@article {pmid42374043,
year = {2026},
author = {Wu, J and Zhang, B and Ma, Y and Kuang, C and Hong, Y},
title = {Recovery of 178 metagenome-assembled genomes from sediments in subterranean estuary.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07716-z},
pmid = {42374043},
issn = {2052-4463},
support = {42476141//National Natural Science Foundation of China/ ; 42276130//National Natural Science Foundation of China/ ; 2025001//Open Fund of Hainan Xisha Marine Environment National Observation and Research Station/ ; 2024312281//Graduate Innovative Research Grant Program of Guangzhou Education Bureau/ ; 2023B1515120029//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A03J3103//Science and Technology Projects in Guangzhou/ ; },
abstract = {Subterranean estuaries (STEs), the mixing zones between terrestrial groundwater and seawater, function as critical biogeochemical reactors that buffer anthropogenic pollutants from entering the open ocean. To date, microbial diversity and community structure within STEs remain poorly characterized. Here, we reconstructed 178 metagenome-assembled genomes (MAGs) exclusively from bacteria (no archaeal MAGs identified). All MAGs met medium-quality standards (>70% completeness, <10% contamination), including 59 near-complete (>90%), 47 with completeness over 80%, and 23 over 75% complete genomes. These MAGs spanned 17 bacterial phyla, with Pseudomonadota dominating (30.9%). Crucially, 157 MAGs (88%) are unclassified at the species level based on GTDB assessment, potentially representing novel taxa, including 1 candidate family, 28 candidate genera, and 128 candidate species. This study provides a genomic resource for studying the functional roles of these unclassified taxa in STEs.},
}

@article {pmid42374196,
year = {2026},
author = {Ye, J and Mao, P and Li, B and Hao, Y and Chen, Y and Li, K},
title = {Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05346-4},
pmid = {42374196},
issn = {1471-2180},
abstract = {BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort.

METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16 S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis.

RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients.

CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.},
}

@article {pmid42374517,
year = {2026},
author = {Harvey, E and Van Brussel, K and Holmes, EC},
title = {Empowering One Health with metagenomics.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-026-00225-4},
pmid = {42374517},
issn = {2524-4655},
support = {GNT2017197//National Health and Medical Research Council/ ; },
abstract = {In an increasingly connected world a global One Health approach to the management of human, animal and ecosystem health will be critical to effective infectious disease responses. The emergence and rapid global spread of several emerging and re-emerging pathogens in the past decade has highlighted the need for rapid, sensitive and accurate diagnostics. Metagenomics, while commonly used for research purposes for almost two decades, entered the global spotlight during the COVID-19 pandemic. In this review we discuss the impacts that metagenomic studies have had on our understanding of origins, aetiology and ecology of infectious diseases within a One Health context. We also discuss the role of metagenomics in the future of diagnostics and disease surveillance, and outline the challenges and limitations of current metagenomic methods.},
}

@article {pmid42374552,
year = {2026},
author = {Wan, LY and Zou, J and Li, XM and Zhao, R and Yang, G and Zhang, MY and Xiao, QY and Wei, YD and Gao, JM and Yang, BP and Zhang, C and Jiao, YM and Wang, FS and Song, JW},
title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals pathogen spectrum and mortality predictors among patients with advanced HIV-1 disease at a tertiary hospital in China.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03234-x},
pmid = {42374552},
issn = {1743-422X},
support = {No. 20250484882//Beijing Nova Program, China/ ; No. 2025ZD01904603//National Science and Technology Major Project/ ; },
abstract = {BACKGROUND: Central nervous system (CNS) infections remain the major causes of morbidity and mortality among people living with HIV-1 (PLWH), particularly in resource-limited settings. However, the clinical characteristics and prognostic indicators of PLWH with suspected CNS infections are not well defined. In this study, we aim to characterize the spectrum of CNS pathogens, clinical characteristics, in-hospital mortality, and factors associated with death among people with advanced HIV-1 disease (AHD) in Guangxi, China.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed to analyze types of infection in cerebrospinal fluid (CSF) from 61 treatment-naive PLWH with suspected CNS infections. Clinical data, routine laboratory tests, and biochemical tests were collected and analyzed.

RESULTS: Among the 61 CSF samples, primarily with AHD, a total of 206 pathogens were identified. Viral pathogens predominated, with Epstein-Barr virus being the most frequently identified, followed by cytomegalovirus. Compared with patients with single-pathogen infection, those with multiple infections (viral, bacterial, and fungal) exhibited significantly lower CD4 T cell counts, higher C-reactive protein levels, and markedly reduced lipid metabolism parameters. However, infection types were not significantly associated with in-hospital death. Multivariate logistic regression analysis identified plasma low density lipoprotein (LDL) and CSF lactate dehydrogenase (LDH) as independent predictors of in-hospital death.

CONCLUSION: In PLWH with AHD and suspected CNS infections, multiple pathogens frequently coexist in the CSF. Plasma LDL and CSF LDH levels were independent predictors of death, indicating their potential value as early risk stratification in AHD.},
}

@article {pmid42374590,
year = {2026},
author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB},
title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02383-z},
pmid = {42374590},
issn = {2049-2618},
support = {Heritage_2020-005_RESTOROMIC//Österreichischen Akademie der Wissenschaften/ ; },
abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.

RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.

CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.},
}

@article {pmid42375904,
year = {2026},
author = {Panagiotidi, K and Markidis, A and Karamatzanis, I and Almomani, M and Omirou, R and Kosmidou, P},
title = {The Nasopharyngeal Microbiome: A Narrative Review of the Hidden Regulator of Ear, Nose, and Throat (ENT) Inflammations.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109921},
pmid = {42375904},
issn = {2168-8184},
abstract = {The nasopharyngeal microbiome is a central regulator of respiratory health. The upper airway microbial community acts as the primary gatekeeper against respiratory pathogens and maintains homeostasis in the upper respiratory tract (URT). This community is established at birth and influenced by the delivery method and antibiotic exposure. Disruptions to this balance are recognised as a major driver of chronic inflammatory ear, nose, and throat (ENT) diseases. This review analyses the literature on the relationship between the nasopharyngeal microbiome and inflammatory ENT diseases. We searched recent literature (2015-2025) via PubMed and Scopus, focusing on 16S rRNA and metagenomic studies of the upper respiratory tract. We examined papers that linked microbial shifts to clinical outcomes in otitis media, rhinosinusitis, and allergic rhinitis, as well as studies applying machine learning to diagnostic modelling. Clinical health is associated with stable colonisation by Dolosigranulum and Corynebacterium. These commensals protect the host by maintaining the mucosal barrier and competing against pathogens. Chronic disease, in contrast, is marked by a bloom of Streptococcus, Haemophilus, or Moraxella. In chronic rhinosinusitis, loss of bacterial diversity and S. aureus biofilm formation often lead to treatment failure. Machine learning tools like Random Forest and XGBoost classifiers have been applied to nasopharyngeal microbiome data. In published cohorts, these models have achieved sensitivity and specificity values of 80-90% for identifying dysbiotic profiles associated with disease, outperforming standard culture in speed and taxonomic resolution. These findings support a shift from broad antibiotic use toward microbiome-informed treatment. Standardising sampling and sequencing methods remains the next necessary step.},
}

@article {pmid42376027,
year = {2026},
author = {Dong, X and Xiao, R and Gao, C and Huang, S and Meng, X and Yan, X and Bai, Z and Wu, S},
title = {Ruxolitinib combined with azithromycin for scrub typhus-associated hemophagocytic lymphohistiocytosis in a child: a case report and narrative literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1852110},
pmid = {42376027},
issn = {2296-2360},
abstract = {BACKGROUND: Scrub typhus-associated hemophagocytic lymphohistiocytosis (HLH) is a rare but life-threatening complication in children, with reported mortality of 11.9%-30%. Conventional immunomodulation with corticosteroids and intravenous immunoglobulin often provides insufficient control of the hyperinflammatory state, while etoposide-based chemotherapy carries significant toxicity. JAK1/2 inhibition targeting the interferon-gamma pathway represents a promising therapeutic strategy, but its application in scrub typhus-associated HLH has not been previously reported.

CASE PRESENTATION: A 5-year-11-month-old girl with no prior medical history presented with persistent fever, tachypnea, hepatosplenomegaly, and a 0.5 cm eschar in the left axilla after travel to Yunnan Province, China. Laboratory findings revealed pancytopenia (platelets 40× 10[9]/L), hyperferritinemia (>2,000 ng/mL), hypofibrinogenemia (1 g/L), and elevated interferon-gamma (135.48 pg/mL). Bone marrow aspiration demonstrated hemophagocytosis. Metagenomic next-generation sequencing confirmed Orientia tsutsugamushi infection. The patient met six of eight HLH-2004 diagnostic criteria. She was treated with oral ruxolitinib (5 mg twice daily) initiated on the day of admission, followed by intravenous azithromycin (10 mg/kg once daily) after confirmatory testing. Fever resolved within 72 h. Ruxolitinib was temporally associated with rapid clinical improvement, although causal attribution cannot be established due to concurrent therapies. By day 8, platelet count normalized to 240× 10[9]/L, ferritin declined to 1,246 ng/mL, and fibrinogen recovered to 2.4 g/L. The patient was discharged on day 13 with ruxolitinib tapered to 2.5 mg daily. At 3-month follow-up, she remained well with normal laboratory parameters.

LITERATURE REVIEW: Narrative literature review of 66 previously reported pediatric cases from Chinese and English databases (inception to May 2026) plus the present case revealed an overall mortality of 11.94% (8/67). Among these patients, 43 (64.2%) received corticosteroids, 34 (50.7%) received intravenous immunoglobulin, and only 3 (4.5%) received etoposide. The published cases suggest that absence or delay of anti-rickettsial therapy is associated with poor outcomes, though the evidence is limited by case-report bias and confounding.

CONCLUSION: This is the first report of successful JAK1/2 inhibitor therapy in scrub typhus-associated HLH. This case raises a hypothesis worth investigating further-that ruxolitinib combined with azithromycin may achieve rapid disease control with good tolerability. Prospective studies are needed to evaluate the role of targeted JAK inhibition in infection-triggered HLH.},
}

@article {pmid42376290,
year = {2026},
author = {Onumanyi, V and Ogola, HJO and Ijoma, GN and Semenya, K},
title = {PacBio HiFi sequencing datasets of culture-enriched airborne microbial cave communities from dolomitic Sudwala Caves, South Africa.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112970},
pmid = {42376290},
issn = {2352-3409},
abstract = {We present a dataset integrating physico-chemical air quality measurements with long-read PacBio HiFi shotgun metagenomic sequences from culture-enriched airborne samples collected in Sudwala Caves, one of the oldest known cave systems in South Africa. This resource provides baseline characterization of airborne microbial communities and associated environmental parameters within a subterranean karst ecosystem. A total of 106 air samples were collected across six different cave compartments and three external reference sites spanning two seasonal periods, the winter-spring transition (September-October 2024) and the summer-autumn window (February-March 2025). Environmental metadata include temperature, relative humidity, particulate matter (PM1.0, PM2.5, PM10), and formaldehyde (HCHO) concentrations, enabling direct linkage between microbial composition and air quality dynamics. Post-quality control of eighteen (18) culture-enriched metagenome datasets yielded 7.7 × 10[4] to 7.8 × 10[5] HiFi reads per sample corresponding to 0.63-6.71 Gb of high-accuracy sequence data per sample. Kaiju classification assigned 65.1-83.4% of assembled sequences to reference taxa. Domain-level profiles were dominated by Bacteria (98.7-99.9% of classified sequences), with minor representation of Eukaryota (0.06-0.15%) and extremely low abundances of Archaea (0.002-0.009%) and Viruses (0.000-0.001%). At the phylum level, airborne bacterial communities were consistently dominated by Bacillota (mean relative abundance: 46.92%), Pseudomonadota (34.28%), and Actinomycetota (15.71%) across all sampling sites and seasons, with Pseudomonadota and Actinomycetota exhibiting proportionally higher representation within cave interior environments relative to outdoor reference sites. At the genus level, Staphylococcus, Bacillus, Microbacterium, Arthrobacter, and Pseudomonas were among the most consistently detected and abundant airborne genera within cave compartments, whilst outdoor aerobiome communities were characterised by greater relative abundances of Planococcus, Sphingomonas, Stenotrophomonas, and Arthrobacter. Functional annotation using the DRAM pipeline identified 1205,651 predicted genes, with 579,682 KEGG orthologs (KO), 62,261 MEROPs peptidases, 904,193 Pfam domains, and 21,859 CAZy genes annotated. This dataset supports investigations of culturable airborne microbial composition, functional capacity, bioaerosol dynamics, and environmental health indicators in dolomitic subterranean karst systems, providing a reference framework for comparative studies of low-biomass atmospheric environments.},
}

@article {pmid42376319,
year = {2026},
author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S},
title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828012},
pmid = {42376319},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; },
abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.

METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.

RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p = 0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p = 0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p < 0.05).

CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.},
}

Humans
*Colorectal Neoplasms/microbiology
*Feces/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
Male
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Multiomics
High-Throughput Nucleotide Sequencing
Adult
Metagenome

@article {pmid42376322,
year = {2026},
author = {Qin, Q and Ning, YC and Zhu, SN and Ma, JH and Chen, W and Tian, W and Wang, CM and Wu, YF and Li, SL},
title = {Performance of metagenomic next-generation sequencing for bloodstream infections in perioperative critically ill patients- a post-hoc analysis of a prospective, multi-center cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1814969},
pmid = {42376322},
issn = {2235-2988},
mesh = {Humans ; Prospective Studies ; Female ; *Metagenomics/methods ; Critical Illness ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Intensive Care Units ; *Bacteremia/diagnosis/microbiology ; Aged ; Middle Aged ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Blood Culture ; *Sepsis/diagnosis/microbiology ; },
abstract = {BACKGROUND: Bloodstream infections (BSI) in intensive care unit (ICU) patients are associated with high morbidity and mortality, necessitating rapid and accurate pathogen identification to guide early antimicrobial therapy. However, traditional blood culture (BC) is limited by the long turnaround time and low sensitivity. Metagenomic next-generation sequencing (mNGS) has been applied in infectious disease diagnostics, but its clinical utility for perioperative ICU patients with BSI requires further evaluation.

METHODS: This post-hoc analysis included 219 perioperative ICU patients (from a prospective, multi-center cohort, July 2020-June 2023) who underwent concurrent mNGS and BC testing. The study compared pathogen detection differences between the two methods, and evaluated the diagnostic value of mNGS for clinical BSI based on mNGS-assisted clinical diagnostic criteria. Additionally, the impact of mNGS findings on clinical antimicrobial management was assessed.

RESULTS: mNGS demonstrated a higher overall pathogen detection rate than BC in the 219 enrolled patients (25.1% vs. 9.6%, p < 0.001), with significant advantages in detecting Gram-negative bacteria (13.2% vs. 5.9%, p = 0.009), anaerobes (3.6% vs. 0.5%, p = 0.018), and fungi (6.4% vs. 0.9%, p = 0.002). Mixed-pathogen infections were identified in 20% of mNGS-positive clinical BSI cases, whereas BC-positive cases exclusively had single-pathogen infections. Ultimately, 64 patients (29.2%) were diagnosed with clinical BSIs. The sensitivity and specificity of the mNGS were 85.9% (95% CI: 74.5%-93.0%), and 80.6% (95% CI: 73.4%-86.4%), respectively, and the area under the receiver operating characteristic curve was 0.833 (95% CI: 0.772-0.894). The positive predictive value and negative predictive value were 64.7% (95% CI: 53.5%-74.6%) and 93.3% (95% CI: 87.3%-96.7%), respectively. Additionally, mNGS led to a positive impact in 56 patients (25.6%), manifested by the identification of new pathogens and guidance for targeted therapy, a negative impact in 11 patients (5.0%), and no clinical impact in 152 patients (69.4%).

CONCLUSIONS: For perioperative ICU patients, mNGS demonstrated superior pathogen detection rates, broader microbial spectrum coverage, and enhanced polymicrobial infection detection capability versus BC. mNGS exhibited high diagnostic value for clinical BSI, with the potential to facilitate targeted antimicrobial therapy adjustments.},
}

Humans
Prospective Studies
Female
*Metagenomics/methods
Critical Illness
*High-Throughput Nucleotide Sequencing/methods
Male
Intensive Care Units
*Bacteremia/diagnosis/microbiology
Aged
Middle Aged
Sensitivity and Specificity
Bacteria/genetics/classification/isolation & purification
Blood Culture
*Sepsis/diagnosis/microbiology

@article {pmid42376574,
year = {2026},
author = {Biełło, K and Rodríguez-Caballero, G and Becerra-Mora, D and Dorado-Blanco, N and Sáez-Melero, LP and Moreno-Vivián, C and Luque-Almagro, VM and Olaya-Abril, A and Roldán, MD},
title = {Exploring the Tenebrio molitor gut microbiota response to LDPE and PET: putative genetic indicators and methodological insights.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746922},
pmid = {42376574},
issn = {1664-302X},
abstract = {Insect gut microbiomes are recognized as potential reservoirs of enzymatic activities relevant to plastic metabolism. Here, we investigated the taxonomic and functional dynamics of the Tenebrio molitor gut microbiota under dietary exposure to low-density polyethylene (LDPE) and polyethylene terephthalate (PET) using 16S rRNA sequencing and shotgun metagenomics. Significant compositional shifts were detected at the ASV level, with plastic-fed cohorts showing enrichment of taxa implicated in xenobiotic metabolism. Predicted functional changes suggested altered abundance of pathways related to aromatic compound processing and redox homeostasis. Metagenomic assembly and functional annotation, performed through a reproducible open-source workflow, revealed several putative proteins with distant homology to enzymes such as phthalate dioxygenases, urethanases, and polyhydroxyalkanoate depolymerases. A metagenome-assembled genome (MAG) assigned to Enterococcus accounted for most recovered protein-coding sequences. Although gene-level comparisons did not show statistically significant differences, Gene Set Enrichment Analysis (GSEA) highlighted ABC transporter signatures and stress-response ATPases under plastic-exposed conditions. Overall, this exploratory study reveals microbial shifts and putative genetic indicators of metabolic potential within the T. molitor gut, providing a reproducible analytical framework for future investigations into the microbial role in plastic bioconversion.},
}

@article {pmid42376617,
year = {2026},
author = {Lee, YS and Kuo, TF and Yang, G and Liang, YC and Yang, WC},
title = {Bidens pilosa extract and bentonite, a phytogenic formulation, as a feed additive to improve diarrhea and gut microbiota in calves: Effects on feed use and regulation of gut microbiota.},
journal = {Veterinary and animal science},
volume = {34},
number = {},
pages = {100732},
pmid = {42376617},
issn = {2451-943X},
abstract = {Phytogenics are emerging as an alternative approach to maintain animal health and productivity without using antibiotics in the livestock industry. This study investigated the function and mechanism of a phytogenic formulation composed of Bidens pilosa extract and bentonite (BPB) on diarrhea, gut microbiota and growth performance in calves. Twenty-six 15-day-old Holstein Friesian calves were fed control or 0.5% BPB diets for 4 weeks. Their diarrhea, gut microbiota, fecal IgA, and bacterial growth were analyzed using culture-based methods, 16S rRNA sequencing, and statistical analyses. BPB (0.5%) significantly reduced diarrhea, fecal scores, and fecal IgA levels, but increased body weight in calves. Furthermore, metagenomic analysis and selective agar assays indicated that 0.5% BPB decreased three bacterial genera, Campylobacter, Clostridium_sensu_stricto_1, and Escherichia/Shigella, but increased seven other bacterial genera, including Lactobacillus, Ruminococcus, and Bacteroides, in the feces of calves. Mechanistic studies suggested that BPB augmented the proliferation of bacteria associated with beneficial effects, subsequently inhibiting the growth of bacteria associated with harmful effects in the intestines of calves. In conclusion, BPB mitigated diarrhea and gut inflammation and increased body weight gain in calves by modulating the gut microbiota. This modulation involved the upregulation of bacteria with beneficial potential that antagonize the growth of bacteria with pathogenic potential.},
}

@article {pmid42376710,
year = {2026},
author = {Arguelles, EDLR and Mugikura, K and Sato, S},
title = {Impact of the invasive diatom species Cymbella janischii on riverine microbial biofilm communities and a potential role of bacterially produced zeatin.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70195},
pmid = {42376710},
issn = {1529-8817},
support = {21A402//Japan Society for the Promotion of Science/ ; 23K05398//Japan Society for the Promotion of Science/ ; 26K01814//Japan Society for the Promotion of Science/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
abstract = {The diatom Cymbella janischii is an invasive species in Japan, causing nuisance blooms by forming thick mats in rivers. To date, there are no documented studies on the microbiome associations in C. janischii mats or the processes that drive bloom formation. This study used metabarcoding of diatoms, bacteria, and fungi to identify key species and assess the effects of C. janischii blooms on the benthic microbial communities. C. janischii blooms reduced diatom and bacterial species diversity, while fungal diversity remained stable. In addition, the diatom Nitzschia paleacea and the bacterium Flavobacterium sp. were observed to co-occur and vary in abundance, indicating a possible ecological link that may affect mat structure or function. Metagenomic predictions of bacterial functions showed that compared to benthic stones without visible C. janischii mats, mat-associated bacteria had enriched pathways related to the metabolism of carbohydrates, nucleotides, and amino acids, along with zeatin biosynthesis. Zeatin is a cytokinin phytohormone that stimulates plant growth and development. In vitro exposure of C. janischii to varying zeatin concentrations confirmed its growth-promoting effects, inducing cell proliferation and stalk formation. This study shows that zeatin stimulates the growth of C. janischii. The findings of this study provide new insights into microbiome diversity, identifying key taxa associated with C. janischii mats to help better understand bloom formation.},
}

@article {pmid42377028,
year = {2026},
author = {Lenz, C and Seel, W and Dombrowski, T and Hacker, S and Simon, M-C and Zentgraf, K and Dawczynski, C and Krüger, K},
title = {Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048926},
doi = {10.1128/msystems.00489-26},
pmid = {42377028},
issn = {2379-5077},
abstract = {Elite athletes undergo intense physical training and experience substantial physiological stress, which could affect the composition and function of their gut microbiome. This study compared the gut microbiomes of 148 German junior and senior elite athletes with those of 108 healthy adults to identify taxonomic and functional features associated with elite athletic status. Group comparisons were conducted between healthy adults, senior athletes, and junior athletes, and a matched-subgroup analysis was performed in adults only, controlling for age, sex, body mass index, and dietary pattern. Significant differences in taxonomic composition were observed between athletes and healthy adults. Healthy adults exhibited greater microbial evenness and diversity than junior athletes, whereas senior athletes displayed higher microbial richness. Principal coordinate analysis revealed distinct clustering by athletic status. Linear discriminant analysis effect size identified taxa such as Escherichia-Shigella as being enriched in athletes. Predictive metagenomic profiling (PICRUSt2) indicated differences in microbial functional potential between adult athletes and matched controls, including pathways related to amino acid metabolism, glycolysis, fatty acid β-oxidation, and quinone biosynthesis. Together, these findings demonstrate distinct taxonomic and predicted functional microbiome signatures associated with elite athletic status.IMPORTANCEElite athletic training and lifestyle are associated with the gut microbiome. Our research has revealed distinct microbial structures in elite athletes, characterized by reduced evenness in junior athletes and increased richness in senior athletes, compared to healthy adults. Matched-subgroup analyses confirmed these group-specific differences. The gut microbiomes of athletes were enriched in pathways related to amino acid biosynthesis, glycolysis, fatty acid β-oxidation, and quinone synthesis. These microbiome features may be relevant for metabolic efficiency and resilience to oxidative stress. Combining taxonomic and functional prediction data from a uniquely characterized cohort of junior and senior elite athletes provides novel insight into microbiome signatures associated with sustained physical and psychological stress, with potential implications for performance, recovery, and health.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT03582020.},
}

@article {pmid42377463,
year = {2026},
author = {Brenner, T and Skarabis, A and Schaller, SJ and von Groote, T and Putensen, C and Günther, U and Sauer, M and Decker, SO and Dusse, F and Weiss, M and Suchodolski, K and Simon, TP and Rosenberger, P and Moerer, O and Unterberg, M and Schewe, JC and Bracht, H and Hutzl, S and Feißt, M and Marschall, U and Brandenburg, P and Stevens, P and Schmidt, J and Pletz, MW and Berger, MM and , },
title = {Effects of a clinical metagenomics intervention on clinical outcomes, healthcare costs, and health-related quality of life in patients with sepsis or septic shock: results of the randomized-controlled DigiSep trial.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
pmid = {42377463},
issn = {1432-1238},
support = {01NVF20013//German Innovation Fund/ ; },
abstract = {PURPOSE: Early pathogen detection is crucial in sepsis. We hypothesized that detection of microbial circulating cell-free DNA by metagenomic next-generation sequencing (mNGS) improves clinical outcomes and health-related quality of life without increasing healthcare costs.

METHODS: This randomized, controlled, interventional, open-label, multicenter trial was conducted in 24 intensive care units across Germany. The intervention group (n = 200) received mNGS diagnostics in addition to standard-of-care microbiology, compared with standard-of-care microbiology alone (control group; n = 189). The primary endpoint was the Desirability of Outcome Ranking/Response Adjusted for Duration of Antibiotic Risk (DOOR/RADAR) score.

RESULTS: The DOOR/RADAR score was not significantly improved at 28 days after sepsis onset (intervention group: 3.21 ± 1.54; control group: 3.49 ± 1.51; 95% CI - 0.58 to 0.03). However, other secondary endpoints were improved, including a reduced duration of mechanical ventilation (intervention group: 6.6 ± 9.4 days; control group: 9.3 ± 10.6 days; 95% CI - 5.03 to - 0.34) and faster shock resolution (intervention group: 6.9 ± 7.4 days; control group: 8.8 ± 8.5 days; 95% CI - 3.75 to - 0.04). Health-related quality of life at 90 days (EQ-5D-5L) was improved in the intervention group (0.312 ± 0.386) compared with the control group (0.208 ± 0.373; p = 0.047). In the subgroup with available claims data (33.2% of participating patients), healthcare costs over 180 days did not differ.

CONCLUSION: The DOOR/RADAR score as primary endpoint was not significantly improved by mNGS. Exploratory secondary analyses revealed improvements in secondary endpoints. (Funding: German Innovation Fund; ClinicalTrials.gov number, NCT04571801, registration: 25.8.2020).},
}

@article {pmid42377624,
year = {2026},
author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C},
title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42377624},
issn = {1573-0972},
mesh = {*Wastewater/microbiology ; *Microalgae/growth & development/microbiology ; Phylogeny ; *Bacteria/isolation & purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; },
abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.},
}

*Wastewater/microbiology
*Microalgae/growth & development/microbiology
Phylogeny
*Bacteria/isolation & purification/classification/genetics/metabolism
RNA, Ribosomal, 16S/genetics
Biomass
Microbial Consortia
Coculture Techniques
Biofuels
DNA, Bacterial/genetics
Metagenomics
Water Purification

@article {pmid42377631,
year = {2026},
author = {Thakur, A and Gupta, P and Sethi, S and Apreja, M and Ahmed, S and Sharma, L},
title = {Exploring the antibacterial potential of a designed peptide against Gardnerella vaginalis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42377631},
issn = {1573-4978},
mesh = {*Gardnerella vaginalis/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Antimicrobial Peptides/pharmacology ; Female ; Vaginosis, Bacterial/drug therapy/microbiology ; Hemolysis/drug effects ; Cell Survival/drug effects ; *Antimicrobial Cationic Peptides/pharmacology ; Peptides, Cyclic/pharmacology ; },
abstract = {BACKGROUND: Bacterial vaginosis (BV) is a common vaginal dysbiosis caused by Gardnerella vaginalis, a facultative anaerobic bacillus. The failure of conventional antibiotics and recurrence of bacterial vaginosis call for alternative novel therapeutic strategies. Antimicrobial peptides (AMPs) provide a targeted, resistance-sparing alternative with their broad-spectrum activity and distinct mode of action.

METHODS: Two AMPs, i.e., TCCP-1 (cyclic) and ZMLP-2 (linear), were designed in silico from proteome sequences of Thymbra capitata and Zataria multiflora already available in NCBI. The designed peptides were chemically synthesized, evaluated for their antibacterial activity, cytotoxicity, hemolytic effects and mechanism of action against G.vaginalis.

RESULTS: TCCP-1, a cyclic peptide with an MIC of 1.95 µg/mL against G. vaginalis showed minimal cytotoxicity even at 100 µg/mL, which is much higher than its MIC value (1.95 µg/mL). TCCP-1 maintained high cell viability at lower concentrations, while a concentration-dependent reduction in viability was observed at higher concentrations. In contrast, ZMLP-2, a linear AMP, showed weak antimicrobial activity with an MIC of 100 µg/mL, exhibited a moderate reduction in cell viability (~ 70-75%) when tested at 100 µg/mL or a concentration below its MIC. Both peptides showed the disruption of bacterial membranes and, therefore, support the re-establishment of healthy vaginal flora. More significantly, TCCP-1 demonstrated efficient antimicrobial activity against G.vaginalis along with decreased cytotoxicity, making it an excellent candidate for future in vivo studies and possible clinical uses.

CONCLUSIONS: Thus, plant-derived AMPs could prove to be useful, targeted, and sustainable alternatives to BV prevention while treating both resistance and recurrence.},
}

*Gardnerella vaginalis/drug effects
Humans
*Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
*Antimicrobial Peptides/pharmacology
Female
Vaginosis, Bacterial/drug therapy/microbiology
Hemolysis/drug effects
Cell Survival/drug effects
*Antimicrobial Cationic Peptides/pharmacology
Peptides, Cyclic/pharmacology

@article {pmid42377725,
year = {2025},
author = {Yun, S and Seo, Y and Yoon, Y},
title = {Prevalence of Microorganisms and Suggestion for Potential Contribution of Microorganisms to Volatile Basic Nitrogen Production in Beef at Current Purchase Stages.},
journal = {Food science of animal resources},
volume = {45},
number = {6},
pages = {1710-1723},
doi = {10.5851/kosfa.2025.e14},
pmid = {42377725},
issn = {2636-0780},
abstract = {This study investigated the prevalence of microorganisms related to meat quality and analyzed volatile basic nitrogen (VBN) levels in beef samples to suggest potential bacteria that might contribute to VBN production at current purchase stages using metagenomic analysis. Seventy beef samples were analyzed for coliform, Escherichia coli, enterohemorrhagic E. coli, Listeria monocytogenes, Salmonella, Staphylococcus aureus, total aerobic bacteria (TAB), Enterobacteriaceae, lactic acid bacteria (LAB), Pseudomonas spp., yeast and molds (YM), and psychrotrophic bacteria (PB). VBN levels ranged from 0.69 to 22.51 mg%. Microbiota from three samples with the highest and three with the lowest VBN levels were analyzed. S. aureus was detected in only one sample at 1.2 Log CFU/g. The cell counts for TAB, coliform, Enterobacteriaceae, LAB, Pseudomonas spp., YM, and PB were 5.1, 1.7, 2.6, 4.2, 1.9, 2.9, and 5.4 Log CFU/g, respectively. Microbiota analysis revealed that samples with high VBN levels had high relative abundances of Lactobacillus and Leuconostoc. This study showed that these relatively abundant LAB were potential bacteria that might contribute to producing more VBN in beef at current purchase stages. However, the potential bacteria were suggested only by metagenomic analysis with a limited sample size without considering the endogenous meat enzymes. Therefore, further research is necessary to identify and isolate these bacteria with a larger sample size while excluding VBN produced by endogenous enzymes. Additionally, environmental factors not included due to the limited objective of this study could also be considered in further research with the different objectives from this study.},
}

@article {pmid42377908,
year = {2026},
author = {Deng, Y and Borton, MA and Nesbø, CL and Forster, MD and Konhauser, KO and Gingras, MK and Goss, GG and Wrighton, KC and Lanoil, BD and Zhong, C and Alessi, DS},
title = {Geochemistry shapes microbial diversity and selected functional traits in flowback and produced waters from hydraulically fractured formations.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag070},
pmid = {42377908},
issn = {1574-6941},
abstract = {Microbial communities inhabiting hydraulically fractured subsurface waters are increasingly recognized as important components of unconventional oil and gas systems because they can influence water quality, infrastructure integrity, and biogeochemical processes during flowback and production. However, a quantitative cross-basin understanding of their taxonomic diversity, ecological organization, and potential functional variation remains limited. In this study, we analyzed 16S rRNA gene amplicons, metagenomes, and geochemical data from flowback and produced water (FPW) from the Sichuan Basin, China, and conducted a quantitative comparison to data previously reported from the same basin and hydraulic fracturing (HF) regions in North America. Our findings revealed strong co-occurrence patterns among fermentative, sulfidogenic, and methanogenic microorganisms, which emerged as core members of microbial communities across all fractured subsurface environments. Notably, microbial diversity and selected metabolic traits differed across basins in the low-salinity systems of China, whereas high-salinity basins in North America exhibited reduced diversity and more constrained metabolic capabilities. These differences are consistent with salinity acting as an important ecological filter across the analyzed basins. Our results indicate that basin-specific geochemical context, particularly salinity, is closely associated with cross-basin differences in microbial diversity, community composition, and selected metabolic traits in fractured subsurface waters. These findings support the value of integrating geological, geochemical, and microbiological information when interpreting microbial risks and water-management strategies in hydraulic fracturing systems.},
}

@article {pmid42378511,
year = {2026},
author = {Zhang, R and Wang, B and Lu, J and Wu, J and Liu, X and Zhang, R and Marsili, E and Gong, C},
title = {The Food Additives p-Coumaric Acid Production from Corn Stalk Catalyzed by a Cold-Adapted Carboxylesterase.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c05955},
pmid = {42378511},
issn = {1520-5118},
abstract = {p-Coumaric acid is a widely utilized food additive with beneficial biological activities. A novel enzymatic catalysis strategy for the production of p-coumaric acid from lignocellulosic biomass is proposed herein. The gene encoding a carboxylesterase was identified in metagenome-assembled genome and further characterized in the isolated Glutamicibacter soli Em07. The target protein, with a molecular weight of 53 kDa, was successfully obtained through heterologous expression. The carboxylesterase exhibited cold adaptation, with optimal activity at 35 °C and pH 7.0 using 1-naphthyl acetate as substrate, and maintained over 75% of the maximum activity after incubation at 25 °C for 2 h. At 25 °C, 35.9 ± 0.4 μg of p-coumaric acid was obtained from 20 mg of corn stalk via carboxylesterase-mediated catalysis. This work achieves a high p-CA yield from lignocellulosic biomass via low-temperature enzymatic catalysis without pretreatment. The results offer valuable progress toward manufacturing high-value food additives, including p-CA.},
}

@article {pmid42378616,
year = {2026},
author = {Tyler, RS and Charles, DW and Mills, AG and Alkabab, Y},
title = {Disseminated Mycobacterium immunogenum -associated Hemophagocytic Lymphohistiocytosis after Stem Cell Transplantation.},
journal = {International journal of mycobacteriology},
volume = {15},
number = {2},
pages = {179-182},
pmid = {42378616},
issn = {2212-554X},
abstract = {Secondary hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory syndrome most commonly triggered by infection, malignancy, or transplant-related immune dysregulation. Rapidly growing mycobacteria are uncommon causes of disseminated infection and have only rarely been reported as infectious triggers of HLH. A 56-year-old immunocompromised woman with a history of allogeneic hematopoietic stem cell transplant presented with recurrent fever, progressive transaminitis, and laboratory features consistent with secondary HLH. Liver biopsy showed granulomatous hepatitis with iron overload. Initial treatment with dexamethasone and anakinra resulted in transient clinical improvement. Less than 2 weeks later, she was readmitted with worsening hepatic dysfunction and found to have acid-fast bacilli in blood and bone marrow cultures, later identified as Mycobacterium immunogenum. Despite targeted antimicrobial therapy, the patient developed progressive hepatic and renal failure and died. To our knowledge, this case represents the first reported case of disseminated M. immunogenum infection precipitating secondary HLH, expanding the recognized clinical spectrum of this rapidly growing nontuberculous mycobacterium and highlights the diagnostic challenges of atypical mycobacterial infection in immunocompromised hosts.},
}

@article {pmid42378712,
year = {2026},
author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M},
title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {6},
pages = {},
doi = {10.1093/ecco-jcc/jjag080},
pmid = {42378712},
issn = {1876-4479},
support = {//Takeda Pharmaceutical Company Ltd/ ; },
abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.

DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n = 23) or CgF (n = 17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.

RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.

CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.},
}

@article {pmid42378762,
year = {2026},
author = {Liu, J and Tan, Y and Fan, X and Xie, S and Xu, X and Zhu, L},
title = {Exogenous vitamin B12 alleviated inhibition of salinity on anaerobic dichloromethane degradation by reducing cofactor-related constraints and reshaping community functional potential.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142823},
doi = {10.1016/j.jhazmat.2026.142823},
pmid = {42378762},
issn = {1873-3336},
abstract = {Dichloromethane (DCM) frequently co-occurs with high salinity in industrial wastewater, imposing dual stress on anaerobic treatment. However, how anaerobic DCM degraders respond to salt stress and whether exogenous vitamin B12 (VB12, a key cofactor in DCM transformation) can facilitate DCM degradation remain poorly understood. Here, we established long-term enrichments (>800 days) of DCM-degrading consortia under non-saline and salt-stressed conditions (10 g/L NaCl) to investigate how VB12 affected degradation performance, community assembly, and functional potential. Salt stress significantly inhibited DCM degradation, reducing the maximum degradation rate by 71.5%, whereas VB12 substantially alleviated this inhibition and increased the degradation rate to 55.9% of the non-saline control. Metagenomic and co-occurrence network analyses indicated that salinity drove community reassembly and niche differentiation, linking DCM degraders, methanogens/homoacetogens, and fermenters within an inferred producer-cooperator-cross-feeder framework that maintained community stability under salt stress. Functional analyses showed that VB12 was associated with shifts in community functional potential toward hydrogenotrophic/acetoclastic methanogenesis and osmoadaptive metabolism, supporting stress adaptation under saline conditions. Further analysis of the mec (methylene chloride catabolism) cassette suggested that VB12 likely reduced cofactor-related constraints and reinforced downstream product-consuming functions, thereby contributing to the enhanced degradation performance. Notably, a previously uncharacterized Dehalobacteriaceae MAG, D_MAG.168, emerged as a dominant candidate DCM degrader under salt stress. Overall, these findings provide insight into the functional responses of DCM-degrading consortia to VB12 supplementation under salt stress and support the further development of VB12-assisted bioaugmentation strategies for DCM-contaminated saline industrial wastewater.},
}

@article {pmid42378793,
year = {2026},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and Jank, L and Barreto, F and Dorn, M and Cardoso, MRI and Siqueira, FM},
title = {Swine waste stabilization ponds as hotspots for antimicrobial resistance gene accumulation: a longitudinal metagenomic study.},
journal = {International journal of hygiene and environmental health},
volume = {276},
number = {},
pages = {114857},
doi = {10.1016/j.ijheh.2026.114857},
pmid = {42378793},
issn = {1618-131X},
abstract = {Using next-generation sequencing, this study provides a comprehensive longitudinal assessment of bacterial communities, antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs), and metabolic pathways in a full-scale swine waste treatment system in Brazil. Samples were collected from the first (WSP1) and final (WSP4) waste stabilization ponds of a farrow-to-finish farm during four sampling events between October 2022 and January 2023. Antibiotic molecules were additionally identified and quantified using solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry. Bacterial community composition remained remarkably stable over time. Similarly, the resistome and mobilome showed pronounced temporal stability, although a consistently higher relative abundance of ARGs and MGEs was observed in the final treatment process (WSP4). Genes encoding resistance markers of human-health relevance were detected in WSP4, including Paer_PhoP_CST, associated with polymyxin (colistin) resistance; PRC-1, linked to resistance to third-generation cephalosporins; and quinolone resistance determinants such as adeF, Paer_parE_FLO, and Mtub_gyrB_FLO. Genes encoding efflux pump complexes associated with multidrug resistance were also identified, including Paer_CpxR, PmpM, YajC, MuxB, and MexW. Supporting these findings, fluoroquinolones (ciprofloxacin and norfloxacin), lincomycin, and tetracycline molecules were detected in the waste ponds, indicating sustained selective pressure within the system. The accumulation of clinically relevant resistance determinants in the final of the waste treatment process, whose effluent is reused for agricultural irrigation, highlights waste stabilization ponds as potential hotspots for the persistence and environmental dissemination of antimicrobial resistance. These findings underscore the urgent need for improved monitoring and management of livestock waste treatment systems to mitigate antimicrobial resistance dissemination across agroecosystems.},
}

@article {pmid42378969,
year = {2026},
author = {Xing, BS and Wu, YF and Zhang, Y and Wang, XC and Li, YY and Chen, R},
title = {Carbon cloth-mediated direct interspecies electron transfer effect on the intensification mechanism of high-load codigestion dynamic membrane bioreactors.},
journal = {Water research},
volume = {304},
number = {},
pages = {126376},
doi = {10.1016/j.watres.2026.126376},
pmid = {42378969},
issn = {1879-2448},
abstract = {Acidification under high organic loading conditions and control of dynamic membrane (DM) thickness remain major challenges in the development of anaerobic dynamic membrane bioreactors (AnDMBR). In anaerobic digestion (AD), conductive materials can promote electron exchange between electron donors and acceptors, thereby accelerating electron transfer and enhancing direct interspecies electron transfer (DIET). These processes can improve methane yield and process stability at higher organic loading rates (OLRs). In this study, a carbon cloth anaerobic dynamic membrane bioreactor (CC-AnDMBR) was constructed and compared with a common nylon mesh anaerobic dynamic membrane bioreactor (NM-AnDMBR) to investigate the impact of DIET reinforcement on system performance and stability. The maximum load tolerance of the system and changes in microorganisms during this process were further evaluated to elucidate the mechanisms underlying enhanced system resilience. At a hydraulic retention time of 6.25 days (OLR of 20.13 g COD/L/day), the methane production rate of the carbon cloth reactor (313.74 ± 41.06 mL/g COD) was significantly greater than that of the nylon mesh reactor (256.02 ± 63.29 mL/g COD). Metagenomic analysis revealed that carbon cloth membranes are more conducive to the enrichment of Geobacter, which can exchange electrons with the dominant archaeal genus Methanosarcina, thereby accelerating the DIET rate within the CC-AnDMBR. The enhanced performance of the carbon cloth reactor was attributed to the higher electrical conductivity, more negative oxidation-reduction potential value, and higher electron transport system activity of the sludge. These characteristics together created a more conducive environment for conductive microorganisms and improved the system's electron transfer rate.},
}

@article {pmid42378973,
year = {2026},
author = {Min, H and Wang, Y and Wang, Q and Zhang, J and Lin, L and Li, X and Li, B},
title = {Cefpirome biodegradation by enriched bacterial consortia and isolated strain Bosea sp. MYQ: Novel insights on biodegradation pathway and bacterial interaction patterns.},
journal = {Water research},
volume = {304},
number = {},
pages = {126351},
doi = {10.1016/j.watres.2026.126351},
pmid = {42378973},
issn = {1879-2448},
abstract = {Deciphering the metabolic fate of cefpirome is essential for designing more efficient biodegradation strategies. In this study, we integrated second- and third-generation metagenomic sequencing with high-performance liquid chromatography-quadrupole time-of-flight mass spectrometer (HPLC-QTOF-MS) to unravel cefpirome biodegradation by a long-term enriched bacterial consortium and its key isolate Bosea sp. MYQ. Five biodegradation products were detected and mapped onto three cooperative pathways. Among them, four products involved in Pathways 2 and 3 were first identified in cefpirome biodegradation. Genome-scale metabolic modeling and genome-resolved metagenomics jointly revealed a pollutant-degrading network coordinated by two keystone donors, MAG2 (Variovorax) and MAG3 (Bosea sp. MYQ). They were primarily responsible for β-lactam ring-opening and the formation of downstream products, while exporting diverse metabolic intermediates to sustain pathway continuity through cross-feeding. Notably, MAG3 (Bosea sp. MYQ) encodes per-1 and bla, which likely contribute critically to cefpirome degradation by underpinning key β-lactam transformation steps. Complementary functions were provided by auxiliary and rare members, particularly MAG4 (Hyphomicrobium), MAG7 (Pandoraea), MAG10 (Methyloversatilis), and MAG21 (Phenylobacterium). These findings expand the repertoire of cefpirome-degrading microorganisms, reveal previously unrecognized biodegradation pathways, and clarify the microbial interaction network underpinning fourth-generation cephalosporin removal.},
}

@article {pmid42379260,
year = {2026},
author = {Alamri, MM and Proctor, G and Garcia-Guevara, F and Guennec, AL and Mainas, G and Shoaie, S and Nibali, L},
title = {Multiomics Analyses in Young Grade C Molar Incisor Pattern Periodontitis.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106871},
doi = {10.1016/j.jdent.2026.106871},
pmid = {42379260},
issn = {1879-176X},
abstract = {OBJECTIVE: To explore the microbial profiles in plaque and saliva and metabolic profiles in saliva and serum collected from young patients (≤25 years old) with grade C molar incisor pattern periodontitis (C/MIP), to compare them to age-matched controls and integrate both omics to elucidate C/MIP pathogenesis.

MATERIAL AND METHOD: Thirty-one young patients with C/MIP and 31 periodontally healthy age-matched controls were recruited. Bacterial profiles were investigated in unstimulated saliva and subgingival plaque using shotgun sequencing metagenomics while metabolic profiles were assessed in saliva using nuclear magnetic resonance and serum using mass spectrometry. Data from both omics analyses were integrated and visualised as interaction networks using Cytoscape software.

RESULTS: C/MIP showed significantly lower levels of several salivary (e.g., dimethylamine, proline, glycine) and serum metabolites, and higher levels of others including methyl indole-3-acetate and sulfosalicylic acid, compared to controls (P<0.001). Fifteen bacteria, of which twelve were associated with C/MIP, were differentially prevalent between groups. The plaque microbiome in C/MIP was enriched with pathogenic species such as D. oralis, C. rectus, T. denticola, and P. endodontalis, while health-associated bacteria like R. mucilaginosa and L. hongkongensis were more prevalent in controls. D. oralis and GGB10485-SGB49305 emerged as potential microbial biomarkers. Notably, metabolites such as DL-glutamine and taurine were significantly associated with periodontal pathogens.

CONCLUSION: C/MIP is marked by a distinct dysbiotic microbiome and altered metabolic profile. While key pathogens and metabolites likely contribute to disease progression, the underlying mechanisms remain only partially understood due to the complexity and incomplete characterisation of many associated factors.

CLINICAL SIGNIFICANCE: This study highlighted the multifactorial nature of C/MIP, driven by microbial dysbiosis, immune disturbances, and metabolic alterations. A comprehensive multi-omics approach offered a foundation for understanding microbial-metabolite dynamics in young patients, and highlighted candidate biomarkers for future diagnostics and therapeutics.},
}

@article {pmid42379362,
year = {2026},
author = {Piantoni, P and Sardi, MI and Aumiller, T and Khafipour, E and Roman-Garcia, Y and Chakrabarti, A and Dieho, K and Aubert, T and Schroeder, GF},
title = {Effects of increasing doses of a phytogenic product based on condensed tannins and spices on production performance and rumen microbiome of lactating dairy cows fed a low-protein diet.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28174},
pmid = {42379362},
issn = {1525-3198},
abstract = {The objective of this experiment was to determine the effect of increasing doses of a phytogenic product based on condensed tannins and spices (CTS) on production performance of lactating dairy cows fed a low protein diet. Eight rumen-cannulated Holstein Friesian dairy cows (140 ± 86 DIM; 39.0 ± 5 kg/d milk yield; mean ± SD), were used in a replicated 4 × 4 Latin Square design experiment with 4-wk periods. Treatments were: 0, 10, 20 and 30 g/d CTS (CTR, 10CTS, 20CTS, and 30CTS, respectively). The grass silage and corn silage-based diet was 55.2% forage, 38.7% NDF, 21.0% total starch, and 14.6% CP. Orthogonal contrasts were used to evaluate the linear and quadratic effect of increasing doses of CTS. Results follow the order: CTR, 10CTS, 20CTS, and 30CTS. Increasing doses of CTS quadratically increased DMI (25.4, 25.9, 26.1, and 25.1 kg/d) and milk yield (37.1, 38.5, 37.7, and 36.3 kg/d), tended to increase fat-and-protein-corrected milk (36.9, 37.6, 37.4, and 36.1 kg/d), and did not affect feed or N efficiency (1.45 ± 0.2 and 32.0 ± 2.3%, respectively). Treatments did not affect milk fat yield (1.48 ± 0.2 kg/d) but increasing doses of CTS increased milk protein yield quadratically (1.22, 1.27, 1.26, and 1.20 kg/d). Intermediate doses of CTS tended to increase de novo fatty acid yield (352, 369, 373, and 356 g/d) and decrease trans-10 C18:1 (4.31, 4.05, 4.05, and 4.24 g/d) compared with CTR and 30CTS. Treatments did not affect milk urea concentration (17.8 ± 1.7 mg/dL) or milk crude protein (3.39 ± 0.2%) or fat (4.06 ± 0.2%) content. Rumen pH and time below rumen pH of 5.8 were not affected by level of CTS supplementation. A treatment by time interaction for rumen ammonia concentration indicated that 20CTS and 30CTS increased ammonia concentration 3 h post-feeding compared with CTR and 10CTS (7.72, 7.94, 13.7, and 14.1 mg/dL). The 10CTS treatment decreased rumen propionate concentration only at 3 h post-feeding compared with the other treatments. Apparent DM and NDF total-tract digestibility were not affected by treatments. Shotgun metagenomics were used to evaluate the impact of CTS supplementation on the solid- and liquid-associated rumen microbiome. Treatment effects were only observed in the solid-associated microbiome. Supplementation of CTS linearly decreased α diversity at both the taxa and functional levels, indicating promotion of a leaner microbial community with higher doses of CTS. Differential abundance analysis identified 26 species with large fold changes, including some species with a high presence of cellulases and significant correlations with phenotypic parameters such as DMI, N efficiency, and milk production. In conclusion, a mixture of CTS affected microbiome and rumen metabolism, increasing fat-and-protein-corrected milk yield when fed at 10 and 20 g/d only. This experiment demonstrates the importance of in vivo dose response experiments with phytogenic products to determine optimum dosage for improved rumen metabolism and performance.},
}

@article {pmid42282649,
year = {2026},
author = {Boyd, AI and Quintanilla, KA and Escapa, IF and Lewis, MA and Kafer, LA and Zeng, XL and Blutt, SE and Ibberson, CB and Lemon, KP},
title = {D-alanine aminotransferase (Dat) promotes Staphylococcus aureus colonization fitness on human nasal respiratory epithelium.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42282649},
issn = {2692-8205},
abstract = {Nasal colonization by Staphylococcus aureus is an established risk factor for invasive infection, yet bacterial determinants promoting fitness on human nasal mucosa remain incompletely defined. To identify genes required for early colonization of human nasal respiratory epithelium, we colonized human nasal epithelial organoids differentiated at air-liquid interface (HNO-ALI) with a high-density transposon (Tn) library of the methicillin-resistant USA300 strain LAC. TnSeq analysis identified 165 genes that met our threshold for candidate colonization fitness factors. Among these, genes involved in D-alanine biosynthesis and use were enriched, including two encoding the enzymes that separately synthesize D-alanine in S. aureus: alanine racemase 1 (alr1) and D-alanine aminotransferase (dat). Disruption of dat reduced colonization fitness in competition with the parental strain by ≥ 1,000 fold across 4 different strains from clonal complexes 8, 5, and 30. In competition with the parental strain during HNO-ALI colonization, a dat::Tn mutant was 34-fold less fit than an alr1::Tn mutant. Genetic complementation with single-copy dat expressed from its native operon promoter restored parental colonization levels. Supplementation with exogenous D-alanine or L-alanine also rescued the dat::Tn colonization defect, whereas D-glutamate did not, consistent with Dat primarily producing D-alanine on nasal mucosa. Complementation with dat under control of a putative 5' intra-operon promoter substantially restored colonization but failed to support growth in chemically defined medium lacking L-alanine, suggesting a new layer of environment-specific regulation of dat transcription. Together, these findings demonstrate that Dat is a major source of D-alanine during colonization of human nasal mucosa and is required for S. aureus fitness in this environment.},
}

@article {pmid42366391,
year = {2026},
author = {Lai, T and Liu, Y and Duan, Z and Su, S and Ding, H and Dai, Y and Gao, M and Ji, M and Liao, L},
title = {Deep metagenomics uncovers functional adaptations and pathogenic risks in the gut microbiome of Antarctic fur seals (Arctocephalus gazella).},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00919-2},
pmid = {42366391},
issn = {2524-6372},
support = {2022YFC2807501//National Key Research and Development Program of China/ ; 42476264//National Natural Science Foundation of China/ ; },
abstract = {The Antarctic fur seal (Arctocephalus gazella) plays a key role in the Antarctic marine ecosystem by regulating krill, fish, and cephalopod populations through selective foraging, promoting Southern Ocean productivity via excretion, and influencing coastal island ecosystems during breeding season. Despite the importance of the gut microbiota in reflecting diet, health, and environmental adaptation, the gut microbiome of the Antarctic fur seal remains poorly characterized. To address this gap and evaluate its potential as a bioindicator of Antarctic marine environmental health, we employed shotgun metagenomics and 16S rRNA amplicon sequencing on fresh fecal samples collected from four Antarctic fur seals (designated S59, S62, S63, and S64) at King George Island, Western Antarctica. Despite inter-individual variation, both approaches identified Bacillota as the dominant phylum but showed genus-level discrepancies, with Fusobacterium prevailing in metagenomes and Clostridium in 16S amplicons. Viral communities constituted up to 5.3% of the microbiome, including an immunodeficiency-associated Lentivirus. Chitin-degrading capacity was ubiquitous, consistent with the host's krill-based diet. Metagenome-assembled genomes (MAGs) resolved distinct taxonomic contributions to discrete steps of chitin hydrolysis, suggesting that complete depolymerization requires metabolic cross-feeding among functionally complementary taxa. Notably, Helicobacter MAGs were abundant in individual S62, suggesting potential pathogenicity. Additionally, 16 antibiotic resistance gene types were detected, with bacitracin, polymyxin, and multidrug resistance dominating the resistome. These findings not only elucidate the community composition, functional potential, and ecological adaptation of the Antarctic fur seal gut microbiota but also establish a comprehensive baseline for assessing environmental change and human impacts on the Antarctic marine ecosystem, thereby offering valuable scientific data and methodological insights for the conservation of polar marine mammals.},
}

@article {pmid42366413,
year = {2026},
author = {Li, X and Li, Z and Sun, X and Guo, Y and Pang, Z and Niu, G},
title = {Honghe Bunya-like virus: a novel virus identified in mosquitoes from Yunnan, China.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13112-z},
pmid = {42366413},
issn = {1471-2164},
support = {SDYJSJGC2025059//Shandong Provincial Department of Education/ ; },
abstract = {BACKGROUND: Arboviruses represent a persistent and escalating threat to global public health, with mosquitoes serving as the principal vectors in their natural transmission cycles and geographic dissemination. Yunnan Province, southwestern China, is a recognized hotspot for arboviral diversity, yet the full spectrum of mosquito-borne viruses circulating in this region remains incompletely characterized.

RESULTS: A total of 3,300 female mosquitoes of four species across four genera were collected from rural areas of Honghe County, Yunnan Province in 2024, and subjected to viral metatranscriptomic sequencing. A previously undescribed bunya-like virus, designated Honghe Bunya-like virus, was identified in two locally dominant hematophagous mosquito species, with minimum infection rates of 0.2% and 0.3%, respectively. The viral genome comprises three single-stranded negative-sense RNA segments (L, M, and S) encoding the RdRp, glycoprotein, and nucleoprotein, respectively, consistent with the canonical architecture of the genus Orthobunyavirus. Phylogenetic analyses placed the virus within Orthobunyavirus across all three segments, though inter-segment topological incongruence was observed; amino acid identities to known orthobunyaviruses (49.7%-71.6%) fell below conspecific thresholds, suggesting a novel species.

CONCLUSIONS: This study expands the known genetic diversity of mosquito-associated virus in southwestern China and, given the phylogenetic affinity to pathogenic orthobunyaviruses and the hematophagous nature of the vector species, raises the possibility of vertebrate infection potential warranting further investigation.},
}

@article {pmid42366525,
year = {2026},
author = {Kan, J and Morales-Amador, A and Hernandez, Y and Burian, J and Ternei, MA and Brady, SF},
title = {Resistance-CONKAT-seq Guided Discovery of a ClpP Active Natural Product from a Soil Metagenome.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.6c00347},
pmid = {42366525},
issn = {1554-8937},
abstract = {The discovery of natural products with specific molecular targets from metagenomes remains challenging. To address this limitation, we developed resistance-CONKAT-seq (resistance co-occurrence network analysis of targeted sequences) which links metagenomic BGCs (biosynthetic gene clusters) to potential modes of action through the identification of colocalized molecular target-based resistance genes. Applying this approach to a soil metagenomic library, we identified the uncharacterized metagenomic azetidopyrroline (MTA) BGC associated with a potential clpP self-resistance gene. Genetic engineering and heterologous expression of the MTA BGC led to the discovery of metaze A and B, which are structurally related azetidopyrroline- and bicyclocarbamate-based natural products, respectively. Metaze B inhibited Mycobacterium tuberculosis caseinolytic protease proteolytic subunit (ClpP) with an IC50 of 1.35 μM. This study expands the chemical diversity of natural product ClpP inhibitors and further demonstrates the applicability of resistance-CONKAT-seq for target-guided discovery of natural products with specific modes of action from complex metagenomes.},
}

@article {pmid42366537,
year = {2026},
author = {Meusel, I and Manheim, D and Delaney, O and Greene, D and Tobolsky, R and Palya, H and Shapiro, N and Sharma, S},
title = {A Metagenomic Biosurveillance Network for Emerging Infectious Diseases: A Simulation-Based Model.},
journal = {Health security},
volume = {},
number = {},
pages = {23265094261453732},
doi = {10.1177/23265094261453732},
pmid = {42366537},
issn = {2326-5108},
abstract = {In this article, we propose a metagenomic next-generation sequencing (mNGS) system for symptomatic clinical respiratory disease samples in Israel to enable detection early enough to contain novel pathogen outbreaks, limit international spread and expedite countermeasure development. We built an open-source, interactive SEIR (susceptible, exposed, infectious, recovered)-based model extending the work of Sharma et al (2023) for 7 representative known respiratory pathogens with pandemic potential, aiming to estimate costs and detection time for the identification of a novel respiratory pathogen in Israel through a network of mNGS monitoring in hospitals. We find that a novel pathogen with SARS-CoV-2-like characteristics could be detected within 68 days (interquartile range [IQR]: 53 to 80) after the first 2 emergency department presentations and 213 (IQR: 94 to 429) total infections across Israel. This surveillance system would cost US$24 million annually over 10 years when implemented in Israel's 6 largest hospitals, covering 37% of the population. Our open-source interactive model allows policymakers and experts to explore different system configurations and their associated tradeoffs between cost, detection speed, and population coverage.},
}

@article {pmid42366621,
year = {2026},
author = {Tawfiq, R and Kulmanov, M and Hoehndorf, R},
title = {Evaluating completeness, coherence, and consistency of genome-scale function annotations.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
doi = {10.1093/bib/bbag336},
pmid = {42366621},
issn = {1477-4054},
support = {URF/1/5041-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5235-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/4938-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; REI/1/5659-01-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; 5932//King Abdullah University of Science and Technology (KAUST)-KAUST Center of Excellence for Smart Health (KCSH)/ ; 5940//King Abdullah University of Science and Technology (KAUST)-Center of Excellence for Generative AI/ ; //KAUST Supercomputing Laboratory/ ; },
mesh = {*Molecular Sequence Annotation/methods ; Systems Biology/methods ; *Genome ; *Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; },
abstract = {Protein function annotation traditionally follows a reductionist approach, assigning functions to individual proteins acting in isolation. This treats each annotation as an independent fact, disconnected from the broader biological system. However, proteins operate within integrated networks where their functions depend on genomic context and interacting partners. This needs to be reflected in function annotation and evaluation frameworks. We assess whether annotated protein functions could plausibly coexist within a living organism. To achieve this goal, we formalize three criteria grounded in systems biology principles: completeness (presence of essential functions), coherence (satisfaction of functional dependencies), and consistency (absence of mutually exclusive functions). We applied this framework to manually curated function annotations from six model organisms and computational function predictions from seven methods. While model organism annotations largely satisfied our constraints, computational function prediction methods systematically failed to produce biologically plausible genome-scale annotations. Our review reveals a measurable gap between the per-protein objectives of current annotation methods and the system-level criteria that an annotation set must satisfy to describe a viable organism. Our evaluation framework grounded in systems biology principles provides quantitative metrics for evaluating biological plausibility and establishes a foundation for developing system-aware annotation approaches. Augmenting protein-level annotation with system-level criteria offers a tractable path to improving annotation of the rapidly growing collection of sequenced genomes and metagenomes.},
}

*Molecular Sequence Annotation/methods
Systems Biology/methods
*Genome
*Proteins/genetics/metabolism
Genomics/methods
Computational Biology/methods

@article {pmid42366665,
year = {2026},
author = {Kuzbekov, SR},
title = {[Microbiota and microbiome of the lacrimal drainage system].},
journal = {Vestnik oftalmologii},
volume = {142},
number = {3},
pages = {91-100},
doi = {10.17116/oftalma202614203191},
pmid = {42366665},
issn = {0042-465X},
mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.},
}

Humans
*Microbiota
*Lacrimal Apparatus/microbiology/physiopathology/pathology
*Dacryocystitis/microbiology/diagnosis/physiopathology
*Lacrimal Duct Obstruction/diagnosis
Anti-Bacterial Agents/pharmacology

@article {pmid42366735,
year = {2026},
author = {Guo, X and Lai, CY and Zhao, HP},
title = {Targeted Acclimation Unlocks Adaptive Evolution of a Methanotrophic Consortium Enabling 3A5MI Elimination and Enhanced Sulfamethoxazole Biodegradation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02194},
pmid = {42366735},
issn = {1520-5851},
abstract = {Targeted pollutant exposure is widely used to acclimate microbial communities for enhanced biodegradation of recalcitrant contaminants, yet the evolutionary mechanisms underlying functional reinforcement remain poorly understood. Here, we acclimated a methanotrophic consortium achieving efficient removal of 3-amino-5-methyl-isoxazole (3A5MI) (>90%, >5 mg/L/d) and elucidated the adaptive evolutionary processes behind it. Analyses of mobile genetic elements (MGEs) and horizontal gene transfer (HGT) revealed that dominant Methylococcaceae members served as genetic exchange hubs in the acclimation bioreactor. Integrated metagenomic and metatranscriptomic analyses showed that prolonged 3A5MI exposure activated their MGEs and promoted extensive HGT of genes related to energy generation, oxidative stress defense, and biosynthesis. This adaptive evolution enabled community-level metabolic rewiring, including optimized carbon metabolism to relieve energy limitation, niche differentiation, and specialized transcription of C-N bond catalytic functions. Furthermore, batch experiments and transformation product analyses confirmed that 3A5MI-induced functional traits (e.g., heterocycle hydroxylation and C-N bond catalysis) facilitated complete sulfamethoxazole (SMX) biodegradation. Overall, this study demonstrates the evolutionary plasticity of methanotrophic consortia under targeted acclimation and highlights MGE-driven genetic exchange and metabolic adaptation as key mechanisms that both underpin functional enhancement and support the development of methanotroph-based strategies for the biodegradation of recalcitrant isoxazole-based pollutants.},
}

@article {pmid42367190,
year = {2026},
author = {Teng, Y and Saghaï, A},
title = {Fermentative nitrite ammonifiers are abundant in soils and ecologically distinct from NrfA-dependent ammonifiers.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag144},
pmid = {42367190},
issn = {2730-6151},
abstract = {Microorganisms can use different enzymes to perform nitrite ammonification, the reduction of nitrite to ammonium, an important process to retain nitrogen in soils. Yet, the organisms mediating this process and their distribution in terrestrial ecosystems remain poorly resolved. Here, we determined the phylogenetic diversity of bacteria performing fermentative nitrite ammonification via the NAD(P)H-dependent nitrite reductase NirB, assessed their distribution across terrestrial ecosystems, and identified their environmental preferences. We found that these organisms are broadly distributed, spanning 29 phyla including Bacillota, Pseudomonadota and Actinomycetota. Screening 1587 globally distributed soil metagenomes using a phylogeny-based approach revealed that fermentative nitrite ammonifiers are ubiquitous across biomes and particularly abundant in Mediterranean forests and desert soils. In these ecosystems, they outnumbered NrfA-dependent ammonifiers, the best characterized ammonifier group to date, suggesting distinct ecological niches for the two groups. Consistent with this, random forest modelling revealed a negative relationship between fermentative nitrite ammonifiers and the carbon-to-nitrate ratio, which contrasts with a preference for high carbon-to-nitrate conditions in NrfA-dependent ammonifiers. However, moisture and salinity emerged as the strongest predictors of the abundance of fermentative nitrite ammonifiers, indicating a high tolerance to osmotic stress in this group. Overall, our results demonstrate that fermentative nitrite ammonifiers are both phylogenetically diverse and environmentally widespread, calling for future efforts to determine the conditions under which they contribute to nitrogen retention in soils.},
}

@article {pmid42367193,
year = {2026},
author = {Guo, S and McNamara, NP and Bending, GD and Mushinski, RM},
title = {Phosphorus availability mediates pathway-specific nitrogen cycling in stratified peatland microbiomes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag143},
pmid = {42367193},
issn = {2730-6151},
abstract = {Peatland microbiomes regulate nitrogen (N) cycling processes that control nutrient retention and greenhouse gas emissions in carbon-rich ecosystems. Although depth-driven redox gradients structure microbial communities, how physicochemical stratification shapes the functional versus taxonomic organization of N-cycling microorganisms remains unclear. We used shotgun metagenomics to characterize N-cycling gene distributions, taxonomic affiliations, and metagenome-assembled genomes (MAGs) across depth and vegetation gradients in a temperate blanket bog. Depth emerged as the primary structuring factor, creating functional-taxonomic decoupling. Surface peat (0-20 cm) harbored functionally diverse but taxonomically constrained communities assembled deterministically around nitrification and labile N acquisition, while subsurface peat (20-40 cm) supported taxonomically richer but functionally-simpler communities assembled stochastically and enriched in denitrification and dissimilatory nitrate reduction. Linear mixed-effects models revealed pathway-specific controls on N cycling. Denitrification increased with depth (β = 11.53, P < .05), whereas organic N transformation declined (β = -5.81, P < .05); depth effects on nitrification and N fixation became non-significant after accounting for environmental variables. Phosphorus (P) emerged as the strongest environmental predictor, regulating nitrification (β = 95.40, P < .01), N fixation (β = 128.33, P < .01), organic N transformation (β = 80.53, P < .01), and denitrification (β = -109.63, P < .05), highlighting the importance of P availability in structuring microbial N cycling. This challenges traditional N-limitation paradigms in ombrotrophic systems. MAGs revealed Pseudomonadota as the dominant N-cycling lineage, while incomplete denitrification capacity indicated genetic potential for N2O accumulation in subsurface layers. These findings demonstrate that P availability, rather than N content alone, regulates microbial N transformation capacity in peatlands, with implications for predicting nutrient dynamics under altered hydrological and nutrient deposition regimes.},
}

@article {pmid42367641,
year = {2026},
author = {Xu, C and Liu, T and Zhang, X and Feng, S},
title = {Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.},
journal = {Blood science (Baltimore, Md.)},
volume = {8},
number = {3},
pages = {e00304},
pmid = {42367641},
issn = {2543-6368},
abstract = {In patients with hematological disorders, the high risk of complex infections caused by immune dysfunction and intensive therapies poses a major challenge to the use of conventional microbiological tests (CMTs). Plasma cell-free DNA (cfDNA) metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary noninvasive tool that enables unbiased, broad-spectrum, and rapid pathogen identification directly from blood samples. This review summarizes the core applications of plasma cfDNA mNGS in patients with hematological disorders, including the diagnosis of febrile neutropenia, bloodstream infections, focal infections, and infections caused by uncommon/fastidious pathogens. It highlights the advantages of this technology in overcoming antibiotic interference, enabling early detection, and providing diagnostic value in cases without clear infection foci or when invasive sampling is not feasible. This review further discusses how China has facilitated the widespread adoption of this technology through a localized application model, cost reduction, and the development of clinically relevant interpretation models. Nevertheless, challenges remain, such as lower sensitivity than site-specific specimens in focal infections, and the difficulty in predicting antimicrobial resistance (AMR) on the basis of cfDNA mNGS. Future developmental directions should focus on technical optimization (eg, combined plasma cell-fraction testing), quality assurance and quality control management, multidimensional data integration (eg, host immune response analysis), artificial intelligence (AI)-assisted interpretation, and cost reduction through technology popularization and insurance coverage. These efforts will advance cfDNA mNGS from a pathogen detection tool toward an intelligent clinical decision-support platform, ultimately improving the diagnostic accuracy and clinical outcomes of hematological patients with infections.},
}

@article {pmid42367778,
year = {2026},
author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y},
title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1868704},
pmid = {42367778},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; },
abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.

RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P < 0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P = 0.003) and depletion of Roseburia (1.05% vs. 3.77%, P = 0.005) and Ruminococcus (5.98% vs. 7.85%, P = 0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P = 0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.

CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.},
}

Humans
*Arthritis, Rheumatoid/complications/microbiology
*Lung Diseases, Interstitial/microbiology/etiology
Female
*Metagenomics/methods
Male
*Gastrointestinal Microbiome/genetics
Middle Aged
Feces/microbiology
Aged
*Bacteria/classification/genetics
Dysbiosis/microbiology
*Metagenome

@article {pmid42367784,
year = {2026},
author = {Zheng, X and Li, D and Yao, X and Luo, X and Gao, C and Yan, X},
title = {The gut microbiota-immune-brain axis in post-traumatic stress disorder: mechanistic integration and translational prospects.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1859206},
pmid = {42367784},
issn = {1664-3224},
mesh = {Humans ; *Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Translational Research, Biomedical ; Intestinal Barrier Function ; Neuroimmunomodulation ; },
abstract = {Post-traumatic stress disorder (PTSD) is a complex mental disorder triggered by severe traumatic events. Its pathophysiology involves not only abnormalities in fear memory circuits and neuroendocrine imbalances but also immune dysregulation and alterations in gut homeostasis. In recent years, the gut microbiota, as a crucial regulatory factor connecting the periphery and the central nervous system, has garnered widespread attention for its potential role in the development and progression of PTSD, offering a new integrative perspective for understanding this disorder. This article focuses on the "gut microbiota-immune-brain axis" framework, reviewing evidence related to changes in the composition and function of the gut microbiota in PTSD. It summarizes how these changes may influence neuroplasticity abnormalities and PTSD-related behavioral phenotypes through mechanisms involving microbial metabolite production, modulation of intestinal barrier integrity, immuno-inflammatory responses, regulation of neuroendocrine homeostasis, and blood-brain barrier dysfunction. However, these mechanistic pathways remain incompletely validated in human studies. Existing research suggests that this axis holds significant value in explaining the multisystem pathological features of PTSD. Nevertheless, challenges persist, including ambiguous causal relationships in microbiota-host interactions, limited direct clinical evidence, and insufficient translational research. Current evidence primarily stems from observational studies, preclinical models, and preliminary intervention studies. The explanatory power varies across these evidence levels: population studies primarily establish correlations, animal models facilitate mechanistic validation, metagenomic and metabolic analyses yield functional insights, while clinical intervention data remain exploratory. This article aims to elucidate the key molecular and systemic mechanisms underlying this axis in PTSD and to evaluate the potential translational value and practical limitations of microbial intervention and immune modulation strategies.},
}

Humans
*Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology
Animals
*Brain/immunology/metabolism
Translational Research, Biomedical
Intestinal Barrier Function
Neuroimmunomodulation

@article {pmid42367847,
year = {2026},
author = {Sparagon, WJ and Lary, S and Ioh, MT and Lin, A and Dhungana, I and Fullmer, CR and Handel, CR and Paudel, R and Burden, J and Deubel, JN and Tayo, MAG and Rodriguez, FE and Swift, SOI and Nakayama, KK and Maaz, TM and Nguyen, NH},
title = {Soil Resistomes in a Tropical Watershed are Indirectly Structured by Bacterial Community Interactions with Soil Properties.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.18.733189},
pmid = {42367847},
issn = {2692-8205},
abstract = {Soils are recognized as reservoirs of antibiotic resistance genes (ARGs) with the potential to transfer to clinical pathogens, creating antimicrobial resistance (AMR) that poses a threat to human health. While large-scale AMR surveys have profiled how diverse biomes shape soil resistomes, less is known about the influence of specific soil properties. Here, we combined metagenomics and 16S rRNA amplicon sequencing with isolate-based approaches to investigate drivers of soil AMR across a tropical watershed from beach to mountaintop in Waimea Valley, O'ahu, Hawai□i. We leveraged functional- and taxonomic-classification of resistances to unravel how soil properties interact with bacterial taxa to structure resistomes. Metagenomic- and isolate-resistomes showed remarkable consistency, including a general gradient of increasing AMR from ridge to beach. Resistome functional composition was significantly correlated with total bacterial community structure. The relationship between resistances and soil properties was primarily dictated by taxonomic composition of each resistance. Rifampin- and Vancomycin-ARGs associated with Actinomycetes negatively correlated with soil physical properties, while resistant genes and isolates from Gammaproteobacteria positively correlated with enzymatic activity metrics. These findings indicate that soil properties structure the resistome indirectly through taxonomic filtering of microbial hosts and challenge the notion that AMR is decoupled from phylogenetic relatedness.},
}

@article {pmid42367895,
year = {2026},
author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and De Souza, ML and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH},
title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.13.732064},
pmid = {42367895},
issn = {2692-8205},
abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1 - 3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and L-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.},
}

@article {pmid42368165,
year = {2026},
author = {Tinker, KA and Ross, DE and Beebe, MN and Bagwell, CE and Smallwood, CR and Davis, RW and Gulliver, DM},
title = {Biogeochemical Assessment of Short-Term Hydrogen Storage in Methane Reservoirs with Field Sample Characterization and Reactor Experiments.},
journal = {ACS omega},
volume = {11},
number = {24},
pages = {34976-34986},
pmid = {42368165},
issn = {2470-1343},
abstract = {Hydrogen is a valuable commodity due to its high energy density and properties as a flexible energy carrier. It is possible to store hydrogen by blending it with methane and utilizing existing natural gas infrastructure. However, adapting current methane storage strategies to withstand the expected biogeochemical processes caused by H2 injection has not been fully explored. In this study, a series of experiments were designed to identify potential geochemical and microbial challenges of storing hydrogen/methane gas blends in existing methane reservoirs. First, fluid samples were collected from two methane reservoirs located in the western United States. The geochemical composition, microbial taxonomy, and metabolic potential of each fluid sample were characterized by utilizing ion chromatography (IC), inductively coupled plasma optical emission spectroscopy (ICP-OES), a Total Organic Carbon (TOC) analyzer, 16S rRNA gene amplicon sequencing, and metagenomic sequencing. Next, fluid samples from one field site (Site 2) were used to complete a series of short-term reactor experiments at reservoir conditions (80 °C and ∼1000 psi) for natural gas (100% CH4) and hydrogen blend (80% CH4/20% H2) storage environments. Both biotic and abiotic (sterilized) measurements were conducted to accurately understand and decouple abiotic and microbially driven processes, with the goal of linking these processes to storage impacts. Overall, the two reservoirs had a high, but variable, total dissolved solids (TDS) concentration, with various organic acids including acetate and propionate. The field sample was characterized by a diverse microbial community with the metabolic capacity for sulfur reduction, iron reduction, and acetogenesis. Across these reactors, there was minimal change in the fluid geochemistry and a minimal (0-5%) decrease of hydrogen gas during the initial storage event (days 1-3). This work contributes to the understanding of the complexities of hydrogen storage and demonstrates the need for additional research.},
}

@article {pmid42368245,
year = {2026},
author = {Bahr, NC and Kasibante, J and Nsangi, L and Kagimu, E and Ssebambulidde, K and Rutakingirwa, MK and Tugume, L and Ramachandran, PS and Cresswell, F and Meya, DB and Boulware, DR and Wilson, MR and Ellis, J},
title = {Central Nervous System Toxoplasmosis is an Under-Recognized Opportunistic infection in Uganda.},
journal = {Journal of tropical medicine},
volume = {2026},
number = {},
pages = {2158978},
pmid = {42368245},
issn = {1687-9686},
abstract = {In Uganda, Toxoplasma meningoencephalitis remains underdiagnosed due to the low sensitivities and specificities of available diagnostics. In our recent publication, we identified 15 cases of possible Toxoplasma gondii meningoencephalitis by cerebrospinal fluid metagenomic next-generation sequencing in patients with suspected meningitis. We herein discuss, in detail, these cases to highlight the ongoing limitations of utilizing clinical symptoms to diagnose Toxoplasma gondii meningoencephalitis, the importance of access to rapid diagnostics, and the frequency of toxoplasmosis as a possible co-infection with other opportunistic diseases among people with advanced HIV.},
}

@article {pmid42368276,
year = {2026},
author = {Zhu, H and Lin, Y and Liao, H and Li, X and Xie, Q and Zheng, Y},
title = {Infantile pulmonary abscess due to Mycobacterium abscessus subsp. massiliense identified by integrated mNGS and targeted NGS: a rare case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1828339},
pmid = {42368276},
issn = {2296-2360},
abstract = {BACKGROUND: To describe a rare case of pulmonary infection caused by Mycobacterium abscessus in an infant and to evaluate the complementary diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying non-tuberculous mycobacterial (NTM) infections when conventional testing is inconclusive.

CASE PRESENTATION: A 3-month-old male infant presented with a persistent cough and a right upper-lobe mass, initially suspected to be a congenital malformation or neoplasm. Following inconclusive routine examinations, mNGS was performed on bronchoalveolar lavage fluid (BALF). mNGS detected a single read of M. abscessus in BALF, providing an initial diagnostic clue. Subsequently, a tNGS assay was conducted on both BALF and resected lung tissue to achieve precise species identification. tNGS identified 13,272 reads of M. abscessus subsp. massiliense in BALF and 31,474 reads in lung tissue, confirming the pathogen and enabling precise molecular diagnosis. Histopathological examination revealed granulomatous inflammation with multinucleated giant cells, consistent with NTM infection. Guided by these results, the patient initially received azithromycin and was transferred to a specialized chest hospital, where a multidrug anti-NTM regimen was formulated, including azithromycin, imipenem-cilastatin, cefoxitin, and linezolid. After continued treatment at a local municipal hospital, respiratory symptoms resolved, inflammatory markers improved, follow-up CT showed progressive absorption of the right upper-lobe lesion with a small residual cavity, and the patient was discharged in stable condition without recurrent infections during available follow-up.

CONCLUSION: This case highlights the diagnostic utility of integrating mNGS and tNGS for the accurate identification of rare NTM infections in infants, particularly when routine microbiological tests and imaging findings are inconclusive.},
}

@article {pmid42368287,
year = {2026},
author = {Li, M and Sun, Z and Jia, T and Ma, M},
title = {Insights into the mechanism of intestinal flora imbalance and immune disorder in co-morbidity of pneumonia and diarrhea in children.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1836762},
pmid = {42368287},
issn = {2296-2360},
abstract = {Pneumonia and diarrhea are the two leading causes of death in children under five years of age, and these two conditions often present as a comorbidity, where the same child experiences respiratory and digestive system infection symptoms simultaneously or sequentially. Clinical data indicate that the incidence of secondary diarrhea in children hospitalized with pneumonia is high, significantly prolonging hospital stays and affecting prognosis. In recent years, the proposal of the gut-lung axis theory has provided a novel perspective for understanding this comorbidity phenomenon. The gut-lung axis refers to the bidirectional regulatory pathway between the gut microbiota and the pulmonary immune system, with the lungs and intestines sharing embryonic origin and a common mucosal immune system. This review systematically reviews the characteristics of gut microbiota dysbiosis and the mechanisms of immune disorders in the context of pediatric pneumonia-diarrhea comorbidity. Clinical studies have shown that children with comorbidity exhibit significant gut microbiota dysbiosis, characterized by a reduction in beneficial bacteria such as Bifidobacterium, an increase in opportunistic pathogens such as Escherichia coli, and decreased microbial diversity. Gut microbiota dysbiosis leads to immune disorders through multiple mechanisms, including reduced short-chain fatty acids, skewed immune cell differentiation, and dysregulated inflammatory factor networks, resulting in Th1/Th2 imbalance, decreased regulatory T cell function, and exacerbated systemic inflammatory responses. Supplementation with microecological preparations such as Saccharomyces boulardii has been shown to significantly shorten hospital stays, diarrhea duration, and fever resolution time, while improving peripheral blood immunoglobulin levels and T-cell subsets, providing evidence-based support for clinical intervention. This review also systematically reviews clinical laboratory indicators associated with comorbidity, including inflammatory markers, immune status indicators, intestinal barrier function markers, and microbiota detection methods, which have important application value in early identification, disease assessment, and treatment monitoring of comorbidity. Future research should further employ metagenomic approaches combined with longitudinal follow-up designs to elucidate the roles of specific bacterial species/strains in gut-lung axis regulation, providing new strategies for precision prevention and treatment of pediatric pneumonia-diarrhea comorbidity.},
}

@article {pmid42368316,
year = {2026},
author = {Zheng, H and Zhuang, J and Lin, Q and Wang, T and Guo, G and Huang, L and Lin, W},
title = {Study on the role and clinical relevance of gut microbiota in diabetic foot ulcers.},
journal = {3 Biotech},
volume = {16},
number = {7},
pages = {287},
pmid = {42368316},
issn = {2190-572X},
abstract = {UNLABELLED: Diabetic foot ulcers (DFU) are severe and costly complications of diabetes, predisposing to infection, amputation, and mortality, highlighting the urgent need to clarify their mechanisms for optimized clinical management. This study integrated clinical biochemistry data and multi-omics analyses (including metagenomic sequencing) from 11 patients to reveal the critical role of gut microbiota in the pathogenesis of DFU. Results showed significant host metabolic disorders in DFU patients, characterized by hypoalbuminemia (mean ± SD:32.35 ± 6.02 g/L), persistent hyperglycemia (mean ± SD:8.25 ± 3.21 mmol/L), and imbalances in trace elements such as magnesium (mean ± SD:0.84 ± 0.08 mmol/L). Concurrently, the gut microbiota composition was markedly altered, with enrichment of the phylum Bacillota_A (formerly Firmicutes; 48.7% in patients vs. 32.1% in controls) and elevated genetic potential of virulence genes (e.g., type VI secretion systems, capsular polysaccharide gene cps4J/L). Metagenomic tracing revealed that antibiotic resistance genes (ARGs) such as tet(A) and blaOXA-1 were co-localized with mobile genetic elements (MGEs) including IncF plasmids and tnpA transposases. 99.2% of key ARGs shared sequence homology with gut-derived metagenome-assembled genomes (MAGs) and co-localized with MGEs, indicating potential cross-niche transfer capacity. Furthermore, renal (mean ± SD:11.81 ± 5.75 mmol/L) and hepatic (ALT: 35.67 ± 18.22 U/L) dysfunction correlated with aggravated gut dysbiosis and ARG enrichment. In conclusion, this study confirms that host metabolic deficiencies contribute to DFU refractoriness by altering gut microbiota ecology and enhancing horizontal gene transfer of virulence and resistance determinants, providing a novel framework for precision therapies targeting the host-microbe metabolic interface.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04745-8.},
}

@article {pmid42368546,
year = {2026},
author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W},
title = {Erratum: Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1899816},
doi = {10.3389/fpls.2026.1899816},
pmid = {42368546},
issn = {1664-462X},
abstract = {[This corrects the article DOI: 10.3389/fpls.2026.1726191.].},
}

@article {pmid42368826,
year = {2026},
author = {Martínez-Noriega, M and Jean-Louis, P and Philippon, M and Sanchez-Flores, A and Gonzalez-Rizzo, S},
title = {Revealing the bacterial diversity and variation of white filamentous microbial mats in marine mangroves of Guadeloupe Island in relation to human activities.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag034},
pmid = {42368826},
issn = {2633-6685},
abstract = {White filamentous microbial mats are complex benthic communities, typically structured by sulfur-oxidizing bacteria from the Beggiatoaceae family, yet their diversity and ecological responses in mangrove ecosystems remain poorly characterized. Here, we provide a high-resolution analysis of bacterial communities associated with white microbial mats in marine mangrove sediments of Guadeloupe using 16S rRNA metabarcoding. Bacterial community composition was compared across sites with different levels of anthropogenic impact (protected, natural, and urban). While overall diversity remained stable, richness differed significantly between conditions, and beta diversity analyses revealed clear compositional structuring along the disturbance gradient. A conserved core microbiome was identified across all sites, whereas rare taxa were detected exclusively in urban sites, including Ferrimicrobium, Thermonospora, Alcanivorax, and Serratia, which has been previously associated with human-induced environmental changes. In contrast, Prosthecochloris and Chlorobaculum were highly abundant in protected sites, whereas Sulfurovum and Sulfurimonas dominated urban environments. The relative abundance of Beggiatoaceae also varied across sites, suggesting sensitivity to anthropogenic disturbance. Despite these compositional shifts, measured physicochemical parameters did not significantly correlate with the community structure, suggesting that microbial mat organization is influenced by fine-scale or unmeasured environmental gradients. Together, these findings indicate that white microbial mats respond to anthropogenic disturbance primarily through taxonomic restructuring rather than loss of diversity, highlighting their potential as sensitive indicators of environmental change in mangrove ecosystems.},
}

@article {pmid42368984,
year = {2026},
author = {Basbouss-Serhal, I and Fayad, F},
title = {Familial Mediterranean Fever and the Gut Microbiota: A Dual Perspective Review of Current Evidence.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {2},
pages = {302-308},
pmid = {42368984},
issn = {2529-198X},
abstract = {Familial Mediterranean Fever is a well-known autoinflammatory disease resulting from mutations in the MEFV gene. A recent development has linked FMF pathogenesis and mode of expression to the gut micro-biota. There may be a change in the gut microbiota profile of FMF patients, characterised by low diversity and a depletion of beneficial bacteria. Dysbiosis tends to be linked to increased gut permeability, systemic inflammation, and low response to colchicine treatment. Probiotics and prebiotics, in this case, may help restore the previous idyllic state of the microbial balance, along with a reduction in inflammatory markers, thereby demonstrating therapeutic merit. Notably, however, it did argue in some instances that changes in the microbiota were secondary to the genetic and inflammatory nature of FMF itself. It is still important to carry out longitudinal studies of naïve patients that will integrate metagenomics with immune profiling to ascertain whether microbial changes arise from causes, contributions, or coincidence in the pathogenesis of FMF.},
}

@article {pmid42369126,
year = {2026},
author = {Pang, H and Pi, C and Shen, P and Tang, Z and Bao, E and Luo, X and Zhang, Q},
title = {Case Report: pharmaceutical care in a case of complicated urinary tract infection combined with disseminated Nocardia brasiliensis infection.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1839868},
pmid = {42369126},
issn = {2296-858X},
abstract = {Given the increasing prevalence of multidrug-resistant opportunistic pathogens and the high mortality rate associated with delayed diagnosis of disseminated infections, there is an urgent need for rapid diagnostic tools and closely monitored, individualized anti-infective strategies. This study aimed to explore the critical role of comprehensive pharmaceutical care in managing disseminated Nocardia infections complicated by complicated urinary tract infection (cUTI). Through detailed documentation of a 67-year-old male patient, this study focuses on optimizing antimicrobial regimens based on pathogenetic findings and adjusting treatments for severe adverse reactions. The patient was diagnosed with disseminated Nocardia brasiliensis infection complicated by Enterococcus faecalis urinary tract infection using metagenomic next-generation sequencing (mNGS). The treatment process underwent two critical adjustments. First, during the efficacy optimization phase, the initial empirical meropenem therapy was modified to a reinforced regimen centered on trimethoprim-sulfamethoxazole (TMP-SMX), combined with linezolid and short-term amikacin, effectively controlling the spread of infection. Subsequently, during the safety optimization phase, the patient developed severe thrombocytopenia during sequential oral therapy. Prompt identification and switching to amoxicillin/clavulanate potassium resolved the adverse reactions, enabling successful continuation of subsequent treatment. Follow-up revealed a favorable patient recovery. This case demonstrates that for such complex mixed infections, rapid pathogen diagnosis represented by mNGS serves as the starting point for precision treatment, whereas the intensive combination regimen centered on TMP-SMX forms the foundation for controlling disseminated Nocardia infection. More importantly, the core insight from this case is that successful treatment relies not only on appropriate initial medication, but more critically, on proactive, dynamic pharmaceutical monitoring throughout long-term therapy. This enables early intervention for severe adverse drug reactions and timely, flexible adjustments to treatment regimens, which are essential components for ensuring ultimate therapeutic success in patients with such complex infections.},
}

@article {pmid42369553,
year = {2026},
author = {Xu, S and Jia, M and Guo, X and Liang, W and Pan, Y and Lin, Y and Li, X and Qiu, H and Hu, D and Yan, D},
title = {Metagenomics and metabolomics analyses of the mechanism of non-expression of natural mating behavior in captive male Malayan pangolins (Manis javanica).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1828282},
pmid = {42369553},
issn = {1664-302X},
abstract = {Ex situ conservation and captive breeding are important measures for conserving endangered species. However, the reproduction of some wild animals, especially males, is inhibited in captivity, but the underlying mechanism has not yet been elucidated. This study aimed to investigate the microbiota and their functions, metabolites, and their metabolic pathways impacting reproduction employing metagenomics and metabolomics analyses and using male Malayan pangolins with normal (with natural mating behavior) and abnormal (no natural mating behavior) reproduction as the research objects. The results showed that the relative abundance of Proteobacteria, Escherichia coli, and Shigella spp. was significantly higher in the abnormal reproduction (AR) group. However, the relative abundance of Firmicutes and Staphylococcus aureus was significantly higher in the normal reproduction (NR) group. Kyoto Encyclopedia of Genes and Genomes functional pathway enrichment analysis found that citrate cycle (TCA cycle, KO00020) and pyruvate metabolism (KO00620) were significantly enriched in pangolins with AR, whereas gonadotropin-releasing hormone secretion (KO04929) was significantly enriched in pangolins with NR. Metabolites such as tryptophan, arginine, and androgen were significantly enriched in pangolins with AR, whereas L-proline, taurine, choline, and spermidine were significantly enriched in pangolins with NR. Microbiota dysbiosis, energy metabolism disorder, deficiencies in key metabolic pathways and metabolites, and hormonal disturbances are all potential factors contributing to the inability of male Malayan pangolin to express natural reproductive behavior. This study provides evidence for AR of captive pangolins and offers important insights for the conservation of captive endangered species.},
}

@article {pmid42369554,
year = {2026},
author = {Zi, GR and Zhang, DJ and He, DL and Shu, F and Ou, Y and Ke, CX},
title = {Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843102},
pmid = {42369554},
issn = {1664-302X},
abstract = {Rapid and accurate detection of pathogenic microorganisms is the key to clinical diagnosis and treatment as well as public health prevention and control. As a representative of the third-generation sequencing technologies, nanopore sequencing technology has brought revolutionary potential to the field of pathogen detection by virtue of its unique advantages such as long read length, real-time sequencing and portable instruments. This paper aims to review the current application status of this technology and prospect its future development. Firstly, the basic principles and the development of mainstream platforms of nanopore sequencing are outlined. Subsequently, its specific applications in the detection of various pathogens including bacteria, viruses, fungi and parasites are systematically elaborated, with a focus on analyzing the practice and remarkable advantages of this technology in scenarios such as direct metagenomic detection without culture, rapid identification of drug resistance and virulence factors, and point-of-care rapid diagnosis. Meanwhile, this paper also objectively discusses the main technical challenges faced in the current application, including the raw read accuracy, the complexity of bioinformatics analysis and the balance between cost and benefit. Finally, the future technological optimization, standardization of data analysis workflows and the expansion of broader clinical application scenarios are prospected. Importantly, this review aims to equip clinical laboratory professionals with a balanced, evidence-based framework to evaluate the readiness, utility, and implementation pathway of nanopore sequencing for specific diagnostic use-cases (e.g., urgent meningitis/endophthalmitis, culture-negative infections, resistance gene detection) within the constraints of a clinical lab, such as cost, turnaround time, and staff expertise, in order to provide new technical perspectives and theoretical support for the precise diagnosis and active surveillance of infectious diseases.},
}

@article {pmid42369768,
year = {2026},
author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G},
title = {A foundational quantum framework for multi-pattern string matching in k-mer detection.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1802517},
pmid = {42369768},
issn = {2673-7647},
abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.

METHOD: We implement two quantum algorithms for DNA multi-pattern string matching for k-mer detection, leveraging Grover's amplitude amplification under the idealized quantum random access memory (QRAM) framework. The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O (√S) query complexity for S text positions but requiring O (m · L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O (√S · √m) in total. These asymptotic gains highlight the potential advantages that could be unlocked by future large-scale, low-noise QRAM architectures, positioning our results as a promising proof-of-concept foundation.

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

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

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

@article {pmid42369969,
year = {2026},
author = {Wei, M and Xiao, Z and Du, X and Cao, J and Wu, S and Zhang, R and Yang, X and Fan, C and Lian, J and Kang, W and Wang, C and Ye, C},
title = {mNGS-Identified Mycobacterium porcinum Infection in a Newly Diagnosed Person With HIV Presenting With Recurrent Suppurative Cervical Lymphadenitis.},
journal = {Open forum infectious diseases},
volume = {13},
number = {6},
pages = {ofag373},
pmid = {42369969},
issn = {2328-8957},
abstract = {Although reports of human infection caused by Mycobacterium porcinum (M. porcinum) have gradually increased in recent years, cases occurring in people with HIV (PWH) remain rare, and the association between M. porcinum infection and suppurative cervical lymphadenitis in PWH has not been previously reported. In this case, metagenomic next-generation sequencing was used to rapidly identify M. porcinum from a pus specimen obtained from a newly diagnosed person with HIV presenting with suppurative cervical lymphadenitis as the initial manifestation. Recognition of these rare clinical features may improve understanding of non-tuberculous mycobacterial infections in PWH and their diverse clinical presentations.},
}

@article {pmid42370219,
year = {2026},
author = {Niu, X and Yu, Q and Gu, J and Lu, B and Shen, W and Tian, J},
title = {Disseminated Mycobacterium avium Complex Infection in an HIV Patient with a History of Talaromyces marneffei: Diagnostic Value of Blind Subculture and Suspected Management Challenges of Immune Reconstitution Inflammatory Syndrome.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {606947},
pmid = {42370219},
issn = {1178-6973},
abstract = {This study reported a 33-year-old male acquired immune deficiency syndrome (AIDS) patient with a 10-year human immunodeficiency virus (HIV) infection history, poor antiretroviral therapy (ART) adherence, and two previous Talaromyces marneffei infections. Self-discontinuation of ART led to severe immunosuppression and disseminated Mycobacterium avium complex (MAC) infection involving the bloodstream and bone marrow. After the restart of ART, the patient developed persistent high fever, which was clinically suspected to be MAC-associated immune reconstitution inflammatory syndrome (IRIS). However, due to the lack of serial HIV viral load and CD4[+] T lymphocyte data, a definitive diagnosis could not be established. The patient was admitted with fatigue, anorexia, and black stool as the main symptoms. MAC infection was confirmed by blood culture, bone marrow culture, and bone marrow metagenomic next-generation sequencing (mNGS) at a higher-level hospital. Notably, after transfer to our hospital, the microbiology laboratory performed blind subculture on routinely negative blood culture bottles and extended the incubation period to 15 days, successfully isolating MAC. This highlights the crucial significance of close clinical-laboratory collaboration and optimized pathogen detection for diagnosing non-tuberculous mycobacteria (NTM) infections. After initial infection control and ART restart, the patient developed recurrent fever. Given the temporal association with ART reinitiation and the dose-dependent correlation between fever and glucocorticoid adjustments, possible MAC-associated IRIS was suspected. The patient's clinical symptoms improved with glucocorticoid therapy, though this does not confirm the diagnosis. Complications including cytomegalovirus reactivation, adverse drug reactions, and human rhinovirus co-infection were managed in a standardized manner. This case suggests that the diagnosis of disseminated MAC infection in severely immunocompromised AIDS patients relies on efficient collaboration between clinicians and laboratories. However, in the absence of confirmatory immunological and virological evidence, the diagnosis of IRIS remains uncertain. Clinicians should remain vigilant for suspected IRIS when restarting ART while acknowledge that limited data may preclude a definitive diagnosis. Individualized comprehensive strategies covering anti-infection, immunomodulation, anti-inflammation, and supportive treatment are the key to managing such complex HIV-related opportunistic infections.},
}

@article {pmid42370222,
year = {2026},
author = {Chen, M and An, W and Fang, S and Zhang, M},
title = {Efficacy and Safety of Omadacycline in Patients with Mycoplasma Pneumoniae Harboring the 23S rRNA A2063G Mutation.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {601060},
pmid = {42370222},
issn = {1178-6973},
abstract = {OBJECTIVE: Mycoplasma pneumoniae is a major pathogen of community-acquired bacterial pneumonia (CABP). Macrolide-resistant Mycoplasma pneumoniae (MRMP) harboring the 23S rRNA A2063G mutation poses a global therapeutic challenge. Omadacycline, a novel aminomethylcycline approved for CABP, exhibits activity against MRMP. However, real-world data on omadacycline for A2063G-mutated MRMP pneumonia remain limited. In this study, we present our clinical experience with intravenous omadacycline in patients with genetically confirmed A2063G-mutated MRMP pneumonia.

METHODS: We retrospectively analyzed the clinical data of eight patients with MRMP pneumonia confirmed by metagenomic next-generation sequencing (mNGS). All patients had failed prior macrolide or fluoroquinolone therapy and received a 7-day course of intravenous omadacycline. Clinical symptoms, inflammatory parameters, chest CT findings, and safety were evaluated.

RESULTS: Eight patients were included. Significant reductions in inflammatory markers were observed after treatment: the neutrophil count decreased from (6.92 ± 2.13)×10[9]/L to (4.67 ± 1.03)×10[9]/L (P = 0.02), C-reactive protein decreased from (68.17 ± 50.35) mg/L to (14.77 ± 19.34) mg/L (P = 0.01), and serum amyloid A decreased from (497.28 ± 319.79) mg/L to (28.35 ± 32.28) mg/L (P < 0.01). Chest CT showed marked resolution of pulmonary lesions in seven patients. No treatment-related adverse events requiring discontinuation were reported.

CONCLUSION: Omadacycline demonstrates promising clinical efficacy and a favorable safety profile for the treatment of pneumonia caused by A2063G-mutated MRMP, promoting both clinical and radiological recovery. Larger prospective controlled studies are warranted to confirm these findings.},
}

@article {pmid42370333,
year = {2026},
author = {Mahlich, Y and Sohi, H and Veličković, M and Piehowski, PD and McDermott, JE and Gosline, SJC},
title = {spammR: an R package designed for analysis and integration of spatial multi-omic measurements.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag163},
pmid = {42370333},
issn = {2635-0041},
abstract = {MOTIVATION: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics.

RESULTS: To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with the goal of integration across multiple data types (e.g. sequencing, metabolites, proteins) within the same tissue.

spammR is implemented in R. The package is currently installable from GitHub (https://pnnl-compbio.github.io/spammR/).},
}

@article {pmid42370706,
year = {2026},
author = {Schiml, VC and Stalder, K and Várnai, A and Bergaust, LL and Bakken, LR and Arntzen, MØ},
title = {Microbial consortia mediating lignocellulose turnover and denitrification in eutrophic lake sediment enrichments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057726},
doi = {10.1128/msystems.00577-26},
pmid = {42370706},
issn = {2379-5077},
abstract = {Lignocellulose is a major component of plant biomass and is recalcitrant, with efficient degradation typically requiring oxygen-dependent oxidative and carbohydrate-active enzymes (CAZymes). Anaerobic turnover is slower but can be supported by microbes capable of nitrate respiration, including denitrifiers and dissimilatory nitrate reduction to ammonium (DNRA) bacteria, which may use nitrate or nitric oxide as alternative oxidants. Anoxic layers beneath the oxic zones of eutrophic lake sediments, where nitrate penetrates from surface waters, provide a natural habitat for such organisms. To investigate these processes, we established nitrate-amended enrichments from organic-rich sediments of 10 eutrophic lakes and applied gas kinetics alongside metagenomics and metaproteomics to characterize the microbial communities. We identified a set of core microbial metagenome-assembled genomes (MAGs) present in all enrichments, dominated by Pseudomonadota, Bacteroidota, Verrucomicrobiota, and Actinomycetota, which played key roles in denitrification and fermentation. Lignocellulose degradation, however, was largely carried out by species outside the core microbiome-that is, different key degraders between lakes, suggesting lake-specific specialization. Among these, we observed potential respiratory DNRA pathways and a broad repertoire of CAZymes targeting various lignocellulose subfractions. Interestingly, many MAGs also encoded nitric oxide dismutases (NODs), enzymes postulated to convert NO to molecular oxygen and dinitrogen gas. Together, these findings advance our understanding of anaerobic biomass degradation and nitrogen cycling in eutrophic freshwater sediments, while highlighting the unexplored functional diversity of NOD-containing bacteria as an intriguing open question for future research.IMPORTANCELignocellulose, the main structural component of plant biomass, represents a vast reservoir of organic carbon in natural environments. Although lignocellulose breakdown is commonly associated with oxygen-rich conditions, it also occurs in oxygen-depleted habitats such as lake sediments, where the responsible microbes and processes are poorly understood. This study reveals how diverse microbial communities can degrade lignocellulose while respiring nitrate, linking carbon turnover to nitrogen cycling in anoxic environments. By identifying shared and lake-specific microbial strategies, as well as a widespread but poorly characterized class of enzymes associated with nitric oxide metabolism, our work advances our understanding of anaerobic biomass degradation. These insights have implications for ecosystem functioning in nutrient-rich waters and for the development of sustainable, oxygen-free biotechnological processes.},
}

@article {pmid42370707,
year = {2026},
author = {Victorsen, A and Knutson, TP and Bolender, L and Jung, S and Ferrieri, P and Thyagarajan, B and Hilt, EE},
title = {Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0366625},
doi = {10.1128/spectrum.03666-25},
pmid = {42370707},
issn = {2165-0497},
abstract = {UNLABELLED: Metagenomic next-generation sequencing (mNGS) in the infectious disease diagnostic space has been gaining traction and is popular for aiding in the diagnosis of central nervous system infections. However, many challenges and obstacles remain in making this technology a gold standard for infectious disease diagnostic testing. One major challenge is being able to distinguish between the clinically relevant organisms from background contamination. We performed a validation study for mNGS on cerebrospinal fluid (CSF) that utilized positive clinical samples and contrived samples that incorporated a bioinformatics pipeline that can better distinguish between background contamination and clinically relevant organisms and used a three-tiered reporting algorithm meant to decrease the inherent subjectivity that comes with interpreting and reporting data from clinical metagenomic sequencing. The validation of this assay and category-based reporting pipeline revealed an overall concordance of 91.8%, with a sensitivity of 100% and a specificity of 72.4%. In addition, we improved the detection of clinically relevant RNA viruses to almost 100% in the CSF by modifying the wet lab processing of the sample. This bioinformatics pipeline with a category-based reporting algorithm will provide more confidence in reporting microorganisms detected with this technology, mNGS, and improving patient care.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) can offer a broad, unbiased approach for the detection of infectious pathogens and has shown promise in diagnosing central nervous system infections. Despite its potential, clinical implementation remains limited by challenges in distinguishing clinically relevant organisms from background contamination. This study validated an mNGS assay for cerebrospinal fluid that incorporates an optimized bioinformatics pipeline with a three-tiered reporting algorithm designed to reduce subjectivity and enhance diagnostic confidence. The assay also has improved detection of clinically relevant RNA viruses through modified wet-lab processing. These findings support the clinical utility of a structured, category-based reporting approach for mNGS, advancing its reliability as a diagnostic tool in infectious disease testing.},
}

@article {pmid42370713,
year = {2026},
author = {Trubl, G and Roux, S and Kellom, M and Vyshenska, D and Tomatsu, A and Singh, K and Kimbrel, JA and Eloe-Fadrosh, E and Malmstrom, RR and Pett-Ridge, J and Blazewicz, SJ},
title = {Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113625},
doi = {10.1128/msystems.01136-25},
pmid = {42370713},
issn = {2379-5077},
abstract = {Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H2[18]O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant [18]O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 10[10] to 6.59 × 10[10] virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H2[18]O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.},
}

@article {pmid42370731,
year = {2026},
author = {Bresette, N and Ericsson, AC and Woods, C and Lin, A-L},
title = {MeLSI: Metric Learning for Statistical Inference in microbiome community composition analysis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040726},
doi = {10.1128/msystems.00407-26},
pmid = {42370731},
issn = {2379-5077},
abstract = {Microbiome beta diversity analysis relies on distance-based methods, including permutational multivariate analysis of variance (PERMANOVA) combined with fixed ecological distance metrics (Bray-Curtis, Euclidean, Jaccard, and UniFrac), which treat all microbial taxa uniformly, regardless of their biological relevance to community differences. This "one-size-fits-all" approach may miss subtle but biologically meaningful patterns in complex microbiome data. We present Metric Learning for Statistical Inference (MeLSI), a novel machine learning framework that learns data-adaptive distance metrics optimized for detecting community composition differences in multivariate microbiome analyses. MeLSI employs an ensemble of weak learners using bootstrap sampling, feature subsampling, and gradient-based optimization to learn optimal feature weights, combined with rigorous permutation testing for statistical inference. The learned metrics can be used with PERMANOVA for hypothesis testing and with principal coordinates analysis for ordination visualization. Comprehensive validation on synthetic benchmarks and real data sets shows that MeLSI maintains proper type I error control while delivering competitive or superior statistical power for detecting subtle community shifts and, crucially, supplies interpretable feature-weight profiles that clarify which taxa drive group separation. On the DietSwap data set, MeLSI was the only method to achieve significance at α = 0.05, demonstrating that adaptive weighting can detect diet-induced community shifts that fixed metrics miss. Across all data sets, the learned feature weights identified biologically relevant taxa while providing actionable insight that no fixed distance metric can supply. MeLSI therefore offers a statistically rigorous tool that augments beta diversity analysis with transparent, data-driven interpretability.IMPORTANCEUnderstanding which microbes differ between groups of interest could reveal therapeutic targets and diagnostic biomarkers. However, current analysis methods treat all microbes equally (similar to using the same ruler to measure everything, regardless of what matters most). This means subtle but biologically important differences may go undetected, especially when only a few key species drive disease states while hundreds of "bystander" species add noise. Metric Learning for Statistical Inference (MeLSI) solves this by learning which microbes matter most for each specific comparison. In comparing male and female gut microbiomes, MeLSI identified specific bacterial families driving the differences, providing actionable biological insights that standard methods miss. This capability is particularly crucial for detecting early disease biomarkers, where differences are subtle and masked by biological variability. By telling researchers not just whether groups differ, but which specific microbes drive those differences, MeLSI accelerates the path from microbiome data to testable biological hypotheses and clinical applications.},
}

@article {pmid42370747,
year = {2026},
author = {Plominsky, AM and Oliver, A and Henriquez-Castillo, C and Podell, S and Minich, JJ and Augyte, S and Lowell-Hawkins, J and Sims, NA and Allen, EE},
title = {Detoxifying and depolymerizing microorganisms reveal intertwined guild collaborations in the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens.},
journal = {mBio},
volume = {},
number = {},
pages = {e0338225},
doi = {10.1128/mbio.03382-25},
pmid = {42370747},
issn = {2150-7511},
abstract = {The biotransformation of macroalgal biomass represents a major catabolic challenge due to its structurally diverse polysaccharides and inhibitory polyphenols. Unlike terrestrial lignocellulosic substrates, macroalgal polysaccharides contain multiple monomer types, branching patterns, and sulfation states. Additionally, toxic macroalgal polyphenols have been shown to inhibit both microbial growth and their catalytic enzymes. While herbivorous fishes have evolved specialized gut microbiota to process these substrates, the enzymatic pathways remain poorly characterized, with few experimentally validated polysaccharide utilization loci or biochemically defined marine sulfatases, and limited understanding of polyphenol degradation. Here, we developed in vitro microcosms, based on the gut microbiome of the generalist macro-algivorous fish Kyphosus cinerascens, to temporally resolve the activity of the microbial guilds involved in macroalgal polysaccharide and polyphenol transformation. First, parallel cDNA/DNA amplicon sequencing was employed to distinguish the natural active fraction from transient gut microbiome taxa that became inactive/dead after their ingestion. Four medium combinations were able to propagate between 96% and 99% of the active hindgut microbial families, reproducing the cooperative degradation dynamics observed in vivo. Metagenomic and metatranscriptomic profiling of these four optimized in vitro microcosms served as models to assess the stepwise functional successions occurring in the natural gut microbiome. Early Gammaproteobacteria expressed enzymes linked to polyphenol detoxification and alginate degradation, followed by Bacillota, Bacteroidota, and Verrucomicrobiota guilds targeting more recalcitrant sulfated polysaccharides and polyphenols. Together, these results identified temporal and taxonomic coordination as key features of macroalgal biomass deconstruction, providing an experimentally tractable model for discovering novel carbohydrate-active enzymes and elucidating poorly understood pathways of marine polyphenol degradation.IMPORTANCESeaweed represents a source of sustainable biomass for various applications, but scalable industrial methods struggle to break down seaweed biomass into intermediate products due to the complexity of its constituents. Fish of the genus Kyphosus feed on different seaweed types by leveraging gastrointestinal bacteria to neutralize inhibitory polyphenols and convert their polysaccharides into simple sugars. This study identifies microbial groups that are transcriptionally active in natural fish hindgut microbiomes and how to propagate these active microbial communities in vitro. This enabled assessing how distinct microbial guilds act in succession to transform complex polysaccharides and polyphenols. Notably, this is the first study to assess the biotransformation capacities of macroalgal polyphenols by complex in vitro hindgut microbiomes of a generalist herbivorous fish. These findings advance our ecological understanding of cooperative degradation in marine gut symbioses and establish a tractable platform for discovering new enzymes and pathways with potential applications in algal biomass utilization.},
}

@article {pmid42371112,
year = {2026},
author = {Tang, A and Cao, Q and Wang, M and Li, W and Xu, H and Wang, Y and Niu, H and Wang, H and Ma, G and Jia, K and Feng, X and He, C and He, J and Alballa, MM and Liao, X and Tian, T and Qin, B and Yang, N and Wei, J and Sun, J and Wang, Y and Cheng, Y and Wu, Q and Yang, J and Wang, Q and Wang, X and Liu, X},
title = {The effectiveness of a plant-based milk with fermented brown rice on constipation symptoms via gut microbiota modulation: a double-blind randomized controlled trial.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42371112},
issn = {1436-6215},
support = {DW080038K0000004//Xi'an Jiaotong University/ ; 82011530197//National Natural Science Foundation of China/ ; 202405212//Feihe Research Grant/ ; },
mesh = {Humans ; *Constipation/microbiology/diet therapy ; *Oryza ; Double-Blind Method ; Female ; *Plant-based Milk ; Adult ; *Gastrointestinal Microbiome/physiology ; Animals ; Middle Aged ; Fermentation ; Fermented Foods ; },
abstract = {PURPOSE: To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.

METHODS: This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500 ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).

RESULTS: A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all P < 0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus Blautia, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.

CONCLUSION: Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.

CLINICAL TRIAL REGISTRY: This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).},
}

Humans
*Constipation/microbiology/diet therapy
*Oryza
Double-Blind Method
Female
*Plant-based Milk
Adult
*Gastrointestinal Microbiome/physiology
Animals
Middle Aged
Fermentation
Fermented Foods

@article {pmid42371206,
year = {2026},
author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T},
title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42371206},
issn = {1573-0972},
support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; },
mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth & development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenome ; China ; Microbiota/genetics ; },
abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.},
}

*Phosphorus/metabolism
*Soil Microbiology
*Soil/chemistry
*Nitrogen/metabolism
Oryza/growth & development
*Nitrogen Cycle
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenome
China
Microbiota/genetics

@article {pmid42371248,
year = {2026},
author = {Tlaskalová-Hogenová, H and Hrnčíř, T and Štěpánková, R and Trebichavský, I and Hudcovic, T and Šplíchal, I and Šplíchalová, A and Šinkora, M and Funda, D and Sánchez, D and Kverka, M and Jirásková Zákostelská, Z and Kostovčíková, K and Coufal, Š and Procházková, P and Roubalová, R and Vannucci, L and Miler, I},
title = {Gnotobiology: from 19th-century global foundations to 21st-century omics - six decades of Czech contribution to microbiome research.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42371248},
issn = {1874-9356},
support = {22-12533S, 22-21356S, 23-05645S, 25-16094S, 26-21469S//Czech Science Foundation (GAČR)/ ; LUAUS23014//Ministry of Education, Youth and Sports of the Czech Republic/ ; CZ.02.01.01/00/22_008/0004597//European Union - Next Generation EU (Operational Programme Johannes Amos Comenius)/ ; LX22NPO5102//European Union - Next Generation EU (National Institute for Cancer Research, Programme EXCELES)/ ; RVO: 61388971//Institute of Microbiology of the Czech Academy of Sciences/ ; NU21-04-00443, NU22-09-00493, NU22J-05-00056, NU23-01-00288, NU23-04-00381, NU23-05-00133, NW24-06-00509, NW24-07-00042, NW25-04-00079//Czech Health Research Council (AZV ČR)/ ; },
abstract = {Gnotobiology, from the Greek gnotos (meaning 'known') and bios (meaning 'life'), is a research discipline that uses organisms with a defined microbiological status to study the interaction between hosts and microbes. This review traces six decades of Czech gnotobiology, beginning with the launch of a dedicated gnotobiology programme at Nový Hrádek in 1962 by Jaroslav Šterzl, whose visionary aims anticipated by decades the current recognition of the microbiota as a central determinant of immune and broader physiological function. The site - originally established in 1953 as the Biological Station - was thereby transformed into one of only four gnotobiological laboratories worldwide at that time and the first in Central and Eastern Europe. The facility pioneered the rearing of germ-free piglets, rats, rabbits, and mice, establishing the experimental foundation for the laboratory's work on immune ontogeny, mucosal immunity and tolerance, and microbiota-host interactions in immune development and regulation. This review discusses the key discoveries made using these models. Among them, work at the Institute of Microbiology (Prague and Nový Hrádek) demonstrated that germ-free animals have underdeveloped lymphoid tissue and impaired adaptive immunity. The review also describes the subsequent development of gnotobiotic models of human metabolic, immune-mediated, neoplastic, and neuropsychiatric diseases. The completion of the Human Genome Project in 2001 and the emergence of microbial metagenomics in the early 2000s sparked renewed interest in host-microbe interactions and led to a rediscovery of gnotobiotic approaches as essential tools for establishing causation in microbiome research. We examine how integrating these approaches with high-throughput sequencing, metabolomics, and other omics technologies has shifted the focus from cataloguing the microbiome to mechanistically dissecting host-microbe interactions. Finally, we outline future directions, including humanized gnotobiotic models, microbiota-based therapeutics, and the convergence of gnotobiology with personalized medicine and synthetic biology.},
}

@article {pmid42371328,
year = {2026},
author = {Pattani, V and Kaneriya, J and Joshi, K and Sanghvi, G},
title = {Microbial Metabolic Strategies for Environmental Detoxification: From Enzymatic Mechanisms to Synthetic Biology and Omics.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42371328},
issn = {1559-0291},
abstract = {Microorganisms play a pivotal role in environmental detoxification by utilizing their metabolic pathways to degrade, transform, or immobilize toxic pollutants such as hydrocarbons, heavy metals, pesticides, and industrial effluents. This review explores microbial enzymatic systems, including oxidoreductases, hydrolases, and transferases, that facilitate pollutant breakdown. Various bioremediation strategies, such as bioaugmentation, biostimulation, and phytoremediation-assisted microbial degradation, are discussed alongside advances in synthetic biology and metabolic engineering, which enhance microbial efficiency for targeted detoxification. The potential of microbial consortia in tackling complex contamination scenarios is also examined. Additionally, omics-based approaches, including metagenomics, transcriptomics, and proteomics, provide deeper insights into microbial community dynamics and metabolic capabilities. Challenges such as environmental limitations, regulatory concerns, and sustainability issues are critically analyzed. By integrating microbiology with biotechnological innovations, microbial metabolism can be effectively harnessed for large-scale pollution mitigation, offering ecofriendly and cost-effective solutions to address global environmental challenges and promote sustainable industrial practices.},
}

@article {pmid42372060,
year = {2026},
author = {Jiang, H and Zhang, M and Khan, RAA and Zhao, J and Hou, J and Liu, T},
title = {Trichoderma enriches Burkholderia via cross-feeding of degradation intermediates to enhance atrazine degradation and alleviate soybean phytotoxicity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag152},
pmid = {42372060},
issn = {1751-7370},
abstract = {The widespread agricultural use of atrazine threatens soil health, and residual phytotoxicity in corn-soybean rotation systems necessitates sustainable remediation strategies. By leveraging the atrazine-degrading fungus Trichoderma lentiforme HN154, we achieved an 80.3% removal of atrazine (500 mg/kg) in non-sterilized soils from a corn planting system within 14 days, 22.1% higher degradation than in sterilized soil, while concurrently alleviating phytotoxic symptoms in soybean plants. Metagenomic analysis revealed that colonization by T. lentiforme HN154 drove restructuring of microbial networks, enriching the keystone family Burkholderiaceae, which was strongly associated with atrazine catabolism and four key catabolic enzymes (EC 3.5.4.43 (atzB), EC 3.5.1.131 (atzE), EC 3.5.1.54 (atzF), EC 3.5.4.42 (atzC)). Among 23 rhizosphere isolates, the Burkholderia strains Bur-4, Bur-5, and Bur-14 showed the highest atrazine degradation rates (26.3% - 29.4%) within 72 h. A Trichoderma-Burkholderia synthetic consortium further enhanced remediation by boosting plant antioxidant defenses (SOD, POD, CAT) and reducing oxidative damage (MDA). Mechanistically, intermediates (hydroxyatrazine and biuret) generated during T. lentiforme HN154-mediated degradation stimulated Burkholderia chemotaxis, swarming and swimming motility, while cross-feeding on these metabolites synergistically accelerated bioaugmentation (the Trichoderma-Burkholderia synthetic consortium achieved rapid atrazine degradation of 86.3% within 168 h). This study reveals tripartite interactions among exogenous microbial degraders, pollutant metabolites, and indigenous microbiota, offering a strategic foundation for microbiome-guided, precision bioaugmentation to restore soil ecological health and crop resilience.},
}

@article {pmid42372843,
year = {2026},
author = {Capuano, N and Giannattasio, A and Impemba, S and Belgiorno, V and Folliero, V and Buonerba, A and Franci, G},
title = {Microplastics as Emerging Viral Vectors: Nexus, Mechanisms, Ecological Implications and Health Risks.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125138},
doi = {10.1016/j.envres.2026.125138},
pmid = {42372843},
issn = {1096-0953},
abstract = {Microplastics (MPs) have emerged as pervasive environmental pollutants with complex implications for ecological and human health. Beyond their chemical toxicity and persistence, MPs act as dynamic microhabitats supporting microbial colonization and viral adsorption. This review provides a comprehensive overview of the physicochemical characteristics, environmental distribution, and degradation pathways of the most common polymeric MPs, including polystyrene, polyethylene, polypropylene, polyvinyl chloride, polyurethane, polyethylene terephthalate, polydimethylsiloxane, and biobased polyesters. Particular attention is given to the virus-microplastic interface, highlighting how MPs serve as vectors that enhance viral persistence, transport, and infectivity. Experimental and metagenomic evidence demonstrates that both enveloped and non-enveloped viruses can adhere to MPs via electrostatic and hydrophobic interactions, often mediated by biofilm and eco-corona formation. These interactions extend viral stability across environmental compartments and can modulate host immune responses, exacerbating infection outcomes. By integrating physicochemical, microbiological, and toxicological perspectives, this review emphasizes that MPs are not inert residues but active ecological interfaces that can reshape viral ecology and increase public-health risks. Future studies combining molecular, environmental, and epidemiological approaches are essential to quantify the real impact of MP-virus interactions on ecosystem balance and infectious-disease dynamics.},
}

@article {pmid42372850,
year = {2026},
author = {Gong, X and Zhang, L and Xu, A and Huang, Z and Wang, C and Yang, T and Liang, H and Zhang, M and Zhan, X and Peng, Y and Gao, D},
title = {Root Exudates Recruit Beneficial Microbes to Promote Anammox-Driven Nitrogen Cycling in Wetland.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125149},
doi = {10.1016/j.envres.2026.125149},
pmid = {42372850},
issn = {1096-0953},
abstract = {Anammox bacteria serve as a major biological sink in nitrogen (N) cycling within wetland, yet the hydrophyte root exudates-mediated microbial interplay mechanism that sustain their activity and ecosystem function remain unclear. To address this gap, we established flow-controlled microcosms planted with Iris pseudacorus, combined with [15]N stable isotope tracing and metagenome-assembled genomes (MAGs) analysis. Our findings revealed that root exudates significantly enhanced in-situ anammox rates (rhizosphere: 5.9±2.0 mg N/(m[3]·d), non-rhizosphere: 0.4±0.02 mg N/(m[3]·d), p<0.001), leading to a remarkable enrichment of anammox bacteria in the rhizosphere (6.5×10[7] copies/g dry sludge, p<0.001). We further uncovered a previously overlooked partial denitrification pathway that supplied nitrite, substantially increasing anammox contributions to rhizosphere N removal (16.6±4.1%). Key bioactive components, flavonoids and amino acids, selectively recruited beneficial rhizobacteria affiliated to Pseudomonadota and Bacteroidota. MAGs-based analysis revealed that these microbial taxa encoded pathways for producing essential substrates (nitrite loop) and metabolites (cofactor, biotin) supporting anammox metabolism. The symbiotic interaction facilitated the survival and metabolic activity of anammox bacteria in the oligotrophic rhizosphere habitat. These findings unveil a natural plant-microbiota interaction that effectively enhances the sustainability of N cycling and provide new insights for optimizing nitrogen removal strategies in engineered wetland systems.},
}

@article {pmid42372852,
year = {2026},
author = {Wang, Y and Yan, C and Jin, J and Li, Z and Zhou, H and Tang, J and Wang, X and Li, H},
title = {Straw incorporation and strawsphere formation shape the fate of antibiotic-resistant human pathogens in agricultural soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125142},
doi = {10.1016/j.envres.2026.125142},
pmid = {42372852},
issn = {1096-0953},
abstract = {Antibiotic-resistant human pathogens (ARPs) in soil pose a latent threat to public health. However, how ARPs evolve in agricultural soil after straw incorporation remains unclear. This study combined a metagenomic analysis of 230 soil samples from typical straw-incorporated regions in China and controlled microcosm experiments to assess the effects of straw incorporation on soil ARPs. The influence of straw incorporation on ARPs was management practice-dependent. Semi-quantity short (4 cm) straw incorporation significantly decreased the total abundances of ARPs by 17.4%. A redundancy analysis revealed that elevated levels of alkali hydrolyzable nitrogen, available potassium and total organic carbon as well as virus abundance were key factors associated with the reduction in ARPs in straw-incorporated soil. Moreover, scanning electron micrographs revealed that the straw surface developed a coccoid bacterium-dominated biofilm, forming a distinct ecological niche, the strawsphere. A KEGG pathway annotation suggested that lignocellulose-degrading microbes in the strawsphere serve as a potential source of ARP-antagonistic microorganisms. Structural equation models further identified straw fragment length as a critical parameter for the fates of ARPs both in soil and the strawsphere. The study elucidated the critical roles of straw incorporation and the resulting 'strawsphere' in controlling ARPs in agricultural soil.},
}

@article {pmid42372901,
year = {2026},
author = {Edwards, M and Sanchez-Ramos, L},
title = {Likelihood ratios enhance clinical interpretation of metagenomic prediction of early-onset neonatal sepsis in preterm premature rupture of membranes (Letter-to-the-Editor).},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2026.06.023},
pmid = {42372901},
issn = {1097-6868},
}

@article {pmid42372926,
year = {2026},
author = {Kwon, CY and Choi, YH and Kim, H and Han, K and Jang, D and Hwangbo, H},
title = {Gut microbial signature for frailty discrimination: a metagenomic meta-analysis of 28 independent cohorts.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {113223},
doi = {10.1016/j.exger.2026.113223},
pmid = {42372926},
issn = {1873-6815},
abstract = {Frailty, a clinical syndrome of multisystem decline and homeostatic vulnerability, is a critical public health priority. While the gut microbiome regulates immune and metabolic signaling, current evidence remains fragmented. We performed a metagenomic meta-analysis of 955 individuals from 28 independent cohorts across 24 countries to identify universal microbial signatures and develop a generalizable discriminative model. Frailty was determined using a Proxy Frailty Index based on the deficit accumulation model. Following refinement to isolate signatures from disease-specific dysbiosis, we used Firth's penalized regression for biomarker discovery and validated a Random Forest (RF) model via leave-one-study-out cross-validation. Shannon diversity exhibited a significant and sharp decline during the transition from robust to pre-frail states (p = 0.0006), manifesting at the earliest stages of physiological decline. We identified 16 microbial biomarkers characterized by the progressive attrition of core symbionts, such as Coprococcus eutactus, and the opportunistic expansion of pathobionts, including Enterococcus gallinarum. Sensitivity analysis in a healthy sub-cohort (n = 499) confirmed that these shifts occur independently of chronic clinical diagnoses and their associated confounding effects (p = 0.036). The 16-species RF model, predominantly driven by Collinsella massiliensis, achieved a corrected mean area under the receiver operating characteristic curve of 0.7572 across 5 eligible cohorts. Gut microbial restructuring is a sentinel biological hallmark of frailty that occurs independently of aging-related diseases. This study establishes a microbial signature broadly applicable across European and East Asian populations that serves as a high-fidelity, non-invasive metric for precision geriatric assessment.},
}

@article {pmid42372963,
year = {2026},
author = {Cui, Q and Wang, F and Shan, X and Ding, L and Qiu, X and Zhang, B and Li, X and Liang, X and Guo, X},
title = {Biodegradable polylactic acid microplastics affect nutrient cycling during the entire crop growth cycle: Implications for soil ecosystem multifunctionality.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128664},
doi = {10.1016/j.envpol.2026.128664},
pmid = {42372963},
issn = {1873-6424},
abstract = {While microplastics (MPs) have been extensively studied for their effects on soil nutrient cycling, their influence on ecosystem multifunctionality (EMF) across the entire crop growth cycle remains poorly understood. This study systematically investigated the impacts of a model biodegradable MP, polylactic acid (PLA), on soil microbiomes and EMF across different maize incubation periods. Results of 16S rRNA amplicon sequencing and metagenomic analysis revealed that PLA-MPs decreased bacterial community α-diversity, co-occurrence network complexity, and stability throughout the 120-day incubation period. Particularly, PLA-MPs exerted more pronounced effects at early incubation stages (30 and 60 days), and these effects were intensified with increasing PLA-MP concentrations. PLA-MPs suppressed anaerobic carbon fixation (porA, porB, frda) and pyruvate metabolism (ppdk), while promoting fermentation (L-lactate dehydrogenase), nitrogen fixation (nifD, nifH, nifK, anfG), and microbial phosphorus (P) acquisition (phoD, phn cluster). Over the entire incubation period, PLA-MP-induced shifts in nutrient cycling enhanced soil carbon (C) function by 37.6-569%, while decreasing nitrogen (N) and P functions by 8.40-22.4% and 16.8-56.2%, respectively. Path analysis revealed that PLA-MPs altered soil properties and bacterial community diversity, which in turn regulated functional genes and these individual soil functions, thereby reducing EMF by 2.05-27.0% (R[2] = 0.923), with bacterial community diversity as the primary driver of EMF (standardized path coefficient of 0.978). These findings underscore the impacts of PLA-MPs on EMF in the soil-crop system throughout the entire maize growth cycle, advancing the understanding of the agroecological safety of biodegradable MPs.},
}

@article {pmid42373490,
year = {2026},
author = {Shen, Y and Zhang, DT and Shi, WX and Ma, CN and Huo, D and Yang, P and Wang, QY and Feng, ZM},
title = {[Epidemiological characteristics of test-negative severe acute respiratory infections during the 2024-2025 surveillance years in Beijing].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {47},
number = {6},
pages = {1114-1119},
doi = {10.3760/cma.j.cn112338-20260104-00004},
pmid = {42373490},
issn = {0254-6450},
support = {2026-2G-30124//Capital's Funds for Health Improvement and Research/ ; BJRID2026-001//Beijing Research Center for Respiratory Infectious Diseases/ ; 20252D01900800//National Science and Technology Major Project of China/ ; },
mesh = {Humans ; Middle Aged ; Adult ; Adolescent ; Child ; Child, Preschool ; *Respiratory Tract Infections/epidemiology/microbiology ; Male ; Female ; Young Adult ; Infant ; Beijing/epidemiology ; Aged ; Infant, Newborn ; High-Throughput Nucleotide Sequencing ; Acute Disease ; },
abstract = {Objective: To analyze the epidemiological characteristics of cases with severe acute respiratory infection (SARI) in Beijing who tested negative for 22 common respiratory pathogens by nucleic acid testing, and to explore the potential pathogen spectrum using metagenomic next-generation sequencing (mNGS). Methods: Data were obtained from the Beijing Acute Respiratory Infectious Disease Surveillance Network. Hospitalized SARI cases from week 40 of 2024 to week 39 of 2025 were included. All cases were tested for 22 common respiratory pathogens using nucleic acid assays. Among those test-negative results, 50 specimens were randomly selected for mNGS analysis. Multivariable logistic regression was performed to identify factors associated with test-negative results. Results: A total of 7 202 SARI cases were included, of whom 4 212 (58.5%) tested negative for all 22 common respiratory pathogens. The proportion of negative results increased with age, with 32.9% (322/978) in children aged 0-5 years, 69.1% (972/1 407) in adults aged 18-59 years, and 65.0% (2 506/3 856) in those aged ≥60 years, the difference was statistically significant (all P<0.001). Multivariable analysis showed that age was independently associated with negative results (18-59 years: aOR=4.62, 95%CI:3.85-5.55; ≥60 years: aOR=4.08, 95%CI:3.49-4.78). Upper respiratory samples were more likely to test negative. Among 48 valid mNGS samples, 32 pathogens were identified. At least one pathogen was detected in 44 cases (93.6%), and multiple infections were common (37 cases, 84.1%). Human herpesvirus 7 (20 cases) was most frequently detected, followed by Stenotrophomonas maltophilia (16 cases), Human herpesvirus (15 cases), and Streptococcus pneumoniae (12 cases). Conclusions: A high proportion of SARI cases in Beijing tested negative for common respiratory pathogens, and age played an important role. mNGS identified predominantly opportunistic pathogens and herpesviruses, and did not detect novel pathogens with clear respiratory significance. These findings indicate that the current SARI surveillance covers the most common respiratory pathogens.},
}

Humans
Middle Aged
Adult
Adolescent
Child
Child, Preschool
*Respiratory Tract Infections/epidemiology/microbiology
Male
Female
Young Adult
Infant
Beijing/epidemiology
Aged
Infant, Newborn
High-Throughput Nucleotide Sequencing
Acute Disease

@article {pmid42373646,
year = {2026},
author = {Howells, AEG and Robinson, K and Silva, MG and Cook, E and Fifer, L and Boyer, G and Hoehler, T and Shock, EL},
title = {Methanotrophy under extreme alkalinity in a serpentinizing system.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72513-6},
pmid = {42373646},
issn = {2041-1723},
support = {NNA15BB02A//NASA | NASA Astrobiology Institute (NAI)/ ; EAR-1515513//National Science Foundation (NSF)/ ; EAR-1949030//National Science Foundation (NSF)/ ; EAR-2149016//National Science Foundation (NSF)/ ; },
abstract = {Serpentinization produces hyperalkaline, H2- and CH4-rich fluids that support microbial life and serve as analogs for ocean worlds such as Enceladus. While methane production in these systems has been well studied, methane consumption-especially under high pH-remains poorly understood. Here, we present isotopic, geochemical, and genomic evidence for hyperalkaliphilic (pH > 11) methanotrophy in the Samail ophiolite of Oman. Using models that account for fluid mixing and gas exsolution, we identify δ[13]CH4 enrichment that cannot be explained by abiotic processes alone. The enrichment of [13]CH4 co-occurs with methanotroph 16S rRNA gene sequences, particularly in fluids formed by mixing CH4-rich, reduced fluids with oxidant-rich waters. Shotgun metagenome sequencing reveals a metagenome-assembled genome affiliated with Methylovulum, encoding a complete methane oxidation pathway, multiple carbon assimilation routes, and Na[+]/H[+] antiporters-adaptations likely enabling growth above pH 11. Our findings highlight the viability of methanotrophy under extreme high pH conditions and provide a framework for interpreting δ[13]CH4 signals in serpentinizing environments on Earth and beyond.},
}

@article {pmid42374042,
year = {2026},
author = {Chen, X and Chen, C and Zhang, P and OuYang, X and Ma, H and Chen, W and Li, T and Han, J and Wang, Y and Wang, H and Zhou, Q and Cheng, G and Zhou, W and Yu, Z and Zhou, W and Wang, M and Zeng, S},
title = {Bifidobacterium animalis reshapes the bile acid pool and prevents neonatal jaundice: a clinical microbiome study from correlation to causation.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01057-w},
pmid = {42374042},
issn = {2055-5008},
support = {2024YFC2707700//National Key R&D Program of China, Key Special Project for "Reproductive Health and Maternal and Child Health Security"/ ; 82571963//the National Natural Science Foundation of China/ ; 2025A1515012162//Natural Science Foundation of Guangdong Province, China/ ; JCYJ20250604145739052//Shenzhen Science and Technology Innovation Bureau/ ; Y2024001//the Research Initiation Fund of Longgang District Maternity & Child Healthcare Hospital of Shenzhen City/ ; },
abstract = {Neonatal jaundice (NJ) affects 60-80% of neonates, yet the underlying microbial mechanisms remain elucidated, despite known links between gut dysbiosis and bilirubin and bile acid (BA) metabolism. Through two-stage shotgun metagenomic-metabolomic analysis of 150 fecal samples from 120 neonates, we identified key taxa linked to bile acid (BA) metabolism in moderate-to-severe NJ. Furthermore, multi-omics integration revealed significant interkingdom correlations among gut phages, bacteria, and BAs. Dysbiosis featured enriched Streptococcus and Escherichia, depleted Bifidobacterium animalis, and group-specific phage signatures. In the independent clinical validation cohort, jaundice intervention normalized the dysbiotic profile, demonstrating significant suppression of pathogenic taxa concomitant with restoration of B. animalis abundance. In vitro, B. animalis subsp. lactis Y103-OTU5 remodeled BA via deconjugation. In a phenylhydrazine hydrochloride (PHZ)-induced murine model of hemolytic jaundice, oral administration of isolated B. animalis subsp. lactis Y103-OTU5 significantly attenuated hyperbilirubinemia and hepatic inflammation, likely via Cyp7a1/Cyp7b1-dependent modulation of BA synthesis and detoxification pathways. Structural equation modeling revealed a tripartite regulatory network: phages indirectly modulated BA through bacterial remodeling, while B. animalis directly regulated BA pathways, positioning it as a potential therapeutic candidate for hemolysis-associated neonatal jaundice. Collectively, these findings reveal a gut phage-bacteria-BA network in NJ, highlighting B. animalis as a therapeutic candidate with dual modulation of BA metabolism and phage-bacteria interactions.},
}

@article {pmid42365131,
year = {2026},
author = {Zhu, S and Yang, Z and Zhao, H and Ma, Y and Chen, K and Qi, D},
title = {Rainfall Drives Differentiation of Plant Rhizosphere Microbial Communities in Two Different Types of Alpine Wetlands: A Perspective Based on a Carbon-Water Coupling Framework.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02823-1},
pmid = {42365131},
issn = {1432-184X},
support = {Qing[2025]TG04//Demonstration of Techniques for Wetland Protection, Restoration, and Carbon Sink Capacity Enhancement in the Qinghai Lake Basin - Qinghai Provincial Finance Budget/ ; },
abstract = {The alpine wetlands of the Qinghai-Tibet Plateau are confronting significant ecological challenges due to drastic shifts in precipitation patterns. Elucidating the response mechanisms of rhizosphere microbial communities in wetland plants to precipitation events is critical to understanding ecosystem resilience. In this study, sandy wetlands at Niaodao and riverine wetlands at Haergai in the Qinghai Lake basin were selected as study sites. Using Poa alpigena rhizosphere and non-rhizosphere soils as the research subjects, metagenomic DNA sequencing combined with environmental factor analysis was employed to compare the microbial community responses before and after a single pulse precipitation event. The results showed that Proteobacteria and Actinobacteria were the dominant phyla in both wetland types (combined relative abundance > 70%). Rainfall induced a differentiated restructuring of soil microbial community composition across different habitats. In rhizosphere soils, rainfall significantly reduced microbial alpha diversity. Co-occurrence network analysis revealed that the rhizosphere community shifted from a competition-coexistence pattern before rainfall to a cooperative adaptation pattern after rainfall, with significant increases in modular cohesion and the proportion of positive correlations. Metagenomic analysis indicated that the number of differentially abundant metabolic pathways in soil microorganisms increased markedly after rainfall, rising to 46 and 40 pathways in the rhizosphere and non-rhizosphere, respectively (compared to 3 and 31 before rainfall), indicating a shift from carbon reserve metabolism to energy-producing metabolism. Total carbon and water content were identified as the core environmental factors jointly regulating community assembly. This study reveals the mechanism by which regional background, precipitation disturbance, and the rhizosphere effect synergistically drive the succession of microbial communities in alpine wetlands, providing a new paradigm for understanding ecosystem adaptation to climate change.},
}

@article {pmid42365389,
year = {2026},
author = {Park, JH and Lee, KL and Lee, YM and Choi, JY and Heo, YR and Oh, SM and Lee, D and Kim, S and Lee, HW and Poon, CTC and Hong, WH and Moon, HB and Mok, S and Lee, CY and Kim, MA and Yuen, AHL and Seok, SH and Kim, BY and Kim, SW},
title = {From traumatic oral fibroma to fatal pneumonia: a multidisciplinary postmortem investigation in a long-term monitored Indo-Pacific bottlenose dolphin (Tursiops aduncus).},
journal = {BMC zoology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40850-026-00277-z},
pmid = {42365389},
issn = {2056-3132},
support = {No. RS-2025-25432543//National Research Foundation of Korea/ ; No. RS-2022-NR072403//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: An Indo-Pacific bottlenose dolphin (Tursiops aduncus) in the coastal waters of Jeju Island, Republic of Korea, exhibited an oral mass and mandibular deformity over a documented 6-year period, including 3 years of intensive longitudinal monitoring by our research team. A multidisciplinary approach combining imaging, pathology, microbiology, and omics analyses was used to assess the dolphin.

RESULTS: Post-mortem computed tomography confirmed a mandibular fracture at the oral mass site. Histopathological examination of the oral mass revealed prominent fibroblast proliferation and collagen deposition. Fibropapillomas and desmoid tumors were excluded based on viral detection assays and β-catenin accumulation analysis, supporting a diagnosis of trauma-induced fibroma. Transcriptomic analysis of the tumor tissues identified highly expressed genes associated with extracellular matrix remodeling, myofibroblast activation, and epithelial differentiation, supporting a reactive fibrotic rather than malignant phenotype. Gross necropsy revealed multiple suppurative pulmonary lesions, abundant foamy fluid within the respiratory tract, and diatoms within the pulmonary tissue. Metagenomic sequencing revealed a polymicrobial infection, with Parvimonas micra as the predominant organism. Collectively, these findings are most consistent with aspiration pneumonia, with severe secondary pulmonary infection considered a major contributor to death. In addition, analysis of halogenated organic contaminants revealed accumulation levels consistent with those typically observed in aged individuals, and no evidence was identified indicating a direct causal role in the terminal disease process.

CONCLUSIONS: To the best of our knowledge, this is the first study to characterize the pathological features and proposed pathogenic mechanism of traumatic fibroma in a marine mammal, and the first confirmed case of pulmonary abscessation associated with Parvimonas micra infection in this taxonomic group. Overall, these findings provide valuable baseline data for the health monitoring and conservation of marine mammal populations.},
}

@article {pmid42365784,
year = {2026},
author = {Chen, Q and Zheng, J and Zeng, L and You, Y and Zhuang, X and Meng, F and Wang, L},
title = {A 1-year-old boy with near-complete tracheobronchial obstruction from endobronchial tuberculosis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117533},
doi = {10.1016/j.diagmicrobio.2026.117533},
pmid = {42365784},
issn = {1879-0070},
abstract = {A one-year-old boy was referred to our respiratory department for further evaluation of obstructing endobronchial lesions. The lesions were detected on chest computed tomography (CT) performed at another hospital after the patient presented with cough and worsening wheezing. Physical examination revealed tachypnea and diminished breath sounds bilaterally without rales. The patient was receiving supplemental oxygen. Notably, his medical history was significant for an admission at 21 days of age for persistent cough, right upper lung atelectasis, and sputum analysis that revealed Bordetella pertussis, Acinetobacter baumannii, and rhinovirus. Despite advanced testing, including bronchoalveolar lavage acid-fast staining, tuberculin skin testing, and metagenomic next-generation sequencing, the diagnosis was initially missed and was ultimately established only after multi-institutional pathology review with deeper histologic recuts identifying a rare acid-fast bacillus. This case demonstrates a rare but high-risk presentation of pediatric tuberculosis: near-complete tracheobronchial obstruction due to endobronchial tuberculosis (EBTB) in an infant.},
}

@article {pmid42365883,
year = {2026},
author = {Wu, W and Wang, W and Liu, H and Ganigué, R and Zhang, J and Liu, B and Liu, G and Wang, A},
title = {Multi-omics analysis reveals propanol is superior electron donor for odd-chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135265},
doi = {10.1016/j.biortech.2026.135265},
pmid = {42365883},
issn = {1873-2976},
abstract = {Chain elongation from organic wastes has primarily targeted even-chain carboxylates, leaving the production of equally valuable odd-chain compounds underexplored. Propanol, abundant in industrial wastewater, offers a promising electron donor to address this gap, yet the underlying metabolic pathways and microbial consortia driving efficient odd-chain elongation remain unclear. The present study systematically investigated the characteristics of odd-chain elongation. The results demonstrated that the propanol-acetate (PA) group, using propanol as the electron donor and acetate as the electron acceptor, achieved an excellent selectivity of 84% for n-valerate and n-heptanoate, compared with 55% in the conventional ethanol-propionate (EP) group. Multi-omics analysis guided the specialized metabolic route construction, showing that electrons from propanol oxidation are channeled to drive acetyl-CoA synthesis from acetate and activate the reverse β-oxidation pathway. The propionate generated from propanol oxidation serves as the initial three-carbon backbone for odd-chain carboxylates generation. The keystone microorganisms for propanol-based odd-chain elongation are suggested to be Clostridium kluyveri and Oscillibacter valericigenes. Techno-economic analysis confirmed the metabolic selectivity inherent to the PA group confers superior economic resilience, yielding higher profitability than the EP group. This work positions propanol-based chain elongation as an efficient and economically viable strategy for the targeted production of valuable odd-chain carboxylates from propanol-containing wastewater.},
}

@article {pmid42366019,
year = {2026},
author = {Wang, D and Wang, F and Sun, S and Huang, L and Sun, K and Li, Z and Feng, J},
title = {Microbe-Metabolite Interactions in Cave Soils Synergistically Regulate the Environmental Persistence of Pseudogymnoascus destructans.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70367},
doi = {10.1111/1462-2920.70367},
pmid = {42366019},
issn = {1462-2920},
support = {32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Caves/microbiology ; *Ascomycota/isolation & purification/genetics/physiology ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil/chemistry ; China ; Microbiota ; Nitrogen Cycle ; },
abstract = {Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.},
}

*Soil Microbiology
*Caves/microbiology
*Ascomycota/isolation & purification/genetics/physiology
Seasons
*Bacteria/metabolism/genetics/classification/isolation & purification
Soil/chemistry
China
Microbiota
Nitrogen Cycle

@article {pmid42050399,
year = {2026},
author = {Li, CJ and Zhao, Y and Tang, M and Chu, X and Zhan, PC and Jiang, XW and Tian, JY and Hai, X and Lu, YF and Yang, LL and Zhi, XY},
title = {Comparative population genomics reveal the genetic features associated with the plant host adaptation of Clostridium butyricum.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42050399},
issn = {1471-2164},
support = {32560005//National Natural Science Foundation of China/ ; },
mesh = {*Clostridium butyricum/genetics/physiology/classification/isolation & purification ; *Host Adaptation/genetics ; Phylogeny ; Genetic Variation ; *Metagenomics ; Genomics ; Genetics, Population ; Genome, Bacterial ; },
abstract = {BACKGROUND: Plants are increasingly considered as secondary reservoirs for enterics. However, little is known about their population dynamics and the genetic mechanisms during plant colonization. Clostridium butyricum is a gut symbiont of humans and animals and, rarely, a pathogen. Here, 55 strains of C. butyricum isolated from the roots of Paris polyphylla var. yunnanensis provided a new model for understanding plant-host adaptation of enterics. RESULTS: These strains, along with 67 non-endophytic C. butyricum strains (nECB), were examined for population structure, revealing that they diverged into four well-defined lineages, whereas endophytic C. butyricum strains (ECB) from different sources were scattered across two lineages. The population diversity estimate confirmed the genetic distinctiveness among four lineages and uncovered distinct evolutionary processes that might drive the divergence of ECB-related lineages. Frequent gene flow between ECB and nECB suggested that plant-host colonization does not lead to genetic isolation. Extensive recombinations within and between lineages demonstrated the major role of recombination in shaping population genetic structure and diversification in C. butyricum. Additionally, the endophytic variance analysis identified several genes associated with CRISPR, defense systems, and metabolism that contribute to endophytic colonization by C. butyricum. CONCLUSION: This study provides novel insights into the ongoing adaptation of C. butyricum to plant hosts and illuminates the genetic mechanisms underlying this host transition. By elucidating population structure, gene flow, recombination patterns, and candidate adaptive genes, our findings advance the understanding of host-associated evolution in enteric bacteria.},
}

*Clostridium butyricum/genetics/physiology/classification/isolation & purification
*Host Adaptation/genetics
Phylogeny
Genetic Variation
*Metagenomics
Genomics
Genetics, Population
Genome, Bacterial

@article {pmid42363297,
year = {2026},
author = {Wang, Y and Liu, M and Dogra, SK and Vidal, K and Godin, JP and Darwish, N and Wei, X and Reymond, L and Li, Q and Dong, J and Vyllioti, AT and Bettler, J and Kennedy, E and Wang, K and Zhai, Q and O'Regan, J and Samuel, TM and Cai, W},
title = {Effects of an infant formula containing a whey protein concentrate on feeding tolerance and markers of intestinal immune defense in Chinese infants.},
journal = {BMC nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40795-026-01395-0},
pmid = {42363297},
issn = {2055-0928},
abstract = {BACKGROUND: Human milk (HM) bioactive components can have immune modulatory functions, impact the gut microbiome, and may result in functional benefits when added to infant formula (IF). In this single-arm, prospective, intervention study, we tested the effectiveness of an IF with a whey protein concentrate co-enriched in α-lactalbumin, milk fat globule membrane (MFGM), and Sn-2 palmitate resulting in protein and lipid profiles observed in HM. The outcomes tested were feeding tolerance, Bifidobacteria abundance, and intestinal and immune health of Chinese infants.

METHODS: Predominantly formula-fed (FF) and breastfed (BF) infants were enrolled between 3 and 28 days and assigned to the FF (N = 60) or BF (N = 60) group, per their feeding practice, for 6 weeks. The primary endpoint was Infant Gastrointestinal Symptom Questionnaire (IGSQ) index score assessed using a validated IGSQ-13 questionnaire after 6 weeks of intervention; non-inferiority of FF vs BF was tested. Secondary endpoints included fecal Bifidobacteria abundance assessed using shotgun metagenomics sequencing; fecal short chain fatty acids (SCFAs) analyzed by ultra-performance liquid chromatography-tandem mass spectrometry; fecal markers of immune response, inflammation, intestinal barrier integrity (secretory immunoglobulin A sIgA), cytokines, calprotectin, α1 antitrypsin, lipocalin-2) assessed using enzyme-linked immunosorbent assay; stool consistency assessed using gastrointestinal (GI) diary; anthropometric assessments; quality of life; physician reported adverse events; and use of medications.

RESULTS: Good GI tolerance was observed in both groups at V2 (mean ± SD IGSQ score FF: 19.9 ± 7.4; BF: 16.8 ± 4.2); difference of means 1.35 [95% CI: -1.312, 4.012]). After 6 weeks, Bifidobacterium genus relative abundance was not significantly different between the groups. Total SCFAs were significantly higher (p < 0.05) in the FF versus BF group, driven by increased levels of valeric and propanoic acids (p < 0.05 for both). The IGSQ domain scores, stool consistency, fecal markers of immunity, inflammation, and intestinal barrier integrity (except lipocalin-2 which was significantly higher in BF vs FF), anthropometric Z-scores, common illnesses, antibiotic use, and adverse events were not significantly different between groups at week 6.

CONCLUSIONS: Our results support the effectiveness of this tested infant formula in supporting good GI tolerance, growth, specific intestinal and immune health markers, and Bifidobacteria abundance similar to that of the BF group.

TRIAL REGISTRATION: NCT04880083 (2021-05-06).},
}

@article {pmid42363646,
year = {2026},
author = {Torres Sánchez, ED and Martínez Nieto, M and González Alvarez, GE and Rodríguez Montaño, R and Alarcón-Sánchez, MA and Heboyan, A and Gutiérrez Maldonado, AF and Varela Hernández, JJ and Lomelí Martínez, SM},
title = {Helicobacter pylori in oral and gastric pathologies: a narrative review of potential bidirectional pathogenic interactions.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2533434},
doi = {10.1080/07853890.2025.2533434},
pmid = {42363646},
issn = {1365-2060},
mesh = {Humans ; *Helicobacter pylori/pathogenicity/isolation & purification ; *Helicobacter Infections/microbiology/complications/immunology ; *Periodontitis/microbiology ; *Mouth/microbiology ; *Gastritis/microbiology ; },
abstract = {The association between periodontal diseases and gastrointestinal conditions, particularly those associated with Helicobacter pylori and systemic inflammation, has garnered increased scientific attention because of its clinical and public health implications. These diseases, which affect both the oral cavity and the digestive system, have shared pathophysiological mechanisms that link inflammatory processes and bacterial transmission pathways. The possible presence of H. pylori in the oral cavity has sparked interest regarding its potential colonization of periodontal tissues and acting as an extragastric reservoir. This narrative review describes H. pylori's possible survival mechanisms in this oral microenvironment and its clinical significance in the interaction between oral and gastric conditions. We propose that periodontitis might promote gastric H. pylori infection by stimulating systemic inflammation, and oral colonization might serve as a reservoir for gastric reinfection. Future studies may involve advanced technologies such as metagenomics and proteomics. The eradication of H. pylori in the oral cavity may provide a strategy to prevent gastric reinfection. The findings described herein highlight the importance of this bacterium in two different pathologies sharing a close anatomical relationship.},
}

Humans
*Helicobacter pylori/pathogenicity/isolation & purification
*Helicobacter Infections/microbiology/complications/immunology
*Periodontitis/microbiology
*Mouth/microbiology
*Gastritis/microbiology

@article {pmid42363687,
year = {2026},
author = {Redmile, C and Sutherland, D and Devane, M and Taylor, W and Busby, I and Glackin, A and Gilpin, B and Chambers, T},
title = {The Establishment of an Indigenous-Led Drinking Water Monitoring Program Leveraging qPCR and Metagenomics Testing in New Zealand.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {7},
pages = {e70471},
doi = {10.1002/wer.70471},
pmid = {42363687},
issn = {1554-7531},
support = {ESR2411//Ministry of Business, Innovation and Employment/ ; TN/PWC/19/UoOWTC//Ministry of Business, Innovation and Employment/ ; },
mesh = {New Zealand ; *Drinking Water/microbiology/analysis ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; Water Quality ; Water Microbiology ; Maori People ; },
abstract = {An Indigenous-led monitoring program was established in partnership with the South Island Māori (Indigenous population of New Zealand [NZ]) tribe of NZ to understand and improve local drinking water safety. The aims of the project were to: (1) establish an Indigenous-led drinking water monitoring program; (2) utilize a full suite of monitoring tools to understand source water hazards and treatment efficacy; and (3) test the effectiveness of advanced water sampling techniques in Indigenous communities. Advanced sampling techniques were used for fecal source tracking to identify existing public health hazards and to provide assurance that any remedial interventions were effective. The program trained a total of 27 individuals from 16 different Indigenous communities in water quality sampling and helped to identify and address six microbial water quality issues. This project underscored the benefits of engaging Indigenous Peoples in governance and decision-making processes and in alleviating systemic barriers that prevent Indigenous communities from realizing safe water quality and sufficient water infrastructure.},
}

New Zealand
*Drinking Water/microbiology/analysis
*Metagenomics/methods
*Environmental Monitoring/methods
Humans
Water Quality
Water Microbiology
Maori People

@article {pmid42363849,
year = {2026},
author = {Wang, X and Wang, H and Wang, X and Zhang, M and Cui, Y and Liao, H and Yang, J and Zou, Y and Jiang, L and Li, X and Yang, Y},
title = {Metagenome-assembled genome of Oscillospiraceae bacterium strain ZGZL, an anaerobic chloromethane-degrading bacterium enriched from rice paddy soil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0028726},
doi = {10.1128/mra.00287-26},
pmid = {42363849},
issn = {2576-098X},
abstract = {Oscillospiraceae sp. strain ZGZL is an anaerobic bacterium capable of degrading chloromethane. Here, we report the metagenome-assembled genome sequence of strain ZGZL, which has a genome size of 2.04 Mb and a G+C content of 52.56%.},
}

@article {pmid42363855,
year = {2026},
author = {Pham, EQ and Gaulke, CA and Eisen, JA and Dandekar, S},
title = {Metagenome-assembled genomes recovered from the gut microbiomes of simian immunodeficiency virus-infected rhesus macaques.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042826},
doi = {10.1128/mra.00428-26},
pmid = {42363855},
issn = {2576-098X},
abstract = {Rhesus macaques are widely used model organisms for studying human biology, yet relatively few metagenome-assembled genomes (MAGs) are available from their microbiome. Here, we report 159 MAGs recovered from simian immunodeficiency virus-infected macaques, including those treated either with antiretroviral therapy or 10-hydroxystearic acid.},
}

@article {pmid42364055,
year = {2026},
author = {Xu, Q and Sun, L and Han, X and Zhang, Q and Jiang, W and Zhu, S},
title = {Multi-kingdom gut microbiota analyses define bacterial-fungal interplay in multiple type 2 diabetes cohorts.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42364055},
issn = {1869-1889},
abstract = {The role of the gut microbiome in type 2 diabetes (T2D) remains incompletely defined, particularly across microbial kingdoms and diverse populations. Here, we conducted a meta-analysis of 3,857 fecal metagenomes from six international cohorts, profiling bacteria, fungi, archaea, and viruses. Using supervised machine-learning models trained on harmonized multi-kingdom profiles with cross-cohort validation, we identified conserved alterations in T2D, characterized by reduced bacterial and viral diversity and increased fungal and archaeal diversity. A cross-kingdom panel of 33 microbial markers derived from these models achieved robust diagnostic performance (AUR-OC=0.82), outperforming single-kingdom models. Notably, Saccharomyces cerevisiae was consistently depleted in T2D and inversely correlated with glycemic indices. In mice, oral S. cerevisiae supplementation improved glucose tolerance and insulin sensitivity while reducing the abundance of Eggerthella lenta and Klebsiella pneumoniae, bacterial taxa previously linked to adverse metabolic and inflammatory phenotypes. Together, our findings highlight the diagnostic value and mechanistic relevance of multi-kingdom microbial signatures in T2D and position S. cerevisiae as a potential fungal probiotic candidate for metabolic intervention.},
}

@article {pmid42364169,
year = {2026},
author = {Pan, P and Zhou, NY},
title = {Metabolic interactions enable aerobic degradation of the environmental pollutant BDE-47.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag163},
pmid = {42364169},
issn = {1751-7370},
abstract = {As a prevalent congener of polybrominated diphenyl ethers (PBDEs), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) poses significant environmental and health risks due to its persistence and bioaccumulation. However, the limited understanding of the microbial degradation mechanism of BDE-47 has hindered the development of effective bioremediation strategies. Here, we decipher an aerobic catabolic pathway of BDE-47 mediated by metabolic relay within a synthetic consortium composed of two environmental isolates, Rhizorhabdus wittichii YL-JM2C and Cupriavidus necator JMP134. Bioaugmentation with this consortium achieved complete removal of BDE-47 in real wastewater samples. The molecular basis underlying this cooperative degradation was elucidated through the heterologous expression and functional characterization of key enzymes involved. Namely, the dioxygenase TcsAaAb from strain YL-JM2C catalyzed the initial conversion of BDE-47 into 2,4-dibromophenol (2,4-DBP) and 3,5-dibromocatechol (3,5-DBC). As a dead-end intermediate in strain YL-JM2C, the former (2,4-DBP) was subsequently transformed into the latter (3,5-DBC) by the hydroxylase TfdB from strain JMP134. The resulting 3,5-DBC was catabolized through the downstream ortho-cleavage pathway present in both strains. These key enzymes for BDE-47 degradation coexist across diverse environments, including soil, seawater, and marine sediments. Global marine metagenomic profiling revealed a significant enrichment of these catabolic signatures in the Mariana Trench, implying that microorganisms in the hadal zone possess the genetic potential for PBDE catabolism. This study unveils previously unrecognized aerobic catabolic mechanisms for BDE-47 within natural ecosystems, offering promising bioremediation strategies for PBDE-contaminated environments.},
}

@article {pmid42364365,
year = {2026},
author = {Manning, VA and Moore, PA and Medina, AR and Trippe, KM},
title = {Genome-resolved metagenomics of an acid-tolerant nitrifying biofilm suggests cooperative nitrogen cycling at low pH.},
journal = {The Science of the total environment},
volume = {1046},
number = {},
pages = {181954},
doi = {10.1016/j.scitotenv.2026.181954},
pmid = {42364365},
issn = {1879-1026},
abstract = {Ammonia emissions from animal feeding operations are a major source of nitrogen loss and environmental pollution. Nitrifying bacteria used within ammonia scrubbers offers a promising strategy to recover nitrogen for fertilizer; however, the acidic environment within air scrubbers generally inhibits nitrification and sustained nitrification at low pH remains poorly understood. Here, we present a genome-resolved analysis of an acid-tolerant nitrifying community (ATNC) enriched from a laboratory bioreactor operating at pH values between 4 and 4.6 that was previously shown to support nitrification. Long-read metagenomic sequencing yielded 12 high-quality metagenome-assembled genomes accounting for 94.7% of community abundance, including four phylogenetically distinct Nitrospira representing both comammox and canonical nitrite-oxidizing lineages, alongside heterotrophic species of Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and a filamentous Ktedonobacterales strain. Genomic reconstruction suggested niche partitioning in nitrogen cycling, with comammox Nitrospira encoding the capacity for complete nitrification and Rhodanobacteraceae harboring genes associated with denitrification. Acid tolerance and biofilm persistence were associated with diverse ion-transport systems, alternative respiratory complexes, extracellular polymeric substance biosynthesis, and expanded repertoires of secreted proteases and carbohydrate-active enzymes that facilitate matrix turnover and carbon scavenging. Within the biofilm, Chloroflexi likely contribute structural scaffolding, while heterotrophs appear to be adapted for extracellular organic matter turnover and to act as metabolic partners. Together, these findings suggest that metabolic cooperation, functional redundancy, and biofilm-mediated resource sharing may support nitrification under acidic conditions. This work provides genome-resolved insight into the microbial processes potentially underpinning nitrification-enhanced ammonia capture and identifies candidate genomic features relevant to optimizing nitrogen recovery while minimizing denitrification-driven losses in engineered systems.},
}

@article {pmid42364424,
year = {2026},
author = {Chambers, LM and Spakowicz, D and Chalif, J and O'Connor, R and Kistenfeger, Q and Mehra, Y and Mohssen, M and Abdeen, C and Haight, P and Nagel, C and Neff, R and Cohn, D and Copeland, LJ and Backes, F and Cosgrove, C and Hays, J and Dravillas, C and McLaughlin, E and O'Malley, D},
title = {PRO-PLATINUM: A randomized, double-blind, placebo controlled study to investigate the efficacy of a probiotic intervention on the gut and vaginal microbiome of ovarian cancer patients undergoing treatment with platinum chemotherapy.},
journal = {Gynecologic oncology},
volume = {211},
number = {},
pages = {74-78},
doi = {10.1016/j.ygyno.2026.06.016},
pmid = {42364424},
issn = {1095-6859},
abstract = {BACKGROUND: PRO-PLATINUM evaluates whether a 5-strain probiotic formulation can favorably modulate the gut microbiome during platinum-based chemotherapy in ovarian cancer (OC), while assessing feasibility, safety, and translational correlates of response and toxicity.

PATIENTS AND METHODS: PRO-PLATINUM is an IRB-approved, randomized, double-blind, placebo-controlled trial enrolling 124 patients with stage II-IV or platinum-sensitive recurrent high-grade OC receiving platinum-based chemotherapy. The study opened to enrollment in February 2026. Participants are randomized 1:1 to a 5-strain probiotic (WBF-038) or placebo, stratified by newly diagnosed advanced versus recurrent disease. The intervention contains inulin and five microbial strains: Akkermansia muciniphila, Anaerobutyricum hallii, Clostridium beijerinckii, Clostridium butyricum, and Bifidobacterium infantis, and is administered orally twice daily beginning within seven days of cycle 1 and continuing through seven days after the completion of cycle 6. Eligible patients must have ECOG performance status 0-2, adequate organ function, and no major probiotic-related contraindications. Stool, blood, and vaginal samples are collected at baseline, cycle 3, and cycle 6; tumor tissue is collected at surgery when available. The primary endpoint is change in gut microbiome composition by whole-genome metagenomic sequencing. Secondary endpoints include intervention adherence, biospecimen feasibility, recurrence-free survival, and overall survival. Exploratory endpoints include toxicity, postoperative infections, stool consistency, diet, medication and antibiotic exposure, quality of life, symptom burden, serum metabolomic and immune profiling, vaginal and tumor microbiome composition, and associations between microbial features and clinical outcomes.

CONCLUSIONS: PRO-PLATINUM will evaluate treatment feasibility and safety and generate prospective translational data to inform future microbiome-directed strategies to improve treatment tolerance, quality of life, and outcomes in OC patients.},
}

@article {pmid42364687,
year = {2026},
author = {Sun, J and Han, X and Sun, X and Qin, H and Yang, D and Shangguan, M and Lu, J and Li, H and Li, Y and Bao, M},
title = {Geochemical and Microbial Functional Responses of Surface Soil to Simulated Low-Concentration CO2 Leakage from Geological Storage.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125132},
doi = {10.1016/j.envres.2026.125132},
pmid = {42364687},
issn = {1096-0953},
abstract = {Geological CO2 storage may pose environmental risks if leaked CO2 migrates into near-surface soils. To evaluate early surface-soil responses to low-concentration CO2 exposure, a 42-day aerated soil microcosm experiment was conducted using a control group and two CO2 treatment levels of 2,000 and 10,000 ppm. Soil physicochemical properties, dissolved cations, metal fractions, enzyme activities, bacterial community composition, and metagenomic functional profiles were analyzed. Sustained CO2 exposure increased electrical conductivity and HCO3[-] concentrations, whereas soil pH remained within a narrow weakly alkaline range. Sequential extraction showed limited redistribution of selected metals among operationally defined fractions, but no evidence of extensive metal mobilization was observed. Among microbial indicators, FDA hydrolase activity responded significantly to CO2 exposure, whereas microbial community structure, alpha diversity, and overall KEGG and CAZy functional profiles remained largely stable. Representative carbon- and nitrogen-cycling genes were influenced mainly by incubation time rather than CO2 concentration. Under the tested short-term, low-concentration, aerated microcosm conditions, the soil system exhibited considerable buffering capacity and resistance to CO2 exposure. The observed effects were mainly expressed as minor changes in soil solution chemistry and selected functional indicators rather than pronounced geochemical deterioration or microbial community restructuring. These findings provide experimental evidence and insights into the geochemical buffering capacity and microbial response mechanisms of surface soil systems under potential leakage scenarios of underground CO2 storage. The findings offer scientific references for environmental risk assessment of CO2 geological sequestration and the selection and interpretation of sensitive monitoring indicators.},
}

@article {pmid42364737,
year = {2026},
author = {Hajjar, C and Saint-Criq, V and Thomas, M and Butel, MJ and Bazarbachi, A and Abifadel, M},
title = {The Lung Microbiome in Hematopoietic Stem Cell Transplantation: Immune Interactions, Clinical Consequences, and Emerging Interventions.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {109004},
doi = {10.1016/j.rmed.2026.109004},
pmid = {42364737},
issn = {1532-3064},
abstract = {Hematopoietic stem cell transplantation (HSCT) offers curative potential for hematologic malignancies and immune disorders, yet pulmonary complications remain major contributors to non-relapse morbidity and mortality. Traditionally attributed to immune suppression and graft-versus-host disease (GvHD), these complications are increasingly recognized to involve disruption of pulmonary microbial communities. A growing body of clinical and experimental evidence indicates that HSCT-associated perturbations in the lung microbiome, driven by conditioning, antimicrobials, immune injury, and infection, are associated with distinct post-transplant pulmonary phenotypes and, in some cohorts, with mortality risk. Whether these microbial shifts represent causal contributors to lung injury or contextual biomarkers of immune vulnerability remains unresolved, and this distinction carries direct implications for microbiome-targeted intervention. Dysbiotic shifts in the lung have been associated with both infectious and non-infectious complications, including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and fibrotic lung disease. Gut-lung microbial crosstalk may amplify or reflect systemic immune dysfunction, though the directionality of this relationship remains incompletely characterized. Multi-omics approaches, integrating metagenomics, metatranscriptomics, and metabolomics, are beginning to define the host-microbiome interaction signatures that distinguish injury subtypes and predict outcomes. This review synthesizes mechanistic insights into lung microbiome-immune interactions after HSCT, critically appraises the methodological constraints on the current evidence base, and evaluates microbiome-based interventions, including fecal microbiota transplantation, inhaled postbiotics, and precision antimicrobials, as candidate strategies for respiratory protection in transplant recipients, while acknowledging that prospective interventional evidence in this population remains limited.},
}

@article {pmid42364789,
year = {2026},
author = {DiSilvestro, AN and Wesolowski, LT and Williams, BD and Warren, LK and Athrey, G and White-Springer, SH},
title = {Short-term provision of moderate dietary starch alters fecal microbiota but does not exacerbate exercise-induced inflammation in yearling Quarter Horses.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {106071},
doi = {10.1016/j.jevs.2026.106071},
pmid = {42364789},
issn = {0737-0806},
abstract = {BACKGROUND: Energy-dense feeds commonly provided to equine athletes may be high in starch, which alter gastrointestinal microbiota and could promote systemic inflammation.

AIMS/OBJECTIVES: To test the hypothesis that exercise-induced inflammation would be greater in horses receiving a starch- versus fiber-based concentrate.

METHODS: Quarter Horses (mean±SD 16±1mo; 337±30kg) received either a fiber-based control (CON; 7 fillies, 8 geldings) or an isocaloric, isonitrogenous starch concentrate (STARCH; 8 fillies, 7 geldings) for 24d. Fecal metagenomics were evaluated on d0 and 21. Blood inflammatory mediators were quantified on d0, d21, and surrounding a 2-h submaximal exercise test (SET) on d22.

RESULTS: On d21, CON horses had greater Lactobacillaceae (∼5.7% vs. ∼2.4% in STARCH), while STARCH had greater Lachnospiraceae (∼38% vs. ∼32% in CON) but diet alone did not impact inflammatory markers. On d22, CRP increased at 24h post-SET in all horses (P<0.0001). By 48h, CRP returned to pre-SET in STARCH but remained elevated in CON (P=0.0005), resulting in greater CRP in CON than STARCH at 48h (P=0.02). TNFα increased from pre-SET to 1h in STARCH horses (P=0.02), then returned to pre by 6h. In CON horses, TNFα increased at 24h (P=0.04) and remained elevated at 48h (P=0.0005). Throughout the SET, CON had greater IL-10 than STARCH horses (P=0.005). SAA, IL-4, IL-8, and vascular endothelial growth factor (VEGF)-A were differentially impacted by the SET but were unaffected by diet.

CONCLUSION: Contrary to our hypothesis, fiber-fed horses appeared to elicit a more robust acute inflammatory response to exercise than starch-fed horses despite an altered gastrointestinal microbiome.},
}

@article {pmid42364824,
year = {2026},
author = {Zhang, H and Xie, G and Jiang, L and Li, M and Ding, J and Mei, C and Xiong, X},
title = {Effects of different function-oriented hydrochars on anaerobic digestion of hydrothermal wastewater: Focusing on microbial community function and organic degradation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135266},
doi = {10.1016/j.biortech.2026.135266},
pmid = {42364824},
issn = {1873-2976},
abstract = {To elucidate the coupling relationships among hydrochar characteristics, microbial responses, and organic matter removal during anaerobic digestion of hydrothermal treatment wastewater (HTTWW-AD), raw hydrochar (HC), alkali-modified hydrochar (AHC), and iron-modified hydrochar (IHC) were prepared. Excessive microbial anabolic metabolism and limited hydrolysis-acidification efficiency were identified as the main causes of the low methane yield in HTTWW-AD. HC, AHC, and IHC increased methane yield by 115.97%, 148.25%, and 135.42%, respectively, and the methane content also increased by 9.86% - 12.50%. Metagenomic analysis revealed that microorganisms in the control (CK) system were under higher stress, whereas hydrochar addition promoted the enrichment of hydrolytic and acidogenic bacteria (HAB) and alleviated microbial stress. AHC further enriched Methanothrix and Methanobacterium, thereby enhancing both acetoclastic and hydrogenotrophic methanogenesis. The enhanced reductive methanogenesis was likely associated with its high electron-donating capacity (EDC). IHC enriched exoelectrogenic HAB, suggesting that Fe/N-related active sites may facilitate extracellular electron transfer. Gas chromatography-mass spectrometry analysis showed that HC favored the removal of ketones, N-containing heterocycles, and alcohols, whereas AHC was more effective for acids, N-containing heterocycles, and alcohols. IHC promoted the removal of diverse organic compounds, particularly ketones, phenols, and esters. These differences were associated with the enrichment of potential degraders (Hydrogenophaga, Sphaerochaeta, Mesotoga, Bacteroides, and Paludibacter), possible adsorption at surface-active sites, and Fe(III)/Fe(II)-cycle-mediated redox activation. Overall, hydrochars effectively promoted hydrolysis-acidification during HTTWW-AD. Hydrochars enriched with electron-donating functional groups favored methanogenic conversion, whereas Fe/N-related active sites were more beneficial for the removal of recalcitrant organic compounds.},
}

@article {pmid41073888,
year = {2025},
author = {Michel, A and Leoz, M and Nesi, N and Petat, H and Ar Gouilh, M and Charbonnier Le Clezio, C and Marguet, C and Hassel, C and Plantier, JC},
title = {Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {908},
pmid = {41073888},
issn = {1471-2164},
mesh = {*Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Fungi/genetics/isolation & purification/classification ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; *Respiratory System/microbiology ; *RNA/isolation & purification ; },
abstract = {BACKGROUND: The respiratory microbiome, which comprises bacteria, fungi, and viruses, plays a crucial role in respiratory health and disease. However, its study is limited by the low microbial biomass in respiratory samples and the dominance of host RNA. Metatranscriptomics offers comprehensive insights into active microbial communities and their interactions with the host but requires optimized RNA extraction protocols for robust and unbiased analysis. This study evaluated two RNA extraction kits—one employing chemical lysis (CL) and another combining chemical and mechanical lysis (CML)—to determine their effectiveness for metatranscriptomic analysis of respiratory samples. RESULTS: The CML protocol significantly increased double-stranded DNA (dsDNA) library yields, leading to higher sequencing read counts for both sample types (p < 0.0001). The read length was unaffected by the lysis protocol for the BAL and NPS samples. Taxonomic profiling revealed that CML enhanced the detection of robust microorganisms, such as gram-positive bacteria and fungi, without compromising viral detection. CONCLUSIONS: The CML protocol demonstrated superior recovery of genetic material, particularly for fungi and gram-positive bacteria, making it better suited for comprehensive metatranscriptomic analyses. These findings underscore the need for tailored RNA extraction strategies on the basis of sample type and research objectives. Optimized metatranscriptomic protocols are pivotal for advancing our understanding of the respiratory microbiome and its role in health and disease.},
}

*Microbiota/genetics
*High-Throughput Nucleotide Sequencing/methods
Humans
Fungi/genetics/isolation & purification/classification
Metagenomics/methods
Bacteria/genetics/classification/isolation & purification
*Respiratory System/microbiology
*RNA/isolation & purification

@article {pmid42350828,
year = {2026},
author = {Botta, A and Messina, C},
title = {Hantavirus infection: Neurologic manifestations should not be overlooked.},
journal = {Journal of neurovirology},
volume = {32},
number = {4},
pages = {},
pmid = {42350828},
issn = {1538-2443},
mesh = {Humans ; *Orthohantavirus/pathogenicity ; *Hemorrhagic Fever with Renal Syndrome/virology/immunology/diagnostic imaging/complications/pathology ; *Hantavirus Infections/virology/complications ; Blood-Brain Barrier/virology/immunology/diagnostic imaging ; *Hantavirus Pulmonary Syndrome/virology/immunology/diagnostic imaging ; },
abstract = {Hantavirus infection is primarily associated with hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), with predominant renal and pulmonary involvement. However, neurological manifestations affecting both the central nervous system (CNS) and peripheral nervous system (PNS) are increasingly recognized. We conducted a narrative review of the literature to summarize the current evidence regarding hantavirus-associated neurological involvement. Reported CNS manifestations included encephalitis, encephalopathy, seizures, meningitis, neurocognitive alterations, posterior reversible encephalopathy syndrome, transverse myelitis, and cerebral hemorrhage. PNS involvement appeared less frequent and included Guillain-Barré syndrome, cranial nerve palsies, neuropathic pain, and sensory disturbances. Neuroimaging findings were heterogeneous, while cerebrospinal fluid analysis often demonstrated nonspecific inflammatory changes. Advanced molecular techniques such as metagenomic next-generation sequencing may improve diagnostic sensitivity, particularly in immunocompromised patients. Current evidence suggests that neurological involvement may result from endothelial dysfunction, neuroinflammation, immune-mediated injury, blood-brain barrier disruption, and, in selected cases, direct viral neuroinvasion. Greater clinical awareness is needed to improve recognition of neurological complications during hantavirus infection. Further prospective studies are required to better define the epidemiology, pathogenesis, and optimal diagnostic approaches of hantavirus-associated neurological disease.},
}

Humans
*Orthohantavirus/pathogenicity
*Hemorrhagic Fever with Renal Syndrome/virology/immunology/diagnostic imaging/complications/pathology
*Hantavirus Infections/virology/complications
Blood-Brain Barrier/virology/immunology/diagnostic imaging
*Hantavirus Pulmonary Syndrome/virology/immunology/diagnostic imaging

@article {pmid42351266,
year = {2026},
author = {Chen, T and Xiao, J and Li, S and Peng, R and Xu, Y and Zhuang, Y and Zhao, X and Sha, M and Wang, J and Ma, J and Wang, W and Gao, J and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02446-1},
pmid = {42351266},
issn = {2049-2618},
abstract = {BACKGROUND: Significant environmental problems have challenged animal agriculture, improving feed efficiency in animals has become a vital research direction for sustainable agriculture. Bacteria play a critical role in the feed efficiency of animals. However, our current understanding of bacteria communities in the gastrointestinal tract of high-feed efficiency animals and their metabolic mechanisms remains unclear.

RESULTS: Twenty Holstein female calves were used in this multi-omics study that integrated metagenomic and metabolomic analyses of 20 Holstein female calves to investigate feed efficiency, as measured by residual feed intake (RFI). From an initial cohort of 84 calves, the 10 with the highest RFI (HRFI, low efficiency) and the 10 with the lowest RFI (LRFI, high efficiency) were selected at 84 days of age. Rumen fluid, feces, and serum samples from these calves were collected for subsequent analyses. We found that LRFI calves harbored rumen and fecal microbiomes with significantly different community structures and co-occurrence networks compared to HRFI calves. Multi-omics integration identified robust microbial and metabolite biomarkers discriminating RFI groups. These microbiomes were functionally linked to differential nutrient utilization, LRFI calves were characterized by enhanced starch and protein digestibility coupled with propionate-oriented fermentation, associated with key species like Erysipelotrichaceae_bacterium and Hungatella_sp. Conversely, HRFI calves showed higher fat digestibility and acetate production. Notably, serum glutamate was enriched in LRFI calves despite lower intake, correlating with potential microbial metabolites (ribitol, taurine). Subsequent validation confirmed that glutamate supplementation in mice improved nitrogen metabolism and gut barrier function.

CONCLUSIONS: In summary, this multi-omics study reveals that high feed efficiency in calves is associated with distinct microbial ecosystems characterized by functions such as starch degradation and propionate production, where glutamate metabolism serves as a central node. Video Abstract.},
}