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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41026185,
year = {2025},
author = {Borja-Martínez, G and de León-Lorenzana, A and Yanez-Montalvo, A and Hernández-Canchola, G and Falcón, LI and Vázquez-Domínguez, E},
title = {Evolutionary and Ecological Drivers of Gut Microbiota in Wild Rodent Species from the Yucatán Peninsula.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {100},
pmid = {41026185},
issn = {1432-184X},
support = {887756//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT)/ ; IV200421//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica-DGAPA/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mexico ; *Rodentia/microbiology/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Biological Evolution ; Biodiversity ; Symbiosis ; },
abstract = {The host-microbiome association is considered a coevolutionary process, in which the microbiome provides important functions for host development, physiology and health. However, the ecological and evolutionary forces shaping the diversity and structure of the bacterial communities that form the microbiome are still being elucidated. We assessed the composition of gut microbiota in six rodent species from three geographic regions across the Yucatán peninsula, Mexico. We evaluated the contribution of host species identity, phylogenetic relationships, and geography to the rodents' gut microbiota, using 16S rRNA V4 sequences. We performed a comprehensive set of analytical approaches, including Hill numbers, machine learning, and phylogenetic comparative frameworks. Our results show that phylosymbiosis is one of the main mechanisms driving microbiota dissimilitude across species and specific microbiota diversity traits. Additionally, the microbial pool in each region was geographically differentiated, shaped by the rodent community ensemble, while ecological filtering rendered a microbial pool characteristic of each species. The environment also played a significant role for some species like Heteromys gaumeri, while dietary habits showed a stronger signal for Oryzomys couesi. Rodents with more specialized habits like Ototylomys phyllotis (semi-arboreal, folivorous) had higher bacterial diversity. The abundance of eight bacterial families determined key differences of the gut microbiota which, in addition to phylogeny and geography, are associated with distinct diet and metabolic functions among rodents. Distinct metabolic functions were related, among others, to toxins metabolism and digestion of complex food components. Overall findings show that both evolutionary and ecological drivers influence these rodents gut microbial structure and composition.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mexico
*Rodentia/microbiology/classification
Phylogeny
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
*Biological Evolution
Biodiversity
Symbiosis

@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation & purification ; *Bacteria/classification/genetics/isolation & purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}

Animals
*Gastrointestinal Microbiome
*Bacteriophages/genetics/classification/physiology/isolation & purification
*Bacteria/classification/genetics/isolation & purification/virology
*Ecosystem
RNA, Ribosomal, 16S/genetics
*Antelopes/microbiology/virology
Metagenome
Feces/microbiology

@article {pmid41026164,
year = {2025},
author = {Yeo, IC and Shim, KY and Min, JO and Kim, JH and Ha, SY and Jeong, CB},
title = {Vertical Structure and Functional Diversity of Microbial Communities in the Ross Sea, Antarctica.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {99},
pmid = {41026164},
issn = {1432-184X},
support = {KIMST RS-2022-KS221661//Korea Institute of Marine Science and Technology promotion/ ; NRF-2022R1C1C1010575//National Research Foundation of Korea/ ; },
mesh = {Antarctic Regions ; *Seawater/microbiology/chemistry ; *Microbiota ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {The Ross Sea, Antarctica, encompasses distinct water masses, each characterized by unique physicochemical conditions influencing microbial community composition and functional diversity. This study examined microbial communities across five stations covering various water masses, including Antarctic Surface Water (AASW), Circumpolar Deep Water (CDW), and Shelf Water (SW). Despite limited horizontal variability, significant vertical structuring was observed, potentially driven by vertical microbial dispersal from surface waters. Surface communities exhibited lower alpha diversity due to abundant labile organic matter favoring fast-growing heterotrophic taxa, whereas deeper communities displayed increased microbial richness, reflecting adaptation to more refractory organic matter. Functional diversity revealed distinct depth-related patterns, with metabolic pathways associated with organic matter predominantly enriched in surface layers. Concurrently, rare taxa became more abundant with depth, emphasizing their potential role as keystone organisms in deep-ocean nutrient cycling. These findings highlight the critical role of vertical microbial connectivity and organic matter composition in shaping microbial community structure and functional specialization, contributing significantly to our understanding of microbial-mediated biogeochemical processes in polar marine ecosystems.},
}

Antarctic Regions
*Seawater/microbiology/chemistry
*Microbiota
*Biodiversity
*Bacteria/classification/genetics/isolation & purification/metabolism
Ecosystem
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid41025798,
year = {2025},
author = {Damashek, J and Sheik, CS and Petro, C and Reeder, CF and Chowdhury, S and Kramer, BJ and DeVilbiss, SE and Pierella Karlusich, JJ and Marks, JC and Valdespino-Castillo, PM and Furey, PC and Berberich, ME and Marcarelli, AM and Scott, JT and Fulweiler, RW},
title = {DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0089725},
doi = {10.1128/mra.00897-25},
pmid = {41025798},
issn = {2576-098X},
abstract = {Microbial nitrogen fixation (diazotrophy) is a critical ecological process. We curated DiazoTIME (Diazotroph Taxonomic Identity and MEtabolism), a comprehensive database of diazotroph genomes including taxonomic annotation and metabolic prediction. DiazoTIME is unique among databases for classifying diazotrophs because it resolves both taxonomy and metabolic functionality.},
}

@article {pmid41025789,
year = {2025},
author = {Hodgskiss, LH and Kerou, M and Luo, Z-H and Bayer, B and Maier, A and Weckwerth, W and Nägele, T and Schleper, C},
title = {Metabolic response of a chemolithoautotrophic archaeon to carbon limitation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073225},
doi = {10.1128/msystems.00732-25},
pmid = {41025789},
issn = {2379-5077},
abstract = {The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach to the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modeling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon, even in the absence of available genetic tools.IMPORTANCELittle is known about the regulation of carbon metabolism within ammonia-oxidizing archaea (AOA), a widespread clade that plays a critical role in the global nitrogen cycle while also fixing inorganic carbon. To address this missing knowledge, the soil AOA Nitrososphaera viennensis was subjected to various levels of inorganic carbon and analyzed via a systems biology approach to better understand how its core metabolism is regulated. The results demonstrate a strong dependence on the carbon fixation cycle and highlight key connection points between the core metabolic pathways. The analysis additionally revealed tight control on translational processes and elucidated unique cellular responses when the organism was exposed to either exogenous catalase or pyruvate to relieve oxidative stress from reactive oxygen species. The presented data highlight metabolic responses of N. viennensis and provide a better understanding of how the organism, and likely other AOA, respond to various environmental conditions.},
}

@article {pmid41024334,
year = {2025},
author = {Zhan, J and Zhang, L and Lai, S and Guo, J and Lin, T and Liu, G and Rensing, C and Liu, X and Zhou, S},
title = {Fe(III)-dependent Nrf activity determines nitrate reduction partitioning in nitrate-reducing communities.},
journal = {mBio},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/mbio.02220-25},
pmid = {41024334},
issn = {2150-7511},
abstract = {Identifying the factors that affect the nitrate reduction partitioning between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification is crucial for mitigating nitrogen loss in ecosystems. Conventionally, the nutrient status of the environment (e.g., the carbon-to-nitrogen ratio) is recognized as the key determinant of nitrogen conversion pathways. Here, we report that the availability of Fe(III) regulates the nitrate reduction partitioning in Geobacter metallireducens and Alcaligenes faecalis co-culture. We controlled the availability of Fe(III) in the coculture medium and tracked nitrogen conversion dynamics and community composition. The results demonstrated that the coculture performed DNRA, contributed mainly by G. metallireducens under Fe(III)-replete conditions, while performing interspecies synergistic denitrification between both species under Fe(III)-depleted conditions. Nitrate/nitrite reductase activity calculations and mutation analyses indicated that nitrate reduction partitioning in the coculture was governed by the nitrite reductase (Nrf) activity of G. metallireducens, which was Fe(III)-dependent. Further validation in urban river water confirmed that Fe(III) supplementation significantly enhances DNRA activity. Our findings establish Fe(III) as a previously unrecognized regulator of microbial nitrogen retention, showing insights into strategies for managing nitrogen fluxes in agricultural and aquatic systems.IMPORTANCENitrogen is essential for life, but its loss from ecosystems through microbial processes like denitrification harms agricultural productivity and contributes to greenhouse gas emissions. Retaining nitrogen as ammonium via microbial dissimilatory nitrate reduction to ammonium (DNRA) could mitigate these issues, but the factors governing microbial prioritization of DNRA over denitrification remain unclear. Our study reveals that Fe(III) plays a critical, previously unrecognized role in steering this process. We show that Fe(III) availability determines whether the nitrate-reducing community conserves nitrogen as ammonium or releases it as gas, with implications for managing nitrogen in soils and waterways. By demonstrating Fe(III)'s ability to enhance nitrogen retention in environmental systems like urban rivers, our findings offer a new lever for sustainable agriculture and pollution control. This work bridges microbial ecology and environmental management, highlighting how trace metals shape nutrient cycles in ways that can be harnessed to protect ecosystem health.},
}

@article {pmid41023320,
year = {2025},
author = {Musiałowski, M and Mierzwa-Hersztek, M and Gondek, K and Dębiec-Andrzejewska, K},
title = {A novel two-step metabarcoding approach improves soil microbiome biodiversity assessment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33697},
pmid = {41023320},
issn = {2045-2322},
support = {LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Badań i Rozwoju,Poland/ ; LIDER/13/0051/L-11/NCBR/2020//Narodowe Centrum Badań i Rozwoju,Poland/ ; },
mesh = {*Soil Microbiology ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Bacteria/genetics/classification ; Phylogeny ; },
abstract = {The foundation of microbial ecology research is Next-Generation Sequencing (NGS), which allows for reconstruction of the soil microbiome taxonomical structure and the calculation of biodiversity metrics. However, obtaining reliable data on soil biodiversity poses several challenges, with accurate primer selection being one of the most critical. While 16S rDNA primers are widely used for their ability to broadly target bacterial communities, they can introduce biases. These primers may preferentially amplify certain bacterial groups, leading to a skewed representation of the microbial diversity in soil samples. To overcome the bias, we developed a novel, Two-Step Metabarcoding (TSM) approach to obtain more accurate and detailed data on soil microbiome structure and biodiversity. The first step involved sequencing of amplicons generated using universal 16S rDNA primers, provided an initial overview of the microbial community, and allowed the identification of key taxonomical groups. In the second step, we employed sequencing of amplicons generated with taxa-specific primers designed for the most abundant phyla in the community. We used the obtained data for a more reliable reconstruction of microbiome taxonomic structure and biodiversity. This two-step approach ensures a thorough exploration of the soil microbiome and promises to enhance our understanding of soil microbial dynamics and ecology.},
}

*Soil Microbiology
*Biodiversity
*DNA Barcoding, Taxonomic/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing
*Bacteria/genetics/classification
Phylogeny

@article {pmid41018004,
year = {2025},
author = {Neilson, R and King, D and Giles, ME},
title = {The microbiome associated with Trichodorus primitivus is enriched with Janthinobacterium compared to soil.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250043},
pmid = {41018004},
issn = {0022-300X},
abstract = {Although soil biota mediates many key processes that deliver multiple environmental benefits, interactions between soil biota are not well characterized. In an ecological context, studies to date on the associations between nematodes and bacteria have mostly focused on either intracellular bacteria or bacteria that have a potential role in crop pathogenesis by endoparasitic nematode species, that is, those species that have a component of their life cycle within the plant host. Moreover, evolutionary studies have utilized the model nematode species, Caenorhabditis elegans, for studies on survival, behavior, and fecundity. In this study, we characterize the bacterial communities associated with an ectoparasitic nematode species, Trichodorus primitivus, whose complete life cycle is external to the plant host. Compared to the soil from which the nematodes were extracted, the diversity of bacterial communities associated with T. primitivus was reduced. By contrast, the nematode-associated bacterial community was significantly enriched with Janthinobacterium, a known antagonist of soilborne pathogens. This study advances knowledge on the interactions between bacteria and ectoparasitic nematodes, which could help inform the future development of novel strategies for nematode control.},
}

@article {pmid41017558,
year = {2025},
author = {Han, P and Liu, C and Abdal-Hay, A and Reed, S and Liaw, A and Wang, J and Ning, Y and Ivanovski, S},
title = {Proteome and microbiome profiles of polymicrobial salivary biofilms on 3D MEW fibrous scaffolds: biomimetic ECM-inspired structures.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb01410g},
pmid = {41017558},
issn = {2050-7518},
abstract = {Replicating the structural complexity of polymicrobial oral biofilms in vitro remains a significant challenge in biomaterials research. Nevertheless, developing clinically relevant biofilm models is crucial for advancing our understanding of biofilm-host interactions and elucidating how biomaterials influence microbial composition, behaviour, and overall biofilm dynamics. In this work, 3D biomimetic fibrous scaffolds made from medical-grade polycaprolactone (mPCL) were fabricated using the melt electrowriting (MEW) technique. The effects on biofilm viability, activity, microbiome, and proteome profiles were assessed on 3D fibrous scaffolds and conventional 2D tissue culture plates (TCP). Human saliva was cultured on MEW mPCL (3D BF) and TCP (2D BF) for 4 days, followed by microbiome profiling via 16S rRNA sequencing and proteomic analysis using LC-MS/MS, SWATH with GO and KEGG pathway enrichment. The results demonstrated that 3D MEW mPCL scaffolds enhanced biofilm biomass, thickness, and viability. Microbiome analysis revealed that 3D BF was enriched with both commensals and pathogens, including Veillonella, Peptostreptococcus, Porphyromonas gingivalis, and Treponema denticola, alongside probiotic species like Lactobacillus acidophilus. Pooled proteomic data from three technical repeats, along with GO and KEGG analyses, revealed a functionally dynamic biofilm ecosystem characterised by elevated expression of proteins involved in glycolysis, the TCA cycle, and nucleotide metabolism, highlighting pathways essential for biofilm survival, stress adaptation, and host interaction. These 'proof-of-concept' findings highlight the potential of 3D MEW fibrous mPCL scaffolds as a biomimetic 3D platform capable of accurately recapitulating the dynamic spatial and metabolic complexity of oral biofilms, thereby facilitating innovative investigations into microbial ecology, host-pathogen interactions, and the accelerated development of targeted antimicrobial therapies.},
}

@article {pmid41016925,
year = {2025},
author = {Li, C and Wu, M and Tang, W and Yu, B and Saiz-Lopez, A and Poulain, A and Bank, MS and Zhou, Q and Bodelier, PLE and Yan, Z and Frey, B and Hu, H and Chen, J and Jiang, Y and Zhong, H},
title = {Aligning global mercury mitigation with climate action.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7826},
pmid = {41016925},
issn = {2041-1723},
support = {42107223//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41673075//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Mercury/analysis/toxicity ; *Climate Change ; Greenhouse Gases/metabolism/analysis ; Humans ; *Environmental Pollution/prevention & control ; Microbiota/drug effects ; *Environmental Pollutants/analysis ; },
abstract = {Environmental mercury (Hg) pollution affects microbial community structure and functions. Yet, whether and how this influence cascades through microbe-mediated cycling of major greenhouse gases (GHGs) remains poorly understood. This Perspective synthesizes emerging evidence on the Hg-microbe-GHG nexus, exploring the possibility that global Hg emission reductions, while critical for human and planetary health, may cause alterations to microbe-mediated GHG fluxes. Significant knowledge gaps persist, however, regarding the Hg-microbe-GHG nexus, particularly concerning the magnitude and direction of the nexus's net impact on climate and global environmental change. To bridge these gaps, we propose a three-step roadmap aimed at disentangling the potential impacts of global Hg emission mitigation strategies on microbial communities, associated GHG emissions, and subsequent climate change. Collectively, these joint efforts from scientists, industry, community stakeholders, and policymakers are critical to harmonizing global Hg mitigation efforts with climate action and to ensuring a sustainable future for Earth systems and their inhabitants.},
}

*Mercury/analysis/toxicity
*Climate Change
Greenhouse Gases/metabolism/analysis
Humans
*Environmental Pollution/prevention & control
Microbiota/drug effects
*Environmental Pollutants/analysis

@article {pmid41016813,
year = {2025},
author = {Lee, HH},
title = {Iodine Biogeochemical Cycle and Microbial Bioremediation of Radioactive Iodine-129.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508018},
doi = {10.4014/jmb.2508.08018},
pmid = {41016813},
issn = {1738-8872},
mesh = {*Biodegradation, Environmental ; *Iodine Radioisotopes/metabolism ; *Bacteria/metabolism ; *Iodine/metabolism ; Oxidation-Reduction ; Humans ; Hydrocarbons, Iodinated ; },
abstract = {Iodine is an essential biophilic element that plays pivotal roles in both environmental systems and human physiology, particularly as a key constituent of thyroid hormones and a regulator of atmospheric ozone. In contrast, its radioactive isotope, iodine-129 (I-129), predominantly generated through anthropogenic nuclear activities, represents a persistent environmental and public health concern. With an exceptionally long half-life of approximately 15.7 million years and high environmental mobility, especially in groundwater, combined with a strong tendency to bioaccumulate in the human thyroid, I-129 poses a disproportionate and long-term radiological hazard in contaminated sites. The biogeochemical cycling of iodine involves intricate interconversions among multiple oxidation states and phases across the lithosphere, hydrosphere, atmosphere, and biosphere. Microorganisms are central to these processes, mediating oxidation, reduction, methylation, accumulation, and sorption. While microbial methylation can increase I-129 mobility via the production of volatile methyl iodide, other microbial pathways, notably biosorption and binding to organic matter, provide promising mechanisms for immobilization and natural attenuation. Microbial bioremediation offers a sustainable and cost-effective alternative or complement to conventional physicochemical methods for managing radioactive contaminants. Strategies such as bioreduction, biosorption, bioaccumulation, and biomineralization exploit the metabolic versatility of microorganisms to alter radionuclide speciation, solubility, and mobility. However, practical application to I-129 remains challenging due to its extreme persistence, environmental variability, and uncertainties in predicting its long-term geochemical fate. Effective management of I-129 contamination will require an integrated, multidisciplinary approach that combines advanced microbial ecology insights, optimized biotechnological processes, and long-term monitoring frameworks.},
}

*Biodegradation, Environmental
*Iodine Radioisotopes/metabolism
*Bacteria/metabolism
*Iodine/metabolism
Oxidation-Reduction
Humans
Hydrocarbons, Iodinated

@article {pmid41016251,
year = {2025},
author = {Schubert, K and Shosanya, T and García-Bayona, L},
title = {The role of mobile genetic elements in adaptation of the microbiota to the dynamic human gut ecosystem.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102675},
doi = {10.1016/j.mib.2025.102675},
pmid = {41016251},
issn = {1879-0364},
abstract = {The human intestinal microbiota is a dynamic ecosystem shaped by extensive horizontal gene transfer, particularly in individuals from industrialized populations. In this review, we discuss recent advances in our understanding of how mobile genetic elements (MGEs) contribute to microbial ecology and evolution in this diverse community, focusing on MGEs carrying fitness-conferring genes. Bacteroidales species can colonize individuals for decades and serve as major hubs for MGE exchange. Most MGEs are highly variable across individuals and geographies. Occasionally, conserved MGEs can spread across geography and lifestyles. Functional characterizations of MGEs reveal their roles in antibiotic resistance, interbacterial antagonism, biofilm formation, immune evasion, and nutrient acquisition, among others. Substantive progress in our understanding of MGEs in the gut microbiome offers promising avenues for therapeutic microbiome interventions. However, major challenges remain in functional prediction, host-MGE linkage, and experimental characterization.},
}

@article {pmid41013679,
year = {2025},
author = {Ramljak, A and Jurburg, S and Chatzinotas, A and Lučić, M and Žižek, M and Babić, I and Udiković-Kolić, N and Petrić, I},
title = {Identifying the drivers of microbial community changes and interactions in polluted coastal sediments.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {117},
pmid = {41013679},
issn = {2524-6372},
support = {IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; IP-2020-02-6510//Hrvatska Zaklada za Znanost/ ; },
abstract = {Despite over three decades of research into the composition and distribution of microbial communities, gaps remain in our mechanistic understanding of microbial community assembly processes, especially in benthic communities in coastal zones continuously exposed to anthropogenic pressures. We analyzed the microbial communities (prokaryotes, fungi, and protists) in sediment samples from ports and bays located along the Adriatic coast chronically exposed to chemical and nutrient pollution, and explored how selective pressures (pollutants, nutrients, and environmental conditions) and dispersal shape these communities. We found that biogeographic factors (i.e. location) play a key role in structuring microbial communities, with benthic fungi also being shaped by the presence of pollutants and nutrients. Strong correlations between nutrient loads and pollutants were observed, along with weakened interactions between microbial communities, particularly between prokaryotes and protists, in the presence of specific pollutants (bismuth, cadmium, copper, zinc, mercury). These results are an important step in disentangling the complex interactions between pollutants and microbial community dynamics in aquatic ecosystems. Further research is needed to assess how these shifts in microbial community dynamics may affect ecosystem services in vulnerable coastal zones.},
}

@article {pmid41012703,
year = {2025},
author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP},
title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.},
journal = {Viruses},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/v17091275},
pmid = {41012703},
issn = {1999-4915},
support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; },
abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.

METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.

RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.

CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.},
}

*Genome, Viral
*Plant Viruses/genetics/physiology
Host Specificity
Metagenomics
Plant Diseases/virology
Plants/virology

@article {pmid41011533,
year = {2025},
author = {Dai, X and He, Y and Su, Y and Mo, H and Li, W and Li, W and Zi, S and Liu, L and Di, Y},
title = {Pathogen Identification, Antagonistic Microbe Screening, and Biocontrol Strategies for Aconitum carmichaelii Root Rot.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092202},
pmid = {41011533},
issn = {2076-2607},
support = {202403AP140013//The Sino-Vietnamese International Joint Laboratory for Characteristic & Cash Crops Green De-velopment of Yunnan Province/ ; Yunnan Academic Degrees Committee Document [2024] No. 19//The Construction Project for Postgraduate Tutor Team of Yunnan Province in 2024/ ; 2024J0486//Scientific Research Fund of the Educational Department of Yunnan Province/ ; },
abstract = {The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch's postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management.},
}

@article {pmid41011501,
year = {2025},
author = {Dai, L and Hao, X and Niu, T and Liu, Z and Wang, Y and Geng, X and Cai, Q and Wang, J and Ren, Y and Liu, F and Liu, H and Li, Z},
title = {Analysis of Microbial Community Structure and Diversity in Different Soil Use Types in the Luo River Basin.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092173},
pmid = {41011501},
issn = {2076-2607},
support = {30803302//Henan Provincial Finance Forest and Grass Science and Technology (Intermediate Trial) Promo-tion Demonstration Project "Introduction and Cultivation of desia polycarpa Maxim. 'Yulu/ ; 2025-2627//Henan Province Science and Technology Research Project "Innovative Utilization of Germplasm Resources and Breeding of Excellent New Varieties of desia polycarpa Maxim."/ ; },
abstract = {The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, bamboo forest, grassland, and abandoned land) in Luoning County of the Luohe River Basin and employed high-throughput sequencing technology to analyze the characteristics of soil microbial communities and differences in soil nutrients. The results showed the following: There were significant differences in soil nutrients and microbial diversity among different land use types. Specifically, the organic matter content in farmland was significantly higher than that in bamboo forests (p < 0.05), and the available phosphorus content in farmland was significantly higher than that in abandoned land (p < 0.05); the abandoned land had a significant advantage in alkali-hydrolyzable nitrogen and available potassium contents (p < 0.05) but the lowest soil water content (p < 0.05). Microbial diversity indices indicated that Pielou's evenness index (Pieloue) in farmland was significantly higher than that in grassland. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Actinobacteria. At the genus level, available potassium was the key factor affecting the top 20 dominant bacterial genera. Redundancy Analysis (RDA) showed that pH was the core environmental variable driving the variation of bacterial community structure. Metabolic pathway analysis revealed that biosynthetic metabolism was the main pathway, and grassland exhibited outstanding performance in the secondary metabolite synthesis pathway. The results of this study fill the gap in soil microbial ecology research in this region and provide a theoretical basis for the sustainable utilization of land resources and agricultural ecological management in the Luohe River Basin.},
}

@article {pmid41011387,
year = {2025},
author = {Wang, Y and Deng, C and Sui, M and Wei, P and Duan, B and Li, Z and Zou, F},
title = {Acute Toxoplasma gondii Infection Drives Gut Microbiome Dysbiosis and Functional Disruption in Mice as Revealed by Metagenomic Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/microorganisms13092056},
pmid = {41011387},
issn = {2076-2607},
support = {202449CE340019//the Yunnan Key Laboratory of Veterinary Etiological Biology/ ; U2202201//the NSFC-Yunnan Joint Fund/ ; 202401AT070440//the Yunnan Fundamental Research Projects/ ; 2024Y339//the Scientific Research Fund of Education Department of Yunnan Province/ ; No.XXX//the Yunnan Provincial University Key Industry Service Science and Technology Program/ ; },
abstract = {Toxoplasma gondii is a widely distributed intracellular parasite that disrupts host immune and metabolic homeostasis. Although accumulating evidence highlights the role of gut microbiota in parasitic infections, the effects of acute T. gondii infection on host gut microbial ecology remain poorly understood. In this study, metagenomic sequencing technology was used to systematically analyze the composition and functional alterations of the ileal microbiota in BALB/c mice on day 10 post-infection. Compared to uninfected controls, T. gondii infected mice exhibited a significant reduction in microbial diversity and a pronounced shift in community structure. Notably, there was an expansion of Proteobacteria, particularly the Enterobacteriaceae family, alongside a marked decline in beneficial taxa such as Actinobacteria and Bacillota. Functional annotation using the KEGG and CAZy databases revealed enrichment of metabolic pathways related to glycolysis/gluconeogenesis, O-antigen nucleotide sugar biosynthesis, bacterial secretion systems, and biofilm formation-Escherichia coli in the infected microbiota. These findings provide novel insights into the dysbiosis of gut microbiota and host-microbe interactions during acute T. gondii infection.},
}

@article {pmid41010480,
year = {2025},
author = {Duysburgh, C and Fiore, W and Marzorati, M},
title = {Survival and Impact on Microbial Diversity of Lacticaseibacillus paracasei DG in a Simulation of Human Intestinal Microbial Ecosystem.},
journal = {Nutrients},
volume = {17},
number = {18},
pages = {},
doi = {10.3390/nu17182952},
pmid = {41010480},
issn = {2072-6643},
support = {N/A//Alfasigma S.p.A./ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics ; *Lacticaseibacillus paracasei/physiology/growth & development/metabolism ; Microbial Viability ; Hydrogen-Ion Concentration ; Fatty Acids, Volatile/metabolism ; Colon/microbiology ; Lactic Acid/metabolism ; Feces/microbiology ; },
abstract = {Background/Objectives: The probiotic Lacticaseibacillus paracasei DG (LpDG) has shown promising results for various gastrointestinal diseases. This study evaluated the survival, metabolic activity, and impact on colonic microbiota of LpDG in an in vitro gastrointestinal tract simulation. Methods: Encapsulated LpDG was tested under simulated fed, fasted, and shortened fasted conditions compared with a blank control in a modified Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]) reactor. Capsule integrity, and cell culturability and viability were assessed at the end of each digestion phase. Metabolic activity (pH, total gas production, and concentrations of short-chain fatty acids, lactate, and ammonium) was assessed after a 24 h colonic incubation with a faecal inoculum. The impact of LpDG on the colonic microbial community was analysed by quantitative polymerase chain reaction and shallow shotgun sequencing. Results: The capsule was completely degraded at the end of the jejunum under all conditions. A low pH had a minimal impact on LpDG culturability and viability. Compared with blank control, LpDG remained metabolically active in the microbial community following a 24 h colonic incubation (LpDG [0-24 h] vs. blank control [0-24 h]: ΔpH, decreased [0.29-0.38 vs. 0.12-0.34]; Δlactic acid, decreased [1.52-1.69 mM vs. 0.13-0.21 mM]; and Δbutyrate, increased [7.49-10.52 mM vs. 5.19-7.76 mM]). Under fed conditions, treatment with LpDG compared with blank control significantly decreased levels of Escherichia coli and Blautia wexlerae and increased Clostridiaceae, Eubacteriaceae, and Lachnospiraceae. Conclusions: LpDG remains viable and metabolically active in the gastrointestinal tract, positively affecting intestinal microbiota and metabolite production.},
}

Humans
*Gastrointestinal Microbiome
*Probiotics
*Lacticaseibacillus paracasei/physiology/growth & development/metabolism
Microbial Viability
Hydrogen-Ion Concentration
Fatty Acids, Volatile/metabolism
Colon/microbiology
Lactic Acid/metabolism
Feces/microbiology

@article {pmid41009926,
year = {2025},
author = {Dealis Gomes, ML and Afonso, L and Basso, KR and Alves, LC and Macías, EJN and Yamada-Ogatta, SF and Guidi, AC and de Mello, JCP and Andrade, FG and Cabeça, LF and Cely, MVT and Andrade, G},
title = {Liposomal Fluopsin C: Physicochemical Properties, Cytotoxicity, and Antibacterial Activity In Vitro and over In Vivo MDR Klebsiella pneumoniae Bacteremia Model.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/antibiotics14090948},
pmid = {41009926},
issn = {2079-6382},
support = {439754/2018-6 (AMR MCTIC)//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; 406016/2022-4, PPSUS-Aracauria Foundation-PR//Brazilian National Council for Scientific and Technological Development (CNPq)/ ; },
abstract = {Introduction: Antimicrobial resistance has become a global concern, and few new antimicrobials are currently being developed. Fluopsin C has proven broad-spectrum activity, being a promising candidate for new antimicrobial development. To optimize antimicrobial activity, this research aimed at fluopsin C (Flp) encapsulation in liposomes to achieve controlled release and reduce cytotoxicity. Methods: Liposomal formulations were prepared by extruding formulations based on soy phosphatidylcholine (SPC) or poly (ethylene glycol)-distearoylphosphatidylethanolamine (DSPE-PEG) plus cholesterol, and were characterized by their size, polydispersity index, zeta potential, encapsulation efficiency, shelf-life stability, in vitro release profile, cytotoxicity, and antimicrobial activity against Klebsiella pneumoniae in vitro and in vivo. Results: The results indicated that the DSPE-PEG DMSO+Flp formulation presented superior physicochemical stability and unaltered antimicrobial activity. In vitro, CC50 decreased by 54%. No lethal dose was obtained in mice within the concentration range tested. The most effective doses in vivo were 2 × 2 mg/kg for free fluopsin C and 1 × 2 mg/kg for DSPE-PEG DMSO+Flp, resulting in a 40% reduction in mortality from bacteremia. Only discrete inflammatory infiltration was detected in the liver, while kidney necrosis ranged from discrete to moderate. Encapsulation of fluopsin C in liposomes showed promising features supporting to use against infections by MDR K. pneumoniae.},
}

@article {pmid41009119,
year = {2025},
author = {Kiewra, D and Ojrzyńska, H and Czułowska, A and Dyczko, D and Jawień, P and Plewa-Tutaj, K},
title = {Dermacentor reticulatus (Fabricius, 1794) in Southwestern Poland: Changes in Range and Local Scale Updates.},
journal = {Insects},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/insects16090935},
pmid = {41009119},
issn = {2075-4450},
abstract = {The ornate dog tick Dermacentor reticulatus is a key vector of several pathogens and has been expanding its range across Europe, raising concerns about the associated veterinary and public health risks. This study aimed to assess the current distribution and local-scale expansion of D. reticulatus in southwestern Poland, particularly in and around the city of Wrocław. In 2024, host-seeking ticks were collected using the flagging method at 80 sites, including 30 previously monitored locations and 50 newly designated ones, selected based on land cover analysis and field verification. Spatial statistics and kriging method were applied to evaluate changes in the tick's range compared to data from 2014-2019. The presence of D. reticulatus was confirmed at 68 sites, including 13 located beyond the previously estimated range. A shift in the mean center of tick occurrence toward the southeast was observed, along with an increase in the compact area of occurrence. The results indicate a continued expansion of D. reticulatus in the region, with urbanization and landscape structure likely influencing its spread. These findings underscore the importance of local-scale surveillance and spatial modeling in assessing the risk of tick-borne diseases.},
}

@article {pmid41006295,
year = {2025},
author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J},
title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1568},
pmid = {41006295},
issn = {2052-4463},
support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; },
abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.},
}

*Soil Microbiology
*Phospholipids
*Fatty Acids
*Databases, Factual
*Enzymes
Soil/chemistry
Ecosystem

@article {pmid41005096,
year = {2025},
author = {Wang, J and Hao, J and Jing, W and Gao, Y and Qiu, S},
title = {Effects of polyethylene terephthalate microplastics on performance of sequencing-batch membrane bioreactor for simulated municipal wastewater treatment.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139956},
doi = {10.1016/j.jhazmat.2025.139956},
pmid = {41005096},
issn = {1873-3336},
abstract = {Municipal wastewater treatment plants (WWTPs) are recognized as key recipients of microplastics (MPs), with polyethylene terephthalate (PET) being among the most prevalent types in sewage. However, the systemic impact of PET MPs on integrated biological-membrane systems-especially their role in microbial ecology and membrane fouling-remains poorly understood. Therefore, the influence of PET MPs on the performance, microbial community and membrane fouling in a sequencing-batch membrane bioreactor (SMBR) was evaluated in this study. Based on the results, adding PET MPs decreased the MLSS from around 5000 mg/L to 4500 mg/L whereas the MLVSS/MLSS remain basically consistent. The SV30 and SVI increased rapidly to 76 % and 173.2 mL/g on the 3rd day (from 64 % and 128.3 mL/g on the 1st day) of adding PET MPs, however, they could be restored in the following days. For pollutants removal, the COD and NH4[+]-N removal were initially negatively affected but gradually recovered after several days of operation. The addition of PET MPs enhanced denitrification, resulting in a decrease in the effluent TN concentration from 15.1 ± 4.9 mg/L to 10.4 ± 4.4 mg/L. PET MPs changed microbial community structure and decreased the abundance of dominant bacteria and species diversity in activated sludge. Arenimonas and Sphingopyxis had strong relationships with PET MPs addition. PET MPs addition exacerbated membrane biofouling, and the microbial diversity on membrane at was basically consistent with activated sludge whereas the abundance changed significantly. This research provides a comprehensive understanding of how PET MPs affect the performance of integrated biological-membrane systems.},
}

@article {pmid41000638,
year = {2025},
author = {Flores, C and Seekatz, AM},
title = {Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.20.677466},
pmid = {41000638},
issn = {2692-8205},
abstract = {Dietary habits have dramatically altered over recent decades, yet the impact of simplified carbohydrate intake on the gut microbiome's complexity and function remains poorly understood. This study investigates how the variety of dietary carbohydrates - not just their amount - shapes gut microbial diversity and resilience in C57BL/6 mice. Over eight weeks, mice consumed diets varying in carbohydrate complexity but matched for total carbohydrate content. Using 16S rRNA sequencing, we found that reduced carbohydrate diversity led to significant declines in microbial diversity and taxonomic redundancy among important bacterial groups, such as unclassified Lachnospiraceae, Ruminococcaceae, and Muribaculaceae, despite no immediate changes in host physiology. Concurrently, Akkermansia increased under low-complexity diets, suggesting a shift toward mucin degradation when complex polysaccharides are scarce. These changes indicate that loss of carbohydrate complexity narrows microbial niches, potentially disrupting metabolic interactions and functional stability of the gut ecosystem. Given the widespread adoption of processed, low-fiber diets in modern societies, these findings emphasize the importance of macronutrient complexity in maintaining gut microbial health. While short-term host effects were minimal, the microbial shifts observed could presage long-term consequences for gut resilience and disease susceptibility. This study underscores the need to consider carbohydrate diversity in dietary recommendations and microbial ecology research to safeguard gut health in the face of global dietary simplification.},
}

@article {pmid41000006,
year = {2025},
author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF},
title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70205},
pmid = {41000006},
issn = {1365-3040},
support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; },
abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.},
}

@article {pmid40999741,
year = {2025},
author = {Sun, J and Huang, H and Li, J and Xu, J and Jia, J and Li, W and Cheng, J and Zhu, D and Liu, M and Yuan, M and Xiao, S and Xue, C},
title = {Mitochondrial iron transporter ClMrs3/4 regulates iron homeostasis to modulate nitric oxide balance facilitating appressorial development in Curvularia lunata.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70594},
pmid = {40999741},
issn = {1469-8137},
support = {2024YFD1400304//National Key Research & Development Program of China/ ; 2023JH101300163/2022JH2/101300168//Liaoning Provincial Applied Basic Research Program/ ; 2024JH1/11700007-3//Liaoning Provincial Key Projects of Science and Technology/ ; JYTYB2024053//Basic Research Project of the Department of Education of Liaoning Province/ ; },
abstract = {Iron is indispensable for the vast majority of organisms, and iron homeostasis plays a pivotal role in both the physiology and pathogenesis of fungal pathogens. However, the underlying mechanisms by which iron homeostasis modulates fungal pathogenesis remain to be fully elucidated. We therefore focused on investigating the functions of mitochondrial iron transporter ClMrs3/4 in virulence. We conducted targeted gene deletions, expression analyses, biochemistry, and pathogenicity assays, demonstrating that ClMrs3/4 regulates appressorial development via maintenance of cellular iron balance in Curvularia lunata. ClMrs3/4 modulates virulence by influencing appressorial development in C. lunata, which is dependent on iron homeostasis. ClMrs3/4 controls nitric oxide (NO) balance via the nitrate (NO3 [-]) assimilation pathway by modulating cytoplasmic iron levels, a process crucial for turgor pressure accumulation within the appressoria independent of mitochondrial and cytoplasmic Fe-S cluster biosynthesis. Our findings underscore the conserved role of Mrs3/4 in iron homeostasis among pathogenic fungi and propose a novel mechanism by which iron homeostasis regulates virulence, particularly through the NO3 [-] assimilation pathway mediated by cytoplasmic iron levels to regulate appressorial development.},
}

@article {pmid40998779,
year = {2025},
author = {Li, Y and Sun, M and Raaijmakers, JM and Mommer, L and Zhang, F and Song, C and Medema, MH},
title = {Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8400},
pmid = {40998779},
issn = {2041-1723},
support = {24.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
mesh = {*Rhizosphere ; *Bacteria/genetics/metabolism/classification ; *Plant Roots/microbiology ; Soil Microbiology ; Microbiota/genetics ; *Multigene Family ; *Plants/microbiology ; Machine Learning ; Algorithms ; },
abstract = {Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here, we integrate published information on catabolic genes in bacteria that contribute to their rhizosphere competence and develop the rhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria with 58 curated detection rules. Our analysis reveals heterogeneity in rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we demonstrate the predictive value of the presence or absence of rCGCs for rhizosphere competence in machine learning with two case studies. rhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, facilitating microbiome-assisted breeding approaches for sustainable agriculture.},
}

*Rhizosphere
*Bacteria/genetics/metabolism/classification
*Plant Roots/microbiology
Soil Microbiology
Microbiota/genetics
*Multigene Family
*Plants/microbiology
Machine Learning
Algorithms

@article {pmid40997605,
year = {2025},
author = {Wu, G and Ding, Z and Wang, J and Xie, J},
title = {Frontier research on the risk of spoilage microorganisms in refrigerated marine fish: From regional to global perspectives.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111465},
doi = {10.1016/j.ijfoodmicro.2025.111465},
pmid = {40997605},
issn = {1879-3460},
abstract = {Microbial spoilage is creating safety risks and significant wastage of refrigerated marine fish. Spoilage microorganisms possess distinct physiological adaptations that enable them to contribute to the spoilage of refrigerated marine fish, thereby complicating the accuracy of microbial risk predictions and the efficacy of control strategies. This review integrates research findings from diverse geographical regions to elucidate mechanisms of microbial spoilage and underscores the ongoing challenges in cross-regional collaborative studies. Omics serve as guiding tools for elucidating the molecular mechanisms by which metabolite mediate spoilage microorganisms-induced deterioration of flavor, texture, and safety. Quantitative Microbial Risk Assessment (QMRA) provides a critical framework for risk prediction, with its future development being intrinsically linked to the integration of omics data, rapid fluorescence sensing, and artificial intelligence (AI) for enhanced prediction and modeling. In conclusion, this review underscores the critical role of spoilage microorganisms in the deterioration of refrigerated marine fish, highlights the complex interplay between microbial ecology, cold adaptation, and spoilage potential, and emphasizes the necessity for collaborative global efforts. Advancing research on native microbial communities, molecular spoilage mechanisms, and AI-powered QMRA frameworks is paramount for reducing food waste, enhancing food safety risk assessment, and the sustainable development of preservation technology.},
}

@article {pmid40996662,
year = {2025},
author = {Rév, A and Parádi, I and Füzy, A and Juhász, P and Kocsis, K and Cseresnyés, I and Takács, T},
title = {Improvement of soil fertility and enzymatic activity by wastewater sludge compost and arbuscular mycorrhizal fungi in giant reed's rhizosphere.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {40996662},
issn = {2676-8607},
support = {SA-26/2021//Eötvös Loránd Research Network/ ; },
abstract = {The effect of low-dose, commercially available wastewater sludge compost (WSC; 15 t ha[-1]) treatment was examined with or without arbuscular mycorrhizal fungal (AMF) inoculation on the nutritional status, heavy metal (HM) concentration and the rhizosphere activity of giant reed (Arundo donax L. var. BL clone (Blossom)) plants. Funneliformis mosseae (BEG12; AMF1), F. geosporum (BEG11; AMF2) or their combination (AMFmix) were applied as AMF treatments in a short-term pot experiment. The physiological and growth parameters of the host plants, the AMF root colonization and the microbiological enzyme activity of the mycorrhizosphere were examined. We assumed that the combined treatment (WSC + AMF) enhances the fertility of low-fertility acidic sandy soil. Neither the WSC treatment nor the AMF inoculations changed the extent of root colonization. Based on the results of root electrical capacitance and the phosphorous uptake, plant nutritional status was improved by WSC addition, without any negative impacts among the measured parameters. AMF treatments increased the enzyme activity in the soil and decreased the concentrations of the potentially toxic HMs (Cu, Mn, Pb, Zn) in roots, but that mitigation of Cu and Zn was compensated in shoots. According to the results of MicroResp™ measurements, the catabolic activity profile of the soil microbial community was changed in case of the AMF2 treatment. The efficient regulatory mechanism of giant reed might be able to adjust optimal/maximal colonization rate, and to select the preferential AMF partners, this supposed mechanism might be responsible for its invasiveness and tolerance to a wide range of environmental conditions.},
}

@article {pmid40996559,
year = {2025},
author = {Han, SI and Kim, JO and Lee, YR and Ekpeghere, KI and Koh, SC and Whang, KS},
title = {Correction: Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {10},
pages = {157},
doi = {10.1007/s10482-025-02169-7},
pmid = {40996559},
issn = {1572-9699},
}

@article {pmid40995846,
year = {2025},
author = {Stephenson, T and Crowder, DW and Osburn, E and Strickland, M and Jones, M and Bartel, S and Kittipalawattanapol, K and Cunningham, CX and Hudiburg, T and Storfer, A and Piaskowski, J and Lynch, L},
title = {Apex Scavenger Declines Have Cascading Effects on Soil Biogeochemistry and Ecosystem Processes.},
journal = {Global change biology},
volume = {31},
number = {9},
pages = {e70520},
doi = {10.1111/gcb.70520},
pmid = {40995846},
issn = {1365-2486},
support = {DEB-2054716//National Science Foundation/ ; },
mesh = {Animals ; *Soil/chemistry ; *Soil Microbiology ; *Food Chain ; *Marsupialia/physiology ; *Ecosystem ; Seasons ; Microbiota ; },
abstract = {Global apex scavenger declines strongly alter food web dynamics, but studies rarely test whether trophic downgrading impacts ecosystem functions. Here, we leverage a unique, disease-induced gradient in Tasmanian devil (Sarcophilus harrisii) population densities to assess feedbacks between carcass persistence, subordinate scavenger guilds, and biogeochemical cycling. We further explored interkingdom and seasonal interactions by manipulating carcass access and replicating experiments in warmer, drier summer versus cooler, wetter winter periods. We show Tasmanian devil declines significantly extend carcass persistence and increase the flux of carcass-derived nutrients belowground (e.g., by 18-134-fold for ammonium). Greater nutrient availability reduces soil microbiome diversity by up to 26%, increasing the relative abundance of putative zoonotic pathogens. Nutrient subsidies also shift microbial communities toward faster-growing taxa that invest less energy in resource acquisition, with implications for soil carbon sequestration. Rates of carcass decomposition were reduced in the winter, dampening soil biogeochemical responses and interkingdom competition. Notably, while less efficient scavenger guilds clearly facilitate carcass consumption, they were not able to fill the functional role of apex scavengers. Our study illustrates how trophic downgrading effects can ripple across all levels of ecological organization.},
}

Animals
*Soil/chemistry
*Soil Microbiology
*Food Chain
*Marsupialia/physiology
*Ecosystem
Seasons
Microbiota

@article {pmid40993772,
year = {2025},
author = {Dubey, JP and Alić, A and Hodžić, A and Lopez-Flores, J and Baneth, G},
title = {Hepatozoon infections in domestic and wild Carnivora: etiology, prevalence, clinical disease, diagnosis and treatment, and redescription of Hepatozoon silvestris, H. martis, and H. ursi.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {391},
pmid = {40993772},
issn = {1756-3305},
mesh = {Animals ; Prevalence ; *Coccidiosis/veterinary/diagnosis/epidemiology/parasitology/drug therapy/therapy ; *Eucoccidiida/classification/isolation & purification ; *Carnivora/parasitology ; Animals, Wild/parasitology ; Animals, Domestic/parasitology ; Life Cycle Stages ; },
abstract = {Hepatozoon spp. are common pathogens in dogs and other Carnivora in many parts of the world, especially in the tropics. There is considerable taxonomic debate concerning the Hepatozoon species infecting Carnivora. Morphological descriptions of several Hepatozoon species are inadequate and their validity is questionable. Additionally, different terminology has been used for the description of life cycle stages. Here, we provide a comprehensive review of the Hepatozoon species in the Carnivora, using a uniform terminology. Worldwide prevalence of clinical and subclinical Hepatozoon infections for the past century is tabulated and critically evaluated. We also review the epizootiology, clinical signs, diagnosis, and treatment of hepatozoonosis in the Carnivora. The morphology and life cycles of seven valid species with known merogonic stages (Hepatozoon americanum, H. canis, H. felis, H. martis, H. rufi, H. silvestris, H. ursi) are summarized in a table using standard terminology. Additional information on H. apri, H. martis, and H. silvestris life cycle stages is provided. Information lacking for H. procyonis, H. luiperdjie and H. ingwe is discussed. The relevance of H. mustelis, H. banethi and H. ewingi is discussed and they are considered as invalid species. For the benefit of future researchers, worldwide reports of prevalence, clinical disease, diagnosis, and treatment of Hepatozoon infections in domestic and wild Carnivora for the past century are summarized in tables alphabetically and chronologically for each country. Co-infections of H. canis, H. americanum, H. felis, and H. silvestris are summarized and discussed. The role of Hepatozoon infections causing clinical illness in wild Carnivora is discussed, particularly for red foxes, coyotes, and mustelids.},
}

Animals
Prevalence
*Coccidiosis/veterinary/diagnosis/epidemiology/parasitology/drug therapy/therapy
*Eucoccidiida/classification/isolation & purification
*Carnivora/parasitology
Animals, Wild/parasitology
Animals, Domestic/parasitology
Life Cycle Stages

@article {pmid40993491,
year = {2025},
author = {Sun, S and Qiao, Z and Tikhonenkov, DV and Gong, Y and Li, H and Li, R and Sun, K and Huo, D},
title = {Temporal Dynamics and Adaptive Mechanisms of Microbial Communities: Divergent Responses and Network Interactions.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {94},
pmid = {40993491},
issn = {1432-184X},
support = {24-44-00093//Russian Science Foundation/ ; 32361133561//National Natural Science Foundation of China/ ; 2021M703430//China Postdoctoral Science Foundation/ ; },
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Ecosystem ; *Rivers/microbiology ; *Eukaryota/genetics/classification/physiology ; Water Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Microbial communities are vital to aquatic ecosystems, driving biogeochemical cycles, nutrient recycling, and overall ecosystem functioning. However, their instant feedback, particularly in response to environmental fluctuations, remain insufficiently understood. In this study, we investigated the interaction of prokaryotic and eukaryotic microbial communities in riverine ecosystems under temporal dynamics using high-throughput sequencing and co-occurrence network analysis. We observed distinct patterns, with eukaryotic communities showing a consistent increase in alpha diversity, while prokaryotic communities exhibited more variable and directional shifts over time. Two key phases were identified: a dynamic phase characterized by rapid changes in both alpha and beta diversity and a stabilization phase where community composition became more stable, with increased evenness. Co-occurrence network analysis revealed a transition from a modular structure in the dynamic phase to a more centralized and highly connected network in the stabilization phase. While modularity can enhance stability by localizing perturbations within distinct subnetworks, increased centralization and connectivity may weaken this stabilizing effect, potentially making the network less resilient to environmental fluctuations. Our findings provide new insights into the adaptive mechanisms that sustain microbial community stability and resilience in dynamic aquatic ecosystems, emphasizing the importance of diversity and network structure in maintaining ecological stability.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
Biodiversity
Ecosystem
*Rivers/microbiology
*Eukaryota/genetics/classification/physiology
Water Microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40991823,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf199},
pmid = {40991823},
issn = {1751-7370},
}

@article {pmid40991432,
year = {2025},
author = {van Gestel, J and Koo, BM and Stürmer, VS and Garriga-Canut, M and Wagner, J and Zanon, A and Gross, CA},
title = {Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {39},
pages = {e2518989122},
doi = {10.1073/pnas.2518989122},
pmid = {40991432},
issn = {1091-6490},
support = {101116560//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; P400PB_186789//Swiss National Science Foundation (Postdoc.Mobility)/ ; R35GM118061//HHS | National Institutes of Health (NIH)/ ; },
mesh = {*Bacillus subtilis/genetics/physiology/growth & development ; *Dictyostelium/physiology ; *Adaptation, Physiological ; Bacterial Proteins/metabolism/genetics ; Phenotype ; },
abstract = {Single-cell eukaryotic predators in the soil are a primary cause of bacterial cell death. Yet, most functional genomic studies on soil bacteria have been performed without predation, thereby selecting for phenotypes impacting growth rather than survival and biasing our view on the ecological factors driving genomic evolution. Here, we study how predation by the ubiquitous amoebal predator Dictyostelium discoideum affects Bacillus subtilis' growth and survival using both a genome-scale mutant screen and de novo evolution of resistance. We show that predation-related genes (many not previously identified) promote survival by enabling filament or aggregate formation, thereby outsizing D. discoideum and slowing or preventing ingestion. Importantly, we find that predation resistance is costly, causing a trade-off between growth and survival. B. subtilis navigates this trade-off through switch-like adaptations, where cells switch back-and-forth between a slow-growing resistant state and a fast-growing susceptible state. These behaviors are controlled through both genotypic and phenotypic switches, with a central role for the Spo0A phosphorylation cascade, whose ancestral function may have been to evade or slow predation. Taken together, we uncover how the antagonist selection pressure imposed by predation is an important ecological driver of phenotypic heterogeneity in B. subtilis.},
}

*Bacillus subtilis/genetics/physiology/growth & development
*Dictyostelium/physiology
*Adaptation, Physiological
Bacterial Proteins/metabolism/genetics
Phenotype

@article {pmid40990948,
year = {2025},
author = {Basu, A and Mondal, S and Roy, A and Tewari, S and Chattopadhyay, S and Ghosh, A and Sil, AK},
title = {Paraclostridium sp. AKS46 vesicles facilitate extracellular electron transport.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf239},
pmid = {40990948},
issn = {1365-2672},
abstract = {AIMS: Paraclostridium sp. AKS46 was shown to have high exoelectrogenic activity. The current study investigated whether membrane vesicles (MVs) contribute to this electrogenic activity of this organism.

METHODS AND RESULTS: To examine the contribution of MVs to electrogenic activity, formation of MVs was first investigated by microscopic analyses of AKS46 cells at different time points of growth. The results showed increasing MV formation with time, especially in electrode-attached cells. To test electrogenic activity, the redox property and the electrochemical activity of the vesicles were examined. To this end, purified AKS46 vesicles demonstrated robust redox activities, and cyclic voltammetry and electrochemical impedance spectroscopy revealed high electrochemical properties of purified vesicles. Furthermore, proteomic analysis of the vesicles identified the presence of redox-active proteins, particularly flavoproteins, which might significantly contribute to electron carrier properties. AKS46 MVs also harbour enzymes involved in CO2 and nitrogen fixation, suggesting their roles in nutrient cycling and maintaining microbial ecology.

CONCLUSION: The exoelectrogenic gram-positive bacteria Paraclostridium sp. AKS46 produces extracellular vesicles packed with electron-rich molecules and thus, these vesicles act as electron transporters. The work highlights a vesicle-mediated mechanism for energy harvesting from waste degradation in microbial fuel cells.},
}

@article {pmid40990516,
year = {2025},
author = {Wang, Y and Xu, J and Liu, Y and Liu, L and Xiao, S and Wang, X and Zhang, J and Huang, S and Zheng, Q},
title = {Ocean currents and environmental gradients shape prokaryotic community structure and function in the South China Sea.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0102025},
doi = {10.1128/spectrum.01020-25},
pmid = {40990516},
issn = {2165-0497},
abstract = {UNLABELLED: The South China Sea (SCS) is characterized by complex hydrodynamic conditions that influence the structure and function of prokaryotic microbial communities. This study conducted a comprehensive analysis of prokaryotic diversity, community assembly, and functional potential across various water masses within the SCS. Using 16S rRNA gene sequencing and co-occurrence network analyses, we found that geographic distance and environmental gradients, particularly temperature and nutrient levels, significantly impacted community composition. Our findings indicate that ecological drift is the primary mechanism governing community assembly, with spatial turnover primarily driven by the dispersal of microorganisms facilitated by ocean currents. Distinct modules in co-occurrence networks were associated with specific environmental factors, reflecting potential environmental selection processes along the SCS current. Keystone species and biomarkers identified through network analysis and random forest modeling exhibited varying associations with environmental variables, highlighting their adaptability to changing conditions. This work underscores the importance of ocean currents and environmental factors in shaping prokaryotic community dynamics and provides insights into microbial biogeography and ecosystem function in the SCS.

IMPORTANCE: Microorganisms, especially prokaryotes, are fundamental in sustaining marine ecosystems through nutrient cycling and organic matter decomposition. However, understanding what shapes their diversity and distribution remains challenging. Our study highlights the significant role ocean currents and environmental conditions play in influencing prokaryotic communities in the South China Sea-a critical marine environment due to its dynamic currents and ecological complexity. We found that currents facilitate microbial dispersal, shaping community composition over vast areas, while temperature gradients act as key selective pressures, determining which species thrive. Additionally, we reveal that both predictable environmental selection and random ecological drift significantly contribute to community structuring. By identifying keystone microbes and biomarkers sensitive to environmental change, our work offers essential insights into marine microbial ecology. These findings are crucial for predicting how microbial communities, and thus ocean health and productivity, respond to ongoing environmental changes.},
}

@article {pmid40989908,
year = {2025},
author = {Lopez-Alforja, X and Sà, EL and Quiroga, MV and Pernice, MC and Cardelús, C and Balagué, V and Gasol, JM and Coutinho, FH and Massana, R and Vaqué, D},
title = {Long-term decline of marine viruses associated with warming and oligotrophication at a NW Mediterranean coastal site.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf150},
pmid = {40989908},
issn = {2730-6151},
abstract = {Viruses play key roles in controlling microbial abundance and community composition, nutrient cycling, and productivity in marine systems. Rising ocean temperatures, alongside increasing oligotrophy, are expected to alter the availability of inorganic nutrients and oxygen-key environmental factors that shape microbial community structure and virus-host interactions. While many studies have investigated viral abundances and community structure across spatial gradients, less is known about their long-term temporal variations, which is particularly relevant in the current context of global change. To address this gap, we analyzed two decades of surface water data from the Blanes Bay Microbial Observatory, located at the North-Western Mediterranean, to describe how biotic and abiotic variables influence temporal dynamics of viral abundances and community composition. Statistical tools for time series, including GAMMs, anomaly analysis, and neural networks, allowed us to demonstrate that viral abundance follows strong seasonality and a clear decrease starting midway (ca. 2011) through the sampled period (2005-2022). Fingerprint analysis evidenced that viral community composition was significantly influenced by seasonality and some environmental and biotic factors, with strong differences in viral communities between summer and winter months. Our analyses revealed that over the last 18 years, the abundance of most microbial groups, including viruses and their potential hosts, has declined, coinciding with an increase in seawater temperature and transparency, as well as a notable decrease in nutrient concentrations and phytoplankton biomass. We identified the ongoing shift toward more oligotrophic conditions as a potential driver of the observed decline in viral abundance, particularly in the last decade.},
}

@article {pmid40989192,
year = {2025},
author = {Alfahl, Z and O'Connor, L and Morris, D and Smith, TJ and O'Dwyer, J and Hynds, PD and Cormican, M and Burke, LP},
title = {A novel enrichment-free, low-volume filtration and rapid lysis (ELR) method in combination with real-time PCR for detection of Shiga toxin-producing Escherichia coli (STEC) in water.},
journal = {Access microbiology},
volume = {7},
number = {7},
pages = {},
pmid = {40989192},
issn = {2516-8290},
abstract = {Consequences of Shiga toxin-producing Escherichia coli (STEC) infection can range in severity from asymptomatic infection to haemolytic uraemic syndrome, renal failure and death. Groundwater-derived drinking water is an important route for STEC transmission. Detection of STEC in water is crucial for timely response and public health interventions; however, currently used culture-based methods are time-consuming and laborious. Therefore, there is a need for rapid methods that maintain high sensitivity and specificity [1]. We describe a novel, sensitive, enrichment-free water filtration method using a convenient sample volume (100 ml) to detect DNA markers of STEC serogroups and virulence factors within 6 h. Quantitative real-time PCR (qPCR) was used to detect and quantify the most common STEC infection-associated serogroups globally, O157 and O26. Real-time PCR was used to detect genetic determinants of STEC virulence (stx1, stx2 and eae genes) and specific marker genes for the clinically relevant serogroups O111, O103, O145 and O104. Results showed that the novel method can detect as low as 5 c.f.u. ml[-1] of STEC in water. The limit of detection for O157 and O26 qPCR assays was two and six copies, respectively. Groundwater and surface water samples (n=28) were collected and processed using the novel method. STEC O157 and O26 serogroups were detected in 23 out of 28 (82.1%) samples (mean 5.2×10[4] copies/reaction) and 19 out of 28 (67.9%) samples (mean 7.83×10[4] copies/reaction), respectively. Shiga toxin genes stx1 or stx2 were detected in 15 out of 28 (53.6%) and 9 out of 28 (32.1%) samples, respectively. The virulence factor intimin gene eae was detected in 24 out of 28 (85.7%) samples. STEC serogroups O111, O103, O145 and O104 were detected in 15 out of 28 (53.6%), 10 out of 28 (35.7%), 11 out of 28 (39.3%) and 15 out of 28 (53.6%) samples, respectively. This novel method reproducibly detects low copies of STEC in low-volume fresh water and has the potential to be used for the detection and quantification of waterborne bacterial pathogens.},
}

@article {pmid40987850,
year = {2025},
author = {Laso-Pérez, R},
title = {Deep-mining the archaeal proteome for antibiotics.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40987850},
issn = {2058-5276},
}

@article {pmid40987416,
year = {2025},
author = {Liaqat, F and Khazi, MI and Ismail, W},
title = {Microbial transport systems of organic sulfur compounds: Diversity and implications for biocatalysis, healthcare, and environmental biotechnology.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108718},
doi = {10.1016/j.biotechadv.2025.108718},
pmid = {40987416},
issn = {1873-1899},
abstract = {The global sulfur cycle plays a vital role in human health, global warming and biogeochemistry. Organic sulfur compounds constitute a substantial sulfur reservoir and serve as an energy and/or carbon source for prokaryotes. In addition, microbial interactions with organic sulfur compounds are pivotal for several biotechnological applications in petroleum biorefining, industrial biocatalysis, bioremediation, healthcare, and plant growth promotion. Microbial degradation of organic sulfur compounds is hindered by slow degradation rates, substrate specificity, toxicity of by-products, and challenges in scalability and efficiency. While degradation pathways of some organic sulfur compounds have been elucidated, transport systems involved in their uptake and efflux remain less explored. Regulating the uptake and efflux of organic sulfur compounds in microorganisms can help overcome several of the limitations associated with their transformation. Membrane transporters are not only crucial for uptake and efflux of organic sulfur compounds but also play a key role in stress tolerance by facilitating the excretion of toxic metabolites. Understanding the intricacies of these transporters provides valuable insights into microbial ecology and the development of strategies for harnessing microbial sulfur metabolism for important biotechnological applications. This review systematically presents the diversity, mechanisms, and potential evolution pathways of microbial membrane transporters involved in organic sulfur compounds acquisition. Furthermore, it highlights and discusses advances in the characterization of transporter systems and current limitations in using transporter systems for fuel biodesulfurization and organic sulfur compound degradation. Eventually, we explore the implications of organic sulfur compounds transporters in biotechnology and identify future research directions toward leveraging the biotechnological potential of microbial sulfur metabolism, fueled by advanced techniques of systems microbiology, metabolic engineering, as well as artificial intelligence.},
}

@article {pmid40986398,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {10},
pages = {},
doi = {10.1093/femsec/fiaf084},
pmid = {40986398},
issn = {1574-6941},
}

@article {pmid40985999,
year = {2025},
author = {Lennon, JT and Bittleston, LS and Chen, Q and Cooper, VS and Fernández, J and Gilbert, JA and Häggblom, MM and Harper, LV and Jansson, JK and Jiao, N and Kuurstra, EM and Peixoto, RS and Rappuoli, R and Schembri, MA and Ventosa, A and Vullo, DL and Zhang, C and Nguyen, NK},
title = {Microbes without borders: uniting societies for climate action.},
journal = {mBio},
volume = {},
number = {},
pages = {e0213625},
doi = {10.1128/mbio.02136-25},
pmid = {40985999},
issn = {2150-7511},
abstract = {The climate crisis is one of the greatest challenges of our time, yet the role of microorganisms remains underrecognized in climate science and policy. Microbes are highly sensitive to environmental change and regulate essential biogeochemical processes, while also offering solutions for reducing emissions, restoring ecosystems, and enhancing resilience. Microbiology societies from five continents recently convened in Washington, DC, for the inaugural Global Strategy Meeting on Microbes and Climate Change. The gathering launched a global alliance to position microbial science as a pillar of climate action and identified four priorities: building a coalition, embedding microbes in climate frameworks, transforming communication, and advancing real-world demonstration projects. This initiative marks the beginning of coordinated global action to harness microbial life for climate solutions.},
}

@article {pmid40985636,
year = {2025},
author = {Grosso Giordano, F and Mariën, Q and De Belie, N and Rodriguez-Navarro, C and Boon, N},
title = {Characterization of isolates used in bacterial-based strategies for accelerated carbonation of lime mortars.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/aem.00683-25},
pmid = {40985636},
issn = {1098-5336},
abstract = {Portland cement largely replaced hydraulic lime over the past century because of its rapid hardening. Achieving earlier hardening in lime through faster carbonation is thus essential to help overcome one of lime's limiting qualities. Here, we isolated two alkaliphilic bacteria, Shouchella clausii and Shouchella patagoniensis, from a lime mortar wall. S. clausii was then further grown in high pH (>11) by adaptive laboratory evolution to acclimate a third isolate. Bacterial suspensions of all three isolates were followed for 14 days in serum bottles at pH 11, and gas composition of the headspace, intact/damaged cell populations, and pH were measured. In parallel, lime mortar samples were incubated in a closed environment with bacterial suspension of the isolates and analyzed with thermogravimetric analysis after 7 and 14 days to quantify carbonation. S. patagoniensis produced more CO2, close to the estimated maximum CO2 uptake rate of lime, and carbonated the lime mortars to a larger extent than the other isolates. Finally, the bacterial suspensions were directly mixed with lime. A linear and homogeneous carbonation of the paste samples was measured compared to water-based pastes, and the development of Liesegang patterns was observed upon phenolphthalein spreading. All this indicated that the organic addition altered the carbonation dynamics of the material, although bacteria did not accelerate carbonation relative to media alone and inhibited it relative to water-based paste. Still, a relationship between bacterial activity, CO2 emission, and carbonation rate was established, but practical aspects of bacterial delivery into lime must be addressed.IMPORTANCEPortland cement is the dominant binder used in most construction today, but until last century, lime was the ubiquitous construction material. The increase in use of cement has sprung from its higher strength and faster hardening; yet, lime still remains a relevant material, particularly in masonry structures and the built heritage. As such, novel lime materials are necessary to tackle some of the current limitations of lime, such as earlier hardening, which would not only make lime easier to work with but would also limit failure due to environmental conditions. As existing strategies to speed up lime hardening have had limited uptake due to their reliance on expensive and often toxic chemicals, the need for novel solutions is in place. We show that bacterial-based strategies could be a viable option to go beyond the limitations of current strategies, but limitations are in place.},
}

@article {pmid40985445,
year = {2025},
author = {Shen, K and Tang, Y and Shi, J and Hu, Z and He, M and Li, J and Wang, Y and Shao, M and Liu, H},
title = {Relationship Between Aquatic Fungal Diversity in Surface Water and Environmental Factors in Yunnan Dashanbao Black-Necked Crane National Nature Reserve, China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/jof11070526},
pmid = {40985445},
issn = {2309-608X},
support = {2024//Yunnan Provincial Department of Education Scientific and Technological Innovation Team for Development and Utilization of Gastrodia Resources/ ; 202110BA070001-059//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities' Association/ ; 2023-3//Zhaotong "Xingzhao Talent Support Program" Team Project/ ; },
abstract = {Aquatic fungi serve as core ecological engines in freshwater ecosystems, driving organic matter decomposition and energy flow to sustain environmental balance. Wetlands, with their distinct hydrological dynamics and nutrient-rich matrices, serve as critical habitats for these microorganisms. As an internationally designated Ramsar Site, Yunnan Dashanbao Black-Necked Crane National Nature Reserve in China not only sustains endangered black-necked cranes but also harbors a cryptic reservoir of aquatic fungi within its peat marshes and alpine lakes. This study employed high-throughput sequencing to characterize fungal diversity and community structure across 12 understudied wetland sites in the reserve, while analyzing key environmental parameters (dissolved oxygen, pH, total nitrogen, and total phosphorus). A total of 5829 fungal operational taxonomic units (OTUs) spanning 649 genera and 15 phyla were identified, with Tausonia (4.17%) and Cladosporium (1.89%) as dominant genera. Environmental correlations revealed 19 genera significantly linked to abiotic factors. FUNGuild functional profiling highlighted saprotrophs (organic decomposers) and pathogens as predominant trophic guilds. Saprotrophs exhibited strong associations with pH, total nitrogen, and phosphorus, whereas pathogens correlated primarily with pH. These findings unveil the hidden diversity and ecological roles of aquatic fungi in alpine wetlands, emphasizing their sensitivity to environmental gradients. By establishing baseline data on fungal community dynamics, this work advances the understanding of wetland microbial ecology and informs conservation strategies for Ramsar sites.},
}

@article {pmid40983756,
year = {2025},
author = {Dong, S and Wang, S and Li, L and Yu, J and Zhang, Y and Xue, JY and Chen, H and Ma, J and Zeng, Y and Cai, Y and Huang, W and Zhou, X and Wu, J and Li, J and Yao, Y and Hu, R and Zhao, T and Villarreal A, JC and Dirick, L and Liu, L and Ignatov, M and Jin, M and Ruan, J and He, Y and Wang, H and Xu, B and Rozzi, R and Wegrzyn, J and Stevenson, DW and Renzaglia, KS and Chen, H and Zhang, L and Zhang, S and Mackenzie, R and Moreno, JE and Melkonian, M and Wei, T and Gu, Y and Xu, X and Rensing, SA and Huang, J and Long, M and Goffinet, B and Bowman, JL and Van de Peer, Y and Liu, H and Liu, Y},
title = {Bryophytes hold a larger gene family space than vascular plants.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40983756},
issn = {1546-1718},
abstract = {After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.},
}

@article {pmid40981669,
year = {2025},
author = {Riisgaard-Jensen, M and Valença, RM and Peces, M and Nielsen, PH},
title = {Sewer microbiomes shape microbial community composition and dynamics of wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf213},
pmid = {40981669},
issn = {1751-7370},
abstract = {The link between the sewer microbiome and microbial communities in activated sludge wastewater treatment plants is currently poorly understood despite the systems being directly interconnected. Microbial immigration from wastewater has been identified as a key factor determining activated sludge community assembly. Here, we present the first comprehensive study of the sewer microbiome and hypothesize that it harbors a process-critical activated sludge microbes, thus critical for activated sludge community assembly and performance. We integrated species-level microbial analyses of biofilm, sediment, and sewer wastewater in domestic gravity and pressure sewers in Aalborg, Denmark, with samples from influent wastewater and activated sludge from two downstream wastewater treatment plants. By tracing the sources of incoming bacteria and determining their growth fate in the activated sludge, we confirmed the hypothesis that most activated sludge process-critical bacteria were part of the sewer microbiome. Within the sewer system, a gradient was observed, from dominance of gut-bacteria in the wastewater upstream to prevalence of biofilm and sediment bacteria downstream at the wastewater treatment plants inlet, with the relative ratio strongly affected by rain events. A holistic understanding of the sewer system and activated sludge is essential, as the sewers hold massive amounts of active biomass serving as a major microbial source for community composition and dynamics in wastewater treatment plants. Sewer systems should be recognized as a crucial environmental filtration step, and the sewer microbiome as an important source community for activated sludge, helping to explain the observed regional and global differences in activated sludge community structure.},
}

@article {pmid40981467,
year = {2025},
author = {Qiao, Y and Wang, L and Wang, S and Li, S and Wang, F and Wang, B and Lin, S and Liu, Y},
title = {Bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity of the algae-associated microbiome throughout the growth cycle of Alexandrium pacificum.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0135925},
doi = {10.1128/aem.01359-25},
pmid = {40981467},
issn = {1098-5336},
abstract = {The algae-associated microbiome represents a consortium that has been chronically domesticated by specific algae, maintaining a close relationship with the host population. Although the microbes associated with dinoflagellates have garnered significant attention in recent years, the interactions and contributions of microbial generalists and specialists through the growth cycle of a bloom-forming dinoflagellate remain largely unexplored. Herein, the ecological and evolutionary characteristics of free-living generalists and specialists within bacterial and fungal communities were investigated during the growth process of Alexandrium pacificum cultured in the laboratory for years without antibiotic treatment. From an ecological perspective, bacterial generalists and fungal specialists dominated the community, indicating different microbial niche patterns between the bacterial and fungal consortia. Furthermore, microbial specialists were more susceptible to disturbance from algal proliferation, as evidenced by greater community dissimilarity and determinacy-dominated assembly processes. Compared with their counterparts, the molecular networks of bacterial generalists and fungal specialists were more complex and robust, suggesting that they significantly contributed to resistance to environmental stress and functional maintenance. Evolutionarily speaking, bacterial generalists and fungal specialists showed much higher diversification potential, and others featured higher extinction rates. Despite these differences, a continuous transition from the former two to their counterparts was observed, alleviating the "Matthew effect" in the biological world for ecological trade-offs. Collectively, these findings emphasize that bacterial generalists and fungal specialists play important roles in maintaining community stability and regulating microbial diversity during the growth process, which expands the current understanding of the maintenance mechanisms of the diversity and community of phytoplankton-associated microbes in the face of disturbance from bloom-forming dinoflagellates.IMPORTANCELike the microbes residing in the rhizosphere and human gut, bacteria that coexist chronically with microalgae exemplify a relationship, forming potentially intimate partnerships with the host. However, studies on the ecological significance of algae-associated microbiomes with different niches under the interference of bloom-forming species are still lacking. This work investigated the ecological interactions and contributions of generalists and specialists within algae-associated bacterial and fungal communities across the growth cycle of Alexandrium pacificum for the first time. These results increase the understanding of the microbial ecology of algae-associated microbes in the context of interference from the proliferation of harmful algal bloom species.},
}

@article {pmid40981420,
year = {2025},
author = {Wing, AJ and Hegarty, B and Bastien, GE and Denef, VJ and Evans, J and Dick, GJ and Duhaime, MB},
title = {Tracking putative Microcystis viruses and virus-host associations across distinct phases of a Microcystis-dominated bloom.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057525},
doi = {10.1128/msystems.00575-25},
pmid = {40981420},
issn = {2379-5077},
abstract = {Viruses significantly impact microbial community composition and function. Yet their role in the fate of freshwater cyanobacterial harmful algal blooms (cHABs), an increasing threat to freshwater systems, remains poorly understood. Here, we address this with a metagenomic analysis of viruses of bloom-forming Microcystis aeruginosa through a seasonal cHAB in the western basin of Lake Erie. We identified globally distributed Microcystis viruses in Lake Erie based on sequence homology to well-studied isolates. A machine-learning model was then used to predict associations between uncharacterized viral populations and the Microcystis and non-Microcystis hosts of the cHAB. Size fractionation of water samples allowed us to identify significant fraction-specific trends in Microcystis viral diversity that corresponded with Microcystis genetic diversity. Viral diversity was highest in the non-colony-associated fraction and lowest in the colony-associated fraction, suggesting that colony formation may lead to bottlenecks in viral diversity in cHABs. Significant turnover of predicted Microcystis virus populations was observed through time, but not between stations miles apart. The virus-host networks revealed extensive interconnectivity and the potential for virus-mediated cross-species genetic exchange. The networks predicted that Lake Erie Microcystis viruses infect hosts spanning phyla, in agreement with lab studies in other systems but challenging previous notions of "narrow" host-virus associations in this genus. Abundant Microcystis virus genes revealed a potential role in key metabolic pathways and host adaptation. These findings advance our understanding of Microcystis viruses and their potential influence on host metabolism, species interactions, and coevolution in Microcystis-dominated cHABs.IMPORTANCEUnderstanding associations between viruses, their hosts, and environmental factors is key for identifying the mechanisms behind the rise and fall of cyanobacterial harmful algal blooms. This study explores the diversity and host ranges of viruses predicted to infect Microcystis, reporting how these properties vary over time, across sample stations in western Lake Erie, and among different filter size fractions. We found that Microcystis virus diversity is highest in non-colony-associated fractions and the lowest in colony-associated fractions, suggesting a link between Microcystis colony formation and reduced viral diversity. We identify abundant genes belonging to predicted Microcystis viruses and their potential roles in key metabolic pathways and adaptation to environmental changes. These findings enhance our understanding of the interplay among viruses, Microcystis, and co-occurring bacteria in cHABs, offering insights into the mechanisms driving bloom dynamics, species interactions, and coevolutionary processes.},
}

@article {pmid40980873,
year = {2025},
author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR},
title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0060125},
doi = {10.1128/msystems.00601-25},
pmid = {40980873},
issn = {2379-5077},
abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.

IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.},
}

@article {pmid40980756,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {40980756},
issn = {2331-8422},
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologs or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems including human microbiomes, soil, oceans, and extreme environments, and discuss what is known, and still unknown, about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization, and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation, and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}