@article {pmid41259520,
year = {2025},
author = {Usman, H and Molaei, M and House, SD and Haase, MF and Dennis, CL and Niepa, THR},
title = {Magnetically responsive nanocultures for direct microbial assessment in soil environments.},
journal = {Science advances},
volume = {11},
number = {47},
pages = {eady2654},
doi = {10.1126/sciadv.ady2654},
pmid = {41259520},
issn = {2375-2548},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Bioreactors ; Magnetic Iron Oxide Nanoparticles/chemistry ; },
abstract = {Cultivating microorganisms in native-like conditions is vital for bioprospecting and accessing now unculturable species. However, there remains a gap in scalable tools that can both mimic native microenvironments and enable targeted recovery of microbes from complex settings. Such approaches are essential to advance our understanding of microbial ecology, predict community functions, and discover previously unidentified biotherapeutics. We present magnetic nanocultures-a high-throughput microsystem for isolating and growing environmental microbes under near-native conditions. These nanoliter-scale bioreactors are encapsulated in semipermeable membranes that form magnetic polymeric microcapsules using iron oxide nanoparticles within polydimethylsiloxane-based shells. This design offers mechanical stability and magnetic actuation, enabling efficient retrieval from soil-like environments. The nanocultures are optimized for optical and biological properties to support microbial encapsulation, growth, and sorting. Our study demonstrates the feasibility of using magnetically responsive microenvironments to cultivate elusive microbes, offering a promising platform for bioprospecting previously uncultured or unknown microbial species.},
}

*Soil Microbiology
*Soil/chemistry
Bioreactors
Magnetic Iron Oxide Nanoparticles/chemistry

@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/msphere.00683-25},
pmid = {41258716},
issn = {2379-5042},
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}

@article {pmid41258518,
year = {2025},
author = {Cong, D and Liu, J and Yu, S and Wu, P and Qin, M},
title = {Assessment of Anthropogenic Impacts on Water Quality and Microbial Communities in the Heilongjiang Maolan Gou National Nature Reserve.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02645-7},
pmid = {41258518},
issn = {1432-184X},
abstract = {Freshwater ecosystems within protected areas play a vital role in maintaining biodiversity and ecological stability, yet they are increasingly threatened by anthropogenic disturbances such as agriculture and tourism. Understanding the impacts of human activities on water quality and microbial community dynamics is essential for the effective conservation and management. This study investigates the spatial variability of water quality and microbial communities across the core, buffer, and experimental zones of the Heilongjiang Maolan Gou National Nature Reserve. Twelve water samples were collected and analyzed for key physicochemical parameters (turbidity, electrical conductivity (EC), chemical oxygen demand (COD), biochemical oxygen demand (BOD), NH4[+], PO4[3-] and heavy metals). The core zone exhibited excellent water quality with low turbidity (0.4-0.5 NTU), EC (45-130 µS/cm), COD (8-10 mg/L), BOD (1.5-2.2 mg/L). In contrast, the experimental zone showed significant contamination due to agriculture and tourism, with high COD (up to 35 mg/L), BOD (up to 6.5 mg/L), NH4[+] (0.18-0.35 mg/L), and PO4[3-] (0.008-0.035 mg/L). Heavy metal concentrations, particularly Cd (up to 0.24 µg/L), were elevated in the experimental zone, correlating with higher Pollution and Water Quality Indices (HPI up to 96.4, WQI up to 61.28). According to standard classifications, HPI values > 100 indicated heavy pollution and WQI scores between 50 and 100 denoted moderate to poor water quality, highlighting degraded conditions in the experimental zone. Microbial analysis revealed distinct community structures across zones, with enhanced pollutant-degrading taxa such as Pseudomonas (noted for aromatic hydrocarbon degradation) and members of Bacteroidota (associated with organic matter breakdown) in the experimental zone. These findings highlight the need for sustainable management to mitigate human impacts and preserve ecological health within the reserve.},
}

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41258437,
year = {2025},
author = {Romaní, AM and Núria, P and Marta, P and Giulia, G},
title = {Drought Drives Extracellular Polymeric Substances Accumulation and Functional Shifts in Streambed Biofilm Communities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02649-3},
pmid = {41258437},
issn = {1432-184X},
abstract = {This study investigates the adaptive response of streambed microbial biofilms to water scarcity, focusing on the role of extracellular polymeric substances (EPS) production across a gradient of hydrological conditions. Sediment samples from 37 streams in the north-eastern Iberian Peninsula, encompassing both permanent and intermittent flow regimes, were analysed for EPS-polysaccharide content, microbial biomass, chlorophyll-a, and biofilm function (carbon substrate utilization profiles). Drought conditions were characterized based on the number of dry days over the eight months preceding sampling. Results revealed that EPS production increased significantly in intermittent streams, particularly under long-term drought, reaffirming that EPS synthesis is a key microbial strategy to mitigate desiccation stress. Notably, when normalized to prokaryotic density, EPS content exhibited a significant positive correlation with drought duration, emphasizing the dominant role of heterotrophic bacteria over algae in EPS secretion. However, EPS content alone was not a universal indicator of water scarcity, which showed a large variability in permanently flowing streams. Functional profiling showed clear shifts in carbon substrate utilization associated with stream hydrology. Intermittent streams exhibited a broader metabolic range, and particularly a capacity to use phenolic compounds, suggesting an adaptation to terrestrial organic matter inputs. Contrary to expectations, functional diversity increased in drier conditions, challenging assumptions derived from controlled experiments and underscoring the resilience of Mediterranean microbial biofilm communities to drought. These findings provide empirical support for EPS-mediated drought adaptation in natural biofilms and highlight functional diversity as a potential mechanism maintaining ecosystem processes under increasing aridity due to climate change.},
}

@article {pmid41258129,
year = {2025},
author = {Cabrerizo, MJ and González-Olalla, JM and Medina-Sánchez, JM and Vila-Duplá, M and Carrillo, P},
title = {Warming Fluctuations Strengthen the Photo-Phagotrophic Coupling in Mixoplanktonic Protists.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02658-2},
pmid = {41258129},
issn = {1432-184X},
support = {PID2022-136280NA-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund/ ; RYC2023-042504-I//MICIU/AEI/10.13039/501100011033 and the European Social Fund plus (ESF+)/ ; DGP-POST-2024-00283//Junta de Andalucía/ ; TED2021-131262B-I00//MCIN/AEI/10.13039/501100011033 and by the European Union NextGeneration EU/PRTR/ ; FPU19/05924//Ministerio de Ciencia e Innovación/ ; PID2020-118872RB-I00//MICIN/AEI/10.13039/501100011033 and the European Regional Development Fund (ERDF)/ ; },
abstract = {Mixoplankton, a major trophic group in aquatic ecosystems, are being affected by global warming. However, most studies on temperature effects use constant mean conditions, overlooking how short-term thermal fluctuations could deviate from climate projections and impact this group. We experimentally quantified how increasing amplitudes of warming fluctuation (± 1, 3, and 5 °C) alter carbon-specific electron transport (ETR[c]), net photosynthesis (P[c]), respiration (R[c]), phagotrophy (Ph[c]), carbon use efficiency (CUE), and growth (µ) in four protist species (three mixoplanktonic and one strict phototroph). We observed a consistent positive link between photosynthetic efficiency (P[c]:ETR[c] ratio) and Ph[c], and a shift towards a strengthening of the Ph[c] (P[c]:ETR[c] / Ph[c] ratio) with greater thermal fluctuation. A potential explanation is a selective behavior aimed to increase phagotrophy to obtain inorganic nutrients through ingested prey internal re-cycling rather than relying on the environment, to support an enhanced photosynthetic efficiency and growth. An enhanced, coupled photo-phagotrophy activity could boost mixoplankton competitiveness compared to phytoplankton. Our findings underscore the need to incorporate trophic flexibility and its interaction with environmental variability into trait-based models to better predict community dynamics, biogeochemical cycling, and food web structure in aquatic ecosystems.},
}

@article {pmid41254852,
year = {2025},
author = {Alster, CJ and Schipper, LA and Bååth, E},
title = {Thermal Adaptation of Bacterial and Fungal Growth in a Geothermally Influenced Soil Transect.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70605},
doi = {10.1111/gcb.70605},
pmid = {41254852},
issn = {1365-2486},
support = {MFP-UOW1904//Marsden Fund/ ; },
mesh = {*Soil Microbiology ; New Zealand ; *Fungi/growth & development ; *Bacteria/growth & development ; Temperature ; *Soil/chemistry ; },
abstract = {Numerous studies have investigated microbial adaptation to increasing soil temperature, but limitations in experimental design hinder comprehensive understanding. These include short-term laboratory studies with constant environmental conditions and field studies with few distinct temperature treatments. Here, we utilized a long-term natural soil geothermal gradient in Aotearoa, New Zealand, ranging in mean annual soil temperature (MAT) from 17°C to 42°C to explore thermal adaptation of microbial growth rates. We collected soil from 28 locations along the gradient and measured bacterial growth rate (via leucine incorporation) at eight temperatures (4°C-45°C) and fungal growth rate (via Ac-in-ergosterol) at two temperatures (16°C and 39°C). We then fit Macromolecular Rate Theory and the Ratkowsky equation to estimate the temperature minimum (T min $$ {T}_
{min}
$$), optimum (T opt $$ {T}_
{opt}
$$), and inflection point (T inf $$ {T}_
{inf}
$$) for bacterial growth, and a temperature sensitivity index to compare relative fungal and bacterial growth rates. We found predictable changes in thermal adaptation of bacterial growth along the geothermal gradient with temperature response curves shifting 0.22°C-0.27°C per 1°C increase in MAT regardless of the temperature metric (i.e., T min $$ {T}_
{min}
$$ , T opt $$ {T}_
{opt}
$$ , and T inf $$ {T}_
{inf}
$$) used. Thermal adaptation of bacterial and fungal growth increased roughly in parallel. We also compared the bacterial growth results to published temperature response data of microbial respiration (with added glucose) from this geothermal gradient. Rates of thermal adaptation for bacterial growth and microbial respiration were similar, suggesting synchronicity across microbial processes. The less than 1°C change in all measured temperatures metrics per degree increase in MAT resulted in microbial growth and activity closer to in situ temperatures at high soil temperatures and lower than in situ temperatures under non-elevated soil temperatures. Overall, our results highlight the use of geothermal gradients and appropriate temperature models in studying thermal adaptation of soil microbial processes; the predictability of results also underscores potential for incorporating microbial thermal adaptation into soil carbon modeling efforts.},
}

*Soil Microbiology
New Zealand
*Fungi/growth & development
*Bacteria/growth & development
Temperature
*Soil/chemistry

@article {pmid41254344,
year = {2025},
author = {Distante, A and Garino, D and Cerrato, C and Perez-Ardavin, J and Flores, FQ and Lopetuso, L and Mir, MC},
title = {The role of the human microbiome in prostate cancer: a systematic review from diagnosis to treatment.},
journal = {Prostate cancer and prostatic diseases},
volume = {},
number = {},
pages = {},
pmid = {41254344},
issn = {1476-5608},
abstract = {BACKGROUND: Prostate cancer (PC) heterogeneity and treatment resistance remain major clinical challenges, with emerging evidence implicating the microbiome as a key modulator of disease pathogenesis. While microbial dysbiosis has been linked to PC diagnosis, progression, and therapeutic outcomes, the mechanisms underlying these associations are poorly understood. This review synthesizes current evidence on the diagnostic, prognostic, and therapeutic potential of the microbiome in PC.

METHODS: A systematic search of PubMed, Embase, and Cochrane Central Register of Controlled Trials (through April 2024) was conducted following PRISMA guidelines (PROSPERO: CRD42024534899). Controlled and observational studies investigating microbial roles in PC diagnosis (e.g., ISUP grading group), prognosis, or treatment response were included. Data extraction and quality assessment used the QUIPS tool. From 810 screened records, 42 studies met inclusion criteria.

RESULTS: Distinct microbial profiles differentiated PC from controls, with Mycoplasma genitalium and Staphylococcus spp. enriched in prostate tumors (3.1- and 2.7-fold, respectively) and correlated with inflammation (IL-6: r = 0.38, p = 0.002). Urinary microbiota showed diagnostic potential (sensitivity: 58-82%), though sampling methods influenced variability. Prognostically, Betaproteobacteria gut enrichment predicted earlier castration-resistant progression (5.2 months; HR 1.8, 95% CI 1.3-2.5), while ADT-induced dysbiosis (e.g., Klebsiella overgrowth) accelerated resistance (2.1-fold risk). Therapies altered microbial ecology: radiotherapy depleted Bacteroides (linked to proctitis; OR 3.1), and immunotherapy responders harbored higher Akkermansia muciniphila. Microbial androgen synthesis and endotoxin production emerged as resistance mechanisms.

CONCLUSIONS: The microbiome influences PC detection, aggressiveness, and treatment efficacy through direct (tissue-resident) and indirect (gut-derived) mechanisms. Standardized profiling and microbiome-modulating strategies (e.g., probiotics during ADT) may personalize management. Prospective trials are needed to validate causality and translate microbial biomarkers into clinical practice.},
}

@article {pmid41252854,
year = {2025},
author = {Chen, X and Huang, Y and Zhu, X and Gan, C and An, W and Liu, Y and Zhou, S and Xu, M},
title = {Global biogeographic patterns and assembly processes of landfill leachate microbiomes.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124922},
doi = {10.1016/j.watres.2025.124922},
pmid = {41252854},
issn = {1879-2448},
abstract = {Approximately 95 % of municipal solid waste is disposed of in landfill globally, generating leachate that is known as a complex mixture of biodegradable and persistent toxic compounds. Microbes are main forces for tackling the toxic leachate but the patterns of microbial assembly in such treatments are largely unknown, limiting the proper optimization of leachate treatment efficiency. This study, for the first time, presents a global-scale analysis involving 151 landfill leachate treatment samples for uncovering mechanisms of microbial assembly from an ecological perspective. The information of microbiome from 97 treatments in Asia, 41 treatments in Europe, and 13 treatments in North America were collected. The results revealed pronounced biogeographic divergence, with Asian samples (particularly those from India) exhibiting lower microbial diversity and richness compared to Europe and North America counterparts. Geographical-climatic and socio-economic factors significantly influenced microbial composition, with elevation and per capita GDP being primary drivers. Further, the community assembly was predominantly governed by deterministic processes. Co-occurrence network analyses demonstrated distinct microbial interaction patterns across continents, with Asian networks being more vulnerable to collapse under external disturbances. This study provides critical insights into the global microbial ecology of landfill leachate treatment, offering a foundation for developing targeted bioremediation strategies.},
}

@article {pmid41251823,
year = {2025},
author = {Della Mónica, IF and Godeas, AM and Scervino, JM},
title = {Hyphosphere interactions: P-solubilizing fungi modulate AMF phosphatase activity and mycorrhizal symbiosis via exudate-mediated communication.},
journal = {Mycorrhiza},
volume = {35},
number = {6},
pages = {66},
pmid = {41251823},
issn = {1432-1890},
support = {UBACyT 20020220400300BA//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; PIBAA 28720210100694CO//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; PICT 01283-2021//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación/ ; PINI 04/B253//Fundación de la Universidad Nacional del Comahue para el Desarrollo Regional/ ; },
mesh = {*Mycorrhizae/physiology/enzymology ; *Symbiosis ; Plant Roots/microbiology ; *Phosphorus/metabolism ; Acid Phosphatase/metabolism ; *Phosphoric Monoester Hydrolases/metabolism ; Daucus carota/microbiology ; *Glomeromycota/physiology/enzymology ; *Phosphates/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with plant roots, enhancing water and nutrient absorption. Phosphate-solubilizing fungi (PSF) can solubilize and mineralize phosphorus, an essential nutrient with low bioavailability, and eventually interact with AMF. However, the understanding of how they interact in the hyphosphere, where root influence is absent, remains limited. Furthermore, the effect of PSF on the phosphatase activity of AMF, related to the P efficiency in acquisition and utilization, within the hyphosphere and mycorrhizosphere zones, remains unclear. Therefore, this study aimed to assess the effect of three different PSF (Talaromyces flavus, T. helicus, and T. diversus) exudates on extracellular acid phosphatases and alkaline phosphatases associated with intra- and extraradical AMF structures in the hyphosphere and mycorrhizosphere, in vitro. To achieve this aim, the AMF Rhizophagus intraradices was cultured with Ri T-DNA transformed carrot roots in a system using Petri dishes that mimicked the hyphosphere (with 2 sections: (a) with roots and AMF, and (b) with only AMF) and the mycorrhizosphere (with roots and AMF in the same place). Different concentrations of PSF exudates were placed in either the hyphosphere or the mycorrhizosphere, and at the end of the experiment (8 weeks), the phosphatase activity of the AMF was measured. This research highlights that the enzymatic activity of AMF is modulated by PSF exudates, depending on whether these exudates are present in the hyphosphere or the mycorrhizosphere. Exudates in the hyphosphere, where PSF are directly associated with AMF hyphae, have a more pronounced effect on AMF extraradical alkaline phosphatases than acid phosphatases, and promote symbiosis efficiency. In contrast, PSF exudates in the mycorrhizosphere had a neutral or negative effect on symbiosis efficiency, improving the extraradical alkaline phosphatases of AMF and the acid phosphatases of the roots. Also, the effect depends on the fungal identity. AMF act as mediators in this context, improving communication between the roots and the hyphosphere microbiome. When exploring the soil, the hyphae encounter compounds produced by microorganisms, thus establishing a complex network of interactions. These interactions enhance the symbiotic efficiency of AMF, modulating the host plant without direct contact. These results show that microbial interactions not only influence the efficiency of phosphorus transfer to plants but also have broader implications for soil health and fertility management.},
}

*Mycorrhizae/physiology/enzymology
*Symbiosis
Plant Roots/microbiology
*Phosphorus/metabolism
Acid Phosphatase/metabolism
*Phosphoric Monoester Hydrolases/metabolism
Daucus carota/microbiology
*Glomeromycota/physiology/enzymology
*Phosphates/metabolism

@article {pmid41251489,
year = {2025},
author = {Ye, H and Šlipogor, V and Hanson, BT and Séneca, J and Hausmann, B and Herbold, CW and Pjevac, P and Bugnyar, T and Loy, A},
title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (Callithrix jacchus) colony.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0044325},
doi = {10.1128/spectrum.00443-25},
pmid = {41251489},
issn = {2165-0497},
abstract = {Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets (Callithrix jacchus), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets.IMPORTANCEThis study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.},
}

@article {pmid41251323,
year = {2025},
author = {Ferreira, J and Lievens, B and Rediers, H},
title = {Development of a spore-based confrontation assay to screen for biocontrol organisms with antagonistic activity against oomycete and fungal pathogens.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf286},
pmid = {41251323},
issn = {1365-2672},
abstract = {AIMS: Screenings for biocontrol organisms against fungal and oomycete pathogens are typically performed on mycelium. While this allows for high-throughput screenings, it omits a major actor in pathogenicity, i.e. the spores. This study aims to improve the screening strategy using a spore-based confrontation assay (SBCA), as well as comparing its performance to the traditional mycelium-based confrontation assay (MBCA) and microscopy analyses of spore germination.

METHODS AND RESULTS: The SBCA was used to screen for 38 candidate biocontrol bacteria against two relevant broad-spectrum phytopathogens, Botrytis cinerea and Phytophthora cactorum. The performance of the SBCA was benchmarked to the traditional mycelium-based confrontation assay and microscopy observations for spore germination inhibition. The SBCA demonstrated a higher hit rate and reproducibility than its counterparts. The bacteria tested exhibited diverse traits in vitro such as production of lytic enzymes, biosurfactant, bioactive volatile organic compounds, and cell-free extracts. These characteristics suggest potential biocontrol modes of action, such as antibiosis (via diffusible metabolites and enzymes) or competition for nutrients and space. For two Pseudomonas strains, the biocontrol activity against P. cactorum was confirmed in planta in a detached leaf assay.

CONCLUSIONS: This study showcases a versatile and robust spore-based screening that outperforms conventional screening methods. Through the use of the SBCA, two promising biocontrol strains with antagonistic activity against P. cactorum in strawberry were identified.},
}

@article {pmid41250675,
year = {2025},
author = {Gao, Y and Bai, J and Zhou, F and He, Y and Wang, Y and Huang, X},
title = {ICCTax: a hierarchical taxonomic classifier for metagenomic sequences on a large language model.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf257},
pmid = {41250675},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenomic data increasingly reflect the coexistence of species from Archaea, Bacteria, Eukaryotes, and Viruses in complex environments. Taxonomic classification across the four superkingdoms is essential for understanding microbial communities, exploring genomic evolutionary relationships, and identifying novel species. This task is inherently imbalanced, uneven, and hierarchical. Genomic sequences provide crucial information for taxonomy classification, but many existing methods relying on sequence similarity to reference genomes often leave sequences misclassified due to incomplete or absent reference databases. Large language models offer a novel approach to extract intrinsic characteristics from sequences.

RESULTS: We present ICCTax, a classifier integrating the large language model HyenaDNA with complementary-view-based hierarchical metric learning and hierarchical-level compactness loss to identify taxonomic genomic sequences. ICCTax accurately classifies sequences to 155 genera and 43 phyla across the four superkingdoms, including unseen taxa. Across three datasets built with different strategies, ICCTax outperforms baseline methods, particularly on Out-of-Distribution data. On Simulated Marine Metagenomic Communities datasets from three oceanic sites, DairyDB-16S rRNA, Tara Oceans, and wastewater metagenomic datasets, it demonstrates strong performance, showcasing real-world applicability. ICCTax can further support identification of novel species and functional genes across diverse environments, enhancing understanding of microbial ecology.

Code is available at https://github.com/Ying-Lab/ICCTax.},
}

@article {pmid41249638,
year = {2025},
author = {Tinning, Z and Kaestli, M and Nowland, SJ and Siboni, N and Seymour, JR and Gibb, KS and Padovan, AC},
title = {Dynamics of Bacterial and Vibrio Communities in Blacklip Rock Oysters in the Seasonal Tropics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {125},
pmid = {41249638},
issn = {1432-184X},
support = {2020-043//Fisheries Research and Development Corporation/ ; Discovery Project DP240100370//Australian Research Council/ ; },
mesh = {Animals ; *Vibrio/isolation & purification/genetics/classification ; *Ostreidae/microbiology ; Seasons ; Aquaculture ; Seawater/microbiology ; *Microbiota ; Australia ; Tropical Climate ; Shellfish/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Humans ; },
abstract = {Cultivation of the tropical Blacklip Rock Oyster (BRO) (Saccostrea spathulata) is an emerging Indigenous-led aquaculture industry in the seasonal tropics of northern Australia. However, little is currently known about the potential for pathogen outbreaks in this species. We conducted a year-long study to establish a microbial baseline to identify potential oyster and human health risks to inform future food safety decision making in this nascent industry. In healthy oysters, we identified both the core microbiome of this oyster species and the presence of potential oyster and human pathogens. The core bacteriome comprised nine bacterial families, while the core vibriome comprised the animal pathogens Vibrio harveyi and V. owensii. The potential human pathogen V. parahaemolyticus was detected in some oysters during the wet season, during periods of increased rainfall, turbidity and total nitrogen. The bacteriome and vibriome of oysters were significantly different to the adjacent seawater and therefore we concluded that seawater is not an appropriate surrogate for pathogen risk surveillance in this developing industry. These results provide new knowledge on the microbiology of a previously understudied oyster species and will inform monitoring methods, harvesting and shellfish quality compliance in this emerging Indigenous-led industry.},
}

Animals
*Vibrio/isolation & purification/genetics/classification
*Ostreidae/microbiology
Seasons
Aquaculture
Seawater/microbiology
*Microbiota
Australia
Tropical Climate
Shellfish/microbiology
*Bacteria/classification/genetics/isolation & purification
Humans

@article {pmid41249586,
year = {2025},
author = {Zhou, S and Bi, J and Zhou, S and Luo, L and Yan, X and Zou, J and Ji, Y and Zhao, S and Qiu, J and Liu, Z and Jiang, J and Wang, B and Liu, X},
title = {Community Assembly Mechanisms Underlying Divergent Responses of Indica and Japonica Rice Rhizosphere Microbiota to Drought Stress.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {126},
pmid = {41249586},
issn = {1432-184X},
support = {2022YFD2300302//National Key Research and Development Program of China/ ; 42277304//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; XUEKEN2022003//Fundamental Research Funds for the Central Universities/ ; BX20240168//National Postdoctoral Program for Innovative Talents/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Oryza/microbiology/growth & development/physiology/genetics/classification ; *Rhizosphere ; *Droughts ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Stress, Physiological ; Agricultural Irrigation ; },
abstract = {Drought stress markedly reduces rice yield, with notable genotypic variation in drought tolerance. While the rhizosphere microbiome is regarded as the second genome of plants, how the indica and japonica rice rhizosphere microbial communities respond to deficit irrigation and their relationship with yield remain to be elucidated. Here, we conducted field experiments using 12 indica and 12 japonica rice varieties under full and deficit irrigation regimes. Yield-related traits, including filled grain number, seed setting rate, two-plant yield, and thousand grain weight, were measured, and the rhizosphere microbial communities were characterized by 16S rRNA gene sequencing. In line with previous studies, japonica varieties showed superior drought resistance in terms of yield performance. Both rice genotype and irrigation regime significantly influenced the composition and functional potential of the rhizosphere microbiome. Compared to indica rice, the japonica rice rhizosphere was enriched with more beneficial microorganisms. Enrichment of nitrogen‑metabolism‑related groups, such as Microvirga and Nitrososphaeraceae, may contribute to rhizosphere nitrogen cycling and support nitrogen availability for the rice. Similarly, higher abundance of Streptomyces in japonica varieties under drought conditions may be associated with improved drought tolerance. These microbial genera were closely associated with rice yield. Moreover, the japonica rhizosphere microbiome was less disturbed by water limitation, showing higher stability. Overall, the rhizosphere microbiome of japonica rice exhibited functional optimization under drought stress by promoting the enrichment of beneficial and nitrogen-cycling microbes, thereby enhancing drought resistance and yield stability. This study demonstrated a significant correlation between rhizosphere microbial communities and rice yield, providing fundamental insights that may contribute to future strategies for optimizing crop productivity through microbiome management in sustainable agriculture.},
}

*Oryza/microbiology/growth & development/physiology/genetics/classification
*Rhizosphere
*Droughts
*Microbiota
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
RNA, Ribosomal, 16S/genetics
Stress, Physiological
Agricultural Irrigation

@article {pmid41248576,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Evaluation of reclaimed treated wastewater on soil quality, microbial community and function in urban greening irrigation.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127958},
doi = {10.1016/j.jenvman.2025.127958},
pmid = {41248576},
issn = {1095-8630},
abstract = {Reclaimed treated wastewater (TWW) offers a sustainable irrigation alternative for urban greening amid freshwater scarcity. However, its impact on soil quality and microbial ecology in urban landscapes remains underexplored. This study assessed the effects of three TWW types and one TWW-purified water mixture on soil properties, heavy metal accumulation, enzyme activity and microbial community dynamics in Common Nandina (Nandina domestica Thunb.) systems over three- and five-month in Nanjing, China, using a metagenomic approach. The results showed that TWW irrigation significantly increased soil nitrogen, phosphorus content and pH (P < 0.05), with stronger effects observed at three-month (P < 0.05). Soil heavy metal content varied, with Cr and As exhibiting potential accumulation. Enzyme activity (N-acetyl-glucosaminidase and phosphatase) was positively influenced by TWW irrigation at three-month. Metagenomic analysis revealed significant shifts in microbial community composition, particularly fungi, with Mucoromycota increasing and Ascomycota decreasing under TWW. The Normalized Stochasticity Ratio indicated increased stochasticity in microbial assembly under TWW irrigation (P < 0.05). Functionally, TWW increased abundance of functional genes related to amino acid metabolism and peroxisomes (P < 0.05), but decreased degradation genes for aromatic compounds. TWW also increased the abundance of antibiotic resistance genes (ARGs), particularly those related to triclosan and glycopeptide, and plant pathogenic genera like Aspergillus and Fusarium. The findings suggest that while TWW irrigation improves certain soil properties and microbial functions in the short term, it may pose ecological risks from heavy metal and microbial contamination, offering key insights for sustainable urban irrigation strategies.},
}

@article {pmid41247962,
year = {2025},
author = {Wei, D and Hu, S and Tang, T and Yang, Y and Meng, F and Peng, Y},
title = {Confinement Reduces Surface Accumulation of Swimming Bacteria.},
journal = {Physical review letters},
volume = {135},
number = {18},
pages = {188401},
doi = {10.1103/dvc8-tlh1},
pmid = {41247962},
issn = {1079-7114},
mesh = {*Models, Biological ; Hydrodynamics ; *Bacterial Physiological Phenomena ; Movement ; *Escherichia coli/physiology ; },
abstract = {Many swimming bacteria naturally inhabit confined environments, yet how confinement influences their swimming behaviors remains unclear. Here, we combine experiments, continuum modeling, and particle-based simulations to investigate near-surface bacterial swimming in dilute suspensions under varying confinement. Confinement reduces near-surface accumulation and facilitates bacterial escape. These effects are quantitatively captured by models incorporating the force quadrupole, a higher-order hydrodynamic singularity, that generates a rotational flow reorienting bacteria away from surfaces. Under strong confinement, bacterial trajectories straighten due to the balancing torques exerted by opposing surfaces. These findings highlight the role of hydrodynamic quadrupole interactions in near-surface bacterial motility, with implications for microbial ecology, infection control, and industrial applications.},
}

*Models, Biological
Hydrodynamics
*Bacterial Physiological Phenomena
Movement
*Escherichia coli/physiology

@article {pmid41247508,
year = {2025},
author = {Wenten, IG},
title = {Rethinking Biofilm Engineering and Fouling Resistance in Membrane Bioreactors.},
journal = {Langmuir : the ACS journal of surfaces and colloids},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.langmuir.5c03864},
pmid = {41247508},
issn = {1520-5827},
abstract = {Membrane bioreactors (MBRs) are increasingly recognized as a key technology in sustainable wastewater treatment, offering a high effluent quality through the integration of biological degradation and membrane filtration. Among the critical factors influencing their performance are biofilm dynamics and membrane fouling. This article critically examines recent advances in biofilm engineering and antifouling strategies for MBRs, with an emphasis on microbial community modulation, quorum quenching, and hydrodynamic control to improve biofilm stability. In parallel, the review examines material-based and biological methods to mitigate membrane fouling, emphasizing multifunctional surfaces and emerging biocontrol strategies. Key operational challenges, such as energy consumption, cleaning frequency, and membrane aging, are evaluated alongside future research directions in materials design, microbial ecology, and real-time system optimization. The integration of these innovations is essential for advancing MBR technologies that are robust, resource-efficient, and aligned with circular economy principles.},
}

@article {pmid41247324,
year = {2025},
author = {Weagley, JS and Cárdenas, LAC and Romani, A and Sullender, ME and Aggarwal, S and Makimaa, H and Hogarty, MP and Rodgers, R and Kennedy, EA and Foster, L and Schriefer, LA and Baldridge, MT},
title = {Differential Microbial Community Assembly Following Co-housing versus Microbiota Transplant.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf256},
pmid = {41247324},
issn = {1751-7370},
abstract = {Mouse models are vital tools for discerning the relative contributions of host and microbial genetics to disease, often requiring the transfer of microbiota between different mouse strains. Transfer methods include antibiotic treatment of recipients and colonization using either co-housing with donors or the transplantation of faecal or caecal donor material. However, the efficiency and dynamics of these methods in reconstituting recipients with donor microbes is not well understood. We thus directly compared co-housing, faecal transplantation, and caecal transplantation methods. Donor mice from Taconic Biosciences, possessing distinct microbial communities, served as the microbial source for recipient mice from Jackson Laboratories, which were treated with antibiotics to disrupt their native microbiota. We monitored bacterial and viral populations longitudinally over the course of antibiotics treatment and reconstitution using 16S rRNA gene sequencing, quantitative PCR, and shotgun sequencing of viral-like particles. As expected, antibiotic treatment rapidly depleted microbial biomass and diversity, with slow and incomplete natural recovery of the microbiota in non-transfer-recipient control mice. Although all transfer methods reconstituted recipient mice with donor microbiota, co-housing achieved this more rapidly for both bacterial and viral communities. Overall, faecal and caecal transplant resulted in highly similar colonization processes with some minor variation in enrichment for two specific bacterial families. This study provides valuable insights into microbial ecology, as well as the dynamics underlying experimental microbial transfer methods, enhancing reproducibility and informing best practices for microbiota transfer in mouse models.},
}

@article {pmid41247030,
year = {2025},
author = {Van Beek, JM and Robles, G and Mewalal, R and Blaby, I and Hatzenpichler, R},
title = {A collection of archaeal 16S rRNA Clone-FISH cultures for probe validation in fluorescence in situ hybridization experiments.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0113125},
doi = {10.1128/mra.01131-25},
pmid = {41247030},
issn = {2576-098X},
abstract = {We present a collection of 30 Escherichia coli cultures (Clone-FISH cultures), each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from 1 of 30 lineages of archaea, including 17 yet uncultured ones. We make these clones available for use as controls in fluorescence in situ hybridization experiments.},
}

@article {pmid41247018,
year = {2025},
author = {Xiong, M and Kuang, W and Liu, Z and Tong, R and Deng, X and Wang, N and Wan, X and Feng, M and Luo, Y and Zhang, B and Zhang, Z and Zheng, F},
title = {Quercetin alleviates ulcerative colitis via regulating gut microbiota and tryptophan metabolism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070325},
doi = {10.1128/msystems.00703-25},
pmid = {41247018},
issn = {2379-5077},
abstract = {UNLABELLED: Quercetin, a natural flavonoid in traditional Chinese medicinal plants, has shown promise in alleviating ulcerative colitis symptoms despite uncertainties about its exact mode of action. This study explored how quercetin influences tryptophan breakdown and gut bacterial populations in mice with chemically induced colitis. The treatment demonstrated measurable improvements-normalizing body weight, reducing spleen enlargement, lowering clinical severity scores, preserving colon structure, and healing tissue damage. Through advanced microbiome profiling and metabolic analysis, researchers observed increased populations of helpful gut microbes alongside higher concentrations of tryptophan byproducts. These biochemical shifts stimulated the aryl hydrocarbon receptor system, which plays a key role in restoring gut lining integrity. The collective evidence points to quercetin's therapeutic potential through its dual action on microbial ecology and tryptophan-derived signaling pathways.

IMPORTANCE: Ulcerative colitis is a chronic inflammatory disease with limited effective therapeutic options. In this study, quercetin-a flavonoid commonly found in traditional Chinese medicinal herbs-was shown to relieve colitis symptoms by reshaping gut microbiota and restoring tryptophan metabolism. Notably, the increase in indolelactic acid, a key microbial metabolite, led to activation of the aryl hydrocarbon receptor, which supports intestinal barrier integrity and dampens inflammation. These findings reveal a gut microbiota-derived metabolite-host signaling axis as a central mechanism of action, highlighting the potential of quercetin as a microbiota-targeted therapeutic approach for UC.},
}

@article {pmid41246320,
year = {2025},
author = {Dey, P},
title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674913},
doi = {10.3389/fimmu.2025.1674913},
pmid = {41246320},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; },
abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
Humans
Dysbiosis
Mice, Knockout
*Intestines/microbiology/immunology
*Intestinal Mucosa/metabolism/microbiology/immunology
*Host Microbial Interactions/genetics
Mice

@article {pmid41246283,
year = {2025},
author = {Phoo, MTP and Dechathai, T and Singkhamanan, K and Chusri, S and Pomwised, R and Wonglapsuwan, M and Morikawa, K and Surachat, K},
title = {Pseudomonas aeruginosa affects Acinetobacter baumannii's growth, gene expression and antibiotic resistance in in vitro co-culture system.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100499},
doi = {10.1016/j.crmicr.2025.100499},
pmid = {41246283},
issn = {2666-5174},
abstract = {Pseudomonas aeruginosa and Acinetobacter baumannii are opportunistic pathogens co-isolated frequently in the same infection sites. In this study, we aimed to elucidate the interaction between P. aeruginosa and A. baumannii in in vitro co-culture system. Growth analysis showed that P. aeruginosa PA01 unilaterally exerts a negative effect on the growth of A. baumannii SK005. A. baumannii alone exhibited an altered transcriptome pattern, especially in the genes for metabolic pathways. Strong upregulation of genes in iron acquisition systems (acinetobactin, baumannoferrin, 2,3-dihydroxybenzoic acid synthesis cluster, and Feo iron transport system) and downregulation of iron-storage genes (bacterioferritin) were the most prominent changes. In terms of antibiotic resistance, we observed the downregulation of the fosfomycin resistance gene fosB. Strikingly, the phenotypic analysis demonstrated that A. baumannii in co-culture is more vulnerable to fosfomycin than in monoculture conditions, while it is more resistant to cefoxitin and imipenem. This study broadens our understanding of microbial ecology in co-infection settings by highlighting the fact that mixed pathogens do not always undergo interaction to a mutually equivalent extent.},
}

@article {pmid41244671,
year = {2025},
author = {Zhang, Z and Jia, L and Liu, B and Liu, Y and Zhao, J and Wang, Y and Zhang, M and Qiao, W and Yang, B and Luo, L and Chen, L},
title = {Maternal gut microbiota and placenta-derived tissues microbes are important for initial gut microbial colonization in infants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1631590},
doi = {10.3389/fmicb.2025.1631590},
pmid = {41244671},
issn = {1664-302X},
abstract = {BACKGROUND: Early infant gut microbiota colonization, influenced by various factors, significantly affects future growth and development. However, results related to how the initial microbial ecology is established in the infant gut remain inconsistent.

RESULTS: In this study, we collected maternal and infant feces, vaginal secretions, placental tissues, breast milk, amniotic membrane tissues, umbilical cord blood, and breast skin for homology comparisons and for exploring the main sources of infant intestinal microbiota. Our results revealed that early infant gut microbiota originated mainly from the vertical transmission of maternal microbiota, and that vaginal microbiota did not affect infant gut microbiota colonization. Microbiota was detected in the placenta, supporting the idea that the uterus is not sterile. Moreover, we verified microbial composition-related similarities in the amniotic tissues and umbilical cord blood, further validating our hypothesis that gut microbiota in the early stages of infancy are mainly vertically transmitted from the mother and placenta-derived tissues also play a significant role in the formation of the infant's initial gut microbiota. Notably, none of the hereby-mentioned influences (i.e., gender, delivery mode, feeding mode, and Hepatitis B virus) affected significantly infant gut microbiota colonization.

CONCLUSION: This study demonstrated that infant intestinal microbiota resulted from microbiotic co-provision from multiple maternal sites. In addition to the maternal gut microbiota, the placenta-derived tissues is the relevant contributor to initial infant gut microbiota, providing strong evidence for the source colonization of the infant gut microbiota.},
}

@article {pmid41244624,
year = {2025},
author = {Addo, SO and Addo, M and DeWitt, ME and Tawiah-Mensah, CNL and Amoah, S and Obuam, PK and Unicorn, NM and Kyeremateng, ET and Desewu, G and Larbi, JA},
title = {Knowledge, Attitude and Practices of Abattoir Workers in Kumasi Towards Ticks and Tick-Borne Pathogens.},
journal = {Public health challenges},
volume = {4},
number = {4},
pages = {e70167},
doi = {10.1002/puh2.70167},
pmid = {41244624},
issn = {2769-2450},
abstract = {The high dependence on livestock in Ghana comes with the risk of zoonotic tick-borne pathogen infection. Abattoir workers are especially at risk due to their frequent contact with livestock that are infested with ticks and tick-borne pathogens. This study sought to assess the knowledge, attitude and practices of abattoir workers in Kumasi towards ticks and tick-borne pathogens. A total of 130 workers were recruited from the Kumasi abattoir (92), Suame abattoir (24) and Akwatia Line slaughter slab (14). The respondents were males, mostly aged between 46 and 55 years (36.2%), had no form of education (43.8%) and had >10 years (68.5%) of working experience. Given that a significant number of the workers handled live animals (95.4%) or dead animals or animal parts (87.7%), were involved in slaughtering (69.2%) and had experienced tick bites (81.5%), there was a risk of tick-borne pathogen infection. However, only 35.4% thought humans can get diseases from tick bites, and 58.5% of the respondents believed tick bites lead to the development of a tick-borne disease. It was observed that education (p = 0.008) had a significant influence on the risk of zoonotic tick-borne pathogen infection, with 52% of the respondents with no education believing humans cannot get infections from ticks. The findings of this study indicate that the abattoir workers are at risk of zoonotic tick-borne infections, and there is a need for frequent education as well as the adoption of effective tick control and preventive measures.},
}

@article {pmid41242981,
year = {2025},
author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A},
title = {The fetal exposome and Preterm Birth: a systematic synthesis of environmental exposures and multi-omics evidence.},
journal = {Journal of perinatal medicine},
volume = {},
number = {},
pages = {},
pmid = {41242981},
issn = {1619-3997},
abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.

METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.

RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.

CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.},
}

@article {pmid41242561,
year = {2025},
author = {Gloria, LD and Lotti, T and van Loosdrecht, MC and Ramazzotti, M},
title = {Who calls granules "home"? Domain-spanning meta-analysis charting microbial ecosystems underlying aerobic granular sludge reactors.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133657},
doi = {10.1016/j.biortech.2025.133657},
pmid = {41242561},
issn = {1873-2976},
abstract = {The theatre of activity of complex microbial communities underpins the Aerobic Granular Sludge (AGS) systems, resulting in efficient wastewater treatment. Here, we present the first meta-analysis of DNA sequencing data from both published and newly generated AGS samples, aiming to define the "core microbiota" of AGS reactors, consisting of bacteria, archaea, eukaryotes and DNA viruses consistently featured and shared across different scales and operational settings. Briefly, the results indicated that a sequencing depth of at least 10 GB is required to profile the majority of the AGS community, revealed the core taxa, detected the recurrent presence of the uncultured genus ADurb.Bin028 in full-scale reactors and identified Rotaria and Diploscapter, as well as the sessile ciliates Stentor and Thuricola, as the most abundant eukaryotes in AGS. In conclusion, this work provided a taxonomic overview of AGS' common microbes and addressed potential technical caveats, aiming to establish a reference for future studies.},
}

@article {pmid41240073,
year = {2025},
author = {Berkhout, MD and de Ram, C and Boeren, S and Plugge, CM and Belzer, C},
title = {Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {123},
pmid = {41240073},
issn = {1432-184X},
support = {0.24.002.002//Ministerie van Onderwijs, Cultuur en Wetenschap/ ; },
mesh = {*Probiotics ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism ; *Verrucomicrobia/physiology ; Akkermansia ; Polysaccharides/metabolism ; Bacteroides thetaiotaomicron ; },
abstract = {Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. However, it is unknown if consumption of live and active A. muciniphila will be effective in terms of survival and engraftment in the gut microbiome. Furthermore, it is of interest whether introduction of A. muciniphila would influence the resident mucosal microbiota. To this end, we investigate the addition of live A. muciniphila to a stable in vitro microbial mucin glycan-degrading synthetic community. A. muciniphila engrafted in this synthetic community and actively degraded mucin using essential mucin glycan-degrading enzymes. Addition of A. muciniphila did not induce major compositional changes, except that Bacteroides thetaiotaomicron increased in relative abundance at the expense of Bacteroides caccae. At the metaproteomic level, community function was not significantly affected, as peptidase, fucosidase, galactosidase and sulfatase expression remained stable. However, sialidase was significantly enriched after A. muciniphila addition, which can be explained by the relative increase of generalist glycan-degrader B. thetaiotaomicron. Overall, we show that a community without A. muciniphila still harbours a niche for this bacterium, but that A. muciniphila did not induce major changes in the in vitro mucosal synthetic community. This suggests that A. muciniphila applied as a probiotic can engraft and exert its beneficial effects on the host, without major impact on the human gut mucosal microbiota composition and function and warrants further research into A. muciniphila engraftment in vivo.},
}

*Probiotics
*Gastrointestinal Microbiome
Humans
Mucins/metabolism
*Verrucomicrobia/physiology
Akkermansia
Polysaccharides/metabolism
Bacteroides thetaiotaomicron

@article {pmid41240069,
year = {2025},
author = {Cambronero-Heinrichs, JC and Pepori, AL and Pecori, F and Santoiemma, G and Cavaletto, G and Santini, A and Rassati, D},
title = {Microbial Interactions Support the Role of Ambrosia Beetles as Potential Vectors of Dutch Elm Disease.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {124},
pmid = {41240069},
issn = {1432-184X},
support = {National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, project: "Ulmus glabra protection in Italian peninsula - MONTANA", CUP:C53D23003510006//European Union - NextGenerationEU/ ; },
mesh = {Animals ; *Plant Diseases/microbiology ; *Ulmus/microbiology/parasitology ; Symbiosis ; *Coleoptera/microbiology ; *Microbial Interactions ; Female ; *Insect Vectors/microbiology ; Ophiostoma/physiology ; *Weevils/microbiology ; },
abstract = {Dutch elm disease (DED) has caused devastating pandemics in natural elm populations across Europe, North America, and Asia. The primary vectors of DED are native elm-associated bark beetles of the genus Scolytus. However, there is evidence suggesting that ambrosia beetles may also carry Ophiostoma novo-ulmi and potentially transmit it to elm trees. In this study, we explored microbial interactions and host selection mechanisms that could support the role of ambrosia beetles as vectors of O. novo-ulmi. Our study showed that females of Anisandrus dispar, Xyleborinus saxesenii, Xylosandrus crassiusculus, and Xylosandrus germanus emerging from both DED-infected and healthy elm logs carried O. novo-ulmi DNA. Furthermore, we showed that none of the tested ambrosia beetle fungal symbionts was adversely affected by O. novo-ulmi, while Dryadomyces spp. and the bacterial symbiont Erwinia sp. 1C4 partially restricted or inhibited O. novo-ulmi growth without fully suppressing it. Overall, these findings provide additional evidence supporting the potential role of ambrosia beetles as vectors of DED and emphasize the need for further research on this understudied insect-pathogen relationship.},
}

Animals
*Plant Diseases/microbiology
*Ulmus/microbiology/parasitology
Symbiosis
*Coleoptera/microbiology
*Microbial Interactions
Female
*Insect Vectors/microbiology
Ophiostoma/physiology
*Weevils/microbiology

@article {pmid41239036,
year = {2025},
author = {Casanova-Hernández, D and Pinacho-Pinacho, CD and Calixto-Rojas, M and Rubio-Godoy, M and Hernández-Velázquez, IM and Guevara-Avendaño, E and Méndez, O and Velázquez-Velázquez, E and Zamora-Briseño, JA},
title = {Challenging the paradigm: the Asian fish tapeworm (Schyzocotyle acheilognathi, Yamaguti 1934) lacks an intrinsic symbiotic bacterial community.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41239036},
issn = {1618-1905},
abstract = {Schyzocotyle acheilognathi is an invasive generalist cestode with a high capacity for adaptation to multiple hosts and freshwater environments. Recent reports suggest that this parasite possesses an intrinsic symbiotic microbiota distinct from that of its fish hosts, and its presence induces gut dysbiosis in the host. In this study, we reassessed these ideas. For this, we collected naturally parasitized fish specimens from different locations in Mexico, encompassing different host species, including Cyprinus carpio, Pseudoxiphophorus bimaculatus, Tlaloc hildebrandi, and Vieja hartwegi. We also tested whether this parasite induces a dysbiotic process in the gut bacterial community of Tlaloc hildebrandi. Parasites were identified based on morphological and molecular criteria, and their bacterial communities were characterized using metataxonomy. Our results revealed that S. acheilognathi does not harbor a consistent microbial community among the different host species surveyed. We also did not detect any dysbiotic effect on the gut microbiota of Tlaloc hildebrandi. These findings contradict previous data and provide evidence of the loose relationship between this parasite and bacteria, which we propose could be a part of its successful generalist strategy. The results presented herein offer a novel perspective on the quest for understanding the microbial ecology in generalist cestodes of freshwater fish.},
}

@article {pmid41239026,
year = {2025},
author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H},
title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.},
journal = {Acta parasitologica},
volume = {70},
number = {6},
pages = {211},
pmid = {41239026},
issn = {1896-1851},
support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; },
mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Gastrointestinal Microbiome ; Mice ; *Intestinal Mucosa/pathology/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology/pathology ; Disease Models, Animal ; Feces/microbiology/parasitology ; Female ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.

METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.

RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3 months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6 months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3 months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6 months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6 months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P < 0.01), and reduced goblet cell counts (P < 0.05), collectively indicating compromised intestinal barrier integrity.

CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.},
}

Animals
*Echinococcus multilocularis/physiology
*Gastrointestinal Microbiome
Mice
*Intestinal Mucosa/pathology/microbiology/parasitology
RNA, Ribosomal, 16S/genetics
*Echinococcosis/parasitology/pathology
Disease Models, Animal
Feces/microbiology/parasitology
Female
Bacteria/classification/genetics/isolation & purification

@article {pmid41237939,
year = {2025},
author = {Devarajan, B and Sharma, S and Mills, B and Prajna, L and Venkatesh, PN and Dharmalingam, K},
title = {Dysbiosis of Bacterial and Fungal Microbiomes Affects the Disease Process and Treatment Outcome in Fungal Keratitis.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110745},
doi = {10.1016/j.exer.2025.110745},
pmid = {41237939},
issn = {1096-0007},
abstract = {Fungal keratitis (FK) is a severe eye infection mainly caused by Aspergillus flavus and Fusarium solani. We examined the changes in bacterial and fungal microbiome profiles over a week of disease progression, treatment, and clinical status using targeted next-generation sequencing (NGS). Samples were collected from infected and healthy contralateral eyes of 25 FK patients and one eye of 10 healthy, non-infected cataract controls. QIIME (Quantitative Insights into Microbial Ecology) and MicrobiomeAnalyst were utilised for the data analysis. There was a reduction in beneficial bacteria like Prevotella, Lactobacillus, and Leuconostoc in FK patients compared to the control samples. On the other hand, opportunistic bacteria including Clostridium, Bifidobacterium, and Pseudomonas increased in FK patients. Aspergillus, Colletotrichum, and Basidiobolus were more abundant in keratitis patients, whereas Malassezia and Trichoderma were less abundant. This dysbiosis was also evident in the uninfected contralateral eyes of FK patients. Treatment resulted in significant changes in bacterial genera like Dolosigranulum, Sutterella, and Akkermansia, and fungal genera such as Myrothecium, Corynespora, and Penicillium. Further, treatment returned them to the control group levels, except for Akkermansia and Corynespora. Among the treated patients, a large subset remains nonresponsive to treatment. This treatment outcome, responder versus non-responder, was reflected in the abundance of bacterial genera such as Tannerella, Sutterella, Odoribacter, and fungal genera such as Coprinellus and Volutella. This study highlights the clinical relevance of microbiome signatures in FK, demonstrating bilateral dysbiosis, integrated bacterial-fungal profiling, and correlations with treatment outcomes. These findings suggest potential for microbiome-informed diagnostics, prognostic biomarkers, and risk stratification.},
}

@article {pmid41236361,
year = {2025},
author = {Markfeld, M and Titcomb, G and Randriamoria, TM and Sehgal, G and Baksh, N and Kerrigan, A and Soarimalala, V and Nunn, CL and Pilosof, S},
title = {Differential Assembly of Core and Non-Core Host-Microbe Network Structures Along a Land-Use Change Gradient.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70255},
doi = {10.1111/ele.70255},
pmid = {41236361},
issn = {1461-0248},
support = {1281/20//Israel Science Foundation/ ; 2308460//National Science Foundation/ ; R01-TW011493//NIH-NSF-NIFA Ecology and Evolution of Infectious Diseases program/ ; 2022721//United States-Israel Binational Science Foundation/ ; Provost's Collaboratory Award//Duke University/ ; RGY0064/2022//Human Frontier Science Program/ ; //Duke Lemur Center/ ; },
mesh = {Animals ; Rats/microbiology ; Madagascar ; *Microbiota ; *Host Microbial Interactions ; },
abstract = {Microbial communities are fundamental to host health, yet their assembly dynamics under environmental change remain poorly understood. We analysed individual-level host-microbe networks in the non-native wild black rats (Rattus rattus) across a land-use gradient in Madagascar. By applying a moving prevalence threshold, we distinguished between core and non-core microbes and compared the assembly drivers shaping their network structures. Non-core microbes formed fragmented, modular networks shaped mainly by heterogeneous selection, reflecting environmental filtering. In contrast, core microbes exhibited stable, less modular networks driven primarily by stochastic ecological drift. These distinct assembly processes persisted across thresholds, highlighting fundamental differences in microbial structuring. Land-use change significantly influenced the modular structure of non-core microbes but had minimal effects on core microbes, demonstrating the differential sensitivity of microbial groups to environmental variation. This study advances our understanding of host-microbe interactions and provides a framework for assessing microbiome assembly under anthropogenic change.},
}

Animals
Rats/microbiology
Madagascar
*Microbiota
*Host Microbial Interactions

@article {pmid41236145,
year = {2025},
author = {Maillard, F and Klinghammer, F and Beatty, BH and Zou, H and Lara, E and Hammer, EC and Tunlid, A and Kennedy, PG},
title = {Keystone protist suppression triggers mesopredator release and biotic homogenization in complex soil microbial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf253},
pmid = {41236145},
issn = {1751-7370},
abstract = {The keystone species concept holds that certain members of an ecological community, despite their low abundance, exert disproportionately large effects on species diversity and composition. In microbial ecology, experimental validation of this concept has been limited because targeted removal of individual species remains technically challenging. Here, we developed a procedure to test the keystone species concept within a soil microbial food web by selectively suppressing a protist predator at the microscale via UV-induced phototoxicity in a microfluidic soil chip system. We targeted a hypotrich ciliate (subclass Hypotrichia), and combined microscopy with high-throughput amplicon sequencing of microbial taxonomic markers to assess, across multiple trophic levels, how its suppression affected microbial community abundance, diversity, and composition. Over the 20-day incubation, the chip system supported complex communities of bacteria, fungi, and protists. Following Hypotrichia suppression, two distinct ecological responses were observed: first, an increase in the relative abundance of flagellates, consistent with mesopredator release, accompanied by a significant rise in overall protist diversity; second, a convergence in protist community composition, indicative of biotic homogenization. Bacterial community abundance, richness, and composition remained unchanged, likely due to compensatory predation from a relative increase in bacterivorous flagellates. In contrast, fungal diversity decreased, presumably because the altered protist community favored facultative fungal consumers. Collectively, these findings provide direct experimental evidence that low abundance microbial predators can function as keystone species, modulating predator community composition and diversity, and exerting cascading effects on lower trophic levels within microbial brown food webs.},
}

@article {pmid41234770,
year = {2025},
author = {Wang, IC and Swanson, JL and Waters, JL and Kochukov, MY and Buffington, SA and Dooling, SW and Arenkiel, BR and Costa-Mattioli, M},
title = {Alteration of gut microbial ecology by the direct activation of the brain: Inverse gut-microbiome-brain dynamics.},
journal = {iScience},
volume = {28},
number = {11},
pages = {113709},
pmid = {41234770},
issn = {2589-0042},
abstract = {The gut-microbiome-brain axis is a bidirectional communication system influencing host physiology and overall fitness. While "bottom-up" effects-where gut microbes influence brain function and behavior-are well established, direct evidence for "top-down" modulation-where the brain shapes the gut microbial ecology-remains elusive. Here, we show that the selective expression of the bacterial ion channel mNaChBac in glutamatergic lateral habenula (LHb) neurons increases their bursting activity and leads to endophentypes associated with depression. Importantly, this chronic activation leads to changes in the gut microbiome composition over time, as reflected by shifts in alpha-diversity and alterations in specific microbial taxa. These findings provide direct evidence that the persistent activation of the brain acts as a selective pressure that affects the stability and diversity of the gut microbiome, providing a new dimension by which gut-microbiome-brain interactions may cooperate to modulate host physiology and health.},
}

@article {pmid41233937,
year = {2025},
author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M},
title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {231},
pmid = {41233937},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; },
abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.

RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.

CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.},
}

Animals
*Rumen/microbiology/metabolism
*Methane/metabolism/biosynthesis
Cattle
*Seaweed
*Dietary Supplements
*Bacteria/genetics/metabolism/classification/isolation & purification
Animal Feed/analysis
*Gastrointestinal Microbiome
Fermentation
Metagenome
Metagenomics
Hydrogen/metabolism

@article {pmid41233936,
year = {2025},
author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS},
title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {234},
pmid = {41233936},
issn = {2049-2618},
support = {141954/2019-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; },
abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.

RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.

CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.},
}

*Anthozoa/microbiology
Animals
*Symbiosis
*Nitrogen Cycle
Metagenomics/methods
Microbiota
Brazil
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
RNA, Ribosomal, 16S/genetics
In Situ Hybridization, Fluorescence

@article {pmid41233829,
year = {2025},
author = {Sieders, M and Candry, P and El Aidy, S},
title = {Hydrogel-based experimental models of the gastrointestinal tract.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {233},
pmid = {41233829},
issn = {2049-2618},
abstract = {The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical features of the gastrointestinal tract, offering unprecedented opportunities to study microbial behavior, adaptation, and interactions within three-dimensional, tunable architectures. Unlike suspension cultures, hydrogels provide porous, mucosa-like environments that enable the cultivation of mucosa-associated microbes, co-culturing with human cells, and mimicking healthy and disease-related states. This review explores the transformative potential of hydrogel matrices in unveiling the spatial organization, nutrient gradients, and community communication that define microbial ecosystems. By integrating the benefits of in vitro and in vivo models, hydrogel-based platforms promise to accelerate discoveries in microbiome science, with far-reaching implications for understanding human health and developing targeted therapeutics. Video Abstract.},
}

@article {pmid41231796,
year = {2025},
author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S},
title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336337},
doi = {10.1371/journal.pone.0336337},
pmid = {41231796},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.

METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.

RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.

CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
*Tuberculosis, Pulmonary/microbiology/drug therapy
Phylogeny
*RNA, Ribosomal, 16S/genetics
Antitubercular Agents/therapeutic use
Male
Female
Mycobacterium tuberculosis/genetics
Middle Aged
Adult

@article {pmid41230548,
year = {2025},
author = {Mukherjee, A and Tan, BH and Swarup, S},
title = {In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community.},
journal = {Bio-protocol},
volume = {15},
number = {21},
pages = {e5496},
pmid = {41230548},
issn = {2331-8325},
abstract = {The rhizosphere, a 2-10 mm region surrounding the root surface, is colonized by numerous microorganisms, known as the rhizosphere microbiome. These microorganisms interact with each other, leading to emergent properties that affect plant fitness. Mapping these interactions is crucial to understanding microbial ecology in the rhizosphere and predicting and manipulating plant health. However, current methods do not capture the chemistry of the rhizosphere environment, and common plant-microbe interaction study setups do not map bacterial interactions in this niche. Additionally, studying bacterial interactions may require the creation of transgenic bacterial lines with markers for antibiotic resistance/fluorescent probes and even isotope labeling. Here, we describe a protocol for both in silico prediction and in vitro validation of bacterial interactions that closely recapitulate the major chemical constituents of the rhizosphere environment using a widely used Murashige & Skoog (MS)-based gnotobiotic plant growth system. We use the auto-fluorescent Pseudomonas, abundantly found in the rhizosphere, to estimate their interactions with other strains, thereby avoiding the need for the creation of transgenic bacterial strains. By combining artificial root exudate medium, plant cultivation medium, and a synthetic bacterial community (SynCom), we first simulate their interactions using genome-scale metabolic models (GSMMs) and then validate these interactions in vitro, using growth assays. We show that the GSMM-predicted interaction scores correlate moderately, yet significantly, with their in vitro validation. Given the complexity of interactions among rhizosphere microbiome members, this reproducible and efficient protocol will allow confident mapping of interactions of fluorescent Pseudomonas with other bacterial strains within the rhizosphere microbiome. Key features • This method builds upon the widely used MS-based gnotobiotic system for growing plants and a synthetic bacterial community (SynCom) for plant-microbe interaction studies. • It considers the chemical composition of plant growth media (MS) and root exudates to map bacterial interactions. • It provides a method to both predict and validate interactions of fluorescent Pseudomonas with other strains within a SynCom. • This method is scalable for any bacterial pair with distinguishing markers (e.g., fluorescence, antibiotic resistance).},
}

@article {pmid41229186,
year = {2025},
author = {Park, JW and Park, JS and Kook, PR and Cho, YH and Park, SK and Lee, JH and Kang, SK and Kim, SW and Kim, SR},
title = {Impact of Artificial Diet Versus Mulberry Leaves on Silkworm Growth, Nutrient Composition, and Gut Microbiota.},
journal = {Archives of insect biochemistry and physiology},
volume = {120},
number = {3},
pages = {e70113},
doi = {10.1002/arch.70113},
pmid = {41229186},
issn = {1520-6327},
support = {PJ01721401.//This study was supported by the 2025 RDA Fellowship Program of the National Institute of Agricultural Science./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Morus/chemistry ; *Bombyx/growth & development/microbiology/metabolism ; Plant Leaves/chemistry ; Larva/growth & development/microbiology ; *Diet ; *Animal Feed/analysis ; Nutrients/analysis ; RNA, Ribosomal, 16S ; },
abstract = {Silkworms (Bombyx Mori) are traditionally reared on mulberry leaves; however, artificial diets have been developed to enable year-round rearing and automation. The physiological performance and cocoon yield of silkworms fed artificial diets remain inferior to those reared on mulberry leaves. We compared growth and nutrient composition in larvae reared on mulberry leaves (ML) and antibiotic-free artificial diet (ADS), and profiled gut microbiota in ML, ADS, and antibiotic-supplemented artificial diet (ADSA) to assess dietary effects on host physiology and microbial ecology. Proximate analysis revealed that protein accumulation was greater in ML-fed larvae, while ADS-fed larvae showed relatively higher fat content at the late fifth instar. Amino acid profiling showed consistently higher silk-related residues (Gly, Ala, Ser) and the derived Silk Amino Acid Index in ML-fed larvae, indicating enhanced fibroin synthesis potential. Microbiome analysis using 16S rRNA amplicon sequencing demonstrated dominance of Enterococcus mundtii in ADS groups, resulting in reduced alpha diversity and uneven community structure. In contrast, ML-fed larvae harbored diverse taxa, including Methylorubrum and Methylobacterium, while ADSA groups exhibited intermediate profiles with occasional dominance of Bacillus cereus. These findings highlight that artificial diet alters host nutrient metabolism and drives dysbiosis of gut microbiota, underscoring the need for optimized formulations and microbiome-stabilizing strategies, such as probiotics or prebiotics.},
}

Animals
*Gastrointestinal Microbiome
*Morus/chemistry
*Bombyx/growth & development/microbiology/metabolism
Plant Leaves/chemistry
Larva/growth & development/microbiology
*Diet
*Animal Feed/analysis
Nutrients/analysis
RNA, Ribosomal, 16S

@article {pmid41228488,
year = {2025},
author = {Yin, C and Liu, X and Fang, W and Meng, Q and Feng, X and Zhang, W and Dang, G and Zhong, R and Chen, L and Wang, Z and Zhang, H},
title = {Hyocholic Acid Species as the Key Modulator for Cecal Epithelial Homeostasis in Low-Birth-Weight Piglets.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213415},
pmid = {41228488},
issn = {2072-6643},
support = {32202709//National Natural Science Foundation of China/ ; U22A20515//National Natural Science Foundation of China/ ; Y2023QC09//Youth Innovation of Chinese Academy of Agricultural Sciences/ ; },
mesh = {Animals ; *Cecum/microbiology/drug effects/metabolism ; Swine ; *Homeostasis/drug effects ; Gastrointestinal Microbiome/drug effects ; *Intestinal Mucosa/metabolism/drug effects ; Bile Acids and Salts ; Animals, Newborn ; Birth Weight ; Dietary Supplements ; *Cholic Acids/pharmacology ; Dysbiosis ; },
abstract = {Background: Low birth weight (LBW) is correlated with gut microbiota dysbiosis and intestinal barrier function disruption, increasing susceptibility to enteric diseases. These alterations underscore the critical need to identify key regulators of gut homeostasis, among which bile acids are increasingly recognized as pivotal for barrier integrity, microbial ecology, and host metabolism. Methods: Eight pairs of LBW (the initial BW was 0.850 ± 0.053 kg) and normal-birth-weight (NBW; 1.488 ± 0.083 kg) piglets were compared to evaluate cecal morphology and bile acid profiles. Subsequently, sixteen LBW piglets and eight NBW piglets were allocated into three groups: NBW (1.563 ± 0.052 kg), LBW control (LBW-CON; 0.950 ± 0.120 kg), and LBW with bile acid supplementation (LBW-bile powder; 0.925 ± 0.116 kg). Piglets in the LBW-bile powder group received 25 mg/kg BW of bile powder (hyodeoxycholic acid-enriched) by daily oral gavage for 14 days. Results: LBW piglets exhibited retarded cecal development and lower abundance of hyocholic acid species (p = 0.006). Importantly, bile powder supplementation significantly improved cecal length (p = 0.009) and mucosal thickness (p = 0.020) compared with LBW-CON piglets. Microbial analysis showed that the microbial dysbiosis index was restored to near-normal levels. Transcriptomic analysis revealed impaired extracellular matrix structure and mucus secretion in LBW piglets. Notably, bile powder supplementation markedly upregulated the protein expression of WNT8B (p < 0.001) and the bile acid receptors (i.e., GPBAR1 and FXR), alongside enhanced tight junctions and the goblet cell marker mucin-2 expression (p < 0.05). Conclusions: These findings suggest that specific bile acid supplementation improves gut barrier function and partially supports cecal development in LBW piglets.},
}

Animals
*Cecum/microbiology/drug effects/metabolism
Swine
*Homeostasis/drug effects
Gastrointestinal Microbiome/drug effects
*Intestinal Mucosa/metabolism/drug effects
Bile Acids and Salts
Animals, Newborn
Birth Weight
Dietary Supplements
*Cholic Acids/pharmacology
Dysbiosis

@article {pmid41227744,
year = {2025},
author = {Fu, Y and Wang, Y and Zhang, J and Ren, J and Fang, B},
title = {Prebiotic Structural Diversity Shapes Gut Microbial Diversity, Community Composition, and Metabolic Activity In Vitro.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227744},
issn = {2304-8158},
support = {81770558//National Natural Science Foundation of China/ ; 3502Z20149031//Xiamen Joint Projects for Major Diseases/ ; 22278343//National Natural Science Foundation of China/ ; },
abstract = {Prebiotics are selectively utilized substrates that modulate gut microbiota and host health, yet different prebiotic structures may elicit distinct ecological and metabolic responses. In this study, we investigated the effects of five structurally diverse prebiotics-isomaltooligosaccharides (IMO), arabinogalactans (AG), pectin, inulin, and stachyose-on human gut microbiota via a 24 h in vitro anaerobic culture with healthy donors' gut microbiota. Microbial community dynamics were profiled by 16S rRNA gene sequencing, and short-chain fatty acids (SCFAs) production was analyzed. All treatments resulted in decreased α-diversity compared with baseline, with pectin most effectively preserving microbial richness and evenness, whereas stachyose led to the greatest reduction. Community composition and functional profiles shifted in a substrate-specific manner, with AG promoting Bacteroidaceae, IMO stimulating Lachnospiraceae and Faecalibacterium, and pectin supporting balanced microbial structures and SCFA production. Pectin, IMO, and inulin enhanced butyrate levels, whereas AG and pectin promoted propionate formation. These findings demonstrate that prebiotic structural differences strongly shape gut microbial ecology and metabolism, providing a mechanistic basis for rationally selecting and combining prebiotics to beneficially modulate the gut microbiota.},
}

@article {pmid41227660,
year = {2025},
author = {Alfonzo, A and Gaglio, R and Alongi, D and Franciosi, E and Perricone, G and Garofalo, G and Prestianni, R and Naselli, V and Pirrone, A and Francesca, N and Moschetti, G and Settanni, L},
title = {Polyphasic Characterisation of Microbiota Associated with Sant'Agostino Table Olives Flavoured with Foeniculum vulgare.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227660},
issn = {2304-8158},
support = {B7521002300001//Ministry of University and Research in Italy/ ; B73C23000060001//European Union/ ; },
abstract = {Sant'Agostino green table olives, traditionally processed in Apulia and flavoured with Foeniculum vulgare, represent a niche product whose microbial ecology remains largely unexplored. This study aimed to characterise the microbiota of the final product (both brine and fruit) after six months of storage with wild fennel. Four production batches were analysed using a combined culture-dependent and culture-independent approach. Microbiological counts revealed variable levels of aerobic mesophilic microorganisms, yeasts, lactic acid bacteria (LAB), and staphylococci, with yeasts and LAB being predominant. Ten LAB strains were identified, including Enterococcus faecium, Leuconostoc mesenteroides subsp. jonggajibkimchii, Leuconostoc mesenteroides subsp. cremoris, Leuconostoc pseudomesenteroides, Lactiplantibacillus plantarum, and Lactiplantibacillus pentosus. Yeast isolates belonged to Candida tropicalis, Torulaspora delbrueckii, and Saccharomyces cerevisiae. Amplicon sequencing (MiSeq Illumina) revealed distinct bacterial profiles between fruit and brine samples, with taxa from Actinobacteria, Bacteroidetes, Enterococcus, Lactobacillus, Leuconostoc, Alphaproteobacteria, Enterobacteriaceae, and other Gammaproteobacteria. Enterococcus and Leuconostoc were consistently detected, while Lactobacillus sensu lato appeared only in one fruit and one brine sample. These findings provide new insights into the microbial diversity of Sant'Agostino olives and contribute to the understanding of their fermentation ecology and potential for quality and safety enhancement.},
}

@article {pmid41227479,
year = {2025},
author = {Chessari, G and Tumino, S and Castiglioni, B and Biscarini, F and Bordonaro, S and Avondo, M and Marletta, D and Cremonesi, P},
title = {Girgentana's Goat Milk Microbiota Investigated in an Organic Farm During Dry Season.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227479},
issn = {2076-2615},
support = {Agritech National Research Center and received funding from the European Union Next-GenerationEU (National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4-D.D. 1032 17/06/2022, CN00000022//Agritech National Research/ ; },
abstract = {Milk microbiota is a complex microbial ecosystem with implications for product quality, safety, and animal health. However, limited data exist on goat milk microbiota, particularly in local breeds. This study provides the first detailed characterization of the milk microbiota of Girgentana goats, a resilient Sicilian breed valued for high-quality dairy products. Illumina NovaSeq sequencing was used to analyze the 16S rRNA V3-V4 regions of 44 individual and 3 bulk milk samples. Briefly, 16S rRNA-gene sequencing produced a total of 8,135,944 high-quality reads, identifying 1134 operational taxonomic units (OTUs) across all individual samples. On average, each sample showed 864 OTUs with counts > 0. Alpha diversity metrics, based on richness estimators (Chao1: 948.1; ACE: 936.3) and diversity indices (Shannon: 4.06; Simpson: 0.95; Fisher: 118.5), indicated a heterogeneous community with both common and low-abundance taxa. Firmicutes (51%) and Proteobacteria (27%) were the predominant phyla, with Lactobacillaceae (54%) and Bifidobacteriaceae (22%) dominating at the family level. Notably, farm bulk milk profiles closely mirrored individual samples. These results establish a milk microbiota baseline for the Girgentana breed and offer valuable insights into microbial ecology in traditional dairy systems, supporting future comparisons across breeds and farming practices.},
}

@article {pmid41222858,
year = {2025},
author = {Dvořák, P and Skoupý, S and Stanojković, A and Johansen, JR and Villanueva, C and Jung, P and Briegel-Williams, L and Laughinghouse, HD and Lefler, FW and Berthold, DE and Kaštovský, J and Hurley, AC and Casamatta, DA},
title = {A hitchhiker's guide to modern, practical cyanobacterial taxonomy.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70102},
pmid = {41222858},
issn = {1529-8817},
support = {23-06507S//Grant Agency of the Czech Republic/ ; },
abstract = {There has been an explosion of new Cyanobacterial taxa described within the last two decades. Cyanobacteria exhibit incredible ecological versatility and morphological variability, and thousands of species have already been described using "traditional" approaches (e.g., morphological features). However, DNA sequencing and other molecular tools have provided extensive evidence that the diversity of cyanobacteria is not necessarily congruent with morphology, as many morphological genera (e.g., Phormidium, Leptolyngbya, and Nostoc) are polyphyletic, and species within the genera are often morphologically indistinguishable, thus cryptic. Further confounding systematic assessments, newly erected taxa are often based on a single strain with one or two 16S rRNA gene sequences, may have incomplete formal descriptions, and lack indication of the employed species concepts. Here we have proposed a set of guidelines for cyanobacterial taxonomists. We have focused on the whole process of erecting new taxa: sampling, sequencing (including genomes), phylogenetic inference, phenotype characterization, species concepts, formal descriptions, and codes of nomenclature. Our hope is that these guidelines will help with the laborious but ever-rewarding task of identifying and describing the taxa within the world of cyanobacteria.},
}

@article {pmid41221507,
year = {2025},
author = {Clinton, CK and Jackson, FLC},
title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf181},
pmid = {41221507},
issn = {2730-6151},
abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.},
}

@article {pmid41220415,
year = {2025},
author = {Moseeb, HM and Aizaz, MM and Aiza, K and Hafsa, TH and Sania, M and Kamran, Z and Shamama, ZT and Usama, AM and Maroof, QP and Feroze, F and Ahmed, R and Ammara, N and Mahima, G},
title = {From obesity to cancer: Gut microbiome mechanisms, biomarkers, and U.S. public health strategies.},
journal = {Oncoscience},
volume = {12},
number = {},
pages = {175-188},
pmid = {41220415},
issn = {2331-4737},
abstract = {BACKGROUND: Obesity, metabolic syndrome, and colorectal cancer (CRC) remain major public health challenges in the United States, collectively driving substantial morbidity, mortality, and economic burden. Beyond diet and genetics, the gut microbiome has emerged as a pivotal determinant of host metabolism, immunity, and carcinogenesis, influenced by both environmental and behavioral factors.

OBJECTIVE: This review synthesizes current evidence linking gut microbial dysbiosis to obesity, metabolic syndrome, and CRC, emphasizing mechanistic pathways, environmental modifiers, and translational opportunities relevant to U.S. public health and precision medicine.

METHODS: Comprehensive searches of PubMed and Scopus (2000-2025) identified large epidemiologic studies, mechanistic experiments, and clinical trials, prioritizing research from U.S. populations and nationally representative databases including NHANES, SEER, and the Nurses' Health Study.

RESULTS: Microbial alterations such as enrichment of Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli contribute to CRC initiation and progression. In obesity and metabolic syndrome, shifts in Firmicutes-to-Bacteroidetes ratios, altered short-chain fatty acid metabolism, and endotoxin-mediated inflammation disrupt metabolic homeostasis. Environmental and lifestyle exposures, including air pollutants, smoking, and Westernized diets, modulate microbial ecology across the aerodigestive tract, affecting disease susceptibility. The emerging discipline of Molecular Pathological Epidemiology (MPE) integrates lifestyle, microbiome, and biomarker data to elucidate exposure-outcome relationships, enabling personalized prevention and therapeutic strategies.

CONCLUSIONS: The gut microbiome functions as both a biomarker and therapeutic target across metabolic and neoplastic diseases. Integrating microbiome science with environmental epidemiology and MPE frameworks offers transformative potential for precision prevention and equitable public health strategies in the U.S.},
}

@article {pmid41219483,
year = {2025},
author = {Han, J and Fang, Q and Hao, Y and Huang, X and Kong, F and Chen, H and Liu, Y},
title = {Diversity of Yeast and Drosophila Species Associated with Grape Sour Rot in China.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {121},
pmid = {41219483},
issn = {1432-184X},
support = {2022E02073//Special Regional Collaborative Innovation Project of Xinjiang Uygur Autonomous Region (Science and Technology Aid Xinjiang Program)/ ; 32272550//National Natural Science Foundation of China/ ; CARS-29-bc-5//Agriculture Research System of China/ ; 202305AF150129//Expert Workstation Project in Yunnan Province/ ; },
abstract = {Sour rot is a complex disease of grapes, primarily caused by the synergistic effects of yeast and Drosophila species, leading to fruit decay, poor quality, and significant economic losses. The lack of information on species distribution and diversity of these organisms in China limits the efficacy of control strategies. In this study, we sequenced the 26S rRNA D1/D2 region in yeasts and the COI region in Drosophila. Nine yeast genera were identified. Hanseniaspora spp. (45.76% of total) were the most abundant, followed by Starmerella spp. (23.62%) and Saccharomyces spp. (17.34%). At the species level, 14 yeast species were identified. Starmerella bacillaris (23.62%), Saccharomyces cerevisiae (17.34%), H. opuntiae (17.34%), and H. uvarum (15.13%) predominated. Of the five species of Drosophila present, Drosophila melanogaster (63.16%) was the dominant species. This study is the first to characterize the diversity of yeasts and Drosophila across major grape-producing regions in China. The findings provide a scientific foundation for elucidating the key drivers of sour rot and designing targeted control strategies.},
}

@article {pmid41219454,
year = {2025},
author = {Zhang, C and Zhang, X and Wang, F and Li, G and Ding, J and Cao, Y and Wang, H and Wu, S and Shang, X and Wei, K and Yang, L},
title = {Integrated Multi-Omics Analysis Reveals Microbial Community Restructuring and its Role in Key Carbohydrate Metabolic Pathways During Tobacco Leaf Curing.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {122},
pmid = {41219454},
issn = {1432-184X},
support = {1102022202016 / 110202201019 (LS-03)//Science and Technology Project of China Tobacco General Corporation/ ; QKHJC-ZK [2022] YB288//Science and Technology Project of Guizhou Provincial Department of Science and Technology/ ; 2022XM17//Science and Technology Project of Guizhou Tobacco Industry Technology Center/ ; 202111/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Plant Leaves/microbiology/metabolism/chemistry ; *Nicotiana/microbiology/metabolism/chemistry ; *Microbiota ; *Fungi/metabolism/genetics/classification/isolation & purification ; *Carbohydrate Metabolism ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Metabolic Networks and Pathways ; Temperature ; Metabolomics ; Multiomics ; },
abstract = {Microorganisms play a significant role in improving the flavor and quality of plant products. Analyzing how tobacco processing affects the microbial community structure is essential. Understanding the synergistic mechanisms of microorganisms during this process can help optimize the flavor and quality of plant products. In this study, samples were collected from four processing stages (T1: fresh leaves, T2: 42 °C, T3: 54 °C, T4: 68 °C), and metabolite and Phylloplane microbial data of tobacco leaves were generated. A comprehensive multi-omics analysis was conducted. The study shows that the increase in temperature and the decrease in humidity during the processing lead to the reorganization of the microbial community. Brevibacterium, Staphylococcus, Aspergillus, and Ganoderma were identified as core biomarkers. Bacteria dominate in the initial degradation of starch, while fungi promote the accumulation of soluble sugars through the transformation of intermediate products. This study deepens our understanding of the role of microorganisms and their carbohydrate metabolism in the tobacco leaf processing process and proposes a new strategy for constructing regulatory models by integrating multi-omics.},
}

*Plant Leaves/microbiology/metabolism/chemistry
*Nicotiana/microbiology/metabolism/chemistry
*Microbiota
*Fungi/metabolism/genetics/classification/isolation & purification
*Carbohydrate Metabolism
*Bacteria/metabolism/classification/genetics/isolation & purification
Metabolic Networks and Pathways
Temperature
Metabolomics
Multiomics

@article {pmid41218435,
year = {2025},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}

@article {pmid41217184,
year = {2025},
author = {Creagh, JW and Rolfsmeier, M and Evans, KJ and Bizarria, R and Reetz, DC and Badigian, TJ and Fredericks, LR and Hasenoehrl, AM and Brown, AP and Graves, BM and Alexander, CK and Rodrigues, A and Stoffregen, EP and Patel, JS and Ytreberg, FM and Rowley, PA},
title = {The Saccharomyces killer toxin K62 is a protein of the aerolysin family.},
journal = {mBio},
volume = {},
number = {},
pages = {e0142525},
doi = {10.1128/mbio.01425-25},
pmid = {41217184},
issn = {2150-7511},
abstract = {UNLABELLED: K62 is an antifungal killer toxin produced by Saccharomyces paradoxus, encoded by a double-stranded RNA satellite. The toxin exhibits a unique antifungal activity but lacks sequence homology to other killer toxins, and its antifungal mechanism of action remains unknown. To understand the function of K62, its tertiary structure was predicted using AlphaFold, followed by molecular dynamics simulations to create high-confidence molecular models. These analyses revealed that K62 monomers closely resemble the five-beta-strand domain found in pore-forming aerolysin toxins. Models of K62 oligomers yielded a circular complex and beta-barrel with structural and biochemical similarities to aerolysin-family pre-pores and pores. Consistent with the formation of aerolysin-like pores, recombinant K62 assembled into membrane-associated high molecular weight oligomers (>250 kDa) that were heat- and detergent-resistant. K62 has more than 1,000 uncharacterized sequence homologs, which were mostly found in fungi of the Ascomycota, as well as in the Chytridiomycota, Basidiomycota, plants, and bacteria, with evidence of extensive horizontal gene transfer. Homologs were also identified in pathogenic fungal species, including human and plant pathogens from the Candida and Fusarium genera, but unlike aerolysins, K62 appeared to be non-toxic to higher eukaryotes. K62 is the first aerolysin family protein discovered in yeasts, revealing a likely role in fungal niche competition and establishing an entirely new, expansive family of aerolysin-like proteins.

IMPORTANCE: Pore-forming toxins are potent biological weapons used across nature, from virulence factors to immune defense proteins. This study identifies K62, a little-known antifungal toxin produced by a wild yeast, as a structural and functional relative of the aerolysin family, which is well-known for forming damaging pores in cell membranes. Using structure prediction, molecular simulations, and biochemical analysis, we show that K62 assembles into large, stable pore-like complexes. Remarkably, K62 is just one member of a large and previously unrecognized family of similar toxin-like proteins found in fungi, plants, and bacteria, including pathogens that affect humans and crops. These findings uncover an unexpected evolutionary link across kingdoms, suggesting that pore-forming toxins may play a widespread role in fungal pathogenesis and microbial warfare. This work lays the foundation for understanding a new group of antifungal molecules and their potential impacts on health, agriculture, and microbial ecology.},
}

@article {pmid41216320,
year = {2025},
author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M},
title = {A global deep terrestrial biosphere core microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf176},
pmid = {41216320},
issn = {2730-6151},
abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.},
}

@article {pmid41215682,
year = {2025},
author = {Alonso, C and Zanetti, J and Griffero, L and Pereira-Flores, E and González, B and Lescano, C and Pérez-Parada, A and Crisci, C and Amann, R},
title = {Marine Bacterioplankton Composition Predicts Oxygen Consumption During Dissolved Organic Matter Degradation Experiments.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70197},
doi = {10.1111/1462-2920.70197},
pmid = {41215682},
issn = {1462-2920},
support = {ANII_MPI_ID_2017_1_1007663//Agencia Nacional de Investigación e Innovación/ ; Grupos I+D 2022//Comisión Sectorial de Investigación Científica/ ; },
abstract = {Microbial communities play pivotal roles in ocean biogeochemistry, yet linking their composition to ecosystem functions remains a significant challenge. In this study, we demonstrate the predictive power of bacterioplankton taxonomic composition in explaining oxygen consumption during dissolved organic matter (DOM) degradation. Using 4 years of experimental data, we integrated 'omics with statistical modeling, applying feature selection and dimensionality reduction to develop high-performance linear regression models with strong predictive accuracy. Our framework also identifies key microbial groups driving oxygen consumption, including taxa known for their differential capabilities in DOM processing and recently shown to exhibit distinct respiration rates. Flavobacteriales emerge as central contributors to oxygen consumption, underscoring their ecological importance in nutrient-rich, highly productive coastal systems often referred to as 'green seas'. Their consistent dominance across varying oxygen consumption categories highlights their pivotal role in sustaining ecosystem functions in these environments. Beyond oxygen consumption, this framework provides a versatile tool for investigating microbially driven biogeochemical processes. By linking community composition with ecosystem functions, our study advances predictive microbial ecology. These findings deepen our understanding of microbial contributions to the ocean's carbon and oxygen cycles, improving our ability to anticipate their responses to environmental change.},
}

@article {pmid41215000,
year = {2025},
author = {Graça, JS and Sachinelli, LDS and Tobar, N and Guadagnini, D and Cabral, L and Noronha, MF and Coutinho, LL and Cazarin, CBB and Bogusz-Junior, S and Belangero, WD and Brunetto, SQ and Pimentel, TC and Saad, MJA and Sant'Ana, AS},
title = {Fermented probiotic dairy products with buriti and orange byproducts enhance gut and bone health.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117364},
doi = {10.1016/j.foodres.2025.117364},
pmid = {41215000},
issn = {1873-7145},
abstract = {The integration of functional ingredients and probiotics in dairy matrices is a promising strategy to nehance bone and intestinal health and preventing the onset of diseases. This study aimed to evaluate the impact of fortification of fermented dairy products (yogurt and fermented milk) with buriti pulp or orange bagasse added, added or not of a probiotic strain L. acidophilus DSM 13241 (Nu-trish® LA-5®) (Chr. Hansen, Hoersholm, Denmark) (yogurt and fermented milk) on bone and intestinal health of Wistar rats. The experimental design consisted of male Wistar rats (n = 6/group) that received supplementation daily for 60 days. The parameters assessed included the quantification of minerals (Ca, P, and Mg) in the products and femurs, the biomechanical and densitometric parameters, the fecal microbiota composition through the sequencing analysis of the 16S rRNA gene, the short-chain fatty acid (SCFA) content, and the permeability of the intestinal barrier. It was observed that the consumption of buriti pulp was responsible for the bone strength and stiffness of the femurs. The consumption of buriti pulp increased the bone strength and stiffness of the femurs and the relative abundance of the Lachnospiraceae NK4A136 group. The fortification of probiotic yogurt with buriti pulp led to an increase in the production of SCFA (acetic acid) and the daily intake of Ca, Mg, and P. The consumption of orange bagasse increased the magnesium mineral content in the femur and serum calcium values. The consumption of orange bagasse increased the Mg content in the femur and serum values of Ca, improved the permeability of the intestinal barrier (reducing serum levels of lipopolysaccharide), and positively impacted the fecal composition (increases in the relative abundance of Lactobacillus and Muribaculaceae). The concentration of acetic and propionic acid increased after consumption of the two fermented milk formulations containing orange bagasse (LA OB and LA OX OB). The groups that consumed yogurt containing buriti pulp (Y BP) and yogurt containing L. acidophilus DSM 13241 (Nu-trish® LA-5®) and buriti pulp (Y LA BP) presented higher concentrations of acetic acid in the feces compared to the group that consumed only yogurt (Y). The consumption of all fermented products containing the probiotic L. acidophilus DSM 13241 (Nu-trish® LA-5®) (fermented milk or natural yogurts and yogurts fortified with buriti pulp and orange pulp: LA, LA OB, LA OX OB, Y LA, and Y LA BP) increased the abundance of the Lachnospiraceae family NK4A136 group. The findings of this study indicate that fruit byproducts and probiotic fermented dairy products exert synergistic effects on bone and gut microbial ecology health in growing rats. These results support the use of sustainable functional ingredients in food innovation to promote systemic health benefits.},
}

@article {pmid41212898,
year = {2025},
author = {Mihajlovic, L and Hofacker, LM and Lindner, F and Jayakumar, P and Diepold, A and Huwiler, SG},
title = {A molecular toolbox to modulate gene expression and protein secretion in the bacterial predator Bdellovibrio bacteriovorus.},
journal = {PLoS genetics},
volume = {21},
number = {11},
pages = {e1011935},
doi = {10.1371/journal.pgen.1011935},
pmid = {41212898},
issn = {1553-7404},
abstract = {The predatory bacterium Bdellovibrio bacteriovorus kills and consumes other bacteria, thrives in diverse environments and holds great potential to address major challenges in medicine, agriculture, and biotechnology. As a bacterial predator it represents an alternative to traditional antimicrobial strategies to combat multidrug-resistant bacterial pathogens and prevent food waste, while the multitude of predatory enzymes it produces have potential for biotechnological applications. However, while a limited set of genetic tools exist, the lack of secretion assays and fine-tuning of secretion constrain both fundamental studies and bioengineering of B. bacteriovorus. Here, we present a molecular toolbox for B. bacteriovorus by systematically tuning gene expression and secretion of a reporter protein. Building on functional native and synthetic promoters from the Anderson library with varying expression levels of fluorescent reporter protein mScarletI3, we evaluated different ribosomal binding sites (RBS) to fine-tune gene expression. To examine secretion, we established a novel protocol to quantify extracellular release of a Nanoluc luciferase reporter protein in B. bacteriovorus using different native Sec-dependent signal sequences. We anticipate that the newly developed genetic toolkit and techniques will advance research on this fundamental predator-prey system, laying the foundation for its broader application and future bioengineering efforts. This work will pave the way for tailored applications of B. bacteriovorus in microbial ecology, agriculture, biotechnology, and medicine.},
}

@article {pmid41212266,
year = {2025},
author = {Malassigné, S and Valiente Moro, C and Luis, P},
title = {Microbial Volatiles from Human Skin and Floral Nectar: Insufficiently Understood Adult Feeding Cues To Improve Odor-Based Traps for Aedes Vector Control.},
journal = {Journal of chemical ecology},
volume = {51},
number = {6},
pages = {108},
pmid = {41212266},
issn = {1573-1561},
abstract = {Mosquitoes of the genus Aedes, including the invasive Aedes albopictus, are responsible for the transmission of arboviruses such as dengue, chikungunya, and Zika. Their global expansion has intensified public health concerns, while the efficacy of insecticide-based control is declining due to resistance and environmental risks. These limitations have increased interest in odor-baited traps as complementary tools for surveillance and population reduction. Yet, their performance in the field remains inconsistent, largely because lures rely on a restricted set of human skin microbial volatiles and capture mainly host-seeking females. This review highlights the contribution of microorganisms inhabiting human skin and floral nectar to mosquito feeding ecology. Skin microbiota shape odor profiles by producing volatile organic compounds that mediate host attractiveness and species-specific mosquito responses. Likewise, nectar-dwelling yeasts and bacteria alter nectar chemistry and floral scent, generating volatiles that influence insect foraging, although their role in Aedes attraction remains poorly studied. By integrating data from Aedes and other insect models, we highlight microbial semiochemicals with demonstrated or potential roles in guiding blood- and sugar-feeding behaviors. We further discuss how microbial ecology, compound concentration, and chemical interactions drive variability in mosquito responses, raising both opportunities and challenges for trap design. Expanding research to nectar-associated microbial cues, while considering ecological specificity and possible non-target effects, could help create more versatile lures that attract both sexes and multiple feeding stages. This review advances our understanding of microbial-associated cues as critical drivers of mosquito behavior and outlines future directions to improve odor-based surveillance and control of Aedes vectors.},
}

@article {pmid41211947,
year = {2025},
author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A},
title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0054325},
doi = {10.1128/msphere.00543-25},
pmid = {41211947},
issn = {2379-5042},
abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.},
}

@article {pmid41210076,
year = {2025},
author = {Bayer, B and Kitzinger, K and Paul, NL and Albers, JB and Saito, MA and Wagner, M and Carlson, CA and Santoro, AE},
title = {Minor contribution of ammonia oxidizers to inorganic carbon fixation in the ocean.},
journal = {Nature geoscience},
volume = {18},
number = {11},
pages = {1144-1151},
pmid = {41210076},
issn = {1752-0894},
abstract = {Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean and are assumed to dominate carbon fixation below the sunlit surface layer. However, the supply of reduced nitrogen delivered from the surface in sinking particulate organic matter is insufficient to support the amount of nitrification required to sustain measured carbon fixation rates in the dark ocean. Here we attempt to reconcile this observed discrepancy by quantifying the contribution of ammonia oxidizers to dark carbon fixation in the eastern tropical and subtropical Pacific Ocean. We used phenylacetylene-a specific inhibitor of the ammonia monooxygenase enzyme-to selectively inhibit ammonia oxidizers in samples collected throughout the water column (60-600 m depth). We show that, despite their high abundances, ammonia oxidizers contribute only a small fraction to dark carbon fixation, accounting for 4-25% of the total depth-integrated rates in the eastern tropical Pacific. The highest contributions were observed within the upper mesopelagic zone (120-175 m depth), where ammonia oxidation could account for ~50% of dark carbon fixation at some stations. Our results challenge the current view that carbon fixation in the dark ocean is primarily sustained by nitrification and suggest that other microbial metabolisms, including heterotrophy, might play a larger role than previously assumed.},
}

@article {pmid41209725,
year = {2025},
author = {Wang, F and Li, S and Li, P and Feng, C and Zhao, Z and Yang, Y and Han, F and Xue, A and Li, Z and Han, P},
title = {The assembly processes and network characteristics of bacterial, fungal and archaeal communities in the middle Yangtze River and river-connected lakes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1701799},
pmid = {41209725},
issn = {1664-302X},
abstract = {Despite the crucial ecological roles of bacterial, fungal and archaeal communities in rivers and lakes, their interactions and dynamic changes in large, hydrologically-connected river-lake systems remain poorly understood. This study investigated the biogeographic patterns, assembly processes and co-occurrence network characteristics of bacterial, fungal and archaeal communities in the middle reaches of Yangtze River (MYR) and its two largest connected lakes, Dongting Lake (DTL) and Poyang Lake (PYL). Our results revealed significant spatial heterogeneity in microbial diversity and composition, with higher sedimentary microbial diversity in lakes than in the river. Stochastic processes, particularly dispersal limitation, dominated community assembly across all habitats. β-NRI analysis showed that deterministic processes were more influential for planktonic bacterial and archaeal communities in the lakes. Co-occurrence network analysis demonstrated that inter-domain cooperation was prevalent in PYL, whereas intra-domain interactions were more common in MYR and DTL, reflecting distinct hydrological connectivity. Keystone taxa differed between rivers and lakes, with rare taxa prevailing in MYR and both rare and abundant taxa contributing in lakes. Our findings highlight how connectivity and flow dynamics fundamentally shape microbial ecology, providing insights into for the management and conservation of large river-lake ecosystems.},
}

@article {pmid41207985,
year = {2025},
author = {Mei, J and Li, L and Ma, ZS},
title = {Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {119},
pmid = {41207985},
issn = {1432-184X},
abstract = {This study investigates the ecological mechanisms governing the structure and composition of lung microbiome communities within tumor tissue from lung cancer patients. While this field has attracted increasing research attention, the ecological and etiological mechanisms driving microbial community assembly in this environment remain poorly characterized. To address this gap, we applied Sloan's near neutral model, Ning et al.'s normalized stochasticity ratio framework and Harris et al.'s multi-site neutral model to evaluate the influences of stochastic and deterministic factors at species, community and metacommunity levels, respectively. Our findings include: (i) Stochastic drift exhibited predominant influence at both species and community levels in normal adjacent tissue (NT), exceeding its effects in LUAD (lung adenocarcinoma) and LUSC (lung squamous cell carcinoma). (ii) At the metacommunity level, neutrality was not rejected at the metacommunity or local community levels, which is consistent with the previous finding (i). (iii) Elevated metacommunity biodiversity (θ) and immigration rates (m) in LUAD/LUSC compared to NT (observed in ∼50% of cases) suggest that tumor occurrence/progression may actively promote microbial recruitment to tumor microenvironments. We propose three non-exclusive mechanistic interpretations: (i) Tumor-mediated immune modulation creates permissive ecological niches; (ii) structural remodeling of tissue enhances microbial colonization potential; (iii) selective enrichment of opportunistic taxa (e.g., Streptococcus) through tumor-specific microenvironmental changes. Our results demonstrate that LUAD and LUSC microbiomes are shaped by deterministic tumor-driven selection, in contrast to the predominantly stochastic assembly observed in NT microbiomes. These findings reveal substantial reorganization of tumor-associated microbial communities, warranting further biomedical investigation and clinical validation.},
}

@article {pmid41207977,
year = {2025},
author = {Oliveira-Pinto, PR and Oliveira-Fernandes, J and Gramaje, D and Santos, C},
title = {Metabarcoding Profiling Reveals Microbiome Structure and Predicts Functional Shifts in Grapevines Challenged by Phyllosticta ampelicida.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {120},
pmid = {41207977},
issn = {1432-184X},
abstract = {Black rot disease (BRD), caused by the still understudied Phyllosticta ampelicida, is spreading across several grape producing countries, posing a growing threat to the agroindustry. The role of the grapevine microbiome in defending against this pathogen, particularly in terms of microbiota structure and community homeostasis, remains unclear. In this study, we aimed to characterize the epiphytic phyllosphere microbiota of grapevines and identify shifts in microbial genetic structure associated with BRD symptoms. We sampled three vineyards of the cultivar "Touriga Nacional" in the Douro region (Portugal), collecting 20 leaves from (a) five healthy and (b) five BRD-symptomatic grapevines. The presence of P. ampelicida was confirmed in all symptomatic samples. Epiphytic bacterial DNA was extracted and sequenced using next-generation sequencing (NGS). Results indicate that although overall the diversity and richness indexes were not different in diseased plants compared to healthy ones, there was a reduction in OTU richness in black rot-affected grapevines. Diseased plants exhibited significant shifts in microbial network assemblages and showed an increased relative abundance of certain taxa, such as Acinetobacter, suggesting a possible recruitment of beneficial bacteria in response to biotic stress. Additionally, we observed a higher abundance of antibiotic resistance-related KEGG Orthologues (KOS) in symptomatic plants, raising potential concerns for human health. This study presents the first characterization of the grapevine phyllosphere epiphytic bacterial microbiota and its structural shifts in response to BRD.},
}

@article {pmid41206559,
year = {2025},
author = {Fournier, P and Pellan, L and Aubert, J and This, P and Vacher, C},
title = {A new scenario of pathogen-microbiota interactions involving the oomycete Plasmopara viticola.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf111},
pmid = {41206559},
issn = {1574-6941},
abstract = {A key question in microbial ecology is how the microbiota regulates host invasion by pathogens. Several ecological theories link the diversity, abundance and assembly processes of the microbiota with its resistance to invasion, but the specific properties of microbial communities that confer protection to the host are poorly understood. We addressed this question for the oomycete Plasmopara viticola, the causal agent of grapevine downy mildew. Using state-of-the-art microbial ecology methods, we compared microbial communities associated with asymptomatic and symptomatic leaf tissues to elucidate pathogen-microbiota interactions. Despite visible symptoms, P. viticola infection induced only subtle changes in microbial community composition. Symptomatic tissues showed enrichment in basidiomycete yeasts and Bacillus species, both known for their biocontrol activity, and exhibited a higher degree of determinism in community assembly processes. Asymptomatic tissues hosted more diverse microbiota, but lacked consistent associations with known biocontrol agents. Instead, they were often associated with other airborne grapevine pathogens. These findings suggest a novel interaction scenario: upon infection, P. viticola reshapes locally the leaf microbiota, excluding other pathogens and selecting for beneficial microbes. Although further studies are needed to uncover the underlying mechanisms, these findings underscore the relevance of targeting disease lesions in the search for protective microbial consortia.},
}

@article {pmid41204663,
year = {2025},
author = {Budziak, M and Ilicic, D and Grossart, HP and Krztoń, W and Walusiak, E and Fyda, J and Wilk-Woźniak, E},
title = {Phytoplankton Under Pressure: Temperature, Precipitation and Cyanobacterial Blooms as Drivers of Chytrid Infections.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70224},
doi = {10.1111/1758-2229.70224},
pmid = {41204663},
issn = {1758-2229},
support = {Statutory funds//Institute of Nature Conservation Polish Academy of Sciences/ ; GR 1540/48-1//German Research Foundation (DFG)/ ; COST Action ParAqua CA20125//European Cooperation in Science and Technology/ ; life17 env/lt/000407//European Union (EU) Life programme/ ; },
mesh = {Temperature ; *Cyanobacteria/growth & development ; *Phytoplankton/microbiology/growth & development ; Seasons ; Fresh Water/microbiology ; Ecosystem ; Rain ; Diatoms/microbiology ; *Chytridiomycota/isolation & purification ; Chlorophyta/microbiology ; Eutrophication ; },
abstract = {The area of fungal parasitism is attracting growing attention because of its great importance for aquatic organisms and their community dynamics. Despite increasing interest in this area, few studies have addressed baseline data on occurrence and environmental factors associated with chytrid parasite infections in natural ecosystems. This work provides insights into occurrence, prevalence, and dynamics of parasitic infections by studying three freshwater reservoirs over a period of 6 years. Chytrid infections were detected in each of the studied water bodies, infecting species of cyanobacteria, green algae and diatoms. However, recurring and prevalent infections were observed in only one water body, which is classified as a natural aquatic ecosystem. The recorded infection prevalence (IPC) ranged between 0% and 20%, while the mean infection severity remained low. Infection rates were highest in summer and most prominent during cyanobacterial blooms. Yet, the most infected group of phytoplankton consisted of green algae. GLM revealed a significantly positive correlation between IPC and water temperature and precipitation. Overall, these results demonstrate the dynamic nature of chytrid infections, which are shaped by multiple environmental factors across space and time.},
}

Temperature
*Cyanobacteria/growth & development
*Phytoplankton/microbiology/growth & development
Seasons
Fresh Water/microbiology
Ecosystem
Rain
Diatoms/microbiology
*Chytridiomycota/isolation & purification
Chlorophyta/microbiology
Eutrophication

@article {pmid41204024,
year = {2025},
author = {Mileng, K and Mani, S and Bezuidenhout, JJ and Mokgokong, PS and Ramatla, TA and Thekisoe, OMM and Lekota, KE},
title = {Bacterial Communities Harboured by Amblyomma Hebraeum Infesting Small Stock in Mahikeng city, South Africa.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {118},
pmid = {41204024},
issn = {1432-184X},
support = {GUN: CSUR23030681021//National Research Foundation/ ; },
mesh = {Animals ; South Africa ; *Bacteria/classification/genetics/isolation & purification ; Goats/parasitology/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sheep/parasitology ; *Amblyomma/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Goat Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; *Sheep Diseases/parasitology/microbiology/epidemiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Ticks are important vectors of pathogens affecting livestock productivity and public health, yet their bacterial communities remain poorly characterized in many parts of South Africa. This study investigated the bacterial diversity and potential pathogenic bacterial etiology associated with Amblyomma hebraeum ticks collected from sheep and goats in Mahikeng, North West province. A total of 168 adult ticks were sampled across four villages. Microbiome profiling was performed using high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. High-throughput 16S rRNA sequencing revealed 16,193 ASVs in goat-derived ticks and 16,510 ASVs in those from sheep. Proteobacteria emerged as the dominant phylum across all samples, with ticks collected from goats showing a particularly high dominance of Rickettsia spp. (51.64% relative abundance), suggesting potential zoonotic risks. In contrast, ticks from sheep harboured significantly more diverse and evenly distributed bacterial communities, as indicated by Shannon (p = 0.0138) and Simpson (p = 0.0233) diversity indices, despite comparable species richness. A core microbiome comprising 1,374 ASVs (32.3%) was shared across all ticks, alongside 1,504 and 1,372 unique ASVs in goat- and sheep-derived ticks, respectively. Notably, several medically and veterinary-relevant genera, including Coxiella, Ehrlichia, Staphylococcus, Bacillus, Acinetobacter, Corynebacterium, and Streptococcus, were detected across both host groups. While total species richness was comparable between hosts, alpha diversity indices that account for evenness revealed host-based differences, and beta diversity patterns further showed clear separation of bacterial communities by host species. This study indicates that the host plays a crucial role as an ecological driver affecting the diversity of microbial communities associated with ticks. This study improves our understanding of the diversity, composition, and abundance of tick-associated microbiomes and pathogens in South African small ruminants. These insights support the development of microbiome-targeted strategies for detecting and controlling tick-borne diseases.},
}

Animals
South Africa
*Bacteria/classification/genetics/isolation & purification
Goats/parasitology/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Sheep/parasitology
*Amblyomma/microbiology
*Tick Infestations/veterinary/parasitology/epidemiology
*Goat Diseases/parasitology/microbiology/epidemiology
Phylogeny
*Sheep Diseases/parasitology/microbiology/epidemiology
DNA, Bacterial/genetics
High-Throughput Nucleotide Sequencing

@article {pmid41203821,
year = {2025},
author = {Young, JD and Pinnell, LJ and Wolfe, CA and Scott, MA and Lawrence, TE and Cavasin, JP and Ellis, JA and Langsten, KL and Richeson, JT and Morley, PS},
title = {Microbial communities and tight junction protein expression in the gastrointestinal tract of feedlot cattle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39055},
pmid = {41203821},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Tight Junction Proteins/metabolism/genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Male ; Tight Junctions/metabolism ; Bacteria/genetics/classification ; },
abstract = {The gastrointestinal tract (GIT) of cattle plays a vital role in nutrient absorption, immune function, and microbial homeostasis. While the importance of the GIT microbiome and epithelial barrier integrity has been increasingly recognized, the typical composition of microbial communities and the expression of tight junction proteins (TJPs) in feedlot cattle remains poorly characterized. We investigated microbial community structure and TJP expression at three GIT sites: the rumen (RU), small intestine (SI), and large intestine (LI) in 21 finish-fed feedlot steers sourced from 21 commercial feedyards in the Texas Panhandle. Samples of luminal contents and GIT tissue were collected from each region, as well as feces and liver abscess material. Microbial communities were characterized using 16S rRNA gene sequencing. TJP gene expression was quantified by RT-qPCR using synthetic standards, and protein expression was evaluated by immunohistochemistry (IHC) with both computer-generated and pathologist-generated scoring. Microbial community structures varied primarily by GIT region rather than by individual animals raised at different locations. Nine bacterial families were identified as core microbiome members, with Lachnospiraceae being the most abundant across the GIT. TJP gene expression varied considerably by site, with RU having significantly lower Claudin 1, Claudin 2, and E-Cadherin expression than the SI and LI. IHC results paralleled qPCR findings, with region-specific patterns of protein localization and intensity. Computerized and pathologist-generated H-scores showed moderate agreement but differed notably between epithelial and lamina propria regions. This study provides a comprehensive baseline of microbial and host factors associated with gut health in a uniquely diverse population of feedlot cattle. The identification of regional microbial communities and distinct TJP expression patterns offers foundational insights into gastrointestinal physiology and barrier function. This work establishes baseline data to support future investigations into the relationships among microbial ecology, epithelial barrier function, and cattle health and productivity.},
}

Animals
Cattle
*Tight Junction Proteins/metabolism/genetics
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Rumen/microbiology/metabolism
Male
Tight Junctions/metabolism
Bacteria/genetics/classification

@article {pmid41202998,
year = {2025},
author = {Kuang, B and Yang, W and Li, C and Lee, CW and Liu, BY and Bong, CW and Wang, W and Chen, S},
title = {Long-Term Oral Administration of Inactivated Vibrio harveyi Vaccine Triggers Immunosuppression in Penaeus vannamei.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110983},
doi = {10.1016/j.fsi.2025.110983},
pmid = {41202998},
issn = {1095-9947},
abstract = {This study investigated optimal oral vaccination strategies to enhance Vibrio resistance in Penaeus vannamei by comparing two feeding regimens: continuous administration of inactivated Vibrio harveyi (IVH) (CF group) and intermittent IVH feeding (7-day IVH followed by 7-day commercial feed, IF group). Results demonstrated that 7-day IVH feeding effectively induced anti-Vibrio immunity. The IF group maintained >60% relative percent survival (RPS) during challenge tests at 14, 21 and 28 days post-immunization, whereas the CF group exhibited a sharp RPS decline to -22.73% at day 14, with persistently low values thereafter. Specific growth rates were significantly reduced in the CF group compared to controls. Immune enzymatic activity analysis at day 14 revealed sustained high levels in the IF group but marked declines in the CF group. Histopathological examination confirmed severe cellular necrosis in intestinal and hepatopancreatic tissues of the CF group at day 14. Gut microbiota analysis indicated comparable dominant taxa between groups at day 14, while the IF group exhibited higher proportions of Ruegeria genera. Proteomic profiling identified distinct expression patterns between groups, with the CF group displaying significant downregulation of proteins associated with energy metabolism, immune responses, metabolic pathways, and cell/tissue maintenance. These data demonstrated that continuous IVH feeding elicited substantial physiological stress, leading to cellular and tissue damage and consequent immunosuppression in P. vannamei, whereas intermittent feeding mitigated immune impairment and conferred V. harveyi resistance. This study highlights the critical need for temporally optimized vaccination protocols in shrimp aquaculture.},
}

@article {pmid41202458,
year = {2025},
author = {Biswas, A and Saini, N and Chivukula, N and Samal, A and Jansari, MR and Bhadury, P and Darbha, GK},
title = {The dawn of a new air pollutant: inhalable microplastics as emerging vectors of hazardous contaminants and their implications for human health.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109897},
doi = {10.1016/j.envint.2025.109897},
pmid = {41202458},
issn = {1873-6750},
abstract = {This study presents the first comprehensive research on inhalable microplastics (iMPs, <10 μm), a notorious subset of airborne microplastics (AMPs). To identify human health risk, ambient iMPs concentrations were assessed at human breathing height across the markets of four major Indian cities. With winter evening being the highest iMPs concentration, in Kolkata (14.23 µg/m[3]), followed by Delhi (14.18 µg/m[3]), linked to the highest footfalls, use of synthetic clothing, and poor waste management. Coastal cities (Chennai: 4 µg/m[3], and Mumbai: 2.65 µg/m[3]) showed lower levels, likely due to improved air circulation, less winter, and reduced apparel, confirmed by Principal Component Analysis. Py-GC-MS quantified 11 polymers, with PET (Polyester) from textiles as the most abundant, followed by PE and SBR from single-use plastics, packaging, vehicles, and footwear. Urban areas in India show an average iMPs concentration of 8.8 µg/m[3], translating to a lifetime lung load of ∼2.9 g/person. Furthermore, this investigation highlights the risks of iMPs-associated tracers such as diethyl phthalates and lead. This pioneering research is the first-ever study to explore AMPs carrier capabilities for ultrafine particulate matter, PTEs, POPs, PPCPs, and microbes. During peak exposure periods like autumn festivals, AMPs harbored diverse microbial communities, including pathogenic (Aspergillus fumigatus) and new strains of bacteria/fungi with antibiotic resistance and virulence factor genes. This suggests that microbes carried by iMPs possess enhanced pathogenicity and resistance against broad-spectrum drugs like tetracycline and are more likely to be multidrug-resistant. Cross-referencing toxicological databases revealed that exposure to AMPs-linked modern-day contaminants elevates the risk of cancer, gastrointestinal, endocrine, breast, and respiratory diseases.},
}

@article {pmid41201519,
year = {2025},
author = {López-Sandoval, DC and Fernández-González, C and González-García, C and Marañón, E},
title = {Warming Accelerates Phytoplankton Bloom Dynamics and Differentially Affects the Fluxes of Carbon, Nitrogen, and Oxygen Through a Coastal Microbial Community.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {117},
pmid = {41201519},
issn = {1432-184X},
support = {Project POLARIS (PGC2018-094553-B-I00)//Spanish Ministry of Science and Innovation/ ; },
mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; *Phytoplankton/growth & development/metabolism ; *Oxygen/metabolism ; *Microbiota/physiology ; Seawater/microbiology/chemistry ; Biomass ; *Eutrophication ; Carbon Cycle ; Ecosystem ; Global Warming ; Hot Temperature ; },
abstract = {Marine heatwaves affect the abundance and community structure of microbial plankton, with implications for food web and ecosystem processes, but their impact on microbially mediated elemental cycling remains poorly constrained. To determine the biogeochemical effects of increased temperature, we conducted an experiment in September 2023 in which a plankton community from a coastal, productive ecosystem (Ría de Vigo, NW Iberia) was exposed to a warming of + 2 °C and + 4 °C under unamended and nutrient-enriched conditions. The response of microbial plankton was characterized in terms of organic matter production, carbon fixation, nitrogen uptake, and oxygen net production. We found that warming caused increased nutrient consumption and biomass production, as well as faster bloom dynamics, both in unamended and nutrient-enriched treatments, indicating that the community was robust to thermal perturbation. Accelerated nutrient depletion under warming gave way to an earlier decrease in carbon fixation and nitrate uptake rates, together with a shift towards a negative or less positive metabolic balance. Carbon fixation was less sensitive than nitrate uptake to the different temperature and nutrient scenarios, leading to wide changes in the carbon-to-nitrogen uptake ratio, while respiration increased non-linearly with temperature. Overall, the investigated microbial fluxes were more responsive to nutrient availability than to temperature. Our results show that microbially driven ecosystem services in coastal waters have the potential to be enhanced during short-term warming events.},
}

*Nitrogen/metabolism
*Carbon/metabolism
*Phytoplankton/growth & development/metabolism
*Oxygen/metabolism
*Microbiota/physiology
Seawater/microbiology/chemistry
Biomass
*Eutrophication
Carbon Cycle
Ecosystem
Global Warming
Hot Temperature

@article {pmid41199522,
year = {2025},
author = {Chen, HJ and Liu, Y and Zhong, YS and Li, MZ and Lai, JJ and Luo, YY and Huang, SL and Liu, SQ and Yu, GH and Sun, YH and Shao, MW},
title = {Modulating Surfactin Biosynthesis in Bacillus subtilis R31 Enhances Behavioural Traits and Biocontrol Efficacy Against Banana Fusarium Wilt.},
journal = {Microbial biotechnology},
volume = {18},
number = {11},
pages = {e70261},
doi = {10.1111/1751-7915.70261},
pmid = {41199522},
issn = {1751-7915},
support = {202206010083//Guangzhou Municipal Science and Technology Project/ ; 2021ZDJS002//Guangdong Province Key Discipline Research Capacity Enhancement Project/ ; 32302450//National Natural Science Foundation of China/ ; 22-035-31-23KF03//Guangxi Key Laboratory of Crop Pest Biology Foundation/ ; 2023B0202010012//Guangdong Province Key Area Research and Development Program/ ; },
mesh = {*Fusarium/growth & development/drug effects/physiology ; *Bacillus subtilis/genetics/metabolism/physiology ; *Plant Diseases/microbiology/prevention & control ; *Musa/microbiology ; *Lipopeptides/biosynthesis/pharmacology ; *Peptides, Cyclic/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metabolic Engineering ; Quorum Sensing ; Rhizosphere ; Biofilms/growth & development ; Bacterial Proteins/genetics/metabolism ; DNA, Ribosomal/chemistry/genetics ; },
abstract = {Surfactin, a lipopeptide antibiotic and quorum-sensing (QS) mediator from Bacillus subtilis, has dual functions in microbial ecology and plant disease suppression. This study engineered B. subtilis R31 to overproduce comK and phrC, key regulators of surfactin biosynthesis, increasing surfactin yield by 45% compared to the WT strain. While elevated surfactin enhanced antimicrobial potential, comK-mediated overproduction impaired biofilm formation and swarming motility, but rhizosphere colonisation was mostly unaffected. 16S rRNA sequencing of banana rhizospheres showed that surfactin selectively shaped the microbial community by enriching beneficial Bacillus species. Mechanistic studies confirmed surfactin's dual role as an antimicrobial and an intercellular signalling molecule for coordinated development in Bacillus populations. These results reveal the molecular mechanisms of R31-mediated suppression of banana Fusarium wilt and offer a strategy for engineering synthetic microbial consortia by manipulating metabolic signalling pathways.},
}

*Fusarium/growth & development/drug effects/physiology
*Bacillus subtilis/genetics/metabolism/physiology
*Plant Diseases/microbiology/prevention & control
*Musa/microbiology
*Lipopeptides/biosynthesis/pharmacology
*Peptides, Cyclic/biosynthesis
RNA, Ribosomal, 16S/genetics
Metabolic Engineering
Quorum Sensing
Rhizosphere
Biofilms/growth & development
Bacterial Proteins/genetics/metabolism
DNA, Ribosomal/chemistry/genetics

@article {pmid41197919,
year = {2025},
author = {Mohit, and Verma, S and Venkatesh, V and Nityanand, S},
title = {Immuno-Microbial Crosstalk in Aplastic Anemia: Role of Gut and Viral Triggers.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108158},
doi = {10.1016/j.micpath.2025.108158},
pmid = {41197919},
issn = {1096-1208},
abstract = {Aplastic anemia (AA) is a rare but life-threatening hematological disorder, manifested in bone marrow failure and pancytopenia, which occurs worldwide due to the preferential immune mediated destruction of hematopoietic stem and progenitor cells. Despite the autoimmune etiology of AA, recent findings emphasize the key role of microbial and viral factors in the pathogenesis of AA by driving the host immune dysregulation. We delve into the immune-microbial crosstalk that is relevant in AA pathogenesis to provide novel insights related to gut microbial ecology, microbial metabolites, viral infections mediated inflammation and cytotoxicity against bone marrow components. Additionally, providing the roadmap of current knowledge for immune-mediated bone marrow failure focusing on activated cytotoxic T cells, altered regulatory T cells and proinflammatory cytokines. Imbalanced immune activation via defects in gut barrier function which promotes pathogen-associated molecular patterns (PAMPs) signaling through Toll-like receptors (TLRs) and other innate sensors. Considering the role of viral trigger such as Parvovirus B19, Epstein-Barr and Hepatitis as inducers of dysregulated immunity and their ability to affect antigen presentation, T cell receptor repertoires, and interferon pathways. We also delineate the potential of targeting the gut-immune axis for personalized AA therapy, including potential microbiome-directed interventions, antiviral and anti-cytokine approaches, as promising complement lines for standard immunosuppression therapy in AA. This cited approach will provide the advanced and novel clinical paradigm for the interconnected immune-microbial signals in pathogenesis of AA which promotes the host immune surveillance and also lead to precision medicine in AA treatment.},
}

@article {pmid41197741,
year = {2025},
author = {Chen, Y and Chen, Y and Hu, C and Xing, X and Zhang, S and Zeng, K and Yin, Z and Meng, C and Situ, F and Li, J and Chen, C and Ma, K and Chen, J and Li, F},
title = {Simultaneous control of disinfection by-products, opportunistic pathogens, and antibiotic resistance genes in drinking water based on a novel advanced treatment process consisting of Fenton-like reaction and biological activated carbon.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133602},
doi = {10.1016/j.biortech.2025.133602},
pmid = {41197741},
issn = {1873-2976},
abstract = {Disinfection by-products (DBPs), opportunistic pathogens (OPs), and antibiotic resistance genes (ARGs) are typical drinking water quality risks today, and the synchronous control of these factors has always been an important challenge. Herein, a novel drinking water treatment process (Fe3C-NC/PMS-BAC) consisting of Fe3C-NC Fenton-like reaction and biological activated carbon (BAC) was established in this study. Fe3C-NC/PMS caused the decomposition of high molecular weight organic matter into low molecular weight organic matter, which was efficiently biodegraded in the subsequent BAC biofilter (PBAC). In addition, the suspended extracellular polymeric substances (EPS) in the effluent of PBAC contained only a small amount of polysaccharides, markedly weakening the biofilm stability and its protective effect against OPs. The changes in organic matter and EPS ultimately led to the reduction of DBPs precursors. More importantly, the Fe3C-NC/PMS treatment remarkably changed the microbial ecology in subsequent PBAC, including shaping the microbial community, regulating EPS characteristics, weakening quorum sensing, and even inhibiting microbial activities, contributing to the inhibition of horizontal gene transfer of ARGs. Therefore, the Fe3C-NC/PMS-BAC is a promising alternative to BAC treatment for future applications, providing new ideas for the collaborative removal of chemical and microbial water quality risks in drinking water.},
}

@article {pmid41194431,
year = {2025},
author = {Truant, A and Giacometti, F and Losasso, C and Peruzzo, A and Petrin, S and Zancato, I and Di Leva, V and Giaccone, V},
title = {First Metataxonomic Characterisation of Gut Microbiota of Swordfish (Xiphias gladius).},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70199},
doi = {10.1111/1758-2229.70199},
pmid = {41194431},
issn = {1758-2229},
mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Perciformes/microbiology ; Phylogeny ; *Fishes/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Biodiversity ; },
abstract = {Swordfish (Xiphias gladius) is a large, migratory apex predator with a carnivorous diet, occupying a top position in the marine food chain. Although it is a valuable teleost pelagic fish with a significant commercial value, its gut microbiota has never been studied. The gut microbiota of 100 individuals was characterised by sequencing the V3-V4 region of the bacterial 16S rRNA gene. Gut microbiota findings were classified with consideration to diversity, taking into account their weight (10-20; 21-30; over 31 kg) and the FAO fishing areas in which they were caught (FAO 27, 34, 37.1.1 areas). Significant differences in the alpha diversity were observed among the weight categories for all metrics examined (except for the evenness index) and only by Shannon's index among the FAO fishing areas. Beta-diversity analysis revealed no significant differences. The phylum Pseudomonadota dominated the swordfish gut microbiota, followed by Fusobacteriota. Photobacterium was the most abundant genus across all weight categories and FAO fishing areas. Smaller fishes showed a less rich and diverse gut microbiota, dominated almost exclusively by Photobacterium. Conversely, Pseudoalteromonas, Psychrobacter, Psychrilyobacter, and Cetobacterium appeared to increase in abundance with fish weight. Although Photobacterium was dominant across the different FAO fishing areas, distinctive microbial community compositions were observed: Cetobacterium was more prevalent in FAO 27, while Pseudoalteromonas was more prevalent in the other areas. Unlike the gut microbiota of other marine fish species, Vibrio and Lactobacillus were largely absent. This study represents the first metataxonomic characterisation of the gut microbiota of swordfish using next-generation sequencing.},
}

Animals
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Perciformes/microbiology
Phylogeny
*Fishes/microbiology
DNA, Bacterial/genetics
Sequence Analysis, DNA
Biodiversity

@article {pmid41193960,
year = {2025},
author = {Van Goethem, MW and Vikram, S and Cowan, DA and Makhalanyane, TP},
title = {Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {994},
pmid = {41193960},
issn = {1471-2164},
}

@article {pmid41193926,
year = {2025},
author = {Wei, N and Nakaji-Conley, M and Tan, J},
title = {Contrasting Diversity and Network Dynamics of Soil Fungal Functional Groups in the Plant Rhizosphere.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {116},
pmid = {41193926},
issn = {1432-184X},
support = {2300058//Directorate for Biological Sciences/ ; 2300057//Directorate for Biological Sciences/ ; E455990101//Wuhan Botanical Garden, Chinese Academy of Sciences/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification/physiology ; Mycorrhizae/genetics/classification/isolation & purification ; *Biodiversity ; *Plants/microbiology ; Microbiota ; Soil/chemistry ; Plant Roots/microbiology ; },
abstract = {Soil microbiomes, critical for plant productivity and ecosystem functioning, mediate essential functions such as pathogenesis, mutualism, and decomposition through different fungal functional groups. Yet, our understanding of the dynamics of co-existing soil fungal functional groups in the rhizosphere remains limited. By leveraging urban farming-featuring fields of different ages and multiple genotypes-we tracked the relative abundance, richness, and microbial networks of putative plant pathogenic fungi, mycorrhizal fungi, and saprotrophic fungi across fields over two years. We observed an increase in the relative abundance of putative plant pathogenic fungi in the rhizosphere in older fields relative to younger fields, supporting the prediction of pathogen accumulation over time. In contrast, there was a decrease in the relative abundance of mycorrhizal fungi in older fields. The relative abundance of saprotrophic fungi remained similar between younger and older fields. While the richness of putative plant pathogenic fungi and saprotrophic fungi was similar across the examined fields, the community structure of both groups differed between younger and older fields. For mycorrhizal fungi, the richness declined in older fields and over the two years. These dynamics led to distinct microbial networks, with decreased network links for mycorrhizal fungi and increased links for saprotrophic fungi in older fields, whereas the links for plant pathogenic fungi remained similar across fields. Our study reveals contrasting dynamics of essential soil fungal functional groups in the rhizosphere and provides predictive insight into the potential shifts in soil function and their impact on plant productivity.},
}

*Rhizosphere
*Soil Microbiology
*Fungi/classification/genetics/isolation & purification/physiology
Mycorrhizae/genetics/classification/isolation & purification
*Biodiversity
*Plants/microbiology
Microbiota
Soil/chemistry
Plant Roots/microbiology

@article {pmid41193719,
year = {2025},
author = {Sugden, S and Davis, CL and Quinn, MW and Whyte, LG},
title = {Current and projected effects of climate change in cryosphere microbial ecosystems.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41193719},
issn = {1740-1534},
abstract = {Cold environments, including glaciers, ice sheets, permafrost soils and sea ice, are common across the surface of the Earth. Despite the challenges of life at subzero temperatures, the global cryosphere hosts diverse microbial communities that support biogeochemical cycling and ecosystem functioning in areas where few other organisms can survive. However, the composition and function of cryosphere microbial communities, and the continued existence of cryosphere habitats, are threatened by ongoing climate change, which has disproportionate impacts in polar regions. In this Review, we survey the breadth of cryosphere habitats and the composition, function and unique adaptations of the microbial communities that inhabit them. We outline how climate change can affect these communities and the ecosystem services they provide through short-term changes in substrate availability, enzyme activity and redox potentials as well as longer-term changes in community composition. We also explore the wide-ranging consequences these changes may have for local ecosystems, human communities and the global climate. Finally, we outline the knowledge gaps in cryosphere microbial ecology that contribute to uncertainties about the future of these ecosystems in a warming world.},
}

@article {pmid41192073,
year = {2025},
author = {McDonagh, F and Kovarova, A and Tumeo, A and O'Connor, A and McEvoy, N and Lonappan, AM and Venkateswaran, K and Murray, EK and Hallahan, B and Miliotis, G},
title = {Complete genome and comparative genomic analysis of cefpodoxime resistant Pantoea septica strain GABEPS69 isolated from saliva of a patient diagnosed with treatment resistant schizophrenia.},
journal = {International journal of medical microbiology : IJMM},
volume = {321},
number = {},
pages = {151681},
doi = {10.1016/j.ijmm.2025.151681},
pmid = {41192073},
issn = {1618-0607},
abstract = {OBJECTIVES: This study aims to generate the first complete genome of Pantoea septica and provide a thorough genomic characterisation of this under-documented species. The study seeks to enhance understanding of P. septica, clarifying features relevant to opportunistic infection in vulnerable cohorts.

METHODS: P. septica GABEPS69 was an opportunistic coloniser isolated from the saliva of a patient prescribed the antipsychotic clozapine, leading to a dysbiotic oral microbiome. A hybrid sequencing approach yielded a closed genome comprising a 4.1 Mb chromosome and six plasmids. Phenotypic susceptibility was determined by disk-diffusion and minimum inhibitory concentration (MIC) assays. Its chromosomal and plasmidic content was bioinformatically analysed alongside all canonical GenBank available P. septica genomes and the type strains of taxonomic neighbours Pantoea piersonii and "Pantoea latae", with focus on virulence-factors (VFs), antimicrobial-resistance-genes (ARGs), metal-resistance-genes (MRGs) and biosynthetic gene clusters.

RESULTS: GABEPS69 exhibited a narrow resistance spectrum, displaying resistance to the third-generation cephalosporin cefpodoxime. Plasmid pGABEPS69_1 harboured an aerobactin pathogenicity island homologue; a locus implicated in enhanced virulence, that was also identified across most other P. septica genomes and in the closely related human-pathogen Pantoea piersonii. A conserved chromosomal class-A β-lactamase homologue was also identified. Additionally, a universal presence of bioactive thiopeptide biosynthetic-gene-clusters was observed in P. septica genomes, suggesting a potential role in microbiome modulation.

CONCLUSION: This study presents a first complete genome of P. septica, revealing its genomic architecture, resistance, and virulence potential. Detailed plasmid analysis and comparative genomics enhance our understanding of the species clinical relevance and microbiome-modulating capacity. These findings motivate surveillance of transient oral microbiota in at-risk populations, including patients receiving clozapine.},
}

@article {pmid41191617,
year = {2025},
author = {Rivas-Santisteban, J and Fernández-González, N and Laso-Pérez, R and Tamames, J and Pedrós-Alió, C},
title = {Picoplankton nitrogen guilds in the tropical and subtropical oceans: From the surface to the deep.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335222},
doi = {10.1371/journal.pone.0335222},
pmid = {41191617},
issn = {1932-6203},
mesh = {*Nitrogen/metabolism ; Oceans and Seas ; Ecosystem ; *Nitrogen Cycle ; Tropical Climate ; *Plankton/metabolism ; Seawater/microbiology ; *Phytoplankton/metabolism ; },
abstract = {Ecological guilds quantify the incidence and extent of resource transformation functions, irrespective of the species involved. Therefore, tackling the microbial nitrogen guilds is key to our understanding of the oceanic nitrogen cycle, but quantitative estimates of guild contribution across varying depths and under specific environmental conditions have yet to be accomplished. In this study, we examine the main picoplankton guilds participating in nitrogen cycling within the low and mid-latitude ocean ecosystems, from the surface down to 4000 m, using data obtained from 75 samples belonging to 11 stations in the Malaspina dataset. In particular, we used a quantitative approach to investigate the stability of nitrogen acquisition and nitrogen-redox guilds separately. Our results showed that nitrogen acquisition guilds are more stable and redundant than nitrogen-redox guilds across depths and site specific conditions. For example, differential conditions such as nitrogen depletion and oxygen availability affected the two groups of guilds in different ways. These findings have implications for the understanding of global nitrogen fluxes and the biosphere's functional diversification.},
}

*Nitrogen/metabolism
Oceans and Seas
Ecosystem
*Nitrogen Cycle
Tropical Climate
*Plankton/metabolism
Seawater/microbiology
*Phytoplankton/metabolism

@article {pmid41188621,
year = {2025},
author = {Kwon, SL and Seo, CW and Kwon, H and Cho, M and Yoo, Y and Lee, SH and Kwon, DY and Lee, YM and Heo, YM and Kim, GH and Lim, YW and Lee, D and Choi, YS and Lee, H and Kim, JJ},
title = {Exploring Multifaceted Roles of Bambusicolous Apiospora in Phyllostachys bambusoides.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {115},
pmid = {41188621},
issn = {1432-184X},
support = {2021R1A2C1011894//National Research Foundation of Korea/ ; PN24120//Korea Polar Research Institute/ ; },
mesh = {*Endophytes/genetics/physiology/classification/isolation & purification ; Symbiosis ; *Ascomycota/genetics/physiology/classification/isolation & purification ; Plant Diseases/microbiology ; Mycobiome ; Soil Microbiology ; Phylogeny ; *Cyperaceae/microbiology ; Plant Roots/microbiology ; },
abstract = {Bamboo plays a crucial role in mitigating climate change. Among various microorganisms inhabiting bamboo, Apiospora is a common bambusicolous fungus that induces black spots, functioning either as a saprobe or as a plant pathogen. However, the diversity and ecological roles of Apiospora as an endophyte in bamboo remain poorly understood. This study explored the diversity and ecological functions of bambusicolous Apiospora in Phyllostachys bambusoides forests. Bamboo samples representing different stages-young (1-year-old, without black spots), mature (aged 3 years, few black spots), and dead (with many black spots)-were collected. Mycobiome analyses across different tissues (culm, leaf, root) and environmental samples (forest soil) revealed diverse Apiospora species throughout the bamboo lifecycle. Notably, Apiospora hysterina emerged as a prevalent endophyte, inhabiting not only mature but also younger, healthier bamboo stages. Biological activity assays, including antioxidant, antifungal, and plant hormone tests, indicated that A. hysterina exhibits potential mutualistic interactions beneficial to bamboo. Conversely, genomic analyses of carbohydrate-active enzyme profiles, effector/virulence factors, and putative biosynthetic gene clusters suggested potential pathogenic capabilities that may involve secondary metabolites, though functional validation is required. These findings reveal the widespread presence of Apiospora species as endophytes from the early to senescent bamboo stages, highlighting A. hysterina's dual capacity as a symbiont and pathogen. Our study underscores the complexity of bambusicolous Apiospora's ecological roles, emphasizing the need for further investigation into its interactions with bamboo ecosystems.},
}

*Endophytes/genetics/physiology/classification/isolation & purification
Symbiosis
*Ascomycota/genetics/physiology/classification/isolation & purification
Plant Diseases/microbiology
Mycobiome
Soil Microbiology
Phylogeny
*Cyperaceae/microbiology
Plant Roots/microbiology

@article {pmid41188517,
year = {2025},
author = {Hettiarachchi, A and Tuerlings, T and Weekers, T and Marshall, L and Leclercq, N and Wood, TJ and Cejas, D and Gerard, M and Vereecken, NJ and Michez, D and Smagghe, G and Joossens, M and Vandamme, P},
title = {The Gut Microbial Community of Solitary Bees is Acquired through Host and Location Filtering.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {114},
pmid = {41188517},
issn = {1432-184X},
support = {3094785//Fonds Wetenschappelijk Onderzoek/ ; 3094785//Fonds De La Recherche Scientifique - FNRS/ ; },
mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome ; *Fungi/classification/isolation & purification/genetics ; *Bacteria/classification/genetics/isolation & purification ; Europe ; Biodiversity ; },
abstract = {Species traits and environmental conditions are among the many factors that shape bee communities. Their effective conservation is currently challenged due to global changes. The gut microbiome likely contributes to bee plasticity and resilience but is largely understudied in solitary bees. A stable core microbiome in social bees has been identified to be important for health and survival in changing environmental conditions, but knowledge on a host-specific core microbiome in solitary bees is very scarce. In the present study, we analyzed the gut bacterial and fungal communities of eight solitary bee species commonly found in apple orchards along a latitudinal gradient throughout Europe. We aimed to understand the intra- and interspecific variations in the gut microbial communities and the extent to which host species and local environment shape the solitary bee gut microbiota. The bacterial community showed strong host effects, with each bee species having a distinct core bacterial community that was mostly stable across locations. The fungal community was most strongly influenced by the local environment, while different environmental variables were responsible for the variation in bacterial and fungal communities. Our study demonstrated that the examined solitary bee species harbor a distinct microbial diversity and composition, which undergoes host- and location-specific filtering.},
}

Animals
Bees/microbiology/physiology
*Gastrointestinal Microbiome
*Fungi/classification/isolation & purification/genetics
*Bacteria/classification/genetics/isolation & purification
Europe
Biodiversity

@article {pmid41059692,
year = {2025},
author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF},
title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0258324},
pmid = {41059692},
issn = {2165-0497},
support = {1559356, 2129697, 1736030//National Science Foundation/ ; Investigator Award in Marine Microbial Ecology and Evolution//Simons Foundation/ ; },
mesh = {*Genome, Viral/genetics ; Phylogeny ; Pacific Ocean ; *Genetic Variation ; Phytoplankton/virology ; Seawater/virology ; *Chlorophyta/virology ; *Phycodnaviridae/genetics/classification/isolation & purification ; *DNA Viruses/genetics/classification/isolation & purification ; },
abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.},
}

*Genome, Viral/genetics
Phylogeny
Pacific Ocean
*Genetic Variation
Phytoplankton/virology
Seawater/virology
*Chlorophyta/virology
*Phycodnaviridae/genetics/classification/isolation & purification
*DNA Viruses/genetics/classification/isolation & purification

@article {pmid41187907,
year = {2025},
author = {Marrec, L and Bank, C},
title = {Drivers of diversity within and between microbial communities during stochastic assembly.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {232},
pages = {20250329},
doi = {10.1098/rsif.2025.0329},
pmid = {41187907},
issn = {1742-5662},
support = {//HORIZON EUROPE European Innovation Council/ ; //Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Microbiota/physiology ; *Models, Biological ; Stochastic Processes ; *Biodiversity ; },
abstract = {No two microbial communities share the same species richness and abundance profiles. Experiments have shown that the assembly of new microbial communities from the same environmental pool is sufficient to generate diversity within and between communities: when microbial dispersal is slower than division, communities exhibit low richness but high between-community dissimilarity; when dispersal is faster, richness increases while dissimilarity decreases. Here, we study a minimal stochastic model that recovers these empirically observed assembly regimes. Our mathematical framework yields explicit expressions for the abundance fluctuation distributions across low-, intermediate- and high-dispersal regimes, providing a quantitative lens on microbiome assembly. We derive analytical predictions for the bimodality coefficient that quantifies the transition between assembly regimes, which appears as a robust metric to predict community richness and dissimilarity. Additionally, we highlight the mean relative abundance as a complementary metric sensitive to differences in microbial traits (e.g. dispersal or division rates). Applying these metrics to experimental data indicates their practical value for the rapid identification of assembly regimes and trait asymmetries. Overall, our study provides general predictions about how stochasticity, timescales and microbial traits influence both within-community diversity (richness) and between-community diversity (dissimilarity) during the assembly of new microbial communities. Our work thus contributes to a better understanding of the factors driving variation in microbiome formation.},
}

*Microbiota/physiology
*Models, Biological
Stochastic Processes
*Biodiversity

@article {pmid41185310,
year = {2025},
author = {Wu, S and Li, Y and Zhang, H and Pan, Y and Yang, H and Tan, Y},
title = {Microbial community reshaping: Calcium chloride-heat treatment synergy in fresh-cut jackfruit preservation via antagonistic yeast enrichment.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117558},
doi = {10.1016/j.foodres.2025.117558},
pmid = {41185310},
issn = {1873-7145},
mesh = {*Calcium Chloride/pharmacology ; *Food Preservation/methods ; *Hot Temperature ; *Food Microbiology/methods ; *Fruit/microbiology ; *Artocarpus/microbiology ; Penicillium/drug effects/growth & development ; *Yeasts/drug effects/growth & development ; Antibiosis ; },
abstract = {Fresh-cut jackfruit is highly susceptible to microbial contamination and rapid spoilage due to mechanical damage and its nutrient-rich substrate. We evaluated calcium chloride combined with heat treatment (CH, 2 % CaCl2 - 55 °C) for controlling spoilage and preservation of fresh-cut jackfruit. The results identified Gilbertella hainanensis, Penicillium kongii, and P. citrinum as the dominant spoilage fungi in fresh-cut jackfruit. CH inhibited these fungi with in vitro inhibition rates of 80.14 %, 43.75 %, and 52.94 %, and corresponding in vivo rates of 83.1 %, 77.9 %, and 83.7 %, respectively. In vitro assays indicated CH compromises fungal membrane integrity, causing leakage of cellular contents. Further analysis revealed that CH markedly increased the relative abundance of the antagonistic yeast Meyerozyma guilliermondii (42.82 %, 8.13-fold vs. control) and was associated with reduced relative abundance of plant pathogenic and saprotrophic fungi. Correlation analysis linked dominant yeast genera to higher total phenolic content and reduced weight loss and other quality deterioration. Overall, CH treatment effectively delayed spoilage and preserved fruit physicochemical and nutritional quality, likely via direct antifungal effects and beneficial reshaping of the surface microbiome. These findings advance understanding of jackfruit postharvest microbial ecology and CH as a promising preservation strategy for fresh-cut jackfruit fruit.},
}

*Calcium Chloride/pharmacology
*Food Preservation/methods
*Hot Temperature
*Food Microbiology/methods
*Fruit/microbiology
*Artocarpus/microbiology
Penicillium/drug effects/growth & development
*Yeasts/drug effects/growth & development
Antibiosis

@article {pmid41184333,
year = {2025},
author = {Ghosh, A and Maile, A and Nagarajaram, HA},
title = {Prokaryotic co-occurrence patterns in diverse Indian mangrove ecosystems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38283},
pmid = {41184333},
issn = {2045-2322},
mesh = {India ; *Wetlands ; Biodiversity ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Soil Microbiology ; },
abstract = {Mangrove ecosystems are unique coastal zones known to harbour a rich biodiversity of flora and fauna, including microbial communities. These microorganisms play a crucial role in nutrient cycling and sustain the primary productivity driven by plants within this ecosystem. Recent advancements in microbial ecology research emphasise that microbial community structure and composition are critical for an ecosystem to thrive. Studies have focused on the microbial diversity within Indian mangrove forests; however, there is a limited understanding of the co-occurrence patterns and functional roles of microbial communities in these ecosystems. This study explores prokaryotic diversity, primarily focusing on community interactions across three major Indian mangrove forests: the Bhitarkanika mangrove forest in Odisha, the Goan mangroves, and the Sundarbans in West Bengal. By analysing the publicly available 16 S rRNA amplicon datasets of the Indian mangrove microbiomes and performing co-occurrence network analysis on these datasets, we identified positively correlated genera and their predicted functional roles. Furthermore, the findings revealed the co-occurrence of several pathogenic bacteria in two of the mangrove ecosystems. Overall, our study highlights the shared functional roles adopted by co-occurring microbes in three major Indian mangrove ecosystems and suggests the need for large-scale studies in these understudied Indian ecosystems.},
}

India
*Wetlands
Biodiversity
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Ecosystem
Phylogeny
Soil Microbiology

@article {pmid41183683,
year = {2025},
author = {Ali, S and Burke, LP and Fitzpatrick, F and Fitzgerald-Hughes, D},
title = {A Scoping Review of Disinfection Strategies for Carbapenemase-Producing Enterobacterales (CPE) in Hospital Water Systems.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.10.021},
pmid = {41183683},
issn = {1532-2939},
abstract = {BACKGROUND: Carbapenemase-producing Enterobacterales (CPE) pose a global health crisis. Their resistance to conventional antimicrobials and many disinfectants, increases the healthcare costs of treatment and risk mitigation. Hospital water systems are reservoirs for CPE, necessitating targeted infection prevention and control (IPC) strategies.

OBJECTIVE: To review and consolidate current evidence of disinfection strategies for CPE in hospital water systems, focusing on practical application, challenges and IPC integration.

METHODOLOGY: A scoping review was conducted following PRISMA guidelines, encompassing studies from 1[st] December 2014 to 31[st] December 2024. Of 1,188 records screened, 22 met inclusion criteria. Thematic analysis categorised findings into chemical, physical and integrative strategies.

KEY FINDINGS: Sodium hypochlorite and hydrogen peroxide reduced contamination temporarily but were poorly effective against biofilms, while acetic acid showed consistent efficacy with regular use. Quaternary ammonium compounds proved effective but required standardised protocols. Physical interventions, such as steam cleaning and drain covers, reduced contamination; and plumbing modifications minimised biofilm formation. Resource-intensive measures, like removing contaminated sinks or adopting water-free environments were also effective. Integrative approaches combining chemical disinfection, infrastructural upgrades and enhanced sink protocols demonstrated the most sustained outcomes, with novel technologies like UV light and biofilm-targeting foams showing great promise.

CONCLUSION: Effective CPE control in hospital water systems requires multidisciplinary action addressing biofilm-protected reservoirs. Regular application of proven disinfectants, tailored to specific contexts, coupled with infrastructural upgrades and comprehensively implemented IPC strategies, offers the most promising outcomes. Novel technologies and updated guidelines are essential to standardising practices and mitigating the broader threat of antimicrobial resistance.},
}

@article {pmid41180493,
year = {2025},
author = {Choi, JM and Wu, X and Zhang, L},
title = {FastST: an efficient tool for inferring decomposition and directionality of microbial communities.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20161},
pmid = {41180493},
issn = {2167-8359},
mesh = {*Microbiota ; Humans ; Bayes Theorem ; Computer Simulation ; *Software ; *Computational Biology/methods ; },
abstract = {Microbiomes play crucial roles in human health, disease development, and global ecosystem functioning. Understanding the origins, movements, and compositions of microbial communities is essential for unraveling the principles governing microbial ecology. Microbial source tracking (MST) approaches have emerged as valuable tools for quantifying the proportions of different microbial sources within target communities, enabling researchers to track transmissions between hosts and environments, identify similarities between microbiome samples, and determine sources of contamination in various settings. Current MST methods like SourceTracker2 and FEAST have advanced the field by employing Bayesian and expectation-maximization approaches, respectively, but are limited by computational inefficiency with high-dimensional data and inability to infer directionality in source-sink relationships. This study presents a novel computational framework for microbial source tracking called FastST. FastST infers the relative contributions of source environments to sink microbiomes while also determining directionality when source-sink relationships are not predefined. Through extensive simulation studies with varying numbers of sources and complexity, FastST demonstrates superior performance in both accuracy and computational efficiency compared to FEAST and SourceTracker2, maintaining consistent execution times even as the number of source environments increases. Furthermore, the proposed method achieved over 90% accuracy in directionality inference across all tested scenarios, even when multiple major sources are present, broadening its applicability in practical microbiome research and environmental monitoring. FastST and data simulation codes are publicly available at https://github.com/joungmin-choi/FastST.},
}

*Microbiota
Humans
Bayes Theorem
Computer Simulation
*Software
*Computational Biology/methods

@article {pmid41178963,
year = {2025},
author = {Whitehead, K and Eppinger, J and Srinivasan, V and Ugalde, JA},
title = {Microbial cross contamination in household laundering and microbial ecology of household washing machines.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667606},
pmid = {41178963},
issn = {1664-302X},
abstract = {Household washing machines host diverse microbial communities that may include opportunistic pathogens, potentially impacting laundry hygiene and human health. However, our understanding of these communities and their transfer abilities remains limited. We examined microbial communities from 10 household washing machines (five front-load and five top-load) using surface swabs from specific hotspots and sterile sentinel washcloths. Samples were analyzed using culture-based methods and 16S rRNA/ITS metabarcoding. We tested microbial transfer during washing cycles with and without clothing and evaluated the effects of machine drying on this transfer. Front-load machines had significantly higher microbial loads than top-load machines (average bacterial counts: 6.50 ± 2.46 Log10/swab vs. 3.79 ± 1.73 Log10/swab). The microbial community composition was mainly shaped by the machine user rather than the machine type or sampling location. The dominant bacterial genera included Pseudomonas, Micrococcus, and Sphingomonas, while Aspergillus, Cladosporium, and Penicillium dominated the fungal communities. Opportunistic microorganisms were identified, but no highly pathogenic species (pathogenicity score 3) were found. Machine drying did not significantly decrease microbial loads, whereas the presence of soiled clothing impacted community composition. Household washing machines host user-specific microbial communities, including potential opportunistic pathogens. Current laundry practices may be inadequate for the complete elimination of pathogens, especially in immunocompromised individuals. These results support the need for additional household laundry sanitization strategies.},
}

@article {pmid41177050,
year = {2025},
author = {Su, F and Li, Y and Zhu, C and Gurmesa, GA and Fang, Y},
title = {Impact of freeze-thaw cycle on metagenomics in subsurface wastewater infiltration systems: Ecological implications for greenhouse gas emissions.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127839},
doi = {10.1016/j.jenvman.2025.127839},
pmid = {41177050},
issn = {1095-8630},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, with a global warming potential 273 times that of carbon dioxide (CO2) and is a significant byproduct of wastewater treatment. Subsurface wastewater infiltration systems (SWIS) effectively treat nitrate-rich wastewater but can also contribute to N2O emissions, particularly during freeze-thaw cycles. This study used metagenomics and [15]N isotope tracing to investigate the impacts of freeze-thaw on microbial ecology and nitrogen transformation in SWIS. Results show that freeze-thaw significantly increased abundances of denitrifying bacteria (Bradyrhizobium, Streptomyces and Nocardioides), on average, by 16-63 %. Denitrification genes (nirK and norB) were also increased by 40 ± 16 % and 22 ± 5 %, while the N2O reductase gene (nosZ) decreased by 19 ± 0.46 %. These impacts collectively increased N2O emissions by more than 20 %. During freezing, about one-third of the added [15]NO3[-]-N was recovered as gas (25 % as N2O and 13 % as N2), increasing to 43 % during thawing (29 % N2O and 15 % N2). This study underscores the need for targeted strategies N2O emission in SWIS, particularly under freeze-thaw conditions, to maximize their sustainability in wastewater treatment.},
}

@article {pmid41175425,
year = {2025},
author = {Awasthi, A and Sandal, A and Mahajan, R and Kaundal, R and Sharma, N and Sharma, S},
title = {Fermentation induced changes in physicochemical properties, antioxidant activity, total sugars, and comprehensive polyphenolic profiles of the Rhododendron-infused wine blends.},
journal = {Food chemistry},
volume = {496},
number = {Pt 2},
pages = {146743},
doi = {10.1016/j.foodchem.2025.146743},
pmid = {41175425},
issn = {1873-7072},
abstract = {This study evaluated the sensory, physicochemical, and functional attributes of seven experimental wine formulations incorporating apple juice, ginger, honey or sucrose, and varying levels of Rhododendron arboreum flower juice. Sensory scores revealed significant improvements in color, aroma and sweetness in rhododendron-enriched blends, with Treatment T7 (apple + honey + ginger + R. arboreum) achieving the highest overall acceptability. Physicochemical analyses showed variations in titratable acidity (0.19-0.51 %), alcohol (9.50-11.97 %), and ascorbic acid (4.76-8.53 mg/100 mL), influenced by substrate composition and sweetener type. Inclusion of R. arboreum substantially enhanced total phenolic (up to 19.78 mg GAE/mL) and flavonoid levels (25.84 mg QE/mL) alongside targeted compounds such as quercetin and caffeic acid. Antioxidant assays also confirmed superior radical scavenging activity. Multivariate analyses highlighted strong correlations between polyphenolic content and antioxidant performance. Overall, R. arboreum addition improved both sensory appeal and functional properties, supporting its potential in functional wine development.},
}

@article {pmid41174663,
year = {2025},
author = {Waclawiková, B and Schwalbe, M and Ilyaskina, D and Toptas, S and Thome, NU and Du, C and Elsayed, SS and de Jong, A and van Wezel, GP and El Aidy, S},
title = {Serotonin modulation of metabolism and stress response in Pseudomonas fluorescens.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {330},
pmid = {41174663},
issn = {1741-7007},
mesh = {*Pseudomonas fluorescens/metabolism/physiology/genetics ; *Serotonin/metabolism/analogs & derivatives ; Oxidative Stress ; *Stress, Physiological ; },
abstract = {BACKGROUND: Pseudomonas fluorescens is a Gram-negative bacterium with a remarkable metabolic and physiological versatility that enables it to adapt and colonize diverse ecological niches, including the human small intestine. While serotonin is primarily found in high concentrations in gut tissue, its levels in the lumen can be elevated in conditions such as celiac disease, where P. fluorescens is also found in increased abundance. The potential effects of serotonin on P. fluorescens in such contexts remain unclear.

RESULTS: We demonstrate that P. fluorescens metabolizes serotonin primarily into 5-hydroxyindole-3-acetic acid (5-HIAA) and, to a lesser extent, into 5-hydroxytryptophol and N-acetylserotonin. Gene expression analysis revealed significant changes in oxidative stress-related pathways over time, and proteomic analysis confirmed the shifts seen particularly in amino acid catabolic pathways. Serotonin metabolism also enhanced bacterial resistance to oxidative stress, suggesting a protective role.

CONCLUSIONS: The findings reveal a novel mechanism by which serotonin modulates the metabolism and stress responses of P. fluorescens. This study provides insight into how P. fluorescens adapts to serotonin-rich environments, such as in celiac disease, and may inform future research on microbial interactions with host-derived metabolites in disease contexts.},
}

*Pseudomonas fluorescens/metabolism/physiology/genetics
*Serotonin/metabolism/analogs & derivatives
Oxidative Stress
*Stress, Physiological

@article {pmid41174295,
year = {2025},
author = {Afonso, AC and Simões, M and Saavedra, MJ and Simões, L and Lema, JM and Trueba-Santiso, A},
title = {Physicochemical, Structural, and Proteomic Insights into Drinking Water-Isolated Acinetobacter calcoaceticus Aggregation and Biofilm Dynamics.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {113},
pmid = {41174295},
issn = {1432-184X},
mesh = {*Biofilms/growth & development ; Proteomics ; Bacterial Proteins/metabolism/genetics ; *Acinetobacter calcoaceticus/physiology/isolation & purification/genetics ; *Drinking Water/microbiology ; *Bacterial Adhesion ; Proteome ; },
abstract = {Acinetobacter calcoaceticus, a ubiquitous Gram-negative bacterium, exhibits remarkable adaptability across diverse environments, including drinking water distribution systems (DWDS), where its biofilm-forming and coaggregation capabilities pose significant public health challenges. This study integrates physicochemical, structural, and proteomic analyses to elucidate the mechanisms underlying A. calcoaceticus aggregation and biofilm dynamics. Surface characterization through contact angle measurements, zeta potential, and co-adhesion energy assessments revealed a predominantly hydrophilic surface with strong electron donor properties and a highly negative charge, promoting intercellular adhesion. Transmission electron microscopy unveiled dense cellular aggregates with extracellular filamentous structures, indicative of enhanced cell-to-cell interactions and potential extracellular polymeric substance involvement. Proteomic profiling identified 2593 differentially expressed proteins between aggregation stages, highlighting metabolic shifts, stress response activation, and upregulation of biofilm-associated proteins, including chaperones and quorum-sensing regulators. Our multidisciplinary approach emphasizes the importance of surface characterization in understanding bacterial community and underscores the critical role of physicochemical properties and proteomic flexibility in A. calcoaceticus biofilm and aggregation ability.},
}

*Biofilms/growth & development
Proteomics
Bacterial Proteins/metabolism/genetics
*Acinetobacter calcoaceticus/physiology/isolation & purification/genetics
*Drinking Water/microbiology
*Bacterial Adhesion
Proteome

@article {pmid41174268,
year = {2025},
author = {Almansour, A and Akkaya, SN and Akbulut, S and Adiguzel, G and Yilmaz, B and Adiguzel, A},
title = {Biogenic Amine Degradation by Lactic Acid Bacteria Isolated from Home-Made White Cheese: Molecular and HPLC-Based Assessment.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41174268},
issn = {1867-1314},
abstract = {Due to the potential health risks to humans associated with biogenic amines (BAs) accumulation in cheeses and other foods, this study is the first of its kind on Erzurum home-made white cheese to investigate the presence of BA-degrading lactic acid bacteria (LAB). Polymerase chain reaction (PCR) was applied for all putative LAB strains to detect the presence of (hdcA, cadA, tdcA, and odc) genes responsible for BA formation (histamine, cadaverine, tyramine, and putrescine, respectively). Only 72% of all strains showed amplicons for hdcA and tdcA, and no strains were found to have cadA, ldc, and odc genes. High-performance liquid chromatography (HPLC) analysis confirmed these findings. Furthermore, 12% of BA-nonproducing LAB have the sufI gene responsible for Multicopper Oxidases (MCOs) production. HPLC analysis was then applied to these strains to investigate their ability to degrade BAs. Nine strains were found to have degradation abilities with optimal conditions at pH 4.5-5.5 and 32-37 °C. Importantly, analysis of twenty home-made white cheeses revealed that the levels of BAs were within safe limits. This research provides valuable insights into the microbial ecology of these cheeses and highlights the potential of utilizing indigenous LAB for controlling BA formation and improving cheese quality.},
}

@article {pmid41171124,
year = {2025},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1098},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

@article {pmid41169038,
year = {2025},
author = {Buccola, MJ and Satheesh Babu, AK and Paz, HA and Porter, ND and Srinivasan, H and Ricks, RL and Rosquist, K and Torres, JL and Zhong, Y and Jalili, T and Wankhade, UD and Anandh Babu, PV},
title = {Dietary Prebiotics Modulate Omeprazole-Induced Alterations in the Gut Microbial Signature.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70307},
doi = {10.1002/mnfr.70307},
pmid = {41169038},
issn = {1613-4133},
abstract = {Proton pump inhibitors (PPIs) are commonly used to treat heartburn and acid-related disorders. However, their misuse and prolonged use contribute to gut dysbiosis. This study investigated whether well-known prebiotic dietary sources, blueberries or strawberries, can reverse PPI (omeprazole) induced dysbiosis and gut inflammation by modulating gut microbes. Male C57BL/6J mice (7 weeks old) were fed a diet with or without omeprazole (40 mg/kg diet), blueberry (3.7% in the diet; ∼1.5 human servings) or strawberry (2.35% in the diet; ∼2 human servings) for 12 weeks. Metabolic parameters, gut microbes (in the cecum and colon), and inflammatory markers were assessed. In this study, no changes were observed in metabolic parameters in mice fed a diet supplemented with omeprazole or berries. Second, blueberry or strawberry supplementation at nutritional dosages improved alterations in gut microbial ecology induced by omeprazole, with effects varying between the cecum and colon. Third, strawberry supplementation reduced omeprazole-induced gut inflammation. Fourth, selected genera were either positively or negatively associated with markers of gut inflammation, suggesting that dietary berries can ameliorate inflammatory signaling through modifications in the gut microbiome. Dietary berries represent a potential nutritional strategy for improving PPI-induced gut dysbiosis and inflammation.},
}

@article {pmid41168937,
year = {2025},
author = {Brangarí, AC and Knorr, MA and Frey, SD and Rousk, J},
title = {Shifts in Microbial Thermal Traits Mitigate Heat-Induced Carbon Losses in Soils.},
journal = {Global change biology},
volume = {31},
number = {11},
pages = {e70579},
doi = {10.1111/gcb.70579},
pmid = {41168937},
issn = {1365-2486},
support = {2022-01478//Svenska Forskningsrådet Formas/ ; CTS 22: 2131//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; KAW 2023.0384//Knut och Alice Wallenbergs Stiftelse/ ; DEB-1832110//National Science Foundation/ ; DEB-1456610//National Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Hot Temperature ; *Carbon/metabolism/analysis ; *Global Warming ; *Carbon Cycle ; Carbon Dioxide/metabolism ; Forests ; },
abstract = {Global warming is expected to transfer carbon from soil organic matter to atmospheric CO2, with microbial communities playing a crucial role in regulating this exchange. While the immediate impact of temperature on microbial functions is well understood and causes soil carbon losses, the long-term response remains unclear, with losses stabilising over time, reducing the overall effect of chronic warming on soil organic carbon (SOC) stocks. Here, we examined the temperature dependence of microbial respiration and growth after 9 years of +5°C warming in a temperate forest. Using these temperature dependences and field temperature data, we modelled in situ carbon fluxes and changes in SOC stocks. Results showed that the direct effect of temperature initially increased respiration and growth, projecting a potential 31% SOC stock loss if the trend had persisted. However, the gradual optimisation of microbial traits to warming balanced the direct temperature effects, enhanced carbon use efficiency and offset CO2 emissions. Together, these microbial trait shifts limited the heat-induced SOC loss to 15%, closely aligning with empirical observations. These findings suggest that microbial trait optimisation can moderate carbon emissions, providing a parsimonious mechanistic explanation for observations worldwide and underscoring the need to integrate microbial dynamics into models.},
}

*Soil Microbiology
*Soil/chemistry
*Hot Temperature
*Carbon/metabolism/analysis
*Global Warming
*Carbon Cycle
Carbon Dioxide/metabolism
Forests

@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.

RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span ~ 1,075 km and nearly 10° latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n = 327) and fungi (n = 117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.

CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Tracheophyta/microbiology
Metagenome
Phylogeny
*Plant Leaves/microbiology
Pinus/microbiology

@article {pmid41168506,
year = {2025},
author = {Martinez-Urtaza, J},
title = {From clonality to complexity: a journey through microbial ecology and evolution.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {41168506},
issn = {1471-0064},
}

@article {pmid41165314,
year = {2025},
author = {Nauwynck, W and Sakarika, M and Faust, K and Boon, N},
title = {Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0135625},
doi = {10.1128/msystems.01356-25},
pmid = {41165314},
issn = {2379-5077},
abstract = {Microbial chain elongation via reverse β-oxidation offers a more sustainable route to produce medium-chain fatty acids like caproate, commodity chemicals typically produced via (petro)chemical processes. Thermophilic anaerobic microbiomes allow production at a high rate and selectivity but remain poorly understood due to the limited cultivability of their members. To better access functional taxa from a thermophilic chain-elongating reactor community, we applied multiple isolation strategies: conventional anaerobic plating, dilution-to-extinction (DTE), droplet-based microfluidics, and fluorescence-activated cell sorting (FACS). We evaluated the taxonomic range and cultivation success of each method using 16S rRNA gene sequencing. Each method yielded a distinct subset of microbial taxa. While Clostridium acetireducens-related strains were consistently isolated across all strategies, key thermophilic chain elongators (e.g., Thermocaproicibacter melissae-like organisms) only appeared in DTE. Droplet microfluidics enriched the most unique taxa in total, mostly rare taxa, including Caproicibacter and Thermoanaerobacterium spp. Plating yielded the lowest diversity, recovering only dominant taxa. FACS-based approaches failed to yield isolates, likely due to stress during processing. Comparing droplet-based isolation to DTE revealed critical insights: although droplets offer higher throughput, which intrinsically increases the chance of capturing rare taxa, not all DTE-cultivated organisms grew in droplets. This suggests additional contributing factors (apart from an increased throughput), such as encapsulation stress and droplet-specific microenvironments. These findings clarify the advantages and limitations of droplet cultivation strategies, allowing a more informed application of these techniques to access the so-called "microbial dark matter."IMPORTANCEMany environmentally and industrially relevant microbes remain uncultured, limiting our ability to understand and use them. This is especially true in thermophilic anaerobic microbiomes, which are promising systems for producing sustainable chemicals from organic waste streams. In this study, we explored how different cultivation strategies influence which microbes can be isolated from a thermophilic chain-elongating reactor. By comparing traditional and novel methods, including droplet microfluidics, we showed that each method recovers a unique set of microbes. While droplet-based methods enable high sampling depth with minimal effort and excel at isolating rare microbes, we found that they also introduce clear biases, as certain organisms recovered by other methods did not grow in droplets. Our work highlights the importance of the cultivation method in isolation success and helps shine a light on the selective forces at play in droplet-based microbial isolation.},
}

@article {pmid41165014,
year = {2025},
author = {Freudenthal, J and Schlegel, M and Bonkowski, M and Dumack, K},
title = {A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists (Amoebozoa and Rhizaria).},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70064},
doi = {10.1111/1755-0998.70064},
pmid = {41165014},
issn = {1755-0998},
support = {221301018//Deutsche Forschungsgemeinschaft/ ; 447013012//Deutsche Forschungsgemeinschaft/ ; SPP 1991//Deutsche Forschungsgemeinschaft/ ; },
abstract = {The inclusion of functional traits of protists in environmental sequencing surveys, in addition to the traditional taxonomic framework, is essential for a better understanding of their roles and impacts on ecosystem processes. We provide a database of functional traits for a widespread and important clade of protists-the Amoebozoa-based on extensive literature research in eight trait categories: Habitat, locomotion, nutrition, morphology, morphotype, size, spore formation, and disease-relatedness. The comparison of community traits of the Amoebozoa with sympatric but highly divergent Cercozoa (Rhizaria) revealed both convergent evolution of morphology or locomotion and distinct differences in habitat preference and feeding selectivity. Amoebozoa seem to be rather unselective in their prey choice compared to Cercozoa. Indeed, the feeding preferences of Amoebozoa appeared to be related to cell size, whereas Cercozoa selectively feed on prey. Applications to metatranscriptomic data from soil, litter, and bark surfaces revealed differences in the average community trait compositions and ecosystem functioning, such as an increased proportion of disease-related Amoebozoa in soil or different proportions of nutrition types of Amoebozoa and Cercozoa on bark. This database will facilitate ecological analyses of sequencing data and improve our understanding of the diversity of adaptations of Amoebozoa to the environment and their functional roles in ecosystems.},
}

@article {pmid41164406,
year = {2025},
author = {Sierra, AM and Escolástico-Ortiz, DA and Zartman, CE and Derome, N and Lovejoy, C and Villarreal A, JC},
title = {Assembly and co-occurrence networks of nitrogen-fixing bacteria associated with epiphyllous liverworts in fragmented tropical forests.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf173},
pmid = {41164406},
issn = {2730-6151},
abstract = {Understanding the spatial dynamics of plant-associated microbial communities is increasingly urgent in the context of habitat loss and the biodiversity crisis. However, the influence of reduced habitat size and connectivity on the assembly mechanisms underlying microbial associations is fundamental to advancing microbial ecology and conservation. In the Brazilian Amazon, we investigated nitrogen-fixing (diazotrophic) bacterial communities associated with two epiphyllous liverworts, Cololejeunea surinamensis and Radula flaccida, across 11 forest sites within the Biological Dynamics of Forest Fragments Project landscape. Using amplicon sequencing targeting the nitrogenase gene (nifH), we characterized diazotroph community diversity, inferred assembly mechanisms through null models, and analyzed co-occurrence network structure. Host-specific associations were evident: C. surinamensis predominantly hosted Hassallia, while R. flaccida was primarily associated with Fischerella. Despite habitat fragmentation, diazotrophic richness and composition remained similar across habitats of different sizes, consistent with strong homogenizing dispersal. Network analyses revealed that smaller fragments harbored more modular communities with fewer module hubs, pronounced shifts in key species relative abundance, and reduced network robustness. Our findings underscore the influence of habitat size on the stability of liverwort-associated diazotrophs, with smaller fragments exhibiting lower key species specificity and disruption of microbe-microbe interactions. Our results emphasize the importance of conserving large, connected forest habitats to maintain the functional integrity of phyllosphere N-fixing microbiota.},
}