). Microscopy revealed diverse bacterial morphotypes, including bacilli, cocci, and filamentous forms, forming clusters on plastic surfaces. 16S rRNA gene sequencing revealed that Actinobacteria, Firmicutes, and Proteobacteria dominated most samples, with high overall diversity and richness. Beta diversity analysis indicated significant variation in bacterial communities among sites but not among polymer types. Notably, the intI1 gene, associated with the spread of antibiotic resistance, was detected at 67 % of the sampled sites. These findings reveal that landfills act as reservoirs for a wide range of bacteria, some of which may have clinical significance, highlighting their ecological and public health impact. Furthermore, plastics are likely to transport resistance genes originating from human activities, spreading them into nearby ecosystems, such as wetlands and oceans, where they interact with wildlife.},
}

@article {pmid41107717,
year = {2025},
author = {Khan, MSI and Wu, J and Hou, S and Ji, S and Li, H and Chang, Y and Sui, B and Tan, D and Yin, J},
title = {Bile modulates phage-host interactions in multidrug-resistant Pseudomonas aeruginosa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {666},
pmid = {41107717},
issn = {1471-2180},
support = {2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; },
mesh = {*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology ; *Bile/metabolism ; *Drug Resistance, Multiple, Bacterial ; Biofilms/growth & development/drug effects ; *Pseudomonas Phages/physiology ; Lipopolysaccharides/biosynthesis ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions ; },
abstract = {Biliary tract infections (BTIs) arise within a bile-rich environment that profoundly shapes microbial ecology and pathogen adaptation. Pseudomonas aeruginosa, a major opportunistic pathogen in nosocomial settings, exhibits remarkable physiological plasticity, that enable persistence in such challenging niches. However, the influence of bile on P. aeruginosa's adaptive responses and phage-host interactions remains largely unexplored. Here, we demonstrate that ox-bile imposes concentration-dependent stress on P. aeruginosa strain ZS-PA-35, indicative of host-derived selective pressure. Notably, ox-bile enhances biofilm formation and promotes swarming and twitching motilities while concurrently suppressing swimming motility. Moreover, ox-bile modulates phage susceptibility, likely through altered receptor expression: exposure to ox-bile sensitizes P. aeruginosa to the type IV pili (T4P)-dependent phage phipa2, whereas susceptibility to the lipopolysaccharide (LPS)-targeting phage phipa10 remains unchanged. Genome-wide mutagenesis identified resistance-conferring mutations affecting T4P structures, LPS biosynthesis, and associated regulatory pathways. Among these, phage-resistant mutants ΔpilT and ΔgalU retained high fitness under ox-bile stress, accompanied by enhanced swarming and swimming motilities. Furthermore, in a lysogenic context, ox-bile markedly suppressed prophage accumulation in the T4P-dependent strain ZS-PA-05. These findings reveal that bile acts as a critical environmental cue shaping both adaptive physiology and phage susceptibility in P. aeruginosa, with broad implications for microbiome dynamics and the development of phage-based therapies targeting bile-impacted infections.},
}

*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology
*Bile/metabolism
*Drug Resistance, Multiple, Bacterial
Biofilms/growth & development/drug effects
*Pseudomonas Phages/physiology
Lipopolysaccharides/biosynthesis
Pseudomonas Infections/microbiology
*Host-Pathogen Interactions

@article {pmid41107300,
year = {2025},
author = {Urrutia-Angulo, L and Ocejo, M and Yergaliyev, T and Oporto, B and Aduriz, G and Camarinha-Silva, A and Hurtado, A},
title = {Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36350},
pmid = {41107300},
issn = {2045-2322},
support = {PRE2020-096275//MICIU/AEI/10.13039/501100011033 and ESF Investing in your future/ ; },
mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; },
abstract = {The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves' gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.},
}

*Colostrum/microbiology
Animals
Cattle
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
DNA Barcoding, Taxonomic/methods
Female
Phylogeny

@article {pmid41106786,
year = {2025},
author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z},
title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {106935},
doi = {10.1016/j.fitote.2025.106935},
pmid = {41106786},
issn = {1873-6971},
abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.},
}

@article {pmid41106598,
year = {2025},
author = {Khan, KS and Alam, T and Fiaz, S and Azim, R and Qadeer, A and Iqbal, R and Li, L},
title = {Hyphosphere Fungi-Bacteria-Plant Interactions Regulate Phosphorus Tradeoffs in the Soil Plant System.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {112819},
doi = {10.1016/j.plantsci.2025.112819},
pmid = {41106598},
issn = {1873-2259},
abstract = {Tripartite interactions among arbuscular mycorrhizal fungi (AMF), phosphorus-solubilizing bacteria (PSB), and terrestrial plants are pivotal in plant stress resistance, nutritional cycling, and soil-microbe ecological functions. The convoluted association between AMF and PSB may play a significant role in the decomposition and absorption of soil organic phosphorus (P), because AMF dynamically secretes carbon-containing compounds from extraradical hyphae (ERH) to stimulate PSB growth rate and activities. PSB are the main contributors of plant nutrition and could play a pivotal role in making soluble P available to plants. In this context, this comprehensive review critically examined the AMF-PSB interactions in soil P mobilization, with a focus on soil biochemical dynamics, microbial ecology, physiological mechanisms, biochemical pathways, and gene expression. While the explored studies emphasize the role of AMF-PSB interactions in P mobilization, it is important to consider that many experiments used root-free compartments, potentially overestimating mycorrhizal contributions relative to root pathways. Future research should integrate root-inclusive systems to provide a more comprehensive understanding of P acquisition dynamics by regulating indigenous AMF in terrestrial ecosystems.},
}

@article {pmid41106329,
year = {2025},
author = {Hill, RC and Pieńkowska, A and Merbach, I and Reitz, T and Muehe, EM and Vengosh, A},
title = {Impacts of fertilization on metal(loid) transfer from soil to wheat in a long-term fertilization experiment - using [87]Sr/[86]Sr isotopes as metal(loid) tracer.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109851},
doi = {10.1016/j.envint.2025.109851},
pmid = {41106329},
issn = {1873-6750},
abstract = {Fertilizers are widely used to sustain food production but can alter soil chemistry and potentially contribute toxic metal(loid)s to agricultural systems. For the first time, this study examined the occurrence of select metal(loid)s (Zn, Sr, V, As, Cd, Pb, and U) alongside the [87]Sr/[86]Sr isotope ratio in agricultural soil- both total and mobile pools- and wheat grain. Samples were collected from one of four fertilization treatments- mineral (NPK), organic (manure), combined mineral+organic, and unfertilized controls- within the 120-year Static Fertilization Experiment in Bad Lauchstädt, Germany. Fertilization treatments altered soil pH and organic carbon resulting in mineral fertilization lowering pH and increasing cation mobility (Cd, Zn, Sr), whereas organic fertilization increased pH and enhanced the mobility of non-cationic elements (V, As). These effects translated into higher Cd in mineral-fertilized wheat grain and higher As in mineral+organic wheat grain. Fertilization shifted the [87]Sr/[86]Sr ratios in soils and wheat grains toward that of the applied fertilizers, with mineral and mineral+organic wheat grains inheriting the triple super phosphate signature (0.70778) and organic wheat grains matching manure (0.70883). The [87]Sr/[86]Sr ratio in the mobile soil pool was correlated with mobile As, V, and P, demonstrating that the [87]Sr/[86]Sr ratio reflects both fertilizer source and the mobility of select co-occurring metal(loid)s. Overall, this study demonstrates metal(loid) enrichment in soil and wheat from fertilization and establishes [87]Sr/[86]Sr ratio as a robust tracer of fertilizer impacts. These findings underscore the need for targeted fertilization strategies to reduce contaminant accumulation in agroecosystems.},
}

@article {pmid41106081,
year = {2025},
author = {Krimech, A and Sbahi, S and Cherifi, O and Hejjaj, A and Mugani, R and Ouazzani, N and Kerner, M and Oudra, B and Mandi, L},
title = {Seasonal effects on Chlorella sorokiniana UCAM 001 growth and physiology in flat-plate photobioreactors in Morocco's arid climate.},
journal = {European journal of protistology},
volume = {101},
number = {},
pages = {126171},
doi = {10.1016/j.ejop.2025.126171},
pmid = {41106081},
issn = {1618-0429},
abstract = {This study aims to investigate the seasonal variation in growth and physiology of Chlorella sorokiniana UCAM 001 strain using annual optimization monitoring with a groundwater medium in two outdoor flat-plate photobioreactors (PBRs), which were first scaled up at the Faculty of Sciences Semlalia (Marrakech, Morocco). The culture medium was adjusted to ensure non-limiting nutrient concentrations (10 mg·L[-1] and 100 mg·L[-1] of additional phosphorus and nitrate, respectively). Temperature, light, and algal growth were monitored daily. Proline, glycine betaine, and catalase levels were measured every four days to assess the degree of algal stress. Biomass productivity increased during spring, reaching 30 mg·L[-1]·day[-1] with a specific growth rate of 0.73 day[-1]. However, no growth was observed during the summer. Physiological analysis revealed increased proline and glycine betaine levels during autumn and winter due to temperatures as low as 13 °C. In contrast, catalase concentration peaked in spring. Pearson correlation analysis indicated that nutrient limitation, together with temperature and light intensity, induced stress in C. sorokiniana, stimulating catalase production. Algal growth efficiently removed nutrients from the medium, achieving removal rates of 97 % for total phosphorus and 87 % for total nitrogen. Optimized cooling systems will improve PBR efficiency and support algal growth under extreme summer conditions.},
}

@article {pmid41105271,
year = {2025},
author = {Castellano-Hinojosa, A and Llodrà-Llabrés, J and Ramos-Rodríguez, E and Smol, JP and Meyer-Jacob, C and Sigro, J and Pérez-Martínez, C},
title = {Temporal succession of bacterial and archaeal communities in a Mediterranean high-mountain lake over the last 430 years using sedimentary DNA.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {107},
pmid = {41105271},
issn = {1432-184X},
support = {LACEN (OAPN 2403-S/2017)//Ministry of Ecological transition in their National Park Autonomous Agency/ ; LifeWatch-2019-10-UGR-01//Ministry of Science and Innovation through the FEDER funds from the Spanish Pluriregional Operational Program 2014-2020 (POPE), LifeWatch-ERIC action line/ ; BIOD22_001//Consejería de Universidad, Investigación e Innovación and Gobierno de España and Unión Europea - NextGenerationEU/ ; },
mesh = {*Lakes/microbiology/chemistry ; *Archaea/classification/genetics/isolation & purification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Climate Change ; Spain ; Microbiota ; DNA, Archaeal/genetics ; Biodiversity ; Ecosystem ; DNA, Bacterial/genetics ; Nitrogen/analysis ; DNA, Ancient/analysis ; Temperature ; },
abstract = {Despite the known influence of climate change on high-altitude ecosystems, the long-term response of prokaryotic communities in Mediterranean high-mountain lakes remains poorly understood. Here, we investigate the temporal dynamics of prokaryotic communities over the past ~ 430 years in a Mediterranean high-mountain lake, utilizing sedimentary ancient DNA (sedDNA). By examining a sediment core from Borreguil Lake in the Sierra Nevada (Spain), we evaluated bacterial and archaeal abundance, diversity, and community composition (β-diversity) in relation to paleoenvironmental and climate data. Our findings revealed a significant restructuring of prokaryotic communities, particularly since ca. 1960. A Random Forest model identified dissolved organic carbon, organic nitrogen, Saharan atmospheric dust inputs, and temperature as key drivers of the abundance, diversity, and composition of prokaryotic communities, particularly in the modern era. Notably, the abundance and diversity of bacterial communities increased in response to increased dissolved organic carbon, elevated temperatures, and dust deposition, while archaea demonstrated a more nuanced response linked to organic nitrogen availability and dust inputs. The temporal shifts in microbial community composition point to broader ecological changes within the lake, shaped by climate-driven environmental variations. For example, the increased relative abundance of Cyanobacteria and other taxa linked to higher nutrient availability indicates ongoing eutrophication processes, likely intensified by climate warming. This study highlights the importance of high-mountain lakes as indicators of climate change, contributing valuable insights into microbial ecology's response to long-term environmental change. Our findings offer a foundational understanding for predicting microbial responses in sensitive ecosystems under future climate scenarios.},
}

*Lakes/microbiology/chemistry
*Archaea/classification/genetics/isolation & purification
*Geologic Sediments/microbiology
*Bacteria/classification/genetics/isolation & purification
Climate Change
Spain
Microbiota
DNA, Archaeal/genetics
Biodiversity
Ecosystem
DNA, Bacterial/genetics
Nitrogen/analysis
DNA, Ancient/analysis
Temperature

@article {pmid41105270,
year = {2025},
author = {Gamoń, F and Ćwiertniewicz-Wojciechowska, M and Muszyński-Huhajło, M and Miodoński, S and Ziembińska-Buczyńska, A and Cema, G and Tomaszewski, M},
title = {Low-Temperature Anammox Supported by Zero-Valent Iron (ZVI): Microbial and Physicochemical Changes during Treatment of Synthetic and Municipal Wastewater.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {108},
pmid = {41105270},
issn = {1432-184X},
support = {UMO-2017/25/N/NZ9/01159//Narodowe Centrum Nauki/ ; },
mesh = {*Iron/metabolism/chemistry ; *Wastewater/microbiology/chemistry ; Oxidation-Reduction ; Bioreactors/microbiology ; Anaerobiosis ; *Ammonium Compounds/metabolism ; *Bacteria/metabolism/classification/genetics ; *Waste Disposal, Fluid/methods ; Cold Temperature ; },
abstract = {The anaerobic ammonium oxidation (anammox) process offers a sustainable and energy-efficient alternative for nitrogen removal in wastewater treatment, but its performance at low temperatures remains a major challenge. This study investigated the role of zero-valent iron (ZVI) in enhancing anammox activity across a temperature range of 10-30 °C using both synthetic and municipal wastewater (MWW). Short-term batch tests demonstrated that low-dose ZVI (5-10 mg/L) stimulated specific anammox activity (SAA) particularly at 13-20 °C, while ZVI increasing concentration (1-10 mg/L) enhanced the enzymatic activity of HDH and decreased NIR activity, as well as modulated oxidative stress (ROS and GSH balance). In contrast, the long-term operation of the anammox process in sequencing batch reactors (SBR) showed that while ZVI (5 mg/L) improved SAA and microbial stability under synthetic conditions at 13 °C in compared to control (without ZVI), these benefits diminished once real municipal wastewater was introduced, most likely due to biomass stress and organic load. Metataxonomic analysis confirmed that ZVI selectively promoted genera such as Candidatus Brocadia, Denitratisoma, Micavibrionales_unclassified, while reducing overall microbial diversity. These results indicate that low-dose ZVI can temporarily enhance anammox resilience at suboptimal temperatures. However, its long-term application in MWW requires further optimization to mitigate potential inhibitory effects and iron passivation.},
}

*Iron/metabolism/chemistry
*Wastewater/microbiology/chemistry
Oxidation-Reduction
Bioreactors/microbiology
Anaerobiosis
*Ammonium Compounds/metabolism
*Bacteria/metabolism/classification/genetics
*Waste Disposal, Fluid/methods
Cold Temperature

@article {pmid41105260,
year = {2025},
author = {Phauk, S and Assentato, L and Sin, S and Uk, O and Hap, S and Terenius, O},
title = {Symbiont Diversity of Rice-Associated Leafhoppers (Cicadellidae) in the Tropical Floodplains of the Tonle Sap Lake, Cambodia.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {109},
pmid = {41105260},
issn = {1432-184X},
mesh = {Animals ; *Hemiptera/microbiology/physiology/classification ; *Symbiosis ; *Oryza/parasitology ; Cambodia ; Female ; Lakes/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Biodiversity ; Microbiota ; Phylogeny ; },
abstract = {Rice-associated leafhoppers (Cicadellidae) play a significant role in rice agroecosystems, contributing not only to direct crop damage but also to the transmission of plant pathogens. This study investigates the symbiont diversity of seventeen leafhopper species from the tropical floodplains of Tonle Sap Lake (TSL), Cambodia. The dominant symbiont across most species was Candidatus (Ca.) Karelsulcia muelleri, an obligate primary endosymbiont essential for nutrient synthesis. The co-obligate symbiont Ca. Nasuia deltocephalinicola was also consistently detected, particularly in Deltocephalinae hosts. In addition, several secondary symbionts, including Sodalis, Arsenophonus, Diplorickettsia, Rickettsia, Wolbachia, and Ca. Lariskella, were identified, showing species-specific associations and potential roles in host fitness and pathogen transmission. Variations in symbiont diversity were observed across cicadellid species, geographic origins, and between sex-associated symbionts, with notable differences in the bacterial composition of Nephotettix virescens. While geographical differences (Battambang vs. Kampong Thom) did not strongly affect microbial composition, sex-associated variations were evident in N. virescens. Females exhibited a higher abundance of Karelsulcia and Nasuia, suggesting possible microbial adaptation related to reproduction. This study highlights the complex and dynamic nature of cicadellid hosts-symbiont interactions and suggests that microbial communities are primarily structured by host species. While geographic distance can influence these communities, this effect is not the same for every species. These findings provide critical insights into the microbial diversity of rice-associated leafhoppers and their potential for ecological roles in rice farming systems. Further studies, including functional analysis and host-symbiont interactions, are crucial to understanding the ecological roles and evolutionary dynamics of these microbial communities.},
}

Animals
*Hemiptera/microbiology/physiology/classification
*Symbiosis
*Oryza/parasitology
Cambodia
Female
Lakes/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Biodiversity
Microbiota
Phylogeny

@article {pmid41105100,
year = {2025},
author = {Arellano, AA and Prack, JL and Coon, KL},
title = {Host-mediated niche construction of bacterial communities in an aquatic microecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf233},
pmid = {41105100},
issn = {1751-7370},
abstract = {Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered. Hosts exert controls on the composition and function of their internally associated symbionts, but an underappreciated modality of microbiome curation is external to the host through changes to the environmental species pool from which they recruit microbial symbionts. Niche construction theory describes how organisms alter their environment and the selective landscape of their offspring and conspecifics. We hypothesize that host-driven manipulation of environmental microbial communities is an underexplored form of this concept. Using the pitcher plant mosquito (Wyeomyia smithii) as a model, we tested how hosts shape microbial communities across developmental stages and gradients of pre-existing community complexity. We report three lines of evidence supporting host-mediated niche construction, leveraging amplicon sequencing and microbiota manipulation experiments with germ-free (axenic) and selectively recolonized (gnotobiotic) mosquitoes. First, single female egg-laying assays showed repeatable adult inoculation of sterile water with beneficial bacteria capable of sustaining robust larval development. Second, increasing larval density in assays inoculated with complex, field-derived microbial communities selected for environmental and host-associated bacteria that correlated with increased larval fitness. Finally, exposing axenic larvae to mixtures of parentally and environmentally derived microbiota demonstrated that prior conditioning by conspecifics enhanced offspring fitness. Although the bacterial taxa associated with mosquito structuring varied, members of the Actinobacteriota and Acetobacteraceae were consistently associated with increased fitness. Overall, our results provide an example of host-mediated niche construction to favor environmental microbial communities that positively impact host fitness.},
}

@article {pmid41104934,
year = {2025},
author = {Ryan, D},
title = {Gene regulation in Bacteroides fragilis: adaptive control in a dynamic host environment.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0022525},
doi = {10.1128/mmbr.00225-25},
pmid = {41104934},
issn = {1098-5557},
abstract = {SUMMARYBacteroides fragilis occupies a dynamic position within the human gut. Though it comprises a relatively minor fraction of the gut microbiota, it is disproportionately enriched at extraintestinal sites of infection. This ability to survive in contrasting host environments pivots on a regulatory framework that is both modular and highly plastic. Rather than deploying a suite of hierarchical global regulators, B. fragilis employs numerous operon-embedded transcriptional switches, including site-specific DNA inversions, phase-variable epigenetic systems, extracytoplasmic function sigma/anti-sigma factor pairs, and hybrid two-component systems. These networks are further complemented by cis-regulatory elongation checkpoints and post-transcriptional control by small RNAs. This review explores the full spectrum of these regulatory mechanisms, highlighting how they facilitate niche adaptation, surface variation, immune evasion, and metabolic prioritization. It also explores intraspecies variation focusing on glycan metabolism, antibiotic resistance, and virulence. Additionally, it outlines recombination-driven regulation, alongside extracytoplasmic function sigma factor diversification, flexible promoter architecture, and elongation checkpoints, each contributing to the evolution of transcriptional control in B. fragilis. Finally, it outlines unanswered questions, including the largely unexplored sRNA regulon, the coordination of DNA inversions, elongation control, and phase-variable methylation, and proposes experimental strategies to investigate the integration of these regulatory systems during environmental transitions. Taken together, B. fragilis emerges as a model bacterium for studying decentralized gene regulation in complex microbial ecosystems, with implications for both microbial ecology and therapeutic targeting of the gut microbiota.},
}

@article {pmid41104481,
year = {2025},
author = {},
title = {Laila P. Partida-Martínez.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70665},
pmid = {41104481},
issn = {1469-8137},
abstract = {Laila P. Partida-Martínez, Cinvestav-Irapuato (Mexico).},
}

@article {pmid41104383,
year = {2025},
author = {Kumar, P and Chitara, D and Sengupta, S and Banerjee, P and Rai, SN},
title = {Microbial consortia in biotechnology: applications and challenges in industrial processes.},
journal = {3 Biotech},
volume = {15},
number = {11},
pages = {386},
pmid = {41104383},
issn = {2190-572X},
abstract = {Microbial consortia, dynamic communities of interacting microorganisms, outperform single-species cultures in industrial biotechnology by overcoming metabolic bottlenecks and degrading complex compounds. These consortia are vital in bioremediation, bioenergy, bioproduction, agriculture, and wastewater treatment. In bioremediation, they efficiently break down persistent pollutants like polycyclic aromatic hydrocarbons. For bioenergy, they convert organic waste into biofuels such as methane and ethanol through multi-step metabolic processes unachievable by single microbes. They also enable sustainable synthesis of bioplastics, antibiotics, and other high-value compounds while enhancing agricultural productivity through improved nutrient availability and biocontrol of plant pathogens. Consortia degrade complex organic contaminants in wastewater treatment, ensuring cleaner effluents and environmental protection. The industrial application faces challenges, including ensuring microbial community stability, optimising performance, and scaling processes from laboratory to industrial scale. The intricate interactions within consortia complicate control, predictability, and real-time monitoring, while intellectual property and regulatory frameworks pose additional barriers. Limitations include gaps in understanding long-term ecological impacts and scalability in diverse environments. Advancements in microbial ecology, systems biology, and bioprocess engineering are crucial to address these issues. Prospects involve using CRISPR and AI to design robust consortia, improve predictive modelling, and foster interdisciplinary collaborations for sustainable applications. Overcoming these challenges will unlock the full potential of microbial consortia, revolutionise industrial processes, and advance sustainable biotechnology.},
}

@article {pmid41104112,
year = {2025},
author = {Hayes, A and Zhang, L and Snape, J and Feil, E and Kasprzyk-Hordern, B and Gaze, WH and Murray, AK},
title = {Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf169},
pmid = {41104112},
issn = {2730-6151},
abstract = {Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.},
}

@article {pmid41103765,
year = {2025},
author = {Li, M and Bi, J and Wang, X and Li, H},
title = {The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652652},
pmid = {41103765},
issn = {1664-302X},
abstract = {Urban parks play a significant role in environmental greening, cultural heritage, and recreational activities. The diversity and distribution of park environmental microbiota have become a hot focus of microbial ecology. However, there has been limited attention on the functional attributes of microbial communities, highlighting the importance of studying the distribution and diversity of functional genes in urban parks. Here, we employed metagenomic sequencing and binning to explore the diversity, assembly, and functional synergy of nitrogen cycling genes from the grassland soil and water in urban parks. Our results showed that glutamate metabolism and assimilatory nitrate reduction are the predominant nitrogen cycling pathways in both the soil and water. The diversity of nitrogen cycling genes in water was more abundant than in soil. The assembly of nitrogen cycling genes in both the soil and water was primarily driven by stochastic processes. Nutrient factors (such as total sulfur) were the most significant influencers of nitrogen cycling genes in park soil, while bacterial communities were the most critical determinants in water. The gene narH, involved in multiple nitrogen cycling metabolic pathways, was identified as an important marker of nitrogen storage in both soil and water. Through metagenomic binning, we discovered linear arrangements of multiple nitrogen cycling genes, such as narG-narH-narJ-narI, which collectively participate in the reduction of nitrate to nitrite, demonstrating the synergy, functional redundancy, and complementarity among nitrogen cycling genes. Our study holds significant implications for the biochemical cycling and the management of nitrogen pollution in urban parks.},
}

@article {pmid41100058,
year = {2025},
author = {Duncan, AH and Armenta, N and Garcia-Ledezma, F and Heck, CA and Hafner, S and Planer-Friedrich, B and Fendorf, S},
title = {Alternate Wetting and Drying Limits Arsenic in Porewater and Rice Grain under Severe Future Climate Conditions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03552},
pmid = {41100058},
issn = {1520-5851},
abstract = {Climate change, coupled with widespread soil arsenic (As) contamination, is expected to decrease rice yields and increase grain As, threatening food security. One promising mitigation strategy is alternate wetting and drying (AWD) irrigation. However, AWD has not previously been tested under potential future climate conditions. Using rhizoboxes to visualize the rhizosphere, we evaluated the efficacy of AWD for limiting porewater and grain As under both current (daily high of 33 °C and 420 ppmv CO2) and severe warming conditions (daily high of 38 °C and 850 ppmv CO2). Compared to continuous flooding, AWD decreased cumulative As exposure 10 cm below the surface by 8.2× under a 33 °C climate and by 15.9× under a 38 °C climate. Grain total As concentrations decreased by 1.5× with AWD under a 33 °C climate and by 1.3× under a 38 °C climate. Porewater cadmium (Cd) concentrations often increased following drainage but never exceeded 1 μg L[-1], and grain Cd concentrations were 14.7× to 119.7× lower than grain As concentrations. Both AWD and the 38 °C and 850 ppmv CO2 climate conditions enhanced root growth. Our findings indicate that AWD may still be an effective As mitigation strategy under severe future climate conditions.},
}

@article {pmid41099815,
year = {2025},
author = {Price, A and Mog, SYA and Dubach, J and Billington, C and Larsen, P},
title = {Microbiomes of 2024's Periodical Cicada Brood XIII Vary By Species and Location.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {105},
pmid = {41099815},
issn = {1432-184X},
support = {2216567 & 1912104//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Microbiota ; *Hemiptera/microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Illinois ; Male ; Female ; },
abstract = {The 17-year Periodical cicadas (Magicicada spp.) are long-lived insects that emerge in mass synchronized events after 17 years underground. Their survival and ecological success depend heavily on their microbiomes, which include obligate bacterial symbionts essential for nutrient acquisition, as well as occasional pathogens such as the behavior-altering fungus Massospora cicadina. While the periodical cicada lifecycle is well studied, little is known about how cicada microbiomes vary across species and environments during a single emergence event. During the 2024 emergence of Brood XIII in northern Illinois, 17-year cicadas were sampled from four ecologically distinct forest preserves. Cicadas were identified by species and sex; their microbiomes were assayed using 16S rRNA gene sequencing and tested for the presence of the fungal pathogen M. cicadina DNA in asymptomatic individuals. Sampling sites were characterized by plant community composition, historical disturbance, and potential presence of the antifungal compound juglone. Microbiome composition differed significantly by cicada species and site, but not by sex. The obligate symbionts Hodgkinia cicadicola and Sulcia muelleri dominated microbiome profiles, though other bacteria-including Pantoea agglomerans, a potential pheromone producer-were variably abundant. Cicada species distributions were non-random across sites and correlated with local plant diversity. M. cicadina DNA was detected in 23% of otherwise asymptomatic cicadas, with infection rates varying by location and negatively correlated with microbiome diversity. This study highlights complex interactions between cicada species, their microbial communities, and environmental variables such as plant diversity, soil chemistry, and land use history.},
}

Animals
*Microbiota
*Hemiptera/microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Symbiosis
Illinois
Male
Female

@article {pmid41099800,
year = {2025},
author = {Zhang, W and Yang, C and Zhao, K and Jin, M and Han, K and Wang, Y and Jiang, Z},
title = {Endophytic bacterial diversity of Vicatia thibetica collected from Xizang and the association with flavonoid accumulation.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {106},
pmid = {41099800},
issn = {1432-184X},
support = {82260759//National Natural Science Foundation of China/ ; },
mesh = {*Flavonoids/metabolism/analysis ; Plant Roots/microbiology/chemistry ; Rhizosphere ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Endophytes/classification/genetics/isolation & purification/metabolism ; *Soil Microbiology ; China ; Biodiversity ; },
abstract = {Vicatia thibetica de Boiss is a unique medicinal and edible plant endemic to Xizang, China. It is one of the five primary root medicines in Tibetan medicine due to its high content of flavonoids. However, the community composition of endophytic bacteria in its various tissues and their potential role in flavonoid accumulation remain unclear. We employed high-throughput sequencing to compare the diversity of endophytic bacteria in the rhizosphere soil and various tissues of V. thibetica collected from three sampling sites in Nyingchi, Xizang. Concurrently, we assessed the types and concentrations of flavonoids present in the roots. Finally, we investigated the relationship between root endophytic bacteria and flavonoid accumulation through correlation analysis. The results indicated that the diversity and abundance of bacterial communities in the rhizosphere soil exceeded those of the endophytic bacterial communities of V. thibetica. Proteobacteria is the dominant phylum, and Sphingomonas is the dominant genus. Each tissue of a plant exhibits its dominant genus. PICRUSt predictive analysis revealed that RNA processing and modification were the predominant functions among related species. Targeted metabolomics analysis has revealed that the roots of the plants contain 14 flavonoid compounds. Correlation analysis revealed that the concentrations of flavonoids in the roots, including apigenin, rutin, astragalin, quercetin 3-glucoside, L-epicatechin, kaempferol, and luteolin, are associated with the distribution and abundance of specific bacterial genera, such as Lactobacillus, Kurthia, Bradyrhizobium, Phenylobacterium, Novosphingobium, and Mycobacterium, among others. This finding suggests that these bacterial genera may directly influence the production and accumulation of flavonoids in the plant. Our findings will enhance the understanding of plant-microbe interactions and provide crucial insights into the role of endophytes in the production of V. thibetica and its significant secondary metabolites.},
}

*Flavonoids/metabolism/analysis
Plant Roots/microbiology/chemistry
Rhizosphere
*Bacteria/classification/genetics/isolation & purification/metabolism
*Endophytes/classification/genetics/isolation & purification/metabolism
*Soil Microbiology
China
Biodiversity

@article {pmid41099526,
year = {2025},
author = {Lami, R},
title = {From biocides to biology: multispecies biofilms as a sustainable, self-regenerating, and effective antifouling strategy.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0160925},
doi = {10.1128/aem.01609-25},
pmid = {41099526},
issn = {1098-5336},
abstract = {Finding antifouling strategies that are effective and environmentally safe remains a central challenge for maritime operations and ecosystem protection. Amador et al.'s article in Applied and Environmental Microbiology (91:e01392-25, 2025, https://doi.org/10.1128/aem.01392-25) proposes a bioinspired, applied-microbial-ecology solution: deliberately shaping pioneer biofilm communities, so they form a physical barrier against macrofouler settlement, avoiding biocides and low-adhesion inert coatings. Though focused on the ocean, this paradigm could inform broader anti-biofilm interventions across microbiology, reframing control as ecological steering rather than chemical suppression or materials-based design.},
}

@article {pmid41096495,
year = {2025},
author = {Phutthaphol, R and Bunchasak, C and Loongyai, W and Rakangthong, C},
title = {Effects of Vitamin D3 and 25(OH)D3 Supplementation on Growth Performance, Bone Parameters and Gut Microbiota of Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/ani15192900},
pmid = {41096495},
issn = {2076-2615},
support = {//Huvepharma (Thailand) Co., Ltd./ ; },
abstract = {Broiler chickens are commonly reared in closed housing systems with limited exposure to sunlight, thereby relying entirely on dietary sources of vitamin D. The hydroxylated metabolite 25-hydroxycholecalciferol [25(OH)D3] has been proposed as a more potent form than native vitamin D3 (cholecalciferol). This study evaluated the effects of dietary supplementation with vitamin D3 alone or in combination with 25(OH)D3 on growth performance, bone characteristics, and cecal microbiota in Ross 308 broilers. A total of 952 one-day-old male chicks were allocated to four treatments: a negative control (no vitamin D3), a positive control (vitamin D3 according to Ross 308 specifications), and a positive control supplemented with 25(OH)D3 at 1394 or 2788 IU/kg, in a randomized design with 17 replicates per treatment and 14 birds per replicate. Over a 40-day feeding trial, diets containing vitamin D3 (positive control) or supplemented with 25(OH)D3 significantly improved final body weight, weight gain, average daily gain, and feed conversion ratio compared with the negative control (p < 0.01), with no significant differences among the positive control and 25(OH)D3-supplemented groups, with a clear linear dose-dependent response. Although tibia ash and bone-breaking strength were not significantly affected, linear responses indicated a slight numerical trend toward improved skeletal mineralization with increasing 25(OH)D3. Microbiota analysis indicated that 25(OH)D3 affected cecal microbial ecology: low-dose inclusion showed reduced species richness and evenness, whereas high-dose inclusion restored richness to levels comparable to the positive control and enriched taxa associated with fiber fermentation and bile acid metabolism while reducing Lactobacillus dominance. In conclusion, supplementation with 25(OH)D3 in addition to vitamin D3 enhanced growth performance and selectively shaped the cecal microbiota of broilers, with suggestive benefits for bone mineralization. These findings highlight 25(OH)D3 as a more potent source of vitamin D than cholecalciferol alone and support its practical use in modern broiler nutrition to improve efficiency, skeletal health, and microbial balance.},
}

@article {pmid41092097,
year = {2025},
author = {Almeida-Silva, F and Van de Peer, Y},
title = {Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koaf243},
pmid = {41092097},
issn = {1532-298X},
abstract = {Gene and genome duplications expand genetic repertoires and facilitate functional innovation. Segmental or whole-genome duplications generate duplicates with similar and somewhat redundant expression profiles across multiple tissues, while other modes of duplication create genes that show increased divergence, leading to functional innovations. How duplicates diverge in expression across cell types in a single tissue remains elusive. Here, we used high-resolution spatial transcriptomic data from Arabidopsis thaliana, Glycine max, Phalaenopsis aphrodite, Zea mays, and Hordeum vulgare to investigate the evolution of gene expression following gene duplication. We found that genes originating from segmental or whole-genome duplications display increased expression levels, expression breadths, spatial variability, and number of coexpression partners. Duplication mechanisms that preserve cis-regulatory landscapes typically generate paralogs with more preserved expression profiles, but such differences generated by mode of duplication fade or disappear over time. Paralogs originating from large-scale (including whole-genome) duplications display redundant or overlapping expression profiles, indicating functional redundancy or subfunctionalization, while most small-scale duplicates diverge asymmetrically, consistent with neofunctionalization. Expression divergence also depends on gene functions, with dosage-sensitive genes displaying highly preserved expression profiles, and genes involved in more specialized processes diverging more rapidly. Our findings offer a spatially resolved view of expression divergence following duplication, elucidating the tempo and mode of gene expression evolution, and helping understand how gene and genome duplications shape cell identities.},
}

@article {pmid41089691,
year = {2025},
author = {Li, W and Lu, K and Tang, J and Chen, Y and Lu, Y and Hu, X and Zhu, H and Feng, Y},
title = {The alterations of airway and intestine microbiota in asthma: a systematic review and meta-analysis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675124},
pmid = {41089691},
issn = {1664-3224},
mesh = {Humans ; *Asthma/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Respiratory System/microbiology/immunology ; },
abstract = {BACKGROUND: Emerging evidence highlights notable differences in microbial ecology between individuals with asthma and healthy controls (HC). This meta-analysis aims to compile data on microbial diversity indices in the airway and intestinal microbiota of both groups for comparative analysis.

METHODS: We conducted a thorough systematic search of literature in PubMed, Embase, the Web of Science, and the Cochrane Library to find English-language studies focused on airway and intestinal microbiota in asthma, published from May 16, 2020 to May 16, 2025. We extracted data regarding microbial diversity indices to facilitate comparisons between the asthma group and HC.

RESULTS: 26 studies were included in this systematic review. Our analysis revealed no significant differences in alpha diversity between the two participant groups; however, beta diversity exhibited significant differences in 9 of the studies reviewed.

CONCLUSION: Our meta-analysis did not confirm the hypothesis that asthma shows lower alpha diversity than HC. To enhance understanding and inform future diagnostic and therapeutic approaches, further studies should be conducted with larger sample sizes and more robust methodologies.

https://www.crd.york.ac.uk/prospero/, identifier CRD420251113790.},
}

Humans
*Asthma/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Respiratory System/microbiology/immunology

@article {pmid41088478,
year = {2025},
author = {Chen, X and Ma, X and Liu, Z and Gu, H and Fang, H and Shen, Z and Zhang, H and Wan, S and Li, W and Hao, X and Clarke, NJ and Liu, J},
title = {Organic fertilizers increase microbial community diversity and stability slowing down the transformation process of nutrient cycling.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {130},
pmid = {41088478},
issn = {2524-6372},
support = {07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; 07//the Straw Returning Project/ ; CHN-2152, 22/0013 SINOGRAIN III//Norwegian Ministry of Foreign Affairs/ ; CHN-2152, 22/0013 SINOGRAIN III//Norwegian Ministry of Foreign Affairs/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; CX25PT02-01-04//Agricultural Science and Technology Innovation Project of Heilongjiang Province/ ; },
abstract = {BACKGROUND: Soil microbes play a central role in nutrient recycling in soils: however, the genetic mechanisms governing their responses to long-term fertilization remain poorly understood. While the agronomic benefits of long-term fertilization are well-documented, the genetic mechanisms and ecological processes underlying microbial community responses to different fertilization regimes remain poorly understood, particularly in unique soil systems such as black soils (Mollisols), which are critical for global food security. A deeper insight into how organic and inorganic fertilizers influence microbial assembly, functional potential, and community stability is essential for developing sustainable soil management practices.

RESULTS: This study deciphers microbial assembly mechanisms, functional gene dynamics, and community restructuring in black soils subjected to 44 years of chemical fertilizer (CF), manure amendment (M), and integrated chemical fertilizer with manure (CFM) treatments. Results revealed that CF significantly enhances functional gene abundance related to carbon (C) degradation (e.g., starch, cellulose, chitin and lignin) and nitrification, accelerating the conversion of recalcitrant C to labile C pools and ammonium to nitrate. Conversely, M and CFM treatments promote microbial diversity and stability while decelerating nutrient transformation processes. In addition, microbial assembly mechanisms shift from stochastic to deterministic processes with long-term fertilizer application in CF. The structural equation modeling (SEM) indicated that soil chemical properties shape both the diversity and composition of taxonomic and functional gene communities which subsequently regulate microbial -mediated nutrient cycling processes and crop yield.

CONCLUSIONS: Our findings highlight the trade-offs between microbial functional potential and community stability under contrasting fertilization strategies, emphasizing the need to integrate microbial metrics into sustainable land management frameworks.},
}

@article {pmid41086300,
year = {2025},
author = {Peterson, BD and Poulin, BA},
title = {Illuminating the Black Box: Trace Element Biogeochemistry from a Microbial Perspective.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06816},
pmid = {41086300},
issn = {1520-5851},
abstract = {Microbial processes are central to the transformation and fate of trace elements in the environment (e.g., mercury (Hg), arsenic (As)), but the complexities underlying microbial transformation rates and the influence of human impacts present considerable hurdles to developing conceptual and quantitative models of these processes. This perspective highlights processes that govern microbial activity in the environment as it pertains to trace elements, including redox, energy generation, resource limitation, and ecology and evolution. In this context, we compare and contrast the microbial-driven processes of Hg and As cycling, two elements with a genetic basis for microbial transformations (e.g., hgcAB, mer, arsH) that are used for microbial (i) metabolism (e.g., conversion of arsenate to arsenite), (ii) detoxification (e.g., reduction of divalent Hg(II) to volatile Hg(0)), (iii) warfare (e.g., conversion of arsenite to highly toxic trivalent methylated As(III)), or (iv) reasons not yet known (e.g., methylation of Hg(II) to toxic methylmercury). We argue for experimental approaches that quantify contaminant transformation(s) of interest in parallel with relevant metrics of microbial community activity. This microbe-centric framework may catalyze advancement that facilitates microbial integration into conceptual and quantitative models used to forecast environmental and human exposure to contaminants.},
}

@article {pmid41085588,
year = {2025},
author = {Purohit, HV and Chakraborty, J},
title = {Metagenomic approaches for studying ubiquitous yet diverse nucleoid associated proteins in microbial communities: challenges and advances.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {383},
pmid = {41085588},
issn = {1573-0972},
}

@article {pmid41085259,
year = {2025},
author = {Li, S and Ye, X and Luo, K and Yu, L and Shen, Z and Yi, T and Wang, M and Gu, Q},
title = {High-Throughput Absolute Quantification Sequencing Advances Characterisation of Microbial Community Ecology.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70139},
doi = {10.1111/mec.70139},
pmid = {41085259},
issn = {1365-294X},
support = {2023YFD2400902//National Key Research and Development Program of China/ ; 31800388//National Natural Science Foundation of China/ ; 41601203//National Natural Science Foundation of China/ ; 2019JJ50314//Natural Science Foundation of Hunan Province, China/ ; kq2208163//Natural Science Foundation of Changsha, China/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; 2108085ME186//Anhui Provincial Natural Science Foundation/ ; },
abstract = {High-throughput sequencing has been extensively used in microbial ecology research, but this technology typically generates semi-quantitative relative abundance data. The discrepancies of community dynamics delivered by relative and absolute abundances have long been recognised by microbial ecologists. However, few studies have considered the discrepancies and their potential effects on related ecological interpretations. Here, the absolute copy numbers (absolute abundances) of taxa were quantified using a 'spike-in' based 16S absolute quantification sequencing to investigate the dynamics, co-occurrence patterns, and ecological assembly processes of microbial community in the river-connected Lake Dongting, Hunan province, China. Routine sequencing data analysis based on relative abundance was also obtained for comparison. The results indicated that outcomes based on relative and absolute abundances were comparable at the community level but differed significantly at the population level when dynamics and interactions of specific taxa were of interest. Specifically, at the population level, the dynamics of individual taxa were usually masked by their relative abundances, particularly for abundant taxa. The correlation-based co-occurrence network constructed from relative abundance largely underestimated the importance of rare taxa, consisted of massive false negative connections, and was less stable than the one constructed using absolute abundance. At the community level, the diversity and composition of microbial communities in Lake Dongting exhibited significant temporal rather than spatial variations, and temperature was determined to be the most important factor shaping microbial community composition and assembly processes, regardless of which abundance data were used. Nonetheless, relative abundance data yielded stronger environmental and deterministic effects on microbial assembly than absolute abundance. In summary, our study highlights the importance of incorporating absolute quantification to unveil the underlying microbial ecological patterns masked by relative abundance.},
}

@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}

Animals
Larva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome/genetics
*Simuliidae/microbiology
*Citrus sinensis/metabolism
*Diptera/microbiology
Nigeria
Metagenome
Metagenomics
Phylogeny

@article {pmid41081862,
year = {2025},
author = {Bandyopadhyay, A and Sarkar, D and Das, A and Das, A},
title = {Intersections of ABO blood group, secretor status, and the gut microbiome: implications for disease susceptibility and therapeutics.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {296},
pmid = {41081862},
issn = {1432-072X},
mesh = {Humans ; *ABO Blood-Group System/genetics/metabolism ; *Gastrointestinal Microbiome ; Disease Susceptibility ; Galactoside 2-alpha-L-fucosyltransferase ; Bacteria/classification/genetics/isolation & purification ; Probiotics ; },
abstract = {The human gut microbiome is a dynamic ecosystem. It is shaped by host factors, including genetic traits such as ABO blood type and associated secretor status (FUT2 gene). In secretor individuals (~ 80% of the population), ABO antigens are expressed on the gut mucosal surfaces. These antigens serve as adhesion sites and nutrient substrates for select microorganisms. Evidence links blood groups to gut microbial ecology, with taxa such as Bacteroidessp., Eubacteriumsp., and Faecalibacterium sp. exhibiting preferential colonization patterns influenced by mechanisms including mucin glycan foraging, pathogen adhesion, and competitive exclusion. ABO blood type further modulates susceptibility to infectious, metabolic, and autoimmune diseases by affecting microbiome composition. Secretor status impacts microbiota diversity and probiotic colonization Non-secretors exhibit altered Bifidobacterium sp. profiles and reduced norovirus adhesion. These insights suggest possible avenues for tailoring microbiome-based interventions; however, current evidence remains preliminary and requires validation through controlled clinical studies. We outline a conceptual model linking host genetics, microbial ecology, and health outcomes, recognizing that these associations are still being mapped. The idea of incorporating blood type and secretor status into precision microbiome approaches remains exploratory and requires rigorous validation.},
}

Humans
*ABO Blood-Group System/genetics/metabolism
*Gastrointestinal Microbiome
Disease Susceptibility
Galactoside 2-alpha-L-fucosyltransferase
Bacteria/classification/genetics/isolation & purification
Probiotics

@article {pmid41081374,
year = {2025},
author = {Hoshyaripour, S and Mauri, M and Hobbs, JK and Foster, SJ and Allen, RJ},
title = {Cell wall mechanical stress could coordinate septal synthesis and scission in Staphylococcus aureus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0172825},
doi = {10.1128/mbio.01728-25},
pmid = {41081374},
issn = {2150-7511},
abstract = {Staphylococcus aureus divides by building a septum and then splitting into two daughter cells. Scission should be coordinated with septum completion to avoid cell lysis; however, it is not known how this is achieved, or what the relative roles of mechanical forces and the activity of peptidoglycan hydrolase enzymes are. Here, we show using thin-shell mechanics that septum formation causes a localized decrease in mechanical stress at the cell's equator. We propose that this local decrease in stress could act as a mechanical trigger for hydrolase activity, leading eventually to splitting. This mechanical trigger model can explain observed cell division defects, including premature splitting and failure to initiate splitting. The model also shows how cell size, turgor pressure, cell wall thickness and stiffness, and the relative rates of synthesis and hydrolysis combine to determine cell cycle timing and the outcome of antibiotic exposure. Bacterial cell division requires dynamic orchestration of molecular players, in concert with cell wall mechanics. Our work suggests how mechanical forces could coordinate with enzyme activity in the control of this complex process.IMPORTANCEStaphylococcus aureus is a major threat due to its ability to generate antibiotic-resistant strains. Understanding S. aureus division is therefore of great importance, but we do not know how septum formation is coordinated with cell scission. Previous works have shown that both mechanical stress and autolysin activity play key roles in scission, but it is unclear how mechanical and biochemical cues work together. Here, we propose a "mechanical trigger" model for the interplay between mechanical stress and autolysin activation. We use mathematical modeling to show that stress decreases in the S. aureus cell wall close to the division site as the septum is formed, and we propose that this could trigger autolysin activity. Our model explains reports of diverse division outcomes in the presence of mutations and antibiotics and points to a general link between cell geometry and antibiotic resistance.},
}

@article {pmid41080577,
year = {2025},
author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z},
title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1636876},
pmid = {41080577},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; },
abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.},
}

Humans
*Gastrointestinal Microbiome/immunology
Child
*Lung/immunology/microbiology/metabolism
*Lung Diseases/therapy/microbiology/immunology/etiology/metabolism
Dysbiosis
Animals
Fatty Acids, Volatile/metabolism

@article {pmid41079626,
year = {2025},
author = {Papadopoulou, KΚ and Chatzinotas, A and Diaz-Otero, BG and Brader, G and Karpouzas, DG and Garces Ruiz, M and Alonso Prados, JL and Declerck, S and Kellari, LM and Sessitsch, A},
title = {Benefits and challenges of upcoming microbial plant protection applications sustaining planetary health.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113557},
pmid = {41079626},
issn = {2589-0042},
abstract = {Plant disease outbreaks pose severe risks to global food security. Due to climate change, new diseases are expected to emerge, and the current use of chemical pesticides poses risks to environmental and human health. In the last decade, alternative plant protection agents of microbial origin have been developed, which also raise great expectations in the industry. Current products primarily represent individual microbial strains, either fungi or bacteria, which occasionally fail under field conditions due to various factors while their regulatory status differs globally. Recently, more diverse applications have started to emerge, ranging from microbial consortia, phages and protists to microbiome modulation or soil translocation. Integrated solutions, incorporating artificial intelligence are also proposed. In this review, we discuss the opportunities and challenges of these solutions, providing specific examples and discuss the regulatory needs for their market entry as well as their relevance for improving food security and planetary health.},
}

@article {pmid41078603,
year = {2025},
author = {Otto, JFM and Pohnert, G and Wichard, T and Bauer, M and Busch, A and Ueberschaar, N},
title = {Global DNA-methylation in quantitative epigenetics: orbitrap mass spectrometry.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1681568},
pmid = {41078603},
issn = {2296-889X},
abstract = {DNA methylation is the most common epigenetic modification in both prokaryotic and eukaryotic genomes. Here we present a method based on highly efficient acid-hydrolysis of DNA, liquid chromatography, and detection by mass spectrometry to accurately quantify cytosine methylation in highly methylated DNA samples. This approach enables direct, rapid, cost-efficient, and sensitive quantification of the methyl-modified nucleobase 5-methylcytosine and 6-methyl adenine, along with their unmodified nucleobases. In contrast to standard sequencing techniques, our method only gives quantitative information on the overall degree of methylation, but it requires only small amounts of DNA and is not dependent on lengthy bioinformatic analyses. Our method allows rapid, global methylome analysis and quantifies a central epigenetic marker. In a proof-of-principle study, we show that it can also be extended to the monitoring of other DNA modifications, such as methylated adenine. Uncomplicated data analysis facilitates a quick and straightforward comparison of DNA methylation across biological contexts. In a case study, we also successfully identified changes in methylation signatures in the marine macroalga Ulva mutabilis "slender". The advantage of global methylation analysis compared to sequencing allows for generating fast prior knowledge on which sample sequencing is senseful. The great benefit of the presented method is the speed and accuracy of the global methylation analysis, which is independent of the total methylation rate and gives accurate results, whereas competitive based on enzymatic digestion might fail.},
}

@article {pmid41078307,
year = {2025},
author = {He, H and Xiao, M and Song, L and Tian, Y and Jia, Y},
title = {Lipidome-microbiome crosstalk as an outer niche in the skin: regulatory networks in health and disease.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf353},
pmid = {41078307},
issn = {1365-2133},
support = {//Beijing Technology and Business University/ ; //Beijing Municipal Education Commission/ ; 32100254//National Science Foundation of China/ ; },
abstract = {The skin is the outermost barrier to organisms from the external environment. This natural role, endowed by evolution, results in a nutrient-poor skin surface that enables microbial nutrition-dependent lipids to shape microbial ecology by survival pressure and nutrient preference. In turn, the skin microbiota produce microorganism-metabolized bioactive molecules (MBMs) to increase molecular diversity. This crosstalk functions as a crucial component of niche-regulating skin properties via multiple mechanisms. Furthermore, the local and remote effects of different barrier sites provide a more comprehensive explanation for the crosstalk from a global perspective. The variable function and mechanism of crosstalk may represent an evolutionary means by which the skin uses fluctuating commensal signals - the highly dynamic MBMs - to calibrate skin status and provide heterologous protection against invasive pathogens. Elucidating the reasons for the differing selectivity and catalytic efficiency of lipid-metabolizing enzymes in microorganisms and revealing the biologic processes and regulatory mechanisms of the 'co-metabolic systems' on the skin will advance diagnostic and therapeutic strategies for local cutaneous disorders and comorbid diseases of distant organs.},
}

@article {pmid41069707,
year = {2025},
author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A},
title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf157},
pmid = {41069707},
issn = {2730-6151},
abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.},
}

@article {pmid41069527,
year = {2025},
author = {Jiang, W and Gu, S},
title = {Editorial: The oral microbiome and its impact on systemic health: from disease development to biomaterials development.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1697069},
pmid = {41069527},
issn = {2235-2988},
}

@article {pmid41066956,
year = {2025},
author = {Huang, P and Zhou, R and Huang, Z and Wu, C},
title = {Deciphering the environmental response and assembly of rare and abundant taxa in zaopei employing daqu produced by different pressing patterns.},
journal = {International journal of food microbiology},
volume = {445},
number = {},
pages = {111471},
doi = {10.1016/j.ijfoodmicro.2025.111471},
pmid = {41066956},
issn = {1879-3460},
abstract = {Baijiu fermentation relies on complex microbial communities within zaopei, which are significantly shaped by the microbial starter daqu. This study investigated the rare and abundant taxa composition, and flavor characteristics of zaopei (fermented grains) employing Nongxiangxing daqu produced by different pressing patterns (mechanically pressed, artificially pressed) from microbial ecology perspective. Then, the origin, environmental response, assembly patterns and driving factors of rare and abundant taxa were revealed. The results indicated that both Lactobacillus and Acetobacter consistently dominated in rare bacteria and abundant bacteria of zaopei, the dominant abundant fungi were Thermoascus and Issatchenkia, while the dominant rare fungi were Aspergillus and Pichia. The microbial community of zaopei was significantly influenced by fungi originating from daqu, according to Fast expectation-maximization microbial source tracking (FEAST) analysis. Moreover, daqu significantly influenced the assembly process of abundant fungi taxa in zaopei, with the mechanically pressed daqu (MDQ) increased the proportion of heterogeneous selection. Moreover, water, starch and ethanol contents were important factors driving the rare bacteria assembly. Co-occurrence network analysis indicated that artificially pressed daqu (ADQ) enhanced microbial interactions in zaopei, which were closely related to rare bacteria. Meanwhile, Spearman's correlation between microorganisms and differential flavor compounds showed that fungal taxa (abundant Clavispora, rare Pichia and rare Issatchenkia) played a dominant role in flavor synthesis. These results contributed to a better understanding of the functional contributions of rare and abundant taxa in baijiu fermentation and provided theoretical support and technical guidance for regulating baijiu quality.},
}

@article {pmid41065083,
year = {2025},
author = {Cantoran, A and Maillard, F and Bermudez, R and Stefanski, A and Reich, PB and Kennedy, PG},
title = {Warming and Reduced Rainfall Alter Fungal Necromass Decomposition Rates and Associated Microbial Community Composition and Functioning at a Temperate-Boreal Forest Ecotone.},
journal = {Global change biology},
volume = {31},
number = {10},
pages = {e70536},
doi = {10.1111/gcb.70536},
pmid = {41065083},
issn = {1365-2486},
support = {DE-FG02-07ER64456//Biological and Environmental Research/ ; NSF-DBI-2021898//Division of Biological Infrastructure/ ; },
mesh = {*Rain ; *Soil Microbiology ; *Climate Change ; Minnesota ; *Microbiota ; Soil/chemistry ; *Fungi/metabolism ; Taiga ; *Global Warming ; },
abstract = {Changes in temperature and rainfall associated with altered climatic conditions are likely to significantly alter rates of soil organic matter decomposition. To determine how the combined effects of warming and drought impact the decomposition of fungal necromass, a large and fast-cycling portion of the global soil organic carbon (C) pool, we incubated Hyaloscypha bicolor necromass under both ambient and altered conditions (+3.3°C air and soil warming and ~40% reduced rainfall) at the B4Warmed experiment in Minnesota, USA. We conducted two multi-week incubations, one assessing mass loss and microbial community composition on decaying necromass after 1, 2, 7, and 14 weeks and the second characterizing the substrate utilization capacities of necromass-associated microbial communities after Weeks 1 and 7. Warming and reduced rainfall accelerated the initial rate of necromass decay by ~20%, yet slowed overall mass loss by ~6% at the end of the 14-week incubation. These different rates of decay over time paralleled shifting abiotic conditions, with altered plots experiencing warmer and relatively moist conditions early, but hotter and drier conditions later. The microbial community composition also varied by treatment and time, with warming and reduced rainfall stimulating fast-growing fungi as well as fungal relative to bacterial growth overall. Additionally, the functional capacity of the microbial community also changed over time, having a higher metabolic capability to utilize C and N substrates in the altered plots early in decomposition but a lower capability later in decay. Collectively, our findings highlight a dynamic, stage-dependent response of fungal necromass decomposition to altered climate regimes. By linking these decay dynamics to shifts in environmental conditions as well as microbial community composition and function, our study highlights the critical roles of both abiotic and biotic changes in mediating decomposition responses to climate change.},
}

*Rain
*Soil Microbiology
*Climate Change
Minnesota
*Microbiota
Soil/chemistry
*Fungi/metabolism
Taiga
*Global Warming

@article {pmid41064756,
year = {2025},
author = {Lofgren, L and Maillard, F and Michaud, T and Gredeby, A and Tunlid, A and Kennedy, PG},
title = {Diverse nitrogen acquisition strategies of conifer-associated ectomycorrhizal fungi shape unique responses to changing nitrogen regimes.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1666003},
pmid = {41064756},
issn = {1664-462X},
abstract = {Ectomycorrhizal fungi are critical mediators of nitrogen acquisition in forest ecosystems, exhibiting variation in both host association and metabolic traits that mediate differential responses to forest nitrogen availability. However, how nitrogen acquisition strategies vary among closely related fungal species, how these patterns manifest in conifer-associated ECM fungi, and whether they persist over changing nitrogen regimes, remains poorly understood. Using an integrative approach combining in silico genomic analysis, in vitro growth assays, and isotopic analysis of in situ specimens spanning six decades, we provide the first comprehensive examination of nitrogen assimilation in congeneric conifer-associated ectomycorrhizal fungi using six Suillus species. We found highly conserved genes for inorganic nitrogen assimilation across species, but striking interspecific variation in the genetic capacity for organic nitrogen metabolism. Interspecific differences were also observed in fungal growth on varying nitrogen substrates in the growth assays, as well as in the isotopic signatures of historical specimens. For the latter, carbon isotopic patterns showed divergent temporal trends among Suillus species, suggestive of differential N use over time. Collectively, these genomic, physiological, and isotopic findings support the presence of notable interspecific diversity in ectomycorrhizal fungal nitrogen acquisition and suggest that coniferous forests and their fungal symbionts exhibit distinct responses to shifts in nitrogen availability compared to broadleaf forests. The ability of even closely related ectomycorrhizal fungi to employ diverse nitrogen acquisition strategies has important implications for forest ecosystem resilience, as different species may provide complementary services to host trees under varying environmental conditions, potentially reducing competition, and influencing forest responses to altered nutrient availability.},
}

@article {pmid41064004,
year = {2025},
author = {Pérez-Ramos, DW and Caragata, EP},
title = {Fungal communities in Florida salt marsh mosquito midguts vary between species and over time but have low structure.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1648091},
pmid = {41064004},
issn = {1664-3224},
mesh = {Animals ; *Fungi/genetics/classification ; *Mycobiome ; *Culicidae/microbiology ; Florida ; Wetlands ; *Aedes/microbiology ; Species Specificity ; *Culex/microbiology ; *Gastrointestinal Microbiome ; },
abstract = {INTRODUCTION: Microorganisms are intrinsically tied to the developmental and reproductive success of mosquitoes, can influence their ability to resist insecticides, and can strongly influence their ability to harbor and transmit pathogens of medical importance. Although mosquito-associated fungi have oben been overlooked at the expense of bacteria, several different fungal taxa are known to modulate interactions between mosquitoes and pathogens, while others have potential applications as biopesticides due to their entomopathogenic activity. Accordingly, understanding how and why different fungi associate with mosquito tissues is an important step toward elucidaUng the impact the diverse kingdom of microorganisms has on mosquito biology and mosquito- borne disease.

METHODS: In this study, we used Illumina Mi-Seq profiling of the internal transcribed spacer gene to characterize the midgut mycobiota of field collected adult mosquitoes from three species: Aedes taeniorhynchus, Anopheles atropos, and Culex nigripalpus, at two different collection times.

RESULTS: We observed that all mosquito specimens carried high loads of Rhodotorula lamellibrachiae, a common environmental yeast that is known to be involved in nitrogen fixation, although its role in mosquito biology is not clear. We also find that the mycobiome is strongly influenced by mosquito species, that few fungi have both high abundance and prevalence, and that few fungi consistently co- associate across time and host species.

DISCUSSION: These findings suggest that there is limited structure to mosquito associated fungal communities, implying that their assembly may be more driven by stochastic than deterministic processes. Our findings highlight the influence of key variables on mosquito fungal diversity and help facilitate understanding of how and when mosquitoes acquire fungi and the roles that fungi play in mosquito biology.},
}

Animals
*Fungi/genetics/classification
*Mycobiome
*Culicidae/microbiology
Florida
Wetlands
*Aedes/microbiology
Species Specificity
*Culex/microbiology
*Gastrointestinal Microbiome

@article {pmid41063836,
year = {2025},
author = {Chen, X and Ye, L and Zou, X and Zhou, Y and Peng, C and Huang, R},
title = {The role of gut microbiota in myocardial ischemia-reperfusion injury.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1625299},
pmid = {41063836},
issn = {2297-055X},
abstract = {Myocardial ischemia-reperfusion injury denotes the pathological damage resulting from the restoration of blood flow and oxygen supply following acute coronary artery occlusion. Myocardial ischemia-reperfusion injury is commonly seen in acute coronary syndromes and is an important factor in the development of ischemic cardiomyopathy, which severely affects the prognosis of coronary heart disease. The gut microbiota, a complex ecosystem with multifaceted functions, plays a crucial role in host health. Dysregulation of the gut microbiota exerts substantial effects on the onset and progression of cardiovascular diseases, including myocardial ischemia-reperfusion injury. This review elucidates the mechanisms underlying myocardial ischemia-reperfusion injury and the involvement of the gut microbiota in this process, encompassing aspects such as intestinal barrier integrity, microbial dysbiosis, inflammatory responses, oxidative stress, mitochondrial dysfunction, and metabolic alterations. Additionally, we investigate various interventions that modulate myocardial ischemia-reperfusion injury by influencing the gut microbiota. Maintaining a healthy intestinal barrier and a stable microbial ecology is paramount in preventing myocardial ischemia-reperfusion injury. High-fiber diets, probiotic consumption, short-chain fatty acids supplementation, and Traditional Chinese Medicine, can safeguard the heart against myocardial ischemia-reperfusion injury by regulating gut microbiota through diverse mechanisms. As the role of gut microbiota in myocardial ischemia-reperfusion injury continues to be investigated, it provides important therapeutic targets and drug development opportunities for the prevention and treatment of myocardial ischemia-reperfusion injury. However, further in-depth and comprehensive studies are required to fully realize these potentials.},
}

@article {pmid41063423,
year = {2025},
author = {Bartz, PM and Grullón-Penkova, IF and Cavaleri, MA and Reed, SC and Shahid, S and Wood, TE and Bachelot, B},
title = {Experimental warming alters free-living nitrogen fixation in a humid tropical forest.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70592},
pmid = {41063423},
issn = {1469-8137},
support = {1754713//Division of Environmental Biology/ ; 2120085//Division of Environmental Biology/ ; 89243018S-SC-000014//Basic Energy Sciences/ ; 89243018S-SC-000017//Basic Energy Sciences/ ; 89243021S-SC-000076//Basic Energy Sciences/ ; DE-SC-0011806//Basic Energy Sciences/ ; DE-SC-0018942//Basic Energy Sciences/ ; DE-SC0012000//Basic Energy Sciences/ ; DE-SC0022095//Basic Energy Sciences/ ; },
abstract = {Microbial nitrogen (N) fixation accounts for c. 97% of natural N inputs to terrestrial ecosystems. These microbes can be free-living in the soil and leaf litter (asymbiotic) or in symbiosis with plants. Warming is expected to increase N-fixation rates because warmer temperatures favor the growth and activity of N-fixing microbes. We investigated the effects of warming on asymbiotic components of N fixation at a field warming experiment in Puerto Rico. We analyzed the function and composition of bacterial communities from surface soil and leaf litter samples. Warming significantly increased asymbiotic N-fixation rates in soil by 55% (to 0.002 kg ha[-1] yr[-1]) and by 525% in leaf litter (to 14.518 kg ha[-1] yr[-1]). This increase in N fixation was associated with changes in the N-fixing bacterial community composition and soil nutrients. Our findings suggest that warming increases the natural N inputs from the atmosphere into this tropical forest due to changes in microbial function and composition, especially in the leaf litter. Given the importance of leaf litter in nutrient cycling, future research should investigate other aspects of N cycles in the leaf litter under warming conditions.},
}

@article {pmid41062579,
year = {2025},
author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J},
title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35107},
pmid = {41062579},
issn = {2045-2322},
support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; },
mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Microbiota ; },
abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.},
}

China
*Museums
*Air Microbiology
*Bacteria/genetics/classification/isolation & purification/drug effects
Microbiota

@article {pmid40981661,
year = {2025},
author = {Pearl Mizrahi, S and Lee, H and Goyal, A and Owen, E and Gore, J},
title = {Structured interactions explain the absence of keystone species in synthetic microcosms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf211},
pmid = {40981661},
issn = {1751-7370},
support = {//Schmidt Science Polymath award/ ; 542385//Simons Foundation Principles of Microbial Ecology Collaboration/ ; LT000378/2018//HSFP Long-term fellowships/ ; GBMF4513//Gordon and Betty Moore Foundation/ ; T32GM087237//NIH Training/ ; /GM/NIGMS NIH HHS/United States ; },
mesh = {*Ecosystem ; *Bacteria/growth & development/classification ; *Microbial Interactions ; *Extinction, Biological ; },
abstract = {In complex ecosystems, the loss of certain species can trigger a cascade of secondary extinctions and invasions. However, our understanding of the prevalence of these critical "keystone" species and the factors influencing their emergence remains limited. To address these questions, we experimentally assembled microcosms from 16 marine bacterial species and found that multiple extinctions and invasions were exceedingly rare upon removal of a species from the initial inoculation. This was true across eight different environments with either simple carbon sources (e.g. glucose) and more complex ones (e.g. glycogen). By employing a generalized Lotka-Volterra model, we could reproduce these results when interspecies interactions followed a hierarchical pattern, wherein species impacted strongly by one species were also more likely to experience strong impacts from others. Such a pattern naturally emerges due to observed variation in carrying capacities and growth rates. Furthermore, using both statistical inference and spent media experiments, we inferred interspecies interaction strengths and found them consistent with structured interactions. Our results suggest that the natural emergence of structured interactions may provide community resilience to extinctions.},
}

*Ecosystem
*Bacteria/growth & development/classification
*Microbial Interactions
*Extinction, Biological

@article {pmid41061000,
year = {2025},
author = {Cummings, CL and Landreville, KD and Kuzma, J},
title = {Public perceptions and support for introduced microbes to combat hospital-acquired infections and antimicrobial resistance.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332578},
doi = {10.1371/journal.pone.0332578},
pmid = {41061000},
issn = {1932-6203},
mesh = {Humans ; *Cross Infection/prevention & control/microbiology ; Female ; Adult ; Male ; Middle Aged ; *Microbiota ; *Public Opinion ; Surveys and Questionnaires ; Aged ; Young Adult ; *Drug Resistance, Microbial ; Adolescent ; United States ; },
abstract = {Hospital-acquired infections and antimicrobial resistance (AMR) remain major global health threats, prompting interest in microbiome-based interventions that introduce beneficial microbes or genetic interventions to control pathogens and reduce AMR genes in hospital environments. Microbiome engineering, which can use advanced biotechnology, genetics, and microbial ecology principles to restructure microbial communities, is a rapidly growing field with applications in infection control. As researchers explore deploying beneficial microbes and other genetic interventions in clinical settings like hospital sinks, public perception becomes critical to responsible implementation. This study addresses how U.S. adults perceive microbiome evaluation, and education. Drawing on a nationally representative survey (N = 1,000), we conducted hierarchical ordinary least squares regression modeling to assess predictors of support across three domains: implementation of introduced microbiomes (IM), rigorous testing, and education for healthcare stakeholders. Results demonstrate that support for IM in hospital sinks is shaped less by demographic traits and more by emotional responses, trust in institutional efficacy, belief in intervention benefits, and a desire to learn about microbiome science. These findings advance previous knowledge by distinguishing cognitive, affective, and contextual predictors across distinct types of support. Contrary to expectations, prior familiarity and information-seeking were negatively associated with IM support, suggesting that some engagement or exposure to risk-framing may drive skepticism. Meanwhile, emotional reactions and perceived efficacy consistently predicted support for IM, testing, and education (i.e., across all dependent variables), underscoring the need to address affective and trust-based components of public engagement. This research contributes to an emerging empirical foundation for responsible microbiome innovation by grounding the analysis in the Responsible Research and Innovation (RRI) framework. With the technology still in early development, these insights provide critical guidance for biotechnology developers, policymakers, and hospital leaders seeking to align microbiome engineering with societal values through transparent communication, rigorous oversight, and inclusive education.},
}

Humans
*Cross Infection/prevention & control/microbiology
Female
Adult
Male
Middle Aged
*Microbiota
*Public Opinion
Surveys and Questionnaires
Aged
Young Adult
*Drug Resistance, Microbial
Adolescent
United States

@article {pmid41057344,
year = {2025},
author = {Sun, X and Frey, C and McCoy, D and Spieler, MBA and Kelly, CL and Maloney, AE and Garcia-Robledo, E and Lehmann, MF and Ward, BB and Zakem, EJ},
title = {Mechanistic understanding of nitrate reduction as the dominant production pathway of nitrous oxide in marine oxygen minimum zones.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8916},
pmid = {41057344},
issn = {2041-1723},
mesh = {*Nitrous Oxide/metabolism ; *Nitrates/metabolism ; *Oxygen/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ecosystem ; Denitrification ; Nitrites/metabolism ; Bacteria/metabolism ; },
abstract = {Nitrous oxide (N2O), a potent greenhouse gas and ozone-depleting agent, is produced intensely in oxygen minimum zones (OMZs) predominantly through nitrate reduction NO 3 - → N 2 O . However, mechanisms and controls of this pathway remain unclear. Here, we investigate the microbial ecology governing this pathway using experiments and an ecosystem model. We experimentally confirm a critical hypothesis: most NO 3 - → N 2 O denitrifiers do not utilize extracellular nitrite, an intermediate of the pathway. Model results demonstrate that the NO 3 - → N 2 O pathway is compatible with oxygen, and that its response to oxygen is heterogeneous because it is governed by niche partitioning of distinct microbial types and thus may not follow a smooth curve. Lastly, experiments demonstrate that this pathway is sensitive to the type of organic matter, its electron acceptor, in addition to organic matter availability. These findings advance our mechanistic understanding of the primary N2O production pathway, necessary for predictions of marine N2O emissions.},
}

*Nitrous Oxide/metabolism
*Nitrates/metabolism
*Oxygen/metabolism
Oxidation-Reduction
*Seawater/microbiology/chemistry
Ecosystem
Denitrification
Nitrites/metabolism
Bacteria/metabolism

@article {pmid41057270,
year = {2025},
author = {Hallett, EN and Comte, J},
title = {Identification and Global Distribution of a Core Microbiome From High-Arctic Lakes.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70182},
doi = {10.1111/1462-2920.70182},
pmid = {41057270},
issn = {1462-2920},
support = {RGPIN-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; RGPNS-2020-06874//Natural Sciences and Engineering Research Council of Canada/ ; //Natural Resources Canada/ ; },
mesh = {*Lakes/microbiology ; Arctic Regions ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Arctic lakes are sentinels of climate change, yet their microbial community structure and functioning remain poorly understood. This study analysed the genetic content of clear-water Arctic lakes and their surroundings using high-throughput amplicon sequencing of the 16S rRNA gene to identify their core microbiome and its contribution to the overall taxonomy pool. To assess geographical constraints and oligotrophic conditions, these results were compared with a latitudinally diverse multi-basin oligotrophic lake in a temperate climate. Arctic and temperate lakes exhibited different assemblages, but both showed similar transitional gradients of microbial community composition from upstream soils/inlets through the lake system to the outlet, driven mainly by the dissolved organic matter (DOM) characteristics. Distinct core microbiomes were identified for temperate and Arctic lakes, with Arctic lakes appearing more diverse. A limited shared core microbiome was observed between the two regions, composed mostly of typical freshwater bacteria. While core taxa identities differed between regions, most exhibited characteristics of generalist bacteria with a strong global presence. These results provide key insights into the structure of remote high Arctic lakes, contributing to our understanding of aquatic microbial ecology in a transitioning Arctic and identifying microbial communities and individual taxa of interest for further study on oligotrophy.},
}

*Lakes/microbiology
Arctic Regions
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Phylogeny
DNA, Bacterial/genetics
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid41056783,
year = {2025},
author = {Guo, H and Lu, Y and Bulok, Y and Huang, W and Liu, Y},
title = {Advances and challenges of anammox-based PN/A and PD/A coupled processes in treating diverse wastewater qualities: A review.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127484},
doi = {10.1016/j.jenvman.2025.127484},
pmid = {41056783},
issn = {1095-8630},
abstract = {The anammox process is critical for sustainable nitrogen removal, yet widespread use faces operational, environmental and microbial challenges. This review evaluates recent advances in anammox-based coupled processes, particularly PN/A and PD/A, highlighting their adaptation to varied wastewater types. PN/A has been extensively validated at full scale for high-ammonia wastewaters, including sludge digestion liquor, landfill leachate, and industrial effluents, and is now being extended to mainstream municipal applications. However, persistent barriers such as NOB suppression, sensitivity to low temperature, and heterotrophic competition under high C/N conditions continue to limit its performance. In contrast, successful PD/A deployment in mainstream wastewater depends on innovative solutions to temperature-related constraints, including biofilm buffering, metabolic adaptation, and kinetic optimization. The performance of both PN/A and PD/A systems is closely tied to wastewater composition (e.g. such as salinity, organic load, and the presence of toxic compounds) and its influence on microbial kinetics. Emerging innovations, including EPS-enriched biofilms, granular sludge, quorum sensing microbial regulation, and AI-driven controls have enhanced system resilience. Furthermore, integrated approaches enabling simultaneous nitrogen and phosphorus removal and novel reactor configurations are expanding the practical applicability of anammox processes, supporting resource recovery goals. This review synthesizes mechanistic insights, highlights full-scale implementation cases, and outlines emerging frontiers such as nanotechnology-enhanced biofilms and digital twin modelling for process optimization. By bridging microbial ecology with advanced process engineering, this work provides strategic direction for scaling up anammox-based systems in pursuit of energy-neutral and sustainable wastewater treatment under tightening environmental regulations.},
}

@article {pmid41054273,
year = {2025},
author = {Wang, S and Bao, Z and Li, Z and Zhao, M and Wang, X and Liu, F},
title = {The impact of very-low-calorie ketogenic diets on gut microbiota in individuals with obesity: a systematic review and meta-analysis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2566305},
doi = {10.1080/19490976.2025.2566305},
pmid = {41054273},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Ketogenic ; *Obesity/microbiology/diet therapy ; Bacteria/classification/genetics/isolation & purification ; Body Mass Index ; *Caloric Restriction ; },
abstract = {OBJECTIVE: This study aimed to systematically review and meta-analyze the effects of very-low-calorie ketogenic diets (VLCKD) on gut microbiota in individuals with obesity.

METHODS: A comprehensive literature search was conducted across four electronic databases-PubMed, EBSCOhost, Cochrane Library, and Web of Science-up to June 2025. Outcomes included changes in gut microbial diversity and the relative abundance of key taxa. Subgroup analyses were performed based on body mass index (BMI), age, and intervention duration.

RESULTS: A total of 14 studies were included. Random-effects meta-analysis revealed that VLCKD interventions significantly improved gut microbial α-diversity, as indicated by increased Shannon index (SMD: 0.54, 95% CI: 0.03 to 1.04, P = 0.0378) and Faith's Phylogenetic Diversity (PD) index (SMD: 0.77, 95% CI: 0.36 to 1.18, P = 0.0002). In addition, VLCKD significantly increased the abundance of Akkermansia (SMD: 1.76, 95% CI: 0.48 to 3.03, P = 0.0069) and the Firmicutes-to-Bacteroidetes (F/B) ratio (SMD: 1.01, 95% CI: 0.67 to 1.34, P < 0.0001), while significantly reducing the probiotic genus Bifidobacterium (SMD: -1.23, 95% CI: -1.81 to -0.64, P < 0.0001). Subgroup analyses indicated that the increase in Shannon index was more pronounced in participants with BMI ≤ 30 kg/m² and age >30 years. Akkermansia showed a greater increase in those with BMI 30-35 kg/m², age >40 years, and intervention duration ≤6 weeks. Conversely, Bifidobacterium abundance declined significantly in individuals with BMI 30-35 kg/m², age >40 years, and within an intervention period ≤12 weeks.

CONCLUSION: VLCKD appears to be a promising dietary intervention for modulating gut microbiota in individuals with obesity. However, its bidirectional effects on microbial ecology warrant caution. Future studies should further investigate its long-term safety and explore personalized strategies for microbiota-targeted interventions.},
}

Humans
*Gastrointestinal Microbiome
*Diet, Ketogenic
*Obesity/microbiology/diet therapy
Bacteria/classification/genetics/isolation & purification
Body Mass Index
*Caloric Restriction

@article {pmid41053793,
year = {2025},
author = {Ou, HX and Chen, Y and Zheng, DL and Lu, YG and Gan, RH},
title = {Evaluating microbial regulation as a preventive strategy for radiation-related caries: A review.},
journal = {Head & face medicine},
volume = {21},
number = {1},
pages = {67},
pmid = {41053793},
issn = {1746-160X},
support = {2022J01270//Fujian provincial Natural Science Foundation of China/ ; 2021GGA055//Fujian Provincial Health Technology Project/ ; },
mesh = {Humans ; *Dental Caries/prevention & control/microbiology/etiology ; *Microbiota/radiation effects ; *Head and Neck Neoplasms/radiotherapy ; Probiotics/therapeutic use ; *Radiation Injuries/prevention & control/microbiology ; Squamous Cell Carcinoma of Head and Neck/radiotherapy ; },
abstract = {Radiotherapy is a crucial treatment for head and neck squamous cell carcinoma but is associated with several complications, particularly the onset of radiation-related caries (RRC), which severely compromises patients' oral health and quality of life. Most studies have focused on the direct effects of radiation on host organs. Such as radiotherapy/Concurrent Chemoradiotherapy (CCRT) contributing to RRC primarily by inducing salivary gland hypofunction and directly damaging tooth structure. However, emerging evidence implicates additional mechanisms including dietary modifications and oral microbial dysbiosis in driving pathogenic microbial shifts characterized by cariogenic bacterial/fungal proliferation, thereby exacerbating RRC progression. In particular, changes in common cariogenic bacteria/fungi after radiotherapy remain poorly understood. Furthermore, clinical translation of microbial ecology principles into effective RRC prevention strategies remains underexplored. This review centers on radiation-induced oral microbiota alterations, critically analyzing documented microbial shifts characterized by marked proliferation of cariogenic taxa including Streptococcus mutans, Lactobacillus, Prevotella melaninogenica, Veillonella, and Actinomyces, alongside fungal overgrowth of Candida albicans. We propose a dual-focused intervention protocol: initiating probiotic supplementation at radiotherapy commencement to stabilize microbial ecology and preserve salivary function, combined with standardized oral care encompassing mechanical plaque removal, fluoride therapy, and natural anticariogenic agents. While mechanistically plausible, this paradigm requires rigorous validation through multicenter randomized controlled trials assessing ecological stability maintenance and caries incidence reduction.},
}

Humans
*Dental Caries/prevention & control/microbiology/etiology
*Microbiota/radiation effects
*Head and Neck Neoplasms/radiotherapy
Probiotics/therapeutic use
*Radiation Injuries/prevention & control/microbiology
Squamous Cell Carcinoma of Head and Neck/radiotherapy

@article {pmid41051094,
year = {2025},
author = {Cheng, Z and Xia, W and McKelvey, S and He, Q and Chen, Y and Yuan, H},
title = {Building Predictive Understanding of the Activated Sludge Microbiome by Bridging Microbial Growth Kinetics and Microbial Population Dynamics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05925},
pmid = {41051094},
issn = {1520-5851},
abstract = {Modeling microbiomes can provide predictive insights into microbial ecology, but current modeling approaches suffer from inherent limitations. In this study, a novel modeling approach was developed based on the intrinsic connection between the growth kinetics of guilds and the dynamics of microbial populations. To implement this approach, 466 samples from four full-scale activated sludge systems were retrieved. The raw samples were processed using a data transformation method that tripled the data set size and enabled quantification of population dynamics. Of the 42 family level core populations, 36 showed overall dynamics statistically close to zero (within ± 0.05 d[-1]). Bayesian networks were built to classify the core populations into heterotrophic and autotrophic guilds. Topological data analysis was applied to identify keystone populations and time-dependent microbial interactions. The data-driven inferences were validated directly using the Microbial Database for Activated Sludge (MiDAS) and indirectly by predicting community structure using artificial neural networks. The Bray-Curtis similarity between predicted and observed communities was higher with microbial kinetic parameters than without these parameters (0.70 vs 0.66, t test, p < 0.05). Owing to the flexibility of the modeling framework, this proposed hybrid approach might potentially be adapted to time-dependent data from natural systems for predictive understanding of the involved microbiomes.},
}

@article {pmid41049421,
year = {2025},
author = {Yan, J and Zhao, J and Naizemuding, P and Zhao, W and Sun, J and Wang, Y and Yang, J and Li, D and Zhang, F and Cao, H},
title = {Unraveling the Anti-Obesity Potential of White Kidney Bean α-Amylase Inhibitors: Mechanistic Insights From Enzyme Kinetics to Gut Microbiota Modulation.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e71043},
pmid = {41049421},
issn = {2048-7177},
abstract = {The global rise in obesity, driven largely by excessive carbohydrate consumption, highlights the demand for innovative dietary interventions targeting starch digestion. This study investigates the anti-obesity effects of α-amylase inhibitors (α-AI) extracted from white kidney beans, employing a multidisciplinary strategy encompassing botanical screening, enzyme kinetics, clinical trials, and gut microbiota profiling. Among 10 varieties evaluated, the A10 strain from Jilin Province demonstrated the highest α-AI activity, characterized by noncompetitive inhibition that remains effective across varying starch concentrations. In an 8-week randomized controlled trial, α-AI supplementation significantly reduced body weight, BMI, waist circumference, and hip circumference compared to placebo. Further, 16S rRNA sequencing revealed dual mechanisms: enrichment of SCFA-producing bacteria (e.g., Bifidobacterium and Bacteroides ovatus) and modulation of microbial lipid metabolic pathways. These results highlight α-AI as a dual-action anti-obesity agent, combining direct enzymatic inhibition with microbiome-mediated metabolic effects. By bridging phytochemical characterization with clinical outcomes, this work proposes a novel therapeutic approach that simultaneously targets carbohydrate absorption and gut microbial ecology, supporting the development of standardized α-AI formulations as potential nutraceuticals for metabolic syndrome.},
}

@article {pmid41048979,
year = {2025},
author = {Nurhazli, NAA and Tan, JH and Kamaroddin, MF and Shamsir, MS and Yaakop, AS and Goh, KM},
title = {Microbial Community Profiles of Biofilms from Hot Springs: 16S and 18S rRNA Amplicon Sequencing Data.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {112093},
pmid = {41048979},
issn = {2352-3409},
abstract = {This article presents microbial diversity data from biofilms collected from the sides or outflows of several Malaysian hot springs, with temperatures ranging from 38 to 56 °C and pH values between 7.1 and 8.7. Genomic DNA was extracted from the biofilms and subjected to 16S V3-V4 and 18S V4 amplicon sequencing using the Illumina NovaSeq 6000 platform. Reads were processed with various bioinformatic tools including QIIME2, and eventually, amplicon sequence variants (ASVs) were identified. In almost all analyzed biofilms, approximately 50% of the total ASVs belonged to Cyanobacteriota and Chloroflexota, except for one biofilm, labeled DTO, which was dominated by Pseudomonadata and Cyanobacteriota. Besides bacteria, the data also suggest the presence of various eukaryotic organisms, including small animals such as nematodes, rotifers, and arthropods; fungi and fungus-like organisms such as Ascomycota, Zoopagomycota, Oomycota, and Cryptomycota; as well as photosynthetic eukaryotes from the Viridiplantae group. This dataset serves as a valuable resource for microbial ecology studies in hot spring biofilms and is openly available for reuse, providing a foundation for future research on microbial diversity and functional roles in geothermal ecosystems.},
}

@article {pmid41048492,
year = {2025},
author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J},
title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633379},
pmid = {41048492},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.

METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.

RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.

DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.},
}

@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}

New York City
*Metagenome
*Parks, Recreational
Metagenomics
Humans
*Seawater/microbiology
Microbiota/genetics
*Water Microbiology

@article {pmid41047820,
year = {2025},
author = {Lu, Q and Feng, Y and Wang, H and Zhu, K and Teng, L and Yue, M and Li, Y},
title = {Gut microbiota as a regulator of vaccine efficacy: implications for personalized vaccination.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2563709},
doi = {10.1080/19490976.2025.2563709},
pmid = {41047820},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Vaccine Efficacy ; *Precision Medicine ; Vaccination ; Immunity, Innate ; *Vaccines/immunology ; Animals ; Adaptive Immunity ; },
abstract = {Vaccines are one of the most significant achievements in global health, as they have substantially reduced morbidity and mortality from infectious diseases. However, the vaccine efficacy varies markedly across different populations, particularly among infants, older adults, and people living in low- and middle-income countries. Host-intrinsic factors, such as sex, age, and genetic predisposition, contribute to these heterogeneities. However, accumulating data indicate that the gut microbiota also plays a pivotal role in modulating vaccine efficacy. This review summarizes current knowledge, demonstrating that vaccine efficacy is shaped not only by host biology but also by a dynamic, bidirectional interplay between the gut microbiota and immune system. We discuss how the microbiota influences vaccine outcomes through several mechanisms, including priming the innate immune response, regulating adaptive responses through metabolites, and facilitating antigen cross-reactivity. Furthermore, we examine the potential for microbiota-informed precision vaccinology, which integrates multiomics profiling and artificial intelligence to predict and improve vaccine performance. These advancements establish a framework for personalized vaccine development based on microbial ecology.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Vaccine Efficacy
*Precision Medicine
Vaccination
Immunity, Innate
*Vaccines/immunology
Animals
Adaptive Immunity

@article {pmid41046701,
year = {2025},
author = {Yao, H and Yu, J and Yang, X and Xu, J},
title = {Mechanisms of disruption of the gut-brain axis by environmental endocrine disruptors.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119124},
doi = {10.1016/j.ecoenv.2025.119124},
pmid = {41046701},
issn = {1090-2414},
abstract = {Environmental endocrine disruptors (EEDs) are exogenous chemicals that impair physiological health by disrupting endocrine function. The gut-brain axis represents a complex bidirectional communication network integrating the gut microbiome, immune system, neural signaling, and endocrine pathways to maintain systemic homeostasis. Within this interconnected system, gut microbiota influence mood regulation, immune activity modulates neural processes, and neural signaling governs circadian and sleep cycles. This review explores the multi-system impacts of EEDs across four key physiological domains: (1) gut microbial ecology, (2) immune function, (3) neuroendocrine regulation, and (4) developmental processes. Evidence indicates that EED exposure disrupts intestinal microbial composition, leading to dysbiosis marked by the depletion of beneficial taxa and the expansion of pathogenic species. Concurrently, EEDs impair gut-associated immune cell populations (T cells, B cells, and macrophages), undermining mucosal immunity and increasing susceptibility to inflammatory bowel disease, autoimmune conditions, and gastrointestinal malignancies. At the endocrine level, EEDs interfere with the hypothalamic-pituitary-adrenal and hypothalamic-pituitary-gonadal axes, contributing to hormonal imbalances and impaired reproductive development. Neurochemically, they disrupt the synthesis, release, and degradation of key neurotransmitters, including norepinephrine, dopamine, and serotonin, while exerting direct neurotoxic effects such as cerebrovascular abnormalities and delayed cerebellar myelination. In summary, this review delineates the mechanistic pathways through which EEDs perturb gut-brain axis homeostasis. These insights provide a scientific basis for designing targeted therapeutic interventions and shaping evidence-based public health policies.},
}

@article {pmid41044018,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Soil microbes: below-ground defenders against desertification.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.09.014},
pmid = {41044018},
issn = {1872-8383},
abstract = {Soil microbes act as below-ground defenders against desertification by several mechanisms, such as rhizosheath formation, necromass accumulation, biological soil crusts, exopolysaccharide (EPS) production, hyphal networks, and calcium carbonate precipitation. Here, we discuss how soil microbes drive ecosystem recovery in drylands, offering promising, nature-based strategies for restoring soils in the face of desertification.},
}

@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.

METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.

RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p = 0.016) showing both a potentially sex-dependent responses to dietary intervention.

CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

Animals
Larva/microbiology/growth & development
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Metagenome
*Diptera/microbiology/growth & development
Animal Feed/analysis
RNA, Ribosomal, 16S/genetics
Metagenomics
Diet
Phylogeny
Chickens

@article {pmid41037135,
year = {2025},
author = {Cárdenas, P and Carpio-Arias, V and Chávez, M and Benítez, AD and Baldeón, AD and Suárez-Jaramillo, A and Fornasini, M and Robles, J and Loza, G and Baldeón, ME},
title = {Nutritional Status and Fecal Microbiota in School Children from the Galapagos and the Andean Region.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {103},
pmid = {41037135},
issn = {1432-184X},
support = {I+D+I-XVII-2022-03//This work was supported by the Ecuadorian Consortium for the Development of Advanced Internet (CEDIA) and Universidad Internacional del Ecuador, Universidad San Francisco de Quito, and Escuela Superior Politecnica del Chimborazo./ ; },
mesh = {Humans ; Ecuador/epidemiology ; *Feces/microbiology ; *Nutritional Status ; Child ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Intestinal Diseases, Parasitic/epidemiology/microbiology ; },
abstract = {Schoolchildren from the Galapagos and the Andean region present the worst indices of malnutrition in Ecuador and are exposed to distinctive food and water insecurity. We compared the nutritional status, the fecal microbiota composition of schoolchildren from the Galapagos (n = 51; 8.88 ± 2.15 years) and the Andean region (n = 114; 8.69 ± 1.83 years). Children had a nutritional evaluation and provided fecal samples for microbiota analysis by 16S rRNA gene sequencing. Excess weight was more prevalent in Galapagos (41.18%) than in the Andes (24.5%). Additionally, intestinal parasitosis was more prevalent in children from the Andes (76.4%) than in Galapagos (13.0%). Species richness was lower in fecal samples of children from the Galapagos than those from the Andes (Chao1 index p = 0.001). Beta-diversity metrics also showed significant differences between these samples. Bacteroidota and Proteobacteria were enriched in the microbiota of Galapagos children, whereas Firmicutes A and Cyanobacteria were enriched in the Andean children. At the genus level, the top 3 genera present in schoolchildren from the Galapagos were Bacteroides, Phocaeicola, and Escherichia, while in children from the Andes were Cryptobacteroides, Prevotella, and Clostridium. Cyanobacteria were inversely associated with BMI z-score in the Galapagos region (q = 0.009), while, Firmicutes D had a direct relationship with BMI z-score in children from the Andes (q = 0.05). At the genus level, only Butyrivibrio was inversely associated with BMI z-score in children of the Galapagos (q = 0.04). We conclude that schoolchildren with different degrees of malnutrition from two distinct geographical areas have dissimilar fecal microbiota characteristics.},
}

Humans
Ecuador/epidemiology
*Feces/microbiology
*Nutritional Status
Child
Male
Female
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Intestinal Diseases, Parasitic/epidemiology/microbiology

@article {pmid41037127,
year = {2025},
author = {Arunrat, N and Mhuantong, W and Sereenonchai, S},
title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {102},
pmid = {41037127},
issn = {1432-184X},
support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; },
mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; },
abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.},
}

*Soil Microbiology
Thailand
*Bacteria/classification/genetics/metabolism/isolation & purification
Soil/chemistry
*Microbiota
Nitrogen/metabolism
Nitrification
*Agriculture/methods
Nitrogen Fixation
Nitrogen Cycle

@article {pmid41037066,
year = {2025},
author = {Scott, CM and Holman, DB and Gzyl, KE and Ibe, A and Taheri, AE},
title = {Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {104},
pmid = {41037066},
issn = {1432-184X},
mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Fungi/classification/genetics/isolation & purification ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; *Mycobiome ; Biodiversity ; DNA, Fungal/genetics ; Age Factors ; Female ; },
abstract = {The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.},
}

Animals
*Feces/microbiology
Swine/microbiology
*Fungi/classification/genetics/isolation & purification
*Animal Husbandry/methods
*Gastrointestinal Microbiome
*Mycobiome
Biodiversity
DNA, Fungal/genetics
Age Factors
Female

@article {pmid41036845,
year = {2025},
author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M},
title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023425},
doi = {10.1128/msphere.00234-25},
pmid = {41036845},
issn = {2379-5042},
abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.},
}

@article {pmid41033533,
year = {2025},
author = {Kim, YJ and Jung, DH and Jung, JH and Seo, DH and Kim, JS and Park, CS},
title = {Genomic and functional characterization of carbohydrate-active enzymes from Ruminococcoides bili FMB-CY1 reveals modular strategy for resistant starch degradation in the human gut.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147957},
doi = {10.1016/j.ijbiomac.2025.147957},
pmid = {41033533},
issn = {1879-0003},
abstract = {Ruminococcoides bili FMB-CY1, a human gut bacterium, exhibits strong resistant starch (RS)-degrading ability. To elucidate its RS-degradation strategy, we performed comprehensive genomic annotation and biochemical characterization of 19 encoded carbohydrate-active enzymes (CAZymes). Genome analysis revealed glycoside hydrolases (GH13, GH31, GH77), glycosyltransferase (GT35), carbohydrate-binding modules (CBMs), and domains associated with amylosome-like multienzyme complexes, including dockerin and cohesin motifs. All 19 CAZyme genes were heterologously expressed in Escherichia coli, and their enzymatic properties were systematically characterized. Most α-amylases exhibited extracellular activity against raw RS granules, particularly those harboring CBMs. Hydrolysis profiling revealed distinct substrate preferences, leading to functional reannotation of four enzymes. Domain analyses further suggested that select CAZymes form a surface-associated complex analogous to the amylosome. Together, these enzymes suggest a putative RS-degradation system, in which extracellular α-amylases initiate starch breakdown and are followed by pullulanases, glucosidases, and transferases that complete RS degradation. The released sugars support microbial cross-feeding and potentially contribute to host energy metabolism. The study provides molecular insight into RS utilization by Rc. bili FMB-CY1 and identifies enzymatic features relevant to gut microbial ecology and functional food applications targeting RS metabolism.},
}

@article {pmid41031660,
year = {2025},
author = {Wick, LY},
title = {Rebuttal to Correspondence on "DC Electric Fields Promote Biodegradation of Waterborne Naphthalene in Biofilter Systems".},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12499},
pmid = {41031660},
issn = {1520-5851},
}

@article {pmid41029470,
year = {2025},
author = {Cutajar, S and Braglia, C and Alberoni, D and Mifsud, M and Baffoni, L and Spiteri, J and Di Gioia, D and Mifsud, D},
title = {Gut microbiome of Vespa orientalis: functional insights and potential honey bee pathogen dynamics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {95},
pmid = {41029470},
issn = {2524-4671},
support = {TESS 2022//Tertiary Education Scholarships Scheme by the Ministry for Education, Sport, Youth, Research and Innovation in Malta (TESS 2022)./ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; CN00000022//European Union Next-GenerationEU, PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; },
abstract = {Vespa orientalis, the oriental hornet, is an emerging predator of honey bees whose ecological impact and microbial ecology remain poorly understood. Here, we present the first detailed characterisation of its gut microbiota by integrating 16S rRNA gene sequencing, predicted microbial function, pathogen screening, and a three-year beekeeper survey across urban and rural sites in Malta. Hornets were sampled from four locations and classified by observed foraging behaviour, either predation on honey bees or scavenging on cat food.Survey data confirmed consistent V. orientalis sightings and seasonal colony losses, particularly during peak foraging months. Microbiome analysis revealed a conserved core community dominated by Spiroplasma, Arsenophonus, and Rosenbergiella, with overall diversity stable across sites and diets. However, specific taxa varied with foraging behaviour. For example, Arsenophonus was enriched in bee-predating hornets, while Enterobacter and Serratia were more common in scavenging individuals, suggesting environmental and dietary influences on microbiota composition. Predicted functional profiles remained broadly conserved, reflecting robust nutrient metabolism and potential detoxification capabilities, with some variations related to the diet behaviour.Pathogen screening detected Nosema ceranae and Crithidia bombi in a substantial proportion of hornets, including those not observed feeding on bees. Although our findings do not demonstrate pathogen transmission, they support the hypothesis that V. orientalis may act as a transient carrier, potentially contributing to pathogen persistence via environmental exposure.Together, these results reveal the dietary flexibility and microbial flexibility within the gut microbiome of V. orientalis, and highlight its potential involvement in pollinator pathogen dynamics.},
}

@article {pmid41028416,
year = {2025},
author = {Sidharthan, VK and Patel, R and Thiyaharajan, M and Krishnappa, C and Pattanaik, S and Kumar, A},
title = {Metabarcoding reveals unique rhizospheric microbiomes of Rhizophora in Indian Mangroves.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41028416},
issn = {1874-9356},
support = {IFB/T-1/WME/23-1//Indian Council of Forestry Research and Education/ ; },
abstract = {Rhizophora species are ecologically significant true mangroves with a broad tropical distribution. We examined the rhizospheric microbiomes of dominant Rhizophora species from two contrasting Indian mangrove ecosystems-Coringa and Pichavaram-using high-throughput metabarcoding. Soil properties differed significantly between sites: Pichavaram exhibited higher electrical conductivity (24.53 dS/m), organic carbon (1.70%), sodium (8811.86 ppm), sodium adsorption ratio (220.15), and exchangeable sodium percentage (64.27%), while Coringa soils showed higher pH (8.01). Sequencing generated 1.31, 1.24, and 1.22 million high-quality reads for archaea, bacteria, and fungi, respectively. Taxonomic profiling revealed Nitrososphaeria (62.3-91.9%), Gammaproteobacteria (16.8-25.1%), and Sordariomycetes (18.6-27.8%) as dominant classes. Core taxa across both sites included Candidatus Nitrosopumilus, Woeseia, and Aspergillus. Alpha diversity indices (Chao1, Shannon, Simpson) indicated significantly higher bacterial richness and evenness in R. apiculata at Coringa (P < 0.001), while archaeal and fungal diversity showed no marked differences. Beta diversity analysis (PCoA, PERMANOVA) revealed distinct community compositions between Coringa and Pichavaram, with stronger segregation in archaeal and bacterial assemblages than in fungi. Differential abundance analysis identified nine archaeal, fifty-nine bacterial, and three fungal genera enriched between sites, with methanogens (Methanosarcina, Methanocella) predominant in Coringa and halophiles (Halococcus, Haloferax) in Pichavaram. Redundancy analysis showed sodium adsorption ratio as the key determinant of microbial assemblages, while electrical conductivity significantly shaped archaeal and fungal communities. These findings provide the first baseline dataset of the Coringa rhizospheric microbiome and new insights into the microbial ecology of Indian mangroves, with implications for ecosystem functioning, methane emissions, and conservation strategies.},
}

@article {pmid41026240,
year = {2025},
author = {Abdelali, SK and Aissaoui, L and Cano-Argüelles, AL and Piloto-Sardiñas, E and Abuin-Denis, L and Maitre, A and Foucault-Simonin, A and Mateos-Hernández, L and Kratou, M and Wu-Chuang, A and Obregon, D and Cabezas-Cruz, A},
title = {Seasonal Variations in the Microbiome of Hyalomma excavatum Ticks in Algeria.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {96},
pmid = {41026240},
issn = {1432-184X},
mesh = {Animals ; *Seasons ; Algeria ; *Microbiota ; *Ixodidae/microbiology ; Female ; *Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Rickettsia/isolation & purification/genetics ; Biodiversity ; },
abstract = {Ticks are key vectors of zoonotic diseases, with their microbiomes playing a critical role in tick physiology, survival, and vector competence. This study presents the first investigation of the microbiome in Hyalomma excavatum ticks from Algeria, focusing on seasonal variations in bacterial diversity, community composition, and pathogen interactions. Using next-generation sequencing (NGS), the microbiome of 21 female ticks collected during spring, summer, and autumn was analyzed. Beta diversity analysis revealed significant seasonal shifts in microbial community structure, while alpha diversity metrics showed no significant differences in richness and evenness. Co-occurrence network analysis demonstrated seasonal shifts in microbial interactions, particularly between symbionts and pathogens, highlighting Francisella as a key taxon in tick survival and pathogen dynamics. Rickettsia presence varied by season, influencing microbial network stability. These findings underscore the ecological determinants shaping the microbiome and its potential role in pathogen transmission. Understanding seasonal microbiome shifts provides valuable insights for managing tick-borne diseases and could inform the development of targeted, season-specific vector control strategies.},
}

Animals
*Seasons
Algeria
*Microbiota
*Ixodidae/microbiology
Female
*Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
RNA, Ribosomal, 16S/genetics
Rickettsia/isolation & purification/genetics
Biodiversity

@article {pmid41026216,
year = {2025},
author = {Martin-Pozas, T and Fernandez-Cortes, A and Calaforra, JM and Sanchez-Moral, S and Saiz-Jimenez, C and Jurado, V},
title = {Aerobiology and Environmental Zonation in Gypsum Caves: A Comparative Study of Culturing and NGS Approaches.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {95},
pmid = {41026216},
issn = {1432-184X},
support = {PID2020-114978GB-I00 and PDI2023-146299OB-C22//Ministerio de Ciencia e Innovación/ ; },
mesh = {*Caves/microbiology ; *Calcium Sulfate/analysis ; *Bacteria/genetics/classification/isolation & purification/growth & development ; High-Throughput Nucleotide Sequencing/methods ; *Air Microbiology ; *Microbiota ; Spain ; *Fungi/isolation & purification/genetics/classification ; Geologic Sediments/microbiology ; Phylogeny ; Biodiversity ; },
abstract = {Classical aerobiological studies commonly use high-volume air samplers to quantify and identify cultivable airborne bacteria and fungi. However, this approach introduces a significant bias, as it overlooks the non-cultivable fraction, which likely constitutes a major component of the airborne microbiome. The advent of next-generation sequencing (NGS) has addressed this limitation, enabling a more comprehensive characterization of the cave aerobiome. This study analyzes both cultivable and non-cultivable airborne bacteria from Covadura and C3 caves, located in the Gypsum Karst of Sorbas (SE Spain). A total of 24 bacterial genera were identified using culture-based methods, whereas NGS revealed 749 genera. Culture-based methods using the surface air system (SAS) predominantly recovered Gram-positive spore-forming bacteria from the phyla Bacillota and Actinomycetota, which were largely absent or present in low relative abundances in the NGS datasets. In contrast, NGS revealed a broader diversity, including numerous Gram-negative and rare airborne bacteria not detected by culture. The NGS results from airborne samples showed greater similarity to the microbial communities found in cave biofilms and sediments, suggesting that a portion of airborne bacteria originates from within the cave and is influenced by microclimatic conditions such as ventilation and air stagnation. Although the short-read sequencing approach used in this study has limitations, such as reduced taxonomic resolution compared to the culture-based approach, it remains the most effective tool for capturing the diversity and ecological patterns of airborne microorganisms. The integration of gas tracers and other environmental data allowed the identification of zones within the cave with different ventilation patterns and degrees of isolation, which corresponded to different spatial distributions of airborne bacteria. Our findings underscore that reliable aerobiological studies in caves require the combination of non-culture dependent-based sequencing approaches and environmental monitoring to fully understand the origin, diversity, and ecological dynamics of airborne microbial communities.},
}

*Caves/microbiology
*Calcium Sulfate/analysis
*Bacteria/genetics/classification/isolation & purification/growth & development
High-Throughput Nucleotide Sequencing/methods
*Air Microbiology
*Microbiota
Spain
*Fungi/isolation & purification/genetics/classification
Geologic Sediments/microbiology
Phylogeny
Biodiversity

@article {pmid41026209,
year = {2025},
author = {Gutiérrez-Pavón, AJ and Pereyra, MM and Chacón, FI and Monroy-Morales, E and Rebollar, EA and Dib, JR and Serrano, M and Romero-Contreras, YJ},
title = {Bacteria from the Amphibian Skin Inhibit the Growth of Phytopathogenic Fungi and Control Postharvest Rots.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {101},
pmid = {41026209},
issn = {1432-184X},
support = {PICT-2021-GRF-TII-0020//Agencia Nacional de Promoción Científica y Tecnológica/ ; N203023//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica/ ; },
mesh = {Animals ; *Plant Diseases/microbiology/prevention & control ; Botrytis/growth & development ; *Skin/microbiology ; Penicillium/growth & development ; *Antibiosis ; *Bacteria/isolation & purification/metabolism ; Fruit/microbiology ; *Biological Control Agents ; Solanum lycopersicum/microbiology ; Alternaria/growth & development ; *Anura/microbiology ; Citrus/microbiology ; *Fungi/growth & development ; Volatile Organic Compounds/pharmacology ; Aspergillus niger/growth & development ; Pest Control, Biological ; },
abstract = {Postharvest diseases caused by phytopathogenic fungi represent one of the main challenges in the agricultural industry, leading to significant losses in fruit production. Although chemical treatments have been widely used for the control of these pathogens, the emergence of resistant strains and concerns regarding food safety and environmental impact have driven the search for novel effective and eco-friendly alternatives, such as the use of biological control agents (BCAs). Previously, we demonstrated that bacteria isolated from frog skin inhibit the growth of the phytopathogenic fungus Botrytis cinerea. Based on these findings, in this study we aimed to investigate the biocontrol potential of three bacterial isolates obtained from the skin of the frog Craugastor fitzingeri. Dual culture assays showed that these bacteria strongly inhibited the mycelial growth of several postharvest fungal phytopathogens, including Penicillium digitatum, P. italicum, Alternaria alternata, Aspergillus niger, and Alternaria solani. This antagonistic activity was further confirmed through assays using bacterial filtrates (BFs) and volatile organic compounds (VOCs), effectively delaying or suppressing fungal development under in vitro conditions. Additionally, in vivo experiments on citrus fruits, tomato, and blueberry demonstrated that treatments with bacterial cell suspensions or BFs significantly reduced disease incidence caused by P. digitatum, A. alternata, and B. cinerea. However, no inhibitory effects were observed against Geotrichum citri-aurantii, Fusarium sp., Fusarium oxysporum, and Phytophthora capsici, suggesting a degree of specificity. Our findings highlight the potential of frog skin-associated bacteria as a novel source of BCAs for the sustainable management of postharvest diseases in fruits.},
}

Animals
*Plant Diseases/microbiology/prevention & control
Botrytis/growth & development
*Skin/microbiology
Penicillium/growth & development
*Antibiosis
*Bacteria/isolation & purification/metabolism
Fruit/microbiology
*Biological Control Agents
Solanum lycopersicum/microbiology
Alternaria/growth & development
*Anura/microbiology
Citrus/microbiology
*Fungi/growth & development
Volatile Organic Compounds/pharmacology
Aspergillus niger/growth & development
Pest Control, Biological

@article {pmid41026187,
year = {2025},
author = {Cheng, P and Liu, F and Li, L and Wu, S and Xiao, W and Zong, Q and Liu, T and Peng, Y},
title = {Impact of Tebuconazole On the Development and Symbiotic Microbial Communities of Pardosa Pseudoannulata.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {97},
pmid = {41026187},
issn = {1432-184X},
mesh = {*Triazoles/toxicity ; *Symbiosis/drug effects ; Animals ; *Microbiota/drug effects ; Bacteria/drug effects/classification/genetics/isolation & purification ; *Fungi/drug effects/classification/genetics ; *Fungicides, Industrial/toxicity ; *Spiders/microbiology/drug effects/growth & development/physiology ; RNA, Ribosomal, 16S/genetics ; Animals, Poisonous ; },
abstract = {Tebuconazole is a widely used triazole fungicide to control fungal diseases. While there have been reported side effects on non-target arthropods, its ecological risks to natural enemies remain poorly understood. In this study, we evaluated the developmental toxicity and symbiotic microorganism responses of the wolf spider Pardosa pseudoannulata, an important predator in rice ecosystems, following exposure to tebuconazole. The results indicated that tebuconazole did not significantly increase the mortality rate of spiderlings; however, it did lead to a significant decrease in spiderling body weight, as well as the length and width of the carapace. High-throughput sequencing of the 16S rRNA gene V3-V4 regions and the ITS region revealed that tebuconazole significantly reduced bacterial diversity indices in the short term, with a gradual recovery over time. In contrast, the impact on the fungal community was continuous and irreversible, with a significant decrease in the Shannon index observed after 15 days. At the genus level, the relative abundances of Cupriavidus and Staphylococcus in the bacterial community decreased significantly after tebuconazole exposure, while Stenotrophomonas increased. In the fungal community, Fungi_gen_Incertae_sedis decreased significantly, and Simplicillium increased. Our findings highlight the ecological risks of fungicide exposure to beneficial predators and underscore the importance of considering symbiotic microbiota in pesticide risk assessments.},
}

*Triazoles/toxicity
*Symbiosis/drug effects
Animals
*Microbiota/drug effects
Bacteria/drug effects/classification/genetics/isolation & purification
*Fungi/drug effects/classification/genetics
*Fungicides, Industrial/toxicity
*Spiders/microbiology/drug effects/growth & development/physiology
RNA, Ribosomal, 16S/genetics
Animals, Poisonous