@article {pmid40245993,
year = {2025},
author = {Zhang, J and Zhang, B and Duan, F and Xuan, Z and Sun, T and Lu, L},
title = {Metagenomic exploration of novel β-galactosidases for glycosylation engineering.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132546},
doi = {10.1016/j.biortech.2025.132546},
pmid = {40245993},
issn = {1873-2976},
abstract = {β-Galactosidases are important enzymatic tools for glycosylation, but their properties vary greatly with the source. Here, ten putative β-galactosidase genes, designated as bga1 to bga10, encoding proteins Bga1 to Bga10, were mined from an environmental metagenomic dataset comprising 119,152 sequences. Five of the encoded enzyme proteins exhibited less than 80% sequence similarity to known enzymes, but displayed conserved catalytic sites in their predicted three-dimensional models. After heterologous expression and characterization, two recombinant enzymes showed specific hydrolysis activity toward o-nitrophenyl-β-d-galactopyranoside. One of them, Bga4R, exhibited remarkable activity at pH 7.4 and 50℃, with excellent alkaline stability. Notably, Bga4R tolerated a wide range of acceptors for transglycosylation. It catalyzed galactosyl transfer to various monosaccharides and sugar alcohols, and enabling the synthesis of diverse glycosylated derivatives. This study identifies a novel GH 1 β-galactosidase as a powerful tool for glycosylation engineering, with promising potential for synthesizing galactosides valuable to food and pharmaceutical industries.},
}

@article {pmid40245807,
year = {2025},
author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C},
title = {New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation.},
journal = {Water research},
volume = {282},
number = {},
pages = {123607},
doi = {10.1016/j.watres.2025.123607},
pmid = {40245807},
issn = {1879-2448},
abstract = {Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.},
}

@article {pmid40245806,
year = {2025},
author = {Li, J and Zuo, X and Chen, Q and Lin, Y and Meng, F},
title = {Genome-resolved metagenomic analysis reveals a novel denitrifier with truncated nitrite reduction pathway from the genus SC-I-84.},
journal = {Water research},
volume = {282},
number = {},
pages = {123598},
doi = {10.1016/j.watres.2025.123598},
pmid = {40245806},
issn = {1879-2448},
abstract = {Understanding the genomic and ecological traits of partial denitrification (PD) bacteria is of high importance for developing wastewater treatment technologies. In this study, a PD-based bioreactor was operated, resulting in a mixed culture dominated by a potentially novel PD functional bacterium (SC-I-84). Progressively increased activity in both nitrate reduction and nitrite production were observed in the SC-I-84 enrichment system, whereas the nitrite reduction activity was always negligible. The phylogenetic analysis indicated that SC-I-84 was closely related to an uncultured beta-proteobacterium (99 %), whereas its denitrification functional genes (napA, napB, narV, and narY) exhibited evidence of co-evolution with chromosomal genes from the genus Cupriavidus, order Burkholderiales. In the genetic sketch of SC-I-84, only nitrate-reduction genes (nar and nap) were identified, whereas nitrite-reduction genes (nir) were absent. Notably, nitrate reduction genes were adjacent to carbon metabolism genes (sucB/C, mdh, idh) and a high abundance of tricarboxylic acid (TCA) cycling genes were found. This can promote the utilization efficiency of electron donors by nitrate reduction genes in SC-I-84, thus enhancing the denitrification activity. Furthermore, SC-I-84 positively cooperated with some bacteria that participate in nitrogen and carbon metabolism and other PD bacteria, but negatively interacted with full-denitrification bacteria. These results indicate that the enrichment of SC-I-84 restricted the growth of full-denitrification bacteria, aiding in the maintenance of a stable PD process. Taken together, the meta-genomic analysis of the novel PD functional bacterium is expected to enhance our understanding of PD processes and aid in the development of PD-based wastewater treatment processes.},
}

@article {pmid40245686,
year = {2025},
author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, Á and Muñoz, S and García-Cañas, V},
title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {262},
number = {},
pages = {116896},
doi = {10.1016/j.jpba.2025.116896},
pmid = {40245686},
issn = {1873-264X},
abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.},
}

@article {pmid40245533,
year = {2025},
author = {Zhao, J and Wang, Y and Zhang, D and Du, J and Gao, Y and Lu, MY and Guo, JY and Su, HT and Chen, XF and Wen, DH and Jia, SY and Xu, YC and Chen, J and Yang, QW},
title = {Uncovering the unseen: Metagenomic next-generation sequencing improves liver abscess diagnostics.},
journal = {Journal of infection and public health},
volume = {18},
number = {7},
pages = {102708},
doi = {10.1016/j.jiph.2025.102708},
pmid = {40245533},
issn = {1876-035X},
abstract = {BACKGROUND: This study retrospectively analyzed the metagenomic next-generation sequencing (mNGS) results and clinical data from patients with liver abscess (LA) to investigate the clinical value of mNGS in the diagnosis of LA.

METHODS: This retrospective observational study included patients with LA who were admitted to Peking Union Medical College Hospital (PUMCH) between April 2022 and July 2024. We comprehensively analyzed the final clinical etiological diagnosis, traditional pathogen detection through conventional microbiological testing (CMT), and mNGS results in terms of pathogen type and specimen turnaround time.

RESULTS: Among 60 patients with LA, 19 types of pathogens were identified. Using clinical etiological diagnosis as the standard, mNGS identified all pathogens, whereas CMT identified only 42.11 % of pathogens. The true-positivity rate of mNGS (86.67 %) was significantly higher than that of CMT (58.33 %; P < 0.001). The average specimen turnaround time for mNGS (57.66 h) was shorter than that for CMT (86.54 hours, P < 0.001).

CONCLUSIONS: Compared with existing CMT, mNGS offers higher true-positive rates, broader pathogen coverage, and shorter specimen turnaround time. These advantages contribute to more accurate clinical diagnosis and treatment.},
}

@article {pmid40245502,
year = {2025},
author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT},
title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.},
journal = {The Science of the total environment},
volume = {978},
number = {},
pages = {179353},
doi = {10.1016/j.scitotenv.2025.179353},
pmid = {40245502},
issn = {1879-1026},
abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.},
}

@article {pmid40244604,
year = {2025},
author = {Koyanagi, Y and Sajiki, AF and Yuki, K and Ushida, H and Kawano, K and Fujita, K and Shimizu, H and Okuda, D and Kosaka, M and Yamada, K and Suzumura, A and Kachi, S and Kaneko, H and Komatsu, H and Usui, Y and Goto, H and Nishiguchi, KM},
title = {Application of Metagenomic Long-Read Sequencing for the Diagnosis of Herpetic Uveitis.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {4},
pages = {50},
doi = {10.1167/iovs.66.4.50},
pmid = {40244604},
issn = {1552-5783},
mesh = {Humans ; *Aqueous Humor/virology ; Female ; Male ; *Uveitis/diagnosis/virology ; Middle Aged ; *Metagenomics/methods ; *DNA, Viral/analysis/genetics ; *Eye Infections, Viral/diagnosis/virology ; Adult ; Sensitivity and Specificity ; Aged ; Multiplex Polymerase Chain Reaction ; *Herpesviridae/genetics/isolation & purification ; Young Adult ; },
abstract = {PURPOSE: To investigate the sensitivity and specificity of herpes virus detection by nanopore metagenomic analysis (NMA) compared with multiplex polymerase chain reaction (mPCR)-positive and -negative controls.

METHODS: This study included 43 patients with uveitis who had been screened for intraocular herpes virus infection using mPCR from aqueous humor samples. Aqueous humor samples stored after mPCR were subjected to whole-genome amplification, long-read sequencing, and analysis of the phylogenetic microorganism composition using a Flongle flow cell on the Oxford Nanopore MinION platform. For samples that tested positive with mPCR and negative with the Flongle flow cell, additional long-read sequencing was performed using a MinION flow cell, which enabled acquisition of more sequence data. The sensitivity and specificity of herpes virus detection by NMA were compared with the mPCR-positive and -negative controls.

RESULTS: NMA using a Flongle flow cell detected the pathogenic virus in 60.0% of those who tested positive by mPCR (12/20). Further analysis using the MinION flow cell successfully identified viral DNA fragments in three out of the eight initially undetected samples, yielding a collective sensitivity of 75.0% (15/20). All of the virus detected with the long-read sequencing were identical to those diagnosed by mPCR testing, and none of the samples that tested negative by mPCR revealed herpes viral DNA with the use of long-read sequencing.

CONCLUSIONS: For the detection of etiologic herpes virus DNA fragments, NMA revealed a reasonable sensitivity and high specificity. Our study highlights the potential of nanopore sequencing to facilitate further advances in uveitis diagnosis.},
}

Humans
*Aqueous Humor/virology
Female
Male
*Uveitis/diagnosis/virology
Middle Aged
*Metagenomics/methods
*DNA, Viral/analysis/genetics
*Eye Infections, Viral/diagnosis/virology
Adult
Sensitivity and Specificity
Aged
Multiplex Polymerase Chain Reaction
*Herpesviridae/genetics/isolation & purification
Young Adult

@article {pmid40244481,
year = {2025},
author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R},
title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {248},
pmid = {40244481},
issn = {1432-0991},
support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; },
mesh = {Thailand ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; },
abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.},
}

Thailand
*Bacteria/classification/genetics/isolation & purification
*Water Microbiology
*Rivers/microbiology
Metagenomics
*Microbiota
Water Quality
Environmental Monitoring

@article {pmid40244477,
year = {2025},
author = {Li, J and Zhang, Y and He, L},
title = {The role of urine microbiota in culture-negative patients with pyuria.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {227},
pmid = {40244477},
issn = {1433-8726},
mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; },
abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.

METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.

RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p = 0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p = 0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p = 0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p = 0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p < 0.001].

CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.},
}

Humans
*Pyuria/microbiology/virology/urine
Retrospective Studies
Male
Female
*Microbiota
Middle Aged
*Urine/microbiology/virology
Aged
Adult

@article {pmid40244062,
year = {2025},
author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC},
title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf071},
pmid = {40244062},
issn = {1751-7370},
support = {COEVOPRO 802242//European Research Council Starting/ ; },
abstract = {Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.},
}

@article {pmid40243577,
year = {2025},
author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J},
title = {Potential Role of Malassezia restricta in Pterygium Development.},
journal = {International journal of molecular sciences},
volume = {26},
number = {7},
pages = {},
doi = {10.3390/ijms26072976},
pmid = {40243577},
issn = {1422-0067},
support = {IP-2020-02-8921//Croatian Science Foundation/ ; },
mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; },
abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.},
}

Humans
*Pterygium/microbiology/pathology/genetics
*Malassezia/genetics/isolation & purification
Male
Female
Middle Aged
Conjunctiva/microbiology/pathology
Microbiota
Aged
Gene Expression Profiling

@article {pmid40243351,
year = {2025},
author = {Li, Y and Liu, S and Han, P and Lei, J and Wang, H and Zhu, W and Dong, Z and Zhang, Y and Jiang, Z and Zheng, B and Rao, G and Yu, Z and Li, A},
title = {Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0259224},
doi = {10.1128/spectrum.02592-24},
pmid = {40243351},
issn = {2165-0497},
abstract = {UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generation sequencing (mNGS) for rapid antimicrobial susceptibility prediction (mNGS-based AST), which was tailored to five ESKAPEE bacteria: Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. However, the clinical utility remained unvalidated. Assuming that mNGS-based AST results were obtained during clinical management, we assessed its clinical utility using data from a previous observational cohort study of clinical mNGS applications. We collected the data from 114 patients infected with five ESKAPEE bacteria from 07/2021 to 03/2023 and incorporated the sequencing data into the model. We evaluated the performance and hypothetical impact of the method by comparing its results and therapy recommendations with those based on traditional culture-based AST. The primary outcome was the performance of mNGS-based AST (n = 113 strains). mNGS-based AST displayed an overall accuracy of 93.84% and shorter turnaround time (1.12 ± 0.33 days vs 2.81 ± 0.57 days for culture-based AST, t = -27.31, P < 0.05). The secondary outcomes included the proportion of patients who could benefit from mNGS-based AST. It could allow earlier and suitable antibacterial adjustments in 32.05% of culture-positive patients (25/78) and offer actionable antimicrobial susceptibility results in 16.67% of culture-negative cases (6/36). mNGS-based AST offers a promising approach for individualized antibacterial therapy.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS)-based antimicrobial susceptibility prediction (AST) is a novel method for predicting the antimicrobial susceptibility of ESKAPEE bacteria using a machine learning approach and short-read sequencing data. Assuming that mNGS-based AST results were obtained during clinical management, it could significantly reduce turnaround time while maintaining a high level of accuracy, allowing for earlier therapeutic adjustments for patients. Furthermore, mNGS-based AST can be integrated with clinical mNGS to maximize the utility of short-read data without substantial cost increases. This study demonstrates the potential of mNGS-based AST for precise, individualized antibacterial selection and highlights its broader applicability in enhancing clinical antimicrobial use for various infections.},
}

@article {pmid40243342,
year = {2025},
author = {Gruninger, RJ and McCormack, ML and Chomistek, NC and Zaheer, R and McAllister, TA},
title = {Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0042325},
doi = {10.1128/spectrum.00423-25},
pmid = {40243342},
issn = {2165-0497},
abstract = {UNLABELLED: Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

IMPORTANCE: Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.},
}

@article {pmid40243306,
year = {2025},
author = {Wang, Z and Sun, Y and Wang, H and Yun, J and Du, W},
title = {Metagenome-assembled genome of a novel Pseudoalteromonas species from South Mid-Atlantic Ridge deep-sea water suggests potential for chitin degradation.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0018925},
doi = {10.1128/mra.00189-25},
pmid = {40243306},
issn = {2576-098X},
abstract = {We report a high-quality metagenome-assembled genome (MAG) of a novel Pseudoalteromonas species recovered from deep-sea water of the South Mid-Atlantic Ridge. This MAG encodes key chitinase-related genes, suggesting potential involvement in chitin degradation and organic matter remineralization in the deep sea.},
}

@article {pmid40242593,
year = {2025},
author = {Sun, S and He, R and Chen, S and Ren, J and Ma, X and Yang, J},
title = {Odontogenic brain abscess caused by Porphyromonas gingivalis and Streptococcus constellatus: a case report and review article.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2485197},
pmid = {40242593},
issn = {2000-2297},
abstract = {BACKGROUND: Odontogenic brain abscess is a rare, but potentially fatal, central nervous system infection, with insidious onset and unclear etiology.

METHODS: This case reports a 70-year-old male patient who developed an odontogenic brain abscess secondary to periodontal infection and underwent neurological surgery. Extract pus during surgery for the metagenomic next-generation sequencing (mNGS).

RESULTS: The mNGS of pus samples obtained from brain abscess aspiration identified the periodontal pathogens Porphyromonas gingivalis and Streptococcus constellatus. Consequently, he was referred to the department of stomatology for further examination and treatment.

CONCLUSIONS: Our study found that major periodontal pathogens including P. gingivalis and S. constellatus were essential in the development of odontogenic brain abscesses; thus, timely intervention and preventive measures are important for treatment.},
}

@article {pmid40242244,
year = {2025},
author = {Kang, Z and Zhang, R and Li, S and Wang, J and Huang, M and Li, W},
title = {Preliminary investigation of gut microbiota and associated metabolic pathways in the pathogenesis of primary central nervous system lymphoma.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1548146},
pmid = {40242244},
issn = {2234-943X},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) is a rare and highly aggressive form of non-Hodgkin lymphoma, primarily confined to the central nervous system. In recent years, growing evidence has indicated that dysbiosis of the gut microbiota is closely associated with the development of various malignancies. This study aims to systematically explore the potential role of gut microbiota and their metabolic pathways in the pathogenesis of PCNSL by integrating metagenomic and metabolomic approaches.

MATERIALS AND METHODS: A total of 33 PCNSL patients and 32 healthy controls were enrolled in this study, and fecal samples were collected from each participant. The fecal samples were analyzed using metagenomic and metabolomic techniques, followed by KEGG pathway enrichment analysis to investigate the biological pathways enriched by the differential gut microbiota and metabolites.

RESULTS: Significant differences were observed in the composition of gut microbiota and metabolites between PCNSL patients and healthy controls. In the gut microbiota of PCNSL patients, the abundance of the phylum Proteobacteria was markedly increased, while the Firmicutes/Bacteroidetes (F/B) ratio was significantly elevated. Metabolomic analysis revealed that the abundance of oleamide was significantly reduced in the PCNSL group, while the relative abundance of deoxycholic acid was significantly elevated. KEGG pathway analysis indicated that the differential gut microbiota and metabolites were primarily involved in key metabolic pathways such as nitrogen metabolism, phenylalanine metabolism, purine metabolism, and pyrimidine metabolism, with these pathways being more active in PCNSL patients.

CONCLUSION: This study is the first to systematically investigate the differences in gut microbiota and their metabolites between PCNSL patients and healthy individuals, highlighting the potential role of gut microbiota alterations in the pathogenesis of PCNSL.},
}

@article {pmid40241899,
year = {2025},
author = {Chen, L and Weng, W and Li, D and Xie, W and Lu, L and Li, S},
title = {Case Report: A clinically relevant isolation of Gardnerella leopoldii guided by morphological and molecular evidence from a urinary tract infection case.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1548067},
pmid = {40241899},
issn = {2296-858X},
abstract = {BACKGROUND: The genus Gardnerella is commonly found in the vaginal ecosystem and is considered a covert pathogen of the urinary tract. However, Gardnerella vaginalis had been the only recognized species of the genus Gardnerella for decades. Cases regarding the clinical relevance of Gardnerella leopoldii have rarely been reported, which is crucial for fully understanding the various species within the genus Gardnerella.

CASE PRESENTATION: A 72-year-old female patient was admitted to the hospital with gross hematuria and complaints of waist soreness. Physical examinations, including those of the head, chest, and abdomen, along with routine laboratory tests such as white blood cell (WBC) count and proportion, liver function, and renal function, yielded normal results. However, the patient also exhibited significantly elevated levels of serum C-reactive protein (CRP) and abnormal urinary test findings, which revealed positive results for occult blood and leukocyte esterase, and increased counts of erythrocyte and leukocyte. To further evaluate the urinary system, computerized tomography urography (CTU) was performed. The CTU results revealed multiple weakly enhanced foci in the right kidney and thickening of the right ureter, renal pelvis, calyces, and bladder walls. Based on the above findings, the initial diagnosis included hematuria, hydronephrosis, and urinary tract infection (UTI). To identify the causative pathogens, we employed a comprehensive approach that included microscopic morphology, Sanger sequencing, and metagenomic next-generation sequencing (mNGS). Finally, both Mycobacterium tuberculosis and G. leopoldii were identified as the co-infecting etiological agents responsible for the patient's urinary tract infection.

CONCLUSION: This case represents the first documented isolation of clinically relevant G. leopoldii, guided by morphological and molecular evidence from a clinical urine sample. It highlights the potential of mNGS as a promising tool for identifying previously unrecognized species and offers valuable insights to enhance the understanding of clinically relevant microorganisms.},
}

@article {pmid40241768,
year = {2025},
author = {Yao, XQ and Bao, H and La, NT and Jiang, GS and Zhai, PH and Liu, CB and Yu, L},
title = {Gut microbiota contribute to cold adaptation in mammals-primates and ungulates.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112245},
pmid = {40241768},
issn = {2589-0042},
abstract = {Gut microbiota play an influential role in how animals adapt to extreme environments. Two phylogenetically distant mammals, Yunnan snub-nosed monkey and reindeer both adapted to frigid environments. Metagenomic analyses revealed they developed similar cold adaptation strategies in response to food scarcity (enhanced fiber degradation and nitrogen balance maintenance), energy shortages (increased short-chain fatty acid [SCFA] synthesis), and a constant body temperature sustainment (stimulation of non-shivering thermogenesis [NST]). Moreover, they evolved distinct adaptation strategies to cope with different cold ecosystems. Yunnan snub-nosed monkey adapt to high-altitude hypoxia environment through enhancing ability to synthesize lactate and metabolize purine, while reindeer adapt to extreme cold environment through increasing blood flow, strengthening urea cycling, and enriching fat storage associated bacteria. Notably, reindeer microbiota uniquely enriched cholesterol-degrading bacteria, potentially mitigating cardiovascular risks from lipid storage. Our study expands the knowledge of how gut microbiome promotes cold adaptation through shared and specialized mechanisms shaped by different phylogenetic and ecological contexts.},
}

@article {pmid40241748,
year = {2025},
author = {Liu, T and Kress, AM and Debelius, J and Zhao, N and Smirnova, E and Bandyopadhyay, S and Bonham, K and Comstock, SS and Gill, S and Gern, JE and Koinis-Mitchell, D and Klepac-Ceraj, V and Lee-Sarwar, K and Litonjua, AA and McKee, K and McCauley, K and O'Connor, TG and Rosas-Salazar, C and Scheible, K and Stanford, JB and Moore, B and Jacobson, LP and Mueller, NT and , },
title = {Maternal vaginal and fecal microbiota in later pregnancy contribute to child fecal microbiota development in the ECHO cohort.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112211},
pmid = {40241748},
issn = {2589-0042},
abstract = {There is growing interest in the use of microbial-seeding interventions to mitigate the impacts of prenatal antibiotics, C-section, and lack of breastfeeding on mother-child microbe sharing. However, the relative importance of maternal vaginal vs. fecal microbiota in this process is unclear. Analyzing 16S rRNA sequences from five US birth cohorts, we found that maternal vaginal and fecal microbiota became more similar as pregnancy progressed, and both niches influenced the child's fecal microbiota. The relative contribution of maternal vaginal microbiota increased when vaginal sampling occurred later in gestation. As children aged from birth to 5 years, their fecal microbiota increasingly resembled their mother's fecal microbiota as compared to vaginal microbiota. Patterns of sharing appeared to differ by prenatal antibiotic use, birth mode (C-section vs. vaginal), and breastfeeding. Our findings enhance understanding of niche-specific mother-child microbe sharing and may inform microbial-seeding interventions. Metagenomic studies are needed to identify specific shared strains.},
}

@article {pmid40241728,
year = {2025},
author = {Xie, L and Wang, X and Wang, X and Liu, X},
title = {Changes in microbial community succession and volatile compounds during the natural fermentation of bangcai.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581378},
pmid = {40241728},
issn = {1664-302X},
abstract = {INTRODUCTION: Fermented bangcai (Brassica juncea var. crassicaulis) is a traditional Chinese food with unique flavor. However, the formation mechanism of flavor compounds related to the fermentation process of bangcai has not been thoroughly studied.

METHODS: Gas chromatography-ion mobility spectrometry technology combined with metagenomics was used to analyze the characteristic volatile flavor compounds and microbial community structure of bangcai before and after fermentation in this study.

RESULTS: A total of 91 types of volatile organic compounds were detected in this study. The pungent odor brought by allyl isothiocyanate, 1-butene isothiocyanate, and other substances in the raw materials was removed through fermentation. This process led to the formation of flavor substances such as propyl acetate, ethyl acetate, and 2-methyl-3-furanthiol, which imparted bangcai with flavors of flower and fruit, roast meat, and fried coffee. In addition, our study found that after air drying, bangcai mainly contained γ-butyrolactone, nonanal and other flavor compounds, giving the bangcai products a richer floral and fruity flavor profile. Citrobacter, Lactobacillus, and Leuconostoc were the dominant bacteria in the fermentation process of bangcai. They were significantly related to the formation of differential flavor compounds such as γ-butyrolactone, ethyl 2-methylpropanoat, and benzaldehyde-D.

DISCUSSION: These results provide a theoretical basis for improving the flavor quality of fermented vegetable products.},
}

@article {pmid40241696,
year = {2025},
author = {Yang, Z and Xie, Y and Zhu, Y and Lei, M and Chen, X and Jin, W and Fu, C and Yu, L},
title = {Unraveling the flavor formation process of mellow and thick-type ripened Pu-erh tea through non-targeted metabolomics and metagenomics.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102424},
pmid = {40241696},
issn = {2590-1575},
abstract = {Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes (P < 0.05). The contents of free amino acids, L-theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea, Aspergillus, Brachybacterium, and Staphylococcus. By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium. This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters (P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.},
}

@article {pmid40241220,
year = {2025},
author = {Yang, K and Li, G and Li, Q and Wang, W and Zhao, X and Shao, N and Qiu, H and Liu, J and Xu, L and Zhao, J},
title = {Distribution of gut microbiota across intestinal segments and their impact on human physiological and pathological processes.},
journal = {Cell & bioscience},
volume = {15},
number = {1},
pages = {47},
pmid = {40241220},
issn = {2045-3701},
support = {82272812//National Natural Science Foundation of China/ ; 82360018//National Natural Science Foundation of China/ ; },
abstract = {In recent years, advancements in metagenomics, metabolomics, and single-cell sequencing have enhanced our understanding of the intricate relationships between gut microbiota and their hosts. Gut microbiota colonize humans from birth, with their initial composition significantly influenced by the mode of delivery and feeding method. During the transition from infancy to early childhood, exposure to a diverse diet and the maturation of the immune system lead to the gradual stabilization of gut microbiota's composition and distribution. Numerous studies have demonstrated that gut microbiota can influence a wide range of physiological functions and pathological processes by interacting with various tissues and organs through the gut-organ axis. Different intestinal segments exhibit unique physical and chemical conditions, which leads to the formation of vertical gradients along the intestinal tract: aerobes and facultative aerobes mainly live in the small intestine and anaerobic bacteria mainly live in the large intestine, and horizontal gradients: mucosa-associated microbiota and lumen-associated microbiota. In this review, we systematically summarize the distribution characteristics of gut microbiota across six intestinal segments: duodenum, jejunum, ileum, cecum, colon, and rectum. We also draw a conclusion that gut microbiota distributed in different intestinal segments affect the progression of different diseases. We hope to elucidate the role of microbiota at specific anatomic sites within the gut in precisely regulating the processes of particular diseases, thereby providing a solid foundation for developing novel diagnostic and therapeutic strategies for related diseases.},
}

@article {pmid40240641,
year = {2025},
author = {Muñoz-Rivera, MP and Martínez-Morales, F and Guzmán-Morales, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR},
title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40240641},
issn = {1618-1905},
abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.},
}

@article {pmid40240456,
year = {2025},
author = {Bahetjan, K and Yu-Xia, and Lin, S and Aili, N and Yang, H and Du, S},
title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13179},
pmid = {40240456},
issn = {2045-2322},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; },
abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology
*Bronchoalveolar Lavage Fluid/microbiology
Male
Female
Aged
Middle Aged
*Microbiota
Bacteria/classification/genetics/isolation & purification
*Lung/microbiology/physiopathology
Dysbiosis/microbiology

@article {pmid40240384,
year = {2025},
author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, JÉCT and Arruda, P and Dante, RA and Gerhardt, IR},
title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {636},
pmid = {40240384},
issn = {2052-4463},
support = {2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; },
mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.},
}

*Droughts
Seasons
*Soil Microbiology
Brazil
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
*Microbiota
Bacteria/genetics/classification

@article {pmid40240311,
year = {2025},
author = {Liu, D and Abdellah, YAY and Dou, T and Keiblinger, KM and Zhou, Z and Bhople, P and Jiang, J and Shi, X and Zhang, F and Yu, F and Xing, B},
title = {Livestock-Crop-Mushroom (LCM) Circular System: An Eco-Friendly Approach for Enhancing Plant Performance and Mitigating Microbiological Risks.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c12517},
pmid = {40240311},
issn = {1520-5851},
abstract = {Mushroom production using agroforestry biowaste is a great green cycling agriculture alternative. Therefore, the current study explored the Livestock-Crop-Mushroom (LCM) circular production model, starting with co-composting of straw and cow manure as a'St' biofertilizer further used for mushroom cultivation that ultimately produced a'StM' biofertilizer. The two biofertilizers were tested for their impacts on plant growth and potential microbial risks. The results show significant growth of oats stimulated by biofertiliser use. Both'St' and'StM' increased plant biomass, while with the latter, the crude protein content (+5.1%) and root biomass were also higher. Reduced abundances of resistome genes (30%) and pathogens (25%) were observed during the oat growth. Further, metagenomics analysis also indicated a reduction in antibiotic-resistance genes by -20% in soils with oats treated by'St' and -46% in'StM' biofertilizer treatment. The'StM' had a three-fold stronger inhibitory effect on oat rhizosphere soil pathogens than'St'. Moreover, compared to'St','StM' suppressed pathogens in seeds and stems, with specific beneficial biomarker microbes in different plant parts. Overall, the antibiotic resistance gene related to oxytetracycline decreased more than three-fold in the LCM system. This study demonstrates the substantial potential and scalability of the LCM circular system within the agricultural domain.},
}

@article {pmid40239498,
year = {2025},
author = {Chen, M and Grégoire, DS and St-Germain, P and Berdugo-Clavijo, C and Hug, LA},
title = {Microbial diversity and capacity for arsenic biogeochemical cycling in aquifers associated with thermal mobilization.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179357},
doi = {10.1016/j.scitotenv.2025.179357},
pmid = {40239498},
issn = {1879-1026},
abstract = {Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic detoxification and metabolism, which include genes for efflux, methylation, and reduction/oxidation of As(V)/As(III). We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread among community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high‑arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.},
}

@article {pmid40238917,
year = {2025},
author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ},
title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.},
journal = {Science translational medicine},
volume = {17},
number = {794},
pages = {eadq8870},
doi = {10.1126/scitranslmed.adq8870},
pmid = {40238917},
issn = {1946-6242},
mesh = {Animals ; Humans ; *Operon/genetics ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology ; *Pyrimidines/toxicity ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; },
abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.},
}

Animals
Humans
*Operon/genetics
*Fluorouracil/therapeutic use/toxicity/adverse effects
Gastrointestinal Microbiome/drug effects/genetics
Mice
*Colorectal Neoplasms/drug therapy/microbiology
*Pyrimidines/toxicity
*Bacteria/genetics/drug effects
RNA, Ribosomal, 16S/genetics
Female
Male

@article {pmid40238748,
year = {2025},
author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C},
title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321389},
doi = {10.1371/journal.pone.0321389},
pmid = {40238748},
issn = {1932-6203},
mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; },
abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.},
}

Animals
Female
Horses/microbiology/immunology
*Uterus/microbiology/immunology/metabolism
Proteomics/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Vagina/microbiology/immunology
Bacteria/genetics/classification
Proteome

@article {pmid40238740,
year = {2025},
author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X},
title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.},
journal = {PLoS pathogens},
volume = {21},
number = {4},
pages = {e1013069},
doi = {10.1371/journal.ppat.1013069},
pmid = {40238740},
issn = {1553-7374},
mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; },
abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.},
}

Animals
*Succinic Acid/metabolism
Mice
Fibrosis
*Gastrointestinal Microbiome/physiology
*Trichinellosis/complications/metabolism/pathology
*Trichinella spiralis
*Bacteroides/metabolism
Mice, Inbred C57BL
Receptors, G-Protein-Coupled/metabolism
Myocardium/pathology/metabolism
Male

@article {pmid40238414,
year = {2025},
author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Agodi, A},
title = {Monitoring Antibiotic Resistance in Wastewater: Findings from Three Treatment Plants in Sicily, Italy.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {3},
pages = {},
doi = {10.3390/ijerph22030351},
pmid = {40238414},
issn = {1660-4601},
support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; },
mesh = {*Wastewater/microbiology ; Sicily ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) poses a global public health threat. Wastewater analysis provides valuable insights into antimicrobial resistance genes (ARGs), identifying sources and trends and evaluating AMR control measures. Between February 2022 and March 2023, pre-treatment urban wastewater samples were collected weekly from treatment plants in Pantano D'Arci, Siracusa, and Giarre (Sicily, Italy). Monthly composite DNA extracts were prepared by combining weekly subsamples from each site, yielding 42 composite samples-14 from each treatment plant. Real-time PCR analysis targeted specific ARGs, including blaSHV, erm(A), erm(B), blaOXA, blaNDM, blaVIM, blaTEM, and blaCTX-M. The preliminary findings revealed that blaERM-B, blaOXA, blaTEM, and blaCTX-M were present in all samples, with erm(B) (median value: 8.51; range: 1.67-30.93), blaSHV (0.78; 0.00-6.36), and blaTEM (0.72; 0.34-4.30) showing the highest relative abundance. These results underscore the importance of integrating ARG data with broader research to understand the persistence and proliferation mechanisms of ARGs in wastewater environments. Future studies should employ metagenomic analyses to profile resistomes in urban, hospital, agricultural, and farm wastewater. Comparing these profiles will help identify contamination pathways and inform the development of targeted ARG surveillance programs. Monitoring shifts in ARG abundance could signal cross-sectoral contamination, enabling more effective AMR control strategies.},
}

*Wastewater/microbiology
Sicily
*Drug Resistance, Microbial/genetics
*Environmental Monitoring
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Genes, Bacterial

@article {pmid40238256,
year = {2025},
author = {Rueangsri, N and Roytrakul, S and Muangnoi, C and Tongkhao, K and Sae-Tan, S and Treesuwan, K and Sirivarasai, J},
title = {Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071148},
pmid = {40238256},
issn = {2304-8158},
support = {C02F660008//Mahidol University and the Office of National Higher Education Science Research and Innova-tion Policy Council through the Program Management Unit for Competitiveness, Thailand/ ; },
abstract = {Research in metagenomics and metaproteomics can reveal how microbiological interactions in fermented foods contribute to their health benefits. This study examined three types of fermented vegetables: a standard formulation, a probiotic formulation with Lacticaseibacillus rhamnosus GG, and a polyphenol formulation with vitexin from Mung bean seed coat. Measurements were taken at day 0 (after 36 h of fermentation at room temperature) and after 15 days. We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (Lactobacillus and Weissella) and species (Lacticaseibacillus rhamnosus and Levilactobacillus brevis) of lactic acid bacteria (LAB). All of these taxa demonstrated significant relative abundance between 0 and 15 days of fermentation in our metagenomic analysis. Our findings from principal component analysis and clustering analysis categorically distinguished protein expression patterns at various stages of fermentation. By comparing samples from day 0 to day 15, we identified proteins associated with DNA replication and repair mechanisms, including transcription elongation factor GreA, tRNA pseudouridine synthase B, and helicases. We also observed their roles in protein synthesis, which encompasses oxidoreductases and aspartokinase. Furthermore, we identified strong correlations of specific proteins across the three formulations with antioxidant markers. In conclusion, the results of this study decisively enhance our understanding of the role of the proteins related to specific LAB in fermented foods, highlighting their potential to improve texture, flavor, nutritional quality, and health benefits.},
}

@article {pmid40238219,
year = {2025},
author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G},
title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071082},
pmid = {40238219},
issn = {2304-8158},
abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.},
}

@article {pmid40238218,
year = {2025},
author = {Zhadyra, S and Tao, F and Xu, P},
title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071102},
pmid = {40238218},
issn = {2304-8158},
abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.},
}

@article {pmid40238191,
year = {2025},
author = {Ren, C and Zhao, M and Xue, T and Geng, T and Nie, X and Han, C and Wen, Y and Jia, L},
title = {Metagenomic and Physicochemical Analyses Reveal Microbial Community and Functional Differences Between Three Different Grades of Hongxin Low-Temperature Daqu.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071104},
pmid = {40238191},
issn = {2304-8158},
support = {202302140601016//Key R&D Program of Shanxi Province/ ; },
abstract = {Hongxin (HX) is an indispensable Daqu in the production of light-flavor Baijiu (LFB). However, the classification method of HX is highly subjective, and the classification and functional differences in microorganisms in different grades of HX are still unclear. In this study, metagenomics and physiochemical analysis were used to compare three grades of HX (top, first, second) and clarify their brewing functions in LFB. The results showed that a total of 1556 genera and 5367 species were detected in all samples. Bacteria and fungi are the main microorganisms in HX, and the relative abundance of bacteria and fungi is above 4.5:1. Kroppenstedtia (11.43%), Leuconostoc (10.52%), Fructilactobacillus (9.00%) were the top three genera in HX. Although the microbial community composition of the three grades of HX is highly similar, each HX has a specific microbial community structure and macrogene functional characteristics, indicating that they have different brewing functions. The dominant microorganisms in top-grade HX and first-grade HX were mainly positively correlated with energy metabolism and lipid metabolism, while the dominant microorganisms in second-grade HX were mainly positively correlated with carbohydrate metabolism and amino acid metabolism. This study revealed the different fermentation effects of different grades of HX in LFB and provided suggestions for the scientific classification and quality control of HX.},
}

@article {pmid40238188,
year = {2025},
author = {Ugarcina Perovic, S and Ramji, V and Chong, H and Duan, Y and Maguire, F and Coelho, LP},
title = {argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf173},
pmid = {40238188},
issn = {1367-4811},
abstract = {SUMMARY: Currently available and frequently used tools for annotating antimicrobial resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challenging. The comparability of ARG annotation outputs can be improved by mapping gene names and their categories to a common controlled vocabulary such as the Antibiotic Resistance Ontology (ARO). We developed argNorm, a command line tool and Python library, to normalize all detected genes across 6 ARG annotation tools (8 databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.

argNorm is available as an open-source tool at: https://github.com/BigDataBiology/argNorm. It can also be downloaded as a PyPI package and is available on Bioconda and as an nf-core module.},
}

@article {pmid40237937,
year = {2025},
author = {Maimaris, J and Payne, J and Roa-Bautista, A and Breuer, J and Storey, N and Morfopoulou, S and Bamford, A and D'Arco, F and Gilmour, K and Aquilina, K and Hassell, J and Hacohen, Y and Silva, AHD and Merve, A and Jacques, TS and Rao, K and Chiesa, R and Amrolia, P and Silva, J and Braggins, H and Xu-Bayford, J and Goldblatt, D and Worth, A and Booth, C and Ip, W and Qasim, W and Kusters, M and Kaliakatsos, M and Brown, JR and Elfeky, R},
title = {Safety and Diagnostic Utility of Brain Biopsy and Metagenomics in Decision-Making for Patients with Inborn Errors of Immunity (IEI) and Unexplained Neurological Manifestations.},
journal = {Journal of clinical immunology},
volume = {45},
number = {1},
pages = {86},
pmid = {40237937},
issn = {1573-2592},
support = {GN-000707//Brain Tumour Charity/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Brain/pathology ; Male ; Biopsy ; Female ; Child, Preschool ; Infant ; Child ; Retrospective Studies ; *Nervous System Diseases/diagnosis/etiology ; Clinical Decision-Making ; Adolescent ; High-Throughput Nucleotide Sequencing ; },
abstract = {Unexplained neurological symptoms can pose a diagnostic challenge in patients with inborn errors of immunity (IEI) where the aetiology can be varied, and diverse pathologies may require contrasting treatments. Brain biopsy, the process of sampling brain tissue directly, has historically provided histological and microbiological information and can now be exploited for deep metagenomic next generation analysis (mNGS). We conducted a retrospective analysis of clinical and diagnostic data on paediatric patients with IEI who had a brain biopsy between 2010 and 2022 at a UK tertiary centre where 14 patients fulfilled our search criteria. We report on clinical characteristics, adverse events and the additional impact of mNGS of brain biopsies, where these were conducted. We found that brain biopsy enabled diagnostics with manageable complications in most cases, either by tissue or metagenomics analysis (n = 11/14, 79%). We found that mNGS analysis improved the diagnostic yield of brain biopsy in 29% of IEI cases (n = 4/14). Brain biopsy enabled a change in management in 71% of cases (n = 10/14). This series provides compelling evidence for the safe and purposeful use of brain biopsy in children with IEI.},
}

Humans
*Metagenomics/methods
*Brain/pathology
Male
Biopsy
Female
Child, Preschool
Infant
Child
Retrospective Studies
*Nervous System Diseases/diagnosis/etiology
Clinical Decision-Making
Adolescent
High-Throughput Nucleotide Sequencing

@article {pmid40237802,
year = {2025},
author = {Lei, W and Huang, R and Qu, L and Ma, K and Li, J},
title = {Exogenous Mogroside V Drove Microbial Carbohydrate Metabolism and Consequently Enhanced Fruity Aroma in Greengage Wine.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c10783},
pmid = {40237802},
issn = {1520-5118},
abstract = {The microbial community is essential for the formation of aroma development in high-acidity greengage wine fermentation. Recent observations also highlight positive effects of mogroside V (MG V) on microorganisms in fermented foods, but the underlying chemical and biological mechanisms remain inadequate. The results indicated differences in the physicochemical properties among greengage wines, particularly a 50% increase in the ethanol conversion rate. Concurrently, GC-MS and sensory analyses demonstrated that MG V augmented carbohydrate conversion into ethyl esters (twice as much as in the control group), exhibiting tropical fruit and floral aroma profiles. The perceived intensity of these aromatic compounds increased by over 30%, thereby enriching the overall aromatic harmony of the wine. Integrated analysis of KEGG pathways and CAZymes annotations demonstrated that the enhancement of ethyl ester formation by MG V depends on improvement of the transport of carbohydrates and MG V, as well as accelerating the flux of pyruvate to acetyl-CoA in yeast. In conclusion, our study presents a targeted strategy for the high-acidity fruit wine industry of modulating this metabolic node in yeast, thereby achieving a focused enhancement of tropical fruit aroma characteristics in fruit wines.},
}

@article {pmid40237492,
year = {2025},
author = {Hu, T and Meng, Y and Zhao, C and Sheng, D and Yang, S and Dai, J and Wei, T and Zhang, Y and Zhao, G and Liu, Y and Wang, Q and Zhang, L},
title = {Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0298424},
doi = {10.1128/spectrum.02984-24},
pmid = {40237492},
issn = {2165-0497},
abstract = {As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.},
}

@article {pmid40237489,
year = {2025},
author = {Rybicka, I and Kaźmierczak, Z},
title = {The human phageome: niche-specific distribution of bacteriophages and their clinical implications.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0178824},
doi = {10.1128/aem.01788-24},
pmid = {40237489},
issn = {1098-5336},
abstract = {Bacteriophages (phages) play a crucial role in shaping the composition and diversity of the human microbiome across various body niches. Recent advancements in high-throughput sequencing technologies have enabled comprehensive analysis of the human phageome in different body sites. This review comprehensively analyzes phage populations across major human body niches, examining their distribution and dynamics through recent metagenomic discoveries. We explore how phage-bacteria interactions within different body sites contribute to homeostasis and disease development. Emerging evidence demonstrates that phageome perturbations can serve as early indicators of various disorders, particularly in the gut microbiome. Understanding these complex microbial interactions offers promising opportunities for developing novel diagnostic markers and therapeutic approaches. However, the causal relationship between phages, bacteria, and disease development remains unclear. Further research is needed to elucidate the role of phages in human health and disease and to explore their potential as diagnostic or therapeutic tools. Understanding the intricate interactions between phages, bacteria, and the human host is crucial for unraveling the complexities of the human microbiome and its impact on health and disease.},
}

@article {pmid40237482,
year = {2025},
author = {Zhang, C and Bosma, TNP and Atashgahi, S and Smidt, H},
title = {Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150324},
doi = {10.1128/msystems.01503-24},
pmid = {40237482},
issn = {2379-5077},
abstract = {Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.},
}

@article {pmid40237336,
year = {2025},
author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR},
title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2493900},
doi = {10.1080/19490976.2025.2493900},
pmid = {40237336},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; },
abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Breast Feeding
Female
*Bacteria/classification/genetics/isolation & purification
Male
Brazil
Feces/microbiology
Metagenomics
*Delivery, Obstetric/methods
Cohort Studies
Infant, Newborn

@article {pmid40236771,
year = {2025},
author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J},
title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70008},
pmid = {40236771},
issn = {2770-596X},
abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.},
}

@article {pmid40236770,
year = {2025},
author = {Zhang, C and Chen, Y and Duan, R and Zhang, Y and Zheng, H and Zhang, J and Zhang, T and Xu, J and Li, K and Pei, F and Duan, L},
title = {Preconception maternal gut dysbiosis affects enteric nervous system development and disease susceptibility in offspring via the GPR41-GDNF/RET/SOX10 signaling pathway.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70012},
pmid = {40236770},
issn = {2770-596X},
abstract = {Maternal health, specifically changes in the gut microbiota, can profoundly impact offspring health; however, our understanding of how gut microbiota alterations during the preconception period influence the offspring remains limited. In this study, we investigated the impact and mechanisms of preconception maternal gut dysbiosis on the development of the enteric nervous system (ENS) in mice. We found that preconception maternal exposure to antibiotics led to the abnormal development of the ENS in offspring, increasing their susceptibility to water avoidance stress at the adult stage. Metagenomic, targeted metabolomic, and transcriptomic analyses revealed that preconception antibiotic exposure disrupted the expression of genes crucial for embryonic ENS development by altering maternal gut microbiota composition. Multi-omics analysis combined with Limosilactobacillus reuteri and propionate gestational supplementation demonstrated that the maternal gut microbiota and metabolites may influence embryonic ENS development via the GPR41-GDNF/RET/SOX10 signaling pathway. Our findings highlight the critical importance of maintaining a healthy maternal gut microbiota before conception to support normal ENS development in offspring.},
}

@article {pmid40236767,
year = {2025},
author = {Huang, L and Wang, P and Liu, S and Deng, G and Qi, X and Sun, G and Gao, X and Zhang, L and Zhang, Y and Xiao, Y and Gao, T and Maitiabula, G and Wang, X},
title = {Gut microbiota-derived tryptophan metabolites improve total parenteral nutrition-associated infections by regulating Group 3 innate lymphoid cells.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70007},
pmid = {40236767},
issn = {2770-596X},
abstract = {Clinical nutritional support is recognized by Klinefner's Surgery as one of the four pivotal advancements in surgical practice during the 20th century. Surgeons regard clinical nutrition as a "life-saving" discipline, pivotal in preserving the lives of numerous critically ill patients and facilitating the success of many surgical procedures. Parenteral nutrition (PN) support serves as a crucial component of clinical nutritional therapy, while a range of complications associated with total parenteral nutrition (TPN) can significantly undermine the efficacy of patient treatment. Impaired intestinal homeostasis is strongly associated with the occurrence and progression of TPN-related infections, yet the underlying mechanisms remain poorly understood. In this study, RNA sequencing and single-cell RNA sequencing (scRNA-Seq) revealed that reduced secretion of interleukin-22 (IL-22) by intestinal Group 3 innate lymphoid cells (ILC3s) is a significant factor contributing to the onset of TPN-related infections. Additionally, through 16S ribosomal RNA (16S rRNA) gene sequencing of the gut microbiota from patients with chronic intestinal failure and metagenomic sequencing analysis of the gut microbiota from mice, we observed that TPN reduced the abundance of Lactobacillus murinus (L. murinus), while supplementation with L. murinus could promote IL-22 secretion by ILC3s. Mechanistically, L. murinus upregulates indole-3-carboxylic acid, which activates the nuclear receptor Rorγt to stimulate IL-22 secretion by ILC3s. This pathway strengthens gut barrier integrity and reduces infection susceptibility. Our findings enhance our understanding of the mechanisms driving the onset of TPN-related infections, highlighting the critical role of gut microbiota in maintaining immune homeostasis and improving clinical outcomes.},
}

@article {pmid40236616,
year = {2025},
author = {Lu, Y and Zhang, C and Wu, J and Xu, X and Lu, A and Huang, H and Chen, M},
title = {Explore the Application Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid in the Early Diagnosis of Pulmonary Tuberculosis.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1837-1845},
pmid = {40236616},
issn = {1178-6973},
abstract = {OBJECTIVE: Compare the diagnostic efficacy of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) with that of four traditional methods in the diagnosis of pulmonary tuberculosis (PTB), and explore the application value of BALF mNGS in the early diagnosis of PTB.

METHODS: A retrospective analysis was performed on 102 patients with suspected PTB in Wuming Hospital Affiliated with Guangxi Medical University from January 2021 to August 2024, among which 61 cases were PTB and 41 cases were non - PTB. Diagnostic performance metrics (sensitivity, specificity, positive/negative predictive value [PPV/NPV], accuracy) were calculated for BALF mNGS, sputum TB-DNA, sputum acid-fast bacilli (AFB) smear, BALF AFB smear, and BALF TB-DNA, using clinical diagnosis as the reference standard.

RESULTS: BALF mNGS demonstrated a sensitivity of 75.41% (46/61), specificity of 87.80% (36/41), PPV of 90.20% (46/51), NPV of 70.59% (36/51), and accuracy of 80.39% (82/102). Its accuracy was significantly higher than sputum-based methods (53.03-58.82%, P < 0.0125) and second only to BALF TB-DNA (84.13%, P > 0.0125). BALF mNGS exhibited superior sensitivity compared to sputum TB-DNA (38.00%), sputum AFB smear (41.67%), and BALF AFB smear (41.50%) (P < 0.0125). While specificity and PPV showed no significant differences among methods, BALF mNGS had a higher NPV than sputum-based assays (53.03-54.17%) but lower than BALF TB-DNA (82.53%, P < 0.0125). Both BALF mNGS (Kappa = 0.608, P < 0.001) and BALF TB-DNA (Kappa = 0.670, P < 0.001) showed strong concordance with clinical diagnosis.

CONCLUSION: BALF mNGS demonstrates high sensitivity and accuracy for PTB diagnosis, outperforming conventional sputum-based methods. Although BALF TB-DNA achieved the highest specificity and NPV, BALF mNGS serves as a robust supplementary tool, particularly for early-stage or paucibacillary PTB. Integration of these molecular techniques may optimize diagnostic workflows in high-TB-burden settings.},
}

@article {pmid40236150,
year = {2025},
author = {Bommana, S and Olagoke, S and Hu, Y and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, T and Dean, D},
title = {Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with Chlamydia trachomatis infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.02.646699},
pmid = {40236150},
issn = {2692-8205},
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes with Chlamydia trachomatis (Ct) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples from women who, overtime, had Ct persistence, clearance, or no infection to evaluate azithromycin-induced changes in microbial composition, function, and the resistome. Our results show a shift in composition and function that support Ct post-treatment with azithromycin resistance mutations in the Ct rplV gene and significant endocervical enrichment of azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis, the strains of which have moderate/high potential for biofilm formation. These findings highlight the unintended ecological consequences of azithromycin, including resistance gene propagation and microbiome shifts that support persistent/recurrent Ct, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}

@article {pmid40235649,
year = {2025},
author = {Mohamed, AYA and Gill, L and Monleon, A and Pronk, M and van Loosdrecht, M and Saikaly, PE and Ali, M},
title = {Genome-resolved metatranscriptomics unveils distinct microbial functionalities across aggregate sizes in aerobic granular sludge.},
journal = {Environmental science and ecotechnology},
volume = {25},
number = {},
pages = {100560},
pmid = {40235649},
issn = {2666-4984},
abstract = {Microbial aggregates of different sizes in aerobic granular sludge (AGS) systems have been shown to exhibit distinct microbial community compositions. However, studies comparing the microbial activities of different-sized aggregates in AGS systems remain limited. In this study, genome-resolved metatranscriptomics was used to investigate microbial activity patterns within differently sized aggregates in a full-scale AGS plant. Our analysis revealed a weak correlation between the relative abundance of metagenome-assembled genomes (MAGs) and their transcriptomic activity, indicating that microbial abundance does not directly correspond to metabolic activity within the system. Flocculent sludge (FL; <0.2 mm) predominantly featured active nitrifiers and fermentative polyphosphate-accumulating organisms (PAOs) from Candidatus Phosphoribacter, while small granules (SG; 0.2-1.0 mm) and large granules (LG; >1.0 mm) hosted more metabolically active PAOs affiliated with Ca. Accumulibacter. Differential gene expression analysis further supported these findings, demonstrating significantly higher expression levels of key phosphorus uptake genes associated with Ca. Accumulibacter in granular sludge (SG and LG) compared to flocculent sludge. Conversely, Ca. Phosphoribacter showed higher expression of these genes in the FL fraction. This study highlights distinct functional roles and metabolic activities of crucial microbial communities depending on aggregate size within AGS systems, offering new insights into optimizing wastewater treatment processes.},
}

@article {pmid40234711,
year = {2025},
author = {Wu, M and Liu, X and Musat, F and Guo, J},
title = {Microbial oxidation of short-chain gaseous alkanes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40234711},
issn = {2058-5276},
abstract = {Short-chain gaseous alkanes (SCGAs), including ethane, propane and butane, are major components of natural gas and their atmospheric emissions impact global air quality and tropospheric chemistry. Many microbial taxa can degrade SCGAs aerobically and anaerobically to CO2, acting as the major biological sink of these compounds and reducing their negative impacts on climate. Environmental metagenomics and cultivation efforts have expanded our understanding of SCGA-oxidizing microorganisms. In this Review, we discuss recent discoveries in the diversity, physiology and metabolism of aerobic and anaerobic SCGA-oxidizing microorganisms, highlight their climate implications and discuss how knowledge of these processes can help develop biotechnologies for environmental remediation and value-added chemical production.},
}

@article {pmid40234093,
year = {2025},
author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ},
title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {4},
pages = {},
doi = {10.1136/jitc-2025-011706},
pmid = {40234093},
issn = {2051-1426},
mesh = {Humans ; *Melanoma/drug therapy/pathology/mortality ; Female ; Male ; *Azetidines/therapeutic use/pharmacology ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Neoadjuvant Therapy/methods ; *Piperidines/pharmacology/therapeutic use ; *Vemurafenib/pharmacology/therapeutic use ; Aged ; Neoplasm Staging ; Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; *Skin Neoplasms/drug therapy ; },
abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

TRIAL REGISTRATION NUMBER: NCT03554083.},
}

Humans
*Melanoma/drug therapy/pathology/mortality
Female
Male
*Azetidines/therapeutic use/pharmacology
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Middle Aged
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
*Neoadjuvant Therapy/methods
*Piperidines/pharmacology/therapeutic use
*Vemurafenib/pharmacology/therapeutic use
Aged
Neoplasm Staging
Adult
Gastrointestinal Microbiome
Treatment Outcome
*Skin Neoplasms/drug therapy

@article {pmid40233994,
year = {2025},
author = {Jenkins, R and Samec, M and Arment, C and Warrington, KJ and Davis, JM and Koster, MJ},
title = {Use of Metagenomic Microbial Plasma Cell-Free DNA Next-Generation Sequencing Assay in Outpatient Rheumatology Practice.},
journal = {The Journal of rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.3899/jrheum.2024-1211},
pmid = {40233994},
issn = {1499-2752},
abstract = {OBJECTIVE: To assess the utility of a metagenomic microbial plasma cell-free DNA next-generation sequencing assay (Karius TestTM; KT) in the evaluation of patients in an outpatient rheumatology practice.

METHODS: All patients with a KT ordered and obtained by a rheumatology provider in the outpatient setting from 1 January 2020 through 31 December 2022 were retrospectively identified. Demographic, clinical, laboratory, radiologic, histopathology, and microbial studies were abstracted. Indication for KT testing was categorized. KT results were defined based on positive result and clinical relevance regarding the symptoms under investigation at the time of the rheumatologic investigation. Review of cases three months after KT was undertaken to determine clinical outcome.

RESULTS: 150 patients with a KT were included (52.7% female, mean age 52 years). The reason for KT was evaluation of atypical presentation of rheumatic disease (80.0%), assessing flare versus infection in patient on immunosuppression (16.7%), and fever of unknown origin (3.3%). 24 (16.0%) KTs were positive, six of which were considered clinically relevant and altered the final diagnosis and treatment. Of the 126 negative KTs, 5 (4.0%) were found to have a clinically relevant infection by conventional testing methodologies.

CONCLUSION: In this large retrospective cohort study, the most frequent reason for KT utilization was an atypical presentation of rheumatic disease. Twenty-five percent of positive KTs altered the final diagnosis and treatment, whereas a false-negative rate of 4.0% was observed. KT has utility in the outpatient rheumatology assessment. Further delineation of which patients are best suited for KT testing remains to be defined.},
}

@article {pmid40233938,
year = {2025},
author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM},
title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.},
journal = {Journal of applied microbiology},
volume = {136},
number = {4},
pages = {},
doi = {10.1093/jambio/lxaf076},
pmid = {40233938},
issn = {1365-2672},
support = {80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; },
mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation & purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; },
abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.

METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.

CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.},
}

Biodegradation, Environmental
Metagenomics
*Microbiota/genetics
Metals, Heavy/metabolism
*Geologic Sediments/microbiology
*Bacteria/genetics/metabolism/drug effects/isolation & purification/classification
Water Pollutants, Chemical/metabolism
Polychlorinated Biphenyls/metabolism
*Drug Resistance, Bacterial/genetics
Metagenome

@article {pmid40037519,
year = {2025},
author = {Jawale, N and Shenberger, JS and Rodriguez, RJ and Shetty, AK and Garg, PM},
title = {The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis.},
journal = {American journal of perinatology},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2549-6551},
pmid = {40037519},
issn = {1098-8785},
support = {U54GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428//NIGMS of the NIH/ ; },
abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..},
}

@article {pmid40233768,
year = {2025},
author = {Tinker, KA and Anthony, W and Brandi, M and Flett, S and Bagwell, CE and Smallwood, C and Davis, R and Gulliver, D},
title = {Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70076},
doi = {10.1111/1758-2229.70076},
pmid = {40233768},
issn = {1758-2229},
support = {//U.S. Department of Energy's (DOE) Office of Fossil Energy and Carbon Management's Hydrogen with Carbon Management Program and executed through the National Energy Technology Laboratory (NETL) Research & Innovation Center's Natural Gas Decarbonization and Hydrogen Technologies Multi-Year Research Plan/ ; },
mesh = {*Hydrogen/metabolism ; *Groundwater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Illinois ; Methane/metabolism ; Microbiota ; Metagenomics ; },
abstract = {Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.},
}

*Hydrogen/metabolism
*Groundwater/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Illinois
Methane/metabolism
Microbiota
Metagenomics

@article {pmid40233618,
year = {2025},
author = {Fan, C and Hou, D and Zhang, L and Li, C and Chen, L and Zhang, P and Wu, Y and Zou, J},
title = {Bioaugmentation using HN-AD consortia for high salinity wastewater treatment: Synergistic effects of halotolerant bacteria and nitrogen removal bacteria.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125355},
doi = {10.1016/j.jenvman.2025.125355},
pmid = {40233618},
issn = {1095-8630},
abstract = {Bioaugmentation shows promise in enhancing nitrogen removal efficiency of high-salt wastewater, yet the impact of microbial associations on ecosystem function and community stability remains unclear. This study innovatively introduced a novel heterotrophic nitrification-aerobic denitrification bacterial consortium to improve the performance of SBR reactor for removing nitrogen from saline wastewater. The results revealed that the bioaugmented reactor (R2) exhibited superior removal performance, achieving maximum removal efficiencies of 87.8 % for COD and 97.8 % for NH4[+]-N. Moreover, proper salinity (2 % and 4 %) promoted the secretion of EPS and ectoine, further enhancing the resistance and stability of bacterial consortia. 16S rRNA gene sequencing and metagenomics analysis revealed the key denitrifying bacteria Pseudomonas and salt-tolerant bacteria Halomonas were successfully coexistence and the relative abundances of crucial genes (napB, nirS, norB, norC and nosZ) were increased obviously, which were benefit for the excellent nitrogen removal performance in R2. These findings elucidate microbial interactions in response to salinity in bioaugmentation, providing a valuable reference for the efficient treatment of high-saline wastewater.},
}

@article {pmid40233040,
year = {2025},
author = {Pomej, K and Frick, A and Scheiner, B and Balcar, L and Pajancic, L and Klotz, A and Kreuter, A and Lampichler, K and Regnat, K and Zinober, K and Trauner, M and Tamandl, D and Gasche, C and Pinter, M},
title = {Study protocol: Fecal Microbiota Transplant combined with Atezolizumab/Bevacizumab in Patients with Hepatocellular Carcinoma who failed to achieve or maintain objective response to Atezolizumab/Bevacizumab - the FAB-HCC pilot study.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321189},
doi = {10.1371/journal.pone.0321189},
pmid = {40233040},
issn = {1932-6203},
mesh = {Humans ; *Liver Neoplasms/therapy/drug therapy ; *Carcinoma, Hepatocellular/therapy/drug therapy ; Pilot Projects ; *Fecal Microbiota Transplantation/methods ; *Bevacizumab/therapeutic use/administration & dosage ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; Male ; Female ; Gastrointestinal Microbiome ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: The gut microbiota is often altered in chronic liver diseases and hepatocellular carcinoma (HCC), and increasing evidence suggests that it may influence response to cancer immunotherapy. Strategies to modulate the gut microbiome (i.e., fecal microbiota transplant (FMT)) may help to improve efficacy of immune checkpoint inhibitors (ICIs) or even overcome resistance to ICIs. Here, we describe the design and rationale of FAB-HCC, a single-center, single-arm, phase II pilot study to assess safety, feasibility, and efficacy of FMT from patients with HCC who responded to PD-(L)1-based immunotherapy or from healthy donors to patients with HCC who failed to achieve or maintain a response to atezolizumab plus bevacizumab.

METHODS: In this single-center, single-arm, phase II pilot study (ClinicalTrials.gov identifier: NCT05750030), we plan to include 12 patients with advanced HCC who failed to achieve or maintain a response to atezolizumab/bevacizumab. Patients will receive a single FMT via colonoscopy from donors with HCC who responded to PD-(L)1-based immunotherapy or from healthy individuals, followed by atezolizumab/bevacizumab every 3 weeks. The primary endpoint is safety, measured by incidence and severity of treatment-related adverse events. The main secondary endpoint is efficacy, as assessed by best radiological response according to RECISTv1.1 and mRECIST. Additional exploratory endpoints include data on the effect of FMT on recipient gut microbiota, as well as metagenomic analysis of stool samples, analyses of circulating immune cells and serum and stool proteomic, metabolomic and lipidomic signatures.

DISCUSSION: The results of this study will help to define the potential of FMT as add-on intervention in the systemic treatment of advanced HCC, with the potential to improve efficacy of immunotherapy or even overcome resistance.

TRIAL REGISTRATION: EudraCT Number: 2022-000234-42 Clinical trial registry & ID: ClinicalTrials.gov identifier: NCT05750030 (Registration date: 16.01.2023).},
}

Humans
*Liver Neoplasms/therapy/drug therapy
*Carcinoma, Hepatocellular/therapy/drug therapy
Pilot Projects
*Fecal Microbiota Transplantation/methods
*Bevacizumab/therapeutic use/administration & dosage
*Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage
Male
Female
Gastrointestinal Microbiome
Middle Aged
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Aged

@article {pmid40232948,
year = {2025},
author = {Leech, SM and Barrett, HL and Dorey, ES and Mullins, T and Laurie, J and Nitert, MD},
title = {Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001385},
pmid = {40232948},
issn = {2057-5858},
mesh = {Humans ; Female ; Pregnancy ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/genetics ; Adult ; *Diabetes, Gestational/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.},
}

Humans
Female
Pregnancy
*Diabetes Mellitus, Type 2/microbiology/complications
*Microbiota/genetics
Adult
*Diabetes, Gestational/microbiology
Saliva/microbiology
*Mouth/microbiology
Metagenomics/methods
Dysbiosis/microbiology
*Bacteria/classification/genetics/isolation & purification

@article {pmid40232107,
year = {2025},
author = {Ravizza, T and Volpedo, G and Riva, A and Striano, P and Vezzani, A},
title = {Intestinal microbiome alterations in pediatric epilepsy: Implications for seizures and therapeutic approaches.},
journal = {Epilepsia open},
volume = {},
number = {},
pages = {},
doi = {10.1002/epi4.70037},
pmid = {40232107},
issn = {2470-9239},
support = {PE0000006/DN.1553//National Recovery and Resilience Plan (NRRP)/ ; //AICE-FIRE/ ; },
abstract = {The intestinal microbiome plays a pivotal role in maintaining host health through its involvement in gastrointestinal, immune, and central nervous system (CNS) functions. Recent evidence underscores the bidirectional communication between the microbiota, the gut, and the brain and the impact of this axis on neurological diseases, including epilepsy. In pediatric patients, alterations in gut microbiota composition-called intestinal dysbiosis-have been linked to seizure susceptibility. Preclinical models revealed that gut dysbiosis may exacerbate seizures, while microbiome-targeted therapies, including fecal microbiota transplantation, pre/pro-biotics, and ketogenic diets, show promise in reducing seizures. Focusing on clinical and preclinical studies, this review examines the role of the gut microbiota in pediatric epilepsy with the aim of exploring its implications for seizure control and management of epilepsy. We also discuss mechanisms that may underlie mutual gut-brain communication and emerging therapeutic strategies targeting the gut microbiome as a novel approach to improve outcomes in pediatric epilepsy. PLAIN LANGUAGE SUMMARY: Reciprocal communication between the brain and the gut appears to be dysfunctional in pediatric epilepsy. The composition of bacteria in the intestine -known as microbiota- and the gastrointestinal functions are altered in children with drug-resistant epilepsy and animal models of pediatric epilepsies. Microbiota-targeted interventions, such as ketogenic diets, pre-/post-biotics administration, and fecal microbiota transplantation, improve both gastrointestinal dysfunctions and seizures in pediatric epilepsy. These findings suggest that the gut and its microbiota represent potential therapeutic targets for reducing drug-resistant seizures in pediatric epilepsy.},
}

@article {pmid40232020,
year = {2025},
author = {Zhang, X and Chi, H and Peng, D and Jiang, M and Wang, C and Zhang, H and Kang, W and Li, L},
title = {Integrated Metagenomic and LC-MS/MS Analysis Reveals the Biogenic Amine-Producing Strains of Two Typical Chinese Traditional Fish Products: Fermented Mandarin Fish (Siniperca chuatsi) and Semi-Dried Yellow Croaker (Larimichthys crocea).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14061016},
pmid = {40232020},
issn = {2304-8158},
support = {2022TD02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; },
abstract = {Two typical fish products-fermented mandarin fish and semi-dried yellow croaker-are associated with biogenic amines (BAs), which are harmful to human health. The objective of this study was to investigate the bacterial ecology of the two fish products and to determine their capacity for producing BAs. Putrescine and cadaverine were major BAs detected in the fish products. Concentrations of BAs were significantly corrected with microbial count (p < 0.05). BA-producing isolates (33) in the two fish products were all multiple BA producers. Several of them, including Lactobacillus sakei, Bacillus cereus and Hafnia alvei isolated from fermented mandarin fish, as well as Shewanella baltica, Aeromonas veronii, and Photobacterium phosphoreum isolated from semi-dried yellow croaker, showed remarkable BA-producing capacity. Hafnia alvei produced the greatest abundance of putrescine, cadaverine, tyramine and 2-phenylethylamine. Lactobacillus sakei mainly produced tryptamine and putrescine. Photobacterium phosphoreum showed the strongest histamine-producing capacity.},
}

@article {pmid40231916,
year = {2025},
author = {A'yuni, Q and Mok, K and Nakphaichit, M and Jangchud, K and Pirak, T},
title = {Thai Cannabis sativa Leaves as a Functional Ingredient for Quality Improvement and Lactic Acid Bacterial Growth Enhancement in Kombucha.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14060942},
pmid = {40231916},
issn = {2304-8158},
support = {FF(KU)25.66//Fundamental fund of Kasetsart University/ ; //Kasetsart's Agro-Industry Scholarship from Department of Product Development, Faculty of Agro-Industry, Kasetsart University/ ; },
abstract = {Kombucha is a well-known fermented drink that gained interest due to its gut health benefits. However, it has a harsh taste of acetic acid and is hard to consume. Thai Cannabis leaves (Cannabis sativa sp. Hang Kra Rog Phu phan ST1) contain high protein and phytochemicals which can improve the growth of lactic acid bacteria (LAB) and enhance the organoleptic quality of the Kombucha. This study revealed the effect of infusing assam green tea leaves with cannabis leaves on the fermentation rate, microbial communities, volatile compounds, and overall quality and taste of the kombucha. The high protein content (23.10%) of Cannabis leaves was found. Phytonutrients and phytochemicals found in the leaves promotes LAB growth, which resulted in the higher number of LAB in the treatment with cannabis leaves. At the end of fermentation (day 7), the highest LAB count (5.53 log CFU mL[-1]) was presented in kombucha infused with 30% cannabis leaves. Kombucha with better quality, higher pH, and less acidity was obtained in a dose manner. The change in microbial communities was detected using metagenomic analysis. The prominence of Dekkera and Komagataeibacter, with low abundance of Zygosaccharomyces and Weissella were identified. These microorganisms improved flavor by lessening strong fermented odor and harsh acidic taste. From volatile compounds, HS-SPME-GCMS revealed that kombucha infused with 30% cannabis leaves possessed less acetic acid, ethanol, and carbon dioxide and gave a better odor and taste. Hence, cannabis leaves was the novel substrate for kombucha fermentation by enhancing LAB growth and improving the overall qualities.},
}

@article {pmid40231684,
year = {2025},
author = {Glenna, S and Birkeland, EE and Orr, RJ and Gilfillan, GD and Dalland, M and Økstad, OA and Voie, ØA and Rounge, TB},
title = {Skin bacterial community dynamics of hands and forearms before and after military field exercise.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0295324},
doi = {10.1128/spectrum.02953-24},
pmid = {40231684},
issn = {2165-0497},
abstract = {The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.},
}

@article {pmid40230845,
year = {2025},
author = {Gao, Q and Li, Z and Geng, J and Han, B and Yang, T and Feng, S and Zhao, L and Teng, Y and Li, Y and Zhao, R and Zhang, W and Wang, Y and Wang, Y},
title = {The type of pathogen is associated with organ failure and legacy dysfunction in patients with sepsis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1541634},
pmid = {40230845},
issn = {1664-3224},
mesh = {Humans ; *Sepsis/mortality/microbiology/complications ; Male ; Female ; *Multiple Organ Failure/mortality/microbiology/etiology ; Middle Aged ; Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Retrospective Studies ; },
abstract = {INTRODUCTION: Is there a difference in pathogen infection among sepsis patients with different organ dysfunction and Post-sepsis persistent organ dysfunction? Is this related to survival? It is currently unclear.

METHODS: This study reviewed 1982 sepsis patients between December 2019 and September 2023, and included 619 patients after removing patients with missing data. Of these, 332 were tested for metagenomic next-generation sequencing (mNGS). First, the pathogens distribution was assessed in all NGS-positive patients, followed by patients with different organ dysfunction (excluding those who died during hospitalization). Lastly, the survival analysis was conducted on patients infected with different pathogens.

RESULTS: The results showed that the mortality rate in our cohort was 27.63% in patients with sepsis, and patients with Respiratory, Liver, Circulatory, Hematologic, Neurological, and Renal dysfunction had poor survival. And patients with post-sepsis persistent organ dysfunction after sepsis have worse survival rates. In addition, we found the infection rates of Legionella and Betapapillomavirus were higher in patients with liver dysfunction. The infection rates of Mastadenovirus, Enterococcus, and Candida were higher in patients with neurological dysfunction. The infection rates of Candida were higher in patients with renal dysfunction and hematologic dysfunction. The infection rates of Moraxella were higher in patients with circulatory dysfunction. The infection rates of Enterococcus, Pneumocystis, and Acinetobacter were higher in patients with Post-sepsis cardiac dysfunction.The infection rates of Enterococcus, Acinetobacter, and Morganella were higher in patients with Post-sepsis liver dysfunction. The infection rates of Enterococcus, Acinetobacter, and Staphylococcus were higher in patients with Post-sepsis respiratory dysfunction. The infection rates of Enterococcus, Candida, Pneumocystis, Staphylococcus, and Listeria were higher in patients with Post-sepsis renal dysfunction. In addition, we found that patients with Escherichia infection in sepsis had the lowest survival rate. The survival rate of patients with Enterococcus infection combined with post-sepsis persistent respiratory dysfunction is also worse.

DISCUSSION: In conclusion, there are differences in the types and proportions of pathogens infected in patients with different organ dysfunction and Post-sepsis persistent organ dysfunction. The combination of Escherichia infection and Enterococcus infection with post-sepsis persistent respiratory dysfunction can affect the survival of patients. We should strengthen the management of sepsis patients, especially those with Post-sepsis persistent organ dysfunction.},
}

Humans
*Sepsis/mortality/microbiology/complications
Male
Female
*Multiple Organ Failure/mortality/microbiology/etiology
Middle Aged
Aged
High-Throughput Nucleotide Sequencing
Adult
Retrospective Studies

@article {pmid40230330,
year = {2025},
author = {Cui, T and Kushmaro, A and Barak, H and Poehlein, A and Daniel, R and Mägert, HJ},
title = {Enhanced discovery of bacterial laccase-like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70037},
pmid = {40230330},
issn = {2211-5463},
abstract = {Laccases belong to the superfamily of multicopper oxidases (MCO), a group of enzymes with the ability to reduce oxygen to water in a reaction without producing harmful byproducts. Laccase activity is influenced by many factors, such as structure; the number, location and binding status of copper ions; and the substrate-binding status. A large number of sequences that have not been experimentally characterized yet have been annotated as laccases. However, the biological functions of the characterized MCOs are considered to vary, and the substrate spectrum overlaps with that of other MCOs. Here, we identified 34 putative bacterial laccase sequences from metagenome data for industrial wastewater. We used machine-learning tools to screen enzymes with laccase activity by combining the T1 copper-binding capacity, the overall copper-binding capacity and the substrate-binding capacity. We also used the software comparisons to remove sequences with large discrepancies between different software applications. Three-dimensional structures of identified enzymes were predicted using alphafold, the positions of metal ions within the proteins were predicted by metal3d and autodock-vina, and their docking with ABTS [i.e. 2,2'-azinobis(3‑ethylbenzo-6‑thiazolinesulfonic acid)] as a substrate was predicted by rosetta and autodock-vina. Based on the docking results, we selected 10 high-scoring proteins, two low-scoring proteins and one composite protein for expression using the pET-21d (+) vector. In line with our predictions, all selected high-scoring proteins exhibited activity towards ABTS. Overall, we describe a method for discovering and designing novel bacterial laccase-like multicopper oxidases, offering increased possibilities for the degradation of various harmful components derived from environmental pollution.},
}

@article {pmid40230307,
year = {2025},
author = {Liu, B and He, N and Li, H and Yang, Z and Lin, Y and Wu, X and Zhang, H and Zhang, Z and Zhang, Z and Tian, Y and Wu, Z and Zou, Y and Peng, J and Li, S},
title = {3-Fucosyllactose Prevents Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota-Derived Pantothenate in Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00079},
pmid = {40230307},
issn = {1520-5118},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health threat. Human milk oligosaccharides (HMOs) exhibit prebiotic properties that may alleviate NAFLD progression. Herein, our study demonstrates that 3-fucosyllactose (3-FL), a distinctive and crucial HMO, significantly attenuates body weight gain, enhances hepatic lipid metabolism, and reduces inflammation in a high-fat diet (HFD)-induced NAFLD mouse model. These findings suggest its potential as a dietary supplement for preventing and alleviating NAFLD progression. Subsequently, fecal metagenomic and nontargeted metabolomics analyses revealed that 3-FL treatment significantly alleviated HFD-induced gut microbiota dysbiosis, with a specific enhancement of the pantothenate (vitamin B5) metabolic pathways. Our targeted metabolite analysis further revealed a significant increase in both hepatic and fecal pantothenate concentrations, which contributed to the enhancement of the coenzyme A (CoA)-mediated lipid metabolism pathway. Furthermore, the subsequent population cohort analyses revealed a significant correlation between serum pantothenate levels and the progression of NAFLD, thereby reinforcing its candidacy as a noninvasive diagnostic biomarker. These findings show that 3-FL acts as an effective prebiotic to alleviate NAFLD symptoms, in part by enhancing the gut microbiota-mediated pantothenate/CoA metabolic pathway.},
}

@article {pmid40230133,
year = {2025},
author = {Chen, HD and Gao, S and Wang, LJ and Zhao, B and Lu, MQ and Song, YM and Cui, JS and Zhang, LL},
title = {[Spatial and Temporal Differences and Influencing Factors of Mobile Genetic Elements in Urban and Suburban River Sediments in Shijiazhuang City].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {4},
pages = {2250-2262},
doi = {10.13227/j.hjkx.202403034},
pmid = {40230133},
issn = {0250-3301},
mesh = {*Rivers ; China ; *Geologic Sediments/microbiology ; *Interspersed Repetitive Sequences/genetics ; Cities ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Spatio-Temporal Analysis ; },
abstract = {With the widespread use of antibiotics in medicine and agriculture, the spread of antibiotic resistance genes （ARGs） in the environment has become a serious threat to ecological balance and human health, particularly for its role in facilitating the emergence of multidrug-resistant pathogens. The study of riverine environments as a major transmission route for ARGs and closely related mobile genetic elements （MGEs） is of great importance. MGEs exacerbate the spread of resistance genes by facilitating the horizontal transfer of ARGs in bacterial populations. Although studies have been conducted to explore the interactions between MGEs and ARGs, there is still a relative lack of research on the spatial and temporal differences in the distribution of MGEs in rivers and their drivers. This study selected two rural rivers （with a total of six sampling points） and three urban rivers （with a total of nine sampling points） within Shijiazhuang as research subjects, and sediment samples were collected in December 2020 and April 2021. By employing metagenomic sequencing technology, this study comprehensively compared and analyzed the spatiotemporal distribution characteristics and influencing factors of MGEs in the sediment of urban and rural rivers. The results showed that： ① In December, 1 738 types of MGEs （60572 RPKM） and 1 604 types of MGEs （26916 RPKM） were detected in urban and rural rivers, respectively. In April, 1 790 types of MGEs （74354 RPKM） and 1 631 types of MGEs （32062 RPKM） were detected in urban and rural rivers, respectively. ② The types and abundance of MGEs in urban rivers were greater than those in rural rivers, and the types and abundance of MGEs in April were greater than those in December. ③ ISPa38, IS26, and tnpA were the most significantly different typical MGEs among the rivers in urban and suburban Shijiazhuang. ④ PCoA and NMDS analyses showed significant spatiotemporal differences in MGEs between urban and rural rivers. ⑤ Correlation analysis and co-occurrence results indicated that the abundance of MGEs in urban rivers was significantly positively correlated with antibiotic concentration, industrial enterprises, sewage treatment plants, total population, livestock farming, and aquaculture. In suburban rivers, the abundance of MGEs was mainly significantly positively correlated with antibiotic concentration, livestock farming, aquaculture, and total population. Overall, by comparing the spatiotemporal heterogeneity of MGEs in urban and rural rivers and identifying the main driving factors of MGEs in urban and suburban rivers, this study provides data support for subsequent risk management and control of antibiotic resistance in different rivers.},
}

*Rivers
China
*Geologic Sediments/microbiology
*Interspersed Repetitive Sequences/genetics
Cities
Drug Resistance, Microbial/genetics
Environmental Monitoring
Spatio-Temporal Analysis

@article {pmid40229213,
year = {2025},
author = {Hoops, SL and Moutsoglou, D and Vaughn, BP and Khoruts, A and Knights, D},
title = {Metagenomic source tracking after microbiota transplant therapy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2487840},
doi = {10.1080/19490976.2025.2487840},
pmid = {40229213},
issn = {1949-0984},
mesh = {Humans ; *Metagenomics/methods ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Colitis, Ulcerative/therapy/microbiology ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Bayes Theorem ; Feces/microbiology ; },
abstract = {Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.},
}

Humans
*Metagenomics/methods
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/genetics
Colitis, Ulcerative/therapy/microbiology
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Metagenome
Bayes Theorem
Feces/microbiology

@article {pmid40228816,
year = {2025},
author = {Chen, J and Liu, X and Bai, Y and Tang, X and Xue, K and Zhu, Z and Liu, W and Wang, J and Wang, C and Qiao, H and Dang, E and Yin, W and Wang, G and Shao, S},
title = {Tonsillar Microbiota Alterations Contribute to Immune Responses in Psoriasis by Skewing Aged Neutrophils.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf134},
pmid = {40228816},
issn = {1365-2133},
abstract = {BACKGROUND: The interplay between microbiota and the onset of immune-mediated diseases is increasingly coming to light. However, the role of tonsillar microbiota in cutaneous inflammation remains largely unknown.

OBJECTIVE: We aimed to determine how tonsillar microbiota influence skin inflammation in psoriasis and to uncover the underlying molecular mechanisms.

METHODS: Tonsillar microbiota samples were collected from 24 healthy controls and 28 psoriasis patients. Microbial community composition was analyzed using 16S rRNA sequencing and metagenomic sequencing. Serum levels of short-chain fatty acids (SCFAs) were measured via liquid chromatography-mass spectrometry in 10 healthy controls and 14 psoriasis patients. Peripheral blood neutrophils from both groups were then exposed to a representative microbial metabolite, and key pro-inflammatory markers were evaluated using functional immune assays.

RESULTS: We found significant alterations in the diversity and composition of the tonsillar microbial community in psoriasis group, with an increased prevalence of Bacteroidales and a decreased prevalence of Burkholderiales, Micrococcales, and Pasteurellales relative to healthy controls. Notably, a marked reduction in Rothia mucilaginosa correlated inversely with systemic inflammation (neutrophil-to-lymphocyte ratio) and disease severity (psoriasis area and severity index). Metagenomic analysis revealed disruptions in pathways critical for SCFAs production, including propanoate, pyruvate, and butanoate metabolism, which was supported by significantly lower serum SCFAs levels in psoriasis patients. Functional assays demonstrated that SCFAs inhibited neutrophil aging, pro-inflammatory cytokine secretion, and neutrophil extracellular traps (NETs) formation.

CONCLUSION: Our findings reveal that changes in tonsillar microbiota and their metabolic outputs contribute to psoriasis by modulating immune responses, highlighting potential clinical implications.},
}

@article {pmid40228693,
year = {2025},
author = {Ma, JY and Liu, JH and Chen, CZ and Zhang, YZ and Guo, ZS and Song, MP and Jiang, F and Chai, ZT and Li, Z and Lv, SX and Zhen, YJ and Wang, L and Liang, ZL and Jiang, ZY},
title = {Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121559},
doi = {10.1016/j.envres.2025.121559},
pmid = {40228693},
issn = {1096-0953},
abstract = {The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.},
}

@article {pmid40228470,
year = {2025},
author = {Zhang, Y and Ye, Y and Fang, M and Xiang, Y and Chen, J and Tang, X and Yang, Z and Qian, Q},
title = {Biogas production enhancement from anaerobic digestion with magnetic biochar: Insights into the functional microbes and DIET.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125347},
doi = {10.1016/j.jenvman.2025.125347},
pmid = {40228470},
issn = {1095-8630},
abstract = {The application of magnetic biochar in anaerobic digestion (AD) has gained increasing attention. However, the underlying mechanisms remain insufficiently understood. This study systematically investigated the effects of magnetic biochar on functional microbial communities involved in methanogenesis and elucidated its role in promoting direct interspecies electron transfer (DIET) within AD systems. The addition of 40 mg g[-1] TSadded of magnetic biochar significantly enhanced methane production by 42.21 %, reaching 223.08 mL g[-1] TS with highest organic matter degradation efficiency. Microbial community analysis showed that magnetic biochar significantly enriched microorganisms associated with hydrolysis, acidogenesis, and methanogenesis, as well as electroactive microorganisms' abundance such as Geobacter spp., Syntrophus spp., P. aestuarii, and M. harundinacea, providing direct evidence for the DIET process of AD with magnetic biochar. Furthermore, the abundance of key genes involved in the DIET, including pilA, Fpo, and the genes encoded outer-membrane c-type cytochromes, was respectively upregulated by 44.49 %, 22.04 %, and 37.6 % in the presence of magnetic biochar. These findings suggest that magnetic biochar enhances the production of conductive pili and cytochrome c, facilitating extracellular electron transfer between syntrophic microorganisms. This accelerated electron transfer promotes CO2 reduction to CH4, ultimately improving methane production efficiency in the AD system. Moreover, the enhancement of hydrogenotrophic methanogenesis was particularly pronounced with magnetic biochar, further contributing to the improved AD performance. This study provides novel mechanistic insights into biochar-mediated DIET, offering a theoretical basis for optimizing biochar applications in AD.},
}

@article {pmid40226917,
year = {2025},
author = {Lai, Q and Yao, S and Zha, Y and Zhang, H and Zhang, H and Ye, Y and Zhang, Y and Bai, H and Ning, K},
title = {Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.},
journal = {Nucleic acids research},
volume = {53},
number = {7},
pages = {},
doi = {10.1093/nar/gkaf305},
pmid = {40226917},
issn = {1362-4962},
support = {2021YFA0910500//National Key R&D Program of China/ ; 32071465//National Natural Science Foundation of China/ ; },
mesh = {*Multigene Family ; *Biosynthetic Pathways/genetics ; *Neural Networks, Computer ; *Genome, Microbial ; Phylogeny ; Metagenome ; Secondary Metabolism/genetics ; Genome, Bacterial ; },
abstract = {Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet's capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.},
}

*Multigene Family
*Biosynthetic Pathways/genetics
*Neural Networks, Computer
*Genome, Microbial
Phylogeny
Metagenome
Secondary Metabolism/genetics
Genome, Bacterial

@article {pmid40226542,
year = {2025},
author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B},
title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19260},
pmid = {40226542},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Sympatry ; Bacteroidetes/genetics/isolation & purification ; },
abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.},
}

Animals
*Gastrointestinal Microbiome/genetics
China
*Arvicolinae/microbiology
*Murinae/microbiology
*Metagenome
Metagenomics
High-Throughput Nucleotide Sequencing
Proteobacteria/genetics/isolation & purification
Firmicutes/genetics/isolation & purification
Sympatry
Bacteroidetes/genetics/isolation & purification

@article {pmid40226095,
year = {2025},
author = {Ho, JY and Koh, XQ and Kang, DY and Low, A and Hu, D and Haryono, MAS and Williams, RBH and Case, RJ and Boucher, YF},
title = {Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1437936},
pmid = {40226095},
issn = {1664-302X},
abstract = {Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41G[T] as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813[TS] (=BAABNI000000000.1[TS]) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891[T] outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.},
}

@article {pmid40225905,
year = {2025},
author = {Lambisia, AW and Mwita Morobe, J and Moraa, E and Mwarumba, S and K N Korir, F and Seif Athman, R and Kiptui, R and Mbee, M and Mugo, N and Amoth, P and Muange, P and J Houldcroft, C and Barasa, E and Mwangangi, J and Githinji, G and C Holmes, E and Isabella Ochola-Oyier, L and N Agoti, C},
title = {Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {28},
pmid = {40225905},
issn = {2398-502X},
abstract = {BACKGROUND: In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as "red eye" disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.

METHODS: Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.

RESULTS: Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV.

CONCLUSION: The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.},
}

@article {pmid40225898,
year = {2025},
author = {Liu, H and Wang, H and Sun, J and Yang, T and Mo, Z and Huang, H and Pan, Y},
title = {High-Altitude Open-Pit Coal Mining has Changed the Sulfur Cycle and Ecological Network of Plant Rhizosphere Microorganisms.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71183},
pmid = {40225898},
issn = {2045-7758},
abstract = {Ecological restoration of mining sites has a considerable effect on microbial community dynamics; however, its impact on sulfur cycling is unclear. This study explored the changes in functional genes related to sulfur cycling and microbial diversity during different stages of succession following the ecological restoration of a mining site in a cold arid area. A total of three succession stages were selected-natural, secondary, and artificial. The expression of sulfur cycle-related genes and associated microbial drivers was investigated using metagenomics and network analysis. The dominant bacteria in the secondary succession were found to be r-strategy-adopting Proteobacteria and Cyanobacteria. Natural succession primarily comprised Aspergillus and Thermus, whereas artificial succession comprised Proteobacteria, Chlorophyta, and Actinobacteria. Mining disturbances were determined to significantly reduce the abundance of sulfur-cycling archaea. Secondary succession was primarily influenced by soil total phosphorus in the sulfur-cycle gene network. The key bacteria and archaea involved in the sulfur cycle were found to be Bradyrhizobium and Nitrosopumilus, respectively. The abundance of Streptomyces was significantly higher in natural succession than in artificial or secondary succession. Burkholderia, which has biological control and bioremediation effects, was abundant during artificial succession. These results provide a theoretical basis for restoring the sulfur cycle and promoting a positive succession of ecosystems in mining areas.},
}

@article {pmid40225105,
year = {2025},
author = {He, W and Wang, S and Xiong, X and Dai, W},
title = {[18]F-FDG PET/CT Imaging of Talaromyces marneffei Infection with Bone Destruction in an HIV-Negative Patient: Case Report and Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1745-1752},
pmid = {40225105},
issn = {1178-6973},
abstract = {BACKGROUND: Talaromycosis is an opportunistic fungal infection caused by Talaromyces marneffei (T. marneffei), commonly occurs in HIV-positive individuals. While less common, it can also affect HIV-negative individuals. We reported a T. marneffei infection in an HIV-negative patient, whose imaging findings and diagnostic process offer valuable clinical insights.

CASE PRESENTATION: An HIV-negative male adult patient with an intermittent cough for more than two years and worsened for more than one month. Enhanced CT scan indicated lung cancer with rib and lymph nodes metastasis. The lower respiratory tract and bronchial lavage fluid culture of the patient were negative. He received two bronchoscopies, two biopsies and two metagenomic next-generation sequencing (mNGS) tests, which failed to find the malignant cell but sequentially identified the presence of Pasteurella multocida and the Epstein-Barr virus. His condition did not improve after anti-infective treatment for 2weeks. An 18-fluorodeoxy glucose ([18]F-FDG) PET/CT scan revealed increased radioactivity in right supraclavicular lymph node, left lung and the right tenth rib. Ultimately, a biopsy at the hypermetabolic lesion of left lung, and a third mNGS test confirmed the presence of Talaromyces marneffei. Subsequently, the patient started antifungal therapy with amphotericin B and itraconazole and showed a favorable response.

CONCLUSION: We reviewed all reported PET/CT findings of T. marneffei infection patients, suggesting that fungus T. marneffei should be considered in patients identified as infection and exhibited bone destruction and also highlight the role of PET/CT in guiding the biopsy site.},
}

@article {pmid40224142,
year = {2025},
author = {Caille, A and Connan, C and Lyon Belgy, N and Borezée, E and Cherbuy, C and Meunier, N and Meslier, V},
title = {Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103268},
pmid = {40224142},
issn = {2215-0161},
abstract = {Recent advances in the study of the gut microbiota has pointed to its under-utilized source of potentially beneficial bacteria, known as next generation probiotics, offering a promising avenue to restore or compensate impaired gut microbiota toward a healthy state. Aside from the difficulties to achieve in-lab adequate culture conditions, the use of beneficial bacterial isolates is also limited by their bioavailability in the donor itself. In the iTARGET study, we positively selected donors based on their diet enriched in fiber, that has been shown to increase the prevalence of bacterial species associated with health. The iTARGET study is a monocenter, prospective, observational study of adults with healthy lifestyle and high daily fiber consumption. We aim to recruit individuals in two phases, the first one for all individuals that will permit the identification of carriers for bacteria of interest and the second phase for a subset of individuals to allow for culture and isolation of previously identified potentially beneficial bacteria. Our primary outcome is the isolation and culture of at least one potentially beneficial isolate. The secondary outcomes comprised the high throughput metagenomic profiles of the intestinal microbiota and the characterization of the cultured isolates. The study was approved by the French Research Ethics Committees (Comité de Protection des Personnes Sud-Est I) under the National reference ID 2023-A01677-38. Study findings and results will be published in peer-reviewed Open Access journals. (Trial registration number on ClinicalTrials.gov: NCT06166810).},
}

@article {pmid40223813,
year = {2025},
author = {Alp-Baltakesmez, D and Ertürkmen, P and Bulantekin, Ö},
title = {Diversity and Functional Roles of Microorganisms in Anatolian Black Pine Cone Vinegar Fermentation.},
journal = {Food science & nutrition},
volume = {13},
number = {4},
pages = {e70155},
pmid = {40223813},
issn = {2048-7177},
abstract = {The parts of some pine species are a rich source of bioactive compounds that can be used in various food products. The current work, the physicochemical, bioactive, antimicrobial, sensory, and aromatic properties of traditional vinegar produced from Anatolian Black Pine Cones from different provinces of Turkey were determined, as well as the cultivable microbial diversity and metagenomic analysis. The total phenolic content of the vinegars ranged from 163.88 to 174.79 mg GAE/L. Antioxidant activity, measured via DPPH and ABTS assays, varied among the samples. CnB vinegar, made from Burdur province cones, stood out for its bioactive compounds, including terpenes, acetic acid, ascorbic acid, and the highest α-terpineol content (3.13%). CnB also exhibited the strongest antimicrobial activity, with the largest inhibition zone (44.91 mm) against E. coli type A, while CnM showed the lowest activity. Sensory evaluations favored CnB for its balanced flavor, while CnV was criticized for excessive sharpness, and CnM was deemed too mild. The bacterial microbiome of CnB was predominantly composed of acetic acid bacteria, with an average concentration of 7.36 log CFU/mL in the enumeration of culturable microorganisms. The dominant bacterial taxa at the phyla level included Proteobacteria (72.296%), Firmicutes (22.062%), Bacteroidota (3.665%), followed by Acetobacteraceae (71.47%), Clostridia (13.187%), Bacilli (5.066%), Bacteroidetes (3.665%), and C. negativicutes (3.737%) at the phylum level. The fungal microbiome was mainly represented by Ascomycota (78.717%) and Eukaryota Incertae sedis (15.840%). The findings demonstrate that pine cone vinegar can be employed in a multitude of applications, including food preservation and health promotion.},
}

@article {pmid40223739,
year = {2025},
author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A},
title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
doi = {10.4103/sjg.sjg_24_25},
pmid = {40223739},
issn = {1998-4049},
abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.

METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.

RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4, uncultured_crAssphage, Staphylococcus_phage_SPbeta-like, Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.

CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.},
}

@article {pmid40223703,
year = {2025},
author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H},
title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00306},
pmid = {40223703},
issn = {1520-5851},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.},
}

@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods/trends
*Metabolomics/methods
*Genomics/methods
Proteomics/methods
Precision Medicine
Host Microbial Interactions
Multiomics

@article {pmid40223231,
year = {2025},
author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S},
title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2489154},
doi = {10.1080/21505594.2025.2489154},
pmid = {40223231},
issn = {2150-5608},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; },
abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.},
}

Humans
*Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood
*Gastrointestinal Microbiome
*Feces/microbiology/chemistry
Male
Female
Middle Aged
Metagenomics
Aged
Metabolomics
Dysbiosis/microbiology
Bacteria/classification/genetics/metabolism/isolation & purification
Metabolic Networks and Pathways
Case-Control Studies
Adult

@article {pmid40223096,
year = {2025},
author = {Yang, Z and Zhou, Y and Lin, J and Wang, X and Huang, C and Gao, J and Wang, G and Yang, B and Liu, G and Duan, H and Cui, J and Zhao, J and Luo, W and Cheng, S and Liu, Y},
title = {Identification and characterization of pigeon adenovirus 1 as an emerging pathogen in pigeons from Northern and Northwest China.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {266},
pmid = {40223096},
issn = {1746-6148},
support = {BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; },
mesh = {Animals ; *Columbidae/virology ; China/epidemiology ; *Adenoviridae Infections/veterinary/virology/epidemiology/pathology ; *Bird Diseases/virology/epidemiology/pathology ; *Aviadenovirus/genetics/isolation & purification ; Phylogeny ; Genome, Viral ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; },
abstract = {BACKGROUND: In 2022, a new infectious disease characterized by severe acute hepatitis, sudden death, and high mortality among breeding pigeons, was reported in China.

RESULTS: In naturally infected pigeons, key necropsy findings comprised hepatic swelling with patchy hemorrhage and pericardial effusion. Histopathological examination further revealed degeneration, necrosis, and basophilic intranuclear inclusion bodies affecting hepatocytes, cardiomyocytes, and vascular endothelial cells. Transmission electron microscopy revealed a typical icosahedral virus structure and crystal-like arrangement of viral particles in the nucleus. Metagenomic next-generation sequencing (mNGS) of pericardial effusion samples revealed the presence of pigeon adenovirus. Sequencing analysis of the hexon and fiber-2 genes suggested that it constituted pigeon adenovirus 1 (PiAdV-1). The complete genome of CH/BJ/1/2022 was determined to be 48,071 nucleotides in length, with a 10-amino acid deletion in the fiber-2 gene at residues 627-636 and a 95-animo acid insertion in the 100 K gene at residue 75. The same disease was reproduced in pigeons by experimental infection.

CONCLUSION: Collectively, our analyses confirmed that the etiological agent was PiAdV-1, an emerging pathogen that causes severe acute hepatitis and high mortality in pigeons. This virus merits close attention because it could be catastrophic for the pigeon industry.},
}

Animals
*Columbidae/virology
China/epidemiology
*Adenoviridae Infections/veterinary/virology/epidemiology/pathology
*Bird Diseases/virology/epidemiology/pathology
*Aviadenovirus/genetics/isolation & purification
Phylogeny
Genome, Viral
*Communicable Diseases, Emerging/veterinary/virology/epidemiology

@article {pmid40222673,
year = {2025},
author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL},
title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26395},
pmid = {40222673},
issn = {1525-3198},
abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.},
}

@article {pmid40222492,
year = {2025},
author = {Xia, Y and Chen, X and Jiang, X and Shen, J},
title = {Enhanced denitrification under saline Conditions: Glycine betaine as a key osmoprotectant.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132517},
doi = {10.1016/j.biortech.2025.132517},
pmid = {40222492},
issn = {1873-2976},
abstract = {Biological denitrification is significantly inhibited by salinity, which adversely affects microbial activity and reduces efficiency. This study aimed to evaluate the impact of salinity on denitrification performance and assess the potential of glycine betaine (GB) as an osmotic pressure regulator and protective agent. Results indicated that under the optimal conditions, including an influent nitrate concentration of 51.03 mg L[-1], C/N ratio of 5.42, pH value of 8.95, and salinity of 1.05 %, the nitrate removal efficiency was predicted to reach 100 %. However, a sharp decline (56.09 ± 4.52 %) in nitrate removal efficiency occurred when salinity increased from 0 % to 3 % within the initial 6 h. This inhibition was mitigated by adding 25 mg L[-1] GB, which enhanced nitrate removal efficiency by 2.19 times. GB promoted the secretion of extracellular polymeric substances (EPS), especially polymeric protein, a critical contributor to salinity resistance. Metagenomics analysis revealed that GB improved denitrification process by upregulating key genes involved in nitrogen and carbon metabolism. Furthermore, the relative abundance of Na[+] transporter genes, K[+] transporter genes, and GB absorption and synthesis genes rose with GB addition, underscoring the indispensable role of GB in alleviating osmotic stress and accelerating microbial metabolism. These findings emphasize the detrimental effects of salinity on denitrification and demonstrate the potential of GB as an osmoprotectant, enabling efficient nitrogen removal under saline conditions.},
}

@article {pmid40222473,
year = {2025},
author = {Jing, K and Li, Y and Li, Y and Meng, Q and Guan, Q},
title = {The treated wastewater enhances the biodegradation of sulfonamide antibiotics in biofilm-sediment downstream of the receiving river outlet.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121600},
doi = {10.1016/j.envres.2025.121600},
pmid = {40222473},
issn = {1096-0953},
abstract = {Although the treated wastewater meets the discharge standards, it can still become a potential transmitted stressor that affects aquatic organisms in receiving rivers. Biofilms and sediments as the main solid-phase substances in natural aquatic environments can biodegrade micropollutants. However, most of the current studies have selected a single solid-phase material, and there are relatively few studies that comprehensively consider the effect of treated wastewater on the dissipation of micropollutants in a composite biofilm-sediment system. Therefore, this study investigated the dissipation pathways of six sulfonamide antibiotics (SAs) in biofilm-sediment and the effect of treated wastewater on SAs dissipation. The results showed that biodegradation was the main pathway for SAs dissipation in biofilm-sediment. The input of treated wastewater increased the abundance of dominant degradation bacteria Burkholderiales and Pseudomonadale, thereby improving the biodegradation rate of SAs (approximately 1.5 times higher than upstream degradation rate). These genera could also be further integrated into downstream communities to continuously mediate the biodegradation of SAs. Through mass spectrometry and metagenomic sequencing analysis, it was found that the common degradation pathways of SAs in biofilm-sediment affected by treated wastewater are acetylation, formylation, hydroxylation, and bond cleavage. Acetyltransferase played an important role in the biodegradation of SAs. In addition, the enrichment of antibiotic resistant genes during biodegradation increased the risk of their spread in the aquatic environment. These findings provide new insights into the fate of antibiotics in aquatic environments and the impact of treated wastewater on downstream bacterial communities.},
}

@article {pmid40222470,
year = {2025},
author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z},
title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121602},
doi = {10.1016/j.envres.2025.121602},
pmid = {40222470},
issn = {1096-0953},
abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2%) was higher than ammonia-oxidizing bacteria (AOB, 12.0%), but lower than ammonia-oxidizing archaea (AOA, 64.8%). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.},
}

@article {pmid40222255,
year = {2025},
author = {Bobrovska, S and Newcomer, E and Gottlieb, M and McSorley, VE and Kittner, A and Hayden, MK and Green, S and Barbian, HJ},
title = {Hospital air sampling enables surveillance of respiratory virus infections and genomes.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179346},
doi = {10.1016/j.scitotenv.2025.179346},
pmid = {40222255},
issn = {1879-1026},
abstract = {There is an urgent need for early detection and comprehensive surveillance of respiratory pathogens. Environmental surveillance may be key to timely responses for newly emerging pathogens and infections that are unreported or underreported. Here, we employed air sampling in a large urban hospital. Air samples (n = 358) were collected weekly at five locations, including two in the emergency department, two in hospital common areas and one in a storage room, for two respiratory virus seasons (November 2022 to June 2024). Air samples were tested for eight respiratory pathogens by qPCR, including RNA and DNA viruses and a bacterium. Air samples had an average of four detected pathogens per sample and 97 % samples contained SARS-CoV-2. Air sample pathogen positivity and quantity were strongly correlated with clinical surveillance for four seasonal respiratory pathogens: influenza A and B, respiratory syncytial virus, and human metapneumovirus. Targeted amplicon sequencing of SARS-CoV-2 showed that lineages detected in air samples reflected those in contemporaneous regional clinical specimens. Metagenomic sequencing with viral capture enrichment detected myriad human pathogens, including respiratory-associated viruses with recovery of full viral genomes. Detection of viral pathogens correlated well between virus capture sequencing and qPCR. Overall, this suggests air sampling can be an agile and effective tool for pathogen early warning, surveillance and genome characterization.},
}

@article {pmid40222247,
year = {2025},
author = {Suzuki, M and Hayashi, T and Takahashi, K and Nozaki, K and Kasuya, KI},
title = {Exploring biodegradation limits of n-alkanes as polyethylene models using multi-omics approaches.},
journal = {The Science of the total environment},
volume = {977},
number = {},
pages = {179365},
doi = {10.1016/j.scitotenv.2025.179365},
pmid = {40222247},
issn = {1879-1026},
abstract = {Polyethylene (PE) is widely regarded as non-biodegradable in natural environments, despite reports suggesting partial biotic degradation. Using multi-omics analysis, this study investigated the biodegradation mechanisms of n-alkanes-structural analogs of PE-to determine the threshold carbon number in PE that allows for environmental biodegradation. n-Alkanes with 6-40 carbons (C6-C40) were biodegraded in the soil, whereas C44 and PE were not. 16S rRNA gene amplicon sequence analysis identified distinct microbial communities associated with non-degradable compounds (PEs and C44) and biodegradable alkanes (C6-C40). Notably, the microbial community composition for C40 differed from those associated with biodegradable alkanes below C36. Multi-omics analysis identified the genera Aeromicrobium, Nocardia, Nocardioides, Rhodococcus, Acinetobacter, and Fontimonas as key degraders of n-alkanes at C36 and below, utilizing alkane hydroxylases such as alkane monooxygenase (AlkB), LC-alkane monooxygenase from Acinetobacter (AlmA), and cytochrome P450 (CYP153). Conversely, the biodegradation of C40 was facilitated by taxa, including the order Acidimicrobiales and the genera, Acidovorax, Sphingorhabdus, Prosthecobacter, and Roseimicrobium using AlmA and CYP153-type hydroxylases. This difference in key degraders and alkane hydroxylases may explain the reduced biodegradability of n-alkanes above C40, including PE.},
}

@article {pmid40222078,
year = {2025},
author = {Xu, A and Gao, D and Wu, WM and Gong, X and Liang, H},
title = {Enhanced denitrification using iron modified biochar under low carbon source condition: Modulating community assembly, allocating carbon metabolism and facilitating electron transfer.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125354},
doi = {10.1016/j.jenvman.2025.125354},
pmid = {40222078},
issn = {1095-8630},
abstract = {Biochar can modulate microbial community structure to enhance denitrification but the activity is still restricted by the availability of electron transfer (ETS) under metabolic imbalance conditions. Here we developed iron (Ⅲ) modified biochar (FeBC) to substantially mitigate this electron limitation, enhance ETS and accelerate denitrification reaction via intracellular metabolism and community interaction. The results demonstrated that FeBC could significantly improve the denitrification performance, the nitrate removal rate was significantly increased by 30 % at C/N ratio of 3 (W/W) with little nitrite and nitrous oxide accumulation, attributing to the enhanced activities of the ETS and denitrifying reductases and complex microbial interactions via increased abundance of microorganisms involved in carbon and nitrogen transformations. Biochemical quantification and electrochemical analysis, revealed that FeBC activated the acceleration of the ETS process. Comparative metagenome analyses indicated that upregulating key enzymes in the tricarboxylic acid cycle was the potential respiratory enzyme associated with FeBC-mediated ETS. NADH/NAD[+] circulation stimulate the startup of carbon metabolism. This energy-linked mechanism could provide ATP for denitrification. This study revealed the functional roles of FeBC in mediating ETS and regulating the bacterial community to achieve enhanced denitrification.},
}

@article {pmid40221653,
year = {2025},
author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ},
title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {26},
pmid = {40221653},
issn = {2730-6844},
mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.

DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.},
}

*Daucus carota/microbiology
*Metagenomics/methods
*Rhizosphere
*Glycine max/microbiology/growth & development
*Microbiota
Soil Microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40221647,
year = {2025},
author = {Zhang, N and Dou, H and Guo, P and Sun, J and Zhang, F and Chen, T and Gao, C and Wang, Z},
title = {Concurrent invasive disseminated Nocardia farcinica and Candida infections in a patient undergoing long-term glucocorticoid therapy for autoimmune thrombocytopenia: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {520},
pmid = {40221647},
issn = {1471-2334},
support = {gxgnfx2022035//Domestic Visiting Training Program for Outstanding Young Backbone Teachers/ ; 2023SYKFZ05//Open project of Anhui Biochemical Drug Engineering Technology Research Center in 2023/ ; },
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/microbiology/complications ; Middle Aged ; *Nocardia/isolation & purification ; *Candidiasis/drug therapy/diagnosis/microbiology/complications ; *Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications ; *Glucocorticoids/therapeutic use/adverse effects ; Antifungal Agents/therapeutic use ; Candida albicans/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology ; Prednisone/therapeutic use/adverse effects ; Immunocompromised Host ; },
abstract = {BACKGROUND: Nocardia farcinica is a virulent organism known for its high resistance to many antibiotics and its ability to cause disseminated life-threatening infections, particularly in immunocompromised patients or those undergoing organ transplantation. Candida albicans can cause disseminated candidiasis with a mortality rate ranging from 30% to 60%. Cases involving concurrent disseminated N. farcinica and C. albicans, particularly in patients with autoimmune thrombocytopenia, are extremely rare. The presence of two disseminated pathogens complicates both diagnosis and treatment, creating substantial challenges for healthcare providers.

CASE PRESENTATION: A 50-year-old woman who had a history of autoimmune thrombocytopenia and was being treated with prednisone (60 mg qd). She presented with a 40-day history of high-grade fevers (40℃), cough, headache, and multiple abscesses in the skin structure. N. farcinica was found in her skin structure, cerebrospinal fluid, and blood, and C. albicans was cultured in cerebrospinal fluid, sputum, and urine. She was diagnosed with disseminated nocardiosis and disseminated candidiasis. The patient received a prolonged course of multiple anti-bacterial and anti-fungal medications and eventually recovered.

CONCLUSIONS: Due to the atypical clinical presentations, the diagnosis of concurrent invasive disseminated N. farcinica and C. albicans infections might be delayed. A variety of diagnostic testing, including metagenomics next-generation sequencing, can help to identify the pathogen rapidly. Drug susceptibility test can guide the selection and adjustment of antibiotics, which should be in companion with surgical interventions to save lives in affected patients.},
}

Humans
Female
*Nocardia Infections/drug therapy/diagnosis/microbiology/complications
Middle Aged
*Nocardia/isolation & purification
*Candidiasis/drug therapy/diagnosis/microbiology/complications
*Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications
*Glucocorticoids/therapeutic use/adverse effects
Antifungal Agents/therapeutic use
Candida albicans/isolation & purification
Anti-Bacterial Agents/therapeutic use
*Coinfection/microbiology
Prednisone/therapeutic use/adverse effects
Immunocompromised Host

@article {pmid40221512,
year = {2025},
author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y},
title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12568},
pmid = {40221512},
issn = {2045-2322},
support = {82104236//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; },
abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.},
}

Humans
*Tuberculosis, Pulmonary/diagnosis/microbiology
Male
Female
Middle Aged
*Lung/microbiology
*Microbiota/genetics
Adult
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Metagenomics/methods
Bronchoalveolar Lavage Fluid/microbiology
Aged

@article {pmid40221485,
year = {2025},
author = {Wu, Q and Gao, J and Sa, B and Cong, H and Deng, W and Zhang, Y and Zhong, X and Zhang, J and Wang, L and Liu, H and Yan, Y and Zhang, Y and Liu, D and Yan, W},
title = {Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {612},
pmid = {40221485},
issn = {2052-4463},
support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42293292//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Prochlorococcus/genetics ; *Synechococcus/genetics ; *Genome, Bacterial ; Nanopore Sequencing ; *Genome, Viral ; Metagenome ; Pacific Ocean ; Indian Ocean ; Seawater/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Prochlorococcus and Synechococcus are key contributors to marine primary production and play essential roles in global biogeochemical cycles. Despite the ecological importance of these two picocyanobacterial genera, current genomic datasets still lack comprehensive representation of under-sampled ocean regions, associated bacteria and viruses. To address this gap, we used a combination of second- and third-generation sequencing technologies to assemble comprehensive genomic data from 105 Picocyanobacterial enrichment cultures isolated from the Indian Ocean, the South China Sea, and the western Pacific Ocean. This dataset includes 55 Prochlorococcus and 50 Synechococcus genomes with high completeness (>98%) and low contamination (<2%), along with 308 non-redundant associated bacterial genomes derived from 1,457 medium- and high-quality non-cyanobacteria metagenome-assembled genomes (MAGs, completeness ≥50% and contamination ≤10%). Additionally, 2,113 non-redundant viral operational taxonomic units (vOTUs) were derived from a total of 7632 qualified viral contigs. This dataset provides a valuable resource for improving our understanding of the complex interactions among Prochlorococcus, Synechococcus, and their associated bacteria and viruses in marine ecosystems, offering a foundation to study their ecological roles and evolutionary dynamics.},
}

*Prochlorococcus/genetics
*Synechococcus/genetics
*Genome, Bacterial
Nanopore Sequencing
*Genome, Viral
Metagenome
Pacific Ocean
Indian Ocean
Seawater/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40221450,
year = {2025},
author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW},
title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {57},
pmid = {40221450},
issn = {2055-5008},
support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.},
}

*RNA, Ribosomal, 16S/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome
Colitis, Ulcerative/microbiology
DNA, Bacterial/genetics
Republic of Korea
Phylogeny
Feces/microbiology
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid40220806,
year = {2025},
author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q},
title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {142983},
doi = {10.1016/j.ijbiomac.2025.142983},
pmid = {40220806},
issn = {1879-0003},
abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.},
}

@article {pmid40220770,
year = {2025},
author = {Venkatesan, P},
title = {UK launch metagenomic pathogen surveillance programme.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101143},
doi = {10.1016/j.lanmic.2025.101143},
pmid = {40220770},
issn = {2666-5247},
}

@article {pmid40220715,
year = {2025},
author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X},
title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105686},
doi = {10.1016/j.ebiom.2025.105686},
pmid = {40220715},
issn = {2352-3964},
abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.

METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.

FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.

INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.

FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).},
}

@article {pmid40220662,
year = {2025},
author = {Yuan, Q and Ng, C and Goh, SG and Khor, WC and Ong, GHM and Aung, KT and Gin, KY},
title = {Evaluation of public health impact risks associated with bacterial antimicrobial resistome in tropical coastal environments.},
journal = {Water research},
volume = {282},
number = {},
pages = {123621},
doi = {10.1016/j.watres.2025.123621},
pmid = {40220662},
issn = {1879-2448},
abstract = {This study investigated antimicrobial resistance genes (ARGs) and microbial communities in Singapore's tropical coastal environments, comparing natural marine waters with aquaculture sites using metagenomic analysis. Results show consistently low ARG levels in natural ecosystems, whereas aquaculture sites exhibit elevated ARG concentrations, particularly those relevant to human pathogens, with considerably temporal fluctuations likely driven by human activities and seasonal factors. Additionally, aquaculture sites were found to host mobile genetic elements (MGEs) that may facilitate ARG spread, identifying aquaculture as a key reservoir of resistance genes with potential public health implications. These findings underscore distinct prevalence of ARG between natural and managed marine environments and highlight the need for continued surveillance to monitor ARG dynamics in coastal areas. By elucidating the potential for ARGs to transfer from aquaculture environments to the human food chain, this research emphasizes the importance of sustainable aquaculture practices and proactive ARG management strategies to mitigate antimicrobial resistance risks posed by tropical coastal ecosystem.},
}

@article {pmid40220550,
year = {2025},
author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E},
title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.},
journal = {Archives of oral biology},
volume = {175},
number = {},
pages = {106251},
doi = {10.1016/j.archoralbio.2025.106251},
pmid = {40220550},
issn = {1879-1506},
abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.},
}

@article {pmid40220395,
year = {2025},
author = {Zhu, Y and Zhang, X and Tao, W and Yang, S and Qi, H and Zhou, Q and Su, W and Zhang, Y and Dong, Y and Gan, Y and Lei, C and Zhang, A},
title = {Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138221},
doi = {10.1016/j.jhazmat.2025.138221},
pmid = {40220395},
issn = {1873-3336},
abstract = {The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.},
}