@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02318-0},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.

RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.

CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}

@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02309-1},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.

RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.

CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}

@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04678-x},
pmid = {41514203},
issn = {1471-2180},
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}

@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02679-x},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}

@article {pmid41513932,
year = {2026},
author = {Ruiz-Ruiz, S and Piquer-Esteban, S and Pérez-Rocher, B and Pérez-Brocal, V and Arnau, V and Artacho, A and Diaz, W and Jiménez-Hernández, N and Pons, J and Castro, JA and Moya, A},
title = {Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35033-3},
pmid = {41513932},
issn = {2045-2322},
support = {grant number CD15/00067//the Carlos III Health Institute (ISCIII)/ ; project number PMPTA23/00001//the Carlos III Health Institute (ISCIII)/ ; grant Conselleria d´Educació, Cultura, Universitats i Ocupació, cofinançat per la Unió Europea FSE+ 2021-2027, ACIF/2021/341//ACIF fellowship from the Generalitat Valenciana/ ; grant number FPU20/05756//Spanish Ministry of Universities, Vocational Training ans Sports/ ; project number PID2019-105969GB-I00 funding by MICIU/AEI/10.13039/501100011033//the Spanish Ministry of Science and Innovation and Universities/ ; project number SAF2015-65878-R funding by MICIU/AEI/10.13039/501100011033/ and by FEDER Una manera de hacer Europa//the Ministry of Science, Innovation and Universities/ ; project number CIPROM/2021/042//Conselleria d´Educació, Cultura, Universitats i Ocupació/ ; },
}

@article {pmid41513032,
year = {2026},
author = {Liu, S and Liu, Z and Xia, X},
title = {Primary cutaneous blastomycosis in a Chinese-Canadian girl following an insect bite.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108374},
doi = {10.1016/j.ijid.2026.108374},
pmid = {41513032},
issn = {1878-3511},
abstract = {BACKGROUND: Blastomycosis is a disease caused by the dimorphic fungus Blastomyces species. This infection occurs most frequently among individuals residing in the midwestern, southeastern, and south-central United States, as well as in Canadian provinces bordering the Great Lakes and the St. Lawrence Seaway. Sporadic cases have been reported in China, the diagnosis of imported cases remains a significant challenge.

CASE PRESENTATION: We report a diagnostically challenging case of primary cutaneous blastomycosis in a Chinese-Canadian girl, presenting as two nodules of different sizes on her left lower leg and left arm. The patient was initially diagnosed with insect bite dermatitis in Canada, which showed poor response to treatment. Direct microscopic examination revealed large spherical yeast cells, some with broad-based budding, initially interpreted as protothecosis or coccidioidomycosis. However, metagenomic next-generation sequencing (mNGS) indicated B. dermatitidis, which was subsequently confirmed by fungal culture and ITS sequencing. The patient was prescribed oral itraconazole at 50 mg/day and has since returned to Canada to continue treatment.

CONCLUSIONS: For diagnosing infections caused by highly pathogenic pathogens such as imported blastomycosis, the combination of mNGS and direct microscopic examination represents a valuable diagnostic approach.},
}

@article {pmid41512899,
year = {2026},
author = {Chu, VT and Spottiswoode, N and Ward, R and Yokoe, DS and Ramirez-Avila, L and Phelps, MS and Glascock, A and Crawford, ED and Kamm, J and Hao, S and Li, L and Dynerman, D and Waltari, E and Nafees, S and Kalantar, KL and Caldera, S and Madera, S and Guerrero, ES and Ivashin, D and Serpa, PH and Love, C and Mwakibete, LL and Doernberg, SB and Kistler, A and Alvino, R and Engel, J and Chiu, CY and Pak, C and Cunningham, G and Reyes, H and Buie, B and Messacar, K and Leroue, M and Prince, BC and Detweiler, AM and Stanley, K and Caughell, C and McNeil, N and Neff, N and Nichols, A and Miller, S and DeRisi, JL and Tato, CM and Langelier, CR},
title = {Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101277},
doi = {10.1016/j.lanmic.2025.101277},
pmid = {41512899},
issn = {2666-5247},
abstract = {Advances in genomic technologies have revolutionised practices for hospital infection prevention and control programmes. In this Personal View, we describe a genomic epidemiology service called the Rapid Response (RR) programme at University of California, San Francisco, a large academic medical centre. In collaboration with the hospital infection-prevention team, the RR programme uses whole-genome sequencing and metagenomic next-generation sequencing for outbreak investigations, special interest analyses of emerging pathogens, and surveillance of high-priority microbes. Over 7 years (2017-24), the RR programme conducted a diversity of outbreak investigations and other analyses; most investigations ruled out transmission, and the rapid turnaround of genomic results averted further resource-intensive work. Longitudinal surveillance enabled early detection of changing incidence trends and guided timely infection-prevention responses. Our experiences with the RR programme build upon growing evidence that genomic epidemiology programmes enhance hospital infection prevention and control, augment priority pathogen surveillance, and improve patient safety.},
}

@article {pmid41512763,
year = {2026},
author = {Liu, X and Li, J and Ma, C},
title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141076},
doi = {10.1016/j.jhazmat.2026.141076},
pmid = {41512763},
issn = {1873-3336},
abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.},
}

@article {pmid41512751,
year = {2025},
author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R},
title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {140812},
doi = {10.1016/j.jhazmat.2025.140812},
pmid = {41512751},
issn = {1873-3336},
abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.},
}

@article {pmid41512717,
year = {2026},
author = {Li, L and Shang, G and Guo, Y and Zhang, J and Qi, Y and Wang, H and Flores, M and Belloch, C and Liu, Y and Jing, W and Li, X and Woldemariam, KY},
title = {Unlocking the genomic landscape of Staphylococcus equorum and understanding the functional role and technological application in dry-cured fermented meat products: A review.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111618},
doi = {10.1016/j.ijfoodmicro.2025.111618},
pmid = {41512717},
issn = {1879-3460},
abstract = {In Dry-cured fermented meat products, the role of Staphylococcus equorum has been given less attention. S. equorum enhances the flavour, colour, texture, and nutritional quality, and produces antimicrobial compounds that inhibit pathogens in dry-cured fermented meat products. This review aims to provide a comprehensive evaluation of S. equorum as a potential starter culture in dry-cured fermented meat products, examines the main genomic and metabolic characteristics, and highlights the regulatory mechanisms. S. equorum is a gram-positive, catalase-positive coccus with high salt tolerance and optimal growth at 4-10 °C and pH 5-5.6. Modern PCR-based sequencing and metagenomics allow accurate identification of S. equorum using the major genes, including superoxide dismutase (sodA) and recombinase A (recA). Identification of this species has been made from different dry-cured fermented meat products, including Spanish dry-cured ham and "Chorizo" sausages from Spain, artisanal "Soppressata" fermented sausage from Italy. The functional role of S. equorum in protein and lipid hydrolysis contributes to key flavour and aroma compounds. Moreover, it has potential in the prevention of secondary lipid oxidation (superoxide dismutase (SOD)), contributes to nitrate reductase activity (NOS pathway), and biosynthesis of antibacterial peptide (micrococcin P1), which improves the quality and safety of dry-cured fermented meat products. Keeping this into account, the studies conducted on the S. equorum application as a starter culture in dry-cured fermented meat products are in their early stages and require further investigation and analysis.},
}

@article {pmid41512665,
year = {2026},
author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY},
title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106384},
doi = {10.1016/j.psj.2026.106384},
pmid = {41512665},
issn = {1525-3171},
abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.},
}

@article {pmid41511111,
year = {2026},
author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M},
title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/msystems.01405-25},
pmid = {41511111},
issn = {2379-5077},
abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.

IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.},
}

@article {pmid41511092,
year = {2026},
author = {Jabir, T and Venkatachalam, S and Surya Prakash, L},
title = {Metagenome-assembled genomes of bacterial communities in the eastern Southwest Indian Ridge, Indian Ocean.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0087025},
doi = {10.1128/mra.00870-25},
pmid = {41511092},
issn = {2576-098X},
abstract = {This paper presents high-quality metagenome-assembled genomes (MAGs) recovered from hydrothermal plume at the 67.67°E vent field along the eastern Southwest Indian Ridge. A total of 24 high-quality MAGs were obtained having 21 different genera. These MAGs, associated with chemosynthetic pathways including methane, metal, and sulfur metabolism, offer crucial insights into microbial transformation in deep-sea hydrothermal vents.},
}

@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
mesh = {*Feces/microbiology/virology ; Animals ; *Marsupialia/microbiology/virology/classification ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Viruses/genetics/classification ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}

*Feces/microbiology/virology
Animals
*Marsupialia/microbiology/virology/classification
Phylogeny
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Viruses/genetics/classification

@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}

@article {pmid41510448,
year = {2025},
author = {Tohya, M and Murase, K and Minagawa, M and Saiura, A and Nakagawa, I and Kirikae, T and Watanabe, S},
title = {Single-Cell Sequencing of a Bile Sample From an Acute Cholecystitis Patient.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98748},
pmid = {41510448},
issn = {2168-8184},
abstract = {Single-cell sequencing is a novel approach to genome sequencing of clinical samples. However, there are only few studies using single-cell sequencing of genomes for bacterial infections. A 71-year-old woman presented to the emergency department with epigastric pain, 38.5°C fever, and a history of hypertension and hyperuricemia. From blood test results, acute cholecystitis was suspected. The surgery went well and bilirubin calcium stones were found in the gallbladder. Single-cell sequencing was used to investigate a bile sample from a patient with acute cholecystitis. The sample, cultured on a MacConkey agar plate, produced four colonies, all identified as Escherichia coli by bacteriological and biochemical properties. Whole genome sequences of the four strains were determined using the single-cell amplified genome (SAG) sequencing technique. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all four were 99.98-100% and 100%, respectively, indicating that they were the same bacterial species. Compared with type strains, these four strains were closest to Shigella sonnei (ANI 98.65-98.66%; dDDH 88.5%) than E. coli (ANI 96.79-96.80%; dDDH 74.2%), despite lacking stx1, stx2 and ipaH, which Shigella species harbor. 16S metagenome analysis identified E. coli as the predominant bacterial genome in the sample, comprising 93.15%. SAG raw data had a relatively high level of quality, with 98.4-98.7% of the read numbers used after quality trimming. However, the genome sequencing coverage was only 9.45-42.88% when compared to a complete genome of an isolate with a mapping quality set above 99%, resulting in gaps compared to conventional whole genome sequence data of these isolates. The procedures of the SAG sequencing technique should be revised to improve the sequencing coverage and reduce gaps in the sequence data. Nonetheless, single-cell genome sequencing can provide novel information for bacterial infections.},
}

@article {pmid41510411,
year = {2025},
author = {Zhao, J and Wang, Y and Zhang, H and Feng, J},
title = {A Case of Severe Fever With Thrombocytopenia Syndrome Co-infected With Pseudomonas aeruginosa and Aspergillus fumigatus.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98752},
pmid = {41510411},
issn = {2168-8184},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne infectious disease with a high mortality rate. Co-infections with SFTS virus (SFTSV) and other pathogens can exacerbate the condition, leading to rapidly progressive multiple organ failure. We reported a case of SFTS complicated by Pseudomonas aeruginosa and Aspergillus fumigatus. Despite active symptomatic supportive treatment (including anti-virus, anti-infection, anti-antifungal treatment, liver protection, and other advanced life supports), the patient's condition deteriorated rapidly, leading to multiple organ failure. The patient was discharged home and died on the same day. The next day, her blood test results reported that SFTSV, Pseudomonas aeruginosa and Aspergillus fumigatus were detected through metagenomic next-generation sequencing (mNGS). It suggests that early pathogen screening and targeted anti-infective treatment are crucial for improving the prognosis.},
}

@article {pmid41510275,
year = {2025},
author = {De Vlaminck, I and Mzava, O and Djomnang, LA and Cheng, A and Gomez-Escobar, L and Lenz, J and Belcher, E and Schenck, E},
title = {Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8148988/v1},
pmid = {41510275},
issn = {2693-5015},
abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated response to infection. Early identification of pathogens and accurate assessment of organ injury are critical for improving outcomes, but current methods are often inadequate, especially after initiation of antibiotic treatment. Metagenomic sequencing of cell-free DNA (cfDNA) offers a promising alternative, enabling simultaneous pathogen detection and tissue-of-origin profiling. Contamination, however, can limit its accuracy in low-biomass samples. Here, we apply the Sample-Intrinsic Microbial DNA Found by Tagging and Sequencing (SIFT-seq) assay, which reduces contamination and allows detection of pathogens and organ injury simultaneously. We analyzed 142 plasma specimens: 105 from sepsis patients, 103 collected after initiation of antibiotic treatment, 24 from non-sepsis ICU controls, and 13 from healthy controls. SIFT-seq identified sepsis-causing pathogens in good agreement with pre-antibiotic blood cultures, revealed elevated immune activity and organ injury in sepsis patients, and, when combined with the SOFA score in a multivariate model, improved diagnostic performance (AUC = 0.874). These findings highlight the potential of integrated cfDNA profiling to enhance sepsis diagnosis.},
}

@article {pmid41509546,
year = {2026},
author = {Steriade, C},
title = {The Gut Feeling Behind Autoimmune Encephalitis.},
journal = {Epilepsy currents},
volume = {},
number = {},
pages = {15357597251412104},
pmid = {41509546},
issn = {1535-7597},
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.

METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.

RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.

SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}

@article {pmid41509497,
year = {2025},
author = {Shen, Z and Eckert, J and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA},
title = {Skin microbiome composition and function in the development of atopic diseases during infancy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.22.696050},
pmid = {41509497},
issn = {2692-8205},
abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome.

OBJECTIVE: To determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.

METHODS: We analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status.

RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae . At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae . Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.

CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.},
}

@article {pmid41509203,
year = {2025},
author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G},
title = {Quantum implementation of multi-pattern string matching for k-mer detection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.21.695808},
pmid = {41509203},
issn = {2692-8205},
abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.

METHOD: We implement two quantum algorithms for DNA multi pattern string matching for k-mer detection based on Grover's amplitude amplification with quantum random access memory (QRAM). The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O(√S) query complexity for S text positions but requiring O(m·L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O(√S · √m) in total.

RESULTS: We present two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.

CONCLUSIONS: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.

To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.},
}

@article {pmid41508741,
year = {2026},
author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P},
title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70262},
pmid = {41508741},
issn = {1758-2229},
support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Lakes/virology ; *DNA Viruses/genetics/classification/isolation & purification ; *Geologic Sediments/virology ; Tibet ; Metagenomics ; Phylogeny ; *Biodiversity ; Metagenome ; },
abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.},
}

*Lakes/virology
*DNA Viruses/genetics/classification/isolation & purification
*Geologic Sediments/virology
Tibet
Metagenomics
Phylogeny
*Biodiversity
Metagenome

@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Prospective Studies ; Male ; Female ; *Specimen Handling/methods ; Middle Aged ; Australia ; Aged ; Occult Blood ; Adult ; *Neoplasms/microbiology ; Surveys and Questionnaires ; Metagenomics/methods ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.

SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}

Humans
Pilot Projects
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
Prospective Studies
Male
Female
*Specimen Handling/methods
Middle Aged
Australia
Aged
Occult Blood
Adult
*Neoplasms/microbiology
Surveys and Questionnaires
Metagenomics/methods

@article {pmid41421789,
year = {2025},
author = {Wang, X and Wu, J and Huang, J and Zeng, Y and Xu, Z and Li, C},
title = {Ectopic paragonimiasis presenting as massive pericardial effusion in a child: A rare diagnostic challenge.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {164},
number = {},
pages = {108326},
doi = {10.1016/j.ijid.2025.108326},
pmid = {41421789},
issn = {1878-3511},
abstract = {OBJECTIVES: To report a rare pediatric case of ectopic paragonimiasis presenting as isolated massive pericardial effusion and to emphasize key diagnostic clues for early recognition in endemic regions.

DESIGN OR METHODS: We describe a 10-year-old boy from an endemic area in China who presented with acute gastrointestinal symptoms and recurrent massive pericardial effusion without respiratory manifestations. Diagnostic evaluation included pericardial fluid analysis, microbiological testing, echocardiography, cardiac magnetic resonance imaging(MRI), serological testing for Paragonimus IgG, therapeutic response assessment, and histopathological examination following surgery.

RESULTS: Despite repeated pericardiocenteses and empirical anti-infective therapy, the effusion persisted. Laboratory testing revealed exudative pericardial fluid with negative cytology, acid-fast staining, and metagenomic next-generation sequencing(mNGS), while peripheral eosinophilia and stool ova were absent. Echocardiography showed a characteristic "cocoon-like" pericardial pattern, and serology was positive for Paragonimus IgG.The patient improved after praziquantel and corticosteroids, but progressive pericardial thickening required pericardiectomy, which confirmed necrotizing granulomatous inflammation. The patient recovered with no recurrence during follow-up.

CONCLUSION: Paragonimiasis should be considered in children from endemic areas with unexplained or recurrent pericardial effusion, even in the absence of pulmonary involvement or eosinophilia. Epidemiological exposure, characteristic echocardiographic findings, and serology are critical for diagnosis, and timely anti-parasitic therapy with surgical intervention when necessary may prevent constrictive pericarditis.},
}

@article {pmid41388147,
year = {2026},
author = {Osipova, E and Balakrishnan, CN and Spottiswoode, CN and Lund, J and DaCosta, JM and Hauber, ME and Warren, WC and Sorenson, MD and Sackton, TB},
title = {Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism.},
journal = {Nature ecology & evolution},
volume = {10},
number = {1},
pages = {128-139},
pmid = {41388147},
issn = {2397-334X},
support = {DEB-1754397//National Science Foundation (NSF)/ ; IOS-1456524//National Science Foundation (NSF)/ ; DEB-1754406//National Science Foundation (NSF)/ ; DEB-1754311//National Science Foundation (NSF)/ ; DEB-1754643//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Nesting Behavior ; Male ; *Adaptation, Physiological/genetics ; *Biological Evolution ; *Finches/genetics/physiology ; Female ; *Adaptation, Biological ; Metagenomics ; },
abstract = {Parental care evolved as a strategy to enhance offspring survival at the cost of reduced adult survival and fecundity. While 99% of bird species provide parental care, obligate brood parasites circumvent this trade-off by exploiting the parental behaviours of other species. This radical life-history shift occurred independently seven times in birds, offering an outstanding opportunity to test for convergent adaptation. To investigate genomic adaptations underlying this transition, we analyse population resequencing data from five brood-parasitic species across three independent origins of brood parasitism-three parasitic finches, a honeyguide and a cowbird-alongside related non-parasitic outgroups. Using the McDonald-Kreitman framework, we find evidence for adaptation in genes involved in sperm function in multiple parasitic clades, but not in the matched, non-parasitic outgroups, consistent with evidence for increased male-male competition in parasitic lineages following the loss of parental care. We also detect selective sweeps near genes associated with nervous system development in parasitic lineages, perhaps associated with improved spatial cognition that aids brood parasites in locating and monitoring host nests. Finally, we detect more selective sweeps in the genomes of host specialist brood parasites as compared to non-parasitic outgroups, perhaps reflecting ongoing host-parasite coevolutionary arms races.},
}

Animals
*Nesting Behavior
Male
*Adaptation, Physiological/genetics
*Biological Evolution
*Finches/genetics/physiology
Female
*Adaptation, Biological
Metagenomics

@article {pmid41508467,
year = {2026},
author = {Chang, H and Zhang, Q and Soro, PL and Zhang, W and Ma, L and Feng, Z and Gu, C},
title = {Integrative metagenomic, metabolomic, and transcriptomic analyses unravel flavor development driven by a defined starter cocktail in cocoa fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118042},
doi = {10.1016/j.foodres.2025.118042},
pmid = {41508467},
issn = {1873-7145},
mesh = {*Fermentation ; *Cacao/microbiology/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Saccharomyces cerevisiae/metabolism/genetics ; Gene Expression Profiling ; Odorants/analysis ; Transcriptome ; Food Microbiology ; Hanseniaspora/metabolism ; Gas Chromatography-Mass Spectrometry ; },
abstract = {This study investigated the impact of a defined starter cocktail (Hanseniaspora uvarum XY23.1, Saccharomyces cerevisiae XY23.2, Lactiplantibacillus plantarum XY23.1, and Gluconobacter oxydans XY23.2) on Trinitario cocoa fermentation in Hainan, China. A multi-omic approach integrating shotgun metagenomics, metabolomics (LC-MS and GC-MS), and transcriptomics was employed to comprehensively assess microbial succession, metabolite dynamics, and functional gene expression. Starter inoculation accelerated cocoa fermentation and stabilized microbial succession, and the four introduced strains remained dominance during the process. Metabolomic analysis revealed that the inoculated group had a remarkable increase in the content of the aromatic volatiles phenylethyl alcohol, 3-methylbutyl acetate, and delta-decalactone, which contributes to fruity and floral aroma characteristics. Shotgun metagenomics revealed enrichment of genes involved in carbohydrate utilization, amino acid catabolism, and acetate ester biosynthesis. Transcriptomics also indicated that S. cerevisiae upregulated Ehrlich pathway and glyoxylate cycle under co-culture conditions, demonstrating its central role in aroma formation and redox balance, while H. uvarum upregulated sugar transporters and stress-response genes, demonstrating a putative regulatory role in nutrient competition and interspecies interaction. Overall, our findings elucidate that defined starter cultures can shape cocoa fermentation toward improved consistency and aroma outcomes, providing a foundation for designing function-driven microbial consortia for controlled fermentation applications.},
}

*Fermentation
*Cacao/microbiology/metabolism
*Metabolomics/methods
*Metagenomics/methods
Saccharomyces cerevisiae/metabolism/genetics
Gene Expression Profiling
Odorants/analysis
Transcriptome
Food Microbiology
Hanseniaspora/metabolism
Gas Chromatography-Mass Spectrometry

@article {pmid41508436,
year = {2026},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Corrigendum to "Aldehyde metabolism in Maotai-flavor baijiu: insights from integrated metagenomic and metaproteomic analyses" [Food Res. Int. 221(Part 3) (2025) 117518].},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {117954},
doi = {10.1016/j.foodres.2025.117954},
pmid = {41508436},
issn = {1873-7145},
}

@article {pmid41508161,
year = {2026},
author = {Villafuerte, AB and Comeau, AM and Soria, R and Ortega, R and Wright, RJ and Miralles, I},
title = {Linking microbial taxonomy and function in N and P metabolism: a study of organic amendments in semiarid restored soils.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00845-9},
pmid = {41508161},
issn = {2524-6372},
support = {FIRESOIL CNS2023-14150//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; BIOQUALIRES-PID2021-1275910B-100//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; P_FORT_GRUPOS_2023/69//Research Plan of the University of Almeria/ ; TECHBIOSOL-PID2024-156189OB- I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {BACKGROUND: Arid and semi-arid regions cover approximately 41% of Earth's surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments are widely used to restore degraded soils because they improve physical, chemical, and biological properties. However, little is known about how these amendments alter microbial communities and the relationship between microbial taxonomy and function, particularly in nitrogen and phosphorus cycling. To address this knowledge gap, the effects of different organic amendments (gardening compost, greenhouse horticultural compost, sewage sludge and two blends of the above) on soil properties, microbial communities and their contributions to nitrogen metabolism and phosphorus turnover in degraded soils from a limestone quarry in the Gádor Range (Almería, SE-Spain) six months after their application were investigated.

RESULTS: Organic amendments increased nutrient content (total organic carbon, total nitrogen and available phosphorus), microbiological activity, and bacterial biomass compared to unamended soils, with the largest increases in sewage-sludge-treated soils. Shotgun metagenomic assays revealed that organic amendments modified bacterial community composition and differentially influenced potential function pathways, contributing more strongly to nitrogen metabolism than phosphorus turnover, particularly within the phosphonate pathway. Across soils, Pseudomonadota and Actinomycetota were the dominant phyla. Sludge-amended soil showed higher relative abundance of Pseudomonas, associated with denitrification processes (nirK, nosZ, norB) and phosphonate degradation via C-P lyase (phnJ). Genera such as Streptomyces were linked to ammonium assimilation (glnAd, gltBD) and phosphonate synthesis (pmmS), and were more abundant in soil with vegetable-compost and unamended soils. Both nitrogen and phosphorus metabolisms exhibited phylogenetically unrestricted functional patterns, indicating high functional redundancy at phylum and genus levels.

CONCLUSIONS: This research establishes key relationships between taxonomy and function in restored soils and demonstrates how organic amendments rephase microbial communities and their potential roles in nutrient cycling. Although dominant taxa and functions were identified, many microorganisms involved in nitrogen and phosphorus turnover remain insufficiently characterized. Further research across restoration contexts is needed to compare nutrient-cycling responses and to deepen understanding of taxonomy-function linkages in soils amended with organic residues.},
}

@article {pmid41508143,
year = {2026},
author = {Gong, Y and Shen, S and Cao, Z and Zou, X and Zhou, S and Jiang, R and Kang, X and Liu, S and Tian, Y},
title = {Prophylactic impact of cecal fermentation broth against gut microbiota dysbiosis of broiler chickens challenged with Escherichia coli.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00514-9},
pmid = {41508143},
issn = {2524-4671},
support = {2024CXZX009//The Science and Technology Innovation Fund of Henan Agricultural University/ ; 30601985//The Scientific Studio of Zhongyuan Scholars/ ; },
}

@article {pmid41508107,
year = {2026},
author = {Bay, P and Cappy, P and Rodriguez, C and Mongardon, N and Petit, M and Voiriot, G and Sonneville, R and Pineton de Chambrun, M and Urbina, T and Pham, T and Decavèle, M and Benghanem, S and Contou, D and Lepeule, R and Melica, G and de Prost, N and Angebault, C and Mekontso Dessap, A and Woerther, PL and Razazi, K},
title = {Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.},
journal = {Critical care (London, England)},
volume = {30},
number = {1},
pages = {18},
pmid = {41508107},
issn = {1466-609X},
}

@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04707-9},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.

OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.

METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.

RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.

CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04664-3},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

@article {pmid41507619,
year = {2026},
author = {Mohamad, M and Sergaki, C and Patel, VC},
title = {Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {3},
pmid = {41507619},
issn = {2731-8745},
abstract = {Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.},
}

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

@article {pmid41507173,
year = {2026},
author = {Han, Y and Liao, J and Li, C and Xing, F and Peng, J and Liu, X and Xie, W and Wu, F and Jian, H and Cheng, R and Dong, X},
title = {Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68174-6},
pmid = {41507173},
issn = {2041-1723},
abstract = {Cold seeps host diverse microbes and viruses with numerous unexplored defense and anti-defense systems. Analysis of 3813 microbial and 13,336 viral genomes from 191 metagenomes across 17 cold seep sites reveals extensive microbial defense repertoires, with over 60% representing candidate systems. Experimental validation confirms that several candidates protect against viral infection. These defense systems frequently co-occur, suggesting potential synergistic interactions, and are broadly distributed across sediments. In response, viruses have evolved diverse anti-defense genes, and the concurrent presence of multiple viral and microbial systems highlights intricate coevolution. Functionally critical lineages, such as anaerobic methanotrophic archaea, sulfate-reducing bacteria, and diazotrophs, appear to modify their defensive strategies under ecological and environmental pressures; for example, sulfate-reducing bacteria harbor multiple Gabija systems while corresponding viruses carry anti-Gabija genes, illustrating specific coevolutionary adaptations. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in deep-sea ecosystems.},
}

@article {pmid41506580,
year = {2026},
author = {Nichols, S and Estandía, A and Young, CM and Knowles, LS and Palinauskas, V and Okamura, B and Clegg, SM},
title = {Host whole genome sequence data represent an untapped resource for characterising affiliated parasite diversity.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104768},
doi = {10.1016/j.ijpara.2025.104768},
pmid = {41506580},
issn = {1879-0135},
abstract = {Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.},
}

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

@article {pmid41506454,
year = {2026},
author = {Shi, T and Xu, S and Lin, Y and Zheng, X and Ruan, H and Shi, W and Zhang, R and Chen, H and Chen, T and Chen, H and Wang, H},
title = {The Clinical Application of Metagenomic Next-Generation Sequencing in Pathogen Identification of Postoperative Spinal Implant Infection.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2026.01.004},
pmid = {41506454},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Postoperative spinal implant infection (PSII) poses significant diagnostic challenges and can lead to serious clinical outcomes. Traditional microbial culture methods are limited by prolonged turnaround times and low sensitivity, which have long hindered a comprehensive understanding of the pathogen spectrum in PSII. Metagenomic next-generation sequencing (mNGS) offers rapid, broad-spectrum, and highly sensitive pathogen detection, providing a promising solution to the diagnostic difficulties associated with PSII.

PURPOSE: This study aimed to evaluate the clinical utility of mNGS for the pathogenic diagnosis of PSII.

STUDY DESIGN/SETTING: Retrospective cohort study.

PATIENT SAMPLE: A retrospective analysis was conducted on clinical data from 122 patients with suspected surgical site infection following spinal implant-related surgery between January 2020 and July 2025.

OUTCOME MEASURES: Identification of pathogenic bacteria in patients.

METHODS: According to the National Healthcare Safety Network (NHSN) criteria, patients were classified into the PSII group (n = 89) and the non-PSII group (n = 33). Pathogen spectrum characteristics of PSII detected by mNGS were analyzed, and the diagnostic performance of mNGS was compared with that of traditional microbial culture, laboratory tests, and imaging studies.

RESULTS: The pathogen detection rate of mNGS was significantly higher than that of traditional culture (79.78% vs. 38.20%, P < 0.001). mNGS successfully detected pathogens in 42.70% (38/89) of culture-negative PSII cases. The main pathogens identified by mNGS included Staphylococcus aureus and coagulase-negative staphylococci (20.00% each, 15/75), Mycobacterium tuberculosis (18.67%, 14/75), and anaerobic bacteria (14.67%, 11/75). Among the 33 patients positive by both mNGS and culture, species-level concordance was 69.70%. No significant difference in the distribution of major pathogens was observed between early-onset (≤3 months) and late-onset (>3 months) infection groups. Antibiotic appropriateness evaluation revealed that only 32.58% (29/89) of patients had initial antibiotic regimens that provided complete coverage against the detected pathogens. The overall diagnostic performance of mNGS for PSII was superior to that of culture, with significantly higher sensitivity (79.78% vs. 38.20%), specificity (100.00% vs. 93.94%), positive predictive value (100.00% vs. 94.44%), negative predictive value (64.71% vs. 36.05%), accuracy (85.25% vs. 53.28%), and AUC (0.8989 vs. 0.6607).

CONCLUSION: mNGS significantly improves the detection of difficult-to-culture pathogens such as M. tuberculosis and anaerobic bacteria in PSII. It is recommended to combine mNGS with conventional methods, thereby improving diagnostic accuracy, guiding rational antibiotic use, and enhancing treatment outcomes.},
}

@article {pmid41506449,
year = {2026},
author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M},
title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.013},
pmid = {41506449},
issn = {2090-1224},
abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.

OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.

METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).

RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2] = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.

CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.},
}

@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of Sediment Microbial Community Composition and Function to Mangrove Restoration from an Aquaculture Pond in Southern China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}

@article {pmid41505815,
year = {2026},
author = {Liu, F and Sun, S and Zhang, Y and Wang, F and Yang, X and Zhang, B and Fan, S and Jia, H},
title = {Possible tuberculous meningitis presenting with predominant voiding dysfunction in an elderly patient: A case report.},
journal = {Journal of infection and public health},
volume = {19},
number = {3},
pages = {103128},
doi = {10.1016/j.jiph.2025.103128},
pmid = {41505815},
issn = {1876-035X},
abstract = {Tuberculous meningitis (TBM) typically presents with neurological symptoms. Voiding dysfunction in TBM is usually attributed to spinal cord involvement. We report a rare case of possible TBM co-existing with possible prostatic tuberculosis, presenting primarily with urinary symptoms in the absence of spinal pathology. A 69-year-old male presented with a two-year history of progressive urinary retention, urgency, and frequency. Initial management for benign prostatic hyperplasia was ineffective. He subsequently developed fever, headache, and dizziness. Cerebrospinal fluid (CSF) analysis revealed lymphocytic pleocytosis and elevated protein. Despite extensive testing, including CSF culture, Xpert MTB/RIF, and metagenomic next-generation sequencing (mNGS), no pathogen was identified. However, a history of untreated testicular tuberculosis, pulmonary nodules on CT, and a prostatic nodule on MRI raised suspicion of disseminated tuberculosis. A clinical diagnosis of possible TBM was made based on a Marais score of 11. An intensive anti-tuberculosis regimen including moxifloxacin and linezolid led to complete resolution of neurological and urinary symptoms. This case suggests that voiding dysfunction in TBM patients may stem from concurrent genitourinary tuberculosis rather than spinal cord involvement. It highlights the importance of considering hematogenous dissemination from latent genitourinary foci in elderly patients and the utility of the Marais criteria for the diagnosis of TBM when microbiological evidence is elusive.},
}

@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13269},
pmid = {41505640},
issn = {1520-5118},
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}

@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}

*Methane/metabolism
*Plant Bark/microbiology
Australia
*Microbiota
*Forests
*Hydrogen/metabolism
Carbon Monoxide/metabolism
Metagenomics
*Trees/microbiology
*Bacteria/metabolism/genetics/classification
Anaerobiosis

@article {pmid41504847,
year = {2026},
author = {Wang, W and Li, Y and Sun, J and Jiang, C and Hao, J},
title = {Semi-Rational Design of a Deep-Sea Metagenomic Sucrose Phosphorylase for Enhanced α-Arbutin Biosynthesis.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41504847},
issn = {1559-0291},
support = {2022YFC2805101//National Key Research and Development Program of China/ ; 2022QNLM030003-2//Qingdao Marine Science and Technology Center/ ; 2023TD71//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
}

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hyperuricemia/microbiology
Male
Female
*Overweight/microbiology
Middle Aged
Cross-Sectional Studies
Feces/microbiology
Adult
Metagenomics
Metagenome

@article {pmid41503923,
year = {2026},
author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H},
title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70231},
pmid = {41503923},
issn = {1744-7917},
support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; },
abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.},
}

@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
doi = {10.1080/19490976.2025.2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation & purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.

RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.

CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}

Female
Animals
*Dysbiosis/microbiology/virology
*Primary Ovarian Insufficiency/microbiology/virology/therapy
*Gastrointestinal Microbiome
Rats
Humans
Adult
*Virome
Fecal Microbiota Transplantation
*Bacteria/genetics/classification/isolation & purification/virology
Young Adult
Feces/virology
Ovary
Rats, Sprague-Dawley

@article {pmid41503787,
year = {2026},
author = {Wang, Y and Yu, Y and Xu, N and Zhang, Z and Chen, B and Song, M and Zhang, Q and Wang, T and Ma, Y and Lu, T and Sun, L and Qian, H},
title = {Genes for Vitamin B Synthesis and Their Distribution in Microbial Producers.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11883},
pmid = {41503787},
issn = {1520-5118},
abstract = {B vitamins (VBs) are essential micronutrients, yet their microbial production across natural habitats remains poorly understood. We analyzed 126,931 metagenome-assembled genomes to map the distribution of VB producers and constructed a database of 87 VB synthesis genes, identifying VB-independent producers and their environmental drivers. Soil and freshwater habitats harbored the greatest diversity of VB1, VB2, VB7, VB9, and VB12 producers, whereas marine systems contained fewer. Biosynthetic capacity was rare for VB5 and was limited for VB3 and VB6. Gammaproteobacteria are prolific producers, synthesizing up to eight VB types. Soil sulfur content and conductivity significantly enhanced VB production potential, linking beneficial microbes to improved soil health. We further validated VB3 and VB7 synthesis in Acinetobacter kookii, supporting our predictive framework. Because the identified producers include both beneficial and pathogenic taxa, careful evaluation is required. This work provides a robust gene database and a foundation for optimizing microbial VB production in agriculture and biotechnology.},
}

@article {pmid41503705,
year = {2026},
author = {Liu, W and Du, Y and Ning, J and Zheng, S and Qiu, W and Wang, Y},
title = {Geogenic Ammonium Enrichment in Alluvial-Lacustrine Aquifer Systems: Coupled Controls of Microbial Pathways and Organic Matter Composition.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11156},
pmid = {41503705},
issn = {1520-5851},
abstract = {Elevated geogenic ammonium (NH4[+]) reported globally in alluvial-lacustrine aquifer systems is generally attributed to the mineralization of natural organic matter (OM). However, the contribution of microbial nitrogen (N) metabolism remains unclear. This study integrated hydrogeochemical profiling, metagenomic sequencing, and molecular-level OM characterization to elucidate how microbial nitrogen transformation and organic N mineralization could drive geogenic NH4[+] accumulation in groundwater. A distinct shift in microbial N metabolism pathways was identified along the NH4[+] enrichment gradient. Under N-limited and strongly reducing conditions, N fixation and dissimilatory reduction of nitrate to ammonium provided additional NH4[+] sources, whereas nitrification served as the primary sink by oxidizing NH4[+] to nitrate. At low NH4[+] levels, NH4[+] was mainly produced via deamination of simple mono-N compounds (CHO+1N) found in highly unsaturated low-oxygen (O) compounds and low-O polyphenols. In contrast, at high NH4[+] levels, urease-mediated hydrolysis of multi-N compounds (CHO+nN) in highly unsaturated high-O compounds became dominant. Co-occurrence network analysis revealed tight, pathway-specific linkages between functional genes and NH4[+]-associated OM compounds, highlighting the substrate-dependent nature of geogenic NH4[+] production. These findings could advance our understanding of microbially mediated NH4[+] enrichment mechanisms and offer implications for the management of NH4[+] and other geogenic contaminants in organic-rich aquifers.},
}

@article {pmid41503571,
year = {2026},
author = {Bajaj, JS and Fagan, A and Sterling, RK and Sikaroodi, M and Gallagher, ML and Lee, H and Matherly, SC and Bartels, A and Mousel, T and Davis, BC and Puri, P and Fuchs, M and Thacker, LR and McGinley, JP and Khoruts, A and Gillevet, PM},
title = {The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101634},
pmid = {41503571},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of HE recurrence among THEMATIC trial participants.

METHODS: The THEMATIC trial enrolled patients with cirrhosis and HE who received oral or enema FMT vs. placebo (1-3 administrations) and were followed for 6 months. Outcomes included safety and HE recurrence. Serum, urine, and stool samples were collected at baseline and post-FMT for all participants. Stool metagenomics, serum and urine metabolomics, inflammatory cytokines, and clinical data were analyzed. Differences between patients with and without HE recurrence were assessed using pathway, random forest, and latent factor analyses.

RESULTS: HE recurred in 10 of 60 patients (17%), with significantly higher recurrence in the placebo vs. the FMT groups (40% vs. 8%; p = 0.005). Due to the low recurrence rate in the FMT arms, all patients with recurrence were combined and compared with those without recurrence. Stool metagenomics showed that the abundance of short-chain fatty acid (SCFA) producers (Faecalibacterium, Eubacterium, Bacteroides, Blautia spp.) was lower, while that of GABA-producing taxa (Lactobacillus, Bifidobacterium spp.) was higher, in patients with recurrence. Urine and serum metabolomes separated HE recurrence groups on PLS-DA, with serum butyrate and isobutyrate being most significantly associated (p = 0.008). Pathway analyses revealed upregulation of GABA and neurotransmitter pathways in patients with HE recurrence. Random forest and latent factor analysis indicated that SCFA producers and secondary bile acids were protective, whereas IL-6, GABA producers, nicotine metabolites, and primary bile acids were associated with HE recurrence.

CONCLUSIONS: Secondary analysis of the THEMATIC randomized controlled trial indicates that HE recurrence in patients on lactulose and rifaximin is associated with distinct microbiome and metabolomic profiles, particularly involving SCFAs, GABA metabolism, bile acids, and IL-6.

IMPACT AND IMPLICATIONS: Fecal microbiota transplantation (FMT) reduced hepatic encephalopathy (HE) recurrence in patients receiving lactulose and rifaximin in the THEMATIC trial, but the multi-omic mechanisms underlying this effect were unclear. In this secondary analysis, we found that HE recurrence - regardless of FMT or placebo assignment - was associated with distinct multi-omic signatures, including reduced short-chain fatty acid-producing and increased pathobiont taxa, lower urinary and serum short-chain fatty acids, secondary bile acids, and acetaminophen derivatives, and higher GABA-related and nicotine metabolites, along with elevated IL-6 levels. Notably, patients with greater donor microbiota engraftment had lower rates of HE recurrence. These findings suggest that HE recurrence after FMT reflects a multifactorial process involving alterations in gut metagenomics, systemic metabolomics, inflammation, and donor engraftment.

TRIAL REGISTRATION: www.clinicaltrials.gov: NCT03796598.},
}

@article {pmid41503531,
year = {2026},
author = {Burd, EM},
title = {Metagenomic next-generation sequencing reveals cross-reactivity of lateral flow cryptococcal antigen assay with Trichosporon inkin.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503531},
issn = {2996-2684},
abstract = {Metagenomic next-generation sequencing (mNGS) in plasma, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid is a relatively new technology that offers a means to potentially provide a diagnosis in cases where infection is suspected, but conventional diagnostic testing has not revealed a pathogen. There have been many publications of individual cases and overall appraisals of its utility in detecting bacteria, fungi, and DNA viruses associated with otherwise undiagnosed systemic infections. A recent article by Phillips et al. published in ASM Case Reports (2:e00053-25, 2025, https://doi.org/10.1128/asmcr.00053-25) presents a case of meningitis in an immunosuppressed child that was ultimately determined to be caused by Trichosporon inkin using mNGS. Elevated ß-1,3-D-glucan (BDG) levels in CSF and serum projected a diagnosis of fungal meningitis. Bacterial, fungal, and mycobacterial cultures were negative. Positive lateral flow cryptococcal antigen titers in serum and CSF complicated the anticipated diagnosis since Cryptococcus spp. are thought to not have sufficient cell wall BDG to produce positive test results. Given the ultimate diagnosis of T. inkin meningitis and the known cross-reactivity with Trichosporon asahii per package insert, the unexpected cryptococcal antigen results raised the possibility of additional cross-reactivity. The authors uncovered this possibility by testing three known clinical isolates of T. inkin which generated positive results. This case adds to the growing literature that highlights the utility of mNGS in providing a diagnosis in otherwise unresolved cases and shows that mNGS can be further instructive in elucidating limitations in commonly used diagnostic tests.},
}

@article {pmid41503526,
year = {2026},
author = {Phillips, K and Acker, KP and Han, JY and Salvatore, CM and Permar, SR and Rolón, RM and Marino, J and Dysart, C and Berman, DM and Chiu, CY and Kidd, SE and Westblade, LF and Dubois, MM},
title = {Trichosporon inkin meningitis in a pediatric patient diagnosed via metagenomic sequencing.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503526},
issn = {2996-2684},
abstract = {BACKGROUND: Trichosporon has emerged as an important cause of invasive fungal infections in immunocompromised patients. There are limited data on invasive Trichosporon infections in children.

CASE SUMMARY: We report a case of culture-negative Trichosporon inkin meningitis diagnosed via metagenomic next-generation sequencing of plasma and cerebrospinal fluid in an infant with retinoblastoma. In addition, we highlight the role of β-1,3-D-glucan in the diagnosis and therapeutic monitoring of trichosporonosis, and cross-reactivity of the cryptococcal antigen lateral flow assay with T. inkin.

CONCLUSION: This diagnosis, which was challenging to make in the absence of a positive culture, highlights the utility of metagenomic sequencing methods and fungal biomarkers in identifying infectious agents and ensuring timely diagnosis and management of patients with rare fungal infections of the central nervous system.},
}

@article {pmid41503489,
year = {2026},
author = {Goddard, TR and Carlson-Jones, JA and Morton, J and Ooi, CY and Tai, A and Warner, MS and Wong, J and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA},
title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.28.25342520},
pmid = {41503489},
abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.},
}

@article {pmid41503361,
year = {2025},
author = {Uddin, MN and Hartog, C and Murray, E and Loveless, JB and Roberson, L and Aslan, A and Cubas, F and Rowles, LS},
title = {Advancing Circular Bioeconomy through a Systems-Level Assessment of Food Waste and Industrial Sludge Codigestion.},
journal = {ACS environmental Au},
volume = {5},
number = {5},
pages = {479-489},
pmid = {41503361},
issn = {2694-2518},
abstract = {Disposal of food waste (FW) in landfills remains an unsustainable practice for organic waste management. Simultaneously, pulp and paper mills produce significant amounts of recalcitrant organic waste that is difficult to decompose due to its high lignocellulosic content. In this study, we developed an innovative approach to improve the digestion of pulp and paper mill sludge (PPMS) by amending FW to produce a low chemical oxygen demand (COD) sludge while recovering methane in the process. This codigestion process was evaluated through lab-scale biogas production experiments coupled with a comprehensive economic and environmental sustainability assessment. Biomethane production results revealed that the FW-PPMS codigestion methane yield was 36% higher on average than the PPMS monodigestion. Additionally, metagenomic analysis revealed that microbial communities for both systems transitioned from highly heterogeneous to more adapted uniform communities after digestion. Improved microbial communities contributed to higher COD removal (92%) in the FW-PPMS system compared to monodigestion (80% removal). The sustainability analysis revealed that the codigestion of FW-PPMS had median costs of 236.64 USD·tonne[-1]·day[-1] and emissions of 228.30 kg CO2 eq·tonne[-1]·day[-1], a significant reduction compared to directly disposing the FW in landfills (median costs of 405.13 USD·tonne[-1]·day[-1] and emissions of 556.27 kg CO2 eq·tonne[-1]·day[-1]). A nationwide contextual analysis revealed that out of six regions, the US Northeast had the lowest median costs and emissions, while the Mountain Plains region had the highest, highlighting the importance of geographical and infrastructural factors in implementation. Overall, codigesting FW with PPMS is revealed to be a sustainable waste management option to decrease landfill disposal of valuable organic waste.},
}

@article {pmid41502951,
year = {2025},
author = {Oliveira, RA and McSpadden, E and Pandey, B and Lee, K and Yousef, M and Chen, RY and Triebold, C and Haro, F and Aksianiuk, V and Patel, R and Shriram, K and Ramanujam, R and Kuehn, S and Raman, AS},
title = {Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.28.582635},
pmid = {41502951},
issn = {2692-8205},
abstract = {Engineering functional microbiomes is challenging due to complex interactions between bacteria and their environments [1-6] . Using a set of 848 gut commensal strains and clearance of multi-drug resistant Klebsiella pneumoniae (Kp -MH258) as a target function, we engineered a functional 15-member synthetic microbiome-SynCom15-through a statistical approach agnostic to strain phenotype, mechanism of action, bacterial interactions, or composition of natural microbiomes. Our approach involved designing, building, and testing 96 metagenomically diverse consortia, learning a generative model using community strain presence/absence as input, and distilling model constraints through statistical inference. SynCom15 cleared Kp -MH258 across in vitro , ex vivo , and in vivo environments, matching the efficacy of a fecal microbiome transplant in a clinically relevant murine model of infection. The mechanism of suppression by SynCom15 was related to fatty acid production coupled with environmental acidification. SynCom15 also suppressed other pathogens- Clostridioides difficile , Escherichia coli , and other K. pneumoniae strains-but through different mechanisms. Sensitivity analysis revealed models trained on strain presence/absence captured the statistical structure of pathogen suppression, illustrating that community representation was key to our approach succeeding. Our framework, 'Constraint Distillation', could be a general and efficient strategy for building emergent complex systems, offering a path towards synthetic ecology more broadly.},
}

@article {pmid41502900,
year = {2025},
author = {Hou, Y and Xie, W and Duan, J and Li, X and Wu, Z},
title = {Challenge of Cupriavidus gilardii infection in an immunocompromised child: a case report.},
journal = {Translational pediatrics},
volume = {14},
number = {12},
pages = {3498-3503},
pmid = {41502900},
issn = {2224-4344},
abstract = {BACKGROUND: Cupriavidus gilardii is a multidrug-resistant (MDR) pathogen found in soil and water. Human infection is extremely rare, with only two pediatric cases reported to date, and its clinical features and the antimicrobial strategies remain unclear. The pathogen's MDR nature often poses a therapeutic challenge. This case provides valuable clinical evidence regarding the management of C. gilardii infection in immunocompromised pediatric patients.

CASE DESCRIPTION: A 4-year-old boy with acute lymphoblastic leukemia developed severe immunosuppression after reinduction cyclophosphamide, cytarabine (Ara-C), mercaptopurine (CAM) chemotherapy according to the SCCCG-ALL-2023 protocol. The patient initially presented with recurrent fever, septic shock, and progressive respiratory distress. Despite an aggressive empirical antibiotic regimen including meropenem, imipenem, piperacillin-tazobactam, linezolid, and levofloxacin, his condition continued to worsen. Blood cultures and metagenomic next-generation sequencing (mNGS) subsequently confirmed C. gilardii infection. Based on susceptibility testing, therapy was adjusted to a combination of ceftazidime-avibactam (CAZ-AVI) and tigecycline. After this adjustment, the patient showed marked clinical improvement, with decreased inflammatory indicators and nearly completed clearance of the pathogen. Unfortunately, on hospital day 26, he developed sudden massive hemoptysis due to Aspergillus pulmonary artery invasion and died despite emergency treatment.

CONCLUSIONS: This case demonstrates that CAZ-AVI may offer effective antimicrobial control for C. gilardii infection in immunocompromised pediatric patients. Although the patient succumbed to secondary fungal complications, successful microbiological control demonstrates that CAZ-AVI may serve as a potential salvage therapy for rare MDR Gram-negative bacteria and provides clinical insight into the management of uncommon pediatric infections.},
}

@article {pmid41502854,
year = {2025},
author = {Su, JW and Qin, SY and Liu, J and Lei, CC and Zhang, XT and Shi, WH and Xie, LH and Liu, Y and Ni, HB and Yu, MY and Liang, HR and Qin, Y and Jiang, J and Sun, HT and Ma, H and Li, ZY and Zhang, XX},
title = {Blastocystis presence alters gut archaeal communities and metabolic functions in Tibetan antelopes (Pantholops hodgsonii).},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1744013},
pmid = {41502854},
issn = {2297-1769},
abstract = {BACKGROUND: Archaea are vital members of the gut microbiota, yet their diversity and functions in high-altitude wildlife remain poorly understood. Understanding their ecological roles can provide insights into host health and microbial community dynamics.

METHODS: We applied metagenome-assembled genome (MAG)-based approaches to investigate gut archaea in Tibetan antelopes (Pantholops hodgsonii) and assess their shifts in the presence of Blastocystis. A total of 463 non-redundant archaeal MAGs were reconstructed and analyzed for taxonomic diversity and functional potential.

RESULTS: The MAGs encompassed 16,189 protein clusters, with over 70% representing potentially novel species, highlighting substantial unexplored archaeal diversity. Alpha diversity showed no significant differences between healthy and Blastocystis-present groups, but beta diversity analysis revealed marked community restructuring, including decreased Methanobacteriota and increased Halobacteriota and Thermoplasmatota in the Blastocystis-present group. Functional annotation indicated changes in energy and nucleotide metabolism and alterations in carbohydrate-active enzyme composition. Additionally, putative viral sequences were detected within archaeal MAGs, suggesting potential virus-microbe interactions.

CONCLUSION: Our findings provide novel insights into the diversity and ecological functions of gut archaea in Tibetan antelopes, offering a foundation for future research on their contributions to host health and microbial ecology.},
}

@article {pmid41502470,
year = {2026},
author = {Shukla, A and Yadav, M and Malik, MZ and Aditya, AK and Kumar, A and Tandon, R and Shalimar, and Ray, AK},
title = {Soil influences on rural versus urban human gut microbiota and implications on cardio-metabolic health: a comparative pilot study.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {62},
pmid = {41502470},
issn = {2190-572X},
abstract = {UNLABELLED: Humans are exposed to surrounding soil environment and this exposure has reduced with growing urbanisation. Limited evidence exists on how rural and urban soils shape human gut microbiome and related functions. Here, we performed metagenomic analysis, functional prediction, gene ontology using QIIME2, PICRUSt, and DAVID by taking human stool and soil samples (n = 20) from rural and urban settings to characterise gut microbiota and their resemblance to their respective soil microbiota and its functional implications. Our findings demonstrated that soil environment affects gut microbial diversity and abundance of its immediate human inhabitants in both groups and observed shared microbial and functional properties in rural- and urban-guts characteristic of their respective soil microbiota. In rural-group, phylum Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, class Actinobacteria were major overlapping features, while in the urban-counterpart phylum Proteobacteria, Firmicutes, class Gammaproteobacteria were observed. We also demonstrated implication of this differential composition on human health in both settings, and observed enrichment of cytokines like IL-12, IFN-ϒ, and oxidative phosphorylation pathway in rural group vital to metabolic homeostasis. While enrichment of response to toxic substances, methane metabolism, and potentially low levels of alanine in the urban counterpart, linked to impaired immune response and metabolism, suggests urban group may be prone to the cardio-metabolic disease risk. These observations were consistent with other findings emphasising rural groups have healthy sets of microbiome compared to their urban counterpart. In conclusion, our findings unveil the significance of soil microbiota in evolution and shaping of human gut microbiota, thereby potentially beneficial to human health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04675-x.},
}

@article {pmid41502282,
year = {2025},
author = {Sheng, YP and Kong, LJ and Chu, PP and Xia, YL and Shen, CT and Sun, JF},
title = {[Clinical Analysis of Torque Teno Virus Infection after Hematopoietic Stem Cell Transplantation in Children].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {33},
number = {6},
pages = {1784-1789},
doi = {10.19746/j.cnki.issn.1009-2137.2025.06.036},
pmid = {41502282},
issn = {1009-2137},
mesh = {Humans ; *Torque teno virus ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *DNA Virus Infections ; Child ; Male ; Female ; Incidence ; Child, Preschool ; Adolescent ; },
abstract = {OBJECTIVE: To investigate the incidence, clinical characteristics, and complications of Torque teno virus (TTV) in children after hematopoietic stem cell transplantation (HSCT).

METHODS: A total of 40 children with hematological diseases who underwent HSCT were selected, and metagenomic next-generation sequencing (mNGS) technology was used to detect the gene sequences of pathogenic microorganisms in the blood. Combined with clinical data, the characteristics of TTV infection were analyzed.

RESULTS: Among the 40 pediatric patients post-HSCT, the TTV positive rate was 42.5% (17/40). There were no statistically significant differences between the TTV-positive group and the TTV-negative group in sex, age, white blood cell count(WBC), red blood cell count(RBC), hemoglobin, platelet count, neutrophil count, lymphocyte count, and high-sensitivity C-reactive protein (all P >0.05). The incidence of TTV infection was significantly higher in children who underwent haploidentical HSCT and in those with bone marrow stem cells (BMSC) as the transplant source (P <0.05). However, there were no significant differences in the TTV infection rate among patients with different disease types, different HLA matching statuses, or different engraftment times of neutrophils and platelets (all P >0.05). Among 17 children infected with TTV, 13(76.5%) had co-infections with other viruses, mainly including cytomegalovirus (58.8%, 10/17), human polyomavirus (41.2%, 7/17), and Epstein-Barr virus (17.6%, 3/17). In children with TTV infection, the most common complications were sepsis (82.4%), graft-versus-host disease (GVHD) (70.6%), pulmonary infection (41.2%), and hemorrhagic cystitis (17.6%). The incidence of GVHD in the TTV-positive group was significantly higher than that in the TTV-negative group (P <0.05).

CONCLUSION: TTV infection is common in children undergoing HSCT, and it is prone to be complicated with cytomegalovirus infection and GVHD, which has an important influence on the clinical outcomes.},
}

Humans
*Torque teno virus
*Hematopoietic Stem Cell Transplantation/adverse effects
*DNA Virus Infections
Child
Male
Female
Incidence
Child, Preschool
Adolescent

@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; *Liver Cirrhosis/complications ; Indonesia/epidemiology ; *Liver/metabolism ; *Brain/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}

Humans
*Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
*Liver Cirrhosis/complications
Indonesia/epidemiology
*Liver/metabolism
*Brain/metabolism
Cross-Sectional Studies
Feces/chemistry

@article {pmid41502165,
year = {2026},
author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES},
title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70225},
doi = {10.1111/1462-2920.70225},
pmid = {41502165},
issn = {1462-2920},
support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; },
mesh = {*Hot Springs/microbiology ; *Thermus/metabolism/growth & development/genetics ; *Nitrogen/metabolism ; *Carbon/metabolism ; Iceland ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; Metagenomics ; },
abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.},
}

*Hot Springs/microbiology
*Thermus/metabolism/growth & development/genetics
*Nitrogen/metabolism
*Carbon/metabolism
Iceland
Nitrogen Fixation
Carbon Dioxide/metabolism
Metagenomics

@article {pmid41502155,
year = {2026},
author = {Kim, SS and D'Agostino, E and Needham, DM},
title = {Dynamics and Eco-Genomics of Baltic Sea Nitrifiers: Seasonality, Niches, Interactions and Genomic Uniqueness.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70215},
doi = {10.1111/1462-2920.70215},
pmid = {41502155},
issn = {1462-2920},
support = {//Helmholtz Association/ ; NE 2754/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Seawater/microbiology/chemistry ; *Nitrification ; *Archaea/genetics/metabolism/classification/isolation & purification ; Seasons ; Metagenomics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Phylogeny ; Ammonia/metabolism ; Genomics ; Nitrogen/metabolism ; Nitrites/metabolism ; Oceans and Seas ; Nitrates/metabolism ; },
abstract = {Nitrification is widespread across marine systems, yet the ecological and evolutionary drivers shaping nitrifier populations remain largely unknown. The Baltic Sea, a brackish basin with pronounced gradients in salinity, oxygen, nutrients and strong seasonality, is a valuable model environment to investigate these questions. Here, we combined metagenomics and rRNA gene sequencing to characterise the spatiotemporal dynamics and genomic diversity of nitrifiers, alongside physicochemical measurements. Nitrifiers were persistently abundant throughout aphotic waters, with vertical niche partitioning and seasonal peaks in surface waters from late fall to early spring. The seasonal peaks were positively correlated with nitrite, nitrate and diverse other prokaryotes, and negatively correlated with solar radiation and chlorophyll. To probe the genomic basis of these ecological patterns of the numerically dominant nitrifier, we recovered five novel genomes of ammonia-oxidising archaea through metagenomics of bulk samples and selective enrichments, including the dominant taxon from aphotic depths. Comparative genomics showed high gene conservation, with variation largely in genes linked to interactions with the external environment and nitrogen and phosphorus metabolism between central surface and deep types. Together, our study provides insights into niches of Baltic Sea nitrifiers and begins the process of understanding the mechanisms and functional implications of these patterns.},
}

*Seawater/microbiology/chemistry
*Nitrification
*Archaea/genetics/metabolism/classification/isolation & purification
Seasons
Metagenomics
*Bacteria/genetics/metabolism/classification/isolation & purification
Phylogeny
Ammonia/metabolism
Genomics
Nitrogen/metabolism
Nitrites/metabolism
Oceans and Seas
Nitrates/metabolism

@article {pmid41502126,
year = {2026},
author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM},
title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70226},
doi = {10.1111/1462-2920.70226},
pmid = {41502126},
issn = {1462-2920},
support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; },
mesh = {*Oxygen/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Metagenomics ; Pacific Ocean ; *Microbiota/genetics ; *Metagenome ; Photosynthesis/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Chlorophyll/metabolism ; Nitrites/metabolism ; },
abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.},
}

*Oxygen/metabolism/analysis
*Seawater/microbiology/chemistry
*Metagenomics
Pacific Ocean
*Microbiota/genetics
*Metagenome
Photosynthesis/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
Chlorophyll/metabolism
Nitrites/metabolism

@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02300-w},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.

RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.

CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}

@article {pmid41501755,
year = {2026},
author = {Li, JL and Hu, W and Pu, LH and Sun, J and Ortúzar, M and Lv, ZH and Yang, ZF and Zhu, D and Xie, KQ and Yang, LQ and Yin, YR},
title = {Molecular cloning and characterization of a GH10 thermophilic xylanase from hot spring and its potential application in promoting probiotic growth.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-025-01096-9},
pmid = {41501755},
issn = {1472-6750},
support = {202101AU070138 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; 230212528080//the Xingdian Talent Support Program of Yunnan Province/ ; },
}

@article {pmid41501434,
year = {2026},
author = {Zell, R and Groth, M and Selinka, L and Selinka, HC},
title = {A metagenomic analysis of urban river samples reveals high numbers of sequences related to mycoviruses.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {46},
pmid = {41501434},
issn = {1432-8798},
mesh = {*Rivers/virology ; Phylogeny ; Genome, Viral ; *Metagenomics ; *Fungal Viruses/genetics/classification/isolation & purification ; Germany ; Open Reading Frames ; },
abstract = {Mycoviruses have been classified into 35 virus families so far. In addition to numerous mycoviruses with proven fungal or oomycetes hosts, many newly discovered viruses from environmental water and soil samples and various animal or plant specimens exhibit significant similarity to classified mycoviruses, thereby expanding the known sequence space of fungal and related viruses. In this study, we searched for mycoviruses in two environmental water samples that had been collected from the Teltow Canal and the Havel River in Berlin, Germany. Viral sequences with similarity to members of 16 virus families were identified. The most common viruses in our samples were botourmia-like viruses with moderate similarity to members of the genus Ourmiavirus. Notably, 58 of the ourmia-like sequences from the Teltow Canal and Havel River and 10 ourmia-like sequences from other sources exhibited a dicistronic genome layout. The second open reading frame (ORF) of these viruses encoded a putative capsid protein with an S domain that showed little similarity to the structural proteins of the classified ourmiaviruses. The second-largest virus group (59 sequences) was assigned to the order Ghabrivirales, and 13 of these sequences exhibited similarity to members of the suborder Alphatotivirineae (families Orthototiviridae, Pseudototiviridae, Botybirnaviridae, and Chrysoviridae). Thirty-three sequences clustered with members of the suborder Betatotivirineae - three of them with members of the family Artiviridae. Fifteen highly divergent toti-like sequences suggest the need to establish a new higher-order taxon within the order Ghabrivirales. Other virus sequences were assigned to the families Mitoviridae (three unuamitoviruses and 10 highly divergent mitovirus-like sequences), Narnaviridae (five "alphanarnavirus"-like sequences), Amalgaviridae (two zybavirus-like sequences), Hypoviridae (one partial RdRP sequence), and Mymonaviridae (one partial RdRP sequence), and one was not classified (Sclerophthora macrospora B-like virus). Notable results include a clade of highly divergent mitovirus-like sequences with a standard translation code, three narnavirus-like sequences with a reverse-frame ORF, and a clade of four Ghabrivirales-like replicase sequences that were found to have numerous termination codons regardless of which translation table was used.},
}

*Rivers/virology
Phylogeny
Genome, Viral
*Metagenomics
*Fungal Viruses/genetics/classification/isolation & purification
Germany
Open Reading Frames

@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33939-y},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}

@article {pmid41501123,
year = {2026},
author = {Alexandrino, DAM and Semedo, M and Cao, W and Azevedo, J and Magalhães, C and Osório, H and Jia, Z and Campos, A and Mucha, AP and Almeida, CMR and Carvalho, MF},
title = {Insights into the biodegradation of two persistent fluorinated fungicides by coupling metabolic modelling with metaproteogenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31941-y},
pmid = {41501123},
issn = {2045-2322},
abstract = {Epoxiconazole (EPO) and fludioxonil (FLU) are fluorinated fungicides known for their extremely high environmental persistence and significant ecotoxicological impact. Given their decades-old use in the agrochemical sector, EPO and FLU became frequent pollutants of terrestrial and aquatic ecosystems. And yet, not much is known regarding how these pesticides biodegrade in the natural environment or how to develop suitable bioremediation approaches capable of tackling their inherent recalcitrance. As such, this work focused on providing new insights into the bacterial degradation of EPO and FLU, by surveying the catabolic activity of a previously obtained EPO-enriched bacterial consortium through chemical and metaproteogenomic analyses guided by different metabolic modelling tools. The bacterial consortium was capable of extensively degrading EPO and FLU in 21 days, with fungicide removals of over 90% and defluorination efficiencies of up to 80%, but none of the subproducts predicted in silico were identified for either pesticide. Despite this, the combination of metabolic modelling tools and metaproteogenomic surveys suggested that EPO and FLU were first attacked in their N-heterocyclic moieties and that the targets of defluorination were the resulting aromatic fluorinated intermediates. This catabolic cascade is consistent with the experimental data gathered in this study and with the existing literature on this topic. Also, the degrading consortium remained stable at the taxonomical and functional levels, highlighting its catabolic plasticity in biodegrading and defluorinating two chemically distinct fluorinated compounds. This work offers a conceptual framework with novel observations that can guide future efforts to further elucidate the pathways of microbial transformation of these pesticides, ultimately contributing to better environmental risk management practices for these pollutants.},
}

@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}

@article {pmid41500138,
year = {2026},
author = {Bellekom, B and Troman, C and Fitz, S and Akello, JO and Grassly, NC and Shaw, AG},
title = {Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181333},
doi = {10.1016/j.scitotenv.2025.181333},
pmid = {41500138},
issn = {1879-1026},
abstract = {Timely and accurate pathogen detection is critical for the successful implementation of wastewater surveillance and has broad implications for public health. A wide range of surveillance tools are currently available, offering both quantitative and qualitative insights into the wastewater virome. Careful consideration of molecular methodology is required to successfully implement an effective wastewater surveillance scheme. Using SARS-CoV-2 as a model organism, we compared detection success across multiple approaches, including targeted (RT-PCR, qPCR, random priming RT-PCR) and target-agnostic (Rapid SMART-9N metagenomics) methods. We also estimated the copy number required for reliable detection, examined how the ratio of target to off-target genomes in wastewater affects detection and genome coverage using metagenomics, and assessed the efficacy of hybrid capture enrichment of target genomes in improving metagenomic detection. Our results show significant differences between methods, targeted RT-PCR and qPCR were more likely (68 % and 65 % respectively) to detect SARS-CoV-2 than target agnostic approaches. The inclusion of carrier RNA during extraction significantly increased the likelihood of target detection. Our target-agnostic metagenomic approach was consistently unable to detect our target, and, even in the presence of high concentrations that are atypical for wastewater, detection was limited. Target enrichment increased SARS-CoV-2 detection and maximum coverage by metagenomics (SMART-9N), though was outperformed by targeted amplicon sequencing. Overall, our findings support the use of targeted approaches for the routine surveillance of viral pathogens in wastewater. Whilst metagenomics provides broad insights into the virome, enrichment strategies are essential when using it to detect specific viruses, particularly in complex wastewater matrices.},
}

@article {pmid41500047,
year = {2025},
author = {Gutfreund, MC and Callado, GY and Pardo, I and Hsieh, MK and Celeghini, PD and Lopes, GOV and Marra, PS and Cheng, YR and Kobayashi, T and Pinho, JRR and Generoso, JR and Bulgarelli, L and Mendonça, EA and Deliberato, RO and Amgarten, DE and Malta, FM and Edmond, MB and Marra, AR},
title = {Metagenomic next-generation sequencing in pediatric infectious disease diagnosis: A comprehensive systematic literature review and meta-analysis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {4},
pages = {117248},
doi = {10.1016/j.diagmicrobio.2025.117248},
pmid = {41500047},
issn = {1879-0070},
abstract = {BACKGROUND: Diagnosing pediatric infectious diseases is challenging due to nonspecific presentations, small sample volumes, and the limited sensitivity of conventional microbiological tests (CMTs). Metagenomic next-generation sequencing (mNGS) enables broad, hypothesis-free pathogen detection, but its diagnostic performance in children remains insufficiently characterized. This study evaluates the diagnostic accuracy of mNGS in pediatric infectious diseases and compares its performance with CMTs.

METHODS: This systematic review and meta-analysis was registered in PROSPERO (CRD42024542444). Searches were performed using multiple databases through August 2024. Eligible studies evaluated mNGS and CMTs in pediatric patients (≤21 years) with suspected infectious diseases and compared their respective results with clinical diagnosis. Pooled sensitivity, specificity, and diagnostic odds ratios (DORs) were calculated using a bivariate random-effects model.

RESULTS: Thirty-three studies (n = 4,165) met inclusion criteria, and nine were eligible for meta-analysis. Pooled sensitivity and specificity of mNGS versus clinical diagnosis were 0.84 (95% CI: 0.82-0.86) and 0.71 (95% CI: 0.66-0.75), respectively, compared with 0.40 (95% CI: 0.37-0.43) and 0.82 (95% CI: 0.78-0.86) for CMTs. The pooled DOR favored mNGS (18.6 vs. 5.4). Respiratory infections were most frequently investigated, followed by bloodstream and mixed infections. Over two-thirds of studies reported changes in antimicrobial management following mNGS results.

CONCLUSIONS: mNGS demonstrates superior sensitivity and diagnostic accuracy compared with CMTs, enabling comprehensive pathogen detection, including rare and co-infecting organisms, and informing targeted antimicrobial therapy. Despite limitations related to cost, complex interpretation, and methodological standardization, mNGS represents a promising complement to conventional diagnostics in pediatric infectious disease management.},
}

@article {pmid41499937,
year = {2025},
author = {Wu, X and Zhang, T and Feng, J and Park, S},
title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157758},
doi = {10.1016/j.phymed.2025.157758},
pmid = {41499937},
issn = {1618-095X},
abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.

PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.

METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPKα signaling pathways.

RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPKα signaling.

CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPKα signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.},
}

@article {pmid41499920,
year = {2025},
author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S},
title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {57},
number = {},
pages = {106558},
doi = {10.1016/j.clnu.2025.106558},
pmid = {41499920},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.

METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.

RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.

CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.

CLINICALTRIALS: gov ID NCT06317883.},
}

@article {pmid41499832,
year = {2026},
author = {Wang, Y and Yao, C and Zhou, J and Liu, B and Qi, L and Wang, B and Ma, C and Hou, L and Liu, M and Zheng, Y},
title = {Co-occurring aquatic acidification and hypoxia promote methane emissions from estuarine ecosystems.},
journal = {Water research},
volume = {292},
number = {},
pages = {125307},
doi = {10.1016/j.watres.2025.125307},
pmid = {41499832},
issn = {1879-2448},
abstract = {Estuaries worldwide are experiencing intensifying acidification and hypoxia, driven synergistically by anthropogenic activities and global climate change. Nevertheless, their combined impact on the emissions of the potent greenhouse gas methane (CH4) and its underlying regulatory mechanisms remains poorly understood, undermining our ability to project climate feedbacks. Here, we integrated [13]C stable isotope tracing, DNA/mRNA-based qPCR, and amplicon/metagenomic sequencing to unravel how acidification-hypoxia interactions regulate the complex balance between CH4 production and consumption in estuarine sediments. Results showed that aquatic acidification and hypoxia combined to significantly increase CH4 emissions from estuarine sediments (P < 0.05), in a non-additive (antagonistic) manner where oxygen availability was the dominant factor governing this response. Notably, acidification increased CH4 emissions by suppressing methanotrophy more strongly than methanogenesis, whereas hypoxia preferentially stimulated methanogenic activity over CH4 oxidation. These response patterns were further demonstrated by metagenomic sequencing and mRNA-based quantitative PCR analyses, which revealed coordinated shifts in both the relative abundance and transcriptional activity of key functional genes. These findings uncover a previously overlooked mechanism whereby the worldwide co-occurrence of acidification and hypoxia in estuarine ecosystems jointly promote CH4 emissions, providing a scientific basis for improving predictive models of the global CH4 cycle and its climate feedbacks under combined anthropogenic and climatic stressors.},
}

@article {pmid41499829,
year = {2026},
author = {Huang, Z and Liu, H and Wang, C and Wang, J and Tian, C and Feng, J and Shen, J and Wang, X},
title = {Regulation of carbon cycling in plateau lakes by trophic states and seasonal variations: A focus on dissolved organic matter and microbial interactions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125312},
doi = {10.1016/j.watres.2025.125312},
pmid = {41499829},
issn = {1879-2448},
abstract = {Plateau lakes are highly sensitive to climate change and anthropogenic disturbances. The intensification of seasonal variations caused by global warming has complicated the biogeochemical interactions between dissolved organic matter (DOM) and microbial communities. However, how DOM's chemical composition regulates microbial community dynamics and carbon cycling under varying trophic states and seasonal conditions remains unclear. Here, we employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing to investigate the seasonal and trophic controls on DOM composition, microbial communities, and carbon cycling in plateau lakes. The results showed that in the dry season, DOM in the eutrophic lake exhibited pronounced aromaticity, with carboxyl-rich alicyclic molecules (CRAMs) constituting 42.80 % of the molecular pool. Conversely, during the wet season, sulfur- and nitrogen-containing compounds like CHOS and CHONS significantly increased, particularly in the eutrophic lake. The oligotrophic lake displayed the highest molecular lability, characterized by hydrogen-to-carbon (H/C) ratios of 1.24 and molecular lability indices (MLB%) of 34.76 %. Eutrophication altered microbial interaction networks, enhancing interspecies interactions and metabolic specialization. This metabolic shift drove preferential utilization of labile sugars in dry seasons and facilitated the degradation of recalcitrant carbon substrates in wet seasons, thereby optimizing carbon source partitioning. Notably, mesotrophic and oligotrophic lakes fostered resource cooperation by reducing network modularity and shaping carbon cycling through the coordinated action of multiple microbial groups. This study elucidates that carbon cycling in plateau lakes is governed by synergistic effects of trophic states and seasonal dynamics, with DOM serving as a critical mediator in microbial-driven carbon cycling dynamics.},
}

@article {pmid41499817,
year = {2026},
author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z},
title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119669},
doi = {10.1016/j.ecoenv.2025.119669},
pmid = {41499817},
issn = {1090-2414},
abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.

METHODS: C57BL/6 mice (n = 10 per group) were orally gavaged with DnPP (1-100 mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).

RESULTS: DnPP exposure induced dose-dependent villus degeneration (100 mg/kg/d, P < 0.05) and colon shortening (P < 0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-α) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P < 0.001) and elevated antibiotic resistance genes (CARD, P < 0.05).

CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.},
}

@article {pmid41499533,
year = {2026},
author = {Liu, T and Song, Z and Zhang, L and Liu, F and Sun, L},
title = {Clinicopathological Features of Orf Virus Infection in the Human: A Rare Case Report of Extensive Skin Infections and Meta-Analysis.},
journal = {Journal of medical virology},
volume = {98},
number = {1},
pages = {e70794},
doi = {10.1002/jmv.70794},
pmid = {41499533},
issn = {1096-9071},
support = {//Beijing Ditan Hospital, Xuzhou Hospital, Capital Medical University, Special Program for Clinical Research and Scientific Innovation Transformation (KCZL202510)./ ; //Training Program for High-level Public Health Technical Talents Construction Project (academic backbone-03-21)/ ; },
mesh = {Humans ; *Orf virus/isolation & purification/genetics ; *Ecthyma, Contagious/pathology/virology/diagnosis ; Male ; Adult ; Animals ; Female ; Sheep ; Middle Aged ; Skin/pathology/virology ; Young Adult ; },
abstract = {The Orf virus is responsible for causing contagious ecthyma in sheep and goats. Humans are primarily infected with Orf virus result in zoonotic skin diseases. We reported a rare case of orf virus infection affecting the face and thoracodorsal regions and performed pathological examination and metagenomic pathogen detection technology(MethPath[TM]) test on the patient. A meta-analysis of the reported cases was also presented. All cases of human infection with orf virus were searched in PubMed and web of science databases. The pathology revealed eosinophilic inclusion bodies visible in the epidermal cells, and the demonstrated orf virus infection by MetaPath™. We identified 99 articles reporting 159 cases of human orf virus infection. The average (±SD) age of all patients was 34.96 ± 16.82 years. Male gender was predominant; hand infections were the most frequent. 81.3% of the patients were infected by contact with sheep. The observed recovery time averaged 42.7 days, with a median of 40 days. The most typical histopathological finding is characterized by the presence of eosinophilic inclusions within vacuolated epidermal cells. When facial nodular lesions are present, obtaining a detailed medical history is essential to aid in considering orf virus infection in the differential diagnosis.},
}

Humans
*Orf virus/isolation & purification/genetics
*Ecthyma, Contagious/pathology/virology/diagnosis
Male
Adult
Animals
Female
Sheep
Middle Aged
Skin/pathology/virology
Young Adult

@article {pmid41499519,
year = {2026},
author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E},
title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0323038},
doi = {10.1371/journal.pone.0323038},
pmid = {41499519},
issn = {1932-6203},
mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation & purification ; Food Microbiology ; },
abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.},
}

*Microbiota
*Cheese/microbiology/analysis
Bacteria/genetics/classification/isolation & purification
Food Microbiology

@article {pmid41499369,
year = {2026},
author = {Chen, K and Luo, S and Jiang, C and Gu, S and Yang, F and Liu, X and Wang, S and Qu, X and Zhang, Q and Zhang, P and Gong, Y and Zeng, H and Qiu, D and Miao, W and Xiong, J},
title = {HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70092},
pmid = {41499369},
issn = {1755-0998},
support = {2023S016//Ningbo Public Welfare Science and the Technology Program Project/ ; 2022xjkk0204//Third Xinjiang Scientific Expedition Program/ ; SNJNP2022008//Background Resources Survey in Shennongjia National Park/ ; 2019 QZKK0304//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; SNJGKL2022008//Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; 32122015//National Natural Science Foundation of China/ ; 32300355//National Natural Science Foundation of China/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Ecosystem ; *Metagenomics/methods ; *Aquatic Organisms/classification/genetics ; Fungi/genetics/classification ; Computational Biology/methods ; Bacteria/classification/genetics ; },
abstract = {Aquatic ecosystems host diverse organisms across all six life kingdoms, yet their complex interactions remain poorly understood, primarily due to limitations in transkingdom species detection methods. To address this limitation, we developed HiMBar (https://github.com/Xchenkai2019/HIFI_barcoding), a high-fidelity (HiFi) metagenomic barcoding approach that utilises long, highly accurate reads to extract multiple full-length marker genes (such as rRNA genes, COI, rbcL) directly from environmental DNA sequencing reads. These genes are subsequently clustered into operational taxonomic units (OTUs) for species identification, eliminating the need for PCR amplification or sequence assembly. HiMBar outperforms existing DNA-based methods in accuracy, recall and consistency. Applying HiMBar, we identified a stable interaction network among Cyanobacteria, Planctomycetota, Verrucomicrobiota and Fungi. Further analysis revealed that glucose metabolism plays a key role in maintaining these interactions. Our study offers a powerful tool for transkingdom species monitoring and provides a case study for exploring transkingdom interactions and their molecular mechanisms.},
}

*DNA Barcoding, Taxonomic/methods
*Ecosystem
*Metagenomics/methods
*Aquatic Organisms/classification/genetics
Fungi/genetics/classification
Computational Biology/methods
Bacteria/classification/genetics

@article {pmid41499358,
year = {2026},
author = {Cao, A and Lin, Y and Guan, S and Chen, Y and Zhai, W and Zhou, Y and Feng, S and Guan, Y and Zhang, Y and Huang, M and Wang, X and Long, H},
title = {Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.},
journal = {Clinical and translational medicine},
volume = {16},
number = {1},
pages = {e70579},
pmid = {41499358},
issn = {2001-1326},
support = {82474002//National Natural Science Foundation of China/ ; 82020108031//National Natural Science Foundation of China/ ; 82404752//National Natural Science Foundation of China/ ; 81973398//National Natural Science Foundation of China/ ; WKZX2023CX020006//Development Center for Medical Science & Technology National Health Commission of the People's Republic of China/ ; 2025A1515012521//Natural Science Foundation of Guangdong Province/ ; 2020B1212060034//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017B030314030//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017YFC0909300//National Key Research and Development Program/ ; B16047//The 111 project/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy ; Female ; Male ; *Neoadjuvant Therapy/methods ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy ; Gastrointestinal Microbiome/drug effects ; Metabolomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Neoadjuvant anti-programmed cell death 1 (PD-1) immunochemotherapy has shown promising efficiency in the treatment of early-stage non-small-cell lung cancer (NSCLC), but it has not consistently yielded durable responses. Biomarkers for the prediction of efficacy are warranted.

METHODS: We performed shotgun metagenomic and plasma/faecal metabolomic studies in 44 NSCLC patients who underwent neoadjuvant tislelizumab plus platinum-based doublet chemotherapy. Samples were collected at baseline and before surgical resection, and the major pathologic response (MPR) was evaluated.

RESULTS: MPR patients showed a significantly higher gut-microbial alpha diversity, an enrichment of Ruminococcaceae, Lachnospiraceae and Clostridiales species, and an increased plasma level of tryptophan metabolites at baseline. On the contrary, non-MPR patients were characterized by enrichment of Prevotella species in faecal samples and higher plasma levels of linoleic acid metabolites. A high predictive accuracy was achieved using a small panel of differential microbial (Clostridium sp. M62/1 and Eisenbergiella tayi) or metabolomic features (linoleic acid, oxindole-3-acetic acid and quinolinic acid) with AUCs > .85.

CONCLUSIONS: The baseline characteristics of the gut microbiota and plasma metabolites could provide early predictions of the response to neoadjuvant anti-PD-1 immunochemotherapy.

TRIAL REGISTRATION: NCT05244837.

KEY POINTS: Baseline metagenomic and metabolomic signatures were significantly associated with the major pathologic response of neoadjuvant anti-PD-1 immunochemotherapy. Integrated microbial model (consists of Clostridium sp. M62/1 and Eisenbergiella tayi) and metabolomic model (consists of linoleic acid, oxindole-3-acetic acid and quinolinic acid) could provide early predictions of the response.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/drug therapy
Female
Male
*Neoadjuvant Therapy/methods
Middle Aged
Aged
*Lung Neoplasms/drug therapy
Gastrointestinal Microbiome/drug effects
Metabolomics/methods
Multiomics

@article {pmid41498995,
year = {2026},
author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A},
title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {32},
pmid = {41498995},
issn = {1573-0972},
support = {42430404//National Natural Science Foundation of China/ ; },
}

@article {pmid41498484,
year = {2026},
author = {Huang, T and Ge, H and Wu, Z and Zhang, Y and Wang, L and Dang, C and Fu, J},
title = {Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70155},
pmid = {41498484},
issn = {1097-0290},
support = {22306068//National Natural Science Foundation of China/ ; 42476142//National Natural Science Foundation of China/ ; //2022 HUST-UTS Key Partnership Research Seed Funding/ ; 2024AFD091//Hubei Provincial Natural Science Foundation of China/ ; },
abstract = {Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 [+]-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.},
}

@article {pmid41497396,
year = {2025},
author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T},
title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.},
journal = {iScience},
volume = {28},
number = {12},
pages = {114029},
pmid = {41497396},
issn = {2589-0042},
abstract = {Metagenomic read classification is a fundamental task in computational biology but remains challenging due to the scale and diversity of sequencing data. We present a run-length compressed BWT-based index using the move structure for efficient multi-class classification. Our method finds all super-maximal exact matches (SMEMs) of length ≥ L between a read and a reference and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs and their class identifiers into a single classification. We are the first to perform run-length compressed read classification using full rather than semi-SMEMs. We evaluated on long and short reads across two datasets: a large bacterial pan-genome with few classes and a smaller 16S rRNA gene database spanning thousands of genera. Our method outperforms SPUMONI 2 in accuracy and runtime while maintaining run-length compressed memory complexity and surpasses Cliffy in memory efficiency with comparable accuracy.},
}

@article {pmid41497123,
year = {2026},
author = {Mehmood, MS and Hajj, F},
title = {Noninvasive early detection of colorectal cancer through gut microbiome-derived biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {997-998},
pmid = {41497123},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) remains a major global burden, with 1.9 million new cases and 935000 deaths reported in 2024. Despite available screening tools, nearly 45% of cases are still diagnosed at advanced stages, where the 5-year survival rate falls below 14%, compared to >90% in early detection. The limitations of colonoscopy its invasiveness, cost, and poor compliance (<40% globally) demand innovative, noninvasive diagnostic solutions. Gut microbiome profiling has recently emerged as a transformative approach, with specific bacterial signatures such as Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius showing AUC values between 0.85 and 0.93 for early CRC identification. Integrating metagenomic and metabolomic data enhances diagnostic accuracy to 89% sensitivity and 91% specificity. Moreover, altered microbial metabolites including decreased short-chain fatty acids and elevated secondary bile acids correlate with a 2.3- to 3.1-fold higher risk of carcinogenesis. Novel CRISPR-Cas13a-based assays further allow sub-attomolar detection of microbial RNA transcripts, underscoring a new frontier in microbiome-driven cancer diagnostics. Collectively, gut microbiome-derived biomarkers represent a noninvasive, mechanistically grounded, and highly sensitive platform for early CRC detection with significant translational potential.},
}

@article {pmid41496931,
year = {2026},
author = {Mehmood, MS and Danaf, N},
title = {Helicobacter pylori persists in pancreatic ductal adenocarcinoma despite eradication therapy.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {1},
pages = {955-956},
pmid = {41496931},
issn = {2049-0801},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with global 5-year survival below 12%. Recent molecular analyses have revealed that Helicobacter pylori may persist within the pancreatic ductal microenvironment despite successful gastric eradication. In a 2024 multicenter study, H. pylori DNA was detected in 41.6% of PDAC tissues, including patients with documented eradication. Metagenomic sequencing identified H. pylori 16S rRNA reads comprising up to 2.5% of total microbial DNA, supporting selective intrapancreatic survival. Mechanistically, CagA/VacA-mediated STAT3 and NF-κB activation drives cytokine release, oxidative stress, and mismatch repair suppression, enhancing oncogenic inflammation and genomic instability. Chronic colonization increased pancreatic intraepithelial neoplasia by more than 60% in murine models, underscoring its pathogenic potential. These findings suggest that H. pylori persistence represents a novel microbial co-factor in PDAC, warranting further exploration as a diagnostic biomarker and therapeutic target.},
}

@article {pmid41350554,
year = {2025},
author = {Protic, D and Bascarevic, D and Dimitrijevic, S and Pesovic, J and Nikolic, V and Nikolic, S and Novicevic, V and Markovic, J and Arandjelovic, I and Savic-Pavicevic, D and Diricks, M and Belheouane, M and Merker, M},
title = {Microbiome modulation and behavioural improvements in children with fragile X syndrome following probiotic intake: A pilot study.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {560},
pmid = {41350554},
issn = {2045-2322},
abstract = {UNLABELLED: The gut microbiome (GM) is increasingly recognized as a key modulator of neurodevelopment via the microbiome-gut-brain axis. Fragile X syndrome (FXS), the most common inherited monogenic cause of intellectual disability, shares behavioural and molecular features with other neurodevelopmental disorders (NDDs), yet the role of the GM in FXS remains largely unexplored. In this open-label, single-arm trial, 15 children with genetically confirmed FXS received a daily probiotic formulation containing Lactobacillus casei, Lactobacillus salivarius, and Bifidobacterium breve for 12 weeks. Behavioural analysis and metagenomic sequencing with network and pathway analyses were performed before and after probiotic supplementation. Significant improvements were observed in irritability (-3.9, SD: ± 5.2; p = 0.027), communication (+ 1.7, SD: ± 2.5; p = 0.022), socialization (+ 1.4, SD: ± 2.1; p = 0.033), and adaptive behaviour (+ 1.3, SD: ± 1.4; p = 0.004). While overall microbial diversity remained stable, SparCC network analysis revealed increases in connectivity measures such as edge count and clustering coefficient, indicating denser microbial interactions and greater community coordination after probiotic supplementation. Functional profiling showed trends toward increased microbial activity in fatty acid biosynthesis, NAD salvage, and starch degradation pathways. This pilot study provides initial evidence that probiotics may modulate structural and functional properties of the GM, with potential links to improved behavioural outcomes in children with FXS. Larger, controlled trials are needed to validate the therapeutic potential of GM-targeted interventions in FXS and related NDDs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-29896-1.},
}

@article {pmid41496864,
year = {2025},
author = {Shi, H and Zhang, X and Liu, L and Thompson, F and Li, X and Sun, H and Mi, H and Zhang, XH and Zhang, Y},
title = {Vertically stratified carbon fixation and coupling processes in deep-sea sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf242},
pmid = {41496864},
issn = {2730-6151},
abstract = {Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH4[+]) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.},
}

@article {pmid41496862,
year = {2025},
author = {Rojas-Vargas, J and Samperio-Ramos, G and Camacho-Ibar, VF and Pajares, S},
title = {Taxonomic and functional stability of sedimentary microbial communities in a pristine upwelling-influenced coastal lagoon.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf241},
pmid = {41496862},
issn = {2730-6151},
abstract = {Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.},
}

@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
doi = {10.1080/19490976.2025.2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Clostridiales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}

Humans
*Immunoglobulin A/metabolism
Animals
Phylogeny
*Campylobacter jejuni/physiology
*Campylobacter Infections/microbiology/immunology
*Gastrointestinal Microbiome
Mice
*Clostridiales/enzymology/genetics/classification
Neutrophils/immunology/microbiology
*Bacterial Proteins/genetics/metabolism
China
Phagocytosis
Epithelial Cells/microbiology
Serine Endopeptidases

@article {pmid41496335,
year = {2026},
author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K},
title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118923},
doi = {10.1016/j.biopha.2025.118923},
pmid = {41496335},
issn = {1950-6007},
abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.

OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.

METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).

RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.

CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.},
}

@article {pmid41496236,
year = {2025},
author = {Huang, C and Huang, P and Zhang, Y and Bartlam, M and Wang, Y},
title = {Ecological filtering enhanced by smaller PBS biodegradable microplastics constrains ARG dynamics in the soil plastisphere.},
journal = {Environment international},
volume = {207},
number = {},
pages = {110030},
doi = {10.1016/j.envint.2025.110030},
pmid = {41496236},
issn = {1873-6750},
abstract = {Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.},
}

@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
doi = {10.1097/MD.0000000000046594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTDã€"2025〕046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.

METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.

RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.

CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}

Humans
*Asthma/microbiology/immunology
*Bibliometrics
*Gastrointestinal Microbiome
Child
Dysbiosis
*Biomedical Research/trends

@article {pmid41495893,
year = {2026},
author = {Bouras, G and Grigson, SR and Mirdita, M and Heinzinger, M and Papudeshi, B and Mallawaarachchi, V and Green, R and Kim, RS and Mihalia, V and Psaltis, AJ and Wormald, PJ and Vreugde, S and Steinegger, M and Edwards, RA},
title = {Protein structure-informed bacteriophage genome annotation with Phold.},
journal = {Nucleic acids research},
volume = {54},
number = {1},
pages = {},
doi = {10.1093/nar/gkaf1448},
pmid = {41495893},
issn = {1362-4962},
mesh = {*Genome, Viral ; *Molecular Sequence Annotation/methods ; *Bacteriophages/genetics ; *Viral Proteins/chemistry/genetics ; *Software ; Protein Conformation ; },
abstract = {Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here, we introduce Phold, an annotation framework utilizing protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high-quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency, and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveal that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold.},
}

*Genome, Viral
*Molecular Sequence Annotation/methods
*Bacteriophages/genetics
*Viral Proteins/chemistry/genetics
*Software
Protein Conformation

@article {pmid41495863,
year = {2026},
author = {Ali, H and Rafiq, M and Manzoor, M and Gillani, SW and Degen, A and Iqbal, A and Wang, W and Rafiq, MK and Shang, Z},
title = {Seasonal shifts in vegetation, soil properties, and microbial communities in Western Himalayan forests.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00842-y},
pmid = {41495863},
issn = {2524-6372},
support = {31961143012//Natural Science Foundation of China/ ; ANSO-SBA-2023-02//Science-based Advisory Program of The Alliance of National and International Science Organizations for the Belt and Road Regions/ ; },
abstract = {BACKGROUND: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.

RESULTS: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p < 0.001) in summer than in winter while the community maturity index was higher (p < 0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p < 0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p < 0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p < 0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R = 0.222, p = 0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R[2]=0.64-0.72 for key paths) than in winter (R[2]=0.52-0.63).

CONCLUSIONS: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.},
}

@article {pmid41495321,
year = {2026},
author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K},
title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34186-x},
pmid = {41495321},
issn = {2045-2322},
support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; },
abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.},
}

@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02654-6},
pmid = {41495312},
issn = {1432-184X},
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}

@article {pmid41494802,
year = {2026},
author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C},
title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337480},
pmid = {41494802},
issn = {1468-3288},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.

OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.

DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, Índice de Alimentación Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6 months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.

RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.

CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.},
}

@article {pmid41494342,
year = {2026},
author = {Hu, P and Chen, S and Qian, Y and Hong, Y and Lin, JG and He, B and Gu, JD},
title = {Efficient nitrogen removal by coupling with methane metabolism in three landfill leachate wastewater treatment systems.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141035},
doi = {10.1016/j.jhazmat.2026.141035},
pmid = {41494342},
issn = {1873-3336},
abstract = {High concentration of ammonium-nitrogen (NH4[+]-N) is a widley known characteristic of landfill leachate, and therefore, a thorough understanding of the active nitrogen-related microorganisms is essential for designing an efficient landfill leachate treatment system. Here, we analyze the microbial nitrogen cycling and metabolic interactions at three full-scale landfill leachate treatment plants. Specifically, using metagenomics and metatranscriptomics techniques, we elucidate the mechanisms underlying high NH4[+]-N removal rates achieved through distinct N removal strategies (nitrification-denitrification system at Jilong (JL), denitrification-ammonia oxidation-partial nitrification system at Xinfeng (XF), and simultaneous nitrification-denitrification-ammonia oxidation system at Wenshan (WS)), all three plants achieved efficient NH4[+]-N removal of 96 %, 97.96 % and 97.33 % for JL, XF, and WS, respectively. Highly active methane (CH4)-associated microorganisms, particularly CH4-catabolizing bacteria, exhibited strong interactions with denitrifying bacteria in all three treatment plants, promoting effective nitrogen removal in the landfill treatment systems. In addition, enhanced anammox activity in WS treatment plant in 2023 and 2015 was compared using nitrogen-15 isotope labeling and in situ transcriptome analysis. By comparing microbial metabolic activity, strong interactions were observed between anammox bacteria and other nitrogen-transforming microbes. Meanwhile, detailed physicochemical parameter analysis revealed that optimal Fe[3] [+] concentrations significantly promote the enrichment and enhanced activity of anammox bacteria. Collectively, this study highlights strategies for microbial-mediated high-efficiency ammonia nitrogen removal in full-scale landfill leachate and explains the underlying mechanisms that may lead to increased abundance and activity of anammox bacteria.},
}

@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
doi = {10.1016/j.redox.2026.104005},
pmid = {41494287},
issn = {2213-2317},
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}