@article {pmid42748823,
year = {2026},
author = {Yang, R and Liu, C and Liu, J and Liu, Y and Wang, C and Guo, D and Zhou, J and Tai, X and Zhang, G and Zhang, B},
title = {Antibiotic resistome patterns across wheat soil microdomains under cadmium exposure and their associations with rhizosphere metabolite profiles.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143642},
doi = {10.1016/j.jhazmat.2026.143642},
pmid = {42748823},
issn = {1873-3336},
abstract = {The co-contamination of heavy metals and antibiotic resistance genes (ARGs) poses an increasing challenge to agroecosystems, yet its relationships with rhizosphere metabolism and microbial communities remain poorly understood. We integrated metagenomic sequencing, untargeted metabolomics, and absolute qPCR in a wheat pot experiment to characterize resistome patterns across unplanted bulk soil (O), root-zone soil (PS), and rhizosphere soil (PR) under three Cd treatments. At the booting stage, observed ARG subtype richness and total TPM-normalized ARG abundance were higher in root-associated compartments, whereas responses to cadmium within PR were heterogeneous and non-monotonic. Absolute qPCR broadly supported enrichment of selected resistance genes in root-associated soils. Community analyses identified Pseudomonadota and Actinomycetota as potential ARG-associated taxa. Metabolomic differentiation between PR and O was substantially greater than the differences among Cd treatments within PR, while metabolite-ARG associations partly reflected compartment-level covariation. ARG and metal resistance gene abundances showed strong covariation relationship, and contig-level analysis identified genetic contexts consistent with potential linkage among resistance determinants across both control and Cd-amended treatments. Overall, spatial differentiation among soil microdomains was more consistent than treatment-associated Cd patterns. These findings identify the wheat rhizosphere as an important zone of ARG enrichment under Cd exposure while highlighting the need for host-resolved and functional validation.},
}

@article {pmid42749142,
year = {2026},
author = {Zhang, Y and Wang, H and Ling, Y and Wang, H and Wang, S and Wang, X and Liu, F},
title = {Carbon-sulfur regulation for deep nitrogen removal in Arundo donax straw/elemental sulfur-amended surface flow constructed wetlands: Metagenomic and metabolomic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135874},
doi = {10.1016/j.biortech.2026.135874},
pmid = {42749142},
issn = {1873-2976},
abstract = {Plant-derived carbon can sustain heterotrophic denitrification in low carbon-to-nitrogen (C/N) constructed wetlands, but how the relative loading of elemental sulfur (S[0]) and solid carbon regulates mixotrophic nitrogen removal remains unclear. In this study, six surface flow constructed wetlands (SFCWs) amended with different Arundo donax straw/S[0] ratios were operated for 96 days to treat simulated secondary effluent. Under the tested conditions, the 1:1 ratio (450 g/450 g) showed the best performance, with a stable-period total inorganic nitrogen (TIN) removal efficiency of 77.6 ± 5.7 % and a relatively low net SO2-4 accumulation per unit TIN removed (1.47 mg SO2-4/mg N). Insufficient S[0] weakened late-stage NO-3-N removal; the excess S[0] configuration showed HS[-]/S[2-] accumulation and was associated with a higher risk of dissimilatory nitrate reduction to ammonium without improving nitrogen removal; and carbon-limited configurations showed insufficient electron donor availability. Vertical profiles showed that carbon release and NO-3-N reduction were concentrated in the lower layers. Metagenomic analysis showed that the 1:1 configuration enriched representative functional taxa, including hydrolytic/fermentative bacteria (Clostridium), sulfur-transforming bacteria (Sulfuritalea, Thiobacillus), and nitrogen reduction-related taxa (Azonexus). Functional gene abundances suggested greater potential for anaerobic carbon oxidation and sulfur transformation in the 1:1 configuration. Metabolomic analysis indicated substrate-associated changes in sulfur-related metabolites and in pathways related to nicotinamide adenine dinucleotide and coenzyme A. Network analysis further showed that carbon metabolism and sulfur transformation were closely associated with nitrogen removal performance. These results provide new insights into substrate regulation of mixotrophic denitrification in SFCWs treating low C/N wastewater.},
}

@article {pmid42749360,
year = {2026},
author = {Zhang, K and Gorelik, MG and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G},
title = {Divergent microbial preludes to necrotising enterocolitis defined by gut phages and bacterial resistomes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338976},
pmid = {42749360},
issn = {1468-3288},
abstract = {BACKGROUND: Translating microbiome correlations into robust predictive features for complex gut disorders remains elusive, partly due to oversimplified models of pathogenesis and neglect of the virome, a key player in microbial ecosystems. Necrotising enterocolitis (NEC), a devastating disease of preterm infants with no reliable clinical predictors, exemplifies this challenge.

OBJECTIVE: To determine the predictive potential of the gut prophageome and polymicrobial aetiologies for NEC.

DESIGN: We applied integrated metagenomic and metatranscriptomic analyses and machine learning to 1825 longitudinal stool samples from 43 preterm infants who later developed NEC and 86 gestational age-matched and birthweight-matched controls across three US hospitals. We characterised gut prophageome acquisitions and their association with clinical exposures, including antibiotics, diet and pharmacotherapies. To predict NEC risk, we integrated pre-onset prophageome, antibacterial resistome and bacteriome profiles with neonatal pathology, stratifying the cohort by disease onset timing (early: ≤40 days; late: >40 days) for separate analysis.

RESULTS: NEC cases exhibited distinct viral diversity trajectories before disease onset. Early-onset NEC was best predicted by phage-bacterial interaction signatures (75% accuracy, 81% sensitivity). Metatranscriptomics revealed increased phage DNA abundance with low gene expression, suggesting a lysogenic lifestyle that may stabilise pathobionts. These phages encode metabolic genes potentially enhancing pathobiont resilience. Late-onset NEC was best predicted by antibacterial resistome profiles (83% accuracy).

CONCLUSION: The gut prophageome serves as both a source of pre-symptomatic predictive signals and an active modulator of NEC pathogenesis, with distinct microbial mechanisms driving early-onset and late-onset disease. These polymicrobial etiologies inform strategies for early detection, risk stratification and the development of microbiome-targeted preventive and therapeutic interventions.},
}

@article {pmid42749361,
year = {2026},
author = {Qian, Z and Han, J and Lyu, B and Ainiwaer, A and Zhao, Q and Wang, S and Cheng, J and Li, Y and Sun, Y and Zhang, X and Lu, Y},
title = {Longitudinal gut microbiome dynamics during immunotherapy identify microbial features of clinical benefit in advanced primary liver cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339115},
pmid = {42749361},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiome has been linked to immune checkpoint inhibitor (ICI) outcomes, but the temporal dynamics of microbial communities during treatment remain poorly characterised.

OBJECTIVE: To characterise gut microbiome trajectories during ICI therapy and evaluate whether on-treatment microbial states improve the identification and generalisability of pretreatment biomarker signatures.

DESIGN: We performed a large prospective longitudinal shotgun metagenomic study of 315 patients with advanced primary liver cancer receiving ICI-based therapy, profiling 777 serial stool metagenomes collected at baseline and at approximately 3-month intervals on treatment. Responders (durable clinical benefit ≥6 months) contributed extended follow-up beyond 18 months. On-treatment windows were used for feature discovery; baseline-trained models were evaluated across all nine public ICI cohorts (n=1204).

RESULTS: Responders showed higher baseline alpha diversity and distinct community structure. Longitudinal profiling revealed marked ecological remodelling during therapy in both response groups, characterised by reduced network connectivity, increased modularity and strong time point specificity of discriminatory species. Using the on-treatment contrast at ~6 months (T2) as a discovery window, we identified a 16-species panel. A baseline model built from this panel outperformed models based on baseline-only feature discovery and generalised across nine public ICI studies. The resulting gut microbiome-derived immunotherapy outcome score stratified overall and progression-free survival in the discovery cohort (HRs 0.49 and 0.44) and across multiple external datasets, including stable-disease subsets.

CONCLUSION: The gut microbiome undergoes structured ecological remodelling during ICI therapy; on-treatment longitudinal windows improve pretreatment signature portability and support microbiome-guided stratification in immuno-oncology.},
}

@article {pmid42749373,
year = {2026},
author = {Gao, H and Shen, J and Chen, D and Mol, BW and Hu, W and Liang, Z and Bai, X and Han, X and Zhu, J and Wang, H and Liu, X and Su, C and Chen, Y and Weng, R and Liu, Y and Li, W and Zhang, D},
title = {Labour induction in low-risk women at 39 weeks of gestation: a randomised trial in China (LIRIC) - protocol of an open label, randomised controlled trial.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e123251},
pmid = {42749373},
issn = {2044-6055},
mesh = {Humans ; Female ; Pregnancy ; China ; *Labor, Induced/methods ; *Cesarean Section/statistics & numerical data ; Randomized Controlled Trials as Topic ; Infant, Newborn ; Gestational Age ; Adult ; Infant ; Pregnancy Trimester, Third ; Perinatal Mortality ; },
abstract = {INTRODUCTION: The A Randomized Trial of Induction Versus Expectant Management (ARRIVE) first demonstrated that elective induction of labour (IOL) at 39 weeks in low-risk pregnancies reduced the likelihood of caesarean section (CS) without compromising perinatal safety; however, the generalisability of these findings remains debated, leading to uncertainty in clinical practice. The Labour Induction in Low-risk Women at 39 Weeks of Gestation: a Randomised Trial in China (LIRIC) aims to evaluate whether 39-week elective IOL reduces CS rates compared with expectant management while exploring its impact on infant neurodevelopment and multiomics profiles.

METHODS AND ANALYSIS: This is a single-centre, open-label, randomised controlled trial in China. A total of 1074 low-risk pregnant women (nulliparous or multiparous) will be randomly assigned (1:1 ratio) to either 39-week IOL or expectant management. The primary outcome is the CS rate. Secondary outcomes include a composite of severe neonatal morbidity and perinatal mortality and infant neurodevelopmental scores (Bayley Scales of Infant Development; Bayley-4 and Ages and Stages Questionnaires; ASQ-3), among others. Data analysis will follow the intention-to-treat principle. Biospecimen will be collected for metagenomic and metabolomic analyses, with results to be reported separately.

ETHICS AND DISSEMINATION: The protocol has been approved by the Ethics Committee of Women's Hospital, School of Medicine, Zhejiang University. Informed consent will be obtained from all participants. Results will be disseminated via peer-reviewed journals, and standardised infant developmental reports will be provided to participants to enhance study benefit.

TRIAL REGISTRATION NUMBER: NCT07082530.},
}

Humans
Female
Pregnancy
China
*Labor, Induced/methods
*Cesarean Section/statistics & numerical data
Randomized Controlled Trials as Topic
Infant, Newborn
Gestational Age
Adult
Infant
Pregnancy Trimester, Third
Perinatal Mortality

@article {pmid42749445,
year = {2026},
author = {Agusetyaningsih, I and Lestari, DA and Pandupuspitasari, NS and Setiaji, A and Philco, SV and Sugiharto, S},
title = {Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {3},
pages = {100775},
doi = {10.1016/j.jgeb.2026.100775},
pmid = {42749445},
issn = {2090-5920},
abstract = {Antibiotic resistance is a growing global health concern, with poultry systems acting as important reservoirs of antibiotic resistance genes (ARGs). However, resistome and functional profiles of indigenous chickens raised under traditional systems remain underexplored. This study aimed to characterize the antibiotic resistome, virulence factor genes, and metabolic potential of gut microbiota in Indonesian Kedu chickens using a shotgun metagenomic approach. Digesta samples from five gastrointestinal segments of 21 healthy adult chickens were analyzed through high-throughput sequencing. ARGs were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Antibiotic Resistance Genes Databases (ARDB), while virulence factors and functional genes were annotated using Virulence Factor Database (VFDB), Clusters of Orthologous Groups (COG), and Carbohydrate-Active EnZymes (CAZy) databases. Results revealed a diverse resistome dominated by multidrug resistance and efflux pump mechanisms, with prominent genes associated with fluoroquinolone, tetracycline, β-lactam, and glycopeptide resistance. The detection of clinically relevant ARGs suggests that genetic determinants associated with antimicrobial resistance are present in the gut microbiota of traditionally raised Kedu chickens, although metagenomic data alone cannot determine whether these genes are actively expressed or confer phenotypic resistance. Virulence factor analysis showed functions related to adherence, immune evasion, iron acquisition, quorum sensing, and efflux activity, reflecting strong microbial adaptability. Functional profiling demonstrated enrichment in translation, carbohydrate and amino acid metabolism, genome maintenance, and cell envelope biogenesis. Additionally, CAZyme analysis indicated a high capacity for complex polysaccharide degradation, supporting efficient utilization of fiber-rich traditional diets. In conclusion, this study provides a comprehensive metagenomic overview of antibiotic resistance and functional potential in Kedu chicken gut microbiota, emphasizing the importance of incorporating indigenous poultry into antimicrobial resistance surveillance within a One Health framework.},
}

@article {pmid42750334,
year = {2026},
author = {Zhang, S and Xiao, L and Mo, G},
title = {[Progress in the application of bronchoalveolar lavage fluid in the diagnosis of infectious lung diseases].},
journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology},
volume = {42},
number = {9},
pages = {844-850},
pmid = {42750334},
issn = {1007-8738},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/cytology/immunology ; *Lung Diseases/diagnosis/microbiology/immunology ; },
abstract = {Bronchoalveolar lavage fluid (BALF) contains diverse cellular components and pathogens, directly reflecting the local immune status at sites of pulmonary infection. By detecting pathogens such as bacteria, fungi, and viruses within these samples and analyzing changes in the immune cell composition and cytokine levels, it will help to assess the immune microenvironment of infected lung regions and to predict disease prognosis. In recent years, the application of artificial intelligence in BALF analysis has significantly enhanced the efficiency of cell classification and counting. Combined with molecular diagnostic methods such as metagenomic next-generation sequencing, this approach deeply explores the diagnostic value of immune cells, pathogens, and their molecular characteristics in BALF for infectious lung diseases. It will provide more precise support for early disease identification, personalized treatment, and clinical decision-making.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology/cytology/immunology
*Lung Diseases/diagnosis/microbiology/immunology

@article {pmid42750336,
year = {2026},
author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YPR},
title = {Alamandine/MrgD pathway modulates gut-bone marrow axis in ageing.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70656},
pmid = {42750336},
issn = {1476-5381},
support = {AG056881/NH/NIH HHS/United States ; P20GM103442/NH/NIH HHS/United States ; U42 OD010918/NH/NIH HHS/United States ; },
abstract = {BACKGROUND AND PURPOSE: Ageing is associated with colon epithelial barrier disruption and up-regulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in ageing via modulating gut-BM axis.

EXPERIMENTAL APPROACH: Mice, 2-3 (Young) or 22-24 months (Old), were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Faecal microbiome was analysed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Caecal or serum bacterial metabolites were analysed and the caecal supernatants (CS) were tested for myelopoietic potential.

KEY RESULTS: MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in ageing was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels and this was antagonized by NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the microbiota with decreased Bacillota/Bacteroidota in ageing. Ala decreased the CD80[+] and increased CX3CR[+] macrophages in the Old colons. Old-CS induced myelopoiesis in BM cells with higher number of pro-inflammatory macrophages, which was prevented by Ala treatment.

CONCLUSIONS AND IMPLICATIONS: Targeting Ala/MrgD pathway is a promising approach for ameliorating the inflammatory stress in ageing by restoring homeostasis in the gut-BM inter-organ communication.},
}

@article {pmid42750565,
year = {2026},
author = {Pothikamjorn, TL and Gonzales, JA},
title = {Molecular biomarker profiling in noninfectious uveitis: a chronological review of discovery.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
pmid = {42750565},
issn = {1531-7021},
abstract = {PURPOSE OR REVIEW: Noninfectious uveitis (NIU) encompasses a heterogeneous group of immune-mediated intraocular inflammatory diseases whose complexity has driven systematic molecular biomarker discovery. This review presents NIU molecular biomarkers organized by biological category; autoantigens, human leukocyte antigens (HLA) and genetic markers, cellular immune subsets, cytokines, chemokines, and multiomics platforms including proteomics, microbiome metagenomics, metabolomics, and single-cell transcriptomics with each category presented in strict chronological order of landmark discovery.

RECENT FINDINGS: We present a review organized along two nested timelines. Categories are presented in the order they historically emerged in the field, and within each category, landmark discoveries appear in chronological sequence. This allows the reader to trace how each biomarker category evolved: from foundational autoantigen identification in experimental uveitis models, through the genomic revolution of HLA association studies, into cellular immunophenotyping, cytokine profiling of aqueous humor, chemokine mapping of intraocular trafficking, and finally the emerging omics platforms that may potentially anchor precision medicine in NIU. Each biomarker is paired in line with its linked targeted therapeutic.

SUMMARY: Biomarker research has transformed the understanding of NIU from a clinically defined syndrome into a group of molecularly distinct immune disorders. Advances spanning autoantigens, genetics, immune-cell profiling, cytokines, chemokines, and multiomics have revealed novel pathogenic mechanisms and therapeutic targets. Integration of these biomarkers with targeted therapies may accelerate the transition toward precision medicine in uveitis care.},
}

@article {pmid42750609,
year = {2026},
author = {Ma, X and Zhong, L and Wang, T and Zhang, Y and Liu, X and Ma, S and Dang, D},
title = {Clinical and etiological characteristics of severe community-acquired pneumonia: A two-center retrospective analysis from Xi'an and Jiaxing in China.},
journal = {The Journal of international medical research},
volume = {54},
number = {9},
pages = {3000605261489324},
doi = {10.1177/03000605261489324},
pmid = {42750609},
issn = {1473-2300},
mesh = {Humans ; *Community-Acquired Pneumonia/microbiology/epidemiology ; Male ; Female ; Retrospective Studies ; China/epidemiology ; Aged ; Severity of Illness Index ; Anti-Bacterial Agents/therapeutic use ; Sputum/microbiology ; *Community-Acquired Infections/microbiology ; },
abstract = {ObjectiveThis study was conducted to evaluate the baseline clinical profile, causative pathogens, and treatment patterns of severe community-acquired pneumonia across two medical centers (Xi'an and Jiaxing) from January 2023 to August 2025.MethodsWe extracted data regarding medical profile, demographic characteristics, comorbidities, laboratory parameters, treatments during hospitalization, and outcomes for these patients from electronic records. Pathogens were detected using a combination of sputum culture/throat-swab polymerase chain reaction with metagenomic next-generation sequencing or targeted next-generation sequencing.ResultsAmong the 204 severe community-acquired pneumonia patients, majority were men (72.55%, 95% confidence interval: 66.05%-78.21%); the age range of the population was 65-79 years (41.18%, 95% confidence interval: 34.65%-48.03%), and chronic obstructive pulmonary disease was the predominant chronic pulmonary condition, present in 28.92% of the study participants. Laboratory evaluations revealed high illness severity scores (Acute Physiology and Chronic Health Evaluation II score: 19.00 (14.00, 24.00) and Sequential Organ Failure Assessment score: 7.00 (6.00, 10.00)). Pathogens were identified using metagenomic next-generation sequencing or targeted next-generation sequencing of blood/sputum/bronchoalveolar lavage fluid and polymerase chain reaction of sputum culture/throat-swab in 117 and 85 cases, respectively. Klebsiella pneumoniae was the most common pathogen, present in 20.10% of the participants (95% confidence interval: 15.18%-26.13%), followed by coronavirus 2019 (16.18%, 95% confidence interval: 11.76%-21.85%), and influenza A virus (12.75%, 95% confidence interval: 8.85%-18.02%). Most frequently administered medicines were β-lactam/β-lactamase-inhibitor combinations (89.22%) and carbapenems (60.78%). All patients received respiratory support, with 15.69% undergoing continuous renal-replacement therapy and 5.39% receiving extracorporeal membrane oxygenation. The in-hospital mortality rate was 38.73% (79/204, 95% confidence interval: 32.31%-45.56%).ConclusionSevere community-acquired pneumonia, which is most often caused by K. pneumoniae in our region, regularly complicates chronic obstructive pulmonary disease and other chronic pulmonary diseases, requires broad-spectrum antibiotics and life-support, and is associated with a relatively high mortality rate.},
}

Humans
*Community-Acquired Pneumonia/microbiology/epidemiology
Male
Female
Retrospective Studies
China/epidemiology
Aged
Severity of Illness Index
Anti-Bacterial Agents/therapeutic use
Sputum/microbiology
*Community-Acquired Infections/microbiology

@article {pmid42750770,
year = {2026},
author = {Saha, S and Dutta, M and Bosu, A},
title = {Reframing Technology and Ethics in Corneal Xenotransplantation: A Scoping Review of Standards and Safety in Ophthalmology.},
journal = {Health care science},
volume = {},
number = {},
pages = {},
pmid = {42750770},
issn = {2771-1757},
abstract = {Xenotransplantation offers a potential solution to the critical global organ shortage by allowing the transplantation of organs from non-primate animals to humans. To address the critical barriers of biological safety, zoonotic infections, and immunological rejection, this review evaluates current innovations in genetically engineered donor species strategies and assesses existing ophthalmological standards, employing specific expression of human regulatory proteins (hCD46/hCD55) and genetically modified triple knockout (GGTA1/B4GalNT2/CMAH), biophysical thresholds, porcine cytomegalovirus screening, bacterial/mycotic cultures, and DNA sequencing for unidentified organisms. Employing a snowball strategy across PubMed Central, ResearchGate, and Wiley Online Library, 47 articles were selected and reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews. The feasibility of xenotransplantation relies heavily on advancements in donor technology and genotype transparency, animal husbandry and biosafety, infectious testing and surveillance, recipient monitoring and lifetime surveillance, biosafety incident and response plan, data governance, sharing and oversight, and animal welfare and social license, necessitating pathogen observation, biosecure storage, bioexclusion monitoring, and good manufacturing practice-style manual, quantitative polymerase chain reaction for porcine cytomegalovirus, porcine reproductive and respiratory syndrome virus, hepatitis E virus, alongside porcine endogenous retrovirus-A/B/C; metagenomic sequencing initially, followed by 1, 3, 6, and 12 months, and subsequently once every year, systematic and preliminary persistent sampling evaluations, independent data safety monitoring board, collaborative guidelines, encrypted databases, and data retention. The integration of endothelium-protective human genes, including hA20 or hHO-1, into genetically altered donor corneas in non-human primate xenografts, is expected to minimize initial post-transplant endothelial cell density loss by ≥ 20% compared to existing models. While clustered regularly interspaced short palindromic repeats-based modifications offer transformative potential for xenotransplantation, their reliability currently depends on establishing stringent biosafety standards.},
}

@article {pmid42750901,
year = {2026},
author = {Musleh, L and Montilli, M and Ammendolia, MG and Sciarra, A and Riccioli, A and Maurizi, L and Longhi, C},
title = {More than an infection: the ecological puzzle of recurrent urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1927507},
pmid = {42750901},
issn = {2235-2988},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology ; Recurrence ; Microbiota ; Reinfection/microbiology ; Host Microbial Interactions ; Dysbiosis ; Urinary Tract/microbiology ; },
abstract = {Recurrent urinary tract infections (rUTIs) represent one of the most common infectious conditions worldwide, yet their pathophysiology extends far beyond repeated episodes of acute bacterial cystitis. Increasing evidence indicates that recurrence may arise through overlapping mechanisms including reinfection from intestinal or periurethral reservoirs, intracellular bacterial persistence, microbial dysbiosis, impaired mucosal immunity and chronic inflammatory remodelling of the bladder microenvironment. Current diagnostic frameworks remain largely based on symptom-based definitions and standard urine culture, approaches that incompletely capture the biological complexity of recurrent disease. This limitation is evident even at the definitional level, where clinically pragmatic categories often fail to reflect the heterogeneous mechanisms underlying recurrence. Advances in expanded urine culture techniques, metagenomics and metabolomics have reshaped the understanding of the urinary tract as a dynamic ecological system interconnected with vaginal, intestinal and prostatic microbial compartments. These approaches have identified diverse microbial communities, virulence-associated functional profiles and host-microbe interactions linked to recurrence-prone phenotypes. Significant challenges continue to persist in elucidating the biological mechanisms driving recurrence. Addressing these gaps is essential to improve disease characterization and support the development of more effective diagnostic and therapeutic approaches.},
}

Humans
*Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology
Recurrence
Microbiota
Reinfection/microbiology
Host Microbial Interactions
Dysbiosis
Urinary Tract/microbiology

@article {pmid42751327,
year = {2026},
author = {De La Hoz, A and Kovac, V and Woolley, AE and Issa, NC and Letourneau, A and Baden, LR and Hammond, SP and Little, JS},
title = {Plasma Microbial Cell-Free DNA Sequencing for the Diagnosis of Chronic Disseminated Candidiasis in Patients with Hematologic Malignancies.},
journal = {Open forum infectious diseases},
volume = {13},
number = {9},
pages = {ofag543},
pmid = {42751327},
issn = {2328-8957},
abstract = {Diagnosis of chronic disseminated candidiasis (CDC) is frequently delayed because clinical manifestations are nonspecific and conventional diagnostic tests have limited sensitivity. We describe a series of 19 CDC cases in which plasma microbial cell-free DNA sequencing was performed due to diagnostic uncertainty. Results influenced antifungal management in most cases.},
}

@article {pmid42751339,
year = {2026},
author = {Segura, MG and Schwem, B and Sakamuri, RM and Grimes, CZ and Horne, M and Wanger, A and Truong, TT and Lieberman, JA and Litvinseva, AP and Ostrosky-Zeichner, L and Smith, DJ},
title = {Molecular Evidence of Autochthonous Environmental Acquisition of Fonsecaea Pediatric Infection in the United States.},
journal = {Open forum infectious diseases},
volume = {13},
number = {9},
pages = {ofag529},
pmid = {42751339},
issn = {2328-8957},
abstract = {Fonsecaea species cause chromoblastomycosis and phaeohyphomycosis, but links between environmental exposure and infection are poorly defined. We describe a 4-year-old boy with finger swelling after oak tree laceration in Houston, Texas. Broad-range polymerase chain reaction identified F. pedrosoi or F. monophora, and metagenomic sequencing of tree bark and soil detected Fonsecaea DNA.},
}

@article {pmid42751541,
year = {2026},
author = {Victor, MP and Al Shehri, N and Grevskott, DH and Alarif, WM and Ali, AM and Marathe, NP},
title = {High-throughput sequencing dataset of raw and treated wastewater from Jeddah, Saudi Arabia.},
journal = {Data in brief},
volume = {68},
number = {},
pages = {113174},
pmid = {42751541},
issn = {2352-3409},
abstract = {Wastewater is a major point source of pollution and antimicrobial resistance (AMR) in the environment. The aim of this study was to determine the microbiota and antimicrobial resistance genes present in both the influent and effluent from a biological wastewater treatment plant situated in Jeddah Second Industrial City, Saudi Arabia, using metagenomics. Water samples were collected, and the DNA extracted from these samples was subjected to metagenomic sequencing (one influent and one effluent) using Illumina NovaSeq. Our analysis yielded ∼88 Gigabases. The predominant bacterial genera identified were Actinomycetota, Psuedomonadota, and Bacillota, and β-lactamases emerged as the most common class of resistance genes. Eventhough these are unreplicated single observations they are expected to be a valuable resource for researchers focusing on wastewater studies, especially in the middle East, offering insights into bacterial diversity and the spectrum of resistomes associated with these microbial communities.},
}

@article {pmid42751774,
year = {2026},
author = {Shao, J and Hung, W and Yin, P and Huang, P and Zhao, W and Yu, L and Tian, F and Chen, W and Xu, J and Zhai, Q and Li, J and Zhao, J},
title = {Efficacy of Bifidobacterium animalis subsp. lactate BL-99 in relieving functional constipation: a randomized placebo-controlled clinical trial.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03175c},
pmid = {42751774},
issn = {2042-650X},
abstract = {Current therapies for functional constipation (FC) often exhibit limited long-term efficacy. Probiotics, particularly Bifidobacterium animalis subsp. lactis BL-99 (BL-99), may offer a novel approach to alleviate FC symptoms. This randomized, double-blind, placebo-controlled trial (No. WXSY-YXLL-AF/SC-11/01.0) enrolled 41 FC patients who completed the full 6-week study. Participants were randomly assigned to receive either BL-99 (1 × 10[11] colony-forming units per day) or placebo for 4 weeks in this population trial. After completing the 4-week intervention period, administration was discontinued and participants entered a 2-week observation following-up period for continued monitoring. Primary endpoint data collected after trial completion were the changes in the Patient Assessment of Constipation Symptoms (PAC-SYM, 12-item scale) score, evaluated on the first day (0 day), the 28th day (week 4), and the 42th day (week 6). Secondary outcomes included fecal metagenomic profiling to evaluate gut microbiota alterations. After 4 weeks of intervention, the BL-99 group demonstrated significant reductions in PAC-SYM scores compared to the placebo, particularly in domains of "abdominal discomfort" (Δ = 1.8 vs. 0.9, p = 0.007) and "pain during defecation" (Δ = 2.1 vs. 1.0, p = 0.003). These improvements persisted at the 2-week post-treatment follow-up (p < 0.05). Metagenomic analysis revealed that BL-99 enriched Bifidobacterium and Faecalibacterium while suppressing Clostridium species, shifting gut microbiota composition closer to that of the healthy controls. Functional annotation highlighted significant downregulation of infection-related pathways (e.g., bacterial invasion and LPS biosynthesis) and metabolic disease-associated pathways (e.g., insulin resistance) in the BL-99 group (q < 0.05). This trial suggests that 4-week BL-99 supplementation effectively alleviates FC symptoms, partially through microbiota modulation and metabolic pathway regulation. The sustained post-treatment effects warrant further investigation into its long-term benefits.},
}

@article {pmid42752346,
year = {2026},
author = {Pothikamjorn, TL and Doan, TA and Hinterwirth, A and Stewart, JM and Gonzales, JA},
title = {Metagenomic Deep Sequencing Identifies Gene Mutations Associated with Chemotherapeutic Resistance in Vitreoretinal Lymphoma.},
journal = {Ocular immunology and inflammation},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/09273948.2026.2677102},
pmid = {42752346},
issn = {1744-5078},
abstract = {PURPOSE: To identify gene mutations associated with chemotherapeutic resistance in patients with vitreoretinal lymphoma (VRL) using metagenomic deep sequencing (MDS) of intraocular specimens.

METHODS: Patients with VRL confirmed by cytopathology and immunohistochemistry, flow cytometry, and/or polymerase chain reaction for MYD88, were included. Intraocular specimens underwent MDS of the host genome. Gene mutations were identified and cross-referenced with the Catalogue of Somatic Mutations in Cancer database to determine associations with chemotherapeutic resistance.

RESULTS: Forty-nine patients with VRL underwent MDS, with six specimens from four patients revealing eight gene mutations associated with chemotherapeutic resistance. Four specimens from three patients harbored mutations associated with methotrexate resistance, the mainstay of VRL treatment. In one patient, serial sampling from the initial vitrectomy and two subsequent recurrences revealed distinct resistance-associated mutations at each time point. Despite multi-agent therapy including rituximab, consolidation regimens, and lenalidomide, this patient ultimately succumbed to the disease, whereas the other three patients remained in long-term remission.

CONCLUSIONS: Our findings demonstrated that specific gene mutations associated with chemotherapeutic resistance may be harbored by VRL. The detection of different resistance mutations at sequential time points in one patient may reflect clonal selection, treatment pressure, or variable detection sensitivity. The ability to easily sample ocular fluid and detect different mutations associated with tumor recurrence or persistence may provide insights into tumor pathogenesis and could inform prognosis and influence treatment decisions. These findings establish a foundation for developing targeted PCR assays for identified resistance genes, which could transform clinical practice in VRL.},
}

@article {pmid42752928,
year = {2026},
author = {Maurya, S and Sharma, P and Yadav, BNS and Gupta, GP and Tiwari, N and Yadav, RK},
title = {Fungi to the rescue: recent advances, mechanistic insights and omics-based perspectives in heavy metal mycoremediation.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42752928},
issn = {1432-072X},
mesh = {Biodegradation, Environmental ; *Metals, Heavy/metabolism ; *Fungi/metabolism/genetics ; Multiomics ; Proteomics ; *Environmental Pollutants/metabolism ; },
abstract = {Heavy metal (HM) contamination arising from rapid industrialization poses critical threats to global ecosystem integrity and public health. Conventional physicochemical approaches are limited by high costs, incomplete removal, and toxic waste generation, necessitating sustainable alternatives. Mycoremediation, which harnesses the remarkable, diverse capacities of fungi to tolerate and mitigate HM stress through sophisticated biological mechanisms, has emerged as a promising and sustainable approach to address HM pollution. This review examines the sources and ecotoxicological impacts of HM pollution, alongside the intracellular and extracellular mechanisms underlying fungal tolerance and removal, including biosorption, precipitation, membrane transport, antioxidant defense, chelation, bioaccumulation, and biotransformation. It further synthesizes fungal-based bioremediation strategies, while examining how metagenomic, metatranscriptomic, transcriptomic, proteomic, and metabolomic approaches are advancing understanding of fungal community structure and active detoxification pathways. This work uniquely integrates community- and isolate-level multi-omics data, explicitly bridges mechanistic understanding with omics-driven insights, and extends this into translational roadmap for applied bioremediation.},
}

Biodegradation, Environmental
*Metals, Heavy/metabolism
*Fungi/metabolism/genetics
Multiomics
Proteomics
*Environmental Pollutants/metabolism

@article {pmid42753294,
year = {2026},
author = {Saleh, ZH and El Enbaawy, MI and Kamal, MA and Mahmoud, H and Hassan, M},
title = {Heat stress, respiratory dysbiosis, and poultry pathobiome: A comprehensive review of chronic respiratory disease in chickens.},
journal = {Veterinary microbiology},
volume = {322},
number = {},
pages = {111225},
doi = {10.1016/j.vetmic.2026.111225},
pmid = {42753294},
issn = {1873-2542},
abstract = {The poultry respiratory microbiome is increasingly recognized as a critical determinant of poultry health, mucosal immunity, and host resistance to opportunistic pathogens. Chronic Respiratory Disease (CRD) exerts a severe economic toll on the global broiler industry. While conventionally attributed to specific etiological agents such as Mycoplasma gallisepticum, disease progression is fundamentally tied to broad ecological dysbiosis within the respiratory tract. This comprehensive review synthesizes current knowledge on the functional roles and compositional dynamics of the poultry respiratory microbiome in both healthy and diseased states. Notably, we acknowledge the emerging threat of climate change, elucidating how heat stress physically and immunologically disrupts the respiratory mucosal microenvironment, acting as a primary catalyst for microbiome destabilization and CRD susceptibility. By shifting the paradigm from a single-pathogen model to a comprehensive pathobiome perspective, we detail the microbial shifts that characterize CRD. Furthermore, because investigating this low-biomass environment presents unique analytical challenges, we critically evaluate current technical methodologies. We address critical bottlenecks in sample collection, DNA extraction biases, and the comparative efficacy of 16S rRNA amplicon versus shotgun metagenomic sequencing. Ultimately, this synthesis provides a foundational framework for optimizing diagnostic methodologies and developing microbiome-targeted interventions -such as next-generation probiotics- to mitigate CRD in an era of escalating environmental stressors.},
}

@article {pmid42753435,
year = {2026},
author = {Xue, P and Huang, B and Wang, Y and Zhao, L and Mao, L},
title = {Environmental fate and risk of diverse oxygenated isomeric prothioconazole biotransformation products in soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143509},
doi = {10.1016/j.jhazmat.2026.143509},
pmid = {42753435},
issn = {1873-3336},
abstract = {Isomeric biotransformation products (TPs) of organic pesticides substantially expand structural diversity and may exhibit distinct environmental behaviors compared with their parent compounds. However, the formation mechanisms and ecological risks of such isomers (regioisomers) in soil remain poorly understood. In this study, the triazole fungicide prothioconazole (PTC) was incubated in agricultural soil, and 21 isomeric TPs were identified and classified into six structural groups using high-resolution mass spectrometry (HR-MS) based on diagnostic fragmentation patterns. These secondary oxygenated isomeric TPs were derived from three primary intermediates (PTC-desthio, PTC-dehydrated, and PTC-S-methyl) via site-selective oxygenation. Toxicity predictions indicated substantial variability among isomers, with certain hydroxylated derivatives exhibiting higher predicted ecotoxicity than others, challenging the assumption that biotransformation necessarily leads to detoxification. Metagenomic analysis showed that PTC exposure significantly altered the soil microbial community, enriching genes associated with xenobiotic degradation and central carbon metabolism. Notably, functional microbial shifts, particularly involving the genus Acinetobacter, were strongly associated with specific isomer profiles. These results suggest a potential link between microbial metabolic responses and the formation of structurally diverse isomeric TPs. The widespread occurrence of such isomers highlights that assessments based solely on parent compounds may underestimate the environmental fate and risks of PTC in agroecosystems.},
}

@article {pmid42709897,
year = {2026},
author = {Guss, HD and Francioli, YZ and Grover, EN and Hill, A and Zou, W and Wade, KJ and Pike, H and Gopalan, SS and Yang, L and Bo, Z and Pollock, DD and Carlton, EJ and Castoe, TA},
title = {Population genomics reveals multi-scale mechanisms sustaining schistosomiasis re-emergence in a near-elimination setting.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014202},
doi = {10.1371/journal.pntd.0014202},
pmid = {42709897},
issn = {1935-2735},
mesh = {Animals ; Humans ; *Schistosoma japonicum/genetics/isolation & purification/classification ; China/epidemiology ; Genetic Variation ; *Schistosomiasis japonica/epidemiology/parasitology/transmission/prevention & control ; Genome, Helminth ; Snails/parasitology ; Metagenomics ; Disease Eradication ; },
abstract = {In China, sustained snail control, environmental management, and mass drug administration with praziquantel reduced schistosomiasis to near-elimination levels, yet re-emergence in Sichuan Province during the early 2000s exposed vulnerabilities in elimination efforts. We used population genomics to investigate the multi-scale population processes underlying Schistosoma japonicum re-emergence in Sichuan. We sequenced whole genomes from 270 miracidia collected from 53 human hosts across 17 villages in 2007, one year after re-emergence was documented. Population genomic analyses identified a broadly cohesive regional schistosome population with weak geographic structuring. Genome-wide diversity remained substantial, and demographic reconstructions revealed no recent decline in effective population size, suggesting that parasite populations had not undergone regional demographic collapse prior to re-emergence and were likely maintained in non-human reservoir hosts. At finer spatial scales, several villages exhibited reduced genomic diversity and elevated inbreeding, consistent with localized transmission maintained by relatively small founding populations. Estimates of pairwise genetic relatedness revealed dense within-village sibling clusters alongside second- and third-degree relationships spanning villages, and rare first- and second-degree cross-village links, supporting predominantly local transmission embedded within a connected regional transmission network. Genomic inference of minimum reproducing worm pairs identified substantial heterogeneity in host-level worm burden, ranging from one to eleven adult worm pairs, although uneven sampling limited absolute estimates. Together, these findings indicate that parasite persistence in this near-elimination setting was sustained by interacting processes operating across multiple biological scales, including diverse regional parasite populations, localized transmission networks connecting villages, and marked heterogeneity in host-level worm burden. More broadly, this work demonstrates how population genomics can reconstruct otherwise hidden patterns of parasite persistence and transmission, providing a valuable complement to conventional epidemiological surveillance in complex, multi-host parasite systems.},
}

Animals
Humans
*Schistosoma japonicum/genetics/isolation & purification/classification
China/epidemiology
Genetic Variation
*Schistosomiasis japonica/epidemiology/parasitology/transmission/prevention & control
Genome, Helminth
Snails/parasitology
Metagenomics
Disease Eradication

@article {pmid42743804,
year = {2026},
author = {Chen, ZY and Gao, FZ and Li, P and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Multi-omics evidence reveals robust airborne-human resistome connectivity driven by high-risk ARGs and mediated by Staphylococcus.},
journal = {Environment international},
volume = {216},
number = {},
pages = {110525},
doi = {10.1016/j.envint.2026.110525},
pmid = {42743804},
issn = {1873-6750},
abstract = {Airborne microbiomes are considered an important source of human antimicrobial resistance (AMR) exposure, yet multi-omics evidence linking airborne and human nasal resistomes remains limited. Here, we integrated metagenomic sequencing and whole-genome sequencing of antibiotic-resistant Staphylococcus isolates to investigate the connectivity between air and human nasal resistomes in dairy farm environments. Metagenomic taxonomic profiling showed that Staphylococcus was prominent in total suspended particles (TSP) and consistently detected across all samples. Among environmental reservoirs, TSP resistomes exhibited the strongest similarity to human nasal resistomes. This connectivity was supported by multiple lines of evidence, including highly similar resistome profiles, extensive homologous antibiotic resistance gene (ARG) pairs, strain-level similarity of resistant Staphylococcus isolates, and conserved mobile ARG genetic contexts. Notably, this connectivity was primarily driven by high-risk ARGs, while Staphylococcus was frequently associated with mobile ARGs and represented the only shared pathogenic genomes carrying both ARGs and virulence factor genes between airborne and nasal samples. Although lower ARG diversity, nasal resistomes exhibited higher ARG burden, risk scores, antibiotic-resistant bacterial genome abundance, and prevalence of resistant Staphylococcus. Occupational exposure further increased total and high-risk ARG burdens among farm workers. Together, these findings indicate that TSP can serve as an important route of occupational AMR exposure, with high-risk ARGs and Staphylococcus contributing to connectivity between airborne and nasal resistomes. Incorporating the host microbiome may therefore provide a more complete assessment of human-associated AMR exposure within a One Health framework.},
}

@article {pmid42743807,
year = {2026},
author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C},
title = {Involvement of cross-genus phages in bacterial resistance to chlorine disinfection.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126886},
doi = {10.1016/j.watres.2026.126886},
pmid = {42743807},
issn = {1879-2448},
abstract = {Chlorine disinfection resistance in pathogenic microorganisms poses severe environmental concerns and public health risks. While phages play critical roles in host adaptation to environmental stress, how poly-host phages contribute to bacterial resistance to chlorine disinfectants remains poorly understood. Here, we investigated shifts in the population dynamics, transcriptional profiles, and function potentials of cross-genus phage-bacterial communities under exposure to chlorine disinfectants in a continuously operated anaerobic-anoxic-oxic system over a 92-day period, using integrated metagenomic and metatranscriptomic approaches. In the presence and absence of chlorine disinfectants, the genomic abundance and diversity of phage and bacterial communities showed similar variation trends, and the community structures of both exhibited clear differences. A strong significant positive correlation was observed between phage and bacterial diversity under chlorine exposure (R = 0.975, p = 0.00,057), whereas no significant correlation was detected in the absence of chlorine disinfection (R = -0.314, p = 0.613), suggesting that chlorine disinfectants may enhance phage-bacteria interactions. Host-associated phages exhibited high consistency with their corresponding putative hosts in terms of genomic abundance (M[2] = 0.0945, p = 0.001) and transcript abundance (M[2] = 0.3668, p = 0.001), and they were also significantly correlated with cross-genus phages in both genomic abundance (R = 0.97, p < 2.2e-16) and transcript abundance (R = 0.83, p < 2.2e-16), which collectively suggests the critical role of cross-genus phages in the resistance of microbial communities to chlorine disinfectants. Bipartite association network analysis shows that cross-genus phages carry highly homologous genes to their putative hosts and may be involved in the horizontal transfer of these genes among bacteria. These homologous genes are involved in DNA repair, redox balance regulation, environmental stress adaptation and efflux pump functions, suggesting a synergistic role between cross-genus phages and their putative hosts in chlorine resistance. Our findings reveal that cross-genus phages can contribute to the resistance of bacterial communities to chlorine disinfectants, providing the theoretical foundation for evaluating the role of poly-host phages in microbial communities.},
}

@article {pmid42743809,
year = {2026},
author = {Chen, S and Wu, H and Chen, Y and Wang, F and Zhang, Y and Chen, N},
title = {An inundation threshold regulates nitrate reduction pathways in mangrove sediments.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126911},
doi = {10.1016/j.watres.2026.126911},
pmid = {42743809},
issn = {1879-2448},
abstract = {Estuarine hydrological regimes are increasingly altered by dam operations and extreme climate events, reshaping inundation in intertidal wetlands. However, how inundation regulates nitrate (NO3[-]) fate remains unclear. We conducted an 18-month, elevation-controlled marsh-organ experiment with Avicennia marina-planted and unvegetated sediments across a 0 %-65 % gradient in mean inundation frequency. We combined [15]N isotope tracing and metagenomics to quantify NO3[-] reduction pathways and associated microbial attributes. In unvegetated sediments, increasing inundation reduced the contribution of denitrification (DNF) from 62 % to 48 % and increased dissimilatory nitrate reduction to ammonium (DNRA) from 25 % to 34 %. In planted sediments, NO3[-] reduction shifted nonlinearly at approximately 24 % mean inundation frequency. Below this threshold, DNF dominated, contributing 83 %-87 % of NO3[-] reduction, whereas DNRA contributed only 2 %-6 %. Above the threshold, DNF declined to 45 % at the highest inundation frequencies, while DNRA increased to 42 %-48 %, indicating a shift from nitrogen removal toward retention. This transition coincided with plant failure, more reducing conditions, and changes in microbial community and functional profiles. Plant survival was associated with DNF-related taxa (e.g., Pseudomonas and Flavobacterium), nirK, and oxidative metabolism, whereas plant failure was associated with DNRA-related taxa (e.g., Shewanella and Geobacter), nrfA, and fermentative metabolism. These findings identify a vegetation-dependent inundation threshold beyond which nitrogen removal declines and nitrogen retention increases in mangrove sediments.},
}

@article {pmid42743975,
year = {2026},
author = {Pang, SJL and Wee, SK and Yap, EPH},
title = {Phage bioinformatics tools: a review of computational approaches for bacteriophage research.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42743975},
issn = {1477-4054},
support = {//Research Center for Excellence IDMxS/ ; //NTU Research Scholarship/ ; },
mesh = {*Computational Biology/methods ; *Bacteriophages/genetics ; Metagenomics/methods ; Machine Learning ; Genome, Viral ; *Software ; },
abstract = {Rising clinical interest in phage therapy and the exponential growth of metagenomic sequence catalogues have driven a rapid expansion of bacteriophage bioinformatics. More than 80 dedicated tools, mostly published since 2020, now span identification, assembly, annotation, taxonomy, lifestyle prediction, defence-system detection, and host prediction. Aimed at experienced practitioners and developers, this review synthesizes the field through the lens of three successive computational paradigms: sequence homology, bounded by database completeness; machine learning, constrained by labelled training data; and foundation models, which now achieve Matthews correlation coefficients above 0.95 in identification tasks and, through structure-informed prediction, raise functional annotation to over half of phage genes. Furthermore, we map the upstream components, namely, gene callers, homology engines, protein language models, and structural search tools, that underpin most downstream pipelines, exposing shared infrastructure and ecosystem-level fragility when dependencies change. To translate this into practice, we propose web-based and command-line reference workflows calibrated to user expertise and sample types. Finally, we set an agenda for the next wave of tool development. Roughly half of phage genes still resist functional annotation despite structural methods; no broadly generalizable strain-level host predictor exists for phage therapy; varying true-positive rates (0%-97%) underscore the absence of standardized community benchmarks analogous to Critical Assessment of Structure Prediction or Critical Assessment of Metagenome Interpretation. As generative genome models begin designing synthetic phages, progress will depend less on producing standalone tools than on rigorous evaluation, interoperable infrastructure, and clinically meaningful prediction targets.},
}

*Computational Biology/methods
*Bacteriophages/genetics
Metagenomics/methods
Machine Learning
Genome, Viral
*Software

@article {pmid42744171,
year = {2026},
author = {Xu, X and Yin, J and Peng, D and Li, J and Yang, Z and Qiao, L and Xu, J and Hu, X and Ren, Y and Cheng, B and Mu, Y},
title = {Enrofloxacin metabolism and antibiotic resistance in Monopterus albus differs between pond cage and greenhouse micro-flow aquaculture systems.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125688},
doi = {10.1016/j.envres.2026.125688},
pmid = {42744171},
issn = {1096-0953},
abstract = {Enrofloxacin (ENR) is a fluoroquinolone antibiotic widely used in aquaculture, yet its metabolic fate and resistance selection dynamics remain poorly characterized. Here, we investigated ENR metabolism, tissue distribution, withdrawal periods, gut microbial communities, and antibiotic resistance genes (ARGs) in Monopterus albus reared under pond net cage (PNC) and greenhouse micro-flow (GMF) systems following a 5-day medicated feed treatment (20 mg ENR/kg body weight). Eight ENR metabolites were tentatively identified, with ciprofloxacin (CIP) as the predominant metabolite. The GMF system significantly shortened the estimated withdrawal period to 4050 °C·d compared to 5550 °C·d for PNC (about 30% reduction). Critically, the PNC withdrawal period exceeded the current Chinese regulatory standard of 500 °C·d by more than 10 folds, revealing a substantial gap between existing guidelines and on-farm food safety requirements. Sediment analysis showed that 7.8% of the administered ENR dose persisted as a long term environmental reservoir. Metagenomic sequencing revealed that even a single ENR treatment induced an approximately 10-fold increase in fluoroquinolone resistance genes by day 60 post-treatment, with cross-resistance extending to multiple other antibiotic classes. Aeromonadaceae and Enterobacteriaceae were identified as the primary ARG hosts, and ARG abundance was significantly correlated with mobile genetic element prevalence, suggesting enhanced horizontal gene transfer potential. These findings demonstrate that aquaculture system design profoundly influences antibiotic fate and resistance selection, and that current withdrawal standards are inadequate for scaleless species. System-specific withdrawal guidelines and strengthened antimicrobial stewardship are urgently needed to mitigate environmental and food safety risks from aquaculture antibiotic use.},
}

@article {pmid42744253,
year = {2026},
author = {Dessai, U and Reynolds, JL and Kabera, C and Alt, L and Birhane, MG and Boxrud, D and Caidi, H and Ceric, O and Chandler, JC and Cook, K and Cooley, LA and Folster, JP and Ford, L and Fortenberry, GZ and Francois Watkins, LK and Franklin, AB and Franklin, AM and Frye, JG and Garland, JL and Ge, B and Harbottle, H and Haro, J and Huebner, KL and Kissler, B and Logan, N and Medley, A and Merrill, A and Miller, RA and Ottesen, A and Rockwell, CA and Shaw, S and Shivley, C and Simmons, M and Tadesse, DA and Tagg, KA and Tyson, GH and Webb, HE and Whichard, JM and Zhao, S and McDermott, PF and Tate, H},
title = {National Antimicrobial Resistance Monitoring System: Three Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100917},
doi = {10.1016/j.jfp.2026.100917},
pmid = {42744253},
issn = {1944-9097},
abstract = {Antimicrobial resistance (AMR) occurs when bacteria and other microorganisms adapt in ways that make medicines less effective, causing infections that are harder to treat and more likely to spread. According to the Centers for Disease Control and Prevention (CDC), AMR infections affect millions of Americans each year and contribute to thousands of deaths (CDC, 2019). After three decades of operation, the U.S. National Antimicrobial Resistance Monitoring System (NARMS) stands as a model of sustained, collaborative public health surveillance. What began in 1996 as an effort to track resistance in Salmonella and E. coli O157 has evolved into a One Health surveillance network monitoring AMR across the farm-to-fork continuum. Through a partnership among CDC, the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), state and local health departments, and universities, NARMS has become the backbone of foodborne AMR surveillance in the United States. The past decade has been particularly transformative. NARMS explored new sampling to include companion animals, minor livestock, aquaculture, surface water, and wildlife. Whole-genome sequencing (WGS) revolutionized the program's capabilities, enabling timely identification of emerging pathogens and revealing how resistance genes spread. Near real-time public dashboards make NARMS data accessible to researchers, clinicians, regulators, and policymakers. NARMS data shape decisions about new animal drug approvals, guide stewardship programs, and inform clinical treatment guidelines nationwide. As NARMS enters its fourth decade with a 2026-2030 strategic plan, the program will leverage artificial intelligence and metagenomics while expanding surveillance to fill remaining gaps ensuring this vital system continues to protect the food supply and both human and animal health from AMR.},
}

@article {pmid42744979,
year = {2026},
author = {},
title = {Ambient temperature is encoded in the metagenome of microbial communities.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42744979},
issn = {2058-5276},
}

@article {pmid42744981,
year = {2026},
author = {Yu, T and Yuan, S and Wang, Y and Wang, F},
title = {Evidence of direct methane production from long-chain fatty acids by thermophilic Archaeoglobi.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42744981},
issn = {2058-5276},
support = {42230401//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42276139//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methanogenic degradation of long-chain fatty acids has traditionally been thought to occur through syntrophic partnerships between fatty acid-degrading bacteria and methanogenic archaea. However, recent genomic evidence suggests that certain archaea may independently carry out the entire process. Here we report the enrichment of an archaeon from the class Archaeoglobi, Candidatus Methanoglobus sphaerolipidus DLY3, from hot spring sediments in Tengchong, China. The results of selective enrichment, growth experiments, microscopy, stable isotope tracing, metagenomics and metatranscriptomics suggest that Ca. M. sphaerolipidus directly converts long-chain fatty acids to methane. This transformation involves the beta-oxidation pathway, the Wood-Ljungdahl pathway and methanogenic methyl-coenzyme M reductase and methyltransferase complexes-a process we term liparotrophy. In addition to oleic acid, Ca. M. sphaerolipidus is also capable of utilizing methanol as a substrate for methanogenesis. Our findings expand the known substrate range for methanogenic archaea beyond carbon dioxide reduction, acetoclastic methanogenesis, methylotrophy, methyl reduction, methoxydotrophy and the recently reported alkylotrophy.},
}

@article {pmid42745084,
year = {2026},
author = {Chen, Y and Zhou, J and Yuan, L and Xie, M and Wang, J and Zheng, J and Zhou, L and Zhang, D and Han, D},
title = {Clinical and Genomic Insights into the Allodiploid Hybrid Pathogen Aspergillus latus: A Retrospective Case Series.},
journal = {Mycopathologia},
volume = {191},
number = {5},
pages = {},
pmid = {42745084},
issn = {1573-0832},
support = {2024ZD0533100 & 2024ZD0533106//National Science and Technology Major Project/ ; 82472371//National Natural Science Foundation of China/ ; },
mesh = {Retrospective Studies ; *Aspergillus/genetics/isolation & purification/classification/drug effects/cytology ; Humans ; China ; Antifungal Agents/pharmacology ; *Aspergillosis/microbiology/pathology/diagnosis ; High-Throughput Nucleotide Sequencing ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; Metagenomics ; },
abstract = {Aspergillus latus is an emerging cryptic allodiploid hybrid pathogen within Aspergillus section Nidulantes that closely resembles related species and therefore prone to misidentification by routine diagnostic methods. Therefore, its true clinical burden is likely underestimated. In this study, we retrospectively characterized five patients with A. latus infections identified by metagenomic next-generation sequencing (mNGS) at a tertiary hospital in China. Clinical manifestations varied according to host immune status, ranging from a subclinical pulmonary lesion in an immunocompetent individual to aggressive disease in highly immunocompromised patients. Conventional microbiological methods showed limited sensitivity and consistently misidentified the isolates as A. nidulans, whereas mNGS enabled accurate detection of A. latus together with complex co-infections. Three viable clinical isolates were recovered for morphological characterization, antifungal susceptibility testing, and whole-genome sequencing (WGS). All tested isolates demonstrated reduced susceptibility to echinocandins but remained susceptible to mold-active triazoles and amphotericin B. Furthermore, WGS and macrosynteny analyses confirmed their allodiploid hybrid nature, revealing a mosaic genome derived from A. spinulosporus and an A. quadrilineatus-related lineage. Collectively, these findings highlight that A. latus may be missed by routine diagnostic methods and may exhibit a distinct antifungal susceptibility profile. Molecular approaches such as mNGS and WGS may therefore help achieve accurate species-level identification and support targeted antifungal therapy. Given this small retrospective case series, larger prospective and multicenter studies are needed to validate these observations and better define the epidemiology, clinical spectrum, and therapeutic implications of this emerging allodiploid hybrid pathogen.},
}

Retrospective Studies
*Aspergillus/genetics/isolation & purification/classification/drug effects/cytology
Humans
China
Antifungal Agents/pharmacology
*Aspergillosis/microbiology/pathology/diagnosis
High-Throughput Nucleotide Sequencing
Microbial Sensitivity Tests
Whole Genome Sequencing
Metagenomics

@article {pmid42745387,
year = {2026},
author = {Kunnummal, SP and Abdulla, A and Khan, M},
title = {Novel Ferulic Acid Esterase From Human Gut Microbiome: Cloning and Application in Crop Residue Valorization.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70208},
pmid = {42745387},
issn = {1470-8744},
support = {5/7/1741/CH/Adhoc/2021-RMBCH//Indian Council of Medical Research/ ; },
abstract = {Ferulic acid esterases (FAEs) are enzymes that interact with esterified components of plant cell walls, facilitating the release of free ferulic acid (FA) from plant materials. Therefore, they hold significant importance across multiple industries, including pharma, food, and cosmetics. This investigation involved the cloning, expression, and characterization of FAE from the human fecal metagenome. Sequence analysis revealed that the cloned gene was approximately 750 bp in length and contained an open reading frame encoding a protein of 252 amino acids. The resulting recombinant protein displayed a molecular weight of 28 kDa and 49.7% identity with the chlorogenic acid esterase from Lactobacillus helveticus. The hydrolytic activity of the recombinant FAE was validated using p-nitrophenyl-ferulate (pNPF) as the substrate, with optimal activity at a pH of 7 and a temperature of 35°C. The enzyme showed stability within a pH range of 5.0-7.0 and temperatures from 5°C to 35°C. High-performance liquid chromatography (HPLC) results indicated that the FAE enzyme could release up to 49.7% of total alkali-extractable FA from dehydrated rice bran, followed by wheat bran and sugarcane bagasse. The total phenolic content of sugarcane bagasse increased by approximately 100% after in situ enzymatic fermentation compared with the chemically extracted fraction. These results indicate that cloned FAE can be used as a potential biocatalyst in industrial applications.},
}

@article {pmid42745810,
year = {2026},
author = {Huang, H and Fu, Y and Liu, E and Bai, K and Li, J and Liu, C and Deng, Y and Xu, F},
title = {Application of metagenomic next-generation sequencing in children with pneumonia of unknown etiology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1922924},
pmid = {42745810},
issn = {2235-2988},
mesh = {Humans ; Female ; Male ; Child, Preschool ; *High-Throughput Nucleotide Sequencing/methods ; Infant ; *Metagenomics/methods ; Retrospective Studies ; Child ; Adolescent ; *Pneumonia/microbiology/diagnosis/etiology ; Bacteria/genetics/classification/isolation & purification ; Coinfection/microbiology ; Immunocompromised Host ; Viruses/genetics/classification/isolation & purification ; },
abstract = {OBJECTIVE: To investigate the pathogen spectrum and clinical application value of metagenomic next-generation sequencing (mNGS) in lower respiratory tract specimens from children with pneumonia of unknown etiology.

METHODS: A retrospective analysis was conducted on children hospitalized in the intensive care unit (ICU) and respiratory department ward of Children's Hospital of Chongqing Medical University from January 2025 to December 2025. All enrolled cases presented negative results for conventional respiratory pathogen tests and received mNGS testing of lower respiratory tract specimens for etiological identification. The mNGS findings and clinical data of the included children were analyzed.

RESULTS: A total of 92 children were enrolled, including 54 males and 38 females, with ages ranging from 2 months to 13 years and 8 months. Causative pathogens were detected in 77 cases (83.7%). The clinically adjudicated etiological diagnosis rates of bacteria, viruses, fungi and atypical pathogens were 75.0% (69/92), 37.0% (34/92), 13.0% (12/92) and 5.4% (5/92), respectively. Thirty-eight cases were complicated with polymicrobial infection, among which bacterial-viral infection was predominant, accounting for 23.1% (24/92). Children with immunocompromised conditions exhibited higher incidences of clinically adjudicated bacterial, fungal and polymicrobial infection than immunocompetent patients. The most common clinically confirmed causative pathogens in immunocompromised children were Streptococcus pneumoniae, human cytomegalovirus, Haemophilus influenzae, Stenotrophomonas maltophilia and Enterococcus faecalis. Treatment regimens were adjusted in 58 cases (63.0%) based on mNGS findings, switching to pathogen-targeted anti-infective therapy.

CONCLUSION: For pediatric pneumonia with negative conventional etiological tests, mNGS of lower respiratory tract specimens significantly enhances pathogen detection rates, effectively identifies polymicrobial infection and opportunistic pathogens. Immune status serves as a critical stratification factor influencing pathogen spectrum and infection patterns, with immunocompromised children being more susceptible to opportunistic infections. Adjustment of anti-infective regimens based on mNGS results can effectively facilitate personalized anti-infective therapy.},
}

Humans
Female
Male
Child, Preschool
*High-Throughput Nucleotide Sequencing/methods
Infant
*Metagenomics/methods
Retrospective Studies
Child
Adolescent
*Pneumonia/microbiology/diagnosis/etiology
Bacteria/genetics/classification/isolation & purification
Coinfection/microbiology
Immunocompromised Host
Viruses/genetics/classification/isolation & purification

@article {pmid42745851,
year = {2026},
author = {Yue, Z and Sheng, S and Peng, L and Xu, W and Zhang, J and Wu, D and Liu, B and Li, Q and Dong, R and Cheng, H and Zou, Y},
title = {Impact of Chamaecrista rotundifolia cover cropping on soil elemental cycling in karst agroecosystems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1906173},
pmid = {42745851},
issn = {1664-302X},
abstract = {Karst desertification causes severe soil erosion, hydrological imbalance, and biodiversity loss, thereby threatening ecosystem resilience and agricultural productivity. Soil carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling underpin ecosystem stability, yet how agricultural management practices regulate multi-element cycling in degraded karst agroecosystems remains poorly understood. Here, we conducted a four-year field trial in a karst mango orchard in southwestern China and integrated metagenomic sequencing with comprehensive soil environmental profiling to investigate how C. rotundifolia cover cropping reshapes soil elemental cycling. Compared with conventional tillage (CK), C. rotundifolia cover cropping (Y) significantly (p < 0.05) altered topsoil microbial functional profiles and nutrient availability. Carbon cycling potentials, including gene associated with aerobic respiration (cox1/3), fermentation, and CO2 assimilation-were enriched under C. rotundifolia cover cropping. Nitrogen cycling potentials were enhanced through increased representation of genes involved in denitrification (nirK/S, nosZ), nitrogen acquisition, and nitrate reduction (nirA, narB), while phosphorus cycling was promoted through enrichment of the PhoR-PhoB phosphate regulatory system. Sulfur transformation potentials were also altered, with increased representation of genes involved in sulfate reduction, oxidation, and sulfonate utilization. Cover cropping substantially improved soil fertility, increasing SOC (+35.4%), NH4 [+]-N (+31.8%), TN (+35.1%), and AP (+105.9%), while reducing exchangeable Al[3+] concentration by 60.9%. Microbial community restructuring was characterized by decreased Actinobacteriota and Chloroflexota and increased Bacteroidota and Proteobacteria, which exhibited central roles in elemental cycling networks. Mantel analyses identified exchangeable Al[3+] as a dominant environmental constraint shaping microbial communities involved in C, N, P, and S cycling. Collectively, these findings demonstrate that C. rotundifolia cover cropping enhances karst soil resilience through a coupled microbial-geochemical pathway, in which improved soil chemical conditions and microbial functional reorganization jointly restore elemental cycling capacity.},
}

@article {pmid42745968,
year = {2026},
author = {Liu, X and Chen, R and Li, Y and Li, D and Xu, Z},
title = {Next-generation sequencing in the etiological diagnosis of severe childhood pneumonia.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1864412},
pmid = {42745968},
issn = {2296-2360},
abstract = {Pneumonia is the leading cause of death for children, particularly those aged 3-5 years old. The majority of the 740,000 annual global deaths of children under five years old occurred in developing countries in 2019. Severe childhood pneumonia (SCAP) causes death and disability in children, as it may trigger pleural effusion, respiratory failure, bacteremia and multiple organ failure. Traditional pathogen detection techniques including microscopy, culture and polymerase chain reaction (PCR) feature narrow detection coverage, lengthy detection cycles and low sensitivity. These defects frequently lead to undetermined infectious etiology, forcing clinicians to administer empirical broad-spectrum antibiotics. Metagenomic next-generation sequencing (mNGS) has emerged as an innovative, high-throughput, untargeted detection technology in recent years, which greatly promotes the etiological diagnosis of infectious diseases. Published meta-analyses show that the pathogen detection rate of mNGS using bronchoalveolar lavage fluid (BALF) samples collected from children can reach 85.83%, which is markedly higher than the 49.97% detection rate of conventional testing approaches. This review systematically elaborates how mNGS reconstructs the cognition of pathogen spectrum in children with severe pneumonia: this technology accurately identifies complex mixed infection patterns, detects pathogens that cannot be captured by traditional testing, and redefines the clinical boundary between microbial colonization and invasive infection. Combined with latest clinical research data, this paper analyzes the core value of mNGS in optimizing treatment schemes, reducing irrational antibiotic use and realizing precision therapy for severe pneumonia in children. Meanwhile, the current limitations and future development directions of this technology are discussed.},
}

@article {pmid42746154,
year = {2026},
author = {Huang, L and Wang, L and Wang, X and Zhang, X and Yu, X and Yang, J and Zhang, W and Yang, J and Ji, W and Cao, Y and Zheng, Y and Gai, W and Jiang, M and Liang, Y},
title = {Metagenomic Next-Generation Sequencing Analysis of Pathogens in Infected Wounds from Dog and Cat Bites - China, 2021-2025.},
journal = {China CDC weekly},
volume = {8},
number = {34},
pages = {1055-1062},
pmid = {42746154},
issn = {2096-7071},
abstract = {Dog and cat bites frequently develop polymicrobial wound infections requiring prompt and appropriate antimicrobial treatment. However, conventional culture-based methods often fail to identify all pathogens, particularly anaerobic and fastidious microorganisms.

WHAT IS ADDED BY THIS REPORT?: This study used metagenomic next-generation sequencing (mNGS) to analyze infected dog- and cat-bite wounds. Distinct microbial profiles were identified between dog and cat bites, and between domestic and stray animals. Anaerobes were predominant in both groups.

These findings highlight the value of mNGS and support empirical antimicrobial strategies to improve infection management and reduce complications.},
}

@article {pmid42746171,
year = {2026},
author = {Zhang, J and Wu, S and Deng, C and Zhang, E and Yu, B and Luo, A and Sun, C and Zhang, H and Zheng, C and Zhou, H and Li, W and Lu, J and Chen, Q and Fan, R and He, X and Ye, B and Shi, X and Wang, P and Wei, J},
title = {Epidemiological Investigation and Source Tracing of an Inhalation Anthrax Case with Traceability to Yunnan Province - Guangdong Province, China, March 2026.},
journal = {China CDC weekly},
volume = {8},
number = {33},
pages = {1037-1041},
pmid = {42746171},
issn = {2096-7071},
abstract = {Anthrax is a zoonotic disease caused by the bacterium Bacillus anthracis (B. anthracis). Inhalation anthrax, caused by inhalation of B. anthracis spores, is the rarest and most fatal form of anthrax. Historically, naturally acquired inhalation anthrax cases have mainly been associated with occupational exposure to infected animals or animal products, such as in wool mills or tanneries.

WHAT IS ADDED BY THIS REPORT?: This report documents the first case of inhalation anthrax in China that was linked to environmental exposure in a historically endemic area, without direct contact with sick animals or animal products. The case was reported in Guangdong Province, however, the source was traced to the patient's newly built residence in Zhenxiong County, Yunnan Province, where environmental samples tested positive for B. anthracis nucleic acid. Three anthrax outbreaks have occurred in this region since 1990.

In anthrax-endemic areas, environmental exposure to contaminated soil or dust can pose a significant risk of anthrax infection, even without direct animal contact. Although rare, inhalation anthrax can occur naturally as B. anthracis spores can survive extreme environmental conditions in the soil or hay for long periods. As it is difficult to distinguish acute pulmonary infection from inhalational anthrax, severe cases were frequently initially suggested by metagenomic sequencing of the alveolar fluid, with similar findings reported for meningeal anthrax in the cerebrospinal fluid.},
}

@article {pmid42746328,
year = {2026},
author = {Kuzuya, K and Maeda, Y and Funakoshi, K and Mizuno, Y and Fujimoto, K},
title = {Autoimmune disease-associated pathobionts: mechanisms and therapeutic potential of phage-based approaches.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1884094},
pmid = {42746328},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/therapy/immunology/microbiology ; Animals ; *Phage Therapy/methods ; *Gastrointestinal Microbiome/immunology ; *Bacteriophages/immunology ; Bacteria/immunology/virology ; Host Microbial Interactions/immunology ; },
abstract = {The gut microbiota is a critical regulator of systemic immune homeostasis; accumulating evidence implicates specific commensal bacteria, termed "pathobionts," in autoimmune disease pathogenesis. However, the definition of pathobionts remains context-dependent, as their effects are influenced by host genetics and host-microbe interactions. In this review, we summarize representative pathobionts supported by functional evidence in selected extraintestinal autoimmune diseases and discuss how these mechanisms may inform phage-based microbiome-targeted interventions. Mechanistically, pathobionts contribute to autoimmune disease through multiple pathways, including molecular mimicry, induction of intestinal T helper 17 and T follicular helper cell responses, disruption of regulatory T cell homeostasis, intestinal barrier dysfunction, and bacterial translocation from the gut to extraintestinal sites. These processes highlight the central role of gut-associated lymphoid tissue in initiating systemic autoimmunity, and targeting disease-associated microbes represents a promising therapeutic strategy. Whole-phage therapy, which enables highly specific bacterial elimination, has shown efficacy in preclinical immune-mediated disease models, but may be affected by variable in vivo replication, bacterial receptor-mediated resistance, anti-phage immune responses, and ecological effects on the resident microbiome. Phage-derived enzymes that lyse bacterial cell walls, such as endolysins, represent a complementary therapeutic modality that specifically targets bacterial peptidoglycan through cell wall-binding and catalytic domains. Collectively, these findings support the concept that pathobiont-targeted interventions, particularly phage-based strategies, may provide microbiome-directed, immunosuppression-sparing therapeutic approaches for selected patient subsets.},
}

Humans
*Autoimmune Diseases/therapy/immunology/microbiology
Animals
*Phage Therapy/methods
*Gastrointestinal Microbiome/immunology
*Bacteriophages/immunology
Bacteria/immunology/virology
Host Microbial Interactions/immunology

@article {pmid42746344,
year = {2026},
author = {Chooklin, S and Chuklin, S},
title = {Beyond the Pancreas: The Gut Microbiota in Acute Pancreatitis - From Mechanisms to Therapeutic Perspectives.},
journal = {Clinical and experimental gastroenterology},
volume = {19},
number = {},
pages = {636881},
pmid = {42746344},
issn = {1178-7023},
abstract = {Acute pancreatitis is a heterogeneous inflammatory disease in which severe forms are frequently complicated by intestinal barrier failure, dysbiosis, bacterial translocation, infected necrosis, systemic inflammation, and organ dysfunction. Growing clinical and experimental evidence suggests that the gut microbiota may contribute to disease progression and represents a potential, although incompletely validated, therapeutic target. Importantly, acute pancreatitis-associated dysbiosis involves not only taxonomic shifts but also functional metabolic reprogramming, including reduced short-chain fatty acid production, altered microbial bile acid transformation, and disturbances in amino acid and lipid metabolism that may contribute to barrier dysfunction and systemic inflammation. This review synthesizes current evidence on microbiota-oriented strategies in acute pancreatitis, with emphasis on clinical applicability, mechanistic rationale, and safety. This narrative review integrates clinical guidelines, randomized trials, meta-analyses, cohort studies, metagenomic and metabolomic investigations, and experimental studies published mainly between 2002 and 2026. Among clinically supported strategies, early oral or enteral nutrition has the strongest evidence base and may help preserve mucosal integrity while limiting the ecological consequences of fasting and critical illness. Antimicrobial stewardship is also fundamental, because unnecessary antibiotic exposure may aggravate dysbiosis, impair colonization resistance, and promote resistant organisms. Selective digestive decontamination has historical clinical evidence but is not established for routine contemporary practice. Prebiotics, dietary fibers, postbiotics, and metabolite-oriented approaches are mechanistically promising, but clinical evidence remains limited. GV-971 is currently supported predominantly by preclinical experimental data. Probiotics and synbiotics require caution, particularly in predicted severe disease, because clinical benefits are inconsistent and important safety concerns have been reported. Fecal microbiota transplantation and washed microbiota transplantation remain investigational and should not be used routinely outside controlled protocols. At present, microbiota-oriented management should prioritize evidence-based supportive measures, particularly early oral or enteral nutrition and rational antimicrobial use. Future studies should combine clinical outcomes with standardized microbiome, metabolome, barrier, and resistance endpoints to determine whether direct microbiota modulation can become a safe and reproducible component of personalized therapy.},
}

@article {pmid42746455,
year = {2026},
author = {Abril, AG and Freire, J and Magadán, S and Villa, TG and Pazos, M and Carrera, M},
title = {A metagenomic analysis of the gut microbiota in a mouse model of fish allergy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1886359},
pmid = {42746455},
issn = {1664-302X},
abstract = {BACKGROUND: Fish are among the most frequent causes of immunoglobulin E (IgE)-mediated food allergies (Type I). Currently, there is no known cure for fish allergy and individuals who are sensitized have to practice strict, lifelong avoidance of fish products in their diets. The relationship between gut microbiome and food allergies is currently a major topic of discussion; these pathologies involve the development of dysbiosis, which is a microbial imbalance resulting from immune-related mechanisms. Recent studies have provided evidence that individuals suffering from food allergies, display an intestinal microbiota with a different microbial composition compared to healthy subjects.

OBJECTIVES AND METHODS: In this work, we have described for the first time the differences in microbiome composition in a mouse model of fish allergy with previous sensitization to the main allergen, beta-Parvalbumin (β-PRVB), compared to mouse individuals without allergic response.

RESULTS: The metagenomic analysis has shown differences in taxonomic composition between the treatments. Regarding phyla, an increase in the relative abundance of Patescibacteria, specifically Saccharimonas genus and Candidatus_Saccharimonas group, were observed in the allergic animals (Prvb_Alum group) when compared to the other groups. In contrast, the relative abundance of the RF39 group (Bacilli), Atopobiaceae family, Erysipelotrichaceae, and the Coriobacteriaceae_UCG-002 group, was higher in the animals that did not develop an allergic response, despite being exposed to the allergen (Prvb group). Furthermore, an increase in the relative abundance of Lachnospiraceae ASF356 group was observed in the control group compared to the other treatments. This family, has been reported to be inversely associated with the progression of intestinal inflammation and anaphylactic diseases. For the first time, the gut microbiota composition of individual mice with and without fish allergies is described in detail in this work. This study may shed light on the potential contribution of gut microbiota to the onset and avoidance of food allergies.},
}

@article {pmid42746483,
year = {2026},
author = {Liu, F and Luo, J and Feng, L and Xia, Y and Chen, X and Xu, Y and Liu, Y},
title = {The association between neonatal respiratory distress syndrome and gut microbiota dysbiosis: evidence from metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1925400},
pmid = {42746483},
issn = {1664-302X},
abstract = {OBJECTIVE: Neonatal respiratory distress syndrome (NRDS) is a common and life-threatening respiratory disorder that affects newborns, significantly impacting their health and survival rates. In recent years, the potential role of the gut-lung axis in NRDS has garnered increasing attention; however, the specific mechanisms involved remain unclear. This study aimed to investigate the association between NRDS and gut microbial composition and functional profiles using shotgun metagenomic sequencing.

METHODS: This case-control study recruited 25 infants diagnosed with NRDS and 15 healthy newborns, all aged between 2 and 6 days. Fecal samples were collected from all participants for subsequent metagenomic sequencing and bioinformatics analysis.

RESULTS: There was no significant difference in α-diversity between the NRDS group and the control (CON) group (p = 0.3335). However, β-diversity exhibited a significant difference (p = 0.001). In the NRDS group, the gut microbiota was enriched with Bacillota, Klebsiella, and Enterococcus, while Bifidobacterium and butyrate metabolism-related bacteria (Bacteroides/Butyricicoccus) were significantly reduced (p < 0.05). Functional analysis indicated that Staphylococcus aureus infection and the Phosphotransferase system (PTS) pathway were enriched in the NRDS group, whereas Butanoate metabolism and Glutathione metabolism were significantly enriched in the CON group. A 10-species classifier achieved 96% AUC for NRDS prediction.

CONCLUSION: NRDS was associated with differences in gut microbial composition and shotgun-metagenomic functional profiles. These preliminary findings characterize group-level microbial differences but do not establish whether the observed alterations preceded or resulted from NRDS. Longitudinal studies are required to clarify their temporal relationship and clinical relevance.},
}

@article {pmid42746583,
year = {2026},
author = {Saadeh, JE and Saad, R and Assaf, F and Osman, R and Chami, AA and Harb, BA and Ghanem, W and Badra, M and Moucharafieh, R},
title = {Current Concepts in Periprosthetic Joint Infection: Modern Biomarkers, Microbiome Insights, Molecular Diagnostics, and Emerging Prevention Strategies.},
journal = {Orthopedic research and reviews},
volume = {18},
number = {},
pages = {634292},
pmid = {42746583},
issn = {1179-1462},
abstract = {AIM: Periprosthetic joint infection (PJI) remains one of the leading causes of revision arthroplasty and is associated with substantial morbidity, mortality, and healthcare costs. Diagnosis remains challenging because of heterogeneous clinical presentations, the limited sensitivity of conventional inflammatory markers in chronic and low-grade infections, culture-negative cases, and biofilm-mediated pathogen persistence. This narrative review summarizes recent advances in the diagnosis and prevention of PJI, with a particular focus on synovial and serum biomarkers, microbiome-related susceptibility, molecular diagnostics, artificial intelligence, and emerging anti-biofilm and implant-surface technologies. Synovial biomarkers, including alpha-defensin, leukocyte esterase, calprotectin, and D-lactate, have demonstrated improved diagnostic performance, particularly in equivocal and culture-negative cases. However, none has sufficient evidence to replace established diagnostic criteria, and current data support their use as adjunctive tools in selected clinical scenarios rather than as standalone tests. Serum biomarkers beyond erythrocyte sedimentation rate and C-reactive protein, such as fibrinogen and protein fraction alterations, may provide additional diagnostic value but require further validation and standardized diagnostic thresholds. Molecular approaches, particularly metagenomic next-generation sequencing, improve pathogen detection in complex infections but remain limited by cost, protocol variability, and challenges in distinguishing clinically relevant pathogens from contaminants. Preventive strategies targeting bacterial adhesion and biofilm formation through local antibiotic delivery, surface modification, and nanotechnology-enabled implants are promising, although long-term efficacy, safety, and cost-effectiveness remain to be established. Overall, PJI management is evolving toward integrated, multimodal diagnostic strategies and biologically informed prevention. Current evidence supports the selective clinical use of synovial biomarker testing as an adjunctive tool within established diagnostic criteria, while continued research is needed before widespread routine implementation can be recommended.

Modern synovial biomarkers provide valuable adjunctive information that may improve diagnostic confidence in challenging periprosthetic joint infection cases when incorporated into a multidisciplinary diagnostic approach involving clinical assessment, laboratory evaluation, microbiological analysis, and established consensus criteria. Emerging preventive strategies targeting biofilm formation and host-microbe interactions represent promising approaches, although their ability to reduce revision rates and improve patient outcomes requires further clinical validation.},
}

@article {pmid42747097,
year = {2026},
author = {Listmann, L and Peters, C and Labecot, A and Rousseau, R and Baux, C and Santelia, ME and Manirakiza, E and Grimsley, N and Yau, S and Gourbiere, S and Schaum, CE and Piganeau, G},
title = {Bridging the gap between genomic, phenotypic, and modeling data in picophytoplankton-virus interactions.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70229},
pmid = {42747097},
issn = {1529-8817},
support = {ANR-10-LABX-0041//Agence Nationale de la Recherche/ ; ANR-18-EURE-0019//Agence Nationale de la Recherche/ ; ANR-21-CE02-0026//Agence Nationale de la Recherche/ ; ANR-21-CE20-0041//Agence Nationale de la Recherche/ ; 2154/8-1//Deutsche Forschungsgemeinschaft/ ; 2154/9-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {We present a comprehensive synthesis of recent developments in methodological approaches to combine experimental and genomic studies of picophytoplankton-virus interactions. This synthesis will not only enhance our understanding of these relationships but also stimulate new hypotheses for the interpretation of metagenomic data and enrich current modeling efforts. Marine picophytoplankton are significant primary producers despite their low contribution to biomass. Pan-oceanic metagenomic studies have revealed an astounding genetic diversity within these communities and the astronomical abundance of viruses that infect them. Despite recent advances in understanding the genetic and genomic diversity of picophytoplankton and viruses, the interpretation of these data relies heavily on ecological and physiological insights. Specifically, our understanding of the mechanisms and dynamics governing host-virus interactions is limited because the current wealth of sequence data has not yet been matched with corresponding life-history traits. Linking phenotypes to genotypes in picophytoplankton-virus systems is also essential for accurately modeling their interactions and their impact on the global carbon cycle. Ultimately, the synergy of the three domains allows for a mechanistic interpretation of environmental data.},
}

@article {pmid42747125,
year = {2026},
author = {Saavedra-Benítez, D and Ampuero, M and Gaggero, A and Chnaiderman, J},
title = {Synchronized Detection of Adenovirus F41 in Wastewater and Fecal Samples Confirms a Small Outbreak in Santiago, Chile.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71148},
doi = {10.1002/jmv.71148},
pmid = {42747125},
issn = {1096-9071},
support = {1181656//Agencia Nacional de Investigación y Desarrollo/ ; },
mesh = {Chile/epidemiology ; *Wastewater/virology ; *Feces/virology ; Phylogeny ; Humans ; *Adenoviridae Infections/epidemiology/virology ; *Disease Outbreaks ; Genome, Viral ; *Adenoviruses, Human/isolation & purification/genetics/classification ; *Adenoviridae/isolation & purification/genetics/classification ; },
abstract = {We conducted systematic surveillance of circulating viruses in two cities in Chile through regular wastewater analysis between 2018 and 2021. Samples were concentrated, nucleic acids were extracted, and the samples were analyzed by massive sequencing. After bioinformatic processing, we detected a significant number of Adenovirus F41 genomes in samples collected during a specific period (January-March 2020), particularly in treatment plants from Santiago de Chile. To confirm whether the virus was circulating in the city during that period, we analyzed stool pools collected at one of the city's main pediatric hospitals. We detected Adenovirus F41 sequences only in the same period as in wastewater. Phylogenetic analysis showed that the virus detected in wastewater and stool samples was almost identical and classified as Lineage 2B. These results demonstrated the effectiveness of wastewater surveillance for detecting enteric viruses in the community, shed light on the efficiency of treatment processes, and revealed a small outbreak of a virus strain previously reported in Europe.},
}

Chile/epidemiology
*Wastewater/virology
*Feces/virology
Phylogeny
Humans
*Adenoviridae Infections/epidemiology/virology
*Disease Outbreaks
Genome, Viral
*Adenoviruses, Human/isolation & purification/genetics/classification
*Adenoviridae/isolation & purification/genetics/classification

@article {pmid42747196,
year = {2026},
author = {Lou, D and Cui, J and Duan, J and Zhou, B and Wang, Y and Wang, D and Tan, J and Duan, H},
title = {Genomic prospecting and biochemical characterization of a novel thermostable 3-quinuclidinone reductase from hot spring metagenomes for efficient biocatalysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0149026},
doi = {10.1128/aem.01490-26},
pmid = {42747196},
issn = {1098-5336},
abstract = {This study presents the discovery and characterization of a novel thermophilic 3-quinuclidinone reductase (ScQR) identified through metagenomic mining of hot spring environments. ScQR, a member of the short-chain dehydrogenase/reductase (SDR) superfamily, was heterologously expressed in Escherichia coli, and its catalytic properties were systematically characterized. The enzyme demonstrates exceptional thermal stability, retaining 86% of its activity after 48 hours at 70°C. Furthermore, K[+] and Mg[2][+] ions significantly enhanced ScQR's activity at specific concentrations. Structural analysis revealed that ScQR adopts a typical SDR fold with a conserved catalytic triad (S141-Y155-K159), and it is NAD(H) dependent. Enzyme assays indicated that ScQR is highly stereoselective for (R)-3-quinuclidinol, with no activity against its enantiomer, (S)-3-quinuclidinol. The enzyme exhibits optimal activity at pH 9 and 85°C, making it a promising candidate for industrial applications requiring high thermal stability. Molecular dynamics simulations further revealed that ScQR preserves global structural integrity up to 360 K, whereas higher temperatures induce destabilization, predominantly in the C-terminal region and residues 95-100. In addition, structure-guided computational design enabled by LigandMPNN and UniKP yielded three ScQR variants with improved substrate affinity and catalytic efficiency while maintaining the overall fold and function. This work underscores the power of metagenomics with structure-driven protein design in discovering novel enzymes with unique catalytic properties from extreme environments and establishes ScQR as a promising biocatalyst for biotechnological and pharmaceutical applications.IMPORTANCEThis study reports the discovery of ScQR, a novel thermophilic 3-quinuclidinone reductase identified via metagenomic mining. ScQR represents one of the most heat-resistant members of the SDR superfamily discovered to date, maintaining 86% activity after 48 hours at 70°C. These findings establish ScQR as a robust biocatalyst for high-temperature pharmaceutical applications and demonstrate a scalable workflow for optimizing enzymes from extreme environments, offering significant value to the fields of biocatalysis and protein engineering.},
}

@article {pmid42747298,
year = {2026},
author = {Nguyen, MH and Schatz, MC},
title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag687},
pmid = {42747298},
issn = {1367-4811},
abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.

RESULTS: We present Perseus, a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.

Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus.},
}

@article {pmid42747315,
year = {2026},
author = {Sun, W and Li, Y and Liu, X and Yu, S and Li, W and Wang, H and Geng, H and Li, L and Hu, J and Huo, J and Zhang, W and Fu, J and Jin, X and Li, H and Zhou, X and Zhu, X},
title = {Gut microbiota functional remodeling and butyrate depletion amplify anti-Ro/La antibody-driven type I interferon activation in neonatal lupus.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2728464},
doi = {10.1080/19490976.2026.2728464},
pmid = {42747315},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Interferon Type I/immunology ; Infant, Newborn ; *Autoantibodies/immunology/blood ; *Lupus Erythematosus, Systemic/immunology/microbiology ; *Butyrates/metabolism ; Female ; Bacteria/classification/genetics/isolation & purification/metabolism ; Male ; },
abstract = {The early-life gut microbiome may influence susceptibility to antibody-mediated neonatal autoimmunity, but the underlying mechanisms remain poorly understood. We investigated whether gut microbial functional capacity and metabolites influence autoantibody-dependent immune activation in 90 neonates, including healthy controls, anti-Ro/La-exposed neonates without neonatal lupus erythematosus (No-NLE), and neonates with NLE (n = 30 per group). Shotgun metagenomic profiling demonstrated progressive remodeling of the neonatal gut microbiome across the three groups, with anti-Ro/La exposure associated with depletion of early-life commensal-associated taxa, including Bifidobacterium, Rothia, and Clostridium, and enrichment of taxa with opportunistic potential, including Klebsiella and Enterococcus, with greatest ecological divergence in neonates with NLE. Functional profiling identified altered microbial carbohydrate-processing capacity, marked by enrichment of glycosyltransferase family 4 (GT4) and depletion of GT2 in NLE. These alterations coincided with broad reductions in plasma short-chain fatty acid metabolites, most prominently butyrate, together with increased serum immunoglobulin G (IgG) and interferon-α (IFN-α) and decreased complement component 4 (C4). A GT4-Klebsiella-Rothia-IFN-α signature distinguished NLE from No-NLE (AUC = 0.883; 95% CI, 0.799-0.967). In functional assays, pooled bacteria-depleted fecal filtrates from neonates with NLE potentiated IFN-α production by neonatal peripheral blood mononuclear cells in the presence of anti-Ro/La-positive plasma. Conversely, sodium butyrate suppressed anti-Ro/La-associated IFN-α production and reduced 28 inflammation-related proteins, including CXCL10, ADA, and PD-L1, involved in cytokine, IL-17, and TNF signaling. Together, these findings provide functional evidence supporting a microbiota-associated butyrate-type I interferon pathway that may amplify maternal autoantibody-dependent immune activation and contribute to the clinical manifestation of NLE.},
}

Humans
*Gastrointestinal Microbiome
*Interferon Type I/immunology
Infant, Newborn
*Autoantibodies/immunology/blood
*Lupus Erythematosus, Systemic/immunology/microbiology
*Butyrates/metabolism
Female
Bacteria/classification/genetics/isolation & purification/metabolism
Male

@article {pmid42747396,
year = {2026},
author = {Huang, Y and Feng, X and Hu, X and Sun, Y and Song, Z and Xie, M and Liao, T and Liu, X and Lv, X and Liu, R and Liu, Q and Voolstra, CR and Luo, H},
title = {Environmental Gradients as a Dominant Force in the Macroevolution of a Host-Associated Marine Bacterium.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag244},
pmid = {42747396},
issn = {1751-7370},
abstract = {Natural selection is imposed by both abiotic environmental filtering and biotic interactions, yet their relative roles in shaping the deep phylogeny of widespread, generalist host-associated bacteria remain unclear. Here, we integrate large-scale phylogenomics, environmental sequencing, functional genomics, and global metagenomic analysis to demonstrate that tidal zonation overrides host association as the dominant macroevolutionary force structuring the marine bacterial genus Ruegeria. Analysis of 533 genomes and 74 global coastal metagenomes reveals that the intertidal-subtidal boundary structures the deepest phylogenetic splits, driving the repeated evolution of distinct ecotypes through independent zonation transitions across global coastlines. These ecotypes possess divergent genomic toolkits: intertidal strains are enriched for genes coding for stress resistance and anaerobic metabolism, whereas subtidal strains specialize in high-affinity nutrient scavenging. Our findings establish that predictable physicochemical gradients act as filters that generate foundational diversity from which specialized host symbionts subsequently emerge, reframing how environmental gradients shape microbial evolution at the eco-evolutionary interface.},
}

@article {pmid42747454,
year = {2026},
author = {Bi, K and Sandoval, M and Nguyen, T and Perez, I and Ghosh, L and Krause, T and Cazaban, CG and Pasco, R and Meyers, L and Wu, F and Rios, J and Tisza, M and Clark, J and Maresso, A and Boerwinkle, E and Bauer, C},
title = {Temporal Alignment of Wastewater Signals with Clinical Indicators of Respiratory Illness Postpandemic, Texas, USA.},
journal = {Emerging infectious diseases},
volume = {32},
number = {13},
pages = {43-52},
doi = {10.3201/eid3213.260141},
pmid = {42747454},
issn = {1080-6059},
mesh = {Texas/epidemiology ; Humans ; *Wastewater/virology ; *COVID-19/epidemiology/diagnosis ; SARS-CoV-2/isolation & purification/genetics ; *Influenza, Human/epidemiology/diagnosis ; *Respiratory Syncytial Virus Infections/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; },
abstract = {In the COVID-19 postpandemic era, declining clinical testing for SARS-CoV-2 has led to the exploration of complementary early detection methods. We evaluated metagenomic wastewater-based epidemiology (WBE) in Texas, USA, by comparing viral signals with the National Syndromic Surveillance Program tracked emergency department visits and Texas All-Payer Claims Database insurance claims across several Texas counties during 2022-2024. By analyzing SARS-CoV-2, influenza, and respiratory syncytial virus, we found moderate-to-strong temporal correlations between wastewater and clinical indicators. Influenza showed the most stable associations (r<0.98), whereas SARS-CoV-2 signals generally preceded clinical metrics. Respiratory syncytial virus exhibited higher geographic and temporal heterogeneity, reflecting differences in clinical data capture. Despite sampling frequency and geographic alignment challenges, metagenomic WBE consistently tracked community trends. Our findings suggest WBE can offer valuable situational awareness and a resilient complement to clinical surveillance, supporting public health preparedness in an evolving respiratory disease landscape.},
}

Texas/epidemiology
Humans
*Wastewater/virology
*COVID-19/epidemiology/diagnosis
SARS-CoV-2/isolation & purification/genetics
*Influenza, Human/epidemiology/diagnosis
*Respiratory Syncytial Virus Infections/epidemiology
*Wastewater-Based Epidemiological Monitoring

@article {pmid42747640,
year = {2026},
author = {Redding, LE and Hu, W and Daniel, S and Okumura, M and Hiehle, ME and David, MZ and Hunter, L and Cole, SD},
title = {Antimicrobial-resistant organism carriage and metagenomic characterization of the microbiome and resistome in veterinary workers.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42747640},
issn = {1573-7446},
support = {NI25AHDRXXXXG042 Formula Funds//U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Microbiota ; *Drug Resistance, Bacterial ; Hospitals, Animal ; Methicillin-Resistant Staphylococcus aureus/isolation & purification/drug effects/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Male ; Escherichia coli/drug effects/isolation & purification/genetics ; Female ; *Animal Technicians ; *Carrier State/microbiology/epidemiology ; *Veterinarians ; Feces/microbiology ; Metagenome ; RNA, Ribosomal, 16S ; Adult ; },
abstract = {BACKGROUND: Veterinary personnel work in environments with high exposure to antimicrobials and antimicrobial-resistant pathogens. However, the extent to which these occupational exposures influence their carriage of antimicrobial-resistant (AMR) organisms and the composition of their microbiome and resistome remains poorly understood. The objective of this study was to characterize AMR pathogen carriage and microbiome/resistome composition in veterinary personnel and to assess whether workplace setting and patient-related exposures were associated with detectable differences in these outcomes.

METHODS: Personnel from a large academic veterinary hospital and a convenience sample of private-practice small-animal veterinary hospitals provided nasal swabs, stool samples, and exposure survey data; environmental samples were also collected from the academic hospital. Nasal swabs were cultured for methicillin-resistant Staphylococcus aureus, and stool samples were cultured for extended spectrum cephalosporin resistance (ESCR) Escherichia coli. Samples also underwent shotgun metagenomic sequencing or 16S rRNA gene sequencing for taxonomic and antimicrobial resistance gene profiling. Alpha/beta diversity were compared across groups, beta diversity by Permutational Multivariate Analysis of Variance, linear models tested differential abundance, and logistic regression was used to assess covariates associated with MRSA and ESCR carriage. A subset of academic-hospital participants also submitted additional samples after time away (1-2 weeks) from the hospital.

RESULTS: Among academic-hospital personnel (n = 38), MRSA and ESCR-E. coli carriage prevalence were 18.4% and 11.1%, respectively. In private-practice personnel (n = 8), carriage was 12.5% and 25%, respectively. Within the academic hospital, MRSA carriage was associated with administering antibiotics to patients. Microbial composition differed modestly by worksite (R[2] = 0.02) when assessed using unweighted UniFrac metrics only, suggesting subtle site-related differences in low-abundance phylogenetically distinct taxa. Global resistome composition did not differ significantly by site or clinical exposure, although a small number of individual AMR ontologies and broad AMR gene families varied across groups, including those associated with commonly-administered oral antibiotics at the hospital. Paired on/off-clinic analyses did not show a clear directional shift after time away from the hospital.

CONCLUSIONS: Veterinary personnel carried MRSA at a notable frequency, while workplace effects on the microbiome and resistome were subtle, with limited evidence for large-scale shifts in community structure by site or patient exposure.},
}

Humans
*Microbiota
*Drug Resistance, Bacterial
Hospitals, Animal
Methicillin-Resistant Staphylococcus aureus/isolation & purification/drug effects/genetics
Animals
Anti-Bacterial Agents/pharmacology
Male
Escherichia coli/drug effects/isolation & purification/genetics
Female
*Animal Technicians
*Carrier State/microbiology/epidemiology
*Veterinarians
Feces/microbiology
Metagenome
RNA, Ribosomal, 16S
Adult

@article {pmid42747765,
year = {2026},
author = {Gueddari, NE and Philip, M and Camoin-Jau, L and Gouriet, F},
title = {Contemporary diagnostic strategies for blood culture-negative infective endocarditis: from conventional microbiology to emerging molecular and multimodality approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42747765},
issn = {1439-0973},
abstract = {BACKGROUND: Blood culture-negative infective endocarditis (BCNE) remains one of the most challenging presentations of infective endocarditis (IE) because the absence of microbiological confirmation delays diagnosis and complicates therapeutic management. BCNE may result from prior antibiotic exposure, infection with fastidious or intracellular microorganisms, fungal pathogens, or non-infectious conditions mimicking IE.

METHODS: This narrative review provides a clinically oriented overview of contemporary diagnostic strategies for BCNE based on current evidence and recent international guidelines. The diagnostic performance, limitations, and clinical applicability of biomarkers, microbiological methods, multimodality imaging, and pathological analysis were critically evaluated and integrated into practical diagnostic algorithms.

RESULTS: Targeted serology and polymerase chain reaction (PCR), particularly on excised valve tissue, remain the most clinically validated microbiological tools for routine BCNE diagnosis. Emerging molecular approaches, including droplet digital PCR (ddPCR) and metagenomic next-generation sequencing (mNGS), show promising diagnostic potential but remain insufficiently standardized for routine implementation. Echocardiography remains the first-line imaging modality, while cardiac computed tomography, 18 F-FDG PET/CT, and white blood cell SPECT/CT (WBC SPECT/CT) provide complementary diagnostic information, particularly in prosthetic valve endocarditis (PVE) and other diagnostically challenging cases. Histopathological examination combined with molecular analysis of surgical specimens remains an important complementary diagnostic approach when valve tissue is available.

CONCLUSIONS: Optimal diagnosis of BCNE requires an integrated multidisciplinary strategy combining clinical assessment, microbiology, multimodality imaging, and pathology. Future progress will depend on evidence-based diagnostic algorithms integrating emerging technologies according to their level of validation, local epidemiology, and available expertise.},
}

@article {pmid42748603,
year = {2026},
author = {Xing, BS and Wang, ZY and Zhang, ZZ and Fu, YL and Cui, YX and Wang, XC and Chen, R and Li, YY},
title = {Spatiotemporal niche differentiation enables stable autotrophic nitrogen removal in a continuous-flow system coupling microalgae, ammonia oxidizers and anammox bacteria.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126938},
doi = {10.1016/j.watres.2026.126938},
pmid = {42748603},
issn = {1879-2448},
abstract = {Natural aquatic aggregates use diel fluctuations in dissolved oxygen and microscale redox gradients to support aerobic and anaerobic processes, providing an ecological blueprint for continuous-flow microalgal-bacterial systems; however, this coupling remains difficult because photosynthetic oxygen supports ammonia oxidation but inhibits oxygen-sensitive anaerobic ammonium-oxidizing bacteria (AnAOB). In this study, a continuous-flow light-driven microalgal-bacterial system was developed. Long-term reactor operation, pathway contribution tests, extracellular polymeric substance (EPS) characterization, granule and FISH-CLSM analysis, and metagenomics were conducted to elucidate the stabilization mechanism of autotrophic nitrogen removal without external organic carbon. During 530 days of operation, the 8 h light/16 h dark regime maintained the dissolved oxygen concentration at 0.2-0.4 mg/L, while TNRE reached 86.2% before external nitrite supplementation and remained approximately 90% during the nitrite-assisted final phase. Pathway contribution tests indicated that the estimated microalgal-associated assimilation contribution was 36.48% during illumination, whereas denitrification and anammox dominated under dark conditions, contributing 40.53% and 39.67%, respectively. During reactor maturation, the average granule size peaked at 450 μm on day 400, the protein/polysaccharide (PN/PS) ratio increased from approximately 3.0 to 5.0, and the amount of tightly bound EPS protein (TB-EPS-PN) increased to approximately 35 mg/g VSS, indicating enhanced granule cohesion and resistance to disturbance. Metagenomic analysis revealed enrichment of Candidatus Kuenenia to 11.62% and coordinated increases in key nitrogen transformation genes. During reactor maturation, granule development, EPS accumulation, and the algal-bacterial association observed by FISH-CLSM were associated with increasing structural organization, while stage-dependent changes in stress- and adaptation-related genes supported a gene-EPS-structure adaptation framework. Collectively, these findings support a spatiotemporal niche‑differentiation framework in which light/dark cycling may temporally partitions nitrogen pathways, while EPS‑associated granule development and structural heterogeneity may enhance diffusion limitation and provide spatial buffering favorable for oxygen‑sensitive anaerobic functions.},
}

@article {pmid42748612,
year = {2026},
author = {Zhang, X and He, J and Lv, L and Cui, H and Wang, Y and Zhang, X and Lv, J},
title = {Methane and carbon dioxide emissions from wastewater treatment units linked to DOM stabilization and phosphonate-scavenging microbiomes.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126932},
doi = {10.1016/j.watres.2026.126932},
pmid = {42748612},
issn = {1879-2448},
abstract = {Municipal wastewater treatment plants (WWTPs) are major engineered facilities for urban carbon removal, yet methane (CH4) formation and source mechanisms in downstream stages after aeration and biological nutrient removal remain poorly resolved. Process resolved monitoring at a full-scale WWTP showed that CH4 emissions were concentrated upstream, while measurable fluxes persisted in downstream sedimentation and denitrification units. Dissolved CH4 profiles showed strong attenuation of influent derived CH4 during upstream treatment, followed by a local increase after secondary clarification. Carbon dioxide (CO2) emissions peaked in the biochemical tank, consistent with rapid oxidation of labile organic carbon. Fluorescence and molecular analyses revealed a shift in dissolved organic matter (DOM) from protein like to more humic and processed molecules, while community assembly remained predominantly deterministic despite greater stochasticity in later stages. The C-P lyase catalytic core was enriched in these units, accompanied by higher phnJ transcript abundance, candidate organophosphonate features, and genomic potential. Together with BES insensitive CH4 formation in independent microcosms, these observations supported C-P lyase mediated organophosphonate utilization as a contributing pathway to local CH4 formation. Integrated evidence indicated that DOM stabilization, deterministic community filtering, potential succinate mediated cross feeding, and phosphonate scavenging jointly shaped this process. These findings show that advanced treatment units are not CH4 hotspots, but neither are they CH4 inactive zones; process resolved GHG assessments should therefore consider persistent local CH4 generation and its association with substrate restructuring and alternative phosphorus acquisition.},
}

@article {pmid42748661,
year = {2026},
author = {Iqbal, S and Xu, Y and Ni, L and Dang, H and Luan, X and Zhang, D},
title = {Biogeographic patterns and metabolic potential of chemoautotrophic communities in cold seep sediments across subarctic to tropical regions.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108410},
doi = {10.1016/j.marenvres.2026.108410},
pmid = {42748661},
issn = {1879-0291},
abstract = {Cold seeps are hotspots of chemoautotrophic primary production, yet how chemoautotrophic community structure and dark carbon fixation (DCF) vary across climatic regions remains unclear. We combined incubation experiments and metagenomics to compare chemoautotrophic communities in cold seep sediments across northwestern Pacific marginal seas, from the subarctic Okhotsk Sea to the tropical South China Sea. Incubation experiments demonstrated higher DCF rates in tropical (1.20 μg C g[-1] day[-1]) than subarctic (0.35 μg C g[-1] day[-1]) sediments (p = 0.002). Analyses of 133 cold seep sediment metagenomes (26 in this study and 107 from NCBI, spanning 0-240 cmbsf) revealed that subarctic chemoautotrophs were dominated by Chloroflexota, Asgardarchaeota, Campylobacterota, and Thermoproteota, whereas tropical chemoautotrophs were dominated by Pseudomonadota and Asgardarchaeota, with higher alpha diversity and integrated co-occurrence networks observed in tropical sediments. Representative genes of the Calvin-Benson-Bassham (CBB) cycle, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, and the 3-hydroxypropionate (3HP) bicycle were enriched in tropical sediments, whereas reductive tricarboxylic acid (rTCA) cycle and Wood-Ljungdahl (WL) pathway genes predominated in subarctic sediments. Genome-resolved analysis showed that CBB cycle potential was concentrated in Pseudomonadota in tropical sediments and in Asgardarchaeota in subarctic sediments, and was most strongly correlated with nitrogen metabolism genes, whereas rTCA cycle potential was concentrated in Campylobacterota across both sediments, coupled strongly to sulfur metabolism. Depth profiling revealed surface communities dominated by Campylobacteria using rTCA cycle in subarctic sediments, and Alphaproteobacteria and Gammaproteobacteria using CBB cycle in tropical sediments, whereas the WL pathway predominated in Dehalococcoidia and Lokiarchaeia in the deeper layers of both regions. This study provides a comparative framework for chemoautotrophic biogeography across climatically distinct seeps.},
}

@article {pmid42748814,
year = {2026},
author = {Gao, J and Li, Y and Feng, K and Zheng, H and Li, W and Cheng, Z and Zhao, J and Li, W and Ye, L and Li, S},
title = {Decoupling biodegradation from substrate concentration via quorum sensing: A cell density-responsive strategy for robust chlorobenzene removal.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143600},
doi = {10.1016/j.jhazmat.2026.143600},
pmid = {42748814},
issn = {1873-3336},
abstract = {Chlorinated aromatic compounds are important industrial pollutants that pose persistent environmental risks due to their toxicity and recalcitrance. Biological treatment is a sustainable approach for chlorinated VOC removal. However, conventional bioremediation is constrained by an inherent dilemma in native regulatory systems: trace substrate concentrations trigger insufficient gene expression, while shock loads induce severe metabolic inhibition and cytotoxicity. To overcome these limitations, we leveraged quorum sensing (QS) to reprogram gene regulation in Pseudomonas putida, redirecting degradation control from substrate concentration to cell density. The native, pollutant-inducible promoter of the tod operon was replaced with the QS-responsive promoter PlasA, generating the engineered strain F1-QS. At low chlorobenzene concentrations, F1-QS increased tod transcription by 9.7‑fold, reduced the lag phase from 6 h to 2 h, and enhanced the degradation rate by 38.91%. Critically, this advantage extended to high pollution loads. At 325 mg/L chlorobenzene, F1-QS achieved 88.0% removal within 32 h, outperforming the wild-type strain (35.9%) by more than two-fold. In a synthetic microbial community, the F1-QS strain accelerated consortium degradation by 70.93% and maintained stable performance during long-term operation, highlighting its superior efficacy and resilience under substrate-limited conditions. Metagenomic analysis revealed that enhanced degradation performance was associated with higher abundance of key chlorobenzene degradation genes, suggesting an enhanced functional potential of the microbial consortium. This study shows that QS‑based rewiring resolves the trade‑off between weak induction at low concentrations and toxicity at high concentrations, offering a robust strategy for chlorinated VOC bioremediation.},
}

@article {pmid42003319,
year = {2026},
author = {Jaskiel, JE and Aichelman, HE and Anderson, G and Claassens, L and Fifer, JE and Hernandez, CM and Huzar, AK and Llopiz, JK and Witting, JW and Mullen, SP and Rotjan, RD},
title = {Larval Genomics as a Viable, Fisheries-Independent Tool for Investigating Population Structure in Tropical Pacific Tunas.},
journal = {Molecular ecology},
volume = {35},
number = {8},
pages = {e70335},
pmid = {42003319},
issn = {1365-294X},
support = {CI-113205//Blue Nature Alliance/ ; 55207252//Waitt Foundation/ ; },
mesh = {Animals ; *Tuna/classification/genetics ; Larva/genetics ; *Fisheries ; Pacific Ocean ; *Metagenomics/methods ; Species Specificity ; Linkage Disequilibrium ; Reproduction ; },
abstract = {Understanding how dispersal, life history, and environmental variability shape genetic connectivity in the open ocean remains a central challenge in evolutionary biology. Highly migratory marine predators like tunas have traditionally been considered genetically homogeneous across ocean basins, yet emerging genomic evidence suggests that cryptic population structure can persist even in species with high gene flow and large effective population sizes. We used 2bRAD sequencing of 348 larval and subadult skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), and bigeye tuna (T. obesus) collected from the central Pacific across 7 years of sampling to examine species boundaries, population genetic information, genetic structure, and connectivity. Larval sampling revealed consistent spawning by all three species and enabled unbiased detection of genetic patterns prior to recruitment bottlenecks. We found strong divergence amongst species, no evidence of structuring within skipjack or bigeye, and a divergent yellowfin population detected in 2 consecutive sampling years north of American Samoa. Comparisons between larvae and subadults suggest that sampling early life history stages can be a valuable tool for assessing population genetic information before recruitment bottlenecks, selective harvest by fisheries, adult dispersal, and selective pressures acting on adult populations, thereby contributing novel insights to the research and effective management of these species. These results highlight how larval genomics can complement traditional population genomic studies of adult tunas and reveal fine-scale structure in highly vagile species, providing new perspectives on connectivity in the open ocean.},
}

Animals
*Tuna/classification/genetics
Larva/genetics
*Fisheries
Pacific Ocean
*Metagenomics/methods
Species Specificity
Linkage Disequilibrium
Reproduction

@article {pmid42734183,
year = {2026},
author = {Chen, W and Pan, Y and Chen, M and Zhou, S and Liu, X and Sun, M and Yang, Z and Zhi, Y},
title = {Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726620},
pmid = {42734183},
issn = {1949-0984},
mesh = {Humans ; *Stroke/complications/metabolism ; Metabolomics ; Metagenomics ; *Depression/metabolism/etiology/microbiology ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Middle Aged ; Aged ; Cytokines/blood ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Biomarkers/blood ; },
abstract = {Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.},
}

Humans
*Stroke/complications/metabolism
Metabolomics
Metagenomics
*Depression/metabolism/etiology/microbiology
Female
Multiomics
Male
*Gastrointestinal Microbiome
Inflammation/metabolism
Middle Aged
Aged
Cytokines/blood
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
Biomarkers/blood

@article {pmid42734327,
year = {2026},
author = {Sahu, K and Aich, P},
title = {A robustness-first cross-disease framework supports a candidate shared microbial redox axis and disease-specific metabolic divergence in colorectal cancer, Crohn's disease, and liver cirrhosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0083626},
doi = {10.1128/msystems.00836-26},
pmid = {42734327},
issn = {2379-5077},
abstract = {UNLABELLED: Gut microbiome dysbiosis is associated with colorectal cancer (CRC), Crohn's disease (CD), and liver cirrhosis (LC), yet whether these diseases share conserved microbial vulnerabilities remains unresolved. Analytical pipeline choices alone can shift apparent performance from near-zero to near-perfect on identical data, rendering cross-disease comparison unreliable. Here, in a secondary cross-sectional analysis of public data sets, maximin optimization is introduced as a proposed pipeline-selection criterion guaranteeing worst-case performance across all tasks simultaneously. Benchmarking 1,152 preprocessing-model configurations across six tasks using gut metagenomics and serum metabolomics from CRC, CD, and LC reveals a candidate 19-species microbiome signature in which Firmicutes bacterium CAG:41 is the sole threshold-stable cross-disease taxon, depleted in all three diseases. Microbiome pathway enrichment converges on sulfur-selenium redox metabolism and B-vitamin biosynthesis, while host metabolomic responses are predominantly disease-specific. CD and LC are dominated by single discriminative taxa; CRC requires community-level integration. Exploratory external evaluation was adequately powered only for CRC (AUC = 0.769, 95% bootstrap CI 0.678-0.849); CD and LC assessments were exploratory only.

IMPORTANCE: Cross-disease microbiome comparison has lacked a principled analytical foundation: arbitrary preprocessing choices can shift apparent classification performance from near-random to near-perfect on identical data, making biological conclusions unreliable when pooled across diseases. Maximin optimization addresses this by providing a decision-theoretic guarantee that every classification task contributes valid signal, enabling the first analytically controlled cross-disease comparison of gut metagenomics and serum metabolomics across three major gut-associated diseases. The identification of Firmicutes bacterium CAG:41 as the sole threshold-stable cross-disease taxon, harboring predicted functions in sulfur-selenium metabolism, offers a concrete target for experimental characterization and prospective screening validation. The two-layer dysbiosis architecture-universal microbial vulnerability with disease-specific host metabolic responses-provides a conceptual template for cross-disease microbiome study design in other gut-associated conditions, pending prospective confirmation.},
}

@article {pmid42734355,
year = {2026},
author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Gürkan Yardımcı, G and Merritt, JL},
title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0155026},
doi = {10.1128/spectrum.01550-26},
pmid = {42734355},
issn = {2165-0497},
abstract = {Across human mucosal sites, dysbiotic inflammatory diseases are characterized by compositional shifts in the resident microbiota, in which commensal-dominated communities give way to pathobiont-enriched communities where "inflammophilic" species often predominate. Effective treatments for these complex polymicrobial infections remain limited, in part, because the ecological mechanisms driving their emergence and persistence are still poorly understood. To address this gap, we analyzed a unique cohort of pediatric patient-matched, disease-free dental plaque and odontogenic abscess specimens, providing a clinically relevant model to examine microbiome transitions from commensal to inflammophilic states. Using complementary community ecology modeling approaches and inferred metagenomic analyses, we identified microbial taxa and functional programs associated with inflammatory selective pressure and dysbiotic community emergence. Dental plaque communities are characterized by anabolic metabolic processes and carbohydrate-derived ATP generation, whereas abscess microbiomes are highly biased for catabolic metabolism, amino acid-derived ATP generation, and antimicrobial resistance. The results suggest that abscess communities are much less reliant upon interspecies metabolic complementation compared to dental plaque communities, which would imply an obligate dependence upon host inflammatory responses to provide the key metabolites required for growth. These findings support a model in which an inflammophilic community ecology is largely the net result of a combination of enhanced resistance to innate immunity and compatibility with the inflammatory nutrient environment. By defining the metabolic requirements and selective pressures governing these dysbiotic transitions, it may be possible to suppress inflammatory dysbiotic diseases using ecologically focused therapeutic strategies that exploit the limited biosynthetic capacity of commensal depleted inflammophilic communities.IMPORTANCEDysbiotic inflammatory diseases are frequently sustained by complex microbial community interactions, but the ecological processes involved remain poorly understood. In this study, we leveraged pediatric patient-matched, disease-free dental plaque and odontogenic abscess clinical specimens to examine how oral microbial communities shift from health-associated to inflammation-associated states. We found that abscess microbiomes are enriched for features consistent with adaptation to inflammatory environments, including antimicrobial resistance, catabolic metabolism, and utilization of host-derived nutrients. These findings support a model in which host inflammation functions as a selective ecological pressure, favoring the establishment of metabolically specialized, inflammophilic microbial communities. By defining the ecological and functional features that distinguish abscess-associated communities from disease-free plaque microbiota, this work provides a framework for understanding inflammatory dysbiosis and for developing ecological strategies to disrupt pathobiont-enriched communities while promoting the restoration of stable, health-associated microbiota.},
}

@article {pmid42734361,
year = {2026},
author = {Luo, G and Zhao, J and Xie, L-l and Li, Y and Rao, Y-z and Sun, Y and Lu, X and Eden, J-S and Chen, L and Shi, M},
title = {Library strategies differentially shape microbial, functional, and host signals in clinical metagenomic sequencing.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0089726},
doi = {10.1128/msystems.00897-26},
pmid = {42734361},
issn = {2379-5077},
abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly used in infectious disease diagnostics, yet how library preparation shapes the microbial, functional, and host signals recovered from clinical samples remains poorly defined. Here, we performed a within-sample parallel comparison of three mNGS library preparation strategies-DNA-based libraries (DNAlib), RNA-based libraries (RNAlib), and total nucleic acid-based libraries (TNAlib)-across a diverse range of clinical specimens spanning five sample types. Using a curated clinical infectome as a benchmark, we show that library strategies are not interchangeable but capture distinct biological dimensions of the same specimen. RNAlib provided the most comprehensive standalone recovery of the clinical infectome, with improved detection of RNA viruses and cellular pathogens, enhanced resolution of resistance and virulence signals, and preservation of infection-associated host immune signatures. DNAlib showed stronger baseline recovery of DNA viruses and broader host genome coverage, whereas the TNAlib workflow evaluated here largely behaved as an intermediate strategy rather than a consistent improvement over dedicated DNA- or RNA-based workflows. Together, these results establish that the library preparation protocol is a major determinant of how clinical mNGS data should be interpreted and provide a framework for selecting sequencing strategies according to specific diagnostic and biological questions.IMPORTANCEMetagenomic sequencing is increasingly used in infectious disease research and clinical diagnostics, but different library preparation strategies may recover fundamentally different biological signals from the same sample. These signals include not only pathogens but also background microbes, microbial functional activity, and host immune-response patterns. Here, we systematically compared DNA-, RNA-, and total nucleic acid-based metagenomic sequencing libraries using the same clinical samples processed in parallel. We found that the three strategies did not provide equivalent information. RNA-based sequencing generated the most informative single-library view of infection, particularly for RNA viruses, cellular pathogens, functional microbial signals, and host immune-response patterns. DNA-based sequencing was more effective for DNA virus and host genome recovery, whereas the total nucleic acid sequencing workflow evaluated here generally behaved as an intermediate strategy. These findings show that library preparation can substantially influence the interpretation of metagenomic data.},
}

@article {pmid42734522,
year = {2026},
author = {Liu, S and Gao, X and Wang, J and Li, Z and Liu, Y and Wang, Y and Hou, T and Liu, F and Liu, Y},
title = {PPsAMP: A Novel Computational Framework for Short Antimicrobial Peptide Identification by Fusing Fine-Tuned Semantic and Physicochemical Features via Cross-Attention.},
journal = {Journal of chemical information and modeling},
volume = {66},
number = {17},
pages = {11491-11502},
doi = {10.1021/acs.jcim.6c01300},
pmid = {42734522},
issn = {1549-960X},
support = {NA//Fundamental Research Funds for the Central Universities/ ; 20250203113SF//Science and Technology Development Plan Project of Jilin Province/ ; 62303193//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Antimicrobial Peptides/chemistry/pharmacology ; Prediction Algorithms ; },
abstract = {The widespread misuse of antibiotics has led to a global antimicrobial resistance crisis, highlighting the urgent need for novel antibacterial strategies. Short antimicrobial peptides (sAMPs), while maintaining strong antimicrobial activity, offer superior bioavailability and synthetic feasibility, thus holding great promise in the development of next-generation antibiotics. In recent years, AI-based approaches have achieved notable progress in AMP prediction; however, most existing models are trained primarily on medium and long peptides, resulting in limited accuracy and representation capability when applied to identify sAMPs. To address this problem, a novel prediction model, PPsAMP, is proposed in this paper. First, the protein language model ProtBert-BFD is fine-tuned by sAMPs and non-sAMPs to extract more discriminative representations, which are then integrated with physicochemical features through a cross-attention mechanism. The fused representation is further processed by a feature learning module to achieve the identification of sAMP. The feature learning module consists of a multihead self-attention mechanism and feedforward layers, with residual connections added to enhance generalization ability. Experimental results demonstrate that PPsAMP significantly outperforms state-of-the-art models for identifying sAMPs. Moreover, PPsAMP has identified 14,839 candidate sAMPs from environmental metagenomes, most of which have not been previously reported. The predicted MIC values indicate that they possess potential antibacterial activity. PPsAMP is freely available at https://github.com/shengxiliu/PPsAMP.},
}

*Antimicrobial Peptides/chemistry/pharmacology
Prediction Algorithms

@article {pmid42734665,
year = {2026},
author = {Naik, S and Kousar, H},
title = {Synergistic Biodegradation and Detoxification of High Alkaline Textile Effluent by Acinetobacter indicus KUHKSN-02 and Native Microbiome Aided Bioaugmentation.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42734665},
issn = {1432-0991},
mesh = {Biodegradation, Environmental ; *Acinetobacter/metabolism/isolation & purification/genetics ; *Wastewater/microbiology/chemistry ; *Microbiota ; *Water Pollutants, Chemical/metabolism ; Textiles ; Textile Industry ; Azo Compounds/metabolism ; Industrial Waste/analysis ; },
abstract = {Textile effluent is a chemically complex wastewater containing azo dyes, high alkalinity and recalcitrant organic pollutants. Its untreated discharge poses serious ecological risks and requires sustainable management before release. The comparative efficiency of monoculture treatment and native microbiome assisted bioaugmentation in real highly alkaline textile effluent remains insufficiently documented. This study evaluated the biodegradation and detoxification potential of Acinetobacter indicus KUHKSN-02, isolated from effluent-contaminated soil, under sterile monoculture and non-sterile native microbiome aided conditions. Results shown reduced pollution load evidenced by drastic decrease in physicochemical parameters by both monoculture (COD to 391 ± 6 mg/L and BOD to 18.73 ± 0.25 mg/L) and native bacterial community (COD to 194.3 ± 2.51 mg/L, BOD to 13.5 ± 0.36 mg/L, and TDS to 998.3 ± 6.5 mg/L), with a highest decolorization of 97.72%. FTIR analysis confirmed alterations in functional groups, while HR-LCMS Orbitrap detected Acid Red 18, Acid Orange 7, and Acid Yellow 36 in the raw effluent and in degradation intermediates such as aniline, 2-oxindole, anthranilic acid and betaine after treatment. The Oryza sativa phytotoxicity assay confirmed detoxification, with germination increasing from 0% in raw effluent to 73.33-93.33% after treatment. These findings demonstrate that native microbiome-aided bioaugmentation enhanced biodegradation and detoxification efficiency compared with monoculture treatment. Future studies should validate this approach under field conditions using metagenomic and metatranscriptomic analysis.},
}

Biodegradation, Environmental
*Acinetobacter/metabolism/isolation & purification/genetics
*Wastewater/microbiology/chemistry
*Microbiota
*Water Pollutants, Chemical/metabolism
Textiles
Textile Industry
Azo Compounds/metabolism
Industrial Waste/analysis

@article {pmid42735627,
year = {2026},
author = {Meng, N and Zhu, J and Yan, J and Zhao, Y and Liu, J and Li, G and Zhang, J and Wu, M and Zhou, H and Ma, Q},
title = {Unraveling anaerobic indole degradation in an acclimated sludge consortium: Candidate pathways and microbial division of labor inferred from metagenomic and metatranscriptomic analyses.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143606},
doi = {10.1016/j.jhazmat.2026.143606},
pmid = {42735627},
issn = {1873-3336},
abstract = {Indole is a widespread nitrogen-containing heterocyclic compound in manure, sludge, and wastewater systems, yet the enzymes and microbial populations involved in its anaerobic transformation remain poorly resolved. Here, we established a long-term acclimated anaerobic sludge consortium and combined degradation assays, metabolite profiling, metatranscriptomics, and genome-resolved metagenomics to investigate the functional basis of anaerobic indole degradation. After 120 days of acclimation, the consortium stably degraded 100 mg/L indole, whereas skatole was not effectively removed under the same strategy, indicating substrate-specific adaptation of the microbial community. Metabolite profiling detected oxindole, dioxindole, isatin, and anthranilic acid, supporting a putative transformation route involving pyrrole-ring oxidation and ring cleavage toward anthranilate-like intermediates. Metatranscriptomic analysis identified 16,660 differentially expressed genes after indole addition, with strong transcriptional responses involving oxidoreductases, hydrolases, cofactor-dependent redox metabolism, aromatic-CoA-related metabolism, and methane metabolism-associated pathways. Transcriptional responses highlighted the xanthine dehydrogenase-like molybdenum-enzyme system and isatin hydrolase as candidate contributors to upstream indole transformation, whereas those of abmG-like, bcrC, and oah genes were consistent with possible anthranilic acid activation and downstream CoA-type processing. MAG-resolved analysis further suggested that these candidate functions may be distributed among populations affiliated with Bacteroidota, Chloroflexota, Desulfobacterota, and Methanobacterium. Together, these findings establish a stable anaerobic indole-degrading consortium and provide a testable functional framework for syntrophic interactions linking upstream indole transformation, aromatic-CoA metabolism, and methanogenesis-associated carbon flow.},
}

@article {pmid42735789,
year = {2026},
author = {Chen, J and Wang, M and Li, W and Li, X and He, L and Li, Y and Zheng, M and Du, S and Zhou, Y and Ye, W},
title = {Comprehensive evaluation of new sequencer T20 and well-established T7 with 507 human samples.},
journal = {Genomics},
volume = {},
number = {},
pages = {111320},
doi = {10.1016/j.ygeno.2026.111320},
pmid = {42735789},
issn = {1089-8646},
abstract = {The DNBSEQ-T20x2 (T20) sequencer, developed by MGI Tech, enables cost-effective human whole-genome sequencing (WGS) at 30× coverage for less than $100 per genome. Here, we evaluate the sequencing performance and data quality of the T20 platform by benchmarking it against the established DNBSEQ-T7 (T7) sequencer using 507 samples derived from blood (N = 75), stool (N = 242), and saliva (N = 190). The T20 exhibited lower sequencing quality metrics compared with the T7, with Q20 scores of 95.76%-95.83% and Q30 scores of 87.25%-87.40%, compared with 97.81%-97.93% and 93.26%-93.60%, respectively, for T7 data. Quality differences were more evident toward the end of reads, and PCR-free libraries sequenced on the T20 showed similar reductions in quality scores. The median empirical base error rate estimated from 102 ZymoBIOMICS samples was 0.33%. The T20 demonstrated comparable coverage uniformity to the T7 and showed high concordance in microbiome composition analysis, with a median Bray-Curtis dissimilarity of 0.02. Variant calling performance was highly consistent between the two platforms. Among variants with non-missing genotype calls on both platforms, 94.92% of SNPs and 87.20% of indels showed concordant genotypes between T20 and T7. Overall, the T20 delivers reliable sequencing accuracy and reproducibility for large-scale genomic and microbiome studies, providing a cost-effective alternative for high-throughput sequencing applications.},
}

@article {pmid42735830,
year = {2026},
author = {Ma, Y and Ge, Y and Liu, C and Wang, M and Xiao, Z and Liu, X and Song, T and Zhou, Q and Xiao, L},
title = {Pathogenic microbiomes on jellyfish reveal health risks beyond envenomation.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {109307},
doi = {10.1016/j.toxicon.2026.109307},
pmid = {42735830},
issn = {1879-3150},
abstract = {Jellyfish stings pose a growing public health concern in coastal regions, yet secondary bacterial infections arising from venom-induced tissue damage remain largely unexplored. Here we used shotgun metagenomics to characterize the surface microbiomes of Rhopilema esculentum, Chrysaora quinquecirrha and Stomolophus meleagris, profiling bacterial composition, virulence factors, antibiotic resistance genes and mobile genetic elements. We observed distinct host-specific microbiome signatures, with R. esculentum harboring the highest abundance of virulence-associated genes and notable enrichment of WHO priority pathogens including Staphylococcus aureus and Acinetobacter baumannii. Resistance genes conferring tetracycline, glycopeptide and fluoroquinolone resistance were prevalent across all species. Transposases comprised over 45% of mobile genetic elements, indicating substantial horizontal gene transfer potential. Validation using newly developed TaqMan qPCR assays across eight jellyfish species including the three aforementioned and five additional species, confirming that all harbored at least one opportunistic pathogen. These findings establish jellyfish surfaces as underappreciated reservoirs of antibiotic-resistant pathogens and highlight a potential, but as yet unproven, route of pathogen exposure following envenomation.},
}

@article {pmid42735856,
year = {2026},
author = {Li, D and Hao, DC and Wang, F and Xiao, P},
title = {Integrating multiphysics simulation and biological insights to optimize fungal-bioaugmented soil microbial fuel cells.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135853},
doi = {10.1016/j.biortech.2026.135853},
pmid = {42735856},
issn = {1873-2976},
abstract = {Soil contamination by persistent herbicides like haloxyfop-P-methyl (B) poses substantial environmental risks. Microbial fuel cells (MFCs) offer a solution but require in-depth optimization. We designed a single-chamber soil MFC with a graphite felt anode and air cathode. A 2D equivalent model coupling secondary current distribution and diluted species transport was built in COMSOL Multiphysics. A specific factor (ffungi) for fungal bioaugmentation was introduced, alongside a substrate promotion-toxicity inhibition function (fB(x)) for the herbicide. The model validated the experimental performance ranking (2B + Myrothecium verrucaria (Mv) > B + Mv + Carbon fiber > B + Talaromyces > B + Mv/Talaromyces) and achieved high calibration accuracy, with relative errors below0.6% for current density(CD) and5.7% for power density (PD) across multiple groups. Parameter scans revealed that increasing ffungi linearly boosts performance, with CD and PD enhancements of approximately 2.5 times at ffungi=5. The initial pollutant concentration exhibited a non-monotonic "substrate promotion-toxicity inhibition" window based on model-predicted extrapolations beyond the experimentally tested x = 1 and x = 2 cases, suggesting an optimal concentration range (x = 2-4) that requires future experimental validation.Carbon fibers predominantly lower interfacial contact impedance and enhance the effective reaction area. Mechanistically, the simulated electrochemical behavior is consistent with the reported biological data (e.g. metagenomics and EIS), suggesting that the "xeno-fungusphere" formed by M. verrucaria promotes biofilm formation and electron transfer. The model serves as a robust tool for designing efficient fungal-augmented MFC for herbicide remediation and energy recovery.},
}

@article {pmid42735857,
year = {2026},
author = {Wang, YG and Chen, H and Sun, XX and Li, LH and Wang, ZY and Chen, R and Xing, BS},
title = {Elucidating how calcium inhibits anammox systems and a novel recovery strategy using cation exchange resin: Performance and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135851},
doi = {10.1016/j.biortech.2026.135851},
pmid = {42735857},
issn = {1873-2976},
abstract = {The application of anaerobic ammonium oxidation (anammox) process is hindered by the susceptibility of anaerobic ammonium-oxidizing bacteria (AnAOB) to inhibitors including excessive Ca[2+] concentrations. In this study, the mechanisms of Ca[2+] inhibition and subsequent recovery using cation exchange resin (CER) were systematically investigated by analyzing the characteristics of anammox granular sludge combined with metagenomic analysis. Under 400 mg/L Ca[2+] stress, the nitrogen removal rate (NRR) remained stable despite a sharp decrease in AnAOB abundance. This resilience was attributed to increased extracellular polymeric substance secretion for Ca[2+] sequestration and functional compensation owing to the activation of the nitrification-denitrification process. When Ca[2+] concentration raised to 800 mg/L, a dense CaCO3 precipitate layer formed on the granules, protecting the internal AnAOB but severely limiting substrate mass transfer, leading to a reduction in the NRR from 2.0 to 1.5 kg N/m[3]/d. Under this dense shield, metabolic pathways shifted toward biosynthesis, and carbon fixation and nucleotide metabolism were activated to support cellular proliferation. CER treatment removed the precipitate layer, restored mass transfer, and fully restored nitrogen removal performance. This recovery was accompanied by peak abundances of auxiliary bacteria (Fimbriimonas and Chthonomonas) and metabolic signatures, indicating a transition from stress defense to growth-oriented homeostasis. This study elucidated the response behavior of the anammox system under graded Ca[2+] stress and during the recovery process, and proposed a novel recovery method suitable for industrial application.},
}

@article {pmid42736576,
year = {2026},
author = {O'Sullivan, RJ and Nordfors, U and Saari, NJ and Majander, K and Taavitsainen, JP and Salo, K and Rohrlach, AB and Salmela, E and Lamnidis, TC and Traverso, L and Krause, J and Peltola, S and Onkamo, P},
title = {Population genomics, demography, and circum-Baltic connectivity of Early Medieval southwestern Finland.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42736576},
issn = {1474-760X},
support = {352727//Research Council of Finland/ ; 160003//Jane ja Aatos Erkon Säätiö/ ; },
mesh = {Humans ; Finland ; *Genetics, Population ; Demography ; History, Medieval ; Genomics ; DNA, Ancient ; Genome, Human ; Scandinavians and Nordic People ; *Metagenomics ; },
abstract = {BACKGROUND: Knowledge of Early Medieval Finland (1050-1250 CE) relies primarily on archaeological evidence, as contemporary sources are scarce. The available evidence indicates two distinct cultural-economic zones: coastal and inland. Using newly generated genomic data from 34 ancient individuals alongside modern Finnish genomes, we characterise Late Iron Age and Early Medieval ancestry in southwestern Finland, reconstruct demographic patterns, and place individuals within a circum-Baltic relatedness network.

RESULTS: Early Medieval ancestry in inland southwestern Finland was very similar to that of present-day inhabitants. Ancient coastal and inland individuals were genetically indistinguishable, whereas modern coastal populations showed substantially more Scandinavian ancestry, and less Baltic ancestry compared to their ancient counterparts. IBD (identity-by-descent) analyses also indicate a major genetic shift in the coastal zone since the Early Medieval Period. Effective population size increased throughout the study period and was ~ 13,000 by 1250 CE. IBD links between Scandinavia and Early Medieval Finland align with known archaeological connections. Furthermore, we identify IBD links between individuals from Early Medieval Finland and victims of the Kronan warship sinking.

CONCLUSIONS: We demonstrate nearly a millenium of population continuity in the inland zone of southwestern Finland, contrasted by a large, contemporaneous genetic shift in the coastal zone. This ancestry shift corresponds with documented medieval emigration from Sweden to Finland. The regional population rapidly expanded during this time period, likely due to new agricultural practices and favourable climatic conditions. Our circum-Baltic IBD network indicates that southwestern Finland was firmly embedded into the wider, pre-modern Baltic world.},
}

Humans
Finland
*Genetics, Population
Demography
History, Medieval
Genomics
DNA, Ancient
Genome, Human
Scandinavians and Nordic People
*Metagenomics

@article {pmid42736748,
year = {2026},
author = {Dirican, N and Yardibi, F},
title = {Scientific research dynamics on community-acquired pneumonia: Bibliometric analysis and future perspectives.},
journal = {Medicine},
volume = {105},
number = {37},
pages = {e50602},
pmid = {42736748},
issn = {1536-5964},
mesh = {*Bibliometrics ; *Community-Acquired Pneumonia ; Humans ; COVID-19/epidemiology ; *Biomedical Research/trends ; SARS-CoV-2 ; Community-Acquired Infections ; },
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is a leading cause of morbidity, mortality, and hospitalization worldwide. This study aimed to provide physicians and researchers with a comprehensive overview of the most influential publications and research trends in CAP.

METHODS: Research articles and reviews on CAP published in English and indexed in the Web of Science from 1978 to 2023 were analyzed. Network visualization and comprehensive bibliometric analyses of publication output, countries, journals, authors, cited references, and keywords were performed using CiteSpace and VOSviewer software.

RESULTS: A total of 4141 publications, including 3665 original research articles and 476 reviews, were included in the analysis. Publication output increased after 1991 and showed an overall upward trend, particularly after 2000. The United States, Spain, and China were the most productive countries. Chest published the most articles, whereas Clinical Infectious Diseases received the highest number of citations. Torres A was the most prolific author, whereas Fine MJ was the most cited. The most cited clinical studies published in the past 5 years focused on COVID-19, severe CAP (sCAP), and corticosteroid therapy. Co-citation analysis identified sCAP, healthcare-associated pneumonia, prospective cohort studies, and metagenomic next-generation sequencing as active research clusters. Keyword co-occurrence analysis identified sCAP as the largest and most prominent cluster, whereas the other current clusters included atypical pathogens, antibiotic resistance, chronic obstructive pulmonary disease, and β-lactam monotherapy.

CONCLUSIONS: This bibliometric analysis highlights the evolving research landscape of CAP and suggests that future research will increasingly focus on sCAP and its treatment, the identification of rare or emerging pathogens, rapid diagnostic technologies, appropriate initial treatment selection, personalized therapeutic strategies, and vaccination. These findings provide valuable insights into the current research hotspots on CAP and future priorities for researchers and clinicians.},
}

*Bibliometrics
*Community-Acquired Pneumonia
Humans
COVID-19/epidemiology
*Biomedical Research/trends
SARS-CoV-2
Community-Acquired Infections

@article {pmid42737259,
year = {2026},
author = {O'Bryan, CA and Stalford, B and Obe, T and Crandall, PG},
title = {Emerging Microbiological and Sensor-Based Approaches for Biofilm Detection in Meat and Poultry Processing Environments.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737259},
issn = {2304-8158},
abstract = {Biofilms remain a major challenge in meat and poultry processing because conventional sanitation verification methods provide only indirect evidence of attached microbial communities. Emerging microbiological and sensor-based technologies offer new opportunities to improve biofilm detection by providing information on biofilm structure, cellular membrane integrity, composition, and spatial distribution. This review evaluates advanced imaging techniques, molecular assays, extracellular polymeric substance (EPS)-focused analyses, and real-time sensor platforms for their potential to strengthen risk-based biofilm monitoring in meat and poultry processing environments. Confocal and epifluorescence microscopy, scanning electron microscopy, optical coherence tomography, and in situ fluorescence imaging provide detailed visualization of biofilm architecture and viability, supporting validation of routine monitoring methods and assessment of sanitation practices. Quantitative PCR, digital PCR, amplicon sequencing, and metagenomics characterize biofilm communities, identify persistent microorganisms, and evaluate sanitation effectiveness, while EPS analyses of polysaccharides, proteins, extracellular DNA, and lipids indicate biofilm maturity and resilience. Electrochemical impedance, quartz crystal microbalance, surface acoustic wave sensors, and microfluidic platforms show promise for near-real-time detection of attached biomass. Collectively, these technologies provide a framework for more targeted, data-driven biofilm surveillance that can improve sanitation verification and reduce pathogen persistence in meat and poultry processing facilities.},
}

@article {pmid42737331,
year = {2026},
author = {Olanbiwoninu, AA and Awotundun, TA and Afolabi, JF and Fashogbon, RO and Fagunwa, O},
title = {Ethnogeographic Distribution of Nigerian Fermented Foods and the Prospects for Bioeconomy Improvements.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737331},
issn = {2304-8158},
abstract = {Fermented foods and beverages represent a cornerstone of Nigerian food culture, yet their scientific documentation remains fragmented, and their potential within global bioeconomy frameworks is largely unrealised. This review addresses two interrelated gaps: the absence of a comprehensive ethnogeographic analysis of Nigerian fermented foods that integrates ecological, cultural, and agricultural drivers of regional diversity, and the limited examination of these foods as models for circular bioeconomy development. Using a narrative synthesis of peer-reviewed literature spanning 1986-2025, we systematically map the distribution of fermented tuber, cereal, legume, dairy, and fruit products across Nigeria's major geopolitical zones, demonstrating that agroecological endowment, ethnic composition, trade routes, and cross-cultural interactions shape regional variation. Beyond their socio-cultural significance, Nigerian fermented foods contribute meaningfully to food security by extending shelf life, enhancing nutrient bioavailability, and reducing post-harvest losses. This review further positions ogi (fermented maize gruel) and garri (fermented cassava granules) as model systems for circular bioeconomy integration, demonstrating how by-product valorisation can generate value-added outputs, including animal feed, bioethanol, biodegradable packaging, and organic acids. Key challenges, including food safety deficits, absence of standardised production protocols, and limited regulatory frameworks, are critically assessed. Three priority research directions are identified: metagenomics-based microbiome profiling, development of culturally appropriate starter cultures, and formulation of gender-responsive regulatory instruments. Nigerian fermented foods, properly documented and integrated into innovation systems, represent an underutilised asset for sustainable food system transformation in Sub-Saharan Africa.},
}

@article {pmid42737401,
year = {2026},
author = {Li, W and Guo, R and Zu, Z and Xu, S and Zhang, G and Dai, Y and Li, Y},
title = {Iron-Amended Pleurotus citrinopileatus Residue Composting: Lignocellulose Degradation and Microbial Functional Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42737401},
issn = {2304-8158},
support = {2025ZDYFNS05//Changchun City Science and Technology Development Plan Project/ ; N/A//the Project of "Tiānchí Yīngcái" Talent Introduction Program of Xinjiang Uygur Autonomous Region/ ; N/A//NYGG/ ; },
abstract = {Spent mushroom substrate (SMS) from Pleurotus citrinopileatus cultivation is a lignocellulose-rich by-product whose efficient composting is hindered by lignocellulose recalcitrance and slow humification. This study compared the effects of Fe3O4-based magnetic powder (MP), Fe[0] beads (IB), and Fe2O3-rich crude iron ore (RI) with those of an unamended control during 30-day aerobic co-composting with chicken manure. Physicochemical characterization and metagenomic sequencing were combined to assess compost maturity, lignocellulose degradation, humic substance transformation, microbial succession, and functional potential. MP achieved the most balanced overall performance, exhibiting the highest total lignocellulose degradation (59.48%), the lowest final organic matter content (357.70 g/kg), a final C/N ratio of 13.04, and the highest germination index (151.50%). RI achieved the highest hemicellulose degradation and final contents of humic acid and total humic substances, whereas IB promoted rapid initial heating and relatively high cellulose degradation but caused greater physicochemical fluctuations. Metagenomic analyses revealed amendment-specific microbial succession and distinct CAZy-annotated gene and MetaCyc pathway profiles associated with lignocellulose transformation and carbon metabolism. Overall, Fe3O4-based magnetic powder showed the greatest potential for simultaneously promoting lignocellulose degradation, organic matter transformation, and compost maturity, providing a practical basis for the sustainable valorization of edible mushroom industry by-products.},
}

@article {pmid42737628,
year = {2026},
author = {Ghaffar, A and Abdul-Careem, MF},
title = {Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737628},
issn = {1422-0067},
support = {10036367//Egg Farmers of Alberta/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Metagenomics/methods ; *Housing, Animal ; *Metagenome ; *Bacteria/genetics/classification ; Genome, Bacterial ; Manure/microbiology ; Archaea/genetics ; Microbiota/genetics ; },
abstract = {Culture-independent techniques are playing a major role in exploring unique and novel microbial communities from complex ecosystems, leading to an outstanding impact on our basic understanding of the tree of life. Microbial communities are not extensively studied in layer chicken housing environments, particularly from the point of view of taxa carrying antimicrobial resistance genes, virulence genes and their functional potential. This study aimed to extract metagenomic-assembled genomes (MAGs) from the Illumina short-reads shotgun metagenomics sequenced data that originated from an Alberta poultry barn environment and then to study host tracking of antimicrobial resistance genes (ARGs) and the roles of genes involved in functions related to ammonia production, short-chain fatty acid (SCFA)-related pathways, sulfur metabolism, methane emission, stress and disinfectant-related pathways. A total of 251 high-quality MAGs were extracted, including 249 bacterial and two archaeal genomes from sequencing data of 30 metagenomic sequencing samples comprising 15 air and 15 manure samples collected from 15-layer farms. Interestingly 22 bacterial MAGs were not classified to species levels using GTDB-based classification. ARGs were mainly harbored by the genera Staphylococcus, Alistepes, Romboutsia, and Enterococcus. Bacteroides is a main taxon carrying ARGs in air samples. Ammonia production-related genes were mainly tracked in Staphylococcus, Ruminococcus and Corynebacterium genera. The assimilatory sulfate reduction genes responsible for sulfur metabolism and hydrogenase-related genes responsible for hydrogen cycling were traced from Staphylococcus originated from both air and manure. The current study provides characterizations of MAGs from a poultry housing environment by linking microbial taxa with virulence, resistance, and metabolic functions. The findings emphasize the role of microbiota in shaping gas emissions and AMR, with implications for poultry health and worker's safety and the ultimate aim of sustainable poultry production.},
}

Animals
*Chickens/microbiology
*Metagenomics/methods
*Housing, Animal
*Metagenome
*Bacteria/genetics/classification
Genome, Bacterial
Manure/microbiology
Archaea/genetics
Microbiota/genetics

@article {pmid42737764,
year = {2026},
author = {Kozhakhmetov, S and Vinogradova, E and Sergazy, S and Chulenbayeva, L and Kossumov, A and Kovenskiy, A and Mukhanbetzhanov, N and Ospankulova, G and Saduakhasova, S and Khamitova, D and Kamanova, S and Toimbayeva, D and Shaimenova, B and Kalemshariv, B and Aitmukhanbetov, D and Kushugulova, A},
title = {Enteral Nutrition Is Associated with a Distinct Gut Microbiome Composition and Fermentation Capacity Profile After Acute Colonic Injury in Rats.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737764},
issn = {1422-0067},
support = {BR22883587//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
mesh = {Animals ; Rats ; *Gastrointestinal Microbiome ; *Enteral Nutrition/methods ; *Fermentation ; Male ; *Colon/injuries/microbiology/pathology ; Dextran Sulfate ; Metagenomics ; Disease Models, Animal ; *Colitis/microbiology/therapy/chemically induced ; Rats, Sprague-Dawley ; },
abstract = {Enteral nutrition (EN) is known to promote mucosal healing in inflammatory bowel disease, and multi-omics data suggest that the gut microbiome mediates its therapeutic effects. However, the impact of EN and its components on the gut community during recovery from acute epithelial injury remains incompletely understood. We used whole-genome metagenomic sequencing to investigate the effect of an EN formula based on extruded amaranth flour and pea protein on the gut microbiome in a dextran sulfate sodium (DSS) rat model of acute colonic injury. Three groups were compared, as follows: an unchallenged control (n = 9) with standard chow, a colonic injury (5% DSS; n = 9) group with standard chow, and a colonic injury (5% DSS; n = 9) group with EN. Injury was confirmed histologically (median MCHI score was 2, indicating epithelial damage without inflammation). DSS caused significant weight loss. Animals receiving EN regained baseline weight faster, by day 14, whereas animals on standard chow achieved recovery only by day 21. Differences in energy intake should be further investigated to validate the effect of EN on body weight recovery. At day 21, both injury groups demonstrated higher relative abundances of Bacteroidaceae and Erysipelotrichaceae, including the mucin-degrader Allobaculum mucilyticum, compared with the control group. Conversely, Lactobacillus abundance, notably Lactobacillus acidophilus, was higher in the EN group than in both other groups, as was the inferred capacity for lactate-producing fermentation. These findings suggest that EN is associated with a distinct microbial composition and inferred metabolic profile during the post-injury period, with lactobacilli as one of the potential mediators of its effects.},
}

Animals
Rats
*Gastrointestinal Microbiome
*Enteral Nutrition/methods
*Fermentation
Male
*Colon/injuries/microbiology/pathology
Dextran Sulfate
Metagenomics
Disease Models, Animal
*Colitis/microbiology/therapy/chemically induced
Rats, Sprague-Dawley

@article {pmid42737832,
year = {2026},
author = {Wei, L and Liu, H and Shen, Z and Song, Z and Huang, S and Lin, Z and Huang, X},
title = {Epithelial Inflammatory iNOS-Nitrate Axis Enhances P. gingivalis Pathogenicity via V. parvula in Diabetes-Associated Periodontitis.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737832},
issn = {1422-0067},
support = {82201056//National Natural Science Foundation of China/ ; 2023A04J2154//Guangzhou Experimental Station/ ; 2023A0505050158//China International Science and Technology Cooperation/ ; },
mesh = {Animals ; *Nitric Oxide Synthase Type II/metabolism/genetics ; *Porphyromonas gingivalis/pathogenicity ; *Periodontitis/microbiology/metabolism/pathology/etiology ; Humans ; Mice ; *Nitrates/metabolism ; Epithelial Cells/metabolism/microbiology ; *Veillonella/pathogenicity ; Male ; Gingiva/microbiology/metabolism/pathology ; Female ; *Diabetes Mellitus, Experimental/complications/microbiology ; Inflammation/microbiology/metabolism ; Virulence ; },
abstract = {The mechanisms by which host inflammatory responses reshape the pathogenic potential of oral microbiota in mucosal inflammatory diseases remain poorly defined. Metagenomic sequencing of subgingival plaque and single-cell RNA sequencing of gingival tissues were performed in patients with diabetes-associated periodontitis (DP) and non-diabetic periodontitis (P). A diabetic mouse model was used to evaluate inflammation and bone resorption following oral inoculation with Porphyromonas gingivalis (P. gingivalis), Veillonella parvula (V. parvula), or both. Human gingival epithelial cells (HGECs) were cultured under high glucose conditions with or without an iNOS inhibitor 1400 W to assess iNOS and nitrate levels. A P. gingivalis-V. parvula co-culture system with nitrate supplements was used to evaluate P. gingivalis growth and virulence. Higher abundance of P. gingivalis and V. parvula was found in DP subgingival plaque. In diabetic mice, these bacteria worsened bone resorption and increased iNOS[+] epithelial cells. Single-cell sequencing showed higher iNOS expression in DP patients, linked to V. parvula. In vitro, high glucose increased iNOS and nitrate in HGECs, and these effects were reversed by 1400 W. With V. parvula, nitrate over 200 μM enhanced P. gingivalis growth and virulence. Diabetic epithelial iNOS-derived nitrate boosts P. gingivalis pathogenicity through V. parvula, worsening periodontal inflammatory bone damage.},
}

Animals
*Nitric Oxide Synthase Type II/metabolism/genetics
*Porphyromonas gingivalis/pathogenicity
*Periodontitis/microbiology/metabolism/pathology/etiology
Humans
Mice
*Nitrates/metabolism
Epithelial Cells/metabolism/microbiology
*Veillonella/pathogenicity
Male
Gingiva/microbiology/metabolism/pathology
Female
*Diabetes Mellitus, Experimental/complications/microbiology
Inflammation/microbiology/metabolism
Virulence

@article {pmid42737915,
year = {2026},
author = {Promariya, A and Treenarat, S and Duangsri, C and Lansubsakul, N and Powtongsook, S and Khetkorn, W and Raksajit, W},
title = {Dynamics of Microbial Communities and Antibiotic Resistance Genes During Arthrospira platensis Cultivation in Swine Wastewater.},
journal = {Biology},
volume = {15},
number = {17},
pages = {},
pmid = {42737915},
issn = {2079-7737},
support = {//The High-Quality Research Graduate Development Cooperation Project between Kasetsart Uni-versity and the National Science and Technology Development Agency (NSTDA)/ ; FF(KU)18.66, FF(KU)50.67//Kasetsart University Research and Development Institution (KURDI)/ ; },
abstract = {Swine wastewater is a nutrient-rich waste stream with considerable potential for cyanobacterial cultivation and resource recovery. However, its impacts on microbial community dynamics and antibiotic resistance genes (ARGs) remain poorly understood. This study evaluated the cultivation of Arthrospira platensis in a medium containing 25% swine wastewater and 75% Zarrouk medium (SWW25) using a flat-panel photobioreactor. A. platensis achieved a biomass concentration of 1.58 ± 0.02 g/L, a biomass productivity of 0.11 ± 0.01 g/L/d, and a specific growth rate of 0.26 ± 0.01 d[-1]. Simultaneously, the system removed 98.5% of ammonium nitrogen and 80% of orthophosphate. Metagenomic analysis indicated changes in bacterial community composition during A. platensis cultivation. Microbial community analysis revealed shifts in relative abundance after cultivation, likely associated with changes in community composition following Arthrospira biomass enrichment, while Proteobacteria, Firmicutes, and Synergistota remained among the dominant phyla. In addition, ARG profiling indicated a decline in ARG diversity and read counts during cultivation, whereas tet(X) remained the only detectable ARG after A. platensis cultivation. Collectively, these findings suggest that A. platensis cultivation under non-axenic conditions was associated with biomass production, nutrient removal, and changes in microbial community composition and ARG profiles in swine wastewater.},
}

@article {pmid42737961,
year = {2026},
author = {Tang, J and Li, N and Zhou, W and Pan, R and Suo, L and Li, B and Zhao, H},
title = {Spatially Specialized Nasopharynx-Rectal Microbiomes in Golden Snub-Nosed Monkeys (Rhinopithecus roxellana).},
journal = {Biology},
volume = {15},
number = {17},
pages = {},
pmid = {42737961},
issn = {2079-7737},
support = {32270536//National Natural Science Foundation of China/ ; 32371563//National Natural Science Foundation of China/ ; //Shaanxi Special Support Plan for High-level Talents/ ; 32672006//National Natural Science Foundation of China/ ; 2024P-02, 2025k-13, 2025K-32, 2026K-32//Special Foundation of Shaanxi Academy of Sciences, China/ ; 2026RS-CXTD-73//Shaanxi Provincial Key Science and Technology Innovation Team/ ; 2024JC-YWGCZ-05, 2024JC-YBQN-0242, 2025JC-YWGCZ-05, 2025JC-GXPT-037//Shaanxi Key Research and Development Program/ ; },
abstract = {BACKGROUND: Understanding the nasopharyngeal (NAS) and rectal (INT) microbiomes is critical to maintain host health. However, their functional roles in shaping microbial network structure and niche differentiation remain unexplored in most animal species, especially endangered primates. Here, we compared the NAS and INT microbiomes of golden snub-nosed monkeys (Rhinopithecus roxellana) using full-length 16S rRNA amplicon sequencing and metagenomics, focusing on taxonomic composition, functional profiles (KEGG, CAZy, PHI), and microbial co-occurrence networks.

RESULTS: Our results indicate that microbial community structure and diversity (Shannon evenness) differ significantly between the two niches. Taxonomically, both sequencing approaches consistently show that, at the relative-abundance level, NAS is dominated by genera such as Dolosigranulum and Vibrio, whereas the INT is characterized by Campylobacter, Helicobacter, and Aerococcus. Notably, metagenomic analysis indicates a relatively high abundance of potential pathogens, including Helicobacter pylori and Chlamydia psittaci. LEfSe analysis shows Dolosigranulum and Campylobacter are key microbial markers for the NAS and INT niches, respectively. KEGG pathway analysis reveals that the NAS microbiome is enriched in valine/leucine/isoleucine degradation and glutathione metabolism, while the INT microbiome is enriched in amino sugar and nucleotide sugar metabolism and ribosome pathways. At the CAZy level, all 29 differentially abundant families (e.g., GH13_29, GH103, AA3_2) were enriched in the NAS. Distinct pathogen-host interaction profiles further reflect niche-specific adaptations. Exploratory Spearman-based co-occurrence networks (in which no genus-CAZy edge survived Benjamini-Hochberg (FDR) correction) linked core commensals to KEGG pathways and CAZy families (e.g., GT35, GH0). In the INT, Campylobacter and Helicobacter form high-connectivity modules associated with pathways such as those involving the two-component system and ABC transporters.

CONCLUSIONS: The nasopharyngeal and rectal microbiomes in golden snub-nosed monkeys differ not only taxonomically but also functionally, exhibiting clear spatially specialized functional differentiation. Given the small sample size (n = 8), these findings provide preliminary evidence for niche-specific microbial and functional partitioning and suggest that the nasopharynx may harbor a relatively high abundance of potential zoonotic pathogens. This study provides a basis for further exploration with a larger sample size.},
}

@article {pmid42737970,
year = {2026},
author = {Suo, L and Bian, K and Tang, J and Li, F and Chang, S and Yang, T and Zhao, X and Dong, W and Sun, K and Yang, C},
title = {Dynamics of Antibiotic Resistance Gene Profiles in Captive Forest Musk Deer (Moschus berezovskii) Along a Breeding Duration Gradient.},
journal = {Biology},
volume = {15},
number = {17},
pages = {},
pmid = {42737970},
issn = {2079-7737},
support = {2024k-08//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025k-26//Science and Technology Projects of Shaanxi Academy of Science/ ; 2025NC-YBXM-120//Shaanxi Key Research and Development Program/ ; },
abstract = {BACKGROUND: To conserve wild populations and ensure a sustainable supply of musk, China initiated the captive breeding of forest musk deer. The temporal dynamics of gut antibiotic resistance gene (ARG) profiles in captive forest musk deer along a breeding duration gradient remain poorly characterized.

METHODS: In this study, we employed metagenomic sequencing to systematically characterize the profiles and potential mobility of ARGs. Samples were divided into short-term, medium-term and long-term groups according to breeding durations.

RESULTS: A total of 331 ARG subtypes and 71 mobile genetic element (MGE) subtypes were annotated across all samples. ARG Shannon diversity differed overall across groups (Kruskal-Wallis, p = 0.03); Bonferroni-adjusted Dunn's test showed no significant pairwise differences. PCoA (Bray-Curtis) demonstrated distinct separation of the ST group (p = 0.002), and shared core ARG subtypes gradually increased with extended breeding years. A strong positive correlation between ARG and MGE abundances was identified (r = 0.85, p = 0.0001). In total, 63 contigs carrying co-localized ARG-MGE complexes were recovered. The ST group contained the highest proportion of such contigs. The ST group displayed tight physical ARG-MGE linkage within 1-3 kb genomic intervals.

CONCLUSIONS: Our results reveal that breeding duration is associated with the gut ARG characteristics of captive forest musk deer. Short-term captivity has higher ARG-MGE co-localization, suggesting a higher possibility of mobilization.},
}

@article {pmid42737978,
year = {2026},
author = {Jiang, L and Wright, R and Raudonis, R and Banskota, AH and Glick, BR and Mitchell, RJ and Scur, M and Wang, Z and Zhang, W and Zhang, T and Luo, Q and Langille, MGI and Cheng, Z and Wen, G},
title = {The Biotechnological Applications of Marine Bacteria.},
journal = {Biology},
volume = {15},
number = {17},
pages = {},
pmid = {42737978},
issn = {2079-7737},
support = {RGPIN-2023-05928, RGPIN-2022-05010//Natural Sciences and Engineering Research Council of Canada/ ; CARS-41//China Agriculture Research System/ ; RS-2025-02263513//Korea National Institute of Health/ ; },
abstract = {Marine bacteria represent a vast and largely untapped resource for biotechnological innovation, offering solutions to global challenges in health, sustainability, and environmental conservation. The ocean's unique conditions have driven marine bacteria to evolve diverse metabolic capabilities, resulting in the production of bioactive compounds, enzymes, and other metabolites with wide-ranging applications. Recent advances in high-throughput sequencing, metagenomics, and analytical chemistry have unlocked new opportunities for leveraging these microorganisms in fields as varied as medicine, agriculture, and bioremediation. This review highlights the role of marine bacteria in the One Health framework, showcasing their contributions to antimicrobial discovery, nutraceutical development, pathogen biocontrol, and environmental cleanup, including microplastic degradation. This review also examines emerging methodologies such as microbiome mining and advanced culturing techniques, which hold the key to realizing the full potential of marine bacteria in a sustainable bioeconomy. By bridging fundamental research with applied sciences, marine biotechnology promises to deliver transformative impacts on human, animal, and environmental health.},
}

@article {pmid42738539,
year = {2026},
author = {Chen, M and Zhang, Z and Du, L and Yu, J and Wang, H and Yu, X and Zhang, S and Lin, L and Long, C and Huang, P and Kong, X and Liang, X and Li, J and Xiong, X and Yin, Y},
title = {Supplementation with Agrobacterium sp. FN01-Derived Crude Product Dominated by L-β-Galactoglucan Enhances Growth Performance and Nutrient Utilization and Modulates Intestinal Microbiota in Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {17},
pages = {},
pmid = {42738539},
issn = {2076-2615},
support = {32130099; 32573243//National Natural Science Foundation of China/ ; },
abstract = {Polysaccharides are well known for their immunomodulatory properties and gut microbiota-regulating functions; however, their digestive stability and structure-dependent biological mechanisms remain poorly understood. This study investigated the in vitro enzymatic resistance and intestinal regulatory effects of a novel L-β-galactoglucan (Mw 400-520 kDa) derived from Agrobacterium sp. FN01, and further evaluated the in vivo effects of its corresponding crude fermentation product on growth performance and intestinal metabolism in pigs. Twenty-seven-day-old weaned piglets were randomly allocated to three treatments, with 16 pens per treatment and 13 piglets per pen, and fed basal diets supplemented with 0, 200, or 400 mg/kg of the crude product. The results showed that L-β-galactoglucan exhibited strong resistance to pancreatic α-amylase and glucoamylase under the tested in vitro conditions, with minimal release of low-molecular-weight oligosaccharides during hydrolysis. The 400 mg/kg crude product supplementation significantly improved growth performance, reduced the feed-to-gain ratio, and increased the apparent total tract digestibility of dry matter, crude protein, crude fat, and gross energy (p < 0.05). In addition, dietary supplementation with this crude product increased intestinal microbial diversity, enriched Halalkalibacter urbisdiaboli, and increased colonic concentrations of isobutyrate and isovalerate (p < 0.05). Functional metagenomic analysis further revealed enhanced microbial carbohydrate metabolism and energy metabolic pathways. In conclusion, under the in vitro conditions tested in this study, the novel L-β-galactoglucan exhibited resistance to the two tested enzymes. In the pig trial, this polysaccharide improved growth performance and nutrient utilization, and modulated the intestinal microbial composition. These observations suggest that the fermentation product may be promising for animal feeding applications.},
}

@article {pmid42738552,
year = {2026},
author = {Luo, X and Zhang, J and Yang, Q and Sun, Y and Zhao, Y and Hu, X and Wang, X and Hu, L and Xu, H and Huang, L and Lei, M and Li, C and Kuang, L and Fu, W},
title = {Integrated Metagenomic and Untargeted Metabolomic Analyses Characterize Enramycin-Associated Colonic Microbial and Metabolic Changes in Weaned Rabbits.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {17},
pages = {},
pmid = {42738552},
issn = {2076-2615},
support = {ZYN2025261//Fundamental Research Funds for the Central Universities of Southwest Minzu University/ ; SASA2026CZYX004//Sichuan Special Project for Financial Operation/ ; SCCXTD-2024-26//Modern Agricultural Industrial System of Sichuan Rabbit Innovation Team/ ; 2026YFYZ0033//Livestock Breeding Project of Sichuan Province/ ; },
abstract = {Enramycin is used as a dietary antimicrobial in young animals, but its effects on rabbit colonic ecology remain insufficiently characterized. This study evaluated the effects of enramycin in 60 weaned rabbits randomly assigned to a control or enramycin-treated group (60 mg/kg) for 14 days (n = 30/group). Clinical outcomes were evaluated in all rabbits, whereas paired colonic multi-omics profiling was performed in six randomly selected survivors per group with no recorded diarrhea. Enramycin reduced diarrhea incidence without affecting body-weight development, organ indices, or mortality. Metagenomic analysis revealed unchanged alpha diversity but significant alterations in microbial community structure, including decreased Verrucomicrobiota, Akkermansia, and Alistipes and increased Cyanobacteria and Avigastranaerophilus. Untargeted metabolomics identified 332 features meeting the predefined screening criteria, including 143 upregulated and 189 downregulated metabolites. Prominent pathway annotations included phenylpropanoid biosynthesis and arachidonic acid metabolism. Resistome analysis demonstrated that treatment drove shifts in streptothricin-, aminoglycoside- and glycopeptide-related resistance signatures. The integrated analysis identified associations between four selected genera and the top 30 differential metabolites. Overall, dietary enramycin was associated with a short-term reduction in diarrhea incidence and concurrent changes in selected colonic microbial, metabolic, and resistance gene features. These findings extend enramycin evaluation beyond conventional clinical outcomes and highlight the importance of considering broader ecological effects when assessing dietary antimicrobial exposure in weaned rabbits.},
}

@article {pmid42738866,
year = {2026},
author = {Jiménez-Ortega, RF and Ortega-Meléndez, AI and Montes-García, JF and Negrete-Abascal, E and Patiño, N and Ramírez-Salazar, EG and Sevilla-Montoya, R and Velázquez-Cruz, R and Hidalgo-Bravo, A},
title = {Genome-Resolved Functional Profiling of Osteoporosis-Associated Gut Bacteria Highlights Putative Metabolic and Immunogenic Signatures of the Gut-Bone Axis.},
journal = {Cells},
volume = {15},
number = {17},
pages = {},
pmid = {42738866},
issn = {2073-4409},
mesh = {*Osteoporosis/microbiology/immunology/genetics/metabolism ; Humans ; *Bone and Bones/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; *Bacteria/genetics/metabolism/classification ; },
abstract = {The gut microbiota has emerged as a potential regulator of bone metabolism, but the genome-encoded functional repertoire of osteoporosis-associated gut bacteria remains insufficiently characterized. This study performed in silico functional profiling of gut bacterial taxa associated with osteoporosis, low bone mineral density, or comparator bone-related phenotypes. Twenty candidate taxa were selected from evidence in the human microbiome and represented by 26 curated bacterial reference genomes. Genome-wide annotations were used to map predicted gut-bone axis signatures, carbohydrate-active enzyme (CAZyme) repertoires, selected Kyoto Encyclopedia of Genes and Genomes pathways, and gutSMASH-predicted metabolic gene clusters. Functional burdens were normalized as hits per 1000 annotated proteins and integrated into metabolic, immunogenic, CAZyme, KEGG, and metabolic gene cluster profiles. Twelve predicted gut-bone axis signatures were identified, comprising 3337 primary candidate protein hits and a strict high-confidence subset of 2497 hits. Dominant signatures included vitamin B12/cobalamin metabolism, folate/one-carbon metabolism, peptidoglycan/cell-wall biosynthesis, and short-chain fatty acid-related functions. Dialister invisus, Dialister succinatiphilus, Megamonas funiformis, and Megamonas hypermegale showed the strongest normalized predicted gut-bone axis signal. These hypothesis-generating findings prioritize microbial metabolic and immunogenic features for future metagenomic, metabolomic, and experimental validation studies.},
}

*Osteoporosis/microbiology/immunology/genetics/metabolism
Humans
*Bone and Bones/metabolism/microbiology
*Gastrointestinal Microbiome/genetics
*Genome, Bacterial
*Bacteria/genetics/metabolism/classification

@article {pmid42738945,
year = {2026},
author = {Pawłowski, P and Kościołek, O and Jeżak, M and Jakubik, K and Kościołek, A and Samardakiewicz, M},
title = {The Gut-Brain Axis and Dietary Patterns in Shaping Long-Term Neurocognitive and Psychosocial Outcomes in Adolescent and Young Adult Survivors of Childhood Cancer: A Systematized Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42738945},
issn = {2072-6643},
mesh = {Humans ; Adolescent ; *Cancer Survivors/psychology ; *Gastrointestinal Microbiome/physiology ; Young Adult ; *Diet ; *Brain-Gut Axis/physiology ; *Neoplasms/psychology ; Dysbiosis ; Child ; *Brain ; },
abstract = {Background: The dynamic advancement of pediatric hemato-oncology and intensified therapeutic protocols have significantly increased survival rates while simultaneously highlighting the challenge of long-term treatment complications. Within the cohort of adolescent and young adult (AYA) survivors, delayed neurocognitive deficits, often manifesting as the chemobrain phenotype, and psychosocial disorders constitute a particularly substantial burden. Contemporary neurogastroenterological evidence indicates a fundamental role of persistent dysbiosis and gut-brain axis dysfunction in the pathogenesis of these alterations. This review aims to critically synthesize translational evidence elucidating the impact of iatrogenic gut microbiota damage and modifiable dietary patterns on the development of long-term neurocognitive sequelae in survivors of early childhood cancer. Methods: A systematized narrative review was conducted in accordance with the SANRA guidelines by integrating data from in vivo models and observational studies. A comprehensive literature search across the PubMed, Embase, Cochrane Central, Scopus, and Web of Science databases up to June 2026 was performed utilizing the Population, Exposure, and Outcomes (PEO) framework. Results: Oncological therapies, including myeloablative conditioning and broad-spectrum antibiotic therapy, induce a microbial scar phenomenon characterized by the depletion of commensal Firmicutes in favor of resistant pathobionts. The subsequent decline in the synthesis of neuroprotective short-chain fatty acids (SCFAs) alongside the pathological activation of the kynurenine pathway disrupts central nervous system homeostasis. Translocation of lipopolysaccharides (LPSs) across the compromised intestinal barrier generates systemic inflammation recognized as inflammaging, which, in turn, stimulates neurotoxic microglial hyperreactivity. This pathophysiological cascade is accelerated by a pro-inflammatory Western diet, whereas anti-inflammatory interventions such as the MIND diet and postbiotics demonstrate measurable restorative potential. Conclusions: The pathophysiology of delayed neurotoxicity is largely a consequence of systemic neuroinflammation driven by intestinal dysbiosis. Implementing individualized dietary and microbiome-targeted strategies into survivorship care protocols constitutes a crucial direction for clinical prophylaxis. Validating their clinical efficacy in the AYA population necessitates prospective randomized controlled trials integrated with shotgun metagenomic sequencing.},
}

Humans
Adolescent
*Cancer Survivors/psychology
*Gastrointestinal Microbiome/physiology
Young Adult
*Diet
*Brain-Gut Axis/physiology
*Neoplasms/psychology
Dysbiosis
Child
*Brain

@article {pmid42738989,
year = {2026},
author = {Nyambal, T and Lkhamsuren, K and Hübner, A and Khuygaa, SO and Bromage, S and Stahl, R and Rest, M and Reichhardt, B and Battulga, A and Odonchimed, S and Dambadarjaa, D and Tulgaa, K and Warinner, C and Tsolmon, S},
title = {Distinctive Patterns of Gut Bifidobacterium Diversity in Mongolian Adults: Regional Variation and Dairy Intake Associations.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42738989},
issn = {2072-6643},
support = {804884/ERC_/European Research Council/International ; },
mesh = {Humans ; *Bifidobacterium/classification/genetics/isolation & purification ; Mongolia ; Adult ; Male ; Female ; *Dairy Products ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Diet ; Middle Aged ; Young Adult ; },
abstract = {Background/Objectives: Despite increasing interest in the human gut microbiome, particularly in Bifidobacterium, studies focusing on traditionally living populations with high habitual dairy consumption remain limited. This study investigated species-level diversity, abundance, and regional variation of Bifidobacterium among healthy Mongolian adults and contextualized these findings within a global comparative framework. Methods: A total of 100 healthy adults were recruited from four Mongolian regions. Fecal samples were analyzed using species-resolved shotgun metagenomics, and dietary intake was assessed through a standardized food frequency questionnaire. Alpha- and beta-diversity metrics, differential abundance tests, and diet-microbe correlations were performed on members of the Bifidobacterium species. To assess the broader significance of the Mongolian Bifidobacterium profile, Shannon diversity was further compared against a curated global dataset comprising 1286 healthy adults from 29 countries using harmonized bioinformatic and statistical pipelines. Results: Shannon diversity within the Bifidobacterium genus was significantly higher in nomadic Mongolians, particularly those from Khuvsgul and Dundgobi, and strong geographic structuring was observed in beta-diversity analyses (PERMANOVA, p < 0.001). Nomadic populations showed higher relative abundances of B. adolescentis and B. angulatum, whereas B. pseudocatenulatum predominated in Ulaanbaatar. Although overall Bifidobacterium abundance was lowest in Bulgan, B. longum remained the dominant species in this region. Spearman correlation analysis with false discovery rate correction identified significant associations between dairy intake and specific Bifidobacterium species. Homemade yogurt and traditional dairy intake were positively associated with B. angulatum. B. catenulatum was positively associated with homemade yogurt, traditional dairy, and total fermented dairy intake, whereas factory milk intake was negatively associated with B. angulatum but positively associated with B. pseudocatenulatum. Mongolia ranked among the top eight of 30 countries for Bifidobacterium Shannon diversity though total Bifidobacterium abundance showed substantial inter-individual and regional variation. Conclusions: Mongolian adults exhibit relatively high Bifidobacterium diversity at both national and global scales. Traditional dairy consumption was associated with species-specific variation in Bifidobacterium composition, supporting the contribution of dietary practices to regional gut microbiota patterns.},
}

Humans
*Bifidobacterium/classification/genetics/isolation & purification
Mongolia
Adult
Male
Female
*Dairy Products
Feces/microbiology
*Gastrointestinal Microbiome
*Diet
Middle Aged
Young Adult

@article {pmid42739046,
year = {2026},
author = {Szabó, J and Maróti, G and Solymosi, N and Andrásofszky, E and Tuboly, T and Bersényi, A and Bruckner, G and Fébel, H},
title = {Effects of Dietary Glucose, Fructose, and Monosaccharide-to-Lard Energy Ratios on Cecal Microbiota Composition and Ecological Organization in Rats.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42739046},
issn = {2072-6643},
mesh = {Animals ; *Fructose/administration & dosage/pharmacology ; *Cecum/microbiology ; Male ; *Glucose/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Monosaccharides/administration & dosage/pharmacology ; *Dietary Fats/administration & dosage ; Rats, Sprague-Dawley ; *Dietary Carbohydrates/administration & dosage ; Bacteria/classification ; Diet ; Energy Intake ; },
abstract = {Background: Although dietary fat and carbohydrates are major determinants of gut microbiota composition, their interactive effects across changing dietary monosaccharide-to-lard energy ratios remain incompletely understood. This study descriptively examined treatment-level cecal microbiome profiles across dietary gradients in which lard (L) was progressively replaced with glucose (G) or fructose (F). Methods: A carbohydrate-free, lard-rich control diet was formulated, and lard was progressively replaced with glucose or fructose while maintaining a constant protein-to-energy ratio. Cecal contents from eight rats per dietary group were pooled in equal amounts, yielding one composite microbiome sample per treatment. Pooled samples were characterized by shotgun metagenomic sequencing. Sequencing/classified read counts (CRs) and relative abundance (RA) were treated as complementary sequencing-derived representations rather than measures of absolute bacterial abundance. Microbiome outcomes were interpreted descriptively at the treatment level. Results: Across the pooled treatment profiles, CRs and RA showed non-linear patterns and did not consistently change in parallel, providing complementary descriptions of treatment-level taxonomic responses. CR patterns indicated a combined effect of L and monosaccharide content, with several mixed L-monosaccharide diets showing lower CRs than both the L6.03 reference and the lard-free endpoints. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions, although their magnitude and direction varied among taxa. Hierarchical clustering and exploratory correlation networks provided complementary descriptions of treatment-level community organization. Conclusions: The pooled treatment-level microbiome profiles revealed non-linear responses to changing dietary L-monosaccharide composition, with CRs and RA providing partly different information on taxonomic patterns. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions.},
}

Animals
*Fructose/administration & dosage/pharmacology
*Cecum/microbiology
Male
*Glucose/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Rats
*Monosaccharides/administration & dosage/pharmacology
*Dietary Fats/administration & dosage
Rats, Sprague-Dawley
*Dietary Carbohydrates/administration & dosage
Bacteria/classification
Diet
Energy Intake

@article {pmid42739393,
year = {2026},
author = {Wang, H and Hao, R and Gao, X and Yang, W and Ma, Q and Zhang, L and Zheng, R and Wu, H},
title = {Genotype-Specific Interactions Between Wheat and Rhizosphere Microbiome Under Drought Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42739393},
issn = {2223-7747},
support = {2022YFD1200902-02//China National Center for Biotechnology Development/ ; },
abstract = {Drought severely limits global wheat production, and plants can mitigate this stress by recruiting beneficial rhizosphere microbiomes. However, the role of host genotype in shaping this recruitment and influencing microbial inoculant efficacy is poorly understood. Here, we aimed to elucidate the interplay among host genotype, drought stress, and inoculation with Trichoderma citrinoviride. A factorial pot experiment investigated the responses of two wheat genotypes (JN 14-95, constitutively drought-tolerant; JN 72, drought-responsive) to water regimes and inoculation with T. citrinoviride. Metagenomic analysis was performed to characterize rhizosphere bacterial community structure and functional potential. Host genotype was the primary driver of bacterial community structure (42.3% of variation), exceeding water stress (23.8%) and inoculation (11.5%). JN 14-95 adopted a "physiological autonomy" strategy with constitutive high root-to-shoot ratio and inferred enrichment of auxin and SOD biosynthesis genes. JN 72 employed a "microbial outsourcing" strategy, enriching beneficial bacteria (Pseudomonas, Bacillus, Streptomyces) and showing inferred enrichment of central carbon metabolism genes. T. citrinoviride amplified these genotype-specific responses, increasing the total dry matter by 21.3% in JN 14-95 and 30.3% in JN 72 under drought. Our findings suggest a need to move from uniform inoculation practices toward genotype-informed microbiome management. The two strategies provide a framework for leveraging host genetics in sustainable agriculture, highlighting that breeding and microbiome management should be integrated.},
}

@article {pmid42739503,
year = {2026},
author = {Jiang, S and Ye, S and Wang, Y and Zhu, H and Wu, Y and Li, Z and Hang, J and Li, X and Yin, Y and Lu, Q and Guo, X},
title = {Performance Profiles of Short DNA Barcode Segments for Family Level Detection of Asteraceae Within Asterales.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
pmid = {42739503},
issn = {2223-7747},
support = {32372124//National Natural Science Foundation of China/ ; 82504949//National Natural Science Foundation of China/ ; YLS-2026-ZY01016//Yuelu Mountain Laboratory Project/ ; 2024M750883//China Postdoctoral Science Foundation/ ; 2026M792817//China Postdoctoral Science Foundation/ ; 2025JJ60641//Hunan Provincial Natural Science Foundation of China/ ; 2025JJ40024//Hunan Provincial Natural Science Foundation of China/ ; 2026JJ60385//Hunan Provincial Natural Science Foundation of China/ ; H20250813//National Foreign Experts Program/ ; },
abstract = {Short DNA barcodes may facilitate sequence recovery from degraded material, but their ability to retain target-family identity while excluding related taxa varies among genomic regions. We computationally evaluated 16 nuclear, plastid, and mitochondrial marker regions from 11 Asterales families using 279,956 NCBI locus-record matches and an accession-disjoint discovery/test design. Thirty-one candidate segments of 50-200 bp (mean, 98.55 bp) were screened in discovery data and evaluated for within-Asteraceae sequence recall, differentiation from non-Asteraceae Asterales, in silico primer behavior, phylogenetic placement, and exploratory matching across 808 metadata-defined metagenomic samples. Conserved regions such as matR and rbcL showed high within-Asteraceae identity, whereas ITS1, ITS, and trnH-psbA showed larger differences from related-family backgrounds; ITS2 and ycf1 showed intermediate profiles. Candidate segments were placed within or immediately adjacent to Asteraceae reference branches in segment-specific maximum-likelihood analyses, although support and topology varied among regions. Metadata-defined target-containing groups had higher mean query coverage and identity than background groups; because target presence was not independently verified and no classifier was fitted, these comparisons were descriptive and did not estimate diagnostic accuracy. Definitionally linked sequence statistics were interpreted as structural associations rather than evidence of causal evolutionary mechanisms. These results provide a family-level computational comparison of candidate short segments for Asteraceae detection within Asterales. Species identification, operational marker combinations, threshold robustness, and laboratory performance require validation using taxonomically dense, voucher-linked, and experimentally characterized datasets.},
}

@article {pmid42740607,
year = {2026},
author = {Lee, J and Minot, S and Dey, N},
title = {Pangenome analysis reveals both niche-specific "specialists" and microbial "side hustlers" in colorectal cancer microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2728331},
doi = {10.1080/19490976.2026.2728331},
pmid = {42740607},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; },
abstract = {The gut microbiome is reproducibly implicated in colorectal cancer (CRC), yet the inter-study and interpersonal variability of certain species associations suggests that CRC microbiomes may be defined by convergent functional states achievable by phylogenetically diverse organisms. Distinguishing lineage-conserved "specialists" from taxonomically diverse "side hustlers"-organisms whose shared functional traits are dispersed across phylogenetically distant lineages-offers complementary translational insights: "specialists" are primary candidates for lineage-targeted biomarkers and inhibitors, while the shared functional architecture of "side hustlers" may reveal high-priority potential therapeutic targets robust to inter-individual variability. Here, we quantify phylogenetic coherence (monophyly) of 3,711 co-associated gene bins (CAGs) across 13 bacterial species and evaluate CRC associations across three independent cohorts, identifying hundreds of CAGs associated with CRC or health across a spectrum of monophyly scores, indicating that both states harbor a mixture of "specialist" and "side hustler" gene content. Strikingly, in Faecalibacterium prausnitzii-a species with a complex relationship to CRC-health-associated CAGs exhibited significantly higher monophyly scores than CRC-associated CAGs, consistent with health-linked traits being lineage-conserved while CRC-linked traits behave as polyphyletically distributed, potentially mobile "side hustlers." Across multiple CRC-associated species, we observe functional convergence in gene bins encoding Type IV secretion systems (T4SS), TonB-dependent receptors, and RagB/SusD nutrient uptake proteins. Fusobacterium animalis strains encode T4SS elements across bins with variable phylogenetic origins, representing simultaneous "specialist" and "side hustler" strategies within a single species. Pairwise interaction analysis further reveals synergistic interspecies associations, including co-occurrence of F. animalis and Clostridium scindens gene bins associated with a CRC probability of > 90%, suggesting that microbial "side hustlers" may amplify oncogenic risk through ecological interactions invisible to species-level analysis. These findings provide proof-of-principle that an ecological and evolutionary lens on the CRC microbiome can identify shared functional vulnerabilities and lineage-specific targets for microbiome-based cancer prevention.},
}

*Colorectal Neoplasms/microbiology
Humans
Phylogeny
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics

@article {pmid42741071,
year = {2026},
author = {Zhaxi, D and Yu, C and Wang, J and Yang, D and Wang, Z and Yang, W and Zhang, Y and Yang, C and Li, Z},
title = {Multi-omics reveals the associations between cecal candidate bacteria and muscle fatty acid composition variations in Daheng and Luning chickens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1907226},
pmid = {42741071},
issn = {1664-302X},
abstract = {INTRODUCTION: Accumulating evidence underscores the profound impact of the gastrointestinal ecosystem on skeletal muscle lipid dynamics.

METHODS: This study was designed to investigate the systemic associations connecting the gut microbiota, intermediate metabolomes, and intramuscular fatty acid (FA) deposition in chicken.

RESULTS: Phenotypic and lipophilic profiling revealed distinct FA compositions between Daheng chickens (DHC) and Luning chickens (LNC), with DHC exhibiting significantly higher concentrations of 26 distinct FAs including flavor-precursor MUFAs (C18:1n9c) and functional omega-3 (n-3) PUFAs (C20:5n3 and C22:5n3) within the leg muscle. High-throughput metagenomic sequencing subsequently identified positive correlations between dominant cecal bacterial taxa and these specific muscle FAs. Concurrently, multi-compartment metabolomics mapped a spectrum of differential metabolites spanning the cecum, serum, and leg muscle, which were fundamentally enriched in the "cysteine and methionine metabolism" and "pantothenate and CoA biosynthesis" pathways. Through an integrative multi-omics framework paired with statistical mediation modeling, we identified a candidate functional axis: the Agathobaculum-Collinsella-Enorma consortium strongly co-varies with muscle FA deposition, a process bridged by key intermediate nodes including Pyruvic acid, S-adenosylmethionine, and Spermine.

CONCLUSION: Collectively, these findings suggest that the gut microbiota is closely coupled with muscle lipid composition via a structured gut-metabolite-muscle axis, offering candidate microbial markers for precision management of meat quality in poultry production.},
}

@article {pmid42741165,
year = {2026},
author = {Yao, H and Haire, A and Wang, Z and Ge, T and Liu, Y and Hou, M and Cui, W},
title = {Analysis of differences in gut microbiota structure and function in Bactrian camels under different breeding patterns from northern and southern Xinjiang, China.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1892252},
pmid = {42741165},
issn = {2297-1769},
abstract = {INTRODUCTION: The lactating Xinjiang Junggar camel is a major dairy breed with excellent milk production performance. In northern Xinjiang, camels are mainly reared under traditional grazing, while those in southern Xinjiang are raised under barn feeding due to grassland scarcity.

METHODS: Nine lactating camels aged 6-7 years old and nine juvenile camels aged 8 months old were selected from each region. Fresh fecal samples were collected from the rectum of each camel for metagenomic sequencing analysis.

RESULTS: The findings indicated that the diversity and abundance of gut microbiota in the BJT group were significantly increased compared with those in the NJT group. Furthermore, the diversity and abundance of gut microbiota in adult lactating camels from both regions were superior to those in juvenile camels. Among the gut microbiota, Actinomycetota, Campylobacterota, Ascomycota, and Thermoplasmatota presented significantly higher relative abundance in the BJT group than in the NJT group (p < 0.05). The relative abundance of Acinetobacter and Halomonas was also significantly elevated in the BJT group, whereas Escherichia and Prevotella were significantly less abundant. Furthermore, the relative abundance of Bifidobacterium and Lactobacillus declined significantly in adult lactating camels compared to that in juvenile camels. There were notable differences in the functional annotations of metabolic pathways, suggesting that the gut microbiota in the BJT group was primarily engaged in nitrogen cycling, decomposition of various organic compounds, and fatty acid metabolism, which were linked to nutrient metabolism, detoxification, and biosynthesis. In contrast, the gut microbiota in the NJT group was associated with such functions as cell recognition, signal transduction, and immune response. Glycoside Hydrolases and Glycosyltransferases constituted the primary carbohydrate-active enzymes within the gut microbiota in Bactrian camels, and they were conducive to the degradation of plant cellulose.

DISCUSSION: Since the intestines of juvenile camel are in the developmental stage, the genera Bifidobacterium and Lactobacillus potentially play significant roles in intestinal maturation. Notably, the gut microbiota in Bactrian camels from northern Xinjiang are characterized by high relative abundance of microorganisms that are halophilic and involved in crude fiber degradation. In contrast, Bactrian camels under barn feeding in southern Xinjiang exhibit higher abundance of the genera Escherichia and Prevotella, implying geographical and feeding conditions are associated with the variations in gut microbiota variations.},
}

@article {pmid42741189,
year = {2026},
author = {Liu, D and Morikawa, S and Izumi, R and Kurozumi, S and Kiyose, M and Shimizu, M},
title = {Effect of different chitosan molecular weights on microplastic excretion.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1869140},
pmid = {42741189},
issn = {2296-861X},
abstract = {INTRODUCTION: Microplastic (MP) ingestion poses a considerable health risk to organisms, including humans, and the environment. The previously established average molecular weight of chitosan that promotes MP excretion is approximately 800,000; however, the effects of chitosan with different molecular weights on MP excretion and the intestinal environment remain unclear. This study aimed to clarify the effects of different chitosan molecular weights on MP excretion and gut microbiota.

METHODS: Sprague-Dawley rats were fed a diet containing MPs with an average particle size of 50 μm.

RESULTS: Compared with the control group, fecal weight increased in all chitosan groups across different molecular weights (low: 83,000; medium: 673,000; high: 1,877,000). Furthermore, the medium and high molecular weight chitosan groups exhibited a significantly higher MP excretion rate and lower MP retention rate in the gastrointestinal tract. The 16S rRNA metagenomic analysis revealed a decrease in Firmicutes and an increase in Bacteroidota and Proteobacteria abundance in the high-molecular-weight chitosan group. Additionally, the abundance of beneficial bacterial genera, such as Akkermansia and Bacteroides, increased. These findings confirm that chitosan with ≥673,000 molecular weight promotes MP excretion. Additionally, chitosan intake may help protect the intestinal environment by improving gut microbiota.},
}

@article {pmid42741332,
year = {2026},
author = {Wang, QH and Liu, YF and Wang, B and Xiao, Q and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Oil composition determines microbial preference for carbon source between hydrocarbons and Necromass in water droplets within crude shale oil.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag242},
pmid = {42741332},
issn = {2730-6151},
abstract = {Water droplets entrapped in crude oil have recently been recognized as unexpected but metabolically active microbial habitats in shale oil reservoirs. However, the key environmental drivers that shape the community composition and metabolic profiles of these droplet microorganisms remain poorly understood. Here, we investigated three shale oil samples from Jiangsu oilfield, all of which contained abundant water droplets (>10[5] droplets/ml oil) of ancient formation water origin. Integrated microscopy, metagenomics, and metabolomics revealed that the physicochemical properties of the enclosing oil, primarily API gravity and viscosity, are associated with droplet size and may influence the droplet microbiomes. These factors appear to jointly drive a fundamental metabolic dichotomy, where in light oil with low-salinity water, communities are enriched with hydrocarbon degraders together with molecular signatures of active petroleum hydrocarbon metabolism. In more viscous, light-to-medium oil with high-salinity water, however, communities shift towards necromass recycling and strong genetic adaptations to osmotic stress. Our findings demonstrate that microbial life in water droplets enclosed in shale oil is widely found in the shale oil reservoirs examined, and selected by carbon quality and environmental pressure. This study provides a mechanistic framework for understanding microbial ecology and biogeochemical processes in shale oil reservoirs and offers insights for microbial enhanced oil recovery in heavy oil reservoirs.},
}

@article {pmid42741704,
year = {2026},
author = {Jiang, Y and Zeng, Q and Ma, L and He, Y and Zhu, S and Xiong, Y and Jing, Y and Zhang, Q and Qi, S and Hu, J and Li, Q and Yang, S},
title = {Gut microbiome dysbiosis is associated with aldosterone overproduction in idiopathic hyperaldosteronism.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117426},
pmid = {42741704},
issn = {2589-0042},
abstract = {Idiopathic hyperaldosteronism (IHA) is a significant cause of secondary hypertension. Emerging evidence links the gut microbiota to endocrine and cardiovascular diseases. We integrated human genetics, multi-omics, and fecal microbiota transplantation (FMT) to investigate the association between IHA and gut microbiome. Two-sample Mendelian randomization identified seven bacterial taxa associated with IHA. Metagenomic analysis of 30 patients with IHA and 30 healthy control subjects revealed lower microbial diversity and depletion of protective genera identified by Mendelian randomization. Plasma metabolomics showed alterations in tryptophan metabolism and other metabolic pathways that overlapped with microbial functional changes. Tryptophan-derived metabolites correlated with the abundance of protective genera. FMT from patients with IHA increased serum aldosterone and elevated 5-hydroxy-L-tryptophan in germ-free mice. These findings support an association between gut microbiome dysbiosis, metabolic alterations, and aldosterone dysregulation, highlighting the gut microbiome as a potential target for the diagnosis and treatment of IHA.},
}

@article {pmid42741729,
year = {2026},
author = {Zhang, H and Kang, Z and Ning, K},
title = {Foundation Models for Microbiome Research: From Sequence Semantics to Community Dynamics and Multimodal World Models.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {7},
number = {3},
pages = {e70046},
pmid = {42741729},
issn = {2641-6573},
abstract = {Microbiome sequencing has advanced faster than microbiome understanding. Although large-scale 16S, metagenomic, metatranscriptomic, and proteomic datasets have accumulated rapidly, most analyses remain cohort-specific and association-driven, limiting mechanistic insight, cross-study transferability, and robustness to technical confounding. Foundation models offer a new computational framework by learning reusable biological representations from large unlabeled datasets. In this Review, we present microbiome foundation models as a hierarchy spanning biological scales. Sequence-centric models capture the syntax and semantics of DNA and proteins for taxonomic inference, functional annotation, and generative design. Community-centric models learn ecological structure from abundance profiles, while addressing compositionality, sparsity, and the unordered nature of microbial communities. Emerging multimodal frameworks integrate sequence-derived functional potential with community-level ecological dynamics under host and environmental context. We discuss key design choices, including tokenization, representation granularity, self-supervised objectives, and evaluation strategies, and highlight challenges in interpretability, domain shift, causal reasoning, and biological validation. Finally, we propose a transition from static representation learning toward intervention-aware microbiome world models capable of simulation, digital twinning, and generative microbiome engineering.},
}

@article {pmid42741868,
year = {2026},
author = {Dong, X and Hu, X and Hu, K and Li, Z and Wang, W},
title = {Nutrient Transfer Hypothesis for the Fluctuation and Regional Variation of Microbial Diversity in the Pacific Ocean.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70427},
doi = {10.1111/1462-2920.70427},
pmid = {42741868},
issn = {1462-2920},
support = {25FV0CWZ02//Fujian Ocean Innovation Center/ ; 42577318//National Natural Science Foundation of China/ ; T2017002//Fundamental Research Funds for the Central University and 111 Program/ ; },
mesh = {Pacific Ocean ; *Biodiversity ; *Seawater/microbiology/chemistry ; *Nutrients/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Food Chain ; Metagenomics ; },
abstract = {Microbial diversity affects marine biogeochemical cycles and sustainability. However, the processes and feedbacks that control the spatial and temporal trends in species diversity and functional gene diversity remain largely unknown at the global marine scale. We analysed 1582 marine metagenomic samples and 19 variables related to marine climate and microbial community dynamics. Over the past 12 years, marine microbial species diversity has significantly decreased across the surface ocean, especially in the Pacific. The greatest decrease reached 24.29% in the central region of the North Pacific Ocean (NPO). We propose a food chain-based nutrient transfer hypothesis in which a decrease in grazing intensity is associated with a decrease in microbial diversity. This hypothesized relationship was further examined using 27 years of independent time series data from a Pacific site. The Pacific Ocean presented high sensitivity to grazing intensity coupled with environmental fluctuations of < 5%, in which species diversity in the NPO and South Pacific Ocean (SPO) regions changed from -9.62% to 13.02% and from -8.38% to 15.03%, respectively. The incorporation of nutrient transfer concepts to reduce the unpredictable uncertainty in marine biogeochemical cycles and ecological stability related to microbial diversity is urgent, especially in the vulnerable Pacific Ocean.},
}

Pacific Ocean
*Biodiversity
*Seawater/microbiology/chemistry
*Nutrients/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Food Chain
Metagenomics

@article {pmid42742016,
year = {2026},
author = {Chen, JX and Wu, HH and Feng, S and Wang, C and Han, Y and Liu, S and Zheng, P and Ji, XN and Chen, Q},
title = {[Clinical characteristics of intracranial suppurative infections caused by Streptococcus intermedius in 4 children].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {64},
number = {10},
pages = {1147-1152},
doi = {10.3760/cma.j.cn112140-20260611-00465},
pmid = {42742016},
issn = {0578-1310},
abstract = {Objective: To investigate the clinical features, therapeutic strategies, and outcomes of intracranial suppurative infections caused by Streptococcus intermedius (S. intermedius) in children. Methods: A case series study was conducted involving 4 children diagnosed with central nervous system (CNS) infections attributed to S. intermedius at the Capital Center for Children's Health, Capital Medical University from January 2020 to January 2026. Their demographics, clinical presentations, laboratory findings, neuroimaging features, microbiological results, treatment regimens, and prognoses were reviewed. Results: Among 4 children 3 were male and 1 was female, aged 10-15 years. All 4 children presented acutely with fever and headache as the initial symptoms; 3 children presented with vomiting, 2 children with drowsiness and seizures. Cerebrospinal fluid (CSF) analysis showed elevated white blood cell counts in all 4 children, elevated protein levels in 3 children. Brain MRI revealed sinusitis in all 4 children, with predominant right-sided involvement. All intracranial suppurative lesions were adjacent to the right-sided sinus inflammatory foci, including multiple brain abscesses in 1 child, subdural empyema in 2 children, and concurrent brain abscess with subdural empyema in 1 child. S. intermedius was confirmed in all 4 children via various microbiological methods: metagenomic next-generation sequencing (mNGS) of subdural pus in 1 child, targeted NGS (tNGS) of CSF in 1 child, culture of deep sinus pus obtained intraoperatively in 1 child, and both culture and tNGS of brain abscess pus in the remaining child. All 4 children received comprehensive treatment, including targeted antimicrobial therapy, anticonvulsant therapy, intracranial pressure reduction management, and multidisciplinary surgical interventions including craniotomy with abscess excision, burr-hole drainage of subdural empyema, and endoscopic sinus surgery. One child developed secondary hemophagocytic lymphohistiocytosis during the disease course. After a follow-up period of 1.5-5.5 years, all 4 children achieved clinical recovery, resumed normal academic and daily activities, and exhibited no significant neurological sequelae. Conclusions: Pediatric intracranial infections caused by Streptococcus intermedius primarily affecting older children and adolescents. These infections are highly associated with adjacent infectious foci, particularly sinusitis, and exhibiting a propensity for localized abscesses or empyema formation. Timely and targeted antibiotic therapy coupled with surgical intervention is associated with favorable prognosis in this population.},
}

@article {pmid42742021,
year = {2026},
author = {Liu, Y and Zhang, M and Gu, BY and Xu, XY and Wang, K and Ji, W and Guo, Y and Gao, W and Zhang, HB and Dong, W and Zheng, JH and Zhang, H and Liu, TL},
title = {[Clinical analysis of infectious endocarditis in children with concomitant septic pulmonary embolism].},
journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics},
volume = {64},
number = {10},
pages = {1179-1184},
doi = {10.3760/cma.j.cn112140-20260601-00426},
pmid = {42742021},
issn = {0578-1310},
support = {2023ZZ02024//Shanghai Research Center for Pediatric Cardiovascular Diseases/ ; },
abstract = {Objective: To analyze the clinical characteristics, diagnosis, and treatment of infectious endocarditis (IE) with septic pulmonary embolism (SPE) in children. Methods: A case series study was conducted. Clinical data of 10 children with IE complicated by SPE admitted to the Department of Cardiovascular Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine from January 2023 to September 2025 were analyzed. The detection rates of three pathogen detection methods, including blood culture, metagenomic next-generation sequencing (mNGS), and vegetation culture, were compared. The clinical diagnosis, treatment, and follow-up outcomes were summarized. Results: Among the 10 children, there were 3 males and 7 females, with an age at presentation of 8.5 (6.6, 11.0) years. Congenital heart disease was present in 9 cases, and intracardiac implants were present in 4 cases. The main clinical manifestations included fever in 10 cases, cough in 4 cases, dyspnea in 4 cases, and chest pain in 3 cases. Six cases had dental caries. A total of 10 pathogens were detected in 9 children, including 2 fungi, 7 bacteria, and 1 Coxiella burnetii. Blood culture was positive in 7 cases, mNGS was positive in 8 cases, and vegetation culture was positive in 4 cases. Echocardiography revealed right-sided vegetations in all cases, and cardiac CT angiography showed multiple pulmonary lesions, including pulmonary artery filling defects, patchy opacities, and streaky shadows. Nine children underwent surgical treatment, and the duration of antimicrobial therapy was 3.0 (2.5, 8.0) months. Under multidisciplinary management, 4 cases were cured, 5 cases improved, and 1 case was under control at discharge. After 6 months of follow-up, pulmonary lesions resolved in 9 cases, and valvular regurgitation improved in 8 cases. Conclusions: Embolization of right-sided IE vegetations is an important cause of SPE in children. Adjunctive mNGS testing, when required, contributes to a higher pathogen detection yield in patients with IE.For right-sided IE, early surgical intervention is often required in addition to antimicrobial therapy.},
}

@article {pmid42742206,
year = {2026},
author = {Boldogkői, Z and Tombácz, D},
title = {The canine gut microbiome as a translational model for human health and aging.},
journal = {mBio},
volume = {},
number = {},
pages = {e0195126},
doi = {10.1128/mbio.01951-26},
pmid = {42742206},
issn = {2150-7511},
abstract = {The domestic dog is increasingly recognized as a complementary translational model for microbiome research relevant to human health while also offering direct benefits for veterinary medicine. Dogs share environments and dietary exposures with humans and show substantial taxonomic and gene-content similarity to the human gut microbiome, although the apparent degree of similarity depends strongly on whether read recruitment, gene-catalog overlap, or functional overlap is assessed. Dogs also develop spontaneous chronic enteropathies, obesity-associated metabolic dysfunction, cancers, cognitive dysfunction, and behavioral disorders in which gut microbial changes can be examined under clinically realistic conditions. Their shorter, breed- and body-size-dependent lifespan permits repeated sampling across development, aging, disease progression, and treatment within practical timeframes. Breed structure, full-sibling cohorts, controlled dietary interventions, and access to clinically indicated samples from multiple anatomical compartments can strengthen selected study designs, although they do not provide the tighter genetic, environmental, and microbial control achievable in rodents. Here, we evaluate the research questions for which canine cohorts are especially informative, synthesize evidence linking canine and human disease-associated microbiomes, and critically assess aging, causal inference, and One Health applications. Major limitations include the need for breed and body-size stratification, heterogeneous diet and husbandry, incomplete treatment histories, the lack of routinely available gnotobiotic canine systems, and gaps in canine-specific reference resources. The canine system is therefore most informative when study designs exploit its clinical realism while acknowledging the tighter experimental control offered by reductionist models, positioning the dog as a complementary rather than a universally superior model.},
}

@article {pmid42742264,
year = {2026},
author = {Keller-Costa, T and Tignat-Perrier, R and Marques, M and Ferrier-Pagès, C and Pogoreutz, C},
title = {Symbiotic interactions and climate change implications of the octocoral microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag246},
pmid = {42742264},
issn = {1751-7370},
abstract = {Octocorals are vital components of tropical, temperate, and cold-water benthic marine ecosystems. Their associated microbiomes, comprising microeukaryotes, prokaryotes, and viruses, are increasingly recognised as central to host health, nutrient cycling, and chemical defence. Metagenomics and amplicon sequencing have uncovered taxonomic and functional complexity within these microbial communities, revealing patterns of host specificity and health status, along with seasonality and geographic structuring. However, anthropogenic stressors, particularly those associated with global climate change, exert intense pressure on coral-dominated ecosystems, leading to complex and poorly understood local and regional patterns of octocoral expansion and mortality. Microbial interactions may be a main driver of these contrasting outcomes by mediating the ecological resilience of octocorals to environmental stress. We synthesise the current state of research on the diversity, organisation, and function of the octocoral microbiome, and identify critical knowledge gaps on octocoral holobionts relative to scleractinian corals. Our meta-analysis of 79 publicly available bacterial genomes from octocorals reveals group-specific specialisation in denitrification and nitrate assimilation, along with widespread capacities for essential amino acid, cofactor, and vitamin production, suggesting important contributions to nutrient cycling in the holobiont. While sampling efforts between cultured and uncultured lineages are even, our genomic survey reveals strong sampling bias toward the Atlantic Ocean, temperate gorgonians, and healthy host states, whereas bacterial genomes representing the pathobiome, tropical and/or deep-sea regions, and other octocoral taxa remain underrepresented. Accordingly, we propose future research directions to advance understanding of octocoral microbiome ecology and its role in the resilience of tropical, temperate and cold-water coral reefs.},
}

@article {pmid42742644,
year = {2026},
author = {Dhiman, K and Devi, M and Kumar, A and Pandey, SS and Dkhar, J},
title = {Characterization of culturable endophytes and microbial communities in the rhizosphere and pitcher fluid of the carnivorous plant Nepenthes khasiana.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42742644},
issn = {1432-072X},
support = {MLP-202//Council of Scientific and Industrial Research, India/ ; SRG/2020/001139 (GAP 273) and EEQ/2022/000015 (GAP 318)//Science and Engineering Research Board/ ; },
mesh = {*Rhizosphere ; *Endophytes/isolation & purification/classification/genetics ; *Bacteria/isolation & purification/classification/genetics ; *Fungi/isolation & purification/classification/genetics ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota ; Phylogeny ; *Carnivorous Plant/microbiology ; Metagenomics ; *Caryophyllales/microbiology ; },
abstract = {Endophytes colonize plant tissues through roots and shoots without causing harm and can move throughout the plant via its vascular system. However, little is known about culturable endophytes, particularly bacteria, in pitcher plants, and their possible entry through pitcher fluid remains unexplored. To address this gap, we isolated endophytes from the pitcher plant Nepenthes khasiana, and performed metagenomic analysis of its rhizospheric soil and pitcher fluid, from which bacteria and fungi were also isolated, to investigate the possible origin of these endophytes. We found that culturable endophytic bacteria were predominantly associated with roots and seeds, whereas endophytic fungi were more abundant across the N. khasiana pitcher. Although most endophytes were restricted to specific tissues, some exhibited a broader distribution across nearly the entire plant. Several OTUs from the rhizospheric soil matched endophytes at the genus level, including some that were also detected in the pitcher fluid. Specifically, three bacterial genera - Enterobacter, Staphylococcus and Bacillus - and one fungal genus, Cladosporium, detected in the pitcher fluid, matched the isolated endophytes. These findings suggest that endophytes in N. khasiana most likely originate from the rhizosphere, with possible migration into the pitcher fluid.},
}

*Rhizosphere
*Endophytes/isolation & purification/classification/genetics
*Bacteria/isolation & purification/classification/genetics
*Fungi/isolation & purification/classification/genetics
Soil Microbiology
Plant Roots/microbiology
*Microbiota
Phylogeny
*Carnivorous Plant/microbiology
Metagenomics
*Caryophyllales/microbiology

@article {pmid42742736,
year = {2026},
author = {Sheoran, N and Gogoi, R and Venkadasamy, G and Vijayan, V and Kumar, N and Jat, SL and Rakshit, S and Kumar, A},
title = {Recurrent and niche-specific functional bacteriome of maize hybrid revealed by integrated metabarcoding and culturomics.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42742736},
issn = {1432-072X},
mesh = {*Zea mays/microbiology ; Soil Microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Microbiota ; DNA Barcoding, Taxonomic ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Rhizosphere ; },
abstract = {The plant microbiome plays a pivotal role in plant survival in natural habitats by facilitating nutrient acquisition, stress adaptation, and disease suppression, while also offering opportunities to enhance crop productivity and climate resilience. However, the distribution of persistent and culturable bacteriome across maize-associated niches and their functional potential remain poorly resolved. This study integrated metagenomic next-generation sequencing (mNGS-based metabarcoding) and culturomics to characterise the maize-associated bacteriome of bulk soil, rhizoplane, phylloplane, and cob of the maize hybrid PHM-1 under contrasting cropping and tillage systems, and to identify recurrent and agriculturally promising bacteriome components. The bacteriome exhibited pronounced niche-specific structuring, whereas overall bacterial community composition did not differ significantly across cropping and tillage treatments (ANOSIM, R = 0.038, p = 0.306). Proteobacteria predominated in the culturable bacteriome (69-84%; mean, 76.2%) but accounted for only 1% of the total bacteriome, whereas Patescibacteria and Firmicutes were relatively enriched. Niche-specific dominance was evident, with Pantoea accounting for 40.79% of the total and 56.27% of the culturable phylloplane bacteriome under cereal monocropping, while Serratia represented 31.59% and 59.40% of the total and culturable cob bacteriomes, respectively. Across niches, mNGS captured substantially greater bacteriome diversity, particularly uncultured and unidentified taxa in soil-associated compartments, whereas culturomics recovered a narrower but functionally accessible fraction. Culturomics yielded 99 isolates representing 32 species across 12 genera, including six genera shared with the mNGS-derived recurrent bacteriome: Bacillus, Enterobacter, Pantoea, Pseudomonas, Serratia, and Stenotrophomonas. Functional screening identified strong biocontrol and plant-beneficial traits among core-associated isolates. Pseudomonas oryzihabitans ZM-DL-PA10 inhibited Rhizoctonia solani, Macrophomina phaseolina, and Bipolaris maydis by up to 40.6%, 43.9%, and 45.2%, respectively, through secreted and volatile metabolites; exhibited P, K, and Zn solubilisation; and produced IAA and siderophores. It also recorded the lowest B. maydis disease index (ADI) of 1.00. Pantoea ananatis ZM-BH-EA4 showed 52.4% and 68.5% inhibition of R. solani and B. maydis, respectively, through volatile metabolites. Collectively, the integration of mNGS and culturomics revealed a strongly compartmentalised maize bacteriome and identified recurrent, culturable, and functionally promising bacterial taxa, providing a targeted resource for microbiome-based crop protection and climate-resilient maize production.},
}

*Zea mays/microbiology
Soil Microbiology
*Bacteria/classification/isolation & purification/genetics/metabolism
*Microbiota
DNA Barcoding, Taxonomic
Metagenomics
High-Throughput Nucleotide Sequencing
Rhizosphere