@article {pmid42685249,
year = {2026},
author = {Zhang, B and Xu, X and Zhang, M and Qi, B and Ma, H and Yan, P and Lens, PNL and Shi, W},
title = {Free Ammonia Stress Rewires Microbial Signaling Networks and Constrains Metabolic Cooperation in Oxygenic Photogranules.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag225},
pmid = {42685249},
issn = {1751-7370},
abstract = {Free ammonia (FA) is a prevalent chemical inhibitor in wastewater ecosystems, yet its ecological impacts on microbial communication and cooperation remain poorly understood. Here, we demonstrated that FA stress restructured the community function of oxygenic photogranules (OPGs) by rewiring signaling-associated regulatory networks and redirecting cellular energy allocation. Temporal profiling of extracellular signaling molecules and intracellular regulatory molecules, integrated with metagenomic and metatranscriptomic analyses, revealed a concentration-dependent reconfiguration of microbial signaling. Under low FA exposure (≤ 1.0 mg/L), diffusible signal factor (DSF)- and indole-3-acetic acid (IAA)-associated pathways were more active, coinciding with photogranules consolidation and efficient nitrogen removal. At moderate FA stress (5.0 mg/L), the regulatory landscape shifted toward acyl-homoserine lactone (AHL)-associated signaling and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)-mediated intracellular regulation, consistent with enhanced aggregation and stress adaptation. In contrast, severe FA stress (25.0 mg/L) broadly attenuated signaling-associated pathways, weakened metabolite cross-feeding networks, impaired energy generation, and increased maintenance-related energetic demands. Under these constraints, microbial populations appeared to shift from cooperative metabolism toward self-maintenance-oriented carbon metabolism, evidenced by activation of the carbon-efficient glyoxylate shunt. Collectively, these findings suggest that FA-induced signaling disruption constrains microbial cooperation through cellular energy limitation, highlighting energy allocation as a key determinant of microbial social stability in phototrophic wastewater microbiomes.},
}

@article {pmid42685266,
year = {2026},
author = {Colajanni, A and Uricaru, R and Darko, S and Subramanian, R and Douek, DC and Thiébaut, R and Thebault, P},
title = {Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag454},
pmid = {42685266},
issn = {1477-4054},
mesh = {Humans ; *Microbiota/genetics ; Benchmarking ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; },
abstract = {Human RNA sequencing (RNA-seq) data originally generated for human transcriptome profiling are overwhelmingly dominated by host sequences, yet they often contain a small fraction of non-human reads that can be exploited for microbial detection. When such datasets are repurposed for secondary microbiome-oriented analyses, extracting and accurately classifying this weak microbial signal becomes technically challenging, and no ready-to-use pipeline currently exists. In this study, we evaluate computational strategies for filtering host reads and classifying microbial transcripts in host-dominated RNA sequencing data. We compare assembly-based approaches similar to those used in a previous study focusing on microbial translocation with state-of-the-art assembly-free methods, and assess their respective strengths and limitations using simulated datasets reflecting low microbial abundance. Our results show that assembly-based methods yield accurate taxonomic predictions but struggle at low read depth, whereas assembly-free methods are more robust in sparse settings at the cost of reduced precision. To leverage the complementarity of both approaches, we propose a hybrid pipeline that integrates assembly-based and assembly-free classification. On simulated data, this hybrid strategy improves microbial classification performance compared with either approach alone. Application to a real human metatranscriptomic dataset analyzed in a microbial translocation context illustrates the broader microbial signal captured by the hybrid approach, despite intrinsic challenges related to the absence of reliable ground truth and the risk of host read misclassification. Our work provides a framework for extracting microbial signals from host-dominated human metatranscriptomes, enabling the reuse of existing transcriptomic datasets for microbiome-related analyses, including but not limited to microbial translocation studies.},
}

Humans
*Microbiota/genetics
Benchmarking
*Transcriptome
*Gene Expression Profiling/methods
Sequence Analysis, RNA/methods
*Computational Biology/methods

@article {pmid42685579,
year = {2026},
author = {Hartono, S and Røder, HL and Boeren, S and Swarts, DC and Abee, T and Smid, EJ and van Mastrigt, O},
title = {Stressostat cultivation of Lactococcus lactis improves lactate stress resistance through mutations in RNA polymerase.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128706},
doi = {10.1016/j.micres.2026.128706},
pmid = {42685579},
issn = {1618-0623},
abstract = {Adaptive laboratory evolution is used to improve the phenotypes of microorganisms and to characterise the mechanisms underlying resistance against complex growth inhibition. Here we focused on lactic acid bacteria (LAB) as starter cultures for food fermentations. Production of LAB starter cultures is challenging due to growth inhibition by organic acids, mainly lactate, produced during fermentation. By utilising stressostat cultivation we generated Lactococcus lactis isolates with enhanced lactate resistance. Using a combination of (meta)genomics, proteomics and pH-controlled batch fermentations, we deciphered the lactate resistance mechanisms of these L. lactis isolates. Proteome responses of L. lactis, combined with similar growth inhibition at high salt, suggest that high lactate mainly causes osmotic stress. We identified RNA polymerase (RNAP) mutations in subunits β (rpoB) and β' (rpoC) as key mutations, causing pleiotropic effects in the proteome. These proteome adaptations are linked to enhanced lactate resistance, particularly the resistance to hyperosmotic stress in absence of glycine-betaine. Combined, our study shows that RNAP mutations enhanced lactate resistance through pleotropic effects in the proteome that changed L. lactis responses against multiple stresses.},
}

@article {pmid42685687,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Chang, K and Li, S and Zhang, Y and Yu, H and Wang, C and Yao, X and Chen, S and Nie, X and Zhao, J and Lu, B and Li, Y and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {The human oral and airway viral genome catalog from metagenomes enables virome characterization informing respiratory health.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {101269},
doi = {10.1016/j.medj.2026.101269},
pmid = {42685687},
issn = {2666-6340},
abstract = {BACKGROUND: Viral communities of the upper aerodigestive tract represent an important component of the human microbial ecosystem but remain poorly characterized due to the limited availability of habitat-specific reference resources.

METHODS: We integrated 19,997 public and 2,673 newly sequenced oral and airway metagenomes to establish the Oral and Airway Viral Genome Catalogue (OAVGC). Viral genomes were reconstructed and characterized through taxonomic assignment, prokaryotic host prediction, functional annotation, and assessment of putative antibacterial activity. Our prospective longitudinal aging cohort, alongside 5 in-house datasets and publicly cohorts, were analyzed to investigate associations between airway virome profiles and respiratory health.

FINDINGS: The OAVGC comprised 141,459 high-quality viral genomes (completeness ≥90%) clustered into 68,708 viral operational taxonomic units (vOTUs). Approximately half of these viruses and families are previously undescribed, with independent cross-cohort detection and PCR assays providing additional support for their occurrence. Across multiple respiratory infection cohorts, the virome exhibited convergent diversity reductions and compositional signatures. In the prospective cohort, the baseline airway virome was correlated with host lung function and geriatric health scores. Virome-based machine learning classifiers demonstrated potential for predicting the future occurrence of upper respiratory tract infections up to 12 months in advance, outperforming bacteriome-based models in our prediction analyses.

CONCLUSIONS: The OAVGC provides an unprecedented genomic and functional resource for investigating the ecological and clinical associations of the oral-airway virome, revealing its potential impact on respiratory health and capacity to predict future infections.

FUNDING: National Natural Science Foundation of China (82341113) and National Key R&D Program of China (2022YFA1304303).},
}

@article {pmid42685930,
year = {2026},
author = {Babenkova, PI and Golovina, NA and Reprintseva, VN and Karaulova, SO and Vostrikova, AD and Burakova, IY and Pogorelova, SV and Smirnova, YD and Morozova, PD and Shutikov, VA and Mikhailov, EV and Kozin, SV and Dzhimak, SS and Gureev, AP and Syromyatnikov, MY},
title = {Comenic acid as a modulator of the gut-testis axis in pyridaben-induced toxicity.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {},
number = {},
pages = {109342},
doi = {10.1016/j.reprotox.2026.109342},
pmid = {42685930},
issn = {1873-1708},
abstract = {Pyridaben is an acaricide that inhibits mitochondrial complex I, which disrupts mitochondrial viability and causes oxidative stress. Pyridaben administration was associated with significant damage to mitochondrial DNA (mtDNA) in mice. The oxidative stress related to pyridaben exposure also co-occurred with alterations in the morphology of the testes and intestines, leading to the activation of the Nrf2-dependent protective pathway in testicular tissue, reduction of the seminiferous tubule lumen accompanied by interstitial tissue swelling, and adaptive changes in the intestinal epithelial tissue. Comenic acid (CA) exhibits active antioxidant properties; in the group receiving CA, the mtDNA copy number increased. Functionally, pyridaben considerably reduced the alpha diversity of the intestinal microbiome, while CA administration appeared to normalize this indicator, also mitigating shifts in beta diversity. Taxonomic analysis revealed that pyridaben elevated the abundance of the families Bacteroidaceae and Muribaculaceae, which aligned with a functional upregulation of endotoxic dTDP-β-L-rhamnose and L-lysine biosynthesis pathways. Conversely, CA treatment attenuated these shifts, reducing opportunistic taxa while concurrently upregulating protective pathways, including folate transformations and CDP-diacylglycerol biosynthesis. These findings suggest that CA, potentially due to its antioxidant properties and modulation of the intestinal microbial and functional profiles, may exert a compensatory effect against pyridaben-induced toxicity via the gut-testis axis.},
}

@article {pmid42685938,
year = {2026},
author = {Zhao, Z and Zhou, J and Li, H and Yu, C and Zhou, L and Luo, Z and Wang, Y and Liang, D and Li, W and Yang, J},
title = {Modulating bile acid isomerization and brain distribution by multiflorin A mitigates neuroendocrine stress and ameliorates anxiety-like behavioral alterations.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {122338},
doi = {10.1016/j.jep.2026.122338},
pmid = {42685938},
issn = {1872-7573},
abstract = {Bile acids (BAs) have long been recognized in traditional ethnic medicines as a regulator of emotion and mental states; however, the underlying biological mechanisms by which BAs influence neuropsychological functions remain largely unclear. Multiflorin A (MA), an acetylated flavonoid glycoside and the signature bioactive constituent of Pruni Semen, is believed to ameliorate psychological stress via targeting the bile system.

AIM OF THE STUDY: This study aimed to investigate alterations in bile acid metabolism and distribution in SPS-induced PTSD-associated anxiety-like behavioral alterations and the therapeutic effects of MA and ursodeoxycholic acid (UDCA).

MATERIALS AND METHODS: SPS-stressed mice exhibiting anxiety-like behaviors were treated with MA. Behavioral tests, histopathology, targeted BAs metabolomics, metagenomics, neurotransmitter profiling, proteomics, and immunofluorescence were performed. UDCA was used as a reference compound to explore the involvement of BAs in MA-mediated neuroprotective effects.

RESULTS: SPS exposure induced anxiety-like behavioral deficits, accompanied by dysregulation of systemic BAs homeostasis, characterized by peripheral BAs depletion, central accumulation of hydrophobic BAs, partial blood-brain barrier disruption, and synaptic impairment. MA and UDCA treatment significantly improved behavioral performance, alleviated histopathological damage, and partially restored gut microbiota composition and BAs profiles, including increased levels of isomerized bile acids such as UDCA and alloLCA. These changes were accompanied by restoration of tight junction, PSD-95 expression, and neurotransmitter balance. Proteomics showed partial reversal of SPS-induced synaptic and neurotransmitter dysregulation, consistent with reduced neural hyperexcitability.

CONCLUSION: MA may ameliorate PTSD-associated anxiety-like behavioral alterations through modulation of the gut microbiota-bile acid-brain interactions, supporting a role for BAs metabolism in neuropsychiatric regulation.},
}

@article {pmid42687165,
year = {2026},
author = {Wang, Y and Wang, L and Cai, Z and Yu, L and Guo, Y and Zhang, L and Zhu, M and Liu, Z and Zhao, Y and Liu, L and Cao, A},
title = {Comparison of clinical efficacy and gut microbiota characteristics in children with ASD treated with fecal microbiota transplantation and ketogenic diet.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42687165},
issn = {1471-244X},
mesh = {Humans ; *Diet, Ketogenic ; *Fecal Microbiota Transplantation ; Female ; Male ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/therapy/microbiology/diet therapy ; Child ; Child, Preschool ; Treatment Outcome ; },
abstract = {OBJECTIVE: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and interaction, along with restricted, repetitive patterns of behavior. It is often accompanied by gastrointestinal dysfunction and gut microbiota dysbiosis. Fecal Microbiota Transplantation (FMT) and the Ketogenic Diet (KD) are interventions targeting the gut microbiota for ASD.

METHODS: 30 participants were diagnosed with ASD according to DSM-5 and ADOS-2. ASD core symptoms were evaluated with CARS and ABC. Gut microbiota composition was analyzed by shotgun metagenomic sequencing.

RESULTS: Both groups demonstrated significant improvements in core symptoms. In the FMT group, the mean CARS score significantly decreased from 34.87 to 33.53 (p < 0.01); in the KD group, it declined from 35.13 to 33 (p < 0.01). The mean ABC score reduced from 79.93 to 69.33 (p = 0.064) in the FMT group and from 63.07 to 42.73 (p < 0.01) in the KD group. Following the intervention, no statistically significant changes were observed in α-diversity or β-diversity within either group. LEfSe analysis revealed distinct post-intervention microbial signatures: FMT significantly enriched butyrate-producing taxa (Wujia chipingensis, Eubacterium sp. MSJ-33, and Butyrivibrio crossotus), while KD elevated Blautia massiliensis and decreased propionate metabolism -associated taxa (Veillonella sp. S12025-13 and Veillonella nakazawae). KEGG enrichment analysis revealed that KD enriched propionate metabolism (Fold enrichment = 3.747, q = 0.010) and aromatic compound degradation (Fold enrichment = 3.591, q = 0.010).

CONCLUSIONS: Both interventions significantly improved clinical symptoms among children with ASD, potentially through distinct patterns of gut microbiota modulation.

CLINICAL TRIALS NUMBER: NCT06348433 (03/21/2024).},
}

Humans
*Diet, Ketogenic
*Fecal Microbiota Transplantation
Female
Male
*Gastrointestinal Microbiome
*Autism Spectrum Disorder/therapy/microbiology/diet therapy
Child
Child, Preschool
Treatment Outcome

@article {pmid42687643,
year = {2026},
author = {Jeon, D and Unno, T},
title = {Long-read sequencing reveals putatively mobilizable resistance genes and multi-drug resistance plasmids underestimated by short-read metagenomics.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {8},
pages = {e2605007},
doi = {10.71150/jm.2605007},
pmid = {42687643},
issn = {1976-3794},
support = {RS-2025-02633155//Rural Development Administration/ ; },
mesh = {Animals ; *Metagenomics/methods ; Cattle ; *Plasmids/genetics ; Swine ; Humans ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Drug Resistance, Multiple, Bacterial/genetics ; Metagenome ; },
abstract = {While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms (Illumina, Oxford Nanopore, and PacBio HiFi) and seven assembly strategies on gut metagenomes from cattle, pig, and human as case studies. Long-read assemblies recovered 5- to 7-fold more plasmid sequence than Illumina in cattle and pig (mean 17.0 Mb vs. 3.1 Mb), while Illumina performed comparably in the less diverse human gut where high per-species coverage enabled effective short-read plasmid assembly. Long reads also detected more resistance genes on plasmid contigs. Hybrid assembly results depended on the algorithm: scaffolding-based OPERA-MS preserved long-read contiguity and recovered more plasmid-borne resistance genes, while the short-read-centric metaSPAdes hybrid mode produced fragmented assemblies. After collapsing haplotype redundancy, PacBio HiFi identified 2 and 49 unique multi-drug resistance plasmid lineages in cattle and pig, respectively. On the other hand, only 2 and 4 were identified from Illumina. Long reads also placed far more ARGs in a putative mobilization context (50-73%) compared to 14-21% for short reads. Platform and assembly strategy are thus key variables in mobilome and resistome characterization and should be accounted for in antimicrobial resistance surveillance.},
}

Animals
*Metagenomics/methods
Cattle
*Plasmids/genetics
Swine
Humans
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
*Drug Resistance, Multiple, Bacterial/genetics
Metagenome

@article {pmid42687714,
year = {2026},
author = {Velsko, IM and Hübner, A and Fagernäs, Z and Yates, JAF and Mann, AE and Hofman, CA and Ozga, AT and Lewis, CM and Speller, C and Fiddyment, S and Francken, M and Wahl, J and Krause, J and Radini, A and King, T and Warinner, C},
title = {The Oral Microbiome of King Richard III of England.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70350},
pmid = {42687714},
issn = {2692-7691},
support = {//Werner Siemens Stiftung/ ; //Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy/ ; //Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM)/ ; //Max Planck Society/ ; },
mesh = {Humans ; *Microbiota/genetics ; England ; *Dental Calculus/microbiology/history ; DNA, Ancient/analysis ; History, 15th Century ; *Mouth/microbiology ; History, Medieval ; History, Ancient ; Phylogeny ; Metagenome/genetics ; },
abstract = {OBJECTIVES: Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452-1485).

MATERIALS AND METHODS: Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of nearly 400 million reads. The metagenomic data were taxonomically profiled and compared to new and previously published dental calculus metagenomes from England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Sequencing data were de novo assembled, and metagenome-assembled genomes assigned to the genus Tannerella were investigated for phylogenetic relatedness and virulence. Putative dietary DNA was assessed for authenticity.

RESULTS: The dental calculus of King Richard III was well-preserved and yielded an exceptionally high quantity of DNA. Oral microbiome species diversity fell within the range previously observed among other northern European populations, suggesting that a royal lifestyle and a rich diet did not substantially impact his oral microbiota. The reconstructed Tannerella genomes contained many virulence factors found today among oral Tannerella species. No putative dietary DNA could be authenticated.

DISCUSSION: The dental calculus of King Richard III produced one of the richest ancient oral metagenomes published to date, yet the species diversity was indistinguishable from that of commoners living in northern Europe over the last 7000 years. Insufficient plant and animal DNA were recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA even when exceptionally well-preserved.},
}

Humans
*Microbiota/genetics
England
*Dental Calculus/microbiology/history
DNA, Ancient/analysis
History, 15th Century
*Mouth/microbiology
History, Medieval
History, Ancient
Phylogeny
Metagenome/genetics

@article {pmid42688005,
year = {2026},
author = {Guo, Z and Qi, H and Zhang, Q and Wang, Y and Du, Y},
title = {Severe co-infection with influenza A virus H3N2 and community-acquired methicillin-susceptible Staphylococcus aureus in a child presenting with septic shock, acute respiratory distress syndrome, and necrotizing pneumonia: a rare case report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1941945},
pmid = {42688005},
issn = {2235-2988},
mesh = {Humans ; Male ; *Pneumonia, Necrotizing/microbiology/diagnosis/complications ; *Influenza, Human/complications/virology ; *Shock, Septic/microbiology/diagnosis ; *Coinfection/microbiology/virology ; *Respiratory Distress Syndrome/microbiology/diagnosis ; *Influenza A Virus, H3N2 Subtype/isolation & purification ; Anti-Bacterial Agents/therapeutic use/adverse effects ; *Staphylococcus aureus/drug effects/isolation & purification ; *Staphylococcal Infections/complications/microbiology ; Community-Acquired Pneumonia ; Linezolid/therapeutic use/adverse effects ; Community-Acquired Infections/microbiology/complications ; Extracorporeal Membrane Oxygenation ; Pneumonia, Staphylococcal ; },
abstract = {BACKGROUND: Influenza co-infection with Staphylococcus aureus (S. aureus) can cause rapidly fatal necrotizing pneumonia, septic shock, and acute respiratory distress syndrome (ARDS) in children. Although methicillin-resistant S. aureus is often highlighted, community-acquired methicillin-susceptible S. aureus (CA-MSSA) can also produce equally severe disease.

CASE PRESENTATION: We report an 8-year-4-month-old male with influenza A (H3N2) who developed septic shock and refractory hypoxemia, requiring immediate intubation. Due to persisting respiratory failure despite maximal ventilation, veno-venous extracorporeal membrane oxygenation (VV-ECMO) was initiated on day 1. Metagenomic next-generation sequencing identified S. aureus as the dominant pathogen, and bronchoalveolar lavage fluid culture later confirmed MSSA. After vancomycin failed clinically, the regimen was switched to linezolid. However, on day 15 of linezolid therapy, the patient developed severe linezolid-induced lactic acidosis (LILA), which resolved within 3 days of stopping the drug. The clinical course was further complicated by pneumothorax and multidrug-resistant organism superinfections. After 54 days of intensive care, the patient was discharged in good condition.

CONCLUSION: This case underscores that during influenza seasons, early empirical anti-staphylococcal therapy should be considered in children with rapidly progressive pneumonia and shock, even when CA-MSSA is suspected. Additionally, routine lactate monitoring is critical during linezolid therapy to enable prompt recognition and management of life-threatening LILA.},
}

Humans
Male
*Pneumonia, Necrotizing/microbiology/diagnosis/complications
*Influenza, Human/complications/virology
*Shock, Septic/microbiology/diagnosis
*Coinfection/microbiology/virology
*Respiratory Distress Syndrome/microbiology/diagnosis
*Influenza A Virus, H3N2 Subtype/isolation & purification
Anti-Bacterial Agents/therapeutic use/adverse effects
*Staphylococcus aureus/drug effects/isolation & purification
*Staphylococcal Infections/complications/microbiology
Community-Acquired Pneumonia
Linezolid/therapeutic use/adverse effects
Community-Acquired Infections/microbiology/complications
Extracorporeal Membrane Oxygenation
Pneumonia, Staphylococcal

@article {pmid42688072,
year = {2026},
author = {Chen, J and Chen, X and Yu, W and Chen, T and Liu, Z and Hu, J},
title = {Multi-omics integration identifies a gut-microbiota-associated plasma metabolite signature for alzheimer disease diagnosis and metabolic pathway targeting.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1933454},
pmid = {42688072},
issn = {1663-9812},
abstract = {BACKGROUND: Alzheimer's disease (AD) is the leading cause of dementia, with early diagnosis remaining constrained by the invasiveness and limited accessibility of current biomarkers. The gut-brain axis has emerged as a critical communication network linking intestinal homeostasis with central nervous system function, yet the diagnostic utility of gut-microbiota-associated circulating metabolites in AD remains largely unexplored.

METHODS: In this case-control study, 85 participants (37 AD patients and 48 cognitively normal controls) were enrolled. Targeted plasma metabolomics using four complementary UPLC-MS/MS assays covering 375 endogenous metabolites was integrated with fecal metagenomic sequencing in 72 participants with paired samples. Differential metabolites were screened using the Mann-Whitney U test, orthogonal partial least squares discriminant analysis, and fold-change thresholds. Gut-microbiota-associated plasma metabolites were defined through Spearman correlation with linear discriminant analysis effect size-identified differential bacterial species. A diagnostic panel was constructed using least absolute shrinkage and selection operator logistic regression with stability selection, and its performance was evaluated by support vector machine with repeated cross-validation, with age and sex evaluated as covariates.

METHODS: We identified 27 differential plasma metabolites enriched in tricarboxylic acid cycle and amino acid metabolic pathways. Correlation analysis identified 10 gut-microbiota-associated plasma metabolites significantly associated with gut microbial alterations. A three-metabolite panel (citric acid, 3-hydroxyoctanoic acid, and glyoxylic acid) achieved a cross-validated area under the curve of 0.865, with a modest sensitivity of 62.2% and specificity of 100.0%, positioning it as a confirmatory auxiliary tool rather than a broad screening instrument. The panel score correlated negatively with Mini-Mental State Examination scores (r = -0.544, P < 0.001), and integration with clinical cognitive assessment yielded an area under the curve of 0.978.

CONCLUSION: These findings potentially advance the translational understanding of the gut-brain metabolic axis in neurodegeneration and support the exploratory clinical utility of microbiota-linked peripheral metabolic signatures as non-invasive auxiliary diagnostic tools for AD, awaiting external validation in larger, multi-center cohorts.},
}

@article {pmid42688151,
year = {2026},
author = {Cai, S and Xu, X and Sun, X and Luo, Q and Chen, W and Wang, X and Zhu, J and Liu, Y and Xiao, L and Zhang, H and Zou, Y and Zhong, Y},
title = {Alleviation of allergic rhinitis symptoms in an animal model by Lactiplantibacillus plantarum BGI-N6.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1923543},
pmid = {42688151},
issn = {1664-3224},
mesh = {Animals ; *Probiotics/therapeutic use ; Disease Models, Animal ; *Rhinitis, Allergic/immunology/therapy/microbiology ; Rats ; *Lactiplantibacillus plantarum/immunology ; Cytokines/blood ; *Gastrointestinal Microbiome/immunology ; Nasal Mucosa/immunology/pathology ; Male ; },
abstract = {Allergic rhinitis (AR) is a chronic inflammatory disease with rising global prevalence and a substantial public health burden. Current treatments have limited efficacy and tolerability, highlighting the need for new strategies. Probiotics represent a promising approach due to their ability to modulate gut microbiota and host immunity. Here, we investigated the preventive potential of Lactiplantibacillus plantarum BGI-N6 in an OVA/ALUM-induced AR rat model. BGI-N6 administration alleviated AR symptoms and nasal mucosal pathology, reduced key allergic mediators, shifted serum immunoglobulin and cytokine levels toward normal, and restored the Th1/Th2/Th17/Treg balance. Metagenomic sequencing of cecal contents showed that these effects were accompanied by expansion of Bacteroidota-affiliated SCFA-producing taxa, restoration of microbial functional capacity, and identification of 41 core functional genes (KEGG Orthologues) consistently shifted across all three dose groups, with Bacteroides showing the strongest enrichment. Correlation analyses further connected these microbial shifts with immune parameters. These findings support BGI-N6 as a probiotic intervention for AR and implicate gut microbiota remodeling as a central correlate of probiotic-induced immunomodulation.},
}

Animals
*Probiotics/therapeutic use
Disease Models, Animal
*Rhinitis, Allergic/immunology/therapy/microbiology
Rats
*Lactiplantibacillus plantarum/immunology
Cytokines/blood
*Gastrointestinal Microbiome/immunology
Nasal Mucosa/immunology/pathology
Male

@article {pmid42688251,
year = {2026},
author = {Li, L and Liu, R},
title = {Metagenomic sequencing reveals structural and functional differentiation of the rhizosphere bacterial communities associated with available potassium in Atractylodes lancea affected with root rot.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1923567},
pmid = {42688251},
issn = {1664-302X},
abstract = {BACKGROUND: Atractylodes lancea is an economically valuable medicinal herb indigenous to China, and its yield and quality are severely threatened by root rot disease. The rhizosphere microenvironment plays a critical role in plant health. Yet, its relationship with root rot in A. lancea is poorly understood.

METHODS: This gap was addressed by collecting rhizosphere soils from healthy A. lancea plants and those infected with root rot. The physicochemical properties of the soil were determined, and metagenomic sequencing was performed to determine differences in the diversity, structure, composition, and functional characteristics of the rhizosphere bacterial communities between the two groups.

RESULTS: Compared with healthy plants, the contents of total nitrogen, total potassium, and available potassium in the rhizosphere soil of diseased plants increased significantly, by 8.11, 3.42, and 38.66%, respectively. Concurrently, the bacterial community diversity increased significantly, and the community structure exhibited an obvious separating trend between the two groups, with a marginally non-significant difference (P = 0.098). Pseudomonadota, Streptomyces, and Trinickia were relatively more abundant in the healthy group, while Acidobacteriota, Cyanobacteriota, Gemmatimonadota, Gemmatimonas, and Sphingomicrobium were significantly enriched in the diseased group according to independent samples Student's t-tests (P < 0.05). LEfSe analysis (LDA score > 4) revealed that all the differential genera in the healthy group belonged to the Burkholderiaceae family within Pseudomonadota. Functional prediction demonstrated that rhizosphere bacteria of healthy plants were predominantly enriched for genes involved in ABC transporter pathways, whereas diseased samples were enriched for secondary metabolite biosynthesis alongside significantly elevated abundance of auxiliary oxidoreductase genes. The abundance of auxiliary oxidoreductase genes was also significantly higher in the diseased group. Redundancy and correlation analyses showed that available potassium was strongly correlated with the divergence in the composition and function of the rhizosphere bacterial community.

CONCLUSIONS: This study revealed that the occurrence of root rot was associated with imbalanced physicochemical properties of rhizosphere soil, shifts in bacterial community composition and structure, and alterations in metabolic functions of A. lancea. These findings elucidate rhizosphere responses linked to root rot and inform the sustainable cultivation of A. lancea.},
}

@article {pmid42688289,
year = {2026},
author = {Buzgó, L and Freytag, C and Göbhardter, D and Laczkó, L and Miló, L and Holub, L and Hanczvikkel, A and Ungvári, E and Majoros, L and Kamotsay, K and Papp, K and Kristóf, K and Kardos, G and Tóth, Á},
title = {Coexistence of carbapenemase and hypervirulence-associated genes among Klebsiella pneumoniae high-risk clones in Hungary.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1870558},
pmid = {42688289},
issn = {1664-302X},
abstract = {INTRODUCTION: Strains of Klebsiella pneumoniae carrying hypervirulence and carbapenemase genes represent a rapidly emerging global public health threat. Our study aimed to comprehensively characterise the genomics of hypervirulence-associated and carbapenemase genes carrying K. pneumoniae (hv(a)CpKp) isolates in Hungary.

MATERIALS AND METHODS: Between January 2022 and April 2024, 89 aerobactin (iucA-D/iutA)-positive non-duplicate carbapenemase-producing K. pneumoniae isolates from 15 Hungarian healthcare institutes underwent short-read (Illumina, MiSeq, NextSeq) whole-genome sequencing, followed by detailed plasmid analysis using long-read sequencing (Nanopore, MinION) in a representative subset of 32 strains.

RESULTS: Most isolates (79/89) belonged to the high-risk clone ST147. Hypervirulence-associated (hva) genes-including rmpA/rmpA2, peg344, shiF, iucA-D, and iutA-were universally present, and 59 isolates possessed chromosomally integrated yersiniabactin loci. Most isolates (87/89) carried the bla NDM-1 carbapenemase gene. Hypervirulence-associated genes were most frequently (29/32) associated with IncHI1B/IncFIB(Mar) plasmids. Notably, we identified plasmids carrying both hva and carbapenemase genes-designated as hybrid plasmids-in 13 of 32 strains. The bla NDM-1 was linked to the IS26 transposase and was present in conserved, identical cassettes on all bla NDM-1-carrying plasmids.

DISCUSSION/CONCLUSION: Our study identified hv(a)CpKp strains, particularly the ST147 clone, circulating in Hungary. Our findings highlight the need for routine virulence gene monitoring and continuous genomic and plasmid-based surveillance to mitigate the clinical and epidemiological impact of emerging hv(a)CpKp lineages.},
}

@article {pmid42688585,
year = {2026},
author = {Liu, S and Huang, L and Xiao, S and Li, Y and Luo, S and Hou, E and Zhang, Y and Jin, M and Wang, Y and Zong, X},
title = {Astaxanthin Alleviates Intestinal Ferroptosis through Gut Commensal Lepagella muris-Mediated Retinoic Acid Production and SLC7A11 Activation.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1421},
pmid = {42688585},
issn = {2639-5274},
abstract = {Intestinal epithelial injury is increasingly linked to ferroptosis, yet how dietary bioactives engage the gut microbiota to restrain this process remains largely unresolved. Here, astaxanthin (ASTA) was identified as a microbiota-engaged regulator of intestinal ferroptosis and lipid peroxidation. ASTA markedly ameliorated dexamethasone-induced intestinal injury, and this protection was closely associated with the attenuation of epithelial ferroptosis. Depletion of the gut microbiota largely abolished the protective effect of ASTA, establishing the gut microbiota as an essential mediator of its intestinal bioactivity. Microbiome and metabolome profiling further revealed that ASTA reshaped the microbial metabolic landscape, with retinol metabolism emerging as a dominant pathway linked to ferroptosis resistance. Among the altered metabolites, retinoic acid was identified as a pivotal ASTA-associated metabolite that connected microbial remodeling with the restoration of epithelial anti-ferroptosis capacity. Metagenomics combined with in vitro bacterial metabolic assays identified Lepagella muris as a candidate ASTA-responsive bacterium capable of contributing to retinoic acid production. Mechanistically, retinoic acid protected intestinal epithelial cells from ferroptosis and barrier disruption through activation of SLC7A11, thereby reinforcing the anti-ferroptosis defense system. This study moves beyond the conventional view of ASTA as a direct antioxidant and reveals a microbiota-enabled redox metabolic mechanism that may be therapeutically exploited for ferroptosis-associated diseases.},
}

@article {pmid42688840,
year = {2026},
author = {Li, J and Liu, Y and Gao, T and Ding, H and Hu, R and Wang, Y and Wu, B},
title = {Progress in interventions for vaginal microecology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1888581},
pmid = {42688840},
issn = {2235-2988},
mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota ; *Probiotics/administration & dosage/therapeutic use ; *Dysbiosis/therapy/microbiology ; Prebiotics/administration & dosage ; Synbiotics/administration & dosage ; },
abstract = {A balanced vaginal microbiome is fundamental to reproductive and gynecologic health, yet dysbiosis is common and clinically consequential. This narrative review synthesizes recent advances in microecological interventions, including probiotic, prebiotic, and synbiotic regimens; combination therapies; and vaginal microbiota transplantation. We place a particular focus on emerging delivery platforms like hydrogel-based carriers, which improve probiotic viability, mucosal adhesion, and controlled release. The review also explores how metagenomic analysis is refining community state typing, identifying pathogenic consortia, and enabling data-driven patient stratification and response monitoring. Despite these advances, key challenges remain, such as strain selection, functional validation, colonization durability, heterogeneous clinical endpoints, and clear regulatory pathways for live biotherapeutics. Future priorities must include developing functionally defined strain consortia, standardizing clinical outcomes, integrating multi-omics with biomaterials engineering, and conducting rigorous multicenter trials to deliver durable, safe, and truly individualized therapies.},
}

Humans
*Vagina/microbiology
Female
*Microbiota
*Probiotics/administration & dosage/therapeutic use
*Dysbiosis/therapy/microbiology
Prebiotics/administration & dosage
Synbiotics/administration & dosage

@article {pmid42689786,
year = {2026},
author = {Zhen, Y and Xia, J and Qiu, YY and Guo, J and Jiang, F},
title = {Prophage Activation as an Overlooked Mechanism Underlying the Biocidal Effect of Free Nitrous Acid in Sewers.},
journal = {Environmental science & technology},
volume = {60},
number = {34},
pages = {24165-24176},
doi = {10.1021/acs.est.6c01580},
pmid = {42689786},
issn = {1520-5851},
support = {SML2024SP024//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 52425001//National Science Fund for Distinguished Young Scholars/ ; U23A2049//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Nitrous Acid ; *Prophages ; *Sewage/microbiology ; Desulfovibrio vulgaris/drug effects ; },
abstract = {Biogenic hydrogen sulfide produced in sewer systems causes odor nuisance and concrete corrosion, necessitating effective biocidal control. Free nitrous acid (FNA) has emerged as a promising biocide, but its unclear mechanisms complicate dosage optimization and risk assessment. Here, using Desulfovibrio vulgaris as a model lysogenic bacterium, we demonstrate that low-dose FNA (0.2-4.0 mg N/L) induces bacterial inactivation via prophage activation-associated lysis in addition to chemical oxidation. Reactive nitrogen species (RNS) scavenging tests revealed that RNS-mediated oxidative stress was closely associated with prophage activation. Activated phages further infected new hosts, reducing the viability of freshly cultured D. vulgaris cells by 25.7% and increasing total phage production 15.2-fold. The phenomenon was further validated in real sewage biofilms, where increased phage production and decreased bacterial viability were observed at a low FNA dose of 0.2 mg N/L, below the dose required for cell destruction by chemical oxidation. Furthermore, metagenomic analysis of 896 sewage samples worldwide revealed that 71.9% of recovered sewage-derived microbial genomes harbor prophages, indicating a widespread genomic basis for prophage activation-mediated bacterial inactivation. Overall, this study expands current understanding of the biocidal mechanisms of FNA and contributes to the development of environmentally sustainable biocidal strategies.},
}

*Nitrous Acid
*Prophages
*Sewage/microbiology
Desulfovibrio vulgaris/drug effects

@article {pmid42689808,
year = {2026},
author = {Ruiz-Haddad, L and Shaw, DR and Ali, M and Pronk, M and van Loosdrecht, MCM and Samonina, O and Saikaly, PE},
title = {Genome-Resolved Metagenomics Revealed the Functional Potential of Core Novel and Known Genera Key to Processes in Full-Scale Aerobic Granular Sludge Plants.},
journal = {Environmental science & technology},
volume = {60},
number = {34},
pages = {24177-24193},
doi = {10.1021/acs.est.6c03437},
pmid = {42689808},
issn = {1520-5851},
support = {NA//Royal HaskoningDHV/ ; NA//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Sewage/microbiology ; Metagenomics ; Polyphosphates ; Wastewater ; },
abstract = {Microbial communities are critical for nutrient removal in aerobic granular sludge (AGS) wastewater treatment plants (WWTPs). Despite the stable long-term operation of full-scale AGS WWTPs, the microbial populations and functional traits sustaining stable long-term performance remain poorly resolved. To address this gap, the recovered MAG catalog from nine full-scale AGS WWTPs across five countries was analyzed. From this catalog, 74 high-quality core MAGs were identified and used for downstream taxonomic characterization and functional analyses. These high-quality core MAGs spanned 48 established and 7 novel genera, representing 31 known and 43 novel species. Functional analysis linked core MAGs to key WWTP processes: polyphosphate accumulation (9), glycogen accumulation (12), denitrification (62), and nitrification (1). These included four novel MAGs with glycogen-accumulating (3) and polyphosphate-accumulating (1) potential and 11 capable of nitrous oxide reduction, critical for mitigating greenhouse gas emissions. Ca. Phosphoribacter was the most abundant genus, highlighting its underestimated role caused by misclassification as Tetrasphaera in 16S rRNA surveys. Specifically, Ca. P. hodrii was the dominant species, exhibiting enhanced sugar uptake and amino acid synthesis as likely drivers of its enrichment in the AGS WWTPs. Overall, this study resolves for the first time the taxa and functional traits consistently enriched in full-scale AGS systems, enabling a shift from an empirical performance assessment toward biologically informed process interpretation.},
}

*Sewage/microbiology
Metagenomics
Polyphosphates
Wastewater

@article {pmid42690060,
year = {2026},
author = {Rahman, N and Rahman, ASMZ and Levin, DB and McAllister, TA and Cicek, N and Derakhshani, H},
title = {Optimizing a culture-enriched hybrid metagenomics pipeline to assess the AMR footprint of livestock manure in anaerobic digestate.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0247226},
doi = {10.1128/spectrum.02472-26},
pmid = {42690060},
issn = {2165-0497},
abstract = {The role of environmental samples from livestock production systems, including manure and anaerobic digestate, as reservoirs of antimicrobial resistance genes (ARGs) is likely underestimated because conventional metagenomic approaches can overlook low-abundance ARGs and often lack the resolution to associate these genes with their microbial hosts and co-localized mobile genetic elements (MGEs). We evaluated whether culture-enriched metagenomics (CEMG), with and without antibiotic selection, enhances ARG detection in anaerobic digestate and improves the resolution of ARG-MGE-host associations using hybrid short- and long-read metagenomic assembly. CEMG increased ARG recovery; mean ARG abundance rose from 15.4 counts per million (CPM) in metagenomic fresh digestate (FD) to 124 CPM in CEMG without antibiotics and 160 CPM in antibiotic-selective CEMG. In FD, only 9 unique ARGs were detected, whereas CEMG recovered 112, including ARGs of clinical importance, such as glycopeptide resistance, beta-lactamase genes, and the cfr 23S rRNA methyltransferase conferring cross-resistance to multiple antibiotic classes. Antibiotic selection induced targeted, class-specific shifts in ARG profiles, with ARGs associated with tetracycline resistance consistently enriched across treatments. Hybrid metagenomic assembly resolved the genomic context of 784 ARGs, of which 59.3% were co-localized with at least one class of MGEs, predominantly plasmids and integrative conjugative elements/integrative mobilizable elements. Biocide and metal resistance genes frequently co-occurred with ARGs on the same contigs. Together, these findings demonstrate that antibiotic-selective culture enrichment enhances resistome surveillance by improving detection of low-abundance ARGs, while hybrid assembly provides critical genomic context for assessing their mobility and host associations.IMPORTANCELivestock manure and its byproducts, such as anaerobic digestate, are recognized as important environmental reservoirs of antimicrobial resistance genes (ARGs) and resistant bacteria, yet current metagenomic approaches may underestimate this risk by failing to detect low-abundance but clinically relevant ARGs. Here, we show that integrating culture enrichment with hybrid metagenomics improves ARG recovery and reveals ARG co-localization with mobile genetic elements and putative bacterial hosts. This approach captures a cultivable and condition-responsive fraction of the resistome that is not readily accessible through direct metagenomic sequencing alone, providing a more informative framework for environmental AMR surveillance.},
}

@article {pmid42690065,
year = {2026},
author = {Langlois, A and Vincent, AT and Lauzon, K and Brouard, J-S and Bueno Dalto, D and Gagnon, N and Talbot, G and Lapointe, J and Poulin-Laprade, D},
title = {Characterization of the gut microbiome and resistome of piglets supplemented with low, moderate, and high concentrations of zinc oxide.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0005926},
doi = {10.1128/spectrum.00059-26},
pmid = {42690065},
issn = {2165-0497},
abstract = {UNLABELLED: The livestock sector is standing out for its substantial use of antimicrobials but is also investing in the development of mitigation strategies. Supranutritional concentrations of zinc (Zn) are served to piglets to prevent post-weaning diarrhea. This practice is detrimental to the piglet's assimilation of nutrients and can impact the environment through the excretion of unassimilated Zn, contributing to the persistence of antibiotic resistance by co-selection. In this study, the ileum and colon microbiome of piglets fed low (175 ppm), moderate (953 ppm), or high (2,991 ppm) concentrations of zinc oxide for 21 days after weaning were investigated using metagenomics and 16S rRNA amplicon sequencing. The pH and volatile fatty acids (VFA) were measured in cecum and colon. The colon resistome was investigated using metagenomics and PCR. The high Zn supplementation led to an increase in pH and a decrease in the VFA in both the cecum and colon. The bacterial diversity in colon was negatively impacted by the high Zn diet, with thriving Clostridiaceae and depletion of beneficial populations (e.g., Lactobacillaceae and Selenomonadaceae). Of concern, higher abundances of blaCTX-M and intI1 were observed in piglets fed with the moderate Zn diet. The findings from this study support the limitation of Zn to low concentrations.

IMPORTANCE: Developing alternatives to antibiotics is imperative to mitigate the global antimicrobial resistance crisis, particularly within the livestock sector, the predominant consumer of these agents. Yet, interventions introduced without due consideration may precipitate unintended consequences. In North American swine production, supranutritional zinc supplementation in pig feed has been adopted to prevent post-weaning diarrhea and sustain profitability. However, excessive zinc disrupts iron and copper metabolism and perturbs mitochondrial homeostasis, impairing energy metabolism, antioxidant defenses, and innate immunity. Moreover, high dietary zinc increases the excretion of this heavy metal, contributing to environmental pollution and fostering antibiotic-resistant bacteria through co-selection. This study provides further evidence supporting the restriction of zinc supplementation to nutritional needs, as supranutritional diets compromised the fermentative capacity of the pig gut microbiome and increased the frequency of clinically relevant antimicrobial resistance markers.},
}

@article {pmid42690073,
year = {2026},
author = {Fraley, AE and Rust, M and Wagner, M and Hipfinger, IR and Böhm, PJN and Dieterich, CL and Field, CM and Page, MJ and Owen, JG and Keyzers, RA and Sunagawa, S and Piel, J},
title = {Noncanonical Peloruside A Biosynthesis by an Uncultivated Verrucomicrobiota Symbiont.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e2011872},
doi = {10.1002/anie.2011872},
pmid = {42690073},
issn = {1521-3773},
support = {//Gordon and Betty Moore Foundation/ ; 205320_185077/SNSF_/Swiss National Science Foundation/Switzerland ; 10.002.732/SNSF_/Swiss National Science Foundation/Switzerland ; //Boehringer Ingelheim Fonds/ ; },
abstract = {Peloruside A, a polyketide macrolide identified in the marine sponge Mycale hentscheli, is a promising anticancer drug candidate due to its ability to stabilize tubulin at a nontaxoid binding site. Substantial efforts were made to improve the supply of this scarce substance through chemical synthesis and mariculture, however, sustainable production has yet to be achieved. Recent microbiome sequencing suggested that bacterial producers are responsible for all M. hentscheli bioactive compounds, but the identity of the peloruside producer remained unknown. Furthermore, a candidate peloruside polyketide synthase (PKS) was identified in silico, but its highly aberrant architecture prevented a confident biosynthetic prediction for the pharmacologically important exocyclic double bond. Here, we reveal an unusually complex modular PKS pathway comprising nonelongating ketosynthases (KSs), two internal thioesterases (TEs), and an acetyl coenzyme A ligase that orchestrate O-acetylation/elimination, acetyl-CoA recycling, and configurational proof-reading to facilitate selective Z-double bond incorporation. The first internal TE falls into a previously characterized O-acylating TE family but contains key amino acid substitutions that facilitate bifunctional acylation/elimination activity. Furthermore, we identified the peloruside producer as 'Candidatus Pelorusia occulta', a member of the biochemically underexplored Lentisphaeria class within the phylum Verrucomicrobiota. This work provides the biochemical and microbiological foundation for heterologous peloruside production.},
}

@article {pmid42690220,
year = {2026},
author = {Liu, B and Chen, W and Wang, Z and Wu, M and Zeng, Y and Zeng, A and Tang, B and Guo, Z and Yin, H},
title = {Bacillus smithii XT-3 inoculation reduces ammonia emissions and promotes humification during co-composting of Siraitia grosvenorii residue and pig manure.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/09593330.2026.2727073},
pmid = {42690220},
issn = {1479-487X},
abstract = {The co-composting of Siraitia grosvenorii residue and pig manure frequently faces challenges associated with substantial nitrogen loss and insufficient humification. To address these issues, the Bacillus smithii strain XT-3 was inoculated into the co-composting system to enhance nitrogen retention and promote humus formation during composting. The underlying mechanisms were further elucidated through metagenomic analysis. Inoculation with strain XT-3 reduced cumulative NH3 emissions by 27.8% and increased humic acid content by 17.02%. Temporal variations in humic substances presented a synchronous decline in fulvic acid coupled with humic acid accumulation, facilitating faster attainment of compost maturity thresholds. Furthermore, XT-3 reshaped the microbial community involved in nitrogen metabolism by enhancing the relative enrichment of Bacillota during the thermophilic stage and elevating the relative abundance of Pseudomonadota and Bacteroidota during the cooling stage, along with strengthened positive microbial interactions. Functional annotation of KEGG orthologs indicated that XT-3 improved the genetic potential of ammonia assimilation pathways throughout composting. Collectively, these findings demonstrate that XT-3 may facilitate synergistic nitrogen retention and enhanced humification by modulating microbial community structure, strengthening positive microbial interactions, thereby providing a theoretical basis for the precise regulation of functional microorganisms during composting.},
}

@article {pmid42690486,
year = {2026},
author = {Wen, Y and Luo, Z and Li, Z and Li, K and Li, J and Yin, S and Zou, Y and Zhang, H and Zhang, Y and Chen, K and Zhang, Y and Liu, S and Chen, Z and Yu, L and Ding, Y},
title = {Oral and gut microbiota profiles in patients with locally advanced rectal cancer with varying responses to neoadjuvant chemoradiotherapy.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42690486},
issn = {1438-7948},
support = {2023A0060//Science and Technology Plan Project of Jiangxi Provincial Administration of Traditional Chinese Medicine/ ; 2024A1515013292//Guangdong Basic and Applied Basic Research Fundation/ ; 2025A1515010567//Guangdong Basic and Applied Basic Research Fundation/ ; 2026A1515012094//Guangdong Basic and Applied Basic Research Fundation/ ; 32300085//National Natural Science Foundation of China/ ; 82504340//National Natural Science Foundation of China/ ; 82473567//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy/pathology ; *Neoadjuvant Therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Chemoradiotherapy ; Aged ; Feces/microbiology ; Saliva/microbiology ; },
abstract = {Recent research has focused on gut bacteria in colorectal cancer, but the influence of other microbiota, including oral and nonbacterial gut microbiota, on treatment efficacy remains insufficiently explored. This study aimed to investigate their relationship with the efficacy of neoadjuvant chemoradiotherapy (nCRT) in locally advanced rectal cancer (LARC). Saliva and fecal samples were collected from patients with LARC before treatment. Shotgun metagenomic sequencing was used to profile bacterial, archaeal, eukaryotic, and viral taxonomic groups and to examine oral and gut microbial functions. An artificial intelligence-based prediction model was developed by integrating oral and gut microbiome data with clinical information. Statistical analyses compared diversity and response-associated microbial features between responders and non-responders to nCRT. Response-associated differences were observed in bacterial and nonbacterial taxonomic profiles and in oral and gut microbial functional profiles. In the internal test subset, the integrated analysis yielded an observed AUC of 0.917. Given the small cohort and the exploratory comparison of candidate classifiers, this estimate requires confirmation in larger, independent cohorts. Baseline oral and gut microbiome profiles were associated with response to nCRT. Integrating microbiome and clinical features showed potential for response prediction, but the model remains exploratory and requires validation in larger, independent cohorts before clinical application. Retrospectively registered on 01/08/2026, NCT07346729.},
}

Humans
*Rectal Neoplasms/microbiology/therapy/pathology
*Neoadjuvant Therapy
*Gastrointestinal Microbiome/genetics
Male
Female
Middle Aged
*Chemoradiotherapy
Aged
Feces/microbiology
Saliva/microbiology

@article {pmid42691590,
year = {2026},
author = {Hou, J and Xu, GL and Tan, S and Mao, YL and Xin, YJ and Cheng, M and Cui, HL},
title = {Halolitoreus marinus gen. nov., sp. nov. and Halolitoreus rarus sp. nov., halophilic archaea isolated from diverse coastal tidal flats, and proposal of the novel family Halolitoreaceae fam. nov. in the order Halobacteriales within the class Halobacteria.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126760},
doi = {10.1016/j.syapm.2026.126760},
pmid = {42691590},
issn = {1618-0984},
abstract = {Coastal tidal flats represent dynamic saline environments that harbor largely unexplored haloarchaeal communities. In this study, amplicon sequencing, metagenomic analyses, and cultivation-based approaches revealed substantial haloarchaeal diversity in tidal flats from four provinces of eastern China despite their relatively low salinity. Five haloarchaeal strains, designated YSMS36[T], DYSN1, QDMS2, CMSO5[T], and ZSTT2, were isolated from diverse tidal flats. Theses strains shared 16S rRNA gene sequence similarities of 92.1-92.2% with their closest validly named relative, Salinilacihabitans rarus AD-4[T]. Phylogenetic analyses based on 16S rRNA and rpoB' gene sequences showed that the five strains formed a distinct and well-supported monophyletic lineage, separated from currently recognized members of the class Halobacteria. Average amino acid identity (AAI), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) values between these five strains and the related Halobacteria representatives were 49.3-62.7%, 66.9-74.9%, and 16.2-29.5%, respectively, and well below the accepted thresholds for species and genus delineation. Phylogenomic analyses further supported their placement within a novel family of the order Halobacteriales. Based on phylogenetic, genomic, chemotaxonomic, and phenotypic analyses, these five strains represent two novel species of a novel genus within a novel family. The names, Halolitoreaceae fam. nov., Halolitoreus marinus gen. nov., sp. nov., and Halolitoreus rarus sp. nov. are herein proposed.},
}

@article {pmid42691671,
year = {2026},
author = {Han, L and Li, L and Ye, W and Huang, J and Liu, Y and Duan, C and Zhan, B and Guo, S and Peng, X},
title = {Micro-aeration unlocks endogenous nitrogen removal in anaerobic digesters via metabolically versatile fermentative bacteria.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126838},
doi = {10.1016/j.watres.2026.126838},
pmid = {42691671},
issn = {1879-2448},
abstract = {Ammonia inhibition represents a significant bottleneck in the anaerobic digestion (AD) of high-nitrogen organic wastes. This study employed a batch reactor system subjected to alternating carbon-sufficient and carbon-limited phases to investigate whether pulsed micro-aeration, with a peak oxidation-reduction potential ranging from -150 to -50 mV, could promote the conversion of total ammonia nitrogen (TAN) to N2 in anaerobic digesters maintained under bulk anaerobic conditions, while simultaneously elucidating the competitive interplay between this nitrogen removal process and methanogenesis. The investigation integrated reactor performance monitoring, [15]N stable-isotope tracing, and combined metagenomic and metaproteomic analyses. Compared to the strictly anaerobic control, the pulsed micro-aeration group exhibited a significant decrease in TAN concentration, with a maximum removal rate of 23.41 mg·L[-1]·d[-1]. Isotope analysis revealed that approximately 82.49% of the transformed [15]NH4[+]-N was recovered as [15]N2, thereby confirming the conversion of TAN to N2. The transient accumulation of NO2[-] and NH2OH, coupled with the absence of sustained NO3[-] accumulation and the enhanced expression of Hao, Nir, Nor, and Nos proteins, collectively suggested the involvement of a hydroxylamine/nitrite-associated pathway in conjunction with denitrification within the micro-aerated system. This nitrogen removal process was primarily mediated by native fermentative/facultative heterotrophic bacteria in the AD system, including Ottowia and Comamonas, which exhibited pronounced metabolic flexibility in response to carbon availability. When carbon was abundant, nitrogen removal was predominantly driven by heterotrophic denitrification; under carbon limitation, the system transitioned towards endogenous maintenance modes characterized by potential hydrogen utilization, mobilization of intracellular reserves (such as polyhydroxybutyrate and fatty acids), scavenging of residual organic matter, and the glyoxylate cycle. However, the activation of nitrogen removal through micro-aeration was accompanied by a suppression of methanogenesis, resulting in a methane loss of 1.31-2.77 mL per mg of TAN removed. Consequently, a paradigm of "mainstream methanogenesis-side-stream micro-aerobic nitrogen removal" is proposed, offering a novel strategy for developing robust processes to mitigate ammonia inhibition in AD.},
}

@article {pmid42691674,
year = {2026},
author = {Chen, Z and Chen, Y and Jia, Y and Zhang, J and Ge, L and Wang, H and Chen, J and Mao, R and Zhang, S and Gao, H and Xia, S},
title = {Co-utilization of manganous nitrate and pyrolusite enables concurrent mitigation of arsenic mobilization and greenhouse gas emissions in paddy-field wetlands.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126845},
doi = {10.1016/j.watres.2026.126845},
pmid = {42691674},
issn = {1879-2448},
abstract = {Constructed wetlands face the dual challenge of arsenic (As) mobilization and greenhouse gas (GHG) emissions under flooded anoxic conditions. Moving beyond single-process remediation, this study developed a synergistic strategy through the co-application of manganous nitrate (Mn(NO3)2) and pyrolusite (MnO2) in microcosms simulating As-contaminated paddy-field wetlands. The results demonstrated that the Mn(NO3)2+MnO2 treatment achieved near-complete As(III) immobilization in the overlying water, significantly outperforming other amendments (KNO3-alone, MnO2-alone and KNO3+MnO2) during a 24d-incubation period. Concurrently, it substantially suppressed cumulative emissions of CH4 and N2O by approximately 35% and 61% than that of the KNO3-alone treatment. Metagenomic analysis revealed that this dual amendment reshaped the microbial community and metabolism. It enriched key taxa such as the dissimilatory nitrate reduction to ammonium (DNRA)-associated archaeon Candidatus Methanoperedens nitroreducens and nitrate-reducing coupled with Fe/Mn-oxidizing bacteria (e.g., Propioniciclava, Zoogloea, and Bryobacter). Meanwhile, the combined amendment also significantly increased the abundance of critical functional genes, including the N2O-reductase gene nosZ, DNRA marker gene nrfA and CH4-oxidation genes (pmoA and reverse methanogenesis-associated mcrA). The underlying mechanism relies on a regenerative Mn(II)/Mn(IV) cycle driven by the biotransformation of Mn(NO3)2. This cycle strategically redirects electron flow from pollutant‑mobilizing pathways, e.g., methanogenesis and dissimilatory Fe/As reduction toward As(III) immobilization and low‑carbon‑emission processes. These processes specifically include anaerobic oxidation of methane coupled to Mn(IV) reduction (AOM‑MnR), nitrate-dependent anaerobic methane oxidation (n-DAOM) and complete denitrification. Overall, this work provides a novel "mineral-electron switch coupled with nitrate-metabolic trigger" framework, offering an effective and sustainable synergy-based approach for the co-management of metalloid and GHG pollution in flooded anoxic environments.},
}

@article {pmid42691912,
year = {2026},
author = {Zhou, Q and Wang, Y and Liang, H and Huang, J and Zhang, J and Yu, K and Lin, L and Li, X and Li, B},
title = {Deciphering the effects of sulfonamide antibiotics on denitrification from a metagenomic perspective: Inhibition of nitrite reduction and succession patterns of functional microorganisms.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143476},
doi = {10.1016/j.jhazmat.2026.143476},
pmid = {42691912},
issn = {1873-3336},
abstract = {Limited research has thoroughly elucidated the impact mechanisms of antibiotics on the denitrification process at the genomic and gene levels, which has hindered the optimization and development of nitrogen removal technology for antibiotic-containing swine wastewater. Lab-scale sequencing batch reactors were constructed in this study to treat synthetic wastewater containing different sulfonamides and nitrate. Investigations were carried out on denitrification performance, microbial community diversity, denitrifier succession patterns, and functional gene distribution. The stress of sulfonamides inhibited the nitrite reduction process, transforming complete denitrification into partial denitrification and causing significant nitrite accumulation. The average nitrogen removal efficiency in the treatment groups decreased from 81.0% ± 2.2-40.1% ± 6.1%. Alicycliphilus and Thauera were identified as the key taxa, accounting for 32.2% and 16.9% of all potential denitrifying bacteria, respectively. Although metagenome-assembled genomes (MAGs) from Thauera were enriched with genes encoding nitrate reductases (nap, nar) and nitrite reductases (nir), this genus preferentially utilized nitrate as an electron acceptor, resulting in the preferential nitrate reduction and subsequent nitrite accumulation. In contrast, Alicycliphilus MAGs developed tolerance to the sulfonamides stress during later stages, with concomitant enrichment of associated functional genes. They replaced Thauera to reemerge as the dominant group, thereby restoring complete denitrification. This study provides new insights into the regulatory mechanisms governing complete versus partial denitrification in nitrogen removal from antibiotic-containing wastewater.},
}

@article {pmid42692038,
year = {2026},
author = {Riella, LV and Borges, TJ and Rosales, IA and Avillach, CT and Palsson, R and Hullekes, F and Verhoeff, R and Pomahac, A and Chen, JY and Santagata, S and Giarraputo, A and Smith, RN and Le, HN and Barth, JA and Low, SC and Getchell, K and Curtis, M and Perrin, S and Kolev, M and Bercovici, S and Lindner, MS and Ribas, GT and Tanguturi, VK and Bapat, AC and Pattanayak, V and Longchamp, A and El-Khoury, J and Duggan, M and Shah, S and Pierson, R and Madsen, JC and Fishman, JA and Elias, N and Colvin, RB and Kawai, T},
title = {Porcine kidney xenotransplantation as a bridge to allotransplantation: a first-in-human study.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(26)01295-X},
pmid = {42692038},
issn = {1474-547X},
abstract = {BACKGROUND: Kidney xenotransplantation offers a potential solution to the organ shortage, but questions remain regarding durability, zoonotic infection risk, and whether the immunological response to the xenograft elicits sensitisation that could complicate subsequent allotransplantation. We report outcomes from a porcine kidney xenograft in a living recipient followed by human allotransplantation.

METHODS: A patient with end-stage kidney disease, a prolonged anticipated waiting time for deceased donor transplantation, and with no suitable living donor underwent transplantation at Massachusetts General Hospital (Boston, MA, USA) with a gene-edited porcine kidney (EGEN-2784; eGenesis [Cambridge, MA, USA]) incorporating the deletion of major glycan xenoantigens, inactivation of porcine endogenous retroviruses, and insertion of seven human transgenes. The recipient received costimulation blockade-based immunosuppression with complement inhibition. Monitoring included renal function, flow cytometric crossmatch, anti-HLA antibodies, and porcine microbial surveillance, including metagenomic sequencing. This report describes the first recipient in a planned three-patient study conducted under a US Food and Drug Administration Expanded Access Investigational New Drug application.

FINDINGS: The xenograft functioned immediately after transplantation on Jan 25, 2025, and sustained dialysis independence for 271 days. A biopsy on day 14 showed T-cell-mediated rejection, which resolved with treatment. Graft function remained stable for approximately 6 months until immunosuppression was reduced in the setting of non-zoonotic bacterial infection. Microvascular inflammation with endothelial injury subsequently emerged, progressing to thrombotic microangiopathy despite persistently negative donor-specific crossmatch, leading to graft failure and nephrectomy. Tissue analysis showed a macrophage and natural-killer-cell-predominant infiltrate with minimal T-cell involvement. No porcine pathogen transmission was detected. Anti-HLA antibodies remained unchanged. 82 days after explantation, the patient underwent human kidney allotransplantation with immediate graft function and no evidence of sensitisation during 231 days of follow-up.

INTERPRETATION: This case shows that porcine kidney xenotransplantation can provide prolonged renal support and be discontinued without clinically significant allosensitisation or zoonotic infection. Early cellular rejection resolved with treatment, whereas later graft failure was associated with microvascular injury progressing to thrombotic microangiopathy despite a negative donor-specific crossmatch, supporting the possibility that mechanisms beyond conventional antibody-mediated rejection contributed to late graft injury. Kidney xenotransplantation has the potential to provide prolonged dialysis-free support while also serving as a bridge to subsequent human allotransplantation.

FUNDING: Massachusetts General Hospital and eGenesis.},
}

@article {pmid42692179,
year = {2026},
author = {Sinaei, Z and Zobba, R and Rizzi, B and Kholik, K and Chisu, V and Cacciotto, C and Bazzoni, E and Giua, L and Pasetto, C and Faridah, TG and Astolfi, N and Masala, G and Alberti, A},
title = {Mycoplasma and Bartonella in Cats from the Tropical Tourist Gili Islands, Indonesia.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108309},
doi = {10.1016/j.actatropica.2026.108309},
pmid = {42692179},
issn = {1873-6254},
abstract = {Bartonella spp. and haemotropic Mycoplasma spp. are important vector-borne bacteria of veterinary and zoonotic relevance, yet information on their circulation in Indonesian island ecosystems remains limited. We investigated their occurrence and molecular diversity in 117 domestic and free-roaming cats from the Gili Islands, Indonesia, using full-length 16S rRNA nanopore metagenomics followed by targeted PCR, sequencing, phylogenetic analysis and multilocus sequence typing (MLST). Bartonella DNA was detected in 18/117 (15.4%) cats and haemotropic Mycoplasma DNA in 40/117 (34.2%). Sequence analysis identified Bartonella henselae as the predominant species together with Bartonella clarridgeiae. MLST of B. henselae revealed three sequence types (ST1, ST16 and ST42), with ST1, a lineage reported in both feline and human isolates, predominating. Comparison with the PubMLST database showed significant geographical differences in the distribution of ST1 and ST42, supporting regional variation in the circulation of B. henselae lineages. Haemoplasma characterization identified Candidatus Mycoplasma haemominutum, Mycoplasma haemofelis, Candidatus Mycoplasma turicensis and a Mycoplasma feliminutum-like organism, comprising ten distinct sequence variants. Haemoplasma positivity was significantly associated with age, with adults showing higher positivity than younger animals (P < 0.001), whereas Bartonella infection was not associated with age, sex or island of origin. The detection of zoonotically relevant B. henselae lineages and the genetic diversity of feline haemoplasmas provide evidence of the circulation of vector-borne bacteria among cats in this tropical island ecosystem. These findings provide the first molecular epidemiological baseline for this region and contribute to understanding the circulation and genetic diversity of feline vector-borne pathogens in Southeast Asia.},
}

@article {pmid42692306,
year = {2026},
author = {Song, W and Yao, J and Fu, Y and Li, Y and Wang, C and Clough, T and Shi, Z and Qin, S},
title = {Stimulatory effects of Mn-embedded root plaques on N2O emissions from paddy soil depend on light intensity.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135761},
doi = {10.1016/j.biortech.2026.135761},
pmid = {42692306},
issn = {1873-2976},
abstract = {Iron (Fe) plaques on rice roots are naturally occurring redox-active mineral interfaces and recognized hotspots for nitrous oxide (N2O) production in paddy rhizospheres. However, the role of trace manganese (Mn) naturally co-deposited within Fe plaques remains poorly understood. Here, we used experimentally induced Fe plaques and Mn-embedded Fe plaques as a controlled model to evaluate whether plaque-associated Mn modifies rhizosphere redox conditions and N2O production. Compared with Fe-only plaques, Mn-embedded Fe plaques showed a greater increase in N2O emissions and were associated with higher hydroxyl radical (•OH) production. Under illuminated conditions, quenching •OH with terephthalic acid reduced N2O emissions most strongly in the Mn-embedded Fe plaque treatment, supporting an association between plaque-associated •OH and light-enhanced N2O accumulation. Despite the shading-induced decrease in rhizosphere O2, N2O production remained higher in the Mn-embedded Fe plaque treatment than in the Fe plaque and control treatments. In anaerobic incubations, EDTA addition reduced the Mn-associated response, whereas exogenous Mn(II) increased N2O production. Metagenomic profiling provided supporting evidence for these responses, showing shifts in denitrification-related taxa and functional genes, including norB and nosZ. Together, these findings identify Mn incorporation into rice root Fe plaques as a previously overlooked factor modulating rhizosphere N2O production and highlight the need to consider trace-metal composition when evaluating the biogeochemical function of root plaques.},
}

@article {pmid42692351,
year = {2026},
author = {Liu, P and Li, J and Zhu, C and Mao, S and Xie, F and Jin, W},
title = {Dietary supplementation of resveratrol alters rumen microbiome and reduces urinary trimethylamine/trimethylamine N-oxide excretion in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28661},
pmid = {42692351},
issn = {1525-3198},
abstract = {Trimethylamine (TMA) is a major product of ruminal choline metabolism. Understanding the microbial pathways associated with TMA formation may provide opportunities to improve rumen fermentation efficiency and animal productivity; however, effective strategies to regulate rumen TMA production remain poorly understood. In this study, in vitro and in vivo experiments were combined to investigate the effects of resveratrol on rumen TMA production and urinary excretion in dairy cows. In vitro rumen fermentation was conducted with 4 resveratrol doses (0, 0.5, 5, and 50 mmol/L). Concentrations of TMA were significantly lower in the 5 and 50 mmol/L resveratrol treatments compared with the control (0 mmol/L). The in vivo experiment was conducted using 36 mid-lactation Holstein cows with an average days in milk (DIM) of 171 ± 7 d and an average parity of 3.2 ± 0.4. The experiment lasted for 5 weeks, consisting of a 1-week adaptation period followed by a 4-week experimental period. Cows were blocked according to parity, milk yield, and days in milk and then randomly assigned to CON (basal diet), RES2.4 (basal diet + 2.4 g resveratrol/cow/day), and RES4.8 (basal diet + 4.8 g resveratrol/cow/day). The total concentrations of TMA and trimethylamine N-oxide (TMAO) in plasma and urine were reduced in cows in the RES4.8 group. Resveratrol did not affect dry matter intake, apparent nutrient digestibility, and milk performance, but it altered rumen fermentation parameters. Resveratrol also increased serum globulin and glutathione peroxidase levels and reduced serum IL-6, malondialdehyde, and superoxide dismutase. Metagenomic analysis showed that resveratrol shifted the structure of bacterial and archaeal communities but did not affect those of protozoa and fungi. The relative abundance of Prevotella was significantly lower in the RES4.8 group, whereas Eubacterium_S and the archaeal orders Methanobacteriales, Methanomicrobiales, and Methanococcales were higher. Functional profiling showed that resveratrol did not affect the overall composition of carbohydrate-active enzymes but decreased the abundance of pathways related to oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, terpenoid backbone biosynthesis, lipopolysaccharide synthesis, and phenylpropanoid biosynthesis. Collectively, these findings provide new insights into the mechanisms underlying resveratrol-mediated regulation of rumen function and host TMA/TMAO metabolism.},
}

@article {pmid42692396,
year = {2026},
author = {Li, T and Lv, J and Tu, Y and Cheng, L and Xiao, H and Sun, Y and Li, JX and Lv, M and Yang, J and Wang, G and Tang, Z and Liu, Y and Song, H and Zhao, S and Shao, PL and Zhang, B},
title = {Global Freshwater Resistomes Reveal Environmental Signatures Associated with the Burden of Drug-resistant Tuberculosis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129105},
doi = {10.1016/j.envpol.2026.129105},
pmid = {42692396},
issn = {1873-6424},
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, yet the extent to which environmental resistomes reflect human disease burden remains unclear. In this study, we provide the first attempt to bridge freshwater resistomes with human disease burden using machine learning models, with a focus on identifying environmental signatures associated with drug-resistant tuberculosis (DR-TB) burden. By analyzing 1280 freshwater metagenomes from 45 countries, we characterized the compositional distribution of the resistomes and further developed an integrated environmental AMR Risk Score. Integrating the AMR Risk Score with socio-economic variables provided complementary information associated with variation in multidrug-resistant tuberculosis burden beyond socio-economic factors alone. In complementary income-stratified analyses, feature selection identified recurrent environmental signatures associated with different drug-resistant tuberculosis subgroups. These findings indicate that freshwater resistome characteristics contain geographically structured information associated with DR-TB burden within the sampled datasets and support the potential value of freshwater metagenomic surveillance for characterizing environmental AMR patterns.},
}

@article {pmid42692606,
year = {2026},
author = {Ma, C and Geng, R and Hou, Q and Zhao, Y and Yue, Y and Xue, T and Wen, L and Li, T and Yang, J and Hu, J},
title = {Structure and protection of Cichorium glandulosum polysaccharides against sarcopenic obesity through activating mitophagy via butyrate-GPR43-AMPK pathway.},
journal = {Carbohydrate polymers},
volume = {390},
number = {},
pages = {125722},
doi = {10.1016/j.carbpol.2026.125722},
pmid = {42692606},
issn = {1879-1344},
mesh = {Animals ; *Mitophagy/drug effects ; *Butyrates/metabolism ; AMP-Activated Protein Kinases/metabolism ; *Obesity/drug therapy/metabolism ; Mice ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/drug effects ; *Asteraceae/chemistry ; *Polysaccharides/chemistry/pharmacology ; Male ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; },
abstract = {Sarcopenic obesity (SO) is a major complication of type 2 diabetes with limited therapeutic options. This study characterized CGP-A, a novel branched fructan (6.722 kDa) from Cichorium glandulosum. Its backbone consists of →1)-β-D-Fruf-(2→ and →6)-α-D-Glcp-(1→ residues, interspersed with →1,6)-β-D-Fruf-(2→ branching points. The side chains consist of terminal β-D-Fruf-(2→ units attached to the C-6 position of the fructofuranosyl residues in the backbone. In db/db mice, CGP-A dose-dependently ameliorated insulin resistance, hepatic steatosis, muscle loss and intestinal barrier dysfunction. Importantly, CGP-A significantly improved grip strength, reflecting an enhancement in muscle quality. Integrated multi-omics analysis combining metagenomics, multi-organ proteomics, and metabolomics revealed that CGP-A altered the gut microbiota, specifically enriching Ligilactobacillus, Bacteroides and Alistipes, while elevating serum butyrate. These findings suggest that butyrate may activate the GPR43-AMPK signaling pathway in both liver and skeletal muscle. Hepatic AMPK activation upregulated PPARα to enhance fatty acid oxidation; concurrently, muscular AMPK stimulated PINK1/Parkin-mediated mitophagy, restoring mitochondrial function and attenuating protein degradation. Antibiotic depletion abolished these effects, establishing the microbiota as a crucial mediator. These findings elucidate the gut microbiota-butyrate-GPR43-AMPK pathway through which CGP-A contributes to multi-organ metabolic improvements, offering a promising prebiotic strategy for managing SO.},
}

Animals
*Mitophagy/drug effects
*Butyrates/metabolism
AMP-Activated Protein Kinases/metabolism
*Obesity/drug therapy/metabolism
Mice
Receptors, G-Protein-Coupled/metabolism
Signal Transduction/drug effects
*Asteraceae/chemistry
*Polysaccharides/chemistry/pharmacology
Male
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL

@article {pmid42692637,
year = {2026},
author = {Zhang, G and Cao, L and Zhang, G and Fu, R and Wu, Y and Zhao, J and Zhang, Z},
title = {Bacillus subtilis exopolysaccharide enhances Lactobacillus johnsonii-kynurenic acid to restore intestinal T helper 17/regulatory T cell balance via aryl hydrocarbon receptor.},
journal = {Carbohydrate polymers},
volume = {390},
number = {},
pages = {125768},
doi = {10.1016/j.carbpol.2026.125768},
pmid = {42692637},
issn = {1879-1344},
mesh = {Animals ; *Bacillus subtilis/chemistry ; *T-Lymphocytes, Regulatory/drug effects/immunology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; *Polysaccharides, Bacterial/pharmacology/chemistry ; *Kynurenic Acid/metabolism/pharmacology ; *Th17 Cells/drug effects/immunology/metabolism ; *Lactobacillus johnsonii/metabolism ; Mice ; Colitis/drug therapy/chemically induced ; Intestinal Barrier Function ; Mice, Inbred C57BL ; },
abstract = {Weaning-induced intestinal dysfunction remains a significant challenge, characterized by microbial dysbiosis and immune suppression. However, the precise molecular mechanisms by which specific structural features of levan-fructans influence host homeostasis through microbial metabolic pathways are not fully understood. Here, a branched levan-type exopolysaccharide from Bacillus subtilis BS21 (BS21EPS), characterized by a β-(2 → 6)-D-fructofuranosyl backbone and β-(2 → 1) linkages, reduces colonic damage and systemic inflammation. Metagenomic sequencing shows that BS21EPS supplementation selectively increases Lactobacillus johnsonii 428 in the colon, which contains specialized GH32 enzymes for levan degradation. Integrative metabolomics identifies kynurenic acid (KYNA) as the primary microbial metabolite consistently increased both in vivo and in vitro, which mechanistically serves as a potent endogenous ligand for the aryl hydrocarbon receptor (AhR). In a mouse colitis model, supplementation with L. johnsonii 428 or KYNA enhances intestinal barrier function and reduces inflammation by influencing T-cell lineage decisions, especially by promoting Treg expansion while inhibiting Th17 differentiation. Notably, AhR antagonism with CH223191 abrogates these immunomodulatory effects, confirming the crucial role of the KYNA-AhR axis in maintaining immune balance. Collectively, these findings reveal a structural-functional link between dietary levans, providing a targeted nutritional strategy for managing weaning-related dysfunction and inflammatory bowel diseases.},
}

Animals
*Bacillus subtilis/chemistry
*T-Lymphocytes, Regulatory/drug effects/immunology/metabolism
*Receptors, Aryl Hydrocarbon/metabolism
*Polysaccharides, Bacterial/pharmacology/chemistry
*Kynurenic Acid/metabolism/pharmacology
*Th17 Cells/drug effects/immunology/metabolism
*Lactobacillus johnsonii/metabolism
Mice
Colitis/drug therapy/chemically induced
Intestinal Barrier Function
Mice, Inbred C57BL

@article {pmid42680271,
year = {2026},
author = {Zhu, D and Xie, J and Li, P and Mei, J},
title = {Decoding the spatiotemporal patterns of food spoilage microbial communities: Integrating multi-omics and artificial intelligence to enable precision preservation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {119937},
doi = {10.1016/j.foodres.2026.119937},
pmid = {42680271},
issn = {1873-7145},
mesh = {*Multiomics ; *Food Microbiology/methods ; *Artificial Intelligence ; *Food Preservation/methods ; *Microbiota ; Metabolomics ; Metagenomics ; },
abstract = {In the global food supply chain, food wastage caused by spoilage has resulted in significant economic losses, food shortages, and environmental pressure. This process is fundamentally driven by the spatiotemporal dynamics of microbial communities. However, traditional research methods struggle to elucidate the complex mechanisms of spatial heterogeneity, interspecies interactions, and functional succession. This limits the development of effective preservation strategies. This review systematically reviews the cutting-edge progress of integrating multi-omics technologies and artificial intelligence (AI) to study food spoilage microbial communities, breaking through this bottleneck. We propose an intelligent theoretical framework that could potentially analyze microbial metabolic activities and predict dynamic shelf life if implemented. The conceptual framework integrates multidimensional data, including spatial metabolomics, temporal metatranscriptomics, single-cell transcriptomics, and longitudinal metagenomics. It can also be combined with AI models, such as graph neural networks. The article elaborates on the principles and applications of spatio-temporal monitoring technologies, such as nano secondary ion mass spectrometry, hyperspectral imaging, and the Internet of Things sensing. Through illustrative cases of typical perishable foods, it also explores how such a multi-omics - AI system might be applied to spoilage warning and precise intervention. Additionally, the article addresses the current challenges in data coverage, model generalization, and federated learning implementation. Then the research further explores emerging areas such as engineered probiotics, edge AI, and microfluidic sensing. These areas are targeted at transforming food preservation from an empirical control approach to a data-driven, precise regulatory framework. This transformation provides theoretical support and technical approaches for developing a smart, sustainable food preservation system.},
}

*Multiomics
*Food Microbiology/methods
*Artificial Intelligence
*Food Preservation/methods
*Microbiota
Metabolomics
Metagenomics

@article {pmid42680349,
year = {2026},
author = {Li, S and Zhang, H and Yang, Y and Xia, Y and Ni, B and Ai, L},
title = {Comparative profiling of microbial community structure, enzyme potential, metabolic features, and volatile composition in craft and Jiafan Huangjiu processes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {242},
number = {Pt 3},
pages = {120059},
doi = {10.1016/j.foodres.2026.120059},
pmid = {42680349},
issn = {1873-7145},
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; *Food Microbiology ; Bacteria/metabolism/genetics/classification ; Metabolomics ; *Fermented Foods/microbiology/analysis ; Metagenomics ; Ethanol/analysis ; },
abstract = {Craft Huangjiu and Jiafan Huangjiu represent two distinct industrial Huangjiu product outcomes with contrasting volatile profiles. This study compared craft Huangjiu (L70) and Jiafan Huangjiu (L79) to characterize their physicochemical, microbial, gene-level functional, metabolic, and volatile features. Because L70 involved mid-fermentation addition of finished Huangjiu, this comparison was not intended to isolate the sole effect of fermentation interruption versus continued fermentation. L79 showed more extensive carbon and nitrogen utilization, with lower residual substrates and higher ethanol and acetic acid contents than L70, whereas L70 retained a less complete fermentation state. At the volatile level, GC-MS and volatile metabolomics consistently showed an ester-enriched profile in L79 and a more alcohol-dominant profile in L70. FlavorDB-based putative annotation and threshold-based OAV analysis further indicated distinct database-assigned descriptor distributions and potential odor-active compounds, with more OAV > 1 ester-related compounds in L79. Metagenomic analysis showed that L70 was dominated by Lactobacillus acetotolerans, whereas L79 contained higher relative abundances of Saccharomyces cerevisiae, Aspergillus oryzae, Aspergillus flavus, and Fructilactobacillus fructivorans. Metagenomic functional annotation showed higher representation of hydrolysis-related CAZy genes and ester-related enzyme annotations in L79. KEGG-based pathway mapping further indicated greater gene-level potential for ethanol-, acetate-, and acetyl-CoA-related metabolism in L79. Accordingly, the L70 profile should be interpreted as the integrated final-product outcome of process intervention, exogenous input, and subsequent fermentation. The findings provide a comparative basis for future flavor regulation and process optimization in Huangjiu and other fermented alcoholic beverages.},
}

*Volatile Organic Compounds/analysis/metabolism
Fermentation
*Alcoholic Beverages/microbiology/analysis
*Microbiota
Gas Chromatography-Mass Spectrometry
*Food Microbiology
Bacteria/metabolism/genetics/classification
Metabolomics
*Fermented Foods/microbiology/analysis
Metagenomics
Ethanol/analysis

@article {pmid42680378,
year = {2026},
author = {Zhou, Y and Zhao, Z and Ke, T and Wang, Z and Wang, J},
title = {The global potential of freshwater microbes for plastic degradation.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {215-224},
doi = {10.1016/j.jes.2026.03.008},
pmid = {42680378},
issn = {1001-0742},
mesh = {*Plastics/metabolism ; *Biodegradation, Environmental ; *Fresh Water/microbiology ; *Water Pollutants, Chemical/metabolism ; *Water Microbiology ; Bacteria/metabolism ; Metagenome ; },
abstract = {Plastic pollution is becoming increasingly severe on a global scale, and the potential for biodegradation as a treatment method that is environmentally friendly merits greater attention. A significant number of genes that associated the degradation of plastic (PDAGs) have been identified, however, the distribution of these genes among microorganisms in global inland waters remains to be elucidated. A global-scale meta-analysis was conducted, incorporating approximately 1000 metagenome datasets of inland waters across seven continents. A total of 13,109 metagenome-assembled genomes (MAGs) were obtained by means of metagenomics binning, and 22,621 PDAGs were identified from these. Among these recognized PDAGs, phenylacetaldehyde dehydrogenase (PAD) was the most dominant (n = 16,664), followed by catalase (n = 5931). The predominant hosts for PAD and catalase were identified as Gamma-proteobacteria and Bacteroidia, respectively. The largest number of both PAD and catalase was found in MAGs from North America, while the average gene number in single MAG was highest in MAGs from Oceania. In accordance with the prediction of traits, PDAG-carrying MAGs from Europe demonstrated the fastest growth rate and the lowest optimal growth rate. Furthermore, 25 styrene monooxygenase (StyA) enzymes were identified, which were found to cluster into two distinct groups hosted by Alpha-proteobacteria and Gamma-proteobacteria, respectively. Moreover, 11 MAGs were observed to possess the complete pathway of polystyrene degradation. These results explored the potential of inland water microorganisms as a biological resource for plastic degradation and provided valuable microbial reference information that can be used to develop biological treatment technologies for mitigating plastics.},
}

*Plastics/metabolism
*Biodegradation, Environmental
*Fresh Water/microbiology
*Water Pollutants, Chemical/metabolism
*Water Microbiology
Bacteria/metabolism
Metagenome

@article {pmid42680395,
year = {2026},
author = {Zhang, Q and Nie, B and Yang, C and Wei, F and Deng, L and Chen, Z and Hua, S},
title = {Boosting domestic wastewater treatment with quorum signal-augmented heterotrophic nitrification-aerobic denitrification bacterial-algal aerobic granular sludge.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {381-391},
doi = {10.1016/j.jes.2026.03.078},
pmid = {42680395},
issn = {1001-0742},
mesh = {Denitrification ; Sewage/microbiology ; Nitrification ; *Waste Disposal, Fluid/methods ; *Wastewater/microbiology/chemistry ; Quorum Sensing ; Bacteria/metabolism ; Aerobiosis ; },
abstract = {The aerobic bacterial-algal granular sludge (ABGS) enhanced with heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria, as a novel symbiotic technology, exhibits fluctuating treatment efficiency and unstable performance primarily due to the unstable symbiotic relationship. This study proposes an innovative approach to strengthening the bacteria-algae symbiosis by introducing exogenous signaling molecules. Concurrently, high-throughput, correlation analysis of environmental factors and metagenomic sequencing techniques are employed to elucidate the enhancement mechanisms of the signaling molecules. The results demonstrate that signaling molecule enhancement boosted total nitrogen (TN) removal efficiency by 24.51 % in the bacteria-algae symbiotic system (X1). Scanning electron microscopy (SEM) characterization revealed that the addition of signaling molecules resulted in more compact aerobic granular sludge (AGS) and markedly improved stability. High-throughput sequencing showed signaling molecules enriched denitrifying bacteria (Hydrogenophaga, Pseudoxanthomonas, Thauera, Zoogloea) and organic-degrading Desulfomicrobium, optimizing microbial diversity and enhancing nitrogen/organic removal. Correlation analysis of environmental factors indicate that the addition of C8-HSL facilitates the enrichment and functional activation of specific genera. Metagenomic analysis revealed that signaling molecules enhanced the system's denitrification performance by modulating gene expression and associated metabolic pathways. Quantitative polymerase chain reaction (qPCR) analysis further confirmed that the signaling molecules upregulated the expression of the napA, nirK, and nirS genes. An increased abundance of the napA gene facilitated aerobic denitrification (NO3[-]-N→NO2[-]-N), while upregulated abundance of the nirK and nirS genes accelerated nitrite reduction (NO2[-]-N→N2). This study aims to provide theoretical and practical foundations for implementing advanced bacteria-algae symbiotic technologies.},
}

Denitrification
Sewage/microbiology
Nitrification
*Waste Disposal, Fluid/methods
*Wastewater/microbiology/chemistry
Quorum Sensing
Bacteria/metabolism
Aerobiosis

@article {pmid42680398,
year = {2026},
author = {Mao, Y and Wang, C and Zhang, L and Zou, B and Han, M and Wang, Z},
title = {Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.},
journal = {Journal of environmental sciences (China)},
volume = {168},
number = {},
pages = {400-412},
doi = {10.1016/j.jes.2025.12.004},
pmid = {42680398},
issn = {1001-0742},
mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology/chemistry ; China ; Bacteria ; Eutrophication ; *Microbial Interactions ; *Environmental Monitoring ; Nitrogen Cycle ; },
abstract = {Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.},
}

*Lakes/microbiology/chemistry
*Geologic Sediments/microbiology/chemistry
China
Bacteria
Eutrophication
*Microbial Interactions
*Environmental Monitoring
Nitrogen Cycle

@article {pmid42680679,
year = {2026},
author = {Yang, X and Peng, AD and Cheng, JH and Huang, YH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG and Wen, G},
title = {A legacy pollutant deciphered by multiomics toxicology and targeted remediation by a synthetic microbial consortium: a case study of 2-chloroacetophenone from abandoned chemical weapons.},
journal = {Water research},
volume = {},
number = {},
pages = {126776},
doi = {10.1016/j.watres.2026.126776},
pmid = {42680679},
issn = {1879-2448},
abstract = {2-Chloroacetophenone (2-CA) is a typical organic poison found in abandoned Japanese chemical weapons, yet systematic research on its ecological risks and bioremediation strategies in aquatic environments remains scarce. Through a 120-day exposure experiment across three concentration gradients (10, 50, and 100 mg·L[-1]) coupled with multiomics analysis (physicochemical profiling, ionomics, 16S rRNA sequencing, metagenomics, and metabolomics), we systematically characterized the toxic effects of 2-CA on aquatic microbial communities and their molecular response mechanisms. The glutathione (GSH) metabolic pathway was identified as the core defense hub against 2-CA-induced oxidative stress, with multiomics data revealing its transition from compensatory activation to irreversible collapse. Guided by these mechanistic insights, we directionally isolated three cascade-degrading bacteria (Pseudomonas abietaniphila, Bacillus sp., and Arthrobacter agilis) harboring the key genes hapA, yjfP, and catA, which encode the three consecutive steps of Baeyer-Villiger oxidation, ester bond hydrolysis, and aromatic ring cleavage. The synthetic microbiome assembled from these three wild-type strains achieved 100% removal of 100 mg·L[-1] 2-CA within 24 h in vitro and within 10 days in simulated contaminated water, with the sequential detection of predicted intermediates (phenyl 2-chloroacetate, phenol, and pyruvic acid) confirming the operation of the cascade pathway. This study establishes a "toxicology diagnosis-functional deconstruction-synthetic reconstruction" paradigm, providing mechanistic understanding and a potential bioremediation strategy for organic toxicants at sites contaminated by relic Japanese chemical weapons, although direct ecotoxicological validation of detoxification remains to be confirmed.},
}

@article {pmid42680729,
year = {2026},
author = {Della Sala, S and Papadimitriou, V and Polymenakou, P and Kutterolf, S and Frieling, J and Pyle, DM and Mather, TA and Kilias, S and Jones, CK and Druitt, T and Preine, J and Hübscher, C and Nomikou, P and Koukousioura, O and Ronge, TA and Beethe, S and Pank, K and Berthod, C and Chen, H and Chiyonobu, S and Clark, A and DeBari, S and Gertisser, R and Johnston, R and Manga, M and McCanta, M and McIntosh, I and Peccia, A and Tominaga, M and Yamamoto, Y and Woodhouse, A and Bernard, A and Fernandez Perez, T and Joshi, KB and Kletetschka, G and Morris, A and Li, X and Papanikolaou, D},
title = {A prolonged hydrothermal past at Santorini Caldera revealed by sedimentary trace metal and microbial signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42680729},
issn = {2041-1723},
support = {NE/L002612/1//RCUK | Natural Environment Research Council (NERC)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1326927//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 527924707//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 527924707//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC-2018-COG-8187 17-V-ECHO//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
mesh = {*Geologic Sediments/chemistry/microbiology ; *Hydrothermal Vents/microbiology/chemistry ; Volcanic Eruptions ; *Trace Elements/analysis ; *Metals/analysis ; Bacteria/genetics ; Metagenomics ; },
abstract = {Hydrothermal systems in volcanic calderas are critical in signalling volcanic unrest, forming ore deposits, and sustaining chemosynthetic microorganisms. Analysis of a ~3500-year sequence of sediments collected from the Santorini caldera, Greece, during International Ocean Discovery Program (IODP) Expedition 398 reveals the behaviour of a prolonged paleo-hydrothermal system. Sediment geochemical and metagenomic data record vigorous hydrothermal activity and metal fluxes for ~1100 years, within a 2270-year window between two major eruptions. Sediment hydrothermally-derived trace metals are significantly enriched over background (~200-fold for As and Hg, and 10-50-fold for Mn, Sb, Mo, and V), with long-term metal fluxes (9 t yr[-1] As, 2.5 t yr[-1] Cu, 7 kg yr[-1] Ag) comparable to fluxes from present-day geothermal fields in the Taupo Volcanic Zone. Metagenomic analysis identifies elevated metal resistance genes-signals of microbial adaptation to heightened hydrothermal stressors. Here we integrate geological and genomic evidence to decipher the paleoenvironmental and biogeochemical history of the past hydrothermal system at Santorini caldera.},
}

*Geologic Sediments/chemistry/microbiology
*Hydrothermal Vents/microbiology/chemistry
Volcanic Eruptions
*Trace Elements/analysis
*Metals/analysis
Bacteria/genetics
Metagenomics

@article {pmid42680742,
year = {2026},
author = {Low, A and Yang, Z and Anantaya, KT and Zhao, S and Tan, WC and Perez, RL and Chung The, H and Lim, SZY and Liu, L and Gounot, JS and Kwah, JS and Ong, RT and Nagarajan, N and Lee, JWJ and Mo, Y},
title = {Microbiome features associated with persistent intestinal carriages of Escherichia coli ST131 in a Southeast Asian cohort study.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42680742},
issn = {2041-1723},
mesh = {Humans ; *Escherichia coli/genetics/isolation & purification/classification ; *Escherichia coli Infections/microbiology/epidemiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Metagenomics ; *Carrier State/microbiology ; Asia, Southeastern/epidemiology ; Intestines/microbiology ; },
abstract = {Escherichia coli sequence-type 131 (ST131) is the dominant global extraintestinal pathogen capable of asymptomatic intestinal carriage and sustained household transmission, challenging infection control. Despite its clinical significance, the ecological determinants of gut persistence remain poorly understood. We performed shotgun metagenomics on fecal samples to investigate gut microbiome features associated with ST131-positive samples, distinct host carrier statuses (persistent, intermittent and non-carriers) and household risks in a study of a Southeast Asian cohort. Here, we show that ST131 carriage was associated with compositional shifts without reducing species alpha-diversity. Regression analyses identified depletion of commensal taxa and the 1,5-anhydrofructose degradation pathway in ST131-positive samples. Persistent carriers exhibited highly perturbed microbiome enriched with pathobionts, aerobactin- and lipopolysaccharide (LPS)-biosynthesis pathways. Comparing household risk groups to control, revealed that biotin biosynthesis and 1,5-anhydrofructose degradation may influence ST131 co-colonization through both direct and indirect mechanisms. Machine learning analyses identified metabolic pathways as stronger discriminators of persistent carriage than taxonomic features. Genomic-resolved analysis of clinical ST131 isolates revealed conserved genes for iron-acquisition, LPS and antibiotic resistance determinants. Overall, while commensals and metabolism may influence initial ST131 colonization, persistent carriage is associated with specific microbial and metabolic adaptations, providing potential targets to limit intestinal ST131 persistence.},
}

Humans
*Escherichia coli/genetics/isolation & purification/classification
*Escherichia coli Infections/microbiology/epidemiology
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Cohort Studies
Metagenomics
*Carrier State/microbiology
Asia, Southeastern/epidemiology
Intestines/microbiology

@article {pmid42680886,
year = {2026},
author = {Liu, CC and Dong, SS and Guo, J and Xu, Z and Wang, C and Li, YX and Meng, LL and Yang, XC and Li, M and Fu, K and Guo, Y and Yang, TL},
title = {MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42680886},
issn = {2058-5276},
support = {2023M732810//China Postdoctoral Science Foundation/ ; 2024M762573//China Postdoctoral Science Foundation/ ; 82372458//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401762//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370653//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Recovering high-quality microbial genomes from metagenomic sequencing data is essential for accurate profiling and understanding microbial variation. However, existing clustering methods often suffer from limited accuracy and scalability. Here we present MetaCAT (Metagenome Clustering and Association Tool), a framework that combines recovery of microbial genomes from metagenomic data and analysis of their associations with host traits. MetaCAT incorporates a Sparse Weighted Dirichlet Process Gaussian Mixture Model (SWDPGMM) to accurately and efficiently decompose complex datasets and combines k-mer frequency with read coverage to improve genome reconstruction. It also provides a dedicated workflow for microbial single-nucleotide polymorphism identification and metagenome-wide association studies with the host. MetaCAT outperforms existing methods in both clustering accuracy and computational efficiency across diverse datasets. Using metagenomic data from colorectal cancer cohorts, it revealed previously unrecognized marker species and microbial single-nucleotide polymorphisms associated with colorectal cancer. MetaCAT provides a scalable framework for microbial community profiling and advances our understanding of host-microbe interactions.},
}

@article {pmid42681283,
year = {2026},
author = {Grasso, G and Marmeisse, R and Bianciotto, V},
title = {Metagenomics Approach for Identification of Arbuscular Mycorrhizal Fungal Sequences in Historical Herbarium Specimens.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3045},
number = {},
pages = {209-215},
pmid = {42681283},
issn = {1940-6029},
mesh = {*Mycorrhizae/genetics/classification ; *Metagenomics/methods ; Soil Microbiology ; DNA, Fungal/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomics offers a powerful alternative to amplicon-based approaches for investigating arbuscular mycorrhizal fungi (AMF) in samples characterized by highly degraded DNA, such as historical herbarium specimens. Here, we present a dedicated bioinformatic pipeline for the retrieval and authentication of AMF sequences from shotgun metagenomic datasets generated from herbarium-associated soils. The workflow integrates quality control and reads preprocessing, taxonomic classification using Kraken2, targeted extrafction of AMF reads, and mapping to reference genomes using short-read-optimized alignment strategies. Authentication of historical DNA is achieved through the analysis of post-mortem damage patterns, including fragment length distributions and cytosine deamination profiles, using MapDamage2. This pipeline enables the detection of ancient AMF DNA, and it could provide a framework for studying long-term dynamics of plant-mycorrhizal associations from historical soil archives.},
}

*Mycorrhizae/genetics/classification
*Metagenomics/methods
Soil Microbiology
DNA, Fungal/genetics
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid42681569,
year = {2026},
author = {Zhang, Z and Ran, X and Lu, S and Chen, X and Ran, Y},
title = {Refractory Cutaneous Cunninghamella bertholletiae Infection Post-Polypectomy: Reversal With Amphotericin B Therapy Adjustment.},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.70672},
pmid = {42681569},
issn = {1365-4632},
}

@article {pmid42681574,
year = {2026},
author = {Campani, S and Stocco, S and Moriondo, M and Chiappini, E and Trapani, S},
title = {Oropharyngeal Kingella kingae Detection and Spondylodiscitis in Early Childhood-A Causal or Casual Association?: A Case Report and a Systematic Literature Review.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000005385},
pmid = {42681574},
issn = {1532-0987},
abstract = {BACKGROUND: Pediatric spondylodiscitis is a rare condition, primarily affecting children aged 6-48 months. Kingella kingae is the leading pathogen in this age group, often presenting with mild or atypical features, which delay diagnosis.

METHODS: We retrospectively reviewed pediatric spondylodiscitis cases discharged from our hospital between January 2010 and May 2026, identifying those attributable to K. kingae. In parallel, we conducted a systematic literature review using PubMed/MEDLINE and Embase (2000-2025) to identify pediatric cases confirmed by culture, nucleic acid amplification or metagenomic sequencing of plasma microbial cell-free DNA.

RESULTS: One case of K. kingae spondylodiscitis was identified at our center. The literature review yielded 59 cases (mean age 24 months). Clinical presentation was indolent: refusal to sit, limping, hip/back pain and minimal systemic symptoms. Laboratory findings were nonspecific, with erythrocyte sedimentation rate being the most elevated marker. All blood cultures were negative. Definitive diagnosis was achieved through molecular detection on blood or biopsy/drainage material; oropharyngeal swab-positive cases were considered presumptive. The lumbar spine (L4-L5) was the most involved site. Most patients responded well to antibiotic treatment; surgical intervention was rarely required.

CONCLUSIONS: Kingella kingae should be considered in young children with persistent gait disturbance or hip/back pain, even without fever or marked laboratory abnormalities. Early magnetic resonance imaging and molecular diagnostics on blood or infectious tissue enable timely, definitive diagnosis and targeted therapy. When isolation from a sterile site is not possible, K. kingae spondylodiscitis remains likely if age, clinical presentation, laboratory findings and polymerase chain reaction detection on a pharyngeal swab are consistent.},
}

@article {pmid42681733,
year = {2026},
author = {Ellis, EK and Ióca, LP and Liu, J and Chen, M and Bruner, SD and Ding, Y and Paul, VJ and Donia, MS and Luesch, H},
title = {Characterization of Dapalides D and E and Genomic Comparison of the Two Co-Occurring Dapalide-Producing Dapis spp.},
journal = {Journal of natural products},
volume = {89},
number = {8},
pages = {2373-2383},
doi = {10.1021/acs.jnatprod.6c00607},
pmid = {42681733},
issn = {1520-6025},
support = {R35GM128742/GM/NIGMS NIH HHS/United States ; RM1GM145426/GM/NIGMS NIH HHS/United States ; NA//University of Florida/ ; NA//Debbie and Sylvia DeSantis Chair professorship/ ; },
mesh = {*Cyanobacteria/genetics/chemistry ; *Depsipeptides/chemistry/pharmacology/isolation & purification ; Molecular Structure ; Phylogeny ; Guam ; Humans ; },
abstract = {Marine cyanobacteria are a rich source of diverse bioactive natural products, targeting proteins involved in many diseases. Here, we combined metagenomic analysis to enhance the structure elucidation process of two new cyclodepsipeptides named dapalides D (1) and E (2) from a collection of a cyanobacterial mat containing multiple Dapis species from Guam. Dapalides D/E are composed of 11 amino acids, including multiple identical units with different configurations. Enantioselective amino acid identification of the acid hydrolyzate established the identity of amino acids, including the configuration of α/β-stereogenic centers. Identification and analysis of the dapalides D/E biosynthetic gene cluster from a metagenome-assembled genome aided the elucidation of α-configuration and establishment of the order of individual building blocks, collectively revealing the total structure. Phylogenomic analysis indicates that the dapalides D/E producer belongs to Dapis sp. (Dapis sp. VPG23-80 MAG-2), which shares a 95.2% average nucleotide identity with Dapis sp. VPG23-80 MAG-1, the producer of dapalides A-C that cooccurs in the same assemblage. Dapalide D (1) showed moderate growth inhibitory activity against various cancer cell lines. This work expands the dapalide structure class and further highlights the use of combined chemical and metagenomic analyses for natural product structure elucidation.},
}

*Cyanobacteria/genetics/chemistry
*Depsipeptides/chemistry/pharmacology/isolation & purification
Molecular Structure
Phylogeny
Guam
Humans

@article {pmid42682513,
year = {2026},
author = {Zhang, W and Chen, M and Guo, T and Kuang, G and Ma, N},
title = {Gut microbiota dysbiosis and aromatic amino acid metabolism alterations: a multi-omics analysis of cognitive impairment following aneurysmal subarachnoid hemorrhage.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1870309},
pmid = {42682513},
issn = {1664-302X},
abstract = {BACKGROUND: Aneurysmal subarachnoid hemorrhage (aSAH) is frequently followed by persistent cognitive impairment, characterized by a complex and multifactorial pathological mechanism. While the role of the "microbiota-gut-brain axis" in neurocognition has garnered increasing attention, the specific ways in which gut microbiota and their derived metabolites might be associated with the development and progression of post-aSAH cognitive impairment remain largely undefined. Consequently, there remains a lack of systematic multi-omics evidence to elucidate these potential underlying associations.

METHODS: In this prospective observational study, we enrolled 48 patients with intracranial aneurysms. Among them, patients with aSAH (n = 33) were divided into a cognitive impairment group (aSAH-CI, n = 18) and a group without cognitive impairment (aSAH-WCI, n = 15) based on a 6-month longitudinal neurocognitive assessment. Patients with unruptured intracranial aneurysms (UIA, n = 15) served as the control group. We integrated a multi-omics approach encompassing fecal metagenomics, untargeted metabolomics, and serological profiles of inflammation, oxidative stress, and apoptosis to explore the potential correlations between the host and the microbiome, as well as to identify early diagnostic biomarkers.

RESULTS: Fecal metagenomics revealed distinct gut dysbiosis in aSAH-CI patients, characterized by reduced alpha diversity, depletion of beneficial commensals (e.g., Agathobacter), and expansion of opportunistic pathogens (e.g., Enterococcus). Functional and metabolomic analyses identified a significant alteration in aromatic amino acid biosynthesis. Specifically, tyrosine metabolism was altered, marked by reduced levels of neurotransmitter precursors and elevated neurotoxic trace amines (tyramine and phenylethylamine). Serologically, aSAH-CI patients exhibited heightened systemic inflammation, oxidative stress, and apoptosis. Integrated multi-omics network analysis underscored a strong correlation between elevated trace amines, depleted Agathobacter, and systemic pathological indices. Notably, Agathobacter rectalis and tyramine demonstrated robust potential as early diagnostic biomarkers for cognitive impairment following aSAH.

CONCLUSION: Our findings suggest a potential dual-hit correlative signature via the microbiota-gut-brain axis in cognitive impairment following aSAH. We hypothesize that the depletion of aromatic amino acid-producing microbiota correlates with reduced neurotransmitter precursors, theoretically impairing synaptic repair. Concurrently, observed associations among opportunistic pathogens, trace amines, and systemic inflammatory and oxidative stress markers suggest a synergistic effect potentially linked to further neuronal damage.},
}

@article {pmid42682792,
year = {2026},
author = {Lao, C and Li, Z and Lin, G and Li, C and Wang, Y},
title = {Employing Metagenomics Capture targeted next-generation sequencing for the etiological diagnosis of bloodstream infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905007},
pmid = {42682792},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; *Bacteremia/diagnosis/microbiology ; *Sepsis/diagnosis/microbiology ; *Molecular Diagnostic Techniques/methods ; Bacteria/genetics/classification/isolation & purification ; Female ; Male ; },
abstract = {BACKGROUND: Bloodstream infections (BSIs) represent a significant public health concern. Metagenomic Capture targeted next-generation sequencing technology, as a newly emerging method for pathogen detection, has been applied in the etiological diagnosis of various infectious diseases and demonstrates good diagnostic efficacy. However, there is relatively limited research on the diagnostic value of this technology for the etiological diagnosis of BSIs.

METHODS: A comprehensive retrospective analysis was performed on patients suspected of having BSIs who were admitted to the Affiliated Guangdong Second Provincial General Hospital of Jinan University in 2024. These patients underwent both blood culture analysis and Metagenomic Capture targeted next-generation sequencing technology for diagnostic testing, and a detailed comparison of the results was conducted.

RESULTS: It was found that the Metagenomic Capture-targeted next-generation sequencing method has a shorter time to result [1.33 (1.18 - 1.69) vs 2.73 (1.89 - 3.84) days, p < 0.001], more pathogenic microbial species detected, higher positive detection rate and higher sensitivity than blood culture.

CONCLUSIONS: Metagenomic Capture targeted next-generation sequencing technology is a promising tool for pathogen identification in BSIs, offering substantial methodological advantages in terms of turnaround time, detection breadth, and sensitivity. These diagnostic performance characteristics support its potential utility in clinical microbiology practice.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Sensitivity and Specificity
*Bacteremia/diagnosis/microbiology
*Sepsis/diagnosis/microbiology
*Molecular Diagnostic Techniques/methods
Bacteria/genetics/classification/isolation & purification
Female
Male

@article {pmid42682809,
year = {2026},
author = {Gao, S and Song, L and Feng, Q and Li, Y and Liang, H and Lei, K and Li, Z and Kisembo, P},
title = {First case of neonatal bloodstream infection caused by Malassezia furfur in mainland China diagnosed via metagenomic next-generation sequencing: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {32},
number = {4},
pages = {267},
pmid = {42682809},
issn = {1792-1015},
abstract = {The present study reports, to the best of our knowledge, the first case of neonatal bloodstream infection caused by Malassezia furfur in mainland China identified using metagenomic next-generation sequencing (mNGS). Traditional microbiological methods have failed to identify causative organisms, highlighting the diagnostic limitations of neonatal sepsis with atypical presentations. Using this case as a clinical entry point, a systematic review was conducted to consolidate the epidemiological, clinical and prognostic characteristics of previously reported neonatal Malassezia infections and critically evaluate current diagnostic challenges. This case suggests the need to expand the pathogen spectrum of neonatal sepsis, particularly among extremely preterm and extremely low-birth-weight infants. Furthermore, it demonstrates the transformative potential of mNGS as an adjunctive diagnostic modality capable of identifying rare, fastidious organisms that evade conventional detection. Integrating mNGS into routine clinical workflows may not only facilitate early and precise pathogen identification but also redefine clinical decision-making paradigms in neonatal infectious disease management.},
}

@article {pmid42682910,
year = {2026},
author = {Jin, Y and Zhou, M and Gao, Y and Zhou, X and Tao, X},
title = {Lawsonella clevelandensis: a normal flora that bites deep.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1914466},
pmid = {42682910},
issn = {2235-2988},
mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; *Abscess/microbiology/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial ; },
abstract = {Since its formal description in 2016, Lawsonella clevelandensis-a strictly anaerobic, partially acid-fast bacterium-has been increasingly recognized as a cause of deep-seated abscesses, yet its fastidious nature and absence from routine diagnostic databases contribute to significant underdiagnosis. This narrative review synthesizes current knowledge on its microbiology, expanding clinical spectrum, diagnostic strategies, and treatment, based on a literature search of PubMed and Web of Science up to April 2026. Analysis of 27 documented publications, comprising 18 clinical cases, reveals a potential association with host risk factors including diabetes, immunosuppression, and prior surgical procedures, alongside a notable predilection for fat-rich tissues such as the breast and abdomen. While metagenomic next-generation sequencing and 16S rRNA gene amplification have become indispensable for definitive identification, antimicrobial susceptibility data-derived primarily from a single strain-demonstrate uniformly low minimum inhibitory concentrations for penicillins, carbapenems, clindamycin, and metronidazole, with no acquired resistance genes identified by whole-genome sequencing. However, the absence of established clinical breakpoints and limited tested isolates precludes definitive conclusions about universal susceptibility. Clinicians should maintain a high index of suspicion for L. clevelandensis in culture-negative deep abscesses, particularly those with acid-fast rods, as prompt diagnosis and empirical therapy with β-lactam/β-lactamase inhibitors or carbapenems appear reasonable based on current in vitro and clinical evidence, though further susceptibility surveillance is essential.},
}

Humans
Anti-Bacterial Agents/pharmacology/therapeutic use
RNA, Ribosomal, 16S/genetics
Microbial Sensitivity Tests
*Abscess/microbiology/diagnosis/drug therapy
High-Throughput Nucleotide Sequencing
Drug Resistance, Bacterial

@article {pmid42682993,
year = {2026},
author = {Wang, Y and Zhang, Y and Li, C and Liu, R and Zhang, S},
title = {Severity-stratified gut microbiome dysbiosis and systemic neuroinflammation in acute traumatic brain injury: a metagenomic and cytokine profiling study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1845360},
pmid = {42682993},
issn = {1664-302X},
abstract = {BACKGROUND: The gut-brain axis has increasingly been implicated in the pathophysiology of traumatic brain injury (TBI). However, few human studies have simultaneously examined gut functional metagenomics and peripheral cytokine profiles across mild to moderate-to-severe TBI, which limits our understanding of how gut health may influence recovery outcomes in TBI patients.

METHODS: This cross-sectional case-control investigation involved the collection of fecal and matched serum samples within 7 days post-injury from 60 mild TBI patients (MT; GCS 13-15), 45 moderate-to-severe TBI patients (MST; GCS ≤ 12), and 113 healthy controls (HC). Shotgun metagenomic sequencing examined gut microbiota. Serum IL-1β, IL-6, IL-8, and TNF-α were measured using a 4-plex Luminex test. Spearman correlation was utilized to construct a hypothesis relating cytokine levels to microbial severity-stratified abundance patterns.

RESULTS: TBI was associated with severity-dependent remodeling of the gut microbiota. Alpha diversity decreased from HC to MST (p < 10[-6]), and community structure varied significantly among all three groups (PERMANOVA, p = 0.001). Serum TNF-α increased in a severity-associated manner (MST vs. HC and MT, p adj < 0.015). Among 332 differentially abundant species, butyrate-producing commensals fell abruptly at MT with no additional decline in MST, suggesting an apparent floor-like pattern rather than confirming a true biological floor effect. For example, Faecalibacterium prausnitzii dropped from 9.02% in HC to 4.29% in MT. In terms of function, metagenomic inference indicated that pathways for fermentative metabolism and short-chain fatty acid (SCFA) biosynthesis were largely suppressed, suggesting a predicted reduction in microbial SCFA production capacity. On the other hand, secondary bile acid synthesis was specifically increased in MST-dominant KOs (85%). Systemically, reduced commensals showed weak, directionally consistent correlations with pro-inflammatory cytokines (|ρ| = 0.16-0.25), although none of the species-cytokine associations survived FDR correction.

CONCLUSION: Acute TBI is associated with severity-specific gut dysbiosis, which is accompanied by systemic neuroinflammation. The early reduction of butyrate-producing taxa in mild TBI suggests that the early post-injury period may represent a potential window for future gut-targeted intervention studies.},
}

@article {pmid42683082,
year = {2026},
author = {Khan, M and Patil, P and Rathored, J},
title = {Carbapenem-resistant Gram-negative pathogens: molecular epidemiology, diagnostic advances, and emerging therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1913726},
pmid = {42683082},
issn = {1664-302X},
abstract = {Carbapenem-resistant Gram-negative pathogens (CR-GNPs) have become an important global health problem, contributing significantly to healthcare-associated infections, extended hospital stays, high mortality rates, and higher healthcare costs. The dissemination of carbapenem resistance is mainly attributed to the spread of carbapenemase-encoding genes, such as the Klebsiella pneumoniae carbapenemase (KPC), the New Delhi metallo-β-lactamase (NDM), the Verona integron-encoded metallo-β-lactamase (VIM), the imipenemase (IMP), and the oxacillinase-48 (OXA-48)-like enzymes associated with clinically important Gram-negative pathogens, including Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa. As well as carbapenemase production, resistance can also develop via alteration of porins, upregulation of efflux pumps, and the buildup of several resistance factors, generating highly adaptable and hard-to-treat microbes. Phenotypic resistance patterns may not predict the underlying mechanism and accurate laboratory detection remains challenging. The identification and monitoring of carbapenem-resistant organisms have undergone improvement in recent years thanks to molecular diagnostics, rapid phenotypic tests, whole-genome sequencing and metagenomics. At the same time, new drugs have been developed, such as ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol and combinations of aztreonam, offering increased treatment options, but with emerging resistance an issue. This mini review covers the molecular epidemiology of CR-GNPs, the latest developments and challenges in diagnosing these infections, new therapeutic options, and future perspectives on genomic surveillance, antimicrobial stewardship, and precision medicine strategies to address the increasing threat of carbapenem resistance.},
}

@article {pmid42683437,
year = {2026},
author = {Audemard, J and Creusot, N and Leloup, J and Duval, C and Halary, S and Mary, L and Eon, M and Forjonel, T and Mouffok, M and Puppo, R and Belmonte, E and Gautier, V and Got, J and Lefebvre, M and Markov, GV and Muller, C and Marie, B and Diémé, B and Frioux, C},
title = {Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivated Microcystis phycospheres.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag226},
pmid = {42683437},
issn = {2730-6151},
abstract = {Favored by global changes, freshwater cyanobacterial harmful blooms generate major ecological, economic, and public health challenges. Microcystis, one of the most widespread cyanobacterial genera, grows within a phycosphere where specialized interactions with its microbiome occur, that are suspected to influence bloom appearance and its potential toxicity. Using a combination of metagenomics, metabolomics, and metabolic modeling, we characterized the culture-associated phycospheres of 12 Microcystis strains isolated from a French pond. The distribution of metabolic reactions within Microcystis was consistent with their genospecies, whereas the metabolic landscape at the community level diverged from cyanobacterial phylogeny, indicating partial functional decoupling between cyanobacteria and their associated microbiomes. Bacteria associated with the simplified phycospheres substantially expanded the metabolic repertoire of the system, while maintaining functional redundancy within and across communities. On the other hand, endometabolomic profiles were largely driven by cyanobacterial metabolic outputs, whereas exometabolomic analysis did not reveal metabolites involved in exchange processes. Metabolic modeling, together with the identification of toxic specialized metabolites produced by specific biosynthetic gene clusters, further highlighted differences in metabolic potential among phycospheres. Together, these findings deepen the understanding of Microcystis' phycosphere functioning and demonstrate the value of multi-omics systems biology approaches, while suggesting that metabolic complementarity between species and across phycospheres could play a role in bloom-associated microbiome structure.},
}

@article {pmid42683603,
year = {2026},
author = {Fu, MX and Perdomo, MF and Lumley, SF and Ringlander, J and Kean, K and Reid, K and Mayne, R and Montaguth, OET and Forrest, L and Buddle, S and Botha, JC and Stenbäck, JB and Dickson, Z and Kent, C and Chai, H and Byott, M and Hannolainen, L and Secret, S and Airey, G and Hedman, K and Andersson, MI and Ansari, MA and Nastouli, E and Breuer, J and Matthews, PC and Golubchik, T and Irving, WL and Simmonds, P and Harvala, H},
title = {Next-Generation Sequencing Methods for Sensitive Hepatitis B Viral Genome Analysis: A European Study.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71130},
doi = {10.1002/jmv.71130},
pmid = {42683603},
issn = {1096-9071},
support = {NIHR203338//National Institute for Health and Care Research/ ; PG-23-0435//Svenska Sällskapet för Medicinsk Forskning/ ; GLS-1001038//Gothenburg Society for Medicine/ ; 220549/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; 220171/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; GNT2025445//National Health and Medical Research Council/ ; CC2223//Francis Crick Institute/ ; },
mesh = {*Hepatitis B virus/genetics/isolation & purification ; Humans ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Europe ; DNA, Viral/genetics/blood ; Viral Load ; *Hepatitis B/virology/diagnosis ; Metagenomics/methods ; Sensitivity and Specificity ; Polymerase Chain Reaction ; Genotype ; },
abstract = {This multicentre study investigated the utility of next-generation sequencing (NGS) to detect and generate hepatitis B virus (HBV) genomes in samples of low viral load (from 0.2 to 6207 IU/mL). 23 HBV DNA-positive plasma samples of genotypes A-E and one HBV-negative control sample were assayed blindly via 9 established NGS methods from 6 European laboratories. Methods included untargeted metagenomics, pre-enrichment by probe-capture followed by Illumina sequencing, and HBV-specific PCR pre-amplification followed by sequencing with Nanopore or Illumina. Full HBV genomes were obtained only from samples with viral loads > 1000 IU/mL using probe-capture methods, > 200 IU/mL using PCR-Illumina methods, > 10 IU/mL using PCR-Nanopore methods, and in no samples using metagenomic methods. Contamination was observed in the negative control and samples with very low viral loads in PCR-based methods. Probe-capture and metagenomic methods detected additional viruses not routinely screened in blood donations, including polyomaviruses and herpesviruses; positive results were confirmed by PCR. In conclusion, NGS may delineate whole-genome sequences at low viral loads if supported by a PCR pre-amplification step. Probe-capture methods also reliably detect HBV without pre-amplification but show limited genome coverage for samples with low viral loads; they may additionally detect a wide range of blood-borne viruses.},
}

*Hepatitis B virus/genetics/isolation & purification
Humans
*Genome, Viral
*High-Throughput Nucleotide Sequencing/methods
Europe
DNA, Viral/genetics/blood
Viral Load
*Hepatitis B/virology/diagnosis
Metagenomics/methods
Sensitivity and Specificity
Polymerase Chain Reaction
Genotype

@article {pmid42683728,
year = {2026},
author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G},
title = {Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725403},
doi = {10.1080/19490976.2026.2725403},
pmid = {42683728},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; Animals ; *Metagenome ; Mice ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Feces/microbiology ; Irritable Bowel Syndrome/therapy/microbiology ; Computer Simulation ; },
abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable and donor-selection strategies remain limited, in part because the role of donor‒recipient metabolic interactions in shaping the post-FMT community remains poorly understood. Here, we leverage metagenome-scale metabolic modeling to quantify metabolic niche complementarity between donor and recipient microbiomes and predict post-FMT community composition. Using MICOM-derived metabolic models, we show that donor genomes whose metabolic flux profiles are more dissimilar from the recipient community colonize at significantly higher rates in a murine FMT model. In a human IBS trial, the same metric predicted post-FMT community composition via leave-one-out cross-validation and captured known disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to evaluate personalized donor screening, identifying super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition. Together, these results support metabolic niche complementarity as a potential determinant of post-FMT community composition and provide a mechanistic basis for evaluating donor-recipient metabolic compatibility. This framework offers a scalable approach for generating testable hypotheses for personalized donor selection.},
}

*Fecal Microbiota Transplantation
Humans
Animals
*Metagenome
Mice
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Feces/microbiology
Irritable Bowel Syndrome/therapy/microbiology
Computer Simulation

@article {pmid42684052,
year = {2026},
author = {Chen, M and Grégoire, DS and Bain, JG and Blowes, DW and Hug, LA},
title = {Diverse microbial metal resistance and novel metal cycling organisms in copper/nickel mine tailings.},
journal = {Metallomics : integrated biometal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/mtomcs/mfag028},
pmid = {42684052},
issn = {1756-591X},
abstract = {Mine tailings contribute to environmental heavy metal contamination through the formation of acid mine drainage (AMD). Microbially-mediated processes such as iron and sulfur redox cycling influence metal mobility. Here, we applied an integrated metagenomic and metaproteomic approach to profile microbial communities across vertical geochemical gradients in legacy copper/nickel tailings in Sudbury, Ontario, Canada. From 43 samples, we recovered 454 non-redundant metagenome-assembled genomes (MAGs), revealing diverse populations within the Actinobacteriota, Desulfobacterota, and uncultured lineages such as Candidatus Eremiobacterota and SZUA-79. Functional profiling identified 301 putative iron- and sulfur-cycling MAGs, including those within the Ca. Eremiobacterota and SZUA-79 phyla. A custom set of Hidden Markov Models (HMMs) was used to annotate metal resistance genes, which were widespread and diverse, but whose abundances did not correlate with measured Cu, Ni, or Fe concentrations. This observation suggests that resistance traits are broadly encoded in these microbial communities regardless of environmental metal concentrations. Proteomic data confirmed in situ expression of selected metal resistance genes and iron/sulfur metabolism genes, although protein recovery was limited due to the difficult nature of mine tailings as an extraction matrix. Our findings highlight both the depth of microbial diversity in metal resistance and metal biogeochemical cycling in mining waste, as well as the technical challenges that currently limit genomic and proteomic sequencing coverage in low-biomass, metal-rich matrices.},
}

@article {pmid42684853,
year = {2026},
author = {Hassan, J and Matsuda, S and Ishii, E and Uda, T and Motooka, D and Iida, T},
title = {A plasmid-encoded T3SS underlies the virulence of enteropathogenic Providencia alcalifaciens strains isolated from a large foodborne outbreak in Japan.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0015126},
doi = {10.1128/iai.00151-26},
pmid = {42684853},
issn = {1098-5522},
abstract = {Providencia alcalifaciens is a gut commensal bacterium and also an emerging enteric pathogen associated with sporadic infections and outbreak cases in humans. The most notable outbreak caused by this bacterium occurred in 1996 in Fukui Prefecture, Japan, affecting 270 individuals. However, the pathogenic mechanisms responsible for this outbreak remain unknown. In this study, we identified the key virulence determinants of the Fukui outbreak strains through genomic and functional analyses. These strains uniquely carry a ~162 kb large plasmid encoding a type III secretion system (T3SS) closely homologous to the Salmonella SPI-1 T3SS. We also show that the plasmid-encoded T3SS (T3SSp) constitutes a functional secretion system and is essential for the pathogenicity of the Fukui outbreak strain, including the invasion of cultured epithelial cells and the induction of diarrhea in a rabbit model. Secretome analysis identified effectors secreted in a T3SSp-dependent manner, among which PipA-sharing limited sequence similarity with SipA, a SPI-1 T3SS effector-plays a crucial role in inducing diarrhea. Ectopic expression of PipA in HeLa cells caused focal accumulation of F-actin, indicating its cytoskeleton-modulating activity. Comparative genomics with other Providencia species revealed the dissemination of the large plasmid, with structural variations among enteropathogenic strains of P. alcalifaciens and Providencia rustigianii associated with clinical cases in humans and animals. Thus, our findings underscore the molecular basis of P. alcalifaciens pathogenicity in the Fukui outbreak and highlight the significance of the large plasmids encoding T3SS in driving pathogenic evolution among Providencia species.},
}

@article {pmid42684889,
year = {2026},
author = {Mueller, NT and Xiao, S and Liu, T and Debelius, J and Kress, AM and Zhao, N and Moore, B and McKee, KS and Jacobson, LP and Comstock, SS and , },
title = {Mother-infant sharing of gut and vaginal microbes at the species and strain level.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117920},
doi = {10.1016/j.celrep.2026.117920},
pmid = {42684889},
issn = {2211-1247},
abstract = {Mother-to-offspring microbial transmission is a foundational process for seeding the infant gut microbiome, yet the relative contributions of maternal body sites and the influence of birth delivery mode remain incompletely understood. We use shotgun metagenomic sequencing in 68 mother-infant dyads to investigate species- and strain-level sharing of the maternal gut and vaginal microbiomes with the infant gut during the first year of life. At 2-4 months of age, infants share an average of 35% of species with their mother's microbiomes, with markedly greater sharing from the maternal gut than the vagina. Vaginally delivered infants exhibit higher levels of sharing than those born by cesarean section (C-section). Strain-level analyses reveal persistent mother-infant transmission across multiple Bacteroides and Bifidobacterium species genome bins, with strain-sharing frequencies varying by species and birth mode. C-section reduces the extent of mother-infant species- and strain-level sharing.},
}

@article {pmid42685246,
year = {2026},
author = {Lei, S and Qiu, X and Wang, Z and Zhang, Z and Zha, A and Zhou, Y and Chen, H and Huang, J and Yu, Z},
title = {Gut microbial H2S promotes metabolic dysfunction in mice via hepatic PPARα suppression.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag226},
pmid = {42685246},
issn = {1751-7370},
abstract = {This study investigates the role of gut microbiota-derived hydrogen sulfide (H2S) in obesity and glucose metabolism disorders. By integrating human gut metagenomic data, intervention experiments in mouse models, and in vitro cellular assays, we identified a signature of microbial sulfur metabolism in human cohorts and provided experimental evidence for its causal role and underlying metabolic mechanisms in mice. In clinical cohorts with obesity and glucose metabolism disorders, we observed a notable enrichment of genes involved in sulfur transport and H2S production. In mouse models, administration of H2S-producing Desulfovibrio desulfuricans, engineered Escherichia coli expressing phsABC, and the H2S donor NaHS consistently induced body weight gain and impaired glucose tolerance. Transcriptome analysis and cellular experiments indicated that H2S was associated with downregulation of the PPAR signaling pathway and lipid metabolism pathways in the liver, which may contribute to the abnormal accumulation of lipids and glycogen. Furthermore, rescue experiments using a PPAR agonist and an H2S adsorbent partially reversed these metabolic abnormalities. Collectively, our work provides experimental evidence in mouse models demonstrating that gut microbial H2S promotes metabolic dysfunction through hepatic PPARα suppression, providing potential targets for microbiome-based therapeutic interventions.},
}

@article {pmid42341325,
year = {2026},
author = {Young, G and Angchaisuksiri, P and Apte, S and Frandsen, RB and Chan, AKC and Chowdary, P and Eichler, H and Lyu, CJ and Martinez Garcia, MF and Matsushita, T and Trakymienė, SŠ and Tran, H and Trinchero, A and Windyga, J and Astermark, J},
title = {Concizumab in patients with hemophilia A or B without inhibitors: 56-week cutoff results of the phase 3 explorer8 study.},
journal = {Blood advances},
volume = {10},
number = {17},
pages = {6032-6042},
doi = {10.1182/bloodadvances.2026019931},
pmid = {42341325},
issn = {2473-9537},
mesh = {Humans ; Male ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacokinetics/adverse effects/administration & dosage/pharmacology ; *Hemophilia A/drug therapy/blood ; Adult ; *Hemophilia B/drug therapy/blood ; Adolescent ; Treatment Outcome ; Young Adult ; },
abstract = {Concizumab is a novel nonfactor replacement therapy for once-daily subcutaneous prophylactic treatment of hemophilia A/B (HA/HB) with and without inhibitors. Concizumab was superior to on-demand treatment in patients with HA/HB without inhibitors in the prospective, multicenter, open-label phase 3 explorer8 study. Here, longer-term efficacy and safety results from the start of the study up to the 56-week cutoff are presented. Males aged ≥12 years with HA/HB were randomized 1:2 to no prophylaxis (group 1) or concizumab (group 2) or allocated to concizumab (groups 3 and 4). Assessments at the 56-week cutoff included efficacy, pharmacokinetics/pharmacodynamics, and safety. The 56-week cutoff was defined as when all patients in groups 2 to 4 had completed the visit at 56 weeks or permanently discontinued treatment. Of 148 patients in the full analysis set, 21 were randomized to no prophylaxis (group 1: HA, n = 9; HB, n = 12), 42 to concizumab (group 2: HA, n = 18; HB, n = 24), and 85 to the nonrandomized concizumab groups (groups 3 and 4: HA, n = 55; HB, n = 30). After ≥24 weeks of treatment, 17 patients in group 1 switched to concizumab. Low median annualized bleeding rates for treated spontaneous and traumatic bleeding episodes were maintained at the 56-week cutoff in patients receiving concizumab (HA, 1.7 [interquartile range (IQR), 0.0-4.5]; HB, 2.8 [IQR, 0.0-6.4]), consistent with 32-week cutoff results. Concizumab plasma concentration remained stable, with no new safety concerns. Concizumab showed longer-term efficacy in patients with HA/HB at the 56-week cutoff and was considered safe and well tolerated. This trial was registered at www.clinicaltrials.gov as #NCT04082429.},
}

Humans
Male
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacokinetics/adverse effects/administration & dosage/pharmacology
*Hemophilia A/drug therapy/blood
Adult
*Hemophilia B/drug therapy/blood
Adolescent
Treatment Outcome
Young Adult

@article {pmid42673797,
year = {2026},
author = {Li, L and Zhang, Z and Pang, H and Yang, J and Liu, Y and Lu, J},
title = {Antipyretic pharmaceuticals intensify sewer H2S accumulation linked to biofilm matrix remodeling and altered sulfur metabolic potential.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143343},
doi = {10.1016/j.jhazmat.2026.143343},
pmid = {42673797},
issn = {1873-3336},
abstract = {Pharmaceuticals enter sewer systems before wastewater treatment, but their role in hazardous gas accumulation remains poorly understood. This study used long-term gravity sewer reactors to examine how acetaminophen (APAP) and ibuprofen (IBU) affect headspace hydrogen sulfide (H2S) accumulation, the properties of extracellular polymeric substances (EPS), and microbial functional potential in sewer biofilms. Both pharmaceuticals changed H2S from a stable baseline to a staged pattern with early suppression followed by accumulation above the control level. IBU showed earlier and higher H2S peaks than APAP, with the peak under 500 μg/L IBU exceeding that under 5000 μg/L APAP. Pharmaceutical exposure depleted extracellular proteins, enriched polysaccharides and humic acid, and promoted the retention of matrix-forming components in tightly bound EPS. QCM-D analysis showed marked decreases in |ΔD/ΔF| from 0.35 in the control to 0.03 and 0.09 under 5000 μg/L APAP and IBU exposure, respectively, indicating EPS interfacial rigidification. Metagenomic profiling further indicated reduced flagellar assembly, enhanced attachment-related potential, increased dsrA/B-associated terminal sulfite reduction potential, and reduced sulfide oxidation potential. These findings suggest that enhanced sewer H2S accumulation under antipyretic pharmaceutical exposure is associated with EPS interfacial rigidification and shifts in sulfur metabolic potential. These results identify antipyretic pharmaceuticals as underrecognized biofilm-structuring stressors associated with intensified sewer H2S accumulation and altered sulfur metabolic potential.},
}

@article {pmid42673827,
year = {2026},
author = {Du, Q and Xu, R and Qin, Y and Cai, X and Zhan, C and Song, Z and Yu, L and Wang, Z and Li, C and Tang, Z and Li, Y and Wang, S and Zhu, G},
title = {Elevated water levels drive greenhouse gas mitigation in the riparian zone profile.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130803},
doi = {10.1016/j.jenvman.2026.130803},
pmid = {42673827},
issn = {1095-8630},
abstract = {Wetlands are critical for climate regulation, with their hyporheic zone serving as sensitive interfaces for groundwater-soil-atmosphere exchange. These zones are active hotspots for carbon-nitrogen cycling and greenhouse gas (GHG) emissions (CO2, CH4, N2O), yet the impact of water level fluctuations on these emissions and their microbial drivers in freshwater wetlands remains poorly understood. This study investigated the spatiotemporal dynamics of GHG emissions and carbon-nitrogen coupling processes along riparian soil profiles of Baiyangdian Lake during water level fluctuations. Employing static chamber measurements, microcosms, quantitative PCR, Metagenome-Assembled genome (MAG) analyses, and Structural Equation Modeling (SEM), we observed that GHG emissions were significantly affected by water level fluctuations. Specifically, CO2 and N2O fluxes, as well as CO2 production potential were significantly lower at high-water-level conditions. Water level also emerged as a key driver of microbial community structure, with Methylococcaceae and Methanosarcinaceae as key regulators of CH4 emission, and Anaeromyxobacteraceae as central to N2O dynamics. A high-quality Methylomirabilales-like MAG, possessing the complete pathway for coupled nitrate reduction and methane oxidation, was identified. Its abundance negatively correlated with water level, suggesting that these C-N coupling bacteria contribute to reducing GHG emissions. This study provides crucial theoretical insights and identifies microbial targets for mitigating wetland GHG emission through hydrological management.},
}

@article {pmid42673922,
year = {2026},
author = {Ning, J and Du, Y and Deng, B and Li, M and Wu, T and Lin, L and Yu, T and Gan, Y and Si, D and Zhang, W and Wang, Y},
title = {Seasonal dynamics of geogenic phosphorus in alluvial-lacustrine aquifers: Coupling of phosphorus-containing dissolved organic matter and microbes as a key driver.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126797},
doi = {10.1016/j.watres.2026.126797},
pmid = {42673922},
issn = {1879-2448},
abstract = {Geogenic phosphorus (P) enrichment in groundwater driven by dissolved organic matter (DOM) degradation has been well documented worldwide but remains underexplored regarding temporal dynamics. As microbial metabolism regulates P-containing DOM mineralization, resolving seasonal shifts in microbial strategies is essential for clarifying geogenic P mobilization. In this study, seasonal field monitoring was integrated with molecular DOM characterization and metagenomic analyses to elucidate the coupling among geogenic P, P-containing DOM, and microbial functional pathways. Dissolved inorganic phosphorus (DIP) fluctuations were controlled by a degradation gradient of P-containing DOM and concurrent adjustments in microbial metabolism. The seasonal oxidant influx from dry to wet seasons modified redox conditions and promoted the transformation of high-molecular-weight humic substances into low-molecular-weight polar compounds, thereby weakening the microbial degradation of P-containing DOM and reducing DIP enrichment. Meanwhile, microbial P metabolism shifted from multi-pathway degradation involving dephosphorylation and C-P bond cleavage to a single dominant dephosphorylation pathway. These findings indicate that seasonal redox dynamics restructure microbial metabolic strategies and ultimately regulate temporal DIP enrichment in groundwater system.},
}

@article {pmid42674139,
year = {2026},
author = {Jiang, K and Pan, X and Zhu, S and Dang, Z and Yang, Z and Huang, L and Pan, X and Zou, X and Zhang, J and Guo, Y and Zhang, W and Li, Z and Cong, X and Wang, Z},
title = {Cellulose/polyester-blended microplastics amplify plastisphere pathogen and antibiotic resistome risks.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135752},
doi = {10.1016/j.biortech.2026.135752},
pmid = {42674139},
issn = {1873-2976},
abstract = {Microplastics (MPs) are important vectors for antibiotic resistance genes (ARGs) in anaerobic digestion systems, yet the risks posed by cellulose/polyester-blended materials remain poorly understood. In this study, commercial airlaid paper (AP; 45 % cellulose and 55 % polyester), polyethylene (PE), polypropylene (PP), and polystyrene (PS) were incubated in anaerobic reactors for 60 days. Biofilm characterization, extracellular polymeric substances (EPS) analysis, 16 S rRNA sequencing, and metagenomics were used to compare plastisphere formation, microbial assembly, ARG/mobile genetic element (MGE) profiles, and potential pathogen composition. Owing to its fibrous structure and bioavailable cellulose fraction, AP exhibited the highest biofilm biomass and EPS content. In contrast, PE, PP, and PS induced stronger interfacial stress, especially PS, as indicated by increased reactive oxygen species, lactate dehydrogenase release, and enrichment of oxidative stress, SOS response, and multidrug efflux pump related genes. Metagenomic analysis showed that fully synthetic MPs mainly enriched multidrug resistance genes, whereas AP selectively enriched polymyxin resistance genes, particularly Mcr-5.1 and Mcr-5.2. AP also exhibited the highest ARG-MGE co-localization rate (12.7 %) and antibiotic resistance risk. Overall, these findings identify polymer composition as a key factor shaping plastisphere resistome assembly and indicate that cellulose/polyester-blended materials require specific consideration in sludge-associated antimicrobial resistance risk assessments.},
}

@article {pmid42674950,
year = {2026},
author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H},
title = {Retraction notice to "A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic" [Sci. Total Environ. 930 (2024) 172601].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {182281},
doi = {10.1016/j.scitotenv.2026.182281},
pmid = {42674950},
issn = {1879-1026},
}

@article {pmid42674953,
year = {2026},
author = {Bilal, M and Wang, Z and Cui, J and Ferreira, LFR and Bharagava, RN and Iqbal, HMN},
title = {Retraction notice to "Environmental impact of lignocellulosic wastes and their effective exploitation as smart carriers - A drive towards greener and eco-friendlier biocatalytic systems" [Sci. Total Environ. 722 (2020) 137903].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {182284},
doi = {10.1016/j.scitotenv.2026.182284},
pmid = {42674953},
issn = {1879-1026},
}

@article {pmid42675165,
year = {2026},
author = {Villada, JC and Vasquez, YM and Szabó, G and Whittaker-Walker, E and Romero, MF and Qin, S and Varghese, N and Eloe-Fadrosh, EA and Kyrpides, NC and , and Visel, A and Woyke, T and Schulz, F},
title = {A genomic catalog of Earth's bacterial and archaeal symbionts.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42675165},
issn = {1546-1696},
support = {https://ror.org/04xm1d337//DOE | Office of Science (SC)/ ; https://ror.org/04xm1d337//DOE | Office of Science (SC)/ ; },
abstract = {Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth yet remains underexplored because of culturing challenges. This study used machine learning (ML) to predict symbiotic lifestyles in more than a hundred thousand microbial genomes from diverse environmental metagenome samples and reference genomes. Predictions were performed using symclatron, an ML framework developed to identify genomic signatures of symbionts. Predictions were deposited in a catalog we established called Symbiont Genomes (SymGs). The results indicate that 15-23% of uncultivated microorganisms likely engage in symbiotic relationships with other organisms, categorized as host-associated or obligate intracellular lifestyles, and are present in half of all known bacterial and archaeal phyla. We also identify genomic signatures of symbiotic lifestyles, including the loss of certain metabolic functions and the differential presence of metabolic modules that may enable host-dependent living. The symclatron software and the SymGs catalog represent valuable resources for studying symbioses, potentially facilitating future mechanistic investigations and engineering of host-microorganism associations.},
}

@article {pmid42675216,
year = {2026},
author = {Gong, J and Muranaka, H and Choi, SY and Tighiouart, M and Bhute, S and Aja, ER and Jacobs, JP and Stotland, A and Van Eyk, J and Elmadbouh, OHM and Edderkaoui, M and Tanaka, S and Furuya, H and Osipov, A and Lorber, J and Billet, S and Morris, A and Ten Hoeve-Scott, J and Graeber, T and Pandol, SJ and Hendifar, A and Bhowmick, NA},
title = {L-Glutamine in combination with first-line gemcitabine and nab-paclitaxel in advanced pancreatic ductal adenocarcinoma: an open-label, single-arm, phase 1 GlutaPanc trial.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {42675216},
issn = {2662-1347},
support = {UL1 TR001881-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P01CA233452//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; CA232859-01//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P01CA233452//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P01CA233452//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Exogenous L-glutamine has preclinical antitumor activity although formal clinical translation has not been attempted. We conducted a single-arm phase 1 trial to assess the safety and preliminary efficacy of clinical-grade, US Food and Drug Administration-approved L-glutamine therapy with gemcitabine and nab-paclitaxel (GA) in participants with treatment-naive, advanced pancreatic cancer (n = 16). The primary endpoint was to determine the recommended phase 2 dose (RP2D) by adaptive Bayesian design across standard doses of GA and a dose range of 0.1-0.3 g kg[-1] twice-daily oral L-glutamine. Secondary endpoints included safety and preliminary efficacy of the study combination. The primary endpoint was met with the RP2D reached at maximum doses of L-glutamine and GA. The grade ≥3 treatment-related adverse event rate was 66.7%, primarily from GA. Addition of L-glutamine to GA induced tumor shrinkage in 94% of subjects with a best overall response rate (ORR) of 44% (12.5% complete response). Median progression-free survival and overall survival (OS) were 8.5 months (95% confidence interval (CI) 6-not reached (NR)) and 22 months (95% CI 11-NR), respectively. L-Glutamine induced distinct metagenomic and metabolomic signatures on exploratory analyses in glutamine-treated subjects as a single agent, while the combination of L-glutamine and GA nearly doubled the ORR and tripled the OS compared to historical GA alone (ClinicalTrials.gov registration: NCT04634539).},
}

@article {pmid42675508,
year = {2026},
author = {Guo, W and Yu, Y and Wang, W and Yu, J and Zhou, M and Long, R},
title = {Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42675508},
issn = {1674-9782},
support = {32402705//National Natural Science Foundation of China/ ; XZ202502ZY0058//Science and Technology Projects of Xizang Autonomous Region, China/ ; },
abstract = {BACKGROUND: As a diverse and abundant component of the rumen ecosystem, viruses interact with other microorganisms and are thought to influence microbial metabolism and host productivity. However, how the rumen virome responds to seasonal fluctuations in extreme environments remains poorly understood. Here, metagenomic analyses were used to investigate temporal dynamics of viral diversity, functional potential, and virus-host associations in the rumen virome of yak and cattle on the Qinghai-Tibet Plateau across warm and cold seasons.

RESULTS: Rumen viral communities exhibited pronounced seasonal variation in both yaks and cattle, with higher alpha diversity observed during the cold season than in the warm season. Across seasons, the yak rumen virome showed greater alpha diversity and community stability than that of cattle. In total, 27,353 temperate and 31,976 virulent viral operational taxonomic units (vOTUs) were identified, predominantly belonging to the class Caudoviricetes. These viruses were linked to microbial hosts spanning 24 bacterial and 8 archaeal phyla, with Bacteroidota and Bacillota representing the dominant lineages. Virus-host associations were more numerous in the cold season and showed distinct host-specific patterns between yaks and cattle. Cold-season virome exhibited reduced diversity of anti-defense genes and enrichment of auxiliary metabolic genes (AMGs) associated with fatty acid metabolism and hemicellulose degradation. Notably, greater divergence between yaks and cattle was observed during the cold season: the yak rumen virome was enriched in pathways related to amino acid, lipid, and energy metabolism, as well as cellulose-degrading CAZyme families, whereas the cattle rumen virome showed enrichment in general carbohydrate metabolism and replication and repair processes.

CONCLUSION: Seasonal plasticity of rumen DNA virome and pronounced interspecific divergence between yaks and cattle provide insight into their distinct microbial processes in the harsh environment of the Qinghai-Tibet Plateau. These findings suggest that the rumen DNA virome exhibits complex ecological and functional responses to seasonal variation and may be associated with host-microbiome interactions and nutrient utilization under environmental stress. This study highlights the ecological relevance of rumen viral genomes in understanding virus-microbiome interactions, microbial adaptation, and nutrient utilization in high-altitude ruminants.},
}

@article {pmid42675564,
year = {2026},
author = {Akyol, CK and Bilaç, Ö and Çam, FS},
title = {Does the Gut Microbiota Play a Role in Attention-Deficit/Hyperactivity Disorder in Childhood? A Pilot Study From Turkey.},
journal = {Developmental neurobiology},
volume = {86},
number = {4},
pages = {e70057},
doi = {10.1002/dneu.70057},
pmid = {42675564},
issn = {1932-846X},
support = {2022-146//Manisa Celal Bayar University Scientific Research Projects Coordination Unit/ ; },
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology ; Male ; Pilot Projects ; *Gastrointestinal Microbiome/physiology ; Turkey ; Female ; Child ; Feeding Behavior/physiology ; Sleep/physiology ; },
abstract = {The pathophysiology of attention-deficit/hyperactivity disorder (ADHD) is not fully understood, but increasing evidence suggests that gut microbiota may play a role. This study compared the gut microbiota of children with ADHD with that of a control group of healthy children, and examined their dietary and sleep habits. Ten medication-naïve children aged 612 years who had recently been diagnosed with ADHD and ten healthy controls were included. ADHD diagnoses were confirmed using the Schedule for Affective Disorders and Schizophrenia for School-Age ChildrenPresent and Lifetime Version (K-SADS-PL). Sleep and eating habits were assessed using the 2nd Level Sleep Disorder Short Form, the Children's Eating Behaviour Inventory, and a form to collect sociodemographic and clinical information. The gut microbiota were analysed using 16S NGS metagenome analysis. A significant decrease in the Shannon and Simpson diversity index values was observed in the ADHD group compared to the control group. Despite the presence of a percentage difference, no statistically significant differences were observed between the groups with respect to species, genus, family, order, class or phylum. Following evaluation of the sleep and eating habit scale scores, no statistically significant difference between the groups was determined.These findings suggests that children with ADHD may alter gut microbiota diversity.However, the absence of significant taxonomic differences and the small sample size mean that these results should be interpreted with caution. Further, larger, adequately powered studies are needed to validate these findings and clarify the potential role of gut microbiota in the pathophysiology of ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/microbiology/physiopathology
Male
Pilot Projects
*Gastrointestinal Microbiome/physiology
Turkey
Female
Child
Feeding Behavior/physiology
Sleep/physiology

@article {pmid42675742,
year = {2026},
author = {Shaikh, SS and Malek, F},
title = {Healthy subjects gut microbiome modulation by Bacillus coagulans BCP92: A randomized, double-blind, placebo-controlled clinical trial.},
journal = {Medicine},
volume = {105},
number = {35},
pages = {e50435},
doi = {10.1097/MD.0000000000050435},
pmid = {42675742},
issn = {1536-5964},
mesh = {Humans ; *Probiotics/administration & dosage ; *Bacillus coagulans/physiology ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Male ; Adult ; Fatty Acids, Volatile/analysis/metabolism ; Female ; Healthy Volunteers ; Young Adult ; Metagenome ; },
abstract = {BACKGROUND: Probiotics are recognized for their ability to restore balance in the gut microbiome during dysbiosis. However, their effects on the gut microbiota of healthy individuals have rarely been investigated. This study aimed to evaluate the safety and efficacy of Bacillus coagulans (Heyndrickxia coagulans) BCP92 and its influence on microbiota composition in healthy subjects.

METHODS: In the present investigation, healthy participants (n = 48) were allocated into 2 groups and administered either Bacillus coagulans BCP92 capsules (1 billion CFU/capsule) or a placebo containing maltodextrin for 42 days. Microbiome composition and short-chain fatty acid analyses were subsequently conducted.

RESULTS: Analysis of metagenomes showed no major alterations in gut microbiome composition among participants who received B. coagulans BCP92 supplementation. However, subtle beneficial changes were observed in the treatment group, suggesting that probiotic administration may increase advantageous phyla, classes, orders, families, and some genera, while decreasing potentially harmful groups. A slight increase in short-chain fatty acids (SCFA) was also observed in the fecal samples.

CONCLUSIONS: This study implies that extended supplementation with the probiotic B. coagulans BCP92 may lead to substantial improvements in gut microbiome composition and SCFA levels.},
}

Humans
*Probiotics/administration & dosage
*Bacillus coagulans/physiology
Double-Blind Method
*Gastrointestinal Microbiome/drug effects
Feces/microbiology/chemistry
Male
Adult
Fatty Acids, Volatile/analysis/metabolism
Female
Healthy Volunteers
Young Adult
Metagenome

@article {pmid42675750,
year = {2026},
author = {Chang, K and Xie, H and Wang, Y and Zhao, X and Na, W and Xian, N and Liu, Y and Jiang, Z and Liu, C},
title = {An Aspergillus luchuensis isolated from a patient with hemoptysis insights from a comprehensive genome-based analysis: Case report.},
journal = {Medicine},
volume = {105},
number = {35},
pages = {e50486},
doi = {10.1097/MD.0000000000050486},
pmid = {42675750},
issn = {1536-5964},
support = {2026434//Chengdu Medical Research Project/ ; 2022346//Chengdu Medical Research Project/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Hemoptysis/microbiology/etiology ; Antifungal Agents/therapeutic use ; *Aspergillus/genetics/isolation & purification/pathogenicity ; *Invasive Pulmonary Aspergillosis/microbiology/drug therapy/diagnosis ; Voriconazole/therapeutic use ; Tomography, X-Ray Computed ; Amphotericin B/therapeutic use ; },
abstract = {RATIONALE: Asp luchuensis, a member of the A niger group, is widely used in food fermentation and rarely causes invasive pulmonary aspergillosis (IPA) in humans. Clinical cases of IPA induced by this strain are extremely scarce, and its genomic characteristics, virulence profiles, and pathogenic mechanisms remain poorly understood, resulting in insufficient clinical recognition of its invasive infection potential.

PATIENT CONCERNS: A 57-year-old immunocompetent non-neutropenic male patient with a long-term smoking and drinking history presented with unexplained severe cough and massive hemoptysis (approximately100 mL) without other typical infectious symptoms.

DIAGNOSES: Combined with chest computed tomography (CT) inflammatory lesions, positive galactomannan test, fungal PCR and metagenomic next-generation sequencing results, the patient was definitively diagnosed with probable A luchuensis-induced IPA. Genomic and transcriptomic analyses confirmed the pathogen as a variant A luchuensis strain with 3 key hypervirulence genes, highly active mitochondrial energy metabolism, and no specific antifungal resistance genes.

INTERVENTIONS: The patient received standardized intravenous antifungal combination therapy with voriconazole and amphotericin B after confirmed diagnosis.

OUTCOMES: The patient's cough and hemoptysis were significantly relieved after 10 days of treatment, with stable vital signs and no adverse drug reactions or disease progression.

LESSONS: A luchuensis possesses strong invasive pathogenicity and can trigger IPA even in non-neutropenic immunocompetent individuals. Negative conventional microbial tests cannot exclude its infection, and mNGS is a reliable diagnostic tool. This strain is susceptible to routine antifungal drugs, and clinicians should raise awareness of atypical Asp species-induced invasive pulmonary infections.},
}

Humans
Male
Middle Aged
*Hemoptysis/microbiology/etiology
Antifungal Agents/therapeutic use
*Aspergillus/genetics/isolation & purification/pathogenicity
*Invasive Pulmonary Aspergillosis/microbiology/drug therapy/diagnosis
Voriconazole/therapeutic use
Tomography, X-Ray Computed
Amphotericin B/therapeutic use

@article {pmid42676636,
year = {2026},
author = {Sabti, O and Lialin-Tzadikov, K and Ivanova, V and Dori-Bachash, M and Uzi-Gavrilov, S and Tik, Z and Mashiach, R and Zorea, A and Mizrahi, I and Segal, A and Moyal-Attias, K and Elinav, E and Meijler, MM},
title = {Disrupted terminal bilirubin catabolism links Lachnospiraceae depletion to inflammatory bowel disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1871609},
pmid = {42676636},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome mediates the reductive catabolism of bilirubin into urobilinoids, yet the bacteria and enzymes responsible for the later steps of this pathway remain largely unknown.

METHODS: Here, we combine untargeted UPLC/HRMS metabolomics with shotgun metagenomic sequencing of fecal samples from 119 participants, including patients with Crohn's disease, ulcerative colitis, and healthy controls, to map disruptions in the bilirubin catabolic pathway in inflammatory bowel disease (IBD).

RESULTS: We show that stercobilinogen and stercobilin, the terminal metabolites of this pathway, are depleted (p < 0.01) in IBD patients irrespective of disease subtype, while upstream intermediates, D-urobilinogen, remain unchanged. This metabolic bottleneck coincides with a marked reduction in members of the Lachnospiraceae family, specifically Blautia sp. SG-772 and three uncharacterized species, which show strong positive correlations with stercobilinogen and stercobilin levels.

DISCUSSION: These findings implicate Lachnospiraceae as key mediators of the yet unknown enzymatic conversion of I-urobilinogen to stercobilinogen, extending the family's known metabolic repertoire beyond short-chain fatty acid production. Given that bilirubin and its reduced metabolite stercobilinogen possess antioxidant properties, their depletion may contribute to the oxidative burden in the IBD gut. Conversely, the concurrent elevation of D-urobilin, which lacks these protective properties and has been linked to metabolic dysfunction in other contexts, may further exacerbate inflammation. Our results identify fecal bilirubin metabolites as candidate biomarkers of microbial dysbiosis in IBD and nominate specific Lachnospiraceae taxa for functional characterization of the missing stercobilinogen reductase.},
}

@article {pmid42676837,
year = {2026},
author = {Xia, Y and Peng, S and Yu, J and Wang, Y and Ye, Y and Liu, M and Shang, L and Cui, X and Wang, P and Ding, Z},
title = {Severity-dependent alterations in oral microbiota and antibiotic resistance in children with dental fluorosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2714622},
pmid = {42676837},
issn = {2000-2297},
abstract = {BACKGROUD: Dental fluorosis is a prevalent endemic condition, yet its impact on the oral microbiota structure and resistance in children remains understudied.

OBJECTIVE: To assess the microbial composition, diversity, functional pathways and co-occurrence patterns among urinary fluoride (UF), bacterial taxa and antibiotic resistance genes in relation to fluorosis severity. Design: Metagenomic analysis of dental plaque was conducted on 96 school-aged children, who were grouped into normal, dubious, very mild, mild, moderate and severe base on fluorosis severity.

RESULTS: Microbial diversity increased with fluorosis severity. Actinomyces sp. HMT 175, Actinomyces oris and Corynebacterium matruchotii, Fusobacterium nucleatum and Rothia dentocariosa were significantly enriched in the moderate and severe groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed a reduced relative abundance of genes involved in carbohydrate metabolism and genetic information processing in moderate and severe groups. Network analysis revealed positive correlations among Actinomyces sp. HMT 175, UF levels and GRD33_1 (a carbapenem resistance gene).

CONCLUSIONS: These findings highlight severity-dependent shifts in the oral microbiota and resistance, warranting further investigation into fluoride's public health implications.},
}

@article {pmid42677031,
year = {2026},
author = {Ceja-Navarro, JA and Patel, D and Genco, G and Byer, A and Ning, D and Wan, KH and Celniker, SE and Zhou, J and Dijkstra, P and Hungate, BA and Pett-Ridge, J and Brodie, EL},
title = {Ecosystem retrogression enhances cross-domain microbial stability and increases the genetic potential for nutrient cycling.},
journal = {mLife},
volume = {5},
number = {4},
pages = {486-506},
pmid = {42677031},
issn = {2770-100X},
abstract = {Ecosystem retrogression drives nutrient depletion, reduced productivity, and profound reorganization of soil microbial communities. Using amplicon sequencing and genome-resolved metagenomics, we examined how cross-domain microbial networks and functional gene potential respond to long-term phosphorus and nitrogen limitation along the well-characterized Ecological Staircase chronosequence in Mendocino, California, USA. Microbial diversity and abundance declined sharply with terrace age for prokaryotes, predatory protists, and bacteriophages, whereas fungi and phototrophic protists increased in nutrient-depleted, acidic soils. These compositional shifts were accompanied by major changes in reconstructed microbial networks: relative modularity increased alongside robustness, indicating adaptive reorganization that may sustain ecosystem function under resource scarcity. Fungi emerged as central stabilizers in these restructured networks, carrying enriched genetic potential to degrade plant polymers and mobilize phosphorus and nitrogen. Despite a decline in overall phage diversity, the relative abundance of phages encoding phosphorus-mobilizing auxiliary metabolic genes increased, suggesting that viral contributions to host phosphorus metabolism may be enhanced under nutrient limitation. Together, these results demonstrate that ecosystem retrogression drives cross-domain microbial reorganization toward fewer but more interconnected lineages, characterized by greater integration of functional genetic potential. This reorganization enhances the potential for functional resilience under extreme nutrient limitation, revealing how microbial networks adapt to maintain the capacity for nutrient cycling and stability as soils age and fertility declines.},
}

@article {pmid42677317,
year = {2026},
author = {Daniel, SG and Matute, JD and Dhudasia, MB and Rosewood, H and Wilson, NG and Patterson, A and Hao, F and Underwood, M and Bittinger, K and Mukhopadhyay, S},
title = {Gut microbiome in preterm infants with different weight gain outcomes.},
journal = {Gut microbiology},
volume = {2},
number = {},
pages = {},
pmid = {42677317},
issn = {3051-1720},
abstract = {BACKGROUND: Inadequate in-hospital weight gain among very low birth weight (VLBW; <1500g) infants is associated with adverse outcomes. Although microbiome alterations are linked to malnutrition in older children, their association with VLBW weight gain outcomes remains unclear.

OBJECTIVE: To evaluate associations between fecal microbiome composition, functional gene pathways, and metabolomic profile, and abnormal weight gain in VLBW infants.

METHODS: Prospective cohort study of VLBW infants from birth to hospital discharge with weekly fecal sampling. Inadequate weight gain was defined at 36 weeks post-menstrual age, as growth faltering (decline in weight-for-age z-scores from birth) and growth failure (<3[rd] percentile weight-for-age). Growth faltering was categorized as mild (0.8-1.2 decline) and moderate-severe (>1.2 decline). Fecal samples underwent shotgun metagenomic sequencing with KEGG-based functional annotation; [1]H NMR-based metabolomics was performed in a subset.

RESULTS: Among 101 enrolled infants, 54% had growth faltering (28 mild; 26 moderate-severe), and 18% had growth failure. The two outcomes rarely co-occurred (n=7). Microbiome diversity and taxonomic composition changed with age but did not differ by growth outcomes. Infants with moderate-to-severe faltering had reduced abundance of the glycolysis/gluconeogenesis pathway. Infants with growth failure showed a significant lag in microbiome maturity. Metabolite concentrations measured in a subset (n=46) were not significantly different in the study groups.

CONCLUSION: Abnormal weight gain in VLBW infants was not associated with major differences in microbial compositional or fecal metabolite levels. Differences identified in pathway analysis and in microbiome maturation may help focus future efforts to investigate the gut microbiome's role in VLBW weight gain.},
}

@article {pmid42677482,
year = {2026},
author = {Wu, Q and Xu, X and Guo, Y and Li, H and Hao, Y and Zhang, Z and Cai, Z and White, JC and Ma, C},
title = {Nano-boron nitride enhances soybean growth and symbiotic nitrogen fixation by modulating the rhizosphere microbiome and biogeochemical cycling.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6nr02400a},
pmid = {42677482},
issn = {2040-3372},
abstract = {Nanotechnology offers promising strategies for sustainable agriculture, yet the systemic mechanisms by which nanomaterials enhance legume nitrogen fixation remain insufficiently understood. The multi-scale impacts of nano-boron nitride (nano-BN) on soybean growth, biological nitrogen fixation, and rhizosphere microbial communities were investigated. Soil addition of 50 mg kg[-1] nano-BN significantly promoted plant biomass, nodule biomass, and leghemoglobin content by 10.0%, 27.4%, and 39.4%, respectively, compared to the untreated control. Nano-BN also enhanced the NH4[+]-N and NO3[-]-N content by 24.3% and 19.9% in root tissues, while reducing these levels in rhizosphere soil. Additionally, nano-BN enriched rhizosphere-dissolved organic matter, particularly humic-like components. Metagenomic analysis revealed that nano-BN reshaped carbon and nitrogen cycling functional genes, enhancing CO2 fixation and aerobic respiration; the nitrogen fixation functional gene nifH was upregulated by 27.7%. Microbial community analysis demonstrated increased bacterial diversity and abundance of beneficial taxa, particularly Bradyrhizobium, which increased by 24.9%. Co-occurrence network analysis revealed enhanced positive interactions and greater topological complexity upon the addition of nano-BN compared to the untreated control, indicating improved community stability. Collectively, these findings demonstrate that nano-BN promotes soybean growth through integrated regulation of nutrient cycling, symbiotic nitrogen fixation, and rhizosphere microbiome assembly. Nano-BN represents an innovative nano-fertilization strategy for enhancing biological nitrogen fixation, improving nutrient use efficiency, and advancing sustainable agricultural systems.},
}

@article {pmid42677827,
year = {2026},
author = {Chen, K and Yang, Z and Peng, J and Liu, C and Yu, Y and Cai, X and Liu, B and Li, S and Chen, T and Jung, S and Tian, Y and Xu, Q and Rao, X and Wu, Z and Wang, H and Di, Y and Wang, L and Wang, J and Lee, MS and Zou, Y and He, N and Li, S},
title = {Bacteroides cellulosilyticus-derived 2-hydroxyphenylacetic acid rectifies hepatic lipid homeostasis in MASLD by targeting the PPARγ-CD36 axis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725392},
doi = {10.1080/19490976.2026.2725392},
pmid = {42677827},
issn = {1949-0984},
mesh = {*PPAR gamma/metabolism/genetics ; *CD36 Antigens/metabolism/genetics ; Humans ; *Phenylacetates/metabolism ; *Lipid Metabolism/drug effects ; Homeostasis ; *Fatty Liver/metabolism/microbiology ; *Bacteroides/metabolism ; *Liver/metabolism ; Hepatocytes/metabolism ; Signal Transduction/drug effects ; Gastrointestinal Microbiome ; },
abstract = {The gut microbiota plays an important role in the occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD), but the specific molecular mechanisms involved have not been fully elucidated. In this study, human cohort studies were performed to identify that the relative abundance of Bacteroides cellulosilyticus (B. cellulosilyticus) was significantly decreased in patients with MASLD. Through the integration of metagenomic and metabolomic analyses, it was confirmed that B. cellulosilyticus and its metabolite 2-hydroxyphenylacetic acid (2HPAA) are key factors regulating the occurrence and development of MASLD. Single-cell sequencing and lipidomic analyses revealed that 2HPAA can enter the liver through the enterohepatic circulation to exert regulatory effects. Specifically, 2HPAA inhibits the peroxisome proliferator-activated receptor γ (PPARγ) signaling pathway, thereby suppressing the expression of the fatty acid transporter CD36. Meanwhile, 2HPAA regulates lipid metabolism in hepatocytes by significantly enhancing palmitate conversion efficiency and inhibiting CD36 palmitoylation. This dual regulatory effect on CD36 expression and palmitoylation can reduce lipid accumulation in hepatocytes and ultimately alleviate MASLD progression. These findings reveal the mechanism by which B. cellulosilyticus and 2HPAA alleviate MASLD by targeting the PPARγ-CD36 pathway. This work provides a new perspective for the study of gut microbiota-host interactions in regulating liver diseases.},
}

*PPAR gamma/metabolism/genetics
*CD36 Antigens/metabolism/genetics
Humans
*Phenylacetates/metabolism
*Lipid Metabolism/drug effects
Homeostasis
*Fatty Liver/metabolism/microbiology
*Bacteroides/metabolism
*Liver/metabolism
Hepatocytes/metabolism
Signal Transduction/drug effects
Gastrointestinal Microbiome

@article {pmid42677877,
year = {2026},
author = {Fukuda, Y and Horiba, K and Hashino, M and Kawabe, S and Miura, H and Kawamura, Y and Tanaka, M and Suzuki, T and Torii, Y and Muramatsu, H and Takahashi, Y and Yoshikawa, T and Kawada, JI},
title = {Comprehensive Viral Detection and Profiling of Plasma Cell-Free RNA in Patients With Suspected Hemophagocytic Lymphohistiocytosis.},
journal = {Journal of medical virology},
volume = {98},
number = {9},
pages = {e71122},
doi = {10.1002/jmv.71122},
pmid = {42677877},
issn = {1096-9071},
support = {24K10975//Japan Society for the Promotion of Science/ ; 24FC1001//Health Labour Sciences Research Grant/ ; },
mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/virology/diagnosis ; Female ; Child ; Child, Preschool ; Male ; High-Throughput Nucleotide Sequencing ; *RNA, Viral/blood/genetics ; Infant ; *Cell-Free Nucleic Acids/blood/genetics ; Metagenomics ; Herpesvirus 4, Human/genetics ; Herpesvirus 6, Human/genetics/isolation & purification ; },
abstract = {Hemophagocytic lymphohistiocytosis (HLH) is a severe, rapidly progressive disease. While viral infection is considered a common etiology of pediatric HLH, specific causative viruses other than the Epstein-Barr virus (EBV) have been rarely identified. This study utilized metagenomic next-generation sequencing (NGS) to identify potential causative pathogens in plasma samples from 17 pediatric patients with suspected HLH. Additionally, one case each of confirmed EBV- and cytomegalovirus (CMV)-associated HLH was analyzed for methodological validation. Plasma cell-free RNA (cfRNA) profiling was performed using NGS data to assess the host transcriptome response. Significant viral reads of human herpesvirus-6B, human herpesvirus-7, and Hubei reo-like virus (HRLV) 14 were detected using metagenomic NGS in one patient each. Plasma cfRNA profiles from five patients with viral infection (including EBV and CMV) were compared to those of 14 patients without viral infection. By comparing the two patient groups, 1053 differentially expressed genes were identified. The gene ontology (GO) term of "adaptive immune response" (GO: 0002250) was significantly enriched among upregulated genes in the virus-positive group. Furthermore, an isolated cluster consisting specifically of mitochondrial RNAs, was identified in the upregulated genes of the virus-positive group. Using metagenomic NGS, several candidate viral pathogens were identified in patients with suspected infection-related HLH. The viral genome of HRLV 14, previously undetected in human clinical samples, was identified in one patient. The results from plasma cfRNA profiling suggest that mitochondrial RNAs may reflect the underlying pathogenesis of virus-associated HLH and have potential utility as disease biomarkers.},
}

Humans
*Lymphohistiocytosis, Hemophagocytic/virology/diagnosis
Female
Child
Child, Preschool
Male
High-Throughput Nucleotide Sequencing
*RNA, Viral/blood/genetics
Infant
*Cell-Free Nucleic Acids/blood/genetics
Metagenomics
Herpesvirus 4, Human/genetics
Herpesvirus 6, Human/genetics/isolation & purification

@article {pmid42678156,
year = {2026},
author = {Wu, Q-Q and Li, C-Y and Chen, S-S and Xu, J and Yan, W-H and Lu, L-N and Feng, H-X and Zhou, J-A and Wang, L and Liu, N-N and Jiang, L and Wang, Y},
title = {Multi-kingdom gut microbiota analyses identify biomarkers of different types of pediatric short bowel syndrome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0031626},
doi = {10.1128/msystems.00316-26},
pmid = {42678156},
issn = {2379-5077},
abstract = {Despite recent advances in bacterial profiling across the three anatomical types of pediatric short bowel syndrome (SBS), the gut multi-kingdom remains unexplored. We characterized the four-kingdom gut microbiota using modified DNA extraction and deep shotgun metagenomic sequencing of fecal samples from 26 healthy controls and 34 pediatric SBS patients comprising three types (8 SBS I, 15 SBS II, and 11 SBS III). Overall, children with SBS exhibited a significant reduction in α-diversity compared with controls, with no difference observed among SBS types. Compared with controls, the proportion of archaea was significantly decreased in all SBS types, while bacteria, fungi, and viruses remained similar across types. Different types of SBS exhibited distinct microbial signatures: SBS I was enriched with pathogens (such as species from the Streptococcus and Klebsiella genera); SBS II was marked by a depletion of beneficial short-chain fatty acid-producing species (such as Faecalibacterium prausnitzii); and SBS III displayed loss of bile acid-metabolizing species, alongside a significant expansion of Lactobacillus species. Ecological networks were rewired in SBS, with disruption pronounced in SBS I. Functional analysis revealed that core metabolic pathways were markedly suppressed in SBS I compared with controls. Integrated correlation analyses revealed ileocecal valve loss as the primary determinant of SBS I microbial profiles, linking it to impaired secretory functions and hepatic injury. Our findings deciphered type-specific alterations in the multi-kingdom microbiota and their functional profiles, providing the basis for designing precision microbial therapies aimed at improving long-term outcomes for children with SBS.IMPORTANCEPediatric short bowel syndrome (SBS) is a primary cause of intestinal failure, yet prior research characterizing the gut microbiota has focused almost exclusively on bacteria. In this study, we characterized the multi-kingdom microbiome (including bacteria, fungi, archaea, and viruses) across the three anatomical types of pediatric SBS. We found that different SBS subtypes showed distinct microbial patterns: SBS I was enriched in pathogens, SBS II exhibited a depletion of beneficial short-chain fatty acid-producing species, and SBS III was characterized by a loss of bile acid-metabolizing microbes with an expansion of Lactobacillus. Functional analysis showed that SBS I had markedly suppressed core metabolic pathways, and integrated analyses identified the ileocecal valve as a key determinant of microbial gene profiles, with its loss linked to impaired secretion and liver injury. These findings provide a comprehensive multi-kingdom view of the pediatric SBS microbiome and highlight anatomical determinants shaping host-microbiome dysfunction.},
}

@article {pmid42678158,
year = {2026},
author = {Kaur, S and Anand, A},
title = {xoxF-linked methanol oxidation signals recur across wetland metagenomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0088926},
doi = {10.1128/spectrum.00889-26},
pmid = {42678158},
issn = {2165-0497},
abstract = {UNLABELLED: Wetlands are globally important methane-cycling ecosystems, but methanol oxidation remains less frequently emphasized than methane oxidation in community-level metagenomic analyses. Recent studies have highlighted the ecological importance of the lanthanide-dependent methanol dehydrogenase XoxF, yet wetland-focused xoxF literature remains comparatively limited relative to marine, freshwater, and other environmental systems. Here, we screened wetland-associated records in IMG/M using methane-metabolism and enzyme-centered queries focused on EC 1.1.2.10/xoxF and related methanol-oxidation annotations. Wetland-associated data sets repeatedly returned xoxF-linked annotations. We then examined a representative data set, a Wetland Surface Sediment combined assembly, to assess the relative representation of methanol-oxidation-associated annotations. In this co-assembly, xoxF/EC 1.1.2.10 was the most frequently recovered methanol-oxidation-associated annotation in the queried annotation space, with 1,996 genes, compared with 428 genes assigned to mxa-like EC 1.1.2.7 functions and 235 genes assigned to mdo/EC 1.1.99.37. KEGG-linked organism context included canonical methanotrophic and methylotrophic genera, including Methylococcus, Methylomonas, Methylotuvimicrobium, Methylovulum, and Methylophaga, while also extending into broader environmental Proteobacteria. Together, these data indicate that xoxF-linked methanol oxidation annotations recur across wetland metagenomes and are strongly represented in a representative wetland surface sediment co-assembly. Because this study relies on database annotations rather than organism-resolved pathway reconstruction or activity measurements, the results are best interpreted as community-level functional potential rather than evidence of xoxF-mediated activity, flux, or ecological dominance. These findings support wetlands as an underexamined but relevant setting for future clade-resolved, genome-resolved, and activity-resolved studies of xoxF-associated methanol oxidation.

IMPORTANCE: Wetlands play a major role in Earth's methane cycle, but studies of wetland microbes often focus more on methane itself than on the downstream step of methanol oxidation. Our study shows that wetland metagenomes repeatedly contain strong signals for xoxF, a gene linked to lanthanide-dependent methanol oxidation. In a representative wetland surface sediment co-assembly, xoxF-associated annotations were much more abundant than classical methanol dehydrogenase annotations, suggesting that this pathway may be especially important in wetland microbial communities. Because most previous xoxF studies have focused on marine, freshwater, or other non-wetland systems, these findings highlight wetlands as an underexplored setting for methanol-processing metabolism. This work provides a foundation for future studies connecting these signals to specific microbes, environmental conditions, and methane-cycling processes in wetlands.},
}

@article {pmid42678565,
year = {2026},
author = {Xu, W and Wang, Y and Yuan, C and Yue, Z},
title = {Microbial signal profiles and organism-level concordance between plasma metagenomic sequencing and blood culture in suspected bloodstream infection.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42678565},
issn = {1573-0972},
mesh = {Humans ; *Blood Culture/methods ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Sepsis/diagnosis/microbiology/blood ; *Bacteria/genetics/isolation & purification/classification ; *Bacteremia/diagnosis/microbiology ; },
abstract = {Plasma metagenomic next-generation sequencing (mNGS) and blood culture detect different components of the microbial signal and frequently produce discordant organism reports. We characterized microbial signal class, report-derived burden, organism-level concordance, and independent clinical attribution in a retrospective, single-center, episode-level cohort. Among 329 episodes with evaluable plasma mNGS reports, 315 had blood culture performed; 232 were mNGS positive/culture negative and 53 were positive by both methods. In the 232 discordant episodes, the recorded routine-care diagnosis classified 124 as bloodstream infection (BSI) and 108 as non-BSI. Nonviral signals were present in 78.2% and 42.6%, respectively (P < 0.001), and median maximum report-derived sequence counts were 98.5 and 11.5 (P < 0.001). Two laboratory physicians then independently reviewed source records using structured criteria while masked to the recorded BSI label and mNGS organism and sequence-count information. Initial agreement for the five-category BSI assessment was 97.6% (Cohen's kappa, 0.960). Within the mNGS-positive/culture-negative subgroup, adjudicated BSI likelihood showed a modest ordinal association with report burden (Spearman rho = 0.190; P = 0.004), while mNGS organisms were considered supported in 1 episode, plausible in 158, unlikely or contaminant in 72, and unresolved in 1. Among 53 dual-positive episodes, 33 (62.3%) shared at least one species, but only 5 (9.4%) had complete species-set concordance. Plasma mNGS and blood culture therefore frequently generated non-equivalent organism sets. Signal class and report burden contributed graded contextual evidence, but organism-level attribution required clinical review and orthogonal microbiology rather than binary positivity alone.},
}

Humans
*Blood Culture/methods
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Sepsis/diagnosis/microbiology/blood
*Bacteria/genetics/isolation & purification/classification
*Bacteremia/diagnosis/microbiology

@article {pmid42679008,
year = {2026},
author = {Egholm Bruun Jensen, E and Nzoyikorera, N and Ivanova, M and Leekitcharoenphon, P and Noelle Uwineza, M and Diawara, I and Nyandwi, J and M Aarestrup, F and Otani, S},
title = {Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {9},
pages = {e0014175},
doi = {10.1371/journal.pntd.0014175},
pmid = {42679008},
issn = {1935-2735},
abstract = {BACKGROUND: Cholera outbreaks remain a major public-health challenge in sub-Saharan Africa, where diagnostic capacity is limited and clinical case definitions are non-specific and re ly heavily on syndromic diagnosis. Rapid identification of Vibrio cholerae is critical, yet cholera-suspected diarrhoea can have multiple infectious causes not captured by targeted diagnostics.

METHODS: We evaluated a mobile, culture-independent metagenomic sequencing workflow for on-site detection of gastrointestinal pathogens directly from faecal samples in Burundi. The offline workflow combined long-read Oxford Nanopore Technologies (ONT) sequencing with rapid, laptop-based taxonomic and antimicrobial resistance (AMR) screening and was deployed across a health centre, a district hospital, and a refugee transit camp. The frontline and real-time results were verified using both conventional culturing and in-depth bioinformatic analyses.

RESULTS: V. cholerae signals were only detected in a subset of suspected cholera cases, while many samples were dominated by alternative bacterial taxa, most frequently Escherichia coli. V. cholerae abundance correlated strongly with detection of the C holera T oxin P hage CTXφ, supporting differentiation between toxigenic signal and background exposure. AMR genes were detected across samples, providing early situational insight into resistance determinants among gastrointestinal bacteria.

CONCLUSIONS: Mobile, offline metagenomic sequencing enables rapid frontline characterization of gastrointestinal disease, especially cholera-suspected, in resource-limited settings and complements existing diagnostics by improving etiological resolution and outbreak response.},
}

@article {pmid42679417,
year = {2026},
author = {Li, H and Gao, H and Fu, J and Yang, S and Chen, L and Zhou, J},
title = {Comparative analysis of microbial communities, assembly processes, and life-history strategies in a mariculture-impacted eutrophic bay and adjacent coastal sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120750},
doi = {10.1016/j.ecoenv.2026.120750},
pmid = {42679417},
issn = {1090-2414},
abstract = {Coastal embayments are increasingly subjected to intensive mariculture, which delivers sustained nutrient, organic matter, and antibiotics to sediments, yet microbiome responses remain poorly understood. Here we compared sediment microbiomes of the eutrophic Xiangshan Bay (XSB) and oligotrophic East China Sea (ECS), integrating cell counts, 16S rRNA amplicon, metagenomics, and cultivation-based resistance assays. Cell counts and amplicon data showed that XSB harbored higher microbial abundance (1.28 ×10[8]-1.34 ×10[9] vs. 2.07 ×10[7]-4.43 ×10[8] cells g[-1]), Chao1 richness (10,374-16,674 vs. 8311-12,281), and Shannon diversity (6.31-7.43 vs. 5.95-6.68). Amplicon-based null and neutral models indicated that community assembly in XSB was less stochastic and more deterministically selected than in the ECS. Life-history traits inferred directly from metagenomic data were consistently elevated in XSB relative to ECS, including 16S rRNA gene copy number (3.35 vs. 2.37), codon usage bias (0.0219 vs. 0.0188), maximum growth potential (0.1208 vs. 0.0844 h[-1]), genome size (5.63 vs. 5.38 Mb), GC content (56.26% vs. 54.48%), and transposase abundance (3.91% vs. 2.55%), collectively indicating a transition from K- to r-selected life-history strategies. Moreover, metagenomic annotation revealed a similarly expanded resistome in XSB, with 4.5-fold higher antibiotic resistance gene abundance (17.40-45.37 vs. 7.96-25.96 RPM) dominated by efflux-pump mechanisms, while plate assays showed roughly two-fold higher phenotypic resistance to macrolides, tetracyclines, and sulfonamides. These findings demonstrate that microbial community, life-history strategies, and antibiotic resistance respond as a coupled system to mariculture-driven eutrophication, providing a trait-based framework for predicting microbiome trajectories under anthropogenic nutrient enrichment.},
}

@article {pmid42679669,
year = {2026},
author = {Yao, D and Xie, H and Hu, Z and Wu, H and Liang, S and Zhang, J},
title = {Root exudates stabilize denitrification yet amplify CO2 emissions by priming effect in constructed wetlands.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126787},
doi = {10.1016/j.watres.2026.126787},
pmid = {42679669},
issn = {1879-2448},
abstract = {Root‑exudated carbon is a key microbial substrate in constructed wetlands (CWs), yet its net impact remains unclear due to its relatively low flux and quantification challenges. Here, we traced its allocation and metabolic pathways using [13]C-DNA-stable isotope probing coupled with metagenomics, thereby decoupling its role under gradient exogenous carbon inputs. The denitrification potential derived from root‑exudated carbon remained stable regardless of exogenous carbon fluctuations, reducing 1.2-1.44 mg·L[-1] N per mg·L[-1] C. Root‑exudated carbon significantly enhanced the priming effect by 0.9-1.54 times with exogenous carbon inputs (p < 0.05), resulting in an amplification of CO2 emissions. The denitrification and carbon emissions derived by root exudates was non-linear effects mediated by microbial regulation. DNA-SIP coupled with metagenomics indicated that differences in denitrification and CO2 emissions response to root‑exudated carbon from substrate quality, microbial community dynamics, and metabolic strategies. The microbial community of the [13]C-labeled heavy fractions was characterized by active denitrifiers, including Pseudomonas, Aeromonas, and Pseudoxanthomonas, which contributed the highest direct positive effect (20.23 %) to denitrification. Root‑exudated carbon influenced CO2 emissions by directly altering the DOM composition (contributing 37.01 %) and upregulating C-degrading genes (contributing 13.04 %). These findings revealed root exudated-carbon differentially regulate carbon and nitrogen metabolisms, challenging our understanding of the synergistic enhancement of water purification and climate mitigation functions in CWs.},
}

@article {pmid42679805,
year = {2026},
author = {Samarra, A and Alcañiz, AJ and Quijada, NM and Renwick, S and George, S and Sinha, T and Martínez-Costa, C and Segata, N and Zhernakova, A and Bode, L and Collado, MC},
title = {Maternal secretor status and human milk oligosaccharides influence the infant gut resistome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103007},
doi = {10.1016/j.xcrm.2026.103007},
pmid = {42679805},
issn = {2666-3791},
abstract = {The infant gut resistome is established early in life and is shaped by perinatal exposures, yet the mechanisms underlying its modulation remain unclear. We combined shotgun metagenomics of fecal samples from 57 one-month-old infants and paired milk samples from 50 mothers in the MAMI cohort to investigate the influence of maternal secretor status on early-life resistome development. Longitudinal follow-up at 6 and 12 months, and also further validation in the independent Lifelines NEXT (LLNEXT) cohort, support our findings. Cesarean section (C-section) was associated with increased antibiotic resistance gene (ARG) diversity, whereas exclusive breastfeeding reduced ARG abundance and diversity. Maternal secretor status further modified resistome composition among exclusively breastfed infants. Human milk oligosaccharide profiling identified specific glycans underlying these associations, with 2'-fucosyllactose and 6'-sialyllactose showing negative correlations with distinct ARG classes. These findings identify human milk composition as a key determinant of early-life resistome assembly and a potential target for modulating antimicrobial resistance.},
}

@article {pmid42679877,
year = {2026},
author = {Chen, Y and Li, W and Ma, X and Chen, F and Zhang, Y and Rittmann, BE},
title = {Bioaugmentation enabled simultaneous biodegradation of sulfadiazine and nitrification.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125595},
doi = {10.1016/j.envres.2026.125595},
pmid = {42679877},
issn = {1096-0953},
abstract = {Antibiotics are detected in surface waters in part because classical wastewater-treatment processes are ineffective for biodegrading them. Furthermore, the presence of antibiotics can inhibit the performance of biological treatment, particularly for nitrification, but an effective strategy for simultaneous antibiotics and nitrogen removals was not reported so far. This work targeted biodegradation of the common sulfanilamide antibiotic sulfadiazine (SDZ) and its inhibition of nitrification. The experimental results showed that nitrification rate decreased to 3.4 mg/(L·h) and 1.9 mg/(L·h) (from 19 mg/(L·h)) when normal nitrifying biomass (NNB) was exposed to SDZ at 10 mg/L and 20 mg/L due to inhibition by SDZ. Bioaugmentation of NNB with a SDZ-acclimated biomass (SDAB) enabled biodegradation of SDZ, which relieved its inhibition of nitrification. In the presence of 20 mg/L of SDZ, the NH4[+]-N removal rate reached at 7.8 mg/(L·h), which was more than 4-fold faster with SDAB bioaugmentation. Metagenomic analysis supported that NNB was responsible for nitrification, while bioaugmented SDAB was responsible for SDZ biodegradation that allowed simultaneous removal of NH4[+]-N and SDZ. For example, metagenomic analysis further showed that SDAB contained 4 genes for monooxygenations critical to initiating SDZ biodegradation, but NNB was enriched in genes for oxidations of NH4[+] and NO2[-].},
}

@article {pmid42680085,
year = {2026},
author = {Liang, J and Zou, W and Du, Z and Tao, X and Wang, X and Zhang, Y and Zhang, G and Lv, L},
title = {Enhanced volatile fatty acid production from co-fermentation of spent mushroom waste and food waste with rumen microbes: Performance and mechanism.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103079},
doi = {10.1016/j.anaerobe.2026.103079},
pmid = {42680085},
issn = {1095-8274},
abstract = {OBJECTIVE: Co-fermentation of lignocellulosic biomass and food waste (FW) can enhance the production of volatile fatty acids (VFAs) during anaerobic fermentation. However, the effect and mechanism of co-fermentation of Auricularia auricula waste (AW) with FW remains unclear. This study aimed to investigate the effect and mechanism of co-fermentation of Auricularia auricula waste (AW) with food waste (FW) on volatile fatty acid (VFA) production.

METHODS: Anaerobic fermentation experiments were conducted at different AW/FW ratios (1:0, 1:1, 2:1, 3:1, 4:1, 0:1) based on volatile solids (VS). VS removal and VFA concentration were measured, and metagenomic sequencing was performed to elucidate the underlying enhancement mechanism.

RESULTS: Co-fermentation significantly improved VS removal and VFA production, with both parameters increasing as the proportion of FW increased. The highest VS removal (48.9%) and VFA concentration (7929 mg/L) were achieved at an AW/FW ratio of 1:1, which were approximately double those of AW alone (22.4% and 3659 mg/L, respectively). Metagenomic analysis revealed that co-fermentation enriched bacterial genera such as Rummeliibacillus (25.4%) and Leuconostoc (9.2%), while Fungal genera Piromyces and Neocallimastix became dominant. Moreover, co-fermentation increased the relative abundance of carbohydrate-active enzymes and activated key functional genes in the VFA production pathway (e.g., ackA, PTA, MDH, HBD).

CONCLUSION: Co-fermentation of AW and FW significantly enhanced the hydrolysis and VFA production. The enhancement mechanism of VFA production during co-fermentation primarily involved the synergistic interaction between substrate nutrient complementation and efficient microbial community. This study provides a feasible strategy for efficient VFA production from spent mushroom waste.},
}

@article {pmid42667585,
year = {2026},
author = {Zhang, D and Chen, C and Xie, Y and Zhou, S and Li, D and Zeng, F and Huang, S and Lv, Y and Huang, X and Mao, F and Chen, R and Mo, Y and Huang, Y and Chen, R and Zhang, X and Yao, Q and Du, Y and Bai, F},
title = {Gut Microbiota from Patients with Long COVID Persisting for 2 Years Result in Alterations in Mice that Resemble Post-COVID Symptoms.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42667585},
issn = {1867-1314},
support = {XSTS2025001//Hainan Medical University Academic Enhancement Support Program/ ; WSJK2024MS150//Joint Project on Health Science and Technology Innovation in Hainan Province/ ; YSPTZX202313//the specific research fund of The Innovation Platform for Academicians of Hainan Province/ ; hnjg2024-67//Hainan Province Education Reform Project/ ; 202330//National Clinical Key Speciality Capacity Building Project/ ; 2021818//Hainan Province Clinical Medical Center/ ; },
abstract = {Human gut microbiota (GM) has been identified as a potentially important factor influencing the development of long COVID (LCOVID). The aim of this study was to understand the GM of LCOVID, which lasted for two years, in order to improve public awareness. Human gut microbiota and its metabolites were assessed in a healthy control group (n = 11) (HC) unexposed to SARS-CoV-2 and an LCOVID group (n = 11) in Hainan, China, using Shotgun metagenomics and liquid chromatography-mass spectrometry (LC-MS) of feces. The causal role of the microbiota in LCOVID was further validated by transplanting feces from the subjects into ABx mice using Histopathology and 16 S rRNA sequencing. Fecal microbial diversity was lower in patients with LCOVID compared with that in HC. Pro-inflammatory bacteria such as Streptococcus_salivarius and Streptococcus_parasanguinis increased, whereas anti-inflammatory bacteria such as Faecalibacterium_SGB15346 and Alistipes_onderdonkii decreased. Fecal metabolites from LCOVID were impaired in carbohydrate degradation, indole production, SCFA production, and fatty acid degradation. Transplantation of feces from patients with LCOVID into mice results in lung inflammation, intestinal inflammation, and anxiety. In addition, transplanted mice showed worse outcomes during Klebsiella_pneumoniae infections. Transplanted mice and the key bacteria Streptococcus_salivarius had the same worse outcomes in the D-IBS model by limb binding. GM from patients with LCOVID was altered significantly and sufficiently to promote LCOVID symptoms in mice, suggesting that it may be a potential therapeutic target.},
}

@article {pmid42668212,
year = {2027},
author = {Huang, X and Luo, R and Wang, Y and Zheng, W and Lu, X and Liu, G and Abdulla, P and Niu, R and Tu, Y and Xing, J and Hong, J and Zheng, W and Liu, J},
title = {Correlation between microbial communities, metabolites, and bioactivities in fermented mare's milk revealed by metagenomics and metabolomics.},
journal = {Food microbiology},
volume = {141},
number = {},
pages = {105278},
doi = {10.1016/j.fm.2026.105278},
pmid = {42668212},
issn = {1095-9998},
mesh = {Animals ; Metagenomics ; Fermentation ; Metabolomics ; *Microbiota ; Horses ; *Milk/microbiology/chemistry/metabolism ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Cultured Milk Products/microbiology/analysis ; Lactobacillales/metabolism/genetics/isolation & purification/classification ; Female ; Antioxidants/metabolism/analysis ; },
abstract = {Koumiss exhibits various functional properties, including antioxidant, hypoglycemic, and antihypertensive effects; however, natural fermentation is characterized by an uncontrollable microbial community structure, significant fluctuations in product quality, and a lack of specialized fermentation agents. The mechanisms underlying the links between microbial communities, functional metabolites, and bioactivity in natural and inoculated fermentation systems remain unclear. Therefore, this study employed bioactivity assays, metagenomics, and non-targeted metabolomics to systematically analyze differences in microbial communities, metabolite composition, and functional activities of mare's milk under different fermentation regimes. The results indicated that, compared with natural fermentation, inoculated fermentation with a mixed lactic acid bacteria (LAB) culture significantly enhanced the antioxidant, α-glucosidase, α-amylase inhibitory activities, and ACE inhibitory activity of mare's milk; microbial diversity in fermented samples was significantly reduced, with a more pronounced decrease in the inoculated group. Metabolomic analysis revealed that inoculated fermentation significantly enriched functional metabolites, including lipids and organic acids. Correlation analysis indicated that the abundance of Lactiplantibacillus and Limosilactobacillus was significantly positively correlated with beneficial metabolites (e.g., linoleic acid, α-linolenic acid) and functional activities. The lipid and amino acid metabolic pathways are closely associated with the differences in in vitro biological activity of inoculated fermented mare's milk. This study provides a fermentation starter that can improve the in vitro functional activity of mare's milk and reveals the potential metabolic links between LAB fermentation and the altered functional traits of mare's milk, thereby providing a theoretical basis and technical support for the development of high-value-added fermented mare's milk products.},
}

Animals
Metagenomics
Fermentation
Metabolomics
*Microbiota
Horses
*Milk/microbiology/chemistry/metabolism
*Bacteria/genetics/classification/isolation & purification/metabolism
*Cultured Milk Products/microbiology/analysis
Lactobacillales/metabolism/genetics/isolation & purification/classification
Female
Antioxidants/metabolism/analysis

@article {pmid42668680,
year = {2026},
author = {Sommer, AJ and Auch, B and Khoruts, A and Bajaj, JS},
title = {Proximity-ligation metagenomics reveals differential plasmid and chromosomal antimicrobial resistance gene carriage in disrupted gut ecosystems.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117312},
pmid = {42668680},
issn = {2589-0042},
abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance genes (ARGs) and virulence genes in the gut microbiome. In this study, we used proximity ligation shotgun metagenomics to characterize bacterial host-mobilome relationships associated with antimicrobial resistance and virulence genes in two disease cohorts with microbiome dysbiosis: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. Microbiome dysbiosis in patients with rCDI is primarily driven by prolonged antibiotic exposure, whereas dysbiosis in patients with cirrhosis results from altered gut physiology. We found an increased relative abundance of chromosomally linked antibiotic resistance determinants in both disease cohorts compared with healthy controls. The rCDI cohorts additionally exhibited increased relative abundance of plasmid-mediated ARGs.},
}

@article {pmid42668932,
year = {2026},
author = {Yan, F and Lin, M and Fu, Q and Gao, Y and Hu, Y and Zhou, M},
title = {Ureaplasma parvum meningitis in neonates: A retrospective case study and literature review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {8},
pages = {2178-2184},
pmid = {42668932},
issn = {1682-024X},
abstract = {OBJECTIVE: To investigate the clinical characteristics and advances in diagnosis and treatment of neonatal Ureaplasma parvum (U. parvum) meningitis.

METHODOLOGY: Clinical manifestations, diagnosis, treatment, and follow-up data of a neonate with persistent fever, normal blood routine, but persistently abnormal cerebrospinal fluid (CSF) results due to U. parvum meningitis were retrospectively analyzed. A literature review was conducted to identify relevant studies reporting on neonatal U. parvum meningitis published until May 2025.

RESULTS: A male infant born at 35+2 weeks of gestation with eight hours of premature rupture of membranes (PROM) was admitted at 17 days of age with persistent fever. The routine blood test was normal, while the CSF suggested purulent meningitis. Empirical treatment was ineffective, and metagenomic next-generation sequencing (mNGS) of CSF confirmed U. parvum meningitis. The infant recovered after three weeks of azithromycin treatment, but a language delay was found at two-year follow-up. The literature review identified 16 previously reported cases of U. parvum meningitis, which were combined with the current case, totaling 17 cases. Main manifestations included fever and convulsions, or initial circulatory and respiratory symptoms. CSF in the included studies showed leukocytosis, decreased glucose, and elevated protein. Diagnosis was mainly based on mNGS, and the predominant treatment consisted of macrolides, sometimes combined with quinolones, for 3-10 weeks. Two patients relapsed after drug withdrawal, and one had elevated liver enzymes. Major neurological complications included lateral ventricular dilatation and hydrocephalus, cerebral hemorrhage, infarction, malacia, and herniation. Most cases had a favorable prognosis, with rare developmental delay.

CONCLUSION: Clinical manifestations of neonatal U. parvum meningitis are nonspecific. Some patients present with normal blood routine but purulent CSF. U. parvum meningitis should be suspected in patients with poor response to empirical antibiotics and confirmed by CSF mNGS. Macrolides are biologically rational and commonly used for neonatal U. parvum meningitis; however, the optimal regimen and duration remain unclear due to limited and heterogeneous case-based evidence.},
}

@article {pmid42669226,
year = {2026},
author = {Gongpan, P and Yang, J and Fu, H and Wu, S and Zhu, X and Chen, R and Liu, L and Geng, CA},
title = {Preparation and chemical characterization of polyphenol-rich extract from Tsaoko Fructus: alleviation of ulcerative colitis in mice by modulating gut microbiota and suppressing the JNK1-cJun signaling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {161},
number = {},
pages = {158752},
doi = {10.1016/j.phymed.2026.158752},
pmid = {42669226},
issn = {1618-095X},
abstract = {BACKGROUND: Tsaoko Fructus, a traditional Chinese medicinal herb, has long been used to alleviate gastritis and enteritis. Nevertheless, the active constituents and underlying anti-inflammatory mechanisms remain insufficiently characterized.

PURPOSE: This study aims to optimize a polyphenol-rich fraction (3CB) from Tsaoko Fructus, evaluate its effects against ulcerative colitis (UC), and reveal the underlying mechanisms of action.

METHODS: The preparation of 3CB was optimized using response surface methodology (RSM), and its major constituents were identified by LC-PDA-MS analysis. A murine UC model was established by administering dextran sulfate sodium (DSS). To evaluate the effects of 3CB on UC mice, metagenomic sequencing of the intestinal microbiome and RNA sequencing of colon tissues were conducted. The anti-inflammatory activity of 3CB and its principal constituents was further verified by quantitative real-time PCR (qPCR), Enzyme linked immunosorbent assay (ELISA), Western blotting, immunohistochemical staining, and histopathological analysis. Network pharmacology, molecular docking, and surface plasmon resonance (SPR) assays were employed to elucidate the molecular mechanisms underlying the anti-inflammatory effects of 3CB.

RESULTS: 3CB significantly alleviated UC symptoms in DSS-induced mice, reshaped the gut microbiota with reducing pathogenic Pseudomonadota and Deferribacterota while enriching beneficial Bacteroidota, and restored microbial amino sugar and nucleotide sugar metabolism pathways of intestinal flora. Additionally, 3CB preserved colonic oxidative phosphorylation, protected the mucus barrier, and suppressed inflammatory cell infiltration and the expression of cytokines. Seven major polyphenols were identified in 3CB, with epicatechin (3) and epiafzelechin (6) being the most abundant. Mechanistic investigation revealed that the anti-inflammatory effect of 3CB was partially dependent on the JNK1-modulated MAPK signaling pathway. JNK1 was identified as a direct target of 3CB, with epiafzelechin (6) exhibiting a high binding affinity (Kd = 10.4 μM).

CONCLUSION: 3CB ameliorates UC potentially through modulation of gut microbiota, protection of the mucus barrier, and JNK1-targeted anti-inflammatory effects, highlighting its potential as a protective intervention for inflammatory bowel disease (IBD).},
}

@article {pmid42669365,
year = {2026},
author = {Meng, Q and Xia, Y and Liu, F and Yan, B and Yang, J and Shi, L and Zhang, M and Wu, J},
title = {In situ fermentation-coupled symbiosis of polyphosphate-accumulating organisms and microalgae for efficient nutrient removal and sludge reduction in low carbon-to-nitrogen ratios wastewater.},
journal = {Bioresource technology},
volume = {463},
number = {},
pages = {135748},
doi = {10.1016/j.biortech.2026.135748},
pmid = {42669365},
issn = {1873-2976},
abstract = {Microalgae-bacteria consortia (MBC) integrated with polyphosphate-accumulating organisms (PAOs) treat wastewater sustainably, but face excess sludge and light-dark mismatch issues. This study developed in situ fermentation-coupled photo simultaneous nitrification-denitrification phosphorus removal (F/P-SNDPR) systems by incorporating fermentative PAOs into MBC for low carbon-to-nitrogen ratios (C/N) wastewater. The effects of light-dark cycles on nutrient removal, sludge fermentation, and microbial dynamics were investigated. Under an optimal 16 h dark/8h light cycle, the F/P-SNDPR system achieved > 83% nitrogen and > 95% phosphorus removal, with low sludge production (312.21 mgVSS/d) and low net CO2 emissions. Prolonged light and dark phases promoted early microbial apoptosis and subsequent cell lysis, respectively, thereby facilitating fermentation. Combined dark duration and photoinhibition suppress nitrite-oxidizing bacteria, enabling stable partial nitrification. Flow cytometry and metagenomic results identified Candidatus Phosphoribacter as the primary fermentative microorganism. Its fermentation-associated genes, including LivFGHMK and Pta, facilitated volatile fatty acid (VFA) production during the dark phase. The generated VFA supported Candidatus Accumulibacter/Candidatus Competibacter to enhance nutrient removal, driven by key functional genes for polyphosphate metabolism (Ppk and Ppx) and denitrification (NirS, NirK, and NosZ). Overall, The F/P-SNDPR system offers a low-carbon strategy for efficient low C/N wastewater treatment without mechanical aeration or external carbon addition, while reducing sludge production.},
}

@article {pmid42669658,
year = {2026},
author = {Huey, SL and Cole, NL and Pagani, I and González, A and Finkelstein, JL and Haas, JD and Udipi, SA and Ghugre, P and Potdar, RD and Knight, R and Mehta, S},
title = {Effect of a complementary feeding intervention based on iron- and zinc-biofortified pearl millet on the gut microbiota in 12-18-month-old children: a randomized trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42669658},
issn = {2041-1723},
support = {2021-67017-34008//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 5T32HD087137//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
mesh = {Humans ; *Zinc/administration & dosage ; *Pennisetum/chemistry ; Infant ; *Iron ; *Gastrointestinal Microbiome/drug effects ; Female ; Male ; *Food, Fortified ; *Infant Nutritional Physiological Phenomena ; Dietary Supplements ; Feces/microbiology ; },
abstract = {Iron supplementation studies in children under five suggest potentially adverse gut microbiota shifts. Given iron's importance during early childhood, food-based approaches may offer a more viable supplementation strategy. Using shotgun metagenomics, we examined the effects of 9 months' daily consumption of iron/zinc-biofortified pearl millet (FeZnPM; 8.70 mg/100 g iron) versus control pearl millet (CPM; 3 mg/100 g iron) on the gut microbiome in 12-18-month-old children without severe anemia (hemoglobin ≥9.0 g/dL) from Mumbai urban slums through a randomized controlled trial, the primary outcomes of which were iron status biomarkers and infant growth (ClinicalTrials.gov ID: NCT02233764). In paired (n = 81) and endpoint (n = 108) analyses, FeZnPM consumption was not associated with detectable adverse effects on developing microbiomes and exploratory analyses suggest that it may support beneficial metabolic adaptations via direct modulation of antibiotic, antioxidant, and pollutant degradation pathways. This suggests biofortified crops could provide a sustainable approach to addressing iron deficiency while maintaining healthy microbiome development in early life.},
}

Humans
*Zinc/administration & dosage
*Pennisetum/chemistry
Infant
*Iron
*Gastrointestinal Microbiome/drug effects
Female
Male
*Food, Fortified
*Infant Nutritional Physiological Phenomena
Dietary Supplements
Feces/microbiology

@article {pmid42669679,
year = {2026},
author = {Zheng, R and Wang, C and Sun, C},
title = {Multi-omics and cultivation reveal laminarin-degrading PVC bacteria in the deep sea.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42669679},
issn = {2041-1723},
mesh = {*Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Glucans/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Multiomics ; Microbiota/genetics ; Phylogeny ; Glycoside Hydrolases/metabolism/genetics ; },
abstract = {The deep sea is home to a vast and largely unexplored microbial biosphere, along with large amounts of complex organic matter (COM). However, the functional capacity of the deep-sea microbiome to metabolize organic matter across diverse regions remains poorly understood. Here, we combine 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics to comprehensively characterize prokaryotic communities across different years (2018 and 2022) and habitats (cold seeps, hydrothermal vents, and seamounts). Our results reveal spatio-temporal community heterogeneity driven by geochemical gradients, alongside a widespread genetic potential for organic matter metabolism. Notably, the PVC (Planctomycetota-Verrucomicrobiota-Chlamydiota) superphylum exhibits extensive polysaccharide degradation capabilities, exemplified by the isolation of Planctomycetota strain WC338 and Lentisphaerota strain WC36 via laminarin enrichment. Growth experiments and transcriptomics confirm their strict laminarin dependence and characterize the underlying catabolic machinery-specifically, the deployment of different glycoside hydrolase (GH) families, which are broadly distributed and prevalent across the PVC superphylum. Furthermore, we demonstrate that laminarin acts as an effective selective substrate for enriching and isolating the deep-sea PVC superphylum bacteria. Collectively, these findings reveal that PVC bacteria-an overlooked group in laminarin degradation-possess specialized adaptations for polysaccharide breakdown and actively participate in laminarin turnover in deep-sea environments.},
}

*Seawater/microbiology
RNA, Ribosomal, 16S/genetics
*Glucans/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Multiomics
Microbiota/genetics
Phylogeny
Glycoside Hydrolases/metabolism/genetics

@article {pmid42669940,
year = {2026},
author = {Jesús, IDY and Zárate-Nicolás, B and Aragón-Magadan, MA and Pérez-Pacheco, R and Pacheco-Esteva, MC and Martínez-Tomás, SH and Vásquez-López, A and Ambrosio-Martínez, CN and Quiroz-González, B},
title = {Chemical, biological, and metagenomic profile of biofertilizers containing native forest and whey microbiota and enriched with macronutrients and micronutrients.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.71026},
pmid = {42669940},
issn = {1097-0010},
support = {//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI) and the Instituto Politécnico Nacional for supporting the SIP 20260212 and SIP INNOVACIÓN 2025-A101 projects./ ; //Secretaría de Ciencia/ ; //Humanidades, Tecnología e Innovación (SECIHTI), Mexico/ ; 20260212//Instituto Politécnico Nacional/ ; },
abstract = {BACKGROUND: Biofertilizers are gaining interest as sustainable nutrient sources that enhance nutrient and soil biological quality. The chemical, biological, and metagenomic profiles of biofertilizers produced from native forest microbiota and acidic whey, and enriched with macronutrients and micronutrients through anaerobic fermentation, were evaluated.

RESULTS: Fermentation of the biofertilizer base over 4 days increased pH (3.0-3.8) and decreased oxidation-reduction potential (ORP, 178 to -173 mV), while electrical conductivity (EC) remained stable (3.7-4.1 mS cm[-1]). After enrichment with macronutrients and micronutrients, 35 days of fermentation, and formulation of the model nutrient solution (MNS), pH stabilized around 4.8, and EC decreased to 1.72 mS cm[-1]. Most biofertilizers, when enriched individually, maintained negative ORP values; however, the increase in ORP observed in the MNS (140 mV) suggests that incorporating the copper-enriched biofertilizer may have contributed to more oxidizing conditions. Biological analysis suggested enhanced nutrient transformation, as revealed by chromatographic complexity in most enriched treatments. The 16S rRNA gene amplicon-based metagenomic profiling showed higher amplicon sequence variant (ASV)-level richness and taxonomic diversity in MNS (592 ASV records and 57 resolved genera) than in the unenriched biofertilizer (342 ASV records and 41 resolved genera). At the genus level, both profiles shared a dominant taxonomic backbone but showed measurable differences in relative abundance patterns (Bray-Curtis = 0.266). Fermentative taxa, including lactic-acid-bacteria-associated genera and Clostridium, dominated both biofertilizers.

CONCLUSIONS: Mineral-source fermentation by native forest microbiota modified the chemical environment, increased microbial diversity and complexity, and enhanced biological indicators of nutrient transformation; these changes suggest potential for increased nutrient bioavailability. © 2026 Society of Chemical Industry.},
}

@article {pmid42670142,
year = {2026},
author = {Su, HB and Li, MJ and Qian, X and Fan, YF},
title = {[Impact of Microplastics in Sediments on Microbial Carbon Cycling Functions in Qinhuai River].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {8},
pages = {5723-5733},
doi = {10.13227/j.hjkx.202506279},
pmid = {42670142},
issn = {0250-3301},
mesh = {*Geologic Sediments/chemistry/microbiology ; Rivers/chemistry ; *Microplastics/analysis ; China ; *Water Pollutants, Chemical/analysis ; *Carbon Cycle ; Environmental Monitoring ; Bacteria/metabolism ; },
abstract = {Microplastics （MPs）， as emerging contaminants， have attracted widespread attention in recent years. Microorganisms， as key regulators of the cycling of elements such as carbon， are sensitive to MPs pollution. Urban river sediments are sinks for environmental MPs and also important habitats for microbial communities. MPs pollution may bring ecological risks to urban rivers by affecting the structure and function of microbial communities. To examine the impact of MPs on microbial carbon cycle functions， this study investigated the sediments from the Qinhuai River， a typical urban river. Sediment samples were collected in October 2024， and MPs analysis combined with metagenomic sequencing was performed to characterize MPs pollution and its effects on microbial community structure and carbon cycling functional genes in both sediments and the plastisphere. The results showed a 100% detection rate of MPs in sediments， with an average abundance （based on dry weight） of （520.56±202.01） n·kg[-1]. MPs were predominantly between 200-300 μm and 1 000-2 000 μm， transparent in color， and exhibited fibrous or fragmental morphologies. Metagenomic analysis revealed significant differences in microbial community structure between the plastisphere and sediments， with higher abundance of Methanomicrobia in the plastisphere， potentially driving the significant enrichment of methane metabolism genes （Wilcoxon rank-sum test， P<0.05）. The Mantel test further indicated that the abundance of carbon cycling genes in the plastisphere was significantly correlated with total nitrogen and a specific MP polymer type （epoxy resin） （P<0.05）. This study uncovered the mechanism by which MPs shape distinct ecological niches and modulate microbial carbon cycling in urban river sediments， providing a scientific basis for evaluating the ecological impacts of MPs.},
}

*Geologic Sediments/chemistry/microbiology
Rivers/chemistry
*Microplastics/analysis
China
*Water Pollutants, Chemical/analysis
*Carbon Cycle
Environmental Monitoring
Bacteria/metabolism

@article {pmid42670399,
year = {2026},
author = {Alemneh, T and Molla, W and Abdela, S and Medjekal, S and Guetouache, M},
title = {Avian malaria: an in-depth overview on its biology, epidemiology, pathogenesis, clinical features, economic impacts, diagnostic, treatment and control strategies.},
journal = {Journal of parasitic diseases : official organ of the Indian Society for Parasitology},
volume = {50},
number = {3},
pages = {538-577},
doi = {10.1007/s12639-025-01887-z},
pmid = {42670399},
issn = {0971-7196},
abstract = {UNLABELLED: Avian malaria is a serious disease affecting diverse bird species worldwide, caused by protozoan parasites of the genus Plasmodium and transmitted exclusively by infected mosquitoes. The parasite completes its life cycle in both the avian host and the mosquito vector, undergoing multiple developmental stages. Clinical signs range from mild to severe and may include lethargy, anemia, respiratory distress, altered feeding behavior, and reduced activity, with young or immunocompromised birds particularly vulnerable to mortality. Diagnosis relies on a combination of clinical observations and laboratory methods, including traditional blood smears and serology alongside molecular tools such as Polymerase Chain Reaction (PCR), Next-Generation Sequencing (NGS), metagenomics, and transcriptomics. Treatment options are limited, typically involving antimalarial drugs such as chloroquine phosphate, primaquine phosphate, mefloquine, sulfachloropyrazine, sulfaquinoxaline, Trimethoprim, and Pyrimethamine-sulfadoxine combination along with supportive care and environmental management. Control strategies target both vectors and hosts, including habitat modification, chemical application, chemo-sterilization, the use of endosymbionts like Wolbachia, housing management, drainage of water bodies, biosecurity measures, vaccination, and the rearing of genetically resistant avian breeds. Ongoing research into the ecology of avian malaria and its vectors is essential for developing effective prevention strategies and mitigating its impact on vulnerable bird populations. This review synthesizes current knowledge on the epidemiology, transmission dynamics, and ecological consequences of avian malaria, with the goal of informing conservation and management strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s12639-025-01887-z.},
}