@article {pmid41807604,
year = {2026},
author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L},
title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807604},
issn = {2045-2322},
abstract = {UNLABELLED: Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41655-4.},
}

@article {pmid42014993,
year = {2026},
author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C},
title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05043-2},
pmid = {42014993},
issn = {1471-2180},
}

@article {pmid42015023,
year = {2026},
author = {Peng, Z and He, H and Zhou, S and Qiao, L and Wang, Q and Li, M and Zhao, Y},
title = {Rhino-orbito-cerebral Rhizopus delemar infection in a patient with anti-melanoma differentiation-associated-5-positive dermatomyositis diagnosed by metagenomic next-generation sequencing: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13359-7},
pmid = {42015023},
issn = {1471-2334},
}

@article {pmid42015434,
year = {2026},
author = {Wang, S and Deng, F},
title = {Clinical Features and Coinfection Factors of Severe Community-Acquired Pneumonia with <em>Mycoplasma Pneumoniae</em> in Children.},
journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP},
volume = {36},
number = {4},
pages = {483-488},
doi = {10.29271/jcpsp.2026.04.483},
pmid = {42015434},
issn = {1681-7168},
mesh = {Humans ; *Community-Acquired Infections/microbiology/epidemiology/diagnosis ; Male ; Female ; *Coinfection/epidemiology/microbiology/diagnosis ; Child ; Retrospective Studies ; *Pneumonia, Mycoplasma/epidemiology/diagnosis/microbiology ; *Mycoplasma pneumoniae/isolation & purification/genetics ; Child, Preschool ; China/epidemiology ; Infant ; Adolescent ; Anti-Bacterial Agents/therapeutic use ; Severity of Illness Index ; Community-Acquired Pneumonia ; },
abstract = {OBJECTIVE: To characterise the clinical features of children with severe community-acquired pneumonia (CAP) associated with Mycoplasma pneumoniae (Mp) infection and to identify factors influencing polymicrobial coinfections.

STUDY DESIGN: A descriptive study. Place and Duration of the Study: Department of Internal Medicine, Anhui Provincial Children's Hospital, Anhui, China, from January to December 2023.

METHODOLOGY: A retrospective cohort study was conducted on 207 hospitalised children aged <16 years with confirmed CAP who underwent BALF testing due to severe symptoms, antibiotic-unresponsive fever, or unclear aetiology. Those with chronic comorbidities were excluded. BALF pathogens were detected via multiplex PCR and metagenomic next-generation sequencing (mNGS). Patients were divided into Mp mono-infection and coinfection groups; demographic, clinical, and laboratory data were compared, and logistic regression analysis was performed to identify factors associated with coinfection.

RESULTS: The coinfection group was significantly younger (4.12 ± 2.83 vs. 6.56 ± 2.47 years, p = 0.013) and had longer hospital stays (11.21 ± 4.26 vs. 9.90 ± 3.68 days, p = 0.049) than the mono-infection group. Inflammatory markers differed significantly: the coinfection group had higher IL-6 (28.64 ± 8.03 vs. 15.86 ± 14.21 pg/mL, p <0.001), but lower IL-2R (1774.15 ± 104.18 vs. 2157.39 ± 382.76 U/mL, p <0.001) and ESR (30.31 ± 14.79 vs. 40.08 ± 13.66 mm/h, p <0.001). Logistic regression confirmed IL-6 (p <0.001), IL-2R (p <0.001), and complications (p = 0.0281) as independent factors associated with coinfections, while chest CT findings showed no correlation (p >0.05).

CONCLUSION: Younger age, elevated IL-6 levels, reduced IL-2R levels, and the presence of complications are closely correlated with polymicrobial coinfections in children with severe Mp-associated CAP.

KEY WORDS: Pneumonia, Mycoplasma pneumoniae, Paediatrics, Coinfection, Metagenomic sequencing, Clinical characteristics.},
}

Humans
*Community-Acquired Infections/microbiology/epidemiology/diagnosis
Male
Female
*Coinfection/epidemiology/microbiology/diagnosis
Child
Retrospective Studies
*Pneumonia, Mycoplasma/epidemiology/diagnosis/microbiology
*Mycoplasma pneumoniae/isolation & purification/genetics
Child, Preschool
China/epidemiology
Infant
Adolescent
Anti-Bacterial Agents/therapeutic use
Severity of Illness Index
Community-Acquired Pneumonia

@article {pmid42015472,
year = {2026},
author = {Song, M and Zhang, Z and Huang, H and Zou, Z and Wen, S and Cui, Y and Liu, S},
title = {Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.},
journal = {The American journal of case reports},
volume = {27},
number = {},
pages = {e951840},
doi = {10.12659/AJCR.951840},
pmid = {42015472},
issn = {1941-5923},
mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Spinal/diagnosis/drug therapy ; *Renal Dialysis ; *Metagenomics/methods ; *Kidney Failure, Chronic/therapy/complications ; *Mycobacterium tuberculosis/genetics/isolation & purification ; },
abstract = {BACKGROUND Spinal tuberculosis is difficult to diagnose in patients undergoing maintenance hemodialysis (MHD) because of immunosuppression, atypical clinical manifestations, and the limited sensitivity of conventional microbiological assays. Rapid and accurate pathogen identification is essential to distinguish spinal tuberculosis from other causes of vertebral destruction, including metastatic malignancy and bacterial spondylitis. This report aims to illustrate the diagnostic value of capture-based targeted sequencing for detecting Mycobacterium tuberculosis in extrapulmonary infection when routine tests and metagenomic next-generation sequencing (mNGS) yield inconclusive or misleading results. CASE REPORT A 64-year-old woman with end-stage renal disease secondary to IgA nephropathy, receiving long-term MHD, presented with progressive low back pain. Imaging revealed multilevel vertebral involvement with pathological fractures, raising suspicion of metastatic disease or infectious spondylitis. Histopathological examination demonstrated granulomatous inflammation, while acid-fast staining and routine cultures were negative. Initial mNGS of spinal tissue identified Staphylococcus aureus, leading to targeted antibacterial therapy. Although inflammatory markers declined, the patient's symptoms worsened and pancytopenia developed. Subsequent analysis of spinal pus using metagenomic capture (MetaCAP)-based targeted sequencing detected the Mycobacterium tuberculosis complex with high confidence. Anti-tuberculosis therapy was promptly initiated, resulting in rapid clinical improvement and radiological resolution. CONCLUSIONS This case shows the limitations of conventional microbiological methods and unbiased mNGS in diagnosing extrapulmonary tuberculosis in immunocompromised patients. Capture-based targeted sequencing offers enhanced sensitivity for Mycobacterium tuberculosis detection and may facilitate timely diagnosis and appropriate treatment of spinal tuberculosis in patients undergoing MHD.},
}

Humans
Female
Middle Aged
*Tuberculosis, Spinal/diagnosis/drug therapy
*Renal Dialysis
*Metagenomics/methods
*Kidney Failure, Chronic/therapy/complications
*Mycobacterium tuberculosis/genetics/isolation & purification

@article {pmid42016528,
year = {2026},
author = {Xu, H and Guo, J and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H and Shao, X},
title = {Metagenomics reveals the functional profiles of soil microorganisms and nutrient cycling under long-term grass vegetation cropping.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100583},
pmid = {42016528},
issn = {2666-5174},
abstract = {Soil microbes are crucial for biogeochemical cycles and their functional potential is greatly affected by ecosystem management. Yet, how does grass vegetation affect the composition of soil microbial communities and the abundance of key nutrient-cycling functional genes? In this study, based on an experimental plot built for 7 years, the long - term influence of two grass vegetation types (Carex breviculmis and Festuca arundinacea Schreb) on soil microbial community structure and C, N, P, and S cycles were explored by metagenomics. The results showed that both plants significantly increased the diversity and richness of soil bacteria and fungi, and the abundance of Pseudomonadota and Ascomycota in Carex breviculmis increased significantly, while those of Actinomycetota and Mucoromycota decreased. Microbial network analysis shows that Carex breviculmis forms a highly modular, low - complexity microbial interaction network, indicating specialized and stable microbial community functions. Conversely, Festuca arundinacea Schreb has a more complex and less modular network, suggesting enhanced microbial interactions. Carex breviculmis significantly increased the abundance of genes related to carbon fixation (fumA/B, pps, ppc) and phosphorus mineralization (phoR/P/B, phnF/P), and also enhanced soil denitrification potential. In contrast, Festuca arundinacea Schreb showed a enrichment of soil nitrogen fixation genes (nifh). Additionally, growing Carex breviculmis and Festuca arundinacea Schreb induced the growth of sulfur - oxidizing bacteria (e.g., Thiobacillus), enriching the abundance of sulfur - metabolism - related genes (apr, sox). Genes related to microbial C, N, P, and S cycles are positively correlated with soil pH, available P, and alkali-hydrolyzed nitrogen. Overall, this study reveals how different grass vegetation types regulate microbial community structure and functional gene abundance to drive nutrient cycling differentiation in grassland ecosystems, thereby providing a theoretical basis for optimizing grass vegetation configuration in managed and restored grasslands to enhance soil ecological functions.},
}

@article {pmid42016568,
year = {2026},
author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ},
title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101401},
pmid = {42016568},
issn = {2665-9271},
abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.},
}

@article {pmid42016597,
year = {2026},
author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG},
title = {Investigating the role of bacterial raw milk community members in chlorate reduction.},
journal = {Access microbiology},
volume = {8},
number = {4},
pages = {},
pmid = {42016597},
issn = {2516-8290},
abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.},
}

@article {pmid42016660,
year = {2026},
author = {Qu, Y and Liu, Y and Zhou, X and Xu, P and Wang, L},
title = {Polymicrobial Pasteurella multocida-Anaerobic Coinfection Followhing a Cat Bite: Limb Salvage Through Metagenomic Next-Generation Sequencing-Guided Diagnosis and Multidisciplinary Management.},
journal = {Clinical case reports},
volume = {14},
number = {3},
pages = {e72304},
pmid = {42016660},
issn = {2050-0904},
abstract = {Successful management of a Pasteurella multocida and polymicrobial infection following a cat bite on the left leg entailed debridement, split-thickness skin grafting with vacuum-sealing drainage, and targeted antibiotic treatment. This approach enabled successful incorporation of the skin graft, preserving the limb and eliminating the necessity for amputation.},
}

@article {pmid42016731,
year = {2026},
author = {Chen, G and Tang, S and Wang, H and Liang, Z and Lv, X and Han, J and Ni, L},
title = {Integration of volatile flavor metabolomics and metagenomics reveals microbial-enzymatic pathways governing key aromatic volatile compound biosynthesis in Hongqujiu fermentation.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103811},
pmid = {42016731},
issn = {2590-1575},
abstract = {The anabolic pathways of key volatile flavor compounds (VFCs) in Hongqujiu (HQJ) remain insufficiently elucidated. In this study, dynamic changes in volatile flavor profiles and microbial communities throughout HQJ brewing, were systematically investigated using an integrated multi-omics strategy combining metabolomics, flavoromics and metagenomics. The results demonstrated that the ethanol content, titratable acidity, amino nitrogen and higher alcohols increased progressively throughout fermentation. Quantitative flavor metabolomic profiling identified 18 key VFCs, maining comprising ethyl esters, acetate esters and higher alcohols. Metagenomic sequencing revealed that Weissella, Lactobacillus, Saccharomyces, Aspergillus, Talaromyces and Monascus were the predominant microbal genera throughout HQJ fermentation. Functional gene annotation further indicated that key enzymes involved in flavor metabolism are primarily associated with Lactobacillus, Aspergillus, Talaromyces, Saccharomyces, Cyberlindnera and Monascus. Overall, this study elucidates the microbial-enzymatic basis of VFC biosynthesis and establishes a comprehensive flavor metabolic framework for HQJ fermentation, providing a theoretical foundation for aroma quality improvement.},
}

@article {pmid42016742,
year = {2026},
author = {Funada Barbosa, MR and Ramos, EDSF and Villanova, F and Oliveira Silva, RL and Garcia, SC and de Araújo, RS and Mendes-Correa, MC and Tozetto-Mendoza, TR and Zhang, W and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E},
title = {Exploring the Genomics of Marnaviridae Family: Identification, Characterization, and Taxonomic Implications.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {7188239},
pmid = {42016742},
issn = {1687-918X},
abstract = {In this study, we characterized sequences similar to Marnaviridae obtained from water samples in the state of São Paulo, Brazil. Sixteen complete or nearly complete genomes were determined, all of them positive-sense single-stranded RNA, with lengths between 7074 and 10,198 base pairs, containing one or two open reading frames (ORFs). The amino acid sequences derived from the ORFs showed similarity and protein domains typical of the Marnaviridae family. Phylogenetic analysis based on RNA-dependent RNA polymerase (RdRp) revealed clusters closely related to viruses that have not yet been classified by the International Committee on Taxonomy of Viruses (ICTV). Some sequences showed proximity to established genera such as Salicharnavirus, Locarnavirus, and Labynarvirus, while others formed three distinct clades, suggesting the presence of new genera. Furthermore, one sequence displayed an RdRp identity of less than 90% and a capsid identity of less than 75%, indicating that it represents a novel species related to Marnaviridae. These findings expand current knowledge of Marnaviridae diversity, contributing to a better understanding of evolutionary relationships and emphasizing the need for taxonomic reorganization.},
}

@article {pmid42016964,
year = {2026},
author = {Sun, X and Peng, Y and Hao, X and Dong, R and Wang, Z and Wang, L and Wang, C and Wu, X and Chen, Z and Zhang, W and Tang, X},
title = {Safeguarding a Flagship Species: Integrated Surveillance of Cross-Species Pathogen Transmission in Giant Panda Ecosystems.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73260},
pmid = {42016964},
issn = {2045-7758},
abstract = {Emerging infectious diseases, driven by increasing interactions among humans, wildlife, and livestock, pose an escalating threat to global health, biodiversity, and economies. As a flagship endangered species, the giant panda (Ailuropoda melanoleuca) plays a pivotal role in biodiversity conservation in China. This review synthesizes current knowledge on pathogens threatening giant panda health, including viruses, bacteria, and parasites alongside their potential transmission pathways within nature reserves. We emphasize the roles of domesticated animals, sympatric wildlife, and ectoparasites as reservoir hosts or vectors. Special focus is placed on cross-species transmission dynamics and the critical need for integrated monitoring systems utilizing metagenomics and viromics. We propose a framework for establishing early warning systems and surveillance networks at the domestic-wild animal interface to enhance pathogen detection, disease prevention, and biodiversity conservation.},
}

@article {pmid42016980,
year = {2026},
author = {De Panis, D and Priotto, O and Padró, J},
title = {Mitogenomic and Metabarcoding Resources for the Study and Conservation of Keystone Neotropical Raptors.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73262},
pmid = {42016980},
issn = {2045-7758},
abstract = {Neotropical raptors are among the most threatened birds, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the mitochondrial genomes of nine high-priority raptors from the Neotropics, including the threatened Chaco Eagle (Buteogallus coronatus), Black-and-Chestnut Eagle (Spizaetus isidori), Rufous-tailed Hawk (Buteo ventralis), and Harpy Eagle (Harpia harpyja), as well as the Near Threatened Orange-breasted Falcon (Falco deiroleucus), Crested Eagle (Morphnus guianensis), Ornate Hawk-Eagle (Spizaetus ornatus), Plumbeous Hawk (Cryptoleucopteryx plumbea), and Solitary Eagle (Buteogallus solitarius). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagle's Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. Our study provides essential molecular tools for monitoring and protecting these ecologically vital yet threatened raptors across the Americas.},
}

@article {pmid42017035,
year = {2026},
author = {Yang, Y and Ren, Y and Ma, T and An, J and Jin, S and Dong, Y},
title = {Research advances in the role of circulating microorganisms in gastrointestinal tumors (Review).},
journal = {Molecular and clinical oncology},
volume = {24},
number = {6},
pages = {40},
pmid = {42017035},
issn = {2049-9469},
abstract = {Gastrointestinal tumors are common malignant tumors of the digestive system, which globally threaten human health. Notably, it has been discovered that blood and other circulating body fluids are not completely sterile; instead, they harbor complex and dynamic microbial DNA and signatures [circulating microorganisms (CM)]. These microorganisms primarily originate from the microbial translocation (including bacterial fragments, DNA and metabolites) through a compromised intestinal barrier, and are closely associated with the initiation and progression of gastrointestinal tumors, thus providing novel perspectives for early tumor diagnosis and prognosis. Although there is currently no evidence that CM can directly cause cancer, their metabolites and exosomes may contribute to tumor microenvironment remodeling. On one hand, they activate pattern recognition and inflammatory signaling pathways, such as Toll-like receptor/signal transducer and activator of transcription, potentially inducing and maintaining low-grade chronic inflammation. On the other hand, they may facilitate immune evasion, potentially promoting the 'inflammation-cancer' transition. With the development of metagenomic technologies and the maturation of next-generation high-throughput sequencing technologies, CM have shown potential as liquid biopsy biomarkers for the early diagnosis of gastrointestinal tumors. Interventions targeting specific CMs have also shown prospects for enhancing efficacy in early clinical trials. However, the field still faces numerous challenges, including insufficient depth of mechanistic validation and a lack of standardized detection protocols. Future efforts should aim to conduct further systematic research to clarify the biological functions and clinical translational value of CM in gastrointestinal tumors.},
}

@article {pmid42017731,
year = {2026},
author = {Su, DM and Ni, T and Yu, XL},
title = {Invasive streptococcus pneumoniae infection in the hip joint and thigh muscle group of an adult diagnosed by Q-mNGS: a case report.},
journal = {JPMA. The Journal of the Pakistan Medical Association},
volume = {76},
number = {3},
pages = {451-454},
doi = {10.47391/JPMA.22494},
pmid = {42017731},
issn = {0030-9982},
mesh = {Humans ; Male ; Adult ; Thigh ; *Hip Joint/microbiology ; *Pneumococcal Infections/diagnosis/therapy/microbiology ; *Streptococcus pneumoniae/isolation & purification/genetics ; Debridement ; *Soft Tissue Infections/microbiology/therapy/diagnosis ; *Abscess/microbiology/therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; *Myositis/microbiology ; *Arthritis, Infectious/microbiology/diagnosis ; Muscle, Skeletal/microbiology ; Drainage ; },
abstract = {Joint infections and myositis due to S. pneumoniae are rare. We report the case of a young adult male presenting with right hip joint infection complicated by thigh muscle abscess, successfully treated by surgical debridement, drainage tube placement, and aggressive antimicrobial therapy. A 38-year-old male presented with right buttock and thigh swelling, pain, night sweats, and limited mobility for 45 days. Imaging examination indicated soft tissue infection around the right hip joint with abscess formation. Quantitative meta-genomic next-generation sequencing (Q-mNGS) of joint fluid confirmed S. pneumoniae as the pathogen. Surgical intervention was performed due to lack of significant improvement after six days of anti-inflammatory therapy. The patient recovered well post-operatively and was discharged with medication after a total hospital stay of 31 days. This case highlights the importance of considering S. pneumoniae as a potential pathogen in joint and soft tissue infections in adults.},
}

Humans
Male
Adult
Thigh
*Hip Joint/microbiology
*Pneumococcal Infections/diagnosis/therapy/microbiology
*Streptococcus pneumoniae/isolation & purification/genetics
Debridement
*Soft Tissue Infections/microbiology/therapy/diagnosis
*Abscess/microbiology/therapy/diagnosis
Anti-Bacterial Agents/therapeutic use
*Myositis/microbiology
*Arthritis, Infectious/microbiology/diagnosis
Muscle, Skeletal/microbiology
Drainage

@article {pmid42018084,
year = {2026},
author = {Han, D and Pan, X and Pan, F and Han, B and Wu, Q and Zhou, Y and Liu, H and Xu, H and Sun, W and Cheng, H and Liu, W and Wan, R and Weng, W and Zhang, H},
title = {Translating Host-Derived Signals from Cerebrospinal Fluid Metagenomic Sequencing into a Diagnostic Tool for Autoimmune Encephalitis in Children.},
journal = {Journal of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10875-026-02023-z},
pmid = {42018084},
issn = {1573-2592},
support = {82471882//National Natural Science Foundation of China/ ; 21ZR1452900//Natural Science Foundation of Shanghai Municipality/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; shslczdzk06902//Shanghai Municipal Key Specialty/ ; },
}

@article {pmid42018438,
year = {2026},
author = {Sun, X and Jiang, X and Zhang, L and Li, M},
title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.},
journal = {Cell reports},
volume = {45},
number = {5},
pages = {117284},
doi = {10.1016/j.celrep.2026.117284},
pmid = {42018438},
issn = {2211-1247},
abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.},
}

@article {pmid42018637,
year = {2026},
author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM},
title = {Defining metabolic niches for marine microbial heterotrophs.},
journal = {Science advances},
volume = {12},
number = {17},
pages = {eadz0537},
doi = {10.1126/sciadv.adz0537},
pmid = {42018637},
issn = {2375-2548},
mesh = {Phytoplankton/metabolism ; *Heterotrophic Processes ; Ecosystem ; Carbon Cycle ; *Microbiota ; *Aquatic Organisms/metabolism ; Biomass ; *Seawater/microbiology ; Metagenomics ; },
abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.},
}

Phytoplankton/metabolism
*Heterotrophic Processes
Ecosystem
Carbon Cycle
*Microbiota
*Aquatic Organisms/metabolism
Biomass
*Seawater/microbiology
Metagenomics

@article {pmid42019101,
year = {2026},
author = {Ramírez-Arenas, PJ and López-Cortés, A and Martínez-Mercado, MA},
title = {Novel Methanosarcinaceae species Methanohalophilus methylutens sp. nov., Methanolobus methylotrophicus sp. nov., and Methanococcoides guerreronegronense sp. nov. from Guerrero Negro hypersaline microbial mats in accordance with the SeqCode.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {3},
pages = {126716},
doi = {10.1016/j.syapm.2026.126716},
pmid = {42019101},
issn = {1618-0984},
abstract = {The Methanosarcinaceae family is the most versatile among methanogenic archaea, utilizing a wide variety of substrates for methanogenesis. It includes all known halophilic, methylotrophic methanogens. Despite evidence of their presence and even dominance over other methanogenic taxa in Guerrero Negro hypersaline microbial mats, no archaeal species have been cultured or described to date. Consequently, a significant gap remains in our understanding of their metabolic potential and diversity. In this study, seven high-quality metagenome-assembled genomes (MAGs) affiliated with the Methanosarcinaceae family were reconstructed. Three MAGs (E22BA4_117[TS], E22_A5_bin58[TS], and E22bin_1538[TS]) serve as the nomenclatural type for the novel proposed species Methanohalophilus methylutens, Methanolobus methylotrophicus, and Methanococcoides guerreronegronense, according to the SeqCode rules and representing the first Methanosarcinaceae species described from microbial mats of Guerrero Negro. Based on genomic content and phylogenetic features, we infer that these MAGs are cytochrome-containing methanogens supported by the presence of core methanogenesis genes (fwd/fmd, ftr, mch, mtd, mer, mtr and mcr). They exhibit distinct metabolic strategies: E22BA4_117[TS] is a generalist with broad substrate versatility, E22_A5_bin58[TS] is an expanded methylotrophic specialist, and E22bin_1538[TS] is a narrow-range methylotroph. All three MAGs encode the complete set of genes for the methylotrophic pathway, multiple Na[+]/H[+] antiporters and both transport and biosynthesis genes for compatible solutes, collectively indicative of their adaptations to hypersaline conditions. These novel species enrich the phylogenomic resolution of Methanosarcinaceae and expand current understanding of the diversity and ecological relevance of these methanogenic archaea in hypersaline ecosystems, while providing genomic evidence that clarifies their metabolic potential and adaptations.},
}

@article {pmid42019198,
year = {2026},
author = {Zhang, C and Geng, H and Li, X and Dai, X and Xu, Y},
title = {Magnetically controlled non-conductive microbial carrier-mediated anaerobic digestion of sewage sludge.},
journal = {Water research},
volume = {300},
number = {},
pages = {125963},
doi = {10.1016/j.watres.2026.125963},
pmid = {42019198},
issn = {1879-2448},
abstract = {Magnetic porous microspheres (MPMs) have been used to enhance the anaerobic digestion (AD) of sludge. However, the feasibility of using MPMs as magnetically controlled microbial carriers in long-term AD remains unclear. Herein, without replenishment of MPMs, the methanogenic performance, main physicochemical properties of sludge and methanogenic metabolomics in 150-day MPM-mediated AD were comprehensively investigated. A substantial highly active anaerobes were found to adhere to MPMs, which maintained strong magnetic controllability and structural stability and significantly enhanced methane production (P < 0.001) and the methane proportion in biogas (P < 0.05) from AD at different hydraulic retention times (HRTs). The significant positive correlations between the interfacial Lewis acid-base (AB) interaction (R[2] > 0.79, P < 0.01) and daily methane production (R[2] > 0.52, P < 0.01) with water-mediated proton-coupled electron transfer (PCET) indicate that MPM-enhanced AB interactions can accelerate electron transfer by promoting proton movement in interfacial water molecules, thus enhancing methanogenesis during AD. Statistical analyses of variations in activities or contents of key bioenergetic substances on and within anaerobic cell membranes in AD confirmed this observation and simultaneously indicated that MPMs significantly enhanced the bioenergetics of CO2-reduction methanogenesis by promoting intracellular water-mediated PCET. Microbial community changes show that during the AD under different HRTs, MPMs significantly enriched bacteria capable of decomposing complex organics into acetate and hydrogen in an attached state, as well as free acetotrophic methanogens and attached hydrogenotrophic and hydrogen-dependent methylotrophic methanogens, thereby optimising the spatial distribution of methanogenic consortia. Metagenomics and genome-centric metagenomic analyses confirmed that MPMs significantly enhanced the hydrogen-dependent methanogenesis pathways of the attached methanogenic consortia and promoted energy-conserving metabolic cooperation between free and attached methanogenic consortia, reducing resource competition. Basic economic and environmental analyses revealed that the annual economic benefit increased by 112.2% and carbon emissions decreased by approximately 1.34 × 10[5] tons CO2/year with MPM-mediated AD relative to conventional AD. These findings can provide an important reference for the development of exogenous material-mediated AD technology.},
}

@article {pmid42019199,
year = {2026},
author = {Liu, S and Wei, W and Wang, C and Ni, BJ and Zhu, S},
title = {Persulfate-driven sludge biorefinery toward value-added medium-chain fatty acids.},
journal = {Water research},
volume = {300},
number = {},
pages = {125935},
doi = {10.1016/j.watres.2026.125935},
pmid = {42019199},
issn = {1879-2448},
abstract = {Transforming waste activated sludge (WAS) into high-value biofuels is a key pathway toward sustainable waste management and carbon neutrality, yet the recalcitrance of extracellular polymeric substances (EPS) and microbial cell walls severely limits medium-chain fatty acids (MCFAs) production during anaerobic fermentation. Here, we propose a persulfate (PDS)-based pretreatment strategy that enhances MCFAs synthesis by driving sludge disintegration and substrate transformation. Treatment with 7.5 mM PDS increased MCFAs yield by ∼50%, reaching 13,341.4 mg COD/L. Mechanistic investigations reveal that SO4·[-] and ·OH radicals preferentially degrade tightly bound EPS, reducing protein and polysaccharide content by 38% and 46%, respectively, and increasing soluble chemical oxygen demand (SCOD) 5.05-fold. This transformation produces nitrogen-rich, low-molecular-weight dissolved organic matter (DOM). The resulting DOM exhibited high H/C ratios, low O/C ratios, and low aromaticity indices (AImod), significantly enhancing its bioavailability during anaerobic fermentation. Integrated metagenomic functional annotation and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that EPS-derived DOM reshaped the microbial metabolic network, stimulating glycolysis, amino acid metabolism, and carbon chain elongation. Moreover, the formation of unsaturated and aromatic-like fermentation products indicated enhanced DOM humification, which facilitated carbon chain elongation and microbial metabolic activity. Life cycle assessment and techno-economic analysis confirmed the environmental sustainability and economic feasibility of this radical-driven strategy. By elucidating the radical-EPS-DOM-metabolism cascade, this study provides mechanism-guided strategies for efficient sludge biorefinery, advancing the field from empirical operation toward targeted, high-efficiency design.},
}

@article {pmid42019232,
year = {2026},
author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X},
title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.},
journal = {International journal of food microbiology},
volume = {456},
number = {},
pages = {111785},
doi = {10.1016/j.ijfoodmicro.2026.111785},
pmid = {42019232},
issn = {1879-3460},
abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.},
}

@article {pmid42019335,
year = {2026},
author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A},
title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129718},
doi = {10.1016/j.jenvman.2026.129718},
pmid = {42019335},
issn = {1095-8630},
abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.},
}

@article {pmid42019341,
year = {2026},
author = {Zhao, Y and Chen, Y and Dang, Z and Li, K and Zhu, Y and Xu, C and Wan, X and Jia, B and Cao, G and Shen, Q and Zhao, Z},
title = {Metagenomic and transcriptomic insights into microbial activity maintenance strategies in a pilot-scale biosorption-biodegradation system for in situ sewer overflow treatment.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129750},
doi = {10.1016/j.jenvman.2026.129750},
pmid = {42019341},
issn = {1095-8630},
abstract = {Sewer overflow is a widely recognized issue in urban water environment pollution. Traditional in situ treatment technologies based on filtration and flocculation often fail to remove soluble pollutants effectively. Conventional in situ biological systems also struggle to maintain activity under fluctuating and nutrient-imbalanced influent conditions. Here, a compact in situ biological treatment process based on biosorption-biodegradation technology with a shortened hydraulic retention time (HRT) is proposed. During a 180-day pilot-scale experiment integrating ballasted flocculation, the system achieved average removal efficiencies of 75-94% for CODCr, NH4[+]-N, TP, BOD5, and SS. Effluent concentrations met Chinese surface water quality standards. The system maintained stable performance during wet weather events and after multiple dry periods of up to 30 days, demonstrating effective microbial activity maintenance. Based on the metagenomic and transcriptomic analyses, this stability is potentially related to nutrient supplementation through carbon metabolism of mixotrophic organisms and pollutant adsorption by biosorption sludge. Additionally, the reduced HRT prevents endogenous respiration and sludge degradation. The compact biosorption-biodegradation process offers an efficient and space-saving strategy for maintaining microbial activity during dry periods. It provides a promising solution for mitigating sewer overflow pollution in high-density urban areas.},
}

@article {pmid42019423,
year = {2026},
author = {Xu, C and Feng, Y and He, S and Wu, M and Hu, S},
title = {Mining of FDRs-carrying microbes involved in aflatoxin B1 degradation.},
journal = {Food chemistry},
volume = {515},
number = {},
pages = {149316},
doi = {10.1016/j.foodchem.2026.149316},
pmid = {42019423},
issn = {1873-7072},
abstract = {Aflatoxin B1 (AFB1), a potent hepatocarcinogenic mycotoxin commonly found in food and feed, poses significant threats to food safety and public health. Microbes reduce AFB1 via biotransformation, so mining degrading strains is key. In this study, a novel AFB1 degrader, Mycobacterium sp. strain HM-7, was isolated from an AFB1-degrading bacterial consortium (designated A-2). Genomic analysis of the reconstructed metagenome-assembled genome (MAG) 12 and strain HM-7 revealed six putative F420H2-dependent reductases (FDRs), which are essential for the biotransformation of AFB1. When strain HM-7 was applied to animal feed, it achieved a significant reduction in AFB1 levels. Furthermore, bioinformatics mining based on the Genome Taxonomy Database (GTDB) identified a wide diversity of FDRs-carrying microbes involved in AFB1 degradation, mainly those belonging to the phylum Actinomycetota, highlighting their potential for bioremediation applications. This study provides valuable insights into the diversity of FDRs-carrying microbes involved in AFB1 degradation.},
}

@article {pmid42019451,
year = {2026},
author = {Wei, ZW and Li, HQ and Wang, XH and Yang, XR and Su, JQ},
title = {Non-biodegradable microplastics amplify antibiotic resistance and pathogen spread in bay plastisphere.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142147},
doi = {10.1016/j.jhazmat.2026.142147},
pmid = {42019451},
issn = {1873-3336},
abstract = {Microplastics (MPs) serve as reservoirs that facilitate the dissemination of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), posing significant threats to public health. However, quantitative evaluations of high-risk ARGs in the plastisphere and comprehensive assessments of their associated health implications are still scarce. In this study, we employed in-situ incubation combined with high-throughput quantitative PCR and metagenomic sequencing to systematically compare the prevalence of ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and HBPs between biodegradable and non-biodegradable MPs. Our findings revealed a marked enrichment of ARGs, VFGs, MGEs, and HBPs in non-biodegradable MPs (polypropylene, polyethylene, and polystyrene) relative to the biodegradable MPs (polyhydroxyalkanoates, polylactic acid, and polybutylene adipate terephthalate). Furthermore, an integrated risk assessment combining high-risk ARGs quantification with a Projection Pursuit Regression model revealed significantly elevated microbial risks associated with non-biodegradable MPs. Taxonomic analysis further indicated that Pseudomonas and Aeromonas act as key HBP vectors carrying ARGs and VFGs in the plastisphere, underscoring their role in facilitating the spread of antimicrobial resistance and virulence. These results highlight how plastic properties mediate microbial colonization patterns under complex field conditions, providing a robust framework for environmental risk evaluation and the targeted management of plastic-associated biological hazards.},
}

@article {pmid42019469,
year = {2026},
author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH},
title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106914},
doi = {10.1016/j.psj.2026.106914},
pmid = {42019469},
issn = {1525-3171},
abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.},
}

@article {pmid42019695,
year = {2026},
author = {Liu, X and Wang, H and Zhou, S and Xie, Y and Wang, J and Wang, X and Xu, S and Wang, L and Jiang, C and Zhuang, X},
title = {Nanobubbles drive advanced anaerobic treatment of swine wastewater for efficient methane recovery: Performance gains and multi-pathway enhancement.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134692},
doi = {10.1016/j.biortech.2026.134692},
pmid = {42019695},
issn = {1873-2976},
abstract = {Swine wastewater contains recoverable energy, but anaerobic digestion is often limited by complex organics and slow hydrolysis. To overcome this limitation, this study introduced nanobubble technology using three gas media (air, O2, and O3) and systematically studied their effects on methane recovery during the anaerobic digestion of swine wastewater. Batch experiments showed that O3 nanobubbles achieved the strongest enhancement, increasing cumulative methane production by 87.5% compared with the control. This improvement may result from the strong oxidative capacity of O3 nanobubbles to degrade recalcitrant organics, as indicated by the second methane production peak observed only in the O3 nanobubbles. In contrast, O2 nanobubbles provided the weakest improvement, potentially because excess dissolved oxygen stimulated facultative aerobic respiration, converting substrates to CO2 and lowering availability for methanogenesis. Further analysis revealed that all nanobubble treatments accelerated volatile fatty acid turnover and enriched key hydrolytic and acidogenic microbes, particularly under O3 nanobubbles. The enrichment of Methanothrix and downregulation of the energy-intensive PilA gene suggest promoted electron transfer. Negatively charged nanobubbles may act as abiotic mediators that facilitate direct interspecies electron transfer. Metabolic analysis indicated enhanced hydrogenotrophic, methylotrophic, and acetoclastic methanogenesis, implying strengthened synergy among pathways. Overall, O3 nanobubbles show promise for resource recovery from organic waste.},
}

@article {pmid42019770,
year = {2026},
author = {Xie, M and Kong, L and Hou, L and Chen, Y and Hou, J},
title = {Atopic Dermatitis: Multi-omics Insights into Microbiota-Driven Modulation of the Gut-Skin Axis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108504},
doi = {10.1016/j.micpath.2026.108504},
pmid = {42019770},
issn = {1096-1208},
abstract = {Atopic dermatitis (AD) is a heterogeneous inflammatory skin disease resulting from complex interactions among host genetics, immune dysregulation, and microbial imbalance. Recent advances in multi-omics technologies have revealed distinct AD endotypes characterized by specific genetic variants, microbial enterotypes, and metabolite profiles. Emerging evidence highlights the gut-skin axis as an important regulatory pathway, in which alterations in gut microbiota influence the production of key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan-derived aryl hydrocarbon receptor (AHR) ligands, thereby modulating Th2-dominant inflammatory responses. Integrated analyses combining metagenomics, metabolomics, and single-cell transcriptomics have further identified endotype-specific signatures, such as Bacteroides-enriched profiles associated with lipopolysaccharide-driven inflammation and Prevotella-dominant clusters linked to enhanced AHR activation and epithelial barrier repair. These findings provide a basis for precision stratification and the development of targeted therapeutic strategies, including genotype-guided biologics, microbiota modulation, engineered probiotics, phage therapy, and fecal microbiota transplantation. This review summarizes current evidence integrating host genetics, microbiota networks, and multi-omics biomarkers to provide a comprehensive framework for understanding AD endotypes and to highlight potential avenues for precision diagnosis and targeted interventions.},
}

@article {pmid42020064,
year = {2026},
author = {Peters, BA},
title = {Evidence grows for the gut-kidney axis, but questions still remain.},
journal = {Kidney international},
volume = {109},
number = {5},
pages = {832-834},
doi = {10.1016/j.kint.2026.02.015},
pmid = {42020064},
issn = {1523-1755},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney/microbiology/metabolism ; Metabolomics ; Cross-Sectional Studies ; Metagenomics ; },
abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.},
}

Humans
*Gastrointestinal Microbiome
*Kidney/microbiology/metabolism
Metabolomics
Cross-Sectional Studies
Metagenomics

@article {pmid42020421,
year = {2026},
author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T},
title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72303-0},
pmid = {42020421},
issn = {2041-1723},
support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.},
}

@article {pmid42020426,
year = {2026},
author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ},
title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42020426},
issn = {2041-1723},
support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; },
mesh = {*Milk, Human/chemistry/metabolism ; Humans ; *Oligosaccharides/metabolism ; *Escherichia coli/physiology/growth & development/genetics/metabolism ; *Symbiosis/physiology ; Female ; *Bifidobacterium bifidum/physiology/genetics/metabolism/growth & development ; Gastrointestinal Microbiome ; Feces/microbiology ; Infant, Newborn ; Infant ; Breast Feeding ; Trisaccharides/metabolism ; Male ; Metagenomics ; Adult ; },
abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.},
}

*Milk, Human/chemistry/metabolism
Humans
*Oligosaccharides/metabolism
*Escherichia coli/physiology/growth & development/genetics/metabolism
*Symbiosis/physiology
Female
*Bifidobacterium bifidum/physiology/genetics/metabolism/growth & development
Gastrointestinal Microbiome
Feces/microbiology
Infant, Newborn
Infant
Breast Feeding
Trisaccharides/metabolism
Male
Metagenomics
Adult

@article {pmid42020430,
year = {2026},
author = {Zhou, L and Li, D and Huang, Y and Kang, J and Lu, Y and Zhang, L and Liu, SQ},
title = {Lactiplantibacillus plantarum-mediated modulation of volatile flavor and quality in low-salt spontaneously fermented yellow capsicum sauce.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00854-z},
pmid = {42020430},
issn = {2396-8370},
support = {32302036//National Natural Science Foundation of China/ ; NHXXRCXM202312//'Nan Hai Xin Xing' Science and Technology Innovation Talent Platform Project Funding of Hainan Province, China/ ; 202407560053//China Scholarship Council/ ; KYQD(ZR)-21122//Scientific Research Foundation of Hainan University, China/ ; },
abstract = {Yellow capsicum sauce (YCS) is a special fermented condiment in Hainan province, China, and its fermentation typically occurs in a high-salt environment. In this study, the effects of different salt contents (5, 10, 15, and 20%, w/w) on microbial communities and volatile flavor profiles in YCS were systematically investigated by metagenomic approach and HS-SPME-GC-MS. The results revealed that Lactiplantibacillus (54.66%) was the dominant genus in low-salt samples (SF5), while its abundance was less than 6% in higher salinity levels (SF15 and SF20). A total of 48 volatile flavor compounds (VFCs) were detected in the naturally fermented YCS, with alcohols and esters being the primary VFCs. Low-salt fermentation facilitated the accumulation of VFCs, and the total VFCs content in SF5 was the highest. Aroma compounds showed a strong correlation with Lactiplantibacillus plantarum. To further validate the findings, L. plantarum MA1 isolated from SF5 was inoculated into the low-salt YCS substrate for bioaugmented fermentation. This strain significantly increased key aroma components, such as cis-3-hexenyl isovalerate, hexyl 3-methylbutanoate, and ethyl acetate. Moreover, it significantly increased the lactic acid content while reducing the nitrite content, thereby more effectively preserving the fresh yellow color of capsicum sauce and the stability of its spiciness.},
}

@article {pmid42020464,
year = {2026},
author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH},
title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37419-9},
pmid = {42020464},
issn = {2045-2322},
support = {5850.0109317.18.9 and 21167-2//Petróleo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.},
}

@article {pmid42020750,
year = {2026},
author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS},
title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42020750},
issn = {1476-4687},
abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.},
}

@article {pmid41814236,
year = {2026},
author = {Xiao, H and Zhang, Y and Zhu, L and Guo, M and Yao, K and Dong, F and Duan, X and Liu, G},
title = {Meningitis and subdural empyema caused by group A streptococcal infection.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41814236},
issn = {1471-2431},
support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; },
abstract = {BACKGROUND: Group A streptococcus (GAS) could lead to various disease types in children, but central nervous system (CNS) infections are uncommon. In this paper, we analyzed the clinical features of a GAS case with meningitis and subdural empyema, and characterized the GAS clone.

CASE PRESENTATION: A thirteen-year-old boy complained of fever, headache, and left hemiplegia. Physical examination also showed central facial palsy of left side. The examinations of blood and cloudy cerebrospinal fluid (CSF) showed bacterial meningitis. Blood cultures and metagenomic sequencing (mNGS) of CSF showed GAS, and GAS antigen of throat swab was positive. The first anti-streptolysin (ASO) was negative, but increased obviously after 2 weeks. The examination of emm type showed emm 12.0 isolate. The head MRI showed restricted diffusion in the right frontal lobe, subdural empyema in the right side of cerebral falx, and meningitis. The CT revealed rhinosinusitis and mastoiditis. Bacterial meningitis, subdural empyema, sepsis, and sinusitis were diagnosed, and vancomycin and ceftriaxone were given. The patient also received dexamethasone in the beginning. Gradual improvement was seen in the patient’s clinical status, laboratory parameters (blood/CSF), and radiographic manifestations.

CONCLUSIONS: The contiguous spread from rhinosinusitis could lead to meningitis and intracranial abscess in adolescent. GAS infection could be the pathogen for subdural empyema in patients with an abrupt onset of symptoms and rapidly deteriorating clinical course.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06722-9.},
}

@article {pmid41814258,
year = {2026},
author = {Zhou, Y and Yu, D and Li, S and Ruan, S and Ye, J and Zhou, D and Chen, Q and Jin, J and Song, K},
title = {Case Report: diagnosis of mixed Scedosporium apiospermum infection assisted by bronchoalveolar lavage fluid morphology.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {41814258},
issn = {1471-2466},
support = {2025HZZD01//The Construction Fund of Key Medical Disciplines of Hangzhou, Laboratory Diagnostics/ ; 2025JK256//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; },
abstract = {BACKGROUND: Scedosporium apiospermum is a highly aggressive opportunistic pathogen, widely distributed in natural environments. Infections predominantly occur in immunocompromised individuals but may also affect immunocompetent individuals with predisposing factors such as trauma, drowning, exposure to contaminated water, diabetes, or malnutrition.

CASE PRESENTATION: In the reported case, morphological abnormalities were initially identified in bronchoalveolar lavage fluid (BALF). Subsequent microbial culture identification and metagenomic next-generation sequencing (mNGS) confirmed a mixed infection involving S. apiospermum.

CONCLUSIONS: This case highlights the importance of improving laboratory personnel’s morphological recognition of S. apiospermum in routine examinations. The combined use of multiple diagnostic methods enhances detection rates, shortens the time to identification, ensures timely and effective treatment for patients, and ultimately reduces mortality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-026-04215-0.},
}

@article {pmid41814359,
year = {2026},
author = {Lai, C and Zhang, J and Xiong, Y and Wang, Y and Liu, Z and Shi, M and Ye, S and Zeng, J},
title = {Multi-omics analysis reveals the association of cesarean delivery with altered gut microbial profiles and a Th2-biased immune response in neonates.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41814359},
issn = {1479-5876},
support = {Z-A20241044//Guangxi Zhuang Autonomous Region Health Department/ ; Z20210019//Guangxi Zhuang Autonomous Region Health Department/ ; Z-A20240946//Guangxi Zhuang Autonomous Region Health Department/ ; 2024GXNSFBA010112//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in providing essential stimulatory signals for the development of the immune system during the early stages of life. Cesarean delivery is associated with altered vertical microbial transmission and may affect early immune priming. Currently, only a limited number of studies have investigated the interactions among gut microbiota, fecal metabolites, and immune function in neonates delivered by cesarean section, which underscores the necessity for further research.

METHODS: We performed metagenomic sequencing and untargeted metabolomics to compare the gut microbiota and fecal metabolites of neonates born through cesarean delivery (n = 18) and vaginal delivery (n = 20). RNA sequencing (RNA-Seq) was utilized to identify differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs). Immune profiling involved flow cytometry analysis to determine the proportions of Th1 and Th2 cells, ELISA-based quantification of plasma IFN-γ, IL-12p70, IL-4, and IL-10, and assessment of STAT4 and STAT6 expression via ELISA and Western blot. Multi-omics integration was applied to elucidate the systemic impact of cesarean delivery on the neonatal gut microbiome, metabolome, and immune system.

RESULTS: The composition and functional features of the gut microbiota, and fecal metabolite profile, were significantly altered in Cesarean group. PBMC gene expression also showed marked differences, presenting a Th2-biased immune response and enrichment of genes associated with systemic lupus erythematosus and primary immunodeficiency. Flow cytometry and ELISA confirmed a Th1/Th2 imbalance, while Western blot revealed decreased STAT4 and increased STAT6 expression in the Cesarean group. Multi-omics analysis indicates that Bacteroides sp. is associated with alterations in fecal metabolite in neonates delivered via cesarean section. The reduced abundance of Bacteroides sp. and Bacteroides fragilis correlated with Th1/Th2 dysregulation. Additionally, gut microbiota changes were correlated with variations in the host oxidative phosphorylation pathway via fecal phosphate levels.

CONCLUSIONS: This multi-omics study reveals an association between the mode of delivery and distinct gut microbiota structure, fecal metabolite profiles, and immune development during early life. This provides a framework for investigating the potential connection between early-life immune programming and mode of delivery.

CLINICAL TRIAL NUMBER: Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07988-4.},
}

@article {pmid42007817,
year = {2026},
author = {Chen, M and Kang, Y and Cheng, M and Li, X and Keng, J and Zhao, P and Sui, H and Dong, J and Sun, L and Liu, B and Hu, Y and Jiang, J and Yang, F},
title = {Co-circulation of multiple arboviruses in acute febrile patients in Yunnan, China, identified by metagenomic sequencing.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0167025},
doi = {10.1128/jcm.01670-25},
pmid = {42007817},
issn = {1098-660X},
abstract = {UNLABELLED: Arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are transmitted by Aedes mosquitoes and mainly circulate in tropical and subtropical regions. With global warming, their geographic range is expanding, increasing their threat to public health. Yunnan Province, China, bordering Southeast Asia, is a hotspot for viral importation due to intensive cross-border mobility. However, systematic surveillance for these arboviruses among acute febrile patients remains insufficient. We performed metagenomic sequencing on serum specimens from 990 acute febrile patients at the China-Myanmar border between 2017 and 2023. The pathogens were confirmed by PCR and viral isolation. Phylogenetic and spatiotemporal analyses were used to infer viral origins and transmission dynamics. In this study, a CHIKV outbreak was confirmed in 2019, with strains closely related to those from Myanmar and Thailand. Four DENV serotypes 1-4 were identified, with the predominant serotype varying annually. ZIKV was detected and closely related to strains from Myanmar. Co-infections were identified, including one case each of CHIKV with DENV-1, CHIKV with DENV-3, CHIKV with ZIKV, and DENV-1 with DENV-2. Bayesian spatiotemporal analysis of CHIKV reconstructed global transmission routes, indicating that the 2019 outbreak in China likely originated in India and spread sequentially through Bangladesh, Thailand, and Myanmar. In addition, we also detected enterovirus, hepatitis virus, Saffold virus, and rhinovirus. This study reveals a comprehensive spectrum of pathogens, including the co-circulation of DENV, CHIKV, and ZIKV, and underscores the potential risk of arbovirus importation into China, highlighting the need for strengthened border surveillance.

IMPORTANCE: Arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV), are expanding their range and threatening global public health. Yunnan, situated along the China-Southeast Asia border, is highly susceptible to viral introduction. By applying viral metagenomic sequencing to acute febrile patients, this study uncovered a comprehensive spectrum of pathogens and the co-circulation of DENV, CHIKV, and ZIKV. Phylogenetic analyses revealed that arboviruses were closely related to strains from Myanmar and Thailand, indicating possible frequent cross-border viral introductions. Meanwhile, we reconstructed the global transmission pathways of CHIKV through Bayesian spatiotemporal analysis, providing valuable insights for regional prevention and control of arboviruses. These findings demonstrate that Yunnan serves as a critical interface for viral importation and underscore the urgent need to strengthen border surveillance and early warning systems to mitigate the spread of arboviruses.},
}

@article {pmid42008001,
year = {2026},
author = {Hu, C and Yu, J and Chu, T and Wang, Q and Chen, L and Yu, Y and Wang, Y},
title = {Uncovering novel virophages and giant viruses in high-altitude Lake Namtso: diversity and evolution of host-virus-virophage tripartite interaction systems.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42008001},
issn = {1432-072X},
}

@article {pmid42008944,
year = {2026},
author = {Liu, J and Li, Y and Wang, H and Wang, L and Wu, G and Zhao, B},
title = {Biphasic dynamics of N-nitrosodimethylamine precursors in effluent-receiving rivers: Insights from multi-omics into microbial nitrogen metabolism regulation.},
journal = {Water research},
volume = {300},
number = {},
pages = {125933},
doi = {10.1016/j.watres.2026.125933},
pmid = {42008944},
issn = {1879-2448},
abstract = {Wastewater effluent introduces substantial dissolved organic nitrogen into rivers, thereby increasing the risk of carcinogenic N-nitrosodimethylamine (NDMA) formation from its precursors. However, the microbial metabolic mechanisms governing dynamics of these precursors along receiving rivers remain unclear. Here, through a 21-day time-series incubation of sediments from upstream, outfall, and downstream areas of a representative wastewater treatment plant, combined with multi-omics analyses i.e., 16S rRNA gene sequencing, metagenomics, and metabolomics, the transformation of precursors and microbially mediated nitrogen metabolism were elucidated. A biphasic pattern of NDMA precursors measured as formation potential (FP) was observed during incubation, characterized by a rapid formation from days 0 to 3 followed by a remarkable degradation until day 7 and subsequent stabilization. Nitrate peaked paralleling NDMA FP, with nitrite accumulation following the onset of precursors degradation. Multi-omics analysis revealed that this turnover was driven by strong functional coupling between key nitrogen-cycling taxa and specific metabolites, particularly short-chain peptides. Community structure in the early phase was dominated by r‑strategists e.g., Bacillota, which promoted organic nitrogen degradation and nitrification, resulting in the accumulation of NDMA precursors. As anoxia developed, the community shifted toward K‑strategists such as Pseudomonadota and Chloroflexota, which likely degraded precursors through co-metabolism and consumption of ammonia source. Metabolomics revealed the conversion of precursors into short-chain peptides and amino acid analogues. Notably, effluent exposure established a functionally specialized legacy effect in downstream sediments, stabilizing into a microbial metabolic hotspot with a peak NDMA FP of 1285 ng/L, 158% and 80.7% higher than those in the upstream and outfall area, respectively. This study establishes a mechanistic framework for evaluating the transformation and risk of NDMA precursors in river systems, with direct implications for monitoring strategies and designing of the wastewater outfall location.},
}

@article {pmid42010118,
year = {2026},
author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV},
title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42010118},
issn = {1546-170X},
support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i Përbashkët i BE-së për Kërkimet mbi Sëmundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; },
abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.},
}

@article {pmid42010313,
year = {2026},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Feng, XY and Pan, YP and Zhang, CJ and Liu, Y and Li, M},
title = {A seven-year metagenomic genome catalogue of mangrove and mudflat sediments from the Futian Reserve, China.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07291-3},
pmid = {42010313},
issn = {2052-4463},
support = {42430707//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32225003, 32393970, 92251306//National Natural Science Foundation of China/ ; JCYJ20230808105711023//General Program supported by Shenzhen Natural Science Foundation in Basic Research Fund/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; 2024T001//Shenzhen University Special Funding Initiative/ ; },
abstract = {Mangrove wetlands are ecologically and biogeochemically important "blue-carbon" ecosystems, yet long-term genomic resources for their microbial communities remain scarce. Here we present a seven-year (2017-2023) metagenomic dataset from the Futian Mangrove National Nature Reserve, China, comprising 65 sediment samples collected from paired habitats (mangrove forest and adjacent mudflat) across multiple depths. Sequencing produced ~5.3 Tbp of data, from which 6,922 metagenome-assembled genomes (MAGs) were reconstructed and dereplicated into 3,404 representative genomes (336 Archaea and 3,068 Bacteria). Quality control ensured that all genomes achieved medium- or high-quality standards, with assembly statistics and read recruitment rates supporting robustness and representativeness. Taxonomic annotation revealed broad phylogenetic diversity spanning 13 archaeal and 69 bacterial phyla, with many lineages lacking formal nomenclature and representing potential novel taxa. All raw sequences, genome assemblies, and detailed metadata have been deposited in public repositories, providing a standardized, time-resolved resource for comparative genomics, microbial ecology, and ecosystem restoration studies in coastal wetlands.},
}

@article {pmid42010457,
year = {2026},
author = {Guo, J and Liang, C and Cairang, L and Si, L and Yan, J and Liu, D},
title = {Metagenomics reveals gut microbial differences and ecological adaptation in plateau zokor (Eospalax baileyi) populations.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05069-6},
pmid = {42010457},
issn = {1471-2180},
support = {LHZX-2023-02//Sanjiangyuan National Park Joint Grant from the Chinese Academy of Sciences and the People's Government of Qinghai Province/ ; },
}

@article {pmid42010710,
year = {2026},
author = {Long, L and An, Y and Zhu, LT and Xu, XL and Lin, JJ and Xu, WJ and Chen, JY and Liu, FY and Liu, XY and Huang, Q},
title = {Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02353-5},
pmid = {42010710},
issn = {2049-2618},
support = {(42177362)//National Natural Science Foundation of China/ ; (2025J02030, 2025J01256)//Fujian Provincial Natural Science Foundation of China/ ; (NO. NBSDC-DB-21)//National Basic Science Data Center "Environment Health DataBase"/ ; },
abstract = {BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries.

RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39 × 10[5] and 2.83 × 10[6] DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens.

CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.},
}

@article {pmid42010711,
year = {2026},
author = {You, C and Zhang, W and Guan, Y and Liang, Q and Nong, C and Yang, T and Li, M and Banerjee, S and Zhou, X and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02393-x},
pmid = {42010711},
issn = {2049-2618},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; KJYQ2025034, KJYQ2024039//Fundamental Research Funds for the Central Universities/ ; BK20240194//the Natural Science Foundation of Jiangsu Province/ ; },
abstract = {BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.

RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.

CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.},
}

@article {pmid42010713,
year = {2026},
author = {Tang, J and Wang, L and Yang, Z and Song, Y and Wu, S and Liang, Q and Li, Z and Zhou, S and Xiong, H and Chen, D and Li, J and Li, F},
title = {Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02401-0},
pmid = {42010713},
issn = {2049-2618},
support = {32272874//National Natural Science Foundation of China/ ; 2021YFF1000601//National Key R&D Program of China/ ; 2662025DKPY008//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Male infertility represents a global health concern, with emerging evidence linking gut microbiota dysbiosis to dysspermatogenesis and subfertility. However, the molecular mediators and regulatory mechanisms by which gut microbiota influences testicular functions remain poorly defined.

RESULTS: This study demonstrates that male gamma-glutamyl transferase 1-deletion (Ggt1[-/-]) mice exhibits infertility phenotypes, including reduced germ and testicular Leydig cell numbers, increased rates of abnormal sperm, and altered reproductive hormone levels. Metabolomic analysis reveals elevated levels of the gut microbial-derived metabolite phenylacetylglycine (PAGly) in serum and testes of Ggt1[-/-] mice, with in vivo injection experiments indicating its role in impairing spermatogenesis. Moreover, blocking PAGly effectively restores the impaired spermatogenesis in Ggt1[-/-] mice. Fecal metagenomic and metabolomic analyses show that gut microbiota in Ggt1[-/-] mice induces elevation of phenylacetic acid, a precursor metabolite of PAGly. Strikingly, fecal microbiota transplantation from Ggt1[-/-] mice (Ggt1[-/-]-FMT) recapitulates the infertility phenotypes including reduced germ cells and increased rates of abnormal sperm. Mechanistically, integrated CUT&Tag and ATAC-Seq analyses reveal that transcription factor STAT5B occupies regulatory elements near Klk1b transcription start sites (TSS), confirming that transcription factor STAT5B directly regulates Klk1b gene transcription. Concretely, PAGly activates β2-adrenergic receptor (β2AR) on Leydig cells, triggering STAT3 phosphorylation, subsequent SOCS3 upregulation, and STAT5B phosphorylation suppression; p-STAT5B with transcriptional activation function is reduced, then Klk1b gene transcription is compromised, and therefore spermatogenesis is disrupted.

CONCLUSION: Ggt1 deletion-induced gut microbiota dysbiosis disrupts spermatogenesis via β2AR-STAT3-SOCS3-STAT5B-Klk1bs signaling pathway. Specifically, PAGly-induced β2AR activation promotes STAT3 phosphorylation, which induces SOCS3 to suppress p-STAT5B dependent Klk1bs transcription. This mechanism underscores the critical role of gut-derived metabolites in regulating testicular function and identifies potential targets for microbiota-modulated male infertility. Video Abstract.},
}

@article {pmid42010746,
year = {2026},
author = {Yun, CS and Kim, JK and Kwon, H and Her, M and Moon, JS},
title = {Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00565-6},
pmid = {42010746},
issn = {2524-4671},
}

@article {pmid42010766,
year = {2026},
author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K},
title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2661415},
doi = {10.1080/19490976.2026.2661415},
pmid = {42010766},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Animals ; *Exercise/physiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Physical Conditioning, Animal ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/metabolism
Animals
*Exercise/physiology
Bacteria/classification/genetics/metabolism/isolation & purification
Physical Conditioning, Animal
Fatty Acids, Volatile/metabolism

@article {pmid42010993,
year = {2026},
author = {Wu, Y and Guo, X and Wang, X and Guo, F},
title = {Fatal Non-Hepatic Hyperammonemia Post-Glofitamab: Ureaplasma and Genetic Susceptibility: A Case Report.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {4},
pages = {e70443},
doi = {10.1002/iid3.70443},
pmid = {42010993},
issn = {2050-4527},
mesh = {Humans ; Male ; *Hyperammonemia/etiology/chemically induced/diagnosis ; Middle Aged ; Fatal Outcome ; Genetic Predisposition to Disease ; *Antibodies, Bispecific/adverse effects/therapeutic use ; *Lymphoma, Large B-Cell, Diffuse/drug therapy ; *Ureaplasma Infections/complications ; *Ureaplasma ; },
abstract = {BACKGROUND: Although primarily reported in solid organ transplant recipients and patients undergoing chimeric antigen receptor T-cell immunotherapy (CAR-T), non-hepatic hyperammonemia (NHHA) is a rare but lethal complication in the broader context of post- chemo-immunotherapy hematologic malignancies. It often presents with unexplained encephalopathy that mimics primary central nervous system (CNS) progression, leading to diagnostic delays. With the expanding use of bispecific antibodies (e.g., glofitamab), the etiology of NHHA, particularly the complex interplay between opportunistic infections and potential metabolic susceptibility, remains poorly understood.

CASE PRESENTATION: We report a fatal case of NHHA in a 58-year-old male with diffuse large B-cell lymphoma (DLBCL) following glofitamab-based chemo-immunotherapy. The patient developed sudden onset altered mental status with extreme hyperammonemia (peak blood ammonia 638.9 µmol/L) despite preserved liver function. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Ureaplasma urealyticum. Furthermore, post-mortem whole-exome sequencing (WES) identified a heterozygous variant of SLC25A13 (NM_014251.3:c.2 T > C). As biochemical confirmation of citrin deficiency was not available, the clinical significance of this variant remains uncertain, though it may represent a contributory metabolic susceptibility factor. Despite aggressive ammonia-lowering strategies, including continuous renal replacement therapy (CRRT) and targeted antibiotics, the patient succumbed to fulminant cerebral edema.

CONCLUSION: This case highlights the Ureaplasma urealyticum infection as a critical precipitant of fatal NHHA following glofitamab therapy, occurring in the background of possible genetic metabolic susceptibility (an unverified heterozygous SLC25A13 variant of uncertain functional significance). These findings underscore the critical need for early blood ammonia monitoring and rapid mNGS screening in immunocompromised patients with unexplained encephalopathy. We propose a structured diagnostic algorithm to expedite the recognition and management of this reversible yet life-threatening condition.},
}

Humans
Male
*Hyperammonemia/etiology/chemically induced/diagnosis
Middle Aged
Fatal Outcome
Genetic Predisposition to Disease
*Antibodies, Bispecific/adverse effects/therapeutic use
*Lymphoma, Large B-Cell, Diffuse/drug therapy
*Ureaplasma Infections/complications
*Ureaplasma

@article {pmid42011017,
year = {2026},
author = {Sadia, H and Amin, A and Ahmed, I},
title = {Metagenomic and Phenotypic Insights Into Biofilm-Forming Pathogens in Patients With Nosocomial Sepsis.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e8989667},
pmid = {42011017},
issn = {2314-6141},
mesh = {*Biofilms/growth & development ; Humans ; *Sepsis/microbiology/genetics ; *Cross Infection/microbiology/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Male ; Female ; Phenotype ; },
abstract = {Biofilm-related infections significantly contribute to bacterial diseases, with estimates suggesting that at least 80% of such infections are associated with biofilms. These infections often involve opportunistic pathogens, which not only influence the type of infection but also impact the microenvironment by interacting with other polymicrobial pathogens, thereby altering microbial diversity within the infection site. The present study was designed to assess potential changes in bacterial communities across various infection types. The 50 samples were collected and pooled from different anatomical locations: II-H1 (calf), ul-H2 (thighs), ft-H3 (upper leg), ct-H4 (chest), and Ca-H5 (catheter). The 16S rDNA sequencing was performed on 10 representative samples using the Sanger method to identify bacterial taxa, whereas the metagenomic analysis was conducted on the Illumina MiSeq platform (Illumina, Inc., San Diego, California). Sanger sequencing identifying several bacterial strains including Bacterium MS-AsIII-61, Bacterium HB33-1, Mammaliicoccus sciuri SSB38, multiple Staphylococcus species (S. aureus DA101 and S8, Staphylococcus sp. C0021-01R and TSA25S, S. cohnii FC2265, and S. saprophyticus A), and Enterobacter hormaechei D15. The metagenomics analysis revealed variations and diversity in the different location across the organ by relative abundance of 5 bacterial phyla and 38 species. The Proteobacteria phylum was the most abundant phylum across all sites, with the highest prevalence observed in Ca-H5, followed by ul-H2, ct-H4, II-H1, and ft-H3 in the decreasing order. In contrast, the Bacteroidetes phylum exhibited the highest abundance in ft-H3. Catheter-associated infections (Ca-H5 site) show a homogeneous ARG profile, dominated by genes supporting biofilm formation and persistence. MSA samples reflect diversity in methicillin and multidrug resistance genes, consistent with surgical-site and opportunistic infections. Trypto samples may represent an environmental or experimental condition leading to alternative ARG expression, highlighting site- or condition-specific variations. The different virulence factor responsible for the boost in the establishment of biofilms in these pathogens includes, surface adhesion proteins, increasing resilience to environmental, efflux pumps, quorum-sensing regulators, stresses, and antibiotic treatments. The study demonstrates the dynamic nature and impact of biofilm-related infections at anatomical sites. It also focused on biofilm-associated infections at surgical sites, their progression into chronic conditions, and the corresponding treatment patterns. The integration of metagenomic analysis with phenotypic studies provided deeper insights into the roles of key genes and their mechanisms in biofilm formation.},
}

*Biofilms/growth & development
Humans
*Sepsis/microbiology/genetics
*Cross Infection/microbiology/genetics
*Metagenomics/methods
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Metagenome
Male
Female
Phenotype

@article {pmid42011181,
year = {2026},
author = {Li, Z and Zhang, Y and Xu, H and Wang, D and Yuan, L and Su, N and Lu, H and Li, W},
title = {Prosthetic Joint Infection Caused by Staphylococcus argenteus: mNGS-Guided Diagnosis and Whole-Genome Characterization of an ST2250 Strain.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {594406},
pmid = {42011181},
issn = {1178-6973},
abstract = {BACKGROUND: Staphylococcus argenteus, a member of the Staphylococcus aureus complex, has increasingly been recognized as a human pathogen but is frequently misidentified as S. aureus in routine clinical laboratories. Reports of prosthetic joint infection (PJI) caused by this species remain rare.

METHODS: We describe a case of delayed-onset PJI in a 71-year-old woman following total knee arthroplasty. Repeated conventional cultures were negative after empirical vancomycin therapy. Metagenomic next-generation sequencing (mNGS) of wound exudate detected S. argenteus, which guided extended culture and subsequent isolation of low-abundance colonies. Species identification was confirmed by whole-genome sequencing (WGS), multilocus sequence typing (MLST), and reinterpretation of MALDI-TOF MS results. Antimicrobial susceptibility testing (AST) was performed and compared with WGS-based resistance prediction. Phylogenetic analysis was conducted using 452 publicly available S. argenteus genomes.

AIM: This study aimed to describe the clinical diagnosis, microbiological identification, and genomic characterization of a Staphylococcus argenteus strain causing prosthetic joint infection.

RESULTS: The isolate was identified as sequence type ST2250 and lacked the staphyloxanthin operon, consistent with the non-pigmented phenotype. WGS and phenotypic AST showed 100% concordance across 11 clinically relevant antibiotics. Phylogenomic analysis revealed that the strain clustered closely with Southeast Asian lineages. Following targeted therapy with intravenous vancomycin and surgical wound management, the patient showed rapid clinical improvement with resolution of local inflammation and complete wound healing.

CONCLUSION: This is the first confirmed case of S. argenteus PJI in Suzhou, China. The case highlights the diagnostic value of mNGS in culture-negative PJI, the importance of molecular tools for correctly differentiating S. argenteus from S. aureus, and the potential of WGS to support resistance prediction for rare staphylococcal pathogens.},
}

@article {pmid42011762,
year = {2026},
author = {Lu, J and Wang, HN and Wang, CM and Xu, J and Ikechukwu, CK and Li, W and Ning, SY and Wu, P and Liu, YW and Shen, Q and Ji, LK and Wang, XC and Yang, SX and Zhou, CL and Wang, XL and Zhang, W and Shan, TL},
title = {Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.},
journal = {Zoological research},
volume = {47},
number = {2},
pages = {606-620},
doi = {10.24272/j.issn.2095-8137.2025.134},
pmid = {42011762},
issn = {2095-8137},
mesh = {Animals ; *Mammals/virology ; *Animals, Zoo/virology ; *Bacteriophages/genetics ; *Genetic Variation ; *Virome/genetics ; Phylogeny ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome ; },
abstract = {Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.},
}

Animals
*Mammals/virology
*Animals, Zoo/virology
*Bacteriophages/genetics
*Genetic Variation
*Virome/genetics
Phylogeny
*Viruses/genetics/classification
*Gastrointestinal Microbiome

@article {pmid42011768,
year = {2026},
author = {Oba, S and Okuno, K and Watanabe, S and Yamamoto, Y and Takaoka, A and Hanaoka, M and Yamauchi, S and Kagawa, H and Tokunaga, M and Ban, D and Kinugasa, Y},
title = {Intratumoral fungal burden of Candida tropicalis as a novel prognostic biomarker for recurrence and mortality in colorectal cancer.},
journal = {Cancer},
volume = {132},
number = {8},
pages = {e70408},
doi = {10.1002/cncr.70408},
pmid = {42011768},
issn = {1097-0142},
support = {JP23K19499//Japan Society for the Promotion of Science/ ; JP24K18571//Japan Society for the Promotion of Science/ ; 2023DI008//Kobayashi Foundation for Cancer Research/ ; },
mesh = {Humans ; *Candida tropicalis/isolation & purification/genetics ; Female ; Male ; *Colorectal Neoplasms/microbiology/mortality/pathology ; Prognosis ; Middle Aged ; *Neoplasm Recurrence, Local/microbiology/pathology/mortality ; Aged ; Biomarkers, Tumor ; Adult ; Disease-Free Survival ; },
abstract = {BACKGROUND: The crucial role of gut fungus dysbiosis in the carcinogenesis and progression of colorectal cancer (CRC) has recently garnered increasing attention. In this study, the potential role of Candida tropicalis, commensal gut fungi, in predicting CRC prognosis was investigated.

METHODS: A total of 304 frozen surgical cancer tissue specimens were obtained from patients with CRC and evaluated the intratumoral C. tropicalis burden using quantitative polymerase chain reaction assays. Mycobial composition and diversity analyses were performed by analyzing publicly available metagenomic datasets.

RESULTS: Metagenomic dataset analysis revealed significant differences in fungal composition and diversity of Candida species among adjacent normal and CRC tissues. The 5-year recurrence-free survival and disease-specific survival rates were significantly worse in patients with a high intratumoral C. tropicalis burden than in those with a low burden (78.0% vs. 86.6%; p = .03 and 88.9% vs. 98.0%; p < .01, respectively). Furthermore, multivariate Cox regression analysis revealed that increased intratumoral C. tropicalis burden was a significant independent predictor for recurrence-free survival (hazard ratio [HR]: 1.92; 95% CI, 1.08-3.44; p = .03) and disease-specific survival (HR: 4.29; 95% CI, 1.36-13.5; p = .03).

CONCLUSIONS: These results have demonstrated, possibly for the first time, the potential of intratumoral C. tropicalis burden as a novel prognostic biomarker for recurrence and mortality in patients with CRC.},
}

Humans
*Candida tropicalis/isolation & purification/genetics
Female
Male
*Colorectal Neoplasms/microbiology/mortality/pathology
Prognosis
Middle Aged
*Neoplasm Recurrence, Local/microbiology/pathology/mortality
Aged
Biomarkers, Tumor
Adult
Disease-Free Survival

@article {pmid42012066,
year = {2026},
author = {Guo, R and Gao, J and Zhang, C and Chang, Z and Sun, Y},
title = {Multi-Omics Analysis Reveals Coordinated Adaptations in Genes, Metabolism, and Gut Microbiota Underpinning Herbivory in Lordiphosa Flies.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70110},
pmid = {42012066},
issn = {1749-4877},
support = {202401BC070011//Yunnan Fundamental Research Projects/ ; 32060112//Natural Science Foundation of China/ ; },
abstract = {Herbivorous insects are among the most ecologically successful animal groups. However, the adaptive mechanisms that allow them to exploit plant hosts, which are often nutrient-poor (low in simple sugars, high in structural carbohydrates) and defended by toxic secondary metabolites, are not fully resolved. Here, we investigated the evolutionary basis of herbivory in Lordiphosa clarofinis, a drosophilid species feeding on living plant tissues, using multi-omics approaches. Behavioral experiments revealed a strong oviposition preference for Galinsoga parviflora (a host rich in secondary metabolites), accompanied by elevated expression of chemosensory genes linked to host discrimination. Comparative genomic analyses revealed lineage-specific expansions of gene families associated with detoxification (e.g., cytochrome P450s) and carbohydrate metabolism, alongside positive selection on genes involved in fatty acid utilization and glycogen synthesis. Transcriptomic data showed differential expression of energy metabolism pathways in response to low-sugar plant diets, with upregulation of genes linked to lipid oxidation and gluconeogenesis. Metagenomic profiling of gut microbiota identified key taxa (e.g., Bacteroidetes) capable of degrading plant polysaccharides and synthesizing essential vitamins, potentially complementing host nutritional intake. Our results demonstrate that herbivory in L. clarofinis is associated with coordinated genomic, transcriptional, and microbial changes, rather than being attributable to a single adaptive mechanism. This study highlights how multi-level biological features covary with plant-based feeding and provides a framework for investigating the complex evolutionary and ecological correlates of herbivory in insects.},
}

@article {pmid42012165,
year = {2026},
author = {Werner, A and Chibani, CM and Schmitz, RA},
title = {Navigating prokaryotic viral genome analysis from metagenomic data.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124925},
doi = {10.1128/msystems.01249-25},
pmid = {42012165},
issn = {2379-5077},
abstract = {Viruses play crucial roles in microbial ecosystems, yet viromic analysis remains challenging due to the field's complexity and rapid evolution. This minireview supports non-specialists through the evolving landscape of viromics, focusing on the analysis of bacterial and archaeal DNA viruses from metagenomic data. We address major challenges, including viral diversity, methodological biases, and the overwhelming array of available tools and pipelines. While describing a typical viromic workflow, we provide users with background information for each of the steps from data acquisition, preprocessing, and quality control to viral characterization and common downstream analyses. The included references and resources will provide users with the information needed to confidently start their own virome analysis.},
}

@article {pmid42012213,
year = {2026},
author = {Couto-Rodriguez, M and Danko, DC and Wells, HL and Rey, S and Jirau Serrano, X and Fidler, G and Papciak, J and Combs, PF and Plourde, A and Augenbraun, M and Mason, CE and Otto, C and O'Hara, NB and Nagy-Szakal, D},
title = {Analytical validation of a highly accurate and reliable next-generation sequencing-based urine assay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0202625},
doi = {10.1128/spectrum.02026-25},
pmid = {42012213},
issn = {2165-0497},
abstract = {Urinary tract infections (UTIs) are diagnosed based on symptoms and confirmed by urine culture, despite its limitations in sensitivity. False-negative cultures can lead to inappropriate antimicrobial use or urosepsis in high-risk patients. Next-generation sequencing (NGS)-based metagenomics offers a comprehensive and precise alternative but is rarely applied clinically. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for pathogen detection in urine. Remnant clinical and spiked urine samples underwent extraction, metagenomic library preparation, and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning to identify pathogens and resistance markers. BIOTIA-DX was intentionally designed and trained to increase stringency and reduce false positive detection of urogenital commensals or opportunistic microbes present at colonization levels. Internal controls ensured standardized, high-stringency results. The assay was validated on 1,470 urine specimens evaluating over 14.5k analytes. The clinical validation achieved a 97.2% sensitivity and 99.6% specificity with a limit of detection (LoD) of <15,000 CFU/mL for most bacterial species and <5,000 CFU/mL for fungal species. Discordant results were reconciled by target-specific qPCR or 16S Sanger sequencing, and 87% of the NGS results were concordant with the comparator. A subset of 332 clinical specimens was tested and validated for antimicrobial resistance (AMR). sul and blaSHV genes were commonly associated with Escherichia coli and Klebsiella pneumoniae, while cfxA was found in Prevotella and Pseudomonas spp. detected by BIOTIA-ID. Overall, these data demonstrate that BIOTIA-ID is a comprehensive, highly accurate end-to-end diagnostic assay with notable advantages over current culture-based diagnostics.IMPORTANCEUrinary tract infections (UTIs) are among the most common infections, yet current diagnostic methods, including urine culture, often fail to detect pathogens accurately, leading to delayed treatment and inappropriate antimicrobial use. Clinical metagenomics offers a powerful alternative, especially in complicated cases. BIOTIA-ID is a validated, clinical-grade next-generation sequencing (NGS)-based assay that provides highly accurate pathogen identification and antimicrobial resistance profiling. By incorporating machine learning and stringent quality controls, BIOTIA-ID minimizes false positives and enhances diagnostic precision. Our study demonstrates its superior performance over culture, with potential to improve UTI diagnostics, guide targeted therapy, and support antimicrobial stewardship. The implementation of urine metagenomic diagnostics could support recurrent and complicated UTI patient management, providing a more reliable alternative to traditional methods.},
}

@article {pmid42012671,
year = {2026},
author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC},
title = {Correction to: Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
doi = {10.1007/s00284-026-04870-w},
pmid = {42012671},
issn = {1432-0991},
}

@article {pmid42012901,
year = {2026},
author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T},
title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c16498},
pmid = {42012901},
issn = {1520-5118},
abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.},
}

@article {pmid42013836,
year = {2026},
author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and , and , and Korten, I and Xavier, RJ},
title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.019},
pmid = {42013836},
issn = {1934-6069},
abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.},
}

@article {pmid42013844,
year = {2026},
author = {Bargheet, A and Bø, GH and Hetland, MAK and Justine, M and Moyo, SJ and Löhr, IH and Blomberg, B and Langeland, N and Klingenberg, C and Pettersen, VK},
title = {Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102752},
doi = {10.1016/j.xcrm.2026.102752},
pmid = {42013844},
issn = {2666-3791},
abstract = {Early-life probiotics that strengthen gut resilience in infants are a promising strategy to combat the global emergency of antibiotic resistance. Still, their effects on antibiotic-resistant opportunistic pathogens, i.e., pathobionts, remain unclear. We evaluate the effects of probiotic supplementation in 152 full-term Tanzanian infants enrolled in the ProRIDE trial. Oral probiotics during the first 4 weeks of life increase gut colonization by Bifidobacterium species, while suppressing pathobionts, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E). Integrated metagenomics and metabolomics show that probiotics reduce resistome load and mobilome richness at 6 weeks, accompanied by concurrent shifts in the fecal metabolome. Specifically, the intervention increases lactate and pyruvate and reduces cross-feeding pathways that lead to propionate and butyrate, which partly explains the reduction in ESBL-E carriage. Our study documents putative pathways by which probiotic-driven Bifidobacterium colonization modulates the infant gut toward a lower level of antibiotic resistance.},
}

@article {pmid42013850,
year = {2026},
author = {Qin, Y and Zhang, YX and Liu, LP and Xie, YH and Ma, XY and Hao, Y and Zhao, LC and Dong, JJ and He, Y and Sun, K and Zhong, H and Zhu, S and Liu, M and Fang, JY and Zhou, CB},
title = {Distinct signatures in the human gut and oral microbiomes of gastric cancer.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102761},
doi = {10.1016/j.xcrm.2026.102761},
pmid = {42013850},
issn = {2666-3791},
abstract = {Microbiome dysbiosis is increasingly recognized as a hallmark of gastric cancer (GC). Here, we analyzed gut and oral shotgun metagenomic data from 317 individuals across two independent cohorts, with validation in a Harbin cohort. We identify 20 oral-gut shared species enriched in the gut of GC, predominantly lactic acid bacteria (LAB). While most gut microbial markers are abundant in saliva, none are significantly altered in GC. Strain-level analysis of 87 matched saliva-stool metagenomes confirms oral-gut transmission of Streptococcus species. GC-enriched LAB form robust co-abundance networks in oral and gut microbiomes, suggesting synergistic interactions. Functional analysis reveals enriched lactate fermentation pathways in GC stool, aligning with LAB dominance and previous findings on gastric microbiota. Moreover, microbiome-based classifiers achieve high predictive accuracy (area under receiver operating characteristic curve [AUROC] = 0.85 for stool, 0.87 for saliva) for GC diagnosis, highlighting translational potential. Collectively, these findings underscore the critical role of the oral-gut microbiome axis in GC.},
}

@article {pmid42013936,
year = {2026},
author = {Nie, Z and Wang, Y and Ya, T and Dang, T and Wang, X and Liu, C and Hu, Z and Wang, X},
title = {Rapid recovery from starvation stress in low-temperature anammox system: extracellular polymeric substances protection and dissimilatory nitrate reduction to ammonium synergistically promote nitrogen metabolism recovery.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134677},
doi = {10.1016/j.biortech.2026.134677},
pmid = {42013936},
issn = {1873-2976},
abstract = {Understanding the response of the anammox system to starvation disturbances under low-temperature conditions is of great importance. In this study, we explored the performance, microbial community structure, and microbial metabolic in a low-temperature anammox system following a 15-day starvation period with the aim of identifying their response and recovery mechanisms after starvation stress. It was found that the low-temperature anammox system was able to regain its initial performance within 5 days. After system stabilization, the total nitrogen removal efficiency increased from 85% to 88%. The upregulation of hydrazine synthase (hzs) and hydrazine dehydrogenase (hdh) genes involved in anammox process was identified as part of a response mechanism of anammox bacteria. During the starvation period, the increased secretion of extracellular polymeric substances (EPS) served as a protective mechanism. Additionally, the synergistic interaction between dissimilatory nitrate reduction to ammonium (DNRA) bacteria and anammox bacteria contributed to the enhancement of nitrogen removal efficiency. The EPS-mediated synergistic interaction between anammox bacteria and heterotrophic bacteria was conducive to the survival of microorganisms during starvation and their prompt recovery upon the restoration of substrate supply.},
}

@article {pmid42013937,
year = {2026},
author = {Zhu, Y and Hou, Q and Hu, F and Zhuang, G and Ma, A},
title = {Functional activators-facilitated FeS transformation enhances petroleum hydrocarbon degradation by promoting functional microbial proliferation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134631},
doi = {10.1016/j.biortech.2026.134631},
pmid = {42013937},
issn = {1873-2976},
abstract = {Bioremediation of total petroleum hydrocarbon (TPH)-contaminated sites often faces a major challenge in sulfur-rich environments, where ferrous sulfide (FeS) immobilizes pollutants and sharply reduces their bioavailability, thereby stalling remediation. This study demonstrates that the bottleneck can be overcome by applying a composite functional activator to induce a targeted shift of the site microenvironment. The activator first selectively suppresses competing iron- and sulfur-reducing bacteria, reducing their relative abundance by 92%, thereby shifting the microbial community structure. Concurrently, a controlled decrease in local pH converts FeS from a pollutant sink into an active catalyst. The transformed FeS then activates molecular oxygen (O2) to generate reactive oxygen species (•OH and SO4[•-]), which chemically mobilize and pre-oxidize TPH, producing a "priming effect". This priming effect subsequently restructures the indigenous microbial community. Consequently, under optimized niche conditions and increased nutrient availability, TPH-degrading Bacillus populations expand significantly in the remediation environment: their relative abundance increases by 57%, and their niche breadth widens by 34%. Metagenomic analysis confirms upregulation of genes related to pollutant degradation, substance transport, and energy metabolism, strengthening the metabolic network. Ultimately, the integrated chemical-biological process achieves 90% TPH degradation. This study realizes the functional shift of FeS from remediation barrier to degradation booster, offering an innovative chemo-biological synergistic strategy and engineering paradigm for long-term stable remediation of TPH-contaminated sites.},
}

@article {pmid42014006,
year = {2026},
author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W},
title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152109},
doi = {10.1016/j.ijbiomac.2026.152109},
pmid = {42014006},
issn = {1879-0003},
abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.},
}

@article {pmid42014453,
year = {2026},
author = {Treichel, NS and Pauvert, C and Séneca, J and Pjevac, P and Berry, D and Penders, J and Hitch, TCA and Clavel, T},
title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42014453},
issn = {2058-5276},
support = {460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 10.55776/DOC69//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776/COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
abstract = {Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.},
}

@article {pmid42014512,
year = {2026},
author = {Vijayasimha, M and Srikanth, M and Trivedi, NS},
title = {From Diagnostic Accuracy to Decision-Grade Respiratory Nanopore Metagenomics: Minimum Standards, Stewardship Endpoints, and Equitable Implementation.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42014512},
issn = {1432-0991},
}

@article {pmid42014682,
year = {2026},
author = {Lee, EM and McNulty, NP and Hibberd, MC and Cheng, J and Ahsan, K and Chang, HW and Cohen, BA and Gordon, JI},
title = {Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71871-5},
pmid = {42014682},
issn = {2041-1723},
support = {DK30292//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; },
abstract = {Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential. While differential expression testing is essential for RNA-sequencing analysis, current metatranscriptomic approaches have only been benchmarked on simulated data, resulting in a lack of standard practices for analysis of real datasets. Here, we use mock communities (defined mixtures of microbial cells with known properties) to quantitatively assess robustness and susceptibility of current approaches to various confounders including organisms' low relative abundance, differential abundance, low prevalence, global transcriptional output changes, and compositional effects. We show that no current method is robust to all confounders and method performance on simulated data does not generalize to real datasets. We then apply the same approaches to MTX datasets generated from gnotobiotic mice colonized with defined consortia of human bacterial strains and show that the method nominated by the mock community comparisons successfully inferred cross-feeding dynamics that were subsequently validated in vitro. Finally, using metagenome-assembled genomes from a human clinical study, we leverage genome-level sequencing depth and detection of genes to exclude low information samples on a per-organism basis to overcome confounding low prevalence and enhance differential expression inference. We conclude that MTX benchmarking on real, non-simulated datasets can and should guide choice of methods and their implementation, enabling inference and validation of microbial metabolic strategies and interactions in vivo.},
}

@article {pmid42014730,
year = {2026},
author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W},
title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07250-y},
pmid = {42014730},
issn = {2052-4463},
support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; },
abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.},
}

@article {pmid42001834,
year = {2026},
author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A},
title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158119},
doi = {10.1016/j.phymed.2026.158119},
pmid = {42001834},
issn = {1618-095X},
abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.

OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.

METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and typeⅡinnate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.

RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-α, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.

CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.},
}

@article {pmid42002156,
year = {2026},
author = {Jeon, J and Nguyen, HT and Yeo, G and Lee, C and Cho, SK and Oh, S},
title = {Integrating metagenomics and explainable artificial intelligence for modeling of food waste treatment using full-scale anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134649},
doi = {10.1016/j.biortech.2026.134649},
pmid = {42002156},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD), a biochemical process that can convert food waste (FW) into methane, offers great promise as a sustainable form of energy production. While several attempts have been made to optimize AD systems using various mathematical models, more precise modeling approaches that fully consider the complexity of the AD process are required, leading to the adoption of artificial intelligence (AI) as a suitable alternative to numerical modeling. In line with this, the present study tested 11 AI-based models on their prediction of the methane yield for a full-scale AD process using FW as a feedstock. The models incorporated operational parameters, environmental conditions, and microbial information to improve their predictive performance, and the most precise model was a one-dimensional convolutional neural network (1D-CNN) with optimized hyperparameters. Explainable AI (XAI) was then used to determine the most important input features contributing to the predictions of the optimal AI model, thus allowing for detailed model interpretation. Methanothrix was identified as a key predictor of methane yield, and metagenomic analysis provided independent genome-level evidence broadly consistent with the XAI results. Overall, this study proposes a novel approach to the interpretation and optimization of AD performance, rather than focusing only on enhancing the predictive performance of a discrete model.},
}

@article {pmid42002784,
year = {2026},
author = {Liu, T and Fan, S and Li, J and Wang, T and Zhang, J and Wang, C},
title = {Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02396-8},
pmid = {42002784},
issn = {2049-2618},
support = {2023YFD1301005//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.

RESULTS: In the experimental setup, 800 mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500 μg/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH3-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-κB-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.

CONCLUSIONS: Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.},
}

@article {pmid42002835,
year = {2026},
author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E},
title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659397},
doi = {10.1080/19490976.2026.2659397},
pmid = {42002835},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Piperidines/adverse effects/therapeutic use ; *Adenine/analogs & derivatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Feces/microbiology ; Treatment Outcome ; *Antineoplastic Agents/adverse effects/therapeutic use ; Adult ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Piperidines/adverse effects/therapeutic use
*Adenine/analogs & derivatives/adverse effects/therapeutic use
Male
Female
Middle Aged
Aged
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Feces/microbiology
Treatment Outcome
*Antineoplastic Agents/adverse effects/therapeutic use
Adult

@article {pmid42003340,
year = {2026},
author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H},
title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70143},
doi = {10.1111/1755-0998.70143},
pmid = {42003340},
issn = {1755-0998},
support = {2023.06155//Fundação para a Ciência e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovación/ ; //The University of Melbourne's Research Computing Services/ ; },
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Genome, Plastid ; *Eukaryota/genetics/classification ; *Software ; Phylogeny ; Metagenome ; },
abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.},
}

*Metagenomics/methods
*Computational Biology/methods
*Genome, Plastid
*Eukaryota/genetics/classification
*Software
Phylogeny
Metagenome

@article {pmid42003642,
year = {2026},
author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE},
title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0008526},
doi = {10.1128/mra.00085-26},
pmid = {42003642},
issn = {2576-098X},
abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.},
}

@article {pmid42003644,
year = {2026},
author = {Iizuka, R and Moriya, T and Oshima, T and Uemura, S and Yohda, M},
title = {Amplicon sequence collection of putative polyethylene terephthalate hydrolases from two different composts in Japan.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017326},
doi = {10.1128/mra.00173-26},
pmid = {42003644},
issn = {2576-098X},
abstract = {We report a collection of amplicon sequences of putative polyethylene terephthalate (PET) hydrolases from two different composts in Japan. Employing previously designed degenerate primers, we identified 31 and 22 sequences from industrial and agricultural composts, respectively, confirming the presence of highly homologous PET hydrolase genes across different compost environments.},
}

@article {pmid42003651,
year = {2026},
author = {Kocakahya, İ and Şahin, G and Büyükkahraman, E and Arıkan, M},
title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/mra.01405-25},
pmid = {42003651},
issn = {2576-098X},
abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.},
}

@article {pmid42004019,
year = {2026},
author = {Yuan, G and Zhu, X and Zhang, L and Wang, X and Wang, Y and Guo, D and Zhang, T and Wang, G and Wang, N},
title = {Shading affects the nitrogen cycling process and plant nitrogen uptake by altering the rhizosphere microbial community.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1780344},
pmid = {42004019},
issn = {1664-462X},
abstract = {Plants adapt to environmental changes by affecting the rhizosphere environment and microbial pathways. Shading affects nitrogen absorption and accumulation in plants by directly or indirectly altering the light intensity. However, the effects this has on the rhizosphere micro-environment and especially the microbial community are not fully understood. Utilizing non-targeted metabolomics and metagenomics, we investigated the changes in the microbial community structure in the cigar tobacco rhizosphere and the nitrogen cycling process and its relationship with nitrogen absorption by the plants under artificial shading conditions. Shading significantly increased the rhizosphere soil organic carbon, hydrolyzable nitrogen, ammonium nitrogen, nitrate nitrogen, and nitrogen contents in tobacco plants. Metabolomics revealed that shading significantly affected the arginine biosynthesis pathway in the rhizosphere soil, with the expression levels of L-oxornithine, citrulline and L-arginine significantly increasing. Metagenomics analysis indicated that shading significantly altered the rhizosphere microbial community structure and the nitrogen cycling process. The abundances of organic nitrogen-decomposition (gdh A, ansB) and nitrification genes (amoA_B, amoB_B, amoC_B, hao) significantly increased. Flavobacterium and Stenotrophomonas may play important roles in the nitrogen cycle in the rhizosphere. Correlation analysis indicated that Flavobacterium and Stenotrophomonas were significantly positively correlated with L-glutamic acid, L-ornithine and L-arginine (p < 0.05). These results reveal the biological mechanism by which shading affects nitrogen absorption in crops via changes in the rhizosphere microbial community and the nitrogen cycling process, providing a scientific foundation for guiding nutrient management strategies in shaded cultivation.},
}

@article {pmid42004152,
year = {2026},
author = {You, G and Wang, S and Hua, Y and Su, J and Yang, Y and Shi, B and Cen, S},
title = {A four-year misdiagnosis of spinal Burkholderia pseudomallei infection: A case report and literature review.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02558},
pmid = {42004152},
issn = {2214-2509},
abstract = {Melioidosis, traditionally an endemic disease, is increasingly reported in non-endemic regions. Its causative pathogen, Burkholderia pseudomallei, exhibits distinct characteristics from common pathogens but is prone to misdiagnosis due to clinical overlap with other infections. Despite advances in diagnostics, metagenomic next-generation sequencing (mNGS) has not been featured in case reports. We present a case of melioidosis, misdiagnosed for four years, where mNGS proved pivotal for definitive diagnosis. Based on our findings and literature review, we advocate for mNGS in melioidosis diagnosis. Furthermore, we identify subtle distinctions between melioidosis and tuberculosis amidst their similarities and propose integrating these features into a differential diagnostic framework.},
}

@article {pmid42004164,
year = {2026},
author = {Chong, KL and Liew, KJ and Salleh, FM and Chong, CS},
title = {Metagenomic insights into mangrove lignocellulolytic bacteria and functional analysis of a glucose-tolerant GH 1 β-glucosidase.},
journal = {3 Biotech},
volume = {16},
number = {5},
pages = {163},
pmid = {42004164},
issn = {2190-572X},
abstract = {UNLABELLED: Mangrove ecosystems contain abundant lignocellulosic biomass and mangrove microorganisms that are capable of degrading plant polymers. In this study, a shotgun metagenomic approach was employed to explore the bacterial communities from Tanjung Piai National Park, Malaysia and their genes involved in lignocellulosic biomass degradation. A total of 148 of carbohydrate active enzymes (CAZy) genes spanning GH, CE, and AA families were identified with lignocellulolytic abilities. These enzymes included 20 cellulases, 46 hemicellulases, and 82 lignin-modifying enzymes. Approximately 89.19% of these genes were found from underexplored bacterial lineages. A set of lignocellulolytic genes derived from diverse bacterial taxa highlighted the synergistic action of mangrove bacteria in lignocellulose degradation. To validate the functionality of these genetic resources, one of the genes (BGL3_GH1) encoding a β-glucosidase was selected for expression and characterisation. The recombinant enzyme showed optimal activity at 60 ℃ and pH 7, retained up to 75% activity at 10% (w/v) NaCl. The enzyme exhibited a 1.6 to 2.1-fold in enzyme activity with glucose concentration up to 2 M. In a two-step saccharification assay using sugarcane bagasse, supplementation with recombinant BGL3_GH1 enhanced the saccharification yield (0.0674 g g[- 1] biomass) compared with treatments using commercial cellulase or recombinant BGL3_GH1 alone. These findings reveal the functional diversity of lignocellulose-degrading genes in mangrove bacteria and identify recombinant BGL3_GH1 as a potential enzyme candidate for biomass conversion application.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04788-x.},
}

@article {pmid42004407,
year = {2026},
author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H},
title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73367},
pmid = {42004407},
issn = {2045-7758},
abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.},
}

@article {pmid42004633,
year = {2026},
author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D},
title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e174893},
pmid = {42004633},
issn = {1314-2828},
abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.

NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).},
}

@article {pmid42004896,
year = {2026},
author = {Pourghasem, M and Tabatabaii, SA and Modarresi, SZ and Jafari Nodoushan, A and Fadavi, N and Soflaee, M and Hosseini Vajari, A and Khazaii, F and Shahhosseini, B and Fakhimi Derakhshan, K and Sadat Mansouri, S},
title = {Fungal Infections in Pediatric Patients With Hematologic Malignancies and Stem Cell Transplantation: Impact on the Upper and Lower Respiratory Systems.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2026},
number = {},
pages = {8766717},
pmid = {42004896},
issn = {1712-9532},
abstract = {Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality in children with hematological malignancies as well as those undergoing hematopoietic stem cell transplantation (HSCT). Extreme immunological dysregulation secondary to severe neutropenia, T-cell lymphopenia, graft-versus-host disease (GVHD), intensive chemotherapy regimens, and conditioning therapy for HSCT, as well as primary immunodeficiencies (PIDs), render these patients highly susceptible to both opportunistic and pathogenic fungal infections. Despite advances in antifungal drugs and diagnostic tools, it is very difficult in these children to provide timely diagnosis and optimal management of IFIs because of the nonspecific clinical manifestations, the invasiveness of present diagnostic modalities in pediatric patients, and biomarker kinetics differences in various pediatric age groups, along with a lack of incorporation of immunological-pharmacological maturity-associated variability in the existing scoring systems borrowed from adults. This narrative review provides a comprehensive and contemporary assessment of the epidemiology, host-related risk factors, clinical presentations, diagnostic criteria, and management practices for IFIs in children with hematological malignancies and following HSCT. It also highlights the role of EORTC/MSGERC criteria in defining IFIs as probable, proven, and possible infections and explores the sensitivity and specificity of noninvasive methods such as the galactomannan index, polymerase chain reaction (PCR), ß-D-glucan assay, high-resolution CT scans (HRCTs), and the latest approaches including next-generation sequencing (NGS) and metagenomics. This review points out significant gaps in pediatric research studies and supports efforts to optimize healthcare use with risk-prediction models rather than just relying on current algorithms.},
}

@article {pmid42005541,
year = {2026},
author = {Naitchede, LHS and Ihearahu, OC and Saha, K and Igwe, DO and Yan, J and Osano, AA and Ray, S and Ude, G},
title = {Microbial community characterization in semi-hydroponic systems of Starbor kale (Brassica oleracea L.) grown under normal gravity and simulated microgravity.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100592},
pmid = {42005541},
issn = {2666-5174},
abstract = {Kale is a member of the Brassicaceae family and contains a range of beneficial compounds. Given the global context of climate change, various vegetable production systems using advanced technologies, such as hydroponics, are being explored to alleviate food insecurity. Herein, we characterized the comprehensive microbial community associated with Starbor kale cultivation systems under normal gravity and simulated microgravity in coco coir, representing an innovative approach compared to previous studies. The kale seedlings were planted in growth vessels set into custom 2D clinostats and placed in a CONVIRON growth chamber for 43 days. The microbial DNA from coco-coir and root samples of grown kale was extracted and subjected to shotgun metagenomic sequencing. Comparisons between components revealed a higher abundance of bacteria in the soilless, while the kale roots were dominated by Eukaryota and archaea. The phyla Pseudomonadota and Actinomycetota were highly prevalent across all samples, with relatively high abundance in the coco coir samples from horizontal clinostats (HCR) under simulated gravity and from rotating vertical clinostats (VCR). The HCR group was associated with the highest number of biomarkers (28). Both CAZymes, glycoside hydrolases and carbohydrate esterases, exhibited higher relative abundances in the coco coir samples under normal gravity, whereas carbohydrate-binding modules were more abundant in HCR and VCR. The root samples showed much higher abundances of polysaccharide lyases (ranging from 0.00088 to 0.00097) and carbohydrate esterases (ranging from 0.030 to 0.033). The top four prevalent antibiotic resistance genes were adeF, vanY, vanT, and qacG. The findings of this investigation are crucial for the cultivation of kale and leafy green agriculture in hydroponic systems.},
}

@article {pmid42005844,
year = {2026},
author = {Ibañez-Lligoña, M and Colomer-Castell, S and Campos, C and González-Camuesco, Á and Llauradó, A and Garcia-Larroy, J and Sánchez-Tejerina, D and Rando-Segura, A and Andrés, C and Esperalba, J and Nadal, P and Ferrer, R and Cortese, MF and Tabernero, D and Gregori, J and Riveiro-Barciela, M and Ruiz-Cobo, JC and Ruiz, A and Del Barco, E and Buti, M and Goya, M and Antón, A and Cano, A and Juntas-Morales, R and Quer, J},
title = {Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786985},
pmid = {42005844},
issn = {1664-302X},
abstract = {INTRODUCTION: Shotgun metagenomic sequencing (mNGS), an untargeted approach that sequences all nucleic acids in a sample, has emerged as a powerful tool for pathogen detection and genome characterization. However, its implementation in clinical diagnostics remains limited due to technical challenges such as contamination and reduces sensitivity, especially in low-biomass samples.

METHODS: We applied mNGS to 144 clinical samples representing chronic infections, acute infections, and respiratory co-infections. To address contamination, we established a framework integrating negative controls, lab-specific contaminant watchlists, and computational filtering. Viral detection performance and genome recovery were assessed across sample types and viral loads.

RESULTS: Viral load was shown to be the primary determinant of sensitivity, with reliable recovery achieved only at higher titers. Our framework substantially improved contamination management, reducing false-positive signals and enhancing viral genome recovery. mNGS enabled the detection of clinically relevant co-infections and refined viral classification beyond targeted diagnostics, while also revealing the substantial risk of spurious detections in the absence of contamination-aware workflows.

DISCUSSION: These findings define practical sensitivity thresholds for clinical mNGS and underscore the need for contamination-aware workflows, particularly for low-biomass samples, while providing an open-source contaminants watchlist that enhances reliability and utility of clinical metagenomics.},
}

@article {pmid42005864,
year = {2025},
author = {Steindler, L and Durán Canché, MA and Ilan, M and Bar-Shalom, R and Lopez, JV and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {466},
doi = {10.12688/wellcomeopenres.24763.2},
pmid = {42005864},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases. Most of the assembly (98.57%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length. Sixty-four binned genomes were generated from the metagenome assembly, of which 46 were classified as high-quality metagenome assembled genomes (MAGs). The microbial signature is typical of HMA sponges, including the Pseudomonadota, Chloroflexota and Acidobacteriota as dominant phyla and several candidate phyla (Poribacteria, Binatota, Latescibacterota) as well as the archaeal clade Nitrosopumilaceae in lower abundance.},
}

@article {pmid42005923,
year = {2026},
author = {Lafon, T and Weingart, M and Vaidie, J and Calfee, CS and Jacob, ST and Freund, Y and Shapiro, NI and Barraud, O and Monneret, G and van der Poll, T and Fromage, Y and François, B},
title = {Challenges in early detection and prognostication of sepsis: new approaches from the emergency department and intensive care unit.},
journal = {EClinicalMedicine},
volume = {94},
number = {},
pages = {103864},
pmid = {42005923},
issn = {2589-5370},
abstract = {In this narrative review, we aimed to provide a comprehensive overview of emerging diagnostic strategies and precision medicine approaches in sepsis, while explicitly acknowledging the heterogeneity of clinical contexts. In the Emergency Department (ED), timely recognition of infection and sepsis represents one of the most frequent and challenging tasks, which may delay management directly increasing morbidity and mortality. Even if very popular and widely used, traditional scores and routine biomarkers remain of limited interest to confirm diagnosis and predict deterioration. Nevertheless, emerging point-of-care tools hold promise such as "real-time microbiology", bedside immune profiling, and echocardiography for on-time hemodynamic phenotyping. More advanced strategies, such as omics technologies and transcriptomic signatures, offer deeper biological precision, while machine learning and artificial intelligence can integrate high-dimensional ED data to anticipate deterioration and capture the dynamic evolution of sepsis subphenotypes. Many of these tools are already feasible at the bedside and only await integration into routine ED workflows. Embedding them within dedicated sepsis pathways and multidisciplinary teams could optimize global patient care and accelerate the transition toward precision medicine in acute sepsis. Sustainable improvements in sepsis outcomes will most likely not come from isolated devices but from their integration into coordinated and sepsis-specific pathways.},
}

@article {pmid42006114,
year = {2025},
author = {Dorobantu, S and Grigorescu, A and Fratea, A and Mirauta, B and Neghina, A and Bica, G and Neacsu, A and Dumitrescu, F and Streata, I and Netea, M and Riza, AL},
title = {Strength of Omics in Uncovering Sepsis Mechanisms-A Perspective.},
journal = {Current health sciences journal},
volume = {51},
number = {4},
pages = {425-436},
pmid = {42006114},
issn = {2067-0656},
abstract = {BACKGROUND: Sepsis is a significant life-threatening condition due to a dysregulated response to infection. Large datasets yield unprecedented views and transformative insights into processes through various computational frameworks. Our aim was to highlight significant contributions from genomics, transcriptomics, proteomics in the field of sepsis, as modeled from human data. We are showcasing key findings in each omics that have improved the understanding of sepsis pathophysiology, while presenting a perspective from the group's own contribution to the field.

DISCUSSION AND CONCLUSIONS: Each of the presented omics has advanced our mechanistic understanding on sepsis pathogenicity, biomarker identification for diagnosis, prognosis, and molecular stratification purposes. Multi-omics sepsis research shows strong input from genomics, transcriptomics, proteomics. These have revealed mechanistic links and produce robust endotypes but faces challenges on the path to clinical integration. Integrative sepsis studies combine large-scale omics, paired sampling, and computational multi-omics frameworks to link molecular layers to phenotype. Addressing gaps in standardization, and age/ethnicity representation could yield actionable biomarkers, stratified therapies and improved outcomes.},
}

@article {pmid42006125,
year = {2026},
author = {Azuma, N and Wada, N and Aoki, R and Sampei, M and Mawatari, T and Saito, Y},
title = {Administration of bifidobacteria and dietary fiber improves cognitive function by increasing short-chain fatty acid-producing bacteria and reducing inflammation.},
journal = {Bioscience of microbiota, food and health},
volume = {45},
number = {2},
pages = {139-148},
pmid = {42006125},
issn = {2186-6953},
abstract = {Bifidobacterium animalis subsp. lactis GCL2505 (GCL2505), commercially known as the "BifiX" strain in Japan, reaches the intestine alive, proliferates after a single intake, and is associated with several positive health effects. A randomized, double-blind, placebo-controlled, parallel-group clinical trial of this probiotic strain in combination with inulin (a prebiotic) reported an improvement of cognitive function in the elderly. In the present study, a follow-up analysis was performed to elucidate the underlying mechanism, using a multi-omics approach that integrated a high-throughput assay of blood inflammatory markers and metagenomic analysis of the fecal bacterial composition. After probiotic and prebiotic administration, short-chain fatty acid producers such as Faecalibacterium and Bifidobacterium were increased in the gut. Moreover, in the subgroup with greater improvement in cognitive function scores, the levels of inflammatory markers were decreased. Subgroup analysis revealed that the improvement of cognitive function was associated with a reduction of inflammation and an increase of Faecalibacterium. These results suggest that GCL2505 and inulin can improve cognitive function by alleviating inflammation via an increase of short-chain fatty acid-producing bacteria, which appears to elevate levels of short-chain fatty acids, particularly acetate and butyrate, in the gut. The present results contribute to a deeper comprehension of the gut-brain axis and propose new avenues for potential therapeutic intervention in cognitive disorders.},
}

@article {pmid42006869,
year = {2026},
author = {Li, Y and Zhu, H and Zhan, Z and Li, G and Zhou, Q and Zheng, C and Huang, F},
title = {Clinical features and prognostic factors of Chlamydia psittaci pneumonia: a retrospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1804156},
pmid = {42006869},
issn = {2296-858X},
abstract = {BACKGROUND: Chlamydia psittaci pneumonia (CPP) is frequently misdiagnosed and can progress to severe illness. A deeper understanding of its clinical and imaging features is crucial for early detection and effective treatment.

METHODS: This retrospective study analyzed 74 patients diagnosed with CPP via metagenomic (mNGS) and targeted next-generation sequencing (tNGS) between January 2022 and September 2025. Patients were categorized into severe (n = 21) and non-severe (n = 53) groups based on established criteria for severe community-acquired pneumonia. Data on demographics, clinical manifestations, laboratory findings, and imaging characteristics were collected and compared.

RESULTS: The cohort had a median age of 60 years, with a male predominance (62.2%). A history of poultry/bird exposure was reported by 87.8% of participants. Common symptoms included fever (94.6%), cough (63.5%), and fatigue (29.7%), with no significant differences between groups. Hospitalization was significantly longer in the severe group (12.95 ± 6.08 days) than in the non-severe group (8.13 ± 3.30 days) (p < 0.001). Chest CT revealed consolidation and ground-glass opacities in all patients. Pleural effusion was significantly more common in the severe group (76.2% vs. 45.3%, p = 0.016), as was bilateral lung involvement (52.4% vs. 22.6%, p = 0.013). Multivariate analysis identified elevated D-dimer (OR = 2.737, p = 0.007) and reduced lymphocyte percentage (L%) (OR = 0.813, p = 0.026) as independent predictors of severe disease. ROC curve analysis showed an AUC of 0.765 for D-dimer and 0.739 for L% reduction. Following tetracycline or quinolone therapy, 94.6% of patients recovered, with an overall mortality rate of 5.4%.

CONCLUSION: Severe CPP is associated with prolonged hospitalization, bilateral pulmonary infiltrates, and pleural effusion. D-dimer and lymphocyte percentage are valuable prognostic indicators for disease severity. Early targeted antibiotic therapy is effective, but timely respiratory support is critical for severe cases.},
}

@article {pmid42006894,
year = {2026},
author = {Cui, T and Huang, M},
title = {Case Report: A case of refractory tuberculous peritonitis mimicking and complicating suspected encapsulating peritoneal sclerosis in a long-term peritoneal dialysis patient.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1777805},
pmid = {42006894},
issn = {2296-858X},
abstract = {BACKGROUND: Tuberculous peritonitis (TBP) is a rare but severe complication in peritoneal dialysis (PD) patients, often presenting with non-specific symptoms. Its diagnosis is particularly challenging in patients with pre-existing or co-existing peritoneal pathology, such as changes suggestive of encapsulating peritoneal sclerosis (EPS).

CASE PRESENTATION: A 59-year-old male on PD for 14 years with no prior history of peritonitis presented with recurrent abdominal pain, fever, and cloudy effluent, following a recent episode of Staphylococcus caprae peritonitis. Initial contrast-enhanced computed tomography (CT) revealed diffuse peritoneal thickening, omental "caking," and localized ascites, raising strong suspicion for EPS. However, the patient's condition relapsed despite broad-spectrum antibiotic therapy. Metagenomic next-generation sequencing (mNGS) of peritoneal fluid definitively identified Mycobacterium tuberculosis complex. The diagnosis was thus revised to TBP manifesting with secondary peritoneal inflammatory changes mimicking EPS. Management involved laparoscopic PD catheter removal, transition to hemodialysis, and initiation of a renal-adjusted anti-tuberculous regimen (levofloxacin and linezolid), leading to gradual clinical and biochemical improvement.

CONCLUSION: This case highlights that TBP can clinically and radiologically mimic EPS in long-term PD patients, leading to diagnostic delay. High clinical suspicion and the utilization of advanced molecular diagnostics like mNGS are crucial for accurate diagnosis. Catheter removal combined with appropriate anti-tuberculous therapy forms the cornerstone of management in such complex scenarios.},
}

@article {pmid42007374,
year = {2026},
author = {Jeong, UJ and Ali, M and Park, YJ and You, JS and Yoon, SS},
title = {A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {2},
pmid = {42007374},
issn = {2771-5965},
abstract = {Aim: Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. Methods: Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. Results: Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8[+] T cells and natural killer cells, with concordant immune trends in peripheral compartments. Conclusion: A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into in vivo validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.},
}

@article {pmid42007699,
year = {2026},
author = {Carroll, AC and Hinz, A and Hicks, AMA and Khov, E and Van Bakel, T and Doukhanine, E and Fralick, M and Nott, C and Kassen, R and Thampi, N and Hug, LA and MacFadden, D and Wong, A},
title = {Targeted metatranscriptomic detection of viruses from floors for simultaneous evaluation of respiratory disease burden and viral variant identification.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0008626},
doi = {10.1128/msphere.00086-26},
pmid = {42007699},
issn = {2379-5042},
abstract = {UNLABELLED: Built environment surveillance is a proven approach for tracking disease burden of some viruses within hospitals and long-term care facilities. However, studies in clinical settings are lacking for simultaneously surveying targets in a built environment using targeted metatranscriptomics. We swabbed six discrete floor locations within an acute care center's emergency department (ED) in Ottawa, Canada, and sequenced cDNA using a 132 viral taxa panel, identifying viral burden across sampling locations and time. The determined SARS-CoV-2 variant profile across time was matched to provincial variant prevalence. The correlation between metatranscriptomic read abundances and reported cases of influenza A, SARS-CoV-2, and RSV was assessed. We quantified these via qPCR and assessed the correlation of Cq versus metatranscriptomic reads for these viruses. We sequenced a median of 1,302,882 reads per sample from 38 floor swabs collected during peak respiratory viral season (November 2022-February 2023). Diversity of viral communities varied significantly across locations in the ED. SARS-CoV-2 variant abundance shifts matched the changing infection landscape concurrently reported in Ontario. Relationships between targeted metatranscriptomic read ratios and clinical burden were not statistically significant, although we found modest correspondence between qPCR signal and read depth for RSV and SARS-CoV-2. This approach characterized the viral communities and the within-species diversity within an ED. Correlating sequencing-derived data with disease burden for three key respiratory viruses was inconsistent, with the exception of significant correlation between metatranscriptomic reads and Cq data for SARS-CoV-2. We were able to recover the distribution of clinically reported SARS-CoV-2 variants from the floor swab data.

IMPORTANCE: Environmental surveillance is useful for estimating the disease burden for certain viruses. qPCR is commonly used for surveillance of wastewater and built environments, including during the COVID-19 pandemic, but single, multiplexed reaction targets are limited. Targeted metagenomic or metatranscriptomic approaches can accurately quantify microbial populations of interest in an environment, reduce off-target sequencing, and evaluate a broader number of targets than qPCR assays. Here, we assessed the capacity of a targeted viral metatranscriptomic panel to correlate viral abundance in the hospital built environment with key pathogens of interest, including influenza A, RSV, and SARS-CoV-2. Our results suggest that targeted metatranscriptomics may identify viral communities in healthcare facilities, including strain-level detection capability. However, this approach must be validated for its effectiveness in viral surveillance that accurately reflects disease burden. This work contributes to a growing toolkit for pathogen surveillance, a critical endeavor to safeguard against outbreaks of known and emerging pathogens.},
}

@article {pmid42001152,
year = {2026},
author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J},
title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00892-w},
pmid = {42001152},
issn = {2524-6372},
support = {2021-PR-284297//Fonds de recherche du Québec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Québec - Nature et technologies/ ; },
abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.},
}

@article {pmid42002296,
year = {2026},
author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C},
title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70304},
doi = {10.1111/1462-2920.70304},
pmid = {42002296},
issn = {1462-2920},
support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; },
mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth & development ; *Gastrointestinal Microbiome ; Bacteria/metabolism/genetics/classification/isolation & purification ; Metabolome ; Biological Products/metabolism ; },
abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.},
}

Animals
*Coleoptera/microbiology/metabolism/growth & development
*Gastrointestinal Microbiome
Bacteria/metabolism/genetics/classification/isolation & purification
Metabolome
Biological Products/metabolism

@article {pmid42002357,
year = {2026},
author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z},
title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.},
journal = {Carbohydrate polymers},
volume = {382},
number = {},
pages = {125292},
doi = {10.1016/j.carbpol.2026.125292},
pmid = {42002357},
issn = {1879-1344},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Curcuma/chemistry ; Dextran Sulfate/toxicity ; *Fructans/pharmacology/chemistry/isolation & purification/therapeutic use ; Mice, Inbred C57BL ; Male ; Metabolic Networks and Pathways/drug effects ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; *Colitis/chemically induced/drug therapy ; Disease Models, Animal ; },
abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Curcuma/chemistry
Dextran Sulfate/toxicity
*Fructans/pharmacology/chemistry/isolation & purification/therapeutic use
Mice, Inbred C57BL
Male
Metabolic Networks and Pathways/drug effects
*Colitis, Ulcerative/drug therapy/chemically induced/metabolism
*Colitis/chemically induced/drug therapy
Disease Models, Animal

@article {pmid41803433,
year = {2026},
author = {Jalal, RS and Alshehrei, FM},
title = {Rhizospheric glycosyltransferase repertoires as a resource for enabling sustainable bioprocessing and green biocatalyst discovery.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41803433},
issn = {2045-2322},
support = {UJ-25-DR-1837//University of Jeddah/ ; },
abstract = {UNLABELLED: The rhizospheric microbiomes associated with wild plant species Moringa oleifera and Abutilon fruticosum, endemic to the arid northwestern Mecca region of Saudi Arabia, represent untapped reservoirs of genetic capability with significant implications for agriculture, biotechnology, medicine, and environmental sustainability. Leveraging high-throughput metagenomic sequencing and advanced bioinformatics, this study systematically cataloged carbohydrate-active enzymes (CAZymes), with a particular focus on glycosyltransferase (GT) families, within these root-associated microbial consortia. The analysis revealed pronounced compositional divergence between rhizospheric and bulk soil microbiomes, underscoring the influence of plant species and edaphic factors in shaping niche-specific microbial assemblages and functional repertoires. The two rhizospheric microbiomes were consistently enriched in all six CAZy classes, with lineage-specific CAZymes of GT families (GT2 and GT84 in M. oleifera and GT31, GT39, and GT66 in A. fruticosum). These lineage-specific CAZymes catalyze the synthesis of structurally diverse polysaccharides, including cellulose, chitin, β-glucans, mannans, and chondroitin, thereby positioning the rhizospheric microbiomes of Moringa oleifera and Abutilon fruticosum as promising reservoirs of biocatalysts for possible future applications in industrial applications, biomedical engineering, and environmentally sustainable technologies. The evolutionary history of these enzymes in hot, oligohydric soils suggests adaptation to thermal and water-limited conditions, which may render them particularly suitable for deployment in industrial and biotechnological bioreactors. These CAZymes are predicted to be positioned as pivotal assets for sustainable bioeconomy initiatives and possible therapeutic glycoengineering.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42974-2.},
}

@article {pmid41998767,
year = {2026},
author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD},
title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {41998767},
issn = {1348-8945},
support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.},
}

@article {pmid41998806,
year = {2026},
author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z},
title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.},
journal = {Journal of medical primatology},
volume = {55},
number = {3},
pages = {e70074},
doi = {10.1111/jmp.70074},
pmid = {41998806},
issn = {1600-0684},
support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; },
abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.},
}

Animals
*Macaca mulatta/immunology
*Gastrointestinal Microbiome
*Diarrhea/veterinary/microbiology/immunology
*Monkey Diseases/immunology/microbiology
Longitudinal Studies
Transcriptome
Male
Anti-Bacterial Agents/therapeutic use
Female
Chronic Disease
Multiomics

@article {pmid41999333,
year = {2026},
author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG},
title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02641},
pmid = {41999333},
issn = {1520-5851},
abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.},
}