@article {pmid40503892,
year = {2025},
author = {He, B and Wang, Y and Xu, M and Hutchins, DA and Fu, F-X and Xia, X and Duan, R and Lin, T-H and Jiao, N and Zheng, Q},
title = {Distinct survival strategies in oligotrophic and eutrophic ecotype Synechococcus-bacteria co-cultures under iron limitation and warming conditions.},
journal = {mBio},
volume = {},
number = {},
pages = {e0109825},
doi = {10.1128/mbio.01098-25},
pmid = {40503892},
issn = {2150-7511},
abstract = {Phytoplankton-bacteria interactions underpin primary production and nutrient cycling in both oligotrophic and eutrophic aquatic environments, profoundly influencing marine biogeochemical cycles. Despite their importance, how these interactions vary under simultaneous environmental stressors such as warming and iron (Fe) limitation remains largely unexplored, especially across differing ecotypes. Here, we compared the responses of oligotrophic (strain YX04-1) and eutrophic (strain XM-24) ecotype Synechococcus-heterotrophic bacteria interactions to concurrent warming and Fe limitation, using the 16S rRNA gene amplicon sequencing alongside metagenomic and metatranscriptomic analyses. Our results revealed that community composition and gene expression in the oceanic Synechococcus sp. YX04-1 co-culture were more sensitive to warming, whereas the coastal Synechococcus sp. XM-24 co-culture responded more strongly to Fe limitation. The resilience of oligotrophic YX04-1 and its bacterial partners to iron deficiency may result from potential mutualistic triangular dynamics, involving complex carbohydrate decomposition, low-molecular-weight organic substrate transfer, and feedback of public goods. In contrast, the eutrophic XM-24 co-culture experienced intensified competition and opportunistic exploitation of organic resources by dominant mixotrophic bacteria under concurrent warming and Fe limitation conditions. These findings reveal contrasting survival strategies of oligotrophic and eutrophic Synechococcus-bacteria co-cultures, highlighting the tighter and mutually beneficial interactions in the oligotrophic co-culture that may assist oligotrophic species in adapting to changing ocean conditions.IMPORTANCEPhytoplankton-bacteria interactions serve as a crucial biological network linking primary production and nutrient cycling in marine ecosystems. In the context of global change, the upper ocean inevitably faces increased warming and iron limitation, which will shift primary producer composition toward Synechococcus and impact its nutrient exchanges with co-existing bacteria. The changes in this fundamental and widespread microbial interaction may affect the stability of nutrient cycling, yet its universal response under warming and iron limitation remains poorly understood. Our research reveals contrasting responses of oligotrophic and eutrophic Synechococcus-bacteria interactions under the same stress, driven by stronger metabolic dependencies in the oligotrophic co-culture but greater individual competitiveness in the eutrophic one. These findings emphasize the importance of cooperative heterotrophic bacteria for host survival and imply a non-uniform co-evolution of in situ microbial interactions across different marine ecosystems in the future.},
}

@article {pmid40503882,
year = {2025},
author = {Jonas, L and Lee, Y-Y and Bachvaroff, T and Hill, RT and Li, Y},
title = {Two novel Patescibacteria: Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov., both associated with microalgae optimized for carbon dioxide sequestration from flue gas.},
journal = {mBio},
volume = {},
number = {},
pages = {e0123125},
doi = {10.1128/mbio.01231-25},
pmid = {40503882},
issn = {2150-7511},
abstract = {The functional roles of bacterial symbionts associated with microalgae remain understudied despite the importance of microalgae in biotechnology and environmental microbiology. 16S rRNA gene sequencing was conducted to analyze bacterial communities associated with two microalgae optimized for growth with flue gas containing 5%-10% CO2. Two dominant bacteria with no taxonomic classification beyond the class level (Paceibacteria) were discovered repeatedly in the most productive algal cultures. Long-read metagenomic sequencing was conducted to yield high-quality metagenomes, from which two novel species were discovered under the Seqcode (seqco.de/r:ywe1blo2), Phycocordibacter aenigmaticus gen. nov. sp. nov. and Minusculum obligatum gen. nov. sp. nov. The genus Phycocordibacter gen. nov. was proposed as the nomenclatural type of the family Phycocordibacteraceae fam. nov. and the order Phycocordibacterales ord. nov. Both bacteria possessed features typical of Patescibacteria such as reduced genomes (<800 kbp), lack of complete glycolysis and tricarboxylic acid (TCA) cycle pathways, and inability to synthesize amino acids. Instead, they rely on the reductive pentose phosphate pathway (Calvin cycle) for essential biosynthesis and redox balance. P. aenigmaticus may also rely on elemental sulfur oxidation (sdo), partial nitrite reduction (nirK), and sulfur-related amino acid metabolism (SAMe → SAH). Both bacteria were found in high relative abundance in cultures of Tetradesmus obliquus HTB1 (freshwater) and Nannochloropsis oceanica IMET1 (marine), suggesting a tight association with microalgae in various environments. The absence of full metabolic pathways for energy production suggests extreme metabolic limitations and obligate symbiosis, most likely with other bacteria associated with the microalgae.IMPORTANCETo our knowledge, this is the first report of Patescibacteria as dominant bacteria associated with microalgae or within a biologically mediated carbon capture system. Two novel Patescibacteria were found in two ecologically distinct microalgal cultures (one freshwater strain and one marine) regardless of whether the cultures were bubbled with air, 5% CO2, or 10% CO2. This unexpected and unprecedented dominance led to long-read sequencing and the assembly of high-quality metagenomes for both Patescibacteria, as well as five other bacteria in the system. The discovery of two novel species belonging to two novel genera, one novel family, and one novel order has enabled us to fill in gaps of a major, uncharacterized branch within the bacterial tree of life. Additionally, the extreme gene loss found in both Patescibacteria, Phycocordibacter aenigmaticus and Minusculum obligatum, contributes knowledge to a rapidly advancing body of research on the scavenging metabolic nature of this enigmatic and largely unclassified phylum.},
}

@article {pmid40503829,
year = {2025},
author = {Zhao, J and Zhuge, R and Guo, K and Tang, J and Sun, Y and Zhang, Y and Yuan, L and Qiu, C and Yan, Y and Wang, K and Jiang, Q and Chen, J and Hua, Z and Qiu, L and Fang, H and Zhuge, J},
title = {The clinical utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing in immunocompromised critically ill patients with invasive pulmonary aspergillosis: a multicenter retrospective study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0058425},
doi = {10.1128/spectrum.00584-25},
pmid = {40503829},
issn = {2165-0497},
abstract = {UNLABELLED: The clinical utility of metagenomic next-generation sequencing (mNGS) in immunocompromised critically ill patients with invasive pulmonary aspergillosis (IPA) remains poorly studied. Given the diagnostic challenges and high mortality associated with IPA in this population, further research on the use of mNGS for early diagnosis and targeted therapy is urgently needed. This multicenter, retrospective, observational study enrolled immunocompromised patients admitted to the intensive care units of six tertiary hospitals in China from April 2021 to November 2024. Comprehensive clinical data were systematically collected, including demographic information, underlying conditions, and detailed records of specimen types and microbiological examination methods. The primary objective was to evaluate the diagnostic and prognostic values of mNGS in comparison to conventional microbiological tests (CMTs) for IPA in this high-risk population. Kappa analysis results indicated a significant agreement between the results of mNGS and CMTs in both groups (Kappa value = 0.638, P < 0.001). The receiver operating curve demonstrated that mNGS exhibited comparable sensitivity (94.03% vs. 95.52%) and higher specificity (96.20% vs. 78.85%), as well as a higher area under the curve (AUC) (0.951 vs. 0.872) in diagnosing IPA compared to CMTs. Moreover, mNGS was significantly superior to other single methods, including cultures (AUC: 0.620, sensitivity: 27.88%, specificity: 96.15%), galactomannan test (AUC: 0.711, sensitivity: 53.73%, specificity: 88.46%), and PCR (AUC: 0.770, sensitivity: 62.69%, specificity: 91.35%). The clinical application of mNGS-guided antibiotic adjustments significantly decreased the 28-day mortality rate (46.51% vs. 66.67%, P < 0.05). mNGS is a feasible and highly sensitive diagnostic tool for detecting Aspergillus infections in immunocompromised critically ill patients compared to CMTs and other single conventional methods. It also performs well in identifying mixed infections, facilitating appropriate antibiotic regimen adjustments and improving patient prognosis.

IMPORTANCE: mNGS demonstrated significantly higher specificity and area under the curve for diagnosing IPA in immunocompromised critically ill patients compared to CMTs. mNGS showed superior diagnostic performance over single methods, such as cultures, galactomannan test, and PCR, with higher sensitivity and specificity for Aspergillus detection. The use of mNGS-guided antibiotic adjustments led to a significant reduction in 28-day mortality (46.51% vs. 66.67%) among immunocompromised patients. mNGS demonstrated utility in identifying mixed infections, supporting targeted therapy and better patient outcomes. The application of mNGS in diagnosing IPA and guiding treatment in ICU patients helped optimize antibiotic regimens, ultimately improving clinical prognosis.},
}

@article {pmid40503491,
year = {2025},
author = {Dong, J and Xu, C and Jin, S and Xie, T and Xu, Z and Hao, D and Dong, L},
title = {Gut Microbiota and Tryptophan Metabolism as Therapeutic Targets for Spinal Cord Injury: Insights From Probiotic Treatment.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {7337-7355},
pmid = {40503491},
issn = {1178-7031},
abstract = {BACKGROUND: Probiotics have been demonstrated to repair spinal cord injuries (SCI) by improving gut microbiota dysbiosis; however, the specific mechanisms underlying their therapeutic effects on SCI remain incompletely elucidated.

OBJECTIVE: This study aims to investigate the therapeutic effects of probiotics and analyze the mechanisms of probiotic treatment for SCI through the gut-spinal cord axis.

METHODS: A rat model of SCI was established to evaluate the therapeutic effects of probiotics. Fecal samples were analyzed to assess gut microbiota composition and metabolite profiles, while differential gene expression in spinal cord tissue was examined.

RESULTS: Pathological assessments demonstrated that probiotic treatment facilitated structural restoration of the spinal cord tissue. Behavioral evaluations via the Basso Mouse Scale (BMS) and inclined plane tests revealed significant improvements in locomotor recovery after SCI. Metagenomic sequencing showed that probiotics enhanced gut microbiota diversity, particularly enriching the relative abundance of Bacillota (formerly Firmicutes) and Clostridia. Metabolite profiling identified an enrichment of key tryptophan metabolites, including 3-Indoleacetonitrile, Xanthoxic acid, Serotonin, and Tryptophanol. Transcriptomic analysis identified 468 upregulated and 173 downregulated genes in spinal cord tissues. Furthermore, gut microbiota, microbial metabolites and spinal cord gene expression were integrated to construct a "gut microbiota-tryptophan metabolites-signaling pathway network" using Cytoscape v.3.10.2. This network linked 19 microbial species (17 belonging to Bacillota and Clostridia, including seven Lactobacillus species) with tryptophan metabolites and downstream signaling pathways. Among these, tryptophan metabolites activated 17 genes predominantly involved in anti-inflammatory and neuroregenerative processes. Protein-level validation confirmed the neuroprotective and anti-inflammatory effects of probiotics.

CONCLUSION: The "Gut microbiota-tryptophan metabolites-signaling pathway network" offers novel therapeutic targets for SCI injury treatment. Probiotics exert their effects by modulating gut microbiota and enhancing tryptophan metabolism, thereby influencing multiple signaling pathways in the spinal cord that can lead to anti-inflammatory and neuroprotective outcomes.},
}

@article {pmid40503301,
year = {2025},
author = {Tang, K and Li, S and Luo, Y and Feng, W and Zhang, Z and Wang, L and Zhao, H and Chen, X and Li, X and Wu, Z},
title = {Integrating metagenomics and untargeted metabolomics to analyze the relationship between microbial dynamics and non-volatile metabolomic profiles in plant-derived microbial fuel cells (MFCs).},
journal = {RSC advances},
volume = {15},
number = {25},
pages = {19582-19597},
pmid = {40503301},
issn = {2046-2069},
abstract = {Microbial Fuel Cells (MFC) are an emerging biomass energy technology that harnesses the power of electroactive bacteria living on a bacterial biofilm to convert biomass energy within waste materials into usable electricity. A pivotal aspect of MFC research involves understanding the behavior and underlying mechanisms of electroactive bacteria during extracellular electron transfer to the anode, which plays a crucial role in energy conversion. In this paper, four MFCs were operated at external resistances of 500 and 1000 ohms, and the changes in the biofilm's electroactive bacterial composition due to altered external resistances were indicated by the voltage and power differences. After stable power generation, total DNA was extracted from the biofilm for sequencing, and metabolites were tested. The expression trends of genes and the differences in final metabolites from the whole period indicate that electron transfer gene families are associated with Shewanella, Pseudomonas, Trichococcus, and Enterococcus, while tyrosine and purine metabolism showed significant differences in effective metabolite accumulation among communities with varying energy output efficiency. Omics techniques revealed, to some extent, the coordination mechanisms and bacterial interactions within biofilms during microbial community succession.},
}

@article {pmid40503221,
year = {2025},
author = {Fehér, E and Kemenesi, G and Görföl, T and Wazzani, Y and Bodó, K and Lanszki, J and Máté, D and Kaszab, E and Domán, M and Zádori, Z and Lanszki, Z},
title = {Occurrence of Recombinant Canine Coronavirus, Picodicistrovirus, and Circovirus in Red Foxes (Vulpes vulpes) Implies Frequent Virus Transmission Events Among Carnivores.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {6681119},
pmid = {40503221},
issn = {1865-1682},
mesh = {Animals ; *Foxes/virology ; *Coronavirus, Canine/genetics/isolation & purification ; *Circovirus/genetics/isolation & purification ; Phylogeny ; *Coronavirus Infections/veterinary/virology/epidemiology/transmission ; Hungary/epidemiology ; Genome, Viral ; *Circoviridae Infections/veterinary/virology/epidemiology/transmission ; Carnivora/virology ; Recombination, Genetic ; },
abstract = {Although their pathogenicity is most often unclear, some canine viruses have been found to infect carnivores other than dogs. This study relies on the surveillance of coronaviruses in 206 saliva and fecal samples of huntable, sympatric canid and mustelid species captured in Hungary, such as the native red fox (Vulpes vulpes), European badger (Meles meles), golden jackal (Canis aureus), and stone marten (Martes foina), as well as the recently settled alien raccoon dog (Nyctereutes procyonoides). Metagenomics-based and direct sequence analysis were deployed to determine the genome sequence of coronaviruses identified in two specimens collected from red foxes. Near-complete genome sequences of two canine coronaviruses (CCoVs) were obtained, together with the complete genome sequence of a canine circovirus (CanineCV) and the near-complete genome sequence of a canine picodicistrovirus (CPDV) from one of the samples. These provided the first fox origin CCoV and CPDV sequence data, and the first recorded appearance of the CPDV in Europe. The results suggested that recombination is of great importance in the evolution of CCoV, CanineCV, and CPDV infecting dogs and wild-living carnivores, including the red fox and golden jackal. These are widespread in Central and Southeast Europe, and have large ranges, facilitating transmission of the multihost canine pathogens.},
}

Animals
*Foxes/virology
*Coronavirus, Canine/genetics/isolation & purification
*Circovirus/genetics/isolation & purification
Phylogeny
*Coronavirus Infections/veterinary/virology/epidemiology/transmission
Hungary/epidemiology
Genome, Viral
*Circoviridae Infections/veterinary/virology/epidemiology/transmission
Carnivora/virology
Recombination, Genetic

@article {pmid40502641,
year = {2025},
author = {Lu, L and Li, Y and Su, H and Ren, S and Liu, Y and Shao, G and Liu, W and Ji, G and Xu, H},
title = {Huangqin decoction inhibits colorectal inflammatory cancer transformation by improving gut microbiome-mediated metabolic dysfunction.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {5},
pages = {101138},
pmid = {40502641},
issn = {2214-0883},
abstract = {Colorectal inflammatory cancer transformation poses a major risk to patients with colitis. Patients with chronic intestinal inflammation have an approximately 2-3 folds increased risk of developing colorectal cancer (CRC). Unfortunately, there is currently no effective intervention available. Huangqin decoction (HQD), a well-known traditional Chinese medicine (TCM) formula, is frequently clinically prescribed for treating patients with colitis, and its active ingredients have effective antitumour efficacy. Nonetheless, the mechanism of HQD-mediated prevention of colorectal inflammatory cancer transformation remains unclear. A strategy integrating metagenomic, lipidomic, and messenger RNA (mRNA) sequencing analysis was used to investigate the regulatory effects of HQD on the gut microbiome, metabolism and potential mechanisms involved in colorectal inflammatory cancer transformation. Our study revealed that HQD suppressed colorectal inflammatory cancer transformation, which was associated with enhanced intestinal barrier function, decreased the inflammatory response, and regulation of the gut microbiome. Notably, cohousing experiments revealed that the transfer of the gut microbiome from HQD-treated mice largely inhibited the pathological transformation of colitis. Moreover, gut microbiome transfer from HQD-treated mice primarily resulted in the altered regulation of fatty acid metabolism, especially the remodeling of arachidonic acid metabolism, which was associated with the amelioration of pathological transformation. Arachidonic acid metabolism and the key metabolic enzyme arachidonic acid 12-lipoxygenase (ALOX12) were affected by HQD treatment, and no obvious protective effect of HQD was observed in Alox 12 [-/-] mice, which revealed that ALOX12 was a critical mediator of HQD protection against colorectal inflammatory cancer transformation. In summary, multiple omics analyses were applied to produce valuable data and theoretical support for the application of HQD as a promising intervention for the transformation of inflammatory CRC.},
}

@article {pmid40502184,
year = {2025},
author = {Verna, G and De Santis, S and Islam, B and Sommella, EM and Licastro, D and Zhang, L and De Almeida Celio, F and Merciai, F and Caponigro, V and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.31.657160},
pmid = {40502184},
issn = {2692-8205},
abstract = {UNLABELLED: Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors, including the gut microbiome. Since ulcerative colitis (UC), a significant risk factor for CAC, is rising in prevalence worldwide, an integrative approach is essential to identify potential triggers linking inflammation to cancer. In the present study, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a relevant missense mutation in the Muc2 gene. Upon transfer from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice exhibited a more severe colitis phenotype, and notably, spontaneous CAC as early as four weeks of age, which progressively worsened over time. In contrast, CONV Winnie developed only mild colitis but with no overt signs of tumorigenesis. Notably, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis or colon tumor development, indicating an essential role for the gut microbiome in the initiation and progression of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of donor, only FMT from SPF Winnie donors resulted in CAC, revealing a microbiota-driven, host-specific susceptibility to tumorigenesis in Winnie mice. Our studies present a novel and relevant model of CAC, providing further evidence that the microbiome plays a key role in the pathogenesis of CAC, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.

LAY SUMMARY: This study reveals a distinct metagenomic, metabolomic, and lipidomic profile associated with tumorigenesis in a murine model of ulcerative colitis, highlighting the risks of specific intestinal dysbiosis in genetically predisposed subjects.

WHAT YOU NEED TO KNOW: Background and context: Colitis-associated colorectal cancer arises from complex host-environment interactions, including gut microbiome influences, driving chronic inflammation, with the intestinal lumen environment remaining a largely unexplored potential risk factor in cancer development.New findings: Winnie mice in specific pathogen-free conditions developed severe colitis, and a novel juvenile colon dysplasia and cancer, with gut microbiome changes driving colitis-associated cancer initiation and progression.Limitations: We identified a pro-inflammatory microbial/metabolic signature promoting colitis-to-CAC transition in Winnie mice, with FMT confirming microbiota-driven tumor susceptibility. However, further research is needed to pinpoint the key bacteria-metabolite-lipid combination driving CAC.Clinical research relevance: This newly characterized microbiota-metabolome-based model of CAC, challenges the dogma of cancer as a non-transmittable disease, providing a foundation for developing microbiota-based strategies for CAC prevention and treatment.Basic research relevance: Unlike genetic or chemically induced models, the Winnie mouse model uniquely serves as a dual model for spontaneous colitis and juvenile CAC, offering a fast, 100% penetrant phenotype that enhances reliability, accelerates research, and provides valuable insights into IBD and CAC.},
}

@article {pmid40502000,
year = {2025},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {The Spinal Cord-Gut Axis Regulates Gut Microbial Homeostasis: Insights from a New Murine Metagenomic Catalog.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.27.656368},
pmid = {40502000},
issn = {2692-8205},
abstract = {The spinal cord, a nexus for brain-body crosstalk, controls gut physiology and microbial homeostasis. Here, >6,500 microbial metagenome-assembled genomes were recovered de novo , from male and female C57BL/6 mice gut metagenomes before and up to 6 months after disrupting the "spinal cord-gut axis". This "Mouse B6 Gut Catalog" improved or doubled species- and strain-level representation in other published catalogs. Analyses showed that breaking the spinal cord-gut axis caused persistent microbial changes that varied by sex, spinal lesion level, and time. A key bacterium, Lactobacillus johnsonii , was consistently reduced, and feeding this to mice with a clinically relevant spinal cord injury improved host health. Genome-resolved, community-contextualized metabolic profiling showed that spinal-dependent effects on microbe-encoded carbohydrate metabolism explain the reduction of L. johnsonii . These data improve murine microbiome catalogs and emphasize that mammalian health and gut ecosystem function depend on a functional spinal cord-gut axis.},
}

@article {pmid40501659,
year = {2025},
author = {Vemuganti, V and Kang, JW and Zhang, Q and Aquino-Martinez, R and Harding, S and Harpt, JL and Deming, Y and Johnson, S and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.08.657719},
pmid = {40501659},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome modulates metabolic, immune, and neurological functions and has been implicated in Alzheimer's disease (AD), though the specific mechanisms remain poorly defined. The bacterial metabolite imidazole propionate (ImP) has been previously associated with several AD comorbidities, such as type 2 diabetes and cardiovascular disease. Here, we show that elevated plasma ImP levels are associated with lower cognitive scores and AD biomarkers in a cohort of >1,100 cognitively unimpaired individuals. Metagenomic profiling identified gut bacteria encoding putative orthologs of the ImP-synthesizing enzyme, urocanate reductase (UrdA), whose abundance correlated with both cognitive measures and multiple AD biomarkers. Chronic ImP administration to mice activated neurodegenerative pathways, worsened AD-like neuropathology, and increased blood-brain barrier (BBB) permeability. Complementary in vitro studies showed that ImP compromised the integrity of human brain endothelial cells. Collectively, these findings implicate ImP in AD progression via both neurodegenerative and cerebrovascular mechanisms, identifying it as a potential target for early intervention.

ONE SENTENCE SUMMARY: Gut bacterial metabolite increases dementia risk.},
}

@article {pmid40500775,
year = {2025},
author = {Liang, T and Dong, J and Zhou, W and Huang, X and Liu, H and Zhang, Y and Yang, Q and Ahmad, M and Chen, L and Ling, J},
title = {Investigation on the aerobic methanotrophic community and the dominant taxon Methylomarinum in seagrass ecosystem.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {67},
pmid = {40500775},
issn = {2524-6372},
support = {Mangrove Wetland Blue Carbon Sequestration Technology Innovation Team//Nansha District High-Level Talent Innovation Team Project in 2021/ ; Mangrove Wetland Blue Carbon Sequestration Technology Innovation Team//Nansha District High-Level Talent Innovation Team Project in 2021/ ; 2023B1212060047//Science and Technology Planning Project of Guangdong Province of China/ ; 42206129//the National Natural Science Foundation of China/ ; 41676163//the National Natural Science Foundation of China/ ; 2023A1515012124//Guangdong Basic and Applied Basic Research Foundation/ ; 2022KJCX07//Sanya Science and Technology Innovation Special Project/ ; GDNRC[2024]38//the Marine Economy Development Project of Guangdong Province/ ; 2023ZD012//Nansha Key Scientific and Technological Project, Guangdong Province/ ; ZDYF2023SHFZ172//Hainan Province Science and Technology Special Fund/ ; },
abstract = {BACKGROUND: Methanotrophs are a key biological methane sink, and aerobic methanotrophs critically reduce wetland methane emissions under global climate change. However, despite their ecological significance, investigations on aerobic methanotrophs within seagrass ecosystems remain scant. In this study, microcosmic culture experiments were used to assess aerobic methane oxidation (AMO) potential and its drivers across a vertical gradient of seagrass sediments. Moreover, the methanotrophic community structure was characterized by amplicon sequencing, and the dominant methanotroph's metagenome-assembled genome (MAG) and metabolic pathway was investigated.

RESULTS: Sediments of Halophila ovalis exhibited notable vertical differences in both physicochemical properties and methane oxidation rates. Furthermore, ammonium nitrogen (NH4[+]-N) decreased with sediment depth, and was suggested by structural equation modeling (SEM) to significantly contribute to the vertical methane oxidation variability. Microbial community structure analysis revealed that type I methanotrophs were stimulated by methane addition and significantly impacted the oxidation of elevated methane, with Methylomarinum being the dominant taxon. Through metagenomic analysis, we assembled a phylogenetically novel methanotroph, Candidatus Methylomarinum sp. MAG81, which is distantly related to the extant Methylomarinum vadi IT-4. We conducted a comparative analysis of the two genomes and discovered that MAG81 not only possesses the capability for methane oxidation but also has the ability to participate in methanol oxidation via Xox-MDH. Furthermore, MAG81 also harbors nitrogen metabolism genes, particularly those involved in nitrogen fixation (nifHDK). This genetic characteristic suggests a potential role for MAG81 in facilitating the carbon and nitrogen cycles within seagrass ecosystems.

CONCLUSIONS: In summary, our study revealed that the vertical variation of NH4[+]-N significantly affected methane oxidation and that type I methanotrophs, especially the genus Methylomarinum played an important role in oxidizing methane in seagrass sediments, shedding new insights into the methane abatement in the seagrass ecosystem, which is essential for climate change mitigation.},
}

@article {pmid40500757,
year = {2025},
author = {Sussfeld, D and Lannes, R and Corel, E and Bernard, G and Martin, P and Bapteste, E and Pelletier, E and Lopez, P},
title = {New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {65},
pmid = {40500757},
issn = {2524-6372},
support = {615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; 615274/ERC_/European Research Council/International ; },
abstract = {BACKGROUND: Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the known Tree of Life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters.

RESULTS: Here, we used an iterative, network-based approach for remote homology detection, to probe a dataset of 40 million ORFs predicted in marine environments. We assessed the environmental diversity of 53 core gene families broadly distributed across the Tree of Life, with essential functions including translational, replication and trafficking processes. For nearly half of them, we identified clusters of remote environmental homologues that showed divergence from the known genetic diversity comparable to the divergence between Archaea and Bacteria, with representatives distributed across all the oceans. In particular, we report the detection of environmental clades with new structural variants of essential SMC (Structural Maintenance of Chromosomes) genes, divergent polymerase subunits forming deep-branching clades in the polymerase tree, and variant DNA recombinases in Bacteria as well as viruses.

CONCLUSIONS: These results indicate that significant environmental diversity may yet be unravelled even in strongly conserved gene families. Protein sequence similarity network approaches, in particular, appear well-suited to highlight potential sources of biological novelty and make better sense of microbial dark matter across taxonomical scales.},
}

@article {pmid40500753,
year = {2025},
author = {Bograd, A and Oppenheimer-Shaanan, Y and Levy, A},
title = {Plasmids, prophages, and defense systems are depleted from plant microbiota genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {163},
pmid = {40500753},
issn = {1474-760X},
support = {1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1535/20//Israeli Science Foundation/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 1001695377//Israeli Ministry of Innovation, Science, and Technology/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 81259//Israel Innovation Authority/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; 12-12-0008//Ministry of Agriculture and Rural Development/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; ZN4041//Volkswagen Stiftung/ ; },
mesh = {*Prophages/genetics ; *Plasmids/genetics ; *Plants/microbiology ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/virology ; },
abstract = {Plant-associated bacteria significantly impact plant growth and health. Understanding how bacterial genomes adapt to plants can provide insights into their growth promotion and virulence functions. Here, we compare 38,912 bacterial genomes and 6073 metagenomes to explore the distribution of mobile genetic elements and defense systems in plant-associated bacteria. We reveal a consistent taxon-independent depletion of prophages, plasmids, and defense systems in plant-associated bacteria, particularly in the phyllosphere, compared to other ecosystems. The mobilome depletion suggests the presence of unique ecological constraints or molecular mechanisms exerted by plants to control the bacterial mobilomes independently of bacterial immunity.},
}

*Prophages/genetics
*Plasmids/genetics
*Plants/microbiology
*Genome, Bacterial
*Microbiota/genetics
Metagenome
*Bacteria/genetics/virology

@article {pmid40500273,
year = {2025},
author = {Wang, H and Zhao, B},
title = {Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing for pulmonary infections in patients with connective tissue disease: A retrospective study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20042},
pmid = {40500273},
issn = {2045-2322},
support = {2024KY1510//the Medical and Health Science and Technology Project of Zhejiang Province/ ; },
mesh = {Humans ; *Connective Tissue Diseases/complications/microbiology ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Adult ; Aged ; *Respiratory Tract Infections/diagnosis/microbiology ; },
abstract = {Pulmonary infection is common in connective tissue diseases (CTDs) patients because of immunodeficiency. The basic characteristics of pathogens in this set of patients may differs from immunocompetent patients and largely unclear. We aimed to understand these characteristics by metagenomic next-generation sequencing (mNGS) detection in bronchoalveolar lavage fluid (BALF) from CTDs and explored the primary disease features of this group of patients. Eighty-one CTD patients who were suspected pulmonary infection and received mNGS of BALF as well as conventional microbiologic testing (CMT) were enrolled consecutively. We analysed the types of CTDs, whether accompanied with interstitial lung disease, comparison between performance of mNGS and CMT, and distribution of clinically relevant pathogens, etc. Of the 81 cases, 62 were clinically diagnosed with pulmonary infection. Among all patients, idiopathic inflammatory myopathy accounted for the highest proportion of cases infected, especially anti-MDA5 dermatomyositis and anti-synthetase syndrome. Patients in the pulmonary infection group had been previously treated with higher percentages of anti-rheumatic drugs than those in the non-infection group. The sensitivity of mNGS was higher than that of CMT (80.6% vs. 66.1%). Among the microbes detected by mNGS, the most common bacterial pathogen was Pseudomonas aeruginosa, and the most frequently fungi was Pneumocystis jirovecii. As for the specific pathogens, mNGS had great advantages over CMT in identifying Pneumocystis jirovecii. Idiopathic inflammatory myopathy was the disease most susceptible to pulmonary infections among CTDs. mNGS showed high efficiency for the detection of pathogens that cause pneumonia in BALF from patients with CTDs, especially for Pneumocystis jirovecii.},
}

Humans
*Connective Tissue Diseases/complications/microbiology
Female
*Bronchoalveolar Lavage Fluid/microbiology
Male
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Metagenomics/methods
Adult
Aged
*Respiratory Tract Infections/diagnosis/microbiology

@article {pmid40499773,
year = {2025},
author = {Ma, Y and Dong, X and Sun, Y and Li, B and Ma, H and Li, H and Zhao, X and Ran, S and Zhang, J and Ye, Y and Li, J},
title = {Diversity and Functional Roles of Viral Communities in Gene Transfer and Antibiotic Resistance in Aquaculture Waters and Microplastic Biofilms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126636},
doi = {10.1016/j.envpol.2025.126636},
pmid = {40499773},
issn = {1873-6424},
abstract = {This study presents a comprehensive metagenomic analysis of viral communities in seawater and microplastic biofilms, uncovering their diversity, functional roles, and ecological significance. We identified 4,999 DNA and 22 RNA viral operational taxonomic units. Seawater samples exhibited greater viral diversity, while microplastic biofilms harbored specialized viral assemblages with enriched metabolic functions, particularly in carbohydrate and amino acid metabolism. Auxiliary metabolic genes were detected, suggesting viral involvement in microbial metabolism and nutrient cycling. The dominance of lytic viruses (98 and 100%) indicates a significant role in microbial regulation. Moreover, antibiotic resistance genes and virulence factors were found, highlighting microplastic biofilms as potential re2servoirs for gene transfer, raising concerns about antibiotic resistance dissemination. The detection of Klebsiella pneumoniae OmpK37 in viruses further underscores the risk of horizontal gene transfer. These findings emphasize the ecological implications of virus-host interactions in marine environments and the urgent need for continued monitoring of viral dynamics in anthropogenically influenced ecosystems.},
}

@article {pmid40499635,
year = {2025},
author = {Wen, C and Guan, J and Uea-Anuwong, T and Shang, J and Peng, C and Tang, X and Magouras, I and Sun, Y and Li, F},
title = {Dissecting the gut microbial communities and resistomes of wild rats from different ecological areas in Hong Kong.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122108},
doi = {10.1016/j.envres.2025.122108},
pmid = {40499635},
issn = {1096-0953},
abstract = {Antimicrobial resistance (AMR) is one of the top global public health issues shared across all One Health domains. Wild rats, as one of key intersections of the animal and environmental domains, are understudied reservoirs and spreaders for AMR. Our study employed the whole-metagenome shotgun sequencing to characterize the caecal microbiome of wild rats and examine the presence of antimicrobial resistance genes (ARGs) from different ecological areas in Hong Kong. We trapped 88 live rats, belonging to the species of Rattus norvegicus (n=57), R. tanezumi (n=24), and R. andamanensis (n=7), from city regions, livestock farms, and stables of horse-riding schools (referred to as "suburbs"). We identified 9,672 ARGs belonging to 29 ARG types and 554 ARG subtypes. Among them, aminoglycosides, macrolide-lincosamide-streptogramin and chloramphenicol, known to be predominant in livestock gut resistome or manure compost were significantly more abundant in rats from livestock farms. Moreover, some ARGs with high-risk levels, including tetM, tetL, floR, mecR1 and lnuA , as well as plasmid-borne ARGs were significantly more abundant in rats from livestock farms than from city regions or suburbs. Furthermore, zoonotic antimicrobial-resistant bacteria (ARB) were detected, including but not limited to, prioritized antimicrobial-resistant Klebsiella pneumoniae, Proteus mirabilis, Escherichia coli, Enterococcus faecium, Acinetobacter baumannii, Campylobacter jejuni, and Staphylococcus aureus. Notably, resistant zoonotic bacteria of Streptococcus suis, Campylobacter coli, and Campylobacter jejuni were more abundant in wild rats from livestock farms. Our findings provides insights into the gut resistomes and zoonotic bacteria in wild rats in Hong Kong, highlighting the potential role of wild rats in the dissemination of ARGs and zoonotic pathogens, especially for those from agricultural settings.},
}

@article {pmid40499416,
year = {2025},
author = {Ye, PZ and Yang, Q and Zhang, CY and Yang, TT and Jiang, SF and Lan, R and Gao, SM and Huang, LN},
title = {Comparative metagenomic analyses of viral genomic diversity and ecosystem functions in extremely acidic copper mine tailings.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138862},
doi = {10.1016/j.jhazmat.2025.138862},
pmid = {40499416},
issn = {1873-3336},
abstract = {Sulfidic mine tailings represent a major source of acid mine drainage (AMD), a significant environmental problem worldwide. While the prokaryotic communities in extremely acidic tailings have been extensively studied to reveal their adaptation strategies and roles in acid generation, the diversity and putative ecosystem functions of viruses potentially infecting these extremophilic prokaryotes remain unexplored. Here, we used comparative metagenomics to investigate the viral communities in a massive copper mine tailings impoundment. Our analyses identified 932 viral operational taxonomic units (vOTUs) in 22 tailings samples, with the majority of them being taxonomically unaffiliated. The viral communities were significantly more diverse in the surface tailings (mean = 531 vOTUs) than the deeper layers (mean = 249 vOTUs). Viral communities are shaped mainly by physicochemical factors related to tailings oxidation and salinity in the surface and deeper tailings, respectively. In silico prediction uncovered archaeal viruses significantly enriched in the deeper tailings layers as compared to the surface tailings, especially those putatively infecting Thermoplasmataceae. Predicted hosts included key functional microbes associated with Fe/S redox, linking the prevalent viral infection with AMD generation/bioremediation. Notably, viral-encoded auxiliary metabolic genes (AMGs) potentially contributing to the stress resistance of hosts were identified in the tailings, exhibiting higher abundance in the deeper layers. Global metatranscriptomic analyses further demonstrated the infective and functional activity of tailings viruses across diverse AMD-associated environments. Overall, our findings provide initial insights into the viral populations and putative ecosystem functions in this extreme habitat and have important implications for mitigating AMD generation in situ.},
}

@article {pmid40499367,
year = {2025},
author = {Wang, X and Shen, Z and Zhang, Q and Lyu, T and Ding, Y and Bai, S},
title = {Biochar amendment and water level optimization enhance nitrogen removal and reduce N2O emissions in vertical flow constructed wetlands via metagenomic analysis.},
journal = {Journal of environmental management},
volume = {389},
number = {},
pages = {126133},
doi = {10.1016/j.jenvman.2025.126133},
pmid = {40499367},
issn = {1095-8630},
abstract = {To explore how biochar influences nitrogen cycling in unsaturated, capillary, and saturated zones of partially saturated vertical flow constructed wetlands (VFCWs), three parallel VFCWs were established to examine the effects of biochar's better water holding capacity on nitrogen removal and N2O emissions. Microbial mechanisms involved were studied by conducting ETS activity, metagenomic sequencing and performing high-throughput sequencing of 16S rRNA. Results indicated that the combination of adding 40 % biochar and maintaining water level of 45 cm facilitated TN removal and suppressed N2O emissions, achieving TN removal efficiency of 73.4 % and N2O/removed TN value of 0.3 %. Within the unsaturated zone, the relative abundance of amoA, hao, and nxrB increased by 929 %, 454 %, and 38.3 %, respectively, enhancing nitrification capacity microorganisms carrying these genes and involved in the oxidation of NH4[+]-N to NO3[-]-N included Nitrosomonas, Methylosarcina, Nitrosospira, and Methylomonas, whose relative abundance increased by 75.2 %. In the capillary zone, the 19.2 % increase in nosZ (involved in the reduction of N2O to N2) transformed it into a potential N2O consumption layer. The functional genera involved in N2O reduction (Ferrovibrio, Thauera, Ramlibacter, and Hyphomicrobium) in the capillary zone increased by 1724 %, 357 %, 707 %, and 78.5 %, respectively, and the ETS activity in the 40W-CW capillary zone was 72.5 % higher than that of QS-CW. Within the saturated zone, the relative abundance of amoA increased by 591 %, hao by 149 %, and nxrB decreased by 20.0 %, potentially facilitating short-cut denitrification.},
}

@article {pmid40499078,
year = {2025},
author = {Xue, K and Wang, P and Lin, Q and Xie, J and Cong, L and Yan, Z},
title = {Uncovering the Single Amino-Acid Polymorphisms of the Human Gut Ecosystem.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00108},
pmid = {40499078},
issn = {1535-3907},
abstract = {Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in the gut microbial metagenome and the host genome, but they could not adequately represent the protein-level variants. Single amino-acid polymorphisms (SAP) derived from nonsynonymous SNPs can cause functional changes of proteins and are important forces of adaption. However, SAP remains quite unexplored for the human gut microbiome. Here, we present a comprehensive large-scale analysis of SAP in the gut ecosystem, introducing a rigorous computational pipeline for detecting such protein variation from 992 published human metaproteomes. We find varied yet elaborate SAP patterns, capturing both known and novel functions and adaptive strategies of gut microbes. Microbial SAP is enriched in the outermost shell, motility devices, and ribosomes. Generally, gut microbial SAP is more convergent in metabolic subpathway regions and is enriched in the initial steps of carbohydrate metabolism pathways that catalyze the formation and isomerization of phosphorylated sugars. Furthermore, microbial and host mutant peptide patterns were altered and exhibited significant correlations in both inflammatory bowel disease and type 1 diabetes. Our results highlight the functional and clinically relevant implications and potential host-microbial interactions of gut ecosystem SAP.},
}

@article {pmid40497682,
year = {2025},
author = {Lei, X and Xu, X and Liu, C and Zhong, L and Yin, S and Li, B and Cao, L and Xie, Z and Li, J and Zhang, X and Guo, Y and Zhang, L and Lin, H and Zhang, S and Zhang, C and Gong, T},
title = {Clinical evaluation of two pathogen enrichment approaches for next-generation sequencing in the diagnosis of lower respiratory tract infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0092225},
doi = {10.1128/spectrum.00922-25},
pmid = {40497682},
issn = {2165-0497},
abstract = {The underdevelopment of microbiological tests has contributed to diagnostic delay and inappropriate use of antibiotics in patients with lower respiratory tract infections, which is ranked as the seventh leading cause of death globally. Next-generation sequencing (NGS) has emerged as a promising platform for the diagnosis of infectious diseases, albeit with high costs and challenges in result interpretation. Here we evaluated two NGS-based pathogen detection assays for the etiological diagnosis of pneumonia in a prospective cohort of 257 patients. Both assays utilized multiplex polymerase chain reaction (PCR) for pathogen enrichment. One assay was designed to promiscuously amplify and identify more than 1,000 pathogens (broad-spectrum targeted next-generation sequencing [bs-tNGS]), while the other specifically targeted 194 pathogens (pathogen-specific targeted next-generation sequencing [ps-tNGS]). The analytical and diagnostic performances of both assays were compared using a composite clinical reference standard. The specificity of ps-tNGS was higher than that of bs-tNGS (84.85% vs. 75.00%), while the sensitivities of both assays were similar (>89%). In addition, a significant overlap in the frequently detected pathogens by the two methods was observed. Moreover, the enrichment of pathogens via multiplex PCR for ps-tNGS has alleviated the requirement for deep sequencing in the shotgun metagenomic workflows and thus dramatically lowered the assay cost. This study demonstrated that ps-tNGS achieved a better overall diagnostic performance and may potentially replace bs-tNGS in the clinical application.IMPORTANCEMicrobial enrichment in metagenomic next-generation sequencing has been achieved through differential cell lysis, but the results varied, depending on experimental procedures and sample types. Therefore, direct enrichment of pathogen DNA/RNA was attempted via multiplex PCR or hybrid probe capture (targeted next-generation sequencing [tNGS]). We evaluated two enrichment methods based on multiplex PCR. One method utilized a primer design strategy to amplify over 1,000 respiratory pathogens (bs-tNGS), while the other specifically targeted 194 pathogens (ps-tNGS). Our findings disavowed the notion that "the more, the better" in tNGS workflows, since ps-tNGS exhibited equivalent sensitivity and, notably, higher specificity than bs-tNGS in a prospective cohort of 257 patients who were suspected of having pneumonia. In future evaluations of tNGS assays, researchers should pay more attention to diagnostic specificity, rather than focusing solely on sensitivity, since a low specificity may potentially lead to misdiagnosis and overuse of antibiotics in cases of non-infectious diseases.},
}

@article {pmid40497681,
year = {2025},
author = {Fan, Y and Li, Y and Wang, L and Zhao, D and Zhou, Y and Houpt, ER and Liu, J},
title = {Fecal microbiome profiling of children with Shigella diarrhea from low- and middle-income countries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0057325},
doi = {10.1128/spectrum.00573-25},
pmid = {40497681},
issn = {2165-0497},
abstract = {Shigella is one of the leading pathogens causing diarrhea in children globally. Stool culture remains the standard for diagnosing Shigella infections; however, quantitative PCR (qPCR) offers greater sensitivity. In this study, we evaluated the fecal microbiomes of 27 diarrheal children with and without Shigella identified by culture and quantitative PCR, respectively, aiming to characterize the fecal microbiome profiles of children with Shigella diarrhea and to explore the differences in microbiome and the mechanisms associated with the culturability of Shigella. Our results showed that Shigella qPCR positive cases were characterized by a significantly higher abundance of Shigella and other Proteobacteria, alongside a lower abundance of the probiotic genus Bifidobacterium. This profile was associated with specific virulence factors (VFGs) and antimicrobial resistance genes (ARGs), indicating a unique pathogenic module related to Shigella infection. While no significant difference in Shigella abundance was found between the Shigella culture positive and culture negative groups, genera Bifidobacterium and Ligilactobacillus were enriched in the culture positive group. Interestingly, the culture positive group also possessed a higher abundance of virulence factors associated with pathogenicity, likely resulting from the higher copy number of pINV plasmid. The fecal metagenomic analyses from diarrheal children suggested a potentially distinct intestinal microbial profile associated with Shigella infection and a possible correlation between increased pathogenicity and the Shigella culturability. These findings might contribute to a more comprehensive understanding of Shigella pathogenicity and improving diagnostic methods for Shigella.IMPORTANCEDiarrhea represents the fifth leading cause of mortality among children under the age of five, with Shigella representing the second most common pathogen responsible for diarrhea-related mortality. In the current study, we employed metagenomics to comprehensively characterize the fecal microbiome profiles of children infected with Shigella and to investigate the factors affecting Shigella culturability. We identified a distinct intestinal microbial profile associated with Shigella-infected diarrheal children, observed a correlation between increased pathogenicity and the Shigella culturability, and also proposed some potential factors that might promote the in vitro growth of Shigella strains. These findings might provide evidence for improving diagnostic methods for Shigella.},
}

@article {pmid40497237,
year = {2025},
author = {Feng, Y and Kuang, G and Pan, Y and Wang, J and Yang, W and Wu, WC and Pan, H and Wang, J and Han, X and Yang, L and Xin, GY and Shan, YT and Gou, QY and Liu, X and Guo, D and Liang, G and Holmes, EC and Gao, Z and Shi, M},
title = {Small mammals in a biodiversity hotspot harbor viruses of emergence risk.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwae463},
pmid = {40497237},
issn = {2053-714X},
abstract = {Metagenomic sequencing has transformed the understanding of viral diversity in wildlife and the potential threats these viruses pose to human health. Despite this progress, such sequencing studies often have lacked systematic and ecologically informed sampling, thereby likely missing many potential human pathogens and the drivers behind their ecology, evolution and emergence. We conducted an extensive search for viruses in the lungs, spleens and guts of 1688 mammals from 38 species across 428 sites in Yunnan Province, China-a hotspot for zoonoses emergence. We identified 162 mammalian viruses, including 102 new ones and 24 posing potential risks to humans due to their relationships with known human pathogens associated with serious diseases or their ability to cross major host species barriers. Our findings offer an in-depth view of virus organotropism, cross-host associations, host sharing patterns, and the ecological factors influencing viral evolution, all of which are critical for anticipating and mitigating future zoonotic outbreaks.},
}

@article {pmid40496755,
year = {2025},
author = {Gui, X and Qiu, X and Gao, Y and Chen, T and Qiu, Y and Liu, J and Xiao, Y},
title = {Chlamydia psittaci infection-associated acute fibrinous and organizing pneumonitis: A case report.},
journal = {IDCases},
volume = {40},
number = {},
pages = {e02217},
pmid = {40496755},
issn = {2214-2509},
abstract = {Acute fibrinous and organizing pneumonia (AFOP) is a rare type of lung injury, and while Chlamydia psittaci pneumonia is a zoonotic disease, secondary AFOP has not been previously reported. We present a 53-year-old female with a 13-day history of cough, fever, and shortness of breath. High-resolution computed tomography (HRCT) showed multiple bilateral patchy shadows and consolidations in the left lung lower lobe. Empirical treatment was ineffective, and lung lesions worsened. Metagenomic next-generation sequencing (mNGS) confirmed Chlamydia psittaci infection. After minocycline treatment, the patient's fever improved, but shortness of breath persisted. CT-guided lung biopsy revealed "fibrin balls" in the alveolar space and interstitial inflammatory infiltrates. Shortness of breath improved after glucocorticoid therapy, with significant lesion absorption noted on follow-up chest CT. This case suggests a possible association between AFOP and C. psittaci infection, supporting the use of combined antibiotic and glucocorticoid therapy.},
}

@article {pmid40496059,
year = {2025},
author = {Lv, Y and Jiang, G and Gao, S and Wang, H and Zhang, Y},
title = {Severe and Rapid Progression of Tropheryma whipplei-Related Pneumonia With Septic Shock: A Case Report.},
journal = {Respirology case reports},
volume = {13},
number = {6},
pages = {e70231},
pmid = {40496059},
issn = {2051-3380},
abstract = {A 54-year-old Chinese male was admitted to our department with fever, vomiting and dyspnea. His condition rapidly worsened within 12 h with acute respiratory distress syndrome and septic shock. We performed routine laboratory tests and metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) and peripheral blood, the results of which indicated the presence of Tropheryma whipplei (TW) in BALF and no pathogens in peripheral blood. We treated him with mechanical ventilation, continuous renal replacement therapy (CRRT) for 3 days, and meropenem and trimethoprim/sulfamethoxazole (TMP/SMX), as well as other therapies for 12 days. The patient survived and showed clinical improvement, with chest computed tomography (CT) scan showing absorption of lesions. During the follow-up period, the patient was given oral TMP/SMX and cefdinir for up to 33 days, and the chest CT scan showing almost complete absorption of lesions. Clinicians should strengthen the awareness of the presence of severe TW-related pneumonia in a patient without immunodeficiency diseases. Rapid detection characteristics of mNGS can guide us to diagnose rare pathogenic bacteria and improve survival for those severe pneumonia patients.},
}

@article {pmid40495714,
year = {2025},
author = {Mars Brisbin, M and McIlvin, MR and Wilburn, DB and Saunders, JK and Cohen, NR and Bhatia, M and Kujawinski, E and Searle, BC and Saito, MA},
title = {Validation and Community Sharing of Ocean Spectral Libraries Generated by Machine Learning for Data Independent Acquisition Ocean Metaproteomic Analyses.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e13971},
doi = {10.1002/pmic.13971},
pmid = {40495714},
issn = {1615-9861},
support = {//Simons Foundation/ ; R01-GM135709//NSF/ ; },
abstract = {Ocean metaproteomics provides valuable insights into the structure and function of marine microbial communities. Yet, ocean samples are challenging due to their extensive biological diversity, which results in a very large number of peptides with a large dynamic range. This study characterized the capabilities of data independent acquisition (DIA) mode for use in ocean metaproteomic samples. Spectral libraries were constructed from discovered peptides and proteins using machine learning (ML) algorithms to remove the incorporation of false positives in the libraries. When compared with 1-dimensional and 2-dimensional data dependent acquisition analyses (DDA), DIA outperformed DDA both with and without gas phase fractionation. We found that larger discovered protein spectral libraries performed better, regardless of the geographic distance between where samples were collected for library generation and where the test samples were collected. Moreover, the spectral library containing all unique proteins present in the Ocean Protein Portal (OPP) outperformed smaller libraries generated from individual sampling campaigns. However, a spectral library constructed from all open reading frames (ORFs) in a metagenome was found to be too large to be workable, resulting in low peptide identifications due to challenges in maintaining a low false discovery rate with such a large database size. Given sufficient sequencing depth and validation studies, spectral libraries generated from previously discovered proteins can serve as a community resource, saving resequencing efforts. The spectral libraries generated in this study are available at the OPP to enable future ocean proteomic studies.},
}

@article {pmid40495477,
year = {2025},
author = {Hurst, C and Zobel, G and Young, W and Olson, T and Parkar, N and Bracegirdle, J and Hannaford, R and Anderson, RC and Dalziel, JE},
title = {Social Isolation Induces Sex-Specific Differences in Behavior and Gut Microbiota Composition in Stress-Sensitive Rats.},
journal = {Brain and behavior},
volume = {15},
number = {6},
pages = {e70621},
doi = {10.1002/brb3.70621},
pmid = {40495477},
issn = {2162-3279},
support = {//Smarter Lives: New opportunities for dairy products across the lifespan/ ; C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Rats ; *Social Isolation/psychology ; *Stress, Psychological/microbiology/physiopathology ; *Behavior, Animal/physiology ; Rats, Inbred WKY ; Anxiety ; *Sex Characteristics ; Sex Factors ; Cecum/microbiology ; },
abstract = {BACKGROUND: Social isolation (SI) is an established rat model of chronic stress. We applied this to the stress-sensitive Wistar Kyoto (WKY) strain to explore brain-to-gut interactions associated with mood. Whether SI stress-induced behavioral changes are sex-specific or if they affect the microbiome in WKY is unknown. We hypothesized individually housed (IH) animals would be more anxious than pair-housed (PH), with sex differences. Male and female rats were either IH or PH from 70 to 112 days old and behavior was assessed in modified open field (OFTmod), elevated plus maze (EPM), and novel object recognition (NOR) tests. Cecal content DNA was analyzed by shotgun metagenome sequencing.

RESULTS: IH rats, particularly females, spent more time in the center of the OFTmod where the semi-novel feed was presented compared to PH group rats. There was a tendency for greater distance traveled, or potential hyperactivity, in IH female rats. Males stayed in the EPM closed arms more than females. No treatment difference occurred for recognition memory. SI altered cecal microbiome composition in females where housing was associated with seven differentially abundant taxa and 49 differentially abundant KEGG Level 3 ortholog/gene categories. Several relationships were noted between behavioral traits and relative abundance of microbiome taxa. There was a greater shift in female microbiome composition.

CONCLUSIONS: In summary, behavioral responses to the housing treatment were minimal. IH animals, particularly females, spent more time in the center of an OFT that contained food; this may have been an indication of depression, as opposed to anxiety. Housing status had a differential impact on the microbiome for females compared to males. The associations between cecal microbiota and activity in the modified OFT suggest that dietary interventions that influence the relative abundance of Bifidobacteria, Alistipes, and Muribaculaceae should be explored.},
}

Animals
Male
Female
*Gastrointestinal Microbiome/physiology
Rats
*Social Isolation/psychology
*Stress, Psychological/microbiology/physiopathology
*Behavior, Animal/physiology
Rats, Inbred WKY
Anxiety
*Sex Characteristics
Sex Factors
Cecum/microbiology

@article {pmid40495233,
year = {2025},
author = {Ndione, MHD and Ndiaye, EH and Dieng, M and Diouf, B and Sankhé, S and Diallo, D and Kane, M and Sene, NM and Mbanne, M and Sy, FA and Diop, SMBS and Doukanda, SFM and Sall, AA and Faye, O and Dia, N and Weaver, SC and Faye, O and Diallo, M and Fall, G and Gaye, A and Diagne, MM},
title = {Mosquito-based detection of retroviruses and arboviruses in Senegal: expanding the scope of xenosurveillance.},
journal = {One health outlook},
volume = {7},
number = {1},
pages = {32},
pmid = {40495233},
issn = {2524-4655},
support = {U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151758/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151758/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; U01AI151801-01/NH/NIH HHS/United States ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; 4306-22-EIPHLSSGENOMICS//Africa CDC Pathogen Genomics Initiative funds/ ; },
abstract = {BACKGROUND: Mosquitoes are well-known vectors for arthropod-borne viruses, yet their role as passive carriers of non-arthropod-borne viruses remains underexplored. Xenosurveillance, a method that utilizes blood-feeding arthropods to sample host and pathogen genetic material, has emerged as a valuable tool in viral ecology. In this study, we investigated the viral landscape of blood-fed mosquitoes from Senegal and report the first detection of Jaagsiekte Sheep Retrovirus (JSRV)-related and Enzootic Nasal Tumor Virus 2 (ENTV-2)-related sequences, alongside endemic arboviruses. Our study aimed to investigate whether mosquitoes can serve as sentinels for detecting both pathogens and host-derived markers in complex ecosystems.

METHODS: Mosquitoes were collected between 2016 and 2019 from three ecologically significant regions in Senegal (Louga, Barkedji, and Kedougou). Blood-fed mosquitoes were pooled and subjected to RNA extraction and metagenomic sequencing using Illumina NextSeq550. Sequencing data were analyzed with CZ-ID and BLAST for viral identification. RT-qPCR assays were designed to validate the presence of JSRV-related sequences, targeting conserved regions of the envelope gene and 3' untranslated region. Phylogenetic analysis was conducted using MAFFT and IQ-TREE to compare the detected sequence with global exogenous and endogenous JSRV references.

RESULTS: Sequencing revealed a broad viral diversity across mosquito species, including insect-specific viruses, arboviruses (West Nile, Sindbis, Bagaza, Usutu, Barkedji), and two retroviral sequences. A JSRV-related sequence was confirmed in a pool from Barkedji (2019) and clustered phylogenetically with endogenous JSRV. A nearly complete ENTV-2 genome, closely related to pathogenic Chinese strains, was recovered from the same pool. Other viruses grouped within established African lineages, supporting persistent regional circulation.

DISCUSSION: This study presents the first report of retroviral sequences detected in mosquitoes, alongside the identification of actively circulating arboviruses and insect-specific viruses, highlighting the broader potential of mosquitoes as environmental sentinels. While mosquitoes are not biological vectors for retroviruses, their ability to capture both host-derived retroviral material and pathogenic viral genomes through bloodmeals reinforces the value of xenosurveillance for monitoring livestock-vector-environment interactions. These findings contribute to broader efforts in integrated disease surveillance and underscore the utility of combining metagenomics with molecular diagnostics to detect diverse viral signals in high-risk ecological settings.},
}

@article {pmid40495179,
year = {2025},
author = {Liu, W and Zhou, X and Xiao, L and Huang, X and Chang, D and Zhong, X and Zeng, M and Xian, Y and Zheng, Y and Huang, W and Huang, R and Huang, M},
title = {The gut microbiota-mediated ferroptosis pathway: a key mechanism of ginsenoside Rd against metabolism-associated fatty liver disease.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {83},
pmid = {40495179},
issn = {1749-8546},
support = {2022YFC3501200//National Key Research and Development Program of China/ ; 82274080//National Natural Science Foundation of China Projects/ ; X2024019//School Management Project of Fujian University of Traditional Chinese Medicine/ ; X2024035//School Management Project of Fujian University of Traditional Chinese Medicine/ ; 2024Y9511//Fujian Provincial Science and Technology Innovation Joint Fund Project/ ; },
abstract = {BACKGROUND: Ginsenoside Rd (G-Rd), found in Panax species, has shown therapeutic potential against metabolism-associated fatty liver disease (MAFLD), but its mechanism has not been well elucidated. This study investigated the key mechanisms of G-Rd in modulating the gut microbiome and lipid peroxidation-mediated ferroptosis pathway in MAFLD.

METHODS: A high-fat diet-induced MAFLD model was established. Ultrastructural changes in liver tissue were observed using transmission electron microscopy. Metagenomics were employed to detect alterations in gut microbiota and their metabolites. Biochemical analysis and immunohistochemistry were used to examine liver injury, blood lipids, lipid peroxidation-related indicators, and tissue iron content.

RESULTS: G-Rd significantly reduced liver injury and steatosis in MAFLD mice and downregulated the elevated relative abundance of Firmicutes and the Firmicutes/Bacteroidetes ratio. It also significantly reduced the abundances of Faecalibaculum rodentium while increasing Muribaculum intestinale, with its functional role being relevant to lipid metabolism regulation. Moreover, G-Rd ameliorated mitochondrial damage and inhibited the ferroptosis pathway in the liver, which was associated with antioxidant-related factors mediated by Nrf2 signaling. The liver protective effect of G-Rd was driven by the regulation of gut microbiota, as demonstrated by antibiotic cocktail treatment and fecal microbiota transplantation.

CONCLUSIONS: G-Rd attenuated HFD-induced MAFLD by alleviating liver oxidative stress, lipid peroxidation, and ferroptosis through modulation of the gut microbiota. The antioxidant and anti-ferroptotic actions of G-Rd, mediated via the Nrf2 pathway, were found to contribute to the amelioration of liver injury and hepatic steatosis in MAFLD.},
}

@article {pmid40494644,
year = {2025},
author = {Ma, R and Shi, Y and Wu, W and Huang, C and Xue, F and Hou, R and Zhou, Y and Gu, J and Feng, F and Yu, X and Liu, J and Li, Z and Zhang, L and Lan, G and Chen, C and Bi, W and Song, X and Fu, M and Yang, H and Gu, H and Yang, J and Qi, D},
title = {The bacterial diversity and potential pathogenic risks of giant panda-infesting ticks.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0219724},
doi = {10.1128/spectrum.02197-24},
pmid = {40494644},
issn = {2165-0497},
abstract = {UNLABELLED: As common parasites in the wild, ticks significantly limit the population growth of wild giant pandas and hinder the process of reintroducing captive giant pandas into their natural habitats. Research on microbial communities and pathogens in ticks infesting giant pandas is limited, emphasizing the need for a comprehensive investigation. To thoroughly investigate the microbial communities in giant panda-infesting ticks, particularly potential pathogens, we analyzed 246 ticks collected from the ears of wild-living giant pandas using 16S rRNA and metagenomic sequencing. We found that the microbial diversity in female ticks was significantly enriched in summer. The microbial community structure carried by ticks is more significantly influenced by seasonal changes than by sex. Metagenomic results indicated that giant pandas have a higher risk of Coxiella burnetii infection in summer and a higher risk of Anaplasma phagocytophilum, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Rickettsia amblyommatis infections in autumn. Over 90% of the ticks carried pathogens, with 82.54% harboring a single potentially pathogenic symbiont and the remaining 17.46% carrying multiple pathogens, all involving Coxiella burnetii. Using the CARD database, we identified a total of 121 antibiotic resistance genes (ARGs), with 76% exhibiting antibiotic efflux mechanisms. Based on the significantly associated ARGs, we provided antibiotic treatment recommendations for infections potentially caused by pathogenic symbionts. This study provides a clear answer to the potential microbial pathogen risks of ticks infesting giant pandas and offers a framework for tick-borne diseases in reintroduced wild panda populations.

IMPORTANCE: Importance: The emergence of tick-borne bacterial diseases poses a serious threat to the population health of wild-living giant pandas. Ticks are obligate hematophagous ectoparasites that survive by feeding on the blood of various animal hosts and spreading pathogens. Although some previous studies have confirmed that wild ticks carried various viruses, the role of wild giant panda-infesting ticks in the bacterial community remains unknown. Here, the identification of the microbial community and antibiotic resistome in giant panda-infesting ticks revealed that most Ixodes ovatus ticks are potentially pathogenic symbionts, including Anaplasma phagocytophilum, Coxiella burnetii, and Rickettsia amblyommatis. Tick-borne disease control also needs to take into account the effects of season, sex, and antibiotic efflux resistance genes. Our findings highlight the contribution of the scientific management of tick-borne diseases in the giant panda population.},
}

@article {pmid40494317,
year = {2025},
author = {Kane, F and Cissoko, Y and Collins, J and Diallo, D and Diarra, B and Kone, A and Dabitao, DK and Sako, O and Coulibaly, TA and Keita, D and Togo, ACG and Coulibaly, G and Tangara, CO and Diakite, M and Konate, I and Lu, XJ and Briese, T and Lipkin, WI and Odio, DC and Katzelnick, CL and Aboulhab, J and Akpa, E and Fouth-Tchos, K and Neal, AT and Shaw-Saliba, K and Dao, S and Chen, RY and Wickiser, JK and Doumbia, S},
title = {Analyzing Transmission Patterns of Two Dengue Virus Serotypes during the 2023 Outbreak in Mali, West Africa.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.25-0113},
pmid = {40494317},
issn = {1476-1645},
abstract = {Dengue fever, a vector-borne disease caused by four serotypes of dengue virus (DENV), ranges from asymptomatic to severe illness, including hemorrhagic fever and shock syndrome. A 2023 outbreak (August 2023-May 2024) in Mali affected six districts in Bamako, causing 1,422 confirmed cases with a 2.7% fatality rate. In this study, viral sequencing provided insights into the molecular epidemiology and transmission dynamics of this outbreak. From September to October 2023, 23 of 42 suspected cases detected through national dengue surveillance activities were tested using the pan-vertebrate virus metagenomics method (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Sequencing data were analyzed using the Rapid Identification of Microbes pipeline, and Bayesian phylogenetic inference with Monte Carlo methods was used to assess viral genomic evolution. Among 23 patients, 61% were male, and the median age was 37 years (range: 20-74). The most common symptoms were fever (93.1%), headache (56.5%), and asthenia (47.8%). The largest proportion experienced dengue with warning signs (65.2%), followed by dengue without warning signs (30.4%) and severe dengue (4.4%). The successful sequencing of 19 samples revealed dengue virus serotype 3 (DENV-3; genotype III) in 15 (65.21%) samples and dengue virus serotype 1 (DENV-1; genotype III) in 4 (17.39%) samples. The DENV-1 sequences were analogous to West African sequences, and the DENV-3 were clustered with West African, Asian, and Caribbean sequences. In this study of DENV in Mali, we offer insights into the molecular epidemiology of the virus and underscore the benefits of the genomic surveillance of arboviruses in West Africa.},
}

@article {pmid40494297,
year = {2025},
author = {Hibbett, D and Nagy, LG and Nilsson, RH},
title = {Fungal diversity, evolution, and classification.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R463-R469},
doi = {10.1016/j.cub.2025.01.053},
pmid = {40494297},
issn = {1879-0445},
mesh = {*Fungi/classification/genetics ; Phylogeny ; *Biodiversity ; *Biological Evolution ; },
abstract = {Fungi include mushrooms, molds, lichens, yeasts, and zoosporic forms that occur as free-living or symbiotic organisms in every ecosystem on Earth. About 155,000 species of Fungi have been described, and possibly millions more remain to be named. Recent focus on aquatic habitats has illuminated major groups near the boundary between Fungi and protists. Fungal systematists have made remarkable progress toward resolving the major branches of the phylogeny, although some deep nodes have proven recalcitrant. Fungal taxonomists steadily describe about 3,000 new species per year, and fungal molecular ecologists routinely detect many thousands of unidentifiable 'dark fungi' through metagenomic analyses. To assemble the complete fungal tree of life, it will be necessary to connect the main branches of the phylogeny to information on all described species and integrate the vast and rapidly growing corpus of dark fungi.},
}

*Fungi/classification/genetics
Phylogeny
*Biodiversity
*Biological Evolution

@article {pmid40494146,
year = {2025},
author = {de Basanta, DW and Lado, C},
title = {Phagocytes of the forest: Are myxomycetes defensive mutualists for host plants?.},
journal = {European journal of protistology},
volume = {99},
number = {},
pages = {126158},
doi = {10.1016/j.ejop.2025.126158},
pmid = {40494146},
issn = {1618-0429},
abstract = {Myxomycetes are microscopic eukaryotic organisms classified within the phylum Amoebozoa. They are naked amoebae, with or without a flagellated stage in their life cycle, capable of forming a multinucleate cell (plasmodium) and producing fruiting bodies for spore dispersal. Myxomycetes are natural bacterivores and fungivores, consistently associated with plants or plant remains in terrestrial habitats. They are commonly found on decaying wood but also occur in living plants, where they may act as mutualists. Here, we propose that these microorganisms function as primary endophytic symbionts of plants, potentially protecting them from other endophytes. We comment on published studies that support this relationship and suggest that further evidence could be obtained through molecular or genomic approaches.},
}

@article {pmid40493700,
year = {2025},
author = {Han, C and Chen, Z and Xiao, Y and Yang, T and Shi, H and Cao, H and Yang, W and Gong, P},
title = {Characterizing nitrogen cycling microorganisms and genes in sediments of the Three Gorges Reservoir.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324051},
doi = {10.1371/journal.pone.0324051},
pmid = {40493700},
issn = {1932-6203},
mesh = {*Geologic Sediments/microbiology ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; *Bacteria/genetics/metabolism/classification ; *Lakes/microbiology ; Denitrification ; Nitrification ; },
abstract = {Microorganisms play a central role in driving the biogeochemical cycles in lakes (reservoirs). This study aims to refine the microbial-driven nitrogen cycle processes in the sediments of the Three Gorges Reservoir and assess the overall state of nitrogen cycling within these sediments. The study focuses on the Three Gorges Reservoir as the research area, using metagenomic sequencing as a research method and measuring various environmental factors in the sediment of the region, systematically investigates the nitrogen cycle microorganisms and corresponding functional gene abundance characteristics attached to sediments from upstream, midstream, and downstream areas within the region, and explores key factors that may influence the composition of nitrogen cycle microbial communities. The outcomes of the present study manifest that within the sediments of the Three Gorges Reservoir, seven principal nitrogen cycling pathways exist. These pathways are specifically nitrogen fixation, nitrification, denitrification, nitrogen transport, organic nitrogen metabolism, assimilatory nitrate reduction, and dissimilatory nitrate reduction. Furthermore, the results of this study also reveal that the anaerobic ammonium oxidation genes are barely present in the sediments of this region, which indicates that the probability of the occurrence of anaerobic ammonium oxidation reactions in this area is negligible. The abundance of nitrogen cycle related functional genes and the diversity, composition and community structure of nitrogen cycling microorganisms differ among the upstream, midstream, and downstream regions. This suggests that as sediment particle size decreases along the course from the upstream to the downstream, it may have an impact on the distribution and community structure of nitrogen cycling microorganisms.},
}

*Geologic Sediments/microbiology
*Nitrogen Cycle/genetics
Nitrogen/metabolism
*Bacteria/genetics/metabolism/classification
*Lakes/microbiology
Denitrification
Nitrification

@article {pmid40493399,
year = {2025},
author = {Han, S and Zhang, Q and Zhang, H and Ma, J},
title = {Eucommia ulmoides and its inhibitory effects on prevotella in piglet gut microbiome through metagenomic and metabolomic analysis.},
journal = {Animal biotechnology},
volume = {36},
number = {1},
pages = {2503753},
doi = {10.1080/10495398.2025.2503753},
pmid = {40493399},
issn = {1532-2378},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Prevotella/drug effects ; Swine/microbiology/growth & development ; *Eucommiaceae/chemistry ; Animal Feed/analysis ; Metagenomics ; Metabolomics ; Diet/veterinary ; Dietary Supplements ; Feces/microbiology ; },
abstract = {Eucommia ulmoides (EU) is a traditional medicinal plant widely cultivated across China. The combination of EU and feed significantly affects the growth performance, intestinal microbiota composition, and metabolic characteristics of weaned piglets. Forty Landrace x Yorkshire piglets were randomly assigned to four groups: a control group receiving a basal diet, three treatment groups receiving a basal diet supplemented with EU and EU with mix energy (EU+ME), and EU with high protein and energy (EU+HPE), respectively. Growth performance was monitored over a 25-day feeding period, and fecal samples were collected for subsequent metagenomic sequencing and metabolomic analysis. Piglets supplemented with EU, EU+ME, and EU+HPE exhibited significantly improved growth performance, compared to the control group. Metagenomic analysis revealed significant alterations in gut microbiota composition, with increased beneficial bacterial classes and suppression of Prevotella spp. Metabolomic profiling demonstrated distinct metabolic alterations among the treatment groups, with pathway impact analysis highlighting enhanced protein synthesis and energy metabolism. Furthermore, EU supplementation did not affect porcine epidemic diarrhea virus activity in vitro but reduced LPS-induced intestinal inflammation. These findings suggest that EU could be a promising natural additive for improving piglet health and growth, with potential implications for managing post-weaning challenges in swine production.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Prevotella/drug effects
Swine/microbiology/growth & development
*Eucommiaceae/chemistry
Animal Feed/analysis
Metagenomics
Metabolomics
Diet/veterinary
Dietary Supplements
Feces/microbiology

@article {pmid40493087,
year = {2025},
author = {Qayyum, H and Ishaq, Z and Ali, A and Kayani, MUR and Huang, L},
title = {Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {124},
pmid = {40493087},
issn = {1438-7948},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Metagenome ; Humans ; Computational Biology/methods ; },
abstract = {Genome-resolved metagenomics is a computational method that enables researchers to reconstruct microbial genomes from a given sample directly. This process involves three major steps, i.e. (i) preprocessing of the reads (ii) metagenome assembly, and (iii) genome binning, with (iv) taxonomic classification, and (v) functional annotation as additional steps. Despite the availability of multiple bioinformatics approaches, metagenomic data analysis encounters various challenges due to high dimensionality, data sparseness, and complexity. Meanwhile, integrating artificial intelligence (AI) at different stages of data analysis has transformed genome-resolved metagenomics. Though the application of machine learning and deep learning in metagenomic annotation started earlier, the emergence of better sequencing technologies, improved throughput, and reduced processing time have rendered the initial models less efficient. Consequently, the number of AI-based metagenomics tools is continuously increasing. The recent AI-based tools demonstrate superior performance in handling complex and multi-dimensional metagenomics data, offering improved accuracy, scalability, and efficiency compared to traditional models. In this paper, we reviewed recent AI-based tools specifically developed for short-read metagenomic data, and their underlying models for genome-resolved metagenomics. It also discusses the performance of these tools and overviews their usability in metagenomics research. We believe this study will provide researchers with insights into the strengths and limitations of current AI-based approaches, serving as a valuable resource for selecting appropriate tools and guiding future advancements in genome-resolved metagenomics.},
}

*Metagenomics/methods
*Artificial Intelligence
*Metagenome
Humans
Computational Biology/methods

@article {pmid40492778,
year = {2025},
author = {Buthelezi, ZM and Pierneef, RE and Bezuidt, OKI and Makhalanyane, TP},
title = {High-quality metagenomic-assembled genomes from sea ice and seawater of the Southern Ocean.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129824},
doi = {10.1128/mra.01298-24},
pmid = {40492778},
issn = {2576-098X},
abstract = {We provide high-quality metagenome-assembled genomes (MAGs) derived from seawater and sea ice samples collected in the Southern Ocean. Several MAGs encode genes associated with dimethylsulfoniopropionate (DMSP) lyase activity and methane oxidation. This resource provides insights regarding the role of microbial communities in the production of key volatile compounds.},
}

@article {pmid40492767,
year = {2025},
author = {Musundi, S and Okanda, D and Lambisia, A and Morobe, JM and Muthanje, E and Ochola-Oyier, LI and Carter, DP and Agoti, CN and Kiiru, J and Githinji, G},
title = {The genome sequence of varicella-zoster virus (Varicellovirus humanalpha3) obtained by metagenomics from a patient presenting with an exanthem rash.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0024825},
doi = {10.1128/mra.00248-25},
pmid = {40492767},
issn = {2576-098X},
abstract = {Here, we report a partial genome sequence of varicella-zoster virus, recovered through metagenomic sequencing from a skin lesion sample collected from a 31-year-old male from Mombasa, Kenya, in August 2024. Phylogenetic analysis placed this isolate in varicella-zoster virus clade 5.},
}

@article {pmid40492765,
year = {2025},
author = {Jin, W and Wang, M and Wang, Y and Zhu, B and Wang, Q and Zhou, C and Li, P and Hu, C and Liu, J and Pan, J and Chen, J and Hu, B},
title = {Targeted next-generation sequencing: a promising approach for Mycobacterium tuberculosis detection and drug resistance when applied in paucibacillary clinical samples.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0312724},
doi = {10.1128/spectrum.03127-24},
pmid = {40492765},
issn = {2165-0497},
abstract = {Tuberculosis (TB) returns to be the leading infectious killer globally after coronavirus disease 2019. The World Health Organization (WHO) formally included targeted next-generation sequencing (tNGS) in its list of recommendations for Mycobacterium tuberculosis (MTB) and drug resistance (DR). In this study, we explored the application of various clinical sample types for TB diagnosis and DR profiles. In comparison to the composite reference standard, the overall sensitivity values of culture, Xpert, metagenomic next-generation sequencing (mNGS), and tNGS were 0.458, 0.614, 0.772, and 0.760, respectively. tNGS had sensitivity similar to mNGS, which had advantages over culture and Xpert, respectively, despite different classification of sample types. In comparison to the microbiological reference standard, the overall sensitivity values of culture, Xpert, mNGS, and tNGS were 0.606, 0.811, 0.856, and 0.884, respectively. Suprisingly, in extrapulmonary tissue and serous effusion, mNGS and tNGS had advantages over Xpert. DR-related mutations were detected in 15 cases (13.2%). There were 51 (44.7%) applicable for all DR genes, with 22 (19.3%) not applicable for DR genes. DR genes were partially applicable in 41 (36.0%) samples. However, in culture-negative TB cases, tNGS can additionally provide 52.7% first-line DR profiles. Sanger sequencing was performed on 14 samples to confirm gene mutation identified by tNGS, and the results were entirely consistent. It was concluded that the tNGS assay was a promising approach in the initial diagnostic test of MTB and DR-related genes in different clinical samples, even for the smear- and culture-negative paucibacillary samples.IMPORTANCEtNGS combines gene-specific amplification with next-generation sequencing to detect MTB and drug-resistant genes by amplifying numerous loci directly from clinical samples. The WHO implemented tNGS for the purpose of monitoring respiratory specimens for MTB detection and DR-TB due to its high sensitivity and specificity, culture independence, and ability to report heterogeneous/silent mutations. The sensitivity outperformed both culture and Xpert, and the turnaround time was significantly less than that of culture-based assays. The tNGS assay used in this study costs USD 96 and has a 12 hour turnaround time. Nonetheless, tNGS has a great deal of promise for enhancing TB detection while also addressing DR strains.},
}

@article {pmid40492742,
year = {2025},
author = {Edwin, NR and Duff, A and Deveautour, C and Brennan, F and Abram, F and O'Sullivan, O},
title = {Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0105924},
doi = {10.1128/msystems.01059-24},
pmid = {40492742},
issn = {2379-5077},
abstract = {Microbes play an important role in soil functioning, underpinning food production systems and delivering an array of essential ecosystem services. To elucidate how these microbes relate to ecosystem functions, accurate identification and classification of soil microorganisms are important. We evaluated the comparability of shotgun and amplicon sequencing approaches by profiling soil microbiota from 131 diverse temperate grassland soils across Ireland. We assessed method comparability in terms of (i) detection and classification of the most abundant phyla, (ii) their capacity to differentiate samples based on their microbial community, and (iii) their capacity to link microbial communities to measured nitrogen cycle functions. Our findings reveal that both methods offer moderately similar outcomes, providing consistent detection of major phyla, similar microbial community differentiation patterns, and largely identifying the same relationships between the phyla and nitrogen functions. The variations observed between the two methods were mostly associated with differences in the choice of reference taxonomy. Amplicon sequencing represents a cost-effective, less computationally demanding option, while shotgun sequencing provides deeper taxonomic resolution and access to the latest databases, making it suitable for detailed microbial profiling. Our study underscores the need for careful method selection based on project requirements, database availability, and financial resources.IMPORTANCEStudying the microorganisms in soil remains a challenge as soils are one of the most complex and diverse environments. Compounding these challenges is the lack of culturable representatives in soil, with over 99% of soil microorganisms yet to be cultivated in a laboratory setting. Leveraging next-generation sequencing technologies, which bypass traditional culture-dependent methods, scientists are now able to attain low-cost, high-throughput DNA sequencing that can detect even the rarest microorganisms within samples. The present study rigorously compares amplicon and shotgun sequencing techniques in profiling microbial communities across diverse temperate grassland soil samples, focusing on how different databases, classifiers, and sequencing methods influence the results. Our study underscores the crucial need for a harmonized taxonomic database that could greatly enhance comparability and accuracy in the understanding of soil microbiomes.},
}

@article {pmid40492740,
year = {2025},
author = {Green, EA and Klepacki, I and Klassen, JL},
title = {Isolation and characterization of mollicute symbionts from a fungus-growing ant reveals high niche overlap leading to co-exclusion.},
journal = {mBio},
volume = {},
number = {},
pages = {e0089325},
doi = {10.1128/mbio.00893-25},
pmid = {40492740},
issn = {2150-7511},
abstract = {UNLABELLED: Two mollicute species belonging to the Mesoplasma and Spiroplasma genera have been detected in several species of fungus-growing ants using molecular methods. However, their ecological roles remain largely inferred from metagenomic data. To better understand their diversity and specialization, we cultured both of these Mesoplasma and Spiroplasma symbionts from the fungus-growing ant Trachymyrmex septentrionalis, providing the first isolated mollicutes from any fungus-growing ant species. The genomes of our isolates and related metagenome-assembled genomes (MAGs) from T. septentrionalis fungus gardens comprise two unique phylogenetic lineages compared to previously described Mesoplasma and Spiroplasma species, and from related MAGs previously sequenced from the leaf-cutting ant Acromyrmex echinatior. This suggests that the T. septentrionalis symbionts comprise undescribed species that can exclude each other from a niche that is largely shared between them. Mesoplasma genomes and MAGs also demonstrate regional specificity with their T. septentrionalis ant hosts. Both Mesoplasma and Spiroplasma strains from T. septentrionalis can catabolize glucose and fructose; both sugars are common in the ant's diet. Similarly, both these Mesoplasma and Spiroplasma can catabolize arginine, but only Mesoplasma can catabolize N-acetylglucosamine; both could produce ammonia for the ants or fungus garden. Based on our genomic and phenotypic analyses, we describe these T. septentrionalis symbionts as Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov., providing insight into their genomic and phenotypic diversity and cultures to facilitate future studies of how these common but poorly understood members of the fungus-growing ant symbiosis separately colonize different ant colonies despite having highly overlapping niches.

IMPORTANCE: Fungus-growing ants partner with multiple microbial symbionts to obtain food and remain free from disease. Of these symbionts, those inhabiting the ant gut remain the least understood and are known only from environmental surveys. Such surveys can infer potential functions of gut symbionts, but cultures are required to experimentally validate these hypotheses. Here, we describe the first cultures of the ant gut symbionts of the fungus-growing ant Trachymyrmex septentrionalis, using comparative genomics and phenotypic experiments to describe them as two novel species: Mesoplasma whartonense sp. nov. and Spiroplasma attinicola sp. nov. This genomic analysis suggests that these species are highly specialized to T. septentrionalis and are distinct from related environmental data generated from the related ant species Acromyrmex echinatior, implying substantial host specificity. Our phenotypic experiments and genomic reconstructions highlight the highly overlapping niches and likely costs and benefits of these symbionts to their ant host, setting the stage for further experimentation.},
}

@article {pmid40462952,
year = {2025},
author = {Zhou, H and Chen, J and Zhang, X},
title = {BMDD: A Probabilistic Framework for Accurate Imputation of Zero-inflated Microbiome Sequencing Data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40462952},
issn = {2692-8205},
abstract = {Microbiome sequencing data are inherently sparse and compositional, with excessive zeros arising from biological absence or insufficient sampling. These zeros pose significant challenges for downstream analyses, particularly those that require log-transformation. We introduce BMDD (BiModal Dirichlet Distribution), a novel probabilistic modeling framework for accurate imputation of microbiome sequencing data. Unlike existing imputation approaches that assume unimodal abundance, BMDD captures the bimodal abundance distribution of the taxa via a mixture of Dirichlet priors. It uses variational inference and a scalable expectation-maximization algorithm for efficient imputation. Through simulations and real microbiome datasets, we demonstrate that BMDD outperforms competing methods in reconstructing true abundances and improves the performance of differential abundance analysis. Through multiple posterior samples, BMDD enables robust inference by accounting for uncertainty in zero imputation. Our method offers a principled and computationally efficient solution for analyzing high-dimensional, zero-inflated microbiome sequencing data and is broadly applicable in microbial biomarker discovery and host-microbiome interaction studies. BMDD is available at: https://github.com/zhouhj1994/BMDD.},
}

@article {pmid40492738,
year = {2025},
author = {Mori, K and Hidaka, K and Tamazawa, S and Hosoyama, A and Tamaki, H and Kakegawa, T and Hanada, S},
title = {Isolation and characterization of a bacterium affiliated with the hitherto uncultured candidate phylum WOR-3 from a deep-sea hydrothermal fluid.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0018825},
doi = {10.1128/aem.00188-25},
pmid = {40492738},
issn = {1098-5336},
abstract = {UNLABELLED: A pure cultured representative, designated strain sy37, in the candidate WOR-3 lineage was obtained from a deep-sea hydrothermal fluid. This lineage was named as the candidate phylum, "Candidatus Caldipriscota," "Candidatus Hydrothermota," or "Candidatus Stahliibacteriota," based on metagenome-assembled genomes of samples from various environments. The isolated strain was a thermophilic, microaerophilic, and chemoheterotrophic rod and obtained energy through aerobic/anaerobic respiration using oxygen and elemental sulfur. The strain could not use thiosulfate, sulfate, sulfite, fumarate, nitrate, nitrite, selenate, selenite, arsenate, ferric citrate, or ferrihydrite as an electron acceptor. Genomic annotation suggested that strain sy37 possesses a novel sulfur reduction mechanism. Among members of the WOR-3 lineage, only the group containing strain sy37 possessed the oxidative phosphorylation pathway with V-type ATPase and cytochrome c oxidase and may be capable of evolving to adapt to modern oxidative environments.

IMPORTANCE: Genome analysis from various environments has revealed the overall diversity of microorganisms. However, there are many lineages for which culture representatives do not yet exist, and the characteristics and ecological significance of many of these microorganisms remain unclear: the WOR-3 lineage is one of these and has been found in various environments through the 16S rRNA gene analysis. In recent years, the metagenome-assembled genomes have been determined from the environments. In this study, we report on the successful isolation of a thermophilic microaerobic chemoorganoheterotroph, strain sy37, which is phylogenetically belonging to the WOR-3 lineage, from a deep-sea hydrothermal environment for the first time.},
}

@article {pmid40492703,
year = {2025},
author = {Alam, I and Marasco, R and Momin, AA and Aalismail, N and Laiolo, E and Martin, C and Sanz-Sáez, I and Foix, BB and Sá, EL and Kamau, A and Guzmán-Vega, FJ and Jamil, T and Acinas, SG and Gasol, JM and Gojobori, T and Agusti, S and Daffonchio, D and Arold, ST and Duarte, CM},
title = {Widespread distribution of bacteria containing PETases with a functional motif across global oceans.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf121},
pmid = {40492703},
issn = {1751-7370},
abstract = {Accumulating evidence indicates that microorganisms respond to the ubiquitous plastic pollution by evolving plastic-degrading enzymes. However, the functional diversity of these enzymes and their distribution across the ocean, including the deep sea, remain poorly understood. By integrating bioinformatics and artificial intelligence-based structure prediction, we developed a structure- and function-informed algorithm to computationally distinguish functional polyethylene terephthalate-degrading enzymes (PETases) from variants lacking PETase activity (pseudo-PETase), either due to alternative substrate specificity or pseudogene origin. Through in vitro functional screening and in vivo microcosm experiments, we verified that this algorithm identified a high-confidence, searchable sequence motif for functional PETases capable of degrading PET. Metagenomic analysis of 415 ocean samples revealed 23 PETase variants, detected in nearly 80% of the samples. These PETases mainly occur between 1000 and 2000 m deep and at the surface in regions with high plastic pollution. Metatranscriptomic analysis further identified PETase variants that were actively transcribed by marine microorganisms. In contrast to their terrestrial counterparts-where PETases are taxonomically diverse-those in marine ecosystems were predominantly encoded and transcribed by members of the Pseudomonadales order. Our study underscores the widespread distribution of PETase-containing bacteria across carbon-limited marine ecosystems, identifying and distinguishing the PETase motif that underpins the functionality of these specialised cutinases.},
}

@article {pmid40492429,
year = {2025},
author = {Meng, R and Li, J and Wang, W and Liang, D and Li, Z and Mao, C and Li, Q and Zhang, Y and Chen, H and Tang, J and Hu, P and Niu, Q and Huang, X and Shen, B and Zhang, J},
title = {Engineered Cas12j-8 is a Versatile Platform for Multiplexed Genome Modulation in Mammalian Cells.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e02593},
doi = {10.1002/advs.202502593},
pmid = {40492429},
issn = {2198-3844},
support = {2022YFC2702705//National Key Research and Development Project of China/ ; 82221005//Creative Research Groups of China/ ; 32371546//National Natural Science Foundation of China/ ; 82071434//National Natural Science Foundation of China/ ; 81971398//National Natural Science Foundation of China/ ; },
abstract = {Cas12j-8 is a compact Cas nuclease discovered from the metagenome of giant bacteriophages, consisting of only 717 amino acids and recognizing the '5-TTN-3' protospacer adjacent motif (PAM) sequence. However, its low gene editing efficiency in mammalian cells limits its application in therapeutic gene editing. To address this limitation, structure-guided mutagenesis is employed to replace key negatively charged residues with arginine, strengthening DNA binding. The resulting quintuple mutant, engineered Cas12j-8 (enCas12j-8), demonstrates robust on-target editing efficiency comparable to LbCas12a while maintaining low off-target effects. Cytosine base editors (CBEs) and adenine base editors (ABEs) are developed using enCas12j-8, achieving up to 29.54-fold C-to-T and 36.57-fold A-to-G conversion efficiency compared with the wild-type at the dominated sites, respectively. Notably, enCas12j-8 enables multiplexed editing of three genomic loci simultaneously via a single crRNA array, achieving efficiencies comparable to single-guide approaches. Additionally, enCas12j-8-ABE facilitates the disruption of splice acceptor sites, effectively inducing exon skipping in the SOD1 gene. This strategy holds potential significance for therapeutic genome modulation. These findings establish enCas12j-8 as a versatile, high-precision tool for genome engineering, combining efficient delivery, multiplexing capability, and compatibility with diverse editing modalities.},
}

@article {pmid40491974,
year = {2025},
author = {Nyström-Persson, J and Bapatdhar, N and Ghosh, S},
title = {Precise and scalable metagenomic profiling with sample-tailored minimizer libraries.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf076},
pmid = {40491974},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; Algorithms ; *Gene Library ; *Software ; *Metagenome ; },
abstract = {Reference-based metagenomic profiling requires large genome libraries to maximize detection and minimize false positives. However, as libraries grow, classification accuracy suffers, particularly in k-mer-based tools, as the growing overlap in genomic regions among organisms results in more high-level taxonomic assignments, blunting precision. To address this, we propose sample-tailored minimizer libraries, which improve on the minimizer-lowest common ancestor classification algorithm from the widely used Kraken 2. In this method, an initial filtering step using a large library removes non-resemblance genomes, followed by a refined classification step using a dynamically built smaller minimizer library. This 2-step classification method shows significant performance improvements compared to the state of the art. We develop a new computational tool called Slacken, a distributed and highly scalable platform based on Apache Spark, to implement the 2-step classification method, which improves speed while keeping the cost per sample comparable to Kraken 2. Specifically, in the CAMI2 'strain madness' samples, the fraction of reads classified at species level increased by 3.5×, while for in silico samples, it increased by 2.2×. The 2-step method achieves the sensitivity of large genomic libraries and the specificity of smaller ones, unlocking the true potential of large reference libraries for metagenomic read profiling.},
}

*Metagenomics/methods
Algorithms
*Gene Library
*Software
*Metagenome

@article {pmid40491912,
year = {2025},
author = {Li, Y and Ye, J and Zhang, C and Gao, W and Zhang, H and Zheng, C and Feng, Z and Song, M and Hao, J and Zuo, H and Zhao, Z and Guo, Y and Zhang, L},
title = {Case Report: Pulmonary mixed infection by Nocardia cyriacigeorgica, Stenotrophomonas maltophilia, and human cytomegalovirus in a patient with minimal change nephrotic syndrome.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1599958},
pmid = {40491912},
issn = {1664-3224},
mesh = {Humans ; Male ; *Stenotrophomonas maltophilia ; Adolescent ; *Cytomegalovirus Infections/diagnosis/drug therapy ; *Nocardia Infections/diagnosis/drug therapy ; *Nocardia ; *Cytomegalovirus ; *Gram-Negative Bacterial Infections/diagnosis/drug therapy ; *Coinfection/diagnosis/microbiology/drug therapy ; },
abstract = {To our knowledge, this is the first reported case of a pulmonary mixed infection involving Nocardia cyriacigeorgica, Stenotrophomonas maltophilia, and human cytomegalovirus (HCMV) in a patient with minimal change nephrotic syndrome (MCNS), which is of great clinical significance. We report the case of an 18-year-old male with a two-month history of MCNS who was admitted due to fever, cough, and bright red hemoptysis. Upon admission, he was treated with piperacillin/tazobactam and moxifloxacin for one week; however, the therapeutic response was suboptimal. Metagenomic Next-Generation Sequencing (mNGS) and microbiological culture of bronchoalveolar lavage fluid identified a pulmonary mixed infection involving N. cyriacigeorgica, S. maltophilia, and HCMV. Following the initiation of combination therapy with linezolid, trimethoprim-sulfamethoxazole, and ganciclovir, the patient's condition improved markedly, and he was discharged in a stable condition. One-year follow-up revealed complete recovery with no recurrence. This case highlights the critical role of incorporating advanced molecular diagnostic tools such as mNGS into clinical practice and the need to be vigilance about opportunistic infections involving multiple pathogens, especially in patients receiving immunosuppressive therapy.},
}

Humans
Male
*Stenotrophomonas maltophilia
Adolescent
*Cytomegalovirus Infections/diagnosis/drug therapy
*Nocardia Infections/diagnosis/drug therapy
*Nocardia
*Cytomegalovirus
*Gram-Negative Bacterial Infections/diagnosis/drug therapy
*Coinfection/diagnosis/microbiology/drug therapy

@article {pmid40491838,
year = {2025},
author = {Tian, C and Zhang, Z},
title = {Sociobiome signals by high income for increased mobile genetic elements in the gut microbiome of Chinese individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1596101},
pmid = {40491838},
issn = {1664-302X},
abstract = {INTRODUCTION: Mobile genetic elements (MGEs) play a crucial role in the dissemination of antibiotic resistance genes (ARGs), posing significant public health concerns. Despite their importance, the impact of socioeconomic factors on MGEs within the human gut microbiome remains poorly understood.

METHODS: We reanalyzed 1,382 publicly available human gut metagenomic datasets from Chinese populations, including 415 individuals from high-income eastern regions and 967 individuals from low- and middle-income western regions. MGEs were identified and categorized into functional groups, and statistical analyses were conducted to assess regional differences and correlations with economic indicators.

RESULTS: A total of 638,097 nonredundant MGEs were identified. Among these, MGEs related to integration/excision had the highest mean abundance, while those involved in stability/transfer/defense had the lowest. The abundance of MGEs was significantly higher in the eastern population compared to the western population. Moreover, MGE abundance was positively correlated with regional GDP per capita and with ARG abundance within individuals.

DISCUSSION: Our findings suggest that socioeconomic development and industrialization are associated with increased MGE abundance in the human gut microbiome, which may in turn facilitate the spread of ARGs. These results highlight a potential unintended consequence of economic advancement on public health through microbiome-mediated antibiotic resistance.},
}

@article {pmid40491516,
year = {2025},
author = {Xue, Y and Cerqueira, FM and Stevenson, HL and Williams-Bouyer, N and Fang, R},
title = {Culture-negative liver abscess identified with plasma microbial cell-free DNA sequencing: A case report.},
journal = {Infectious medicine},
volume = {4},
number = {2},
pages = {100180},
pmid = {40491516},
issn = {2772-431X},
abstract = {Pyogenic liver abscess (PLA) is a potentially life-threatening disease. Early diagnosis and appropriate treatment are crucial to ensure high-quality healthcare for patients with PLA. However, this is complicated by their non-specific clinical symptoms. In addition, the etiologic organisms responsible for PLA are frequently culture-negative, thus complicating clinical decision-making. Here, we report a case of PLA caused by Streptococcus intermedius, as identified via DNA metagenomic sequencing of plasma.},
}

@article {pmid40491436,
year = {2025},
author = {Li, D and Zhang, DY and Chen, SJ and Lv, YT and Huang, SM and Chen, C and Zeng, F and Chen, RX and Zhang, XD and Xiong, JX and Chen, FD and Jiang, YH and Chen, Z and Mo, CY and Chen, JJ and Zhu, XL and Zhang, LJ and Bai, FH},
title = {Long-term alterations in gut microbiota following mild COVID-19 recovery: bacterial and fungal community shifts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1565887},
pmid = {40491436},
issn = {2235-2988},
mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; *Fungi/classification/genetics/isolation & purification ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Feces/microbiology ; SARS-CoV-2 ; *Mycobiome ; Probiotics ; Metagenomics ; China ; },
abstract = {OBJECTIVE: COVID-19 has had a profound impact on public health globally. However, most studies have focused on patients with long COVID or those in the acute phase of infection, with limited research on the health of individuals who have recovered from mild COVID-19. This study investigates the long-term changes in bacterial and fungal communities in individuals recovering from mild COVID-19 and their clinical relevance.

METHODS: Healthy individuals from Hainan Province were enrolled before the COVID-19 outbreak, along with individuals recovering from COVID-19 at 3 months and 6 months post-recovery. Stool, blood samples, and metadata were collected. Metagenomic sequencing and Internal Transcribed Spacer (ITS) analysis characterized bacterial and fungal communities, while bacterial-fungal co-occurrence networks were constructed. A random forest model evaluated the predictive capacity of key taxa.

RESULTS: The gut microbiota of COVID-19 recoverees differed significantly from that of healthy individuals. At 3 months post-recovery, probiotics (e.g., Blautia massiliensis and Kluyveromyces spp.) were enriched, linked to improved metabolism, while at 6 months, partial recovery of probiotics (e.g., Acidaminococcus massiliensis and Asterotremella spp.) was observed alongside persistent pathogens (e.g., Streptococcus equinus and Gibberella spp.). Dynamic changes were observed, with Acidaminococcus massiliensis enriched at both baseline and 6 months but absent at 3 months. Co-occurrence network analysis revealed synergies between bacterial (Rothia spp.) and fungal (Coprinopsis spp.) taxa, suggesting their potential roles in gut restoration. The bacterial random forest model (10 taxa) outperformed the fungal model (8 taxa) in predicting recovery status (AUC = 0.99 vs. 0.80).

CONCLUSION: These findings highlight the significant long-term impacts of mild COVID-19 recovery on gut microbiota, with key taxa influencing metabolism and immune regulation, supporting microbiome-based strategies for recovery management.},
}

Humans
*COVID-19/microbiology
*Gastrointestinal Microbiome
*Fungi/classification/genetics/isolation & purification
Female
*Bacteria/classification/genetics/isolation & purification
Male
Adult
Middle Aged
Feces/microbiology
SARS-CoV-2
*Mycobiome
Probiotics
Metagenomics
China

@article {pmid40491430,
year = {2025},
author = {Chen, Z and Liu, X and Tan, L and Lyu, X and Long, Q and Wu, W and Guo, Z and Liu, Z and Li, Z and Hu, M},
title = {Comparative of metagenomic and targeted next-generation sequencing in lower respiratory tract fungal infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1534519},
pmid = {40491430},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Sensitivity and Specificity ; Aged ; Adult ; China ; *Fungi/genetics/isolation & purification/classification ; *Respiratory Tract Infections/microbiology/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung Diseases, Fungal/diagnosis/microbiology ; Young Adult ; },
abstract = {OBJECTIVES: This study aims to compare the diagnostic efficiency and consistency of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in patients with lower respiratory tract fungal infections.

METHODS: A total of 115 patients with probable pulmonary infection between September 2022 and April 2023 were enrolled at the Second Xiangya Hospital, Changsha, China, of which 61 were clinically diagnosed with invasive pulmonary fungal infection (IPFI) and 54 were non-IPFI cases. All patients received bronchoalveolar lavage, with mNGS, tNGS, and cultures being conducted paralleled. Diagnostic effectiveness and consistency in detecting microorganisms were compared.

RESULTS: Both mNGS and tNGS showed high sensitivity rates of 95.08% each, with specificity of 90.74% and 85.19%, respectively. They also demonstrated positive predictive values (PPVs) of 92.1% and 87.9% and negative predictive values (NPVs) of 94.2% and 93.9%, respectively, in diagnosing IPFI. The sensitivity and NPV of mNGS and tNGS were superior to that of any individual or combined conventional microbiological tests (CMTs) (P < 0.05). The consistency of culture with mNGS and tNGS was 48.70% and 50.43%, respectively. For fungal detection, Pneumocystis jirovecii (26/61, 42.6%; and 28/61, 45.9%), Candida albicans (19/61, 31.1%; and 21/61, 34.4%), and Aspergillus fumigatus (16/61, 26.2%; and 15/61, 24.6%) are most prevalent for mNGS and tNGS in enrolled cases, and the detection rate was greatly higher than that of culture. Furthermore, mNGS and tNGS were capable of diagnosing mixed infections in 65 and 55 out of the 115 cases, whereas only nine cases of bacterial-fungal infection were detected by culture.

CONCLUSION: The diagnostic efficacy of mNGS and tNGS was comparable to that of identified IPFI. NGS-based methodologies present a promising tool for detecting IPFI, which can be a good supplement to CMT.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Male
Middle Aged
Sensitivity and Specificity
Aged
Adult
China
*Fungi/genetics/isolation & purification/classification
*Respiratory Tract Infections/microbiology/diagnosis
Bronchoalveolar Lavage Fluid/microbiology
*Lung Diseases, Fungal/diagnosis/microbiology
Young Adult

@article {pmid40491146,
year = {2025},
author = {Li, YH and Zhao, YX and Liu, PL and Wang, YY and Tian, CL and Dong, YJ and Zhang, LJ and Chen, G},
title = {[Severe pneumonia, intracranial infection, and reversible splenial lesion syndrome caused by chlamydia psittacosis infection].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {6},
pages = {557-559},
doi = {10.3760/cma.j.cn112147-20240809-00474},
pmid = {40491146},
issn = {1001-0939},
mesh = {Humans ; *Psittacosis/complications/drug therapy ; Male ; Chlamydophila psittaci/isolation & purification ; Minocycline/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {A patient with severe pneumonia, central nervous system infection, and reversible splenial lesion syndrome was described in this article. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid and cerebrospinal fluid revealed chlamydia psittacosis. After treatment with minocycline, the patient was cured. His respiratory and neurological symptoms all disappeared.},
}

Humans
*Psittacosis/complications/drug therapy
Male
Chlamydophila psittaci/isolation & purification
Minocycline/therapeutic use
Anti-Bacterial Agents/therapeutic use
*Pneumonia/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid40490984,
year = {2025},
author = {Vargas, BO and Carazzolle, MF and Galhardo, JP and José, J and de Souza, BC and Correia, JBL and Santos, JRD and Pereira, GAG and de de Mello, FDSB},
title = {Engineering Saccharomyces Cerevisiae With Novel Functional Xylose Isomerases From Rumen Microbiota for Enhanced Biofuel Production.},
journal = {Biotechnology journal},
volume = {20},
number = {6},
pages = {e70050},
doi = {10.1002/biot.70050},
pmid = {40490984},
issn = {1860-7314},
support = {//National Agency of Petroleum, Natural Gas and Biofuels/ ; JPG: 88887.479699/2020-0//National Council for the Improvement of Higher Education/ ; JRS: 142340/2020-0//National Council for the Improvement of Higher Education/ ; BCS: 2022/05001-4//Fundação de Amparo à Pesquisa no Estado de São Paulo/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism/enzymology ; Animals ; *Rumen/microbiology ; *Biofuels ; Sheep ; Xylose/metabolism ; Cattle ; Camelus/microbiology ; *Metabolic Engineering/methods ; Ethanol/metabolism ; Fermentation ; Microbiota/genetics ; Aldose-Ketose Isomerases ; },
abstract = {Xylose metabolism in Saccharomyces cerevisiae remains a significant bottleneck due to the difficulty in identifying functional and efficient xylose isomerases (XI). In the present study, publicly available metagenomic and metatranscriptomic datasets of rumen microbiota from different herbivorous mammals were used to prospect novel XIs sequences. Seven putative XIs from moose, camel, cow, and sheep were cloned into a strain modified for xylose metabolism. Out of those, five XIs demonstrated activity and efficiently converted xylose into xylulose, resulting in ethanol as the final product. A XI from camel rumen microbiota exhibited a KM of 16.25 mM, indicating high substrate affinity. The strains expressing enzymes XI11 and XI12, obtained from sheep rumen microbiota, were able to deplete 40 g/L of xylose within 72 and 96 h, achieving theoretical ethanol yields of 90% and 88%, respectively. These results are comparable to those obtained with Orpinomyces sp. ukk1 XI, a benchmark enzyme previously reported as highly efficient in S. cerevisiae. This study also provides the first report on the successful expression of XIs mined from the ruminal microbiotas of sheep and camels in S. cerevisiae, expanding the perspectives for the optimization of fermentation processes and the production of lignocellulosic biofuels from xylose.},
}

*Saccharomyces cerevisiae/genetics/metabolism/enzymology
Animals
*Rumen/microbiology
*Biofuels
Sheep
Xylose/metabolism
Cattle
Camelus/microbiology
*Metabolic Engineering/methods
Ethanol/metabolism
Fermentation
Microbiota/genetics
Aldose-Ketose Isomerases

@article {pmid40490486,
year = {2025},
author = {Hendricks, H and Israel, S and Weitkamp, JH and Pakala, S and Rajagopala, S and Banerjee, R},
title = {Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia.},
journal = {Journal of perinatology : official journal of the California Perinatal Association},
volume = {},
number = {},
pages = {},
pmid = {40490486},
issn = {1476-5543},
support = {5UL1TR002243-03//Vanderbilt Institute for Clinical and Translational Research (VICTR)/ ; },
abstract = {BACKGROUND: Neonatal microbiome dysbiosis is associated with infectious complications.

METHODS: Prospective weekly stools were collected over 1 year from hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months. Neonates with bacteremia (cases) were matched to uninfected controls. Stools were analyzed using whole metagenome sequencing. Intensity of antibiotic exposure was compared using an Antibiotic Spectrum Index (ASI).

RESULTS: We analyzed 398 stools from 40 cases and 39 controls. Cases had lower α diversity beyond 4 weeks PNA. Cases with subsequent infections after index bacteremia had persistently lower α diversity, while cases without subsequent infections demonstrated recovery of microbiome diversity. Compared to controls, cases had greater ASI at multiple timepoints, higher Enterococcus spp. and lower anaerobe abundance.

CONCLUSIONS: Compared to controls, premature neonates with bacteremia had intestinal microbiomes with lower α diversity, higher Enterococcus spp. and lower anaerobe abundance. These changes were associated with recurrent infectious complications.},
}

@article {pmid40489796,
year = {2025},
author = {Andersen, S and Kennedy, GA and Banks, M and Flanagan, BM and Henden, AS},
title = {Prebiotic fibre enteral supplementation post allogeneic transplantation; feasibility and impact on the microbiome.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024015703},
pmid = {40489796},
issn = {2473-9537},
abstract = {The decline in diversity of the gastrointestinal microbiome during haematopoietic stem cell transplantation (HSCT) is associated with poorer clinical outcomes. While provision of enteral nutrition (EN) is common during HSCT, provision of a prebiotic fibre containing formula has not been explored. This pilot study compared tolerance, clinical, microbiome and metabolomic outcomes between patients who received standard EN (n= 10) versus prebiotic fibre EN (n=20) post allogeneic HSCT. Stool samples were collected at baseline and at peri-engraftment and were analysed with shotgun metagenomic sequencing. Provision of prebiotic EN increased daily fibre intake post-transplant to an average 22g per day compared with 4g per day in the standard care group. High tolerance of both EN formulas was observed with only 20% (n=2) of the standard and 15% of the prebiotic group (n=3) requiring parenteral nutrition (p=1.0). There was no difference in the amount of EN provided, EN duration or clinical outcomes. Microbial diversity declined in both groups with no difference post EN provision (p=0.93), however, there was a significant difference in relative abundance of lactobacillus_C rhamnosus with an increase in the prebiotic group only (p=0.022). The relative abundance of faecalicatena gnavus increased in the standard group and declined in the prebiotic group (p=0.0027). Functional analysis of the microbial genome showed decreased expression of antibiotic resistance genes in the prebiotic group only post EN provision (p = 0.00035). A longer fibre intervention should be trialled to optimise clinical outcomes and a more diverse microbiome. The trial was registered at www.anzctr.org.au as ACTRN12621000832875.},
}

@article {pmid40489603,
year = {2025},
author = {Cao, J and He, Q and Zhang, M and Zhou, R and Feng, C},
title = {Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.},
journal = {Polish journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.33073/pjm-2025-011},
pmid = {40489603},
issn = {2544-4646},
abstract = {Gut microbiota acts on the lungs through the gut-lung axis and play an important role in lung diseases. However, there are no reports on the gut microbiota characteristics in patients with invasive pulmonary aspergillosis (IPA). We aimed to analyze changes in gut microbiota in IPA patients, correlate these changes with clinical indicators and disease prognosis, and explore the application value of these characteristic changes in diagnosing IPA. The objective was to provide a theoretical basis for preventing and treating individual immunity. We conducted metagenomic next-generation sequencing of fecal samples from 43 patients with IPA and 31 healthy controls to analyze changes in the gut microbiota of these patients. We also built a random forest model for diagnosing IPA based on the gut microbiota. Compared to healthy controls, IPA patients showed a decrease in gut microbiota diversity and metabolic levels. Changes in the microbiota were characterized by a significant reduction in anti-inflammatory species that produce short-chain fatty acids, such as Faecalibacterium, Blautia, Roseburia, Phocaeicola, and Bacteroides. In contrast, opportunistic pathogens, such as Enterococcus, Corynebacterium, Escherichia, Staphylococcus, Haemophilus, and Finegoldia, were significantly enriched. The classification model based on Clostridium fessum, Blautia wexlerae, Streptococcus pseudopneumoniae, Corynebacterium striatum, and Faecalibacterium prausnitzii showed high value in distinguishing patients with IPA from healthy controls. Patients with IPA exhibit gut microbiota imbalance. The gut microbiota can serve as a biomarker that helps in diagnosing IPA. Our findings support the potential use of gut microbiota as a target for IPA prevention and treatment.},
}

@article {pmid40489326,
year = {2025},
author = {Sun, Y and Guo, K and Tang, J and Zhao, J and Zhang, X and Yan, Y and Yuan, L and Zhang, Y and Qiu, C and Luo, J and Zhang, W and Fang, H and Chen, J},
title = {Changes of respiratory microbiota associated with prognosis in pulmonary infection patients with invasive mechanical ventilation-supported respiratory failure.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2514093},
doi = {10.1080/07853890.2025.2514093},
pmid = {40489326},
issn = {1365-2060},
mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Respiration, Artificial/methods/adverse effects ; Prognosis ; *Respiratory Insufficiency/therapy/microbiology/mortality ; Middle Aged ; Aged ; *Microbiota/genetics ; Intensive Care Units/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/microbiology/mortality ; Anti-Bacterial Agents/therapeutic use ; Risk Factors ; },
abstract = {BACKGROUND: Respiratory failure (RF) is an important cause of intensive care unit (ICU) admission and mortality due to respiratory diseases. This study aimed to evaluate the clinical performance of metagenomic next-generation sequencing (mNGS) testing in pathogen diagnosis, medication guidance and to explore dynamic changes in the respiratory microbiota associated with prognosis.

METHODS: This multicenter retrospective study enrolled ICU patients from five hospitals who underwent invasive mechanical ventilation (IMV) and had pathogenic microorganisms identified by both mNGS and conventional microbiological tests (CMT) from December 2021 to April 2024. Patients were classified into two groups based on discharge outcomes: survivors (n=122) and non-survivors (n=35).

RESULTS: Compared with the survivors, non-survivors had a significantly higher proportion of smokers, dyspnea, type I RF, blood urea nitrogen, and C-reactive protein (p < 0.05). All the above indicators were identified as independent risk factors for mortality, except for type I RF. mNGS showed a better performance for pathogen identification than CMT in both groups, and nearly 60% showed consistent results between the two methods. Among survivors, antibiotic adjustment was mainly based on mNGS results (35.25%), whereas non-survivors more frequently received adjustments based on mNGS and CMT results (34.29%). The richness and abundance of lung microorganisms in the non-survivors were significantly lower than those in the survivors (p < 0.05).

CONCLUSIONS: mNGS is a promising method for identifying pathogens in pulmonary infections in IMV-supported RF patients and for exploring changes in lung microbial composition to provide a reference for patient prognosis.},
}

Humans
Male
Female
Retrospective Studies
*Respiration, Artificial/methods/adverse effects
Prognosis
*Respiratory Insufficiency/therapy/microbiology/mortality
Middle Aged
Aged
*Microbiota/genetics
Intensive Care Units/statistics & numerical data
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/microbiology/mortality
Anti-Bacterial Agents/therapeutic use
Risk Factors

@article {pmid40489211,
year = {2025},
author = {Gautam, P and Yadav, R and Vishwakarma, RK and Shekhar, S and Pathak, A and Singh, C},
title = {An Integrative Analysis of Metagenomic and Metabolomic Profiling Reveals Gut Microbiome Dysbiosis and Metabolic Alterations in ALS: Potential Biomarkers and Therapeutic Insights.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00254},
pmid = {40489211},
issn = {1948-7193},
abstract = {ALS is a severe neurodegenerative disorder characterized by motor neuron degeneration, gut dysbiosis, immune dysregulation, and metabolic disturbances. In this study, shotgun metagenomics and [1]H nuclear magnetic resonance (NMR)-based metabolomics were employed to investigate the altered gut microbiome and metabolite profiles in individuals with ALS, household controls (HCs), and nonhousehold controls (NHCs). The principal component analysis (PCA) explained 33% of the variance, and the partial least-squares discriminant analysis (PLS-DA) model demonstrate R[2] and Q[2] values of 0.97 and 0.84, respectively, indicating an adequate model fit. The relative bacterial abundance was 99.34% in the ALS group and 98.94% in the HC group. Among the ten identified genera, Bifidobacterium, Lactobacillus, and Enterococcus were more prevalent in ALS individuals, while Lactiplantibacillus and Klebsiella were more abundant in the HC group. We identified 70 metabolites, including short-chain fatty acids (SCFAs), branched-chain amino acids (BCAAs), carbohydrates, and aromatic compounds, using NMR. Orthogonal partial least-squares discriminant analysis (O-PLS-DA) explained 15.8% of the variance, with a clear separation between the ALS and HC groups. Univariate receiver operating characteristic (ROC) analysis identified three fecal metabolites with AUC values above 0.70, including butyrate (0.798), propionate (0.727), and citrate (0.719). These metabolites may serve as potential biomarkers for ALS. The statistical model for metabolic pathway analysis revealed interconnected pathways, highlighting the complexity of metabolic dysregulation, as well as potential microbial and metabolic biomarkers in ALS. These results highlight the role of gut microbiome alterations in ALS and suggest potential avenues for therapeutic intervention.},
}

@article {pmid40488951,
year = {2025},
author = {Liu, Y and Huang, G and Wei, F and Hu, Y},
title = {Non-negligible role of gut morphology in shaping mammalian gut microbiomes.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40488951},
issn = {1869-1889},
abstract = {Because of the overemphasis on the roles of diet and phylogeny in shaping the gut microbiome, the gut morphology is seldom independently considered and even often ignored. To address this research gap, we investigated a large-scale dataset of mammalian gut microbiomes, comprising 16S ribosomal RNA and metagenomic sequencing data from 292 species spanning 20 orders. We dissected the effects of various factors on the gut microbiome across four distinct gut morphology categories (foregut/hindgut/simple, foregut/hindgut, functional ruminant/ruminant-like, and colon fermenter/cecum fermenter) and uncovered the synergistic effect between phylogeny and gut morphology. Moreover, we identified the significant role of gut morphology in the gut microbiomes of hosts occupying specific niches, as well as those within the same taxonomic order but with different gut morphologies. We also identified three enterotype indices-Fusobacterium, UCG-005, and Prevotella-which could predict the three gut morphology types of mammals: simple, foregut, and hindgut. These findings enhance our understanding of mammalian gut microbial assembly and provide novel insights into host-microbe coevolution.},
}

@article {pmid40488937,
year = {2025},
author = {Paul, C and Roy, T and Roy, M and Rajeev, AC and Pan, A and Maitra, M and Das, N},
title = {Genome wide analysis of Priestia aryabhattai_OP, an endobacterium, modulating growth, development and biochemical compositions of sporophores in edible oyster mushroom Pleurotus ostreatus (MTCC 1802).},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {6},
pages = {194},
pmid = {40488937},
issn = {1573-0972},
support = {G.O. No. 52-Edn (B)/5B-15/2017//by Higher Education Department, Govt. of West Bengal, India as fellowship/ ; BT/INF/22/SP41296/2020//Department of Biotechnology (DBT), Govt. of India as DBT Builder Grant/ ; },
mesh = {*Pleurotus/growth & development/metabolism ; *Genome, Bacterial ; Phylogeny ; Laccase/metabolism/biosynthesis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Siderophores/metabolism ; Whole Genome Sequencing ; Fruiting Bodies, Fungal/growth & development ; },
abstract = {The increasing global interest in the consuming and producing of edible oyster mushrooms (Pleurotus spp.) is driven by their well-documented nutritional and health benefits. The metagenomic analysis of fruiting body revealed a distinct microbial composition in P. ostreatus, predominantly comprising Pseudomonodota (~ 82%) and Bacillota (~ 10%). An endobacterium Priestia aryabhattai_OP, associated with internal tissue of P. ostreatus (MTCC 1802), was isolated and characterized through biochemical and microscopic analyses as well as 16 S rRNA and whole genome sequencing. Co-cultivation of P. ostreatus with this bacterium significantly enhanced the in vitro production of laccase, a key growth-promoting enzyme. Additionally, the endobacterium improved the biological efficiency (BE) of the mushroom, enriched its nutraceutical profile, and facilitated the biosynthesis of beneficial compounds, including IAA, siderophores, and antimicrobials like lassopeptides, phosphonates, non-ribosomal iron-binding siderophores (NI- siderophore), carotenoids, paeninodins, synechobactins, and surfactins. The present findings offer novel insights into microbe-microbe interactions and their pivotal roles in fungal biology, with significant implications for sustainable mushroom production as well as nutrient enrichment and biotechnological advancements.},
}

*Pleurotus/growth & development/metabolism
*Genome, Bacterial
Phylogeny
Laccase/metabolism/biosynthesis
RNA, Ribosomal, 16S/genetics
Metagenomics
Siderophores/metabolism
Whole Genome Sequencing
Fruiting Bodies, Fungal/growth & development

@article {pmid40488750,
year = {2025},
author = {Jin, L and Huaijie, J and Shuaiyang, Z and Qiaoyun, R and Qingli, N and Jifei, Y and Obaid, MK and Guiquan, G and Guangyuan, L and Hong, Y},
title = {Microbial Pathogen Community in Ornithodoros lahorensis (Acari: Argasidae) in China.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {11},
pages = {e70694},
doi = {10.1096/fj.202500105R},
pmid = {40488750},
issn = {1530-6860},
support = {2021YFD1800101//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Animals ; *Ornithodoros/virology/microbiology ; China ; Phylogeny ; Genome, Viral ; *RNA Viruses/genetics ; },
abstract = {The prevalence of tick-borne bacterial and viral diseases, which pose a serious threat to human and livestock health, is increasing worldwide. At present, only a limited number of tick-borne pathogens have been reported, and no analysis of the microbial pathogen community in ticks has been carried out. We sequenced the viral metagenome of Ornithodoros lahorensis species of ticks from the Chinese mainland and identified 390 RNA viruses with unique microbial compositions. A total of 992 assembled viral transcriptomes revealed the breadth and diversity of the genome structure of tick-borne viruses, reflecting the importance of ticks as RNA viral pools. We analyzed the phylogeny of different virus families to investigate virus evolution and found that the most diverse tick-associated viruses belonged to the family Siphoviridae, which diverged earlier in evolutionary time than other arboviruses. There were only a few tick-specific viruses, whereas the number of vertebrate-infecting viruses in ticks was greater. We hope that our virus sequencing dataset will facilitate future important research on viruses carried by ticks that can infect vertebrates.},
}

Animals
*Ornithodoros/virology/microbiology
China
Phylogeny
Genome, Viral
*RNA Viruses/genetics

@article {pmid40488653,
year = {2025},
author = {Shajahan, RM and M, A and A, FT and Sreekumaran, S and Lakshmanan, D and Jaiswal, M and K, RE},
title = {Targeted Antimicrobial Resistance Gene Screening from Metagenomic DNA of Raw Milk Samples Identifies the Presence of Multiple Genes Including the mcr9.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {},
doi = {10.1089/fpd.2024.0187},
pmid = {40488653},
issn = {1556-7125},
abstract = {The current study has investigated the prevalence of antimicrobial resistance (AMR) genes in cow and goat raw milk samples. The misuse of antibiotics in the livestock sector has already been reported to be a major factor contributing to AMR risk. For the study, milk samples were collected from five different farms, and metagenomic DNA was extracted. Then, PCR amplification was carried out using primers specific to 15 different AMR genes. From the results obtained, the prevalence of β-lactam resistance genes, particularly blaTEM (24%), along with other genes like blaZ (12%) and blaSHV (8%), were observed in addition to the transmissible mcr9 gene (12%) conferring resistance to colistin. These findings underscore the urgent need for monitoring AMR genes and regulating antibiotic use in dairy farming to safeguard public health, as it poses a potential risk with the consumption of unpasteurized milk.},
}

@article {pmid40488505,
year = {2025},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Mapping of urban garden soil microbiomes in Bangladesh.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037525},
doi = {10.1128/mra.00375-25},
pmid = {40488505},
issn = {2576-098X},
abstract = {Shotgun metagenomics revealed distinct microbiome profiles in the garden soils of Dhaka and Gazipur district, Bangladesh, with Bacillus spp. demonstrating ecological dominance (>53% relative abundance) and location-specific distribution patterns. These findings highlight Bacillus species as prevalent microbes in urban garden soils.},
}

@article {pmid40488500,
year = {2025},
author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Ballesteros, G and Egas, C and Molina-Montenegro, M and Castro-Nallar, E},
title = {Rhizosphere and soil metagenomes and metagenome-assembled genomes from the Byers Peninsula, Livingston Island (62°S), Antarctica.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017125},
doi = {10.1128/mra.00171-25},
pmid = {40488500},
issn = {2576-098X},
abstract = {Rhizosphere microbes establish functional interactions with their hosts, impacting plant fitness. To further understand plant effects on microbial composition and functional diversity, we present 52 metagenomes and 1,484 metagenome-assembled genomes (MAGs) from soil and the rhizosphere of Colobanthus quitensis and Deschampsia antarctica.},
}

@article {pmid40488474,
year = {2025},
author = {Li, P and Chen, Y and Cao, X and Wang, Z and Sai, L and Wang, L},
title = {Diagnosis of invasive pulmonary aspergillosis using metagenomic next-generation sequencing and conventional microbial tests post-COVID-19 pandemic.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0012125},
doi = {10.1128/spectrum.00121-25},
pmid = {40488474},
issn = {2165-0497},
abstract = {UNLABELLED: Early recognition and timely diagnosis are crucial for improving the clinical outcome of invasive pulmonary aspergillosis (IPA) patients. Metagenomic next-generation sequencing (mNGS) shows immense advantages in identifying responsible complex pathogens, especially with the gradual ease of COVID-19 control policies in China since 2022. A total of 327 patients with suspected Aspergillus infection in non-neutropenic populations were enrolled in the current study. The diagnostic efficacy with mNGS and conventional microbial tests (CMTs) in suspected IPA patients was assessed, and the incidence and risk factors for Aspergillus infection were also investigated. mNGS exhibited excellent performance in detecting Aspergillus. The sensitivity of mNGS (80.58%) was superior to that of CMTs, as demonstrated by comparisons with smears (22.30%, P < 0.001), culture (30.94%, P < 0.001), serum GM (22.62%, P < 0.001), BALF GM (55.40%, P < 0.001), and combined CMTs (61.87%, P < 0.001). The results of mNGS caused a direct shift in the management of 212 (64.8%) positive effect patients, making a clear diagnosis and instructing antifungal therapy. Notably, in addition to the common risk factors, the patients with a history of COVID-19 infection were more prone to IPA. The occurrence of IPA increased significantly with the gradual ease of COVID-19 control policies (47.62% vs 30.21%, P = 0.004). Meanwhile, mixed infections were commonly observed in IPA patients, with Human gammaherpesvirus and Acinetobacter baumannii being the most common co-pathogens. Our study demonstrated that mNGS might present a feasible and remarkably sensitive approach for detecting Aspergillus, thereby serving as a valuable auxiliary tool for CMTs.

IMPORTANCE: Our study is the first to focus on Aspergillus infection after the COVID-19 pandemic and find that (i) mNGS is a feasible and highly sensitive method for detecting Aspergillus post-COVID-19 pandemic, thereby serving as a valuable auxiliary tool for CMTs. (ii) mNGS has the potential to revolutionize the management of fungal infections. (iii) The history of COVID-19 infection is an independent risk factor for IPA. Identification of this risk factor for IPA may raise clinical attention and require careful follow-up of high-risk individuals post-COVID-19 infection. (iv) Mixed infections were commonly observed in IPA patients, with Human gammaherpesvirus and Acinetobacter baumannii being the most common co-pathogens.},
}

@article {pmid40488469,
year = {2025},
author = {Rissanen, AJ and Mangayil, R and Tveit, AT and Maanoja, ST and Khanongnuch, R},
title = {Dissolved organic matter and sulfide enhance the CH4 consumption of a psychrophilic lake methanotroph, Methylobacter sp. S3L5C.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0313324},
doi = {10.1128/spectrum.03133-24},
pmid = {40488469},
issn = {2165-0497},
abstract = {Gammaproteobacterial methanotrophic bacteria (gMOB) are dominant methanotrophs in the water column of oxygen-stratified boreal and subarctic lakes and ponds. (Meta)genomic data suggest that, besides methane (CH4), gMOB potentially use dissolved organic matter (DOM) and reduced sulfur compounds (e.g., sulfide) as electron sources. To study the DOM and sulfide metabolism of lake gMOB, we subjected a psychrophilic lake water strain, Methylobacter sp. S3L5C, first to different sulfide levels (Na2S, 0-5 mM) to test the toxicity, and subsequently, to freshwater DOM (60 mg L[-1]) either alone or with sulfide (0.05 mM) at 1 and 20% CH4 levels. The growth, CH4 and O2 consumption, CO2 production, and mRNA expression patterns of S3L5C were analyzed. Sulfide concentrations of 0-0.5 mM had no effect, while 1 and 5 mM concentrations inhibited the strain's growth. At 20% CH4, DOM addition enhanced CH4 consumption, CO2 production, and growth of S3L5C, while the addition of sulfide+DOM led to further increases in these variables. The addition of sulfide+DOM enhanced CH4 consumption even at 1% CH4. The effect of DOM on the S3L5C's metabolism was accompanied by enhanced expression of the cyc2 gene, which has been suggested to mediate the extracellular electron transfer from DOM. Furthermore, the addition of sulfide+DOM enhanced the expression of the sqr and soxB genes encoding dissimilatory sulfide and thiosulfate oxidation, respectively. Together with previous metagenomic data, these results suggest that the usage of DOM and reduced sulfur compounds as electron sources is a trait that enhances methanotrophy among gMOB of boreal and subarctic lakes and ponds.IMPORTANCEGammaproteobacterial methanotrophic bacteria (gMOB) are crucial mitigators of methane emissions of many ecosystems, like boreal and subarctic lakes and ponds. Metagenomic data suggest that besides using methane, gMOB have genetic potential to use dissolved organic matter (DOM) and sulfide, typically present in lakes and ponds, as electron donors. To test the effect of DOM and sulfide on the methane metabolism of gMOB of oxygen-stratified boreal lakes, we subjected our recently isolated lake gMOB strain, Methylobacter sp. S3L5C, to additions of freshwater DOM and sulfide. We show that DOM and sulfide enhance methane consumption and growth of S3L5C. Furthermore, the expression of genes mediating the electron transfer from DOM and sulfide is enhanced. Our results suggest that the usage of DOM and reduced sulfur compounds as electron sources is a trait that enhances methanotrophy among gMOB and adds significantly to the growing body of literature highlighting the enormous metabolic versatility of gMOB.},
}

@article {pmid40488467,
year = {2025},
author = {Liu, Y and Qiu, Q and Chen, Y and Deng, Y and Huang, W and Sun, C and Shang, X and Chen, X and Wang, C and Han, L and Chen, S and Yuan, J and Xu, F and Yang, Z and Fang, X and Huang, L},
title = {Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145924},
doi = {10.1128/spectrum.01459-24},
pmid = {40488467},
issn = {2165-0497},
abstract = {Pre-diabetes (PD) represents a critical stage in the progression toward type 2 diabetes, with significant alterations observed in the human microbial community among pre-diabetic individuals in observational studies. However, understanding the interaction between human microbiota and the host during pre-diabetes remains limited. Therefore, this study aims to understand the alterations in the human microbial community during pre-diabetes, a critical stage toward type 2 diabetes. Using an integrated analysis of human microbiota and metabolomics data, we seek to identify the functional signature associated with PD and gain insights into potential mechanisms driving its progression to type 2 diabetes. These findings could inform the development of early intervention strategies for those at high risk. Samples were collected from pre-diabetes, diabetes, and healthy control groups. Through metagenome and 16S rRNA sequencing, we analyzed the gut microbial and tongue coating compositions, respectively. Untargeted metabolomics techniques were also applied for comprehensive plasma data. Using integrated multi-omics analysis, we aim to understand the metabolic potentials of the human microbiome, its molecular links with host targets, and their effects on pre-diabetes, thereby deepening our understanding of microbiome-host interactions in this context. The pre-diabetes group exhibited distinct clinical characteristics, particularly in blood glucose levels and a higher average level of γ-glutamyl transferase. We identified 509 intestinal bacterial species, with Megamonas funiformis and Parabacteroides merdae showing higher abundance in the PD group. In tongue coating samples, we found 1,122 bacterial genera, with the PD group showing altered levels of Corynebacterium and Johnsonella. Furthermore, we detected 795 metabolites, primarily involved in carbohydrate and lipid metabolism. Importantly, our integrated multi-omics analysis suggested Flavonifractor plautii's role in modulating blood glucose through influencing carbohydrate metabolism. Our integrated multi-omics analysis revealed significant alterations in several regulatory pathways associated with pre-diabetes, particularly emphasizing the impact of gut bacterium Flavonifractor plautii on blood glucose levels through its influence on carbohydrate metabolism. These intricate relationships among gut microbiota, metabolites, and blood glucose levels underscore the significance of personalized treatment approaches and preventive strategies for pre-diabetes. The insights gained from this research hold considerable promise for advancing our understanding and management of pre-diabetes.IMPORTANCEThis study investigates alterations in the human microbial community during PD, a critical stage leading to type 2 diabetes. Through integrated analysis of metagenomic and metabolomics data from pre-diabetes, diabetes, and healthy control groups, we identified distinct clinical characteristics in the PD group, including elevated blood glucose levels and γ-glutamyl transferase. A total of 509 intestinal bacterial species were identified, with Flavonifractor plautii playing a key role in modulating blood glucose levels via its influence on carbohydrate metabolism. Our findings underscore the complex interactions among gut microbiota, metabolites, and blood glucose levels, highlighting the potential for personalized treatment approaches and early intervention strategies for individuals at high risk of developing type 2 diabetes.},
}

@article {pmid40488405,
year = {2025},
author = {Ricci, F and Leung, PM and Hutchinson, T and Nguyen-Dinh, T and Frank, AH and Hood, AVS and Salazar, VW and Eate, V and Wong, WW and Cook, PLM and Greening, C and McClelland, H},
title = {Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf117},
pmid = {40488405},
issn = {1751-7370},
abstract = {Photosynthetic microbial mats are macroscopic microbial ecosystems consisting of a wide array of functional groups and microenvironments arranged along variable redox gradients. Light energy ultimately drives primary production and a cascade of daisy-chained metabolisms. Heterotrophic members of these communities remineralise organic material, decreasing net primary production, and returning nutrients to the aqueous phase. However, reduced inorganic and one-carbon substrates such as trace gases and those released as metabolic byproducts in deeper anoxic regions of the mat, could theoretically also fuel carbon fixation, mitigating carbon loss from heterotrophy and enhancing net primary production. Here, we investigated the intricate metabolic synergies that sustain community nutrient webs in a biomineralising microbial mat from a hypersaline lake. We recovered 331 genomes spanning 40 bacterial and archaeal phyla that influence the biogeochemistry of these ecosystems. Phototrophy is a major metabolic potential found in 17% of the genomes, but over 50% encode enzymes to harness energy from inorganic substrates and 12% co-encode chemosynthetic carbon fixation pathways that use sulfide and hydrogen as electron donors. We experimentally demonstrated that the microbial community oxidises ferrous iron, ammonia, sulfide, and reduced trace gas substrates aerobically and anaerobically. Furthermore, carbon isotope assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and organic matter production alongside photosynthesis. Chemosynthesis in microbial mats results from a complex suite of spatially organised metabolic interactions and continuous nutrient cycling, which decouples carbon fixation from the diurnal cycle, and enhances the net primary production of these highly efficient ecosystems.},
}

@article {pmid40488306,
year = {2025},
author = {Yoshimura, E and Hamada, Y and Hatamoto, Y and Nakagata, T and Nanri, H and Nakayama, Y and Iwasaka, C and Hayashi, T and Suzuki, I and Ando, T and Ishikawa-Takata, K and Tanaka, S and Ono, R and Araki, M and Kawashima, H and Chen, YA and Park, J and Hosomi, K and Mizuguchi, K and Kunisawa, J and Miyachi, M},
title = {Effect of short-term dietary intervention on fecal serotonin, gut microbiome-derived tryptophanase, and energy absorption in a randomized crossover trial: an exploratory analysis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2514137},
doi = {10.1080/19490976.2025.2514137},
pmid = {40488306},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/chemistry/microbiology ; Cross-Over Studies ; Male ; *Serotonin/analysis/metabolism ; Adult ; Female ; Young Adult ; *Tryptophanase/metabolism/analysis/genetics ; Energy Metabolism ; *Diet ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, we investigated the effects of short-term energy loads on changes in gut microbiome-derived tryptophanase and fecal serotonin levels and their association with variations in energy absorption. This randomized crossover energy-load intervention study included 15 healthy participants subjected to three dietary conditions - overfeeding, control, and underfeeding - for eight days. The effects of the dietary conditions on energy absorption (digestible and metabolizable energy) were assessed using a bomb calorimeter. Fecal serotonin levels were assessed using LC-MS/MS, and the gut microbiota was analyzed using the 16S rRNA gene and metagenomic shotgun analysis. Significant differences were observed in digestible energy (p < 0.001), with higher values in the overfeeding than in the control (p = 0.032) conditions. Furthermore, significant differences were noted in metabolizable energy and gut transit time (p < 0.001), both of which were higher in the overfeeding than in the control (metabolizable energy: p = 0.001; gut transit time: p = 0.014) and underfeeding (metabolizable energy: p < 0.001; gut transit time: p = 0.004) conditions. Fecal serotonin levels differed significantly (p < 0.001), with significantly lower levels in the overfeeding than in the control (p = 0.005) and underfeeding (p < 0.001) conditions. Tryptophanase exhibited significant differences (p = 0.0019), with lower gene abundance in the overfeeding than in the underfeeding (p = 0.001) condition. Tryptophanase positively correlated with Bacteroides abundance under all conditions (correlation coefficient: 0.696-0.896). Intra-individual variability in fecal serotonin levels was significantly negatively associated with digestible energy (β = -0.077, p = 0.019). The findings suggest that short-term energy loads dynamically alter fecal serotonin, Bacteroides, and tryptophanase levels. Moreover, changes in fecal serotonin levels might be indirectly associated with energy absorption.},
}

Humans
*Gastrointestinal Microbiome
*Feces/chemistry/microbiology
Cross-Over Studies
Male
*Serotonin/analysis/metabolism
Adult
Female
Young Adult
*Tryptophanase/metabolism/analysis/genetics
Energy Metabolism
*Diet
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics

@article {pmid40487918,
year = {2025},
author = {Boak, EN and Bowen, BP and Louie, KB and Northen, TR and Kroeger, ME},
title = {Bacterial and fungal composition and exometabolites control the development and persistence of soil water repellency.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf084},
pmid = {40487918},
issn = {2730-6151},
abstract = {Soil water repellency (SWR), the reduced affinity of soil for water, is a phenomenon that affects soils globally. With worsening climate change, SWR is expected to increase emphasizing the need to understand the mechanisms driving SWR development and persistence. The importance of the soil microbes in SWR has been postulated for decades, but limited research has been conducted into whole-community interactions and the role of community metabolic activity. To address this gap in knowledge, we investigated the direct effect of microbial community composition, activity, and diversity, as well as their associated metabolites on the development and persistence of SWR by inoculating microcosms containing model soils with 15 different microbial communities and quantified respiration and SWR over time. Six communities that consistently produced either a hydrophobic or hydrophilic phenotype were characterized using metagenomics and metabolomics to determine the impact of microbial and metabolite composition and diversity on SWR. We identified several bacterial genera with significant changes in abundance between SWR phenotypes including Nocardiopsis and Kocuria in hydrophilic and Streptomyces and Cutibacterium in hydrophobic. We discovered that hydrophilic communities were more positively connected when compared to hydrophobic communities, which could be due to an increase in defense mechanism genes. Additionally, we identified specific metabolites associated with hydrophilic and hydrophobic phenotypes including an increase in the osmolyte ectoine in hydrophilic and an increase in plant-derived decomposition products in hydrophobic communities. Finally, our research suggests that fungi, previously thought to cause hydrophobicity, may actually contribute to hydrophilicity through their preferential consumption of hydrophobic compounds.},
}

@article {pmid40487916,
year = {2025},
author = {Okazaki, Y and Nishikawa, Y and Wagatsuma, R and Takeyama, H and Nakano, SI},
title = {Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf086},
pmid = {40487916},
issn = {2730-6151},
abstract = {Characterizing virus-host pairs and the infection state of individual cells is the major technical challenge in microbial ecology. We addressed these challenges using state-of-the-art single-cell genome technology (SAG-gel) combined with extensive metagenomic datasets targeting the bacterial and viral communities in Lake Biwa. From two water layers and two seasons, we obtained 862 single-cell amplified genomes (SAGs), including 176 viral (double-stranded DNA phage) contigs, which identified novel virus-host pairs involving dominant freshwater lineages. The viral infection rate, estimated by mapping the individual SAG's raw reads to viral contigs, showed little variation among samples (12.1%-18.1%) but significant variation in host taxonomy (4.2%-65.3%), with copiotrophs showing higher values than oligotrophs. The high infection rates of copiotrophs were attributed to collective infection by diverse viruses, suggesting weak density-dependent virus-host selection, presumably due to their nonpersistent interactions with viruses resulting from fluctuating abundance. In contrast, the low infection rates of oligotrophs supported the idea that their codominance with viruses is achieved by genomic microdiversification, which diversifies the virus-host specificity, sustained by their large population size and persistent density-dependent fluctuating selection. Notably, we discovered viruses infecting CL500-11, the dominant bacterioplankton lineage in deep freshwater lakes worldwide. These viruses showed extremely high read coverages in cellular and virion metagenomes but were detected in <1% of host cells, suggesting a low infection rate and high burst size. Overall, we revealed highly diverse virus-host interactions within and between host lineages that were overlooked at the metagenomic resolution.},
}

@article {pmid40487915,
year = {2025},
author = {Wu, X and Liu, Y and He, Z and Zhou, X and Liesack, W and Peng, J},
title = {Coevolution and cross-infection patterns between viruses and their host methanogens in paddy soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf088},
pmid = {40487915},
issn = {2730-6151},
abstract = {Methanogens play a critical role in global methane (CH4) emissions from rice paddy ecosystems. Through the integration of metagenomic analysis and meta-analysis, we constructed a CRISPR spacer database comprising 14 475 spacers derived from 351 methanogenic genomes. This enabled the identification of viruses targeting key methanogenic families prevalent in rice paddies, including Methanosarcinaceae, Methanotrichaceae, Methanobacteriaceae, Methanocellaceae, and Methanomassiliicoccaceae. We identified 419 virus-host linkages involving 56 methanogenic host species and 189 viruses, spanning the families Straboviridae, Salasmaviridae, Kyanoviridae, Herelleviridae, and Demerecviridae, along with 126 unclassified viral entities. These findings highlight a virome composition that is markedly distinct from those observed in gut environments. Cross-infection patterns were supported by the presence of specific viruses predicted to infect multiple closely related methanogenic species. Evidence for potential virus-host coevolution was observed in 24 viruses encoding anti-CRISPR proteins, likely facilitating evasion of host CRISPR-mediated immunity. Collectively, this study reveals a complex and dynamic network of virus-host interactions shaping methanogen communities in rice paddy ecosystems.},
}

@article {pmid40487637,
year = {2025},
author = {Chen, M and Peng, Y and Hu, Y and Kang, Z and Chen, T and Zhang, Y and Chen, X and Li, Q and Yuan, Z and Wu, Y and Xu, H and Zhou, G and Liu, T and Zhou, H and Yuan, C and Huang, W and Zhang, W},
title = {A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {5},
pages = {2511-2528},
pmid = {40487637},
issn = {2211-3835},
abstract = {Metformin has been demonstrated to attenuate hyperglycaemia by modulating the gut microbiota. However, the mechanisms through which the microbiome mediates metformin monotherapy failure (MMF) are unclear. Herein, in a prospective clinical cohort study of newly diagnosed type 2 diabetes mellitus (T2DM) patients treated with metformin monotherapy, metagenomic sequencing of faecal samples revealed that Phocaeicola vulgatus abundance was approximately 12 times higher in nonresponders than in responders. P. vulgatus rapidly hydrolysed taurine-conjugated bile acids, leading to ceramide accumulation and reversing the improvements in glucose intolerance conferred by metformin in high-fat diet-fed mice. Interestingly, C22:0 ceramide bound to mitochondrial fission factor to induce mitochondrial fragmentation and impair hepatic oxidative phosphorylation in P. vulgatus-colonized hyperglycaemic mice, which could be exacerbated by metformin. This work suggests that metformin may be unsuitable for P. vulgatus-rich T2DM patients and that clinicians should be aware of metformin toxicity to mitochondria. Suppressing P. vulgatus growth with cefaclor or improving mitochondrial function using adenosylcobalamin may represent simple, safe, effective therapeutic strategies for addressing MMF.},
}

@article {pmid40487313,
year = {2025},
author = {Wei, H and Thammasit, P and Amsri, A and Pruksaphon, K and Deng, F and Nosanchuk, JD and Youngchim, S},
title = {An overview of rapid non-culture-based techniques in various clinical specimens for the laboratory diagnosis of Talaromyces marneffei.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591429},
pmid = {40487313},
issn = {2235-2988},
mesh = {*Talaromyces/isolation & purification/genetics ; Humans ; *Mycoses/diagnosis/microbiology ; Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Talaromyces marneffei (T. marneffei) is a temperature-dependent biphasic deep opportunistic infectious fungus that primarily affects individuals with advanced HIV disease and other immunocompromised populations. Traditional diagnostic methods rely on fungal culture, but this process, although sensitive, is time-consuming and susceptible to contamination. Therefore, non-culture techniques serve as important complementary and alternative methods for diagnosing talaromycosis. They enable faster and more convenient pathogen identification, improving diagnostic efficiency and facilitating earlier initiation of treatment. Patients with talaromycosis can present with a wide range of clinical symptoms, and different clinical samples require different detection techniques. Blood samples are the most versatile, as laboratory technologists can utilize a wide range of diagnostic methods to obtain accurate results, particularly in the setting of a suspected disseminated infection. In contrast, urine diagnosis relies primarily on immunological methods that detect an antigen abundantly secreted during an infection. Moreover, for invasive samples like bronchoalveolar lavage fluid or cerebrospinal fluid, metagenomic next-generation sequencing is likely to be of significant importance for the early diagnosis due to its high sensitivity and specificity, though this approach is not yet standardized or widely available. For tissue samples, histopathology for light microscopy analysis is a well-established basic method, but it relies on experienced laboratory personnel, is time-consuming, and the histological appearance of other fungi can overlap with T. marneffei. Recent advances in rapid non-culture-based methods diagnostics underscore the growing importance of these tools in clinical settings, particularly for resource-limited areas where culture facilities are inadequate or unavailable. These methods improve diagnostic turnaround time and may lead to better clinical outcomes, especially for vulnerable patient populations. This review emphasizes the need for ongoing development and validation of non-culture diagnostics, with a focus on standardization, accessibility, and integration of rapid molecular and immunological tools to improve early detection and patient management in endemic regions.},
}

*Talaromyces/isolation & purification/genetics
Humans
*Mycoses/diagnosis/microbiology
Sensitivity and Specificity
Molecular Diagnostic Techniques/methods
High-Throughput Nucleotide Sequencing

@article {pmid40487152,
year = {2025},
author = {Leys, SP and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Erpenbeck, D and Niu, H and McKenna, V and , and , and , and , and , },
title = {The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {222},
pmid = {40487152},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Spongilla lacustris (freshwater sponge; Porifera; Demospongiae; Spongillida; Spongillidae). The genome sequence is 248.7 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 28.04 kilobases in length. A 14.6-megabase genome assembly of the green algal cobiont Choricystis sp. (Chlorophyta; Trebouxiophyceae) was scaffolded into 16 chromosomal pseudomolecules. Additionally, three bacterial metagenome bins were recovered from the same sample. Gene annotation of this assembly at Ensembl identified 30,435 protein coding genes.},
}

@article {pmid40486693,
year = {2025},
author = {Witonsky, JI and Elhawary, JR and Eng, C and Oh, SS and Salazar, S and Contreras, MG and Medina, V and Secor, EA and Zhang, P and Everman, JL and Fairbanks-Mahnke, A and Pruesse, E and Sajuthi, SP and Chang, CH and Guerrero, TR and Fuentes, KC and Lopez, N and Montañez-López, CA and Morales, EV and Morales, NV and Otero, RA and Rivera, RC and Rodriguez, L and Vazquez, G and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Morin, A and Nieves, NA and Rios, C and Serrano, G and Williams, BJM and Ziv, E and Moore, CM and Sheppard, D and Burchard, EG and Seibold, MA and Rodríguez-Santana, JR},
title = {The PRIMERO birth cohort: Design and baseline characteristics.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {4},
number = {3},
pages = {100470},
pmid = {40486693},
issn = {2772-8293},
abstract = {BACKGROUND: Although early-life respiratory illnesses (RIs) are linked to childhood asthma, it is unclear whether children are predisposed to both conditions or if RIs induce alterations that lead to asthma. Puerto Rican children, who bear a disproportionate burden of early-life RIs and asthma, are an important population for studying this relationship.

OBJECTIVE: We sought to describe the design and baseline characteristics of the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes (PRIMERO) birth cohort.

METHODS: PRIMERO is designed to examine the role of respiratory viruses on the development of RIs and asthma. Pregnant women were recruited at Hospital Interamericano de Medicina Avanzada-San Pablo in Caguas, Puerto Rico. Questionnaires at birth and annual follow-ups gather clinical, social, and environmental data. Collected samples include postterm maternal blood; infant cord blood; the child's blood at year 2; and the child's nasal airway epithelium at birth, during RIs over the first 2 years, and annually until age 5.

RESULTS: We enrolled 2,100 mother-child dyads into the PRIMERO study between February 2020 and June 2023, representing 59% of births at Hospital Interamericano de Medicina Avanzada. As of April 29, 2024, 2,069 participants remain active, with high rates of biospecimen collection and annual visit participation. Illness surveillance detected 6,076 RIs, with 38.4% involving the lower respiratory tract.

CONCLUSION: The PRIMERO birth cohort study, with its comprehensive data on viral exposures, respiratory outcomes, and airway molecular phenotypes in a high-risk population of Puerto Rican children, is uniquely positioned to address long-standing questions about the early-life determinants and mechanisms underlying virus-related asthma development.},
}

@article {pmid40486234,
year = {2025},
author = {Shilov, S and Korotetskiy, I and Kuznetsova, T and Zubenko, N and Ivanova, L and Solodova, E and Tugeyeva, A and Kaziyev, A and Korotetskaya, N and Izmailov, T},
title = {The chicken gut resistome data from different regions of Kazakhstan.},
journal = {Data in brief},
volume = {60},
number = {},
pages = {111608},
pmid = {40486234},
issn = {2352-3409},
abstract = {Antibiotic resistance (AR) is a serious global health problem affecting both human medicine and animal agriculture. The poultry farming, especially industrial poultry, antibiotics are widely used for disease prevention and growth promotion, leading to the accumulation and dissemination of antibiotic resistance genes (ARGs) within the intestinal microbiomes of birds. Poultry, which often have close contact with humans, can serve as reservoirs for resistant microorganisms, posing potential public health risks. Determination of avian intestinal resistomes through metagenomic sequencing and bioinformatics analysis enables the identification of diversity and transmission dynamics of ARGs, and to evaluate the influence of environmental factors and conditions of poultry on resistance gene distribution. The article presents data of resistome analysis of gut microbiota in populations of chickens from different regions of Kazakhstan. The data obtained will allow to develop a strategy to reduce the spread of antibiotic-resistant pathogens and improve safety in poultry farming, as well as to predict the risk of transmission of resistant microorganisms between animals and humans.},
}

@article {pmid40485833,
year = {2025},
author = {Sibalekile, A and Araya, T and Castillo Hernandez, J and Kotzé, E},
title = {Glyphosate-microbial interactions: metagenomic insights and future directions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570235},
pmid = {40485833},
issn = {1664-302X},
abstract = {Glyphosate [N-(phosphonomethyl) glycine] is the most widely used systematic non-selective herbicide worldwide. However, there is increasing concern about its potential impacts on soil microbial communities, which play crucial roles in maintaining soil functions, plant health, and crop productivity. While glyphosate can be inactivated in soil through strong sorption, desorption remains a significant challenge as glyphosate residues and metabolites can exert toxicity effects on agroecosystems, particularly by altering microbial diversity and functionality. This review synthesizes current knowledge on glyphosate's behavior in soils and advancements in metagenomics approaches (including their limitations) to better understand the complex interactions between glyphosate and microbial communities in genetically modified (GM) cropping systems. Glyphosate has demonstrated antimicrobial properties, inhibiting the growth of various bacteria and fungi. Conversely, other studies suggest that glyphosate may enhance microbial richness, promoting the proliferation of potential glyphosate degraders (e.g., Bacillus, Stenetrophomonas, Pseudomonas, Sphingomonas, and Phenylobacterium) and N2 fixing bacteria (e.g., Bradyrhizobium, Rhizobium, and Devosia) in the bulk soil and rhizosphere of GM crops. These contrasting findings are influenced by factors such as soil types, glyphosate rates, and crop varieties. Moreover, the review highlights that methodological discrepancies, including variations in next-generation sequencing (NGS) platforms and reference databases, contribute significantly to inconsistencies in the literature. These differences stem from varying levels of accuracy or annotation standards in the databases and NGS technologies used. To address these challenges, this study underscores the need for standardized molecular and bioinformatics approaches. Integrating advanced long-read sequencing technologies, such as Oxford Nanopore and PacBio, with compatible reference databases could provide more accurate and consistent analyses of microbial community composition at finer taxonomic levels. Such advancements could improve our understanding of how glyphosate influences the balance between pathogenic microorganisms and plant-growth-promoting microbes in GM cropping systems, ultimately informing sustainable agricultural practices.},
}

@article {pmid40484974,
year = {2025},
author = {Smith, ME and Kavamura, VN and Hughes, D and Mendes, R and Lund, G and Clark, I and Mauchline, TH},
title = {Uncovering functional deterioration in the rhizosphere microbiome associated with post-green revolution wheat cultivars.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {64},
pmid = {40484974},
issn = {2524-6372},
support = {FR2021-02017//Svenska Forskningsrådet Formas/ ; BB/N016246/1//Bilateral BBSRC-Embrapa gran/ ; BBS/E/C/00005196//Bilateral BBSRC-Embrapa grant/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; },
abstract = {BACKGROUND: During the Green Revolution, one of the biggest developments of wheat domestication was the development of new cultivars that respond well to fertilisers and produce higher yields on shorter stems to prevent lodging. Consequently, this change has also impacted the wheat microbiome, often resulting in reduced selection of taxa and a loss of network complexity in the rhizospheres of modern cultivars. Given the importance of rhizosphere microbiomes for plant health and performance, it is imperative that we understand if and how these changes have affected their function. Here, we use shotgun metagenomics to classify the functional potential of prokaryote communities from the rhizospheres of pre-green revolution (heritage) cultivars to compare the impact of modern wheat breeding on rhizosphere microbiome functions.

RESULTS: We found distinct taxonomic and functional differences between heritage and modern wheat rhizosphere communities and identified that modern wheat microbiomes were less distinct from the communities in the surrounding soil. Of the 113 functional genes that were differentially abundant between heritage and modern cultivars, 95% were depleted in modern cultivars and 65% of differentially abundant reads best mapped to genes involved in staurosporine biosynthesis (antibiotic product), plant cell wall degradation (microbial mediation of plant root architecture, overwintering energy source for microbes) and sphingolipid metabolism (signal bioactive molecules).

CONCLUSIONS: Overall, our findings indicate that green revolution breeding has developed wheat cultivars with a reduced rhizosphere effect. The consequences of this are likely detrimental to the development of microbiome-assisted agriculture which will require a strong rhizosphere selective environment for the establishment of a beneficial plant root microbiome. We believe our results are of striking importance and highlight that implementation of microbiome facilitated agriculture will benefit from deliberately incorporating the development of beneficial plant-microbiome interactions, alongside traditional yield traits, to advance sustainable wheat production.},
}

@article {pmid40484531,
year = {2025},
author = {Hu, Q and Cheng, S and Qian, D and Wang, Y and Xie, G and Peng, Q},
title = {Identification of core microbial communities and their influence on flavor-oriented traditional fermented sour cucumbers.},
journal = {Food microbiology},
volume = {131},
number = {},
pages = {104810},
doi = {10.1016/j.fm.2025.104810},
pmid = {40484531},
issn = {1095-9998},
mesh = {Volatile Organic Compounds/metabolism/analysis ; Fermentation ; *Cucumis sativus/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Taste ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Flavoring Agents/metabolism ; Humans ; *Microbial Consortia ; Food Microbiology ; *Microbiota ; },
abstract = {Sour cucumber is a traditional fermented vegetable with global popularity, yet its fermentation process often leads to inconsistencies in quality and flavor due to the reliance on natural fermentation. This study identifies 12 core volatile organic compounds (VOCs) contributing to its unique flavor and investigates the key microbial species involved in the fermentation process. Using a synthetic microbial consortium constructed from core microbial species, we successfully replicated the flavor profile of naturally fermented sour cucumbers while enhancing safety by reducing nitrite levels. This approach also reduced bitterness and astringency, while improving sourness and umami, providing a robust framework for standardized production of high-quality fermented vegetables. These findings offer practical solutions for improving flavor quality and ensuring the safety of fermented foods.},
}

Volatile Organic Compounds/metabolism/analysis
Fermentation
*Cucumis sativus/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Taste
*Bacteria/metabolism/classification/genetics/isolation & purification
*Flavoring Agents/metabolism
Humans
*Microbial Consortia
Food Microbiology
*Microbiota

@article {pmid40484397,
year = {2025},
author = {Adachi, A and Dominguez, JJ and Utami, YD and Fuji, M and Kirita, S and Imai, S and Murakami, T and Hongoh, Y and Shinjo, R and Kamiya, T and Fujiwara, T and Minamisawa, K and Ono, N and Kanaya, S and Saijo, Y},
title = {Field Dynamics of the Root Endosphere Microbiome Assembly in Paddy Rice Cultivated under No Fertilizer Input.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf045},
pmid = {40484397},
issn = {1471-9053},
abstract = {Plants accommodate diverse microbial communities, termed the microbiome, which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and the underlying mechanisms driving them, particularly in crops adapting to the field conditions, are not well understood. Here, we investigate the root endosphere microbiome of rice (Oryza sativa ssp. japonica) across four consecutive cultivation seasons in a high-yield, non-fertilized, and pesticide-free paddy field, compared to a neighboring fertilized and pesticide-treated field. Using 16S rRNA amplicon and metagenome sequencing, we analyzed three Japonica cultivars-Nipponbare, Hinohikari, and Kinmaze. Our findings reveal that the root endosphere microbiomes diverge based on fertilization regime and plant developmental stages, while the effects of cultivar variation are less significant. Machine learning model and metagenomic analysis of nitrogenase (nif) genes suggest enhanced nitrogen fixation activity in the non-fertilized field-grown roots, highlighting a potential role of diazotrophic, iron-reducing bacteria Telmatospirillum. These results provide valuable insights into the assembly of the rice root microbiome in nutrient-poor soil, which can aid in managing microbial homeostasis for sustainable agriculture.},
}

@article {pmid40483623,
year = {2025},
author = {Chi, Y and Luo, M and Ding, C},
title = {The role of microbiota in fish spoilage: biochemical mechanisms and innovative preservation strategies.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {7},
pages = {89},
pmid = {40483623},
issn = {1572-9699},
support = {202411049301XJ//National College Student Innovation and Entrepreneurship Training Program Funding Project/ ; },
mesh = {*Fishes/microbiology ; *Microbiota ; Animals ; *Food Preservation/methods ; *Food Microbiology ; *Seafood/microbiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Fish spoilage is a microbially-mediated biochemical process resulting in quality deterioration, economic losses, and food safety risks. Studies have indicated that spoilage microbiota are phylogenetically diverse, with Gram-negative bacteria (Pseudomonas, Shewanella, Photobacterium) representing primary spoilage organisms, and Gram-positive bacteria (Lactobacillus, Brochothrix) causing spoilage only under specific conditions. Microorganisms cause spoilage through the utilization of three main metabolic processes: (i) proteolytic degradation of muscle proteins, (ii) lipolytic breakdown of triglycerides, and (iii) production of volatile bioactive organic compounds and biogenic amines. By combining high-throughput sequencing with metabolomics, researchers have been uncovering strain-specific metabolic networks and how they are influenced by environmental factors such as temperature, pH, and packaging. This review systematically examines: (1) patterns of taxonomic succession in spoilage microbiota, (2) enzymatic and biochemical pathways involved in spoilage, and (3) innovative preservation strategies targeting spoilage consortia. Emerging technologies, such as bacteriocin-mediated biopreservation, phage therapy, and modified atmosphere packaging, show considerable promise in inhibiting spoilage organisms while maintaining the sensory qualities of the fish. Microbiome-directed interventions combined with predictive modeling and precision storage systems also represent a novel approach to fish preservation. There is a critical need to integrate traditional microbiology with the use of multi-omic technologies for the development of sustainable, microbiota-based preservation strategies that address global seafood security challenges.},
}

*Fishes/microbiology
*Microbiota
Animals
*Food Preservation/methods
*Food Microbiology
*Seafood/microbiology
*Bacteria/metabolism/classification/genetics

@article {pmid40483486,
year = {2025},
author = {Bergholm, J and Tessema, TS and Blomström, AL and Berg, M},
title = {Metagenomic insights into the complex viral composition of the enteric RNA virome in healthy and diarrheic calves from Ethiopia.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {188},
pmid = {40483486},
issn = {1743-422X},
support = {2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; 2021-04343//Vetenskapsrådet/ ; },
mesh = {Animals ; Cattle ; Ethiopia/epidemiology ; *Diarrhea/veterinary/virology ; *Virome ; Metagenomics ; *Cattle Diseases/virology ; Feces/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Genome, Viral ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Viruses and the virome have received increased attention in the context of calf diarrhea and with the advancement of high-throughput sequencing the detection and discovery of viruses has been improved. Calf diarrhea, being the main contributor to calf morbidity and mortality, is a major issue within the livestock sector in Ethiopia. However, studies on viruses and the virome in calves is lacking in the country. Therefore, we utilized viral metagenomics to investigate the diversity of RNA viruses in healthy and diarrheic calves from central Ethiopia.

METHODS: Fecal material from 47 calves were collected, pooled, and sequenced using Illumina. Following sequencing, the virome composition and individual viral sequences were investigated using bioinformatic analysis.

RESULTS: The metagenomic analysis revealed the presence of several RNA viruses, including rotavirus and bovine coronavirus, known causative agents in calf diarrhea. In addition, several enteric RNA viruses that have not been detected in cattle in Ethiopia previously, such as norovirus, nebovirus, astrovirus, torovirus, kobuvirus, enterovirus, boosepivirus and hunnivirus were identified. Furthermore, a highly divergent viral sequence, which we gave the working name suluvirus, was found. Suluvirus showed a similar genome structure to viruses within the Picornaviridae family and phylogenetic analysis showed that it clusters with crohiviruses. However, due to its very divergent amino acid sequence, we propose that suluvirus represent either a new genus within the Picornaviridae or a new species within crohiviruses.

CONCLUSIONS: To our knowledge, this is the first characterization of the RNA virome in Ethiopian cattle and the study revealed multiple RNA viruses circulating in both diarrheic and healthy calves, as well as a putative novel virus, suluvirus. Our study highlights that viral metagenomics is a powerful tool in understanding the divergence of viruses and their possible association to calf diarrhea, enabling characterization of known viruses as well as discovery of novel viruses.},
}

Animals
Cattle
Ethiopia/epidemiology
*Diarrhea/veterinary/virology
*Virome
Metagenomics
*Cattle Diseases/virology
Feces/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Genome, Viral
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40483351,
year = {2025},
author = {Koblitz, J and Reimer, LC and Pukall, R and Overmann, J},
title = {Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {897},
pmid = {40483351},
issn = {2399-3642},
support = {K280/2019//Leibniz-Gemeinschaft (Leibniz Association)/ ; },
mesh = {*Machine Learning ; *Bacteria/genetics ; Phenotype ; Software ; Computational Biology/methods ; },
abstract = {Predicting prokaryotic phenotypes-observable traits that govern functionality, adaptability, and interactions-holds significant potential for fields such as biotechnology, environmental sciences, and evolutionary biology. In this study, we leverage machine learning to explore the relationship between prokaryotic genotypes and phenotypes. Utilizing the highly standardized datasets in the BacDive database, we model eight physiological properties based on protein family inventories, evaluate model performance using multiple metrics, and examine the biological implications of our predictions. The high confidence values achieved underscore the importance of data quality and quantity for reliably inferring bacterial phenotypes. Our approach generates 50,396 completely new datapoints for 15,938 strains, now openly available in the BacDive database, thereby enriching existing phenotypic resources and enabling further research. The open-source software we provide can be readily applied to other datasets, such as those from metagenomic studies, and to various applications, including assessing the potential of soil bacteria for bioremediation.},
}

*Machine Learning
*Bacteria/genetics
Phenotype
Software
Computational Biology/methods

@article {pmid40483244,
year = {2025},
author = {Duong, JT and Hayden, HS and Verster, AJ and Pope, CE and Miller, C and Kelsi Penewit, and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Kelly, A and Schwarzenberg, SJ and Freedman, SD and Hoffman, LR},
title = {Fecal microbiota changes in people with cystic fibrosis after 6 months of elexacaftor/tezacaftor/ivacaftor: Findings from the promise study.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.05.006},
pmid = {40483244},
issn = {1873-5010},
abstract = {BACKGROUND: People with cystic fibrosis (PwCF) often have fecal dysbioses relative to those without CF, characterized by increased pro-inflammatory microbiota and gastrointestinal (GI) inflammation as measured by fecal calprotectin, suggesting that inflammation contributes to CF GI disease. The multicenter observational PROMISE study (NCT04038047) found that calprotectin decreased in PwCF treated with elexacaftor/tezacaftor/ivacaftor (ETI). To better understand the dynamics between fecal dysbiosis and GI inflammation, we characterized the microbiomes of fecal samples from PROMISE and the relationships with calprotectin before, 1-month post, and 6-months post ETI.

METHODS: Fecal microbiota from participants ≥12 y/o were determined by shotgun metagenomic sequencing with random forest modeling and multivariate linear regression analysis to define relationships between microbiota, calprotectin, and deltaF508 genotype before and after ETI.

RESULTS: We analyzed 345 samples from 124 participants. At baseline, we observed community-level differences in the fecal microbiota among participants with abnormal compared to normal calprotectin. With ETI, the relative abundances of 7 bacterial species - Escherichia coli, Staphylococcus aureus, Clostridium scindens, Enterocloster clostridioformis, Clostridium butyricum, Anaeroglobus geminatus, and Ruminococcus gnavus - decreased significantly, correlating with calprotectin decrease. We detected community-level differences in the fecal microbiota based on CFTR genotype and a distinct pattern of microbiota change in F508del homozygous compared to heterozygous participants after ETI.

CONCLUSIONS: We identified 7 species for which fecal abundances decreased with ETI and correlated with calprotectin decrease, supporting a close relationship between fecal microbiota and inflammation in PwCF. Future work will define these relationships with metabolites and GI symptoms during long-term ETI therapy.},
}

@article {pmid40482930,
year = {2025},
author = {Adiningrat, A and Maulana, I and Fadhlurrahman, AG and Yumoto, H},
title = {Probiotic bacteria from asymptomatic necrotic tooth can regulate the microbiome homeostasis.},
journal = {Microbial pathogenesis},
volume = {206},
number = {},
pages = {107791},
doi = {10.1016/j.micpath.2025.107791},
pmid = {40482930},
issn = {1096-1208},
abstract = {OBJECTIVE: This study was performed to identify and isolate the dominant bacteria from a chronic asymptomatic necrotic root canal and investigate in vitro its potential postbiotics effect at the biofilm maturation maintaining root canal microbiome homeostasis.

METHODS: For bacterial identification of an in vivo root canal sample, metagenomic analysis was applied, followed by single colony isolation and PCR analysis. Cell free supernatant (CFS) was then cultivated through serial L paracasei culture procedures prior antibiofilm analysis. Antibiofilm effects of the CFS product were evaluated using in vitro biofilm analysis against S. mutans and E. faecalis. Biofilm mass analysis was measured by using colorimetric approach with cresyl-vast violet staining, morphological appearance was observed using both phase-contrast and scanning electron microscope (SEM). Shapiro-Wilk analysis was applied for normality test, followed by the ANOVA to compare multiple groups or a student t-test for independent two groups mean comparisons.

RESULTS: The isolated root canal bacteria produced biofilm mass that was similar to the Enterococcus faecalis control pathogenic biofilm. From the morphological analysis suggested that population of the isolated bacteria were predominantly occupied by rod-shaped rather than cocci-shaped inhabitants. Further metagenomic analysis indicated that the isolated dominant bacteria in the mixed culture were mainly identified as probiotic bacteria, Lacticaseibacillus paracasei. Moreover, the functional analysis revealed that the L. paracasei cell free supernatant product (CFS) exhibited a promising positive effect in biofilm structure integrity disturbances of S. mutans and E. faecalis.

CONCLUSIONS: The isolated Lacticaseibacillus paracasei from the root canal of a chronic asymptomatic necrotic tooth, produces potential postbiotic products that demonstrated a disruptive ability against Streptococcus mutans and Enterococcus faecalis biofilm integrity.},
}

@article {pmid40482668,
year = {2025},
author = {Garcia-Mauriño, C and Shao, Y and Miltz, A and Lawley, TD and Rodger, A and Field, N},
title = {Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101072},
doi = {10.1016/j.lanmic.2024.101072},
pmid = {40482668},
issn = {2666-5247},
abstract = {BACKGROUND: Early-life gut microbiota affects immune system development, including the lung immune response (gut-lung axis). We aimed to investigate whether gut microbiota composition in neonates in the first week of life is associated with hospital admissions for viral lower respiratory tract infections (vLRTIs).

METHODS: The Baby Biome Study (BBS) is a prospective birth cohort, which enrolled mother-baby pairs between Jan 1, 2016, and Dec 31, 2017, at three UK hospitals. In the present study, we only included BBS babies with a sequenced first-week stool sample and successful data linkage. Stool was collected in the first week of life for shotgun-metagenomic sequencing. We examined the following microbiota features: alpha diversity (Chao1, Shannon, and Simpson indices) and community structures (cluster-partitioning against medoids method). The participants were followed up through linkage to the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database to determine vLRTI hospital admission incidence in the first 2 years of life. We used Poisson mixed-effects models for univariable and multivariable analyses to evaluate the association between microbiota features and vLRTI hospital admission incidence, adjusting for confounders identified through direct acyclic graphs.

FINDINGS: 3305 (95%) of the 3476 BBS-enrolled babies for whom consent to data linkage was obtained were included in the present study. 1111 (34%) babies had a first-week sequenced stool sample, of whom 1082 (97%; 564 born vaginally and 518 born by caesarean section) were successfully linked to HES-APC, and had median follow-up of 2·0 years (IQR 1·4-2·9). Most babies were born at term (996 [92%] ≥37 weeks gestational age and 1070 [99%] >35 weeks gestational age) and healthy (1050 [97%] had no comorbidities), and 520 (48%) were female and 562 (52%) were male. Higher first-week gut microbiota alpha diversity was associated with reduced rates of vLRTI hospital admission (Chao1 Index adjusted hazard ratio [HR] 0·92 [95% CI 0·85-0·99]; Shannon Index adjusted HR 0·57 [0·33-0·98]; and Simpson Index adjusted HR 0·36 [0·11-1·20]). Three microbiota clusters were identified. Cluster 1 had a mixed composition and cluster 2 was dominated by Bifidobacterium breve, with both clusters observed in babies born vaginally and by caesarean section. Cluster 3 was found only in vaginally born babies and was dominated by Bifidobacterium longum. Having cluster 1 (mixed) or cluster 2 (B breve dominated) was independently associated with increased rates of vLRTI hospital admission compared with cluster 3 (B longum dominated; cluster 1 [mixed] 3·05 [1·25-7·41] and cluster 2 [B breve dominated] 2·80 [1·06-7·44]).

INTERPRETATION: We report observational evidence that first-week gut microbiota differences are associated with clinically severe vLRTI in young children. This study identified bacterial species that could be of interest for vLRTI prevention. This finding has important implications for the design of future research and intervention strategies.

FUNDING: The Wellcome Trust and Wellcome Sanger Institute core funding.},
}

@article {pmid40482531,
year = {2025},
author = {Yan, R and Manjunatha, V and Thomas, A and Shankar, V and Lumpkins, B and Hoerr, FJ and Greene, A and Jiang, X},
title = {Comparative effects of vegetarian diet and rendered animal by-product on the chicken gut health.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105360},
doi = {10.1016/j.psj.2025.105360},
pmid = {40482531},
issn = {1525-3171},
abstract = {Rendered animal proteins and fats can provide vital nutrients for poultry at affordable prices. With growing interest in reintroducing rendered animal by-products into poultry diets, this study investigated the effects of replacing a portion of soybean meal and vegetable fat with rendered animal proteins and fats in a standard vegetarian chicken diet. The study focused on the changes in gut and liver histopathology, and gut microbiome composition and functions. Five diet treatments were formulated to be isocaloric and isonitrogenous and balanced for amino acids, including a standard vegetarian control diet and four diets containing rendered animal by-products. A total of 15 pens with 50 chickens each were assigned one of the five diets from hatch to 42 days of age, with three replicate pens per treatment. On days 28 and 42, six birds were randomly selected from two pens per treatment and humanely euthanized by cervical dislocation. Cecal samples were collected for microbial enumeration and DNA extraction, while gut and liver histopathology analyses were conducted on day 42. Enumeration of Clostridium perfringens was performed under anaerobic conditions using selective media and metagenomic sequencing was used to assess taxonomic and functional profiles of the microbiome. Statistical analysis included data transformation, permutational multivariate analysis of variance, and differential abundance testing. No significant differences were observed between the vegetarian control and rendered animal by-product diets in gut or liver histopathology, C. perfringens levels, or microbiome composition, indicating that inclusion of animal by-products did not significantly affect broiler intestinal health or microbial functions over a 42-day period. These findings suggest that partially replacing soybean meal and vegetable fat with rendered animal by-products can be a safe and cost-effective alternative to plant-based ingredients in poultry diets.},
}

@article {pmid40482428,
year = {2025},
author = {Roy, S and King, GM and Hernández, M},
title = {Classification of MAGs associated with trace gas metabolism in volcanic soils named following SeqCode rules.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {4},
pages = {126622},
doi = {10.1016/j.syapm.2025.126622},
pmid = {40482428},
issn = {1618-0984},
abstract = {Trace gas metabolism is important for nutrient flow in all ecosystems, particularly volcanic ecosystems. Microbes in volcanic ecosystems are among the early colonisers and can play key roles in ecological succession. Here, we describe the taxonomic and functional characteristics of two new metagenome-assembled genomes (MAGs), one belonging to Bacteria (MAG_1957-2.1) and one to Archaea (MAG_C2-3), retrieved from soils in volcanoes located in Chile (Llaima) and the USA (Kilauea), respectively. MAG_1957-2.1 has a genome size of 6.36Mb with 96.21 % completeness. MAG_C2-3 has a genome size of 3.02Mb with 97.57 % completeness. Phylogenetic analyses of the bacterial MAGs placed MAG_1957-2.1 in the class Ktedonobacteria, while the archaeal MAG_C2-3 was placed in the class Nitrososphaeria. Functional characterisation for potential trace gas metabolism showed that MAG_1957-2.1 contains a coxL gene encoding the large subunit of form I carbon monoxide dehydrogenase (CoxL), which is associated with the oxidation of carbon monoxide (CO). It also contains the form I cox gene cluster with a coxMSL arrangement. On the other hand, MAG_C2-3 contains gene subunit A (amoA) as well as subunit B (amoB), which encode for ammonia monooxygenase, the enzyme that catalyses the oxidation of ammonia. Based on the sequence characteristics and phylogenomic analyses we propose the names Paraktedonobacter carboxidivorans sp. nov for MAG_1957-2.1 and Nitrososphaera maunauluensis sp. nov for MAG_C2-3. The names are proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}

@article {pmid40482427,
year = {2025},
author = {Mao, YL and Tan, S and Wang, BB and Yang, XY and Hou, J and Cui, HL},
title = {Halosimplex amylolyticum sp. nov., Halosimplex halobium sp. nov., Halosimplex marinum sp. nov., Halosimplex rarum sp. nov., Halovenus amylolytica sp. nov., Halovenus halobia sp. nov., and Halovenus marina sp. nov., halophilic archaea isolated from a marine tidal flat, a marine solar saltern, three coarse sea salts, and two saline lakes.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {4},
pages = {126626},
doi = {10.1016/j.syapm.2025.126626},
pmid = {40482427},
issn = {1618-0984},
abstract = {Seven novel halophilic archaeal strains DYHT-AS-1[T], GDY60[T], TS25[T], XH63[T], SHR40[T], SYNS179[T], and ZY30[T] were isolated from tidal flat, saline lakes, marine solar saltern and coarse sea salts from different regions of China. Metagenomic and amplicon analyses indicated that the abundance of these seven strains in respective habitats was low. Phylogenetic and comparative genomic analyses indicated that strains DYHT-AS-1[T], GDY60[T], TS25[T], and XH63[T] formed a tight cluster with Halosimplex species, exhibiting high 16S rRNA gene sequence similarity (90.4-99.4 %). The ANI, dDDH, and AAI values among these four strains and current Halosimplex species were 80.8-92.3 %, 24.5-53.3 %, and 77.8-91.5 %, respectively. Strains SHR40[T], SYNS179[T], and ZY30[T] were related to Halovenus species, with 16S rRNA gene sequence similarities ranging from 88.8 % to 98.4 %. The ANI, dDDH, and AAI values among these three strains and current Halovenus species were 69.9-77.8 %, 19.4-21.5 %, and 62.1-78.1 %, respectively. These values are significantly lower than the thresholds for species demarcation. The optimal growth conditions for these seven strains in terms of NaCl, MgCl2, temperature, and pH were 3.1-3.4 M, 0.05-0.5 M, 35-40 °C, and 6.5-7.5, respectively. According to phenotypic differences in nutrition, biochemical activity, and antibiotic sensitivity, these seven strains can be distinguished from their related species. Based on the above results, strains DYHT-AS-1[T], GDY60[T], TS25[T], and XH63[T] represent four new species of the genus Halosimplex, and strains SHR40[T], SYNS179[T], and ZY30[T] represent three novel species of the genus Halovenus.},
}

@article {pmid40482059,
year = {2025},
author = {Rendina, M and Turnbaugh, PJ and Bradley, PH},
title = {Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf131},
pmid = {40482059},
issn = {2160-1836},
abstract = {Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We conducted a systematic search for all known human proteins with gut microbial homologs. Because gene fusion and fission can obscure homology detection, we built a pipeline to identify not only full-length homologs, but also cases where microbial homologs were split across multiple adjacent genes in the same neighborhood or operon ("split homologs"). We found that human proteins with full-length gut microbial homologs disproportionately participate in xenobiotic metabolism. While this included many different enzyme classes, short-chain and aldo-keto reductases were the most frequently detected, especially in prevalent gut microbes, while cytochrome P450 homologs were largely restricted to lower-prevalence facultative anaerobes. In contrast, human proteins with split homologs tended to play roles in central metabolism, especially of nucleobase-containing compounds. We identify twelve specific drugs that gut microbial split homologs may metabolize; two of these, 6-mercaptopurine by xanthine dehydrogenase (XDH) and 5-fluorouracil by dihydropyrimidine dehydrogenase (DPYD), have been recently confirmed in mouse models. This work provides a comprehensive map of homology between the human and gut microbial proteomes, indicates which human xenobiotic enzyme classes are most likely to be shared by gut microorganisms, and finally demonstrates that split homology may be an underappreciated explanation for microbial contributions to drug metabolism.},
}

@article {pmid40481853,
year = {2025},
author = {Chaverri, P and Escudero-Leyva, E and Mora-Rojas, D and Calvo-Obando, A and González, M and Escalante-Campos, E and Mesén-Porras, E and Wicki-Emmenegger, D and Rojas-Gätjens, D and Avey-Arroyo, J and Campos-Hernández, M and Castellón, E and Moreira-Soto, A and Drexler, JF and Chavarría, M},
title = {Differential Microbial Composition and Fiber Degradation in Two Sloth Species (Bradypus variegatus and Choloepus hoffmanni).},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {327},
pmid = {40481853},
issn = {1432-0991},
support = {VI 809-C3-102//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; 57592642//Deutscher Akademischer Austauschdienst/ ; },
mesh = {Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Cellulose/metabolism ; *Dietary Fiber/metabolism ; *Fungi/classification/metabolism/genetics/isolation & purification ; Metagenomics ; },
abstract = {Sloths have the slowest digestion among mammals, requiring 5-20 times longer to digest food than other herbivores, which suggests differences in their gut microbiota, particularly in plant-fiber-degrading microorganisms. Bradypus variegatus has a lower metabolic rate and moves less than Choloepus hoffmanni. However, no comprehensive studies have compared the microbiota (e.g., fungi) of these species. We hypothesized that differences in digestion and metabolism between the two species would be reflected in their microbiota composition and functionality, which we characterized using metagenomics, metabarcoding, and cellulose degradation. Results revealed significant differences in microbiota composition and functionality. Both species are dominated by bacteria; fungi comprised only 0.06-0.5% of metagenomic reads. Neocallimastigomycota, an anaerobic fungus involved in fiber breakdown in other herbivores, was found in low abundance, especially in B. variegatus. Bacterial communities showed subtle differences: C. hoffmanni was dominated by Bacillota and Bacteroidota, while B. variegatus showed higher Actinomycetota. Expected herbivore bacterial taxa (e.g., Fibrobacter and Prevotella) were scarce. Functional analysis showed a low abundance of carbohydrate-active enzymes essential for polysaccharide breakdown. Cellulose degradation assays confirmed that sloths digest only ~ 3-30% of ingested plant material. This research sheds light on the potential multidirectional links between the gut microbiota, metabolism, and digestion.},
}

Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
*Gastrointestinal Microbiome
Cellulose/metabolism
*Dietary Fiber/metabolism
*Fungi/classification/metabolism/genetics/isolation & purification
Metagenomics

@article {pmid40481811,
year = {2025},
author = {Baeza, JA and Rosales, SM},
title = {The complete mitochondrial genome of the 'maze' coral Meandrina meandrites (Scleractinia: Vacatina: Meandrinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/24701394.2025.2504422},
pmid = {40481811},
issn = {2470-1408},
abstract = {The shallow water reef-building 'maze' or 'brain' stony coral Meandrina meandrites (fam. Meandrinidae) is currently experiencing major environmental problems in the Caribbean Sea. In this study, we assembled the mitochondrial genome of M. meandrites to support future conservation of this imperiled coral. We also explored the phylogenetic position of this coral in the Class Scleractinia utilizing the phylogenetic signal provided by translated mitochondrial protein-coding genes (PCGs). A complete mitochondrial genome of M. meandrites, 17,196 bp in length, was assembled using short-reads next-generation sequencing (NGS) sequencing with the target-restricted-assembly pipeline GetOrganelle. The newly assembled mitochondrial genome of M. meandrites encoded 13 PCGs, two ribosomal genes (ribosomal RNA), and two transfer genes (tRNAs). It also contains two relatively long non-coding regions 400 and 1,877 bp long. A group I intron bisected the nad5 PCG. Each of the two tRNAs exhibited a canonical 'cloverleaf' secondary structure. The mitochondrial genome of M. meandrites is identical to that of a conspecific assembled using HiFi PacBio long reads (available in GenBank with accession number OY855917 but without a companion paper) with the exception of four single nucleotide variants. The aforementioned comparison indicates that the mitochondrial genome assembled from a short-read NGS dataset is reliable (complete and accurate). A maximum-likelihood phylomitogenomic analysis based on PCGs (translated) supported the monophyly of the order Scleractinia and placed M. meandrites in a moderately to well-supported clade with Astrangia sp. (family Astrangidae). This newly assembled mitochondrial genome can be used as a reference to support conservation planning, including biomonitoring of this stony coral using environmental DNA.},
}

@article {pmid40481438,
year = {2025},
author = {Babalola, OO and Osuji, IE and Akanmu, AO},
title = {Amplicon-based metagenomic survey of microbes associated with the organic and inorganic rhizosphere soil of Glycine max L.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {40},
pmid = {40481438},
issn = {2730-6844},
}

@article {pmid40481394,
year = {2025},
author = {Lu, X and Chen, J and Miao, S and Xie, Y},
title = {Two cases of Talaromyces marneffei tracheobronchial infection in HIV-negative patients.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {800},
pmid = {40481394},
issn = {1471-2334},
abstract = {OBJECTIVES: In recent years, the incidence and prevalence of Talaromyces marneffei (TM) have been on the rise. This infection predominantly affects immunocompromised or immunodeficient individuals, especially those with acquired immunodeficiency syndrome (AIDS). There has been a notable increase in the incidence of TM and its associated infections. The majority of cases occur within immunocompromised or immunodeficient populations, with a high prevalence among AIDS patients. However, cases are also occasionally detected in HIV - negative individuals. Due to the insidious and slow - growing nature of TM, the disease can be misdiagnosed as other conditions such as tuberculosis, bacterial pneumonia, and lung cancer, particularly in non - endemic regions. Such misdiagnosis significantly impacts the patient’s prognosis.

METHODS: Two HIV-negative patients with TM infection from non - endemic areas were hospitalized with a high suspicion of co-infection with lung cancer and poor symptomatic treatment response. These patients underwent a comprehensive diagnostic workup, including lung puncture biopsy, sputum, blood, pleural, and peritoneal fluid cultures, as well as Metagenomics Next Generation Sequencing (mNGS) analysis. Eventually, both patients were diagnosed with TM tracheobronchial infection.

RESULTS: The patients were treated with voriconazole antifungal therapy, combined with methylprednisolone (used for reducing inflammation, relieving spasms, and treating asthma) and acyclovir (used for treating viral infections). The 49 - year - old patient was cured and discharged from the hospital, while the 79 - year - old male patient’s condition continued to deteriorate, and he ultimately died.

CONCLUSION: It has been determined that TM infection, presenting primarily with respiratory symptoms, is highly susceptible to misdiagnosis in the early stages of the disease. This can lead to treatment delays and a negative impact on the prognosis. It is crucial for medical professionals to be more aware of the possibility of TM infection in non - HIV - infected and non - endemic populations. Collecting respiratory and lung tissue specimens from the infection sites at the earliest possible stage is essential for diagnosing TM infection. Integrating mNGS and mass spectrometry results is crucial for improving the detection and early diagnosis of TM infection, which is of great value for enhancing the efficacy of clinical treatment and the prognosis of patients.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid40480048,
year = {2025},
author = {Yang, J and Liu, J and Gu, H and Song, W and Zhang, H and Wang, J and Yang, P},
title = {Gut microbiota, metabolites, and pulmonary hypertension: Mutual regulation and potential therapies.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128245},
doi = {10.1016/j.micres.2025.128245},
pmid = {40480048},
issn = {1618-0623},
abstract = {Pulmonary hypertension is a progressive condition characterized by increased pulmonary vascular pressure and resistance, ultimately leading to right heart failure and death. Increasing evidence has underscored the importance of the gut-lung axis in the development of respiratory and cardiovascular diseases. Notably, significant changes in the gut microbiota, including altered microbial composition and function, have been observed in pulmonary hypertension. Specifically, microbiota-derived metabolites, including short chain fatty acids, trimethylamine N-oxide, bile acids and tryptophan, play a significant role in the development of pulmonary hypertension. The identification of key bacteria and metabolites, along with recent advances in gut microbiota-targeting technologies and metabolic pathway-targeting inhibitors/agonists, holds potential for developing diagnostic, prognostic, and therapeutic strategies for pulmonary hypertension. Emerging research directions include metagenomic analysis of viruses and fungi, artificial intelligence-aided prediction models, novel metabolites and their associated enzymes, drug-microbiota interactions, selective antibiotics, and advanced microbiota transplantation. This review synthesizes clinical and experimental evidence linking the gut microbiota to pulmonary hypertension, highlighting their interplay as a promising avenue for further investigation and translational applications.},
}

@article {pmid40478725,
year = {2025},
author = {Wang, J and den Bakker, HC and Denes, TG},
title = {A critical review of metagenomic approaches for foodborne pathogen surveillance.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/10408398.2025.2503453},
pmid = {40478725},
issn = {1549-7852},
abstract = {High-throughput sequencing methods (e.g., whole-genome sequencing and metagenomics) are rapidly changing multiple fields of microbiology, including food safety and pathogen surveillance. Current foodborne pathogen surveillance relies heavily on resource-intensive, isolate-based approaches, limiting large-scale implementation. To facilitate more efficient public health responses, innovative technologies that can rapidly and accurately identify diverse foodborne pathogens are essential. Metagenomics-based approaches represent a potential transformative advancement in food safety diagnostics. These techniques enable unbiased and comprehensive analysis of foodborne pathogen genetic material from clinical, food product, processing facility, and environmental samples, positioning metagenomics as a promising strategy for foodborne pathogen surveillance. Here, we explore how metagenomics can be applied to foodborne pathogen surveillance and outbreak detection, focusing on recent advances in both short- and long-read sequencing technologies. The challenges limiting potential applications are reviewed, including the detection and characterization of low-abundance pathogens, the complexity of assembly-based analysis, and the identification of antimicrobial resistance genes. Finally, we discuss a future outlook for metagenomics impacting public health response to foodborne pathogens. It is anticipated that through continuous improvements in sequencing and analytical technologies, that metagenomic approaches to foodborne pathogen detection and characterization will become routine, with the potential to reduce the foodborne illness burden.},
}

@article {pmid40478660,
year = {2025},
author = {Nicolas, M and Lemaitre, C and Vicedomini, R and Frioux, C},
title = {Mapler: A pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf334},
pmid = {40478660},
issn = {1367-4811},
abstract = {SUMMARY: Metagenome assembly seeks to reconstruct the most high-quality genomes from sequencing data of microbial ecosystems. Despite technological advancements that facilitate assembly, such as Hi-Fi long reads, the process remains challenging in complex environmental samples consisting of hundreds to thousands of populations. Mapler is a metagenome assembly and evaluation pipeline with a focus on evaluating the quality of Hi-Fi long read metagenome assemblies. It incorporates several state-of-the-art metrics, as well as novel metrics assessing the diversity that remains uncaptured by the assembly process. Mapler facilitates the comparison of assembly strategies and helps identify methodological bottlenecks that hinder genome reconstruction.

Mapler is open source and publicly available under the AGPL-3.0 licence at https://github.com/Nimauric/Mapler. Source code is implemented in Python and Bash as a Snakemake pipeline. A snapshot of the code is available on Software Heritage at swh:1:snp:df4f5f02e22ebbab285ec14af58d4d88436ee5d6.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40478429,
year = {2025},
author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN},
title = {Hydrological regime and niche partitioning drive fungal community structure and function in arid wetlands sediments of South Africa.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40478429},
issn = {1614-7499},
support = {DST/CON0197/2017//Department of Science and Innovation, South Africa/ ; },
abstract = {Arid wetlands are ecologically significant yet understudied ecosystems shaped by extreme conditions and hydrological variability. However, the structure and ecological functional of fungal communities in these habitats remain poorly understood, especially in southern Africa. This study integrated shotgun metagenomics, FUNGuild functional profiling, and multivariate analyses to examine fungal diversity, functional composition, and environmental drivers in seasonal and permanent arid wetlands of South Africa. Distinct fungal assemblages emerged, primarily shaped by hydrological regimes and ionic stress. Seasonal wetlands were dominated by Mucoromycota (79%), particularly arbuscular mycorrhizal (AM) fungus (Rhizophagus, 62%), while permanent wetlands had higher Ascomycota (54%), with Aspergillus (50%) prevalent in oxygen-limited sediments. Although alpha diversity showed no significant difference, beta diversity confirmed significant mycobiome differentiation. Total dissolved solids (TDS), electrical conductivity (EC), and salinity were key predictors of fungal composition, with TDS the strongest determinant (p < 0.01). Functional guild analysis highlighted niche differentiation, with saprotrophs dominating permanent wetlands (59.7% vs. 21.5%; p < 0.05), while symbiotrophs, particularly AM fungi, were enriched in seasonal wetlands (69.3% vs. 36.1%; p < 0.001). Indicator taxa identified via LefSe (LDA > 3, p < 0.05) and random forest modeling included Rhizophagus, Trichoderma, Fusarium, and Entomophthora in seasonal wetlands, and Aspergillus in permanent wetlands. This study provides the first integrative insight into fungal ecology in South Africa's arid wetlands, demonstrating that hydrological regime shapes fungal structure and function through environmental filtering and niche specialization, with implications for guiding conservation and adaptive management of these fragile ecosystems.},
}

@article {pmid40478395,
year = {2025},
author = {Zhang, T and Liu, Y and Li, J and Yuan, M and Qiao, C and Huang, X and Yang, X and Gao, B and Lou, C and Yang, Y and Cao, Y},
title = {Toad's survivability and soil microbiome alterations impacted via individual abundance.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {40478395},
issn = {2676-8607},
support = {CI2021A04012//CACMS Innovation Fund/ ; ZZ16-YQ-04//Fundamental Research Funds of CACMS/ ; H2023406026//Hebei Natural Science Foundation/ ; QN2024119//Science Research Project of Hebei Education Department/ ; },
abstract = {Artificial breeding is a valid strategy for the reverse of current extinction tendency in wild population of amphibian like toads. Considering public health, an alternative to antibiotics is demanded for ameliorating survival of toads during the culture period. Relying on the cognition of probiotics or antagonistic bacteria, the present work investigated viability and soil microorganism variations induced by distribution characteristic on toads using high-throughput sequencing technology. Comparison and analysis of soil metagenome from clustered and depopulated groups distinguished by toad behavior showed differences of bacterial community composition (e.g., Proteobacteria bacterium TMED72 and Nannocystis exedens) and antibiotic resistance genes involving antibiotic efflux and inactivation (e.g., mdtB and acrF). There were 18 and 10 distribution-typical genes independently enriched in Proteobacteria bacterium TMED72 and bacterium TMED88 of clustered group and Nannocystis exedens of depopulated group. In Nannocystis exedens, one of the distribution-typical genes was annotated as 6-phosphogluconate dehydrogenase acting role on bacterial growth restriction. It implied that, compared with the group emerging rare traces, the reduction of soil bacteria which possess genes retarding bacterial growth putatively impairs competitiveness to pathogenic bacteria and results in poor survivability of toads under clustering behavior. With the co-occurrence of virulence genes, more evidences are needed on the antagonistic bacteria Nannocystis exedens as antibiotic substitute.},
}

@article {pmid40476734,
year = {2025},
author = {Marcos-Zambrano, LJ and Lacruz-Pleguezuelos, B and Aguilar-Aguilar, E and Marcos-Pasero, H and Valdés, A and Loria-Kohen, V and Cifuentes, A and Ramirez de Molina, A and Diaz-Ruiz, A and Pancaldi, V and Carrillo de Santa Pau, E},
title = {Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014325},
doi = {10.1128/msystems.00143-25},
pmid = {40476734},
issn = {2379-5077},
abstract = {UNLABELLED: Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient's microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled "Low-grade symptoms," displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named "High-grade symptoms," exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.

IMPORTANCE: Celiac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6-12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.},
}