@article {pmid40557508,
year = {2025},
author = {Schroeder, TH and Vanwynsberghe, M and Dervishi, A and Stäudle, H},
title = {Detection of pathogenic microorganisms using metagenomic next generation sequencing for patients with suspected infection presenting in the emergency department.},
journal = {European journal of emergency medicine : official journal of the European Society for Emergency Medicine},
volume = {32},
number = {4},
pages = {288-290},
doi = {10.1097/MEJ.0000000000001239},
pmid = {40557508},
issn = {1473-5695},
}

@article {pmid40557420,
year = {2025},
author = {Girard, M and Vandamme, L and Cazaux, B and Limasset, A},
title = {OReO: optimizing read order for practical compression.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf128},
pmid = {40557420},
issn = {2635-0041},
abstract = {MOTIVATION: Recent advances in high-throughput and third-generation sequencing technologies have created significant challenges in storing and managing the rapidly growing volume of read datasets. Although more than 50 specialized compression tools have been developed, employing methods such as reference-based approaches, customized generic compressors, and read reordering, many users still rely on common generic compressors (e.g. gzip, zstd, xz) for convenience, portability, and reliability, despite their low compression ratios. Here, we introduce Optimizing Read Order (OReO), a simple read-reordering framework that achieves high compression performance without requiring specialized software for decompression. By grouping overlapping reads together before applying generic compressors, OReO exploits inherent redundancies in sequencing data and achieves compression ratios on par with state-of-the-art tools. Moreover, because it relies only on standard decompressors, OReO avoids the need for dedicated installations and maintenance, removing a key barrier to practical adoption.

RESULTS: We evaluated OReO on both Oxford Nanopore Technologies (ONT) and HiFi genomic and metagenomic datasets of varying sizes and complexities. Our results demonstrate that OReO provides substantial compression gains with comparable resource usage and outperforms dedicated methods in decompression speed. We propose that future compression strategies should focus on reordering as a means to let generic compression tools fully exploit data redundancy, offering an efficient, sustainable, and user-friendly solution to the growing challenges of sequencing data storage.

The OReO code is open source and available at github.com/girunivlille/oreo.},
}

@article {pmid40557317,
year = {2025},
author = {Ding, Y and Jing, C and Wei, J and Wang, D and Li, W and Wang, M and Zhou, J and Qian, Q and Sun, W},
title = {Comparison of the diagnostic capabilities of tNGS and mNGS for pathogens causing lower respiratory tract infections: a prospective observational study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1578939},
pmid = {40557317},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Prospective Studies ; Female ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Sensitivity and Specificity ; Aged ; Adult ; China ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation & purification/genetics/classification ; Fungi/isolation & purification/genetics ; *Molecular Diagnostic Techniques/methods ; },
abstract = {AIMS: Pathogens in lower respiratory tract infections(LRTI) are complex. Conventional microbiological testings(CMTs) are time-consuming and inaccurate. mNGS is widely used to overcome these issues. tNGS, as an emerging NGS technology, has uncertain diagnostic efficacy.

MATERIALS AND METHODS: 136 suspected LRTI patients were included from January 2022 to February 2024 from the Department of Respiratory and Critical Care Medicine at Jiangsu Province People's Hospital,China.We simultaneously submitted the bronchoalveolar lavage fluids (BALFs) for mNGS, tNGS and conventional microbial testing (CMTs) and compared the pathogen diagnostic efficacy of mNGS, and tNGS.

RESULTS: A total of 136 patients were included, and there was no statistically significant difference in the detection sensitivity(74.75% VS 78.64%, p>0,05) and specificity(81.82% vs 93,94%,p>0.05) between mNGS and tNGS. However, tNGS has a higher sensitivity(27.94% vs 17.65%,p=0.043)and specificity(88.78% vs 84.82%,p=0.048) for fungi. According to our diagnostic criteria, tNGS successfully identified 3 cases of Pneumocystis jirovecii(P. jirovecii) individually. In addition, both tNGS and mNGS detected chlamydia psittaci whereas CMTs were unable to detect it.

CONCLUSIONS: tNGS demonstrates diagnostic efficacy for pathogens in lower respiratory tract infections that is comparable to mNGS. However, tNGS has specific advantages in the detection of fungi. Considering the cost-effectiveness of tNGS, it is recommended to implement tNGS clinically for patients with lower respiratory tract infections.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
Male
Prospective Studies
Female
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology/virology
Sensitivity and Specificity
Aged
Adult
China
*High-Throughput Nucleotide Sequencing/methods
Bacteria/isolation & purification/genetics/classification
Fungi/isolation & purification/genetics
*Molecular Diagnostic Techniques/methods

@article {pmid40557154,
year = {2025},
author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M},
title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555441},
pmid = {40557154},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; },
abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.

METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.

RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.

CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*HIV Infections/microbiology/complications/physiopathology
Middle Aged
Dysbiosis
*Lung/physiopathology
*Bacteria/genetics/classification
Adult
*Lung Diseases/microbiology
Respiratory Function Tests
Aged

@article {pmid40556944,
year = {2025},
author = {Chen, Y and Fan, B and Zeng, J and Zou, Y and Tao, C and Chen, C and Zhang, P and Liang, J and Qi, F and Tang, H and Lu, L},
title = {Single-Cell RNA Transcriptomics and Multi-omics Analyses Reveal the Clinical Effects of Acupuncture on Methadone Reduction.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0741},
pmid = {40556944},
issn = {2639-5274},
abstract = {Opioid use disorders (OUDs) pose a substantial global health burden, with methadone maintenance treatment (MMT) widely adopted as an intervention; however, MMT is associated with immunosuppression, metabolic disturbances, and dysbiosis of the gut microbiota. Despite the potential of acupuncture in reducing methadone dosages and opioid addiction, the underlying biological mechanisms remain unclear. Therefore, we aimed to integrate clinical trial data with multi-omics analysis, including single-cell sequencing, transcriptomics, metabolomics, and metagenomics, to evaluate the effects of acupuncture in patients undergoing MMT. We collected peripheral blood mononuclear cells, plasma, and fecal samples from 48 MMT participants in a randomized, placebo-controlled trial. Participants were divided into acupuncture (n = 25) and sham-acupuncture (n = 23) groups. After 8 weeks of intervention, 84% of patients in the acupuncture group achieved ≥20% reduction in methadone dosage, compared to 39% in the sham-acupuncture group (P < 0.01). Our findings revealed that acupuncture may activate the defense response to viruses, with altered immune cell functions in classical monocytes correlating with clinical responses to reduced methadone doses. Acupuncture might ameliorate intestinal microbial disruptions caused by OUD by up-regulating Bilophila and modulating bile acid metabolism. Furthermore, acupuncture up-regulated galectin-9 (LGALS9)-mediated intercellular communication between classical monocytes and other immune subsets. To further validate the mechanistic link between bile acid metabolism and immune regulation, we conducted in vitro experiments using THP-1 monocytes treated with cholic acid. The results showed that bile acid exposure suppressed galectin-9 and IFN-γ expression, while low-dose bile acid (simulating acupuncture effects) partially reversed this effect. These findings support a bile acid-galectin-interferon axis that may be modulated by acupuncture in OUD. Collectively, our results provide clinical and mechanistic evidence supporting acupuncture as a potential adjunct therapy to mitigate the adverse effects of long-term opioid use.},
}

@article {pmid40556900,
year = {2025},
author = {Zhang, Q and Wang, X and Cheng, P and Huo, S and Liu, C and Yu, Z},
title = {Editorial: Recent advances in agricultural waste recycling by microorganisms and their symbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1631828},
doi = {10.3389/fmicb.2025.1631828},
pmid = {40556900},
issn = {1664-302X},
}

@article {pmid40556899,
year = {2025},
author = {Ning, T and Zheng, X and Liang, J and Wang, W and Zhang, G and Wei, X and Tan, L},
title = {Effect of different bulking agents on the quality, microbial community structure and metabolic functions during human feces composting in foam composting device.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1556537},
pmid = {40556899},
issn = {1664-302X},
abstract = {Aerobic composting represents an efficacious strategy for the disposal of human feces, yet investigations into the effects of different bulking agents on this process remain limited. This study investigated the effects of composting human feces with four types of bulking agents-wheat straw, corn straw, millet straw, and sawdust-in a foam composting device, as well as the impacts of the process on the microbial community structure and metabolic functions adopting sequencing data analysis and metagenomic analysis. The results demonstrate that aerobic composting can safely treat human feces, resulting in a mature compost product. Comparative assessments of compost quality and microbial profiles with various bulking agents indicated superior performance of corn straw compost, surpassing those produced with wheat straw, millet straw, and sawdust in terms of humification level (HA/FA = 2.9), peak temperature reached (71.2°C), composting duration (20 days), and nutrient composition (TN 42.87 g/kg). Additionally, the diversity and dominance of certain microbial colonies (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidota) were significantly higher in composts formulated with corn straw. The metagenomic data analysis reveals significant differences in the abundance of "carbon metabolism" and "microbial metabolism" among different groups, further indicating that the addition of different bulking agents affects the utilization of metabolic products, amino acids, and carbohydrates as carbon sources by microbes in human feces compost. Consequently, leveraging corn straw as a bulking agent, given its abundant availability, could potentially improve the efficiency and outcome of the human feces composting process.},
}

@article {pmid40556897,
year = {2025},
author = {Lu, L and Huang, X and Zheng, P and Wei, S and Jiao, N and Zhang, R and Li, X and Yang, Y},
title = {Two novel phages infecting Erythrobacter isolated from the epipelagic ocean.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592355},
pmid = {40556897},
issn = {1664-302X},
abstract = {Erythrobacter, an aerobic anoxygenic photoheterotrophic bacterial genus, plays a vital role in carbon and energy cycling in marine environments. However, their phage predators remain poorly understood, with only two strains previously reported. This study isolated and characterized a novel Erythrobacter phage, vB_EauS-R34L1 (R34L1), and its sub-strain vB_EauS-R34L2 (R34L2), from coastal seawater. Both phages exhibit long-tailed, icosahedral morphologies and relatively narrow but slightly different host ranges. One-step growth curve analysis revealed a 160-min latent period and burst sizes of 81 and 91 PFU/cell for R34L1 and R34L2, respectively. Genomic analysis showed that the phages possess dsDNA genomes of 56,415 bp (R34L1) and 54,924 bp (R34L2), with G + C contents of 61.60 and 61.19%, respectively. Both phages harbor a suite of unique genes, including GapR and GH19, which are crucial for host interaction and ecological functionality. Blastn analysis indicated a 99.73% genome similarity between them. Taxonomic and phylogenetic analyses positioned them in a novel viral genus cluster, Eausmariqdvirus, under the family Casjensviridae, indicating a distant evolutionary relationship with known phages. Metagenomic queries suggested that R34L1- and R34L2-like phages are exclusively abundant in temperate and tropical epipelagic zones. This study expands our understanding of Erythrobacter phages and provides insights into their ecological roles in marine ecosystems.},
}

@article {pmid40556523,
year = {2025},
author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E},
title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf089},
pmid = {40556523},
issn = {1536-4844},
support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; },
abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.

METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.

RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA⁺ plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.

DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.},
}

@article {pmid40556381,
year = {2025},
author = {Zhao, S and Xu, Q and Li, M and Chen, J and Francis, F and Dai, X and Tan, J and Kong, Z},
title = {Exploring the Impact of Dinotefuran Residue on Microbial Community and Flavor Generation in Huangjiu Fermentation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02308},
pmid = {40556381},
issn = {1520-5118},
abstract = {Pesticide residues create food safety hazards while negatively affecting the quality of fermented foods, but the mechanisms of the deterioration response have been a mystery. In this study, headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) and metagenomics sequencing analyses were employed to investigate the effect of dinotefuran residue on the aroma profile and microbial community of Huangjiu. The presence of dinotefuran led to a reduction in the overall concentration of volatile compounds, and some floral, fruity, and sweet aromas such as piperitenol, citronellyl isobutyrate, and trans-2-decenal were no longer detected. Meanwhile, the levels of certain acidic volatiles, including formic acid, propionic acid, and heptanoic acid, increased and contributed to off-flavors. Dinotefuran affected the Huangjiu flavor by modifying the abundance and structure of key genera such as Saccharomyces, Lactococcus, and Cyberlindnera. These changes were associated with disturbances in 16 KEGG tertiary metabolic pathways, including glycolysis, pyruvate metabolism, and amino acid biosynthesis. These results provided some reference for further studies on how pesticide residues affect the flavor and microbial characteristics of traditional fermented beverages like Huangjiu.},
}

@article {pmid40555957,
year = {2025},
author = {Gonçalves, OS and Fernandes, AS and de Sousa, TGG and Santana, MF and Barreto, CC},
title = {From cultivation challenges of Acidobacteriota to biotechnological promises - unveiling what is needed to fully harness their potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {208},
pmid = {40555957},
issn = {1573-0972},
support = {00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 5.10/2022//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 402644/2021-2//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-02381-21//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Biotechnology/methods ; Biodegradation, Environmental ; Genome, Bacterial ; Industrial Microbiology ; Genomics ; },
abstract = {Acidobacteriota are currently well-known for their ubiquity and metabolic versatility. Their environmental importance is the subject of many studies, but their biotechnological applications still need to be explored. Although they are considered hard-to-culture bacteria, many genomes are available, which reveals promising biotechnological potential. Despite these promising features, the application of Acidobacteriota in biotechnology remains underexplored. In this context, we review key findings regarding the potential applications of Acidobacteriota, emphasizing advancements derived from genomic, metagenomic, and culture-based studies. We specifically focus on their ability to produce enzymes and other bioactive molecules, their antimicrobial properties, and their potential applications in agriculture and bioremediation. Furthermore, we discuss strategies to overcome the challenges associated with culturing and manipulating these bacteria, such as heterologous expression and other emerging techniques related to -omics and computational approaches. These strategies could provide deeper insights into Acidobacteriota's metabolism, including their biosynthetic pathways and interactions within microbial consortia. Ultimately, this understanding could lead to broader applications of Acidobacteriota in environmental and industrial biotechnology.},
}

*Biotechnology/methods
Biodegradation, Environmental
Genome, Bacterial
Industrial Microbiology
Genomics

@article {pmid40555791,
year = {2025},
author = {Lin, S and Sun, Z and Zhu, X and Wang, M and Zhang, Q and Qian, J and Zhang, H and Mei, Z and Pu, Y and Kong, M and Guo, P and Zhou, X and Li, J and Sun, X and Ma, L and Zhang, X and Zhao, F and Nie, J and Hong, S and Chen, J and Wang, X and Li, X and Zheng, Y},
title = {Segatella copri and gut microbial ammonia metabolism contribute to chronic kidney disease pathogenesis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40555791},
issn = {2058-5276},
abstract = {Alterations in gut microbiota have been linked to chronic kidney disease (CKD), but large-scale studies and mechanistic insights are limited. Here we analysed gut metagenome data from 1,550 older individuals (aged 65-93 years) with comprehensive kidney function measurements. Segatella copri was positively associated with kidney function through microbial ammonia metabolism-related pathways and the asnA gene, which encodes an ammonia-assimilating enzyme. These associations were replicated in two external studies. In mice, ammonia supplementation increased serum levels of creatinine and blood urea nitrogen, accelerating CKD progression. In vitro cultures of S. copri or asnA-overexpressing Escherichia coli reduced ammonia concentrations, which was markedly attenuated in asnA-knockout S. copri. Gavage of either S. copri or asnA-overexpressing E. coli, but not asnA-knockout S. copri, mitigated ammonia-induced CKD progression in mice. These findings highlight the role of gut microbial ammonia metabolism in CKD pathogenesis and underscore the therapeutic potential of microbial-based interventions.},
}

@article {pmid40555747,
year = {2025},
author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ},
title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {867},
pmid = {40555747},
issn = {2399-3642},
mesh = {Humans ; *Bifidobacterium/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; },
abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.},
}

Humans
*Bifidobacterium/isolation & purification/genetics
*Gastrointestinal Microbiome
*Dysbiosis/epidemiology/microbiology
Infant
United States/epidemiology
Female
Male
Infant, Newborn
Metagenomics

@article {pmid40555322,
year = {2025},
author = {Ying, S and Zhang, Z and Xiang, R},
title = {Metagenomic and Whole-Genome Characterization of Carbapenem-Resistant Acinetobacter baumannii Carrying blaOXA-23 Gene within the Tn2006 Transposon Among ICU Patients.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.06.009},
pmid = {40555322},
issn = {2213-7173},
abstract = {PURPOSE: To characterize carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 genes within the Tn2006 transposon using metagenomic and whole-genome sequencing, focusing on their genetic features, antimicrobial resistance, and potential for clonal spread and horizontal gene transfer among ICU patients.

METHODS: Bronchoalveolar lavage fluid samples from 28 ICU patients were analyzed using mNGS to detect pathogens and resistance genes. A. baumannii isolates underwent whole-genome sequencing for genetic diversity assessment. Antimicrobial susceptibility testing and comparative genomic analysis were performed.

RESULTS: mNGS revealed mixed infections in 71.4% of patients, identifying multiple bacteria, viruses, fungi, and mycoplasma species. A. baumannii was detected in 25 samples, often alongside other pathogens. All isolates harbored blaOXA-23 within Tn2006 on the chromosome and belonged to sequence type ST2, indicating clonal dissemination despite significant genetic diversity (up to 2,969 SNP differences). The isolates were highly resistant to multiple antibiotics but remained susceptible to tigecycline and colistin. Comparative genomic analysis with 238 global CRAB genomes confirmed the prevalence of the Tn2006 transposon carrying blaOXA-23 in ST2 strains, emphasizing the potential for rapid spread of this resistance mechanism.

CONCLUSION: The widespread presence of multidrug-resistant A. baumannii carrying blaOXA-23 within Tn2006 among ICU patients poses a significant public health concern. The high rate of mixed infections and the potential for horizontal gene transfer complicate infection management in critically ill patients. Enhanced infection control measures, continuous surveillance, and targeted interventions are urgently needed to prevent further dissemination of these resistant strains in hospital settings.},
}

@article {pmid40555025,
year = {2025},
author = {Lin, Z and Pang, S and Wu, Y and Xu, T and Zhou, YL and Li, H and Zhang, C and Qian, PY and Zhang, S},
title = {Biodiversity and nitrogen metabolism in the plastisphere impacted by urban nitrogen loading from a coastal mega-city.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139012},
doi = {10.1016/j.jhazmat.2025.139012},
pmid = {40555025},
issn = {1873-3336},
abstract = {The plastisphere, recognized for vast biomass and critical role in nitrogen cycling, is becoming a pertinent component of marine ecosystems. The relationship between plastisphere and increased nitrogen inputs from urban wastewater in coastal zones remains poorly understood. Through metagenomics, metatranscriptomics and metabolomics, this research sought to elucidate the plastisphere's reaction to elevated nitrogen loading and pinpoint key microbial resources that can be harnessed. Although the archaeal community composition within the plastisphere remains largely unchanged by nitrogen loading, bacterial diversity experiences a substantial boost, which is inversely correlated with fungal diversity. Furthermore, such conditions are associated with reduced intricate microbial interactions. Moreover, the plastisphere subjected to nitrogen loading shows an enrichment of genera and genes implicated in ammonium assimilation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Metabolomics analysis highlighted the plastisphere's accumulation of L-glutathione oxidized (GSSG) in response to nitrogen loading. The research further highlighted a quartet of microbial phyla-Actinomycetota, Bacteroidota, Cyanobacteriota, and Pseudomonadota-that not only thrive but also constitute pivotal microbial resources within the plastisphere when confronted with strong nitrogen loading. In essence, this investigation illuminates the plastisphere's biodiversity dynamics and nitrogen metabolic adjustments during augmented nitrogen loading and offers novel perspectives on taking advantage of the plastisphere's untapped microbial potential.},
}

@article {pmid40554894,
year = {2025},
author = {Zheng, SJ and Gao, XY and Diao, XH and Chen, ND},
title = {Dendrobium huoshanense improves atherosclerosis in high-fat-induced ApoE mice by regulating gut microbiota and serum metabolite profiles.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156964},
doi = {10.1016/j.phymed.2025.156964},
pmid = {40554894},
issn = {1618-095X},
abstract = {BACKGROUND: Cardiovascular diseases, particularly atherosclerosis (AS), remain leading causes of mortality, with limited effective treatments available. Dendrobium huoshanense, a traditional medicinal herb, has shown promising anti-inflammatory and antioxidant effects, but its cardiovascular protective potential remains underexplored.

PURPOSE: This study aimed to explore the protective effects of Dendrobium huoshanense polysaccharides (DHP) against AS and elucidate the underlying mechanisms involved.

METHODS: An ApoE(-/-) mice model of AS was established, and DHP was administered at different concentrations via gavage. After 14 weeks, serum and fecal samples were collected. The effects of DHP on lipid profiles, aortic plaques, matrix metalloproteinases (MMP-2 and MMP-9), and the Nrf2/HO-1 pathway were assessed. Additionally, metagenomic sequencing of fecal samples and untargeted metabolomics of serum were conducted and correlations between these findings were explored.

RESULTS: DHP improved lipid profiles, reduced reactive oxygen species (ROS) and malondialdehyde (MDA) levels, and enhanced superoxide dismutase (SOD) activity. It stabilized aortic plaques, suppressed MMP-2 and MMP-9 overexpression, and activated the Nrf2/HO-1 pathway. DHP also promoted gut microbiota balance, increasing Mucispirillum, Bifidobacterium, and Faecalibaculum while decreasing Desulfovibrionaceae and Eubacterium. Metabolomics revealed alterations in metabolites, including taurochenodeoxycholic acid and ursocolic acid, influencing amino acid, glycerophospholipid, and bile acid metabolism.

CONCLUSIONS: DHP effectively lowers lipid levels, stabilizes aortic plaques, restores gut microbiota balance, and corrects metabolic disturbances, thereby inhibiting the progression of atherosclerosis. These findings provide a scientific basis for the clinical use of DHP in AS prevention and treatment.},
}

@article {pmid40554566,
year = {2025},
author = {Calderón-Ezquerro, MC and Brunner-Mendoza, C and Guerrero-Guerra, C and Sanchez-Flores A, A and Salinas-Peralta, I and Toriello, C and Ponce-de León, A and Ortega-Rosas C I, CI},
title = {Genetic sequencing of the airborne fungal spectrum and air quality at a public hospital in Mexico City.},
journal = {PLOS global public health},
volume = {5},
number = {6},
pages = {e0004784},
pmid = {40554566},
issn = {2767-3375},
abstract = {Hospital bioaerosols represent significant risks for nosocomial infections, contributing to patient morbidity and mortality. Exposure to these particles, particularly airborne fungal spores or propagules, can trigger adverse effects on the immune system and cause respiratory diseases. This study evaluated the airborne fungal community in a public hospital in Mexico City using a metagenomic approach, two types of aerobiological samplers as well as temperature, humidity, and suspended particle analysis. Sampling was carried out in three areas within the hospital: and outside the hospital. Airborne sampling was performed for three consecutive days, except in the EU. The results showed that using two different samplers revealed fungal diversity and composition variations. Specifically, the Cμ-Sampler captured a higher abundance and diversity of fungi than the AVPS, with Total Taxonomy Annotations at a Genus level of 626 in F1, 632 in F2, 485 in EU and 617 in OH). In the analysis of fungal presence, Ascomycota and Basidiomycota were identified as dominant phyla. Using the AVPS sampler, Ascomycota showed an overwhelming presence of 90% to 100% inside and outside the hospital, while Basidiomycota was found in a range of 1% to 10%. Using the CμS-Sampler, Ascomycota was observed to vary between 39% and 72% in areas F1 and F2 of the hospital and from 73% to 82% outside it. On the other hand, Basidiomycota presented values between 54% and 61% in F1 and from 18% to 27% outside the hospital. The predominant genera were Aspergillus, Penicillium, Cladosporium and Alternaria. The identification of twenty-seven fungal species, including opportunistic pathogens such as Aspergillus fumigatus, Penicillium chrysogenum, P. expansum, Cladosporium and Alternaria alternata, is a significant result of this study. The results revealed the diversity of fungi in the hospital environment. The proposed complementary use of different samplers could significantly optimise current surveillance methods.},
}

@article {pmid40554279,
year = {2025},
author = {Zhang, Z and Liu, C and Chen, T and Liu, F and Luo, S and Ye, J},
title = {Microorganisms and characteristic volatile flavor compounds in Luocheng fermented rice noodles.},
journal = {Food chemistry},
volume = {490},
number = {},
pages = {145133},
doi = {10.1016/j.foodchem.2025.145133},
pmid = {40554279},
issn = {1873-7072},
abstract = {The association between the appealing flavors of Luocheng fermented rice noodles (LCFN) and microbial succession during long-term fermentation is poorly understood. This study aims to elucidate the mechanism of flavor formation in LCFN during fermentation over a 30-day period. The electronic nose results showed that the LCFN underwent a flavor shift in 7-10 days with maturation in 15-30 days. This transformation was associated with the formation of characteristic flavors of (E)-2-decenal, 2-undecenal, (E, E)-2,4-decadienal, (E)-2-octenal, (E)-2-heptenal, hexanal, nonanal, and 2-pentyl furan, which had significant positive correlation with palmitic acid, oleic acid, and linoleic acid. Changes in lipase activity and the analysis of metagenomics, suggested that the characteristic flavors may be produced by Lactobacillaceae and Geotrichum via lipid metabolism. This study provides theoretical guidance for the screening of safe and efficient microorganisms for the production of flavorful rice noodles.},
}

@article {pmid40554148,
year = {2025},
author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y},
title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.},
journal = {Water research},
volume = {284},
number = {},
pages = {123973},
doi = {10.1016/j.watres.2025.123973},
pmid = {40554148},
issn = {1879-2448},
abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.},
}

@article {pmid40554092,
year = {2025},
author = {Choi, BS and Holm, JB and Brejnrod, A and Fjære, E and Xia, Z and Allingbjerg, ML and Larsen, IS and Kristensen, DM and Dall, M and Myrmel, LS and Koch, J and Danneskiold-Samsøe, NB and Kalliokoski, O and Treebak, JT and Xiao, L and Hansen, AK and Sørensen, H and Madsen, L and Arumugam, M and Kristiansen, K and Jensen, BAH},
title = {Housing matters: experimental variables shaping metabolism in obese mice.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102190},
doi = {10.1016/j.molmet.2025.102190},
pmid = {40554092},
issn = {2212-8778},
abstract = {Diet-induced obesity in mice is an important model for investigating host-diet interactions as well as dietary and pharmacological treatments of metabolic diseases. Experimental reproducibility is, however, a recurrent challenge. To determine key controllable experimental drivers of mouse metabolism, we distributed 338 C57BL/6JBomTac mice (males and females) into six research units across two countries, divided them into a variety of housing conditions (i.e., diets, cage types, temperatures, group-housing vs. single-housing) and kept 26 reference mice at the vendor. We applied linear mixed models to rank the influence of each variable on metabolic phenotype (i.e., body weight gain, glucose intolerance, liver, and visceral adipose tissue weight). Group-housing was the most potent driver of metabolic dysfunction apart from sex and diet. Accordingly, single-housed mice exhibited reduced weight gain (∼50%), increased energy expenditure, and diminished respiratory exchange ratio concomitant with improved glucose tolerance (∼20%) compared to their group-housed counterparts. Our results may aid in clarifying the impact of experimental design and promote rational, transparent reporting to increase reproducibility.},
}

@article {pmid40554085,
year = {2025},
author = {Chen, H and Ruan, F and Wu, W and Liu, J and Wang, Z and Xu, X and Liu, Y and Wu, S and Zhou, J and Ma, J},
title = {Pulmonary fungal infection caused by Rhizopus microsporus in type II diabetic patient:A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116953},
doi = {10.1016/j.diagmicrobio.2025.116953},
pmid = {40554085},
issn = {1879-0070},
abstract = {Pulmonary fungal infections are invasive fungal diseases with high mortality, particularly in immunocompromised patients. This case report describes a patient with type II diabetes mellitus who developed a pulmonary fungal infection. The patient presented with a one-week history of paroxysmal cough and expectoration of yellowish-white, purulent sputum following exposure to cold temperatures. Initial empirical antiviral therapy failed to yield any clinical improvement Subsequent chest computed tomography (CT) scans revealed irregular areas of increased density in the left lower lung, while metagenomic next-generation sequencing (mNGS) identified the infection as caused by Rhizopus microspores. The patient was treated with intravenous amphotericin B and showed clinical improvement without side effects during follow-up. This case highlighted the potential of mNGS as an adjunctive diagnostic tool for rare pathogen infections, especially in immunocompromised patients where conventional microbiological methods may be inconclusive.},
}

@article {pmid40554061,
year = {2025},
author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L},
title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.06.037},
pmid = {40554061},
issn = {2090-1224},
abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.

OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.

METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.

RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.

CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.},
}

@article {pmid40553742,
year = {2025},
author = {Frutkoff, YA and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D},
title = {Whole food diet induces remission in children and young adults with mild-moderate Crohn's disease and is more tolerable than exclusive enteral nutrition: a randomized controlled trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.06.011},
pmid = {40553742},
issn = {1528-0012},
abstract = {BACKGROUND: Tasty&Healthy (T&H) is a whole-food diet for Crohn's disease (CD), which excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized-controlled trial comparing tolerability and effectiveness of T&H vs. exclusive enteral nutrition (EEN).

METHODS: Patients with biologic-naive mild-moderate CD aged 6-25 years were randomized to either T&H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Non-Invasive (MINI) index, calprotectin, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Fecal microbiome was analyzed by metagenomics at baseline, week-4 and week-8. Data were analyzed by the intention-to-treat approach unless specified otherwise.

RESULTS: Among 83 included patients (41 T&H, 42 EEN; mean age 14.5±3.7 years), 88% tolerated T&H vs. 52% for EEN (aOR 7.7 [95%CI 2.4-25]; p<0.001). Calprotectin, CRP and ESR decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of T&H group vs. 38% of the EEN group (aOR 2.5 [0.98-6.3], p=0.1; per-protocol: 67% vs. 76%; p=0.47). Calprotectin <250μg/g was achieved in 34% vs. 33% (aOR 0.97 [0.37-2.6], p=0.84) and MINI<8 in 44% vs. 31% (aOR 1.8 [0.7-4.5]; p=0.33). Microbiome α-diversity improved in the T&H arm and declined in the EEN arm, showing superior species richness at both week-4 and week-8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&H and increased in EEN (q<0.001).

CONCLUSIONS: T&H demonstrated better tolerability than EEN for inducing remission in mild-to-moderate CD, while positively affecting the microbiome (TASTI-MM, NCT#04239248).},
}

@article {pmid40553325,
year = {2025},
author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P},
title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {15-37},
pmid = {40553325},
issn = {1940-6029},
mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; },
abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.},
}

Humans
*Precision Medicine/methods
*Metabolomics/methods
*Metabolome
Metagenomics/methods
*Microbiota
*Artificial Intelligence
Computational Biology/methods
Gastrointestinal Microbiome

@article {pmid40552763,
year = {2025},
author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF},
title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520412},
doi = {10.1080/19490976.2025.2520412},
pmid = {40552763},
issn = {1949-0984},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; *Clostridioides difficile/physiology ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Recurrence ; Aged ; },
abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.},
}

Humans
*Clostridium Infections/therapy/microbiology
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Feces/microbiology
Male
*Clostridioides difficile/physiology
Female
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Adult
Recurrence
Aged

@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}

@article {pmid40551486,
year = {2025},
author = {Yan, F and Wu, SM and Yuan, WQ and Yang, YH and Zhu, H and Cui, DJ},
title = {Thermophiles, Thick-Walled Bacteria, and Pseudomonads in High-Altitude Gut Microbiota.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.17032},
pmid = {40551486},
issn = {1440-1746},
support = {qiankehe2018-5764-11//Cultivation Fund of National Natural Science Foundation/ ; gzwkj2025-268//Science and Technology Fund of Guizhou provincial health committee/ ; },
abstract = {BACKGROUND AND AIM: High-altitude environments are characterized by low oxygen and reduced low pressure, which impose significant physiological challenges on organisms. Among various adaptive systems, the intestinal flora plays a crucial role in maintaining gut health and barrier integrity function under such conditions. This study aimed to elucidate the regulatory mechanisms of intestinal flora in high-altitude environments, focusing on downregulating intracellular Bone Morphogenetic Protein 4 (BMP4) to influence glycolysis metabolism, thereby affecting intercellular communication of the intestinal mucosal barrier and matrix remodeling.

METHODS: High-altitude mouse intestinal flora composition and function were analyzed using 16S rRNA and metagenomic sequencing. Additionally, single-cell sequencing was employed to examine cell population communication and gene expression differences between normal and high-altitude mouse intestinal tissues.

RESULTS: Single-cell sequencing showed significantly reduced interactions between intestinal fibroblasts and epithelial cells in high-altitude mice, accompanied by a marked increase in BMP4 expression. Overexpression of BMP4 was found to activate the glycolysis pathway. Gut microbiota metabolites, including secondary bile acids, lactic acid, and butyrate, exhibited protective effects on hypoxia-induced intestinal mucosal barrier injury, with butyrate showing the most prominent effect. Under hypoxic conditions, butyrate suppressed the BMP4/glycolysis pathway, thereby alleviating hypoxia-induced intestinal mucosal barrier damage.

CONCLUSION: This study uncovered a novel mechanism by which the gut microbiota in high-altitude environments modulate glycolysis metabolism through BMP4 downregulation, thereby affecting intercellular communication and matrix remodeling within the intestinal mucosal barrier.},
}

@article {pmid40551155,
year = {2025},
author = {Mizsei, E and Sos, T and Móré, A and Wenner, B and Rák, G and Mebert, K},
title = {Restriction times on the rise: mechanistic modelling of activity time of grassland vipers (Vipera spp.) in the face of climate change.},
journal = {Frontiers in zoology},
volume = {22},
number = {1},
pages = {10},
pmid = {40551155},
issn = {1742-9994},
support = {LIFE18 NAT/HU/000799//LIFE programme/ ; },
abstract = {Climate change threatens species adapted to cool alpine environments, particularly ectotherms like reptiles. Small-sized grassland specialist vipers inhabit such environments in Eurasia and are highly susceptible to overheating and dehydration as global temperature rises. This study modelled activity restriction times, defined as hours when environmental temperatures exceed the thermal tolerance (i.e. not available for essential activities) of the species, for 20 grassland viper taxa to assess climate change impacts. Under future conditions, hours of activity restriction are projected to increase by 21% by the SSP1-2.6 scenario, and by 52.1% by the SSP5-8.5 scenario. Elevation and latitude significantly influenced restriction time changes, with high-altitude and northern populations predicted to be most affected. The taxa Vipera graeca and Vipera ursinii moldavica are expected to experience the greatest increase in restriction times. Despite warmer conditions potentially increasing hours within preferred thermal ranges, vipers are unlikely to exploit lower-elevation habitats due to competition and ecological constraints. These findings emphasise the urgent need for conservation strategies, including habitat preservation and connectivity, to mitigate the adverse effects of climate change on grassland vipers, particularly the most vulnerable populations.},
}

@article {pmid40550680,
year = {2025},
author = {Lin, M and Hu, L and Hao, L and Wang, Z},
title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2415-2431},
doi = {10.13345/j.cjb.240399},
pmid = {40550680},
issn = {1872-2075},
mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; },
abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.},
}

*Wetlands
*Microbiota/genetics
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification
RNA, Ribosomal, 16S/genetics
China
Cities
Geologic Sediments/microbiology
Archaea/genetics/metabolism/classification
Metagenomics
Metagenome

@article {pmid40550672,
year = {2025},
author = {Wang, X and Wang, S and Yang, K and Tang, Y and Xu, Y and Shen, Q and Wei, Z},
title = {[Methodological breakthroughs and challenges in research of soil phage microecology].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2310-2323},
doi = {10.13345/j.cjb.250258},
pmid = {40550672},
issn = {1872-2075},
mesh = {*Bacteriophages/genetics/isolation & purification/physiology ; *Soil Microbiology ; Ecosystem ; Microbiota ; Metagenomics/methods ; },
abstract = {Phages, as obligate bacterial and archaeal parasites, constitute a virus group of paramount ecological significance due to their exceptional abundance and genetic diversity. These biological entities serve as critical regulators in Earth's ecosystems, driving biogeochemical cycles, energy fluxes, and ecosystem services across terrestrial and marine environments. Within soil microbiomes, phages function as microbial "dark matter," maintaining the soil-plant system balance through precise modulation of the microbial community structure and functional dynamics. Despite the growing research interests in soil phages in recent years, the proportion of such studies in environmental virology remains disproportionately low, which is primarily attributed to researchers' limited familiarity with the research methodologies for phage microecology, incomplete technical frameworks, and inherent challenges posed by soil environmental complexity. To address these challenges, this review synthesizes cutting-edge methodologies for soil phage investigation from four aspects: (1) tangential flow filtration (TFF)-based phage enrichment strategies; (2) integrated quantification approaches combining double-layer agar plating, epifluorescence microscopy, and flow cytometry; (3) multi-omics analytical pipelines leveraging metagenomics and viromics datasets; and (4) computational frameworks merging machine learning algorithms with eco-evolutionary theory for deciphering phage-host interaction networks. Through comparative analysis of methodological principles, technical merits, and application scopes, we establish a comprehensive workflow for soil phage research. Future research in this field should prioritize: (1) construction of soil phage resource libraries, (2) exploration of RNA phages based on transcriptomes, (3) functional characterization of unknown genes, and (4) deep integration and interaction validation of multi-omics data. This systematic methodological synthesis provides critical technical references for addressing fundamental challenges in characterizing soil phages regarding the community structure, functional potential, and interaction mechanisms with hosts.},
}

*Bacteriophages/genetics/isolation & purification/physiology
*Soil Microbiology
Ecosystem
Microbiota
Metagenomics/methods

@article {pmid40550235,
year = {2025},
author = {Howard-Jones, AR and Mahar, JE and Proudmore, K and Butel-Simoes, GI and Eden, JS and Neave, MJ and Mileto, P and Hueston, L and Freeman, K and Ellem, J and Caly, L and Sikazwe, C and Levy, A and Thomas, A and Taylor, C and Kurucz, N and Smyth, K and Jennison, A and Moore, P and Wright, R and Mee, PT and Brischetto, A and Feldman, R and Dwyer, DE and O'Sullivan, MV and Mahony, AA and Warner, MS and Papanicolas, LE and Schlebusch, S and Lim, CK and Baird, R and Speers, D and Williams, DT and Currie, BJ and Kok, J},
title = {Diagnostic and phylogenetic perspectives of the 2023 Murray Valley encephalitis virus outbreak in Australia: an observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101089},
doi = {10.1016/j.lanmic.2025.101089},
pmid = {40550235},
issn = {2666-5247},
abstract = {BACKGROUND: An outbreak of Murray Valley encephalitis virus (MVEV), the largest since 1974, was observed in Australia between Jan 1 and July 31, 2023. This study aims to characterise the utility of diagnostic platforms, testing algorithms, and genomic characteristics of MVEV to facilitate a comprehensive framework for MVEV testing and surveillance in the outbreak setting.

METHODS: In this observational study, we assessed flavivirus diagnostics for all patients with suspected Murray Valley encephalitis in Australia from Jan 1 to July 31, 2023. We included all patients with confirmed Murray Valley encephalitis, probable Murray Valley encephalitis, or acute unspecified flavivirus infection using the Communicable Diseases Network Australia case definition. Cases were excluded if an alternative diagnosis was identified. We collected blood, serum, cerebrospinal fluid, brain tissue, urine, or a combination of these samples, as appropriate and at the discretion of the treating clinician. We conducted multimodal diagnostic testing, which included flavivirus-specific serological and nucleic acid amplification testing. Metagenomic next-generation sequencing, including next-generation deep sequencing, target-enrichment, and targeted amplification, was conducted on human and representative mosquito-derived samples obtained from established mosquito population surveillance programmes for phylogenetic analysis.

FINDINGS: 27 patients with encephalitis were assessed for MVEV between Jan 1, 2023, and July 31, 2023, 23 (85%) of whom fulfilled national case definitions for confirmed Murray Valley encephalitis. Patient ages ranged from 6 weeks to 83 years (median 62·0 years [IQR 31·0-67·5]) and patients were mostly male (21 [78%] male patients and six [22%] female patients). Incidence varied widely by geographical region and was highest in the Northern Territory (32·0 per 1 000 000 population). Diagnostic specimen collection generally occurred promptly (median 6·0 days [IQR 4·0-14·5] from symptom onset to diagnostic specimen collection). In seven patients, case assignation relied on convalescent serum samples to assess for seroconversion or an appropriate rise in antibody titre (to four times the initial value or greater), or both. MVEV-specific IgM was detectable in serum samples of 17 (81%) of 21 patients tested by day 7 and MVEV IgG or total antibody (TAb) were detected in 18 (100%) of 18 patients tested by day 30. MVEV-specific IgM (or TAb) and MVEV RNA were detected in cerebrospinal fluid collected within 14 days of symptom onset in nine (39%) of 23 patients and seven (28%) of 25 patients, respectively. Phylogenetic analysis revealed two circulating MVEV genotypes, G1A and G2, in mosquitoes and humans in 2023. In southeast Australia, only G1A was detected and probably introduced from enzootic foci in northern Australia.

INTERPRETATION: This study provides a comprehensive overview of the diagnostic workflows and phylogenetic evaluations used during the 2023 MVEV outbreak in Australia, emphasising the importance of a multimodal approach for accurate and timely confirmation of flavivirus infection. Further One Health surveillance for MVEV and other zoonotic flaviviruses is key, given potential expanded ecological niches in the context of episodic climatic events.

FUNDING: None.},
}

@article {pmid40549455,
year = {2025},
author = {Goryanin, I and Sorokin, A and Seitov, M and Emilov, B and Iskakov, M and Goryanin, I and Osmonov, B},
title = {Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.},
journal = {Journal of integrative bioinformatics},
volume = {},
number = {},
pages = {},
pmid = {40549455},
issn = {1613-4516},
abstract = {This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.},
}

@article {pmid40549420,
year = {2025},
author = {Podowski, JC and Forrester, S and Yaqub, T and Aqel, A and Abu Lubad, M and Mukhtar, N and Waqar Aziz, M and Sardar, N and Bin Aslam, H and Pervaiz, H and Wolfe, AJ and Schabacker, DS},
title = {Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high-throughput identification and lineage assignment in Pakistan.},
journal = {Microbial genomics},
volume = {11},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001422},
pmid = {40549420},
issn = {2057-5858},
mesh = {*Bacillus anthracis/genetics/classification/isolation & purification ; Pakistan ; *Anthrax/microbiology/epidemiology ; Animals ; *Genome, Bacterial ; Humans ; Genomics/methods ; Phylogeny ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Bacillus anthracis, the causative agent of anthrax, is a highly virulent zoonotic pathogen primarily affecting domesticated and wild herbivores. Human exposure to B. anthracis is primarily through contact with infected animals or contaminated animal products. In Pakistan, where livestock vaccines are largely unavailable and infected carcasses are often disposed of improperly, the risk to humans, wildlife and livestock is significant. Currently, the diagnosis of anthrax infections and outbreak tracing necessitates the isolation and culturing of B. anthracis, a process that requires BSL-3 facilities. In this study, we show that positive identification, genome reconstruction and lineage assignment can be accomplished using bioinformatic analysis of DNA extracted directly from environmental samples that would otherwise provide the starting material for isolation and culturing. This approach does not require laboratory target enrichment as is necessary for other pathogens, due in part to the extremely high bacterial load in the bloodstream in the deceased animals. Using these methods, we greatly expand the knowledge of endemic B. anthracis in Pakistan. We provide the first reference B. anthracis genomes from Pakistan since the 1970s and identify A.Br.014 Aust94 as a minor circulating sublineage alongside the dominant A.Br.047 Vollum. Future work will focus on the limits of detection and will determine if this bioinformatic method can be expanded more broadly for B. anthracis or other pathogens to replace typical culture-based methods.},
}

*Bacillus anthracis/genetics/classification/isolation & purification
Pakistan
*Anthrax/microbiology/epidemiology
Animals
*Genome, Bacterial
Humans
Genomics/methods
Phylogeny
Computational Biology/methods
High-Throughput Nucleotide Sequencing

@article {pmid40548737,
year = {2025},
author = {Ren, G and Ma, L and Yan, C and Xue, Q and Zhang, H and Wang, W and Ren, X and Lei, Y and Li, S and Liu, Y and Zheng, Q and Wei, S and Zhang, Y and Wang, X},
title = {Application of targeted metagenomic next-generation sequencing in pneumonia patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0171324},
doi = {10.1128/spectrum.01713-24},
pmid = {40548737},
issn = {2165-0497},
abstract = {After the coronavirus disease 2019 (COVID-19) pandemic, the incidence rate of mixed infections, especially in critically ill patients with severe pneumonia, increases due to the immunity gap and has also been proven to be associated with mortality, increasing the difficulty in accurate and rapid diagnoses. Here, we evaluated the performance of targeted metagenomic next-generation sequencing (mNGS), including capture hybridization-based mNGS (chNGS) and multiplex PCR-based targeted mNGS (tNGS), in diagnosing pneumonia. Patients admitted to the Pulmonary and Critical Care Medicine, Beijing Aerospace General Hospital, and diagnosed as suspected pulmonary infections from April 2022 to March 2024 were retrospectively evaluated, and 110 patients were finally enrolled. According to the final comprehensive clinical diagnoses, there were 99 patients diagnosed with definite infectious diseases. Single infections accounted for 58.6% of these patients (58/99), while mixed infections occurred in about half of these patients (41.4%, 41/99) and were found in most of the death cases. Pseudomonas aeruginosa (n = 22), Pneumocystis jirovecii (n = 15), and severe acute respiratory syndrome coronavirus 2 (n = 13) were found to be the most common bacterial, fungal, and viral pathogens, respectively. Taking final comprehensive clinical diagnoses as the reference standard, the total coincidence rate (TCR) of chNGS can reach up to 64.1% (95% confidence interval [CI], 54.8%-73.3%), while the TCR of conventional methods was only 39.8% (95% CI, 30.4%-49.3%). The performance of tNGS was slightly superior to that of chNGS, while chNGS yielded more false-negative results, especially for viral detection. Additionally, chNGS combined with tNGS can improve the TCR to 81.3% (95% CI, 62.1%-100.0%).IMPORTANCEThis is the first report on evaluating the performance of capture hybridization-based metagenomicnext-generation sequencing (chNGS), multiplex PCR-based targeted mNGS (tNGS), and conventional methods in diagnosing pneumonia. Our findings emphasized the importance of chNGS and tNGS in diagnosing, managing, and ruling out infections, and an era of widespread application of regional tNGS in monitoring and diagnosing infections with high sensitivity and low economic burden on patients can be expected.},
}

@article {pmid40548531,
year = {2025},
author = {Zhang, J and Li, Y and Zheng, J and Ding, X},
title = {Metagenomic Next-Generation Sequencing Provides a Reliable Method for Early Diagnosis of Pneumocystis jirovecii Pneumonia After Kidney Transplant: A Single-Center Retrospective Cohort Study.},
journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation},
volume = {23},
number = {5},
pages = {334-341},
doi = {10.6002/ect.2024.0250},
pmid = {40548531},
issn = {2146-8427},
mesh = {Humans ; Retrospective Studies ; *Pneumonia, Pneumocystis/diagnosis/microbiology/epidemiology/immunology ; *Pneumocystis carinii/genetics/pathogenicity/isolation & purification ; Female ; Male ; *Kidney Transplantation/adverse effects ; Middle Aged ; Predictive Value of Tests ; Adult ; *High-Throughput Nucleotide Sequencing ; Early Diagnosis ; China/epidemiology ; *Metagenomics ; Time Factors ; Risk Factors ; Treatment Outcome ; Incidence ; },
abstract = {OBJECTIVES: Pneumocystis jirovecii pneumonia, a common pulmonary infection after kidney transplant, cannot be detected by conventional culture methods, and limitations have been shown with lung tissue biopsy, sputum collection, and sample smear staining. Early diagnosis is key as long-term survival is decreased in patients with Pneumocystis jirovecii pneumonia who are not treated in a timely and effective manner.

MATERIALS AND METHODS: From January 2018 to January 2023, our study enrolled 110 patients with pulmonary infection seen at the First Affiliated Hospital of Xi'an Jiaotong University (China). Of these patients, 46 had confirmed Pneumocystis jirovecii pneumonia per metagenomic next-generation sequencing or conventional detection methods. We compared percentages of positive tests, other pathogen species, and other factors between the 2 test methods. Clinical characteristics of patients with (n = 46) and without (n = 64) Pneumocystis jirovecii were analyzed retrospectively.

RESULTS: Overall incidence of PJP was 2.3% (46/1977). Among 46 patients diagnosed with Pneumocystis jirovecii pneumonia, average time of onset post-transplant was 7.21 ± 2.55 months; 42 patients were cured, and 4 patients died. Thirty-three patients had mixed pulmonary infections, with Pneumocystis jirovecii and human cytomegalovirus being the most common pathogen combination, and 13 patients had monotypic pulmonary infections. Sixteen patients were Pneumocystis jirovecii positive according to conventional pathogen detection, for a detection rate of 34.8% (16/46), with significant difference shown between detection methods (χ2 = 92.0, P < .01). Patients who were treated with tacrolimus had insufficient use of sulfamethoxazole-trimethoprim and previous cytomegalovirus infection, and patients with acute rejection were more likely to develop Pneumocystis jirovecii pneumonia (P < .05).

CONCLUSIONS: Metagenomic next-generation sequencing showed more advantages in early diagnosis of Pneumocystis jirovecii pneumonia. Precision medicine can be adopted to reduce costs and improve cure rates based on results of metagenomic next-generation sequencing.},
}

Humans
Retrospective Studies
*Pneumonia, Pneumocystis/diagnosis/microbiology/epidemiology/immunology
*Pneumocystis carinii/genetics/pathogenicity/isolation & purification
Female
Male
*Kidney Transplantation/adverse effects
Middle Aged
Predictive Value of Tests
Adult
*High-Throughput Nucleotide Sequencing
Early Diagnosis
China/epidemiology
*Metagenomics
Time Factors
Risk Factors
Treatment Outcome
Incidence

@article {pmid40548332,
year = {2025},
author = {Pita, L and Maldonado, M and Koutsouveli, V and Riesgo, A and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {283},
pmid = {40548332},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Chondrosia reniformis (kidney sponge; Porifera; Demospongiae; Chondrillida; Chondrillidae). The genome sequence has a total length of 117.37 megabases. Most of the assembly (99.98%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs. Gene annotation of the host organism assembly on Ensembl identified 17,340 protein-coding genes. The metagenome of the specimen was also assembled and 53 binned bacterial genomes were identified, including 40 high-quality MAGs that were representative of a typical high microbial abundance sponge and included three candiate phyla (Poribacteria, Latescibacteria, Binatota).},
}

@article {pmid40548295,
year = {2025},
author = {Diwan, A and Harke, S and Panche, AN},
title = {Exploration of novel bioactive compounds from the microbiome of fish and shellfish as an alternative to replace antibiotic drugs in aquaculture farming.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e8},
pmid = {40548295},
issn = {2632-2897},
abstract = {The use of antibiotics in fish and shrimp aquaculture all over the world was found to be only partially successful in preventing infectious diseases. However, their overuse has resulted in the contamination of closed aquatic ecosystems, reduced antibiotic resistance in organisms that fight infectious diseases, and compromised the effectiveness of various antibiotic medications in controlling diseases. Excessive use of antibiotics damages aquaculture species and impacts human health, also rendering the most potent antibiotics increasingly ineffective, with limited alternatives. Therefore, intensive research efforts have been made to replace antibiotics with other protocols and methods like vaccines, phage therapy, quorum quenching technology, probiotics, prebiotics, chicken egg yolk antibody (IgY), and plant therapy," etc. Though all these methods have great potential, many of them are still in the experimental stage, except for fish vaccines. All these alternative technologies need to be carefully standardized and evaluated before implementation. In recent times, after realizing the importance of the gut microbiome community in maintaining the health of animals, efforts have been made to use the microbiome strains for the prevention of pathogenic bacterial and viral infections. Now it has been experimentally proven that animals should possess a healthy microbiome community in their gut tract to strengthen the immune system and prevent the entry of harmful pathogens. Investigations are now being carried out on the derivation of various bioactive compounds from the gut microbiome strains and their structural profile and functionality using the molecular tools of metagenomics and bioinformatics. Such newly discovered compounds from microbiomes can be used as potential alternatives to replace antibiotic drugs in the aquaculture industry. These alternatives are likely to emerge as breakthroughs in animal health management and farming, with effects on cost efficiency, species health, productivity, and yield enhancement. Therefore, introducing new micro-innovative technologies into an overall health management plan will be highly beneficial.},
}

@article {pmid40547922,
year = {2025},
author = {Yuan, B and Jiang, T and Han, J and Wang, M},
title = {Neurobrucellosis with negative serological examination: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1583891},
pmid = {40547922},
issn = {2296-858X},
abstract = {Neurobrucellosis is an uncommon occurrence that can arise as a consequence of brucellosis. However, its clinical symptoms are severe and have the potential to be life-threatening. Timely detection, prompt diagnosis, and early treatment are crucial factors. Clinically, the gold standard for diagnosing pathogenic microorganisms is through culture. However, this method is hindered by its lengthy culture duration, low rate of positive results, and the absence of typical clinical signs of neurobrucellosis. Consequently, misdiagnosis and delayed treatment are common. Metagenomics next-generation sequencing (mNGS) technology is a novel approach in microbiological diagnosis that enables the simultaneous detection of all microorganisms present in a sample, including viruses, bacteria, fungus, and parasites. This method holds significant diagnostic significance for viral disorders affecting the central nervous system. This paper reports a case of neurobrucellosis detected by mNGS after a negative serological test, as well as a review of the relevant literature.},
}

@article {pmid40547485,
year = {2025},
author = {Su, C and Zhu, M and Guo, Y and Sun, J and Liu, M and Ma, Y and Xu, Y and Bai, Y and Che, X and Zhang, N},
title = {DMAHDM@MPC nanoparticles in orthodontic adhesive inhibit cariogenic bacteria and sugar metabolism to prevent enamel demineralization.},
journal = {Materials today. Bio},
volume = {33},
number = {},
pages = {101969},
pmid = {40547485},
issn = {2590-0064},
abstract = {During orthodontic treatment, poor oral hygiene often facilitates the proliferation of cariogenic bacteria, particularly Streptococcus mutans, leading to lactic acid accumulation and subsequent enamel demineralization. To mitigate this issue, Dimethylaminohexadecyl methacrylate (DMAHDM) was incorporated onto the protein-repellent surface of 2-Methacryloyloxyethyl phosphorylcholine (MPC), resulting in the formation of a DMAHDM@MPC composite. This composite was then integrated into resin-modified glass ionomer cement (RMGIC) to develop an antimicrobial orthodontic adhesive, termed RMGIC + MPC + DMAHDM (RMD). This study demonstrated that DMAHDM@MPC nanoparticles self-assembled into a core-shell structure, thereby enhancing the antimicrobial activity. A six-month randomized controlled trial (RCT) involving 29 orthodontic patients, along with metagenomic and metabolomic analyses, revealed that RMD significantly reduced plaque accumulation by selectively inhibiting pathogenic bacteria while preserving beneficial microbiota. Additionally, MPC was shown to competitively bind to sucrose-6-phosphatase (SPP) in pathogenic bacteria, inhibiting sucrose synthesis and carbohydrate metabolism, thus reducing the production of organic acids. In conclusion, RMD effectively prevents enamel demineralization by selectively targeting cariogenic bacteria and their associated sugar metabolism pathways during orthodontic treatment.},
}

@article {pmid40546666,
year = {2025},
author = {Jeyaraman, N and Jeyaraman, M and Dhanpal, P and Ramasubramanian, S and Nallakumarasamy, A and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF},
title = {Integrative review of the gut microbiome's role in pain management for orthopaedic conditions.},
journal = {World journal of experimental medicine},
volume = {15},
number = {2},
pages = {102969},
pmid = {40546666},
issn = {2220-315X},
abstract = {The gut microbiome, a complex ecosystem of microorganisms, has a significant role in modulating pain, particularly within orthopaedic conditions. Its impact on immune and neurological functions is underscored by the gut-brain axis, which influences inflammation, pain perception, and systemic immune responses. This integrative review examines current research on how gut dysbiosis is associated with various pain pathways, notably nociceptive and neuroinflammatory mechanisms linked to central sensitization. We highlight advancements in meta-omics technologies, such as metagenomics and metaproteomics, which deepen our understanding of microbiome-host interactions and their implications in pain. Recent studies emphasize that gut-derived short-chain fatty acids and microbial metabolites play roles in modulating neuroinflammation and nociception, contributing to pain management. Probiotics, prebiotics, synbiotics, and faecal microbiome transplants are explored as potential therapeutic strategies to alleviate pain through gut microbiome modulation, offering an adjunct or alternative to opioids. However, variability in individual microbiomes poses challenges to standardizing these treatments, necessitating further rigorous clinical trials. A multidisciplinary approach combining microbiology, immunology, neurology, and orthopaedics is essential to develop innovative, personalized pain management strategies rooted in gut health, with potential to transform orthopaedic pain care.},
}

@article {pmid40544959,
year = {2025},
author = {Lin, T and Liu, X and Wu, L and Wu, Q and Zeng, H and Li, W and Tang, H and Zhao, J and Ding, Z},
title = {Clinical efficacy of metagenomic Next-Generation Sequencing for Pathogen Detection in Septic Patients based on Blood Samples in Intensive Care Units.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {100897},
doi = {10.1016/j.ijmmb.2025.100897},
pmid = {40544959},
issn = {1998-3646},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is considered superior to traditional culture for pathogen detection. However, its utility in septic patients based on blood samples remains limited.

METHODS: This research aimed to compare mNGS and culture-based diagnostics in 78 septic patients, with 25 with sepsis and 53 with septic shock.

RESULTS: Among 68 cases with matching sample types, pathogens of 38 cases were solely identified through mNGS, and in contrast, 2 cases had their pathogens detected by microbiological culture only. Moreover, 17 of 63 cases (26.98%) were found to be positive by both mNGS and culture, and 6 of 63 cases (9.52%) came negative under both diagnostic methods. Regardless of prior antibiotic exposure, the positive rate of mNGS, which was 80.77%, was significantly higher than that of culture (37.18%). Significantly, among the 38 septic patients diagnosed solely by mNGS, 23 patients achieved a favorable outcome after physicians adjusted the treatment based on the mNGS findings.

CONCLUSION: In conclusion, mNGS offered a swift and accurate means for pathogen identification, and thus making this approach as a promising technology for detecting sepsis.},
}

@article {pmid40544684,
year = {2025},
author = {Eckermann, C and Klein, CJ and Schäfer, F and Thiel, M and Weiss, AV and Motz, C and Lienkamp, K and Hannig, M and Schneider, M},
title = {Probiotics-embedded polymer films for oral health: Development, characterization, and therapeutic potential.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {255},
number = {},
pages = {114886},
doi = {10.1016/j.colsurfb.2025.114886},
pmid = {40544684},
issn = {1873-4367},
abstract = {The oral microbiome plays a crucial role in maintaining homeostasis, and microbial imbalances contribute to diseases such as periodontitis. Probiotic strains such as Lactobacillus rhamnosus and Lactobacillus reuteri have shown potential in restoring microbial balance in the oral cavity. However, their application remains challenging due to limited survival and adherence under intraoral conditions. Thus, we aimed to develop and evaluate mucoadhesive polymer films for local probiotic delivery. L. rhamnosus and L. reuteri were microencapsulated via spray drying and embedded in films composed of hydroxypropyl methylcellulose-polyvinyl alcohol (HPMC-PVA) and foamed polyvinyl alcohol (PVA). The films were characterized in terms of bacterial viability, tensile strength, folding endurance, and mucoadhesive properties. A proof-of-concept in vivo study was conducted by intraorally exposing enamel samples to two volunteers for eight hours, followed by confocal imaging and morphological analysis of adherent bacteria. Microencapsulation preserved high bacterial viability. The resulting films exhibited suitable mechanical properties and strong mucoadhesion. Biological evaluation revealed clear effects: films containing microencapsulated bacteria led to a statistically significant increase in adherent rod-shaped lactobacilli and a consistent reduction in coccoid bacteria associated with dysbiosis. The foamed PVA formulation showed the most pronounced modulation of the enamel-associated microbiota. These findings demonstrate that probiotic films can enable both bacterial stabilization and effective oral delivery. The system enhances colonization by beneficial bacteria while reducing potentially pathogenic cocci. This approach presents a promising strategy for microbiome-based prevention of oral diseases and merits further clinical investigation.},
}

@article {pmid40544677,
year = {2025},
author = {Bortoluzzi, C and Watson, M and Iuspa, MA and Lumpkins, B and Mathis, G and Jones, M and Hofacre, C},
title = {Precision biotics enhance growth performance in broiler chickens by selectively modifying their intestinal microbiome to better respond to enteric challenges.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105454},
doi = {10.1016/j.psj.2025.105454},
pmid = {40544677},
issn = {1525-3171},
abstract = {Precision biotics (PB) are innovative feed additives designed to influence key metabolic pathways in the microbiome, particularly those involved in short-chain fatty acid (SCFA) production. These SCFAs are crucial for the healthy development and functionality of the gastrointestinal tract (GIT) in chickens. Our hypothesis was that adding a glycan-based PB to the diet would steer microbial metabolism towards increased SCFA production in the ceca, thereby reducing the adverse effects of necrotic enteritis (NE) in chickens. These studies evaluated the supplementation of PB on the cecal microbiome and growth performance in broiler chickens exposed to a necrotic enteritis (NE) challenge. Experiment 1: Day-old chicks were assigned to three treatment groups: a control, a challenged control, and a challenged group supplemented with PB. The birds were vaccinated for coccidiosis at day 0 and challenged with Clostridium perfringens. Cecal content was collected from one bird per pen on days 22 and 42 for microbiome analysis. Experiment 2: Day-old chicks were again assigned to three treatments: control, challenged control, and challenged with PB. All birds were vaccinated for coccidiosis and challenged with Eimeria maxima on day 14 and later with C. perfringens. On day 21, birds were euthanized for NE lesion scoring. In Exp. 1, the supplementation of PB significantly improved (P < 0.05) the growth performance of the challenged birds. An increased relative abundance of species related to SCFA production was observed on day 42, including several Faecalibacterium species (P < 0.05). This was paired with an increased relative abundance of both propionate (P<0.05) and butyrate pathways in birds with PB supplementation. In Exp. 2, on day 21, the challenge impaired growth performance, but the supplementation of PB counteracted this effect (P < 0.05). On day 42, the supplementation of PB improved BW by 10 % (P < 0.0001), and the FCR by 8.4 % (P < 0.0001) when compared to the challenged group. The supplementation of PB reduced NE associated mortality (5.5 vs 0.5 %; P = 0.002) and reduced the lesions characteristic of NE (P < 0.0001). Taken together, the microbiome metabolic shift observed with the supplementation of PB explains the improvement in growth performance, resilience to enteric stress and faster recovery of the intestine, which consequently improves welfare and the sustainability of poultry production.},
}

@article {pmid40544571,
year = {2025},
author = {Cao, J and Xu, Y and Zhang, C and Li, X and Liu, R and Wang, X and Dai, X},
title = {Enhancing the participation of water in the anaerobic digestion of sewage sludge for highly efficient methanogenesis.},
journal = {Water research},
volume = {284},
number = {},
pages = {124047},
doi = {10.1016/j.watres.2025.124047},
pmid = {40544571},
issn = {1879-2448},
abstract = {Water is widely present in sewage sludge, in which it constitutes the largest proportion; however, its participation in the methanogenesis of sludge has been overlooked. Here we revealed the mechanisms enhancing the participation of water in methanogenesis of sludge. Through stable isotope tracing experiments, we observed that isoelectric point pretreatment significantly enhanced the participation of water in CO2-reduction methanogenesis. Experimental results show that solid-liquid non-covalent interactions and interfacial water ordering in sludge were significantly enhanced. The former outcome drove electron transfer, while the latter provided an efficient proton channel. Combined with hydrogen/deuterium kinetic isotope effect (KIE) tests, it demonstrated that the water-mediated proton-coupled electron transfer (PCET) in the sludge were enhanced, accompanied by possible quantum tunnelling effect (KIE >> 10). Variations in the concentrations of key enzymes indicated that enhancing water-mediated PCET promoted both intracellular and extracellular electron-proton flow and accelerated the efficiency of mutual conversion between NADH and NAD[+], strongly driving ATP synthesis. Further genome-centric metagenomic analysis and reaction thermodynamic calculations revealed that enhancing water-mediated PCET triggered enrichment of CO2-reduction methanogenic consortia and effectively bypassed the limitation of H2 partial pressure, providing a thermodynamic advantage to promote collaborative methanogenic metabolisms. These findings provide a theoretical basis for regulating the methanogenesis of perishable organic solid waste by water.},
}

@article {pmid40544520,
year = {2025},
author = {Zhang, E and Gong, GA and Huang, S and Bao, Y and Ji, L and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Zhang, W},
title = {Viral Metagenomics of the Bharal (Pseudois nayaur) within the Qinghai-Tibet Plateau Revealed Diverse Viruses.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {143-152},
doi = {10.33073/pjm-2025-012},
pmid = {40544520},
issn = {2544-4646},
mesh = {Animals ; *Metagenomics ; Phylogeny ; Genome, Viral ; Tibet ; Feces/virology ; *Viruses/genetics/classification/isolation & purification ; Genetic Variation ; },
abstract = {The Qinghai-Tibetan Plateau (QTP) provides a home to diverse flora and fauna, and its ecosystems are unique worldwide. The study focused on the bharal, an endemic species found in the QTP and adjacent regions. We applied viral metagenomics technology to extract samples from the feces of 10 wild bharal. Viral nucleic acids were isolated, enriched, and sequenced from these samples, revealing the presence of a novel strain of Astroviridae virus. Phylogenetic analysis and sequence comparison identified this virus as part of the Mamastro-virus, forming a cluster with other Mamastrovirus species. Recombination analysis confirmed a multiple recombination event, suggesting that the new strain may be a potential recombinant. Additionally, nearly complete genome sequences of viruses belonging to the family Circoviridae were characterized, and a phylogenetic tree was constructed based on genotyping and predicted amino acid sequence analysis of the rep protein. Overall, this study helps us better understand the viral communities in the gut microbiome of the rare bharal. Moreover, the new recombinant discovered in this study will provide insights into the origin, genetic diversity, and evolution of bharal from the QTP and play a crucial role in future research on its presence in the intestinal ecology of sheep.},
}

Animals
*Metagenomics
Phylogeny
Genome, Viral
Tibet
Feces/virology
*Viruses/genetics/classification/isolation & purification
Genetic Variation

@article {pmid40544519,
year = {2025},
author = {Yu, X and Liang, J and Yang, R and Gai, W and Zheng, Y},
title = {Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {192-205},
doi = {10.33073/pjm-2025-016},
pmid = {40544519},
issn = {2544-4646},
mesh = {Humans ; Infant ; *High-Throughput Nucleotide Sequencing ; Male ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; Intensive Care Units, Pediatric ; *Trachea/microbiology ; *Pneumonia/microbiology/diagnosis/virology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; Coinfection/microbiology ; },
abstract = {Pneumonia is a leading cause of mortality in children. While metagenomic next-generation sequencing (mNGS) has the potential to detect all the microorganisms in pneumonia patients, the relationship between these microorganisms and the patients' clinical characteristics remains to be established. Fifty-five children, diagnosed with severe pneumonia and undergoing tracheal aspirate (TA) mNGS for pathogen detection at The Heilongjiang Hospital of Beijing Children's Hospital between July 2021 and November 2022, were included in this study. The clinical characteristics, pathogen distribution, and microbiome features of these children were analyzed. Results showed that the rate of mixed infections was notably high (80%, 44/55), with bacterial-viral infections being the most common. Streptococcus pneumoniae, Mycoplasma pneumoniae (MP), Candida albicans, and Respiratory syncytial virus (RSV) were the most common pathogens in this cohort. Furthermore, RSV and S. pneumoniae were the most prevalent pathogens in children younger than 12 months (infants), while MP and Haemophilus influenzae were more commonly identified in children between 12 and 144 months. Increased richness and diversity of the microbiota were observed in the TA of the older children. Linear discriminant analysis (LDA) effect size (LEfSe) analysis identified that RSV and Streptococcus mitis were the specific species associated with infants. In contrast, Human bocaparvovirus 1 and Prevotella histicola were significantly enriched in the older children. In addition, the top 20 most abundant species exhibited correlations with neutrophil count and C-reactive protein. This study emphasizes the significance of employing mNGS to understand better the clinical characteristics and microbial diversity in pediatric patients with severe pneumonia.},
}

Humans
Infant
*High-Throughput Nucleotide Sequencing
Male
Child, Preschool
Female
*Metagenomics/methods
Child
Intensive Care Units, Pediatric
*Trachea/microbiology
*Pneumonia/microbiology/diagnosis/virology
Microbiota/genetics
Bacteria/genetics/classification/isolation & purification
Coinfection/microbiology

@article {pmid40544513,
year = {2025},
author = {Muccee, F and Mohiuddin, F and Shahab, A and Almajwal, A and Afsar, T and Amor, H and Razak, S},
title = {Whole Genome Shotgun Sequencing-Based Insights into the Benzene and Xylene Degrading Potentials of Bacteria.},
journal = {Polish journal of microbiology},
volume = {74},
number = {2},
pages = {244-261},
doi = {10.33073/pjm-2025-020},
pmid = {40544513},
issn = {2544-4646},
mesh = {*Xylenes/metabolism ; *Benzene/metabolism ; Biodegradation, Environmental ; Whole Genome Sequencing ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Genome, Bacterial ; Soil Microbiology ; Phylogeny ; Soil Pollutants/metabolism ; DNA, Bacterial/genetics ; Shotgun Sequencing ; },
abstract = {Due to their hazardous effects on human health and air quality, benzene and xylene constitute the primary pollutants. Coupling the physicochemical strategies with bacterial bioremediation is an emerging mode of decontamination. Considering the limited understanding of benzene and xylene degradation pathways in the genus Bacillus, failure of earlier documented bacteria to degrade these compounds due to poor optimization and complicated real-world contamination scenarios, we initiated the current project. It is an attempt to explore the gene repertoire and pathways associated with the bioremediation of benzene and xylene in new and efficient bacteria. Eleven bacteria were isolated from tannery industry soil in a previous study. Bacterial DNA was extracted by the organic method. To prepare a sample for whole genome sequencing (WGS) analysis, a mixture of genomic DNA was made by adding DNA from each isolate in equimolar concentration (100 ng). The sample was subjected to WGS. Results obtained as FASTq files were submitted to Sequence Read Archives (SRA), NCBI, to get the accession number assigned. Taxonomic profiling revealed that the sample was composed of phyla Proteobacteria (76%), Firmicutes (16%) and unclassified phyla (8%). Functional annotation unraveled the presence of benzoate, m-, p- and o-xylene isomers, benzene, aminobenzoate, 2-, 3- and 4-fluorobenzoate, toluene, chloroalkane and chloroalkene, naphthalene, polycyclic aromatic hydrocarbons (PAHs), dioxin, caprolactum, atrazine, styrene, and chlorobenzene and chlorocyclohexane degradation enzymes and pathways. It is the first ever study documenting the benzene degradation pathway similar to Gram-negative bacteria, in the genus Bacillus, inhabiting the tannery soil and coexistence of metabolic pathways for multiple organic pollutants.},
}

*Xylenes/metabolism
*Benzene/metabolism
Biodegradation, Environmental
Whole Genome Sequencing
*Bacteria/metabolism/genetics/classification/isolation & purification
*Genome, Bacterial
Soil Microbiology
Phylogeny
Soil Pollutants/metabolism
DNA, Bacterial/genetics
Shotgun Sequencing

@article {pmid40544449,
year = {2025},
author = {Yew, WC and Young, GR and Cheung, W and Nelson, A and Berrington, JE and Smith, DL},
title = {Protocol to study the inter-relationship between phageome and lipidome in low-volume preterm milk.},
journal = {STAR protocols},
volume = {6},
number = {3},
pages = {103917},
doi = {10.1016/j.xpro.2025.103917},
pmid = {40544449},
issn = {2666-1667},
abstract = {Bacteriophages and lipids in human milk may benefit preterm infant health by modulating gut microbiomes. Here, we present a protocol for analyzing the phageome and lipidome in preterm milk using shotgun metagenomics and untargeted lipidomics approaches, respectively. We describe steps for extracting phages and lipids in low-volume milk, characterizing phageome using an in-house bioinformatic pipeline, and statistical analysis to correlate the phageome and lipidome. Finally, we detail an in vitro assay to examine the associations between fatty acid chain length and phage morphotype. For complete details on the use and execution of this protocol, please refer to Yew et al.[1].},
}

@article {pmid40544407,
year = {2025},
author = {Matos, JSS and Demoliner, M and Gularte, JS and Filippi, M and de Abreu Góes Pereira, VM and de Barros, MP and Spilki, FR},
title = {SARS-CoV-2 Spillback in Opossums, Southern Brazil.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40544407},
issn = {1612-9210},
abstract = {This study focuses on monitoring of SARS-CoV-2 in free-living animals in the Vale dos Sinos region, Rio Grande do Sul, Brazil, aiming to verify the presence of this emerging virus using next-generation sequencing (NGS) technique. Rectal and oral swab samples were collected from 52 white-eared opossums (Didelphis albiventris) and submitted to metagenomics and subsequently directed SARS-CoV-2 genome sequencing. Five positive samples were found to originate from these animals' contact with human waste or contaminated water bodies, indicating the spillover of SARS-CoV-2 to D. albiventris.},
}

@article {pmid40544290,
year = {2025},
author = {Chege, MN and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA},
title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {70},
pmid = {40544290},
issn = {2524-4671},
support = {R01 AG071684/NH/NIH HHS/United States ; R01 AG071684/NH/NIH HHS/United States ; DEB 1840223//National Science Foundation/ ; },
abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While high-throughput sequencing is commonly used to characterize bacterial communities in animal microbiota, these methods are less often applied to gut eukaryotic composition. Here we used shotgun metagenomic sequencing to characterize eukaryotic diversity in the microbiomes of wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, sequencing depth, and season of sample collection.

RESULTS: We analyzed a total of 75 fecal samples collected in 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of all samples, respectively (percentages indicate the percent of samples in which each kingdom was observed). Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effects of season, host age, or host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).

CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is important for primate health monitoring and management strategies.},
}

@article {pmid40544256,
year = {2025},
author = {Mannavola, CM and De Maio, F and Marra, J and Fiori, B and Santarelli, G and Posteraro, B and Sica, S and D'Inzeo, T and Sanguinetti, M},
title = {Bloodstream infection by Lactobacillus rhamnosus in a haematology patient: why metagenomics can make the difference.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {47},
pmid = {40544256},
issn = {1757-4749},
support = {PE00000007, INF-ACT//EU funding for the MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; },
abstract = {BACKGROUND: Bloodstream infections (BSIs) pose a persistent threat to hospitalized patients, particularly those who are immunocompromised and susceptible to infections caused by anaerobic or facultative anaerobic bacteria. Alterations in gut microbiota composition can predispose individuals to intestinal domination by one or more pathobionts, increasing the risk of bacterial translocation into the bloodstream and subsequent bacteremia.

CASE PRESENTATION: We report the case of a 20-year-old female with multiple relapsed/refractory Philadelphia-negative B-cell acute lymphoblastic leukemia, initially referred to our hematology center for CAR-T cell therapy. The patient ultimately underwent allogeneic hematopoietic stem cell transplantation, which was complicated by infections, moderate-to-severe graft-versus-host disease, hepatic sinusoidal obstruction syndrome, and transplant-associated thrombotic microangiopathy, all contributing to a fatal outcome. Blood cultures obtained in the final week before the patient succumbed to multi-organ toxicity grew Lactobacillus rhamnosus. A fecal sample collected concurrently for intestinal microbiota characterization revealed a marked predominance of Bacillota (98.5%), with Lacticaseibacillus dominating at 47.9%, followed by Pediococcus (18.59%) and Staphylococcus (3.5%) at the genus level. We performed genomic comparison between the L. rhamnosus isolated from blood cultures and the best-matched strain detected in the intestinal microbiota.

CONCLUSIONS: We report the isolation of L. rhamnosus from blood cultures in a patient post hematopoietic cell transplantation, with genomic similarity to a gut-dominant L. rhamnosus strain. This case highlights the potential link between intestinal domination and subsequent bloodstream infection, supporting the value of gut microbiota profiling as an adjunctive tool for monitoring high-risk patients, such as hematopoietic cell transplant recipients.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13099-025-00722-3.},
}

@article {pmid40543872,
year = {2025},
author = {Yu, PF and Wang, D and Ma, XG and Fu, YB and Han, LY and Wang, A and Jiang, DL and Sun, HW and Li, DX and Jin, X and Yang, KD and Zhang, LC and Tang, YL},
title = {System characteristics of integrated continuous flow simultaneous partial Nitrification, Anammox and Denitrification (SNAD) for NH4[+]-rich wastewater: performance, sludge evolution, metagenomic sequencing analysis.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122175},
doi = {10.1016/j.envres.2025.122175},
pmid = {40543872},
issn = {1096-0953},
abstract = {The integrated process of simultaneous partial nitrification, anammox, and denitrification (SNAD) is designed to achieve efficient nitrogen removal and carbon reduction. This study details the design and successful implementation of an innovative, single-piece continuous flow SNAD system for treating high concentration NH4[+] wastewater. The system leverages simultaneous anammox and denitrification (SAD) granular sludge and employs a strategy of dosing partial nitrification sludge, alongside meticulous control of pH, dissolved oxygen (DO), free ammonia (FA), and free nitrous acid (FNA) was applied to initiate the SNAD process. The spectral analysis results suggest a marginal reduction in the stability and flocculation properties of the SNAD granular sludge. Molecular analysis via 16S rRNA gene sequencing revealed ammonia-oxidizing bacteria, anaerobic ammonia-oxidizing bacteria, and denitrifying bacteria as the predominant microbial populations within the SNAD system. A marked increase in the abundance of related functional genes was observed, alongside a reduction in quorum sensing (QS) and ATP-Binding Cassette (ABC) transporter proteins. These findings suggest a possible attenuation in the secretion of native signaling proteins within the SNAD system.},
}

@article {pmid40543557,
year = {2025},
author = {Nunley, BE and Weixler, A and Kim, HG and Xie, H and Sereewit, J and Hajian, P and Ellis, S and Mills, MG and Pérez-Osorio, AC and Goya, S and Gov, J and Dewar, R and Fernandes, G and Templeton, KE and Maloney, DM and Greninger, AL and Roychoudhury, P},
title = {Clinical performance evaluation of a tiling amplicon panel for whole genome sequencing of respiratory syncytial virus.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmoldx.2025.05.005},
pmid = {40543557},
issn = {1943-7811},
abstract = {Accurate genomic characterization of respiratory syncytial virus (RSV) is crucial for studies of epidemiology and viral evolution, including monitoring potential escape from newly authorized vaccines and prophylactic monoclonal antibodies. We adapted a viral genome tiling amplicon panel (UW-ARTIC) and developed a custom bioinformatic pipeline for high-throughput, cost-effective sequencing of both RSV-A and RSV-B subgroups. We established genome acceptability criteria and determined the performance characteristics of the panel including assay sensitivity, specificity, breadth of genome recovery, accuracy, and precision using contrived and remnant clinical specimens. High-quality genomes (>95% genome completeness; >500X and >1000X average depth for whole genome and fusion gene respectively) were recovered from samples with Ct ≤ 30 (∼594 and 2,004 copies per reaction for RSV-A and RSV-B respectively). Minor variants were accurately identified at >5% allele frequency. The assay showed high accuracy when compared to Sanger, shotgun metagenomic, and hybridization capture-based sequencing, as well as high repeatability and reproducibility. The UW-ARTIC RSV panel has utility for cost-effective RSV genome recovery in public health, clinical, and research applications. It has been used to generate FDA-reportable data for clinical trials of RSV antiviral products, with robust performance in global samples from as recently as the 2023/24 season. Continued genomic surveillance and future updates to primers will be essential for continued recovery of genomes as RSV continues to evolve.},
}

@article {pmid40543442,
year = {2025},
author = {Li, Y and Liu, J and Huang, G and Chen, Z and Ma, X and Huang, L},
title = {Metagenomic diagnosis of congenital tuberculosis with coinfections in an extremely preterm infant conceived via in vitro fertilization.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116960},
doi = {10.1016/j.diagmicrobio.2025.116960},
pmid = {40543442},
issn = {1879-0070},
abstract = {We describe a case of congenital tuberculosis in an extremely preterm infant (24 weeks' gestation, 800 g) conceived via in vitro fertilization, complicated by cytomegalovirus and Klebsiella pneumoniae coinfections. Diagnosis was confirmed by metagenomic next-generation sequencing after conventional tests were inconclusive. Management included anti-tuberculosis, antiviral, and antibacterial therapy, as well as surgical correction of a patent ductus arteriosus. The infant demonstrated significant clinical recovery, with resolution of pulmonary, splenic, and cardiac abnormalities. This case underscores the value of advanced molecular diagnostics and multidisciplinary care in managing life-threatening neonatal infections.},
}

@article {pmid40543441,
year = {2025},
author = {Hong, WL and Yao, LY and Zhong, Z and Meng, FJ and Zhang, WY and Lu, K and She, ZY},
title = {Successful management of Nocardia farcinica brain abscess in an immunocompetent adult with trimethoprim/sulfamethoxazole hypersensitivity: A case report and review.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116954},
doi = {10.1016/j.diagmicrobio.2025.116954},
pmid = {40543441},
issn = {1879-0070},
abstract = {BACKGROUND: Nocardia farcinica brain abscesses are rare in immunocompetent individuals. Trimethoprim/sulfamethoxazole (TMP/SMX) is first-line therapy, but hypersensitivity reactions necessitate alternative regimens. This report details successful management in a TMP/SMX-allergic patient.

CASE REPORT: A 38-year-old immunocompetent male presented with recurrent seizures. MRI revealed expanding left frontal lobe lesions. Surgical excision and metagenomic next-generation sequencing (mNGS) confirmed N. farcinica. Due to hypersensitivity to TMP/SMX, an alternative antibiotic regimen consisting of intravenous imipenem/cilastatin for 18 days and amikacin for 7 days was administered, followed by oral amoxicillin for 435 days and minocycline for 252 days. This therapeutic approach resulted in effective infection control, as evidenced by sustained clinical improvement over a 28-month follow-up period.

CONCLUSION: N. farcinica brain abscess can occur in immunocompetent adults, posing therapeutic challenges with TMP/SMX intolerance. This case demonstrates that alternative regimens-imipenem/cilastatin, amikacin, amoxicillin, and minocycline-can achieve sustained remission. Individualized therapy based on drug susceptibility and patient factors is critical.},
}

@article {pmid40543402,
year = {2025},
author = {Aziz, T and Shabbir, MA and Sarwar, A and Khan, AA and Zhao, L and Yang, Z and Shami, A and Alwethaynani, MS and Al-Asmari, F and Alghamdi, AM and Al-Joufi, FA},
title = {Exploring the multifaceted probiotic potential of Lactiplantibacillus plantarum NMGL2, investigating its antimicrobial resistance profiles and bacteriocin production.},
journal = {Journal of microbiological methods},
volume = {236},
number = {},
pages = {107178},
doi = {10.1016/j.mimet.2025.107178},
pmid = {40543402},
issn = {1872-8359},
abstract = {BACKGROUND: Lactiplantibacillus plantarum is widely recognized for its probiotic and antimicrobial properties, making it a valuable candidate for food and clinical applications. Genomic characterization provides deeper insight into its potential health benefits and safety profile.

AIM: This study aimed to sequence and analyze the genome of L. plantarum NMGL2 to evaluate its antimicrobial resistance, probiotic potential, and genetic suitability for biotechnological applications.

METHODS: The genomic DNA of L. plantarum NMGL2 was extracted and sequenced using Illumina technology. Genome assembly and annotation were performed, followed by gene prediction using Prokka and identification of antimicrobial resistance genes, virulence factors, and probiotic markers via BLAST. Metagenomic analysis of gut microbiota samples and phylogenetic analysis were conducted to assess strain relationships with other L. plantarum isolates.

RESULTS: The genome analysis revealed approximately 3000 protein-coding genes, including those encoding bile salt hydrolase, antimicrobial peptides, and antibiotic resistance determinants. Phylogenetic analysis showed that NMGL2 is closely related to other probiotic L. plantarum strains, supporting its probiotic characteristics and its potential role in combating pathogens.

CONCLUSION: L. plantarum NMGL2 demonstrates promising probiotic traits and carries genes that support its application in food safety and clinical contexts. Further, in vivo studies are needed to validate its health benefits and ensure safety, particularly in treating gastrointestinal disorders.},
}

@article {pmid40543345,
year = {2025},
author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y},
title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138980},
doi = {10.1016/j.jhazmat.2025.138980},
pmid = {40543345},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.},
}

@article {pmid40543204,
year = {2025},
author = {Yang, J and Kim, JS and Jeon, HW and Lee, J and Seo, JH},
title = {Integrated culture-based and metagenomic profiling of airborne and surface-deposited bacterial communities in residential environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126703},
doi = {10.1016/j.envpol.2025.126703},
pmid = {40543204},
issn = {1873-6424},
abstract = {Indoor environments host diverse microbial communities, where airborne and surface-deposited bacteria contribute to human exposure and potential health risks. This study applies metagenomic analysis to examine bacterial diversity in residential apartments, focusing on four key indoor spaces: kitchens, living rooms, toilets, and bedrooms. Airborne bacteria were collected using a culture-based air sampler and surface-deposited bacteria were collected via swabbing of high-contact areas; both were analyzed through 16S rRNA gene sequencing and bioinformatics processing. Airborne bacterial communities were primarily composed of Staphylococcus, Bacillus, and Enhydrobacter, whereas surface-deposited bacteria varied by location, with Streptococcus and Staphylococcus being most common on high-contact surfaces. Overall, surface-deposited bacterial diversity was greater than that of airborne communities, highlighting their distinct but interconnected roles in indoor microbial ecosystems. Functional pathway analysis suggested that indoor bacterial communities may harbor metabolic functions, as well as antibiotic resistance and virulence-related pathways, pointing to potential health concerns. Principal component analysis (PCA) showed clear distinctions between airborne and surface-deposited bacterial communities. These findings highlight the need for space-specific microbial management strategies, such as improved ventilation and surface hygiene, to reduce exposure risks and promote healthier indoor environments.},
}

@article {pmid40542451,
year = {2025},
author = {Ji, S and Ahmad, F and Peng, B and Yang, Y and Su, M and Zhao, X and Vatanen, T},
title = {Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {149},
pmid = {40542451},
issn = {2049-2618},
support = {U22A20365//Joint Funds of National Natural Science Foundation of China/ ; T2341019//National Natural Science Foundation of China/ ; 2023A1515012429//Natural Science Foundation of Guangdong Province/ ; 2024B03J1343//Guangzhou Science and Technology Plan Project/ ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.

METHODS: The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.

RESULTS: Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.

CONCLUSIONS: FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.},
}

@article {pmid40542420,
year = {2025},
author = {Yu, M and Chu, Y and Wang, Y and Mo, L and Tan, X and Guo, S and Yuan, S and Ma, Y},
title = {Metagenomic analysis reveals gut phage diversity across three mammalian models.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {146},
pmid = {40542420},
issn = {2049-2618},
support = {2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; B2302023//Shenzhen Medical Research Fund/ ; B2302023//Shenzhen Medical Research Fund/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; },
abstract = {BACKGROUND: The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.

RESULTS: We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.

CONCLUSIONS: Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.},
}

@article {pmid40542368,
year = {2025},
author = {Liu, F and Zhuang, Y and Huang, X and Papazian, L and Cai, H and Shao, H and Chen, Q and Xie, C and Tang, K and Li, K and Wang, M and Xu, Y and Shen, P and Wang, Q and He, X and Wang, N and Wang, H and Dai, M and Xiong, Y and Zhong, L and Pan, Y and Chu, L and Yang, B and Zhang, G and Zhou, H and Xu, J and Jiang, C and Huang, L},
title = {The Landscape of lower respiratory tract herpesviruses in severe pneumonia patients: a multicenter, retrospective study with prospective validation.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {254},
pmid = {40542368},
issn = {1466-609X},
support = {82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
abstract = {OBJECTIVE: Herpesviruses are widely distributed in the lower respiratory tract, yet no study has comprehensively characterized their clinical features and prognostic impact in severe pneumonia.

METHOD: In this multicenter, retrospective study, we included severe pneumonia patients who underwent bronchoalveolar lavage fluid (BALF) metagenomic testing in intensive care units across 17 medical centers from January 2019 to June 2023. Based on metagenomic results, patients were categorized into herpesvirus-negative, HSV-1, EBV, CMV, HHV-6B, and HHV-7 groups. Propensity score matching and multivariable Cox regression were used to compare mortality between herpesvirus-positive and -negative patients. Interaction analyses were conducted to assess the impact of co-detection of different herpesviruses. Besides, main findings were validated using data from a prospective multicenter cohort.

RESULTS: Among 1,737 enrolled patients, the 28-day mortality rate was 41.3% (718/1,737). Herpesviruses were detected in 828 patients. Detection frequencies were: HSV-1 (26.8%), CMV (17.8%), EBV (16.6%), HHV-7 (5.3%), HHV-6B (2.2%), and VZV (0.5%). Clinical characteristics varied across herpesvirus groups. No single herpesvirus was independently associated with increased mortality compared to the negative group. However, co-detection of HSV-1 and CMV was significantly associated with higher 28-day mortality (vs. both negative: adj-HR = 1.439, 95% CI: 1.093-1.894, P = 0.009). This finding was validated in a prospective cohort (adj-HR = 1.656, 95% CI: 1.061-2.585, P = 0.026).

CONCLUSIONS: Herpesviruses are frequently detected in the lower respiratory tract of patients with severe pneumonia, with distinct clinical features across virus types. Co-detection of HSV-1 and CMV was associated with increased 28-day mortality.},
}

@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}

@article {pmid40541587,
year = {2025},
author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TTY and Dawson, HD},
title = {Broccoli consumption alters microbial diversity, metatranscriptome and host transcriptome in mice fed a Total Western Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.041},
pmid = {40541587},
issn = {1541-6100},
abstract = {BACKGROUND: Cruciferous vegetables (CV) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent CV compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) are unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.

OBJECTIVE: We investigated the effects of a broccoli powder-supplemented Total Western Diet (TWD) on changes in the gut microbiome, the host transcriptome and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.

METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for six weeks followed by supplementation with 0, 0.5, 1 or 2.5% broccoli powder (BP) (reflecting a human intake from ¼ -1 cup per day) for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S rRNA amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess functionality of the microbial communities. The host cecal transcriptome was also assessed.

RESULTS: Beta diversity was significantly higher (p = 1.20E-03) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial RNA transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.

CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.},
}

@article {pmid40541578,
year = {2025},
author = {Tian, J and Hu, J and Xiong, Y and Deng, X and Fang, Y and Wang, G and Chi, R and Xiao, C},
title = {Metagenomic and metabolomic insights into microalgal-bacterial symbiosis under low carbon-to-nitrogen ratios.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132849},
doi = {10.1016/j.biortech.2025.132849},
pmid = {40541578},
issn = {1873-2976},
abstract = {Microalgal-bacterial symbiotic system (MBSS) is expected to efficiently treat ammonia nitrogen (NH4[+]-N) wastewater at low carbon-to-nitrogen ratio (CNR). In this study, MBSS was constructed and operated at CNRs of 0, 2, and 4 for 36 days, named as L (low CNR), M (medium CNR), and H (high CNR). Microbial interaction mechanisms were explored through metagenomics and non-targeted metabolomics. The average NH4[+]-N removal efficiencies of L, M, and H were 9.2 ± 4.3 %, 33.6 ± 10.9 %, and 51.6 ± 14.1 %, respectively. CNR significantly influenced NH4[+]-N removal. Metagenomics and metabolomics showed that bacteria dominate MBSS, with phylum Pseudomonadota having a large advantage. Addition of simple organic carbon sources may inhibit the generation of complex organic compounds by microalgae, consequently leading to bacteria utilizing simple carbon sources. Certain key microorganisms, genes, and metabolites respond to different CNRs to regulate MBSS performance. This study provides new insights into MBSS nitrogen removal at low CNR.},
}

@article {pmid40541123,
year = {2025},
author = {Jiao, Y and Xiao, D and Li, X and Jiang, M and Li, H},
title = {Integrative fMRI and multiomics reveal neuroprotective mechanisms of Astragalus membranaceus in sleep deprivation-induced depression.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156959},
doi = {10.1016/j.phymed.2025.156959},
pmid = {40541123},
issn = {1618-095X},
abstract = {BACKGROUND: Sleep deprivation (SD) is a significant public health concern and a risk factor for neuropsychiatric disorders, including depression. SD disrupts the gut-brain axis, causing dysbiosis and neuroinflammation. Astragalus membranaceus (AST) exhibits antidepressant and anti-inflammatory properties, including modulation of the gut microbiota; however, its neuroprotective effects on SD-induced neuropsychiatric disturbances remain largely unexplored. This study investigates the potential of AST using an innovative integrative multiomics approach.

PURPOSE: This study was conducted to investigate the neuroprotective effects of AST against SD-induced depression-like behavior and to explore the mechanism underlying its regulatory effects on the gut-brain axis.

METHODS: We established a chronic SD mouse model that was subjected to AST intervention and employed a pioneering integrative multiomics approach-combining resting-state functional magnetic resonance imaging for brain function, metagenomics for microbiota profiling, metabolomics for metabolic alterations, and transcriptomics for gene expression in key brain regions. Behavioral tests and cytokine assays complemented these analyses to comprehensively evaluate the therapeutic effects of AST.

RESULTS: SD induced depression-like behavior, neuroinflammation (IL-1β, IL-6, and TNF-α secretion), gut dysbiosis (Proteobacteria expansion, loss of beneficial microbes), and disrupted metabolic pathways. AST alleviated behavioral deficits, normalized brain connectivity, and reduced the levels of proinflammatory cytokines. It also reshaped microbiota, enriching Muribaculum and Butyricicoccus, and restored metabolic profiles, increasing the levels of short-chain fatty acids and promoting bile acid pathways. Integrated analysis linked microbiota restoration to reduced neuroinflammation and improved neuroprotection.

CONCLUSION: AST modulates the gut-brain axis to counteract SD-induced dysbiosis, neuroinflammation, and metabolic imbalance, alleviating depression-like symptoms. These findings offer novel mechanistic insights into the therapeutic potential of AST for SD-related neuropsychiatric conditions.},
}

@article {pmid40540838,
year = {2025},
author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO},
title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128260},
doi = {10.1016/j.micres.2025.128260},
pmid = {40540838},
issn = {1618-0623},
abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.},
}

@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}

@article {pmid40540222,
year = {2025},
author = {Xiao, YY and Lu, AL and Mo, HY and He, ZD and Wen, JL and Yin, X},
title = {Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40540222},
issn = {1434-9949},
support = {81760298//National Natural Science Foundation of China/ ; 2021JJA140699//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; (Grant No. YYZS2023005).//the First Afliated Hospital of Guangxi Medical University/ ; },
abstract = {OBJECTIVES: This study aimed to assess the clinical value of metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) co-infections, thereby establishing a foundation for early infection identification and the development of anti-infective regimens.

METHODS: This retrospective study analyzed 304 CTD patients with suspected infections at the First Affiliated Hospital of Guangxi Medical University between October 2020 and April 2024. The study compared the diagnostic efficacy between mNGS and conventional microbiological testing (CMT), examined pathogen detection rates across different periods and pathogen types, and evaluated the clinical outcomes of mNGS-guided antimicrobial regimen adjustments.

RESULTS: Among the 180 confirmed infections (Group I), mNGS demonstrated superior diagnostic performance compared to conventional microbiological testing (CMT). mNGS exhibited significantly higher sensitivity (89.6% vs. 57.0%; OR = 6.5, 95% CI: 3.7-11.0, p < 0.001), with a specificity of 81.5%, positive predictive value (PPV) of 97.2%, and negative predictive value (NPV) of 52.4%. mNGS outperformed CMT in detecting bacterial and viral pathogens (p < 0.05). Viral infections were the most common. Compared to prior studies, mNGS exhibited improved pathogen detection rates. mNGS-guided treatment optimization significantly enhanced clinical outcomes, with higher cure rates, lower mortality, and shorter hospital stays.

CONCLUSION: Current evidence suggests that while mNGS demonstrates superior diagnostic performance over CMT for detecting infections in CTD patients, their combined use provides optimal pathogen identification accuracy and enhanced clinical management. Key Points • This is the larger-scale retrospective study of mNGS application in patients with CTDs co-infections following the Coronavirus Disease 2019 (COVID-19). • We found that the distribution of pathogens and positivity rates have changed in recent years, especially after the COVID-19. • The clinical value of mNGS was further demonstrated through its impact of mNGS results on antibiotic regimens and the analysis of negative samples.},
}

@article {pmid40539808,
year = {2025},
author = {Sun, H and Chen, Q and Zhang, D and Hu, L and Li, S and Lu, M and Wang, Y and Su, H and Gao, Y and Guo, J and Zhao, Y and Du, J and Liu, C and Xia, H and Xu, Y and Ge, X and Yang, Q},
title = {Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156324},
doi = {10.1128/spectrum.01563-24},
pmid = {40539808},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the diagnostic potential of mNGS for detecting MTB in pulmonary tuberculosis patients. We analyzed pulmonary microbiome data to assess its impact on mNGS diagnostic accuracy and explored the association between microbiome profiles and clinical diagnosis. Bronchoalveolar lavage fluid samples were collected from 236 patients with pulmonary infections, and the diagnostic performance of mNGS was compared with traditional methods in detecting MTB. Furthermore, the incidence of false negatives and false positives, as well as the characteristics of the lung microbiota in TB patients, was analyzed to improve the diagnostic precision of mNGS. We observed that among all detection methods, mNGS showed the highest sensitivity (73.33%), followed by X-pert (60.00%), culture (53.33%), RT-PCR (53.33%), and sputum smear (23.33%). Notably, mNGS produced 3 false positive results in 236 samples, yielding a specificity of 98.54%. Analysis of the pulmonary microbiome revealed significant differences in both α-diversity and β-diversity between patients with TB and uninfected controls (P<0.05). Shannon index and Chao1 index were identified as significant predictors associated with MTB infection. ROC curve analysis demonstrated an AUC of 0.765, indicating good discriminatory performance. This study suggested that integrating wet-laboratory techniques with bioinformatics analysis can further enhance the diagnostic accuracy of mNGS for TB. Furthermore, microbiome analysis holds significant potential for the diagnosis of MTB infection.

IMPORTANCE: This study focuses on the application of next-generation sequencing (NGS) technology in detecting Mycobacterium tuberculosis in bronchoalveolar lavage fluid and explores the impact of M. tuberculosis infection on the pulmonary microbiome. By optimizing the methods and conducting microbial analyses, the accuracy of metagenomic NGS for detecting M. tuberculosis has been improved.},
}

@article {pmid40539782,
year = {2025},
author = {Qi, Y-H and Ye, Z-X and Feng, K-H and Ma, X-W and Zhang, C-X and Hu, M-H and Shi, M and Chen, J-P and Li, J-M},
title = {Diversity and evolutionary history of RNA viruses among different horseshoe crab species.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0016425},
doi = {10.1128/jvi.00164-25},
pmid = {40539782},
issn = {1098-5514},
abstract = {Horseshoe crabs (Xiphosura: Limulidae) are the sole surviving species of the class Merostomata, with only four extant species remaining today. Recent advances in metagenomic next-generation sequencing have unveiled a vast diversity of RNA viruses and non-retroviral endogenous RNA viral elements (nrEVEs) in invertebrates. This raises intriguing questions about the RNA virome and nrEVEs in horseshoe crabs as "living fossils," potentially offering insights into the evolutionary relationships between RNA viruses and these ancient organisms. In this study, 22 novel RNA viruses were identified across the four horseshoe crab species by screening 117 data sets, including picornaviruses, totiviruses, a flavivirus, a rhabdovirus, as well as a plant-associated tombusvirus and a fungi-associated narnavirus. Additionally, 20 nrEVEs were identified in the genomes of the four horseshoe crab species (hcEVEs), with most sharing homology with the viral family Chuviridae (N = 11), supporting the hypothesis that modern negative-sense RNA viruses may trace their origins to ancient oceanic chuviruses. A time-scaled phylogenetic tree based on hcEVEs suggests that at least two independent ancient chuvirus infections and genome integration events occurred in the common ancestor of horseshoe crab species. Interestingly, transcriptional analyses indicated that hcEVE-containing transcripts display typical exon-intron structures in the three Asian horseshoe crab species, suggesting that these hcEVEs may have been co-opted by horseshoe crabs during coevolution. These findings advance our understanding of the RNA viruses associated with horseshoe crabs and shed light on the potential role of RNA viruses in shaping the evolutionary history of this "living fossil" arthropod host.IMPORTANCERecent studies have discovered abundant RNA viruses in invertebrates, revealing that viral genomes may integrate into host genomes, creating a genetic record of past infections. In this study, we explored the evolutionary relationship between RNA viruses and the four extant horseshoe crab species-the last representatives of the class Merostomata, often termed "living fossils"-by analyzing viral sequences embedded in their genomes. The presence of chuvirus-like sequences in the genomes of these horseshoe crabs suggests that modern negative-sense RNA viruses may trace their origins back to ancient chuviruses from the ocean. Furthermore, we identified at least two independent ancient integrations of chuviruses in the evolutionary history of horseshoe crabs, with one orthologous gene containing a chuvirus-derived G protein gene/coding sequence potentially inherited from a common ancestor of the three Asian species before their divergence. Our findings contribute to a deeper understanding of the long-term coevolution between RNA viruses and their arthropod hosts.},
}

@article {pmid40539777,
year = {2025},
author = {Olmsted, CN and Gahler, M and Roden, E and Peterson, B and Lazarcik, J and Tran, PQ and Berg, M and Bryant, DA and Goudeau, D and Malmstrom, RR and Qin, M and McMahon, KD},
title = {Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0178924},
doi = {10.1128/aem.01789-24},
pmid = {40539777},
issn = {1098-5336},
abstract = {The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by Chlorobium and anaerobic respiration (electrogenic metabolism) by Geothrix, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.},
}

@article {pmid40539111,
year = {2025},
author = {Ma, Y and Wu, Q and Wang, X and Sui, W and Zhang, X},
title = {Carbon components in organic amendments drive nitrogen metabolism in one-year-long anaerobic soil microcosms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1588169},
pmid = {40539111},
issn = {1664-302X},
abstract = {INTRODUCTION: Long-term studies on the dynamic changes in nitrogen metabolism and functional microbial communities under anaerobic conditions, particularly those driven by organic amendments, remain scarce.

METHODS: We conducted a year-long anaerobic microcosm experiment using three organic amendments-aerobically fermented pig-manure digestate (ACM), compost (ACP) and straw powder (ACS)-alongside an inorganic fertilizer-only control (ACN).

RESULTS: Temporal shifts revealed that organic amendments drove distinct nitrogen metabolism pathways. Amendments of digestate and compost promoted the proliferation of nitrogen-mineralizing bacteria such as Ramlibacter and Lysobacter, leading to significant ammonium accumulation. After 12-month incubation, the ACM treatment caused a 75.6-fold increase in ammonium, a 43.4% rise in total nitrogen (TN), and a 27.0% increase in total organic carbon (TOC). In contrast, the ACS treatment exhibited superior nitrogen fixation, with an average of 1.69-fold higher rate than ACM and 5.30 fold higher than ACP The ACS treatment enriched cellulolytic nitrogen-fixing bacteria, including Clostridium, and nitrogen-fixing archaea.

DISCUSSION: This study provides profound insights in to the unique nitrogen metabolism pathways influenced by organic amendments under anoxic conditions, ultimately offering valuable insights into improved soil fertility and sustainable nitrogen management practices in agricultural systems.},
}

@article {pmid40539103,
year = {2025},
author = {Lin, ZY and He, SS and Mo, ZT and Liao, XT and Feng, ZS and Kong, J and Zhu, L and Li, Y and Tan, HY and Su, ZW and Jia, CH and Wu, F},
title = {Integrated analysis of serum metabolomics and fecal microbiome in infants with necrotizing enterocolitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584041},
pmid = {40539103},
issn = {1664-302X},
abstract = {BACKGROUND: Necrotizing enterocolitis (NEC), a lethal gastrointestinal disorder in preterm infants, remains poorly understood in its pathology, and early diagnosis are critically limited. Multi-omics approaches present unprecedented opportunities to elucidate NEC pathogenesis and identify clinically translatable biomarkers.

METHODS: Infants with Bell stage II-III NEC and gestational age-matched controls were enrolled. Serum/stool samples from NEC patients at acute (NEC-D) and recovery (NEC-R) phases, and controls (non-NEC) were collected. Fecal metagenomic sequencing and serum untargeted metabolomic profiling were performed. Clinical parameters were compared.

RESULTS: The study comprised seven NEC and seven non-NEC infants. Baseline neonatal characteristics and maternal perinatal parameters showed no significant differences between NEC-D and non-NEC except for markedly lower leukocyte counts in NEC infants. Fecal metagenomics revealed severely diminished alpha diversity in NEC-D versus both non-NEC controls and NEC-R, characterized with lower Chao1 index. NEC-D exhibited elevated Escherichia coli relative abundance alongside reduced Staphylococcus haemolyticus, Staphylococcus aureus, Staphylococcus epidermidis, and Lactobacillus paracasei. Correspondingly, KEGG functional gene analysis demonstrated impaired metabolism in NEC-D. Serum metabolomics identified significantly decreased ornithine, DL-arginine, L-threonine, leucine, and D-proline in NEC-D versus non-NEC. NEC-D also showed lower taurodeoxycholic acid, glycocholic acid, and chenodeoxycholic acid compared to NEC-R. Integrative analysis revealed a positive correlation between the metabolites D-proline and ornithine and the Lactobacillus paracasei, Staphylococcus epidermidis, and Staphylococcus aureus abundance.

CONCLUSION: NEC is characterized by gut microbiota dysbiosis with reduced diversity, altered functional gene expression, and disrupted host-microbiota metabolic crosstalk. The identified serum metabolite-microbiome correlations provide mechanistic insights into NEC pathogenesis and potential diagnostic biomarkers.},
}

@article {pmid40538825,
year = {2025},
author = {Hofman, J and Brenerova, P and Borilova Linhartova, P},
title = {State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.},
journal = {Frontiers in reproductive health},
volume = {7},
number = {},
pages = {1557912},
pmid = {40538825},
issn = {2673-3153},
abstract = {Although the understanding of the causes of infertility is the key to its successful treatment, recent studies have shown that as many as 50% of male-caused infertility cases are considered idiopathic. The microbial colonization of the male reproductive system was shown to be associated with reduced male reproductive fitness. Investigation of the seminal microbiome, however, remains challenging. This article aimed to improve this situation by creating the first comprehensive review of literature on the metagenomic methods (including the pre-analytical and analytical approaches) used in the research on human seminal bacteriome (total bacterial DNA in the matrix), published in 2018-2024. A total of 29 studies addressing the analysis of the human seminal bacteriome were identified. The analysis typically involved DNA extraction from the supernatant using commercial kits, amplification of the gene for 16S rRNA, and sequencing of amplicons. Where the separation of seminal plasma was performed, centrifugation was the dominant method used for this purpose. The significant heterogeneity in individual steps of methodological approaches in the analysis of the human seminal bacteriome complicates the comparison of results among studies and the establishment of standard procedures, hindering clinical advancements. For this reason, a protocol for the analysis of the human seminal plasma bacteriome is proposed here, which could lead to improved comparability of results among studies and make future research more efficient. This protocol is founded on rigorous quality control measures, compliance with the WHO laboratory manual for sample collection, extensive pretreatment involving mechanical and enzymatic lysis, DNA extraction using the QIAamp DNA Mini Kit (Qiagen), and short-read sequencing conducted on the MiSeq platform (Illumina).},
}

@article {pmid40538739,
year = {2025},
author = {Zou, ZL and Shen, ZH},
title = {Amoebic liver abscess co-infected with bacterial liver abscess: A rare case in an immunocompromised patient.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02279},
pmid = {40538739},
issn = {2214-2509},
abstract = {We present a complex case of a 43-year-old HIV-positive Chinese male with co-infection of amoebic liver abscess (ALA) and bacterial liver abscess caused by Salmonella enterica subsp. enterica serotype Typhi (abbreviated as Salmonella Typhi). The patient presented with fever and abdominal pain. Initial bacterial cultures identified Salmonella Typhi, but targeted antibiotic therapy failed to resolve his symptoms, prompting to further investigation. Metagenomic next-generation sequencing (mNGS) of pleural and liver abscess drainage fluids revealed sequences of Entamoeba histolytica, confirming a dual infection. The patient was treated with combination therapy, resulting in clinical improvement. This case highlights diagnostic challenges in immunocompromised patients and underscores the critical role of mNGS in identifying co-infections and guiding treatment. Early recognition and timely intervention are essential for achieving optimal outcomes in such complex cases.},
}

@article {pmid40538403,
year = {2025},
author = {Chengsupanimit, T and Mahajan, A and Farhadian, S and Machiavello Roman, F},
title = {Case Report: Spinal cord abscess due to Nocardia farcinica presenting as longitudinally extensive transverse myelitis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1613770},
pmid = {40538403},
issn = {2296-858X},
abstract = {A middle-aged man, renal transplant recipient, was admitted with lower extremity paralysis, loss of sensation and urinary retention. The initial diagnostic workup revealed extensive inflammatory spinal changes on imaging, consistent with longitudinally extensive transverse myelitis. Cerebrospinal fluid testing demonstrated neutrophilic pleocytosis; routine tests for bacterial and viral pathogens were negative. The patient received high-dose steroids for presumed autoimmune myelitis, but his condition worsened. Repeat spinal imaging revealed an intramedullary spinal cord abscess and a loculated collection in the cauda equina. Nocardia farcinica was isolated from spinal biopsy tissue cultures and metagenomic sequencing of cerebrospinal fluid. He received treatment with trimethoprim-sulfamethoxazole and linezolid, with subsequent improvement of the radiological abnormalities. At outpatient follow-up two months after initiating antimicrobials, the patient endorsed improved upper extremity strength, though remained paraplegic. This case report highlights the protean manifestations of central nervous system nocardiosis and the benefits of using metagenomic sequencing to diagnose complex central nervous system infections.},
}

@article {pmid40537892,
year = {2025},
author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ},
title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503018},
doi = {10.4014/jmb.2503.03018},
pmid = {40537892},
issn = {1738-8872},
abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.},
}

@article {pmid40537881,
year = {2025},
author = {Linghu, Y and Hu, RS and Tang, XM and Li, RT and Li, WY and Wu, JH},
title = {Unveiling viral diversity and dynamics in mosquitoes through metagenomic analysis in Guizhou Province, China.},
journal = {Infectious diseases of poverty},
volume = {14},
number = {1},
pages = {51},
pmid = {40537881},
issn = {2049-9957},
support = {Qian Ke He Platform Talent-GCC [2022] 033-1//The Training Project for High-Level Innovative talents in Guizhou Province, China/ ; Qian Ke He Platform Talent-CXTD [2022] 004//The Science and Technology Innovation Talent team of Guizhou Province, China/ ; Project Contract Number: Xiao Bo He J Zi [2023] 44//The Scientific Research Foundation for Advanced Talents, Guizhou Medical University/ ; NO. 2024GCC16Z//The High-level Talent Research Start-up Project of Sichuan University of Arts and Science/ ; },
abstract = {BACKGROUND: Poverty, disease, and vector ecology intersect to present ongoing health threats, particularly in ecologically sensitive regions. Guizhou Province in China, with its complex karst topography and rich biodiversity, offers a unique environment to study mosquito-borne viral transmission. Despite over 5000 reported cases of Japanese encephalitis in the past two decades and the detection of Zika virus in 2016, the virological landscape of this region remains poorly understood. This study aims to characterize the mosquito-associated virome, assess viral diversity, and identify factors influencing transmission dynamics in Guizhou Province.

METHODS: Between 2021 and 2022, we conducted a 2-year mosquito surveillance across eight ecologically distinct regions in Guizhou Province. Adult mosquitoes were collected using a variety of methods, including BG Mosquitaire CO2 traps, mosquito-killing lamps, manual collection, human bait traps, and oviposition traps. To investigate the virome diversity and dynamics within mosquito populations, we performed metagenomic sequencing and bioinformatics analysis on pooled mosquito samples collected from geographically diverse sampling sites.

RESULTS: We collected more than 40,000 adult mosquitoes, primarily belonging to four genera: Aedes, Anopheles, Armigeres, and Culex. Dominant species included Aedes albopictus, Anopheles sinensis, Armigeres subalbatus, and Culex tritaeniorhynchus. Notably, we report the first provincial record of the Anopheles baileyi complex, expanding the known distribution of mosquito vector in this region. Viral metagenomic sequencing, coupled with bioinformatic analysis, identified 162 viral contigs, including 140 known and 22 previously uncharacterized viruses. We experimentally confirmed the genotypes of three medically important zoonotic viruses: Japanese encephalitis virus (JEV-GI), Getah virus (GETV-GIII) and Banna virus (BAV-A2). Comparative analysis of viral abundance across mosquito species revealed that Aedes albopictus populations in Guizhou harbor a distinct virome composition, diverging from those reported in other geographic regions.

CONCLUSIONS: This study presents the comprehensive characterization of the mosquito-associated virome in Guizhou Province, providing critical insights into viral diversity, vector competence, and transmission dynamics within karst ecosystems. The detection of multiple zoonotic viruses highlights the need for strengthened surveillance and targeted public health interventions in this region.},
}

@article {pmid40537478,
year = {2025},
author = {Sommer, AJ and Skarlupka, JH and Teseo, S and Otani, S and Suen, G and Coon, KL and Sapountzis, P},
title = {Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {111},
pmid = {40537478},
issn = {2055-5008},
support = {WIS04039//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
abstract = {Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms.},
}

@article {pmid40537448,
year = {2025},
author = {Rudi, K and Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Philip, M and Martin, J and Sundt, MØ and Snipen, LG},
title = {The Coastal Seafloor Microbiota Is Structured by Local Selection of Cosmopolitan Taxa.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70123},
doi = {10.1111/1758-2229.70123},
pmid = {40537448},
issn = {1758-2229},
support = {320076//Norges Forskningsråd/ ; },
abstract = {Understanding the assembly processes of the coastal seafloor microbiota is crucial for gaining insights into how ocean ecosystems work. In our study, we addressed the question about how local selection affects the global distribution of coastal seafloor microorganisms. We identified two main clusters of samples by examining the geographical distribution of 356 high-quality prokaryote metagenome-assembled genomes (MAGs) from 94 coastal samples collected along the Norwegian and Icelandic coasts. There was no identifiable correlation between the abundance of MAGs and the geographic distance between them central to the identified clusters (no distance decay). In contrast, noncentral MAGs demonstrate a pronounced distance decay. We also observed significant functional differences between the two sample clusters. One cluster showed enrichment in functions such as dissimilatory nitrate reduction to ammonium (DNRA), acetoclastic methanogenesis, thiosulphate conversion and acetate and butyrate metabolism. The other cluster was enriched in propionate metabolism, nitrite oxidation to nitrate and cobalamin-dependent carbon fixation. These results suggest that localised environmental selection acts on cosmopolitan taxa to shape seafloor microbiota. Our findings therefore profoundly impact the understanding of seafloor ecological processes and their management.},
}

@article {pmid40536635,
year = {2025},
author = {Zhang, X and Feng, Y and Shi, X and Zhang, Y and Wang, W},
title = {Degradable plastic of high-density polyethylene (HDPE)-CaCO3 reduced the abundance of antibiotic resistance genes in soil.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {7},
pages = {773},
pmid = {40536635},
issn = {1573-2959},
support = {20170031//Henan Normal University Outstanding Youth Science Fund/ ; 20170031//Henan Normal University Outstanding Youth Science Fund/ ; 20170031//Henan Normal University Outstanding Youth Science Fund/ ; 41907121//National Natural Science Foundation of China/ ; },
mesh = {*Polyethylene/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Calcium Carbonate/chemistry ; *Biodegradable Plastics ; *Soil Pollutants/analysis ; Soil/chemistry ; Biodegradation, Environmental ; Plastics ; },
abstract = {A large number of degradable plastics have entered the market because traditional plastics are not easy to degrade. However, degradable plastics have problems such as inability to be completely degraded in time. Therefore, evaluating whether degradable plastics pose environmental harm is both urgent and crucial. High-density polyethylene (HDPE) disposable degradable plastic bags which were filled with CaCO3 have been widely circulated in the market. But there has been no reported research on whether HDPE/CaCO3 degradable plastics are harmful to the environment. Therefore, in this study, HDPE-CaCO3 degradable plastics circulated in the market were taken as the research objects, and the antibiotic resistance genes (ARG), a new type of environmental pollution indicator, were used as the evaluation indicators. The HDPE/CaCO3 degradable plastics were made into plastic pieces less than 10 mm in size and then evenly mixed with soil. After 30 days, metagenomic sequencing was performed on the soil microorganisms, and the soil microbial community structure and the abundance of ARGs in the soil were analyzed to evaluate the potential environmental risks of HDPE/CaCO3 degradable plastics. The results showed that comparing with HDPE, the HDPE/CaCO3 degradable plastics could reduce the abundance of soil ARGs and change the soil microbial community structure. Our results indicated that HDPE/CaCO3 degradable plastics imposed a reduced environmental impact compared to conventional HDPE plastics.},
}

*Polyethylene/chemistry
*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Calcium Carbonate/chemistry
*Biodegradable Plastics
*Soil Pollutants/analysis
Soil/chemistry
Biodegradation, Environmental
Plastics

@article {pmid40535544,
year = {2025},
author = {Wang, X and Cao, D and Chen, W and Sun, J and Hu, H},
title = {Metagenomics reveals unique gut mycobiome biomarkers in major depressive disorder - a non-invasive method.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582522},
pmid = {40535544},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Depressive Disorder, Major/microbiology/diagnosis ; *Mycobiome ; Biomarkers/analysis ; Male ; Female ; Adult ; *Metagenomics/methods ; *Fungi/classification/genetics/isolation & purification ; Middle Aged ; Machine Learning ; Support Vector Machine ; Case-Control Studies ; Feces/microbiology ; },
abstract = {BACKGROUND: An increasing amount of evidence suggests a potential link between alterations in the intestinal microbiota and the onset of various psychiatric disorders, including depression. Nevertheless, the precise nature of the link between depression and the intestinal microbiota remains largely unknown. A significant proportion of previous research has concentrated on the study of gut bacterial communities, with relatively little attention paid to the link between gut mycobiome and depression.

METHODS: In this research, we analyzed the composition and differences of intestinal fungal communities between major depressive disorder (MDD) and healthy controls. Subsequently, we constructed a machine learning model using support vector machine-recursive feature elimination to search for potential fungal markers for MDD.

RESULTS: Our findings indicated that the composition and beta diversity of intestinal fungal communities were significantly changed in MDD compared to the healthy controls. A total of 22 specific fungal community markers were screened out by machine learning, and the predictive model had promising performance in the prediction of MDD (area under the curve, AUC = 1.000). Additionally, the intestinal fungal communities demonstrated satisfactory performance in the validation cohort, with an AUC of 0.884 (95% CI: 0.7871-0.9476) in the Russian validation cohort, which consisted of 36 patients with MDD and 36 healthy individuals. The AUC for the Wuhan validation cohort was 0.838 (95% CI: 0.7403-0.9102), which included 40 patients with MDD and 42 healthy individuals.

CONCLUSION: To summarize, our research revealed the characterization of intestinal fungal communities in MDD and developed a prediction model based on specific intestinal fungal communities. Although MDD has well-established diagnostic criteria, the strategy based on the model of gut fungal communities may offer predictive biomarkers for MDD.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Depressive Disorder, Major/microbiology/diagnosis
*Mycobiome
Biomarkers/analysis
Male
Female
Adult
*Metagenomics/methods
*Fungi/classification/genetics/isolation & purification
Middle Aged
Machine Learning
Support Vector Machine
Case-Control Studies
Feces/microbiology

@article {pmid40535541,
year = {2025},
author = {Kato-Kogoe, N and Tsuda, K and Kudo, A and Sakaguchi, S and Omori, M and Komori, E and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Tamaki, J and Ueno, T},
title = {Salivary microbiota and IgA responses are different in pre-diabetic individuals compared to normoglycemic controls.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591285},
pmid = {40535541},
issn = {2235-2988},
mesh = {Humans ; *Saliva/microbiology/immunology ; Female ; Male ; *Immunoglobulin A/analysis/immunology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Microbiota/immunology ; *Prediabetic State/immunology/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Diabetes Mellitus, Type 2/immunology/microbiology ; Aged ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; },
abstract = {INTRODUCTION: In recent years, changes in the oral microbiota of patients with type 2 diabetes mellitus (T2DM) have been increasingly recognized. The salivary microbiota may also be altered in pre-diabetes, which is the earliest stage of abnormal blood glucose regulation and a reversible stage preceding T2DM; however, its characteristics are poorly understood. Salivary immunoglobulin A (IgA) is a host defense factor central to the oral immune system and may play an important role in regulating the salivary microbiota. Given that alterations in immunoreactivity are observed in pre-diabetes, we hypothesized that the salivary IgA response may also be altered; however, limited knowledge exists regarding this. Therefore, in the present study, we aimed to evaluate the characteristics of salivary microbiota and IgA responses against salivary microbiota in individuals with pre-diabetes, comparing them to those in individuals with normoglycemia.

METHODS: Saliva samples were collected from 101 pre-diabetic individuals (PreDM group) and 101 age- and sex-matched normoglycemic controls (Normal group). Further, 16S rRNA metagenomic analysis was performed to compare bacterial microbiota composition. For each of the 19 saliva samples from the PreDM and Normal groups, IgA-enriched and IgA-nonenriched fractions were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. The IgA index was calculated to evaluate the difference in the IgA response to each bacterium between the PreDM and Normal groups.

RESULTS: Bacterial species richness was significantly lower in the PreDM group than in the Normal group (observed operational taxonomic unit index, p = 0.042), and a difference between these groups was noted in the overall salivary microbiota structure (unweighted UniFrac distances, p = 0.009). Salivary IgA responses against several bacterial genera differed between the PreDM and Normal groups. Significantly higher IgA responses were noted against Haemophilus in the PreDM group, with lower responses against Capnocytophaga, Corynebacterium, and Streptococcus relative to those in the Normal group.

CONCLUSIONS: Salivary microbiota and IgA responses differ between pre-diabetic individuals and normoglycemic controls. The current findings advance our understanding of the interaction between oral bacteria and host immune responses in patients with a poor glycemic status.},
}

Humans
*Saliva/microbiology/immunology
Female
Male
*Immunoglobulin A/analysis/immunology
Middle Aged
RNA, Ribosomal, 16S/genetics
*Microbiota/immunology
*Prediabetic State/immunology/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Diabetes Mellitus, Type 2/immunology/microbiology
Aged
Metagenomics
DNA, Bacterial/genetics/chemistry

@article {pmid40535168,
year = {2025},
author = {Huang, J and Ren, W and Hu, W and Ni, J},
title = {Diagnosis of secondary tuberculosis infection in an asymptomatic elderly with cancer using next-generation sequencing: Case report.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20251123},
pmid = {40535168},
issn = {2391-5412},
abstract = {In recent years, there has been a notable increase in the prevalence of tumors and tuberculosis (TB), particularly among elderly and immunocompromised populations. Early diagnosis and treatment are crucial for significantly improving patient outcomes. However, traditional diagnostic methods exhibit certain limitations. The rapid advancement of metagenomic next-generation sequencing (mNGS) has shown promising applications in the field of infectious diseases. We describe an 88-year-old male with multiple comorbidities, including newly diagnosed localized prostate cancer, who presented asymptomatically. Routine mNGS screening unexpectedly identified Mycobacterium tuberculosis, suggesting that malignancy may foster immune conditions favoring latent TB reactivation. This case emphasizes mNGS's role as a rapid, sensitive diagnostic adjunct for occult infections in high-risk populations.},
}

@article {pmid40535082,
year = {2025},
author = {Wang, C and Hu, B and Liang, Q and Jiang, H and Yuan, L and Li, S},
title = {Oral microbiome and risk of lung cancer: results from a two-sample mendelian randomization analysis.},
journal = {Translational lung cancer research},
volume = {14},
number = {5},
pages = {1715-1723},
pmid = {40535082},
issn = {2218-6751},
abstract = {BACKGROUND: Numerous studies have suggested that the oral microbiome may function as a biomarker for lung cancer screening. However, the relationship between oral microbiome and lung cancer has not been thoroughly investigated. Consequently, investigating the causal relationship between oral microbiome and lung cancer was the primary goal of this study.

METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between the oral microbiome and lung cancer. Summary statistics for the oral microbiomes were obtained from large-scale metagenome-genome-wide association studies (mgGWAS), while genome-wide association study (GWAS) summary statistics for lung cancer were sourced from the IEU-OpenGWAS online platform. We employed inverse variance weighted (IVW) analysis and Wald ratio methods to evaluate the causal associations between the oral microbiome and lung cancer. Finally, we performed MR Steiger's test to strengthen the validity of the causal associations.

RESULTS: Three oral microbiomes were causally associated with lung cancer. Gemella haemolysans (pheno.388) from saliva and an unclassified species (pheno.844) of Clostridia from saliva were protective factors for lung cancer, and an unclassified species (pheno.1354) of Prevotella from tongue was a risk factor for lung cancer. And there is no bidirectional association of causality between oral microbiomes and lung cancer.

CONCLUSIONS: The oral microbiomes, Gemella haemolysans (pheno.388) from saliva, an unclassified species (pheno.844) of Clostridia from saliva and an unclassified species (pheno.1354) of Prevotella from tongue, were causally associated with lung cancer. Oral microbiology holds significant potential for clinical applications in etiologic exploration, early screening, prevention, and enhancing survival in lung cancer. Regarding treatment, personalized therapy based on oral flora may provide novel therapeutic strategies for lung cancer.},
}

@article {pmid40535022,
year = {2025},
author = {Blaustein, RA and Smith, JE and Toro, M and Pachepsky, Y and Stocker, MD},
title = {Water metagenomes reflect physicochemical water quality throughout a model agricultural pond.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535096},
pmid = {40535022},
issn = {1664-302X},
abstract = {Agricultural ponds are essential irrigation resources, though may also serve as reservoirs for pathogens and antimicrobial resistance (AMR) genes. While monitoring microbiological water quality is critical for food safety, the influence of sampling factors (e.g., when and where to collect samples) in making risk assessments and potential applications for using environmental covariates as indicators remain unclear. Here, we explored the hypothesis that metagenomes of agricultural waters change with spatiotemporal shifts in physicochemical water quality, i.e., across water depths over time. Water samples and underlying sediments were collected at a model pond at the surface and within the water column (0, 1, 2 m depths) throughout one day (i.e., 9:00, 12:00, 15:00). All samples were processed for shotgun metagenomic sequencing analysis and enumeration of various water quality parameters (e.g., temperature, nutrient concentrations, turbidity, pH, culturable Escherichia coli). At the pond surface, Microcystis aeruginosa and members of Cyanobacteria, along with genes encoding pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. In contrast, within the water column (1-2 m depths) and sediments, diverse members of Proteobacteria and Actinobacteria were more dominant, along with encoded pathways related to respiration and amino acid biosynthesis. Various aspects of water quality (i.e., chlorophyll dissolved organic matter, ammonia, E. coli concentrations) correlated with water metagenome diversity, albeit not with any specific AMR genes or virulence factors. Nevertheless, de novo assembly of sequenced reads uncovered 22 unique strains encoding several AMR, virulence, or stress response genetic elements, thus linking metagenome functional potential to key taxa. Overall, our findings highlight distinctions in agricultural pond water metagenomes at the surface and in the water column and demonstrate the potential for metagenomic surveillance in water quality monitoring to support food safety.},
}

@article {pmid40535021,
year = {2025},
author = {Chen, Z and Li, Q and Li, F and Yin, L and Wang, L and Ye, T and Wang, Y and Fu, S and Wang, W and Huang, X},
title = {Evolution in a plant matrix: adaptive reshaping of kefir grains microbiota and function during long-term soymilk culture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614639},
pmid = {40535021},
issn = {1664-302X},
abstract = {To explore the adaptability of kefir grains in long-term subculture in soymilk, this study tracked the succession and functional changes of its microbial community over 4 months. High-throughput sequencing results showed that the microbial community structure was drastically reshaped, mainly manifested in the relative abundance of Lacticaseibacillus kefiranofaciens decreasing from 95.00 to 15.70%, while Lacticaseibacillus paracasei increased from 0.32 to 76.94%, becoming the dominant bacteria. Metagenomic analysis indicated that L. paracasei possesses key enzymes for metabolizing raffinose, stachyose and sucrose, which is the basis for its efficient utilization of soymilk oligosaccharides and its competitive advantage. The decrease in the abundance of L. kefiranofaciens was associated with a decrease in the synthesis of extracellular polysaccharides (EPS), which in turn caused a reduction in the diameter of kefir grains, an increase in surface viscosity and a partial collapse of the gel matrix structure. The pH and free amino acid content of fermented soymilk did not fluctuate much during the passage process, but the sensory acceptance, antioxidant capacity and angiotensin converting enzyme (ACE) inhibitory activity all showed a downward trend. This work reveals the adaptive evolution mechanism of kefir grains in a plant matrix environment and provides a theoretical basis for the optimization of soymilk fermentation based on limited strains.},
}

@article {pmid40535015,
year = {2025},
author = {Chen, Y and Jiang, X and Zhao, J and Yang, M and Chen, Y and Ling, H and Liu, Y and Deng, F and Wang, Z},
title = {Microbial response under sulfate stress in a sulfur-based autotrophic denitrification system.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615317},
pmid = {40535015},
issn = {1664-302X},
abstract = {This study investigated the responses of the bacterial community structure and metabolic pathways in a sulfur-based autotrophic denitrification filter (SADF) system to fast elevated sulfate salinity, from 0.04 to 1.2% in 30 days. Results showed that the SADF system exhibited robust sulfate salinity stress tolerance at low nitrate concentrations. In the context of sulfate scenarios, the genus Thiobacillus significantly proliferated and was identified as the dominant sulfur-oxidizing player in the SADF system, achieving a relative abundance of 63.79% under 1.2% sulfate salinity. Cooperative and competitive interactions were found in the SADF-related microorganisms, promoting stable denitrification performance under high salinity. Surprisingly, with a low hydraulic retention time (HRT) of 60 min, metagenomic sequencing revealed a upregulated abundance of functional genes encoding for enzymes associated with nitrogen and sulfur metabolism, while positive correlations were observed between these two pathways in response to sulfate salinity. Furthermore, global wastewater treatment plants were thoroughly explored for the distribution of the SADF-related microorganisms identified in this study. Interestingly, one-way ANOVA analysis showed that the SADF-related microorganisms were widely distributed globally, demonstrating their universality in potential engineering applications worldwide.},
}

@article {pmid40535009,
year = {2025},
author = {He, S and Qi, Y},
title = {The microbiota, the malarial parasite, and the mice-a three-sided relationship.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615846},
pmid = {40535009},
issn = {1664-302X},
abstract = {In recent years, the role of gut microbiota in modulating malaria susceptibility and infection progression has emerged as a pivotal focus in interdisciplinary research. While existing reviews have delineated mechanisms by which mosquito-associated gut microbiota regulate Plasmodium development, a systematic synthesis of the tripartite interplay among host gut microbiota, Plasmodium and host immunometabolic networks remains absent. Compared with previous studies predominantly focusing on single species or unitary mechanisms, this review fills the gap in cross-species integrated analysis of host-microbiota-pathogen interactions. By consolidating metagenomic, metabolomic, and immunological data, this review transitions from unitary mechanistic explanations to multi-omics-driven systematic analyses, demonstrating that murine microbiota suppresses Plasmodium proliferation through adaptive immune activation and metabolic product regulation. Meanwhile, Plasmodium infection induces decreased microbial diversity and functional pathway deviation in murine microbiota, exacerbating host immunometabolic imbalance. These advancements not only elucidate core biological principles governing "microbiota-host-pathogen" interactions but also transcend traditional pathogen-centric perspectives by pioneering precise intervention strategies based on microbiota homeostasis restoration. This provides theoretical foundation for developing microbiome-targeted precision prevention approaches, which will continue to make substantial contributions to malaria research.},
}

@article {pmid40535002,
year = {2025},
author = {Xamxidin, M and Zhang, X and Zheng, G and Chen, C and Wu, M},
title = {Metagenomics-assembled genomes reveal microbial metabolic adaptation to athalassohaline environment, the case Lake Barkol, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550346},
pmid = {40535002},
issn = {1664-302X},
abstract = {Salt-tolerant and halophilic microorganisms are critical drivers of ecosystem stability and biogeochemical cycling in athalassohaline environments. Lake Barkol, a high-altitude inland saline lake, provides a valuable natural setting for investigating microbial community dynamics and adaptation mechanisms under extreme salinity. In this study, we employed high-throughput metagenomic sequencing to characterize the taxonomic composition, metabolic potential, and ecological functions of microbial communities in both water and sediment samples from Lake Barkol. We reconstructed 309 metagenome-assembled genomes (MAGs), comprising 279 bacterial and 30 archaeal genomes. Notably, approximately 97% of the MAGs could not be classified at the species level, indicating substantial taxonomic novelty in this ecosystem. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Desulfobacterota, Planctomycetota, and Verrucomicrobiota, while archaeal communities were primarily composed of Halobacteriota, Thermoplasmatota, and Nanoarchaeota. Metabolic reconstruction revealed the presence of diverse carbon fixation pathways, including the Calvin-Benson-Bassham (CBB) cycle, the Arnon-Buchanan reductive tricarboxylic acid (rTCA) cycle, and the Wood-Ljungdahl pathway. Autotrophic sulfur-oxidizing bacteria, alongside members of Cyanobacteria and Desulfobacterota, were implicated in primary production and carbon assimilation. Nitrogen metabolism was predominantly mediated by Gammaproteobacteria, with evidence for both nitrogen fixation and denitrification processes. Sulfur cycling was largely driven by Desulfobacterota and Pseudomonadota, contributing to sulfate reduction and sulfur oxidation pathways. Microbial communities exhibited distinct osmoadaptation strategies. The "salt-in" strategy was characterized by ion transport systems such as Trk/Ktr potassium uptake and Na[+]/H[+] antiporters, enabling active intracellular ion homeostasis. In contrast, the "salt-out" strategy involved the biosynthesis and uptake of compatible solutes including ectoine, trehalose, and glycine betaine. These strategies were differentially enriched between water and sediment habitats, suggesting spatially distinct adaptive responses to local salinity gradients and nutrient regimes. Additionally, genes encoding microbial rhodopsins were widely distributed, suggesting that rhodopsin-based phototrophy may contribute to supplemental energy acquisition under osmotic stress conditions. The integration of functional and taxonomic data highlights the metabolic versatility and ecological roles of microbial taxa in sustaining biogeochemical processes under hypersaline conditions. Overall, this study reveals extensive taxonomic novelty and functional plasticity among microbial communities in Lake Barkol and underscores the influence of salinity in structuring microbial assemblages and metabolic pathways in athalassohaline ecosystems.},
}

@article {pmid40533851,
year = {2025},
author = {Rahman, N and McCullough, T and Orozco, DF and Walkowiak, S and Farzan, A and Shekarriz, S and Surette, MG and Cicek, N and Derakhshani, H},
title = {Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {66},
pmid = {40533851},
issn = {2524-4671},
support = {(RGPIN-2023-04359)//NSERC Discovery Grant/ ; },
abstract = {INTRODUCTION: The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.

RESULTS: We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.

CONCLUSION: Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.},
}

@article {pmid40533761,
year = {2025},
author = {Hosch, S and Hamelin, B and Haslbauer, JD and Field, CM and Heim, A and Boeck, L and Savic Prince, S and Gradistanac, TA and Gander, AE and Keller, PM and Leuzinger, K and Mertz, KD},
title = {Human mastadenovirus pneumonia in two immunocompetent patients.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {198},
pmid = {40533761},
issn = {1743-422X},
mesh = {Humans ; Female ; Lung/pathology/virology/diagnostic imaging ; *Mastadenovirus/isolation & purification/genetics/classification ; *Pneumonia, Viral/pathology/virology/diagnosis ; Middle Aged ; Switzerland ; Tomography, X-Ray Computed ; *Adenovirus Infections, Human/pathology/virology/diagnosis ; Immunocompetence ; Histocytochemistry ; Whole Genome Sequencing ; Aged ; },
abstract = {BACKGROUND: Human adenoviruses (hAdV) are common pathogens associated with acute respiratory tract infections. Mastadenovirus blackbeardi (hAdV-B) has been linked to severe pneumonia and disseminated disease, primarily in immunocompromised patients. The histopathological and clinical features of adenoviral pneumonia remain poorly characterized.

CASE PRESENTATION: We report two cases of hAdV-B pneumonia in immunocompetent female patients with a history of smoking. Both patients are of Caucasian origin and reside in Switzerland. They presented with persistent respiratory symptoms, pulmonary infiltrates on CT scans, and necrotizing granulomatous inflammation in lung tissue. After excluding other pathogens, metagenomic whole-genome sequencing identified hAdV-B in both cases. Both patients recovered fully following wedge resection of the affected lung tissue, without the need for additional therapy.

CONCLUSIONS: These two cases demonstrated a remarkably similar clinical and histopathological profile, characterized by chronic granulomatous lung inflammation. The findings suggest a prolonged inflammatory response leading to persistent tissue damage. Our observations highlight the potential of hAdV-B to cause chronic pneumonia even in otherwise healthy individuals.},
}

Humans
Female
Lung/pathology/virology/diagnostic imaging
*Mastadenovirus/isolation & purification/genetics/classification
*Pneumonia, Viral/pathology/virology/diagnosis
Middle Aged
Switzerland
Tomography, X-Ray Computed
*Adenovirus Infections, Human/pathology/virology/diagnosis
Immunocompetence
Histocytochemistry
Whole Genome Sequencing
Aged

@article {pmid40533170,
year = {2025},
author = {Kumari Nawarathna, TNT and Fujii, N and Yamamoto, K and Kuroda, K and Narihiro, T and Ozaki, N and Ohashi, A and Kindaichi, T},
title = {Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25007},
pmid = {40533170},
issn = {1347-4405},
mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Carbon Cycle ; Metagenomics ; *Microbial Consortia/genetics ; *Ammonia/metabolism ; Folic Acid/metabolism/biosynthesis ; *Seawater/microbiology ; Metagenome ; Bioreactors/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Genome, Bacterial ; Wastewater/microbiology ; Carbon/metabolism ; },
abstract = {Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using [14]C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L[-1] of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.},
}

*Bacteria/metabolism/genetics/classification/isolation & purification
*Carbon Cycle
Metagenomics
*Microbial Consortia/genetics
*Ammonia/metabolism
Folic Acid/metabolism/biosynthesis
*Seawater/microbiology
Metagenome
Bioreactors/microbiology
Metabolic Networks and Pathways
Phylogeny
Genome, Bacterial
Wastewater/microbiology
Carbon/metabolism

@article {pmid40532861,
year = {2025},
author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK},
title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107815},
doi = {10.1016/j.micpath.2025.107815},
pmid = {40532861},
issn = {1096-1208},
abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS analysis result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 Kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties activities. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.},
}

@article {pmid40532815,
year = {2025},
author = {Pan, D and Sun, H and Liu, Y and Wang, J and Kuang, Y and Shi, T and Zhang, H},
title = {Mobilome dominates fomesafen-responsive dissemination of antibiotic resistome in manure-amended agricultural soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126686},
doi = {10.1016/j.envpol.2025.126686},
pmid = {40532815},
issn = {1873-6424},
abstract = {Pesticides are increasingly perceived as emerging drivers in the spread of antibiotic resistance genes (ARGs) within agroecosystems. Pesticides with longer half-lives tend to impose persistent stresses on soil microbiomes, yet the selection for ARG dissemination remains overlooked. Focusing on a widely used long residual herbicide fomesafen, we examined recommended dose-based selection on the dissemination of ARGs in agricultural soils with or without manure amendment. The degradation half-lives of fomesafen in the blank soils and manure-amended soils were 35.77-124.00 and 20.00-73.27 d, respectively. After 42d exposure, the total abundances of ARGs in the fomesafen-treated manure-amended soils at exposure concentrations of 1 and 5 mg/kg were 1.20- and 1.36-fold higher than that in the controls, with the changes of mobile genetic elements (MGEs) reaching 1.24-2.22 folds; while no significant changes were observed in the blank soils. Furthermore, no significant changes were observed in either bacterial communities or ARG-carrying metagenome-assembled genomes in both manure-amended soils and blank soils under fomesafen selection. Variation partition analysis suggested that 24.42%-25.41% of the variations in ARGs could be individually explained by MGEs, while only 13.47%-13.75% by bacterial communities. Overall, these findings demonstrate that MGE-mediated horizontal transfer predominates fomesafen-responsive dissemination of ARGs in manure-amended agriculture soils and underscores the urgency of re-evaluating agricultural practices involving co-application of manures and long residual herbicides.},
}

@article {pmid40532696,
year = {2025},
author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and , and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL},
title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.034},
pmid = {40532696},
issn = {1097-4172},
abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.},
}

@article {pmid40532535,
year = {2025},
author = {Wang, Z and He, Y and Luo, M and Liu, S and Hou, J and Cao, B and An, X},
title = {Transfer toxicity of polystyrene microplastics in vivo: Multi-organ crosstalk.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109604},
doi = {10.1016/j.envint.2025.109604},
pmid = {40532535},
issn = {1873-6750},
abstract = {The accumulation of microplastics (MPs) within the environment caused serious ecological and health problems. Nevertheless, its systemic toxicity to organisms and its mechanisms lack effective evidence. This study established a model of MP exposure through the gavage of polystyrene (PS)-MPs particles to maternal mice on days 1 to 21 of lactation. The results demonstrated that PS-MPs were distributed widely in maternal mice, occurring mainly in the feces, colon, liver and mammary glands. Further experiments revealed that the gut and blood-milk barriers were disrupted, and pathological injury and inflammatory reactions were observed in the liver, gut, and mammary glands. Metabolomic and metagenome analysis indicated abnormalities in hepatic bile acid metabolism and significant alterations in the gut microbiota after exposure to PS-MPs. These alterations led to increased disruption of the intestine-liver axis. Notably, with fecal microbiota transplantation and antibiotic experiments, we observed that elimination of the intestinal microbiota reduced tissue inflammation and improved gut and blood-milk barrier leakage. These findings demonstrated that PS-MPs exaggerated intestine-liver axis disorders by inducing colonic injury, intestinal ecological dysregulation and abnormal hepatic bile acid metabolism. Furthermore, PS-MPs translocated via the intestine-liver axis and exerted broader toxic effects on mammary tissue. Overall, our study uncovered the transfer toxicity of PS-MPs in mice, proposing the possibility of a gut-liver-mammary axis.},
}

@article {pmid40532529,
year = {2025},
author = {Parab, AS and Ghose, M and Manohar, CS},
title = {Metagenomic reconstruction of microbial genomes and biogeochemical pathways: insights into carbon and nitrogen flux dynamics in the eastern Arabian Sea.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107292},
doi = {10.1016/j.marenvres.2025.107292},
pmid = {40532529},
issn = {1879-0291},
abstract = {The eastern Arabian Sea (EAS) experiences seasonal nutrient availability and productivity shifts driven by the Indian monsoon, influencing microbial contributions to biogeochemical cycles. This study explores carbon, nitrogen and sulfur cycling using metagenome-assembled genomes (MAGs) from water samples collected at chlorophyll maxima (C-Max) depths during non-monsoon and monsoon seasons. A total of 49 high-quality MAGs were reconstructed from 12 metagenomic samples, including four novel lineages from the phyla Pseudomonadota and Bacteroidota. These MAGs revealed distinct seasonal shifts in microbial composition and function. During the non-monsoon season, microbial communities dominated by Idiomarina and Marinobacter showed increased gene abundance for C1 compound metabolism, nitrogen cycling and sulfur oxidation, processes essential for managing climate-active gases such as carbon dioxide (CO2) and nitrous oxide (N2O), while also preventing toxic sulfide accumulation. In contrast, monsoon conditions enhanced organic matter influx, promoting nitrogen retention pathways driven by Sinimarinibacterium and Oleibacter, raising concerns about potential nutrient buildup and localized hypoxia. Despite seasonal variations, functional redundancy ensured the stability of nutrient cycling processes. PERMANOVA analysis (p < 0.001) confirmed that microbial functional gene distribution was primarily shaped by taxonomic structure, with genus-level composition playing a dominant role. The study highlights microbial adaptability and resilience, ensuring ecosystem stability in the dynamic EAS environment. Understanding microbial processes at C-Max depths has enhanced our understanding of biogeochemical cycling in the EAS. Although focused on oxygenated depths, these findings offer insights relevant to microbial functions in the OMZ, reflecting the distinct environmental conditions of EASs.},
}

@article {pmid40532377,
year = {2025},
author = {Deng, Y and Li, J and Taherzadeh, MJ and Lu, H and Kong, D and Ma, B and Hu, Y and Chen, G and Ruan, Y},
title = {Metagenomics reveal the mechanisms of integrated heterotrophic and sulfur autotrophic denitrification (HSAD) using PBAT/starch as carbon source.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138943},
doi = {10.1016/j.jhazmat.2025.138943},
pmid = {40532377},
issn = {1873-3336},
abstract = {The accumulation of nitrate in recirculating aquaculture system constrains the sustainable development of aquaculture industry. This study evaluated the performance of two heterotrophic sulfur autotrophic denitrification (HSAD) reactors packed with PBAT/starch granules and supplemented with thiosulfate in the influent, operating at salinities of 0 ‰ (Reactor I) and 25 ‰ (Reactor II) over a 163-day period. Reactor I achieved an average nitrate removal rate of 0.17 kg/m[3]/d with minimal accumulation of nitrite, total ammonia nitrogen (TAN) and dissolved organic carbon (DOC). In contrast, Reactor II exhibited a slower start-up, a lower denitrification rate of 0.08 kg/m[3]/d, and higher fluctuations in water quality parameters. Over time, both reactors transitioned from heterotrophic to sulfur autotrophic denitrification, as evidenced by increased effluent sulfate concentration, acidification and a decline in microbial biomass. Metagenomics and metatranscriptomics analyses revealed the coexistence of autotropic and heterotrophic denitrifying bacteria, with salinity inhibiting the abundance of denitrifying bacteria and expression of functional genes associated with nitrogen and sulfur metabolism. Network analysis further identified positive correlations among microorganisms involved in carbon, nitrogen and sulfur cycling. This study provides insights into the microbial mechanisms in HSAD process and offers a promising approach for the treatment of nitrate-rich aquaculture wastewater.},
}

@article {pmid40531665,
year = {2025},
author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S},
title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.006815},
pmid = {40531665},
issn = {1466-5034},
mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation & purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs & derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; },
abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).},
}

Thailand
*Flavobacterium/classification/genetics/isolation & purification
*Phylogeny
RNA, Ribosomal, 16S/genetics
*Rivers/microbiology
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Base Composition
Bacterial Typing Techniques
Sequence Analysis, DNA
Vitamin K 2/analogs & derivatives/chemistry/analysis
Nucleic Acid Hybridization
Genome, Bacterial
Phospholipids/analysis/chemistry
*Water Microbiology