@article {pmid41443112,
year = {2025},
author = {Cao, Y and Xu, Y and Yan, C and Lu, Z and Zhou, Q and Wang, J and Wang, Y and Cheng, L and Zhang, L and He, Y and Guo, B and Li, B},
title = {Comparing the performance of targeted next-generation sequencing and metagenomic next-generation sequencing in diagnosing pneumonia: A systematic review and network meta-analysis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {3},
pages = {117234},
doi = {10.1016/j.diagmicrobio.2025.117234},
pmid = {41443112},
issn = {1879-0070},
abstract = {BACKGROUND: In terms of diagnosing pneumonia, there is currently limited evidence for a direct comparison of the performance of targeted next-generation sequencing (tNGS) and metagenomic next-generation sequencing (mNGS), and is no comprehensive conclusion yet. This systematic review and network meta-analysis (NMA) aimed to comprehensively compare the diagnostic performance of tNGS and mNGS in patients with pneumonia.

METHODS: A systematic literature search was conducted across PubMed, Embase, the Cochrane Library, and Web of Science. From the establishment of the database to September 10, 2025. Studies providing diagnostic data (true positive, false positive, false negative, true negative) for tNGS and/or mNGS in patients suspected of pneumonia were included. We conducted a frequency theory random effects network meta-analysis, and calculate pooled odds ratios (ORs) with 95 % confidence interval (CI) for sensitivity and specificity, and to rank diagnostic performance using surface under the cumulative ranking curve (SUCRA) values. Subgroup analyses based on sample type and patient status were conducted.

RESULTS: The NMA revealed no statistically significant differences in overall sensitivity (OR = 1.54, 95 % CI [0.47-5.06]) or specificity (OR = 1.29, 95 % CI [0.39-4.28]) between tNGS and mNGS. SUCRA rankings indicated that tNGS had the highest cumulative probability for sensitivity (91.9 %), followed by mNGS (74.6 %), and the cumulative specificity probability of tNGS (37.8 %) is higher than that of mNGS (17.1 %). In subgroup analysis, when multiple sample types were used, tNGS showed significantly higher specificity than mNGS (OR = 4.95, 95 % CI [1.13-21.75]).

CONCLUSION: These findings suggest tNGS may be a more specific and potentially cost-effective option for the etiological diagnosis of pneumonia, particularly when multi-sample testing is employed.},
}

@article {pmid41442943,
year = {2025},
author = {Huang, J and Zhang, J and Klümper, U and Guo, J and Berendonk, TU and Honda, R and Liang, H and Lin, L and Li, X and Li, B},
title = {Combined exposure of enrofloxacin and disinfection byproducts under environmentally relevant concentrations enhances antibiotic resistance risks in livestock wastewater.},
journal = {Water research},
volume = {291},
number = {},
pages = {125189},
doi = {10.1016/j.watres.2025.125189},
pmid = {41442943},
issn = {1879-2448},
abstract = {Livestock wastewater is a crucial source of antibiotic resistance. However, the impact of disinfection byproducts (DBPs), stemming from disinfectants commonly used in livestock farming, on antibiotic resistance has scarcely been explored at the community level. Moreover, the combined effects of these DBPs with antibiotic pressure remain unknown. Herein, we added one antibiotic enrofloxacin, and two typical DBPs trichloromethane (TCM) and trichloroacetic acid (TCAA), individually or in combination to bioreactors simulating the biotreatment of livestock wastewater. Our time-series metagenomic analysis over 120 days showed that pollutant exposure significantly increased the abundance of antibiotic resistance genes (ARGs), elevating the peak ARG abundance by 23.4 % to 85.4 % compared to the control group. An increasing trend of ARG abundance was observed in the TCAA, enrofloxacin+TCAA, and enrofloxacin+TCM groups with increasing exposure time. Exposure to DBPs alone or in combination with enrofloxacin did not significantly increase the ARG copy number per cell compared to individual enrofloxacin exposure. However, under co-exposure to enrofloxacin and DBPs, the diversity of antibiotic-resistant bacteria (ARB) was significantly higher than those in both the control group and the single enrofloxacin group, indicating a stronger driving effect of combined exposure on the dissemination of ARGs. Genomic-centric analysis revealed a significant increase in the relative abundance of ARB when exposed to combined enrofloxacin and DBPs and individual TCM groups at environmentally relevant concentrations. We discovered that plasmids and integrative and conjugative elements (ICEs) play more essential roles in the spread of ARGs compared to that of integrons and phages. The relative abundance of ARB carrying shared ARGs on both chromosome and plasmids remained nearly stable in control groups but increased to varying extents in all treatment groups. The ARG-carrying ICEs were enriched when exposed to enrofloxacin, TCM, and TCAA alone. The long-term exposure of enrofloxacin or DBPs was in relation with the enrichment of putative pathogenic ARB. Overall, the increased antibiotic resistance levels and the co-occurrence of ARGs, virulence factors, and mobile genetic elements (MGEs) resulting from long-term exposure to enrofloxacin or DBPs underscore the considerable microbial risk associated with the release of ARGs from livestock wastewater.},
}

@article {pmid41442899,
year = {2025},
author = {Leonard, SR and Mammel, MK and Richter, TKS and Simko, I and Brandl, MT},
title = {Metagenomic characterization of the antibiotic, biocide, and metal resistome of soil and romaine lettuce from the field through processing and storage.},
journal = {International journal of food microbiology},
volume = {448},
number = {},
pages = {111595},
doi = {10.1016/j.ijfoodmicro.2025.111595},
pmid = {41442899},
issn = {1879-3460},
abstract = {The presence of antimicrobial resistance genes (AMRGs) on crops is of concern to public health since plant-derived foods may serve as vectors of AMRGs to human pathogens. This study mined the bacterial metagenomes of soil and lettuce from harvest through processing and storage to characterize their comprehensive resistomes (antibiotics, metals, and biocides). Cold-stored lettuce had the greatest number of AMRG reads per million of all sample types. AMRGs were overall dominated by metal resistance determinants, except those of processed lettuce (cut, washed in chlorinated water, and rinsed), which were heavily enriched in genes encoding biocide resistance. The greatest percentage of drug resistance genes, when averaged over all sample types, belonged to resistance to β-lactams (30 %) followed by aminoglycosides (6.7 %); and specific allele sequences from both classes were observed in common between lettuce and soil sampled next to lettuce heads. Genes for resistance to β-lactams were in highest relative abundance (RA) on cold-stored lettuce and lowest in soil. Several extended-spectrum β-lactamase genes and the colistin resistance gene mcr-9.1 were detected in the cold-stored lettuce resistome. Harvest season and field type had a significant effect on the comprehensive resistome of most sample types (PERMANOVA, P < 0.05). Notably, the RA of β-lactams resistance genes in the drug resistome of cold-stored lettuce represented 17.4 % and 2.0 % in spring vs. fall, and 11.3 % and 3.9 % in the commercial vs. experimental field, respectively. This study highlights the multifactorial role of the biotic and abiotic environment on the comprehensive resistome of lettuce during production and storage.},
}

@article {pmid41442808,
year = {2025},
author = {Wang, X and Chen, M and Zhang, X and Han, X and Hu, Y and Wang, X and Li, X and Zhang, D},
title = {Effect of sodium percarbonate in mitigating lactic acid inhibition and enhancing system performance during anaerobic digestion of acidified food waste.},
journal = {Journal of environmental management},
volume = {398},
number = {},
pages = {128411},
doi = {10.1016/j.jenvman.2025.128411},
pmid = {41442808},
issn = {1095-8630},
abstract = {Food waste treatment poses a critical environmental challenge amid urbanization, and its resource recovery efficiency is hindered by acidification. In this study, sodium percarbonate (SPC) was used to treat acidified food waste. The results showed that SPC increased the short-chain fatty acids (SCFAs) production during anaerobic digestion from 363.89 ± 11.55 mg COD/L (control) to 15,431.60 ± 329.94 mg COD/L (0.4 g/g TSS). Quenching experiments revealed that CO3·[-] and ·O2[-] were the main reactive species from SPC responsible for promoting SCFAs generation and lactic acid degradation. High-throughput sequencing analysis indicated that SPC pretreatment enhanced the diversity and abundance of functional microbial communities involved in anaerobic digestion. Metagenomic analysis further demonstrated that pretreatment increased gene abundances related to organic matter metabolism, tricarboxylic acid cycle, acidogenesis, and methanogenic modules, thereby contributing to enhanced anaerobic digestion performance. This study elucidated the underlying impact mechanisms of SPC on the anaerobic digestion of acidified food waste, providing valuable insights for optimizing the efficient resource recovery of waste.},
}

@article {pmid41442804,
year = {2025},
author = {Zhang, K and Zheng, J and Liu, K and Gao, L and Bi, R and Ji, F},
title = {Optimizing intermittent rotary aeration to enhance efficiency and reduce greenhouse gas and ammonia emissions during fish manure composting.},
journal = {Journal of environmental management},
volume = {398},
number = {},
pages = {128414},
doi = {10.1016/j.jenvman.2025.128414},
pmid = {41442804},
issn = {1095-8630},
abstract = {The treatment of fish manure from industrial recirculating aquaculture systems (IRAS) is challenging due to its low carbon-to-nitrogen (C/N) ratio and poor separability. This study investigated the optimization of composting efficiency and greenhouse gas mitigation for such manure using a rotating-bin system. A self-developed concentration technique was employed to obtain the feedstock, which was composted under varying rotational aeration frequencies. We comprehensively assessed the process by analyzing physicochemical parameters, product maturity, gas emissions (N2O, CH4, NH3, CO2), and microbial community metagenomics. Results identified an intermittent aeration regime of 5-min rotation followed by a 45-min rest (Treatment D) as optimal. Only Treatment D produced mature compost, achieving a seed germination index of 83.76 %. Critically, this regime reduced cumulative emissions of N2O, CH4, and NH3 by 47.6 %, 56.5 %, and 47.9 %, respectively, compared to continuous aeration, with a 44.2 % reduction in total CO2-equivalent emissions. Metagenomic analysis linked this improvement to a 23.5-31.2 % higher relative abundance of key nitrogen-cycle genes (amoA, hao), enhancing organic nitrogen assimilation and humification. This work demonstrates that optimized intermittent aeration in rotating bins significantly advances the sustainable, low-emission composting of fish manure from IRAS.},
}

@article {pmid41442770,
year = {2025},
author = {Liu, C and Zhang, L},
title = {Biomarkers.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e103718},
doi = {10.1002/alz70856_103718},
pmid = {41442770},
issn = {1552-5279},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; *Apolipoprotein E4/genetics ; Aged ; *Biomarkers ; *Alzheimer Disease/genetics/microbiology ; Feces/microbiology ; Middle Aged ; },
abstract = {BACKGROUND: The gut-brain axis hypothesis proposes a bidirectional communication network between the gut microbiome and the central nervous system, shaping neuroinflammatory processes linked to Alzheimer's disease (AD). Although the APOE4 allele is the strongest genetic risk factor for AD-raising the likelihood of disease by two- to three-fold with even one copy-its association with the gut microbiome remains underexplored. This gap limits our full understanding of the pathways contributing to AD.

METHOD: We investigated the relationship between APOE4 status and gut microbiome composition in 114 healthy participants (average age: 77, 57% women). Stool samples underwent shotgun metagenomic sequencing. Rigorous quality control steps removed low-quality reads and human DNA contaminants. We performed taxonomic profiling and applied rarefaction to normalize sequencing depth. Alpha diversity (richness and evenness) and beta diversity (unweighted UniFrac-based principal coordinates analysis) were assessed. We then used permutational multivariate analysis of variance, adjusting for demographic and clinical variables, to identify group differences. Differential taxonomic analysis pinpointed bacterial taxa enriched in APOE4 carriers versus non-carriers.

RESULT: Alpha diversity metrics did not differ significantly between APOE4 carriers and non-carriers at the species level (p = 0.070). However, beta diversity analysis showed significant differences in overall community composition after adjusted by the covariates (p = 0.003), and APOE4 carrier status remained significant in PERMANOVA (p = 0.039). Furthermore, subgroup analysis of APOE4 genotypes (2/4, 3/4, 4/4) also revealed significant compositional differences (p = 0.030). Differential taxonomic analysis identified 21 species enriched in APOE4 carriers and 20 species enriched in non-carriers. Among non-carriers, Alistipes finegoldii (p = 0.035) and Odoribacter splanchnicus (p = 0.024) were more abundant. These species are involved in metabolic pathways related to short-chain fatty acid production, which can have anti-inflammatory effects. Their presence suggests a protective gut microbiome-mediated mechanism in individuals without the APOE4 allele.

CONCLUSION: Our findings suggest that APOE4 carriers have distinct gut microbiome patterns that may heighten the risk of neuroinflammation through the gut-brain axis, potentially contributing to AD onset or progression. These results highlight the interplay between genetic risk factors and gut microbial communities. They also underscore the potential for microbiome-targeted interventions to reduce AD risk in genetically susceptible individuals.},
}

Humans
Female
Male
*Gastrointestinal Microbiome/genetics
*Apolipoprotein E4/genetics
Aged
*Biomarkers
*Alzheimer Disease/genetics/microbiology
Feces/microbiology
Middle Aged

@article {pmid41442682,
year = {2025},
author = {Monzón, ÁRR and Ramos, JFO and Narvaez, YC and Rosales, MH},
title = {Biomarkers.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e097688},
doi = {10.1002/alz70856_097688},
pmid = {41442682},
issn = {1552-5279},
mesh = {Humans ; *Biomarkers/metabolism ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/metabolism/microbiology ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Metabolomics ; Middle Aged ; Adult ; Aged ; Young Adult ; },
abstract = {BACKGROUND: T2DM and AD are major public health concerns characterized by metabolic and cognitive impairments, respectively, with growing evidence suggesting that gut microbiota alterations contribute to their pathogenesis. Metagenomic and metabolomic analyses provide valuable insights into the microbiota's role in glucose regulation, inflammation, and dementia risk, offering potential for early diagnosis and targeted interventions. Understanding the interplay between gut microbiota and metabolic pathways could lead to novel therapeutic strategies to improve patient outcomes.

METHOD: A descriptive study with a quantitative approach, cross-sectional observational comparative, of relational scope will be conducted. The study population will be segmented into four groups and two subgroups: Control (CTRL) (n = 30), Type 2 Diabetes Mellitus (T2DM) (n = 30), Alzheimer's Disease (AD) without T2DM (n = 30), and AD with T2DM (n = 30). Subgroups include Control (Young adults) (n = 30) and T2DM (Young adults) (n = 30). All groups will undergo characterization, which includes blood chemistry, and clinical, mental, nutritional, and anthropometric evaluations. We obtained urine and stool samples for DNA extraction and library preparation. We used Magnetic Resonance Mass Spectrometry (MRMS) for metabolomic analysis, which uses eluents to detect metabolites. We will apply MetaHit bioinformatics tools to assess sample diversity and perform metabolomic analysis in RStudio.

RESULT: The study revealed distinct patterns of intestinal dysbiosis and metabolic changes in patients with T2DM and AD, categorized by age. A comprehensive taxonomic and functional representation of the gut microbiome highlighted condition-specific differences. Significant correlations were found between microbiological, metabolomic, and clinical biomarkers, particularly those related to cognitive decline. Key metabolic pathways and molecular processes underlying dysbiosis were identified. Fecal metabolite analysis uncovered distinctive compounds such as (+/-)-Ethylketocyclazocine, (-)-Quebrachamine, and (-)-jasmonoyl-L-isoleucine, while urinary metabolites like (Phenylthio) acetic acid and 2,3-Diketo-L-gulonate showed disease-associated variations. These findings support the development of personalized interventions to mitigate cognitive decline through microbiota and metabolomic profile modifications.

CONCLUSION: The study identifies distinct gut microbiota and metabolic patterns linked to cognitive decline in T2DM and AD, offering insights into disease mechanisms and supporting the development of personalized therapeutic strategies to improve patient outcomes.},
}

Humans
*Biomarkers/metabolism
Cross-Sectional Studies
*Diabetes Mellitus, Type 2/metabolism/microbiology
*Alzheimer Disease/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
Male
Female
Metabolomics
Middle Aged
Adult
Aged
Young Adult

@article {pmid41442661,
year = {2025},
author = {Ivanich, K and Yackzan, A and Chang, YH and Aware, C and Govindarajan, M and Kramer, S and Yanckello, LM and Ericsson, A and Lin, AL},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e104646},
doi = {10.1002/alz70855_104646},
pmid = {41442661},
issn = {1552-5279},
mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Mice, Transgenic ; Male ; Apolipoprotein E4/genetics ; *Brain/metabolism ; Mice ; *Diet, Ketogenic ; *Alzheimer Disease/genetics/metabolism ; Apolipoprotein E3/genetics ; Metabolomics ; Disease Models, Animal ; },
abstract = {BACKGROUND: The apolipoprotein ε4 (APOE4) polymorphism is the primary genetic risk factor for Alzheimer's disease (AD). APOE4 carriers exhibit early deficits in brain metabolism and gut microbiome diversity, both elevating AD risk. This study investigated whether a ketogenic diet (KD) can restore brain metabolism and gut microbiome diversity in young, asymptomatic APOE4-positive mice, while also assessing sex-based differences, given the higher AD risk in females. Comparisons were also made with APOE3 mice, which carries a neutral AD risk, to determine genotype differences. Additionally, a correlative analysis explored relationships between microbes and brain metabolites, identifying potential therapeutic and screening targets for AD risk mitigation.

METHOD: Female and male APOE3 (n =  44) and APOE4 (n =  39) transgenic mice were randomly assigned to a control diet (5.1% fat) or a KD (75.1% fat). Mice ate ad libitum for 16 weeks, starting at 12 weeks of age. Brain tissue was collected for untargeted metabolomics (UPLC-MS/MS via Metabolon Inc.), and fecal samples were collected for 16s rRNA shotgun metagenomic sequencing (CosmosID). Gut microbiome species richness and evenness were measured using Shannon index (α-diversity). Bray-Curtis dissimilarity (β-diversity) measured intra-subject dissimilarity for pre- and post-diet gut microbiome composition, and Spearman's correlation heatmaps linked metabolites and microbes to correlations within amino acid, energy, and lipid metabolic pathways.

RESULT: The KD restored brain metabolism in APOE4 females by recovering levels of metabolites associated with mitochondrial function (Figure 1A) and glutamate metabolism (Figure 1B), while exerting variable effects on these metabolites in APOE3 mice and APOE4 males. The KD increased species' richness and evenness in APOE4 females (Figure 2A) and balanced microbiome composition in APOE4 mice, as indicated by limited changes pre- and post-dietary intervention (Figure 2B). Correlation analyses revealed that Bacteroides intestinalis, Clostridium sp. ASF502, Lachnospiraceae bacterium A4, Lactobacillus johnsonii, Lactobacillus reuteri had significant associations with metabolites involved in amino acids and energy (Figure 3A) and lipid (Figure 3B) pathways.

CONCLUSION: The KD effectively restored brain metabolism and gut microbiome diversity in APOE4 female mice. These effects were absent in APOE3 mice and APOE4 males. Correlations between microbes and metabolites provide potential targets for AD interventions and risk assessment.},
}

Animals
*Gastrointestinal Microbiome
Female
Mice, Transgenic
Male
Apolipoprotein E4/genetics
*Brain/metabolism
Mice
*Diet, Ketogenic
*Alzheimer Disease/genetics/metabolism
Apolipoprotein E3/genetics
Metabolomics
Disease Models, Animal

@article {pmid41442536,
year = {2025},
author = {Kazen, AB and Umfleet, LG and Aboulalazm, FA and Cohen, AD and Terhune, S and Mason, L and Obarski, S and Franczak, M and Kindel, T and Wang, Y and Kirby, J},
title = {Biomarkers.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e097652},
doi = {10.1002/alz70856_097652},
pmid = {41442536},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Aged ; Biomarkers ; Magnetic Resonance Imaging ; Neuropsychological Tests/statistics & numerical data ; Feces/microbiology ; *Dysbiosis/microbiology ; *Cerebrovascular Circulation/physiology ; Middle Aged ; Cognition ; },
abstract = {BACKGROUND: Gut dysbiosis and cerebrovascular disease have both been implicated in Alzheimer's disease (AD) progression and pathophysiology. However, the interplay between them is unclear. The goal of this study was to identify relationships between gut microbiota (GMB), cerebrovascular functioning, and cognition in patients diagnosed with amnestic mild cognitive impairment (aMCI) compared to cognitively unimpaired older adult controls.

METHODS: Participants (N = 14 aMCI and 10 controls) provided fecal samples for 16S and shotgun metagenomics GMB sequencing, underwent an MRI, and completed neuropsychological tests. For MRI, cerebral vascular reactivity (CVR), cerebral blood flow (CBF) and arterial transit time (ATT) were assessed. Spearman rho correlational analysis was used to evaluate relationships between discriminatory microbial taxa, cerebrovascular metrics, and cognition.

RESULTS: Sequencing revealed differentially abundant bacterial and viral taxa distinguishing aMCI from controls. Spearman correlations revealed that bacteria known to induce inflammation were negatively associated with cognition and cerebrovascular function, whereas bacteria associated with a healthy gut microbiome had positive associations with cognitive and cerebrovascular function. For example, Alistipes indistinctus, which depletes intestinal urate levels was enriched in aMCI and had significant negative correlations with Trail Making Test-B (TMT-B; rs=-.587) and category fluency (CF) scores (rs=-.422), CVR (rs=-.437), and CBF (rs=-.546). Bilophila wadsworthia was negatively associated (trend-level) with CVR and CBF, and significantly correlated with TMT-B (rs = -.499) and category fluency (rs = -.503). The bile acid modifying bacterium, Turicibacter sp., had a significant positive correlation with CBF (rs=.423). Finally, we found that several bacteriophages had significant correlations with cognitive and cerebrovascular measures, such as a B. wadsworthia phage that was enriched in aMCI and had significant negative correlations with TMT-B (rs=-.491), delayed recall (rs=-.589), and CVR (rs=-.474). Further, this phage contained an acyl-coA synthetase capable of influencing central metabolism.

CONCLUSIONS: Consistent with previous research, we found that persons with aMCI have an altered gut microbiome relative to controls. Further, we demonstrate through metagenomics sequencing that both bacterial and viral taxa are associated with cognitive and neurovascular functioning in aMCI. Knowledge about the relationships between the microbiota, cognition, and cerebrovascular function paves the way for future studies cross-sectional and longitudinal studies.},
}

Humans
Male
Female
*Cognitive Dysfunction/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
Aged
Biomarkers
Magnetic Resonance Imaging
Neuropsychological Tests/statistics & numerical data
Feces/microbiology
*Dysbiosis/microbiology
*Cerebrovascular Circulation/physiology
Middle Aged
Cognition

@article {pmid41441246,
year = {2025},
author = {Nikolova, R and Gatev, E and Kenarova, A and Petkova, M and Dinev, N and Baldrian, P and Radeva, G},
title = {Selective Pressure of Heavy Metals on Soil Microbial Taxa near a Smelting Area.},
journal = {Toxics},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/toxics13121025},
pmid = {41441246},
issn = {2305-6304},
support = {CZ.02.01.01/00/22_008/0004597 and LUC21352//Ministry of Education, Youth and Sports of the Czech Republic/ ; },
abstract = {Soil pollution by heavy metals (HMs) poses a major threat to soil quality and human health, with mining and smelting industries identified as key sources. Soils around smelters are often considered polluted hotspots, being generally unsuitable for agricultural activities. Although many studies have identified microbial taxa able to survive in such environments, most have focused on relatively low HM concentrations. The purpose of the study was to assess the ecological risk and to evaluate the diversity and structural shifts in microbial communities, as well as to predict key metabolic pathways associated with HM resistance in soils near Pb-Zn smelter in Bulgaria. The soils ranged from low-risk to disastrous, with cadmium (Cd) identified as the primary contributor to soil toxicity. High-throughput sequencing of 16S rRNA and ITS amplicons revealed widespread dominance of the phyla Proteobacteria, Actinobacteriota and Acidobacteriota, and Ascomycota, with the prevailing classes Acidobacteriae, Chloroflexia, and Eurotiomycetes, indicating their high tolerance to HMs. Functional predictions suggested enrichment of key pathways in the most polluted soils related to HM resistance, including efflux systems and detoxifying enzymes. These results highlight the necessity of integrating soil microbial indicators into agricultural management strategies to ensure safe food production.},
}

@article {pmid41440831,
year = {2025},
author = {Kuehn, JF and Zhang, Q and Heston, MB and Kang, JW and Harding, S and Davenport-Sis, NJ and Kerby, RL and Schiffmann, EC and Wheeler, JL and Clements, E and Shankar, S and Mickol, A and Zemberi, J and Chow, H and Zhang, E and Harpt, J and Mushtaque, A and Yoo, M and Cook, A and Carlsson, CM and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Ulland, TK and Bendlin, BB and Rey, FE},
title = {Biomarkers.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e098071},
doi = {10.1002/alz70856_098071},
pmid = {41440831},
issn = {1552-5279},
mesh = {Humans ; *Biomarkers/cerebrospinal fluid ; Male ; *Alzheimer Disease/metabolism/diagnosis ; Female ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Feces/chemistry/microbiology ; Aged ; Middle Aged ; Cohort Studies ; Metagenome ; },
abstract = {BACKGROUND: Short-chain fatty acids (SCFA), including acetate, propionate, and butyrate, are abundant gut bacterial metabolites produced via the fermentation of dietary fibers and resistant starch. Several lines of evidence, particularly in preclinical mouse models, suggest a protective role of SCFA against Alzheimer's Disease (AD) pathology. In one study, supplementation of mice with tributyrin, a butyrate prodrug, significantly attenuated AD pathology. However, the relationships between SCFA, the bacterial taxa that produce them, and AD biomarkers require further elucidation in humans.

METHOD: We assessed gut metagenomes and SCFA levels in fecal samples from 213 cognitively unimpaired Microbiome Alzheimer's Risk Study (MARS) participants (Table 1). The cohort was co-enrolled in the Wisconsin Alzheimer's Disease Research Center and Wisconsin Registry for Alzheimer's Prevention, which track preclinical disease progression in middle-aged and older adults at risk for AD. We sequenced DNA extracted from 213 fecal samples (one sample per participant, 30 million reads per sample), created metagenome-assembled genomes (MAGs), and annotated their functions. We measured levels of the major SCFA in fecal samples using headspace gas chromatography. We performed multiple linear regressions between levels of cerebrospinal fluid (CSF) AD biomarkers and each SCFA or MAG, controlling for age, sex, body mass index, and APOE genotype.

RESULT: We found an inverse association between amyloid positive status (CSF Aꞵ42/Aꞵ40 <0.046) and MAGs encoding propionate or butyrate production pathways. Fecal acetate, propionate, and butyrate levels were reduced in females and in participants with amyloid-positive status. Mediation analysis detected a trend indicating that butyrate may mediate the inverse relationship between MAGs with butyrate production pathways and amyloid positive status.

CONCLUSION: Relative abundances of MAGs encoding enzymes for propionate and butyrate production were reduced in amyloid-positive participants in a cognitively unimpaired human cohort enriched for AD risk. These results, combined with the extensive literature in preclinical AD mouse models, suggest that SCFA may play a causal role in AD progression.},
}

Humans
*Biomarkers/cerebrospinal fluid
Male
*Alzheimer Disease/metabolism/diagnosis
Female
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome
Feces/chemistry/microbiology
Aged
Middle Aged
Cohort Studies
Metagenome

@article {pmid41440703,
year = {2025},
author = {Zhang, ZF and Jiang, Y and Mao, J},
title = {Global Distribution Patterns of Dark Matter Fungi in Cold Seep: A Metagenomic Meta-Analysis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120878},
pmid = {41440703},
issn = {2309-608X},
support = {2024A04J3728//Guangzhou Science and Technology Plan Project/ ; 32400044//National Natural Science Foundation of China/ ; },
abstract = {Deep-sea cold seep ecosystems, known for their unique geochemical niches and chemosynthetic communities, harbor numerous "dark matter fungi (DMF)" that remain understudied compared to their bacterial and archaeal counterparts. Integrating 105 metagenomic datasets from 12 global cold seep sites, this study systematically elucidated the diversity, biogeography, and assembly mechanisms of cold seep fungal communities. Our analysis revealed highly diverse and abundant fungi, spanning 21 phyla and 928 genera, characterized by the absolute dominance of Ascomycota and a pervasive presence of unclassified DMF. Crucially, the fungal communities exhibited significant geographical and seep-type heterogeneity, with peak abundance notably in methane seep environments. Further analyses revealed that fungal community diversity and structure are influenced by both spatial and biological factors. Moreover, assembly exhibits multi-scale characteristics: dispersal limitation is the primary determinant globally, while local-scale structure is jointly driven by environmental variables and biological interactions with key chemosynthetic genes. These findings establish the macro-biogeographical pattern of deep-sea cold seep fungi, underscoring their tight coupling with core energy metabolism and providing essential data for future research and potential utilization.},
}

@article {pmid41440692,
year = {2025},
author = {Lv, X and Wang, H and Wang, W},
title = {Agaricus sinodeliciosus and Coprinus comatus Improve Soil Fertility and Microbial Community Structure.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120866},
pmid = {41440692},
issn = {2309-608X},
support = {41761107//National Natural Science Foundation of China/ ; 2025-ZJ-969T//The Natural Science Foundation of Qinghai Province/ ; W2412148//International (Regional) Cooperation and Exchange (ICE) Projects of the National Natural Science Foundation of China (NSFC)/ ; D23029//111 Project/ ; },
abstract = {Agaricus sinodeliciosus (A. sinodeliciosus) and Coprinus comatus (C. comatus) are precious macrofungi found in Qinghai Province, China. As decomposers, they play a crucial role in the terrestrial ecosystem. The article takes A. sinodeliciosus and C. comatus growing in the saline-alkali land of the Qaidam Basin in Qinghai Province as the research objects, and deeply analyzes the influence of the two macrofungi on soil. The results show that, compared with the control soil, the total carbon (TC) content in the soil of A. sinodeliciosus and C. comatus increased by 27.48% and 113.24%, the total nitrogen (TN) content increased by 95.16% and 108.06%, the hydrolyzable nitrogen (HN) increased by 87.36% and 97.90%, and the available potassium (AK) increased by 182.72% and 596.09%, respectively. In addition, C. comatus significantly increased the available phosphorus (AP) by 163.14%. This proves that both macrofungi can enhance soil fertility, and C. comatus has a stronger fertilization effect. In terms of soil microorganisms, A. sinodeliciosus significantly influenced the distribution of soil bacteria and fungi, increasing the abundance of Streptomyces and reducing alpha diversity. C. comatus had a greater impact on bacteria, significantly increasing the relative abundance of Pseudomonas in the soil, but had no significant effect on fungi. Additionally, there was a close relationship between soil microbial abundance and physicochemical properties. pH, AP, TC, and AK were the main factors influencing bacteria, while total salt was the main factor affecting fungi. These findings reveal that A. sinodeliciosus and C. comatus influence the soil microenvironment by regulating soil physicochemical properties and microbial communities.},
}

@article {pmid41440679,
year = {2025},
author = {Boán, J and Fernández-Ruiz, M and Aparicio-Minguijón, E and Aguado, JM},
title = {The Unnoticed Threat: Clinical Characteristics, Risk Factors, and Outcome of Mucormycosis in Solid Organ Transplantation.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120853},
pmid = {41440679},
issn = {2309-608X},
abstract = {Mucormycosis is an uncommon but life-threatening invasive fungal infection caused by molds of the order Mucorales, whose incidence has increased among solid organ transplant (SOT) recipients in recent years. Profound immunosuppression (particularly high-dose corticosteroids), T-cell-depleting therapies, diabetes mellitus, and previous episodes of graft rejection are the main predisposing conditions. This narrative review summarizes the current evidence on epidemiology, pathogenesis, risk factors, clinical presentation, diagnostic strategies, and treatment outcomes of mucormycosis in the SOT population. Pulmonary and rhino-orbital-cerebral infections are the predominant clinical forms, often characterized by rapid angioinvasive progression and mortality rates exceeding 45%. Early diagnosis remains challenging due to nonspecific clinical manifestations and the limited sensitivity of conventional diagnostic tools, although molecular techniques such as the detection of circulating Mucorales DNA in blood and metagenomic next-generation sequencing are promising. Liposomal amphotericin B remains the first-line therapy, ideally associated to surgical debridement and reduction in immunosuppression, while broad-spectrum triazoles (isavuconazole and posaconazole) represent alternative or salvage options. Despite recent advances in diagnostic methods and antifungal therapy, the prognosis of post-transplant mucormycosis remains poor, underscoring the need for multidisciplinary management and collaborative studies to inform the clinical management in this high-risk population.},
}

@article {pmid41440673,
year = {2025},
author = {Rümenapp, M and Becker, B and Pushkareva, E},
title = {Environmental Gradients Shape Fungal Diversity and Functional Traits in Arctic Biocrusts.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
doi = {10.3390/jof11120847},
pmid = {41440673},
issn = {2309-608X},
support = {PU867/1-1//Deutsche Forschungsgemeinschaft/ ; Be1779///Deutsche Forschungsgemeinschaft/ ; },
abstract = {Arctic biological soil crusts (biocrusts) are known to host diverse fungal communities that facilitate nutrient cycling and soil stabilisation in these harsh environments. In this study, the diversity and composition of fungi were assessed across elevation and spatial gradients in biocrusts from Kongsfjorden (Svalbard) using metagenomic sequencing. Within the observed fungal phyla, Ascomycota was dominant across all sites, with Basidiomycota and Rozellomycota also exhibiting high abundances. Furthermore, saprotrophic fungi were most abundant, followed by mycorrhizal and parasitic guilds. Lichen-associated fungi were also detected across the samples, although their read counts were substantially lower. Additionally, the fungal genus richness and guild composition exhibited no significant variation between elevations, but location within the fjord strongly shaped community structure.},
}

@article {pmid41440348,
year = {2025},
author = {Sonets, IV and Galeeva, IS and Krivonos, DV and Pavlenko, AV and Vvedenskiy, AV and Ahmetzyanova, AA and Mikaelyan, KA and Ilina, EN and Yanushevich, OO and Revazova, ZE and Vibornaya, EI and Runova, GS and Aliamovskii, VV and Bobr, IS and Tsargasova, MO and Kalinnikova, EI and Govorun, VM},
title = {In-Depth Multi-Approach Analysis of WGS Metagenomics Data Reveals Signatures Potentially Explaining Features in Periodontitis Stage Severity.},
journal = {Dentistry journal},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/dj13120590},
pmid = {41440348},
issn = {2304-6767},
abstract = {Background: Periodontitis is a chronic inflammatory disease mostly associated with Porphyromonas gingivalis infection and characterized by progressive destruction of the supporting structures of the tooth, including the gingiva, periodontal ligament and alveolar bone. However, the impact of other members of the periodontal microbiome on stage of the severity of the periodontitis remains largely uncharacterized. Methods: This exploratory study employs whole-genome shotgun (WGS) metagenomics to characterize the periodontal microbiome in patients suffering from mild and severe periodontitis, aiming to identify microbial signatures linked to disease severity via analysis of taxonomic composition, predicted metabolic pathways and metagenome-assembled genomes (MAGs). After initial selection, 28 adult patients with a computer tomography (CT)-confirmed diagnosis of mild and severe stage of periodontitis from 2 clinics were included in the research project. Results: Taxonomic analysis confirms the presence of various commensal and pathogenic bacteria detectable at the species level, especially belonging to so-called "red, orange and green periodontal complexes"-P. gingivalis, T. forsythia, C. rectus, and Capnocytophaga spp. that may contribute to disease heterogeneity. The conducted investigation suggests that non-microbial factors such as cardiovascular diseases and antibiotic usage in the last 6 months prior to the hospital admission could explain variance of disease progression and impact on severity. Analysis of microbial functional composition revealed metabolic traits showing positive correlations with severe stage of periodontitis. Robust network analysis suggested interactions between pathogenic bacteria of the red complex and other members of the periodontal microbiome. Conclusions: These findings underscore the multifactorial nature of periodontitis pathogenesis, highlighting the need for integrated approaches combining microbial, host, and environmental data to unravel drivers of disease progression. The study provides a foundation for future large-scale investigations into personalized diagnostic or therapeutic strategies.},
}

@article {pmid41439481,
year = {2026},
author = {Zou, Y and Li, N and Li, X and Kuang, M and Xu, X and Guan, L and Li, X and Zheng, P and Li, L and Wan, J and Lu, N and Liu, J and He, C and Zhu, Y},
title = {Gut microbiota dysbiosis exacerbates acute pancreatitis via Escherichia coli-driven neutrophil heterogeneity and NETosis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606480},
doi = {10.1080/19490976.2025.2606480},
pmid = {41439481},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/microbiology/immunology/complications ; *Gastrointestinal Microbiome ; Mice ; Humans ; *Neutrophils/immunology ; *Extracellular Traps/immunology/metabolism ; *Escherichia coli/physiology ; *Pancreatitis/microbiology/immunology/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Specific Pathogen-Free Organisms ; },
abstract = {Gut microbiota dysbiosis contributes to acute pancreatitis (AP) severity, but the specific microbes and mechanisms remain unclear. In this study, we employed both germ-free (GF) and specific-pathogen-free (SPF) murine models of AP to investigate the role of the intestinal microbiota. Our findings demonstrate that GF mice exhibited markedly attenuated pancreatic injury, inflammatory cell infiltration, and neutrophil extracellular traps (NETs) formation. Through fecal microbiota transplantation (FMT) from AP patients, differential antibiotic modulation, and single-bacterial colonization experiments, we identified Gram-negative bacteria, particularly Escherichia coli (E. coli), as critical microbial drivers of disease exacerbation. Single-cell RNA sequencing revealed that microbiota dysbiosis profoundly reprogrammed both local pancreatic and systemic immune landscapes. Specifically, dysbiosis promoted emergency granulopoiesis in the bone marrow, enhanced neutrophil mobilization and activation, and facilitated the expansion of pro-inflammatory neutrophil subpopulations (Neutrophils_2 and Neutrophils_3). These subsets exhibited upregulated signaling through NETosis-associated pathways, including TLR, NF-κB, and IL-17 axes. Conversely, in GF conditions, we observed a predominance of an anti-inflammatory neutrophil subset (Neutrophils_4), characterized by the expression of tissue repair-associated genes such as Reg1 and Reg2. Shotgun metagenomic profiling of fecal samples from patients with AP revealed an enrichment of E. coli during the acute phase, positively correlating with circulating cell-free DNA, a marker of NETosis. Together, these insights suggest that gut microbiota dysbiosis, notably increased E. coli abundance, may aggravate AP by reshaping immunity and promoting aberrant NETs formation, supporting microbiota or NETs targeted therapies.},
}

Animals
*Dysbiosis/microbiology/immunology/complications
*Gastrointestinal Microbiome
Mice
Humans
*Neutrophils/immunology
*Extracellular Traps/immunology/metabolism
*Escherichia coli/physiology
*Pancreatitis/microbiology/immunology/pathology
Male
Mice, Inbred C57BL
Disease Models, Animal
Fecal Microbiota Transplantation
Female
Specific Pathogen-Free Organisms

@article {pmid41439274,
year = {2026},
author = {Li, Y and Xu, C and Park, H and Omstead, AN and Anees, M and Sherry, C and Khan, AF and Grayhack, E and Weksler, B and Wagner, P and Bartlett, DL and Meltzer, SJ and Zaidi, AH and Goel, A},
title = {A machine-learning informed circulating microbial DNA signature for early diagnosis of esophageal adenocarcinoma.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604334},
doi = {10.1080/19490976.2025.2604334},
pmid = {41439274},
issn = {1949-0984},
mesh = {Humans ; *Esophageal Neoplasms/diagnosis/microbiology/blood ; *Adenocarcinoma/diagnosis/microbiology/blood ; *Machine Learning ; *Early Detection of Cancer/methods ; Barrett Esophagus/diagnosis/microbiology ; Male ; Female ; Middle Aged ; Aged ; Gastroesophageal Reflux/diagnosis/microbiology ; Bacteria/genetics/classification/isolation & purification ; *DNA, Bacterial/blood/genetics ; Liquid Biopsy/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Metagenomics ; Biomarkers, Tumor/blood ; },
abstract = {Esophageal adenocarcinoma (EAC) has seen a dramatic rise in incidence in developed countries over the past three decades. Early detection of its precursors-gastroesophageal reflux disease (GERD), Barrett's esophagus (BE), and high-grade dysplasia (HGD) is critical for cancer prevention. This study presents the development and validation of a novel liquid biopsy assay based on circulating microbial DNA (cmDNA) for the early detection of EAC and HGD. Using metagenomic sequencing, we identified significant differences in microbial diversity and composition between EAC and HGD patients, as well as between BE and GERD patients. A total of 46 microbial candidates in tissue and 419 in serum were upregulated in EAC & HGD, with 11 consistently elevated in both sample types. Following qRT-PCR validation and LASSO regression, a 6-marker cmDNA panel was selected. This signature was incorporated into a diagnostic model trained with the XGBoost algorithm, achieving an AUC of 0.93 in the training cohort (52 HGD & EAC cases vs. 54 BE & GERD controls). Importantly, the model demonstrated robust performance in an independent testing cohort (23 HGD & EAC cases vs. 22 BE & GERD controls), yielding AUCs of 0.91 for EAC and 0.88 for HGD. These findings highlight the diagnostic potential of cmDNA-based profiling and support its utility as a minimally invasive, accurate, and generalizable tool for early detection of esophageal adenocarcinoma.},
}

Humans
*Esophageal Neoplasms/diagnosis/microbiology/blood
*Adenocarcinoma/diagnosis/microbiology/blood
*Machine Learning
*Early Detection of Cancer/methods
Barrett Esophagus/diagnosis/microbiology
Male
Female
Middle Aged
Aged
Gastroesophageal Reflux/diagnosis/microbiology
Bacteria/genetics/classification/isolation & purification
*DNA, Bacterial/blood/genetics
Liquid Biopsy/methods
*Cell-Free Nucleic Acids/blood/genetics
Metagenomics
Biomarkers, Tumor/blood

@article {pmid41439238,
year = {2026},
author = {Kumar, A and Solanki, MK and Kumar, M and Kaushik, A and Arya, A and Saikia, M and Gaur, VK and Singh, RP and Singh, SK and Singh, VK and Dufossé, L},
title = {The microbial strategies for the management of chemical pesticides: A comprehensive review.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100519},
pmid = {41439238},
issn = {2666-5174},
abstract = {Chemical pesticides considered as one of the emerging environmental contaminants that severally affect the human health and soil and water ecosystem. Despite their well-documented adverse effects on fruit quality, soil structure, the emergence of pesticide-resistant pests, and human well-being, chemical pesticides are still widely used for crop protection, particularly in developing countries. Although to manage the chemical pesticides, various traditional approaches have been employed, however the higher cost, and the generation of toxic residues have shifted research attention toward eco-friendly and sustainable bioremediation strategies. Microorganisms including the bacteria, fungi, and algae play a crucial role in pesticide degradation by transforming toxic compounds into less toxic forms. However, to optimize microbial bioremediation, a comprehensive understanding of microbial metabolism and physiology is essential. In this context, omics technologies such as genomics, metagenomics, transcriptomics, proteomics, and metabolomics, offer powerful tools for elucidating the molecular mechanisms involved in pesticide degradation. These approaches facilitate the identification of microorganism, key genes, enzymes, and metabolic pathways responsible for the breakdown of pesticide compounds and their by-products. Furthermore, advanced technology like the gene editing can enhance the efficacy of pesticides biodegradation by knocking out undesirable genes or introducing beneficial ones in the microorganisms. The Artificial intelligence also plays a significant role in analysing big data, understanding microbial communities' structure, identifying nature of pesticides and selecting or predicting the microbial species with enhanced pesticides degrading efficacy.},
}

@article {pmid41439237,
year = {2026},
author = {Wang, J and Asif, A and Gu, F and Gu, S and Ding, Y and Gu, Y and Rafiq, MS and Hao, H},
title = {A naturally isolated symbiotic Lactobacillus murinus suppresses multidrug-resistant Campylobacter jejuni via microbial metabolites.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100520},
pmid = {41439237},
issn = {2666-5174},
abstract = {Multidrug-resistant Campylobacter jejuni (MDR C. jejuni), the leading cause of food-borne gastroenteritis worldwide, poses a significant threat to public health and food safety. The intestinal microbiota prevents MDR C. jejuni colonization, but the specific mechanisms remain poorly understood. In this study, we performed a multi-omics analysis of the gut microbiota in C57BL/6 mice, combined with in vitro experiments, to investigate the role of gut microbiota in C. jejuni colonization. Treatment with tylvalosin, a new macrolide, altered the gut microbiota composition, reducing Bifidobacterium longum communities and decreasing levels of short-chain fatty acids (acetic acid, propionic acid, n-butyric acid, i-butyric acid, and i-valeric acid). This disruption of intestinal homeostasis facilitated C. jejuni colonization. Through metagenomic sequencing, we identified and isolated Lactobacillus murinus (L. murinus) from the mice's intestinal flora, which exhibited inhibitory activity against C. jejuni in vitro. Metabolomic analysis and in vitro validation further revealed the significance of L. murinus-derived metabolites. Our results indicate that L. murinus inhibits and kills C. jejuni in a co-culture system by secreting acids that synergistically induce apoptosis, leading to cell membrane disruption and the release of cellular contents.},
}

@article {pmid41439190,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Portier, SC and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A},
title = {Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf224},
pmid = {41439190},
issn = {2730-6151},
abstract = {Because accessing the small intestine is technically challenging, studies of the small intestinal microbiome are predominantly conducted in patients rather than in healthy individuals. Invasive clinical procedures, such as endoscopy or surgery, usually performed for therapeutic purposes, are typically required for sample collection. Although stomas offer a less invasive means for repeated sampling, their use remains restricted to patient populations. As a result, the small intestinal microbiome of healthy individuals remains largely understudied. This study evaluated a novel ingestible medical device for collecting luminal samples from the small intestine. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics, and culturomics were used to assess the effectiveness of the medical device in characterizing the healthy small intestinal microbiome and identifying potential biomarkers. The small intestinal microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct small intestinal metabolic footprint, with bile acids and amino acids being the most abundant metabolite classes. Host- and host/microbe-derived bile acids were particularly abundant in small intestinal samples. Using a fast culturomics approach on two small intestinal samples, we achieved species-level characterization and identified 90 bacterial species, including five potentially novel ones. This study demonstrates the efficacy of our novel sampling device in enabling comprehensive small intestinal microbiome analysis through an integrative, multi-omics approach. This approach allows distinct microbiome signatures to be identified between small intestinal and fecal samples.},
}

@article {pmid41439189,
year = {2025},
author = {Ghotbi, M and Ghotbi, M and D'Agostino, E and Kanitz, M and Needham, DM},
title = {From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf218},
pmid = {41439189},
issn = {2730-6151},
abstract = {Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating the study of microbial communities where large-volume sample collection is challenging. This can aid where 'conventional' filtrater-based methods miss capturing smaller microbes, or where microscale variability matters, such as the ocean. Here, we develop and validate physical and chemical-based DNA extractions from microvolumes with universal rRNA gene amplicons and metagenomic sequencing of all domains and viruses, on natural surface seawater and experimentally manipulated marine waters. Compared to 500-mL filter-based extraction, direct PCR of 3 μL of lysate from seawater microvolume extractions ranging from 100-1000 μL consistently captured comparable microbial community composition and diversity, with reliable amplification and little to no contamination. Metagenomic results of 10 μL lysates from 15 microvolume samples (100 μL) captured 83 high- and draft-quality, diverse bacterial genomes and 430 complete, high and medium quality viral contigs. Our approach enables scaling of rRNA gene sequencing and metagenomic library prep for high-throughput experimentation for a fraction of the cost of conventional methods and builds upon existing microvolume approaches by removing unnecessary expenses, like excess plasticware and expensive bead clean-up. The method expands opportunities for more comprehensive microbial community monitoring and controlled laboratory experiments by facilitating higher sample numbers and lowering sample volume needs. However, its potential bias against Gram-positive bacteria should be considered when applying to environments where these taxa are abundant.},
}

@article {pmid41439067,
year = {2025},
author = {Patel, B and Vijayan, V and Tran, K},
title = {Microbial Cell-Free DNA Sequencing in the Identification of Rhizopus Arrhizus in an Adolescent With Gastrointestinal Mucormycosis.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97426},
pmid = {41439067},
issn = {2168-8184},
abstract = {Mucormycosis is a rare and often fatal angioinvasive fungal infection, typically occurring in immunocompromised hosts. Gastrointestinal mucormycosis (GM), a rare manifestation of mucormycosis, is particularly challenging to diagnose due to its non-specific clinical presentation and overlap with other abdominal pathologies. We report the case of a previously healthy 15-year-old male with Class I obesity who presented with perforated appendicitis and developed septic shock and multi-organ failure for which he was admitted to the pediatric intensive care unit. Upon arrival, the patient was intubated and placed on mechanical ventilation. He was started on vasopressor support and intravenous antibiotics. An orogastric tube was placed for bowel decompression, but on hospital day 2, he developed profuse bloody output from the orogastric tube. Imaging revealed mixed-density debris surrounding the gastric lumen. His condition deteriorated with ongoing fevers and signs of gastrointestinal bleeding. Conventional infectious disease tests were unrevealing. Metagenomic next-generation sequencing of plasma cell-free DNA (Karius test) detected Rhizopus arrhizus, leading to the initiation of antifungal therapy with liposomal amphotericin B and posaconazole. Exploratory laparotomy revealed necrotic ulcers, extensive gastric and bowel necrosis and infarctions, confirming GM. Despite aggressive antifungal treatment and surgical debridement, the patient ultimately succumbed to his disease. This case underscores the importance of considering mucormycosis in critically ill patients without traditional risk factors and highlights the utility of microbial cell-free DNA sequencing as a non-invasive diagnostic adjunct in children with mucormycosis when tissue sampling is impractical.},
}

@article {pmid41438456,
year = {2025},
author = {Han, P and Yuan, X and Li, C and Zhang, L and Cui, J},
title = {Case Report: Pneumocystis jiroveci pneumonia: report of five children with the nephrotic syndrome and review of the literature.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1687471},
pmid = {41438456},
issn = {2296-2360},
abstract = {OBJECTIVE: To retrospectively analyze the clinical characteristics, treatment, and prognosis of five pediatric patients with nephrotic syndrome who developed Pneumocystis carinii pneumonia (PJP) after long-term use of steroids and tacrolimus.

METHODS: A review was conducted on five cases of nephrotic syndrome in children who developed Pneumocystis pneumonia after long-term treatment with steroids and tacrolimus. The initial symptoms, early clinical characteristics, and imaging changes were summarized. Among these cases, two were diagnosed through alveolar lavage fluid metagenomic testing and three through sputum metagenomic testing (BGI Genomics Co.), all indicating (pneumocystis carinii pneumonia. All five patients received early treatment with sulfa drugs, with three of them also receiving caspofungin.

RESULTS: One child died and four were discharged with symptomatic improvement.

CONCLUSION: PJP is a severe opportunistic infection that can progress rapidly and lead to life-threatening respiratory failure, particularly in immunocompromised individuals. Among children with nephrotic syndrome (NS), prolonged exposure to glucocorticoids, tacrolimus, or other immunosuppressive agents markedly increases susceptibility to PJP. Therefore, heightened clinical vigilance, early etiological diagnosis, and prompt initiation of appropriate therapy are essential to improving clinical outcomes in this population.},
}

@article {pmid41438409,
year = {2025},
author = {Carrera-Faja, L and Jasso, MV and Sarmiento, I and Cabrera-Gumbau, JM and Espunyes, J and Martínez-Urtaza, J and Cabezón, O},
title = {Metagenomic survey reveals Volzhskoe tick virus in Hyalomma ticks for the first time in western Europe, North-Eastern Spain.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101279},
pmid = {41438409},
issn = {2352-7714},
abstract = {Ticks are reservoirs and vectors of several emerging arboviruses, yet their associated virome remains poorly characterized. Using meta-transcriptomic sequencing, we surveyed Hyalomma marginatum and Rhipicephalus bursa ticks collected from areas with contrasting Crimean-Congo haemorrhagic fever virus (CCHFV) seroprevalence in wild ungulates in north-eastern Spain, a region with no reported CCHF cases in humans. While CCHFV RNA was not detected, we identified Volzhskoe tick virus (VTV), a recently described member of the class Bunyaviricetes, first identified in Russia, in H. marginatum from the Ports de Tortosa i Beseit Natural Park-making its first report of VTV in Western Europe. These findings suggest a broader distribution of VTV and raise important questions about its potential interactions with CCHFV, pathogenicity and host range. Moreover, our approach underscores the value of metagenomic surveillance for improving our understanding of tick-borne virus ecology.},
}

@article {pmid41438378,
year = {2025},
author = {Yang, W and Liu, H and Xu, R and Peng, Y and Xu, T and Yang, Y and Li, Y and Xiang, H},
title = {Integrated genomics, metagenomics and metatranscriptomics to reveal the biocontrol mechanism of Bacillus velezensis JY10 against tobacco target spot disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1707097},
pmid = {41438378},
issn = {1664-302X},
abstract = {Tobacco target spot (TTS) disease, a prevalent fungal disease caused by Rhizoctonia solani, severely reduces tobacco yield and quality, imposing substantial economic losses on the tobacco industry. In this study, we employed a biological control approach against TTS using a Bacillus velezensis JY10 isolated from healthy tobacco stems. We further elucidated the mechanism of JY10 in controlling TTS through genomics, metagenomics and metatranscriptomics. The results showed that JY10 exhibited robust inhibitory effects against R. solani, with an inhibition rate exceeding 95%, and achieved a TTS control efficacy of 68.63% in pot experiments. Whole-genome sequencing demonstrated that the JY10 genome spans 3,929,772 bp, contains 4,026 protein-coding genes, and has a GC content of 46.5%. AntiSMASH analysis predicted 12 secondary metabolite biosynthetic gene clusters, encoding antimicrobial compounds such as surfactin, fengycin, difficidin, bacillaene, bacillibactin, macrolactin H, and bacilysin. Metagenomic profiling showed that JY10 treatment had no significant influence on tobacco phyllosphere and rhizosphere microbiome structure, however, it significantly increased the relative abundance of beneficial microbes, including Bacillus, Pseudonocardia, and Pseudomonas. Metatranscriptomic analysis revealed that JY10 might enhance tobacco TTS resistance by modulating oxidative phosphorylation pathway and upregulating several antibiotics biosynthesis. Taken together, JY10 may employ a dual control strategy against TTS, involving the direct production of antifungal compounds, as well as indirectly increasing the abundance of beneficial microbes and modulating their oxidative phosphorylation and antibiotic synthesis pathways in the phyllosphere and rhizosphere of tobacco. These findings provide a theoretical foundation for understanding biocontrol mechanisms of JY10 and introduce a promising bacterial resource for the development of sustainable TTS management strategies.},
}

@article {pmid41438339,
year = {2026},
author = {Van Espen, L and Brol, MJ and Close, L and Schierwagen, R and Gu, W and Keller, MI and Balogh, B and Fullam, A and De Coninck, L and Nakamura, T and Kuhn, M and Bork, P and Laleman, W and Bajaj, JS and Papp, M and Schnabl, B and Trebicka, J and Matthijnssens, J and , },
title = {L actococcus A phages predict ACLF while Enterococcus B phages predict bacterial infection in decompensated cirrhosis.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101622},
pmid = {41438339},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: As portal hypertension progresses in cirrhosis, bacterial translocation across a compromised gut barrier leads to endotoxemia, systemic inflammation and immune dysfunction. Gut phages play a key role in these processes by influencing bacteria-host interactions. This study explores the role of the human gut virome in acute decompensation of cirrhosis and acute-on-chronic liver failure (ACLF).

METHODS: The fecal virome was longitudinally assessed by metagenomic sequencing in two independent cohorts: 93 patients (292 samples) with acute decompensation or ACLF from the PREDICT study, and 94 patients (94 samples) with decompensated cirrhosis undergoing TIPS (transjugular intrahepatic portosystemic shunt) surgery collected in a tertiary care setting. Besides descriptive analysis, phages were grouped according to their predicted bacterial host and lifestyle, and associated with clinical parameters.

RESULTS: Phage alpha-diversity was higher in patients with ACLF and correlated with ACLF severity. In the absence of ACLF, the phageome was dominated by virulent phages, but in ACLF, temperate phages became more prevalent. Genus-level analysis showed that phageomes were highly patient-specific. Lactococcus A phages were the only phage-host group predicting ACLF development (odds ratio [OR] = 14; Fisher test p = 0.0129). Enterococcus B phages (OR = 14.7; p = 0.0015; adj. p = 0.037) and their bacterial hosts (OR = 2.8; p = 0.020) were significantly more prevalent in cases of proven systemic bacterial infection. The presence of both phage families was linked to increased 90-day mortality rates.

CONCLUSION: ACLF is characterized by increased fecal virome diversity and a shift from virulent toward temperate phages at disease onset. Our study links Lactococcus A phages to ACLF development, and Enterococcus B phages to bacterial infection, while both are associated with increased 90-day mortality.

CLINICAL TRIAL NUMBER: NCT03056612.

IMPACT AND IMPLICATIONS: The human gut virome is a poorly investigated part of the human gut microbiome, especially in the context of decompensated cirrhosis and acute-on-chronic liver failure. This study identified two phage groups (Lactococcus A phages and Enterococcus B phages) with particular prognostic value. In the future, virome analysis of fecal samples could be useful for patient stratification in clinical practice.},
}

@article {pmid41437628,
year = {2025},
author = {Barth, P and Förster, F and Jaenicke, S and Thelen, F and Rossbach, O and Weber, F and Shalamova, L and Goesmann, A},
title = {PARANOiD: Pipeline for Automated read ANalysis of iCLIP Data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf673},
pmid = {41437628},
issn = {1367-4811},
abstract = {MOTIVATION: RNA-protein interactions play essential roles in every living organism, with RNA transcription, processing, and translation being just a few examples. Therefore, determining the set of RNAs that are bound by individual RNA-binding proteins, as well as the precise location of the interaction, is crucial for biological understanding. CLIP (UV-cross-linking and immunoprecipitation) is a method developed to study these interactions. Several variations of the CLIP protocol have been developed, e.g., iCLIP (individual-nucleotide resolution CLIP), which offers nucleotide-precise resolution of the cross-linking event.

RESULTS: PARANOiD is a versatile software for fully automated analysis of iCLIP and iCLIP2 data. It contains all steps necessary for preprocessing, the determination of cross-link locations, and several additional steps, which can be used to detect specific characteristics, e.g., definite distances between cross-link events or identify binding motifs. Additionally, results are visualized as statistical plots for a quick overview and as standardized bioinformatics file formats, which can be used for further analysis steps.

AVAILABILITY: PARANOiD is published under the MIT license and is available from https://github.com/patrick-barth/PARANOiD. The documentation is available at https://paranoid.readthedocs.io/en/latest/index.html.

CONTACT: patrick.barth@computational.bio.uni-giessen.de.},
}

@article {pmid41437386,
year = {2025},
author = {Aminu, S and Ascandari, A and Mokhtar, MM and Allali, AE and Benhida, R and Daoud, R},
title = {Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02315-3},
pmid = {41437386},
issn = {2049-2618},
abstract = {BACKGROUND: Human-built environment microbiomes mediate pathogen persistence and antimicrobial resistance (AMR) circulation, yet their ecological organization and resilience remain poorly quantified. Hospitals, sewage systems, ambulances, and public transport form interconnected microbial networks where contamination potential and compositional stability define biosurveillance risk. Understanding these dynamics requires genome-resolved frameworks capable of linking community composition to ecological behavior.

METHODS: We analyzed 767 publicly available Illumina metagenomes from four urban environments using the GRUMB workflow. Quality-filtered reads were assembled into 10,834 metagenome-assembled genomes (MAGs) and dereplicated into 1542 species-level representatives. Functional annotation with CARD and VFDB identified ARG- and VF-carrying species, producing a genome-resolved abundance matrix used for ecological and predictive modeling. Alpha and beta diversity, indicator taxa, and prevalence were assessed in R, while machine learning (Random Forest, scikit-learn) achieved a nested cross-validation balanced accuracy of 0.97 ± 0.01. Synthetic donor-recipient simulations (α = 0-1) implemented in Python modeled compositional blending, entropy-based uncertainty, and Minimal Detectable Contamination (MDC) thresholds.

RESULTS: Microbial communities exhibited strong environment-specific structure (PERMANOVA R[2] = 0.12, p < 0.001). Hospital sewage contained the highest richness and compositional heterogeneity, whereas ambulances and hospital environments showed low-diversity, surface-filtered microbiomes. Machine learning identified consistent ecological predictors (Pseudomonas_E fragi, Sphingomonas sp000797515, Acinetobacter variabilis, Roseomonas mucosa) that delineated environmental identity. Synthetic blending revealed a directional source-sink hierarchy with hospital sewage acting as the primary donor (MDC = 0.2-0.3), while hospital environments displayed the greatest compositional resilience (MDC ≥ 0.8). Entropy-based uncertainty analysis identified tipping zones (α = 0.3-0.5), and dominance mapping highlighted hospital environments as stabilizing ecological nodes. WHO-priority pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli) occupied central positions in the network, bridging environmental and clinical compartments.

CONCLUSIONS: This genome-resolved and simulation-driven framework reveals a directional microbial continuum across urban infrastructures governed by dominance, resilience, and clinical connectivity. Hospital sewage functions as a microbial donor, while hospital environments act as ecological stabilizers anchoring built-environment microbiomes. These findings advance biosurveillance from descriptive profiling to predictive ecological modeling, offering quantitative metrics for risk-informed infrastructure design. Video Abstract.},
}

@article {pmid41437205,
year = {2026},
author = {Dinesh, D and Morgan, XC and Kim, H and Scott, TM and Garelnabi, M and Lee, JS and Mangano, KM and Nguyen, LH and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Gut Microbial Variations Associated With Proton Pump Inhibitor Use in the Boston Puerto Rican Health Study.},
journal = {Pharmacology research & perspectives},
volume = {14},
number = {1},
pages = {e70205},
doi = {10.1002/prp2.70205},
pmid = {41437205},
issn = {2052-1707},
support = {RF1AG075922/AG/NIA NIH HHS/United States ; P01 AG023394/NH/NIH HHS/United States ; P50 HL105185/NH/NIH HHS/United States ; R01 AG055948/NH/NIH HHS/United States ; R01 NS09772/NH/NIH HHS/United States ; //University of Massachusetts/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; Aged ; Middle Aged ; Prospective Studies ; Boston ; Cross-Sectional Studies ; Puerto Rico/ethnology ; Hispanic or Latino ; Feces/microbiology ; White ; },
abstract = {Proton pump inhibitors (PPI), used to treat gastrointestinal disorders, are associated with alterations in the gut microbiome. However, this is understudied in Puerto Ricans who have unique lifestyle characteristics. Puerto Ricans, including participants of the Boston-Puerto Rican Health Study (BPRHS), report high PPI use. Therefore, we examined gut microbial variations associated with PPI use in the BPRHS. BPRHS is a prospective cohort. 309 BPRHS participants self-reported PPI use and self-collected, metagenomically profiled, stool samples. PPI use was classified as any use in the past 30 days. Cross-sectional associations between gut microbial taxa, functional pathways, and PPI use were examined using omnibus analyses, multivariate linear modeling in MaAsLin2, and random forest classifier in feature-wise analyses. We further compared our results with the non-Hispanic Health Professionals Follow-Up Study (HPFS) to validate key findings and examine ethnicity-related differences. Among 309 participants (mean age 68.8 years; female 74.6%), 112 (36%) self-reported PPI use. After adjusting for relevant covariates, we observed an enrichment of Streptococcus parasanguinis (β = 3.16, FDR p = 0.01), S. anginosus (β = 2.89, FDR p < 0.01), S. salivarius (β = 2.56, FDR p = 0.01), S. gordonii (β = 1.98, FDR p = 0.15), and Rothia mucilaginosa (β = 1.54, FDR p = 0.06), among PPI users compared to non-users. Streptococci, Lactobacilli, and Enterococci predominantly contributed to the functional pathways associated with PPI use. The observed enrichment of oral-typical taxa, such as Streptococci, among PPI users in the BPRHS suggests the potential of PPIs to alter gut microbial composition. More studies are needed to understand the impact of PPI use on the gut microbiome in different ethnicities. Trial Registration: Parent study (BPRHS) NCT01231958.},
}

Humans
*Proton Pump Inhibitors/adverse effects/pharmacology
*Gastrointestinal Microbiome/drug effects
Female
Male
Aged
Middle Aged
Prospective Studies
Boston
Cross-Sectional Studies
Puerto Rico/ethnology
Hispanic or Latino
Feces/microbiology
White

@article {pmid41436743,
year = {2025},
author = {Prajapati, SK and Shukla, R and Kumar, V and Yadav, D and Lekkala, L and Szekeres, C and Ma, Y and Jain, S and Yadav, H},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {},
pages = {e102998},
doi = {10.1002/alz70855_102998},
pmid = {41436743},
issn = {1552-5279},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/immunology ; Aged ; Female ; *Cognitive Dysfunction/immunology/microbiology ; Middle Aged ; *Alzheimer Disease/immunology/microbiology ; Aged, 80 and over ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) pathogenesis has been linked to the microbiota-immune-brain axis; however, the relationship between gut microbiota, immune activity, and cognitive impairment remains unclear. Thus, this study examines the connection between intestinal microbial composition, immune cell phenotype, and cognitive function in older adults.

METHOD: Data and biological samples were obtained from participants aged ≥60 years (Control, n = 30; mild cognitive impairment (MCI), n = 30) from the MiaGB (Microbiome in Aging Gut and Brain) consortium, a multi-site, clinical study. Cognitive function was assessed using Montreal Cognitive Assessment (MoCA) scores, immunophenotyping through flow cytometry, stool microbiome analysis using whole-genome metagenomics, and bulk transcriptomics analysis was carried out.

RESULTS: The abundance of immune cells such as granulocytes, lymphocytes, T-cells, and NK cells was significantly decreased in MCI group. Interestingly, the levels of CD4+ were reduced while CD8+ cells increased in MCI participants compared to controls. Microbial profiling revealed distinct bacterial signatures, with MCI participants showing higher relative abundances of Eubacterium hallii, Parabacteroides distasonis, Eggerthella_sp_CAG_298, Dorea formicigenerans and Alistipes finegldii. Differential expression analysis of transcriptomics data identified 1632 upregulated and 240 downregulated genes. Gene ontology and pathway analysis revealed that upregulated genes are involved in several immune functions such as response to stimulus, adaptive immune response, lymphocyte, and T cell activation, while downregulated genes are linked to nervous system functions and signaling processes such as neuron projection. Transcriptomics analysis further highlighted that several downregulated genes are involved in the key pathways that participate in the neural functions.

CONCLUSION: These distinct bacteria, immune cells, and gene expression profiles suggest that alterations in immune cell populations, gene expression, and gut microbiota are associated with cognitive function in aging, highlighting potential interactions between the microbiota-immune-brain axis and cognitive impairment.},
}

Humans
Male
*Gastrointestinal Microbiome/immunology
Aged
Female
*Cognitive Dysfunction/immunology/microbiology
Middle Aged
*Alzheimer Disease/immunology/microbiology
Aged, 80 and over

@article {pmid41436649,
year = {2025},
author = {Sakurai, R and Fukuda, Y and Tada, C},
title = {Culture-independent discovery of a novel thermotolerant lipase and its producer from mesophilic anaerobic digestion sludge.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-025-13674-0},
pmid = {41436649},
issn = {1432-0614},
abstract = {Anaerobic digestion of lipid-rich wastes holds significant potential for enhanced biomethane production, due to the high energy density of lipids. However, to fully harness this potential, a deeper understanding of lipolytic microorganisms is essential, as key microbial players involved in lipid hydrolysis remain largely unidentified. In this study, we employed an integrated approach combining zymography, metaproteomics, and metagenomics to identify the lipolytic microorganisms from anaerobic digester sludge. This activity-based strategy identified a novel lipase distantly related to known lipases. Besides, although this lipase originates from a mesophilic environment, it exhibited unexpected extremophilic-like properties, with maximal activity at 97.5 °C and pH 11. We further reconstructed a metagenome-assembled genome encoding this lipase and demonstrated that it likely represents a novel genus closely related to Candidatus Scatomorpha. Metabolic reconstruction suggested that this bacterium hydrolyzes extracellular lipids and utilizes the resulting hydrolysate, glycerol, to produce lactate and ethanol. Habitat analysis revealed that this bacterium is specifically detected in anaerobic digesters, particularly those processing lipid-rich waste. These findings highlight the pivotal role of this bacterium in anaerobic lipid degradation.},
}

@article {pmid41436448,
year = {2025},
author = {Manghi, P and Antonello, G and Schiffer, L and Golzato, D and Wokaty, A and Beghini, F and Mirzayi, C and Long, K and Gravel-Pucillo, K and Piccinno, G and Gamboa-Tuz, SD and Bonetti, A and D'Amato, G and Azhar, R and Eckenrode, K and Zohra, F and Giunchiglia, V and Keller, M and Pedrotti, A and Likhotkin, I and Elsafoury, S and Geistlinger, L and Blanco-Miguez, A and Thomas, AM and Zolfo, M and Ramos, M and Valles-Colomer, M and Tamburini, S and Asnicar, F and Jones, HE and Huttenhower, C and Carey, V and Davis, S and Pasolli, E and Oh, S and Segata, N and Waldron, L},
title = {Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66888-1},
pmid = {41436448},
issn = {2041-1723},
support = {5R01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Large public datasets of the human microbiome now exist but combining them for large-scale analysis is difficult due to a lack of standardization. We developed curatedMetagenomicData (cMD) 3, a uniformly processed collection of over 22,000 human microbiome samples with manually curated metadata from 94 studies and 42 countries. This large and diverse resource allows for meta-analysis of the links between microbes and human health. Through meta-analysis, we identified hundreds of microbial species and thousands of microbial functions significantly associated with a person's sex, age, body mass index, and disease status, and catalog these as references. We developed an "oral enrichment score" (OES) based on the relative abundance of bacteria typically found in the oral cavity and not in the gut. Higher OES in the gut is a consistent feature in individuals with disease, suggesting that the relative abundance of oral bacteria in the gut is a simple and quantifiable signal of altered microbiome health. These analyses identify modest but widely shared patterns in human microbiomes, serving as a reproducible and readily updatable reference.},
}

@article {pmid41435895,
year = {2025},
author = {Zhang, PP and Cui, MY and Yang, SY and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF},
title = {Astragalus membranaceus improves blood glucose and renal function in diabetic kidney disease mice via gut microbial metabolite axis.},
journal = {Fitoterapia},
volume = {189},
number = {},
pages = {107048},
doi = {10.1016/j.fitote.2025.107048},
pmid = {41435895},
issn = {1873-6971},
abstract = {Recent studies have demonstrated the therapeutic potential of Astragalus membranaceus in diabetic kidney disease (DKD); however, the underlying mechanisms remain incompletely elucidated. In this study, we established a streptozotocin-induced DKD mouse model to evaluate the effects of A. membranaceus extract (AME) on glycemic control, renal function, gut microbiota composition, and metabolic profiles. Biochemical analyzes revealed that A. membranaceus significantly attenuated hyperglycemia and improved renal function, as indicated by reduced serum creatinine and blood urea nitrogen levels. Metagenomic sequencing demonstrated that A. membranaceus reversed microbial dysbiosis by suppressing pathogenic bacteria (e.g., Aerococcus urinaeequi) and enriching beneficial probiotics (e.g., Thomasclavelia cocleata). Furthermore, LC/MS-based metabolomics identified key metabolic pathways, including glycerophospholipid metabolism and bile acid synthesis, as potential mediators of the therapeutic effects. These findings underscore the crucial role of the gut-renal axis in DKD pathogenesis and provide a mechanistic basis for the clinical application of A. membranaceus.},
}

@article {pmid41435665,
year = {2025},
author = {Li, Y and Ma, J and Li, X and Ling, T and Zhang, Y and Xia, X},
title = {Integrating metagenomics analysis and machine learning to identify drivers of antibiotic resistance genes abundance in microplastic-contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140886},
doi = {10.1016/j.jhazmat.2025.140886},
pmid = {41435665},
issn = {1873-3336},
abstract = {Microplastics (MPs) in soil ecosystems significantly influence antibiotic resistance genes (ARGs) transmission and abundance. However, a holistic understanding of how MP characteristics interact with climatic and edaphic factors to drive ARGs fluctuations remain unclear. By integrating global metagenomic datasets, we compared divergence of soil microbial communities and antibiotic resistomes across MP types and applied interpretable machine learning (ML) techniques to explore ARG dynamics. Results revealed distinct microbial community and resistome patterns associated with MP types, explaining 31.0-36.2 % of the variation in bacterial structure and ARG profiles. Moreover, specific microbial biomarkers for 7 MP types underscore their significant role in structuring communities. Biodegradable MPs (e.g., polybutylene succinate, polyhydroxyalkanoates) exhibited reduced bacterial diversity but higher ARG abundance risk than conventional MPs. Among ML models, Gradient Boosted Decision Trees exhibited superior predictive performance for ARG abundance, with average R[2] values of 0.98 for training and 0.93 for testing. Driver importance analysis identified bacterial genera (mean contribution: 69.86 %) as the dominant factor in the abundance of primary ARG subtype, followed by climate (13.89 %), soil properties (9.55 %), and MP characteristics (6.70 %). This study provides novel insights into the environmental drivers of ARG dynamics in MP-contaminated soils, highlighting the importance of incorporating climate scenario projections into future ecological risk management strategies for MPs and ARGs.},
}

@article {pmid41435471,
year = {2025},
author = {Sun, M and Kong, L and Farooq, MA and Che, L and Tian, W and Wang, C and Wang, L and Lou, Z},
title = {Comparison of the plastisphere and surrounding waste in landfills: Bacterial community assembly and functional evolution.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128372},
doi = {10.1016/j.jenvman.2025.128372},
pmid = {41435471},
issn = {1095-8630},
abstract = {Plastic waste in landfills forms unique microbial habitats termed the plastisphere, a critical but underexplored niche in anaerobic, dark landfill environments. To advance plastisphere research in such terrestrial anaerobic settings and inform landfill management, this study employed an integrated approach of 16S rRNA sequencing and metagenomics to systematically investigate the bacterial community structure, assembly mechanisms, and metabolic functions of the plastisphere. Network analysis indicated that the plastisphere sustains a simplified yet highly modular co-occurrence network shaped by competitive niche partitioning. The plastisphere and surrounding waste exhibited no overlap in network keystone taxa. Key plastisphere taxa-including g_Devosia, g_Rummeliibacillus, and g_Dethiobacter-demonstrated enhanced carbon utilization and stress perception capabilities, playing crucial roles in community assembly and plastic degradation. Although stochastic processes dominated community assembly (73.75 %), homogeneous selection (HoS) driven by plastic properties and keystone taxa enriches pathogens (e.g., Microbacterium spp.) and nitrogen-cycling (e.g., Pseudohongiella) guilds. Metagenomic analysis confirmed the enrichment of denitrification (narB, nosZ) and sulfite reduction (sir, cysCDHIJN) genes, indicating elevated risks of N2O and H2S emissions, especially during early landfill stabilization. Redundancy analysis identified pH, biodegradable organic matter (BDM), and total Kjeldahl nitrogen (TKN) as key environmental drivers. These findings establish the landfill plastisphere as a reservoir of plastic-degrading and potentially pathogenic microorganisms, with important implications for greenhouse gas emissions, odor control, and landfill management strategies. This study provides foundational insights into the ecological consequences of anthropogenic microhabitats in terrestrial environments, bridging critical knowledge gaps in plastisphere ecosystems within landfills-an anaerobic, dark environment rich in organic matter.},
}

@article {pmid41435039,
year = {2025},
author = {Elorriaga, IT and Imatz, E and Ibarlucea, B and Cano, A and Sanmartín, E and Tueros, I and Ayala, U and de Heredia, AG and Zaldua, C and Zugaza, JL and Aleman, IT and Garcia-Sebastian, M and Martínez-Lage, P and Erramuzpe, A},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e099250},
doi = {10.1002/alz70860_099250},
pmid = {41435039},
issn = {1552-5279},
mesh = {Humans ; Aged ; *Public Health ; Female ; Male ; Aged, 80 and over ; Biomarkers ; Middle Aged ; *Aging ; *Healthy Aging ; },
abstract = {BACKGROUND: The ITTHACA project is a collaborative initiative involving six research institutions from the Basque Country including Universities, Health, Technology and Basic Research Institutions. It builds upon the ongoing CITA GO-ON) CITA Go-On study, ClinicalTrials.gov, NCT04840030) cohort study, which adapts the Finnish FINGER [Ngandu, T., et al. 2015] model to the local context. ITTHACA focuses on enhancing healthy aging by identifying markers, prediction models and sensors for in vivo monitoring that allow the establishment and implementation of combined intervention strategies in the population.

METHOD: This one-year randomized-controlled trial (total n = 250; 125 control and 125 intervention), focused on 60-85-year-old males and females at risk of dementia, adopts a multimodal approach. Biomarker identification includes proteomics and metabolomics in biological fluids (blood) and 16S metagenomics and lipidomics in the gut microbiome (stool), as well as employing a FINGER-like mice model. Biosensor technology under development includes multi-channel bioimpedance spectroscopy for tissue analysis and electrochemical sensors for real-time detection of aging markers in biofluids. Predictive modeling integrates data from these analyses and multiple domains-cognition, cardiovascular health, voice, food texture perception and habits-to generate diagnostic tools that monitor biological aging and inform early interventions. A proof-of-concept study in an older population sample, with special attention to user experience, will evaluate the potential benefits of these findings in improving the quality of life for older adults.

RESULT: Not applicable. The ITTHACA project is ongoing, with outcomes expected to include validated biomarkers, novel biosensors, and predictive models that facilitate early interventions.

CONCLUSION: ITTHACA demonstrates the power of interdisciplinary collaboration in tackling the complex multidomain challenge of aging. By leveraging the expertise of complementary Basque Country Research Centers, this initiative is poised to produce innovative resources for prolonging healthy and autonomous living. The project's outcomes are expected to support new therapeutic strategies and socio-healthcare interventions that address the rising prevalence of aging-related conditions, including cognitive decline.},
}

Humans
Aged
*Public Health
Female
Male
Aged, 80 and over
Biomarkers
Middle Aged
*Aging
*Healthy Aging

@article {pmid41434599,
year = {2025},
author = {Dinesh, D and Morgan, X and Scott, TM and Garelnabi, M and Mangano, KM and Noel, SE and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e098660},
doi = {10.1002/alz70860_098660},
pmid = {41434599},
issn = {1552-5279},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Aged ; *Public Health ; Puerto Rico/ethnology ; Prospective Studies ; Feces/microbiology/virology ; *Cognition/physiology ; Hispanic or Latino ; Boston ; Cross-Sectional Studies ; Dysbiosis ; *Virome ; Aged, 80 and over ; Middle Aged ; Alzheimer Disease ; White ; },
abstract = {BACKGROUND: Gut bacterial variations and dysbiosis may influence cognitive function via the microbiome-gut-brain-axis. Gut viruses may also, directly or indirectly, impact cognitive function by modulating the gut bacteria. Hispanics/Latinos, who may have unique microbiome characteristics, are at a higher risk of Alzheimer's disease and related dementia. There is a lack of research on the gut microbiome and, especially, the virome in Hispanics/Latinos. Here, we examined variations in the gut bacteriome and virome associated with cognitive function in the Boston Puerto Rican Health Study (BPRHS), a prospective cohort of older Puerto Rican adults residing in the Boston area.

METHOD: This study was conducted in 316 BPRHS participants with fecal metagenomic sequencing and cognitive assessments, summarized as a composite global cognitive score (GCS). Taxonomic profiling of the gut bacteriome was performed using MetaPhlAN 4.0. Gut virome profiles from shotgun sequencing were generated using BAQLaVa 1.0. Cross-sectional associations between bacterial and viral composition and GCS were assessed using alpha (Shannon) and beta (Bray-Curtis) diversity indices. Feature-wise testing was performed using multivariate linear regression (MaAsLin2) to identify bacterial and viral taxa associated with the GCS.

RESULT: Among 316 participants (mean age 68.7 years, 70.9% female), there were no differences in overall bacterial or viral composition, measured by alpha and beta diversity, based on GCS. In feature-wise analyses, adjusted for age, sex, and BMI, among participants with higher GCS (better cognitive function), we observed an enrichment of Faecalibacterium prausnitzii bacterium (β = 0.78, p = 0.01, FDR p = 0.22), and depletion of the phage Carjivirus communis (β = -1.07, p < 0.01, FDR p = 0.09).

CONCLUSION: The observed results suggest an enrichment of F. prausnitzii, a beneficial butyrate producing taxa, among participants with better cognitive function, and enrichment of Carjivirus communis, a Crassvirales dsDNA Bacteroidetes phage, among participants with worse cognitive function. A recent study reported an association between Bacteroidetes phages and amyloid β and Alzheimer's disease pathology. Gut viral variations may modulate gut bacteria, impacting cognitive function. Future work will test interactions of the gut bacteriome, virome and their functional pathways, as related to cognitive function in Puerto Rican adults.},
}

Humans
Female
Male
*Gastrointestinal Microbiome
Aged
*Public Health
Puerto Rico/ethnology
Prospective Studies
Feces/microbiology/virology
*Cognition/physiology
Hispanic or Latino
Boston
Cross-Sectional Studies
Dysbiosis
*Virome
Aged, 80 and over
Middle Aged
Alzheimer Disease
White

@article {pmid41434594,
year = {2025},
author = {Fernando, WM and Martins, RN and Rainey-Smith, SR and Sohrabi, HR and Ramachandra, S and Dissanayaka, SU},
title = {Public Health.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 6},
number = {},
pages = {e096704},
doi = {10.1002/alz70860_096704},
pmid = {41434594},
issn = {1552-5279},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Aged ; *Alzheimer Disease/microbiology/genetics ; *Probiotics ; Apolipoprotein E4/genetics ; *Public Health ; Feces/microbiology ; Middle Aged ; Australia ; Sex Factors ; Age Factors ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is a progressive neurodegenerative disorder, with evidence suggesting gut microbiota plays a critical role in its onset and progression. Shifts in probiotic communities during the preclinical phase may influence disease pathways through gut-brain interactions. This study investigates how age, sex, and APOE ε4 genotype impact probiotic composition and microbial metabolite production in cognitively unimpaired individuals.

METHOD: Stool samples from 123 participants in the Australian Imaging Biomarkers and Lifestyle (AIBL) study and WA Memory Study (WAMS) were analysed. Participants were grouped by age (<70, ≥70 years), sex, and APOE ε4 carrier status. Metagenomic sequencing assessed gut microbial composition, focusing on probiotics like Bifidobacterium and Lactobacillus. Gas-liquid chromatography measured short-chain fatty acids (SCFAs), including butyrate, propionate, and acetate.

RESULT: Gut Microbiota Composition: Dominant bacterial phyla included Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes across all groups. Age-Related Changes: Older participants (≥70 years) showed significant declines in Bacteroidetes and Firmicutes, reflecting reduced microbial diversity. Sex-Specific Differences: Females had lower Firmicutes levels, reducing butyrate production, essential for inflammation control and brain health. APOE ε4 Carriers: Older APOE ε4 carriers showed a decline in butyrate-producing bacteria, particularly Faecalibacterium prausnitzii, leading to reduced butyrate and elevated acetate levels. Sex and APOE ε4: Female APOE ε4 carriers ≥70 exhibited the most pronounced butyrate decline, indicating increased vulnerability to dysbiosis and inflammation. Probiotic Alterations: Key probiotics, including Bifidobacterium and Lactobacillus, were significantly reduced in older APOE ε4 carriers.

CONCLUSION: Age, sex, and APOE ε4 status significantly influence gut microbiota composition and SCFA production at the preclinical stage of AD. Reduced butyrate levels, particularly in older female APOE ε4 carriers, highlight the importance of gut health in mitigating AD risk. These findings suggest targeted probiotic interventions could restore gut balance and delay AD progression.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
Male
Aged
*Alzheimer Disease/microbiology/genetics
*Probiotics
Apolipoprotein E4/genetics
*Public Health
Feces/microbiology
Middle Aged
Australia
Sex Factors
Age Factors

@article {pmid41433308,
year = {2025},
author = {Konganti, K and Kase, JA and Gonzalez-Escalona, N},
title = {Centriflaken: An automated data analysis pipeline for assembly and in silico analyses of foodborne pathogens from metagenomic samples.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0329425},
doi = {10.1371/journal.pone.0329425},
pmid = {41433308},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Foodborne Diseases/microbiology ; *Shiga-Toxigenic Escherichia coli/genetics/isolation & purification ; Food Microbiology ; Computer Simulation ; Metagenome ; Computational Biology/methods ; Data Analysis ; },
abstract = {Rapid and comprehensive analysis of metagenomic data from samples associated with foodborne outbreaks is of critical importance in food safety. Equally important is the need for automated analysis pipelines that allow the rapid and effective construction of metagenomic assembled genomes (MAGs) to enable bacterial source-tracking from metagenomic data. Here, we present centriflaken, an automated precision metagenomics pipeline for detecting and characterizing Shiga toxin-producing Escherichia coli (STEC) from metagenomic data. centriflaken streamlines the process of generating metagenome-assembled genomes (MAGs) and conducting in silico analyses of STECs, significantly reducing the time and manual effort required for comprehensive pathogen profiling. centriflaken was validated using Oxford Nanopore long-read sequencing data from agricultural water enrichments, successfully reproducing results from our previous study that involved multiple manual bioinformatics steps (Maguire et al., 2021). The tool's efficacy was further demonstrated through its application to ZymoBIOMICS microbial community standards and 21 additional irrigation water samples, completing STEC precision metagenomics analyses in less than 7 hours per sample. centriflaken's versatility allows for the analysis of user-defined taxa beyond STEC, including other foodborne pathogens like Listeria monocytogenes or Salmonella. The pipeline generates comprehensive summary plots and tables, accessible through a MultiQC HTML report. Designed for portability, centriflaken packages all software dependencies within containers and virtual environments. This open-source tool is available on GitHub under the MIT license (https://github.com/CFSAN-Biostatistics/centriflaken), offering a powerful resource for rapid, automated pathogen detection and characterization in food safety applications.},
}

*Metagenomics/methods
*Foodborne Diseases/microbiology
*Shiga-Toxigenic Escherichia coli/genetics/isolation & purification
Food Microbiology
Computer Simulation
Metagenome
Computational Biology/methods
Data Analysis

@article {pmid41432724,
year = {2025},
author = {Zhang, Z and Ye, B and He, J and Xiang, L and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Li, Y and Ju, J and Liu, Y and Xia, M},
title = {Microbial metabolites associated with healthy lifestyles in relation to metabolic syndrome and vascular health: a cross-sectional study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143325},
doi = {10.1128/msystems.01433-25},
pmid = {41432724},
issn = {2379-5077},
abstract = {UNLABELLED: Lifestyle behaviors influence the risk of metabolic syndrome (MetS) and affect vascular health. However, the interactions between gut microbiota and lifestyle behaviors in relation to MetS, as well as the specific microbial taxa and metabolites involved, remain unclear. Here, we aimed to investigate the associations among healthy lifestyle behaviors, gut microbiota, and MetS and to explore the potential mediating roles of microbially derived metabolites in these associations. A total of 1,342 participants with complete assessments of the Healthy Lifestyle Score (HLS), MetS, and vascular health were enrolled. Fecal samples were collected and subjected to metagenomic sequencing. Host genetic data were obtained using a high-density genotyping array, and plasma metabolites were quantified by liquid chromatography-mass spectrometry. Using generalized linear models, we found that increased abundances of Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis were associated with higher HLS and a reduced risk of MetS. Eleven microbial metabolic pathways were independently correlated with both HLS and MetS. Furthermore, increased plasma levels of cinnamoylglycine and betaine, driven by enhanced microbial capacity for homolactic fermentation, were identified as potential microbial effectors associated with MetS and vascular health. These findings indicate that the association between HLS and MetS may involve modulation of the gut microbiota and their metabolites and highlight the potential to enhance the beneficial effects of healthy behaviors on MetS and vascular health through microbiota-modifying interventions.

IMPORTANCE: Metabolic syndrome raises the risk of heart disease and diabetes, yet practical levers to prevent it remain limited. We show that everyday healthy habits align with a gut microbial "signature" linked to better vascular health and lower metabolic risk. Using metagenomics, metabolomics, and genetic causal analyses, we identify specific bacteria (Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis) and microbially produced molecules-especially cinnamoylglycine and betaine from enhanced homolactic fermentation-that may mediate these benefits. These findings connect lifestyle, the gut microbiome, and blood metabolites in a single framework, suggesting actionable biomarkers to monitor risk and potential microbiota-targeted strategies (diet and pre/probiotics) to improve cardiometabolic health. By highlighting concrete microbial pathways and metabolites, our work advances the path toward precision prevention and low-cost interventions for metabolic syndrome and vascular disease.},
}

@article {pmid41432437,
year = {2025},
author = {Bowerman, KL and Lu, Y and McRae, H and Volmer, JG and Zaugg, J and Pope, PB and Hugenholtz, P and Greening, C and Morrison, M and Soo, RM and Evans, PN},
title = {Metagenomic analysis of fecal microbiomes reveals genetic potential for diverse hydrogen management strategies in marsupials.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0160825},
doi = {10.1128/msystems.01608-25},
pmid = {41432437},
issn = {2379-5077},
abstract = {Methane is an end product of plant biomass digestion by gut microbiota, though the amount produced and/or released varies between hosts. On a per-unit-of-feed basis, macropodid marsupials (e.g., kangaroos) have been reported to emit less methane than ruminant livestock, despite a similar diet, although measurements exist for only a subset of macropodid species. Competition for hydrogen within the gut microbiome, particularly through alternative hydrogen sinks to methanogenesis, influences methane production; therefore, characterizing hydrogen management strategies within a host system can provide insights into methane emission profiles. In this study, we analyzed 33 fecal microbiomes of 14 marsupial species (predominantly captive animals) to provide the first systematic characterization of methanogen types and hydrogen-cycling genetic capacity across marsupial gut microbiomes. We recovered 1,394 metagenome-assembled genomes and identified host-associated bacterial signatures that varied significantly between marsupial species. Comparative analysis with fecal microbiomes from high- and low-methane-emitting mammals revealed that marsupials display heterogeneous hydrogen management strategies: some harbor elevated methanogenesis genes (mcrA, methanogen-specific hydrogenases), while others show enrichment of bacterial hydrogen-uptake hydrogenases and alternative electron acceptor pathways (nitrate/nitrite reduction, sulfite reduction). This predicted functional variation occurs both between and within marsupial families and gut types, suggesting that hydrogen management capacity may differ within taxonomic and anatomical classifications. These results demonstrate that marsupial gut microbiomes cannot be treated as a functionally homogenous group regarding methane emissions and highlight the need for species-specific measurements to accurately assess their methanogenic potential and inform ecological models of greenhouse gas production.IMPORTANCEHerbivorous marsupials such as kangaroos and wallabies have been reported to produce significantly lower methane emissions than ruminant livestock despite eating a similar diet, yet the microbial mechanisms underlying this difference remain poorly understood. Here, we conduct a comparative study of fecal microbiomes of 14 marsupial species to provide the first investigation of hydrogen-cycling genetic capacity across these animals. Through comparative analysis with fecal microbiomes of high- and low-methane-producing animals, we identify enrichment of bacterial genes for alternative hydrogen uptake and disposal pathways in some marsupials, supporting competition for hydrogen playing a role in the level of methane production. These data also indicate variation in hydrogen management between marsupials, including within species, suggesting methane emission capacity may vary at the level of the individual.},
}

@article {pmid41432416,
year = {2025},
author = {Hu, B and An, L and Wu, M and Xu, J and Nie, Y and Wu, X-L},
title = {Metagenomics reveals potential interactions between Patescibacteriota and their phages in groundwater ecosystems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120425},
doi = {10.1128/msystems.01204-25},
pmid = {41432416},
issn = {2379-5077},
abstract = {UNLABELLED: Patescibacteriota is a vast lineage composed of bacteria with ultra-small size, streamlined genomes, notable defects in core metabolic potential, and symbiotic lifestyle, which are widely detected in groundwater ecosystems. Increasing attention has focused on the physiological and ecological significance of Patescibacteriota, while the potential interactions between Patescibacteriota and their phages still need more exploration. Here, we collected 82 groundwater metagenomic data sets and further derived 1,162 phages with the potential to infect 2,439 groundwater Patescibacteriota metagenome-assembled genomes (MAGs). Notably, the groundwater Patescibacteriota MAGs were predominantly infected by temperate phages, and viral operational taxonomic unit/host Patescibacteriota operational taxonomic unit (OTU) abundance ratios were significantly negatively correlated with the relative abundance of host Patescibacteriota OTUs. Intriguingly, the groundwater Patescibacteriota phages encoded various auxiliary metabolic genes (AMGs) that might promote symbiotic lifestyle and metabolic potential of host Patescibacteriota MAGs. These included AMGs associated with concanavalin A-like lectin/glucanases superfamily and O-Antigen nucleotide sugar biosynthesis, which could enhance surface adhesion of host Patescibacteriota MAGs. Moreover, AMGs related to the ABC transport system and the P-type transporter could strengthen metabolic exchange and uptake of essential nutrients from the surroundings. Additionally, AMGs involved in various metabolic pathways might alleviate metabolic deficiencies in host Patescibacteriota MAGs.

IMPORTANCE: Here, we sought phages that were capable of infecting Patescibacteriota metagenome-assembled genomes (MAGs), and further explored the diversity and novelty of Patescibacteriota phages, as well as the mechanisms underlying phage-Patescibacteriota interactions in groundwater ecosystems. The abundance profiles of phage-Patescibacteriota interactions suggested that lysogenic infection may represent a mutually adapted strategy between Patescibacteriota and their phages in groundwater ecosystems. Furthermore, the groundwater Patescibacteriota phages possessed diverse auxiliary metabolic genes which might facilitate the symbiotic associations and metabolic exchange between host Patescibacteriota MAGs and other free-living microbes and expand the metabolic capabilities of host Patescibacteriota MAGs. This study elucidated the mechanisms of phage-Patescibacteriota interactions and the potential roles of phages in modulating the physiology and ecology of Patescibacteriota within groundwater ecosystems.},
}

@article {pmid41432288,
year = {2026},
author = {Sahakyan, H and Mutz, P and Tobiasson, V and Koonin, EV},
title = {Exploring the protein universe with distant similarity detection methods.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {1},
pages = {e70397},
doi = {10.1002/pro.70397},
pmid = {41432288},
issn = {1469-896X},
support = {/NH/NIH HHS/United States ; },
mesh = {*Proteins/chemistry/genetics ; *Computational Biology/methods ; Protein Conformation ; Databases, Protein ; Sequence Analysis, Protein/methods ; Models, Molecular ; },
abstract = {During the last few years, the body of data on proteins is expanding almost exponentially with the development of advanced methods for gene sequencing, protein structure determination, particularly by cryoelectron microscopy, and structure prediction using artificial intelligence-based approaches. These developments create the potential for a comprehensive exploration of the protein universe, the entirety of the proteins existing in the biosphere. Elucidation of the relationships among proteins including the most distant ones, where only the core fold is shared, is crucial for understanding protein functions, folding mechanisms, and evolution, as well as the evolution of cellular life forms and viruses. In this brief review, we discuss methods that shaped the field of protein bioinformatics, first, through comparative sequence analysis, and the recent developments in protein structure prediction that transformed the state of the art in the comparative analysis of distantly related proteins. The combination of the rapidly growing databases of genome and metagenome sequences with sensitive methods for sequence comparison and the new generation of structure analysis tools can make charting the protein universe at the structural level a realistic goal.},
}

*Proteins/chemistry/genetics
*Computational Biology/methods
Protein Conformation
Databases, Protein
Sequence Analysis, Protein/methods
Models, Molecular

@article {pmid41432253,
year = {2025},
author = {Ricci, F and Hutchinson, T and Leung, PM and Nguyen-Dinh, T and Zeng, J and Jirapanjawat, T and Eate, V and Wong, WW and Cook, PLM and Greening, C},
title = {Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf286},
pmid = {41432253},
issn = {1751-7370},
abstract = {Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of microorganisms colonising the sediment of a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across the entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.},
}

@article {pmid41432242,
year = {2025},
author = {Xie, X and Chen, L and Yuan, J and Zheng, H and Zhang, L and Yu, X and Liu, X and Wei, C and Qiu, G},
title = {Metagenomic characterization of the metabolism, evolution, and global distribution of Candidatus Accumulibacter members in wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf278},
pmid = {41432242},
issn = {1751-7370},
abstract = {Deciphering the genomic basis of ecological diversification in activated sludge microbiomes is essential for optimizing treatment technology and advancing microbial ecology. Here, we present a global genome-resolved investigation of Candidatus Accumulibacter, the primary functional agent of enhanced biological phosphorus removal, based on 828 metagenomes from wastewater treatment plants across six continents. We recovered 104 high-quality Candidatus Accumulibacter metagenome-assembled genomes, discovering a new clade (Clade IV), substantially expanding the known phylogenetic diversity and revealing a ubiquitous yet geographically heterogeneous global distribution. Phylogenomic and pangenome analyses uncovered extensive clade-specific gene gain and loss, particularly in nitrogen metabolism, suggesting divergent evolutionary trajectories shaped by relaxed selection and niche adaptation. Genome-wide patterns of convergent streamlining and enriched antiviral defense systems indicate selective pressures from strong competition and viral predation. Constraint-based metabolic modeling revealed pervasive amino acid autotrophies and metabolic complementarity, coupled with distinct carbon utilization strategies that support ecological specialization across operational settings. Experimental validation reconciled model-phenotype discrepancies, highlighting the importance of transporter promiscuity and gene regulation in carbon substrate assimilation. Collectively, our findings redefine Candidatus Accumulibacter as a dynamic model of microbial genome plasticity, metabolic adaptation, and ecological resilience, providing an insight for understanding how microbial communities adapt and respond under engineered environmental conditions.},
}

@article {pmid41432159,
year = {2025},
author = {Lau, KJX and Ma, A and Chen, B and Thankaraj Salammal, MS and Ramachandran, S and Naqvi, NI},
title = {Controlled irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297025},
doi = {10.1128/spectrum.02970-25},
pmid = {41432159},
issn = {2165-0497},
abstract = {The rhizosphere microbiomes of rice plants under conventional flood irrigation consist of highly complex consortia of microorganisms and, in particular, methanogens purportedly associated with methane emissions therein. Controlled irrigation has been proposed as a cultivation method of choice over continuous flooding to reduce water and fertilizer usage in an aerobic environment. However, a systematic understanding of the assembly and function of microbiota in the rhizosphere under drip and flood irrigation remains unclear. Using empirical analyses, we report a significant reduction in methane emissions in controlled irrigation compared to the flooded environment. Genotypic or varietal differences did not influence such methane emissions under conventional flooded cultivation of rice. Using metagenomic sequencing and computational analyses, we provide a deeper understanding of how drip irrigation or continuous flooding affects the root-associated microbiomes in rice. Rhizosphere soil from two different rice varieties, Huanghuazhan and Temasek rice, grown under drip or flood conditions in a greenhouse, was collected over 2 months post-transplantation for metagenomic analysis. Our results reveal that drip irrigation favors microbes involved in the nitrifying-denitrifying processes, while continuous flooding enriches for methanotrophs and methanogenic archaea. Syntrophic microbiomes associated with methanogenesis were significantly reduced in drip irrigation. Several keystone taxa were evident in the co-occurrence network model related to methanogenic, methanotrophic, nitrifying, sulfur-oxidizing and sulfur-reducing activities. Lastly, oxygen availability and redox potential were identified as key drivers that reshape rhizosphere microbiota and the associated metabolic functional differences observed between the two irrigation regimes, leading up to the microbial mitigation of climate impact.IMPORTANCEUnlike previous studies in alternate wet-dry irrigation systems, this study characterized the rice microbiomes in a controlled drip irrigation setting where water levels were maintained at low levels and soil remained unflooded throughout the entire season in a greenhouse. A reduction of more than 90% in methane emissions was observed with drip irrigation compared to flood irrigation. A significant correlation was found between levels of methane emitted and mcrA gene copies detected, with a Pearson correlation coefficient R of 0.77 and P-value of 2.3e - 10. Methanogens are highly abundant in continuously flooded rice soil and are significantly reduced in drip-irrigated soil. Metagenomic profiling indicates that the shifts in microbial diversity under drip irrigation favor nitrifying microorganisms and are likely influenced by increased oxygen availability due to higher soil redox potential.},
}

@article {pmid41432156,
year = {2025},
author = {Butarelli, ACdA and Nakamura, FM and Vilela Peres, F and Modolon da Silva, F and Bendia, AG and Basti, R and Mahiques, MMd and Sumida, PYG and Pellizari, VH},
title = {Genomic insights into a versatile deep-sea methanotroph constituting the rare biosphere of a Brazilian carbonate mound complex.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0131125},
doi = {10.1128/msystems.01311-25},
pmid = {41432156},
issn = {2379-5077},
abstract = {UNLABELLED: Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments, described in accordance with the SeqCode rules. Recent discoveries of aerobic methanotrophs in non-seep carbonate-rich environments in the deep sea suggest that these organisms may persist as part of the rare biosphere. Recovering rare, active methanotrophs through targeted culturing is essential for understanding their persistence under the oligotrophic non-seep conditions, and for uncovering their genomic adaptations related to the survival in energy-limited ecosystems. In our study, using metagenomic analysis of enrichment cultures from the Alpha Crucis Carbonate Ridge, we discovered Methylotuvimicrobium crucis sp. nov., a novel methanotroph representing the rare biosphere in native sediments, described in accordance with the SeqCode rules. Phylogenomic analysis revealed <95% of Average Nucleotide Identity (ANI) to described species, with genomic evidence of deep-sea specialization including: (i) stress adaptation through cold-shock proteins (CspA) and DNA repair systems (UvrD/LexA), (ii) metabolic versatility via complete methane oxidation (pmoABC), nitrogen fixation (nifHDK), and sulfur cycling (sox/sqr) pathways, and (iii) niche partitioning through biofilm formation (GGDEF/EAL) and heavy metal resistance (CopZ/CzcD). Comparative genomics identified a 1,234-gene deep-sea core shared with Methylotuvimicrobium sp. wino1, enriched in mobile elements (TnpA, prophages) suggesting horizontal gene transfer drives adaptation. While undetected in situ amplicon surveys, Methylotuvimicrobium crucis exhibited enrichment under methane availability, demonstrating its role as a latent methane filter. These findings contribute to the understanding of the ecological significance of aerobic methanotrophs in deep-sea systems, revealing how rare microbial taxa with genomic plasticity have the potential to influence biogeochemical cycling in deep carbonate-rich environments.

IMPORTANCE: Microbial communities in deep-sea sediments play crucial roles in global biogeochemical cycles, yet they remain poorly characterized due to the challenges of sampling and culturing under extreme conditions. This study provides a comprehensive overview of microbial diversity and functional potential in carbonate-rich deep-sea sediments, with an emphasis on methane-oxidizing bacteria. By combining high-throughput metagenomics and comparative genomics, we reconstructed high-quality genomes from previously uncharacterized microbial consortia, including novel members of the genus Methylotuvimicrobium. Our findings shed light on the ecological strategies of methanotrophs in oxygen-limited environments and expand the genomic representation of key players in carbon cycling.},
}

@article {pmid41432144,
year = {2025},
author = {Liu, J and Ni, H-B and Yu, M-Y and Qin, S-Y and Elsheikha, HM and Peng, P and Guo, L and Xie, L-H and Liang, H-R and Lei, C-C and Xu, Y and Tang, Y and Yu, H-L and Qin, Y and Liu, J and Sun, H-C and Zhang, X-X and Qiu, B},
title = {Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144325},
doi = {10.1128/msystems.01443-25},
pmid = {41432144},
issn = {2379-5077},
abstract = {UNLABELLED: Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife.

IMPORTANCE: Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.},
}

@article {pmid41431864,
year = {2026},
author = {Dowrick, JM and Roy, NC and Carco, C and James, SC and Heenan, PE and Frampton, CMA and Fraser, K and Young, W and Cooney, J and Trower, T and Keenan, JI and McNabb, WC and Mullaney, JA and Bayer, SB and Talley, NJ and Gearry, RB and Angeli-Gordon, TR},
title = {Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604871},
doi = {10.1080/19490976.2025.2604871},
pmid = {41431864},
issn = {1949-0984},
mesh = {Humans ; Cluster Analysis ; *Gastrointestinal Diseases/physiopathology/microbiology/classification ; Male ; Female ; *Brain/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Multiomics ; },
abstract = {Rome IV disorders of gut-brain interaction (DGBI) subtypes are known to be unstable and demonstrate high rates of non-treatment response, likely indicating patient heterogeneity. Cluster analysis, a type of unsupervised machine learning, can identify homogeneous sub-populations. Independent cluster analyses of symptom and biological data have highlighted its value in predicting patient outcomes. Integrated clustering of symptom and biological data may provide a unique multimodal perspective that better captures the complexity of DGBI. Here, integrated symptom and multi-omic cluster analysis was performed on a cohort of healthy controls and patients with lower-gastrointestinal tract DGBI. Cluster stability was assessed by considering how frequently pairs of participants appeared in the same cluster between different bootstrapped datasets. Functional enrichment analysis was performed on the biological signatures of stable DGBI-predominant clusters, implicating disrupted ammonia handling and metabolism as possible pathophysiologies present in a subset of patients with DGBI. Integrated clustering revealed subtypes that were not apparent using a singular modality, suggesting a symptom-only classification is prone to capturing heterogeneous sub-populations.},
}

Humans
Cluster Analysis
*Gastrointestinal Diseases/physiopathology/microbiology/classification
Male
Female
*Brain/physiopathology
*Gastrointestinal Microbiome
Adult
Middle Aged
*Gastrointestinal Tract/physiopathology
Multiomics

@article {pmid41431647,
year = {2025},
author = {Lu, X and Dai, H and Gu, X and Xie, J and Zhong, X and Dong, X and Su, B and Su, J and Wang, L and Sun, T and Geng, L},
title = {The clinical significance of gut microbiota of chronic obstructive pulmonary disease with functional abdominal bloating and distension.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20526},
pmid = {41431647},
issn = {2167-8359},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/complications/physiopathology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Case-Control Studies ; Biomarkers ; *Gastrointestinal Diseases/microbiology ; Clinical Relevance ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a disease with high morbidity and mortality. Functional abdominal bloating/distension (FABD), a functional gastrointestinal disorder characterized by recurrent sensations of abdominal fullness and/or visible abdominal distension without identifiable organic causes. FABD mainly impairs gastrointestinal functions-particularly intestinal transit and gas handling-rather than pulmonary function. This study characterized fecal microbiota in COPD patients with FABD to identify precision medicine biomarkers.

METHODS: Fecal samples from 20 COPD & FABD, 20 COPD, and 10 healthy controls (HC) were analyzed via metagenomic analysis. Gut microbiota diversity/composition were compared, and immune parameters (serum IgG, CD4+/CD8+ T cells) were assessed.

RESULTS: COPD/COPD & FABD patients showed significantly higher fecal microbiota α-diversity (COPD vs. HC: Chao1, P = 0.12; ACE, P = 0.14; Shannon, P = 0.0016; Simpson, P = 0.0013; COPD & FABD vs. HC: Chao1, P = 0.031; ACE, P = 0.031; Shannon, P = 0.00032; Simpson, P = 0.0005) vs. HC. β-Diversity analyses (PCA/PCoA) revealed distinct clustering between patients and HC (PCA, P = 0.014; PCoA, P = 0.013), but no separation between COPD and COPD & FABD (P > 0.05). Linear discriminant analysis (LEfSe) identified 50 discriminative biomarkers: 41 enriched in HC (Bacteroides uniformis), five in COPD & FABD (Bacilli, Enterococcus faecium), and four in COPD (Streptococcus parasanguinis). Notably, Enterococcus faecium was highly abundant in patients (22.04-26.92%) but absent in HC, suggesting a potential association with the COPD-FABD condition. Random forest models showed moderate diagnostic accuracy for all microbes (AUC = 0.632) and strong performance for fungal biomarkers (Clostridium fessum, Clostridioides difficile; AUC = 0.856).

CONCLUSION: Gut microbiota signatures, particularly Enterococcus faecium and fungal taxa, may serve as non-invasive biomarkers for COPD progression and FABD diagnosis, warranting clinical validation.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/complications/physiopathology
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Aged
Feces/microbiology
Case-Control Studies
Biomarkers
*Gastrointestinal Diseases/microbiology
Clinical Relevance

@article {pmid41431641,
year = {2025},
author = {Nguyen, BN and Nguyen, LTN and Trinh, DTM and Nguyen, HT and Tran, TTT},
title = {Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20521},
pmid = {41431641},
issn = {2167-8359},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology ; Vietnam ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Pilot Projects ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; },
abstract = {In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam.},
}

Humans
*Arthritis, Rheumatoid/microbiology
Vietnam
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Pilot Projects
Adult
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Aged

@article {pmid41431463,
year = {2025},
author = {Noorian, P and Hamann, K and Hoque, MM and Espinoza-Vergara, G and To, J and Leo, D and Chari, P and Weber, G and Marial, O and Pryor, J and Duggin, IG and Lee, BB and Rice, SA and McDougald, D},
title = {A model, mixed-species urinary catheter biofilm derived from spinal cord injury patients.},
journal = {Biofilm},
volume = {10},
number = {},
pages = {100332},
pmid = {41431463},
issn = {2590-2075},
abstract = {Complex multispecies biofilms consistently colonise urinary catheters, causing persistent asymptomatic bacteriuria and frequent symptomatic episodes in long-term catheterized individuals. Simple single-species models often fail to capture the complexities of mixed-species interactions and lab-based organisms may not reflect the genomic diversity found in real-world infections. Additionally, growth under flow conditions promotes robust, complex-biofilm structures. Therefore, to reflect the dynamics of in vivo infections, biofilm samples from clinical indwelling catheters of spinal cord injury (SCI) participants colonised by 5-10 species were used to establish polymicrobial macro-fluidic models, in catheters. This resulted in final models of 2-4 species biofilms. Metagenomic techniques using short-read Illumina and long-read Oxford Nanopore sequencing was used to assess the taxonomic composition, in vivo to in vitro biofilms diversity shifts, single nucleotide polymorphism (SNP) analysis and complete metagenome-assembled genomes (MAGs). In silico analysis revealed a high number of varied antibiotic resistance genes, virulence factors and biofilm associated factors present in these biofilms. Antibiotic resistance testing using our models highlighted the drastic differences between planktonic bacteria, single-species and multispecies biofilms. While single-species biofilms show considerably increased tolerance to antibiotics compared to their planktonic counterparts, this resistance is even greater in multispecies biofilms. Under flow conditions, all species in the multispecies biofilm showed increased resistance, unlike static conditions where only most did. Models developed and characterised in this study are expected to facilitate testing of effective strategies to prevent and treat catheter-associated infections by enabling more accurate analysis of biofilm inhibition, disruption and microbial interactions.},
}

@article {pmid41431440,
year = {2026},
author = {Wang, W and Huang, H and Zhao, K and Lv, J and Liu, X and Xie, S and Feng, J},
title = {The Differing Responses of Chlorophyta and Bacillariophyta to Available Resources Result in Diverse Community Patterns in Lakes Situated to the East of the Hu Line During the Autumn.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {1},
pages = {e70248},
doi = {10.1002/wer.70248},
pmid = {41431440},
issn = {1554-7531},
support = {32270220//National Natural Science Foundation of China/ ; U22A20445//National Natural Science Foundation of China/ ; 2020KJ029//Excellent Achievement Cultivation Project of Higher education in Shanxi/ ; 2024-007//Research Project Supported by Shanxi Scholarship Council of China/ ; 202203021211313//Sanjin Talent Innovation Teams in Natural Sciences and Engineering Technology/ ; },
mesh = {*Lakes ; *Diatoms/genetics/physiology ; *Chlorophyta/genetics/physiology ; Seasons ; Biodiversity ; Ecosystem ; },
abstract = {Phytoplankton communities are of vital importance to the functioning of freshwater ecosystems, but the role of the metabolic capacity of the community in regulating community dynamics under natural conditions has yet to be sufficiently considered. This study investigated 26 lakes situated along the eastern section of the Hu Line, combining field surveys with metagenome-assembled analyses to ascertain the factors responsible for the divergence in Chlorophyta and Bacillariophyta communities. The results demonstrated that the diversity of Chlorophyta was markedly higher than that of Bacillariophyta whereas the abundance was significantly lower. These discrepancies in community attributes were predominantly attributable to variations in the response of the two algal groups to nutrients. The abundance and diversity of diatom metabolic genes were significantly higher than those of green algae. The greater diversity and extent of metabolic genes in Bacillariophyta confer enhanced metabolic capacity and, consequently, greater adaptive capacity. Such differences in metabolic gene composition may be attributed to the disparate evolutionary pathways that these organisms have followed.},
}

*Lakes
*Diatoms/genetics/physiology
*Chlorophyta/genetics/physiology
Seasons
Biodiversity
Ecosystem

@article {pmid41431054,
year = {2025},
author = {Mei, H and Mei, J and Sun, Y and Shang, Q and Sun, P and Yang, Y and Kan, J and Chen, X and Sun, L},
title = {Antibiotics guided by metagenomic next-generation sequencing to control infection after total knee arthroplasty: A case report and literature review.},
journal = {Medicine},
volume = {104},
number = {51},
pages = {e46734},
doi = {10.1097/MD.0000000000046734},
pmid = {41431054},
issn = {1536-5964},
mesh = {Aged ; Humans ; Male ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; *Arthroplasty, Replacement, Knee/adverse effects ; Coxiella burnetii/genetics/isolation & purification ; Doxycycline/therapeutic use/administration & dosage ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Moxifloxacin/therapeutic use/administration & dosage ; *Prosthesis-Related Infections/drug therapy/microbiology ; *Q Fever/drug therapy/diagnosis ; },
abstract = {RATIONALE: A prosthetic joint infection is a serious complication of joint surgery, with Staphylococcus aureus being the most common pathogen. In contrast, C. burnetii, the agent of Q fever, is a rare zoonotic parasite primarily found in cattle and sheep. It can be transmitted through respiratory, digestive, and cutaneous routes, destroying host cells and leading to diseases such as bone and joint infections, endocarditis, and interstitial lung disease.

PATIENT CONCERNS: A 75-year-old male patient underwent total knee arthroplasty due to degenerative disease in his left knee. After surgery, he was exposed to cattle and their feces. Fifteen months after the operation, he experienced pain, though there was no significant elevation of erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and white blood cell (WBC). Oral nonsteroidal anti-inflammatory drugs (NSAIDs) were administered. The pain intensified and was accompanied by swelling. ESR and CRP were elevated, while WBC remained normal. The patient took oral Rifampicin for 28 days without improvement. The knee joint puncture culture was negative. The metagenomic next-generation sequencing (mNGS) detected C. burnetii, and oral Doxycycline for 1 week. The intravenous infusion of Doxycycline and Moxifloxacin continued for 28 days. After the above indexes stabilized, a 1-stage revision surgery was performed, and Doxycycline and Moxifloxacin were administered for 16 days until the indexes returned to normal and symptoms such as knee joint pain and swelling disappeared.

DIAGNOSES: Left knee radiography, laboratory tests, and knee cavity puncture, culture, and mNGS testing were performed to confirm the diagnosis of the pathogen.

INTERVENTIONS: According to mNGS, the left knee was revised and antibiotics were applied before and after the operation until the infection indexes returned to normal and symptoms such as knee pain and swelling disappeared.

OUTCOMES: ESR, CRP, and WBC indexes were normal. Pain and swelling disappeared. Other symptoms disappeared. Joint flexion and extension mobility was good.

LESSONS: In patients with postoperative prosthetic joint infection after total knee arthroplasty, mNGS can identify pathogenic bacteria, inform the use of antibiotics, and enable prompt surgical intervention.},
}

Aged
Humans
Male
*Anti-Bacterial Agents/therapeutic use/administration & dosage
*Arthroplasty, Replacement, Knee/adverse effects
Coxiella burnetii/genetics/isolation & purification
Doxycycline/therapeutic use/administration & dosage
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Moxifloxacin/therapeutic use/administration & dosage
*Prosthesis-Related Infections/drug therapy/microbiology
*Q Fever/drug therapy/diagnosis

@article {pmid41431015,
year = {2025},
author = {Lin, B and Meng, X and Pu, K and Fu, T and Peng, N and Li, Q},
title = {Early diagnostic strategy for central nervous system bacterial infections after neurosurgery: A retrospective study.},
journal = {Medicine},
volume = {104},
number = {51},
pages = {e46635},
doi = {10.1097/MD.0000000000046635},
pmid = {41431015},
issn = {1536-5964},
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Neurosurgical Procedures/adverse effects ; Adult ; Early Diagnosis ; *Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/etiology ; Aged ; *Postoperative Complications/diagnosis/cerebrospinal fluid ; ROC Curve ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Accurate diagnosis of post-neurosurgical bacterial infection of central nervous system is challenging due to the nonspecific nature of clinical signs and cerebrospinal fluid (CSF) parameters, which often overlap with sterile postoperative inflammation. This study aimed to develop and validate a stepwise diagnostic strategy integrating readily available clinical and basic laboratory indicators to improve the early identification of post-neurosurgical bacterial infection of the central nervous system. A retrospective cohort study was conducted at Tianjin Huanhu Hospital, a tertiary neurosurgical center, from October 2018 to June 2025. We enrolled 176 patients suspected of post-neurosurgical bacterial infection of the central nervous system who underwent CSF metagenomic next-generation sequencing (mNGS). Six diagnostic prediction models, combining clinical features (fever, altered mental status) and CSF parameters (white blood cell count, glucose levels), were constructed. Their diagnostic performance was evaluated against a composite reference standard (mNGS, culture, and clinical treatment response) using receiver operating characteristic analysis. The area under the curve (AUC), sensitivity, and specificity were calculated. Among the 6 models, two demonstrated superior performance. Model 5 (T > 38.0°C + [CSF white blood cell ≥ 2000 × 106/L OR CSF glucose < 2.2 mmol/L OR CSF/Blood glucose ratio < 0.4]) achieved an AUC of 0.768. Notably, Model 6 (T > 39.0°C + Altered Mental Status + Intermittent Fever), relying solely on clinical indicators, achieved a comparable AUC of 0.769. For individual parameters, a high fever threshold (T > 39.8°C) and profoundly low CSF glucose (<1.01 mmol/L) showed high specificities of 99%and 97%, respectively, for ruling in infection. A diagnostic strategy combining severe clinical manifestations (high fever and altered mental status) with high-threshold CSF parameters enables effective risk stratification for post-neurosurgical bacterial infection of the central nervous system. The high performance of a purely clinical model (Model 6) offers a valuable tool for rapid bedside assessment, especially in resource-limited settings. Future prospective, multicenter studies are recommended to validate these algorithms and further refine variable definitions for broader clinical application.},
}

Humans
Retrospective Studies
Male
Female
Middle Aged
*Neurosurgical Procedures/adverse effects
Adult
Early Diagnosis
*Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/etiology
Aged
*Postoperative Complications/diagnosis/cerebrospinal fluid
ROC Curve
Sensitivity and Specificity
High-Throughput Nucleotide Sequencing

@article {pmid41430427,
year = {2025},
author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M},
title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32485-x},
pmid = {41430427},
issn = {2045-2322},
abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.},
}

@article {pmid41430301,
year = {2025},
author = {Wikki, I and Palmu, J and Kauko, A and Havulinna, A and Jousilahti, P and Lahti, L and Knight, R and Salomaa, V and Niiranen, T},
title = {Prospective association between the gut microbiota and incident pneumonia: a cohort study of 6419 individuals.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03453-w},
pmid = {41430301},
issn = {1465-993X},
support = {330887//Research Council of Finland/ ; 321351, 354447//Research Council of Finland/ ; },
abstract = {BACKGROUND: Previous animal studies have identified the protective capacity of the gut microbiota against respiratory infections. Nevertheless, the prospective association between human gut microbiota and pneumonia risk remains unknown.

OBJECTIVES: To evaluate the links between gut microbiota and incident pneumonia in a representative population sample.

METHODS: We performed shotgun metagenome sequencing on stool samples from 6419 FINRISK 2002 participants. Participants were followed up for incident pneumonia using nationwide health register data. We employed multivariable-adjusted Cox regression models and permutational multivariate analysis of variance (PERMANOVA) to assess the association of gut microbiome alpha diversity, compositional variation (beta diversity), and taxonomic composition with pneumonia risk.

RESULTS: Altogether, 685 patients (10.7%) developed pneumonia during a mean follow-up of 17.8 years. Alpha diversity was not associated with incident pneumonia (hazard ratio [HR] 1.00; 95% confidence interval [CI] 0.93 - 1.08), whereas community composition was (PERMANOVA R[2] = 0.03%; P = 0.02). We observed an inverse association between the relative abundance of butyrate-producing bacteria and incident pneumonia (HR per 1-SD increase 0.91; 95% CI 0.85-0.98). The relative abundance of Bacteroides_F pectinophilus, Eubacterium_G ventriosum, Agathobaculum butyriciproducens, Butyribacter intestini, Eubacterium_I ramulus, CAG-1427 sp000435675, and CAG-603 sp900066105 were inversely associated with pneumonia risk. The relative abundance of Clostridium_AQ innocuum was positively correlated with pneumonia risk.

CONCLUSIONS: The gut microbiota composition, and especially the relative abundance of butyrate-producing bacteria, was associated with lower pneumonia risk in the population. These findings warrant further studies to investigate whether microbiome modulation to increase short chain fatty acid production through diet, prebiotics, or probiotics could reduce pneumonia risk.},
}

@article {pmid41430289,
year = {2025},
author = {Williams, GM and Hoedt, EC and Duncanson, K and Gan, L and Prakoso, E and Talley, NJ and Beck, EJ},
title = {Inverse associations between Mediterranean diet constituents and the gut microbiota in metabolic-associated steatotic liver disease (MASLD): a case-control study.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-025-00939-8},
pmid = {41430289},
issn = {1743-7075},
abstract = {BACKGROUND: Dietary therapy, specifically for weight loss, is currently considered first-line therapy for metabolic-associated steatotic liver disease (MASLD). However, increasing recognition of the role of the gut-liver axis in MASLD highlights potential for microbiota-modulating dietary therapy to improve outcomes. This study aimed to explore dietary variables relevant to gut microbiota in MASLD.

METHODS: Twenty-five adults with MASLD and 25 healthy controls were recruited using a retrospective case-control design and characterised using 3-day dietary intake records, clinical markers, and shotgun metagenomic sequencing.

RESULTS: MASLD participants consumed less dietary fibre (p = < 0.01), very long chain omega-3 fatty acids (p = 0.02), nuts and seeds (p = 0.03), whole grains (p < 0.01) and vegetables (p = 0.04). Participants with MASLD had lower abundance of Alistipes senegalensis (r=-0.01, p = 0.04), Coprococcus eutactus (r=-0.07, p = 0.006), Faecalibacterium (r=-0.02, p < 0.001), and higher abundance of Ruminococcus torques (r = 0.04, p = 0.02), and less expression of functional pathways associated with ethanol production, methionine, folate and branched-chain amino acid metabolism. Bacterial species and functional pathways more abundant in MASLD were positively associated with intake of added sugars and saturated fat, and negatively associated with unsaturated fatty acid and dietary fibre intake.

CONCLUSIONS: Microbiota characteristics differ between individuals with and without MASLD, and this is influenced by dietary intake. Future translation-focused research investigating dietary interventions and the gut-liver-axis in MASLD are warranted.},
}

@article {pmid41429819,
year = {2025},
author = {Chen, Q and Xu, J and Yang, J and Qin, X and Fan, J and Ke, H and Yang, Z and Zheng, W and Li, X and Huang, L and Ning, W},
title = {Gut microbiota analysis in children with autism spectrum disorder and their family members.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44282},
pmid = {41429819},
issn = {2045-2322},
support = {Grant No.3502Z20214001//Project of Xiamen Cell Therapy Research Center, Xiamen, Fujian, China/ ; 2022YFC2704300//National Key Research and Development Program of China/ ; 32400532//National Natural Science Foundation of China/ ; 2024GGB18//Fujian Provincial Health Technology Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology ; Child ; Male ; Female ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; Siblings ; Bifidobacterium/isolation & purification/genetics ; Clostridium/isolation & purification/genetics ; Bacteroides/isolation & purification/genetics ; Metagenomics/methods ; Family ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication and interaction, alongside restricted, and repetitive behaviors. Emerging evidence suggests that gut microbiota alterations may contribute to ASD pathogenesis via the gut-brain axis. However, many previous studies have not adequately controlled for confounding genetic and environmental variables. In this study, we examined the gut microbiota profiles of 19 children with ASD, 8 siblings with non-ASD, and 36 parents from 17 families, providing a unique design that minimized biases related to shared genetic and familial environments. Metagenomic sequencing revealed significant differences in gut microbiota diversity and composition between groups. Specifically, children with ASD had lower abundances of Bifidobacterium and higher abundances of both Bacteroides and Clostridium species compared to their siblings, with notable dysbiosis correlated to ASD-specific symptoms. These findings highlight the potential role of microbiota alterations in ASD pathogenesis and suggest familial microbiota traits influenced by both genetic and environmental factors. Further exploration of gut microbial therapies could offer promising avenues for ASD intervention.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Autism Spectrum Disorder/microbiology
Child
Male
Female
Child, Preschool
Dysbiosis/microbiology
Feces/microbiology
Siblings
Bifidobacterium/isolation & purification/genetics
Clostridium/isolation & purification/genetics
Bacteroides/isolation & purification/genetics
Metagenomics/methods
Family

@article {pmid41429339,
year = {2025},
author = {Li, M and Gao, S and Cheng, J and Chen, D and Li, H and Zhang, X and Wu, C and Chang, Y},
title = {Potential biomarkers for human Ascending aortic aneurysm identified through metagenomic and metabolomic Analyses: A case-control study.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.026},
pmid = {41429339},
issn = {2090-1224},
abstract = {INTRODUCTION: Ascending aortic aneurysm (AsAA) is a high-risk cardiovascular condition; recent research indicates a possible association between gut microbiota, plasma metabolites, and the pathogenesis of AsAA.

OBJECTIVE: This study aims to investigate the compositional and metabolic alterations in the gut microbiota of AsAA patients to identify potential biomarkers for AsAA.

METHODS: This study enlisted 72 participants, comprising 44 individuals with AsAA and 28 healthy controls. All participants underwent examination for clinical features, and fecal and plasma samples were obtained for metagenomic and metabolomic studies.

RESULTS: Metagenomic analysis revealed a significant reduction of 23 bacterial species in AsAA patients, including Bifidobacterium adolescentis, Bifidobacterium longum, Lactiplantibacillus plantarum, Enterococcus faecalis, and Streptococcus thermophilus, while 52 bacterial species, such as Prevotella copri, Phascolarctobacterium faecium, and Eubacterium ventriosum, were found to be enriched. Furthermore, we identified seven microbial co-abundance groups (CAGs), of which three (predominantly comprising Roseburia, Agathobacter, and Prevotella) were significantly elevated in AsAA patients, whereas one (predominantly comprising Escherichia) was substantially diminished. KEGG pathway enrichment analysis indicated that the biosynthesis of unsaturated fatty acids pathway displayed the most pronounced differences between groups. Metabolomics data revealed that 22 metabolites, including ceramides, were significantly elevated, while 8 metabolites, such as threonine, were notably downregulated. Moreover, clinical indicators like C-reactive protein (CRP) and complement components C3 and C4 have shown strong correlations with specific gut microbiota (Streptococcus, Prevotella) and plasma metabolites (threonine, ceramides). These findings indicate that inflammatory responses, metabolic dysregulation, and gut microbiota imbalance are pivotal in the etiology of AsAA.

CONCLUSION: This study demonstrates substantial alterations in gut microbiota composition and plasma metabolites in patients with AsAA. Prevotella and ceramides exhibit potential as biomarkers for AsAA diagnosis. Furthermore, a synergy of Prevotella and ceramides may function as a potent disease prediction classifier, offering novel perspectives on the early diagnosis and targeted treatment of AsAA.},
}

@article {pmid41429282,
year = {2025},
author = {Akram, J and Jin, Y and Song, C and Li, C and Chen, C and Liu, G},
title = {Stimulating anaerobic degradation of biodegradable plastics by promoting direct interspecies electron transfer via conductive materials.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133850},
doi = {10.1016/j.biortech.2025.133850},
pmid = {41429282},
issn = {1873-2976},
abstract = {Although biodegradable plastics (BPs) are promoted as environmentally friendly, they exhibit low degradability and slow degradation rates under anaerobic conditions, creating challenges similar to conventional plastics. This study explores the effects of granular activated carbon and magnetite on the anaerobic digestion of BPs. Results showed that conductive materials improved digestion rates for readily degradable BPs but had no effect on recalcitrant ones unless pretreated. Magnetite increased the maximum methane production rates of cellulose diacetate, poly(3-hydroxybutyrate-co-3-hydroxyvalerate), and thermoplastic starch by 18 %, 37 % and 15 %, respectively, at an organic loading (OL) of 8 gVS/L. Supplementation was especially effective at high OLs, where unamended controls were inhibited by excessive acidification. Metagenomic analysis revealed enrichment of direct interspecies electron transfer-capable microorganisms such as Syntrophaceticus and Methanosarcina, along with associated functional genes, in the supplemented groups. Overall, the findings suggest that conductive materials are most beneficial for readily degradable BPs, especially under high OL conditions.},
}

@article {pmid41429225,
year = {2025},
author = {Chen, J and Cao, H and Xu, Y and Chang, Y and Qin, X and Zhang, Z and Yang, W},
title = {Is light-to-moderate alcohol drinking associated with the onset of metabolic dysfunction-associated steatotic liver disease in a Chinese cohort?.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101144},
doi = {10.1016/j.ajcnut.2025.101144},
pmid = {41429225},
issn = {1938-3207},
abstract = {BACKGROUND: The association between light-to-moderate alcohol drinking (≤14 g/d for females; ≤28 g/d for males) and the risk of steatotic liver disease (SLD), including its metabolic dysfunction-associated subtype (MASLD), remains unclear, as does the role of related gut microbiota.

OBJECTIVES: We investigated the association between light-to-moderate alcohol drinking and incident SLD/MASLD, identified gut microbial species associated with such drinking, and evaluated their associations with disease risk.

METHODS: Among 1297 adults from a Chinese community-based cohort, alcohol intake was assessed by validated questionnaire, and SLD was diagnosed by vibration-controlled transient elastography. In a subset with fecal samples at follow-up (n=665), gut microbiota was profiled using shotgun metagenomic sequencing. We used the average alcohol intake from baseline and follow-up to represent long-term drinking habits. Species differentially associated with alcohol intake were identified using zero-inflated Gaussian models with false discovery rate (FDR) correction. Cox and logistic regression were used to estimate hazards ratio (HR) and odds ratio (OR) with 95% confidence interval (CI), respectively.

RESULTS: During follow-up (2020-2025), 513 incident SLD cases were identified. Light-to-moderate drinkers showed higher risks of SLD (HR=1.27, 95% CI: 1.03, 1.58) and MASLD (HR=1.27, 95% CI: 1.01, 1.59) versus abstainers. For the same comparison, liquor consumption was positively associated with SLD (HR=1.29, 95% CI: 1.01, 1.65). We identified 89 microbial species associated with alcohol intake and constructed a microbial score, which was positively associated with SLD (ORT3 vs T1=1.54, 95% CI: 1.03, 2.31, Ptrend=0.05) and MASLD (ORT3 vs T1=1.50, 95% CI: 1.00, 2.26, Ptrend=0.05). Among these species, Stenotrophomonas maltophilia AQ, Olsenella E timonensis, and Firm 11 sp., which were less abundant in drinkers, showed inverse associations with both conditions after FDR correction.

CONCLUSIONS: Light-to-moderate alcohol consumption was associated with increased risks of SLD and MASLD. A gut microbial score based on alcohol-associated species also predicted higher disease risk.},
}

@article {pmid41429195,
year = {2025},
author = {Ji, J and Guo, J and Huang, Y and Chen, K and Xu, Y and Liang, W and Lin, Z and Xiong, C and Han, X and Liu, J and Hei, Z and Chen, S and Yao, W and Chen, C},
title = {Electroconvulsive therapy modulates brain plasticity in male depression: Links to gut microbial metabolites and diet-derived regulation of Wnt/BDNF signaling.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110240},
doi = {10.1016/j.jnutbio.2025.110240},
pmid = {41429195},
issn = {1873-4847},
abstract = {Electroconvulsive therapy (ECT) stands as the most effective intervention for treatment-resistant depression; however, its interaction with dietary regulation of the gut-brain axis has not been thoroughly explored. This study aimed to elucidate the mechanistic link between ECT, gut microbiota remodeling, short-chain fatty acid (SCFA) production, and neural plasticity. In this study, mice were subjected to chronic restraint stress (6 h/day for 28 consecutive days) to establish a depression-like model. Utilizing a translational approach that incorporated behavioral assessments, multimodal neuroimaging techniques such as PET-CT and laser speckle contrast imaging, along with multi-omics analyses including metagenomics, metabolomics, and transcriptomics in rodent models, we demonstrated that ECT induced significant gut microbiota remodeling, characterized by an enrichment of SCFA-producing genera like Lactobacillus and Bifidobacterium. This remodeling was associated with restored intestinal barrier integrity and elevated plasma SCFA levels. Mechanistically, these microbial metabolites activated hippocampal Wnt/β-catenin signaling pathways, enhancing synaptic plasticity restoration, while concurrent probiotic supplementation further amplified brain-derived neurotrophic factor (BDNF) expression via SCFA-dependent epigenetic mechanisms. Neuroimaging corroborated the normalization of cerebral glucose metabolism and hemodynamic function post-ECT. In conclusion, our findings unveil a novel gut-brain communication pathway by which ECT exerts its antidepressant effects, positioning SCFAs as vital mediators connecting microbial metabolic alterations to neural plasticity. This research not only redefines the role of nutritional biochemistry in neuromodulation but also suggests the potential of microbial metabolite monitoring to tailor antidepressant therapies for enhanced efficacy.},
}

@article {pmid41428801,
year = {2025},
author = {Sauša, S and Zodāne, A and Kumar, S and Plūme, J and Baranova, J and Kozlova, T and , and Saušs, H and Kloviņš, J and Pīrāgs, V and Mitravinda, KS and Kistkins, S and Brīvība, M},
title = {Rapid and Selective Gut Microbiome Modulation by Polyherbal Formulation in Type 2 Diabetes.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-25-0463},
pmid = {41428801},
issn = {2049-3614},
abstract = {BACKGROUND: Metformin, the first-line treatment for type 2 diabetes, often induces gastrointestinal side effects, affecting treatment adherence. Recent research suggests that the gut microbiome mediates both the efficacy and tolerability of metformin. This study evaluates the effect of a polyherbal formulation, used as an add-on to metformin, on the gut microbiota in patients with type 2 diabetes and metformin intolerance.

METHODS: We report preliminary findings from the first 7-day intervention phase of an ongoing randomized, placebo-controlled, crossover trial (NCT06846138) in 27 adults with type 2 diabetes. Participants received either polyherbal formulations or a placebo alongside metformin for 7 days. Stool samples were collected pre- and post-intervention for shotgun metagenomic sequencing. Microbial diversity, composition, and pathway functions were analyzed using Kraken2, Bracken, and HUMAnN3. Continuous glucose monitoring was used to assess glycemic metrics.

RESULTS: No significant alpha-diversity changes were observed; however, beta-diversity differed significantly between arms (PERMANOVA R2 = 0.04, p = 0.04). In the polyherbal formulation group, 17 species changed post-treatment (FDR < 0.25), with significant increases in six Bifidobacterium spp. (e.g., B. adolescentis, B. ruminantium). In contrast, the placebo group showed no major microbial shifts. Polyherbal formulation also altered 10 microbial pathways (FDR < 0.25). Continuous glucose monitoring revealed no short-term changes in glycemic levels.

CONCLUSION: Short-term polyherbal formulation co-administration significantly modulates gut microbiota, promoting beneficial taxa like Bifidobacterium in metformin-treated type 2 diabetes patients. This supports the potential role of the polyherbal formulation in microbiome-targeted strategies to improve metformin tolerability and effectiveness.},
}

@article {pmid41428733,
year = {2025},
author = {Yang, Z and Yu, M and Li, P and Li, Z and Teng, Y and Zhou, Y and Zhao, M and Liu, C and Zhao, Z and Wang, Z and Li, J and Jing, Y and Li, Y and Zhao, H and Song, W and Bian, C and Zhao, H and Chen, J and Xin, B and Lai, J},
title = {Casδ, an evolutionary transitional CRISPR system enables efficient genome editing across animals and plants.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1358},
pmid = {41428733},
issn = {1362-4962},
support = {//Agriculture Science and Technology/ ; 2023YFD1202900//National Key Research and Development Program of China/ ; PC2023A01004//Pinduoduo-China Agricultural University/ ; //Agriculture Science and Technology/ ; },
mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; Humans ; Animals ; *CRISPR-Associated Proteins/genetics/metabolism/chemistry ; Genome, Plant ; RNA, Guide, CRISPR-Cas Systems/genetics ; Zea mays/genetics ; Evolution, Molecular ; Oryza/genetics ; },
abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated) adaptive immune systems provide sequence-specific mechanisms for targeting foreign DNA or RNA and have been widely used in genome editing and DNA detection. Type V CRISPR-Cas systems are characterized by a single RNA-guided RuvC domain-containing effector, Cas12. Here, through comprehensive mining of large-scale genomic and metagenomic data from microbial sources, we identified a new Class 2 CRISPR-Cas effector superfamily, designated Casδ, comprising three members with protein sizes ranging from 867 to 936 amino acids. Biochemical analyses revealed that Casδ-1 functions as a single RNA-guided endonuclease with specific recognition of 5'-RYR-3' protospacer-adjacent motifs, where R represents A or G, and Y represents T or C. Casδ-1 exhibits robust double-stranded DNA cleavage activity and target-dependent trans-cleavage activity. Casδ-1 mediates efficient genome editing across species, achieving up to 60% indel rates in human cells while generating homozygous knockout lines in two agriculturally important monocot species (Oryza sativa and Zea mays) through stable transformation. Structural and evolutionary analyses reveal Casδ as an evolutionary transitional nuclease bridging Cas12n and canonical type V systems, featuring a C-terminal loop that is essential for activity. Collectively, Casδ is an evolutionarily distinct, compact (<1000 aa), tracrRNA-free CRISPR system enabling versatile cross-kingdom genome editing.},
}

*Gene Editing/methods
*CRISPR-Cas Systems/genetics
Humans
Animals
*CRISPR-Associated Proteins/genetics/metabolism/chemistry
Genome, Plant
RNA, Guide, CRISPR-Cas Systems/genetics
Zea mays/genetics
Evolution, Molecular
Oryza/genetics

@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
doi = {10.1111/1751-7915.70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth & development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}

Animals
Larva/microbiology
*Gastrointestinal Microbiome
*Salmonella/growth & development
Manure/microbiology
*Diptera/microbiology
Chickens
Bacillus
Metagenomics
*Antibiosis
Bacteria/classification/genetics/isolation & purification

@article {pmid41428487,
year = {2025},
author = {Deng, C and Hu, J and Chen, Q and Zhou, S and Ni, J},
title = {Expanded global groundwater microbial diversity reveals bioprospecting potential.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116760},
doi = {10.1016/j.celrep.2025.116760},
pmid = {41428487},
issn = {2211-1247},
abstract = {Although the terrestrial subsurface harbors a substantial fraction of Earth's microbial biomass, the genomic diversity of groundwater microbiomes and their potential for bioprospecting remain poorly characterized. Here, we recovered 44,320 bacterial and archaeal genomes from in-house and publicly available metagenomic datasets, establishing a large-scale groundwater microbiota catalog (GWMC) spanning 167 phyla, including four candidate phyla and over 12,000 previously uncharacterized species. This unprecedented phylogenetic diversity was accompanied by a bimodal genome size distribution (0.3-12.8 Mbp), revealing divergent strategies of genomic allocation. By mining extensive genomic resources, we found that small genomes prioritized molecular defense and redox regulation, whereas large genomes frequently harbored greater biosynthetic potential. Notably, we establish the largest selenoprotein catalog to date and highlight groundwater as an overlooked hotspot of microbial selenium metabolism. Overall, this work advances our understanding of microbial diversity in aquifers and uncovers underexplored genomic resources with potential for biotechnology and biomedicine.},
}

@article {pmid41428281,
year = {2025},
author = {Yu, J and Cheng, L and Zhan, H and Huang, Y and Wang, S and Li, H and Liu, Y and Xu, Y and Guo, Y and Li, Y},
title = {Potential Mechanisms and Hypotheses for Pathogenic Microorganisms Triggering Kawasaki Disease.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {110},
pmid = {41428281},
issn = {1559-0267},
support = {2024YFA1307604//National Key Research and Development Program of China/ ; 8247082356//Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Host-Pathogen Interactions/immunology ; Dysbiosis ; Disease Susceptibility ; *Virus Diseases/immunology/complications ; Superantigens/immunology ; Immunoglobulin A/immunology/metabolism ; Cytokines/metabolism ; },
abstract = {Kawasaki disease (KD) is an acute, self-limiting systemic vasculitis of early childhood and remains the leading cause of acquired heart disease in developed nations. Despite decades of investigation, its etiology and immunopathogenesis are still not fully understood. This review integrates nearly six decades of histopathological, epidemiological, and immunological research to examine infection-driven mechanisms underlying KD. Current evidence indicates that KD may result from a convergence of microbial and host factors: viral infections can trigger mucosal IgA-mediated immune activation; superantigens may induce T-cell receptor (TCR) Vβ-skewed cytokine release; conventional antigens appear to elicit oligoclonal adaptive immune responses consistent with infection-associated vasculitis; and gut microbiota dysbiosis may amplify systemic inflammation through disruption of intestinal barrier integrity and short-chain fatty acid metabolism. Rather than a single-pathogen infection, KD likely reflects infection-triggered immune dysregulation in genetically susceptible children. By contrasting these mechanistic hypotheses, this review highlights the need for longitudinal, multi-omics studies integrating metagenomic, transcriptomic, and serologic analyses to delineate causal microbial signatures, identify diagnostic biomarkers, and guide precision immunomodulatory strategies for this complex pediatric vasculitis.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology
Gastrointestinal Microbiome/immunology
Animals
Host-Pathogen Interactions/immunology
Dysbiosis
Disease Susceptibility
*Virus Diseases/immunology/complications
Superantigens/immunology
Immunoglobulin A/immunology/metabolism
Cytokines/metabolism

@article {pmid41427949,
year = {2025},
author = {Pan, S and Zhao, X and Shi, Q and Shen, Z and Liu, J and Li, W and Xie, Y},
title = {Significant diversity of human anelloviruses revealed by novel viral sequences identified in human metagenomic data.},
journal = {The Journal of general virology},
volume = {106},
number = {12},
pages = {},
doi = {10.1099/jgv.0.002199},
pmid = {41427949},
issn = {1465-2099},
mesh = {Humans ; Phylogeny ; Metagenomics ; *Anelloviridae/genetics/classification/isolation & purification ; *Genetic Variation ; Genome, Viral ; Open Reading Frames ; Viral Proteins/genetics ; *DNA Virus Infections/virology ; },
abstract = {Human torque teno viruses are emerging infectious agents distributed globally and have increasingly been reported to be associated with human diseases. To identify potential anelloviral sequences in available metagenomic data, an in silico screening was performed mainly employing the ORF1, ORF2 and ORF3 nucleotide/protein queries of known human anelloviruses and identified 217 complete ORF1 regions. Pairwise nucleotide-identity analysis with a 69% cut-off - consistent with ICTV species demarcation - revealed 117 novel species across the 3 major human-infecting genera: 15 in Alphatorquevirus, 51 in Betatorquevirus and 51 in Gammatorquevirus. In nearly all cases, these species assignments correspond precisely to monophyletic clusters in maximum-likelihood phylogenies of ORF1 amino acid sequences. Using AlphaFold3-guided modelling together with representative ORF1 alignments, we delineated capsid motifs - the conserved jelly-roll (JR) β-sandwich core (β-strands B-I) and the outward projection domains P1/P2 - and quantified motif lengths across genera, revealing tightly constrained JR lengths with genus-specific but overlapping variation in P1/P2. A few exceptions - where pairwise-based groupings split or merge slightly differently - highlight ongoing challenges in delineating rapidly evolving viruses. Notably, the two deeply branching isolates retain the canonical JR core while exhibiting a TTMDV-like short P2, indicating preservation of key capsid architecture in the newly proposed genus. This work nearly doubles the known species richness of human anelloviruses and introduces a novel genus, underscoring the vast, hidden diversity of the gut virome and its potential impact on human health. By coupling taxonomy with structure-informed ORF1 motif analysis, our study provides biological context for these lineages and a framework for future functional and immunological investigations.},
}

Humans
Phylogeny
Metagenomics
*Anelloviridae/genetics/classification/isolation & purification
*Genetic Variation
Genome, Viral
Open Reading Frames
Viral Proteins/genetics
*DNA Virus Infections/virology

@article {pmid41427872,
year = {2025},
author = {Gu, T and Chen, Z and Hutchins, DA and Sun, J},
title = {Urea-driven nitrification contributes to N2O production in the oligotrophic euphotic ocean.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf281},
pmid = {41427872},
issn = {1751-7370},
abstract = {Urea is an important alternative nitrogen source to ammonium for nitrification in oligotrophic oceans, yet its role in substrate-driven nitrous oxide (N2O) production remains poorly constrained. Here, we combined N2O isotopomer profiling, 15N-tracer incubations, and metagenomics to quantify and mechanistically resolve substrate-specific archaeal nitrification in the western tropical Pacific euphotic zone. Isotopomer-based mixing and fractionation model indicated that archaeal nitrification accounted for 69.6 ± 14.1% of microbial sources of N2O in oxygenated epipelagic waters. Depth-integrated urea-driven nitrification contributed 14-41% of total nitrification and 21-39% of nitrification-derived N2O, with contributions regulated by substrate proportions. Acidification experiments showed that pH decline inhibited ammonium-driven nitrification (median 21.9%) and enhanced urea oxidation (median 61.9%), whereas N2O production increased for both substrates (median 35.9% and 38.0%). In addition, experimental acidification induced opposite shifts in hybrid versus double-labelled N2O, suggesting pH-driven shifts N-intermediate chemistry and intracellular partitioning. Metagenomic results support the globally widespread urea-type AOA. Together, these results indicate that urea-driven nitrification constitutes a non-negligible, substrate-dependent source of N2O in oligotrophic euphotic zones. We recommend that Earth-system N-cycle models represent urea and ammonium oxidation as distinct pathways with pH-sensitive yields to improve projections of marine nitrification and N2O fluxes under acidification.},
}

@article {pmid41427714,
year = {2025},
author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0183825},
doi = {10.1128/spectrum.01838-25},
pmid = {41427714},
issn = {2165-0497},
abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.

IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.},
}

@article {pmid41427415,
year = {2025},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.09.693354},
pmid = {41427415},
issn = {2692-8205},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug resistant Gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii . This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document potential sources of the corresponding resistance genes. This study searched for potential emerging colistin-resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments which all contained eptA genes. We confirmed their ability to confer significant colistin resistance in E. coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter strains, marking them as potential mcr genes or their precursors. This study highlights the goose fecal microbiome as a potential source for colistin resistance in the environment.},
}

@article {pmid41427287,
year = {2025},
author = {Zhang, A and Boucher, C and Noyes, N and Yu, YW},
title = {RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.05.692407},
pmid = {41427287},
issn = {2692-8205},
abstract = {UNLABELLED: Hybridization (bait) capture combined with long-read sequencing enables targeted profiling within complex metagenomes but introduces systematic biases from bait multiplicity, sequence composition, and species abundance that existing simulators ignore. We present RAmpSim , a fast simulator that models bait-target hybridization and fragment capture using a thermodynamic nearest-neighbor energy model and Boltzmann-weighted sampling of binding sites. Fragments are generated through multinomial sampling parameterized by bait concentration, binding energy, and genomic abundance before being passed to existing long-read simulators for modeling platform-specific errors. Implemented in Rust, RAmpSim reproduces empirical within-genome coverage and cross-species enrichment patterns observed in capture-based metagenomic datasets. Compared to uniform-coverage baselines, RAmpSim 's simulated coverage distributions are up to an order of magnitude closer to real data with respect to earth mover's distance. Classification analysis reveals high recall in classifying high coverage regions between simulated and experimental distributions while outperforming a uniform baseline. Supporting accurate benchmarking and bait-set evaluation, RAmpSim provides an interpretable, efficient framework for simulating capture-based metagenomic sequencing.

CODE AVAILABILITY: https://github.com/az002/RAmpSim.git.},
}

@article {pmid41427275,
year = {2025},
author = {Chen, K and Talesara, A and Thakkar, S and Shao, M},
title = {Minimum flow decomposition guided by saturating subflows.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.11.693570},
pmid = {41427275},
issn = {2692-8205},
abstract = {The minimum flow decomposition problem abstracts a set of key tasks in bioinformatics, including metagenome and transcriptome assembly. These tasks, collectively known as multi-assembly, aim to reconstruct multiple genomic sequences from reads obtained from mixed samples. The reads are first organized into a directed graph (e.g., overlap graph, splice graph), where each edge has an integer weight representing the number of supporting reads. By viewing the graph as a flow network, the underlying sequences and their abundances can be extracted through decomposition into a minimum number of weighted paths. Although this problem is NP-hard, prior work has proposed an efficient heuristic that transforms the graph by identifying nontrivial equations in the flow values. However, for graphs with complex structures, many equations cannot be fully resolved by existing mechanisms, leading to suboptimal decompositions. In this study, we revisit the theoretical framework of the flow decomposition problem and extend the equation-resolving mechanisms to jointly model all equations in the graph, enabling safe merge operations that iteratively simplify the graph. Experimental results demonstrate that our new algorithm substantially improves decomposition quality over existing heuristics, achieving near-optimal solutions for complex graphs, while running several orders of magnitude faster than the ILP formulation. Source code of our algorithm is available at https://github.com/Shao-Group/catfish-LP.git .},
}

@article {pmid41426949,
year = {2025},
author = {Allshouse, T and Amendano, M and Caruso, B and Del Campo, R and Murphy, G and Shaffer, L and Steinberg, E and Sullivan, A and Stowe, E},
title = {The Microbiota of Homemade Tepache Includes Antibiotic-Resistant Microorganisms.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {41426949},
issn = {2578-9430},
abstract = {Tepache is a traditional, homemade Mexican drink made by fermenting pineapple rinds. The natural probiotic bacteria in tepache are said to promote a healthy gut microbiome. This study assessed the microbial community in homemade tepache for diversity, survival in simulated gastric fluid, and antibiotic resistance. Simulated gastric passaging reduced total community numbers but the community density was not strongly impacted by exposure to tetracycline. Metagenomic analysis reveals a community dominated by Bacillus, Meyerozyma and Talaromyces. These results indicate that consuming home fermented beverages may provide helpful probiotic bacteria but could also expose the gut microbiome to antibiotic resistance genes.},
}

@article {pmid41426737,
year = {2025},
author = {Valente, P and Sbrenna, L and Valente, F and Sbrenna, A and Mascolo, A},
title = {Drug-Induced Gingival Overgrowth Associated With Cyclosporine Therapy: A Case Report of a 23-Year Periodontal Follow-Up in a Heart Transplant Recipient.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e97019},
pmid = {41426737},
issn = {2168-8184},
abstract = {Drug-induced gingival overgrowth (DIGO) is a common adverse effect of cyclosporine therapy, which is widely used as an immunosuppressive agent in solid organ transplant recipients. This case report describes the 23-year follow-up of a male patient with a history of orthotopic heart transplantation, performed two years prior to his first dental visit in 2002, who developed DIGO under long-term cyclosporine therapy. At the initial periodontal evaluation, a diagnosis of localized Stage I, Grade A periodontitis associated with gingivitis was made, and nonsurgical mechanical debridement, scaling and root planing, and tailored oral hygiene instruction were provided, yielding favorable early outcomes and long-term periodontal stability. After many years of stability, the patient returned following a three-year lapse in maintenance, presenting with marked gingival enlargement, bleeding on probing, discoloration, and migration of the maxillary central incisors, consistent with progression to Stage II, Grade B periodontitis. Nonsurgical retreatment was performed, and DNA-based metagenomic analysis of subgingival plaque and tongue biofilm revealed a dysbiotic microbial profile, including the persistence of key periodontopathogenic taxa associated with tissue destruction and alveolar bone loss. This case underscores the importance of sustained periodontal maintenance in transplant recipients receiving cyclosporine therapy and illustrates that even after decades of apparent stability, DIGO and periodontal deterioration may reemerge if maintenance care is interrupted. The integration of DNA-based metagenomic analysis provided valuable diagnostic and motivational support, reinforcing a personalized, multidisciplinary approach to long-term periodontal management in immunosuppressed patients.},
}

@article {pmid41426650,
year = {2025},
author = {Wang, C and Wei, H and Duan, R and Jin, S and Wen, J and Li, H and Cheng, A and Gao, C and Xue, H and Hou, Y},
title = {Habitat Diversity Sustains Ecosystem Functioning in Plateau Arid-Region Wetlands.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72747},
pmid = {41426650},
issn = {2045-7758},
abstract = {Plateau arid-region wetlands constitute critical ecosystems for regional ecological security, yet exhibit heightened vulnerability under multiple stressors. Current understanding of the mechanisms sustaining the functions of these systems, particularly the pivotal role of habitat diversity, remains limited. Targeting the Jinzihai Wetland (Qaidam Basin, Qinghai-Tibet Plateau), we integrated metagenomic and geochemical profiling to characterize three representative habitats: sandy meadows, peat bogs, and lake sediments. Our analyses revealed that pronounced cross-habitat physicochemical gradients drive community structure differentiation predominantly through species replacement, establishing habitat diversity as a fundamental driver of wetland biodiversity. Concurrently, community differentiation drives spatial divergence in functional gene composition, manifesting distinct functional dominance: sandy meadows govern assimilation and saline-alkaline stress response; peat bogs orchestrate nutrient enrichment and transformation; lake sediments mediate element release and burial. These functionally complementary habitats collectively catalyze biogeochemical cycling. We demonstrate that within plateau arid-region wetlands, habitat diversity stabilizes ecosystem functioning by sustaining both biodiversity and functional diversity of biogeochemical processes. Consequently, prioritizing habitat diversity conservation is imperative for safeguarding the long-term stability of these vulnerable ecosystems within management frameworks.},
}

@article {pmid41426590,
year = {2025},
author = {Zhang, J and Xu, X and Chen, L and Yang, X and Matsubara, JK and Tian, Y and Liu, J and Jin, X and Chang, H and Xu, M and Zhu, C and Wang, X and Ren, L and Xie, J and Liu, J and Liu, G and Lu, M and Wang, X and Du, L and Ma, Z and Liu, X and Zhao, H and Chen, W and Huo, X and Zheng, G and Xie, C and Xu, C and Zhang, X and Qi, W and Feng, Z},
title = {Circulating microbiome profiling in transjugular intrahepatic portosystemic shunt patients: 16S rRNA vs. shotgun sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1662837},
pmid = {41426590},
issn = {2296-858X},
abstract = {BACKGROUND AND AIM: Current efforts to characterize the circulating microbiome are constrained by the lack of standardized protocols for isolating and sequencing microbial communities in blood. To address this challenge, our study compared 16S rRNA (V3-V4 region) and shotgun metagenomic sequencing for circulating microbiome detection.

MATERIALS AND METHODS: After obtaining ethics committee approval and informed consent, samples were aseptically collected from 10 patients undergoing transjugular intrahepatic portosystemic shunt (TIPS) procedures. Shotgun metagenomic reads were taxonomically classified using the Kraken2-Bracken pipeline. 16S rRNA (V3-V4) data were analyzed through an ASV-based approach, with USEARCH for denoising and VSEARCH for taxonomic annotation. The results from both sequencing methods were then systematically compared.

RESULTS: Shotgun metagenomic sequencing generated 7,024,580,376 raw reads (mean depth: 234,152,679.2 reads/sample), while 16S rRNA sequencing produced 6,612,678 raw reads (mean depth: 220,422.6 reads/sample). 16S rRNA amplicon sequencing captured a broader range of microbial signals. Although the taxonomic profiles from both sequencing methods showed limited overlap, the core microbiota common to both were still identified. These conserved core microbial communities exhibited stable α- and β-diversity indices across separate vascular compartments.

CONCLUSION: In our study, 16S rRNA amplicon sequencing captured more diverse microbial signals than shotgun metagenomics. A stable microbial community structure was observed across vascular compartments, suggesting a homogeneous microbial composition throughout the circulatory system.},
}

@article {pmid41426580,
year = {2025},
author = {Li, S and Tian, Q and Yang, X and Zhang, M and Zheng, M and Li, D and Duan, Z and Li, Y and Qiu, Z and Liu, Z},
title = {Chronic meningoencephalomyelitis caused by Nocardia nova infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1680771},
pmid = {41426580},
issn = {2296-858X},
abstract = {A 25-year-old female zookeeper presented with 3-month history of sore throat and headache, 2-month intermittent fever, and 1-month dizziness. Neurological examination revealed bilateral nystagmus, left-sided sensory loss, ataxia, and subtle meningeal signs. Brain and cervical spinal cord MRI showed multiple enhancing lesions with central vein signs. Cerebrospinal fluid (CSF) analysis demonstrated elevated pressure (240 mmH2O) and leukocytosis (140 × 10[6]/L). Serum MOG-IgG was positive (1:32), while CSF metagenomic next-generation sequencing (mNGS) confirmed Nocardia nova infection. Initial treatment with trimethoprim-sulfamethoxazole (TMP-SMX), amikacin, and imipenem-cilastatin was followed by regimen adjustment to TMP-SMX plus minocycline at 6 weeks. One-month post-therapy, repeat CSF showed normalized pressure, reduced leukocytes, negative mNGS, and MRI evidence of lesion regression. Complete symptom resolution occurred 2 months after treatment initiation. This case exemplifies a rare presentation of N. nova-induced meningoencephalomyelitis with craniospinal involvement in an immunocompetent individual.},
}

@article {pmid41426285,
year = {2025},
author = {Ma, X and Zhang, Q and Ji, X and Xia, Y and Cao, J and Xu, X},
title = {Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluids Improves Pathogen Detection and Antimicrobial Stewardship in Lower Respiratory Tract Infections: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6611-6632},
pmid = {41426285},
issn = {1178-6973},
abstract = {PURPOSE: With the advancement of metagenomic next-generation sequencing (mNGS), its role in diagnosing lower respiratory tract infections (LRTIs) has expanded rapidly. LRTIs remain a major global health burden, particularly in critically ill patients where diagnosis is challenging. Routine microbiological testing (RMT), including culture, microscopy, antigen detection, and PCR-are limited by low sensitivity, long turnaround times, and restricted pathogen coverage. This study assesses the diagnostic performance of mNGS in LRTIs, with emphasis on pathogen detection and resistance gene prediction, and compares it with traditional methods to clarify its clinical benefits and limitations.

METHODS: This retrospective study included 367 hospitalized patients with suspected LRTIs. All patients underwent mNGS testing, which was compared with traditional diagnostic methods. We also used mNGS to explore the pathogen spectrum characteristics in critically ill patients with pneumonia and evaluated its applicability in predicting antimicrobial resistance genes and adjusting antibiotic treatment.

RESULTS: For patients diagnosed with LRTIs, mNGS demonstrated superior microbial detection efficacy, particularly for bacteria and fungi, relative to culture (bacteria: 56.58% vs 17.37%, P < 0.0001; fungi: 49.65% vs 16.78%, P < 0.0001) and PCR (65.14% vs 45.14%, P < 0.05). In contrast to the non-severe pneumonia group, the detection rate of Enterococcus faecium was highest in the severe pneumonia group (P < 0.001), and the severe pneumonia group had more mixed infections (P < 0.001). In addition, mNGS showed high accuracy in predicting antibiotic resistance genes, with 90.57% agreement with antibiotic susceptibility testing (AST) results. Based on the mNGS results, 97.82% of patients underwent active adjustment to their antibiotic treatment regimen.

CONCLUSION: mNGS is an effective tool for diagnosing LRTIs, with significantly higher pathogen detection rates than traditional methods. mNGS also demonstrates high accuracy in predicting antimicrobial resistance, providing crucial support for clinical treatment decisions.},
}

@article {pmid41426281,
year = {2025},
author = {Yang, L and Zhang, Y and Wu, M and Zeng, F and Chen, H and Xie, D and Shi, F},
title = {Recurrent Disseminated Talaromycosis Mimicking Liver Disease in a STAT3-Mutated HIES Patient: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6605-6610},
pmid = {41426281},
issn = {1178-6973},
abstract = {BACKGROUND: Talaromycosis is increasingly recognized in immunocompromised individuals beyond those with HIV, including patients with primary immunodeficiencies such as Hyper-IgE syndrome (HIES). However, diagnosing disseminated infection remains challenging due to nonspecific clinical manifestations and limitations of conventional diagnostic methods.

CASE PRESENTATION: We report a rare case of recurrent disseminated Talaromyces marneffei (T. marneffei) infection in a 25-year-old male with STAT3-mutated HIES. Initially presenting with abnormal liver function tests, the patient had a history of T. marneffei pulmonary infection successfully treated with itraconazole. During the current admission, he developed intermittent fever, jaundice, and splenomegaly. Initial evaluations led to a misdiagnosis of chronic drug-induced liver injury (DILI). Subsequent fever recurrence and worsening liver function prompted further investigation. Metagenomic next-generation sequencing (mNGS) and histopathology of liver revealed T. marneffei, confirming disseminated infection involving the liver. Histopathological examination of the liver showed granulomatous inflammation with IgG4-positive plasma cell infiltration, further complicating the differential diagnosis. The patient responded well to intravenous voriconazole, with significant improvement in liver function and radiological findings.

CONCLUSION: Disseminated talaromycosis should be considered in immunocompromised patients presenting with unexplained fever, hepatosplenomegaly, or organ dysfunction, even in the absence of classic symptoms. Integration of mNGS into diagnostic workflows enhances pathogen detection, and long-term antifungal prophylaxis may be necessary in patients with persistent immune deficiencies.},
}

@article {pmid41424898,
year = {2025},
author = {Chattopadhyay, P and Biswas, I and Banerjee, G},
title = {Analysing the Metagenomic Dynamics of Soil Microbiota Affected by Tea Pruning and Skiffing Methods in Tea Plantations of Dibrugarh, Assam, India.},
journal = {Indian journal of microbiology},
volume = {65},
number = {4},
pages = {2015-2020},
pmid = {41424898},
issn = {0046-8991},
abstract = {Beginning with the centralization of young tea (Yt) to encourage low branch growth, subsequent light pruning (LP) and deep skiffing (DS) techniques are employed to promote branch spread, ensuring an ideal leaf area index and manageable plucking height. This study investigates the effects of LP and DS compared to Yt on soil biota, a previously unexplored topic. Soil samples from Yt, LP, and DS sites within the Rajgarh Tea Estate in Assam, India, were analyzed for standard parameters and metagenomic DNA using Illumina sequencing. While all samples exhibited a clay loam texture with minimal parameter variation, significant variations in soil phyla abundance were observed. Acidobacteria dominated across all samples, but linear discriminant analysis revealed distinct phyla compositions. At the genus level, Geobacter, Verticiella, and Glaciihabitans were most abundant in S11, S7, and S9 samples, respectively. However, the relative abundance of phyla in the soil samples from Yt, LP, and DS sites varies significantly. But the difference in bacterial community at genus level resolution was not significant at p value 0.05 level. These findings indicate that pruning and skiffing primarily impact on the relative abundance of soil phyla, not microbial diversity. Understanding the soil microbiota in relation to tea cultivation practices through metagenomics can pave the way for developing new microbial consortia for an integrated crop management system in tea cultivation.},
}

@article {pmid41423959,
year = {2025},
author = {Bao, Y and Dolfing, J and Chen, R and Qiu, C and Zhang, J and Zhou, X and Liu, L and Wang, Y and Lin, X and Feng, Y},
title = {Phages Shape the Transformation of Organic Matter During Composting.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70291},
doi = {10.1111/1751-7915.70291},
pmid = {41423959},
issn = {1751-7915},
support = {42207365//National Natural Science Foundation of China/ ; 42177297//National Natural Science Foundation of China/ ; 42577330//National Natural Science Foundation of China/ ; 42577352//National Natural Science Foundation of China/ ; BK20221161//Natural Science Foundation of Jiangsu Province/ ; XDA28010302//Chinese Academy of Sciences (CAS) Strategic Priority Research Program/ ; },
mesh = {*Composting/methods ; *Bacteriophages/metabolism/growth & development/genetics ; Manure/microbiology ; *Organic Chemicals/metabolism ; Soil Microbiology ; Biotransformation ; Animals ; Oryza ; Chickens ; Metagenomics ; Bacteria/metabolism/virology ; },
abstract = {Microorganisms drive the biotransformation of dissolved organic matter (DOM) during organic wastes composting, yet the role of phages with different lifestyles (i.e., temperate and virulent) in this process remains poorly understood. Here, bulk metagenomic sequencing combined with electrospray ionisation (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to investigate the dynamics of temperate and virulent phage communities, microbial functional traits represented by the growth yield (Y)-resource acquisition (A)-stress tolerance (S) life-history strategies (Y-A-S) framework, and molecular changes in DOM composition, as well as their potential linkages during the composting of a rice chaff and chicken manure mixture. Our results revealed that the ratio of temperate/virulent phage, microbial Y/A strategy, and microbial-/plant-derived DOM components exhibited highly consistent dynamic patterns, all peaking during mid-composting stage when temperatures are elevated and remaining low at the initial and final stages. Random forest analysis further identified the ratio of temperate/virulent phages and the microbial Y/A strategy as key predictors of the variance in microbial Y/A trade-offs and microbial-/plant-derived DOM components, accounting for 10% and 13% of the explained variance, respectively. Together, our results demonstrate that an increased prevalence of temperate phages promoted the microbial Y-strategy and the accumulation of microbial-derived DOM components, while a greater dominance of virulent phages favoured the A-strategy and plant-derived DOM enrichment. These findings offer new insights into the ecological role of phages in mediating material transformation during organic waste composting.},
}

*Composting/methods
*Bacteriophages/metabolism/growth & development/genetics
Manure/microbiology
*Organic Chemicals/metabolism
Soil Microbiology
Biotransformation
Animals
Oryza
Chickens
Metagenomics
Bacteria/metabolism/virology

@article {pmid41423811,
year = {2025},
author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and Lentine, J and Sockolow, RE and Sonnenberg, GF},
title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf295},
pmid = {41423811},
issn = {1536-4844},
support = {//Weill Cornell Medicine Department of Pediatrics/ ; },
abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.

METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.

RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.

CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.},
}

@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67677-6},
pmid = {41423629},
issn = {2041-1723},
support = {109105z/15/a//Wellcome Trust (Wellcome)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}

@article {pmid41423072,
year = {2025},
author = {Song, MN and Xu, HT and Liang, SM and Fang, SY and Zhang, Y and Zhang, ZZ and Jin, RC},
title = {Ultrasound-assisted breathing revives floated anammox granules by reconnecting intra‑granular metabolic interactions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133838},
doi = {10.1016/j.biortech.2025.133838},
pmid = {41423072},
issn = {1873-2976},
abstract = {The flotation of granular sludge is a critical bottleneck hindering the application of high-load anammox process. Here, we propose and validate an "assisted breathing" strategy, using non-destructive physical treatments to rapidly restore the functionality of floated granules. A systematic comparison of pressure transient (PT), mechanical shaking (MS), and ultrasonic radiation (UR) revealed that intermittent UR treatment was uniquely effective and it propelled the nitrogen removal rate (NRR) to a remarkable 7.19 kg-N m[-3] d[-1] within 60 days, far surpassing the PT, MS, and control reactors. Mechanistic investigations revealed that the efficacy of "assisted breathing" stems from a synergistic physio-ecological cascade. Physically, ultrasonication enhanced granule permeability and mass transfer efficiency by facilitating entrapped N2 gas release. Biologically, intermittent UR treatment stimulated the production of protein-rich extracellular polymeric substances (EPS), repurposing EPS from a pore-clogging obstacle into beneficial public goods. Most critically, metagenomic analysis demonstrated that UR treatment selectively enriched key heterotrophic partners, such as Ignavibacteriaceae sp. SMN043, which formed a tight syntrophic relationship with AnAOB by providing essential metabolites like folate in exchange for amino acids. Intriguingly, this led to a 14.1 % increase in SAA. These results demonstrate that targeted physical intervention can unlock superior performance by reviving and re‑linking the metabolic networks inside anammox granules. This process effectively transforms inert, floated biomass into highly active aggregates, opening a new avenue for active ecological engineering in bioreactors.},
}

@article {pmid41422804,
year = {2025},
author = {Tabuteau, S and Hervé, V and Irlinger, F and Monnet, C},
title = {Metagenomic Profiling and Genome-Centric Analysis Reveal Iron Acquisition Systems in Cheese-Associated Bacteria and Fungi.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70218},
doi = {10.1111/1462-2920.70218},
pmid = {41422804},
issn = {1462-2920},
support = {//ABIES Doctoral School/ ; //MICA Department of INRAE/ ; },
mesh = {*Cheese/microbiology ; *Iron/metabolism ; Siderophores/biosynthesis/metabolism/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Fungi/genetics/metabolism/classification/isolation & purification ; *Metagenome ; Genome, Bacterial ; },
abstract = {Cheese microbial communities are composed of diverse interacting microorganisms, including both inoculated and non-inoculated strains. One limiting factor for microbial growth on cheese surfaces is iron availability. To better understand the role of iron acquisition in cheese microbial ecology, we investigated the diversity and distribution of iron uptake systems across a wide range of cheeses. We analysed 136 metagenomes and 1400 genomes and Metagenome-Assembled Genomes (MAGs) from 44 French Protected Designation of Origin (PDO) cheeses. Using an updated set of Hidden Markov Models targeting iron acquisition genes, we identified a wide diversity of iron uptake systems. Siderophore biosynthesis and import systems were more prevalent in surface-associated species than in those from the cheese core. About 20 different siderophore biosynthesis pathways were detected, with desferrioxamine and enterobactin-type being the most prevalent. Genomic analyses revealed the main bacterial and fungal producers, including Glutamicibacter, Corynebacterium, Staphylococcus, and Penicillium. While siderophore biosynthesis pathways were found in a minority of MAGs, iron/siderophore import systems were widespread, suggesting the potential for cross-feeding interactions involving siderophores. These findings enhance our understanding of microbial interactions in cheese and open perspectives for improving ripening cultures by considering iron acquisition traits.},
}

*Cheese/microbiology
*Iron/metabolism
Siderophores/biosynthesis/metabolism/genetics
Metagenomics
*Bacteria/genetics/metabolism/classification/isolation & purification
*Fungi/genetics/metabolism/classification/isolation & purification
*Metagenome
Genome, Bacterial

@article {pmid41422728,
year = {2025},
author = {Xun, J and Han, Y and Liu, B and Jiang, X and Zhang, J and Hu, Z and Yang, H and Gao, Q and Wu, Z and Wang, X and Yu, X and Zhang, Q},
title = {Baihua Dangen Tang inhibits the peritoneal metastasis of colon cancer by modulating the bacterial metabolite gentisic acid to suppress MDSCs.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157720},
doi = {10.1016/j.phymed.2025.157720},
pmid = {41422728},
issn = {1618-095X},
abstract = {BACKGROUND: The treatment principle of Lingnan traditional compound Baihua Dangen Tang includes 'clearing heat and removing toxins, resolving stasis and dispersing stagnation, and dispelling wind and removing dampness', which is compatible with the pathogenesis of peritoneal cancer, which is characterized by 'dampness, heat, stasis and toxin'. Therefore, Baihua Dangen Tang may be an effective treatment for peritoneal metastasis of colon cancer.

OBJECTIVE: To systematically elucidate the effects and mechanisms of Baihua Dangen Tang in inhibiting the peritoneal metastasis of colon cancer.

METHODS: In this study, a peritoneal metastasis model of colon cancer was constructed by intraperitoneal injection of CT26/MC38 cells (1 × 10[6]) for 14 days. Abdominal circumference, ascites volume, tumor weight and Ki67 expression were analyzed. Mass spectrometry and flow cytometry were used to analyze changes in immune cells, such as MDSCs and T-cell subsets, in ascites and peripheral blood. Changes in the fecal flora and metabolites were analyzed by macrogenomic and untargeted metabolomics to screen for key differential flora metabolites. In vitro experiments were performed to determine the effects of Baihua Dangen Tang and differential flora metabolites on tumor cell migration and invasion and MDSC function.

RESULTS: In this study, we observed that Baihua Dangen Tang significantly inhibited peritoneal metastasis of colon cancer; reduced abdominal circumference, bloody ascites content, and metastatic tumor weight; and decreased metastatic tumor Ki67 expression. Analysis of ascites and peripheral blood by mass spectrometry and flow cytometry revealed that Baihua Dangen Tang increased the numbers of CD4[+] T cells and CD8[+] T cells and decreased the number of MDSCs in ascites and peripheral blood. Combined macrogenomic and metabolomic analyses revealed that the metabolite gentisic acid, which was positively correlated with Lactobacillus spp. and negatively correlated with Desulfovibrio spp., significantly changed. In vivo experiments confirmed that gentisic acid inhibited the progression of CT26 peritoneal metastases. In vitro experiments confirmed that Baihua Dangen Tang and its regulatory bacterial colony metabolite gentisic acid inhibited the migration and invasion ability of colon cancer cells and their recruitment of MDSCs, in addition to directly inhibiting the function of MDSCs, thus enhancing T-cell activity.

CONCLUSION: Baihua Dangen Tang and its microbiota-derived metabolite gentisic acid inhibit cancer cell metastasis and MDSCs function, demonstrating multitarget suppression of colorectal cancer peritoneal metastasis.},
}

@article {pmid41422454,
year = {2025},
author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C},
title = {Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next-generation sequencing.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41422454},
issn = {1439-0973},
abstract = {A Siberian woman in her forties presented to a public hospital in northeastern Germany with chronic back pain and a paravertebral mass, initially misdiagnosed as spinal tuberculosis. Repeated biopsies and metagenomic next-generation sequencing (mNGS) ultimately confirmed vertebral alveolar echinococcosis. Haplotype analysis revealed a novel Asian-cluster variant, supporting the presumed origin of infection.},
}

@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00888-3},
pmid = {41422269},
issn = {2055-5008},
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}

@article {pmid41422081,
year = {2025},
author = {Arnaud-Haond, S and Trouche, B and Liautard-Haag, C and Alain, K and Aubé, J and Bonhomme, F and Brandt, MI and Caillarec-Joly, A and Cambon, MA and Cornette, F and Cueff-Gauchard, V and Durand, P and de Vargas, C and Felix, C and Fuchs, S and , and Günther, B and Henry, N and Hourdez, S and Jollivet, D and Le Port, AS and Lesongeur, F and Maignien, L and Comtet-Marre, S and Matabos, M and Omnes, E and Peyret, P and Pradillon, F and Sarrazin, J and Schauberger, C and Tran Lu Y, A and Ulloa, O and Vaz, S and Zeppili, D and Viard, F and Gavory, F and Gaz, S and Guy, J and Jacoby, E and Oliveira, PH and Samson, G and Aury, JM and Wincker, P and Pesant, S and Poulain, J and Belser, C},
title = {Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-025-06009-1},
pmid = {41422081},
issn = {2052-4463},
support = {ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0003//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-POCE-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; 678760//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 669947//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; ANR-10-INBS-09//Commissariat à l'Énergie Atomique et aux Énergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; },
abstract = {The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within "Pourquoi Pas les Abysses?" and eDNAbyss projects. Together with information ensuring reproducibility, this dataset -combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization- contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.},
}

@article {pmid41421910,
year = {2025},
author = {Zeng, H and Xu, H and Liu, G and Wei, Y and Zhang, J and Shi, H},
title = {Corrigendum to "Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava" [J Hazard Mater 411 (2021) 125143].},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {140878},
doi = {10.1016/j.jhazmat.2025.140878},
pmid = {41421910},
issn = {1873-3336},
}

@article {pmid41421776,
year = {2025},
author = {Gao, L and Chen, Y and Li, S and Yang, Z and Guo, W and Lu, Y and Zhu, G and Gaballah, ES},
title = {Low atmospheric pressure of plateau environments shapes microbial communities, nitrogen conversion, and carbon metabolism in biological nitrogen removal systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123595},
doi = {10.1016/j.envres.2025.123595},
pmid = {41421776},
issn = {1096-0953},
abstract = {Wastewater treatment plants in high-altitude regions often exhibit unstable nitrogen removal under low atmospheric pressure, but the coupled impacts on oxygen transfer, microbial metabolism, and community adaptation remain poorly resolved. In this study, long-term bioreactor operation under different atmospheric pressures was performed to elucidate how low pressure reshapes biological nitrogen removal systems through changes in oxygen transfer, microbial metabolism, and community structure. Low pressure reduced oxygen solubility and gas-liquid/liquid-solid transfer, which suppressed nitrification and caused nitrite accumulation, while simultaneous nitrification-denitrification partly sustained total nitrogen removal. Multi-scale analyses integrating batch tests, enzyme activities, and metagenomics showed a consistent shift from oxidative to more electron-efficient pathways, with strengthened denitrification and expanded carbon metabolism that enhanced the use of carboxylic acids and amino acids and secured carbon and electron supply. The microbial community reorganized toward denitrifying polyphosphate-accumulating organisms (DPAOs), denitrifying glycogen-accumulating organisms (DGAOs), and conventional denitrifiers, with stronger functional associations despite a simpler network structure. These findings explain performance deterioration under plateau atmospheric conditions and indicate feasible control points to sustain nitrogen removal in high-altitude wastewater treatment systems.},
}

@article {pmid41421745,
year = {2025},
author = {Mandelbrot, L and Kennedy, S and Rousseau, J and Goffinet, F and Landraud, L and Plainvert, C and Marcou, V and Desfrère, L and Barral, T and Allal, L and Baud, A and Grall, N and Poyart, C and Ancel, PY and Tazi, A},
title = {Predicting neonatal infection in PPROM with vaginal microbiology and metagenomics: a prospective cohort study.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.12.042},
pmid = {41421745},
issn = {1097-6868},
abstract = {OBJECTIVE: Early-onset neonatal sepsis (EONS) due to ascending infection is a potentially preventable complication of preterm premature rupture of membranes (PPROM). Our objective was to determine whether the analysis of bacteria from vaginal swab samples is predictive of the risk of EONS in PPROM.

STUDY DESIGN: In a prospective 3-center observational cohort, patients with PPROM were enrolled between 22 and 36 weeks' gestation (WG) + 6 days. Vaginal swab samples at delivery were analyzed using two different approaches, classical bacterial cultures and shotgun metagenomic sequencing analysis. A metagenomics score was constructed combining the characterization of the vaginal microbiome and the presence of pathogens and the optimal cut-off to predict EONS was tested on a receiver operating curve.

RESULTS: 563 PPROM cases were enrolled, with 646 liveborn neonates. PPROM occurred < 32 WG in 41.9% and deliveries were < 34 WG in 41.0%. The incidence of EONS was 29/646 (4.5%). When considering all central and peripheral microbiological samples available for 26 neonates, the main pathogens isolated were Escherichia coli in 14 cases (53.8 %), other gram-negatives in 5 (19.2%), strict anaerobes in 3 (11.5%); there was a single case (3.8%) each with Group B Streptococcus (GBS), Streptococcus anginosus, Staphylococcus aureus and Ureaplasma urealyticum. We studied the prediction of EONS among 272 mothers and their 310 neonates (20 EONS, 6.4%) with both culture and metagenomic data available. A culture positive for a major or intermediate pathogen in the vaginal sample at delivery had a sensitivity of 80.0 % (95% CI=56.3-94.3) and a specificity of 37.9% (95% CI=32.3-43.8), adjusted odds ratio (aOR) of 1.6 (95 % CI [0.5-5.0]) to predict EONS. The presence of E. coli was associated with an EONS risk of 10.6% vs 4.9%, in the absence of E. coli (p=0.07). The metagenomics score was highly associated with EONS, with an area under the receiver operating curve of 0.75 (95% CI, 0.61-0.90). At the optimal cutoff value, sensitivity was 70% (95% CI, 64-95%), specificity was 85% (95% CI, 81-89%). A metagenomics score greater than 40 was associated with a significantly increased risk of EONS with an aOR of 8.9 (95 % CI [3.5; 22.3]) in multivariate analysis adjusted for latency period and gestational age, p<0.001.

CONCLUSION: In PPROM, conventional microbial culture of maternal vaginal samples was associated with EONS, but its predictive values remain insufficient to guide perinatal care. Metagenomic microbial signatures improved predictive values. This opens the perspective for a rapid point-of-care test.},
}

@article {pmid41421679,
year = {2025},
author = {Huang, P and Zhou, Y},
title = {Metabolic responses of purple phototrophic bacteria to elevated hydrogen partial pressure: Metatranscriptomic insights into biohydrogen production and consumption.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133831},
doi = {10.1016/j.biortech.2025.133831},
pmid = {41421679},
issn = {1873-2976},
abstract = {During biohydrogen production, self-generated gas accumulation can lead to elevated hydrogen partial pressure (HPP) in the headspace. However, the effects of elevated HPP on hydrogen yield in photo fermentation systems and the metabolic responses of phototrophic bacteria (PPB) under such conditions remain poorly understood. This study investigated the effects of elevated HPP on PPB-based biohydrogen production and examined the underlying metabolic responses using metagenomic and metatranscriptomic analysis. PPB maintained efficient H2 production (0.67 ± 0.09 L H2·g COD[-1]; 0.09 ± 0.01 L H2·L[-1]·d[-1]) until HPP reached about 30 %, after which both H2 production and growth declined. Transcriptomic results showed reduced nitrogenase and increased hydrogenase expression, disturbing electron allocation and redox balance and suppressing the tricarboxylic acid (TCA) cycle, gluconeogenesis, and photosynthesis. When HPP increased to about 40 %, H2 production stopped and shifted to H2 consumption, while alternative electron sinks such as the reverse TCA cycle and branched-chain amino acid synthesis were activated to partially restore metabolism. Upon headspace flushing, H2 production rapidly resumed, demonstrating the robustness of the PPB system to short-term HPP inhibition. This study provides practical insight for PF system operation, highlighting the importance of maintaining HPP below inhibitory threshold to sustain efficient H2 production.},
}

@article {pmid41421358,
year = {2025},
author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P},
title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101106},
doi = {10.1016/j.xgen.2025.101106},
pmid = {41421358},
issn = {2666-979X},
abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.},
}

@article {pmid41421350,
year = {2025},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102516},
doi = {10.1016/j.xcrm.2025.102516},
pmid = {41421350},
issn = {2666-3791},
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}

@article {pmid41421332,
year = {2025},
author = {Wang, Q and Liang, E and Xu, J and Liu, Y and Chao, C and Wan, H and Zhao, Y},
title = {Microbial self-regulation and electron transport reconstruction under Cr(VI)-4-CP stress: From synergistic inhibition to antagonistic interaction.},
journal = {Water research},
volume = {291},
number = {},
pages = {125138},
doi = {10.1016/j.watres.2025.125138},
pmid = {41421332},
issn = {1879-2448},
abstract = {Understanding how microbial communities adapt to multi-pollutant stress is crucial for efficient denitrification. Although previous studies reported the effects of heavy metals and phenolic compounds individually or in mixtures, the deep mechanisms by which combined stressors reshape microbial electron transport and community structure remain unclear. This study explored the denitrification response to combined Cr(VI) and 4-chlorophenol (4-CP) stress, revealing a temporal shift from synergistic inhibition (acute exposure) to antagonistic interaction (long-term adaptation). Acute Cr(VI)-4-CP exposure caused complete inhibition of denitrification within 18T, accompanied by the activation of dissimilatory nitrate reduction to ammonium. Cr(VI) intracellular accumulation (71.78 %) induced oxidative imbalance and 4-CP prioritized metabolism disrupted electron donor availability, collectively causing FMN decreasing, which decreased NAR electron capture efficiency. Prolonged exposure activated microbial self-regulation (denitrification efficiency recovered to 31.42 %), including extracellular Cr(III) immobilization (84.19 %), antioxidant enzyme upregulation, reshaping oxidative-antioxidant homeostasis. Concomitantly, the electron transport was remodeled via FMN/FAD complementarity, enabling partial recovery of NAR activity and suppression of N2O accumulation. Metagenomic analysis further identified functional cooperation among Microbacterium, Thermomonas, Diaphorobacter, and Acidovorax, supporting glucose/4-CP co-metabolism (COD4CP/CODglucose=1/1.26) and stabilized denitrification performance. This study established a mechanistic framework linking microbial self-regulation and electron transport remodeling, providing new insights into the resilience of denitrifiers under multi-pollutant stress.},
}

@article {pmid41421325,
year = {2025},
author = {Yang, Z and Yang, Y and Ning, D and Fan, X and Lv, Y and Zhuang, L and Wu, L},
title = {Metagenomic insights into the global distribution and functional potentials of major polyphosphate-accumulating organisms (PAOs) in activated sludge wastewater treatment plants.},
journal = {Water research},
volume = {291},
number = {},
pages = {125191},
doi = {10.1016/j.watres.2025.125191},
pmid = {41421325},
issn = {1879-2448},
abstract = {Polyphosphate accumulating organisms (PAOs) are essential for phosphorus removal in wastewater treatment plants (WWTPs); however, their global distribution patterns and potential ecological functions across diverse activated sludge systems remain poorly understood. Here, we analyzed 226 activated sludge metagenomes from 142 WWTPs across six continents, encompassing both enhanced biological phosphorus removal (EBPR) and non-EBPR processes. We reconstructed 29 near-complete PAO metagenome-assembled genomes, identifying putative members of several previously unrecognized Candidatus Accumulibacter clades. Our results revealed that Dechloromonas and Ca. Accumulibacter dominated in most WWTPs, while the former Tetrasphaera genus was prevalent in certain European samples. Furthermore, these PAOs demonstrated high metabolic versatility in carbon, nitrogen, and phosphorus cycling, though this functional potential varied significantly across genera. The link between PAOs and plant performance was process-dependent: while pollutant removal across the entire dataset showed comparable associations with both PAO abundance and the total abundance of phosphorus-cycling genes, the relationship was stronger for PAO abundance in EBPR plants. Collectively, these results represent a major expansion of the known genomic diversity of PAOs, and provide a foundational global baseline of PAO diversity that can help inform the future development of region- and process-specific optimization strategies.},
}