@article {pmid41857781,
year = {2026},
author = {Alexander, JE and Appleton, C and Beatty, SSK and Brown, DC and Carvell-Miller, L and McKee, TS and Morrison, J and Patterson-Kane, JC and Reynolds, R and Wadulack, S and , },
title = {Cohort profile of the first 2,000 canine enrolees in the Mars Petcare Biobank: demographic, hematologic and serum biochemistry results from March 2022 to December 2024.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {41857781},
issn = {1746-6148},
abstract = {BACKGROUND: The MARS PETCARE BIOBANK™ (MPB) is a study recruiting pets visiting Mars Veterinary Health hospitals in the USA over a ten-year period, with the aim of analysing longitudinal data from thousands of otherwise healthy dogs and cats at their first presentation to identify novel and actionable pet health insights . The present study summarises the baseline demographic, haematologic, and serum biochemistry data recorded for the first 2000 dogs enroled in the MPB study between March 2022 and December 2024 and considers how representative they are of the general population in the United States.

RESULTS: The median enrolment age was 3.0 years (0.5–10.0 yrs). The population was 52% male and 48% female with approximately 84% of the population having undergone neutering by their initial study visit. The median enrolment body weight was 20.0 kg (2.5 – 71.5 kg) and the median body condition score was 5/9 (range 3–7). One hundred and twenty eight breeds were represented and 47% of the population were described as mixed breed. The median values for all serum biochemistry and complete blood count parameters were within the applicable reference interval. For certain analytes including serum glucose, amylase, cholesterol, phosphorus, creatine phosphokinase, precision pancreatic lipase, platelet count, haematocrit, and haemoglobin more than 5% of dogs had results outside the reference intervals. On review only 0.25% of dogs were subsequently excluded from continuing the MPB study because the results were considered of clinical significance.

CONCLUSIONS: The MPB aims to enable research to deliver insights applicable to the general dog population accessing primary veterinary care in the USA, and recruits accordingly. These data suggest that the first 2,000 dogs recruited in the MPB are comparable in demographics to other studies of the US population. The number of blood test results falling outside of reference intervals (up to 17% depending on analyte), for dogs deemed by veterinarians to be healthy in the context of the clinical history and examination, raises questions around the definition of health and how reference intervals are used. Data gathered during the study is expected to provide valuable information to studies pertaining to genetic, metagenomic, metabolic, dietary, and environmental risk factors associated with early signals of transition to various common diseases.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-026-05419-6.},
}

@article {pmid41959053,
year = {2026},
author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA},
title = {Infant gut microbiomes contribute to metabolic states that impact brain function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41959053},
issn = {2692-8205},
abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.},
}

@article {pmid42043697,
year = {2026},
author = {Lomelí-Álvarez, MF and Escamilla-Montes, R and Diarte-Plata, G and Guo, X and Fierro-Coronado, JA and Rubio-Luque, AM and Vega-Carranza, AS and González, AL},
title = {Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42043697},
issn = {1678-4405},
abstract = {This study evaluated the effects of Bacillus licheniformis and Pediococcus pentosaceus administered in both culture water and feed to Penaeus vannamei over a 47-day experiment. Treatments in triplicate were as follows: (I) Commercial Feed (CF); (II) CF + P. pentosaceus in the water (3 × 10[6] CFU/L); (III) CF + B. licheniformis in the water (3 × 10[6] CFU/L); (IV) P. pentosaceus in fermented feed (51 × 10[5] CFU/g); (V) B. licheniformis in fermented feed (147 × 10[6] CFU/g); (VI) Mix of P. pentosaceus (140 × 10[5] CFU/g) + B. licheniformis (180 × 10[5] CFU/g) in fermented feed + Mix of P. pentosaceus + B. licheniformis (3 × 10[6] CFU/L) in the water. Growth, immune effectors (phenoloxidase and superoxide anion), and gut bacterial profiles via 16S metagenomic sequencing were assessed. Survival was determined after a challenge with Vibrio parahaemolyticus. Probiotics did not affect growth. Only B. licheniformis in water and fermented feed elicited a significant immunostimulatory response, increasing superoxide anion production and phenoloxidase activity, respectively. Probiotic administration also modulated the gut microbiota, significantly increasing the relative abundance of beneficial genera like Ruegeria and Haloferula. Measures of both alpha and beta diversity indicated a significant restructuring of the microbial community in response to probiotics. Most major bacterial groups showed predominantly positive intra-group interactions, while Psychromonadaceae solely exhibited negative interactions with other families. Shrimp survival was significantly higher in shrimp treated with probiotics, excluding treatment II. These results demonstrate that probiotics strengthen innate immunity and improves disease resistance in shrimp by enhancing immunocompetence and enriching beneficial gut microbes, offering a viable strategy for sustainable aquaculture health management.},
}

@article {pmid42050656,
year = {2026},
author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K},
title = {Correction: Bacteriophages in gut metagenomes: from analysis to application.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42050656},
issn = {1743-422X},
}

@article {pmid42050727,
year = {2026},
author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S},
title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00577-2},
pmid = {42050727},
issn = {2524-4671},
}

@article {pmid42050730,
year = {2026},
author = {Seppey, M and Benavides, A and Berkeley, MR and Manni, M and Zdobnov, EM},
title = {LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-04089-9},
pmid = {42050730},
issn = {1474-760X},
support = {ESKAS No. 2022.0531//Federal Commission for Scholarships for Foreign Students for the Swiss Government Excellence Scholarship/ ; 310030_189062//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.},
}

@article {pmid42051014,
year = {2026},
author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L},
title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70280},
pmid = {42051014},
issn = {1744-7917},
support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; },
abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.},
}

@article {pmid42051699,
year = {2026},
author = {Du, Y and Guo, Z and Yao, D and Wang, Y},
title = {Hemophagocytic lymphohistiocytosis secondary to Pneumocystis jirovecii pneumonia: a rare case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1795567},
pmid = {42051699},
issn = {2296-858X},
abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Pneumocystis jirovecii pneumonia (PJP) is extremely rare in children. We present the case of a 10-year-old girl with a history of idiopathic thrombocytopenic purpura (ITP) on long-term oral prednisone, who was admitted for progressive fever, cough, and dyspnea. Metagenomic next-generation sequencing of blood and bronchoalveolar lavage fluid confirmed PJP. Despite targeted antifungal therapy and respiratory support, she developed persistent high-grade fever, pancytopenia, hyperferritinemia, hypofibrinogenemia, and hemophagocytosis on bone marrow aspirate by day 10, meeting diagnostic criteria for HLH. Genetic testing was declined by the parents. Management included dexamethasone, continuous renal replacement therapy, and plasmapheresis. Unfortunately, her condition deteriorated, and she was discharged upon parental request on day 22, succumbing on the same day. To our knowledge, this is the first reported pediatric case of HLH secondary to PJP in China. This case highlights that in children with PJP-especially those on immunosuppressive therapy-the development of persistent fever and cytopenia should prompt immediate evaluation for secondary HLH to enable timely intervention.},
}

@article {pmid42052210,
year = {2026},
author = {Qu, HL and Li, JN and Gao, Y and Xu, XM and Zhang, XB and Yang, SD},
title = {From microscopy to antimicrobial decisions: a clinically grounded roadmap for critical care infectious diseases.},
journal = {Frontiers in artificial intelligence},
volume = {9},
number = {},
pages = {1807400},
pmid = {42052210},
issn = {2624-8212},
abstract = {In the intensive care unit (ICU), antibiotics often begin under extreme uncertainty. Fever, leukocytosis, hypotension, and organ dysfunction may signal bacterial infection, but the same findings are common with aspiration, post-operative inflammation, drug reactions, or sterile systemic inflammation. Cultures take time and their yield falls after antibiotics. Rapid molecular tests and metagenomics can add actionable information, but they also raise the burden of interpreting complex results. Microscopy is one of the few inputs that can shift management within minutes to hours: Gram-stain patterns from positive blood-culture bottles, respiratory specimens, cerebrospinal fluid, and wound material can reshape initial coverage and support early de-escalation when negative. Tissue and cytology help distinguish invasion from key mimics. The gap is consistency-reads vary across observers, workflows differ, and results do not always translate into reliable bedside actions. This review focuses on infectious-disease artificial intelligence (AI) as ICU bedside decision support, rather than as a survey of models. Using ICU sepsis as the primary use case-and neurocritical care as a challenging setting where sedation, brain injury, and noninfectious inflammation often mimic infection-we separate evidence into pathogen signals and host-response signals. We then map both streams to six decisions over the first 72 hours: start now versus pause, choose initial spectrum, reassess and narrow, escalate diagnostics and source control, act on high-risk resistance or invasive pathogens, and stop safely. We summarize where AI is most credible today (Gram-stain assistance, culture-plate triage, urine-culture screening, infection-focused digital pathology, host-response classifiers, and selected metagenomics) and what makes outputs actionable: calibrated probabilities, explicit confidence with safe deferral when uncertain, validation across hospitals and instruments, and endpoints tied to stewardship and safety (time to appropriate therapy, antibiotic days, de-escalation within 72 hours, missed bacteremia). Evidence was updated through February 28, 2026.},
}

@article {pmid42052392,
year = {2026},
author = {Suenaga, H and Fujihara, H},
title = {Molecular basis for adaptive evolution of aromatic degradation enzymes in bacteria revealed by metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1795400},
pmid = {42052392},
issn = {1664-302X},
abstract = {Aromatic hydrocarbons, including persistent polycyclic aromatic hydrocarbons (PAHs), impose strong selective pressures that drive the adaptive evolution of bacterial degradation systems. Metagenomic studies have revealed extensive diversification of key catabolic enzymes, such as ring-hydroxylating and ring-cleavage dioxygenases, through the accumulation of single-nucleotide polymorphisms (SNPs) and structural modifications that increase substrate range and enhance catalytic efficiency in polluted environments. These findings demonstrate that gene mutations that change enzyme properties collectively shape the evolution of aromatic-degrading bacteria. Metagenomics is powerful tools for elucidating these evolutionary processes and advancing applications in bioremediation and industrial biocatalysis.},
}

@article {pmid42052398,
year = {2026},
author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ},
title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794875},
pmid = {42052398},
issn = {1664-302X},
abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.},
}

@article {pmid42052556,
year = {2026},
author = {Chu, T and Liu, J and Zhang, Y and Yang, K and Li, S and Yan, Q and Li, Y},
title = {Metagenome-based virome analysis identifies the oral viral signatures for periodontitis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2662091},
pmid = {42052556},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis (PD) is a chronic infectious disease driven by bacterial biofilms, yet the oral virome's role in pathogenesis remains poorly understood.

OBJECTIVE: This cross-cohort meta-analysis aims to define PD-associated viral signatures, characterize predicted virus-host interactions, and evaluate the diagnostic potential of viral biomarkers.

METHODS: We integrated 89 saliva (44 PD, 45 healthy) and 86 subgingival plaque (48 PD, 38 healthy) metagenomes from six public cohorts for a unified virome analysis.

RESULTS: We identified 156 viral operational taxonomic units (vOTUs) significantly associated with PD (105 in saliva, 66 in subgingival plaque and 15 shared). PD-enriched vOTUs were predicted to target periodontal pathogens including Porphyromonas gingivalis, whereas Streptococcus-targeting phages were decreased. PD-associated vOTUs harbored diverse bacterial defense and anti-defense systems, with those enriched in PD overrepresenting lysozyme and replication-associated genes. Diagnostic models based on key viral markers achieved robust performance, with AUCs of 0.95 (saliva) and 0.92 (subgingival plaque) for classifying PD.

CONCLUSION: This study delineates a distinct oral virome profile in PD, highlights predicted virus-host interactions, and underscores the potential of viral biomarkers for PD diagnosis,providing a basis for future investigations into viral ecology and phage-based interventions.},
}

@article {pmid42052831,
year = {2026},
author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S},
title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {4},
pages = {48982},
doi = {10.31083/FBL48982},
pmid = {42052831},
issn = {2768-6698},
support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.

METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.

RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 ± 0.12, suggesting promising discriminatory potential that warrants further validation.

CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Glomerulonephritis, Membranous/microbiology
*Metagenomics/methods
Male
Female
Middle Aged
Feces/microbiology
Adult
*Bacteria/genetics/classification
Case-Control Studies

@article {pmid42053312,
year = {2026},
author = {Chung, B and Wang, S and Hao, Z and Allison, SD and Malik, AA},
title = {Plant litter chemistry and associated changes in microbial decomposition under drought.},
journal = {mBio},
volume = {},
number = {},
pages = {e0043826},
doi = {10.1128/mbio.00438-26},
pmid = {42053312},
issn = {2150-7511},
abstract = {UNLABELLED: Drought has consequences for microbial decomposition rates, including indirect effects through changes in plant litter chemistry. Here, we studied the impact of a decade-long drought on plant litter chemistry and microbial decomposition traits in a semi-arid ecosystem during an 18-month litter bag experiment. We investigated litter sourced from four conditions: grass and shrub vegetation under ambient and reduced precipitation. We hypothesized that litter chemistry drives microbial decomposition capabilities and enzyme activity due to vegetation differences and drought effects on litter chemistry. We found that carbohydrate-rich grass litter had a higher abundance of decomposition genes detected using metagenomics and enzyme activity than more recalcitrant shrub litter, which was richer in lignin and lipids; these patterns were related to substrate supply. Drought decreased some carbohydrate fractions in grass litter but did not change the lignin fraction in grass and shrub litter, suggesting that drought does not make litter more recalcitrant. Most decomposition genes and enzyme activities were not significantly affected by drought, thereby maintaining decomposition rates. Microbial community succession patterns-decreasing fungal abundance and increasing bacterial abundance with time-corresponded with decreasing chitin gene abundance and increasing peptidoglycan gene abundance over time, indicating microbial necromass recycling. We demonstrate minimal litter chemistry-mediated effects of drought but show significant changes in community composition and their decomposition capabilities over time, highlighting that complex microbial-chemical interactions under climate change can influence ecosystem-scale processes.

IMPORTANCE: Climate change is causing more severe and frequent droughts in semi-arid ecosystems, affecting soil microbes breaking down plant litter. Our research focuses on understanding the less studied pathway of drought impact on microbes via changes in plant litter chemistry. Drought can alter the plant litter chemistry by changing the composition and physiology of plants, which can alter microbial decomposition and ecosystem-level carbon cycling. We investigated litter decomposition traits of microbial communities in grass and shrub litter under long-term drought. There were significant changes in litter chemistry under drought but no increase in lignin fraction. Despite this, microbial communities maintained their decomposition capabilities under drought, highlighting the ability of microbes to adapt and continue functioning. We also demonstrate unique microbial community succession patterns and dead biomass recycling, which can have implications for carbon cycling rates in the ecosystem. This study sheds light on the complex microbial interactions that affect ecosystem functioning under climate change.},
}

@article {pmid42053608,
year = {2026},
author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N},
title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02779-2},
pmid = {42053608},
issn = {1432-184X},
support = {Project number: 116O328//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
}

@article {pmid42053852,
year = {2026},
author = {Peng, Q and Lin, Y},
title = {A case report of infective endocarditis caused by Mycoplasma pneumoniae in a child.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42053852},
issn = {1435-4373},
abstract = {OBJECTIVE: This study aimed to investigate the clinical features and management strategies for infective endocarditis(IE) caused by Mycoplasma pneumoniae(M. pneumoniae) in children, in order to enhance understanding of this rare extrapulmonary complication of M. pneumoniae infection and provide clinical insights for its diagnosis and treatment.

METHODS: We retrospectively analyzed the clinical data and management process of a pediatric patient diagnosed with IE who was admitted to our hospital in September 2025.

RESULTS: A 9-year-old male patient was admitted with initial symptoms of fever and cough and was diagnosed with M. pneumoniae pneumonia. Subsequently, prompted by the detection of a faint blowing murmur on auscultation, transthoracic echocardiography was performed, which revealed a vegetation in the right ventricle. Empirical antibiotic treatment with doxycycline combined with vancomycin and ceftriaxone was initiated. M. pneumoniae was detected in two blood specimens using metagenomic next-generation sequencing (mNGS), while all three conventional blood cultures remained negative. Treatment was subsequently adjusted to doxycycline monotherapy. On hospital day 11, follow-up echocardiography examination showed resolution of the vegetative, with no evidence of thromboembolic events. After discharge, the patient continued oral doxycycline for a total treatment duration of 4 weeks. Follow-up revealed good recovery.

CONCLUSIONS: M. pneumoniae pneumonia in children may be complicated by IE. Antimicrobial agents should be guided by regional antimicrobial resistance patterns and resistance gene testing. The addition of anti-inflammatory and anticoagulant therapies should be considered when clinically indicated. mNGS is a valuable diagnostic tool for identifying pathogens in cases of blood culture-negative IE.},
}

@article {pmid42053938,
year = {2024},
author = {Jang, YJ and Moon, JS and Kim, JE and Kim, D and Choi, HS and Oh, I},
title = {Blending Three Probiotics Alleviates Loperamide-Induced Constipation in Sprague-Dawley (SD)-Rats.},
journal = {Food science of animal resources},
volume = {44},
number = {1},
pages = {119-131},
doi = {10.5851/kosfa.2023.e61},
pmid = {42053938},
issn = {2636-0780},
abstract = {BIOVITA 3 bacterial species (BIOVITA 3), a probiotic blend powder containing Clostridium butyricum IDCC 1301, Weizmannia coagulans IDCC 1201 and Bacillus subtilis IDCC 1101, has been used as a food ingredient for gut health. However, its efficacy in improving constipation has not been reported. Therefore, we aimed to investigate the functional effects of oral administration of BIOVITA 3 as well as its component strains alone (at 1.0×10[9] CFU/day) in Sprague-Dawley (SD) rats with loperamide-induced constipation. The study included fecal analysis, gastrointestinal transit ratio, histopathological analysis, short chain fatty acids (SCFAs), and metagenome analysis. As results, the BIOVITA 3 group showed significant improvements in fecal number, water content, gastrointestinal transit ratio, and thickening of the mucosal layer. In the SCFAs analysis, all probiotic-treated groups showed an increase in total SCFAs compared to the loperamide-constipated group. Changes in microbial abundance and the diversity index of three groups (normal, constipated, and BIOVITA 3) were also defined. Of these, the BIOVITA 3 showed a significant improvement in loperamide-constipated SD-rats. This study suggests the possibility that BIOVITA 3 can be applied as an ingredient in functional foods to relieve constipation.},
}

@article {pmid42054100,
year = {2026},
author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE},
title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001705},
pmid = {42054100},
issn = {2057-5858},
mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; },
abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.},
}

Animals
*Metagenomics/methods
*Food Microbiology
Chickens/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
*Meat/microbiology
Cattle
Sheep
Salmon/microbiology
United Kingdom
Microbiota/genetics
Anti-Bacterial Agents/pharmacology
Swine

@article {pmid42054312,
year = {2026},
author = {Revel, J and Leroy, J and Delbecq, S and Constant, O and Marty, F and Naili, C and Barthès, A and Nagy, A and Schmidt-Chanasit, J and Cadar, D and Abd Rahaman, NY and Lajoix, AD and Desmetz, C and Simonin, Y},
title = {Differential Properties of NS1 Glycoproteins in West Nile and Usutu Viruses.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2667565},
doi = {10.1080/22221751.2026.2667565},
pmid = {42054312},
issn = {2222-1751},
abstract = {AbstractWest Nile virus (WNV) and Usutu virus (USUV) are neurotropic orthoflaviviruses of the Flaviviridae family, transmitted primarily by Culex mosquitoes and maintained in enzootic cycles involving birds. While WNV is a well-established human pathogen causing hundreds of neuroinvasive cases annually in Europe, USUV has emerged more recently, with fewer documented human infections but increasing evidence of neurovirulence. The viral nonstructural protein 1 (NS1) plays a central role in orthoflavivirus pathogenesis by modulating host immune responses, disrupting endothelial barrier integrity, and facilitating viral dissemination. However, the functional and biochemical properties of NS1 from WNV and USUV remain poorly characterized. We combined in vitro, in vivo, and clinical approaches to compare NS1 secretion, stability, and its impact on blood-brain barrier. Our results show that WNV NS1 is secreted at significantly higher levels, exhibits greater thermal stability, and disrupts brain endothelial barrier integrity in vitro. In contrast, USUV NS1 is secreted less efficiently, is slightly less stable, and does not compromise blood-brain barrier integrity, despite inducing distinct transcriptional responses in brain endothelial cells. In mice, WNV infection led to higher serum NS1 levels and stronger systemic inflammation than USUV. Clinically, WNV NS1 was detected mainly in patients with neurological symptoms, whereas USUV NS1 remained undetectable in all cases. Altogether, these findings reveal differential NS1 properties between these closely related viruses, with key implications for orthoflavivirus diagnosis and neurovirulence mechanisms.},
}

@article {pmid42054365,
year = {2026},
author = {Santos-Júnior, CD and Escobar, MC and Huber, P and Niño-Garcia, JP and Cardona, GI and Costa-Pereira, R and Sarmento, H},
title = {Resource availability structures microbial competition through genomic niche partitioning.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2526391123},
doi = {10.1073/pnas.2526391123},
pmid = {42054365},
issn = {1091-6490},
support = {862923//EC | Horizon 2020 Framework Programme (H2020)/ ; 304655/2025-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/15842-6//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 23/02850-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 20/11953-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2025hsqd014//Hubei Hongshan Laboratory/ ; },
mesh = {Humans ; Ecosystem ; Metagenome ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Biodiversity ; Bacteria/genetics/classification ; Metagenomics/methods ; Soil Microbiology ; Genomics ; Microbiota/genetics ; *Microbial Interactions ; },
abstract = {Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo's predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.},
}

Humans
Ecosystem
Metagenome
Phylogeny
*Gastrointestinal Microbiome/genetics
Biodiversity
Bacteria/genetics/classification
Metagenomics/methods
Soil Microbiology
Genomics
Microbiota/genetics
*Microbial Interactions

@article {pmid42054706,
year = {2026},
author = {Vilaseca, A and Toledano, M and Flanagan, EP},
title = {Complexities in evaluation and management of infectious myelopathies.},
journal = {Current opinion in infectious diseases},
volume = {39},
number = {3},
pages = {227-239},
doi = {10.1097/QCO.0000000000001204},
pmid = {42054706},
issn = {1473-6527},
mesh = {Humans ; *COVID-19/complications ; *Spinal Cord Diseases/diagnosis/virology/therapy/etiology ; SARS-CoV-2 ; *Myelitis/diagnosis/virology ; Magnetic Resonance Imaging ; },
abstract = {PURPOSE OF REVIEW: To review recent advances in infectious myelopathies and integrate them into a practical, syndrome-based approach that supports early recognition, guides testing, and avoids pitfalls.

RECENT FINDINGS: Advances in MRI pattern recognition and pathogen-specific diagnostics have refined the evaluation of infectious myelopathies, with strategies tailored to geographic epidemiology, host susceptibility, and distinction from immune-mediated causes. During the COVID-19 pandemic, SARS-CoV-2-associated myelopathy emerged as a rare para- or postinfectious cause of myelitis. The pandemic coincided with a decline in enterovirus outbreaks and acute flaccid myelitis, which are now re-emerging, underscoring the importance of epidemiologic surveillance. Metagenomic next-generation sequencing is useful in suspected infectious myelopathy because it can identify unexpected pathogens from cerebrospinal fluid, but its imperfect sensitivity and contamination risk mean it should complement rather than replace conventional testing. Growing recognition of compartmentalized central nervous system inflammation and cerebrospinal fluid viral escape in HIV myelopathy has shifted management toward antiretroviral resistance patterns and treatment optimization. Therapeutic advances remain limited and largely pathogen-specific, although targeted approaches such as mogamulizumab for HTLV-1-associated myelopathy are promising.

SUMMARY: Recent progress in infectious myelopathies has been driven by improved pathogen detection and more tailored diagnostic strategies, although treatment advances are beginning to emerge.},
}

Humans
*COVID-19/complications
*Spinal Cord Diseases/diagnosis/virology/therapy/etiology
SARS-CoV-2
*Myelitis/diagnosis/virology
Magnetic Resonance Imaging

@article {pmid42055201,
year = {2026},
author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M},
title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110551},
doi = {10.1016/j.cbpc.2026.110551},
pmid = {42055201},
issn = {1532-0456},
abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.},
}

@article {pmid42055262,
year = {2026},
author = {Trinh, HP and Lee, SH and Park, HD},
title = {Mitigating nitrite stress and restoring functional redundancy in anammox reactor via acetate-driven DNRA-anammox coupling.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134732},
doi = {10.1016/j.biortech.2026.134732},
pmid = {42055262},
issn = {1873-2976},
abstract = {Frequent fluctuations in nitrite concentrations and unstable control of partial nitritation often lead to excessive NO2[-] accumulation, resulting in performance deterioration in anammox-based systems. To address this challenge, an anammox reactor was operated for 180 days to investigate the inhibitory effects of elevated NO2[-]/NH4[+]ratios on anammox activity and to evaluate the effectiveness of external carbon supplementation in promoting dissimilatory nitrate reduction to ammonium (DNRA)-related pathways that contribute to NO2[-] reduction. Increasing NO2[-]/NH4[+]ratio from 1.3 to 3.0 decreased the nitrogen removal efficiency from 96.7% to 26.6%, reduced the relative abundance of anammox bacteria (Ca. Kuenenia and Ca. Jettenia) from 41.5% to 7.0% and promoted Nitrospira to 7.7%. In contrast, acetate supplementation at a C/N ratio of 0.2 suppressed Nitrospira to 0.2% and enhanced the abundance of anammox and DNRA-performing bacteria (e.g., Fimbriimonadaceae, Mycobacterium, Anaerolineales, Caldilineaceae, and Ignavibacteriaceae) to 31.2% and 15.7%, respectively. Metagenome-assembled genome analysis confirmed the enrichment of functional genes associated with anammox (hzsABC and hdh) and DNRA metabolism (nirBD and nrfAH), corresponding to the recovery of nitrogen removal efficiency to 82.3%. Quantitative microbial network analysis further revealed that functional redundancy index declined from 0.56 to 0.42 under nitrite stress but recovered to 0.53 following acetate supplementation, indicating the restoration of a functionally buffered microbial community. Overall, these results demonstrate that low-level acetate supplementation, (C/N = 0.2) effectively stimulated DNRA-mediated NO2[-] reduction to NH4[+] by both DNRA-performing bacteria, thereby supporting anammox activity and providing an energy-efficient strategy to mitigate NO2[-] accumulation and stabilize nitrogen removal in anammox-based systems.},
}

@article {pmid42055314,
year = {2026},
author = {Zhang, Y and Xia, J and Qiu, Z and Tian, S and Wang, J and Ren, X and Chen, M},
title = {Successful Treatment of Balamuthia Mandrillaris Amebic Encephalitis Diagnosed by MetaCAP in China: A Case Report and Review of 25 Survival Cases.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108745},
doi = {10.1016/j.ijid.2026.108745},
pmid = {42055314},
issn = {1878-3511},
abstract = {Balamuthia mandrillaris, a free-living amoeba, can cause Balamuthia amebic encephalitis (BAE), a rare and often fatal cerebral infection. The reported mortality rate is >90%, largely attributable to the absence of specific clinical manifestations, sensitive diagnostic methods and effective therapeutic interventions. We herein describe a middle-aged, male patient diagnosed with BAE using Metagenomic Capture sequencing (MetaCAP) who achieved full recovery following early medical therapy without neurosurgical treatment. Our findings indicate that MetaCAP serves as a rapid and sensitive diagnostic approach, and sulfasalazine may confer a potential anti-inflammatory benefit in the management of BAE. In addition, we reviewed 25 survival cases of BAE reported in the PubMed database up to now.},
}

@article {pmid42055803,
year = {2026},
author = {Auwal, AM and Matthews, R and Cook, C and Sargent, B and Easton, A and Ray, STJ and Ellul, MA and Michael, BD},
title = {Suspected encephalitis in adults.},
journal = {Practical neurology},
volume = {},
number = {},
pages = {},
doi = {10.1136/pn-2024-004299},
pmid = {42055803},
issn = {1474-7766},
abstract = {'Query encephalitis' is one of the most common reasons for inpatient neurology referral in the context of an acutely confused patient. Growing evidence suggests that time to treatment is a key determinant of outcome in both infectious and autoimmune encephalitis; hence, these two causes should be considered simultaneously at presentation. However, under-recognition and the existence of several mimics make a rapid diagnosis of encephalitis challenging. Appreciation of clinical syndromes can guide aetiological investigation and consequent treatment. In this article, we discuss clinical phenotypes associated with both infectious and autoimmune encephalitis, as well as a systematic approach to their investigation and up-to-date treatment strategies. We also highlight ongoing areas of research, such as metagenomics and therapeutic trials.},
}

@article {pmid42056322,
year = {2026},
author = {Thakkar, S and Rathour, R and Rana, SS and Samant, S and Kikani, BA and Madamwar, D and Desai, C},
title = {Biochar-augmented microaerophilic fixed-film bioreactor integrated with an aerobic membrane bioreactor effectively reduces persistent, mobile chemicals in the CETP effluent treatment.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42056322},
issn = {1573-0972},
support = {File No. GSBTM/JD(R&D)/662/2022-23/00292469//Gujarat State Biotechnology Mission (GSBTM), Department of Science and Technology, Government of Gujarat/ ; },
mesh = {*Bioreactors/microbiology ; *Charcoal/chemistry ; Aerobiosis ; *Water Pollutants, Chemical/metabolism ; *Waste Disposal, Fluid/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Membranes, Artificial ; *Water Purification/methods ; Biodegradation, Environmental ; Wastewater/chemistry/microbiology ; Biological Oxygen Demand Analysis ; },
abstract = {Different classes of chemical compounds including persistent, mobile chemicals (PMCs) often bypass the conventional treatment processes of common effluent treatment plants (CETPs), resulting in their unmonitored release into aquatic environments. In this study, an integrated treatment system comprising a microaerophilic fixed-film bioreactor (MFB) and an aerobic membrane bioreactor (Ae-MBR) was engineered to treat secondary CETP effluent. Two types of packing materials in the engineered MFBs were evaluated: one with wood charcoal (C-MFB) and another with 30% (w/w) biochar-augmented charcoal (BAC-MFB). The BAC-MFB showed better treatment efficiency, achieving 69.17% colour (Pt-Co units) removal and 93.01% COD removal at an optimal 3d hydraulic retention time (HRT). Integration with Ae-MBR further enhanced the treatment, achieving > 95% COD and > 94% colour removal, with an overall > 85% reduction in total number of parent chemical compounds and a specific > 83% reduction in PMCs from CETP effluent. At 3d HRT, bacterial community analysis revealed dominance of Campylobacterota and Bacillota in BAC-MFB under microaerophilic conditions, whereas Bacillota dominated in the Ae-MBR under aerobic conditions. The predicted metagenome analysis revealed significant enrichment of benzoate and aminobenzoate degradation pathways in the integrated system. While the BAC-MFB treatment alone achieved sufficient COD removal, its integration with Ae-MBR markedly enhanced the reduction in overall chemical complexity including PMCs from the CETP effluent. This study demonstrates that the engineered hybrid BAC-MFB-Ae-MBR system is a sustainable solution for the treatment of industrial CETP effluents.},
}

*Bioreactors/microbiology
*Charcoal/chemistry
Aerobiosis
*Water Pollutants, Chemical/metabolism
*Waste Disposal, Fluid/methods
Bacteria/genetics/classification/metabolism/isolation & purification
Membranes, Artificial
*Water Purification/methods
Biodegradation, Environmental
Wastewater/chemistry/microbiology
Biological Oxygen Demand Analysis

@article {pmid42056687,
year = {2026},
author = {Wedell, E and Shen, C and Warnow, T},
title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2981},
number = {},
pages = {37-52},
pmid = {42056687},
issn = {1940-6029},
mesh = {*Phylogeny ; *Software ; *Metagenomics/methods ; Algorithms ; Likelihood Functions ; *Computational Biology/methods ; },
abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.},
}

*Phylogeny
*Software
*Metagenomics/methods
Algorithms
Likelihood Functions
*Computational Biology/methods

@article {pmid42056742,
year = {2026},
author = {Zhang, X and Li, Q and Yang, H and Li, H and Hu, C},
title = {Active responses of cyanobacterial crusts directly exposed to the extreme stratospheric environment.},
journal = {Life sciences in space research},
volume = {50},
number = {},
pages = {133-145},
doi = {10.1016/j.lssr.2026.01.001},
pmid = {42056742},
issn = {2214-5532},
abstract = {The stratosphere's highly hostile environment offers a unique and relatively accessible setting to evaluate extremophilic adaptation for extraterrestrial colonization. The accelerating pace of the Martian project has underscored the need for a better understanding of the synergistic responses of microbial communities in Mars-like habitats. Here, we loaded the cyanobacterial crust, a model system with multiple trophic levels, onto a balloon-borne astrobiology platform for a direct-exposure experiment in the stratosphere, aligned with the ground-control and indoor-simulated groups. After short-term in-situ exposure, we performed multi-omics analyses to delineate alterations in community composition and the community-level metabolic response. We observed a significant shift in the community composition of active members, with the relative abundance of photoautotrophs (except Scytonema) declining while that of chemotrophs increased. However, we demonstrated the unique thriving of the cyanobacterial genus Scytonema, attributed to its synthesis of the anti-ultraviolet compound scytonemin, its diverse material, and its energy acquisition. Meanwhile, the distinct metabolic profiles exhibited by various species and their interspecies metabolic interactions synergistically facilitated the retention of organic carbon and nitrogen, ultimately sustaining the stability of the biocrust community. Our study underscores the adaptive resilience of cyanobacterial crusts under stratospheric stresses. Notably, the robustness of Scytonema, particularly its unique survival capabilities, highlights its potential for extraterrestrial applications.},
}

@article {pmid42056812,
year = {2026},
author = {Fu, Y and Zhuang, H and Shi, J},
title = {Reshaping of the electron transport chain and carbon metabolism by low-loading Fe3O4@PU for enhanced phenolic compounds degradation in an algal-bacterial biofilm system.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142207},
doi = {10.1016/j.jhazmat.2026.142207},
pmid = {42056812},
issn = {1873-3336},
abstract = {While previous algal-bacterial biofilm systems without magnetite have shown limited resilience to high concentration phenolic compounds, this study demonstrates that introducing low loading (5%) nano-Fe3O4 substantially enhances degradation stability by optimizing electron transfer pathways. Four algal-bacterial reactors with varying Fe3O4 loadings (5-50%) were constructed using polyurethane carriers to treat phenolic wastewater under increasing total phenol (TPh) concentrations (50-300 mg/L). The 5% loading reactor (R1) demonstrated outstanding performance, achieving > 80% TPh removal and approximately 76% COD removal even at the highest loading. Compared to without magnetite systems, R1 achieved 13-15% higher TPh degradation at 300 mg/L. R1 also exhibited the highest electron transfer system activity (0.487 μg O2·gVSS[-1]·h[-1]) and cytochrome c content (72.12 mg/g VSS), indicating that Fe3O4 serves as an electron shuttle, compensating for endogenous electron carrier limitations. Metagenomic analysis revealed that the enhanced performance stemmed from robust carbohydrate metabolism, particularly the upregulation of key glycolytic enzymes (pfkA) and glycogen degrading enzymes (GH13), ensuring efficient NADH/ATP production. This metabolic advantage supplied reducing power to the Fe3O4 optimized electron transport chain, synchronizing electron generation with respiratory utilization. These findings demonstrate that low-dose Fe3O4 optimizes natural electron transfer pathways by coupling metabolic flux with respiratory chain activity, offering a cost effective strategy for treating high strength industrial wastewater.},
}

@article {pmid42046358,
year = {2026},
author = {Chen, K and Huang, L},
title = {[Metagenomic next - generation sequencing for diagnosis of infection of unknown origin in intensive care units: a bibliometric analysis].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {38},
number = {1},
pages = {79-83},
doi = {10.16250/j.32.1915.2026077},
pmid = {42046358},
issn = {1005-6661},
mesh = {*Bibliometrics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Intensive Care Units ; *Metagenomics/methods ; },
abstract = {OBJECTIVE: To investigate the scientific outputs of metagenomic next-generation sequencing (mNGS) for diagnosis of infection of unknown origin in intensive care units (ICUs), and to decipher the latest advances, frontier trends and spatiotemporal evolution of research hotpots in mNGS for diagnosis of infection of unknown origin in ICUs.

METHODS: Publications pertaining to the application of mNGS in diagnosis of infection of unknown origin in ICUs were retrieved from Web of Science Core Collection (WOSCC) from January 1, 2015 to December 31, 2024. The software Scimago Graphica 1.0.30 was employed to generate the network maps of collaboration relationships between countries, international collaborative relationships, author collaborations, institutional collaborative relationships, and a heatmap of journals, and the software VOSviewer 1.6.18 was used to create a heatmap of keywords, and maps of keyword co-occurrence clustering and keyword clustering timelines. In addition, the keyword burst map was created using the software CiteSpace 6.3.R3.

RESULTS: A total of 1 707 publications were included in the final analysis, and the number of publications appeared an overall tendency towards a rise from 2015 to 2024, with the largest number of publications seen in 2024 (545 publications). The largest number of publications was recorded in China (1 390 publications), followed by in USA (190 publications) and United Kingdom (31 publications), and China led the global research in this field, with 81% of global related researches linked with China. Frontiers in Cellular and Infection and Microbiology published the largest number of articles (212 publications, 12.42%), and Joseph Derisi was the most productive author (33 publications). Author collaborations occurred within groups; however, there was a lack of close inter-group collaborations, with University of California, San Francisco and Chan Zuckerberg Biohub-based group seen as the largest collaborative group. High-frequency co-occurrence keywords included mNGS, infection, diagnosis, case report, community-acquired pneumonia and bronchoalveolar lavage fluid, and the 100 most common high-frequency co-occurrence keywords were assigned into four clusters. Keyword clustering timeline analysis revealed that the research hotspots in this field shifted from virus sequencing and sequence alignment to severe pulmonary infections, and keyword burst analysis showed identification, mNGS and virus as top three keywords with the highest burst intensity.

CONCLUSIONS: mNGS was mainly used for identification of viruses among patients with infections of unknown origins in ICUs from 2015 to 2024, and future research priority shifted to pathogen detection for severe pulmonary infections.},
}

*Bibliometrics
*High-Throughput Nucleotide Sequencing/methods
Humans
*Intensive Care Units
*Metagenomics/methods

@article {pmid42046871,
year = {2026},
author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q},
title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {4},
pages = {375-389},
doi = {10.1631/jzus.B2400495},
pmid = {42046871},
issn = {1862-1783},
support = {2021YFA0805904//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; },
abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.},
}

Animals
*Gastrointestinal Microbiome/genetics
Humans
Mice
Germ-Free Life
*Fecal Microbiota Transplantation/methods
Feces/microbiology
*Metagenomics
Reproducibility of Results
High-Throughput Nucleotide Sequencing
Male
*Metagenome
Mice, Inbred C57BL
Female

@article {pmid42047611,
year = {2026},
author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C},
title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.70219},
pmid = {42047611},
issn = {1525-1470},
support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson & Johnson Consumer Inc./ ; },
abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.

METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.

RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.

CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.},
}

@article {pmid42047812,
year = {2026},
author = {Zhu, R and Zhang, J and Shen, HL},
title = {Hip joint infection by Prevotella denticola in rheumatoid arthritis : A case diagnosed with metagenomic sequencing.},
journal = {Wiener klinische Wochenschrift},
volume = {},
number = {},
pages = {},
pmid = {42047812},
issn = {1613-7671},
abstract = {BACKGROUND: Infection, as a complication of rheumatoid arthritis (RA), has attracted increasing attention from rheumatologists. Here, we present the first case of RA with hip joint infection, which was driven by infection with Prevotella denticola. Anaerobic bacterial infection was identified by metagenomic next-generation sequencing (mNGS).

METHODS: We describe the case of a 56-year-old woman with a history of RA who was admitted for intense hip joint pain and intermittent fever following long-term oral glucocorticoid (GC) treatment.

RESULTS: Although blood and hip joint effusion cultures for aerobic and anaerobic organisms were negative, we considered the possibility of a clinical diagnosis of hip joint infection; therefore, empirical antibiotic treatment was initiated but it was ineffective in this case. Prevotella denticola was identified by mNGS from the hip joint effusion obtained via ultrasound-guided puncture and the organism was resistant to the initial antimicrobial treatment. Finally, the adjustment of antimicrobial treatment led to successful treatment.

CONCLUSION: Patients with RA have a significantly greater risk of infections than the general population; however, Prevotella denticola infection of the hip joint has not been previously reported. The combination of ultrasound-guided puncture and mNGS to accurately recognize and treat joint infection in patients with RA in a timely manner is necessary to prevent the development of complications, a strategy worthy of further clinical application.},
}

@article {pmid42048337,
year = {2026},
author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM},
title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347959},
doi = {10.1371/journal.pone.0347959},
pmid = {42048337},
issn = {1932-6203},
mesh = {Colombia ; *Mangifera/microbiology ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Air Pollutants/metabolism ; Microbiota/genetics ; *Metagenome ; Phylogeny ; Cities ; },
abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.},
}

Colombia
*Mangifera/microbiology
*Bacteria/genetics/classification/drug effects
Metagenomics
RNA, Ribosomal, 16S/genetics
*Air Pollutants/metabolism
Microbiota/genetics
*Metagenome
Phylogeny
Cities

@article {pmid42048878,
year = {2026},
author = {Shi, W and Qin, Y and Li, W and Xu, J and Xu, H and Liu, Y},
title = {The dual role of phosphorus regeneration in controlling arsenic speciation: Iron-reducing bacteria in a seasonally ice-covered lake.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142206},
doi = {10.1016/j.jhazmat.2026.142206},
pmid = {42048878},
issn = {1873-3336},
abstract = {While the reductive dissolution of iron (hydro)oxides by dissimilatory iron‑reducing bacteria (DFeRB) can mobilize sediment bound arsenic (As), the role of concomitant phosphorus (P) regeneration in actively governing As speciation transformation, rather than mere release, remains mechanistically unclear, especially under seasonally contrasting redox regimes of ice-covered lakes. This study demonstrated that DFeRB mediated P regeneration exerts a dual, season‑dependent control over As speciation in lacustrine sediments. Through microcosm experiments simulating ice‑bound and summer periods, combined with sequential extraction, X‑ray diffraction, metagenomics, and structural equation modeling (SEM), and partial least-squares path modeling (PLS-PM), resolved that regenerated P not only promote As desorption via competitive adsorption but also redirect a substantial speciation of released As into a stable, pyrite‑coprecipitated pool (As‑S7). This sequestration pathway was particularly pronounced under ice‑bound anoxia, where DFeRB sustained a low‑rate, long‑duration reduction mode, as evidenced by persistent iron‑reduction gene (K02650, K17230) abundance and delayed As(III) peak release. SEM/PLS-PM quantified the seasonal shift in dominant mechanisms: summer release was driven by intensive P competition (including organic phosphorus), whereas ice‑bound conditions favored Fe‑S‑As co‑precipitation, effectively coupling prolonged microbial iron reduction to long‑term As immobilization. These findings establish P regeneration as a decisive switch between As mobility and stability in anaerobic sediments and define the seasonal microbial‑mineral feedbacks that modulate this switch. This work provides a predictive basis for assessing As fate in seasonally stratified water bodies under changing climatic conditions and a process-based basis for risk assessment and eutrophication management.},
}

@article {pmid42049031,
year = {2026},
author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q},
title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102780},
doi = {10.1016/j.xcrm.2026.102780},
pmid = {42049031},
issn = {2666-3791},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.},
}

@article {pmid42049067,
year = {2026},
author = {Khandelwal, S and Mishra, A and Pandey, SK},
title = {Integrating microbial bioremediation, multi-omics, and emerging technologies for polycyclic aromatic hydrocarbon (PAHs) detoxification.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107519},
doi = {10.1016/j.mimet.2026.107519},
pmid = {42049067},
issn = {1872-8359},
abstract = {Environmental organic pollutants, identified as Polycyclic Aromatic Hydrocarbons (PAHs), are widespread and toxic. These hydrocarbons are commonly produced by industrial activities, burning fossil fuels, and crude oil discharges. Their high hydrophobicity, tendency to bioaccumulate, and mutagenic, carcinogenic, teratogenic, and genotoxic properties lead to significant environmental and human health risks. Additionally, their low bioavailability and chemical stability complicate PAHs remediation. In recent years, various methods have been explored to reduce their impact, including conventional physical and chemical treatments; however, these often face issues such as inadequate removal, high costs, lengthy processes, and environmental concerns. Bioremediation has emerged as a promising, environmentally friendly solution. This approach involves microorganisms such as bacteria, fungi, algae, and archaea utilizing specific enzymatic pathways-like dioxygenases, monooxygenases, peroxidases, and laccases-to transform PAHs into less toxic substances. Advances in genomics and metagenomics have identified key catabolic genes (e.g., nah, Phn, nid, pah) and regulatory mechanisms that enhance microbial resistance in PAH-contaminated environments. Since PAHs' low bioavailability and solubility often limit bioremediation alone, integrated strategies are gaining prominence. In-situ and ex-situ methods-including bioaugmentation, bio-stimulation, composting, and phytoremediation-boost microbial degradation of PAHs. Furthermore, advanced technologies such as multi-omics platforms, CRISPR-based genetic engineering, and artificial intelligence (AI) are transforming the field by enabling the development of targeted microbial strains, improving bioremediation efficiency, and creating predictive models. This review offers a recent, comprehensive outline by unifying PAHs toxicity, microbial degradation, traditional remediation, and advanced biotechnological tools into a single framework. A comprehensive and recent update of microbial and biotechnological approaches for sustainable PAHs bioremediation is offered by this review.},
}

@article {pmid42049248,
year = {2026},
author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM},
title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70161},
doi = {10.1002/cph4.70161},
pmid = {42049248},
issn = {2040-4603},
support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus/physiology ; Prospective Studies ; Middle Aged ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Adult ; Aged ; *Hypertension, Pulmonary/microbiology ; Ventricular Dysfunction, Right ; },
abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.

METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.

RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.

CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.},
}

Humans
Male
Female
*Gastrointestinal Microbiome/physiology
*Lactobacillus/physiology
Prospective Studies
Middle Aged
*Pulmonary Arterial Hypertension/microbiology/physiopathology
Adult
Aged
*Hypertension, Pulmonary/microbiology
Ventricular Dysfunction, Right

@article {pmid42049488,
year = {2026},
author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ},
title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338223},
pmid = {42049488},
issn = {1468-3288},
abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.

OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.

DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.

RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.

CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.},
}

@article {pmid42049592,
year = {2026},
author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , },
title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.04.005},
pmid = {42049592},
issn = {1873-5010},
abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.},
}

@article {pmid42049781,
year = {2026},
author = {Manohar, CS and Ghose, M and Parab, AS},
title = {Integrated metagenomic analysis of bacteriomes associated with beach-cast seaweeds reveals metabolic potential for biotechnological and environmental applications.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46393-1},
pmid = {42049781},
issn = {2045-2322},
support = {MLP2019//Council of Scientific and Industrial Research, India/ ; },
}

@article {pmid42050358,
year = {2026},
author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y},
title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70567},
pmid = {42050358},
issn = {1365-3040},
support = {2024CXPT072//Key R&D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; },
abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.},
}

@article {pmid41436515,
year = {2025},
author = {Algarni, AD and Abd El-Samie, FE and Soliman, NF and Emara, HM and Algarni, F and Abd-Alhalem, SM and Marie, HS},
title = {Exploiting fuzzy weights in CNN model-based taxonomic classification of 500-bp sequence bacterial dataset.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44733},
pmid = {41436515},
issn = {2045-2322},
mesh = {Datasets as Topic ; *Fuzzy Logic ; *Convolutional Neural Networks ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics ; Deep Learning ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; },
abstract = {Taxonomic classification plays a crucial role in understanding the diversity and evolutionary relationships among bacteria. Accurately classifying bacterial DNA sequences based on a limited 500-bp segment remains challenging. This paper presents an improved Fuzzy-weighted Convolutional Neural Network (F-CNN) for taxonomic classification of bacterial DNA sequences, specifically focusing on the 500-bp segments. The proposed model aims to overcome the limitations of traditional classification methods by leveraging the power of deep learning and fuzzy logic processing. The improved fuzzy deep learning model is proposed to handle the problem of classifying samples with similar probabilities in the classification layer. It incorporates a feature selection stage using various techniques and a fuzzy weighting system to handle the uncertainty associated with similar classes in the classification layer and optimize parameters using fuzzy weights. The experimental results on the Ribosomal Database Project Release 11 (RDP 11) sequences dataset show the superiority of the proposed model, especially at the 500-bp region. Experimental results on the RDP 11 dataset, which includes over 1.4 million bacterial gene sequences, demonstrate the superior performance of the proposed model, achieving a classification accuracy up to 84.03% at the genus level for 500-bp segments and demonstrating high generalization when applied to longer sequences. This paper has significant implications for various fields, including microbiology, epidemiology, and environmental science, where accurate classification of bacteria is crucial for understanding their roles in different ecosystems and disease outbreaks.},
}

Datasets as Topic
*Fuzzy Logic
*Convolutional Neural Networks
DNA, Bacterial/genetics
*Bacteria/classification/genetics
Deep Learning
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Computational Biology/methods

@article {pmid42036837,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70359},
doi = {10.1111/1751-7915.70359},
pmid = {42036837},
issn = {1751-7915},
support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; },
mesh = {*Microbiota ; *Chitin/metabolism ; Soil Microbiology ; *Bacteria/enzymology/genetics/classification ; Phenotype ; Chitinases/genetics/metabolism ; Genetic Association Studies ; },
abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.},
}

*Microbiota
*Chitin/metabolism
Soil Microbiology
*Bacteria/enzymology/genetics/classification
Phenotype
Chitinases/genetics/metabolism
Genetic Association Studies

@article {pmid42037322,
year = {2026},
author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP},
title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {9},
pages = {e71828},
doi = {10.1096/fj.202600054R},
pmid = {42037322},
issn = {1530-6860},
support = {APIDOM-BACTERIOB//CHU de La Réunion/ ; //Institut National de la Santé et de la Recherche Médicale (Inserm)/ ; //University of La Réunion/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Periodontitis/microbiology/metabolism/complications/pathology ; Male ; Female ; *Intra-Abdominal Fat/metabolism/pathology ; Middle Aged ; Adult ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/metabolism/microbiology/pathology ; *Metabolic Diseases/microbiology/metabolism ; Dysbiosis/microbiology ; Porphyromonas gingivalis ; *Mouth/microbiology ; },
abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Periodontitis/microbiology/metabolism/complications/pathology
Male
Female
*Intra-Abdominal Fat/metabolism/pathology
Middle Aged
Adult
*Obesity, Morbid/microbiology/complications/metabolism
*Inflammation/metabolism/microbiology/pathology
*Metabolic Diseases/microbiology/metabolism
Dysbiosis/microbiology
Porphyromonas gingivalis
*Mouth/microbiology

@article {pmid42037351,
year = {2026},
author = {Chakraborty, S and Mukherjee, D and Sar, P},
title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0005926},
doi = {10.1128/mra.00059-26},
pmid = {42037351},
issn = {2576-098X},
abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.},
}

@article {pmid42037384,
year = {2026},
author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ},
title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0358725},
doi = {10.1128/spectrum.03587-25},
pmid = {42037384},
issn = {2165-0497},
abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.},
}

@article {pmid42037401,
year = {2026},
author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q},
title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0248125},
doi = {10.1128/aem.02481-25},
pmid = {42037401},
issn = {1098-5336},
abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.},
}

@article {pmid42037579,
year = {2026},
author = {Virtuoso, FAS and Boekhorst, J and van Ravenstein, S and Schouten, D and Juanpere-Borràs, M and Broekhuis, F and Vissia, S and Mazebedi, R and Araldi, A and van Langevelde, F},
title = {DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70144},
doi = {10.1111/1755-0998.70144},
pmid = {42037579},
issn = {1755-0998},
support = {//Wageningen University and Research/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Feces/chemistry ; *Diet ; *Carnivora/physiology/classification ; Workflow ; *Metagenomics/methods ; },
abstract = {Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Feces/chemistry
*Diet
*Carnivora/physiology/classification
Workflow
*Metagenomics/methods

@article {pmid42038227,
year = {2026},
author = {Fu, L and Zhang, Y and Wang, L and Li, X},
title = {Primary amoebic meningoencephalitis caused by Naegleria fowleri in a 6-year-old girl: case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1801355},
pmid = {42038227},
issn = {2296-2360},
abstract = {BACKGROUND: Primary amoebic meningoencephalitis (PAM) is caused by Naegleria fowleri, a rare but highly fatal central nervous system infection with a mortality rate exceeding 95%. Early diagnosis is challenging due to the close similarity of its clinical manifestations and cerebrospinal fluid (CSF) findings to those of acute bacterial meningitis. Metagenomic next-generation sequencing (mNGS) has become a vital tool for identifying rare or unexpected pathogens.

CASE PRESENTATION: A previously healthy 6-year-old girl was admitted with fever, vomiting, and headache of 1 day's duration. Six days before symptom onset, she had played in natural freshwater bodies. After admission, she developed persistent high fever and rapidly progressive altered mental status, followed by two episodes of generalized tonic-clonic seizures, hemoptysis, acute respiratory failure, and circulatory shock. Initial cranial magnetic resonance imaging showed no abnormalities. CSF analysis revealed marked inflammatory changes: a white blood cell count of 3,072 × 10[6]/L, markedly elevated protein (3,667.6 mg/L), and significantly decreased glucose (0.08 mmol/L). Despite administration of broad-spectrum antibiotics, glucocorticoids, osmotherapy, and comprehensive intensive care unit management, the patient died approximately 11 h after admission following three cardiac arrests. Two days postmortem, CSF mNGS confirmed infection with Naegleria fowleri (copy number 3 × 10[5] copies/mL), establishing the diagnosis of PAM.

CONCLUSIONS: This pediatric case serves as a warning that PAM should be considered in children with a history of freshwater exposure and rapidly progressive meningoencephalitis, even when early imaging is normal and CSF findings resemble bacterial meningitis. Early lumbar puncture, rapid molecular diagnostics, and heightened clinician vigilance are critical for the timely initiation of targeted therapy.},
}

@article {pmid42038247,
year = {2026},
author = {Li, X and Jiang, Y and Dai, R and Yang, Y and Wang, W},
title = {Rickettsia felis meningoencephalitis in a child: a case report and literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1763281},
pmid = {42038247},
issn = {2296-2360},
abstract = {Rickettsia felis (R. felis) infection occasionally invades the central nervous system, causing encephalitis or meningoencephalitis. Although the disease typically presents as mild to moderate illness, delayed diagnosis and treatment may increase the risk of adverse prognosis in pediatric patients. This article reports a case of R. felis meningoencephalitis in a child diagnosed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid. mNGS analysis detected high-confidence R. felis-specific sequences, and potential background microbial contamination was effectively excluded through a bioinformatics pipeline, thereby providing critical evidence for etiological confirmation. Due to insufficient clinical awareness, limited pathogen detection methods, and the self-limiting nature of the disease, R. felis infection is prone to missed diagnosis and misdiagnosis in febrile children. The clinical manifestations are nonspecific; even with central nervous system involvement, routine laboratory tests are unlikely to suggest the microbial etiology, contributing to the underrecognition and underreporting of pediatric R. felis meningoencephalitis. Therefore, enhancing diagnostic awareness and achieving early precise diagnosis and treatment may help shorten the disease course and improve patient outcomes.},
}

@article {pmid42038299,
year = {2026},
author = {Liu, HJ and Wang, LF and Li, XY and Li, L},
title = {Toxicity-guided dose modification for disseminated Nocardia farcinica brain abscess in a patient with pneumoconiosis: a brief research report.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1805920},
pmid = {42038299},
issn = {1663-9812},
abstract = {BACKGROUND: Optimal antimicrobial strategies for disseminated nocardiosis with central nervous system (CNS) involvement remain poorly defined, particularly regarding trimethoprim-sulfamethoxazole (TMP-SMX) dosing in immunocompromised patients with severe drug intolerance.

METHODS: This observational case study analyzed the clinical course and pharmacological management of a 55-year-old male gold miner with pneumoconiosis and chronic corticosteroid use who developed Nocardia farcinica brain abscess. Diagnosis was established via metagenomic next-generation sequencing (mNGS) and phenotypic culture. An individualized antimicrobial regimen was designed based on toxicity monitoring.

RESULTS: Diagnosis of N. farcinica was confirmed by mNGS within 48 h. The patient initially failed empirical meropenem but responded to combination therapy with imipenem, amikacin, and TMP-SMX. Due to grade III gastrointestinal toxicity (CTCAE v5.0), TMP-SMX was de-escalated from 15 mg·kg[-1]·d[-1]-11.25 mg·kg[-1]·d[-1], with maintenance at 7.5 mg·kg[-1]·d[-1]. Clinical improvement was observed at Day 120, though durable cure remains unconfirmed.

CONCLUSION: In extreme circumstances of severe dose-limiting toxicity, temporary TMP-SMX dose reduction with intensive monitoring may be feasible as a bridge to complete guideline-concordant therapy, though this approach falls below current recommendations and requires robust therapeutic drug monitoring. Species-directed antimicrobial selection and early molecular diagnosis facilitated initial clinical resolution in this high-risk immunocompromised host.},
}

@article {pmid42038409,
year = {2026},
author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ},
title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {2},
pages = {lqag040},
pmid = {42038409},
issn = {2631-9268},
mesh = {Animals ; *Rivers/microbiology ; *Biodiversity ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; *Nanopore Sequencing/methods ; DNA, Environmental/genetics ; Environmental Health ; Animals, Wild/genetics ; Metagenome ; },
abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.},
}

Animals
*Rivers/microbiology
*Biodiversity
*Metagenomics/methods
*Environmental Monitoring/methods
Humans
*Nanopore Sequencing/methods
DNA, Environmental/genetics
Environmental Health
Animals, Wild/genetics
Metagenome

@article {pmid42038418,
year = {2026},
author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Mueller, CL},
title = {Sparse regression, classification, and microbial network estimation in QIIME2 with q2-classo and q2-gglasso.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {42038418},
issn = {2331-8422},
abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.

RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.

AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.},
}

@article {pmid42038553,
year = {2026},
author = {Rodríguez-Rodríguez, Y and Disla, AMM and Ortega, MER and Gandini, G and Tejada-Tejada, P and Guevara, MÁ and Franco, EF and Dantas, CWD and Ramos, RT and Jáuregui-Haza, UJ},
title = {Microbial Profiling and Biosafety Assessment of a Sargassum-Based Liquid Biofertilizer Using 16S rRNA Metagenomics.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {3219583},
pmid = {42038553},
issn = {1687-918X},
abstract = {Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum-based liquid biofertilizer (SBLB-INTEC) with those of a conventional product (LB-BANELINO) using 16S rRNA amplicon sequencing, rather than culture-dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB-INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB-INTEC, but differences in alpha- and beta-diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain-level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus-level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant-associated functions suggests that SBLB-INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant-response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.},
}

@article {pmid42038636,
year = {2026},
author = {Ryder, JH and Turbett, SE},
title = {Mindful diagnostics: a central nervous system infection case study.},
journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE},
volume = {6},
number = {1},
pages = {e96},
pmid = {42038636},
issn = {2732-494X},
abstract = {A clinical case is presented to discuss a framework for use of advanced diagnostics for central nervous system infections. Advantages, limitations, and diagnostic stewardship strategies are discussed for each modality: multiplex molecular meningitis/encephalitis panel, plasma microbial cell-free DNA sequencing, and cerebrospinal fluid metagenomic next generation sequencing.},
}

@article {pmid42039195,
year = {2026},
author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H},
title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1749584},
pmid = {42039195},
issn = {1664-3224},
mesh = {Female ; Humans ; *Virome ; *Mycobiome ; *Vaginosis, Bacterial/microbiology/virology ; *Microbiota ; Papillomavirus Infections/microbiology/virology ; Vagina/microbiology/virology ; *Reproductive Health ; *Genitalia, Female/microbiology/virology ; Bacteriophages ; },
abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.

METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.

RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.

CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.},
}

Female
Humans
*Virome
*Mycobiome
*Vaginosis, Bacterial/microbiology/virology
*Microbiota
Papillomavirus Infections/microbiology/virology
Vagina/microbiology/virology
*Reproductive Health
*Genitalia, Female/microbiology/virology
Bacteriophages

@article {pmid42039480,
year = {2026},
author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y},
title = {16S rRNA k-mer composition encodes microbial functional potential.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.718937},
pmid = {42039480},
issn = {2692-8205},
abstract = {16S rRNA amplicon sequencing is widely used to profile microbiome taxonomic composition and functional potential. Most 16S rRNA-based analysis methods depend on comparing sequenced reads against reference marker genes from previously characterized organisms. Thus, method accuracy declines in environments dominated by uncharacterized microbes. We uncovered a direct link between 16S rRNA and genome-encoded functions. Using fully sequenced bacterial genomes, we show that (i) whole-genome k-mer composition is predictive of functions encoded in the genome and (ii) 16S rRNA k-mer profiles reflect their source genome k-mer compositions. Leveraging these relationships, we developed embeRNA, a neural network-based framework that predicts functions directly from 16S rRNA k-mer embeddings, without taxonomy assignment or phylogenetic placement. Furthermore, by producing per-function probability scores rather than categorical assignments, embeRNA allows users to adapt decision thresholds to match study goals and sample characteristics, e.g. balancing precision vs. recall or accounting for community novelty. We trained embeRNA on a large collection of bacterial function-omes and evaluated it using a stringent "novel microbes" benchmark, where all test 16S rRNA sequences were dissimilar to those seen in training (all <97% identical). On this test set of phylogenetically novel organisms, embeRNA outperformed reference-based methods overall and achieved significantly better performance for the "hard to label" set of functions. In testing on soil metagenomes with paired 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data, embeRNA recovered most WMS-inferred functions and yielded abundance profiles strongly correlated with WMS results. Together, our results indicate that 16S rRNA k-mer composition carries substantial functional signal and that 16S amplicon data can be used to complement WMS-based inference to broaden functional characterization of microbiomes, particularly in understudied environments.},
}

@article {pmid42039609,
year = {2026},
author = {Maldonado Pereira, L and Mutawi, TMA and Singh, A and Sanderson, B and Rekowski, MJ and Barnaba, C and Medina Meza, IG},
title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.12.717948},
pmid = {42039609},
issn = {2692-8205},
abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.},
}

@article {pmid42039751,
year = {2026},
author = {Chen, XG and Zhou, L and Duan, K and Shi, SY and Subi, A and Sun, HW and Lu, YM and Hu, L and Yang, ZT},
title = {Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1786413},
pmid = {42039751},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Male ; Virulence Factors/genetics ; Female ; Middle Aged ; Virulence/genetics ; Aged ; Intensive Care Units ; *Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/microbiology/diagnosis ; *Host-Pathogen Interactions ; Anti-Bacterial Agents/pharmacology ; Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.

METHODS: In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.

RESULTS: mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly β-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.

CONCLUSION: mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Male
Virulence Factors/genetics
Female
Middle Aged
Virulence/genetics
Aged
Intensive Care Units
*Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification
*Drug Resistance, Bacterial/genetics
*Bacterial Infections/microbiology/diagnosis
*Host-Pathogen Interactions
Anti-Bacterial Agents/pharmacology
Adult

@article {pmid42039753,
year = {2026},
author = {Li, X and Fang, J and Li, D and Cai, B and Yin, J and Zheng, Y and Yin, G},
title = {Performance evaluation of mNGS in pathogen diagnosis of skin and soft tissue infections and its optimization effect on antibiotic decision-making.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1771148},
pmid = {42039753},
issn = {2235-2988},
mesh = {Humans ; *Soft Tissue Infections/diagnosis/microbiology/drug therapy ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Antimicrobial Stewardship ; Aged ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification/drug effects ; *Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy ; Young Adult ; Coinfection/diagnosis/microbiology/drug therapy ; Adolescent ; Clinical Decision-Making ; },
abstract = {BACKGROUND: Skin and soft tissue infections (SSTIs), often caused by polymicrobial pathogens, pose diagnostic challenges due to the limitations of conventional methods, including low sensitivity and prolonged turnaround time. This diagnostic gap has perpetuated empirical antibiotic use in clinical practice. Metagenomic next-generation sequencing (mNGS), with its unbiased pathogen detection capability, offers a transformative approach for rapid and precise microbial identification in SSTIs.

OBJECTIVE: To evaluate the clinical utility of mNGS compared to conventional microbiological testing in guiding antibiotic stewardship for complex SSTIs.

METHODS: A retrospective cohort study was conducted at the First Affiliated Hospital of Zhengzhou University from April 2023 to May 2025, enrolling 69 patients with clinically diagnosed complex SSTIs. All patients underwent concurrent mNGS testing, conventional bacterial culture, and pathological examination. The diagnostic performance of mNGS was systematically compared with culture methods, with emphasis on culture-negative cases and polymicrobial infections. The impact of mNGS-guided antibiotic adjustments was assessed.

RESULTS: mNGS demonstrated significantly higher pathogen detection rates than conventional culture (P < 0.001), with a concordance of 37.5% between the two methods. Among 24 culture-negative patients, mNGS identified pathogens in 20 cases (83.3% detection rate). For polymicrobial infections (n = 20), culture detected pathogens in only 2 cases, whereas mNGS successfully identified multiple pathogens in the majority. Antibiotic therapy was adjusted based on mNGS results in 11.9% (8/69) of patients.

CONCLUSION: mNGS substantially improves pathogen detection in complex SSTIs compared to conventional methods. Beyond diagnostic accuracy, its clinical value lies in enabling targeted antibiotic therapy, thereby optimizing antimicrobial stewardship and potentially reducing healthcare costs.},
}

Humans
*Soft Tissue Infections/diagnosis/microbiology/drug therapy
Retrospective Studies
Male
Female
*Anti-Bacterial Agents/therapeutic use
Middle Aged
Adult
*High-Throughput Nucleotide Sequencing/methods
Antimicrobial Stewardship
Aged
*Metagenomics/methods
*Bacteria/genetics/isolation & purification/classification/drug effects
*Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy
Young Adult
Coinfection/diagnosis/microbiology/drug therapy
Adolescent
Clinical Decision-Making

@article {pmid42039757,
year = {2026},
author = {Wu, Y and Zhang, J and Su, W and Zhang, Z},
title = {Global epidemiology of tick-borne Alpharhabdovirinae: a meta-analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1791903},
pmid = {42039757},
issn = {2235-2988},
mesh = {Animals ; Phylogeny ; *Ticks/virology ; Humans ; *Tick-Borne Diseases/epidemiology/virology ; Genome, Viral ; },
abstract = {INTRODUCTION: The Alpharhabdovirinae subfamily of the family Rhabdoviridae encompasses a diverse and expanding group of tick-borne viruses, some of which pose potential risks as emerging human pathogens. Despite increasing detection through metagenomic surveillance, the global diversity, phylogenetic relationships, and taxonomic framework of tick-borne Alpharhabdovirinae (TBA) remain poorly characterized.

METHODS: This study conducted a comprehensive meta-analysis of all publicly available TBA sequences based on phylogenetic analysis of five structural proteins (N, P, M, G, L), combined with host associations and geographic distributions.

RESULTS: 345 TBA strains were classified into 12 distinct phylogenetic clusters, each exhibiting unique evolutionary and ecological characteristics. These clusters include: (1) seven species-level lineages within the genus Alpharicinrhavirus, predominantly associated with Hyalomma and Haemaphysalis ticks across Eurasia; (2) a cluster related to Manly virus, widely distributed in Amblyomma, Haemaphysalis, and Rhipicephalus ticks acrossAustralia and China, exhibiting additional protein-coding genes of unknown function; (3) the genus Ledantevirus (21 species), characterized by broad host tropism including bats, rodents, and humans, with some members displaying phosphoprotein phylogenetic anomalies suggestive of recombination; (4) the genus Lostrhavirus, together with Tongliao Rhabd tick virus 1, forming a cluster associated with Hyalomma and Amblyomma ticks; (5) a Mononegavirus cluster comprising Alpharicinrhavirus heilongjiang, Alpharicinrhavirus skanevik (Norway mononegavirus 1), and Mononegavirales sp. specifically associated with Ixodesticks in Eurasia; and (6) one clusters with incomplete protein repertoires and uncertain taxonomic positions, including Tahe rhabdovirus 3 and Yanbian Rhabd tick virus 1 which lacks phosphoprotein entirely. This study provide a refined phylogenetic framework for TBA viruses, clarify their evolutionary relationships, and highlight critical knowledge gaps, including numerous uncharacterized hypothetical proteins and incomplete genomes that warrant further investigation.

DISCUSSION: This study underscores the importance of enhanced global surveillance and genomic characterization to assess the emergence potential and public health threat posed by this diverse group of tick-borne viruses.},
}

Animals
Phylogeny
*Ticks/virology
Humans
*Tick-Borne Diseases/epidemiology/virology
Genome, Viral

@article {pmid42039802,
year = {2026},
author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P},
title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780132},
pmid = {42039802},
issn = {1664-302X},
abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.},
}

@article {pmid42039826,
year = {2026},
author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C},
title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797687},
pmid = {42039826},
issn = {1664-302X},
abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.

METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.

RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 × 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.

CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.},
}

@article {pmid42039832,
year = {2026},
author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M},
title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761627},
pmid = {42039832},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.

METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.

RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.

CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.},
}

@article {pmid42040306,
year = {2026},
author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q},
title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1782544},
pmid = {42040306},
issn = {1664-462X},
abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.

METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.

RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.

DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.},
}

@article {pmid42040505,
year = {2026},
author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R},
title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag072},
pmid = {42040505},
issn = {2730-6151},
abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.},
}

@article {pmid42040506,
year = {2026},
author = {Zhang, T and Pan, J and Palomo, A and Ouyang, Z and Wen, X and Li, J and Wang, C and Zheng, M},
title = {Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag070},
pmid = {42040506},
issn = {2730-6151},
abstract = {Complete ammonia oxidation (comammox) is a critical biogeochemical process in the nitrogen cycle. In this study, we utilized comammox Nitrospira to convert urine wastewater into ammonium nitrate by operating a laboratory-scale membrane bioreactor at pH 3 ~ 4. During the process, the acid-tolerant comammox Nitrospira was highly enriched. The metagenomic and metatranscriptomic analyses were applied to reveal its unique characteristics. Comparative genomic analysis among previously reported comammox Nitrospira demonstrated that this species was phylogenetically novel, named Candidatus Nitrospira aciditolerans. Key mechanisms were further identified to enable this species to thrive in acidic environments. These include active proton efflux, regulation of proton consumption, inhibition of proton influx, and cellular strategies for acid stress management and repair. Remarkably, different from other comammox Nitrospira and acid-tolerant ammonia-oxidizing bacteria (AOB), Candidatus Nitrospira aciditolerans possesses highly expressed V-type ATPases that are typically associated with acidophilic ammonia-oxidizing archaea (AOA). This may indicate an ecologically significant role for comammox bacteria and AOA in co-maintaining ammonia oxidation activity in low pH environments. Kinetic characterization revealed an apparent ammonium half-saturation coefficient K m of 0.50 ± 0.05 μM NH3 and an apparent ammonium inhibition constant K i of 241.43 ± 45.64 μM NH3. The enrichment culture demonstrated optimal ammonia oxidation activity at neutral pH but maintained functionality across a broader pH range between 4 and 8. Like other nitrifying bacteria, this comammox culture was sensitive to temperature and salinity changes. The findings enhance our understanding of the nitrogen cycle under acidic conditions and also present opportunities for engineering applications of acid-tolerant ammonia oxidizers.},
}

@article {pmid42040549,
year = {2026},
author = {Chen, Q and Yang, Z and Ren, D and Bao, C and Zhao, Y and Shi, Z},
title = {Case Report: Pulmonary tuberculosis with pneumocystis jirovecii colonization in a non-HIV patient: a cautionary tale on interpreting mNGS results.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1782843},
pmid = {42040549},
issn = {2296-858X},
abstract = {The diagnosis and treatment process of this case highlights that mNGS, as a powerful pathogen detection tool, provides a rapid method for the early detection of Pneumocystis jirovecii. However, mNGS testing of lavage specimens alone cannot distinguish between colonization and infection by the pathogen, particularly when a high number of sequences are present. Clinicians should therefore interpret laboratory results with caution to avoid unnecessary treatment that may cause adverse effects to the patient. CT scans offer strong evidence for differentiating between Pneumocystis jirovecii infection and/or Mycobacterium tuberculosis infection. Performing a biopsy at the site of infection, collecting pathological samples, and submitting them for mNGS testing can further assist clinicians in making a definitive diagnosis.},
}

@article {pmid42040584,
year = {2026},
author = {Li, CB and Tang, S and Wen, Y},
title = {Case Report: The complete radiological resolution of diffuse cholangitis in a HIV-positive patient with cryptosporidium infection after anti-retroviral therapy.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1686336},
pmid = {42040584},
issn = {2296-858X},
abstract = {We present a case of an HIV-positive patient with AIDS cholangiopathy secondary to Cryptosporidium infection. Imaging examination showed intrahepatic and extrahepatic cholangitis without papillary stenosis and extrahepatic bile duct strictures, indicating mild bile duct disease. However, it failed to obtain positive results in fecal microscopy examinations. Alternatively, metagenomic next-generation sequencing (mNGS) of a blood sample identified Cryptosporidium infection. The diagnostic power of mNGS is highly sensitive and can simultaneously identify various pathogens. To avoid irreversible damage to the biliary system, the rapid initiation of anti-HIV therapy restored the function of the immune system and led to the clinical resolution of cryptosporidiosis.},
}

@article {pmid42040837,
year = {2026},
author = {Sander, MM and Stoof-Leichsenring, KR and Liu, S and Shen, W and Lisovski, S and Herzschuh, U},
title = {Sedimentary Metagenomics Reveal Avian Community Transitions From the Last Glacial Maximum to the Holocene.},
journal = {Ecology and evolution},
volume = {16},
number = {4},
pages = {e72064},
pmid = {42040837},
issn = {2045-7758},
abstract = {The transition from the Last Glacial to the Holocene was marked by significant warming. This forced a compositional turnover of terrestrial plant and mammal communities discovered by diverse palaeoecological techniques. In this study, we analysed ancient environmental DNA with shotgun metagenomics from eight lake sediment cores, collected in northern Eurasia and Alaska, to elucidate the relationship of past bird communities and vegetation structure across the last 21,000 years. We leveraged all DNA reads assigned to the class 'Aves' to characterise the compositional changes of the bird community. The dominance of chicken birds (Galliformes, mainly ptarmigans) during the Last Glacial Maximum turned into a higher taxonomic bird diversity with increased numbers of songbird, raptor and waterfowl abundances and genera. This went along with the late glacial loss of the steppe-tundra and the increase of shrub and tree cover. Compared to the northern boreal areas, vegetation and bird communities were more stable in the northern tundra sites, where open landscapes prevailed throughout. Metagenomics significantly contribute to the reconstruction of past avian community changes and thus have high potential to support the predictions of distribution changes in the course of future ecosystem change.},
}

@article {pmid42041249,
year = {2026},
author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS},
title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.},
journal = {mBio},
volume = {},
number = {},
pages = {e0286825},
doi = {10.1128/mbio.02868-25},
pmid = {42041249},
issn = {2150-7511},
abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.},
}

@article {pmid42041251,
year = {2026},
author = {Gador-Whyte, AP and Sherry, NL and Brischetto, A and Andersson, P and Bond, KA and van Hal, SJ and Harris, PNA and Howden, BP and , },
title = {Implementation of pathogen genomics in clinical microbiology laboratories.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0017725},
doi = {10.1128/cmr.00177-25},
pmid = {42041251},
issn = {1098-6618},
abstract = {SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.},
}

@article {pmid42041878,
year = {2026},
author = {Carlone, J and Ribeiro, ÁCDS and Parisi, A and Giampaoli, S and Fasano, A},
title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/biology15080600},
pmid = {42041878},
issn = {2079-7737},
abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.},
}

@article {pmid42041929,
year = {2026},
author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J},
title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/biology15080652},
pmid = {42041929},
issn = {2079-7737},
abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.},
}

@article {pmid42043232,
year = {2026},
author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S},
title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.},
journal = {Viruses},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/v18040443},
pmid = {42043232},
issn = {1999-4915},
support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; },
mesh = {Animals ; China ; Phylogeny ; *Virome/genetics ; *Ticks/virology ; Genome, Viral ; *RNA Viruses/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.},
}

Animals
China
Phylogeny
*Virome/genetics
*Ticks/virology
Genome, Viral
*RNA Viruses/genetics/classification/isolation & purification
Metagenomics

@article {pmid42043279,
year = {2026},
author = {Rūmnieks, J and Baltā, I and Šišovs, M and Tārs, K},
title = {ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {5},
pages = {e70582},
doi = {10.1002/pro.70582},
pmid = {42043279},
issn = {1469-896X},
support = {5.2.1.1.i.0/2/24/I/CFLA/001//European Commission/ ; },
mesh = {Open Reading Frames ; *Viral Proteins/genetics/chemistry ; *Metagenome ; Genome, Viral ; *Bacteriophages/genetics ; },
abstract = {The bacteriophages with single-stranded RNA (ssRNA) genomes (class Leviviricetes) are among the simplest known viruses that encode only three core proteins: a receptor-binding protein, a capsid protein, and an RNA-dependent RNA polymerase. The number of isolated ssRNA phages has remained very low, but the accumulating RNA metagenome data have uncovered a large variety of these viruses in many environments. Besides the core proteins, many of these genomes putatively encode additional proteins, which up to now have remained uncharacterized. We looked for non-conserved open reading frames (ORFs) in Leviviricetes sequences from the IMG/VR virus metagenome database and used sequence- and structure-based clustering to organize them into similarity groups. Potential ORFs were found throughout the ssRNA phage genomes but almost exclusively on the positive-sense RNA strand, suggestive of their protein-coding potential. The prevalence of the non-conserved ORFs varied in various phage lineages, and their distribution among different genome positions was markedly uneven. Most of the identified ORFs encode all-α proteins, a portion of which contain transmembrane segments that resemble a group of known ssRNA phage lysis proteins, while many others represent previously uncharacterized families of globular or semi-globular α-helical proteins. We additionally uncovered a major class of globular α/β proteins and experimentally determined the structure of a representative protein of this group. These results pave the way for further functional studies of novel ssRNA phage proteins for a better understanding of this diverse virus group.},
}

Open Reading Frames
*Viral Proteins/genetics/chemistry
*Metagenome
Genome, Viral
*Bacteriophages/genetics

@article {pmid42044527,
year = {2026},
author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ},
title = {Identify contaminants with decontam on the QIIME 2 Framework.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126125},
doi = {10.1128/mra.01261-25},
pmid = {42044527},
issn = {2576-098X},
abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.},
}

@article {pmid42044543,
year = {2026},
author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y},
title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129734},
doi = {10.1016/j.jenvman.2026.129734},
pmid = {42044543},
issn = {1095-8630},
abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.},
}

@article {pmid42044779,
year = {2026},
author = {Zhang, Y and Zeng, M and Guo, P and Zhang, Z and Chen, X and Li, X and Hao, F and Jiao, X and Wu, Y and Feng, W and Zheng, X},
title = {Effects of Rehmannia glutinosa Libosch. Rhizome Water Extract and Rehmapicrogenin on Pulmonary Hypertension: Multi-Omics Insights into Epidermal Growth Factor Receptor/Pyruvate Kinase M2 Pathway and Metabolic Regulation.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121775},
doi = {10.1016/j.jep.2026.121775},
pmid = {42044779},
issn = {1872-7573},
abstract = {Rehmannia glutinosa Libosch. (RG), as one of the 'Four Famous Chinese Medicinal Herbs', has a long history of medicinal use and is classified as belonging to the meridians of the heart, liver, and kidney. RG has the effects of clearing heat and cooling blood, nourishing yin, and generating fluids. Pulmonary hypertension (PH) is a cardiovascular disease, and its pathogenesis can be summarized as 'yin deficiency', 'blood stasis', and 'qi deficiency'. The efficacy of RG is highly compatible with this disease, and the compounds isolated from RG can significantly inhibit the proliferation of pulmonary arterial smooth muscle cells (PASMCs). However, the mechanism by which it intervenes in PH remains unclear.

OBJECTIVE: In this study, the mechanisms and active components of RG were investigated for treating PH by using multi-omics analysis and surface plasmon resonance (SPR) technology, providing experimental support for clinical application.

METHODS: A PH mouse model was established through 5 weeks of hypoxia, with RG administration starting in week four. Cardiorespiratory function was evaluated after treatment. The therapeutic targets of RG were identified via 16S rDNA sequencing, metagenomics, and metabolomics. SPR ligand fishing was performed to isolate rehmapicrogenin (Reh), an RG-derived compound that targets the epidermal growth factor receptor (EGFR). The effects and mechanisms of Reh were assessed by measuring cardiac and pulmonary function, oxidative stress, apoptosis, immune cell activity, and glycolysis. An in vitro model of hypoxia-induced PASMC proliferation was used to validate Reh's mechanism with an EGFR agonist (NSC).

RESULTS: RG extracts improved cardiorespiratory function and regulated gut microbiota, correcting the Firmicutes/Bacteroidetes (F/B) ratio in PH mice. RG also mitigated metabolic disturbances and inhibited glycolysis through pyruvate kinase M2 (PKM2) regulation, as confirmed using immunofluorescence analysis, western blotting, and PCR. SPR identified Reh as the active ingredient, which improved cardiorespiratory function, reduced oxidative stress and apoptosis, and suppressed EGFR and PKM2 expression and glycolysis. In vitro, Reh inhibited PASMC migration and proliferation, alleviated oxidative stress, and reduced mitochondrial damage. These effects were reversed upon NSC addition, confirming the role of EGFR in the mechanism.

CONCLUSION: RG and its active compound Reh mitigate hypoxia-induced PH by targeting the EGFR/PKM2 pathway, reducing glycolysis, and regulating gut microbiota dysbiosis.},
}

@article {pmid42044791,
year = {2026},
author = {Dai, Y and Li, J and Wang, X and Xia, F and Zheng, J and Shen, C},
title = {Synergistic Mechanisms of Bacteria and Fungi in the Biodegradation of Benzo[a]pyrene: Insights from Metagenomic and Metabolomic Analyses.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124602},
doi = {10.1016/j.envres.2026.124602},
pmid = {42044791},
issn = {1096-0953},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants, with benzo[a]pyrene (BaP), a prominent heavy-weight PAH, drawing considerable attention due to its high toxicity and resistance to degradation. While both bacteria and fungi have been demonstrated to effectively remediate BaP, their synergistic mechanisms remain poorly understood. In this study, we employed Pseudomonas nicosulfuronedens DY-8 (bacterium) and Arthrinium acutiapicum DL-5 (fungus) to explore the mechanisms underlying PAH bioaugmentation using metagenomic and metabolomic approaches. Although both strains individually enhanced BaP degradation, their combined application significantly reduced BaP residuals. qPCR analysis revealed that the bacteria promote BaP dissipation by stimulating the abundance of PAH-RHD GP genes in the soil. Correlations between metabolite abundance, enriched microbial populations, functional gene abundance, and fungal growth suggest that fungi enhance the growth of indigenous bacteria, further boosting the degradation of BaP metabolites. Additionally, the synergistic treatment of bacteria and fungi further altered the diversity of soil functional microorganisms, metabolic products, and functional genes. These findings provide insights into potential synergistic mechanisms by which bacterial-fungal interactions drive the degradation of high-molecular-weight PAHs, underscoring the potential of microbial consortia in the bioremediation of persistent organic pollutants in soil environments.},
}

@article {pmid42044793,
year = {2026},
author = {Zhou, Y and Hu, X and Du, L and Gu, Y and Li, J and Jia, M and Zhang, G and Wang, Y},
title = {Antibiotic Resistance Genes Across Divergent Wetland Types: Profiles, Driving Mechanisms, and Risk Assessment.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124601},
doi = {10.1016/j.envres.2026.124601},
pmid = {42044793},
issn = {1096-0953},
abstract = {Wetlands are critical reservoirs and hotspots of antibiotic resistance genes (ARGs). Metagenomic sequencing was employed to profile the ARG and mobile genetic element (MGE) abundance and diversity in coastal (B), constructed (R), and swampy (W) wetlands. In total, 560 ARGs were detected across all sites, primarily conferring resistance to cephalosporins and tetracyclines, with antibiotic efflux being the dominant mechanism of resistance. ARG richness was significantly higher in wetlands R and W than in wetland B (p < 0.001). Non-metric multidimensional scaling (NMDS) further indicated significant differences in ARG β-diversity among the wetlands. Pseudomonadota were identified as the primary hosts of both ARGs and MGEs. Soil salinity and Cr content were the key environmental factors regulating ARG profiles, with salinity exhibiting the broadest influence and linearly correlating with multiple ARG types. In addition, plasmid and insertion sequence (IS) richness positively correlated with ARG richness, showing the strongest explanatory power for ARG richness variation. Risk assessment revealed that rank I and II ARGs were significantly enriched in wetland W (p < 0.05), whereas rank IV ARGs were dominant across most sites. This study demonstrated that soil physicochemical properties, plasmids, and ISs jointly and differentially shaped ARG abundance and diversity in wetlands, accompanied by an assessment of their risk. These findings support the development of targeted strategies to mitigate ARG dissemination in wetland ecosystems.},
}

@article {pmid42044853,
year = {2026},
author = {Weng, H and Wang, H and Zhang, Q and Li, X and Zhang, L and Peng, Y},
title = {Enrichment of comammox Nitrospira with urea: comparative genomics reveals divergent urea response mechanisms among ammonia-oxidizing microorganisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134722},
doi = {10.1016/j.biortech.2026.134722},
pmid = {42044853},
issn = {1873-2976},
abstract = {Urea is a major nitrogen form in natural and engineered ecosystems, yet the traits driving niche partitioning among nitrifiers during urea nitrification remain poorly understood. In this work, a stable urea nitrification microbial community was successfully established over prolonged cultivation characterized using 16S rRNA gene amplicon sequencing, qPCR and genome-resolved metagenomics coupled with comparative genomics. A clade A comammox Nitrospira closely related to Candidatus Nitrospira nitrosa became dominant (OTU330, 13.9%) and yielded the most abundant nitrifier metagenome-assembled genome (MAG). Genomes indicate comammox Nitrospira couples ATP-dependent urea ABC uptake to a streamlined urease-only module characterized by slow substrate turnover, whereas Nitrosomonas relies on passive urea channels and redundant urease/urea-amidolyase pathways, enabling rapid urea metabolism. These contrasting urea acquisition strategies suggest an affinity-capacity trade-off that underpins niche partitioning in urea-fed, oligotrophic nitrifying systems and provide targets for enhancing urea-based wastewater treatment processes.},
}

@article {pmid42045408,
year = {2026},
author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S},
title = {Improving metagenome binning by integrating intrinsic features and taxonomy.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42045408},
issn = {1546-1696},
support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; },
abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.},
}

@article {pmid42045553,
year = {2026},
author = {Wei, D and Xing, C and Zeng, S and Hou, D and Deng, Z and Long, X and Wang, H and Zhou, R and Yu, L and Shu, N and Tao, Z and Zhou, X and Weng, S and He, J and Huang, Z},
title = {The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function.},
journal = {Advanced biotechnology},
volume = {4},
number = {2},
pages = {},
pmid = {42045553},
issn = {2948-2801},
support = {2023YFD2401705//National Key Research and Development Program of China/ ; 2024YFD2401202//National Key Research and Development Program of China/ ; AA23062047//Earmarked Fund for CARS-48-20; Guangxi Science and Technology Major Special Project/ ; SML2021SP203//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0-45.0 mg/g; total organic carbon: 15.0-35.0 mg/g) and sustained redox homeostasis (consistently low oxidation-reduction potential: - 150 to - 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%-50% in CRCE vs. 10%-20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers (Geobacter), sulfur oxidizers (Sulfuricurvum), and nitrifiers (Nitrospira), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.},
}

@article {pmid42045683,
year = {2026},
author = {Boppana, LKT and Bag, R},
title = {Metagenomic Microbial Next-Generation Gene Sequencing as a Noninvasive Diagnostic Tool in Adult Lung Transplantation: A Retrospective Case Series.},
journal = {Lung},
volume = {204},
number = {1},
pages = {},
pmid = {42045683},
issn = {1432-1750},
}

@article {pmid41850677,
year = {2026},
author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J},
title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {20},
number = {7},
pages = {101770},
doi = {10.1016/j.jcmgh.2026.101770},
pmid = {41850677},
issn = {2352-345X},
abstract = {BACKGROUND & AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.

METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-β1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.

RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-β1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-β1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-β1.

CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-β1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.},
}

@article {pmid42033828,
year = {2026},
author = {Liu, X and Li, N and Wu, WM and Ambrosini, R and Zhong, B and Mei, X and Liu, R and Zhou, L and Yi, S and He, Y},
title = {Freeze-thaw aging and microbial colonization converts microplastics into nitrogen cycling hotspots.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142170},
doi = {10.1016/j.jhazmat.2026.142170},
pmid = {42033828},
issn = {1873-3336},
abstract = {As global warming intensifies, the frequency of freeze-thaw events increases, significantly impacting microbial metabolism and biogeochemical cycling. However, the synergistic effects of freeze-thaw cycles (FTCs) and pervasive microplastics (MPs) on microbial community assembly and nitrogen cycling remain poorly understood. Here, we conducted a microcosm experiment integrating metagenomic and random forest model to elucidate the co-regulatory mechanisms of FTCs and MPs on plastisphere microbial communities and nitrogen metabolism. Results revealed that FTCs accelerated the environmental aging of MPs, inducing surface cracking and oxidation, thereby creating microenvironments favorable for microbial colonization. In the experimental microcosms, the combined effects of FTCs and presence of MPs increased microbial richness and diversity, promoted community differentiation between sediment and plastisphere, and increased microbial niche specialization. Functional analyses showed that FTCs induced a functional reconfiguration of the plastisphere nitrogen metabolism, with a selective enrichment of key enzyme genes, such as nitrite reductase, which may enhance nitrite redox activity and N2O emission capacity. In the plastisphere, the contribution of Acinetobacter to nitrogen cycling increased, whereas Nitrospira declined, possibly due to oxygen limitation. Overall, our findings suggested that FTCs may facilitate transformation of MPs from inert pollutants into potentially metabolically active microhabitats, providing critical insights for assessing emerging pollutants and climate change.},
}

@article {pmid42033834,
year = {2026},
author = {Su, S and Lin, M and Li, K and Lin, J and Chen, Z},
title = {Soil aggregates as functional units for cadmium sequestration: Differential regulation by nitrogen enrichment and labile carbon inputs.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142196},
doi = {10.1016/j.jhazmat.2026.142196},
pmid = {42033834},
issn = {1873-3336},
abstract = {While cadmium (Cd) speciation in soil is known to control its environmental risk, how nitrogen (N) enrichment and labile organic carbon (LOC) inputs redistribute Cd fractions within soil aggregates remains unclear. This study examined how ammonium enrichment (AT), nitrate enrichment (NT), and glucose input (CT) altered carbonate-bound Cd (CB-Cd) and organic matter-bound Cd (OM-Cd) within soil aggregates. Both N enrichment and glucose input enhanced CB-Cd formation, with CT increasing CB-Cd by 39.19% via stimulated microbial activity and carbonate precipitation. Different sources of enriched N regulated OM-Cd, with AT decreasing OM-Cd by 15.55%, and NT increasing OM-Cd by 24.61%. This was attributed to competitive adsorption and suppressed microbial decomposition of recalcitrant organic matter. Aggregate hierarchy was also crucial in determining Cd speciation, where macroaggregates, with higher LOC and genes involved in carbonate precipitation, favored CB-Cd partitioning, whereas microaggregates, with greater surface area and enriched alkyl/aromatic C, served as the major OM-Cd sink. Microbial community analysis revealed that glucose reshaped communities, enriching r-strategists like Amycolatopsis and Trichoderma, which were positively correlated with CB-Cd and OM-Cd. Metagenomic data indicated that glucose stimulated genes for labile C degradation, reinforcing CB-Cd formation, while N addition suppressed C-degradation genes. Random forest and PLS path models identified alkyl C, O-alkyl C, and polysaccharide derivatives as primary SOC components regulating CB-Cd, while alkyl C, phenolic, and aromatic compounds regulating OM-Cd. These findings reveal a mechanism for stabilizing Cd in less bioavailable fractions via SOC and N management, leveraging soil aggregates' role in long-term metal sequestration.},
}

@article {pmid42033969,
year = {2026},
author = {Tian, J and Wang, L and Wang, Y and Zheng, M and Sun, C},
title = {Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.},
journal = {Marine environmental research},
volume = {219},
number = {},
pages = {108068},
doi = {10.1016/j.marenvres.2026.108068},
pmid = {42033969},
issn = {1879-0291},
abstract = {As a semi-enclosed marginal sea in China, the Bohai Sea has long been influenced by substantial pollutant inputs from surrounding rivers, making it an important region for investigating the distribution patterns of pollutants and microbial communities. In this study, the concentrations of emerging contaminants (ECs) in 19 sediment samples were determined, and metagenomic sequencing was employed to systematically analyze the structure and functional characteristics of microbial communities. The results showed that the detected ECs included synthetic musks (SMs, 7.96-22.85 ng/g dw), dominated by tonalide (AHTN) and galaxolide (HHCB); organophosphate esters (OPEs, not detected-282.27 ng/g dw), were not detected in most samples, but relatively high concentrations were observed at the NS-33 station; and polyhalogenated carbazoles (PHCZs, 0.70-4.36 ng/g dw), with 3,6-dichlorocarbazole (36-CCZ) constituting 61.87% of PHCZs. The microbial community was dominated by Proteobacteria (68.36%). Further network analysis indicated significant correlations between PHCZs and nitrogen metabolism genes, suggesting that PHCZs may inhibit nitrogen fixation and nitrification, while enhancing denitrification. Overall, this study reveals the distribution patterns of ECs and microbial communities in Bohai Sea sediments and their potential associations, providing insights into their interactions in coastal ecosystems.},
}

@article {pmid42033990,
year = {2026},
author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W},
title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.},
journal = {Biomaterials},
volume = {333},
number = {},
pages = {124234},
doi = {10.1016/j.biomaterials.2026.124234},
pmid = {42033990},
issn = {1878-5905},
abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.},
}

@article {pmid42034087,
year = {2026},
author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z},
title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.},
journal = {Food chemistry},
volume = {516},
number = {},
pages = {149287},
doi = {10.1016/j.foodchem.2026.149287},
pmid = {42034087},
issn = {1873-7072},
abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.},
}

@article {pmid42034426,
year = {2026},
author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H},
title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107059},
doi = {10.1016/j.pestbp.2026.107059},
pmid = {42034426},
issn = {1095-9939},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; China ; },
abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Metagenome
China

@article {pmid42034448,
year = {2026},
author = {Zhang, Y and Zhao, L and Zhang, P and Yang, Y and Wang, A and Xue, C and Yao, Y and Zhang, J and Zhao, M},
title = {Paenibacillus polymyxa EP-4 can effectively control southern corn leaf blight and affect the selectivity of Spodoptera frugiperda to corn.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107047},
doi = {10.1016/j.pestbp.2026.107047},
pmid = {42034448},
issn = {1095-9939},
mesh = {Animals ; *Zea mays/microbiology ; *Plant Diseases/microbiology/prevention & control ; *Spodoptera/physiology/microbiology ; *Paenibacillus polymyxa/physiology ; *Pest Control, Biological/methods ; Plant Leaves/microbiology ; Ascomycota ; Biological Control Agents ; },
abstract = {Southern corn leaf blight (SCLB) and Spodoptera frugiperda pose serious threats to corn yield. In recent years, an increasing number of studies have investigated biological control agents to control plant diseases and insect pests. However, research on the use of one biocontrol bacterium to control plant diseases and insect pests simultaneously is very limited. In this study, the bacterium EP-4, which can significantly inhibit the growth of Bipolaris maydis, was identified as Paenibacillus polymyxa. EP-4 metabolites inhibited hyphal growth, caused hyphal deformities, significantly reduced the spore germination of B. maydis, and damaged cell membranes, leading to DNA leakage. In the greenhouse, EP-4 significantly reduced the disease index of SCLB and the feeding and oviposition preferences of S. frugiperda to corn. Metabolite analysis revealed that inoculation with B. maydis and S. frugiperda after EP-4 pretreatment affected the production of corn resistance-related substances such as brassinolide, quercetin, 2-undecanone and naringin. Metagenomic analysis revealed that EP-4 pretreatment and subsequent inoculation with pests and diseases could induce the recruitment of Pseudomonas, Burkholderia, Azotobacter and Mesorhizobium in corn. EP-4 could significantly reduce the occurrence of SCLB and significantly affect the feeding and oviposition of S. frugiperda on corn. The mechanism of action of EP-4 on pests and diseases has been shown to differ. This strain has great application potential in corn.},
}

Animals
*Zea mays/microbiology
*Plant Diseases/microbiology/prevention & control
*Spodoptera/physiology/microbiology
*Paenibacillus polymyxa/physiology
*Pest Control, Biological/methods
Plant Leaves/microbiology
Ascomycota
Biological Control Agents

@article {pmid42034850,
year = {2026},
author = {Gupta, E and Sharma, S and Dash, PK and Parida, M},
title = {Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49112-y},
pmid = {42034850},
issn = {2045-2322},
}

@article {pmid42034975,
year = {2026},
author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K},
title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04999-5},
pmid = {42034975},
issn = {1471-2180},
support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; },
}

@article {pmid42034994,
year = {2026},
author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B},
title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13117-9},
pmid = {42034994},
issn = {1471-2334},
support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; },
}

@article {pmid42035444,
year = {2026},
author = {Lopez, C and Banker, A and Venkatasamy, V and Garcia, J and Mattiazzi, A and Eidam, L and Preczewski, L and Anjan, S and Nasrallah, A and Vianna, R and Morsi, M and Natori, Y},
title = {Diagnosing Hyperammonemia Syndrome in Non-Lung Solid Organ Transplant Recipients With Metagenomic Next-Generation Sequencing: Utility and Limitations From Two Clinical Cases.},
journal = {Clinical transplantation},
volume = {40},
number = {4},
pages = {e70550},
doi = {10.1111/ctr.70550},
pmid = {42035444},
issn = {1399-0012},
}

@article {pmid42035799,
year = {2026},
author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K},
title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {121858},
doi = {10.1016/j.jad.2026.121858},
pmid = {42035799},
issn = {1573-2517},
abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.

METHODS: Fecal samples were collected from 121 first-episode, drug-naïve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.

RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.

CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.},
}

@article {pmid42035921,
year = {2026},
author = {Liu, H and Xie, B and Zhuo, H and He, B and Dai, J and Zhou, Z and Shen, G and Chen, B and Tang, J and Ren, H and Jiang, X},
title = {Molecular Traces of Microbial Cross-Kingdom Migration: From the Gut Ecosystem to the Intervertebral Disc Microenvironment.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2026.04.027},
pmid = {42035921},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Low back pain is a leading cause of disability worldwide, and lumbar intervertebral disc degeneration (IVDD) is strongly associated with its development. Recent studies have shown that the gut microbiota (GM) and its metabolites may be involved in the occurrence and development of IVDD through the gut-disc axis. However, the key microbes mediating this process and their specific molecular mechanisms remain unclear.

PURPOSE: This study aimed to identify the gut microbes that play a key role in the progression of IVDD using multi-omics approaches and clarify the specific mechanisms by which these microbes participate in IVDD by regulating host cell functions.

STUDY DESIGN/SETTING: A single center, prospective cross-sectional study.

PATIENT SAMPLE: We prospectively included 113 patients who underwent surgical treatment for symptomatic lumbar degenerative diseases from May 2022 to May 2023, and their degenerated lumbar intervertebral disc (IVD) tissues as well as paired feces samples were collected.

OUTCOME MEASURES: Metagenomic next-generation sequencing (mNGS), modified Pfirrmann typing, Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq).

METHODS: Clinical IVD samples and paired fecal samples were prospectively collected and subjected to multi-omics bioinformatics analysis. mNGS was used to analyze the microbial composition in IVD and paired fecal samples. scRNA-seq was employed to resolve the cellular heterogeneity of IVD tissues. Bulk RNA-seq was utilized to identify the characteristics of host response genes related to microbial exposure. Subsequent AUCell scoring was performed to evaluate the abundance of microbes in cell subsets. The CellChat algorithm was applied to analyze the microbe-mediated intercellular communication network of host cells.

RESULTS: The raw detection rate of mNGS in IVD tissues was 100%, with a positive rate of 60.2% (68/113) after excluding background bacteria. A total of 505 genera and 1,528 microbial species were detected, with dominant species including Stutzerimonas stutzeri and Moraxella osloensis. The mNGS detection rate in fecal samples was 100% (322 genera and 789 species), among which Phocaeicola vulgatus (PV) was a dominant species. A total of 7 bacterial species shared by GM and IVD were identified; however, only the relative abundances of PV and Bacteroides thetaiotaomicron (BT) increased gradually with the severity of IVDD. Single-cell RNA-seq identified 10 cell clusters, annotated as chondrocytes, macrophages, fibroblasts, and endothelial cells, with the proportions of the latter three non-chondrocyte populations being significantly higher in the severe IVDD group. Chondrocytes were further divided into subsets. Subsets MDC1 and MDC5 were related to mild degeneration with high expression of ACAN and SOX9, whereas SDC2, SDC3, SDC4, SDC6, and SDC7 were related to severe degeneration. AUCell scoring revealed that PV showed a significantly higher abundance in these pathological subsets, while BT was evenly distributed. Furthermore, chondrocytes with high PV abundance significantly upregulated matrix degradation genes including MMP13 and COL1A1, as well as cell adhesion genes such as POSTN and SPARC. These upregulated genes were significantly enriched in LPS-associated inflammatory cascades, extracellular matrix degradation, and metabolic reprogramming pathways. Crucially, LPS signaling genes including TLR4, MYD88, NFKB1, and RELA were upregulated in chondrocytes with high PV abundance, while short-chain fatty acid receptor genes were minimally expressed with no significant group differences. Finally, CellChat analysis revealed that high PV abundance amplified the communication between chondrocytes and macrophages, fibroblasts, and endothelial cells, which was mediated by the CXCL pathway for immune recruitment, the VEGF and ANGPT pathways for angiogenesis, and the TGF-β pathway for pro-fibrotic remodeling.

CONCLUSION: This study suggests that gut-derived PV may activate the inflammatory response of chondrocytes through the LPS-mediated TLR4-MYD88 signaling axis and reshape the intercellular communication network, thereby potentially contributing to the process of IVDD. These findings provide novel mechanistic insights into the gut-disc axis theory and offer new perspectives on IVDD therapeutic strategies targeting microbe-host interactions.},
}