@article {pmid41089932,
year = {2025},
author = {Zhang, W and Guo, H and Xu, W and Chen, W and Hu, Y and Wang, Z},
title = {Di-(2-ethylhexyl) phthalate-degrading functional microorganisms were identified in black soil based on high throughput analysis.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100479},
pmid = {41089932},
issn = {2666-5174},
abstract = {Di-(2-ethylhexyl) phthalate (DEHP) has become an increasingly serious pollutant in soils. Microbial degradation represents a highly promising approach for its remediation. In this study, four black soils were used to simulate the natural degradation of DEHP over a 75-day microenvironmental experiment. High-throughput analysis was conducted to investigate the distribution and abundance of functional genes in soil microorganisms, aiming to explore functional microbial information. The degradation efficiency of DEHP in black soils was 76.37 %, 74.16 %, 92.21 %, and 75.35 %. The α-diversity of microbial community was positively correlated with the degradation rate. Actinobacteria and Proteobacteria exhibited sensitivity to DEHP contamination. Xanthomonaceae, Sphingomonadaceae, Hypomicrobiaceae, and Comamonadaceae contributed to the upstream metabolism of DEHP. The abundances of Rhodococcus, Sphingomonas, Nocardioides, and Arthrobacter were positively correlated with the abundance of functional genes enriched in the black soil for benzoate degradation. Concurrently, 10 DEHP-degrading bacterial communities were identified, and the taxonomic and functional profiles of certain members within these communities were consistent with the metagenomic data. Bacterial communities JQ104, JQ52, and JQ129 degraded >98 % of DEHP (400 mg/L) in 48 h, demonstrating remarkable degradation efficiency. This study demonstrated the dynamic impact of the indigenous microbiome on DEHP contamination and verified the degradation capabilities of key functional microorganisms.},
}

@article {pmid41089718,
year = {2025},
author = {Takahashi, Y and Fujitani, H and Taniguchi, I and Gotoh, Y and Shimada, Y and Ikeda, S and Hayashi, T and Tago, K and Hayatsu, M and Tsuneda, S},
title = {Acid tolerance and metabolic potential of comammox and nitrite-oxidizing Nitrospira enriched from soil.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf167},
pmid = {41089718},
issn = {2730-6151},
abstract = {Nitrification is the two-step microbial oxidation of ammonia to nitrate via nitrite, and it can contribute to environmental problems in soils. Some nitrifiers have been cultivated from acidic soils at pH <5.5, allowing their metabolic potential and phylogeny to be investigated through genomic analyses. However, the genomic features of the genus Nitrospira remain poorly understood in the context of acid tolerance, despite its wide distribution in acidic environments. This study aimed to characterize the physiology and genomics of acid-tolerant Nitrospira enriched from an acidic soil. Using a metagenomic approach, two closed genomes of Nitrospira were reconstructed: a complete ammonia-oxidizing (comammox) bacterium and a nitrite-oxidizing bacterium (NOB). Both enriched Nitrospira survived at pH <5.5 in physiological tests, and the enriched comammox Nitrospira was phylogenetically close to clones derived from acidic soils. The active-site residues of hydroxylamine oxidase, a key nitrification enzyme, were conserved between the comammox Nitrospira characterized in this study and the previously reported betaproteobacterial ammonia oxidizers. This conservation suggests that existing nitrification inhibitors targeting this enzyme may also inhibit ammonia oxidation by comammox Nitrospira in acidic soils. Although the comammox and NOB Nitrospira in this study shared nearly all key metabolic pathways with Nitrospira species identified from neutral pH environments, both possessed passive urea transporters homologous to those found in acid-tolerant bacteria. These results revealed the acid tolerance of the enriched Nitrospira at pH <5.5, as well as their genomic features shared with acid-tolerant bacteria, rather than with previously reported Nitrospira species.},
}

@article {pmid41089454,
year = {2025},
author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G},
title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666201},
pmid = {41089454},
issn = {1664-302X},
abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.

METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.

RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.

DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.},
}

@article {pmid41089363,
year = {2025},
author = {Park, T and Praisler, G and Wenner, BA},
title = {Treatment of dual-flow continuous culture fermenters with an organic essential oil product minimally influenced prokaryotic microbiome.},
journal = {Journal of animal science and technology},
volume = {67},
number = {5},
pages = {1018-1032},
pmid = {41089363},
issn = {2055-0391},
abstract = {Previous research reported an essential oil (EO) product decreasing methane (CH4) production by dual-flow continuous culture (DFCC); this product could assist organic dairy producers in decreasing emissions. Our objective was to assess the effect of this EO product on the microbial populations within DFCC. Here, we hypothesized that the EO either decreased protozoal population or induced shifts in the bacterial relative abundance to decrease CH4 production. Metagenomic DNA was extracted from previous effluent samples taken from a DFCC system (n = 2) across four experimental periods, after which samples were sequenced the 16S rRNA gene and microbial taxonomy was assigned using the SILVA v138 database. The treatments included a control (CON) diet (60:40 concentrate:orchardgrass pellet mix, 17.1% crude protein, 33.0% neutral detergent fiber, 20.1% acid detergent fiber, and 27.1% starch) fed twice daily for a total of 80 g/d dry matter, or the same CON diet with the addition of EO at 3 mg/d. Protozoa were also quantified in both fermenter contents and unpooled daily effluent samples. The statistical model included fixed effects of treatment and fermenter, and random effect of period, using either MaAsLin2 or the adonis2 function in the vegan package of R for microbial features, or SAS mixed model for protozoal counts. The results were deemed significant at Q < 0.05 and p < 0.05 for the MaAsLin2 and adonis2/SAS analyses, respectively. For the protozoal populations, the treatments had no significant effect (p > 0.10) on the total counts, differentiated groups, or cell outflow. The addition of EO increased the relative abundance of Methanobrevibacter and decreased that of uncultured Methanomethylophilaceae (Q < 0.05). In contrast, EO addition had no significant effect on archaeal α- or β-diversity (p > 0.05). Despite not having a significant effect on the β-diversity of archaeal and bacterial communities, EO decreased (p < 0.05) α-diversity indices in prokaryotic communities. Moreover, EO decreased (Q < 0.01) the relative abundance of Clostridia UCG-014, Rikenellaceae RC9 gut group, and Christenellaceae R7 group, and increased (Q < 0.01) others including Treponema, Succinivibrionaceae UCG-002, and Ruminococcus. Offsetting shifts in the relative abundance of fiber-degrading bacteria and detailed methanogen communities deserves further investigation including predicted metabolic pathways impacted by population shifts induced by this EO combination.},
}

@article {pmid41089014,
year = {2025},
author = {Li, B and Xu, F and Xia, M and Li, X and Hou, X and Lyu, X and Guo, X},
title = {[Retrospective clinical analysis of 31 cases of necrotizing fasciitis of the neck with or without descending necrotizing mediastinitis].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {39},
number = {10},
pages = {971-975},
doi = {10.13201/j.issn.2096-7993.2025.10.014},
pmid = {41089014},
issn = {2096-7993},
mesh = {Humans ; Retrospective Studies ; *Fasciitis, Necrotizing/complications/therapy ; *Mediastinitis/complications ; *Neck/pathology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Prognosis ; },
abstract = {Objective:To summarize the clinical characteristics and management experience of complications in patients with cervical necrotizing fasciitis （CNF） with or without descending necrotizing mediastinitis （DNM）, in order to provide a basis for optimizing diagnosis and treatment strategies. Methods:A retrospective analysis was conducted on the clinical data of 31 patients diagnosed with CNF and DNM at Shandong Provincial Hospital Affiliated to Shandong First Medical University between October 2019 and March 2024. A comprehensive evaluation was performed based on the patients' clinical characteristics, metagenomic next-generation sequencing （mNGS） pathogen detection results, imaging assessments, surgical interventions, management approaches for specific complications, and prognostic outcomes. Results:Among the 31 patients, 10 had severe diabetes mellitus. Etiological analysis was summarized as follows: 5 cases were odontogenic, 3 were of tonsillar origin, 3 were due to endogenous esophageal injury, 2 were due to exogenous cervical trauma, 2 originated from a congenital branchial cleft fistula, and 16 cases had an unknown etiology. Among them, 29 patients underwent surgery via an external cervical approach, 1 patient underwent surgery via an intraoral approach, and 1 patient received ultrasound-guided puncture and drainage therapy. Ultimately, 29 patients were cured and discharged （including 1 patient who experienced two instances of major neck vessel rupture and successfully underwent two interventional embolization procedures for hemostasis）; 2 patients died after failed rescue efforts due to concurrent sepsis and multiple organ dysfunction. The treatment success rate was 93%, and the mortality rate was 7%. In this cohort of CNF and DNM cases, only a minority had a clearly identified odontogenic cause; although the etiology was unknown in most cases, imaging consistently showed oropharyngeal lymph node necrosis, suggesting a possible pharyngeal origin of infection in adults. The mNGS pathogen profile was predominantly Gram-positive bacteria, accompanied by anaerobic bacilli and fungi. Conclusion:CNF and DNM are severe and rapidly progressive conditions that can lead to life-threatening complications within hours. Timely recognition can reduce unnecessary examinations and expedite treatment.},
}

Humans
Retrospective Studies
*Fasciitis, Necrotizing/complications/therapy
*Mediastinitis/complications
*Neck/pathology
Male
Female
Middle Aged
Adult
Aged
Prognosis

@article {pmid41088813,
year = {2025},
author = {Guo, YN and De, R and Wang, FM and Han, ZZ and Liu, LY and Sun, Y and Yao, Y and Ma, XL and Liu, S and Zhu, C and Qu, D and Zhao, LQ},
title = {Molecular Characterization of New Recombinant Human Adenoviruses Detected in Children with Acute Respiratory Tract Infections in Beijing, China, 2022-2023.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {9},
pages = {1071-1081},
doi = {10.3967/bes2025.105},
pmid = {41088813},
issn = {2214-0190},
mesh = {Humans ; *Adenoviruses, Human/genetics/classification/isolation & purification ; *Respiratory Tract Infections/virology/epidemiology ; Child, Preschool ; Child ; *Recombination, Genetic ; Male ; Beijing/epidemiology ; Infant ; Female ; Phylogeny ; *Adenovirus Infections, Human/virology/epidemiology ; Acute Disease ; Genome, Viral ; },
abstract = {OBJECTIVE: Recombination events are common and serve as the primary driving force of diverse human adenovirus (HAdV), particularly in children with acute respiratory tract infections (ARIs). Therefore, continual monitoring of these events is essential for effective viral surveillance and control.

METHODS: Respiratory specimens were collected from children with ARIs between January 2022 and December 2023. The penton base, hexon, and fiber genes were amplified from HAdV-positive specimens and sequenced to determine the virus type. In cases with inconsistent typing results, genes were cloned into the pGEM-T vector to detect recombination events. Metagenomic next-generation sequencing (mNGS) was performed to characterize the recombinant HAdV genomes.

RESULTS: Among 6,771 specimens, 277 (4.09%, 277/6,771) were positvie for HAdV, of which 157 (56.68%, 157/277) were successfully typed, with HAdV-B3 being the dominant type (91.08%, 143/157), and 14 (5.05%, 14/277) exhibited inconsistent typing results, six of which belonged to species B. The penton base genes of these six specimens were classified as HAdV-B7, whereas their hexon and fiber genes were classified as HAdV-B3, resulting in a recombinant genotype designated P7H3F3, which closely resembled HAdV-B114. Additionally, a partial gene encoding L1 52/55 kD was identified, which originated from HAdV-B16.

CONCLUSION: A novel recombinant, P7H3F3, was identified, containing sequences derived from HAdV-B3 and HAdV-B7, which is similar to HAdV-B114, along with additional sequences from HAdV-B16.},
}

Humans
*Adenoviruses, Human/genetics/classification/isolation & purification
*Respiratory Tract Infections/virology/epidemiology
Child, Preschool
Child
*Recombination, Genetic
Male
Beijing/epidemiology
Infant
Female
Phylogeny
*Adenovirus Infections, Human/virology/epidemiology
Acute Disease
Genome, Viral

@article {pmid41088467,
year = {2025},
author = {Osburn, ED and Weissman, JL and Strickland, MS and Bahram, M and Stone, BW and McBride, SG},
title = {Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {131},
pmid = {41088467},
issn = {2524-6372},
support = {2131837//National Science Foundation/ ; 2020-67034-41310//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: To improve our understanding of microbial systems, it is essential to refine the conceptual frameworks that connect microorganisms to their ecological functions. While trait-based approaches can provide nuanced perspectives on how microorganisms influence ecosystem processes, there is ongoing debate over the link between microbial taxonomic classifications and life history traits. Here, we integrate genomic, metagenomic, amplicon sequencing, and experimental (stable isotope probing) data to investigate the scaling of bacterial growth traits from individual taxa to complex assemblages and to identify specific taxonomic groups of soil bacteria that can be used as indicators of community-scale microbial growth.

RESULTS: Our results revealed broadly different distributions of growth rates among bacterial phyla, including significantly different mean and median rates. This, in turn, manifested in strong relationships between relative abundances of some phyla and community-scale growth rates in soil. Specifically, we calculated community weighted mean growth rates using measured growth rates of constituent taxa and found that the fast-growing taxa that had sufficient abundance and ubiquity across samples to contribute to variation in community-average growth were mostly lineages of Proteobacteria (e.g., Sphingomonas). As a result, the relative abundance of phylum Proteobacteria was the single strongest taxonomic predictor of community-average growth, explaining up to ~ 60% of the variation in growth rates across communities. In contrast, Verrucomicrobia were consistent indicators of slower community-average growth. These patterns were especially strong when using taxon-level growth rates measured following carbon and nitrogen additions to soil.

CONCLUSIONS: Our results demonstrate that phylum relative abundances can be strong indicators of community-level bacterial growth despite the wide variation in growth rates observed within phyla. The stronger phylum-growth relationships for whole assemblages than are apparent for individual taxa are due to relative abundance-weighted trait averaging in complex assemblages, i.e., at the community scale, broad differences in growth traits among phyla become more important than variation within phyla. Overall, our results provide clarity regarding the use of bacterial taxonomic information for inferring traits, demonstrating that high taxonomic ranks can be valid indicators of microbial traits in soil provided that inferences are drawn at the appropriate scale.},
}

@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tryptophan/metabolism
Male
*Symbiosis/drug effects
*Benzamides/pharmacology/therapeutic use
*Coronary Vessels/drug effects/physiopathology
*Microvessels/drug effects/physiopathology
Rats
*Microcirculation/drug effects

@article {pmid41088296,
year = {2025},
author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J},
title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1083},
pmid = {41088296},
issn = {1479-5876},
support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; Adolescent ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Male ; Female ; *Emotions ; Quetiapine Fumarate/therapeutic use/pharmacology ; Magnetic Resonance Imaging ; Case-Control Studies ; Brain/physiopathology/diagnostic imaging ; Neuroimaging ; },
abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.

METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.

RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC = 91.12%) and predict the treatment effect (AUC = 91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.

CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
Adolescent
*Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology
Male
Female
*Emotions
Quetiapine Fumarate/therapeutic use/pharmacology
Magnetic Resonance Imaging
Case-Control Studies
Brain/physiopathology/diagnostic imaging
Neuroimaging

@article {pmid41088250,
year = {2025},
author = {Koehler, AV and Wang, T and Stevens, MA and Haydon, SR and Gasser, RB},
title = {Long-term molecular surveillance of Cryptosporidium and Giardia in wildlife in protected drinking water catchments.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {413},
pmid = {41088250},
issn = {1756-3305},
support = {LP160101299//Australian Research Council/ ; },
mesh = {*Cryptosporidium/genetics/isolation & purification/classification ; Animals ; *Giardia/genetics/isolation & purification/classification ; *Cryptosporidiosis/epidemiology/parasitology ; Feces/parasitology ; *Giardiasis/epidemiology/veterinary/parasitology ; *Animals, Wild/parasitology ; *Drinking Water/parasitology ; Victoria/epidemiology ; Genotype ; Longitudinal Studies ; Prevalence ; Epidemiological Monitoring ; },
abstract = {BACKGROUND: This study presents findings from a 15-year longitudinal surveillance program (2009-2024) monitoring Cryptosporidium and Giardia in protected drinking water catchments in Melbourne and environs in the State of Victoria, Australia. As one of the few major cities worldwide sourcing largely unfiltered water from forested catchments, Melbourne presents a unique opportunity to assess the occurrence and prevalence of protozoan parasites in a minimally disturbed ecosystem.

METHODS: A total of 14,960 animal faecal samples were analysed using polymerase chain reaction (PCR)-based sequencing, including 8695 samples collected over the past 9 years.

RESULTS: Cryptosporidium was detected in 3.15% of samples and Giardia in 0.16%. A total of 12 recognised Cryptosporidium species and genotypes were identified, nine of which have known zoonotic potential, as well as two sub-assemblages (AI and AIII) of Giardia duodenalis, including four novel assemblage AI variants. Parasite diversity was the highest in eastern grey kangaroos, which hosted at least 18 Cryptosporidium variants. Temporal analyses revealed significant inter-annual variation, with peak prevalence during the 2023 La Niña year and seasonal differences by host group. Notably, C. ubiquitum, C. muris and C. occultus were recorded for the first time in these catchments. In spite of the low prevalence of high-risk species such as C. parvum and the absence of C. hominis, the detection of emerging and previously uncharacterised genotypes emphasises the importance of sustained surveillance.

CONCLUSIONS: These findings have broad implications for managing zoonotic risk in unfiltered water systems worldwide. Advances in metagenomics and high-throughput sequencing platforms will be critical for enhancing future pathogen monitoring and catchment management strategies in the context of increasing climate and environmental pressures.},
}

*Cryptosporidium/genetics/isolation & purification/classification
Animals
*Giardia/genetics/isolation & purification/classification
*Cryptosporidiosis/epidemiology/parasitology
Feces/parasitology
*Giardiasis/epidemiology/veterinary/parasitology
*Animals, Wild/parasitology
*Drinking Water/parasitology
Victoria/epidemiology
Genotype
Longitudinal Studies
Prevalence
Epidemiological Monitoring

@article {pmid41087996,
year = {2025},
author = {Kruasuwan, W and Pathomchareansukchai, D and Tangsawad, W and Wankaew, N and Arigul, T and Nitayanon, P and Nimsamer, P and Duangjanchot, R and Arayamethakorn, S and Chancharussin, N and Jenjaroenpun, P and Kamolvit, W and Suputtamongkol, Y and Wongsurawat, T and Tansirichaiya, S},
title = {Clinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1299},
pmid = {41087996},
issn = {1471-2334},
}

@article {pmid41087940,
year = {2025},
author = {Li, C and Liu, M and Ji, Y and Pang, S and Tian, J and Li, X and Zhang, M and Gu, Y and Chen, H and He, L and Wu, Y},
title = {Clinical characteristics and prognostic indicators in Listeria monocytogenes meningoencephalitis: A retrospective case series and literature review.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {420},
pmid = {41087940},
issn = {1471-2377},
support = {YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; YKD2022LH060//Inner Mongolia Medical University Joint Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 2023GLLH0034//Inner Mongolia Academy of Medical Sciences Scientific Research Joint Fund key Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; 202202019//Inner Mongolia Region Health Science and Technology Plan Project/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; KC23262//The project of Xuzhou Science and Technology Bureau in 2023/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XZSYSKF2020010//The opening project of key laboratories of colleges and universities in Jiangsu Province in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; XWKYHT20200001//The Youth Medical Science and Technology Innovation Project of Xuzhou Municipal Health Commission in 2020/ ; },
mesh = {Humans ; Middle Aged ; Male ; Retrospective Studies ; Female ; Prognosis ; Adult ; *Listeria monocytogenes ; Aged ; *Meningitis, Listeria/diagnosis/cerebrospinal fluid ; *Meningoencephalitis/diagnosis/cerebrospinal fluid ; *Listeriosis/diagnosis/cerebrospinal fluid ; },
abstract = {BACKGROUND: Listeria monocytogenes meningoencephalitis (LMM) is a rare but severe central nervous system (CNS) infection. This study aimed to characterize the clinical manifestations, diagnostic findings, treatment responses, and prognostic factors associated with LMM.

METHODS: We retrospectively analyzed the clinical data of 13 patients diagnosed with LMM at Xuzhou Medical University Affiliated Hospital between 2018 and 2023. An additional five cases were identified through a literature search in the China National Knowledge Infrastructure (CNKI) and Wanfang databases from 2019 to 2022. Clinical features, cerebrospinal fluid (CSF) and blood test results, imaging findings, treatments, and outcomes were summarized.

RESULTS: Among 18 patients (11 males, 7 females; mean age 51.6 ± 17.2 years), all had acute onset with fever (100%), headache (83.3%), and altered consciousness (77.8%). CSF analysis showed elevated pressure in 83.3%, increased leukocytes and protein in all cases, and variable glucose levels. LM was cultured from CSF in 10 patients and detected via metagenomic next-generation sequencing (mNGS) in 12. Imaging findings included hydrocephalus in 4 cases and meningeal enhancement in 2 cases. Full recovery was observed in 2 cases, improvement in 9, palliative care in 3, and death in 4. Early seizures and hydrocephalus were linked to worse outcomes.

CONCLUSION: Listeria monocytogenes meningoencephalitis is a rapidly progressive CNS infection with variable presentations and significant risk of poor outcomes. Early recognition, appropriate antimicrobial coverage, and timely diagnostic testing are essential to improving prognosis.

TRIAL REGISTRATION: Not applicable.},
}

Humans
Middle Aged
Male
Retrospective Studies
Female
Prognosis
Adult
*Listeria monocytogenes
Aged
*Meningitis, Listeria/diagnosis/cerebrospinal fluid
*Meningoencephalitis/diagnosis/cerebrospinal fluid
*Listeriosis/diagnosis/cerebrospinal fluid

@article {pmid41040331,
year = {2025},
author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM},
title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41040331},
issn = {2692-8205},
abstract = {Human disruption of ecosystems poses a significant threat to global health, driving the need for low-cost, low-power, and easily deployable sensors for environmental and health monitoring. Microbial bioelectronic sensors are particularly well-suited as they generate electrical signals and can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies for bioelectronic sensors lack modularity, are limited to a few microbial chassis, and depend on specialized instruments for signal detection. Here, we present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play platform for bioelectronic sensor development. This system comprises a "sender" bacterium that produces electron mediators in response to analytes and a "receiver" bacterium that utilizes the electron mediators to generate electrical signals via extracellular electron transfer (EET). By modularly swapping the sender bacterium and its associated genetic sensing elements, we achieved bioelectronic sensing of metals, small molecules, and peptides in distinct environmental, food, and human-relevant settings. Moreover, we designed a centimetre-sized bioelectronic device that enables low-cost, portable signal readout from e[-]COSENS using a household digital multimeter. The e[-]COSENS platform greatly simplifies the bioelectronic sensor design and opens unprecedented potential for bioelectronic sensor applications.},
}

@article {pmid40889483,
year = {2025},
author = {Bertrans-Tubau, L and Martínez-Campos, S and López-Doval, JC and Abril, M and Pladelasala-Rocafiguera, G and Ponsá, S and Suñer, AC and Salvadó, V and Hidalgo, M and Doménech-Pascual, A and Romaní, AM and Pico-Tomàs, A and Balcázar, JL and Proia, L},
title = {Improving small urban wastewater treatment plants with a nature-based reactor for tertiary treatment.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126983},
doi = {10.1016/j.jenvman.2025.126983},
pmid = {40889483},
issn = {1095-8630},
mesh = {*Wastewater ; Nitrogen ; Phosphorus ; *Bioreactors ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; Sewage ; Biofilms ; },
abstract = {Urban wastewater treatment has significantly improved in recent decades, reducing the environmental impacts of their effluents and improving the chemical and ecological status of receiving water bodies. However, specific treatments, focused on nitrogen and phosphorus removal, have been implemented principally in large urban wastewater treatment plants (UWWTPs) serving over 10,000 population equivalents (P.E). In contrast, small UWWTPs (<10,000 P.E.) are generally not required to meet nutrient discharge limits despite the revised Urban Wastewater Treatment Directive. Nature-Based Solutions (NBS) offer cost-effective alternatives for small facilities as potential tertiary treatments. This research evaluated a pond-stream system, based on the biological activity of benthic (biofilms) and planktonic microbial communities (biofilm-plankton reactor, BPR), as an additional treatment step for activated sludge UWWTPs. The BPR achieved removal efficiencies for nitrogen (67.4 ± 11.1 %) and Escherichia coli (75.4 ± 37.3 %), while phosphorus, carbon, and targeted contaminants of emerging concern were highly variable and were not consistently removed. Microbial communities' structure and functions were assessed through algal biomass, stoichiometry, and extracellular enzymatic activities, providing a distinctive perspective into the BPR's microbial ecological dynamics related to removal efficiencies. Shotgun metagenomics identified a broad range of nitrogen functional genes, mainly involved in biodegradation and biosynthesis processes. This next-generation sequencing approach complemented conventional E. coli count methods, offering a deeper understanding of potential pathogen hotspots in treated effluents. Overall, the BPR system demonstrated a promising NBS for nitrogen and microbiological contaminant removal in small UWWTPs, whereas further investigation is needed to optimise the removal of other important water quality parameters.},
}

*Wastewater
Nitrogen
Phosphorus
*Bioreactors
*Water Purification/methods
*Waste Disposal, Fluid/methods
Sewage
Biofilms

@article {pmid41087922,
year = {2025},
author = {Wang, Y and Liang, M and Hu, M and Mao, G},
title = {Disseminated Talaromyces marneffei infection in a patient with Ankylosing Spondylitis: a case report and review of the literature.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1316},
pmid = {41087922},
issn = {1471-2334},
abstract = {BACKGROUND: Ankylosing Spondylitis (AS) is a prevalent autoimmune disorder that necessitates the prolonged use of corticosteroids, non-steroidal anti-inflammatory drugs (NSAIDs), and disease-modifying antirheumatic drugs (DMARDs). Immunosuppressive medications are now commonly incorporated into treatment plans; however, this may increase patients' risk of severe infections. Infections caused by Talaromyces marneffei (TM) are rarely seen in patients with AS, yet if left untreated, they could result in severe morbidity and even death.

CASE REPORT: This report presents a comprehensive case study of a 44-year-old Human Immunodeficiency Virus (HIV)-negative male with Ankylosing Spondylitis (AS) complicated by diabetes mellitus, who developed both soft tissue and pulmonary infections. Initial diagnosis suggested a bacterial etiology; however, clinical response to broad-spectrum antibiotics was suboptimal. Subsequent diagnostic procedures, including biopsy and culture of axillary lymph nodes and pulmonary tissue, coupled with Metagenomic Next-Generation Sequencing (mNGS), confirmed the diagnosis of disseminated TM infection. The patient achieved favorable outcomes following targeted antifungal therapy.

CONCLUSION: Patients with compromised immune function due to chronic immunosuppressive treatments require vigilant monitoring for uncommon opportunistic pathogens, particularly fungal infections. Advanced diagnostic techniques for early identification of pathogens, prompt and accurate prescription of antimicrobial agents, tailored dosing schedules, and stringent monitoring for potential complications are crucial for optimizing patient outcomes.},
}

@article {pmid41087898,
year = {2025},
author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C},
title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {660},
pmid = {41087898},
issn = {1471-2180},
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.

METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.

RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.

CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.},
}

@article {pmid41087864,
year = {2025},
author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X},
title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {663},
pmid = {41087864},
issn = {1471-2180},
support = {82100594//National Natural Science Foundation of China,China/ ; },
abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.

METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.

RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.

CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).},
}

@article {pmid41087617,
year = {2025},
author = {Liu, M and Yang, L and Nan, D and Ma, L and Zhang, J and Liang, F and Yang, J and Liu, X},
title = {Hyperbaric oxygen treatment mitigates gut dysbiosis of mice with spinal cord injury.},
journal = {Journal of molecular medicine (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41087617},
issn = {1432-1440},
support = {No. 82101964//National Natural Science Foundation of China/ ; No. 7202055//Natural Science Foundation of Beijing Municipality/ ; CYDXK 202208//Beijing Chao-Yang Hospital Multi-disciplinary Team Program/ ; },
abstract = {Gut dysbiosis impacts the recovery of neurological function after spinal cord injury (SCI). Hyperbaric oxygen (HBO) can alleviate SCI, but its effects on the gut microbiota post-SCI remain unclear. This study aimed to clarify the impact of HBO on SCI-induced gut dysbiosis and to explore the mechanisms of locomotor recovery in HBO-treated SCI mice. After establishing different groups of mouse models, bacterial cultures and Basso Mouse Scale (BMS) scores were performed at various time points post-SCI. Intestinal tissues were collected for intestinal permeability assay, histological analysis, immunofluorescence, and qPCR analysis. Flow cytometry and ELISA were used to detect immune-inflammatory cells and cytokines in intestinal tissue. The composition of gut microbiota in fecal samples from each group was also analyzed. Spinal cord tissues were collected for immunofluorescence and untargeted metabolomics analysis. Spearman correlation analysis was used to correlate differential microbiota with differential metabolites. Our results showed that the expression of tight junction proteins was increased after HBO treatment in SCI mice. Metagenomic analysis of the fecal DNA revealed that HBO altered intestinal bacterial composition. Differential metabolites were mainly enriched in pathways, such as glycerophospholipid metabolism, steroid biosynthesis, and glycolysis/gluconeogenesis. Moreover, differential microbiota showed a strong correlation with differential metabolites related to glycerophospholipids. HBO treatment significantly inhibited immune cells and inflammatory cytokines in the gut after SCI. In addition, HBO treatment significantly increased BMS scores and body weight, and repaired damaged cholinergic neurons. Antibiotic-induced gut dysbiosis impaired the recovery of locomotor function and exacerbated intraspinal pathology. However, these effects could be mitigated by HBO treatment. Overall, HBO treatment may improve neurological recovery through multiple regulatory mechanisms including alleviating gut dysbiosis, reducing intestinal inflammation, and rectifying glycerophospholipid metabolic disorders after SCI. These findings highlight HBO as a promising therapeutic strategy for SCI treatment and support its clinical application. KEY MESSAGES: The intestinal microbiota composition of mice changed after SCI. HBO treatment could preserve intestinal barrier integrity, modulate the composition of intestinal microbiota, rectify glycerophospholipid metabolic disorders, and reduce intestinal immune inflammatory responses. Intestinal microbiota identified as the target for HBO therapeutic in SCI recovery. Alleviating SCI-induced gut dysbiosis may be one of the mechanisms underlying the beneficial effect of HBO on neurological functions.},
}

@article {pmid41087549,
year = {2025},
author = {Chauhan, M and Maniya, H and Mori, P and Nagpal, R and Tirgar, P and Kumar, V},
title = {Assessment of multi-strain probiotics in regulating diet-induced obesity in Balb/c mice model.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {41087549},
issn = {1476-5497},
abstract = {BACKGROUND/OBJECTIVES: This study investigated the efficacy of a novel multi-strain probiotic (MSP), composed of Limosilactobacillus fermentum BAB 7912, Bacillus rugosus PIC5CR, and Bacillus rugosus PIB9CR, in preventing and reverting diet-induced obesity in Balb/c male mice.

SUBJECTS/METHODS: This study used 8-week-old Balb/c mice. A total of 40 mice were divided into five groups namely control negative (CN), control with obesity (CO), and three treatment groups: microbial consortium treated (MCT), Healthy control 1 (HC1), and Healthy control 2 (HC2). Obesity was induced using a high-fat diet. MSP formulation developed indigenously as part of previous study, was fed to Balb/c mice at different time intervals to study its preventive and ameliorative potential. Animals were dissected for the collection of blood as well as various organs to study the effect of MSP feeding on obesity status. Results were validated using histopathological and metagenomic data.

RESULTS: The CN and other treatment groups gained significant weight at the end of 6 weeks, while no significant weight gain was observed among HC1 group animals that were fed with HFD and MSP together. This highlights the preventive effect of continuous MSP feeding in the HC1 animal group. Initial liver histopathology in the HC1 group revealed enlarged hepatocytes and fat droplets. By week 9, the MCT group, which received MSP with a basal diet, showed liver recovery towards normal, accompanied by body weight improvement from 28.02 ± 0.7 g to 26.18 ± 0.96 g. Metagenomic analysis revealed that MSP treatment increased the relative abundance of health-promoting bacteria, notably Lactobacillaceae (specifically Lactobacillus).

CONCLUSIONS: Findings indicated that continuous consumption of MSP contributes significantly in prevention of obesity and associated metabolic disorders. Future studies are needed to explore the mechanisms underlying these effects and to evaluate the potential of MSP for human health.},
}

@article {pmid41087370,
year = {2025},
author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D},
title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35782},
pmid = {41087370},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; },
abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.},
}

*Metagenomics/methods
*Metagenome
*Phosphates/metabolism
*Geologic Sediments/microbiology
Bacteria/genetics
Microbiota/genetics
Phosphoric Monoester Hydrolases/genetics/metabolism

@article {pmid41087364,
year = {2025},
author = {Boulay, A and Leprince, A and Enault, F and Rousseau, E and Galiez, C},
title = {Empathi: embedding-based phage protein annotation tool by hierarchical assignment.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9114},
pmid = {41087364},
issn = {2041-1723},
support = {325947//Fonds de Recherche du Québec - Nature et Technologies (Quebec Fund for Research in Nature and Technology)/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Viral Proteins/genetics/metabolism/classification ; *Molecular Sequence Annotation/methods ; Machine Learning ; Genome, Viral ; Databases, Protein ; *Software ; Bacteria/virology ; *Computational Biology/methods ; },
abstract = {Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of protein sequences. Consequently, the majority of functions carried by phage proteins remain elusive. Current tools to comprehensively identify phage protein functions from their sequence either lack sensitivity (those relying on homology for instance) or specificity (assigning a single coarse grain function to a protein). Here, we introduce Empathi, a protein-embedding-based classifier that assigns functions in a hierarchical manner. New categories were specifically elaborated for phage protein functions and organized such that molecular-level functions are respected in each category, making them well suited for training machine learning classifiers based on protein embeddings. Empathi outperforms homology-based methods on a dataset of cultured phage genomes, tripling the number of annotated homologous groups. On the EnVhogDB database, the most recent and extensive database of metagenomically-sourced phage proteins, Empathi doubled the annotated fraction of protein families from 16% to 33%. Having a more global view of the repertoire of functions a phage possesses will assuredly help to understand them and their interactions with bacteria better.},
}

*Bacteriophages/genetics/metabolism
*Viral Proteins/genetics/metabolism/classification
*Molecular Sequence Annotation/methods
Machine Learning
Genome, Viral
Databases, Protein
*Software
Bacteria/virology
*Computational Biology/methods

@article {pmid41086989,
year = {2025},
author = {Zheng, L and Yao, L and Zhu, B and Chen, S and JinQian, and Liu, S and JinZhao, and Chen, Z and ShuaiXiang, and Xie, Z and Zhu, J and Wang, S and KaiWu, and Chen, J and Zhang, S and Lu, X},
title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120399},
doi = {10.1016/j.jad.2025.120399},
pmid = {41086989},
issn = {1573-2517},
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.},
}

@article {pmid41086964,
year = {2025},
author = {Zhang, X and Qaisar, M and Xu, F and Sun, J and Li, J and Cai, J},
title = {Bio-induced hydroxylated magnesium ammonium phosphate precipitation drives non-biological ammonium removal in sulfide-based denitrification.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133492},
doi = {10.1016/j.biortech.2025.133492},
pmid = {41086964},
issn = {1873-2976},
abstract = {The sulfide-based autotrophic denitrification (SAD) process showed remarkable efficiency in nitrate (98.18 ± 2.13 %) and sulfide (97.4 ± 2.75 %) removal, while also resulting in unintentional ammonium elimination (18.92 ± 9.79 %) through a 138-day continuous-flow experiment. Batch tests demonstrated kinetic decoupling between ammonium removal and SAD activity, with ammonium elimination exhibiting a substantial dependence on pH (p < 0.01), indicating a chemically driven process. XRD and SEM-EDS analysis suggested biologically induced precipitation of magnesium ammonium phosphate-like compounds (Mg3(NH4)2H4(PO4)4·8H2O). Metagenomic analysis further confirmed the absence of biological ammonium conversion pathways, as dominant functional genes were linked to sulfur-oxidizing denitrification (napAB and nosZ), driven by genus Sulfurovum (42.89 % relative abundance). No genes (hdh and hzsA) associated with ammonium oxidation were detected which ruled out the biological nitrogen transformation. These findings definitively confirm that magnesium ammonium phosphate precipitation was the principal mechanism for ammonium removal in SAD systems, offering essential insights for enhancing energy-efficient nitrogen removal in wastewater treatment.},
}

@article {pmid41086845,
year = {2025},
author = {White, AE and Koch, TJ and Jensen, TZT and Niemann, J and Pedersen, MW and Søtofte, MB and Binder, D and Lepère, C and Harb, C and Huber, R and Kramer, L and Mauvilly, M and Ebersbach, R and Wahl, J and Little, A and Wales, N and Regert, M and Schroeder, H},
title = {Ancient DNA and biomarkers from artefacts: insights into technology and cultural practices in Neolithic Europe.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2057},
pages = {20250092},
doi = {10.1098/rspb.2025.0092},
pmid = {41086845},
issn = {1471-2954},
support = {//HORIZON EUROPE European Research Council/ ; //Carlsbergfondet/ ; //HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
mesh = {*DNA, Ancient/analysis ; Archaeology ; Humans ; Europe ; History, Ancient ; Biomarkers/analysis ; Plant Bark/chemistry ; Animals ; },
abstract = {Birch bark tar was widely used throughout prehistoric Europe for hafting stone tools as well as various other purposes. While previous research has mainly focused on the identification and production of birch bark tar, its diverse uses remain to be fully explored. In this study, we combined ancient DNA with organic residue analysis to analyse 30 birch tar artefacts from nine Neolithic sites in and around the Alps. We identified birch tar as the main component, with some samples also containing conifer resin or tar, possibly added to modify its properties. Degradation markers indicate that tar used for ceramic repair was heated repeatedly, probably during cooking. Additionally, the presence of human and oral microbial DNA in some of the samples suggests the tar was chewed, in some cases by multiple individuals. The human DNA also enables us to determine the sex of those who chewed the tar, offering insights into gendered practices in the past, while plant and animal DNA shed light on past diets and the possible use of additives. This study underscores the value of integrating organic residue and ancient DNA analysis of archaeological artefacts to deepen our understanding of past cultural practices.},
}

*DNA, Ancient/analysis
Archaeology
Humans
Europe
History, Ancient
Biomarkers/analysis
Plant Bark/chemistry
Animals

@article {pmid41086610,
year = {2025},
author = {Li, H and Gao, H and Chen, S and Li, X and Zhou, J},
title = {Intensive mariculture shifts microbial communities and life-history strategies in the semi-enclosed bay: Case study in Sansha Bay, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107607},
doi = {10.1016/j.marenvres.2025.107607},
pmid = {41086610},
issn = {1879-0291},
abstract = {Coastal bays often experience significant disturbances from various mariculture activities, frequently leading to severe eutrophication. Yet, the ecological consequences of nutrient inputs derived from mariculture on bay-associated microbial communities remain insufficiently understood. Sansha Bay, known as the world's largest cage mariculture site for Larimichthys crocea, represents a characteristic semi-enclosed bay commonly utilized for studying the environmental impacts of intensive mariculture. In this study, we compared the highly eutrophic Sansha Bay with the relatively undisturbed natural East China Sea to investigate how intensive mariculture influences the bay microbial biosphere, focusing on community composition, assembly mechanisms, functional profiles, and life-history strategies. Amplicon sequencing and metagenomic analyses showed that Sansha Bay had a greater proportion of fast-growing microorganisms, nitrogen and carbon cycling microbes, and antibiotic-resistant bacteria. Null model analysis indicated that while natural coastal microbial assemblages were predominantly shaped by stochastic processes, deterministic selection became increasingly prominent as mariculture activities intensified. Correspondingly, microbial life-history traits, including 16S rRNA gene copy number, codon usage bias, predicted maximum growth rates, genome size, guanine-cytosine content, transposase abundance, and niche breadth, were consistently elevated in the eutrophic bay. These results suggest that eutrophication associated with mariculture drives a shift in life-history strategies from oligotrophs (K-strategists) to copiotrophs (r-strategists). Collectively, this study yields novel mechanistic understanding of how intensive mariculture reshapes microbial community structures, laying the groundwork for forecasting changes in coastal ecosystems subjected to ongoing human disturbances.},
}

@article {pmid41086517,
year = {2025},
author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q},
title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.},
journal = {Virology},
volume = {613},
number = {},
pages = {110712},
doi = {10.1016/j.virol.2025.110712},
pmid = {41086517},
issn = {1096-0341},
abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.},
}

@article {pmid41086499,
year = {2025},
author = {Li, Y and Zheng, X and He, H and Hu, R and Han, Z and Tao, J and Lin, T and Chen, W},
title = {Microalgal-bacterial granular sludge enhances oxytetracycline removal: Microbial responses, degradation pathways, and adaptive mechanisms.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140103},
doi = {10.1016/j.jhazmat.2025.140103},
pmid = {41086499},
issn = {1873-3336},
abstract = {Oxytetracycline (OTC), an emerging "low-concentration, high-toxicity" contaminant, presents considerable hurdles to wastewater treatment processes. This study systematically evaluated for the first time the impacts of OTC on the operational performance, sludge characteristics, and microbial metabolic activity across three treatment systems: microalgal-bacterial granular sludge (MBGS), aerobic granular sludge (AGS), and activated sludge (AS). Results demonstrated that MBGS exhibited superior treatment efficiency, maintaining stable removal of 500 μg/L OTC at 88.06 ± 1.45 % (p < 0.05). MBGS adapted to OTC exposure by increasing ATP content and reducing lactate dehydrogenase release. Acclimated MBGS primarily removed OTC through biodegradation. Moreover, multiple OTC transformation products with reduced toxic potential were detected, signifying that MBGS systems achieve efficient microbial degradation. Metagenomic analyses revealed that Pseudomonadota in MBGS displayed high adaptability under OTC exposure. Additionally, OTC exposure upregulated carbohydrate and energy metabolism in MBGS, thereby enhancing overall microbial metabolic activity. Alphaproteobacteria contributed most significantly to key functional genes, underscoring their critical role in contaminant removal in the MBGS. Redundancy analysis highlights a robust association between Alphaproteobacteria and the abundance of antibiotic resistance genes. This study confirms the MBGS's resilience to OTC-contaminated wastewater, highlighting its potential for efficient antibiotic wastewater treatment.},
}

@article {pmid41086488,
year = {2025},
author = {Chen, L and Lin, Y and Jia, X and Zheng, X and Zhuo, Y and Chen, Q and Fan, H and Fang, Y and Zhang, H and Lin, C},
title = {Dual-Path valorization of organic waste via black soldier fly: Synergistic enhancement of feed efficiency, crop quality, and climate mitigation in closed-loop aquaculture.},
journal = {Waste management (New York, N.Y.)},
volume = {209},
number = {},
pages = {115186},
doi = {10.1016/j.wasman.2025.115186},
pmid = {41086488},
issn = {1879-2456},
abstract = {The rapid expansion of aquaculture generates vast quantities of hyperhydrated organic waste (e.g., eel feces), posing a severe waste management challenge due to its recalcitrance and high disposal costs. This study presents a circular bio-strategy using black soldier fly (BSF, Hermetia illucens) larvae to synergistically convert aquaculture waste and agro-industrial residue (Flammulina velutipes substrate) within a closed-loop system. The process achieved 92.6 % waste utilization efficiency, yielding two valuable co-products: First, BSF larvae accumulated nutrient-rich biomass (17.9 % crude protein, 8.03 % lauric acid). As a 1.0 % supplement in broiler diets, it significantly enhanced feed efficiency by 2.6 % and increased 42-day body weight by 7.5 % (P < 0.01), demonstrating a viable fishmeal alternative. Second, BSF frass was composted into a superior organic fertilizer, which outperformed conventional composting by reducing NH3 emissions by 34 % (P < 0.001) and increasing total nitrogen retention by 15.3 %, attributed to pH modulation and chitin-NH4[+] complexation. The frass also enhanced phosphorus (7.05 %) and potassium (2.76 %) bioavailability. Metagenomics analysis revealed that frass inoculation enriched functional microbes (Azoarcus, LDA > 2.5; Roseisolibacter) driving synchronized nitrogen fixation and phosphate solubilization. Field application of the compost boosted tomato yields by 12.1 % (P < 0.05) and improved fruit quality (vitamin C + 18.6 %, soluble sugars + 20 %). This work establishes a scalable waste-to-resource paradigm that concurrently addresses waste management, livestock feed security, and sustainable crop intensification.},
}

@article {pmid41085836,
year = {2025},
author = {Vidal-Silva, IM and Loza, A and Gutierrez-Rios, RM},
title = {Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {384},
pmid = {41085836},
issn = {1573-0972},
support = {IN202524//PAPIIT-DGAPA/ ; 319234//Ciencia Básica y/o Ciencia de Frontera. Modalidad: Paradigmas y Controversias de la Ciencia 2022/ ; },
}

@article {pmid41085703,
year = {2025},
author = {Sharma, N and Verma, A and Ambardar, S and Raj, S and Vakhlu, J},
title = {Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.},
journal = {Molecular genetics and genomics : MGG},
volume = {300},
number = {1},
pages = {97},
pmid = {41085703},
issn = {1617-4623},
support = {Rashtriya Uchchatar Shiksha Abhiyan//Rashtriya Uchchatar Shiksha Abhiyan/ ; JKST&IC/J/14/2022/160//JKST&IC-JKDST/ ; DST-INSPIRE/03/2022/004594//DST-INSPIRE/ ; BT/AIR01624/PACE-28/22//BIRAC-PACE/ ; },
mesh = {*Crocus/microbiology/genetics ; *Software ; *Metagenome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Algorithms ; },
abstract = {Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.},
}

*Crocus/microbiology/genetics
*Software
*Metagenome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification
*Microbiota/genetics
Algorithms

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

@article {pmid41085530,
year = {2025},
author = {Fan, M and Wang, Z and Yao, M and Li, X and van der Meer, W and Tao, Y and Rose, JB and Liu, G},
title = {Unveiling Chemical-Microbial Cascade Risk Factors from Plastic Pipe Leaching in Drinking Water.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10244},
pmid = {41085530},
issn = {1520-5851},
abstract = {Plastic pipes are increasingly used in drinking water distribution systems, yet their impact on water quality remains insufficiently understood. Here, we systematically investigate the dual outcomes posed by plastic pipes─chemical leaching and cascaded microbial exposure risks─by integrating Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and metagenomic analysis. Our results reveal that plastic pipes continuously release dissolved organic matter (DOM), including organic additives such as bisphenols (BPs) and organophosphate esters (OPEs), which profoundly reshape microbial communities. Under chlorinated conditions, leached DOM alters microbial diversity, promoting chlorine-resistant bacteria and opportunistic pathogens (OPs), while under nonchlorinated conditions, it accelerates microbial growth and enriches antibiotic resistance genes (ARGs), OPs, and virulence factors (VFs). Among plastic materials, polyethylene (PE) exhibited the highest chemical risk, releasing high concentrations of TCPP (700 ng/L) and BPF (200 ng/L) along with 207-227 unique DOM molecules. In contrast, polyvinyl chloride (PVC) supported the highest OP abundance, while polypropylene random copolymer (PPR) fostered the greatest OP diversity. These findings challenge conventional drinking water safety assessments that separate chemical contamination from microbial risk, underscoring the urgent need for an integrated risk assessment framework. Furthermore, they highlight the necessity of paying greater attention to the chemical and cascading microbial issues arising from the leaching of plastic pipes into drinking water, and of conducting a more comprehensive assessment of the associated potential health risks.},
}

@article {pmid41084448,
year = {2025},
author = {Han, Z and Jin, LX and Wang, ZT and Yang, LQ and Li, L and Ruan, Y and Chen, QW and Yao, SH and Heng, XP},
title = {[Regulatory effects of Dangua Humai Oral Liquid on gut microbiota and mucosal barrier in mice with glucolipid metabolism disorder].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {15},
pages = {4315-4324},
doi = {10.19540/j.cnki.cjcmm.20250421.401},
pmid = {41084448},
issn = {1001-5302},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/administration & dosage ; Mice, Inbred C57BL ; Humans ; *Glycolipids/metabolism ; Lipid Metabolism/drug effects ; Administration, Oral ; Disease Models, Animal ; },
abstract = {The gut microbiota regulates intestinal nutrient absorption, participates in modulating host glucolipid metabolism, and contributes to ameliorating glucolipid metabolism disorder. Dysbiosis of the gut microbiota can compromise the integrity of the intestinal mucosal barrier, induce inflammatory responses, and exacerbate insulin resistance and abnormal lipid metabolism in the host. Dangua Humai Oral Liquid, a hospital-developed formulation for regulating glucolipid metabolism, has been granted a national invention patent and demonstrates significant clinical efficacy. This study aimed to investigate the effects of Dangua Humai Oral Liquid on gut microbiota and the intestinal mucosal barrier in a mouse model with glucolipid metabolism disorder. A glucolipid metabolism disorder model was established by feeding mice a high-glucose and high-fat diet. The mice were divided into a normal group, a model group, and a treatment group, with eight mice in each group. The treatment group received a daily gavage of Dangua Humai Oral Liquid(20 g·kg~(-1)), while the normal group and model group were given an equivalent volume of sterile water. After 15 weeks of intervention, glucolipid metabolism, intestinal mucosal barrier function, and inflammatory responses were evaluated. Metagenomics and untargeted metabolomics were employed to analyze changes in gut microbiota and associated metabolic pathways. Significant differences were observed between the indicators of the normal group and the model group. Compared with the model group, the treatment group exhibited marked improvements in glucolipid metabolism disorder, alleviated pathological damage in the liver and small intestine tissue, elevated expression of recombinant claudin 1(CLDN1), occluding(OCLN), and zonula occludens 1(ZO-1) in the small intestine tissue, and reduced serum levels of inflammatory factors lipopolysaccharides(LPS), lipopolysaccharide-binding protein(LBP), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α). At the phylum level, the relative abundance of Bacteroidota decreased, while that of Firmicutes increased. Lipid-related metabolic pathways were significantly altered. In conclusion, based on the successful establishment of the mouse model of glucolipid metabolism disorder, this study confirmed that Dangua Humai Oral Liquid effectively modulates gut microbiota and mucosal barrier function, reduces serum inflammatory factor levels, and regulates lipid-related metabolic pathways, thereby ameliorating glucolipid metabolism disorder.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Intestinal Mucosa/drug effects/metabolism/microbiology
Male
*Drugs, Chinese Herbal/administration & dosage
Mice, Inbred C57BL
Humans
*Glycolipids/metabolism
Lipid Metabolism/drug effects
Administration, Oral
Disease Models, Animal

@article {pmid41083999,
year = {2025},
author = {Holst, BS and Bonnevie, A and Spens, J and Lindahl, JF and Huupponen, A and Syrjä, P and Blomström, AL},
title = {Tick-borne encephalitis virus associated with foetal death in a bitch, a case report.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {326},
pmid = {41083999},
issn = {1743-422X},
mesh = {Animals ; Dogs ; Female ; Pregnancy ; *Dog Diseases/virology/pathology/diagnosis/transmission ; *Encephalitis Viruses, Tick-Borne/isolation & purification/genetics ; *Infectious Disease Transmission, Vertical/veterinary ; *Fetal Death/etiology ; *Encephalitis, Tick-Borne/veterinary/virology/transmission/pathology/diagnosis ; *Pregnancy Complications, Infectious/veterinary/virology ; Placenta/virology/pathology ; },
abstract = {BACKGROUND: For the first time, a case of vertical transmission of TBEV in a dog associated with foetal death is described.

CASE PRESENTATION: A six-year-old beagle bitch experienced foetal death from day 49 in pregnancy. A caesarean section was performed on day 56, and one live and three dead pups in different stages of resorption were delivered. Black mucoid, non-smelling foetal membranes surrounded the dead foetuses. The live-born foetus died despite efforts to save it and was sent for autopsy together with the placenta. Autopsy demonstrated lung atelectasis and no malformations. A mild acute necrotizing placentitis was diagnosed on histopathology. Selective bacteriological cultures for Brucella canis from blood, vagina and the foetus were all negative, as was PCR for canine herpes virus (CHV). Viral metagenomics analysis identified the presence of tick-borne encephalitis virus (TBEV) in the placental tissue and in situ hybridization revealed TBEV in the trophoblasts. The bitch had antibodies to TBEV. One year later, the bitch had a normal pregnancy and whelping.

CONCLUSION: With the spread of both ticks and TBEV, infection with TBEV should be given further consideration as a potential differential diagnosis in cases of foetal death in dogs.},
}

Animals
Dogs
Female
Pregnancy
*Dog Diseases/virology/pathology/diagnosis/transmission
*Encephalitis Viruses, Tick-Borne/isolation & purification/genetics
*Infectious Disease Transmission, Vertical/veterinary
*Fetal Death/etiology
*Encephalitis, Tick-Borne/veterinary/virology/transmission/pathology/diagnosis
*Pregnancy Complications, Infectious/veterinary/virology
Placenta/virology/pathology

@article {pmid41083440,
year = {2025},
author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P},
title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9069},
pmid = {41083440},
issn = {2041-1723},
support = {225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; },
abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Symbiosis
Phylogeny
Metagenome/genetics
*Evolution, Molecular
Biological Evolution

@article {pmid41082849,
year = {2025},
author = {Su, R and Zhu, L and He, X and Zhang, H and Huang, R and Zeng, J and Zhao, D},
title = {Denitrifying anaerobic methane oxidation reduces greenhouse gas emissions in floodplain sediments of the largest freshwater lake in China under flash drought.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127532},
doi = {10.1016/j.jenvman.2025.127532},
pmid = {41082849},
issn = {1095-8630},
abstract = {Climate change-induced extreme heat, flooding and drought events influence the carbon and nitrogen cycling, including the denitrifying anaerobic methane oxidation (DAMO) process which couples the nitrogen removal and methane (CH4) mitigation. To assess the impacts of 2022 record-breaking flash drought (summer FD) on the DAMO process, we collected bulk soils and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during summer FD and winter drought. The in situ CH4 fluxes and potential DAMO rates were determined using static-chamber technique and [13]C stable isotope method. The abundance, composition and metabolic pathways of DAMO archaeal and bacterial communities were investigated using quantitative PCR, high-throughput and metagenomic sequencing techniques. Higher DAMO rates (8.73 ± 3.79 and 16.03 ± 7.45 nmol [13]CO2 g[-1] d[-1] for nitrate-DAMO and nitrite-DAMO respectively) were observed during summer FD compared to winter drought, and nitrite-DAMO (52%∼74%) dominated the DAMO processes. DAMO bacterial pmoA genes (4.7 × 10[4]∼1.1 × 10[6] copies g[-1] dry soil) were more abundant than DAMO archaeal mcrA genes (1.4 × 10[3]∼1.3 × 10[4] copies g[-1] dry soil). Nitrate- and nitrite-DAMO rates were mainly driven by temperature, available nitrogen substrate and the abundance of DAMO archaea and bacteria, possibly contributing to CH4 consumption in the littoral wetlands of Poyang Lake. Several reconstructed metagenome-assembled genomes possessing genes involved in anaerobic methane oxidation and nitrate/nitrite reduction could potentially participate in cooperative DAMO process. This study elucidates the DAMO process and microbial mechanisms under flash droughts, providing a novel insight for the carbon-nitrogen coupling and mitigation of greenhouse gases in aquatic ecosystems.},
}

@article {pmid41082619,
year = {2025},
author = {Huang, PH and Liao, YC and Chen, FJ and Wu, HC and Liu, PY},
title = {Metagenomic Sequencing of Blood Culture Broth for Diagnosing Fastidious Endocarditis.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf554},
pmid = {41082619},
issn = {1537-6591},
}

@article {pmid41082531,
year = {2025},
author = {Mwasi, L and Khamadi, S and Bulimo, W and Kinyua, J and Yalwala, S and Sang, LP and Robert, H and Kellar, GG and Eads, J and Eyase, F},
title = {Identification and genetic characterization of Jingmen tick virus from ticks sampled in select regions of Kenya; 2022-2024.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0329878},
doi = {10.1371/journal.pone.0329878},
pmid = {41082531},
issn = {1932-6203},
mesh = {Animals ; Kenya/epidemiology ; Phylogeny ; *Ticks/virology ; *Flavivirus/genetics/isolation & purification/classification ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Cattle ; },
abstract = {Jingmen tick virus (JMTV), an emerging segmented RNA virus classified as an ungrouped flavivirus, poses a growing public health concern globally. Known for its association with febrile illnesses and wide host range, JMTV has been detected in Rhipicephalus, Hyalomma, and Amblyomma ticks collected from cattle, goats, sheep, camels, and chickens in pastoral regions of Kenya, including Baringo, Mandera, Malindi, Lamu, Mombasa, Wajir, Isiolo, and West Pokot. Using viral metagenomics next-generation sequencing, this study analysed adult ticks (n = 1629, 72 pools). A total of 53% (38/72) pools were positive for at least one viral pathogen, with JMTV detected in 87% (33/38) of these pools across all study sites. Phylogenetic analyses revealed evidence of distinct Kenyan JMTV strains, with sequence segments from Malindi and Wajir clustering uniquely in their own clade; suggesting potential localised evolutionary pressures. Time calibrated phylogeny for the segment 1(RdRp) suggested varied ancestral origins and evolutionary relationships for the JMTV strains. MEME, BUSTED and FUBAR methods implemented in the Data-Monkey, unanimously identified codon 290 in segment 1 and 30 in segment 4 to be undergoing episodic positive selection. Recombination analysis performed using the RDP4 recombination detection tool indicated a recombination event in segment 2 of the Lamu JMTV strain that was confirmed by seven detection methods of the RDP4 tool and visualised in BootScan. These findings suggest that Kenyan JMTV strains are undergoing positive selection, potentially driven by unique ecological and host factors. Segmented genome evidence of recombination highlights the increasing virus's potential for antigenic diversity. Host diversity and virus phylogenetic patterns underscore the zoonotic potential and its capacity for regional spread, emphasizing the critical need for enhanced vector surveillance. Temporal and ecological drivers like seasonal tick activity and livestock movement warrant investigation to elucidate JMTV transmission dynamics. Prioritizing tick-borne virus surveillance in Kenya will strengthen public health strategies and mitigates emerging viral risks.},
}

Animals
Kenya/epidemiology
Phylogeny
*Ticks/virology
*Flavivirus/genetics/isolation & purification/classification
Genome, Viral
High-Throughput Nucleotide Sequencing
Cattle

@article {pmid41082485,
year = {2025},
author = {Zhou, W and Zhang, D and Alhaskawi, A and Ezzi, SHA and Kota, VG and Abdulla, MHAH and Abdulla, AHAH and Abdalbary, SA and Lu, H and Liang, J},
title = {Rare Pathogen in Diabetic Foot Gangrene: A Case of Wohlfahrtiimonas chitiniclastica Infection.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {223},
pages = {},
doi = {10.3791/68877},
pmid = {41082485},
issn = {1940-087X},
mesh = {Humans ; Male ; Aged ; *Diabetic Foot/microbiology ; *Gangrene/microbiology ; *Gram-Negative Bacterial Infections/microbiology/diagnosis ; },
abstract = {Wohlfahrtiimonas chitiniclastica is a rare Gram-negative bacterium typically associated with wound infections, particularly in immunocompromised patients or individuals exposed to unsanitary conditions. Although clinical cases are infrequent, the infection can lead to severe complications such as bacteremia, septic shock, and even death if unrecognized or inadequately treated. We present the case of a 76-year-old diabetic male who developed chronic, non-healing foot ulcers complicated by gangrene and maggot infestation. Diagnostic challenges were addressed using metagenomic next-generation sequencing, which identified W. chitiniclastica alongside Proteus mirabilis and Corynebacterium striatum. Management included aggressive surgical debridement to remove necrotic tissue, local application of gentamicin-impregnated bone cement, systemic antibiotic therapy with ertapenem, and wound reconstruction using a dorsally based fascial flap. This combined approach resulted in significant clinical improvement, progressive wound healing, and marked reductions in infection markers. The case highlights the decisive role of advanced sequencing technologies in identifying rare pathogens within polymicrobial infections, where conventional methods such as MALDI-TOF mass spectrometry may fail. It also emphasizes the importance of integrating precision diagnostics with surgical intervention, targeted antimicrobial therapy, and rigorous postoperative care to achieve successful outcomes. By documenting this unusual presentation, we aim to expand clinical awareness of W. chitiniclastica infections and provide a practical framework for managing similarly complex diabetic foot infections.},
}

Humans
Male
Aged
*Diabetic Foot/microbiology
*Gangrene/microbiology
*Gram-Negative Bacterial Infections/microbiology/diagnosis

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

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

@article {pmid41081627,
year = {2025},
author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M},
title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173025},
doi = {10.1128/spectrum.01730-25},
pmid = {41081627},
issn = {2165-0497},
abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.},
}

@article {pmid41081605,
year = {2025},
author = {Lee, S and Kim, J and Mirdita, M and Gilchrist, CLM and Steinegger, M},
title = {Easy and interactive taxonomic profiling with Metabuli App.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf557},
pmid = {41081605},
issn = {1367-4811},
abstract = {SUMMARY: Accurate metagenomic taxonomic profiling is critical for understanding microbial communities. However, computational analysis often requires command-line proficiency and high-performance computing resources. To lower these barriers, we developed Metabuli App, an all-in-one desktop application that efficiently runs taxonomic profiling locally on a consumer-grade computer. It features user-friendly graphical interfaces for custom database curation, raw read quality control (QC), taxonomic profiling, and interactive result visualization.

GPLv3-licensed source code and prebuilt apps for Windows, macOS, and Linux are available at https://github.com/steineggerlab/Metabuli-App and are archived at https://doi.org/10.5281/zenodo.15876171. Analysis scripts are available at https://github.com/jaebeom-kim/metabuli-app-analysis. The Sankey-based taxonomy visualization component is available at https://github.com/steineggerlab/taxoview for easy integration into other web projects.},
}

@article {pmid41081506,
year = {2025},
author = {Jiang, C and Wu, Y and Qiu, C and Zhu, S and Zhang, Y and Shui, W},
title = {Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0034825},
doi = {10.1128/msphere.00348-25},
pmid = {41081506},
issn = {2379-5042},
abstract = {Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were Proteobacteria, Actinobacteria, and Acidobacteria; the dominant archaea were Crenarchaeota; and the dominant fungi were Ascomycota. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were CeoB, AcrB, and MexF. Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems.IMPORTANCECurrently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.},
}

@article {pmid41081392,
year = {2025},
author = {Rasmussen, AN and Langenfeld, K and Tolar, BB and Perzan, Z and Maher, K and Cardarelli, EL and Bargar, JR and Boye, K and Francis, CA},
title = {Floodplain nitrifiers harbor the genetic potential for utilizing a wide range of organic nitrogen compounds.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0082925},
doi = {10.1128/msystems.00829-25},
pmid = {41081392},
issn = {2379-5077},
abstract = {UNLABELLED: Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (ure) and at least one urea transporter (utp, urt, dur3). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase (cynS), nitrilase (nit1), omega-amidase (nit2), nitrile hydratase (nthA), and genes related to purine degradation, including biuret hydrolase (biuH), oxamic transcarbamylase (allFGH), and catabolic carbamate kinase (allK). AOA often encoded an uncharacterized amidohydrolase collocated with biuH, rather than allophanate hydrolase (atzF). A small number of AOA encoded atzF, functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes (trtA, biuH, and atzH), and in comammox, these genes were also collocated with allFGHK. The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members.

IMPORTANCE: Floodplains are critical ecosystems where terrestrial and riverine systems meet. Floodplain sediments experience many, sometimes dramatic, changes in moisture and oxygen concentrations because of changes in water table height, flooding, and drought, leading to active microbial cycling of contaminants and nutrients. Nitrogen is one such nutrient that is not only essential for the building blocks of life but can also be used as an energy source by some microorganisms. Microorganisms that oxidize ammonia and nitrite are a crucial part of the nitrogen cycle and can lead to eventual nitrogen loss from a system. Investigating the genes present in microorganisms responsible for nitrification in a dynamic floodplain suggests that organic nitrogen-from decaying plants or potentially other sources, such as fertilizers, grazing livestock feces, or contaminants (e.g., pesticides, pharmaceuticals)-is an important nitrogen source to these microorganisms. This study identifies genes not previously described in nitrifying microorganisms, expanding their potential metabolic substrates.},
}

@article {pmid41080808,
year = {2025},
author = {Zhang, Z and Huang, W},
title = {Exoskeleton Robot Gait Training and Its Impact on the Gut Microbiota-Brain Axis in Incomplete Spinal Cord Injury Patients: A Narrative Review of Rehabilitation Mechanisms.},
journal = {Journal of multidisciplinary healthcare},
volume = {18},
number = {},
pages = {6411-6430},
pmid = {41080808},
issn = {1178-2390},
abstract = {Exoskeleton robot-assisted gait training represents a significant advancement in neurorehabilitation for patients with incomplete spinal cord injury (iSCI). While its efficacy in improving motor function is increasingly documented, emerging evidence suggests these interventions may exert therapeutic effects through previously unrecognized physiological pathways involving the gut microbiota-brain axis. This review synthesizes current evidence regarding the bidirectional relationship between exoskeleton-based locomotor training and alterations in gut microbiome composition and function in the context of iSCI. Following spinal cord injury, significant dysbiosis occurs, characterized by reduced microbial diversity and altered taxonomic representation, which correlates with neuroinflammation, autonomic dysfunction, and impaired recovery. Exoskeleton-mediated gait rehabilitation appears to partially restore microbial homeostasis through multiple mechanisms, including autonomic nervous system regulation, altered intestinal transit time, modified intestinal barrier integrity, and immunomodulation. These microbiome modifications potentially facilitate neuroplasticity and functional recovery through microbiota-derived metabolites that traverse the blood-brain barrier or communicate via vagal afferents. The integration of metagenomic analysis with functional neuroimaging and detailed autonomic assessment in prospective studies represents a critical research direction. This emerging perspective extends beyond biomechanical rehabilitation, suggesting a comprehensive neurobiological effect that includes modulation of the microbiota-gut-brain axis, with significant implications for optimizing therapeutic strategies for individuals with incomplete spinal cord injury.},
}

@article {pmid41080802,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y},
title = {Metagenomic insights into viral dynamics and funcation in Baijiu.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101189},
pmid = {41080802},
issn = {2665-9271},
abstract = {Baijiu fermentation represents a sophisticated microbial-driven biochemical process mediated by complex microbial consortium. Despite extensive characterization of bacterial and fungal roles in fermentation systems, the virus remains a critical knowledge gap. In this study,we employed metagenomics to profile the dynamics of viral community in fermented grains across five stages (day 0, 5, 10, 20 and 30) of a Baijiu fermentation. The metagenomics revealed 101 viral families, dominated by Metaviridae, Parvoviridae, Aliceevansviridae, Herelleviridae, Geminiviridae, Iridoviridae, and Genomoviridae, and lactic acid bacteria was identified as primary phage hosts. The results revealed that ssRNA viruses and ssDNA viruses were more abundant during 0-5 days, dsDNA viruses became dominant during 10-30 days. Multivariate analysis indicated that the viral community dynamics during the fermentation were primarily governed by microbes in succession, environmental factors (temperature,pH, moisture and glucose) and metabolites (lactic acid, acetate and ethanol) in the biosystem. Notably, predicting phages exhibited strong positive correlations with their respective hosts (P < 0.01, r > 0.6). We have identified viral auxiliary metabolic genes (AMGs) related to amino acid metabolism and vitamin biosynthesis. At 30 days of fermentation, the number and abundance of AMGs significantly increased. Our findings provide novel insights into the viral ecology in complex Baijiu fermentation ecosystem, shedding light on the intricate interactions within fermentation microbial communities.},
}

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

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

@article {pmid41080528,
year = {2025},
author = {Wu, XT and Qiu, M and He, YQ and Wu, K and Zhao, JY and Wang, J and Ren, HY and Su, JY and Bao, P},
title = {Disproportionation of elemental sulfur by Exiguobacterium from marine sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf168},
pmid = {41080528},
issn = {2730-6151},
abstract = {Elemental sulfur disproportionation is an ancient microbial metabolic process, and the phylogenetic distribution of elemental sulfur disproportionators may be broader than previously thought. We enriched a bacterial community capable of this process, with Exiguobacterium making up 99.45% of the total population. The results indicate that Exiguobacterium facilitates the formation of thiosulfate and sulfide through elemental sulfur disproportionation. This study represents the first report documenting elemental sulfur disproportionation by Bacilli. Metagenomic analysis shows that rhodanese-like sulfur transferase genes are significantly more abundant in the experimental group than in the control group, suggesting that they are implicated in elemental sulfur disproportionation in Exiguobacterium. These findings support the idea that Bacilli and/or Firmicutes are the oldest extant bacterial phyla. Our research fills a critical gap in understanding sulfur biogeochemical cycles. Given the widespread occurrence of Exiguobacterium across various environments, direct microbial transformations between elemental sulfur and thiosulfate are likely prevalent throughout ecological systems.},
}

@article {pmid41080188,
year = {2025},
author = {Geniselli da Silva, V and Smith, NW and Mullaney, JA and Roy, NC and Wall, C and McNabb, WC},
title = {Mathematical models of the colonic microbiota: an evaluation of accuracy using in vitro fecal fermentation data.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1623418},
pmid = {41080188},
issn = {2296-861X},
abstract = {Traditional approaches for studying diet-colonic microbiota interactions are time-consuming, resource-intensive, and often hindered by technical and ethical concerns. Metagenome-scale community metabolic models show promise as complementary tools to overcome these limitations. However, their experimental validation is challenging, and their accuracy in predicting colonic microbial function under realistic dietary conditions remains unclear. This study assessed the accuracy of the Microbial Community model (MICOM) in predicting major short-chain fatty acid (SCFA) production by the colonic microbiota of weaning infants, using fecal samples as a proxy. Model predictions were compared with experimental SCFA production using in vitro fecal fermentation data at the genus level. The model exhibited overall poor accuracy, with only a weak, significant correlation between measured and predicted acetate production (r = 0.17, p = 0.03). However, agreement between predicted and measured SCFA production improved for samples primarily composed of plant-based foods: acetate exhibited a moderate positive correlation (r = 0.31, p = 0.005), and butyrate a trend toward a weak positive correlation (r = 0.21, p = 0.06). These findings suggest that the model is better suited for predicting the influence of complex carbohydrates on the colonic microbiota than for other dietary compounds. Our study demonstrates that, given current limitations, modeling approaches for diet-colonic microbiota interactions should complement rather than replace traditional experimental methods. Further refinement of computational models for microbial communities is essential to advance research on dietary compound-colonic microbiota interactions in weaning infants.},
}

@article {pmid41080146,
year = {2025},
author = {He, X and Yang, F and Qu, G and Zhang, H and Yi, M and Wang, X and Sun, S},
title = {Integrated microbial and proteomic analysis elucidates quality degradation mechanisms of fresh milk through the industrial processing stage.},
journal = {Food chemistry: X},
volume = {31},
number = {},
pages = {103062},
pmid = {41080146},
issn = {2590-1575},
abstract = {Fresh milk quality deterioration during processing is a major dairy challenge, with microbial-driven protein degradation mechanisms unclear. This study pioneers an integrated microbiome-proteome approach to systematically elucidate the dynamic interplay between microbial succession and protein quality changes during industrial processing. Microbial community analysis revealed oscillatory richness, with 2.3-fold and 1.8-fold increases during pre-treatment (PL) and refrigerated transport (RC), respectively. Pseudomonas (12.4 % → 31.7 %) and Acinetobacter (8.1 % → 19.3 %) dominated key phases, with proteomics showing significant nutrient loss (IgM: -69.8 %; IgG: -54.15 %). Integrating microbial metagenomics with proteolytic pathway analysis identified proteases from Pseudomonas and Acinetobacter as key drivers of protein degradation (68 % activity). Pasteurization cut microbial load by 82 % but paradoxically intensified nutrient loss via protein denaturation. Crucially, our data establish a time-dependent degradation model, revealing that combined microbial enzymatic action and thermal effects account for 76 % of total protein hydrolysis, providing a theoretical framework for developing targeted intervention strategies in dairy processing optimization.},
}

@article {pmid41079703,
year = {2025},
author = {Akinnola, OO and Samuel, AE and Omonhinmin, CA},
title = {Dataset on characterisation of microbiome of prostate tissue and expressed prostatic secretions.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112098},
pmid = {41079703},
issn = {2352-3409},
abstract = {Prostate cancer (PCa) is the second most prevalent cancer in men, particularly affecting those of Black African descent. Nigeria currently has the fourth highest risk for PCa mortality in the world. The microbiome of the prostate has emerged as a critical factor in understanding the aetiology and progression of prostate diseases, such as prostate cancer (PCa), benign prostatic hyperplasia (BPH) , benign stromal hyperplasia (BSH) and prostatitis (PRO). This study to comparatively characterise the microbiome present in prostate tissue and expressed prostatic secretion (EPS) from 30 study subjects diagnosed with PCa, BPH, BSH and PRO and sampled from the urology clinic of Lagos State University Teaching Hospital Ikeja. Bacterial species community composition and diversity were analysed based on 16S rRNA metagenome nucleotide data to ensure the accuracy, reproducibility, and broader applicability of microbiological and genomic research. Data information allows for precise identification of organisms at the species or strain level, essential for verifying experimental results and comparisons of the isolated organism's genome with related strains, providing insights into genetic diversity, virulence factors, and metabolic pathways of the sample population microbiome.},
}

@article {pmid41079637,
year = {2025},
author = {Tóth, AG and Nagy, SÁ and Lakatos, I and Solymosi, N and Stágel, A and Paholcsek, M and Posta, K and Gömbös, P and Ferenczi, S and Szőke, Z},
title = {Impact of mycotoxins and glyphosate residue on the gut microbiome and resistome of European fallow deer.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113539},
pmid = {41079637},
issn = {2589-0042},
abstract = {Some mycotoxins and herbicide residues pose threats to animal health. These toxins might affect the gut microbiome of fallow deer. The analyzation of the intestinal content samples of this valuable game species exposed to varying levels of zearalenone (ZEA) and other toxic compounds such as aflatoxin B1, deoxynivalenol, fumonisin B1, and glyphosate residues was performed. Metagenomic analysis revealed significant alterations in the bacterial community composition. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. Changes in the abundance of antibiotic resistance genes (ARGs) were also observed, suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.},
}

@article {pmid41079385,
year = {2025},
author = {van Ede, JM and van der Steen, S and van der Kraan, GM and van Loosdrecht, MCM and Pabst, M},
title = {Discovery of microbial glycoside hydrolases via enrichment and metaproteomics.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41079385},
issn = {2633-0679},
abstract = {The immense microbial diversity on Earth represents a vast genomic resource, yet discovering novel enzymes from complex environments remains challenging. Here, we combine a microbial enrichment with metagenomics and metaproteomics to facilitate the identification of microbial glycoside hydrolases that operate under defined conditions. We enriched microbial communities on the carbohydrate polymer pullulan at elevated temperatures under acidic conditions. Pullulan is a natural polysaccharide composed of maltotriose units linked by α-1,6-glycosidic bonds. Pullulan, along with its hydrolyzing enzymes, has broad applications across various industries. The enrichment inocula were sampled from thermophilic compost and from soil from the bank of a pond. In both cases, Alicyclobacillus was identified as the dominant microorganism. Metaproteomic analysis of the enriched biomass and secretome enabled the identification of several pullulan-degrading enzyme candidates from this organism. These enzymes were absent in the metagenomic analysis of the initial inoculum, which is highly complex with a wide diversity of species. This underscores the effectiveness of combining microbial enrichment with multi-omics for uncovering novel enzymes and sequence variants that operate under defined conditions from complex microbial environments.},
}

@article {pmid41078880,
year = {2025},
author = {Goudarzi, R and Jahanshahi, DA and Kavousi, A and Ariaeenejad, S},
title = {Discovery and engineering of bifunctional enzymes for lignocellulose degradation: Metagenomic and computational approaches.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {48},
number = {},
pages = {e00926},
pmid = {41078880},
issn = {2215-017X},
abstract = {Efficient degradation of lignocellulosic biomass is vital for converting plant-based waste into renewable fuels and chemicals. Owing to its complex composition of cellulose, hemicellulose, and lignin, its enzymatic breakdown often requires multiple enzymes to act synergistically. Bifunctional enzymes that combine two catalytic activities in a single protein offer a promising solution. This review highlights recent advances in the identification and engineering of bifunctional enzymes for lignocellulose degradation, particularly through metagenomics, protein fusion and computational design. Functional pairings, such as cellulase/xylanase, were examined with a focus on their synergistic effects, substrate specificity, and stability. Promiscuous and naturally evolved bifunctional enzymes from extreme or uncultured environments are also discussed. Advances in silico modeling and directed evolution have enhanced enzyme properties such as thermostability and substrate range. The review concludes with an outlook on the challenges and opportunities of implementing bifunctional enzymes to improve the economic and technical viability of biomass conversion.},
}

@article {pmid41078518,
year = {2025},
author = {Liu, J and Wang, L and Su, L and Chen, J and Su, R},
title = {Exploring the gut microbiota-Parkinson's disease link: preliminary insights from metagenomics and Mendelian randomization.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654418},
pmid = {41078518},
issn = {1664-302X},
abstract = {INTRODUCTION: The relationship between the gut microbiome and Parkinson's disease (PD) has recently attracted significant attention, with most studies focused on analyzing microbial composition. However, our understanding of the potential causal relationship between the gut microbiota and PD remains limited.

METHODS: We extracted microbiome data from the metagenome for broad taxonomic coverage and accurate functional analysis. Subsequently, Mendelian randomization was employed to elucidate the causal relationship between the gut microbiome and PD.

RESULTS: The gut microbiota in PD patients was found to be systemically imbalanced, characterized by an abnormal enrichment of potential pathogenic bacteria, a significant reduction in key beneficial bacteria, and a reorganization of intestinal metabolic functions. This state of imbalance involves significant abnormalities in multiple metabolic and regulatory pathways, including the glucose metabolism, oxidative stress response, protein homeostasis regulation, and immune signaling pathways. These findings suggest that dysbiosis may influence host neural function through multilevel metabolic interventions. Additionally, specific microbial communities are clearly associated with disease risk, with some bacterial populations promoting disease onset and others demonstrating a potentially protective effect. Although metagenomic findings require validation in larger cohorts, the results of this study indicate that changes in gut microbiota composition and function are closely related to PD onset and progression.

CONCLUSION: This study revealed that certain microorganisms traditionally considered beneficial may contribute to PD risk. This finding challenges previous assumptions and highlights the complexity of host-microbiome interactions. The identification of altered metabolic and immune pathways, particularly those involving bacteria that produce short-chain fatty acids, underscores the critical role of the gut microbiota in PD pathophysiology. However, the relatively small sample size of the current metagenomic analysis limits the generalizability of these findings. Larger, more diverse cohorts are needed to validate these results. Despite this limitation, the study provides important insights into microbiome-targeted therapeutic strategies, emphasizing the need to reconsider the roles of both beneficial and harmful microorganisms in PD.},
}

@article {pmid41078512,
year = {2025},
author = {Li, Y and You, J and Liao, Y and Wang, D and Wang, H and Su, Y},
title = {Daily fluctuation of genus Prevotella in porcine colon under ad libitum feeding and its association with nutrient substrates.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1688301},
pmid = {41078512},
issn = {1664-302X},
abstract = {The circadian rhythms of the gut microbiota are biologically significant for the host. However, the association between fluctuations in the relative abundance of the microbiota and nutrient substrates in the gut remains incompletely understood. Using swine as a model, this study employed continuous sampling at 9 time points over 24 h via a colonic T-shaped fistula. It investigated the temporal dynamics of nutrient substrates and Prevotella abundance in the colon of pigs over a 24-h period and further explored dynamic interactions among KEGG level-3 pathways, genes, and Prevotella using metagenomic approaches. Results revealed a significant 24-h periodicity in Prevotella abundance, peaking at T06-T09 and declining to minimal levels at T18-T21, with the nadir at T18. Dynamic correlation network analysis uncovered significant temporal associations between Prevotella rhythms and nutrient substrates: negative correlations with true protein (TP) and ammonia nitrogen (NH3-N), in contrast to positive correlations with starch and cellulose, exhibiting time lags ranging from -2 to 4 h. Prevotella copri exhibited high relative abundance and pronounced daily fluctuations, while Prevotella sp. MGM2 showed relatively high abundance but lacked daily fluctuations. Furthermore, differences existed in the dynamic correlations of genes and KEGG level-3 metabolic pathways of these two Prevotella species with nutrient substrates. The results revealed that the two Prevotella species in the colon exhibited different response strategies to nutrient substrates: Prevotella copri likely adopted a "rhythmic substrate-responsive strategy," while Prevotella sp. MGM2 followed a "sustained response strategy," which may explain their distinct daily fluctuations.},
}

@article {pmid41078511,
year = {2025},
author = {Ren, G and Shi, W and Li, W and Wang, J and Wang, C and Zhao, G},
title = {Pyrolysis temperature shapes biochar-mediated soil microbial communities and carbon-nitrogen metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1657149},
pmid = {41078511},
issn = {1664-302X},
abstract = {INTRODUCTION: Biochar derived from agricultural residues has potential to improve soil quality and regulate microbial communities, but its effect depends strongly on pyrolysis temperature.

METHODS: In this study, biochar prepared from Flammulina velutipes residue at 200 °C, 300 °C, and 400 °C was applied to cucumber seedling cultivation to evaluate its influence on soil physicochemical properties, microbial community structure, and functional metabolism.

RESULTS: Results showed that soil pH increased significantly with biochar addition, from 5.00 in the control to 6.17 at 400 °C, while soil organic matter reached the highest level in the 400 °C treatment (90.03 g·kg[-1]). Available phosphorus and potassium were also enhanced, with maximum values of 731.81 mg·kg[-1] and 481.68 mg·kg[-1], respectively. Seedling growth responded differently to pyrolysis temperatures: the 300 °C biochar treatment increased above-ground biomass to 0.18 g and total biomass to 0.214 g per plant, significantly higher than the control (0.124 g). Metagenomic sequencing revealed shifts in dominant microbial phyla, with Acidobacteriota enriched at higher temperatures, and alpha diversity indices (Chao1, ACE, Sobs) increased under 400 °C biochar. Functional analysis indicated that carbon metabolic genes (e.g., acetyl-CoA synthesis, TCA cycle) were optimized at moderate to high temperatures, whereas nitrogen metabolism showed divergent responses, with nitrate reduction favored at 300 °C and nitrite reduction at 400 °C. Regression analysis demonstrated a positive correlation between microbial diversity and carbon metabolism genes (R [2] = 0.75), but a negative correlation with nitrogen metabolism genes (R [2] = 0.56). Redundancy analysis further identified ammonium nitrogen, acid phosphatase, and catalase as key drivers of microbial community and functional gene structure.

DISCUSSION: Overall, these findings highlight that biochar from mushroom residue, particularly produced at 300-400 °C, improves soil fertility, regulates microbial community composition, and modulates carbon and nitrogen metabolic processes, thereby enhancing cucumber seedling growth.},
}

@article {pmid41078118,
year = {2025},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70379},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}

@article {pmid41078079,
year = {2025},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70102},
pmid = {41078079},
issn = {1398-9995},
support = {/NH/NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; //Massachusetts General Hospital/ ; //the Harvard University William F. Milton Fund/ ; //American Lung Association Innovation Award/ ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.

METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age < 1 year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24 h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR] < 0.05), regions (mbDMRs, FDR < 0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6 years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR < 0.10).

RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).

CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}

@article {pmid41077897,
year = {2025},
author = {Rachtman, E and Jiang, Y and Mirarab, S},
title = {Machine Learning Enables Alignment-Free Distance Calculation and Phylogenetic Placement Using k-Mer Frequencies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70055},
doi = {10.1111/1755-0998.70055},
pmid = {41077897},
issn = {1755-0998},
support = {2137603//National Science Foundation (ACCESS Program)/ ; 2138259//National Science Foundation (ACCESS Program)/ ; 2138286//National Science Foundation (ACCESS Program)/ ; 2138296//National Science Foundation (ACCESS Program)/ ; 2138307//National Science Foundation (ACCESS Program)/ ; ACI-1540112//National Science Foundation (NRP/Natulius Program)/ ; CNS-2100237//National Science Foundation (NRP/Natulius Program)/ ; ACI-1541349//National Science Foundation (NRP/Natulius Program)/ ; CNS-1730158//National Science Foundation (NRP/Natulius Program)/ ; CNS-2120019//National Science Foundation (NRP/Natulius Program)/ ; OAC-1826967//National Science Foundation (NRP/Natulius Program)/ ; OAC-2112167//National Science Foundation (NRP/Natulius Program)/ ; 1R35GM142725/NH/NIH HHS/United States ; //Minderoo Foundation/ ; //Schmidt Foundation/ ; },
abstract = {A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between long query sequences and reference genomes. Our proposed method, kf2vec, requires no alignment and can work on any region of the genome (needs no marker genes), thus simplifying analysis pipelines. A rich literature exists on using short k-mers frequencies to measure distances that correlate with phylogeny. Existing methods, however, have had moderate practical success despite enjoying strong theory. Instead of using predefined metrics, we train a deep neural network to estimate a distance from k-mer frequency vectors such that those distances match the path lengths on the reference phylogeny. The trained model is then used to characterise new samples. We demonstrate that kf2vec outperforms existing k-mer-based approaches in distance calculation and allows accurate phylogenetic placement and taxonomic identification of new samples from various types of long sequences.},
}

@article {pmid41077635,
year = {2025},
author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , },
title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.},
journal = {Comprehensive Physiology},
volume = {15},
number = {5},
pages = {e70058},
doi = {10.1002/cph4.70058},
pmid = {41077635},
issn = {2040-4603},
support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.

METHODS: We performed metagenomic whole genome sequencing (mWGS; > 25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.

RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p = 0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p = 0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p = 0.05) but reduced compared to healthy individuals (0.20; p < 0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p = 0.06) and healthy (0.01; p = 0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.

CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Renal Insufficiency, Chronic/microbiology
*Acute Kidney Injury/microbiology
Metagenomics/methods
Precision Medicine/methods
Female
Male
Middle Aged
Adult
Feces/microbiology

@article {pmid41077176,
year = {2025},
author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R},
title = {Microbiome Signatures and Their Role in Uveitis: Pathogenesis, Diagnostics, and Therapeutic Perspectives.},
journal = {Progress in retinal and eye research},
volume = {},
number = {},
pages = {101409},
doi = {10.1016/j.preteyeres.2025.101409},
pmid = {41077176},
issn = {1873-1635},
abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.},
}

@article {pmid41076761,
year = {2025},
author = {Jin, Y and Ping, J and Huang, X and Dai, J and Wang, X and Wang, S},
title = {Nanoscale zero-valent iron coupled with microorganisms enhances the removal of organochlorine pesticides in groundwater: Insights from the role of cascading effects and horizontal gene transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124745},
doi = {10.1016/j.watres.2025.124745},
pmid = {41076761},
issn = {1879-2448},
abstract = {Nanoscale zero-valent iron (nZVIs) represent a promising approach for the remediation of organic chlorine-contaminated groundwater. However, the interaction between nZVIs and indigenous dechlorinating microorganisms is complex, which may have unpredictable effects on the dechlorination of organic chlorine, necessitating further investigation. In this study, we investigated an abandoned pesticide factory in southwest China, combined with microcosm experiment to reconstruct the metabolic pathway of biological dechlorination, and quantified the functional contribution of dechlorination genes and microorganisms. The results showed that the combined treatment of nZVIs and microorganisms significantly enhanced the degradation efficiency of HCHs, DDTs, and their six isomers, achieving removal rates of up to 99 % for HCHs and 87.73 % for DDTs. The concentrations of Cl[-] and Fe[2+] had a direct positive effect on the enrichment of microbial communities harboring HCHs degradation genes. Haloalkane dehalogenase encoded by the dhaA gene was identified as a key enzyme in the degradation of β-HCH precursors, which not only promoted the growth of facultative dehalogenators (particularly Acidovorax and Methyloversatilis) but also enhanced overall dechlorination activity. Importantly, we successfully reconstructed 7 near-complete bacterial metagenome-assembled genomes (MAGs) carrying the dhaA gene, representing taxonomically diverse novel dechlorinating microorganisms. Additionally, nZVIs significantly increased the abundance of mobile genetic elements (MGEs), with 17 MGEs detected within scaffolds harboring dhaA in the 7 MAGs. Integrases and transposases were identified as key drivers facilitating the spread of dhaA. This finding was supported by the shift of dhaA-harboring hosts, and by the incongruent evolutionary patterns observed between the genome-based tree and the dhaA protein phylogenetic tree. To be specific, cascading effects and horizontal gene transfer synergistically promoted the proliferation of dechlorinating microbes, providing novel strategies for managing and remediating organic chlorine-contaminated ecosystems.},
}

@article {pmid41076729,
year = {2025},
author = {Burdon, IA and Psaltis, AJ},
title = {Changes in the sinus microbiome in health and chronic rhinosinusitis.},
journal = {Current opinion in otolaryngology & head and neck surgery},
volume = {},
number = {},
pages = {},
pmid = {41076729},
issn = {1531-6998},
abstract = {PURPOSE OF REVIEW: This article synthesises the recent sinus microbiome literature, identifying common themes in research findings as well as surveying the varied methodological approaches used across these studies.

RECENT FINDINGS: While there remains no clear consensus as to which microbes define dysbiosis in chronic rhinosinusitis (CRS), certain trends are emerging. Increasingly, the evidence points towards a pathogenic role in the overabundance of Moraxella, Haemophilus and Pseudomonas species, whilst the genera Cutibacterium, Anaerococcus and Dolosigranulum tend towards commensalism. However, the roles of the most common genera in the sinus microbiome, Staphylococcus and Corynebacterium, remain uncertain. Given the diversity and abundance of species within these genera, species and function-level analyses are needed to clarify their contributions to the aetiopathogenesis of CRS. Comprehensive study of the sinus microbiome in healthy individuals further shows that community composition shifts with age, suggesting that dysbiosis may manifest differently across the lifespan. Beyond bacteria, growing evidence highlights the importance of fungi and viruses, underscoring the need to incorporate these microbionts into future analyses.

SUMMARY: Progress towards a clinically meaningful consensus will require standardised approaches to sequencing, species-level resolution in these analyses, and consideration of the heterogeneous clinical and immunological subgroups of CRS.},
}

@article {pmid41075638,
year = {2025},
author = {Yin, D and Wang, K and Sun, S},
title = {Efficient sulfide bio-chemical removal by different crystalline FeOOH (α, β, γ, δ and amorphous) in sewers.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140072},
doi = {10.1016/j.jhazmat.2025.140072},
pmid = {41075638},
issn = {1873-3336},
abstract = {H2S corrosion in sewers causes huge economic losses. However, effective control solutions have remained lacking for decades. This study proposes FeOOH as a long-lasting and cost-effective alternative to iron salts for H2S control in sewers. The effect of FeOOH crystalline structures, electrochemical activity, acid and thermal stability, and surface morphology on S and Fe microbial redox were investigated. δ-FeOOH exhibited nearly 100 % H2S removal efficiency and the highest S[2-] removal capacity of 369.6 mg S/g FeOOH (1.10 mol S/Fe) followed by α-, AMO-, β- and γ-FeOOH. α-FeOOH treatment showed the highest FeS-S precipitation (304.2 mg S/g) and longest duration for sulfide control. This was contributed to α-FeOOH's low surface area and high structure stability. SO4[2-]-S bio-reduction inhibition was highest in δ-FeOOH (92.4 mg S/g), attributed to its highest Fe(Ⅲ)/Fe(Ⅱ), abundant sulfide oxidation genes (fccB, soxY and SUOx), and minimal electron transfer resistance. Moreover, sewer microbes enhanced the sulfide removal capacity of FeOOH by up to 6.0 times. FeOOH redirected microbial electron transfer away from SO4[2-] reduction and formed hydrogen bond with proteins that influenced SO4[2-] transport and uptake. This study provides comprehensive insights into the impact of FeOOH crystalline structure on microbial sulfur metabolism and electron transfer in sewers.},
}

@article {pmid41075532,
year = {2025},
author = {Ghafoor, D and Hayakijkosol, O and Prasetsincharoen, N and Chen, CCM and Noman, M and Chomchat, P and Kinobe, R},
title = {Characterisation of the gut microbiome and surveillance of antibiotic resistance genes in green sea turtles (Chelonia mydas).},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107605},
doi = {10.1016/j.marenvres.2025.107605},
pmid = {41075532},
issn = {1879-0291},
abstract = {Green sea turtles (Chelonia mydas) are globally endangered marine herbivores that maintain the health of seagrass and coastal ecosystems. Their populations are declining due to human activities, including environmental pollution, which can disrupt gut microbial communities and compromise nutrition, immunity, and overall health. In this study, cloacal swabs from 139 green sea turtles categorised as captive juveniles, captive adults and wild stranded animals in the Gulf of Thailand, were analysed via shotgun metagenomic sequencing to elucidate bacterial taxonomic diversity and ARG profiles. In captive juveniles, Pseudomonadota was the most abundant phylum, followed by Ascomycota and Basidiomycota. In captive adults, Pseudomonadota exhibited an even greater predominance, with only minor contributions from unclassified bacteria and other taxa. In wild stranded green sea turtles, Pseudomonadota was dominant in their gut microbiome, but this was accompanied by notable levels of Actinomycetota, Bacteroidota, and Bacillota. Stranded turtles exhibited highest microbial diversity and variability, while captive adult turtles showed the lowest. Resistome profiling also revealed significant differences in the relative abundance of antibiotic resistance genes across all three groups. MacB (macrolide resistance) was the most abundant gene overall, with the highest abundance observed in juveniles (4.8 %). Stranded turtles exhibited elevated levels of TetA(58) (tetracycline resistance, 2.6 %) and msbA (nitroimidazole resistance, 2.2 %), while adults showed the greatest enrichment of Ecol_fabG_TRC (triclosan resistance, 3.8 %) and TxR (tetracycline resistance, 3.6 %). These data demonstrate that marked variability existed in the gut microbiome and resistome of green sea turtles across different life stages in captive or wild environments. This offers critical insights for the development of targeted conservation strategies and health management practices for both wild and captive green sea turtles. Strategies to mitigate the spread of antibiotic resistance should be developed.},
}

@article {pmid41073934,
year = {2025},
author = {Zhu, X and Yan, J and Lai, X and Chen, M and Wang, Q},
title = {Hematogenous pulmonary abscess and septicemia due to infection with hypervirulent Pseudomonas aeruginosa in a nonimmunodeficient adolescent: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1280},
pmid = {41073934},
issn = {1471-2334},
support = {No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.LGF22H190004//Basic Public Welfare Research Project of Zhejiang Province, China/ ; No.2022KY927//, Health Science and Technology Planning Project of Zhejiang Province, China/ ; },
abstract = {BACKGROUND: Pseudomonas aeruginosa is a non-glucose-fermenting gram-negative bacillus and an opportunistic pathogen that typically causes localized or systemic infections in immunocompromised middle-aged and elderly individuals or children with congenital immune deficiencies. However, cases of pulmonary abscess with severe sepsis in normal individuals are rare and should be taken seriously.

CASE PRESENTATION: A 15-year-old nonimmunodeficient adolescent was hospitalized due to high fever and other clinical symptoms. The patient was diagnosed with a pulmonary abscess with severe sepsis. Etiological Examination showed that sensitive Pseudomonas aeruginosa. Subsequent inspection revealed this clinical isolate produces virulence factors ExoA and Pyocyanin, which was highly virulent. The patient’s symptoms were improved after imipenem (IPM) treatment and discharged. At follow-up 3 months later, he had recovered well.

CONCLUSIONS: We report a case of a pulmonary abscess with severe sepsis caused by Pseudomonas aeruginosa in an immunocompetent patient. Compared with the vast majority of infections caused by P. aeruginosa, this patient was younger and had no immunodeficiency or basic diseases, and the characteristics of the lesions were also unique. For this P. aeruginosa isolate, the testings of antimicrobial drugs were generally sensitive, and the virulence factors ExoA and Pyocyanin by quantitative metagenomics next-generation sequencing may be the main factors for the severity.},
}

@article {pmid41075379,
year = {2025},
author = {Pichler, I and Krischer, E and Obenhuber, T and Hirsch, B and Reinhold, I and Wiedmer, C and Ziltener, G and Weller, D and Roth, P and Weiss, T and Kufner, V and Bloemberg, GV and Trkola, A and Müller, NJ and Huber, M},
title = {Viral metagenomic sequencing reveals rare pathogens and improves diagnostic accuracy in neuroinflammatory disorders.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117140},
doi = {10.1016/j.diagmicrobio.2025.117140},
pmid = {41075379},
issn = {1879-0070},
abstract = {BACKGROUND: Neuroinflammatory disorders are frequently of unknown aetiology. Unbiased metagenomic next-generation sequencing of cerebrospinal fluid could help bridge the current diagnostic gap by identifying more infectious pathogens inducing central nervous system disorders. This study examined the advantages of adding viral metagenomics to standard testing procedures.

METHODS: Patients presenting with symptoms indicative of a neuroinflammatory disorder were enrolled at a Swiss tertiary care hospital through prospective and retrospective recruitment. Participants were diagnosed with infectious or autoimmune neuroinflammatory disorders based on the results of routine diagnostics and viral metagenomic sequencing.

RESULTS: Of the 70 study participants, 50 were classified as having an infectious disorder. Among these, a total of 37 pathogens were identified in 29 individuals (56 %), including 32 viral, three bacterial, one fungal, and one prion infection. Conventional virus testing and viral metagenomic sequencing produced the same positive and negative results for 13 and 21 cases, respectively. This resulted in an overall percent agreement of 59 %. Disparate viral results were observed in 19 cases. Ten cases were detected only by conventional testing, and nine were detected only by viral metagenomics. Notably, we report the detection of Toscana virus by viral metagenomic sequencing, a relatively rare pathogen in Switzerland that is not routinely screened for, underscoring the advantages of integrating viral metagenomics with conventional testing.

CONCLUSIONS: Viral metagenomic sequencing as a first-line diagnostic tool in combination with conventional methods yields the most comprehensive results to diagnose patients with infectious neuroinflammatory disorders. Its unbiased approach enables the detection of rare or unconsidered viruses.},
}

@article {pmid41075335,
year = {2025},
author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF},
title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.},
journal = {Research in veterinary science},
volume = {196},
number = {},
pages = {105930},
doi = {10.1016/j.rvsc.2025.105930},
pmid = {41075335},
issn = {1532-2661},
abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.},
}

@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}

Humans
Adolescent
*Dysbiosis/microbiology
Female
Male
*Mouth/microbiology
*Obesity/microbiology
Microbiota/genetics
Saliva/microbiology
Body Mass Index
Kuwait

@article {pmid41074769,
year = {2025},
author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS},
title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf216},
pmid = {41074769},
issn = {1751-7370},
abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.},
}

@article {pmid41074341,
year = {2025},
author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z},
title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117155},
doi = {10.1016/j.foodres.2025.117155},
pmid = {41074341},
issn = {1873-7145},
mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; },
abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.},
}

*Taste
China
*Hot Temperature
*Wine/microbiology/analysis
Odorants/analysis
*Food Microbiology
Bacteria/classification/genetics/metabolism
Metagenomics
Microbiota
Fermentation
Humans

@article {pmid41073968,
year = {2025},
author = {Onohuean, H and Choonara, YE},
title = {Epidemiological distribution of bacterial meningitis infections in South Africa: a systematic review and meta-analysis.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1284},
pmid = {41073968},
issn = {1471-2334},
mesh = {Humans ; South Africa/epidemiology ; *Meningitis, Bacterial/epidemiology/microbiology ; Prevalence ; Child ; Adolescent ; Child, Preschool ; Female ; Male ; Adult ; Infant ; Middle Aged ; Young Adult ; },
abstract = {Scientific evidence from public health findings can enhance the management, treatment, and prevention policies for bacterial meningitis (BM) infections. However, comprehensive epidemiological data on BM prevalence in South Africa is limited. We aimed to assess the prevalence and characteristics of laboratory-confirmed BM cases at the national population level. Using PRISMA standards, we retrieved data from electronic databases and selected reference articles. Out of 115,626 participants, 57,964 (50.13%) were infected with BM, with the highest prevalence (7.67%) in the age group 6-17 years. Our meta-analysis of 19 studies revealed an overall pooled prevalence of 38.01%, 95% confidence interval (CI: 0.26-0.50), with significant heterogeneity (I[2] = 99.86%, Q = 13117.45, p < 0.0001). The Egger test indicated publication bias (z = 3.4977, p = 0.0005). Subgroup analyses showed a higher prevalence in studies with sample sizes over 1000 (60.22%, 95% CI: 0.3899-0.7819, I[2] = 99.92%), over long study years (37.50%, 95% CI: 0.2642-0.5005, I[2] = 99.84%), cross-sectional study design (58.69%, 95%CI: 0.4906-0.6770, I2 = 99.72%), and particularly in Gauteng province (60.42%, 95% CI: 0.4539-0.7371, I[2] = 98.45%). The infectious types included Listeria (83.33%, 95% CI: 0.1936-0.9905, I[2] = 0.00%) and Neisseria (62.64%, 95% CI: 0.6126-0.6400, I[2] = 0.00%). Significant heterogeneity was noted in study design (R[2] = 52.93%, p < 0.0001), sample size (R[2] = 0.00%, p = 0.0117), and province (R[2] = 0.0%, p < 0.0001). These findings underscore a high prevalence of BM infections in South Africa's epidemiological landscape, highlighting the urgent need for targeted surveillance for effective prevention and treatment strategies.},
}

Humans
South Africa/epidemiology
*Meningitis, Bacterial/epidemiology/microbiology
Prevalence
Child
Adolescent
Child, Preschool
Female
Male
Adult
Infant
Middle Aged
Young Adult

@article {pmid41073886,
year = {2025},
author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y},
title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {658},
pmid = {41073886},
issn = {1471-2180},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration & dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.},
}

Animals
Cattle/growth & development/microbiology
Rumen/microbiology/metabolism
*Creatine/pharmacology/administration & dosage
Metabolomics
Metagenomics
Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Animal Feed/analysis
*Pyruvic Acid/pharmacology
Bacteria/genetics/classification/metabolism

@article {pmid41073868,
year = {2026},
author = {Leoni, C and Marzano, M and Filomena, E and D'Erchia, AM},
title = {Digital Droplet PCR (ddPCR) for Absolute Quantification of 16S rRNA Copy Number in Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2969},
number = {},
pages = {235-247},
pmid = {41073868},
issn = {1940-6029},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Gene Dosage ; DNA Copy Number Variations ; Fluorescent Dyes/chemistry ; },
abstract = {Digital Droplet PCR (ddPCR) is a quantitative PCR method that offers high sensitivity and accuracy in measuring the amount of nucleic acid in a sample, without the need of a standard curve. In ddPCR, a single sample is partitioned into up to 20,000 droplets, using the water-oil emulsion technology, and the amplification reaction occurs within each droplet using a fluorescent hydrolysis probe (Taqman) or a DNA-binding fluorescent dye. Following PCR, the emitted signals are individually measured in each droplet. Here, we describe a ddPCR optimized protocol for accurately quantifying the total copy number of the 16S rRNA gene in a metagenomic DNA sample. The protocol utilizes a primer pair, targeting the 16S V5-V6 hypervariable regions, in combination with a double-strand DNA-binding fluorescent dye.},
}

*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Polymerase Chain Reaction/methods
*Gene Dosage
DNA Copy Number Variations
Fluorescent Dyes/chemistry

@article {pmid41073663,
year = {2025},
author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF},
title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41073663},
issn = {2058-5276},
support = {K01-DK102771//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; },
abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.},
}

@article {pmid41073345,
year = {2025},
author = {Guo, WB and Wang, TT and Song, ZK and Liu, QY and Sun, JJ},
title = {[One case of occupational pulmonary anthrax].},
journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases},
volume = {43},
number = {9},
pages = {705-707},
doi = {10.3760/cma.j.cn121094-20240719-00326},
pmid = {41073345},
issn = {1001-9391},
mesh = {Humans ; *Anthrax ; Male ; Bacillus anthracis ; *Occupational Diseases ; *Anthracosis ; Adult ; },
abstract = {Pulmonary anthrax is an acute zoonotic infectious disease caused by Bacillus anthracis infecting the human body. Humans can be infected by coming into contact with diseased animals and their products or by consuming diseased animals. According to the different infection routes, it can be classified into cutaneous anthrax, pulmonary anthrax and intestinal anthrax, etc. Among them, cutaneous anthrax is the most common, while case reports of pulmonary anthrax are rare. This article analyzes the clinical data of a case of occupational pulmonary anthrax diagnosed by metagenomic next-generation sequencing (mNGS) and successfully treated, so as to provide a reference for the clinical treatment of pulmonary anthrax.},
}

Humans
*Anthrax
Male
Bacillus anthracis
*Occupational Diseases
*Anthracosis
Adult

@article {pmid41072965,
year = {2025},
author = {Odukwe, C and Abdelrahman, A and Zaidi, AN and Love, B and El-Hamamsy, I and Ghesani, M and Hopkins, KA},
title = {Culture-Negative Transcatheter Pulmonary Valve Endocarditis.},
journal = {JACC. Case reports},
volume = {30},
number = {31},
pages = {105324},
doi = {10.1016/j.jaccas.2025.105324},
pmid = {41072965},
issn = {2666-0849},
abstract = {CLINICAL CONDITION: We present a case of transcatheter pulmonary valve endocarditis in a 38-year-old woman with a history of atrial septal defect, pulmonary stenosis, and bicuspid aortic valve, all previously repaired with mechanical and bioprosthetic valve replacements. Despite negative initial studies, [18]F-fluorodeoxyglucose positron emission tomography-computed tomography revealed septic pulmonary emboli and abnormal uptake at the pulmonary valve. Metagenomic sequencing identified Haemophilus parainfluenzae as the pathogen.

KEY QUESTIONS: What is the differential diagnosis of a cardiac mass in this context? How should imaging and laboratory testing be approached in prosthetic valve endocarditis with negative studies? What surgical factors matter in patients with prior cardiac repairs?

OUTCOME: The patient underwent successful replacement of the pulmonary and aortic valves and completed a course of antibiotics, with full recovery.

TAKE-HOME MESSAGE: Consider bioprosthetic valve endocarditis in patients with persistent fevers and negative cultures. Use advanced diagnostics early when the clinical suspicion is high.},
}

@article {pmid41072853,
year = {2025},
author = {Li, Y and Sun, C and Zhao, T and Ni, Y and Liu, Q and Song, M and Xu, X and Sun, W and Li, Y and Zhou, J and Li, D and Zhang, Q and Feng, C and Shi, J and Cao, M and Huang, B and Su, N and Lu, X and Wang, L and Lei, J and Sang, L and Zhou, W and Cai, X and Wang, J and Wang, Y and Cai, Y and Lu, Y and Zhong, J and Su, X},
title = {Etiology of Initial Treatment Failure in Non-immunosuppressed Adult Patients with Community-acquired Pneumonia.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108110},
doi = {10.1016/j.ijid.2025.108110},
pmid = {41072853},
issn = {1878-3511},
abstract = {OBJECTIVES: Initial treatment failure (ITF) of community-acquired pneumonia (CAP) is a significant clinical problem. The study aimed to explore the etiology of ITF using metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), and to provide optimized management strategies for patients with CAP.

METHODS: From June 2022 to August 2024, we conducted a prospective, multicenter study in 15 hospitals of non-immunosuppressed adult CAP patients with ITF in Jiangsu Province, China. Conventional microbiological tests (CMTs), mNGS, and tNGS were applied to detect microorganisms in bronchoalveolar lavage fluid.

RESULTS: ITF was mainly caused by responsible pathogens not covered by initial treatment (59.0%) despite the high compliance with guideline-recommended regimens. The top 5 responsible pathogens were Chlamydia psittaci (21.5%), Mycoplasma pneumoniae (16.7%), influenza virus (14.6%), SARS-CoV-2 (8.3%), and Pseudomonas aeruginosa (6.3%). The positive pathogen identification rate for mNGS and tNGS was 74.4% and 72.7%, respectively, while for CMTs it was 12.2%. Based on NGS results, treatment was optimized in 53.5% of patients, and 95.8% were improved or cured.

CONCLUSIONS: Atypical pathogens and viruses not covered by empirical treatment regimens were the main causes of ITF. mNGS and tNGS outperformed CMTs in identifying responsible pathogens and could optimize the treatment of patients with ITF.},
}

@article {pmid41072822,
year = {2025},
author = {Chen, Z and Zhang, J and Lin, L and Sun, Y and Li, XY and Li, B},
title = {Enhanced fermentation for lactic acid production from food waste via hydrothermal pretreatment: performance evaluation and metagenomic analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133456},
doi = {10.1016/j.biortech.2025.133456},
pmid = {41072822},
issn = {1873-2976},
abstract = {Mixed-culture lactic acid fermentation of food waste (FW) commonly requests low pH conditions. However, this can pose the challenge of insufficient substrate hydrolysis. To address this, we investigated hydrothermal pretreatment coupled with centrifugal supernatant recovery as a technical strategy to enhance the FW hydrolysis and lactic acid production. The study characterized the supernatant substrate after the pretreatment at different temperatures (80-140 °C), focusing on organic solubilization, supernatant-solid separation for organic recovery, grease removal, and subsequently evaluated lactic acid production in 8-day batch fermentation. The results showed that hydrothermal pretreatment significantly boosted FW hydrolysis, improved organic recovery in the supernatant, and enhanced lactic acid yields. Optimal lactic acid production (12.4 g/L) representing a 68 % increase over the control without hydrothermal pretreatment, was achieved at 120 °C, despite the maximum hydrolysis occurring at 140 °C. Metagenomic sequencing further revealed that the pretreated substrate fostered the development of a lactic acid bacteria-dominated microbial community at low pH, notably enriched with Lactobacillus amylolyticus and Lactobacillus delbrueckii, along with functional genes associated with lactic acid production. Crucially, the absence of genes related to propionate and butyrate pathways in the dominant bacteria would explain the reduced byproduct spectrum and enhanced fermentation stability. These findings indicate that hydrothermal pretreatment improves both the quantity and quality of FW supernatant substrate, promoting a lactic acid bacteria-dominated community that drives favorable metabolic pathways under low pH conditions for more efficient and stable lactic acid production.},
}

@article {pmid41072348,
year = {2025},
author = {Tang, Y and Khan, E and Gu, AZ and Tsang, DCW},
title = {Graphitic biochar-anammox achieved by multi-heme-based extracellular electron transfer.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124704},
doi = {10.1016/j.watres.2025.124704},
pmid = {41072348},
issn = {1879-2448},
abstract = {The anammox process decarbonizes nitrogen removal by avoiding greenhouse gas emissions and organic carbon demand, yet its reliance on nitrification and denitrification undermines these advantages. To address this, we developed a biochar-assisted anammox system that leverages graphitic defects as redox-active sites to enable interspecies, multi-heme extracellular electron transfer (EET). Biochar produced at 800 °C for 4 h (BC800-4 h) exhibited the greatest graphitic defect density and the highest electron accepting capacity, uniquely exceeding the daily stoichiometric electron demand for complete ammonium oxidation in the present study. Metagenomic and in vitro assays revealed that BC800-4 h promoted hydroxylamine-dependent ammonium oxidation by anaerobic ammonia-oxidizing bacteria (AnAOB) via EET. A cooperative microbial network was identified: AnAOB in suspension supplied heme precursors, while ammonia-oxidizing and denitrifying bacteria colonizing the biochar facilitated heme assembly and transport. This partitioning enabled direct electron transfer to biochar, achieving 62 % nitrogen removal without exogenous nitrite and reducing N2O emissions by 28 %. The pore-size-dependent reduction in graphitic defects suggests that large molecular-weight biological channels (>10 kDa) are essential for electron transfer between anammox consortia and biochar. Our findings indicate an opportunity to develop a biochar-anammox reactor-with suspended AnAOB and a fixed-bed biochar biofilm-to exploit this synergy for efficient and low-emission nitrogen removal.},
}

@article {pmid41072344,
year = {2025},
author = {Yu, K and Xia, J and Zhu, D and He, B and Yu, Z and Zhu, DZ and Yao, Z},
title = {Public risk of sewage sediments in different functional areas - deciphered by metagenome assembly.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124691},
doi = {10.1016/j.watres.2025.124691},
pmid = {41072344},
issn = {1879-2448},
abstract = {Understanding public risk of sewage sediments, particularly those risks related to methane, sulfide emission and bio-risk, is critical for ensuring citizen safety. However, the underlying microbial mechanisms causing these risks remain unclear. This study employed metagenomic assembly to analyze methane/sulfur cycling pathways and bio-risks in sewage sediments from three typical functional areas: commercial, multifunctional, and residential. Results demonstrated that the sewage sediments in the multifunctional area exhibited the highest potential public risk levels, characterized by intensified methane/sulfur metabolic activity and increased abundance of mobile gene elements (MGEs) and high-risk antibiotic resistance genes (ARGs). In addition, the co-occurrence network complexity of ARGs, MGEs and pathogens were higher in the multifunctional sewage sediments. Intriguingly, we found genus Thiobacillus which participated in sulfur cycling, as the host of high risk ARGs, significantly enriched in the multifunctional area, also distributed in sewer systems around the world. Additionally, total organic carbon (TOC) emerged as key driver of sediment public risks. These findings highlight variations in sewage sediment public risks across different functional areas, providing a foundation for targeted risk mitigation strategies.},
}

@article {pmid41072198,
year = {2025},
author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E},
title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180681},
doi = {10.1016/j.scitotenv.2025.180681},
pmid = {41072198},
issn = {1879-1026},
abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.},
}

@article {pmid41072177,
year = {2025},
author = {Uribarri, A and Henriquez, L and Beguiristain, I and Rodriguez, I and Alfaro, M and Sancho, I and Portillo, ME},
title = {Toward a clinical algorithm for the detection of periprosthetic joint infections using targeted NGS.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {2},
pages = {117133},
doi = {10.1016/j.diagmicrobio.2025.117133},
pmid = {41072177},
issn = {1879-0070},
abstract = {OBJECTIVES: Periprosthetic joint infection (PJI) represents a severe surgical complication, and despite advances have been made in PJI diagnosis, many cases remain microbiologically negative. In this context, metagenomic Next-Generation Sequencing (mNGS) emerged as a promising diagnostic tool for PJI. This study aimed to establish objective, widely-usable methodology and criteria for diagnosing PJI based on sequence analysis.

METHODS: We retrospectively analyzed sonication fluid samples from 34 patients who underwent surgical treatment for PJI in 2022. A 16S rRNA-based targeted NGS (tNGS) approach was carried out amplifying 16S rRNA gene for 25 and 35 cycles. Sequencing was performed on the Illumina MiSeq platform and data was processed using nf-core/ampliseq.

RESULTS: A significantly higher number of classifiable reads was observed in PJI cases (p < 0.0001). A negative control database was created using negative tNGS controls and samples from patients classified as aseptic failure. The database was then employed to establish three tNGS diagnostic criteria. The diagnostic efficacy of tNGS employing these criteria was assessed through receiver operating characteristic (ROC) curve analysis, which revealed optimal results after 25 cycles of 16S rRNA amplification (AUC = 0.924, p < 0.0001). An optimal cut-off of >12 % was calculated, obtaining a sensitivity of 100 % (95 % CI 75.3 %-100 %) and a specificity of 90.5 % (95 % CI 69.9 %-98.8 %). In both of our culture-negative PJI cases potential pathogens were detected: Listeria and Cutibacterium.

CONCLUSIONS: To the best of our knowledge, this is one of the few studies that attempts to establish standardized criteria and diagnostic cut-offs for the analysis of PJI tNGS data. We believe that these results could serve as a valuable reference for future PJI metagenomics diagnostic studies.},
}

@article {pmid41071829,
year = {2025},
author = {Akanbi, DO and Abaye, BB and Averhoff, F and Berg, MG and Orf, GS and Lawan, KM and Beckett, GA and Omotoso, AB and Mata, M and Cloherty, GA and Chabuka, L and de Oliveira, T and Mac-Fisi, KW and Walter, A and Mark, II and Edeki, G and Sinayoko, A and Nasrullah, M and Justina, BI and Balogun, MS},
title = {Detection of dengue, malaria, and additional causes of acute febrile illness: The need for expanded testing, Bayelsa State, Nigeria.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {10},
pages = {e0013060},
doi = {10.1371/journal.pntd.0013060},
pmid = {41071829},
issn = {1935-2735},
abstract = {Dengue virus (DENV) infection has not been previously reported from Bayelsa State, Nigeria. We aimed to determine the prevalence of dengue virus (DENV) infection, malaria, and coinfection, and other pathogens among febrile patients in the capital city, Yenagoa.We conducted a cross-sectional study among persons aged ≥1 year who presented with acute febrile illnesses (AFI) at four hospitals in Bayelsa State during 20 May - 15 June 2022. Blood samples from 443 participants were tested for DENV seromarkers (NS1, IgM, IgG), using serology and RT-PCR, and malaria was diagnosed by thick smear microscopy. Sociodemographic and risk factor data were collected using electronic questionnaires administered via smart phones/tablets and analyzed using univariate and multivariate methods. Metagenomic libraries were prepared and enriched by viral target capture and sequenced by NGS. The seroprevalence of acute DENV infection was 14.5% (n = 64) while the prevalence of malaria was 42.4% (n = 188); 6.5% (n = 29) of participants were coinfected with acute DENV infection and malaria. An additional 17.6% (n = 78) of participants had markers for past DENV infection. Rural/suburban residence and age ≥ 31 years were significantly correlated with having any dengue seromarker. Residence in a larger household (≥5 persons), and borehole water-use were predictors for malaria fever. RT-PCR results revealed multiple DENV serotypes, with serotype 3 dominant. Sequencing of unknown AFI cases revealed numerous viral causes such as adenovirus, EBV, and hepatitis A, as well as additional dengue and malarial infections missed by conventional testing. Of interest were Coxsackievirus A5 (hand, foot and mouth disease; HFMD) which has been diversifying locally for years in Nigeria and an mPox clade IIb (lineage A.2.3) strain that emerged in Nigeria during the 2022 global outbreak. The results of this study provide the first documentation of human DENV infection in Bayelsa State, Nigeria and suggests that dengue is an emerging and important cause of febrile illness in this area. Our findings support the need for routine testing to identify DENV among patients who present with acute febrile disease. Metagenomic NGS results highlight the benefits of unbiased surveillance to identify circulating and emerging pathogens.},
}

@article {pmid41070991,
year = {2025},
author = {Brennan, C and Shaffer, JP and Belda-Ferre, P and Mohanty, I and Weng, Y and Cantrell, K and Ackermann, G and Allaband, C and Bryant, M and Farmer, S and González, A and McDonald, D and Martino, C and Meehan, MJ and Rahman, G and Salido, RA and Schwartz, T and Song, SJ and Tribelhorn, C and Tubb, HM and Dorrestein, PC and Knight, R},
title = {Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191225},
doi = {10.1128/spectrum.01912-25},
pmid = {41070991},
issn = {2165-0497},
abstract = {UNLABELLED: An essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a variability that clinical sample collection alone cannot fully capture. At-home sample collection enables the inclusion of a larger and more diverse group of participants, accounting for differences in ethnicity, age, and other factors. However, managing large studies is challenging due to the complexities involved in sample acquisition, processing, and analysis. Building on our previous work demonstrating the effectiveness of single 1 mL barcoded, racked Matrix Tubes in reducing sample processing time and well-to-well contamination for paired DNA and metabolite extraction, we further validate this method against a previously benchmarked plate-based approach using the same extraction reagents. This validation focuses on samples from the built environment, human skin, human saliva, and feces from mice and humans. Importantly, we explore the impact of using a mix of bead sizes during bead-beating for cell lysis, demonstrating that it enhances taxonomic recovery compared to a single bead size. Finally, we assess the potential of 95% isopropanol for room-temperature sample preservation. Our results show that isopropanol performs comparably to 95% ethanol in many cases, suggesting it is viable as an alternative when ethanol is unavailable. Beyond minimizing contamination, halving processing time, eliminating human error during sample plating, and streamlining metadata curation, the Matrix tube approach produces metabolomic, 16S, and shotgun metagenomic data consistent with the Plate-based Method for both high- and low-biomass samples.

IMPORTANCE: Numerous studies have linked the microbiome to human and environmental health, yet many fundamental questions remain unanswered. Large-scale studies with robust statistical power are required to identify important covariates against a background of confounding factors. Cross-contamination, limited throughput, and human error have been identified as major setbacks when processing large numbers of samples. We present a streamlined method for sample accession and extraction of metabolites and DNA for both high- and low-biomass samples. This approach, previously shown to significantly reduce cross-contamination, employs an automation-friendly, single barcoded tube per sample. Additionally, we demonstrate that 95% isopropanol serves as an effective ambient-temperature storage solution for many sample types, providing an alternative in regions where ethanol is unavailable or restricted. This method has significant implications for the field, enabling large-scale studies to generate accurate insights with greater efficiency and expanded accessibility in situations in which ethanol is more costly or otherwise not available.},
}

@article {pmid41070134,
year = {2025},
author = {Li, Q and Liu, F and Zhong, J and Fang, X and Zhang, X and Xiong, H and Li, G and Chen, H},
title = {Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656016},
pmid = {41070134},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is strongly associated with alterations in the gut microbiome. While numerous studies have examined this association, most focus on genus- or species-level taxonomic classifications, overlooking functional heterogeneity at the strain level.

METHODS: We integrated 1,123 metagenomic samples from seven global CRC cohorts to conduct multi-level metagenome-wide association studies (MWAS). Fecal microbial load (FML) correction was applied to mitigate technical confounding. We evaluated the performance of taxonomic models at various resolutions strain, species, and genus levels in classifying CRC status both within and across cohorts.

RESULTS: Strain-level analysis revealed conspecific strains with divergent associations to CRC. For instance, distinct strains of Bacteroides thetaiotaomicron exhibited both protective and risk-increasing effects across different cohorts. Genomic functional annotation suggested potential mechanistic bases for these opposing roles. Correction for FML reduced confounding and significantly improved the performance of within-cohort and cross-cohort CRC classification models. Interestingly, genus- and species-level models demonstrated superior predictive robustness compared to strain-level models, likely due to higher microbial abundance and greater cross-population conservation at these taxonomic ranks.

CONCLUSION: Our study underscores the biological relevance of strain level analysis in elucidating functional diversity within the microbiome. However, higher taxonomic levels provide more robust and clinically translatable diagnostic markers for CRC. Integrating FML correction with multi-level taxonomic profiling enhances both mechanistic insight into microbiom CRC interactions and the generalizability of diagnostic models across diverse populations.},
}

@article {pmid41070121,
year = {2025},
author = {Long, C and Fu, X and Wu, Q and Wang, S and Zhou, X and Mao, J and Guo, L and Shi, W and Yang, H and Yang, T and Du, Y and Yue, J and Wu, D and Liu, H},
title = {Poncirus trifoliata vs. Citrus junos rootstocks: reshaping lemon rhizosphere microecology through microbial and metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1650631},
pmid = {41070121},
issn = {1664-302X},
abstract = {INTRODUCTION: Trifoliate orange (Poncirus trifoliataL. Raf) and "Ziyang Xiangcheng" (Citrus junos Sieb. ex Tanaka) are the predominant rootstocks for lemon production in China, exhibiting distinct adaptations to soil pH and differential impacts on plant resilience. As pivotal mediators of scion-soil interactions, rootstocks have emerged as key research targets for their regulatory potential in rhizosphere microbial communities and metabolites.

METHODS: Pot-cultured systems were established with lemon (Citrus × limon "Eureka") saplings grafted onto trifoliate orange (PTL) and "Ziyang Xiangcheng" (CJL) rootstocks. Integrated metagenomic and GC-MS metabolomic approaches were employed to analyze rhizosphere microbial communities and metabolites.

RESULTS: The results demonstrated no significant difference in rhizospheric microbial α-diversity (richness) between PTL and CJL, although PTL exhibited higher evenness. β-Diversity and LEfSe analysis revealed significant structural divergence in communities. A total of 15 differentially enriched genera across three phyla were identified, among which Pseudomonas, Cupriavidus, and Burkholderia in CJL, along with Sphingobium in PTL, exhibited strong effects. Random forest modeling identified 15 key differential metabolites, with 4 significantly upregulated in CJL and 11 in PTL. Microbial-metabolite correlation and GSEA analysis uncovered 10 core pathways involving genetic information processing, energy metabolism, environmental adaptation, and disease resistance mechanisms. Soil analysis showed CJL significantly surpassed PTL in organic matter content, catalase activity and plant height, whereas PTL exhibited superior cellulase, sucrase and urease activities. Mechanistically, PTL appears to recruit Pseudomonas mediterranea via 1-Monostearin secretion to activate glycerolipid metabolism, enhancing drought tolerance. Its caffeate and salicyl alcohol-β-glucoside secretions potentially mobilize Sphingobium and Ensifer adhaerens to regulate amino sugar metabolism, promoting carbon sequestration and root defense. Conversely, CJL likely employs L-alanine exudation to recruit Pseudomonas putida, triggering exopolysaccharide biosynthesis through arginine-proline metabolism as a key tolerance mechanism (such as drought tolerance and alkali tolerance).

DISCUSSION: The findings elucidate rootstock-specific modulation of rhizosphere microecosystems, highlighting distinct microbial-metabolite interactions and tolerance mechanisms. These results provide theoretical support for precision rootstock selection and microbiome engineering to advance sustainable citrus production.},
}

@article {pmid41070117,
year = {2025},
author = {He, C and Yang, S and Dong, S and Wang, S and Zhang, P and Yang, Y and Xu, D and Yang, R and Zeng, B and Hu, Y and Zhang, Q},
title = {Fermentation-driven microbial and metabolic shifts in filler tobacco leaves of different grades.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651289},
pmid = {41070117},
issn = {1664-302X},
abstract = {INTRODUCTION: Filler tobacco leaves (FTLs) serve as the primary raw material for cigar production, and notable differences in physicochemical properties and fermentation responsiveness exist across different grades. However, the underlying mechanisms governing microbial and metabolic evolution during FTL fermentation remain poorly understood. This study systematically investigated the microbial community structures and metabolomic profiles of FTLs of varying grades before and after fermentation using metagenomic sequencing and untargeted metabolomics.

RESULTS: Metagenomic analysis revealed marked differences in microbial composition among FTL grades at the onset of fermentation. The fermentation process further facilitated the enrichment of functional genera such as Bacillus, Escherichia, and Alternaria, while low-grade FTLs exhibited excessive accumulation of Corynebacterium, potentially contributing to off-flavors and undesirable odors. Untargeted metabolomics identified numerous significantly differential metabolites after fermentation, primarily enriched in pathways related to amino acid biosynthesis, sugar metabolism, and carotenoid biosynthesis. Principal component analysis and hierarchical clustering indicated partial continuity in metabolomic profiles within the same grade before and after fermentation. Correlation analysis further revealed strong positive associations between several dominant genera and flavor-related metabolites.

CONCLUSION: This study demonstrates that FTLs of different grades exhibit distinct patterns of microbial succession and metabolic remodeling during fermentation. The initial leaf grade plays a pivotal role in shaping microbial communities and metabolite accumulation. These findings offer mechanistic insights into the fermentation process of FTLs and provide theoretical and practical guidance for optimizing raw material grading and fermentation management in the cigar industry.},
}

@article {pmid41070051,
year = {2025},
author = {Zhang, Y and Chen, A and Yang, C and Guan, L and Wang, C},
title = {Metagenomic next-generation sequencing assists in diagnosing Pneumocystis Jirovecii pneumonia in non-HIV patients: a case report.},
journal = {Respiratory medicine case reports},
volume = {58},
number = {},
pages = {102289},
pmid = {41070051},
issn = {2213-0071},
abstract = {BACKGROUND: Pneumocystis jirovecii Pneumonia (PJP) is a pulmonary opportunistic fungal infection with an incompletely elucidated pathogenesis. In recent years, non-human immunodeficiency virus (HIV) -infected PJP patients have exhibited rapid progression, poor prognosis, and a greater mortality rate compared to their HIV equivalents, necessitating timely detection and management, which are both critical and problematic.

CASE REPORT: We report a young patient admitted with diabetic ketoacidosis characterized by rapidly progressing acute respiratory failure with negative pathogen blood cultures, serum antibodies and polymerase chain reaction results, and a normal CD4[+] lymphocyte count. Anti-HIV antibody were negative. A computed tomography scan of the chest revealed patchy opacities in both lower lungs, a nonspecific manifestation. However, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected high Pneumocystis jiroveci sequence counts and a markedly elevated 1,3-β-D-glucan test titer. Following the diagnosis of non-HIV-infected PJP, the patient was discharged after 13 days with a positive outcome, attained through systematic management involving Trimethoprim-sulfamethoxazole anti-infective medication and stringent glycemic control.

CONCLUSION: Insufficient glucose management may be an important susceptibility factor for immunocompetent persons with non-HIV-infected PJP patients. MNGS serves as an effective method for rapid diagnosis and medication adjustment when signs, symptoms, and imaging findings of PJP are nonspecific.},
}

@article {pmid41069861,
year = {2025},
author = {George, C and Dharan, HM and Drescher, L and Lee, J and Qi, Y and Wang, Y and Chang, Y and Teo, SLM and Wainwright, BJ and Yung, C and Lauro, FM and Hazen, TC and Pointing, SB},
title = {Tropical intertidal microbiome response to the 2024 Marine Honour oil spill.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100623},
pmid = {41069861},
issn = {2666-4984},
abstract = {Marine fuel oil (MFO) spills in tropical coastal environments are under-characterized despite increasing risk from maritime activities. Microbial and geochemical responses to the June 2024 Marine Honour MFO spill on Singapore's intertidal sediments were analyzed in real time over 185 days. Using metagenomics and hydrocarbon profiling, microbial community shifts and hydrocarbon degradation were quantified across visibly oiled (high-impact) and clean (low-impact) sites. Microbiomes at all sites adapted rapidly to the spill through increased diversity and abundance of genes encoding alkane and aromatic compound degradation, detoxification, and biosurfactant production. The dominant hydrocarbon-degrading bacteria differed markedly from those reported in other crude oil spills and in regions with different climates. Oil deposition intensity strongly influenced microbial succession and hydrocarbon-degrading gene profiles, and this reflected early toxicity constraints in heavily oiled areas. The persistence of hydrocarbon degradation genes beyond hydrocarbon detection in sediments suggested long-term functional priming may occur. The study provides novel genome-resolved insight into the microbial response to MFO pollution, advances understanding of marine environmental biodegradation, and provides urgently needed baseline data for oil spill response strategies in Southeast Asia and beyond.},
}

@article {pmid41069710,
year = {2025},
author = {Burakova, I and Smirnova, Y and Gryaznova, M and Morozova, P and Kotarev, V and Lyadova, L and Ivanova, N and Denisenko, L and Syromyatnikov, M},
title = {Effect of interferon on broilers' fecal microbiome composition.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {2},
pages = {487-496},
pmid = {41069710},
issn = {2311-7710},
abstract = {OBJECTIVE: The purpose of our study was to investigate the effect of chicken interferon on the intestinal microbiota of broiler chickens.

MATERIALS AND METHODS: The study used next-generation sequencing on the Ion Torrent pragmatic general multicast platform to target the V3 16S ribosomal ribonucleic acid hypervariable region gene, allowing us to analyze in detail changes in the composition of the broiler chicken microbiome.

RESULTS: Forty-one bacterial genera were identified in the studied groups of broilers. The highest abundance in both groups was observed for Lactobacillus, which was 31.08% ± 6.52 in the control group and 36.08% ± 7.25 in the interferon group. There was no clustering between the microbiome communities of the groups studied. We found a decrease or complete absence of Escherichia-Shigella, Eubacterium fissicatena group, Lachnospiraceae CHKCI001, and Pediococcus in the interferon-treated broiler group compared to the control group and an increase in the number of genera Ruminococcaceae CAG-352 and Turicibacter in the interferon group.

CONCLUSION: A decrease in E.-Shigella may indicate normalization of the intestinal microbiota of broilers, and it can also be concluded that the introduction of interferon helps to suppress opportunistic bacteria. In the interferon group, a sharp increase in the number of Turicibacter was observed. Representatives of this genus are among the most common members in the intestines of broilers.},
}

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

@article {pmid41069598,
year = {2025},
author = {Wang, Z and Lin, X and Wu, J and Su, C and Luo, Y and Yu, G},
title = {Radix Pseudostellaria polysaccharides alleviate sepsis-induced liver injury by modulating the gut microbiota via the TLR4/NF-κB pathway.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1658147},
pmid = {41069598},
issn = {1663-9812},
abstract = {BACKGROUND: Sepsis-induced liver injury (SLI) is a life-threatening complication with limited therapeutic options. Radix Pseudostellariae polysaccharides (RPPS), a component of traditional Chinese medicine, exert immunomodulatory, anti-inflammatory, and antioxidant properties. Herein, we investigated the therapeutic effects and mechanisms of RPPS on SLI.

METHODS: A murine sepsis model was established using cecal ligation and puncture. Mice were pretreated with RPPS or saline for 14 days. Subsequently, multi-omics integration-including metagenomics, proteomics, and network pharmacology-was employed to elucidate the mechanisms of RPPS. Liver injury was assessed via serum biomarkers, histopathology, and transmission electron microscopy, while intestinal barrier integrity was evaluated through histopathological analysis. Gut microbiota composition and functional pathways were examined using metagenomic sequencing. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analyses of gut microbiota, liver proteomics, and network pharmacology data were integrated to predict key target pathways, which were experimentally validated in mice.

RESULTS: RPPS pretreatment significantly improved survival, reduced liver injury markers, attenuated hepatic necrosis and inflammation, and restored intestinal barrier integrity. RPPS also modulated the gut microbiota by enriching beneficial taxa and suppressing pathogens. Multi-omics integration identified the toll-like receptor 4 (TLR4)/nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway as the core mechanism, and experimental validation confirmed that RPPS inhibited TLR4 membrane expression, MyD88/IKKα/β activation, NF-κB p65 phosphorylation, and nuclear translocation. In conclusion, RPPS alleviates SLI by protecting the intestinal barrier, modulating gut microbiota, and suppressing the TLR4/NF-κB signaling pathway.

CONCLUSION: This study provides a scientific foundation for RPPS as a potential therapeutic candidate in sepsis treatment.},
}

@article {pmid41069450,
year = {2025},
author = {Chen, W and Yang, P and Hu, J and Liu, X and Jiang, C and Wu, H and Wang, Y and Yan, Q and Lu, S and Xiong, J and Huang, X and Pan, Y and He, F and Chen, Q and Hu, S and Chen, M and Xiong, C},
title = {Echoes in the Deep: Revealing Influenza A Viruses' Persistence and Microbial Associations in Aquatic Ecosystems.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {5586400},
pmid = {41069450},
issn = {1865-1682},
mesh = {*Influenza A virus/isolation & purification/genetics/classification ; China/epidemiology ; Animals ; *Seawater/virology/microbiology ; Phylogeny ; Lakes/virology ; Ecosystem ; Humans ; *Water Microbiology ; Fresh Water/virology ; },
abstract = {BACKGROUND: Influenza A viruses (IAVs) are significant pathogens with complex transmission dynamics in aquatic ecosystems, yet their persistence, evolutionary relationships, and associations with environmental microorganisms remain poorly understood. This study aimed to elucidate the phylogenetic characteristics and ecological associations of IAV in freshwater and seawater ecosystems in Eastern China to inform public health strategies.

METHODS: Water samples were collected from three freshwater lakes and a coastal seawater site. Viral particles were concentrated, and nucleic acids were extracted for metatranscriptomic and metagenomic sequencing. Phylogenetic analyses, population dynamics assessments, and microbial association networks were constructed using bioinformatic tools. Statistical tests, including Tajima's D and Fu and Li's tests, were applied to evaluate evolutionary trends.

RESULTS: IAV fragments in seawater showed high homology with recent human H3N2 strains from North America (2021-2024), while freshwater-derived fragments aligned with historical avian strains from Asia. Microbial association networks revealed significant associations between IAV and environmental bacteria (e.g., Brevundimonas aurantiaca) and fungi (e.g., Thamnidium), implying potential ecological associations that may underpin viral persistence. Freshwater environments with higher abundances of Uroviricota exhibited more frequent IAV detection. PERMANOVA confirmed distinct overall microbial community compositions in IAV-positive versus IAV-negative samples across both freshwater and seawater ecosystems (p < 0.05).

CONCLUSION: Aquatic ecosystems, particularly freshwater habitats, may serve as reservoirs for IAV persistence and evolution, driven by complex microbial associations. Regional disparities in viral strain origins highlight the role of migratory waterfowl and environmental transmission routes. Integrated surveillance of aquatic IAV dynamics is critical to anticipate zoonotic risks and mitigate future outbreaks.},
}

*Influenza A virus/isolation & purification/genetics/classification
China/epidemiology
Animals
*Seawater/virology/microbiology
Phylogeny
Lakes/virology
Ecosystem
Humans
*Water Microbiology
Fresh Water/virology

@article {pmid41069107,
year = {2025},
author = {Ozel, B and Agirman, B and Simsek, O and Erten, H},
title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.70003},
pmid = {41069107},
issn = {1097-0061},
support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; },
abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.},
}

@article {pmid41069041,
year = {2025},
author = {Koketsu, A and Fukase, S and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Kumada, K and Li, B and Shimada, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Bacterial Involvement in Oral Squamous Cell Carcinoma and Potentially Malignant Oral Disorders.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70115},
pmid = {41069041},
issn = {1601-0825},
abstract = {OBJECTIVE: To clarify the relationship between oral squamous cell carcinoma (OSCC), potentially malignant oral disease (OPMD), and bacterial flora using metagenomic analysis.

METHODS: This cross-sectional observational study included 50 patients in the control group and 77 patients with OPMDs, 41 with early OSCCs, and 20 with advanced OSCCs. Patient saliva samples were subjected to high-throughput sequencing of 16S rRNA gene amplicons to evaluate the composition and diversity of the oral microbiome.

RESULTS: No significant differences were observed in patient backgrounds, other than sex. Patients with advanced OSCCs had greater oral bacterial diversity than those with early OSCC or OPMD. The advanced OSCC group formed a distinct cluster separate from the other groups. Sixteen and 275 species were identified at the phylum and genus levels, respectively. Compared with the control group, Actinomycetia and Streptococcus were significantly elevated in the early OSCC and OPMD groups. Peptostreptococcus and Fusobacterium were significantly higher in the advanced OSCC group than in the control, OPMD, and early OSCC groups.

CONCLUSIONS: The composition and diversity of oral microbiota may be associated with OPMD development and progression to OSCC. Consequently, the salivary microbiome may serve as a biomarker for oral cancer and help predict cancer progression.},
}

@article {pmid41068938,
year = {2025},
author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S},
title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {345},
pmid = {41068938},
issn = {1474-760X},
support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; },
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.

RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.

CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.},
}

Animals
*Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
*Gastrointestinal Microbiome
Epithelium/metabolism/microbiology
Fatty Acids, Volatile/metabolism
Female
*Goat Diseases/microbiology
Hydrogen-Ion Concentration
*Microbiota
Transcriptome
Multiomics

@article {pmid41068590,
year = {2025},
author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B},
title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {653},
pmid = {41068590},
issn = {1471-2180},
support = {2023ZSLC24//Zhongshan Hospital/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Adult ; },
abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.

METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.

RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio = 0.29; 95% confidence interval = 0.12-0.73; P = 0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score = 1.0; log2FoldChange = 3.6) and Dolosigranulum (NetMoss score = 0.6; log2FoldChange = 1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.

CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.},
}

Humans
Male
*Microbiota
Female
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
*Lung/microbiology
Prognosis
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Nontuberculous Mycobacteria/genetics/isolation & purification/classification
Bacteria/classification/genetics/isolation & purification
Metagenomics
Adult

@article {pmid41068306,
year = {2025},
author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X},
title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35375},
pmid = {41068306},
issn = {2045-2322},
support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; },
abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology/metabolism
Female
*Gastrointestinal Microbiome
Male
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Adult
Middle Aged
Bile Acids and Salts/metabolism
Constipation/microbiology
Metagenome
Diarrhea/microbiology
Bacteria/classification/genetics/metabolism