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

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

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

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

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

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

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

@article {pmid42351291,
year = {2026},
author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y},
title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02448-z},
pmid = {42351291},
issn = {2049-2618},
abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.

RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.

CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.},
}

@article {pmid42351509,
year = {2026},
author = {Wang, M},
title = {Nanopore Sequencing in Mycobacterial Diagnostics: Clinical and Laboratory Roles of mNGS and tNGS.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/diagnostics16121850},
pmid = {42351509},
issn = {2075-4418},
support = {No. 20220919Y060//Hangzhou Science and Technology Commission/ ; },
abstract = {Background/Objectives: Nanopore sequencing is increasingly used in mycobacterial diagnostics, where clinical microbiologists and diagnostic laboratories must decide when broad metagenomic next-generation sequencing (mNGS) or focused targeted next-generation sequencing (tNGS) is most appropriate. This review examined reported clinical and laboratory roles of nanopore mNGS and tNGS in tuberculosis (TB) and nontuberculous mycobacterial (NTM) settings. Methods: Targeted searches of PubMed/MEDLINE, Embase, Web of Science Core Collection, and Scopus were refreshed on 4 April 2026. Thirty-five records spanning original clinical studies, evidence syntheses, and guideline-context documents were included. Results: Nanopore mNGS is most useful for broad organism detection and diagnostic rescue in unresolved pulmonary and extrapulmonary presentations, particularly when first-line testing is negative, discordant, low-yield, or when mixed infection is suspected. Nanopore tNGS appears better aligned with predefined TB confirmation and resistance-focused workflows because targeted regions allow more standardized interpretation. Agreement is strongest for rifampicin- and isoniazid-related resistance targets. In NTM settings, evidence is stronger for detection and species identification than for disease-level diagnosis. Common implementation constraints include pre-analytical variation, contamination control, host-background interference, inconsistent bioinformatics, and limited workforce capacity. Conclusions: A practical tiered approach is supported in which mNGS is positioned mainly for diagnostic rescue and discovery, whereas tNGS is considered for predefined workflows requiring standardized target interrogation and resistance-associated mutation reporting under local validation and quality systems.},
}

@article {pmid42351718,
year = {2026},
author = {Tîrziu, AT and Romanescu, M and Ciordas, PD and Mercea, N and Munteanu, M and Horhat, FG and Chis, AR and Preda, MA},
title = {Metagenomic Profiling of the Gut Microbiome in Age-Related Macular Degeneration-A Pilot Study.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061290},
pmid = {42351718},
issn = {2227-9059},
support = {CNFIS-FDI-2024-F-0451//Consiliul National pentru Finantarea Invatamantului Superior/ ; },
abstract = {Background/Objectives: Age-related macular degeneration (AMD) is a multifactorial retinal disease involving inflammatory, metabolic, and genetic factors. Increasing evidence suggests that the gut microbiome may contribute to systemic pathways involved in retinal homeostasis. This exploratory pilot study investigated gut microbiome alterations in AMD patients and controls using long-read whole-genome sequencing. Methods: Bacterial DNA was extracted from fecal samples and analyzed using Oxford Nanopore sequencing, followed by taxonomic profiling, alpha and beta diversity analyses, and differential abundance testing. Results: AMD patients showed significantly reduced microbial diversity, reflected by lower richness, Shannon and Simpson indices. Species-level beta diversity analyses revealed significant differences in microbial community composition, particularly with Bray-Curtis metrics, alongside increased inter-individual microbial heterogeneity in AMD samples. Differential abundance analyses identified the depletion of several potentially beneficial commensal taxa, including Faecalibacterium prausnitzii and Parabacteriodes distasonis, whereas Staphylococcus aureus was enriched in AMD patients. Comparisons between wet and dry subtypes showed no significant differences in alpha or beta diversity. Conclusions: Overall, the findings support the presence of gut microbial dysbiosis in AMD characterized by reduced diversity, abundance-driven community shifts, and increased microbiome heterogeneity. Given the small cohort size, cross-sectional design and lack of functional analysis, these results should be considered preliminary and hypothesis-generating.},
}

@article {pmid42351858,
year = {2026},
author = {Chen, X and Yuan, H and Li, X},
title = {Methane Yield, Substrate Conversion, Microbial Community Structure and Metabolic Pathways During Anaerobic Digestion of Natural Cellulosic Biomass.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/bioengineering13060613},
pmid = {42351858},
issn = {2306-5354},
abstract = {Three natural celluloses (softwood pulp, straw grass pulp, and degreased cotton) were used for anaerobic digestion tests to research methane yield, substrate conversion and microbial community structure, and further supplemented and clarified the metabolic pathway mechanisms of anaerobic digestion of cellulosic biomass. The results showed that natural cellulose could be significantly degraded and converted into methane by anaerobic microorganisms. The cumulative specific methane yields of wood pulp fiber (F1), straw pulp fiber (F2), and degreased cotton fiber (F3) were 373.57 ± 10.70 mL/g VS, 349.15 ± 13.20 mL/g VS and 346.16 ± 1.60 mL/g VS, respectively. The corresponding biodegradability values were 93.97%, 85.95% and 84.32%. Although the fermentation cycles in F1, F2, and F3 were identical (T95 was 12 days), the three groups exhibited distinct biogas production patterns. Metagenomic analysis indicated that F1 and F2 were dominated by the acetoclastic methanogenesis pathway, while the proportion of the hydrogenotrophic methanogenesis pathway increased in F3. Meanwhile, the cell motility pathway category was significantly enriched in F3. These results supplement the existing research on the anaerobic digestion of natural cellulose and provide theoretical support for the efficient anaerobic bioconversion of natural cellulosic biomass.},
}

@article {pmid42352020,
year = {2026},
author = {Zhang, BY and Wang, YQ and Yang, R and Zhang, Y and Jiang, DZ and Ji, LH and Mao, YF and Tang, B and Zhang, XM},
title = {Gut Microbiota-Mediated Histidine Deficiency Drives Testicular Ferroptosis Induced by Bisphenol F Exposure.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/antiox15060714},
pmid = {42352020},
issn = {2076-3921},
support = {No. 32573319 and No. 32172803//National Natural Science Foundation of China/ ; },
abstract = {Bisphenol F (BPF), a widespread environmental contaminant and a major substitute for the restricted bisphenol A (BPA), has raised increasing concerns regarding its potential male reproductive health risks, yet its underlying mechanisms remain poorly understood. This study investigates the mechanisms underlying BPF-induced testicular damage, focusing on the interplay among gut microbiota (GM) dysbiosis, histidine metabolism disruption, and ferroptosis. Using a mouse model exposed to BPF (50, 100, and 200 mg/kg/day) for 28 days, we observed significant testicular pathology, including seminiferous tubule atrophy, vacuolation, and blood-testis barrier (BTB) impairment. Metagenomic and metabolomic analyses revealed GM dysbiosis and suppressed intestinal histidine metabolism, accompanied by decreased abundance of beneficial taxa (e.g., Bacteroides, Ligilactobacillus) and increased potential pathobionts (e.g., Akkermansia, Mucispirillum). BPF exposure was associated with reduced testicular histidine levels and decreased expression of the histidine transporter-related marker LAT1, suggesting impaired histidine availability and a possible alteration in LAT1/CD98-mediated transport; however, direct inhibition of LAT1/CD98 transport activity was not experimentally demonstrated. BPF exposure was accompanied by ferroptosis-related alterations in the testes, including mitochondrial damage, iron accumulation, lipid peroxidation, and downregulation of the xCT-GSH-GPX4 antioxidant axis. In vitro experiments using mouse Sertoli cells (mSCs) confirmed BPF-induced ferroptosis, which was mitigated by the exogenous histidine supplementation. Histidine administration in vivo ameliorated testicular damage, restored BTB integrity, and reversed ferroptotic markers. Our findings support a working model in which a GM-histidine-testis axis may contribute to BPF-induced reproductive toxicity, while further functional studies are required to establish direct causality and transporter-level mechanisms.},
}

@article {pmid42352268,
year = {2026},
author = {Tita, GV and Fogas, CR and Slavescu, KC and Tantau, VM and Medan, SA and Serban, DE},
title = {Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study.},
journal = {Biomolecules},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/biom16060801},
pmid = {42352268},
issn = {2218-273X},
mesh = {Humans ; *Crohn Disease/microbiology ; *Dysbiosis/microbiology/genetics ; Pilot Projects ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics ; *High-Throughput Nucleotide Sequencing ; Prospective Studies ; Adolescent ; Metagenomics ; Eubacteriales ; },
abstract = {Background: Crohn's disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.},
}

Humans
*Crohn Disease/microbiology
*Dysbiosis/microbiology/genetics
Pilot Projects
Female
Male
Child
*Gastrointestinal Microbiome/genetics
*High-Throughput Nucleotide Sequencing
Prospective Studies
Adolescent
Metagenomics
Eubacteriales

@article {pmid42352384,
year = {2026},
author = {Brown, JL and Mahadevan, P and Middlebrooks, M},
title = {Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea Slug Elysia papillosa.},
journal = {Biomolecules},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/biom16060918},
pmid = {42352384},
issn = {2218-273X},
support = {OURI//University of Tampa/ ; },
mesh = {Animals ; *Gastropoda/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Phylogeny ; },
abstract = {Certain sacoglossan sea slugs, often known as "solar-powered sea slugs", are a group of marine gastropods that have the unique ability to photosynthesize by stealing functional chloroplasts from algae. The sacoglossan Elysia papillosa can maintain functional chloroplasts for up to two weeks after feeding. The microbiome of these slugs may play a crucial role in their metabolism, immunity, development, but more importantly their photosynthesis. Shotgun metagenomic sequencing was conducted on four samples of E. papillosa in order to characterize their microbiome. Sequences were classified and relative abundance was quantified with Centrifuger and functional data was examined using SqueezeMeta. Bacteria were analyzed by taxonomic groups and hypothesized function to the sea slug was determined with literature analysis. All samples were dominated by phyla Actinomycetota, Bacillota, Patescibacteriota, and Pseudomonadota. The presence of the phyla Bacteroidota and Bacillota was notable in all samples, which contain species known to produce enzymes that break down polysaccharides. It is possible that these bacteria could assist in degradation of the polysaccharide xylan found in the cell walls of Penicillus, the algal food source of E. papillosa. One species that was found in all samples was Cutibacterium acnes which has been shown to be an important component of the gut microbiota in other marine invertebrates and may provide the host with vitamin B12 and other beneficial nutrients. Many of these bacteria may be opportunistic rather than commensal. As a result, more research is required to describe the interactions between the slug and its microbiome, but this preliminary report provides a valuable starting point for identifying the microbiome make-up to further understanding of these relationships.},
}

Animals
*Gastropoda/microbiology
*Microbiota
*Bacteria/genetics/classification
Phylogeny

@article {pmid42353029,
year = {2026},
author = {Xu, HJ and Liu, QL and Zhang, YF and Cuan, SN and Jia, Z and Qiao, D},
title = {Metagenomic Insights into Gut Microbiota Alterations Following Dendrobium huoshanense Water Extract Intervention in Streptozotocin-Induced Type 1 Diabetic Rats.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
doi = {10.3390/ijms27125308},
pmid = {42353029},
issn = {1422-0067},
support = {no//the platform of the Traditional Chinese Medicine Institute of Anhui Dabie Mountain/ ; },
mesh = {Animals ; *Dendrobium/chemistry ; Rats ; *Plant Extracts/pharmacology/chemistry ; *Diabetes Mellitus, Experimental/drug therapy/microbiology ; *Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; Male ; Metagenomics/methods ; *Hypoglycemic Agents/pharmacology ; Rats, Sprague-Dawley ; Streptozocin ; Water/chemistry ; Metagenome ; },
abstract = {Dendrobium huoshanense water extract (DHWE) exhibits hypoglycemic effects in streptozotocin-induced type 1 diabetic (STZ-T1D) rats. However, its regulatory impact on the gut microbiota of T1D rats remains largely unclear. In this study, metagenomic sequencing was employed to characterize alterations in the gut microbiota of STZ-T1D rats following DHWE intervention, aiming to explore associations between DHWE-mediated gut microbial changes and T1D-related phenotypes. The results showed that 1300 mg/kg·BW/day DHWE did not significantly affect gut microbial α-diversity (p > 0.05), but drove the β-diversity structure toward that of normal rats. Meanwhile, DHWE significantly reduced the Bacteroidota/Bacillota ratio (p < 0.05), Megamonas (p < 0.01), Megamonas funiformis (p < 0.01), and notably increased the relative abundances of Adlercreutzia (p < 0.01), Adlercreutzia equolifaciens (p < 0.01) in STZ-T1D rats. Furthermore, functional annotation revealed that DHWE enriched multiple metabolic pathways, including streptomycin biosynthesis, ansamycins biosynthesis, galactose metabolism, ether lipid metabolism, and caprolactam degradation. Collectively, these findings demonstrate that DHWE reshapes gut microbiota composition and function in STZ-T1D rats, offering new clues regarding how gut microbial changes may contribute to the modulatory effects of Dendrobium huoshanense in T1D conditions.},
}

Animals
*Dendrobium/chemistry
Rats
*Plant Extracts/pharmacology/chemistry
*Diabetes Mellitus, Experimental/drug therapy/microbiology
*Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced
*Gastrointestinal Microbiome/drug effects
Male
Metagenomics/methods
*Hypoglycemic Agents/pharmacology
Rats, Sprague-Dawley
Streptozocin
Water/chemistry
Metagenome

@article {pmid42353070,
year = {2026},
author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Koralnik, IJ},
title = {Cross-Compartment Virome Profiling in Human Immunodeficiency Virus Infection and Substance Use Disorder Reveals Brain-CSF-Periphery Discordance and Hepatitis B Virus in Central Nervous System.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
doi = {10.3390/ijms27125349},
pmid = {42353070},
issn = {1422-0067},
mesh = {Humans ; *Brain/virology ; *HIV Infections/virology/cerebrospinal fluid/complications ; *Substance-Related Disorders/virology/cerebrospinal fluid/complications ; *Virome ; *Hepatitis B virus/genetics/isolation & purification ; Female ; *Central Nervous System/virology ; Male ; *Hepatitis B/virology/cerebrospinal fluid ; Viral Load ; Adult ; },
abstract = {The diversity and abundance of the brain virome is an active field of investigation. However, how the brain virome relates to the presence of viruses outside of the nervous system remains unclear. The rationale for this study is that analyses across multiple biologically linked compartments within the same individuals provide an important opportunity to evaluate virome discordance and viral burden. To characterize viral prevalence and burden across anatomical compartments, we applied the targeted viral enrichment method ViroFind to matched postmortem brain (n = 66), cerebrospinal fluid (CSF; n = 24), and peripheral samples (spleen, peripheral blood mononuclear cells, and lymph nodes; n = 66) from individuals with and without human immunodeficiency virus (HIV) infection and substance use disorder (SUD) in the National NeuroAIDS Tissue Consortium. We detected nucleic acids from 27 viruses representing 12 taxa. Several viruses, including adenovirus, torque teno virus, Epstein-Barr virus, human herpesvirus 6 and 7, cytomegalovirus, parvovirus, and JC polyomavirus, showed significant inter-compartment differences in prevalence or burden. CSF exhibited lower overall viral diversity than brain or peripheral samples, whereas peripheral samples showed the highest viral burden. CNS viral detection was more likely when the same virus was also detected in the periphery. We also detected HBV and HCV in CNS samples despite them not being classically regarded as neurotropic. Broader virome profiling showed greater peripheral viral burden and diversity in HIV-positive than HIV-negative individuals, whereas SUD was not associated with overall viral burden differences. These findings highlight important cross-compartment differences in viral detection, including occurrence of occult HBV infection within the CNS, and support the value of CNS-periphery comparisons in virome studies. These findings can contribute to improved diagnosis and management of viral infections.},
}

Humans
*Brain/virology
*HIV Infections/virology/cerebrospinal fluid/complications
*Substance-Related Disorders/virology/cerebrospinal fluid/complications
*Virome
*Hepatitis B virus/genetics/isolation & purification
Female
*Central Nervous System/virology
Male
*Hepatitis B/virology/cerebrospinal fluid
Viral Load
Adult

@article {pmid42353346,
year = {2026},
author = {Wang, Y and Han, Y and Wang, C and Wang, Z and Guan, Z and Li, N and Pan, J},
title = {Microbial Contamination, Degradation Characteristics of Dominant Bacteria on the Hull of the Nanhai No. 1 Shipwreck.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
doi = {10.3390/ijms27125631},
pmid = {42353346},
issn = {1422-0067},
mesh = {*Wood/microbiology/metabolism ; *Bacteria/isolation & purification/genetics/classification/metabolism ; Biodegradation, Environmental ; Anti-Bacterial Agents/pharmacology ; },
abstract = {To clarify the microbial contamination and wood degradation risk of the Nanhai No. 1 shipwreck hull and verify on-site antibacterial agent effectiveness, microbial samples were collected and analyzed via SEM, metagenomic sequencing, bacterial isolation, enzyme activity detection, and antibacterial experiments. The results showed that Actinomycetota was the dominant phylum, and Brachybacterium, Microbacterium, and Brevibacterium were the dominant genera. Seven bacterial strains were isolated and purified, among which Brevibacterium sp. (NH.SH-B6) had the strongest wood degradation ability, possessing cellulase, LiP, MnP, and Lac activities. When cultured with hull wood as the sole carbon source, LiP was the dominant degrading enzyme of NH.SH-B6, and its maximum enzyme activity was achieved under the optimal conditions of pH = 7, 10% NaCl, 1000 mg/L FeSO4, and no PEG400 added. 50 mg/mL cinnamaldehyde and 0.5% isothiazolinone K100 had good inhibitory effects on the isolated bacteria, and bacterial proliferation was due to incomplete antibacterial agent spraying. This study clarifies the microbial degradation risk of the Nanhai No. 1 shipwreck hull and provides a scientific basis for optimizing the on-site protection strategy of the shipwreck.},
}

*Wood/microbiology/metabolism
*Bacteria/isolation & purification/genetics/classification/metabolism
Biodegradation, Environmental
Anti-Bacterial Agents/pharmacology

@article {pmid42353397,
year = {2026},
author = {Walther, B and Bouilloux, F and Vayer, P and Douablin, A and Walther, F},
title = {An Ecological Framework for Interpreting the Canine Gut Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/ani16121787},
pmid = {42353397},
issn = {2076-2615},
abstract = {The intestinal microbiome is increasingly recognized as an important determinant of canine gastrointestinal health. However, interpreting microbiome sequencing data remains challenging because most analytical approaches rely on taxonomic descriptions, alpha diversity indices, or dysbiosis indices derived generally from a limited number of microbial ecological interpretation targets. While shotgun metagenomic approaches increasingly allow the identification of microbial communities, such analyses remain costly and are not yet widely accessible in routine veterinary settings. The objective of this study was to develop an integrative interpretation framework based on widely accessible biomarkers combining fecal calprotectin and 16S rRNA gene sequencing data. These data enabled the generation of complementary ecological dimensions of gut microbiome organization: biological inflammation assessed through fecal calprotectin, microbiological inflammatory pressure estimated through a Microbiological Inflammatory Score (MIS), and microbiome stability measured by a Microbiome Resilience Score (MRS) derived from alpha diversity, functional balance, and dominance structure. Fecal microbiome profiles obtained by 16S rRNA gene sequencing were analyzed in a real-life cohort of privately owned dogs. Alpha diversity, taxonomic weighting, abundance-dependent dominance rules, beta diversity based on Bray-Curtis dissimilarity, distance to a reference microbiome core, and a 16S-derived dysbiosis score were integrated into a multidimensional interpretation model. Strong ecological associations were observed between resilience, microbial diversity, and dysbiosis-related metrics. Microbiome resilience strongly correlated with Shannon diversity (Spearman ρ = 0.98, p < 0.001), while the reconstructed 16S-derived dysbiosis score showed a more moderate positive correlation with MIS (Spearman ρ = 0.41, p = 0.004), supporting the partially independent ecological dimensions captured by the framework. The results revealed a continuum ranging from stable microbiomes to inflammatory dysbiosis. Most dogs clustered near a reference microbiome core characterized by low microbiological inflammatory pressure and high resilience, whereas a subset of microbiomes showed elevated MIS values, reduced resilience, increased compositional distance from the reference core, and higher dysbiosis index values. These findings support the value of a multidimensional experimental framework integrating inflammation, dysbiosis, and resilience to improve interpretation of canine microbiome profiles under real-life conditions.},
}

@article {pmid42353476,
year = {2026},
author = {Kiani, A and Jurgens, G and Gonzalez-Ortiz, G and Walk, CL and Rinttilä, T},
title = {Investigation of the Effect of TiO2 as a Dietary Marker on Broiler Intestinal Fermentation: Combination of Ex Vivo Simulation and In Vivo Approach.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/ani16121867},
pmid = {42353476},
issn = {2076-2615},
abstract = {The impact of dietary inert digestibility markers on gut microbiota and intestinal fermentation remains poorly understood. This study investigated the effects of dietary titanium dioxide (TiO2) supplementation at 4 kg/t feed, representing a typical dose used in animal nutrition studies, on fermentation dynamics and microbial composition in broiler chickens using combined ex vivo and in vivo approaches. Ex vivo fermentations were conducted using ileal and caecal microbiota and substrates collected from 32-day-old broiler chickens. Titanium dioxide (TiO2) was supplemented directly to the fermentations, and gas production and short-chain fatty acid (SCFA) profiles were used as the main outcome measures. In parallel, 392 broiler chickens were fed diets with or without TiO2 for 32 days, and ileal and caecal digesta were analysed for fermentation end-products and microbial composition using shotgun metagenomic sequencing. A second ex vivo experiment was performed using microbiota adapted to dietary TiO2. In the first ex vivo model, TiO2 reduced gas production and acetic acid concentration in the ileum (p < 0.05), whereas in the caecum it increased gas production, total eubacterial counts, and branched-chain fatty acids (BCFAs) (p < 0.05). In vivo, TiO2 did not affect growth performance or organ development but significantly increased isobutyric acid and total BCFA concentrations in the caecum (p < 0.05). Metagenomic analysis revealed increased caecal alpha diversity (Shannon index) and enrichment of taxa associated with amino acid metabolism, including Massilicoli timonensis, Blautia merdavium, Rubneribacter badeniensis, and Mediterraneibacter caccavium. The second ex vivo experiment showed similar trends, with increased gas and BCFA production. Collectively, these findings indicate that TiO2 can modulate intestinal fermentation and microbial composition in a segment-specific manner, suggesting that dietary markers may not be biologically inert.},
}

@article {pmid42353508,
year = {2026},
author = {Shi, K and Zhou, X and Li, K and Dai, J and Shen, Y and Wu, Z and Zhang, X and Yu, Q and Chen, S},
title = {Multi-Omics Analysis Reveals the Gut-Mediated Mechanism Underlying the Seasonal Non-Laying Phenotype in Zhedong White Geese (Anser cygnoides domesticus).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/ani16121899},
pmid = {42353508},
issn = {2076-2615},
abstract = {As a precious indigenous goose resource in China, the Zhedong white goose occupies an essential position in the domestic goose industry. However, this breed spontaneously enters a prolonged non-laying period of over two months per year, which greatly limits egg production capacity and restricts the economic development of the goose industry. Herein, this study systematically compared serum physiological indices and serum and fecal metabolome, as well as fecal microbial communities, between laying and non-laying Zhedong white geese, aiming to reveal the key regulatory mechanisms underlying reproductive stage transition. Physiological analyses indicated that non-laying geese had higher serum levels of GnRH, PRL, APOA, and T-AOC, whereas the concentrations of LH, E2, TNF-α, IL-1, and calcium were significantly reduced; FSH, PROG, and BA levels showed no significant differences between the two groups. Metabolomic analysis identified 277 upregulated and 403 downregulated DAMs in feces, and 386 DAMs in serum. The shared enriched pathways across serum and fecal samples encompassed arginine biosynthesis, histidine metabolism, and pantothenate and CoA biosynthesis, as well as steroid hormone biosynthesis. A total of 120 DAMs overlapped in two specimens, and the non-laying geese presented pronounced depletion of tryptophan-derived metabolites and steroid hormone-related metabolites. Metagenomic results showed no significant difference in gut microbial alpha diversity between groups, while their microbial community structures were clearly differentiated. A total of 774 upregulated and 854 downregulated microbial species were screened in non-laying geese, and these differential microbes were primarily enriched in pathways associated with reproductive hormone signaling, steroid biosynthesis and energy metabolism. Multi-omics correlation analysis verified close associations between differential microbes and reproductive-related metabolites. Certain probiotic strains, including Pediococcus pentosaceus and Lactococcus raffinolactis, were positively correlated with steroid hormones and tryptophan metabolites, and their abundances declined obviously in the non-laying stage. Collectively, this study elaborates the holistic changes in serum biochemistry, gut metabolome and microbiome in geese at different reproductive stages. The dysregulation of amino acid and steroid hormone metabolism, combined with the loss of beneficial intestinal microbes, jointly induces the non-laying phenotype. This study provides new perspectives for understanding the gut-reproductive axis and supplies promising biomarkers to improve the laying performance of geese.},
}

@article {pmid42353537,
year = {2026},
author = {Liu, Y and Zhang, G and Gao, H and Fang, M and Jiang, L and Kong, Y and Liu, Q and Wang, P and Zhang, S and Li, Y},
title = {Metavirome Analysis of Viruses Carried by Dairy Cows in Shaanxi, Gansu and Ningxia, China.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/ani16121928},
pmid = {42353537},
issn = {2076-2615},
support = {32130104//National Natural Science Foundation of China/ ; 2023BCF01038, 2024BBF02017//the Ningxia Hui Autonomous Region Key R&D Projects/ ; },
abstract = {Dairy cows are economically significant ruminants in China, and the dairy industry is closely linked to food safety and the agricultural economy. However, various factors such as pathogenic microorganisms often lead to frequent diseases in dairy cows. Furthermore, as potential hosts for diverse viruses, dairy cows can harbor zoonotic pathogens, which pose a threat to public health. The Shaanxi-Gansu-Ningxia region boasts abundant natural resources and extensive pastures. It is a major animal husbandry base in Northwest China, and dairy farming plays a significant role in the local economy. However, research on dairy cow virus diversity in this region remains limited; epidemic prevention and control capabilities are constrained, and the risk of disease outbreaks is elevated. In this study, 790 dairy cow samples were collected from 13 large-scale farms and free-range households in the Shaanxi-Gansu-Ningxia region from 2021 to 2023. Sample types consisted of nasal and anal swabs. Six viral metagenomic libraries were constructed and analyzed using high-throughput sequencing and bioinformatics methods, leading to the identification of 51 viral families. These comprised 16 positive-sense single-stranded RNA virus families, one Retroviridae family, four double-stranded RNA virus families, 21 double-stranded DNA virus families, and nine single-stranded DNA virus families. Among these, RNA viruses were represented by families such as Astroviridae, Coronaviridae, Caliciviridae, Picornaviridae, and Picobirnaviridae; DNA viruses were primarily detected in Circoviridae, Papillomaviridae, Genomoviridae, and Smacoviridae. Alpha diversity analysis revealed no significant differences in viral diversity and abundance among the three regions (p > 0.05); however, significant differences were observed in the read counts and proportions of RNA and DNA viruses across the provinces. Phylogenetic analysis further indicated that viruses carried by dairy cows exhibit considerable genetic diversity and pose potential cross-species transmission risks. This study established a reference database for the dairy cow virome in the Shaanxi-Gansu-Ningxia region, elucidated the phylogenetic relationships of key viruses, and provided a scientific basis for future monitoring and prevention of dairy cow viruses.},
}

@article {pmid42353547,
year = {2026},
author = {Liu, L and Narrowe, AB and Firrman, J and Mahalak, KK and Chetty, VJ and Lemons, JMS and Baudot, A and Van den Abbeele, P},
title = {Perfluorooctanoic Acid (PFOA) Alters the Structure of the Gut Microbial Community and Colonoid Transcription.},
journal = {Current issues in molecular biology},
volume = {48},
number = {6},
pages = {},
doi = {10.3390/cimb48060542},
pmid = {42353547},
issn = {1467-3045},
support = {8072-41000-108-00-D//United States Department of Agriculture/ ; },
abstract = {Perfluorooctanoic acid (PFOA) is an environmentally persistent chemical that enters the gastrointestinal tract (GIT) via the food chain, posing a harmful, long-term threat to human health. In response to this challenge, research on the PFOA-GIT interaction is thriving. Currently, studies on the effect of PFOA on the epithelial cells of the GIT and those on its influence on the microbial community are often implemented separately, and less attention has been paid to the combinational effects of the chemical, the gut microbiome and metabolome. In the present study, we co-cultured fecal samples from healthy adults aged 25-70 in the ex vivo SIFR[®] simulator, adding PFOA at 10 mg/L to represent the accumulated effects of long-term exposure. The results obtained from bacterial cell counting by flow cytometry and shotgun metagenomic sequencing revealed that PFOA was broadly disruptive to the microbiome and that Pseudomonadota emerged as the dominant phylum by replacing Bacteriodota and Bacillota, including key members of short-chain fatty acid-producing groups. Bacterial culture media with and without PFOA were collected and used in human colonoid cell culture for TEER and transcription measurement. It was shown that the PFOA-impacted microbial culture had stronger effects on the cell's protective functions, in terms of tissue junction tightening, mucin biosynthesis, and immune response, than either untreated bacterial culture or PFOA alone. The results point out the possibility that the combination of PFOA and PFOA-impacted bacterial metabolites more strongly induces a change in epithelial cells' protective function than either one alone.},
}

@article {pmid42353629,
year = {2026},
author = {Iorizzo, M},
title = {Microbial α-L-Rhamnosidases: Regioselective Biocatalysts for Flavonoid Biotransformation and Nutraceutical Applications.},
journal = {Current issues in molecular biology},
volume = {48},
number = {6},
pages = {},
doi = {10.3390/cimb48060625},
pmid = {42353629},
issn = {1467-3045},
abstract = {Microbial α-L-rhamnosidases are increasingly recognised as selective biocatalysts in food biotechnology, nutraceutical production, and health-related applications. These glycoside hydrolases catalyse the hydrolysis of terminal alpha-L-rhamnose residues from flavonoids, terpenoids, saponins, and other glycosylated natural products, thereby modulating sensory properties, solubility, intestinal absorption, and biological activity. While their traditional uses include debittering citrus juice and enhancing wine aroma, recent evidence demonstrates their wider value in selective flavonoid biotransformation, production of rare mono-glycosylated derivatives, probiotic fermentations, and microbiome-associated metabolism. This review summarises microbial sources, catalytic mechanisms, CAZy classification, substrate specificity, structure-function relationships, analytical methods, industrial process engineering, and emerging applications in functional foods and targeted nutraceutical applications. Particular attention is given to the distinction between alpha-(1→2)- and alpha-(1→6)-linked substrates, the production of isoquercitrin and prunin, recombinant enzyme platforms, immobilised biocatalysts, and potential future opportunities arising from metagenomics, synthetic biology, and AI-assisted protein engineering.},
}

@article {pmid42353668,
year = {2026},
author = {Kerek, Á and Husz, LH and Szarka, E and Tornyos, GÁ and Jerzsele, Á},
title = {Integrated Phenotypic and Sequencing-Based Resistome Assessment of Antimicrobial Resistance Determinants in a Sample of Commercial Farm-Animal Probiotic Products.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/antibiotics15060544},
pmid = {42353668},
issn = {2079-6382},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; },
abstract = {Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6')-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome-mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings.},
}

@article {pmid42353692,
year = {2026},
author = {Elton, L and Lutimba, S and Mateos, AD and Frosini, SM and Jepson, R and Williams, A and Ali, S and Heaphy, J and Pang, V and Commins, L and O'Brien, C and Yetiş, Ö and Caine, E and Ward, I and Muzslay, M and Yui, S and Karia, K and Shore, E and Rofael, S and Mack, D and Atkinson, C and McHugh, TD and Wey, EQ},
title = {Comparison of Environmental Microbiomes, Resistomes and Plasmidomes from a Human Tertiary Hospital and Companion Animal Veterinary Hospital in London, UK.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/antibiotics15060568},
pmid = {42353692},
issn = {2079-6382},
support = {N/A//Royal Free London NHS Foundation Trust/ ; },
abstract = {Background: Human hospitals and veterinary centres are hotspots for resistant microbes and plasmids, and metagenomic sequencing offers an agnostic insight into microbiomes, resistomes, and mobilomes, informing strategies for reducing AMR spread. Methods: Environmental samples, including wastewater and surface swabs, were taken from a tertiary human hospital ward (36 samples) and a companion animal veterinary hospital (48 samples) in London. Whole DNA was extracted and metagenomic sequencing undertaken using Oxford Nanopore Technologies' MinION. Data were analyzed for microbiomes, resistomes and mobilomes and compared. Results: Microbial diversity analyses highlight higher richness across human hospital (HH) environmental samples, but more evenness in veterinary hospital (VH) environmental samples. Diversity showed distinct microbial communities in the HH and VH samples. There were significantly more total antimicrobial resistance gene (ARG) types (p < 0.0001) in the environmental HH samples compared with the environmental VH samples. There was a significantly higher mean number of Enterobacteriales plasmid types (p ≤ 0.0001) in the HH samples. There were significantly more total Gram-Positive plasmid types (p ≤ 0.0001) in the VH samples. Discussion: This research highlights the presence of human and animal pathogens, ARGs and mobile genetic elements in clinical environments, underscoring the importance of multisectoral surveillance. Integrating taxonomic, resistome, and mobilome analyses provides a better understanding of the potential for AMR dissemination at the human-animal-environment interface. This provides insights relevant for the development of targeted surveillance and mitigation strategies within a OH framework.},
}

@article {pmid42353998,
year = {2026},
author = {Margasoiu, I and Pînzariu, AC and Manole, LM and Spoială, EL and Păduraru, G and Ghiga, G and Popa, IP and Șerban, DN and Șerban, IL and Trandafir, LM},
title = {Gut Microbiome Responses to Nutritional and Lifestyle Interventions in Pediatric Obesity: A Systematic Review Toward Precision Nutrition.},
journal = {Children (Basel, Switzerland)},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/children13060828},
pmid = {42353998},
issn = {2227-9067},
support = {SMIS code 351058//Grigore T. Popa University of Medicine and Pharmacy/ ; },
abstract = {Background: Childhood obesity is increasingly associated with gut microbiome dysbiosis. This systematic review (PROSPERO CRD420251131354) evaluates evidence from studies published between 2020 and 2026 assessing how nutritional and lifestyle interventions influence gut microbiota in children with obesity. Methods: A systematic search of PubMed, EMBASE and EBSCO identified 21 interventional studies involving children aged 5-18 years with obesity, with the last search conducted in April 2026. Interventions comprised prebiotics, probiotics, synbiotics, postbiotics, high-fiber diets, calorie-restricted dietary approaches, and lifestyle modifications such as physical activity. Microbiome outcomes were analyzed using 16S rRNA sequencing, quantitative real-time polymerase chain reaction (qPCR), or metagenomics. Risk of bias was evaluated using the RoB 2 and ROBINS-I (version 2) tools. Due to substantial heterogeneity in study design, participant characteristics, intervention types, and analytical methods, a meta-analysis was not feasible. Results: Across 21 studies, nutritional interventions included measurable but heterogeneous alterations in gut microbiome composition. Inulin supplementation was associated with a significant increase in alpha diversity and with higher relative abundances of Bifidobacterium, Blautia, Megasphaera, Subdoligranulum, and Eubacterium coprostanoligenes. Synbiotic supplementation increased Prevotella and Dialister and reduced the Firmicutes/Bacteroidetes ratio. High-fiber dietary interventions increased Faecalibacterium, Bifidobacterium, and Clostridium, while reducing Bacteroides, and were associated with shifts in metabolic pathways related to carbohydrate, lipid, and nucleotide metabolism. Calorie-restricted diets and combined diet-exercise interventions increased beneficial taxa such as Akkermansia muciniphila, improved microbial diversity, and correlated with favorable metabolic and anthropometric outcomes. Overall, nutritional and lifestyle interventions in pediatric obesity were associated with taxon-specific and context-dependent microbiome changes, rather than uniform restructuring. Conclusions: Nutritional interventions can modulate gut microbiota diversity, composition, and predicted function in pediatric obesity; however, the observed effects vary substantially across studies. The limited number of trials, small sample sizes, and methodological heterogeneity underscore the need for larger, standardized studies to better define clinical and therapeutic implications.},
}

@article {pmid42354149,
year = {2026},
author = {Bai, F and Cai, C and Zhang, T and Xu, L and Liu, Y and Liu, R and Ma, Z and Jiang, M and Gao, J and Zhang, J and Yu, X and Tang, T and Chen, J and Yao, S},
title = {Comparative Analysis of Microbial Community Structure and Functional Traits of Baijiu Daqu Across Diverse Geographical Regions in China.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/foods15122182},
pmid = {42354149},
issn = {2304-8158},
support = {YQY25-SW-210//China National Research Institute of Food and Fermentation/ ; ZQ2023JC-GC03//Science and Technology Innovation Program of Sinolight Corporation/ ; },
abstract = {Daqu is a key starter used in Baijiu production, and its microbial composition and associated metabolic functions play critical roles in fermentation performance and flavor development. This work aimed to reveal how Daqu-making temperature regulates microbial community divergence and subsequent metabolite formation via multi-omics analysis so as to provide theoretical guidance for Daqu quality control. In this study, physicochemical analysis, metagenomic sequencing, and metabolomic profiling were combined to investigate the microbial community structure, functional differentiation, and metabolite characteristics of nine Daqu samples collected from six major Baijiu-producing regions in China. The temperature during Daqu preparation was found to be a primary factor driving microbial community assembly and functional specialization. Medium-temperature Daqu exhibited higher saccharifying activity (up to 867 U) and greater microbial diversity with the enrichment of amino acid metabolism-related pathways, indicating enhanced protein degradation and amino acid utilization for the formation of flavor precursors. In contrast, high-temperature Daqu showed stronger capacities for carbohydrate degradation and conversion, particularly in starch and sucrose metabolism, which were closely associated with the enrichment of thermotolerant fungi and bacteria. LEfSe analysis identified 47 distinct microbial biomarkers (LDA score > 3.0), which could differentiate between medium- and high-temperature Daqu. Redundancy analysis indicated that environmental factors (moisture and acidity) together with functional properties (fermentation, esterification, liquefaction, and saccharification) act as key drivers of microbial functional patterns. Metabolomic analysis further revealed that medium-temperature Daqu had higher abundances of esters and fatty acids, whereas high-temperature Daqu had higher proportions of alcohols and ketones. Taken together, these results provide a multi-omics perspective on temperature-driven microbial functional differentiation in Daqu and offer a scientific basis for quality-oriented regulation and process optimization in Baijiu production.},
}

@article {pmid42354792,
year = {2026},
author = {Pan, Z and Bao, J and Liu, X and Ge, G and Zhao, M},
title = {Metagenomic Insights into Regional Differences in the Rhizosphere Microbial Communities of Stellera chamaejasme L. in Inner Mongolia.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061167},
pmid = {42354792},
issn = {2076-2607},
support = {CARS-34//China Agriculture Research System/ ; },
abstract = {Rhizosphere microorganisms are important components of grassland ecosystems, but the rhizosphere microbiome of the poisonous and medicinal plant Stellera chamaejasme L. remains poorly characterized. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition, community structure, differentially enriched taxa, and KEGG-based functional potential of rhizosphere microbial communities associated with S. chamaejasme from three typical steppe regions in Inner Mongolia. Acidobacteria, Proteobacteria, and Actinobacteria were the dominant phyla, while Sphingomonas, Bradyrhizobium, and Streptomyces were among the dominant genera. Genus-level profiles and ordination analysis showed region-associated community patterns, and rarefaction curves indicated that sequencing depth was sufficient to capture most detectable taxa. LEfSe analysis identified region-associated differentially enriched taxa, including Sphingomonas-, Bradyrhizobium/Nitrospira-, and Streptomyces/Solirubrobacter-associated taxa. KEGG annotation suggested broadly similar major functional categories across regions, with some differences in the relative abundance of metabolic pathways. These results provide baseline metagenomic information on S. chamaejasme rhizosphere communities. Because of the limited replication and lack of soil physicochemical measurements, ecological mechanisms should be tested in future studies.},
}

@article {pmid42354802,
year = {2026},
author = {Hao, D and Yu, X and Sun, X and Cheng, D and Ding, H and Wang, Y and Li, Y and Geng, Z and Xu, G},
title = {Thermophilic Microbial Inoculant Promotes Lignocellulose Degradation During Green Waste Composting.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061177},
pmid = {42354802},
issn = {2076-2607},
support = {PTYX202514//Fundamental Research Funds for the Central Universities/ ; Liao[2025]TG03//China Central Financial Forestry and Grassland Science and Technology Promotion Demonstration Project/ ; },
abstract = {Thermophilic microbial inoculant (CI) has been demonstrated to optimize the green waste composting (GWC) process. The pathways through which it enhances lignocellulose degradation remain unclear. This study evaluated composting performance under four treatments: CI, effective microorganisms (EM), Phanerochaete chrysosporium (WF), and natural composting (CK). To elucidate the biological differences between efficient lignocellulose-degrading systems and CK, metagenomic analyses were conducted on CI and CK based on lignocellulose degradation rates. The results indicated that CI inoculation did not negatively affect the compost heating process and produced a nitrogen-rich, safe, and mature compost product. Compared to other treatments, CI increased the lignocellulose degradation rate by 3.66% to 31.8%. Metagenomic analysis revealed that CI inoculation enriched genes encoding glycoside hydrolases (GHs), glycosyl transferases (GTs), carbohydrate esterases (CEs), and carbohydrate-binding modules (CBMs) across multiple composting phases, positively impacting dominant carbohydrate-active enzyme (CAZyme) families including AA3, CE1, and CE7. CI inoculation also elevated the relative abundance of lignocellulose-degrading microorganisms (0.70~2.73%), simplified microbial network structure, and strengthened microbial cooperation. Within the microbial network, Chryseolinea, Protaetiibacter, and unclassified_f__Burkholderiaceae were identified as core taxa involved in lignocellulose degradation. Redundancy analysis (RDA) identified temperature as the primary factor influencing biological factors, with CI improving composting efficiency by optimizing the microenvironment. Collectively, this work provides a novel strategy for microbial inoculant application in composting and offers new perspectives for identifying core taxa, contributing to advancing composting efficiency.},
}

@article {pmid42354818,
year = {2026},
author = {Yang, Z and Xv, W and Cai, Y and Gu, H and Feng, Y},
title = {Long-Term Application of Fermented Fertilizer Attenuates the Accumulation of Antibiotic Resistance Genes in Aquaculture Sediment.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061193},
pmid = {42354818},
issn = {2076-2607},
abstract = {Aquaculture sediments are increasingly recognized as important reservoirs of antibiotic resistance genes (ARGs). Although thermophilic fermentation is widely used to reduce ARGs and pathogens in manure, most biosafety assessments stop at the fertilizer product itself, leaving unresolved whether these benefits persist after application to aquaculture sediments. Here, we compared inorganic fertilizer (IF), raw manure (RM), and fermented fertilizer (FF) to test whether fermentation confers sustained biosafety benefits in aquaculture pond sediments. After a 6-month co-culture period, sediment samples were analyzed using shotgun metagenomic sequencing, ARG and mobile genetic element (MGE) profiling, antibiotic residue determination, and network analyses. Long-term fertilization significantly altered sediment physicochemical properties, microbial community composition, and resistome structure. Among the three groups, the RM exhibited the highest total ARG abundance and the greatest number of unique ARG subtypes, with significant enrichment of multidrug resistance genes as well as pathogen-, disease-, and host-associated mobile genetic elements (MGEs). In contrast, the FF group showed the lowest total ARG abundance and fewest unique ARG subtypes, along with suppression of pathogen-associated MGEs, indicating that FF can effectively reduce the risk of ARG dissemination. However, the potential impact of residual antibiotics still warrants attention. Redundancy analysis showed that TC and TN primarily explained bacteriome and resistome variation under RM, whereas pH, EC, AP, and AK were more strongly associated with FF. Co-occurrence analysis further suggested that fertilizer-driven microbial community shifts may regulate ARG persistence and potential cross-ecosystem dissemination. Overall, fermented fertilizer attenuated, but did not eliminate, manure-derived resistance risks in aquaculture sediments. These findings support fermented fertilizer as a safer management option than raw manure and highlight the need for integrated risk assessment combining ARGs, MGEs, microbial hosts, and antibiotic residues.},
}

@article {pmid42354826,
year = {2026},
author = {O'Donald, SN and Patel, F and Keen, P and Hanson, LA and Cunningham, F and Lawrence, ML and Tekedar, HC},
title = {Hi-C Metagenome Deconvolution of Double-Crested Cormorant (Nannopterum auritum) Fecal Samples Demonstrates Feasibility of Linking Microbial Genomes, AMR Genes, and Mobile Elements in Avian Microbiomes.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061198},
pmid = {42354826},
issn = {2076-2607},
support = {N/A//New York Institute of Technology/ ; },
abstract = {The double-crested cormorant (Nannopterum auritum), a piscivorous bird endemic to North America, frequently forages in aquaculture ponds during migration and wintering, contributing to economic losses in catfish-producing regions of the southern United States. While interactions between cormorants and aquaculture systems are well documented, their associated microbial communities and genetic elements remain less characterized. In this exploratory study, Hi-C-enabled metagenomics was applied to fecal samples from two cormorants to generate a genome-resolved, descriptive analysis of gut microbial composition and to associate bacterial genomes with mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and putative virulence-associated genes. Metagenome-assembled genomes (MAGs) included taxa reported in aquatic or animal-associated environments, including Edwardsiella tarda, Plesiomonas shigelloides, Clostridium perfringens, and Campylobacter volucris. ARGs were detected across multiple MAGs, with E. tarda harboring the greatest diversity. Hi-C-enabled linkage of plasmids and phages to putative hosts, providing structural insight into microbial organization. Analyses are descriptive (n = 2) and do not include statistical comparisons or diversity metrics. These findings demonstrate the utility of Hi-C for resolving gene-host associations and provide a framework for future studies of microbial connectivity in One Health contexts.},
}

@article {pmid42354835,
year = {2026},
author = {Mohammed, MZ and Linhares, DCL and Zeller, MA and Silva, GS and Rademacher, C and Peterson, C and Trevisan, G},
title = {Genetic Characterization of PRRSV Diversity and Detection of Other Pathogens in Live Virus Inoculation Material Used in Breeding Herd Stabilization Programs.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061207},
pmid = {42354835},
issn = {2076-2607},
support = {GR-028677//American Association of Swine Veterinarians Foundation/ ; IPPA 23-120//Iowa Pork Producers Association/ ; },
abstract = {Live virus inoculation (LVI) is widely used for porcine reproductive and respiratory syndrome virus (PRRSV) stabilization, yet preparation practices and pathogen composition remain poorly characterized. This study aimed to evaluate variability in LVI preparation, quantify PRRSV genomic load, and detect additional swine pathogens. A survey was conducted to document LVI preparation methods, and samples were analyzed using reverse-transcription quantitative PCR (RT-qPCR) for PRRSV quantification and next-generation sequencing for PRRSV and the metagenomic characterization of additional pathogens. Among 61 LVI samples, substantial variability was observed in preparation practices and viral composition, with 31 distinct PRRSV variants identified and seven samples containing multiple strains. PRRSV RNA concentrations ranged from 10[1.69] to 2.52 × 10[8] copies/mL. Metagenomic analysis detected a complete or near-complete genome for PRRSV, porcine parvovirus, and porcine circovirus type 2. Genome fragments of porcine sapovirus, porcine rotavirus, porcine astrovirus, and bacterial genetic material from Salmonella spp., Pseudomonas spp., Streptococcus spp., and Escherichia coli were also detected. These findings highlight substantial heterogeneity in LVI materials and encourage the use of next-generation sequencing to verify LVI PRRSV composition and screen for co-existing pathogens, reinforcing the need for standardized preparation protocols and further investigation into optimal viral dosing for effective immunization.},
}

@article {pmid42354848,
year = {2026},
author = {Gou, F and Zhao, Q and Han, Y and Sun, Y and Ding, W and Chen, J and Jin, S},
title = {Effects of Dietary Concentrate-to-Roughage Ratio on Rumen Microbiota, Functional Profiles, and Fermentation Characteristics in Yak.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061223},
pmid = {42354848},
issn = {2076-2607},
support = {2024-NK-109//Qinghai Provincial Science and Technology Department/ ; },
abstract = {This study investigated the effects of different concentrate-to-roughage ratios on the rumen microbial community, functional potential, and fermentation characteristics in yak. Forty Qinghai Plateau-type yaks (8-9 months, 68.725 ± 18.973 kg) were randomly assigned to four dietary groups with concentrate-to-roughage ratios of 80:20 (C80), 65:35 (C65), 50:50 (C50), and 35:65 (C35). After a 15-day adaptation period, animals were fed for 105 days. Rumen contents were analyzed using metagenomic sequencing combined with fermentation parameter measurements. High-concentrate diets (C80 and C65) were associated with increased relative abundance of starch-degrading and propionate-producing bacteria, such as Prevotella and Succiniclasticum, whereas low-concentrate diets (C50 and C35) were associated with higher abundance of cellulolytic bacteria, including Ruminococcus and Fibrobacter. Functional analysis indicated increased relative abundance of genes involved in glycolysis (ko00010), propanoate metabolism (ko00640), and energy-related pathways in high-concentrate groups, while fiber degradation and methane-related pathways were relatively higher in low-concentrate groups. Rumen fermentation parameters showed a significant decrease in pH with increasing concentrate level (p = 0.001), and NH3-N concentrations differed among treatments (p = 0.036). Dietary concentrate-to-roughage ratio significantly influences rumen microbial composition, functional potential, and fermentation characteristics in yak. A moderate concentrate level (approximately 65:35) may contribute to a more balanced rumen microbial and fermentation profile under the conditions of this study.},
}

@article {pmid42354871,
year = {2026},
author = {Qiu, Q and Sun, X and Li, H and Zhou, D and Huo, H},
title = {Plastic Degradation Potential and Metagenomic Analysis of an Enriched Gut Microbial Consortium from Tenebrio molitor.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061246},
pmid = {42354871},
issn = {2076-2607},
support = {52230003//National Natural Science Foundation of China/ ; },
abstract = {Plastic pollution has become an increasingly severe global environmental issue, highlighting the urgent need for efficient and sustainable biodegradation strategies. In this study, an enriched gut microbial consortium, NE-01 derived from Tenebrio molitor, exhibited significant degradation activity toward polystyrene (PS), polyethylene (PE), and polyethylene terephthalate (PET). Metagenomic sequencing revealed that Pseudomonas and Proteobacteria were the dominant taxa, maintaining high community diversity and providing a microbial foundation for the degradation of plastics and other complex organic compounds. Functional annotation and metabolic pathway analysis indicated that xenobiotic biodegradation and metabolism occupied a large proportion of the metabolic network, suggesting the consortium's potential for degrading exogenous pollutants. Several key genes associated with the degradation of aromatic and halogenated compounds, such as benzoate, toluene, styrene, and bisphenol A, were identified. Metabolic reconstruction further suggested possible degradation pathways for PS, PE, PET, and the plasticizer di(2-ethylhexyl) phthalate (DEHP). This study preliminarily demonstrated that the T. molitor gut-derived microbial consortium harbors multiple plastic-degrading genes and provides a theoretical basis for developing green, microbe-based strategies for plastic degradation.},
}

@article {pmid42354876,
year = {2026},
author = {Yue, Y and Jiang, Y and Zhang, Y and Xiao, T and Hao, H and Wang, Q and Tong, Z and Zhang, J and Chen, H},
title = {Duration of Spent Mushroom Substrate Return Affects Microbial Assembly and Nitrogen Metabolism to Promote Functional Stabilization in Rice-Mushroom Crop Rotation Systems.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061251},
pmid = {42354876},
issn = {2076-2607},
support = {T2024310//Shanghai Agricultural Science and Technology Innovation Project/ ; 24YF273800//Shanghai Sailing Program/ ; 202509/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Spent mushroom substrate (SMS) return is a vital strategy for agricultural waste recycling and soil fertility improvement, yet its ecological impacts of duration remain poorly understood. This study employed metagenomic sequencing to explore soil fertility, microbial dynamics, and nitrogen cycling across different SMS return durations (0, 1, and 3 years) within rice-mushroom crop rotation systems. Soil nutrients (organic matter, total nitrogen, total phosphorus) initially decreased and then increased throughout the rice growth cycle. The one-year return (y1) induced early nutrient depletion, whereas the three-year return (y3) significantly enhanced late-stage nutrient accumulation. With increasing duration, bacterial and archaeal assembly shifted from stochastic toward deterministic processes, while fungal diversity and stochasticity decreased continuously. Co-occurrence network analysis demonstrated that SMS return increased network complexity and intercommunity competition. This transition was accompanied by a functional shift in keystone taxa from those responsive to exogenous organic matter in y1 to those mediating nitrogen fixation, anammox, and sulfur metabolism in y3. Nitrogen cycling in y1 increased potential N2O emission risks through nirS upregulation and nosZ downregulation, whereas y3 mitigated inorganic nitrogen loss by upregulating gene abundances of ammonia assimilation, nitrification, and DNRA genes. Notably, the structure of nitrogen-cycling genes fluctuated in y1 but was resilient to y0 levels in y3. These findings demonstrated that while initial SMS return triggered ecological fluctuations and environmental risks, continuous return (y3) achieved functional stability by reshaping microbial niches. This study highlights the importance of SMS return duration in balancing soil fertility enhancement with environmental risk mitigation in sustainable paddy ecosystems.},
}

@article {pmid42354906,
year = {2026},
author = {Cao, YF and Wang, YR and Zheng, PX and Wang, XC and Xu, L and Sun, C},
title = {Multi-Omics Reveals the Impact of Domestic Wastewater Input on the Dissolved Organic Carbon Pool and Microbial Community in the Qiantang River Estuary.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061282},
pmid = {42354906},
issn = {2076-2607},
support = {32370006//National Natural Science Foundation of China/ ; Y24C010009//Zhejiang Provincial Natural Science Foundation/ ; },
abstract = {Estuarine ecosystems face intense anthropogenic pressures, yet systematic research on how domestic wastewater influences the dissolved organic carbon (DOC) pool via microbial community regulation remains limited. In this study, we conducted a microcosm experiment simulating wastewater input into the Qiantang River and integrated multi-omics (16S rRNA sequencing, metagenomics, metatranscriptomics, and FT-ICR MS) to elucidate the mechanism. Results showed that: (1) Wastewater input increased initial DOC and changed its degradation pattern: slower decay but higher removal. (2) Compared to the control, the wastewater-amended group exhibited a decreased fluorescence intensity contribution of carboxyl-rich alicyclic molecule (CRAM)-like compounds, indicating reduced chemical stability of recalcitrant DOC (RDOC). (3) Wastewater drove directional microbial succession from catabolic-dominant taxa (e.g., Comamonas, Citrobacter) to anabolic-dominant taxa (e.g., Reyranella), shifting metabolism from pollutant degradation to endogenous synthesis, thereby lowering the system's efficiency in forming stable RDOC. (4) Multi-omics revealed a "stimulation-balance" functional response: early activation of xenobiotic degradation and signal transduction (day 2), followed by a shift to anabolic metabolism (day 28). This functional transition, driven by microbial succession, ultimately reduced RDOC stability. Our findings reveal that wastewater reshapes the microbial carbon pump, providing a theoretical basis for assessing estuarine carbon sink responses to pollution control measures.},
}

@article {pmid42354916,
year = {2026},
author = {Zhang, X and Lu, C and Lu, L and Meng, L and Liu, Y and Ma, B},
title = {Metagenome-Assembled Genomes Support the Proposal of Candidatus Flavobacterium genomatis from the Northeast Black Soil Ecosystem.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061292},
pmid = {42354916},
issn = {2076-2607},
support = {2024YFD1501800//National Key R&D Program of China/ ; 2024ZD1000603//National Key Science and Technology Special Project for Deep Earth Research/ ; 42277283//National Natural Science Foundation of China/ ; 2024C03131//Key R&D Program of Zhejiang Province/ ; 2024Z267//Key R&D Program of Ningbo/ ; GZC20251786//National Program for Funding Postdoctoral Researchers/ ; },
abstract = {Soils are critical microbial habitats that support terrestrial ecosystem functioning and harbor numerous uncultured and functionally uncharacterized microbial groups. The black soil region in northeast China is a key agricultural ecosystem globally, yet the classification and functional understanding of its crucial microbial groups remain underexplored. In this study, we identified three high-completeness metagenome-assembled genomes (MAGs) from the Global Mollisols Genomic Atlas (GMGA). Phylogenetic and comparative genomic analyses identified these genomes as representing a novel evolutionary branch within the genus Flavobacterium, classified under the phylum Bacteroidota. Their novel taxonomic position is further supported by average nucleotide identity (ANI) and average amino acid identity (AAI) thresholds, demonstrating significant divergence from all known reference genomes. Functional annotation indicated that this species possesses strong plant polysaccharide degradation potential and a chemoheterotrophic lifestyle, together with environmental stress tolerance and a specialized nitrogen metabolic network adapted to agricultural inputs, thereby conferring a metabolic advantage in black soil environments characterized by high organic matter input and marked seasonal fluctuations. In addition, global distribution analysis showed that this lineage is widely distributed across diverse ecosystems and is significantly enriched in soil habitats, particularly in environments with fluctuating carbon sources and high organic matter inputs. The new species is most abundant in temperate soils, with the northeast black soil region of China emerging as a key hotspot. Based on these findings, and because no pure culture is currently available, we propose Candidatus Flavobacterium genomatis based on genome-resolved metagenomic evidence and in alignment with the International Code of Nomenclature of Prokaryotes rules for uncultivated prokaryotes. Our results expand the known species diversity of the genus Flavobacterium and suggest potential ecological roles of uncultured black-soil microbes in carbon and nitrogen cycling, including possible involvement in N2O reduction under suitable environmental conditions.},
}

@article {pmid42354965,
year = {2026},
author = {He, Z and Wang, B and Jin, D and Tian, M and Gong, L},
title = {Effects of Rice Straw Incorporation on Paddy Soil Microbiome and Metabolome Throughout the Crop Growth Period.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061341},
pmid = {42354965},
issn = {2076-2607},
support = {2024BS1002;2026CY3515;2025XKJS8528//Liaoning Academy of Agricultural Sciences/ ; 2025JH2; 101300068//Liaoning Province Applied Basic Research Program/ ; },
abstract = {Rice straw incorporation is a paddy soil management practice that can reduce environmental pollution, mitigate soil degradation, and minimize nutrient loss. In this study, temporal shifts in soil microbial communities and metabolic profiles were investigated across three key rice growth stages-pre-planting (BS), tillering (TI), and harvest (HA)-to elucidate the ecological effects of straw incorporation. The Shannon diversity and Pielou evenness indices were significantly higher under straw incorporation than under the control at the BS and TI stages, but significantly lower at the HA stage. Straw incorporation also increased the relative abundance of key bacterial taxa, including Polaromonas sp. AER18D145, Sphingomonas sediminicola, and Thiobacillus denitrificans. Functional annotation indicated that the microbial community was mainly associated with amino acid biosynthesis and glycolysis. Metabolomic analysis revealed significant changes in steroids and their derivatives, terpenoid lipids, and carboxylic acids and their derivatives. Three metabolites-3-hexa-isoprenyl-4,5-dihydroxybenzoic acid, LysoPE (16:1(9Z)/0:0), and stachyose-differed significantly across all stages, suggesting their potential as metabolic indicators of straw incorporation. KEGG enrichment analysis identified significant alterations in arachidonic acid, purine, galactose, and pyrimidine metabolism. Redundancy analysis further revealed positive associations of LysoPE (16:1(9Z)/0:0) and stachyose with Brevundimonas sp. Root608 and Polaromonas sp. AER18D145.},
}

@article {pmid42354967,
year = {2026},
author = {Romero-Ricardo, L and López, Y and Lopez-Mejia, Y and García, A and Contreras-Martínez, H and Galeano, K and Gastelbondo, B and Fragoso, P and Paternina, L and Arrieta, G and Mattar, S},
title = {Metagenomic Analysis Reveals Viral Diversity in Phlebotomine Sand Flies from Caribbean Region in Colombia.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061343},
pmid = {42354967},
issn = {2076-2607},
support = {BPIN 2020000100322//Ministry of Science, Technology and Innovation/ ; },
abstract = {Phlebotomine sand flies are dipterans that transmit leishmaniasis, bartonellosis, and arboviruses of public health importance. Colombia is a tropical country with high annual incidences of arboviruses, such as dengue and, more recently, yellow fever, all of which have similar symptoms. This study characterized the viruses circulating in phlebotomine sand flies in two departments in the Colombian Caribbean. Between August 2023 and December 2024, a descriptive study was conducted in the Departments of Córdoba and Cesar in Colombia. Four municipalities were selected per department, and four insect captures were performed using CDC light traps. Specimens were taxonomically identified and organized into groups according to species and study area, and total RNA was extracted for NGS analysis. Short sequences were quality-assessed, assembled using MEGAHIT to obtain contigs, and classified using DIAMOND-MEGAN6 to select viral genomic sequences for phylogenetic analysis. Thirteen viral families were identified, including a virus from the family Rhabdoviridae in Pi. evansi in the department of Cesar and another from the family Dicistroviridae in Lutzomyia gomezi in both departments. Two genome segments of the family Phenuiviridae were found in Lutzomyia gomezi in the department of Córdoba, Colombia. Sand flies harbor a diverse range of viral families, some of which are previously undescribed, and can be studied to determine their taxonomy and assess their potential to infect vertebrate cells or their interactions with medically important pathogens such as Leishmania spp.},
}

@article {pmid42354972,
year = {2026},
author = {Diakoumopoulou, D and Slavko, A and Papadimitriou, K and Karoussis, IK and Nikolaou, C and Chatzipanagiotou, S and Ioannidis, A},
title = {Subgingival Microbiota Shifts Following Diode Laser-Activated Indocyanine Green Treatment in Periodontitis: A Pilot 16S rDNA Study.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061347},
pmid = {42354972},
issn = {2076-2607},
support = {485/03-07-2023/OPN: 9Ρ5Ι46Ψ8Ν2-83Φ//National and Kapodistrian University of Athens/ ; },
abstract = {Periodontal disease is driven by a dysbiotic subgingival microbiota enriched in anaerobic pathogens, and novel antimicrobial strategies are needed to complement conventional therapy. This pilot study assessed changes in the subgingival microbiota following diode laser-activated indocyanine green-based treatment (EmunDo) using 16S rDNA amplicon sequencing of paired samples collected before and after therapy. Microbiome analysis revealed compositional shifts across all taxonomic levels, with reductions in disease-associated genera including Porphyromonas, Treponema, Fretibacterium, and Prevotella, and relative increases in taxa more commonly associated with periodontal health, such as Streptococcus, Actinomyces, and Haemophilus. Functional prediction further suggested treatment-associated variation in metabolic categories. Overall microbial richness was preserved between groups. These findings suggest that EmunDo treatment was associated with a restructuring of the subgingival microbiota toward a less dysbiotic profile, warranting further investigation in larger controlled studies using higher-resolution approaches such as shotgun metagenomics.},
}

@article {pmid42354979,
year = {2026},
author = {de Sousa, LC and Caeiro, AJ and de Carvalho, CCCR},
title = {Screening of Marine Bacteria for Lipase Activity and Application as Whole-Cell Biocatalysts.},
journal = {Microorganisms},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/microorganisms14061355},
pmid = {42354979},
issn = {2076-2607},
support = {no. 101000327, project FuturEnzyme//European Union/ ; UID/04565/2025//Fundação para a Ciência e Tecnologia/ ; LA/P/0140/2020//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Several strategies can be employed for the identification of novel microbial lipases. Despite the increasing importance of metagenomics in bioprospecting, significant limitations in the expression of recombinant proteins, and lipases in particular, remain. Culture-based bioprospecting approaches are, therefore, still valuable. In this work, a collection of bacterial isolates, mainly of marine origin, was screened for lipase activity through a culture-based approach. Screening for lipolytic bacteria was performed in solid media containing olive oil emulsions and rhodamine B. Positive isolates were subsequently grown in liquid media, to confirm lipase production. Significant hydrolytic activity towards the triglyceride substrates tributyrin and triolein could be observed with the biomass produced, although no lipase activity could be detected in the culture supernatants. Six isolates presenting high activity were characterized as whole-cell biocatalysts, and all were found to be active at temperatures ranging between 25 and 65 °C, and at pH values between 6 and 10.5. Genomic analyses of two of these Gram-negative lipase-producing isolates revealed the presence of several hypothetical genes encoding for lipolytic enzymes, including outer cell-bound enzymes, predicted through the application of machine-learning tools. These natural isolates, containing cell-associated lipases, may therefore be of special interest for application as whole-cell biocatalysts.},
}

@article {pmid42355557,
year = {2026},
author = {Ang, MY and Chen, L and Song, L and Lipovich, L and Choo, SW},
title = {Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/life16061032},
pmid = {42355557},
issn = {2075-1729},
support = {5000105//High-Level Talent Recruitment Program for Academic and Research Platform Construction/ ; },
abstract = {Large language models (LLMs) are increasingly adopted in life-science research for scientific writing, coding, literature synthesis, workflow troubleshooting, and preliminary data interpretation. In microbial genomics and bioinformatics, their appeal is clear because researchers routinely integrate genome annotations, antimicrobial resistance profiles, virulence determinants, taxonomic assignments, microbiome outputs, workflow scripts, and primary literature. Yet this domain also highlights major risks, including hallucinated biological claims, inaccurate citations, irreproducible code, unsupported genotype-to-phenotype inference, and inappropriate clinical or public health framing. This narrative review examines responsible LLM use in microbial genomics as a representative life-science setting where interpretation depends on database provenance, validated workflows, expert assessment, and reproducible evidence chains. It considers applications in genome annotation, antimicrobial resistance interpretation, virulence analysis, microbiome and metagenomics workflows, coding support, and scientific writing. The review further presents MicrobeGuardGPT as a conceptual reliability framework for assessing LLM-assisted microbial genomics outputs before scientific, clinical, or public health use. By connecting task domains, evidence verification, expert validation, and reliability classification, the framework supports risk-aware LLM integration in bioinformatics. Responsible implementation will require domain-specific benchmarks, curated database linkage, transparent reporting, reproducible workflows, human oversight, and governance standards tailored to biological interpretation across research, diagnostic, surveillance, outbreak-response, educational, and translational contexts.},
}

@article {pmid42355602,
year = {2026},
author = {Schroeder, TH and Eliwi Alsaffan, M and Stäudle, H and Dervishi, A},
title = {Influence of Ongoing Antibiotic Therapy on the Detection of Pathogenic Microorganisms Using Metagenomic Next-Generation Sequencing and Blood Culture in ICU Patients.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/jcm15124434},
pmid = {42355602},
issn = {2077-0383},
abstract = {Background: Blood cultures often yield negative results in critically ill patients, particularly after antimicrobial therapy has started. Plasma metagenomic next-generation sequencing enables culture-independent pathogen detection, but its diagnostic performance relative to blood cultures, especially under ongoing antibiotic exposure in ICU populations, remains unclear. Methods: In this retrospective single-center study, we analyzed adult ICU patients who underwent plasma metagenomic next-generation sequencing testing with paired contemporaneous blood culture between March 2023 and September 2024. Patients were classified according to antibiotic exposure at the time of sampling, and the diagnostic yield and performance of metagenomic next-generation sequencing and blood culture were compared overall and stratified by duration of antibiotic exposure. Results: A total of 393 paired metagenomic next-generation sequencing-blood culture samples from 302 ICU patients were analyzed. Blood culture positivity was significantly lower in patients receiving antibiotics at the time of sampling (10.4% vs. 30.4%), whereas metagenomic next-generation sequencing positivity for bacteria remained stable (52.6% vs. 50.8%). With increasing antibiotic exposure, blood culture yield declined sharply, while metagenomic next-generation sequencing detection showed minimal variation. Overall, the concordance of metagenomic next-generation sequencing compared with blood culture as a comparator was 75.3%, with a negative predictive value of 88.0%. Across all subgroups, metagenomic next-generation sequencing demonstrated a higher diagnostic yield than blood culture, with the greatest relative advantage in antibiotic-treated patients. Conclusions: In critically ill patients receiving antimicrobial therapy, blood culture diagnostic yield is markedly reduced, whereas plasma metagenomic next-generation sequencing maintains pathogen detection across varying durations of antibiotic exposure. Metagenomic next-generation sequencing represents a valuable complementary diagnostic tool alongside blood cultures in pretreated ICU patients.},
}

@article {pmid42355677,
year = {2026},
author = {He, C and Zou, H and Jiang, Z and Zhou, Y and Ying, B},
title = {Metagenomic Next-Generation Sequencing for Pulmonary Tuberculosis Diagnosis and Infection Risk Factor Analysis in AECOPD Patients: A Single-Center Retrospective Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/jcm15124507},
pmid = {42355677},
issn = {2077-0383},
support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; ZYGD23036//1. 3. 5 project for disciplines of excellence from West China Hospital of Sichuan University/ ; 2024YFFK0225//Science and Technology Department of Sichuan Province/ ; },
abstract = {Background: Pulmonary tuberculosis (TB) is a significant trigger of acute exacerbations of chronic obstructive pulmonary disease (AECOPD), so its timely and accurate diagnosis is essential. Also, the risk factors for TB occurrence in this population remain unclear. This study aimed to evaluate the performance of metagenomic next-generation sequencing (mNGS) for TB diagnosis in AECOPD patients, as well as to identify the associated risk factors. Methods: A retrospective observational cohort of 659 AECOPD patients with suspected pulmonary infection was enrolled. The microbial cell-free nucleic acids in bronchoalveolar lavage fluid samples were extracted and subjected to mNGS detection. The clinical data for each patient were collected from the hospital information system. The statistical analyses were performed with SPSS version 25.0. Results: A total of 170 cases, included for final analyses, were categorized into TB (n = 41), bacterial infection (n = 73), and non-infective control (n = 56) groups. Among these groups, the TB group had the highest intensive care unit (ICU) admission rate (46.34%) and longest median hospital stay (19.50 days) (p < 0.01). For TB diagnosis, mNGS demonstrated a greater sensitivity (86.00%), a lower specificity (93.30%), and a higher area under the curve (AUC, 0.877) than TB-DNA detection (70.21%, 100%, 0.848, respectively) and Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay (63.83%, 100.00%, 0.870, respectively). Notably, mNGS identified the bacterial or viral co-infections in 18.00% of TB cases. Furthermore, the stringently mapped read number determined by mNGS showed a positive correlation with ICU admission rate (r = 0.76) and in-hospital mortality (r = 0.77). The lower body mass index (BMI) and reduced natural killer (NK) cell count were identified as the independent risk factors in the TB group (both p < 0.05). Conclusions: For the diagnosis of pulmonary TB in AECOPD patients, mNGS demonstrated comparable performance to TB-DNA detection and Xpert MTB/RIF assay, and also mNGS identified co-infections. In addition, a lower BMI and reduced NK cell count were identified as the independent risk factors for TB occurrence in this cohort.},
}

@article {pmid42355923,
year = {2026},
author = {Mammadov, RA and Roest, HP and Fuhler, GM and Su, J and Visseren, T and Janssen, HLA and Porte, RJ and Murad, SD and Hansen, BE and van der Laan, LJW and Peppelenbosch, MP},
title = {Association of FUT2 rs601338 Genotype with Colonic Mucosal Microbiome Composition, Post-Transplant Bacteremia, and All-Cause Mortality After Liver Transplantation for Primary Sclerosing Cholangitis: A Retrospective Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/jcm15124755},
pmid = {42355923},
issn = {2077-0383},
abstract = {Background/Objectives: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease frequently requiring liver transplantation (LTx). The gut-liver axis, host genetics, and microbial dysbiosis are thought to contribute to disease progression and post-transplant outcomes. The FUT2 rs601338 polymorphism influences mucosal fucosylation, host-microbial interactions, and susceptibility to infection. This study aimed to investigate the association between FUT2 genotype, colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in a retrospective single-center PSC cohort. Methods: This retrospective cohort study included PSC patients who underwent LTx at Erasmus MC University Medical Center (Rotterdam, The Netherlands) between 1987 and 2015. Pre-transplant archival formalin-fixed paraffin-embedded (FFPE) colonic biopsy specimens were available for microbiome analysis. Of 169 transplanted patients, FFPE tissue was available for 98 individuals, and FUT2 rs601338 genotyping was successfully performed in 87 patients. Patients were classified as FUT2 non-secretors (AA, n = 28) and secretors (GA/GG, n = 59). Post-transplant bacteremia was assessed based on clinically indicated blood cultures during follow-up. Colonic mucosal microbiome composition was analyzed using 16S rRNA gene sequencing. Results: FUT2 non-secretors showed a distinct colonic mucosal microbiome profile compared with secretors, characterized by differential abundance of selected taxa within Proteobacteria, Firmicutes, and Bacteroidetes. Post-transplant bacteremia occurred in 30 patients and was more frequent among non-secretors (43%) compared with secretors (15%). Both FUT2 non-secretor status and post-transplant bacteremia were associated with reduced all-cause post-transplant survival in Kaplan-Meier analysis and remained associated with mortality in multivariable regression models. Specific microbial taxa were also showed associations with bacteremia, mortality, and established prognostic scores, including the Amsterdam-Oxford Model and Mayo Risk Score. Conclusions: FUT2 genotype is associated with alterations in colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in PSC patients undergoing liver transplantation. These findings suggest a potential interplay between host genetics, intestinal microbiota, and infectious complications after transplantation. Given the retrospective design, limited sample size, and use of archival FFPE tissue, all findings should be interpreted as exploratory and hypothesis-generating. Prospective multicenter studies using standardized sampling and high-resolution metagenomic approaches are warranted for validation.},
}

@article {pmid42357036,
year = {2026},
author = {Osipov, DO and Rozhkova, AM and Volkov, PV and Zorov, IN and Sinitsyna, OA and Trofimchuk, ES and Moskvina, MA and Grokhovskaya, TE and Yaroslavov, AA and Sinitsyn, AP},
title = {Changes in Mechanical Properties and Structure of PET Films Treated with Metagenome-Derived LCC[ICCG] PETase Heterologously Expressed in Penicillium verruculosum.},
journal = {Polymers},
volume = {18},
number = {12},
pages = {},
doi = {10.3390/polym18121510},
pmid = {42357036},
issn = {2073-4360},
support = {126030218233-1//The Ministry of Education and Science of the Russian Federation/ ; },
abstract = {This study examines the nature of enzymatic degradation of polyethylene terephthalate (PET) films mediated by a novel recombinant LCC[ICCG] PETase enzyme preparation based on P. verruculosum fungus. The investigation was conducted using amorphous PET samples and PET samples with varying degrees of crystallinity as substrates for PETase-catalyzed hydrolysis under different temperature and pH conditions. Mechanical testing revealed that enzymatic treatment reduced the yield stress by 20-25%, tensile strength by approximately twofold, and elongation at break by 5-10 times, while the deformation mechanism remained unchanged. Enzymatic degradation under acidic conditions was ineffective, whereas increasing the pH to 9-10 markedly accelerated PET degradation and the associated deterioration of mechanical properties. Thermal analysis (TGA, DSC) and microscopy (optical and scanning electron microscopy) demonstrated that degradation was localized at the polymer surface, leading to the formation of cavities, cracks, and submicron-sized pores rather than bulk material disintegration. An inverse correlation was observed between PET crystallinity and susceptibility to enzymatic degradation: samples with crystallinity below 13% could be almost completely degraded, whereas samples with crystallinity above 30% exhibited little or no measurable weight loss over the same period. Low-crystallinity PET underwent rapid degradation accompanied by a transient increase in crystallinity, while highly crystalline PET primarily accumulated surface defects that nevertheless caused a substantial loss of mechanical strength. Consequently, the experimental data obtained in this study provide useful information for understanding PET degradation and for future studies on enzymatic PET recycling. The systematization of feedstock characteristics and the elucidated patterns of enzymatic degradation will enable optimization of pretreatment, enzymatic hydrolysis, and monomer recovery process parameters, thereby facilitating the eventual production of secondary raw materials.},
}

@article {pmid42357147,
year = {2026},
author = {Chen, X and Hou, C and Yu, H and Xie, J},
title = {Enhanced Yield of GmJAG1-Edited Soybeans Accompanied by Improved Function of the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/plants15121828},
pmid = {42357147},
issn = {2223-7747},
support = {2023YFF1001600//National Key R&D Program of China/ ; },
abstract = {In the present study, we investigated how soybean yield is enhanced upon editing of the gene GmJAG1 and the consequent influence on the structure and function of the rhizosphere microbiome. Field trials revealed that gene-edited (GE) soybeans had a 55.22% increase in yield without concomitant changes in root length. Metagenomic sequencing of the rhizosphere soil microbiome showed that, compared with the corresponding non-edited line (CK), the alpha diversity of the GE groups remained unaltered, whereas beta diversity differed significantly at the soybean reproductive (R2) stage. Notably, the rhizosphere microbiome of GE soybeans at the R2 stage exhibited enrichment of functional pathways related to transport, amino acid biosynthesis, and central metabolism. These findings suggest that GmJAG1 editing may shape the functional profile of the rhizosphere microbiome, which could potentially contribute to yield gains. This work offers a novel microbiological perspective for understanding the mechanisms by which yield may be improved in GE crops.},
}

@article {pmid42357170,
year = {2026},
author = {Wang, P and Yin, D and Fu, G and Yi, X and Guo, Z},
title = {Nitrogen Input Alters Root Exudation of Kandelia obovata and Nitrogen Cycling in Constructed Mangrove Wetlands.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/plants15121851},
pmid = {42357170},
issn = {2223-7747},
support = {32271704//National Natural Science Foundation of China/ ; 2022A1515010562//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20230808105410020//The Shenzhen Science and Technology Project/ ; },
abstract = {The role of mangrove root exudates in mediating the nitrogen cycle, particularly under high dissolved inorganic nitrogen (DIN) input, in coastal ecosystems remains unclear. This research investigated variation in the root exudates, and nitrogen transformation and output, in constructed mangrove wetlands planted with Kandelia obovata under high, moderate, and low nitrogen-input levels (PCWs-H, PCWs-M, and PCWs-L, respectively). PCWs-H promoted increased root density and biomass accumulation, enhancing soil nitrogen sequestration, whereas PCWs-L induced greater specific root length, specific root surface area, and number of root tips. These changes directly influenced denitrification efficiency. Hydroxymethoxyphenylcarboxylic acid-O-sulfate and Arg-Ser released in root exudates under PCWs-H might act as potential denitrification inhibitors, thereby suppressing denitrifiers and impairing dissolved nitrogen purification. Elevated nitrogen loading predominantly limited denitrification, resulting in relative NO3[-]-N removal rates of PCWs-H < PCWs-M < PCWs-L (p < 0.05). Compared with PCWs-H and PCWs-L, the enhanced soil organic nitrogen storage under PCWs-M was associated with flavonoids in root exudates. Metagenomic analysis showed that denitrification was the dominant nitrogen removal pathway. Nitrogen loading influenced the effects of root exudates on the microbial community. Under PCWs-H, triterpenoids promoted norBC and nirK/S abundance but depressed amoABC abundance. Sterols and flavonoids in exudates under PCWs-L depressed nosZ abundance, instead activating dissimilatory nitrate reduction to ammonium. Compared with PCWs-H and PCWs-L, N2O emissions were minimal under PCWs-M. This study revealed that mangrove root exudates mediate the nitrogen cycle in mangrove wetlands, providing a theoretical basis for local authorities to manage DIN inputs and mitigate N2O emissions.},
}

@article {pmid42357267,
year = {2026},
author = {Dumitru, CN and Dumitru, AO and Goroftei, L and Niculet, E and Ignat, MD and Baroiu, L and Nechita, A and Balan, G},
title = {Pharmacomicrobiomics of Non-Antibiotic Drugs: Mechanisms and Clinical Consequences of Gut Microbiota Alterations.},
journal = {Pharmaceutics},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/pharmaceutics18060651},
pmid = {42357267},
issn = {1999-4923},
support = {NA//"Dunarea de Jos" University of Galati/ ; },
abstract = {Background: The gut microbiota constitutes a metabolically active "second genome" that profoundly modulates drug pharmacokinetics, pharmacodynamics, and adverse reaction profiles. Beyond antibiotics, widely prescribed non-antibiotic pharmacotherapies exert clinically relevant pharmacomicrobiomic effects with implications for therapeutic optimisation and pharmacovigilance. Methods: This narrative review, conducted following PRISMA 2020 reporting principles (without PROSPERO pre-registration), searched PubMed/MEDLINE, Scopus, Web of Science, and Cochrane Library (January 2015-December 2024) for evidence on proton pump inhibitors (PPIs), metformin, NSAIDs, statins, SGLT2 inhibitors, and oral iron. Evidence tables included clinical human studies with molecular microbiota characterisation (16S rRNA or shotgun metagenomics), ≥20 participants, and a control arm; preclinical data informed mechanistic synthesis. Results: Of 68 eligible studies, 20 met criteria for the evidence tables. PPIs significantly remodelled gut microbiota composition with enrichment of oral-origin taxa ("oralisation of the gut"), associating with Clostridioides difficile infection and SIBO. Metformin enriched Akkermansia muciniphila and butyrate producers, contributing causally to glycaemic efficacy. NSAIDs compromised barrier integrity, with synergistic dysbiosis under PPI co-prescription. Statins correlated with reduced prevalence of the dysbiotic Bact2 enterotype. SGLT2 inhibitor data remained discordant. Oral iron consistently enriched Enterobacteriaceae at the expense of beneficial commensals.},
}

@article {pmid42357653,
year = {2026},
author = {Sholes, SL and Norton, S and Gonzalez, A and Gaspar, JM},
title = {MGtree: A Fast and Flexible Alignment-Based Metagenomics Pipeline.},
journal = {Viruses},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/v18060643},
pmid = {42357653},
issn = {1999-4915},
support = {n/a//Merck & Co., Inc., Rahway, NJ, USA (United States)/ ; },
mesh = {*Metagenomics/methods ; Phylogeny ; Humans ; Norovirus/genetics/classification ; Genotype ; *Sequence Alignment/methods ; Computational Biology/methods ; Genome, Viral ; *Software ; Papillomaviridae/genetics/classification ; Human Papillomavirus Viruses/genetics/classification ; },
abstract = {Metagenomics analysis is a critical tool in identifying and typing viral samples to aid surveillance, clinical, epidemiological, and other workflows. Despite advances in sequencing technology and analysis pipelines, there are still limitations that lead to reduced taxonomic resolution or false positives from highly recombinant or challenging samples. Here we describe MGtree, a novel metagenomics pipeline that utilizes a combination of full-length read alignments and phylogenetic analysis to classify samples of interest. We demonstrate that MGtree accurately genotypes viral samples from challenging norovirus and HPV datasets. MGtree outperforms the popular metagenomics programs Kraken2 and Centrifuge, and it succeeds with low-input samples where de novo assembly fails. MGtree's correct assignments across highly mutant and coinfected samples highlights its ability to resolve viral genotypes and its potential to improve classification precision in complex samples.},
}

*Metagenomics/methods
Phylogeny
Humans
Norovirus/genetics/classification
Genotype
*Sequence Alignment/methods
Computational Biology/methods
Genome, Viral
*Software
Papillomaviridae/genetics/classification
Human Papillomavirus Viruses/genetics/classification

@article {pmid42357654,
year = {2026},
author = {Paoli, JE and Trovão, NS and Odoom, T and Mohktar, Q and Buabeng, KB and Adu, B and Tasiame, W and Anderson, B and Tawiah-Yingar, DNY and Subramaniam, K and von Fricken, ME and Mensah, GI and Mietzsch, M and McKenna, R and Johnson, SAM and Mavian, CN},
title = {One Health Genomic Surveillance at Human-Animal Interfaces in Rural Ghana Reveals Underreported Viruses of Zoonotic and Economic Concern.},
journal = {Viruses},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/v18060644},
pmid = {42357654},
issn = {1999-4915},
support = {N/A//University of Florida/ ; },
abstract = {Under a One Health framework, viruses of veterinary and zoonotic importance pose significant threats to animal and human health, food security, and livelihoods, particularly in regions with intense human-animal interactions. In West Africa, despite recent advances in surveillance programs, important gaps remain in understanding viral diversity and cross-species transmission at wildlife-livestock interfaces. We conducted metagenomic surveillance to characterize viruses circulating across livestock, domestic animals, and wildlife in rural Ghana in 165 animals sampled across five regions. Viral RNA from serum and tissue samples was sequenced with the Illumina platform, and genomes were de novo assembled with MEGAHIT. Phylogenetic relationships were reconstructed using Bayesian approaches. We report the first genomic sequences of porcine parvovirus 3, canine parvovirus, rotavirus A genotype R16, and bovine hepacivirus subtype B from Ghana in over a decade. Phylogenetic analyses revealed intercontinental linkages between Africa and Europe for parvoviruses, persistence of hepacivirus lineages, and evidence of cross-species transmission for rotavirus. Notably, detection in apparently healthy animals highlights underrecognized circulation, gaps in vaccination effectiveness, trade-related biosecurity vulnerabilities, and the role of wildlife in viral maintenance and transmission. Our findings reveal dynamic viral diversity and connectivity across animal populations and ecological interfaces, emphasizing the fluid and interconnected nature of pathogen circulation within One Health systems. By integrating metagenomics and phylogenetics, this study provides a scalable framework for enhancing surveillance capacity, enabling the early detection of emerging threats and informing targeted strategies to mitigate zoonotic and economically important viral diseases in West Africa.},
}

@article {pmid42357666,
year = {2026},
author = {Lai, T and Liu, F and Li, G and Hua, L},
title = {ViroBioTree: A Tree-Structured Biological Evidence Retrieval Framework for Viral Protein Function Annotation.},
journal = {Viruses},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/v18060656},
pmid = {42357666},
issn = {1999-4915},
support = {Grant No. 2026GXNSFAA00640099//Natural Science Foundation of Guangxi province/ ; Guike AD25069086//the Science and Technology Project of Guangxi/ ; },
mesh = {*Viral Proteins/genetics/metabolism ; *Molecular Sequence Annotation/methods ; *Computational Biology/methods ; Humans ; Open Reading Frames ; SARS-CoV-2/genetics ; Genome, Viral ; *Software ; },
abstract = {Accurate viral protein function annotation is essential for genomic surveillance, yet conventional retrieval-augmented generation (RAG) pipelines often fragment biological evidence into fixed-length text chunks, disrupting relationships among ORFs, annotations, structural domains, sequence motifs, residue mappings, and model-derived attention evidence. We propose ViroBioTree, a tree-structured biological evidence retrieval framework for downstream viral protein evidence review rather than a new primary annotation classifier. Built as an evidence organization layer on ViralMultiNet-derived ORF-level predictions and annotations, ViroBioTree converts sequence, annotation, structure, and attention evidence into typed biological nodes and traceable edges, then performs deterministic multi-channel recall, evidence-aware reranking, balanced TopK selection, rule-based verification, and node-cited report generation. In a demo benchmark, ViroBioTree achieved its strongest deterministic proxy performance on structure-explanation tasks, with Precision@K = 1.0, Recall@K = 1.0, and diversity = 0.52; these values reflect expected node-type and tag agreement rather than independent biological correctness. A bounded full-scale SARS-CoV-2 index contained 39,800 ORF rows, 80,000 attention records, 199,418 nodes, and 495,886 edges. In a stratified full20k diagnostic evaluation, ViroBioTree showed task-dependent advantages over LlamaIndex vector retrieval for conflict detection, evidence retrieval, and structure explanation, while LlamaIndex remained competitive or stronger for annotation-rich function annotation. A cross-family Influenza A Virus (IAV) diagnostic audit showed that the schema can represent IAV evidence namespaces while explicitly exposing missing formal ORF inputs, missing attention evidence, and unavailable residue/PDB assertions. Supplementary robustness, external sanity-check, diversity-risk, expert-evaluation, domain-tool positioning, and cross-family audit analyses supported traceability, report quality, and conservative evidence handling, but also showed that stable Precision@K under query perturbation does not necessarily imply stable retrieved evidence sets. ViroBioTree operates offline and deterministically, but does not address raw-read assembly, base calling, primary ORF prediction, or wet-lab validation. Its results should be interpreted as proxy and expert-reviewed evidence for traceable viral protein evidence retrieval and report generation rather than as direct validation of biological function annotation.},
}

*Viral Proteins/genetics/metabolism
*Molecular Sequence Annotation/methods
*Computational Biology/methods
Humans
Open Reading Frames
SARS-CoV-2/genetics
Genome, Viral
*Software

@article {pmid42357739,
year = {2026},
author = {Xue, T and Zhang, B and Wang, Z and Ma, Y and Shen, Q and Ding, J and Yang, X},
title = {Rapid Metagenomic Detection of Brucella abortus During a Two-Case Bovine Abortion Investigation in Inner Mongolia, China.},
journal = {Veterinary sciences},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/vetsci13060541},
pmid = {42357739},
issn = {2306-7381},
abstract = {Abortion in cattle entails substantial economic loss, and rapid identification of abortigenic pathogens is critical for timely on-farm response and reduction in human exposure risk. In 2024, two Holstein cows from a small farm in Inner Mongolia aborted in close succession without an obvious cause. Vulvar swabs from both cows, one afterbirth sample, and whole blood from one aborted fetus were collected. Shotgun metagenomic sequencing was performed, followed by host-read removal, taxonomic profiling with Kraken2, de novo assembly of Brucella-aligned reads, and whole-genome comparison. Serological tests, Gram-stained smears, and Brucella genus- and species-specific qPCR assays were used as orthogonal verification. Putative resistance and virulence determinants were screened against CARD and VFDB. Brucella reads were detected in all samples, with the highest relative abundance in the 138-afterbirth (96%). qPCR assays detected Brucella DNA and B. abortus-specific signals in all four samples. A draft Brucella genome was assembled from the 138-afterbirth sample and was phylogenetically placed within B. abortus, showing relatedness to previously circulating Chinese lineages. Cows 138 and 198 were RBT-positive with SAT titres of 1:100 (++). No acquired Brucella resistance genes were identified in CARD. Within 72 h of sample receipt, B. abortus was reported to the farm and local authorities and emergency biosecurity measures were implemented. This field investigation shows that metagenomic sequencing, when combined with conventional serology, microscopy, and targeted qPCR, can support rapid etiological investigation when culture is delayed, hazardous, or biosafety level 3 facilities are unavailable.},
}

@article {pmid42357757,
year = {2026},
author = {Ma, L and Qu, J and Li, X and Liu, Y},
title = {Ecological Reassembly of the Milk Microbiome and Its Associated Resistome During the Dry Period in Dairy Cows.},
journal = {Veterinary sciences},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/vetsci13060559},
pmid = {42357757},
issn = {2306-7381},
support = {2023YFD1800100//National Key Research and Development Program of China/ ; No. IFR-06//the Agricultural Science and Technology Innovation Program/ ; },
abstract = {The aim of this study was to characterize the coordinated dynamics of the mammary microbiome, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the dry period, calving, and early lactation. The mammary microbiome undergoes substantial ecological changes across these stages, yet the coordinated dynamics of microbial composition, ARGs, and MGEs remain poorly understood. Here, shotgun metagenomic sequencing was performed on mammary secretion samples collected before dry-off (BM), immediately after calving (ACM), and one month postpartum (AM). The mammary microbiome exhibited a clear "exposure-bottleneck-reassembly" trajectory. BM was characterized by high microbial diversity and the enrichment of environmentally associated taxa, whereas ACM displayed a pronounced immunological bottleneck with markedly reduced microbial diversity and network complexity. During AM, microbial communities partially recovered but remained distinct from the BM state, indicating persistent ecological restructuring after calving. ARGs and MGEs showed parallel dynamics, with broad resistome and mobilome diversity in BM, a sharp contraction in ACM, and a selective re-expansion in AM. Network analysis further revealed maximal ecological complexity in BM, increased ARGs/MGEs connectivity in ACM, and partial stabilization in AM. These findings demonstrate that host physiological transitions, together with dry cow therapy (DCT), drive the coordinated remodeling of the mammary microbiome, resistome, and mobilome across the dry period.},
}

@article {pmid42358061,
year = {2026},
author = {Morvil, N and Goh, WGW and Zheng, C and Sutjipto, S and Ng, DHL and Zambon, M},
title = {Navigating the Future of Respiratory Infections: Key Insights From International Congress in Singapore, 17-20 September 2025.},
journal = {Influenza and other respiratory viruses},
volume = {20},
number = {7},
pages = {e70276},
doi = {10.1111/irv.70276},
pmid = {42358061},
issn = {1750-2659},
mesh = {Humans ; Singapore ; *Respiratory Tract Infections/prevention & control/diagnosis/epidemiology/drug therapy/therapy/virology ; Antiviral Agents/therapeutic use ; Animals ; },
abstract = {BACKGROUND: The 8th International Society for Respiratory Viruses (ISRV) Antiviral Group Conference, held jointly with the 3rd International Meeting on Respiratory Pathogens in Singapore (17-20 September 2025), examined evolving approaches to prevention and management of respiratory infections. This report summarizes the major themes and perspectives that emerged across the meeting.

METHODS: We reviewed plenary sessions, thematic symposia and panel discussions and synthesized recurring concepts relevant to clinical practice and preparedness. Discussions were organized into key domains, including therapeutics, host response, vaccination, surveillance, diagnostics and research infrastructure.

RESULTS: Presentations highlighted the development of long-acting and broadly active antivirals, interest in combination therapy and early treatment, and increasing recognition that inflammatory host responses contribute substantially to disease severity. Advances in vaccines targeting conserved viral components and long-acting monoclonal antibodies were discussed, along with the growing role of adaptive platform trials and harmonized clinical endpoints. A recurring theme was the transition from pathogen-centred management to a broader framework incorporating host responses. Speakers also emphasized integrated surveillance using genomic sequencing, metagenomics and rapid point-of-care diagnostics within a One Health framework addressing zoonotic spillover.

CONCLUSIONS: The meeting illustrated how clinical care, translational science and public health preparedness are becoming increasingly interconnected. Sustained investment in surveillance systems, clinical trial platforms and access to therapeutics will be necessary to translate scientific progress into routine care and to strengthen readiness for future epidemics and pandemics.},
}

Humans
Singapore
*Respiratory Tract Infections/prevention & control/diagnosis/epidemiology/drug therapy/therapy/virology
Antiviral Agents/therapeutic use
Animals

@article {pmid42358249,
year = {2026},
author = {He, L and Huang, Y and Li, H and Zhu, B and Zhang, Z and Wu, J and Zhou, S and Zhan, Q and Wu, K and Wu, F},
title = {Novel insights into gut microbiota alterations in major depressive disorder with suicidal ideation: a metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843301},
pmid = {42358249},
issn = {1664-302X},
abstract = {INTRODUCTION: Suicidal ideation in major depressive disorder (MDD) is common, yet its biological mechanisms and biomarkers remain unclear. The gut microbiota, a key component of the gut-brain axis, has been implicated, but current evidence is limited.

METHODS: We analyzed fecal samples from 141 participants, including 52 healthy controls (HCs) and 89 first-episode, drug-naïve MDD patients, further classified into suicidal ideation (SI, n = 57) and non-suicidal ideation (NSI, n = 32) groups using the Beck Scale for Suicide Ideation (BSSI). Shotgun metagenomic sequencing with HUMAnN3-based taxonomic and functional profiling was performed. Microbial diversity, differential abundance, and partial correlation analyses with suicidal ideation severity were conducted to identify key microbial taxa associated with suicidal ideation. For functional difference analysis, MaAsLin2 was employed across four levels: KEGG Orthology (KO), KEGG pathways, CAZy, and MetaCyc pathways. Mediation analysis was used to assess potential mediating effects between suicidal ideation and key microbial taxa after adjustment for age, sex, education, and BMI.

RESULTS: No significant differences were observed in overall microbial diversity. Bacteroides cellulosilyticus was enriched in HCs and showed a significant negative association with suicidal ideation severity. Functionally, compared with the NSI group, patients with suicidal ideation exhibited reduced microbial capacities related to peptidoglycan biosynthesis. Mediation analysis further indicated that B. cellulosilyticus may modulate suicidal ideation through pathways involved in carbohydrate transport and metabolism, vitamin K2 biosynthesis, and DNA repair.

CONCLUSION: Bacteroides cellulosilyticus may act as a potentially protective microbial species, negatively regulating suicidal ideation, possibly by enhancing carbohydrate metabolism and short-chain fatty acid production. Notably, this species has received limited attention in the context of psychiatric disorders, highlighting its potential as a novel microbial target. These findings provide new microbiome-based insights into suicidal ideation in MDD.},
}

@article {pmid42358254,
year = {2026},
author = {Duan, G and Kong, L and Duan, S and Nie, S and Gu, W},
title = {Research progress on emerging and important Tick-Borne pathogens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1866307},
pmid = {42358254},
issn = {1664-302X},
abstract = {Ticks are important vector arthropods, which can carry and transmit a variety of pathogenic microorganisms, and pose a serious threat to global public health. This study reviews the research progress of the main and emerging tick-borne pathogens, such as Lyme disease related Borrelia, Rickettsia, Babesia, Thrombocytopenia Syndrome Virus (SFTSV), Tick-borne Encephalitis Virus (TBEV), Alongshan virus (ALSV), etc., focuses on their genomic diversity, pathogenicity, transmission and immune escape, co- infection. In addition, the application of new detection technology [Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), metagenomic next-generation sequencing (mNGS), microfluidics] in Tick-Borne pathogens is summarized.It highlights current research limitations, including delayed vaccine development and inadequate surveillance systems. Finally, future research directions are prospected, providing theoretical references for the prevention and control of tick-borne diseases.},
}

@article {pmid42358269,
year = {2026},
author = {Hou, Z and Shi, M and Gou, S and Liao, D and Hu, C and Zhang, Q and Zhang, X and He, L and Ba, Y and Zhang, Y and Li, Y and Zhou, K and Wang, H and Song, L},
title = {Relative contributions of vegetation and soil properties to microbial community structure and function in alpine and subalpine meadows of the southeastern Tibetan Plateau.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1847498},
pmid = {42358269},
issn = {1664-302X},
abstract = {INTRODUCTION: Ongoing climate warming is expected to promote the upward expansion of subalpine meadows and the gradual replacement of alpine meadows on the southeastern margin of the Tibetan Plateau. However, the mechanisms by which these vegetation transitions reshape belowground microbial taxonomic composition and metabolic functional potential remain poorly understood.

METHODS: We investigated soil microbial community structure and functional potential in alpine meadow (AM) and subalpine meadow (SM) ecosystems in the Napahai Basin by integrating vegetation surveys, soil chemical analyses, enzyme activity assays, and metagenomic sequencing.

RESULTS AND DISCUSSION: Altitudinal differences in hydrothermal conditions were associated with pronounced divergence in plant community composition and soil nutrient status between the two meadow types. Although microbial α-diversity did not differ significantly, β-diversity analyses revealed distinct taxonomic and functional differentiation. Functional annotations based on CAZymes and KEGG indicated that variation in microbial functional potential was closely associated with coordinated changes in carbon, nitrogen, and phosphorus availability, suggesting that microbial metabolic strategies shifted along the environmental gradient. Random forest and partial least squares path modelling further showed that plant community composition exerted a stronger direct influence on microbial functional configuration than soil-mediated indirect effects. These findings highlight the prominent role of vegetation in shaping microbial functional potential and underscore the sensitivity of belowground ecological processes to vegetation transitions along environmental gradients in high-elevation meadow ecosystems.},
}

@article {pmid42358428,
year = {2026},
author = {Chen, Y and Tian, D and Bai, Y and Xu, J and Liu, S and Wang, Y and Li, X},
title = {Case Report: Listeria monocytogenes meningitis complicated by an acute exacerbation of chronic obstructive pulmonary disease: the key diagnostic role of metagenomic high-throughput sequencing.},
journal = {Frontiers in medical technology},
volume = {8},
number = {},
pages = {1801483},
pmid = {42358428},
issn = {2673-3129},
abstract = {BACKGROUND: Listeria monocytogenes is an opportunistic foodborne pathogen that causes severe invasive infections, such as meningitis, primarily in immunocompromised individuals, the elderly, and pregnant women. Diagnosis is often challenging due to nonspecific early symptoms.

CASE DESCRIPTION: A 67-year-old male with a history of chronic obstructive pulmonary disease (COPD) presented with a 4-day history of persistent high-grade fever and altered mental status. Initial empirical antibiotic therapy (meropenem) proved ineffective.Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) definitively identified L.monocytogenes. The patient was diagnosed with "Listeria monocytogenes meningitis complicated by an acute exacerbation of chronic obstructive pulmonary disease". Patients with pathogenic bacterial infections completed a 21-day course of ampicillin and sulbactam sodium and a 14-day course of gentamicin, resulting in a rapid improvement in clinical symptoms and biochemical parameters.

CONCLUSION: This case underscores the critical role of mNGS in the aetiological diagnosis of central nervous system infections, especially when conventional methods are inconclusive. It highlights the need for a high index of suspicion for listeriosis in elderly patients with comorbidities presenting with unexplained fever and neurological decline.},
}

@article {pmid42358480,
year = {2026},
author = {Flores, GD and Damon, ZF and Ford, M and Gancz, NN and Savoca, PW and Esfand, SM and Chu, KA and Querdasi, FR and McCann, CF and Westman, JG and Labus, JS and Clewett, D and Parr, AC and Hsiao, EY and Jacobs, J and Silvers, J and Callaghan, BL},
title = {A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.},
journal = {Brain, behavior, & immunity - health},
volume = {55},
number = {},
pages = {101275},
pmid = {42358480},
issn = {2666-3546},
abstract = {Caregiving-related early adversities (crEAs) are potent risk factors for the development of internalizing psychopathology (e.g., depression, anxiety). Alterations to the dopaminergic mesocorticolimbic system, which supports the construction of reward-related experiences, are commonly observed following crEA exposure and are thought to mediate this risk. Indeed, many internalizing disorders are characterized by disruptions in how reward-related information is represented and used to guide affective and motivational states. Critically, the effects of crEA on mesocorticolimbic functioning may be shaped by input from peripheral systems, such as the gut microbiome, though such bottom-up signaling has been markedly understudied in humans. The Teen Bugs study was thus developed to identify gut microbiome-dependent metabolic pathways linking crEA exposure to mesocorticolimbic functioning and internalizing symptoms in adolescents, a group that experiences a disproportionate incidence of psychopathology relative to other age groups and is underrepresented in the gut microbiome literature. Adolescents aged 12-15 years, with and without histories of crEA exposure, will be followed across three timepoints over five years. At each timepoint, participants will complete a semi-structured clinical interview, a reward-guided decision-making task, and self-report questionnaires assessing mental health, previous caregiving experiences, reward-related behaviors, as well as developmental and lifestyle factors. Participants will also undergo multimodal neuroimaging that leverages MRI-based proxy markers of dopaminergic neurobiology and provide stool and blood samples for metagenomic and metabolomic profiling, respectively. This integrative design has the potential to clarify developmentally salient mechanisms that may serve as novel therapeutic targets for youth most at risk of, or already experiencing, internalizing psychopathology.},
}

@article {pmid42358948,
year = {2026},
author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G},
title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1849216},
pmid = {42358948},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; },
abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.

METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.

RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.

CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.},
}

Humans
*Dysbiosis/microbiology/metabolism
*Guillain-Barre Syndrome/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Female
*Bile Acids and Salts/metabolism/blood
Male
*gamma-Aminobutyric Acid/metabolism/blood
Adult
Middle Aged
Metabolomics/methods
Metabolome
Metagenomics
Feces/microbiology
Aged

@article {pmid42359020,
year = {2026},
author = {Wei, BH and Da, HJ},
title = {Purulent Pericarditis Caused by Polymicrobial Periodontal Pathogens (Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis): A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {598156},
pmid = {42359020},
issn = {1178-6973},
abstract = {BACKGROUND: Purulent pericarditis is a rare, life-threatening infection, most commonly caused by bacteria such as Staphylococcus aureus. We report an exceptional case of hematogenously disseminated infection probably originating from the oral cavity, highlighting a novel pathogen profile.

CASE PRESENTATION: We report a 66-year-old male with no history of periodontal disease or oral procedures presented with purulent pericarditis and a concomitant subphrenic abscess. Metagenomic next-generation sequencing (mNGS) of pericardial fluid revealed a polymicrobial infection with three periodontal pathogens: Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis. The patient was treated with pericardiocentesis, targeted antibiotics, and organ support, resulting in clinical stabilization.

CONCLUSION: This case provides clinical evidence that a consortium of periodontal pathogens can disseminate hematogenously to cause severe metastatic infections in sterile sites, even in individuals without overt oral disease. It underscores the need to consider occult oral origins in infections of unknown source and illustrates the value of comprehensive molecular diagnostics in identifying fastidious organisms, although it remains undetermined whether both conditions were secondary to the same source.},
}

@article {pmid42359168,
year = {2026},
author = {Mundt, B and Kant, R and Grzybek, M},
title = {Viral pathogens in urban rats: A one health systematic review of global surveillance evidence.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101468},
pmid = {42359168},
issn = {2352-7714},
abstract = {BACKGROUND: Commensal rats (Rattus norvegicus and Rattus rattus) thrive in urban environments worldwide, where they live near humans and may act as reservoirs for viral pathogens of public health relevance. Although rats are increasingly recognised as sentinels of urban environmental health, the diversity and distribution of viral infections circulating in urban rat populations remain incompletely characterised within a One Health framework.

OBJECTIVES: This systematic review synthesises global evidence on viral pathogens detected in urban rats, focusing on rat hepatitis E virus/Rocahepevirus ratti and human-associated hepatitis E virus/Paslahepevirus balayani where distinguishable, Seoul virus (SEOV), SARS-CoV-2, and additional viral taxa identified through targeted surveillance or, in rare cases, metagenomic approaches.

METHODS: Following PRISMA 2020 guidelines, five electronic databases were searched for primary studies reporting viral detection in urban Rattus spp. Eligible studies underwent screening, structured data extraction and quality appraisal. Viral prevalence was summarised descriptively by pathogen and geographic region.

RESULTS: A total of 70 studies met the inclusion criteria, spanning Europe, Asia, North America, South America and the Caribbean. HEV and SEOV were the most frequently reported viruses, with prevalence varying widely between regions. HEV prevalence ranged from low levels in parts of Europe and Asia to high levels in North America. SEOV was detected across all regions, with particularly high prevalence in parts of Asia and the Americas. SARS-CoV-2 was not detected in European rats but was reported at low to moderate prevalence in the Americas. Numerous additional viral pathogens were identified.

CONCLUSIONS: Urban rats globally harbour diverse viral communities, including pathogens with zoonotic potential. Surveillance remains uneven and methodologically heterogeneous. Integrating rat biomonitoring into coordinated One Health surveillance systems is critical to strengthen early warning capacity and mitigate zoonotic risk.},
}

@article {pmid42359352,
year = {2026},
author = {Lyu, C and Zhou, Q and Xiao, X and Bai, X and Pu, Y and Zhu, H and Zhao, M and Meng, J and Lyu, H},
title = {Metagenomics next-generation sequencing of plasma combined with blood cells for improving the prognosis of early infection in patients with hematologic disorders: a real-world cohort study in northern China.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1662559},
pmid = {42359352},
issn = {2296-889X},
abstract = {INTRODUCTION: Infection is a leading cause of death in hematologic disorder patients. While plasma metagenomic next-generation sequencing (mNGS) is widely used, no studies have explored the clinical value of whole blood mNGS, combining plasma and blood cells, in these patients.

METHODS: We retrospectively analyzed the results of whole blood mNGS testing from 231 blood samples of hematological disorders patients with suspected infections. The diagnostic performance of whole blood mNGS and its clinical impacts on treatment were assessed based on the final clinical diagnosis.

RESULTS: mNGS testing in both plasma and whole blood showed significantly higher pathogen detection rates than blood culture (72.29%, 77.06% vs. 21.65%, P < 0.001). The total concordance rate of whole blood mNGS was also significantly higher than that of blood culture, conventional microbial testing, and plasma mNGS when compared to the final clinical diagnosis. Of the 101 pathogens detected by whole blood mNGS, 13 were missed by plasma mNGS. As a result, whole blood mNGS demonstrated a broad pathogen detection capability, especially in patients with non-hematologic malignancies or hematopoietic stem cell transplantation. Regarding treatment, whole blood mNGS had a positive impact on 72.73% of all patients, and 75.15% patients with pulmonary infections. It helped rule out infection in a timely manner, reduce or stop unnecessary antibiotic use, and enabled 77.88% of infected patients to benefit from whole blood mNGS sequencing.

DISCUSSION: Whole blood mNGS assays, combining plasma and blood cells, significantly improved pathogen detection rates and optimized antibiotic therapy in patients with hematological diseases and pulmonary infections or bloodstream infection. This approach facilitates the early management of patients with hematologic disorders who are at risk of infection.},
}

@article {pmid42359485,
year = {2026},
author = {Addy, HPK and Amedorme, D and Osei-Poku, P and Kwarteng, A},
title = {Predicted Functional Potentials of Bacterial Communities in Fermented Maize Products From Ghana, Nigeria, and Benin via 16S rRNA Amplicon Sequencing and PICRUSt2.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70272},
doi = {10.1002/mbo3.70272},
pmid = {42359485},
issn = {2045-8827},
mesh = {RNA, Ribosomal, 16S/genetics ; *Zea mays/microbiology ; *Fermented Foods/microbiology ; Ghana ; Nigeria ; Benin ; *Microbiota/genetics ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; Lactobacillus/genetics/metabolism ; DNA, Bacterial/genetics ; },
abstract = {Fermented maize products are integral to the diets of many African communities. Despite their cultural significance and health benefits, little is known about the metabolic potential of their microbial populations. This study utilized 16S rRNA amplicon sequencing data from the NCBI to characterize the functional capabilities of microbiomes in six maize-based fermented foods. Quality assessment and taxonomic classification were performed using QIIME2 with the SILVA 138 database, while functional predictions were generated with PICRUSt2 and analyzed in R. Taxonomic profiling revealed that Firmicutes dominated all samples, reaching peak abundance in Mawe (94.9%) and S37_Fermented_Maize (91.4%). Proteobacteria were elevated in S19_Fermented_maize (up to 36.5%) and S38_Dehulled_Maize (16.0%). At the genus level, Lactobacillus was most abundant in S5_Mawe (82.2%) and S6_Mawe (79.6%), while Acetobacter peaked in S19_Fermented_maize (32.7%). Regarding functional predictions, Lactobacillus appeared to drive key KEGG Orthologs and pathways, specifically ABC transporters, transcriptional regulation, and DNA replication mechanisms. In contrast, Weissella and Streptococcus contributed notably to peptide/nickel transport, L-lactate dehydrogenase (EC 1.1.1.27), and nucleotide biosynthesis. Acetobacter was prominent in Ogi, showing a connection with site-specific methylation (EC 2.1.1.72) and phospholipid synthesis (PHOSLIPSYN-PWY). Notably, commercial Mawe samples exhibited higher predicted activities related to transposase activity (K07496), energy metabolism, and peptidoglycan maturation (PWY0-1586). These findings demonstrate that while traditional fermentation processes maintain a consistent set of metabolic functions predominantly driven by Lactobacillus, distinct variations exist depending on product type and production approach. These predicted functions provide a baseline for further experimental validation of the metabolic contributions of microbial communities in fermented maize products.},
}

RNA, Ribosomal, 16S/genetics
*Zea mays/microbiology
*Fermented Foods/microbiology
Ghana
Nigeria
Benin
*Microbiota/genetics
Fermentation
*Bacteria/classification/genetics/metabolism/isolation & purification
Sequence Analysis, DNA
Phylogeny
Lactobacillus/genetics/metabolism
DNA, Bacterial/genetics

@article {pmid42359789,
year = {2026},
author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ},
title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2691334},
doi = {10.1080/19490976.2026.2691334},
pmid = {42359789},
issn = {1949-0984},
mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth & development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth & development/metabolism ; },
abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.},
}

*Mucins/metabolism/chemistry
Animals
Humans
*Akkermansia/growth & development/metabolism
Mice
Gastrointestinal Microbiome
Polysaccharides/metabolism
*Dietary Sugars/metabolism
Colon/microbiology
Citric Acid Cycle
*Verrucomicrobia/growth & development/metabolism

@article {pmid42360122,
year = {2026},
author = {Banerjee, P and Al-Bayer, S and Calaor, J and Weber, S and Graham, NR and Andersen, JC and Economo, EP and Kennedy, S and Krehenwinkel, H and Gillespie, RG and Roderick, GK and Rogers, HS and Puliafico, KP},
title = {Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70172},
doi = {10.1111/1755-0998.70172},
pmid = {42360122},
issn = {1755-0998},
support = {RC21-1034//Strategic Environmental Research and Development Program/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; *Biodiversity ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; },
abstract = {DNA-based methods offer a rapid and cost-effective way for detecting species occurrence and monitoring biodiversity; among them, bulk DNA metabarcoding is well-established, and recently developed environmental DNA (eDNA)-based methods offer a non-lethal alternative. With a goal to develop suitable methods for assessing insect biodiversity for understudied island ecosystems where DNA reference libraries are incomplete, we compared established bulk DNA metabarcoding methods with eDNA across three replicated terrestrial ecosystem types (degraded forest, limestone forest, and grassland) on the island of Guam. Using two mitochondrial COI primer pairs, we performed bulk DNA metabarcoding of standard entomological collection methods (Malaise traps, pan traps, and vegetation beating), and compared the assessment of biodiversity with that from different eDNA sources (flowers, leaves, tree trunks, and spider webs). In our samples, eDNA and bulk DNA metabarcoding both detected a large proportion of overall taxa (OTUs, 86.6% and 60.3%, respectively). Although bulk DNA metabarcoding detected significantly more taxa, eDNA proved to be a reasonable non-lethal alternative. As expected, because of limitations in existing reference databases for understudied systems, species-level identification was achieved for only a few OTUs. Overall, the sampling approach was the dominant driver of arthropod diversity, explaining ~17% of the observed variation, while habitat type accounted for ~4%. Thus, each sampling approach captured some unique diversity and contributed to the complementary effect of maximizing detection. For rapid biodiversity surveys of terrestrial arthropods, we recommend integrating metabarcoding approaches, and in sensitive ecosystems where specimen capture is undesirable, eDNA offers a powerful non-lethal alternative to monitor diversity and community change.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*DNA, Environmental/genetics
*Arthropods/genetics/classification
*Biodiversity
*Ecosystem
Electron Transport Complex IV/genetics
*Metagenomics/methods

@article {pmid42360286,
year = {2026},
author = {Shi, Q and Chen, C and Bai, T and Zhang, S and Wu, Y and Wu, H and Luo, H and Chen, Y and Zheng, S and Meng, X and Wu, Y and Gao, J and Wang, Z and Chen, H},
title = {Protein-Free Diet Aggravates Food Allergy Response via the Consumption of Glycochenodeoxycholic Acid in a Murine Model.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c03218},
pmid = {42360286},
issn = {1520-5118},
abstract = {Amino acid-based formulas (AAFs) are increasingly consumed in infants with food allergy (FA), while the effects of their long-term consumption on FA remain poorly known. This study investigated the effects of the long-term consumption of AAFs on FA by subjecting neonatal mice to an amino acid-based diet (AAD). Long-term consumption of AAD exacerbated allergic symptoms, Th2 responses, and mast cell activation and concurrently suppressed the differentiation of CD103[+] DCs and Tregs in the MLN. Furthermore, integrated metabolomics and metagenomics analysis revealed that AAD induced intestinal microbiota dysbiosis and altered the systemic metabolome, characterized by a marked depletion of Bacteroides and glycochenodeoxycholic acid (GCDCA). Critically, oral supplementation with GCDCA effectively attenuated the FA response in AAD-fed mice. In summary, our findings suggest that long-term consumption of AAD aggravates FA via GCDCA depletion, which highlights the necessity to avoid the excessive use of AAFs and positions GCDCA supplementation as a promising therapeutic strategy for FA.},
}

@article {pmid42360299,
year = {2026},
author = {Drahun, I and Chukwunta, A and Ayodele, A and Pilling, BG and van Herk, WG and Cassone, BJ},
title = {Bacteriomes, cryptic forms and evolution of a common wireworm pest species, Hypnoidus bicolor.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.70054},
pmid = {42360299},
issn = {1365-2583},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Like other insects, coleopterans harbour dynamic bacteriomes that shape core aspects of their life history. The bacteriomes of several wireworm species (Coleoptera: Elateridae) have been described; however, little research has been undertaken to determine the factors that influence their structure and composition. These soil-dwelling larvae of click beetles are significant agricultural pests in the Canadian Prairies, with the most ubiquitous species, Hypnoidus bicolor, delineated into two genetically distinct clades and both sexual and parthenogenetic populations. In this study, we collected 69 H. bicolor adults and larvae from nine populations spanning three Prairie provinces and subjected them to Sanger and 16S rRNA gene sequencing to determine their clade and characterize their bacteriome, respectively. Combined with long-term surveillance, we provide compelling evidence that the parthenogenetic and sexual populations are associated with different clades. Development, sampling location and host genetics all contributed to the plasticity of H. bicolor bacteriomes. These differences are largely attributed to gut bacterial community composition of larvae, whereas, in adults, they appear driven by overall community structure as well as differences in the presence/absence of taxa and within-clade/population variance. Several notable genera emerged from our study, including Alphaproteobacteria and Rickettsiella endosymbionts that predominated in the parthenogenetic clade. Incorporation of this research into integrative pest management and reclassification of H. bicolor into a cryptic species complex is also discussed. Overall, this study advances our understanding of Elateridae bacteriomes, including factors that contribute to their richness and community composition.},
}

@article {pmid42360358,
year = {2026},
author = {Meier, DV and Greve, A and de Beer, D and Abed, RMM and Woebken, D},
title = {Sulfide-oxidizing potential and hypersalinity tolerance strategies in salt-crust covered coastal microbial mats.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag166},
pmid = {42360358},
issn = {1751-7370},
abstract = {Hypersaline microbial mats are dense microbial ecosystems capable of performing nearly complete element cycling under harsh conditions including near-saturation salinity. Our previous study of salt-crust covered microbial mats showed that oxygenic photosynthesis was inhibited at salt saturation, while phototrophic sulfide oxidation persisted despite well-known sulfide-oxidizing taxa being undetectable. In this study, we analyzed metagenome-assembled genomes (MAGs) from the same mats to identify sulfide-oxidizing taxa and adaptations enabling oxygenic phototrophs to survive salt saturation. We extended the dataset by including morphologically identical mats exposed to lower salinity regimes to identify metabolic capabilities specifically selected for by saturation-level salinity. The phototrophic sulfide oxidation capability was found in nearly all cyanobacterial MAGs, in some Chloroflexota, and in abundant Rhodovibrio populations previously not known to oxidize sulfide. Furthermore, we found clear indications of Haloarchaea-like potassium-based osmoregulation in Bradymonadaceae (Myxococcota) adding another taxon to the few known potassium-accumulating bacteria. Despite lower oxygen concentrations, salt-crust covered mats showed smaller proportions of fermenters and higher proportions of aerobic microorganisms than lower salinity mats. We compared the genetic signatures of hypersalinity and desiccation tolerance in cyanobacterial MAGs from this study to genomes from desiccation-prone environments such as desert soils and small freshwater streams. Genomes of hyperhalophilic cyanobacteria were characterized by lack of certain potassium transporters and catalase genes and presence of additional osmolyte transporter subunits and sulfide-oxidation genes. We hypothesize that during salt saturation the oxidative stress for mat dwelling cyanobacteria is lowered, while the ability to oxidize sulfide provides them with energy when oxygenic photosynthesis is inhibited.},
}

@article {pmid42360629,
year = {2026},
author = {Liu, KJ and Gao, Y and Yang, X and Xia, Y and Lu, C and Li, ZR and Chu, X and Huang, H and Xu, P and Shi, M and Yuan, K and Yang, H},
title = {Diagnostic Performance and Cost-Effectiveness of BALF mNGS in Older Adults with Pulmonary Infections.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {42360629},
issn = {2193-8229},
support = {KQTD20200820145822023//Shenzhen Science and technology innovation Commission foundation/ ; JCYJ20240813120110015//Shenzhen Science and technology innovation Commission foundation/ ; JCYJ20230807095204008//Shenzhen Science and technology innovation Commission foundation/ ; No. LCYJ2021008//Key Program for Clinical Research at Peking University Shenzhen Hospital/ ; },
abstract = {INTRODUCTION: Pulmonary infections in elderly patients cause high morbidity and mortality. Conventional culture has low sensitivity and slow turnaround, delaying targeted therapy. Metagenomic next-generation sequencing (mNGS) is an emerging technology, but its diagnostic performance and cost-effectiveness are unclear. This study therefore aims to evaluate its diagnostic performance compared to conventional culture in older adults with pulmonary infections and to assess its cost-effectiveness.

METHODS: From March 2020 to March 2023, 522 patients (aged 55-69 years) diagnosed with pulmonary infections were enrolled at Peking University Shenzhen Hospital. Of these, 168 patients underwent simultaneous mNGS and conventional culture testing using bronchoalveolar lavage fluid (BALF) samples, while the remaining 354 patients received culture testing alone. Pathogen detection results were compared to assess the diagnostic performance of mNGS versus traditional culture methods. Additionally, cost-effectiveness analyses of the two diagnostic strategies-as well as the impact of mNGS testing timing post-admission-were conducted in the overall cohort and across stratified subgroups.

RESULTS: Among the 168 patients who underwent both tests, mNGS identified a greater diversity and abundance of microorganisms than culture (overall detection: 89.88% vs. 26.79%; pathogen detection: 67.86% vs. 18.45%, p < 0.001). mNGS testing yielded a net economic benefit of 1202.70 CNY per patient overall and 3831.15 CNY among pathogen-positive cases. Delaying mNGS testing tended to be associated with increased hospitalization length of stay (LOS) and costs, with the most pronounced difference observed around 6 days after admission (p < 0.001). Early mNGS testing (within 6 days of admission) provided a net benefit of 6346.00 CNY.

CONCLUSIONS: BALF-based mNGS showed higher positivity rates and a broader pathogen detection spectrum compared to conventional culture methods in this study. Early implementation of mNGS shows strong potential to guide the treatment of pulmonary infections and reduce healthcare costs for elderly and aging patients.},
}

@article {pmid42361430,
year = {2026},
author = {Horowitz, ML and Shrestha, A and Feng, KH and Pelton, CA and Wells, R and Allen, RF and Clauss, TM and Stokka, D and Cavin, JM and Walsh, MT and Holmes, EC and Allison, AB},
title = {Viral etiology of orogenital papillomatosis and squamous cell carcinoma in bottlenose dolphins in the southeastern United States.},
journal = {Virology},
volume = {623},
number = {},
pages = {111015},
doi = {10.1016/j.virol.2026.111015},
pmid = {42361430},
issn = {1096-0341},
abstract = {Orogenital papillomatosis and squamous cell carcinoma is an emerging yet poorly understood complex disease of bottlenose dolphins (Tursiops truncatus and T. erebennus), both in the wild and under managed care. Previous studies have indicated a potential role of papillomaviruses and/or herpesviruses in the development of oncogenesis, although unbiased metagenomic approaches to examine the disease-associated virome in biopsied lesions have not been performed. Herein, we determined the viruses present in oral and genital lesions from both wild and managed care bottlenose dolphins from the southeastern United States through deep sequencing. The sampled dolphins were infected with two closely related but phylogenetically distinct lineages of delphinid gammaherpesvirus. Multiple different papillomaviruses were also detected, including a new species and several novel types of Tursiops papillomaviruses. Delphinid gammaherpesviruses were detected more often and at higher levels than papillomaviruses in both wild and managed care dolphins, although co-infections with both viruses were common. Additionally, we demonstrate that oral and genital swabs are an effective method for detecting viral infection in dolphins with or without lesions, providing a simple, non-invasive surveillance tool and an adjunct to surgical tissue biopsies. To build diagnostic tools for further study on viral diseases of bottlenose dolphins, we immortalized primary cells from oral frenulum biopsies via retroviral transduction of the simian virus 40 large T antigen gene, which was confirmed by immunoassays and chromosomal mapping. Elucidating the etiologic agent(s) and malignant transformation process of this important disease of dolphins may ultimately lead to the development of targeted therapeutics and/or preventative recommendations.},
}

@article {pmid42361635,
year = {2026},
author = {Tian, L and Lu, JN and Zhang, Y and Zhang, Q and Jiang, G and Yin, Y and Li, L and Fei, YH and Yang, Y and Ruan, Z and Guo, Y and Wang, S and Tang, YT and Chao, Y and Qiu, R},
title = {Overlooked dissemination risk of resistomes in mining soil environments.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142779},
doi = {10.1016/j.jhazmat.2026.142779},
pmid = {42361635},
issn = {1873-3336},
abstract = {Global mining significantly alters soil microbial communities and enriches antibiotic resistance genes (ARGs) via metal co-selection. However, the dissemination of mining-associated resistomes into surrounding ecosystems remains poorly understood. We conducted a national-scale metagenomic investigation of 416 soil samples to characterize the mining resistome and its dissemination potential. Mining soils were notably enriched in bacitracin resistance genes. Host analysis revealed that 60% of ARG-carrying genomes in downstream farmland were shared with mining sites, while source tracking indicated that 57% of quinolone resistance genes in farmlands likely originated from mining areas. Bipartite network analysis further supported this resistome connection from mines to agricultural soils. Using an optimized risk assessment framework, we identified 14 high-risk ARGs, 50% of which were previously unreported. These high-risk ARGs exhibited distinct latitudinal distributions, often associated with uncharacterized hosts. This study provides the first systematic, national-scale evidence of ARG dissemination from mining environments to agricultural ecosystems. By identifying overlooked high-risk ARGs, this research fills critical knowledge gaps in evaluating resistomes from extreme environments and offers essential insights for managing ARG dissemination risks.},
}

@article {pmid42361757,
year = {2026},
author = {Lyu, Y and Bi, X and Tan, Y and Jiang, J and Zhang, Y and Zhou, M and Chen, G and Guo, G},
title = {SANI® process enables sustainable coking wastewater treatment: performance, microbial mechanisms and detoxification.},
journal = {Water research},
volume = {304},
number = {},
pages = {126354},
doi = {10.1016/j.watres.2026.126354},
pmid = {42361757},
issn = {1879-2448},
abstract = {Coking wastewater (CW), characterized by high organic concentration, high toxicity, and poor biodegradability, poses significant challenges for biological treatment. The sulfate reduction-autotrophic denitrification-nitrification (SANI®) process, known for its robustness in treating municipal wastewater with high salinity and low sludge production, has not yet been explored for CW treatment under high-toxicity conditions. This study established a lab-scale continuous-flow SANI system treating real CW at stepwise increasing concentrations (30 %→60 %→100 % of real CW ratio) to investigate toxic pollutants removal performance and sulfur-mediated degradation mechanisms. The SANI process achieved efficient and stable removal of carbon (COD 83.5 %, TOC 93.3 %), nitrogen (NH4[+]-N 97.5 %, TN 85.1 %), and characteristic toxic pollutants (volatile phenols >99 %, SCN[-] >99 %) during 100 % CW treatment, with effluent biotoxicity substantially reduced. 16S rRNA gene sequencing revealed functionally complementary microbial consortia: sulfur-reducing genera (Gudongella, Desulfitobacterium) dominated the anaerobic reactor; mixotrophic denitrifiers (Thauera, Comamonas) enriched in the anoxic reactor; and nitrifiers (Nitrospira) coupled with sulfur-oxidizers (Thiobacillus) prevailed in the aerobic reactor. Metagenomic analysis elucidated complete nitrogen/sulfur metabolic networks and typical toxic pollutant degradation pathways: SCN[-] degradation proceeded via the CNO pathway, while phenol degradation followed the meta-cleavage pathway after hydroxylation. This study pioneers SANI process for sulfur-rich real CW treatment, demonstrating it enables simultaneous removal of carbon, nitrogen, and toxic pollutants-offering a breakthrough low-carbon alternative for industrial wastewater.},
}

@article {pmid42361875,
year = {2026},
author = {Liu, C and Che, C and Huang, P and Gao, J and Wang, S and Ji, B},
title = {Dual carbon source driven metabolic coupling shapes microalgal-bacterial granular sludge stability.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125119},
doi = {10.1016/j.envres.2026.125119},
pmid = {42361875},
issn = {1096-0953},
abstract = {Microalgal-bacterial granular sludge (MBGS) is a viable technology for wastewater treatment, yet its operational stability is often limited under single-carbon conditions due to metabolic imbalance. In this study, six dual carbon strategies were evaluated to investigate their roles in regulating system stability and pollutant removal. The results showed that carbon source composition strongly influenced reactor performance, potentially by pH buffering, thereby reshaping microenvironmental conditions and microbial community structure. Among all conditions, the acetate-glucose system achieved the highest stability, with simultaneous removal of COD (91.1%), NH4[+]-N (96.8%), and PO4[3-]-P (96.9%). Metagenomic analysis and system performance indicated that proton consumption during acetate assimilation likely offset acidification from glucose fermentation, maintaining a favorable alkaline niche (pH 10.0-10.2) that enriched functional bacteria (e.g., Thauera, 4.1%) and enabled simultaneous nitrogen and phosphorus removal. In contrast, the glycerol-glucose system induced severe acidification (pH < 4.0), which suppressed bacterial activity and shifted the community toward acid-tolerant fungi (e.g., Fusarium, 38.9%), resulting in functional deterioration. These findings suggest that pH buffering likely serves as a key regulatory parameter linking carbon metabolism to system stability. Rational pairing of carbon sources with complementary proton fluxes may provide a practical strategy to enhance MBGS robustness and offers a generalizable framework for carbon-source design in biological wastewater treatment.},
}

@article {pmid42361876,
year = {2026},
author = {Chen, S and Zhang, C and Li, P and Li, S and Xing, H and Zhao, Z and Zhang, C and Zhou, D and Huo, H},
title = {Tightened Coupling of Organic Nitrogen and Organic Carbon Synthesis Governs Integrity of Soil Organic Matter in Black Soils.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125123},
doi = {10.1016/j.envres.2026.125123},
pmid = {42361876},
issn = {1096-0953},
abstract = {Soil organic matter (SOM) underpins fertility and carbon sequestration in black soils, yet the regulatory role of soil organic nitrogen (SON) in SOM stabilization remains poorly resolved. Herein, a total of 246 cropland black soils samples spanning three SOM gradients (10 g/kg interval) collected before spring plowing were analyzed using integrated multi-spectroscopic techniques and metagenomics to unravel chemical transformations and microbial mechanisms linking nitrogen and carbon processes. Results demonstrated that SOM accumulation drove a compositional transition from labile polysaccharides-C toward persistent alkyl-C, aromatic-C and aromatic-N containing structures. SON emerged as a dominant regulator of both SOM accumulation and stabilization by promoting aromatization and nitrogen incorporation, thereby enhancing aromaticity and structural persistence. Metagenomic evidences revealed intensified microbial coordination between soil organic carbon (SOC) and SON synthesis under high SOM conditions. On average, 64.8% microbial species encoded concurrent capacities for SOC and SON synthesis under favorable SOM enrichment status. 79.4% higher microbial network interaction and 83.3% stronger coupling intensity between SOC and SON synthesis were observed in favorable SOM enrichment status. Above improvements were attributed to coordinated upregulation of five SOC synthesis pathways and six SON synthesis pathways, with increases ranging from 21% to 57.5% and 24% to 99.8%, respectively. Overall, this study demonstrates that SON is not only a passive component but also an active driver that couples microbial carbon-nitrogen metabolism to govern SOM integrity, providing a novel biological perspective for understanding SOM integrity in black soils.},
}

@article {pmid42361879,
year = {2026},
author = {Ge, Z and Wang, S and Zhang, N and Li, Y and Huang, D and Zhang, J},
title = {Habitat-dependent viral dynamics and auxiliary metabolism in ecological floating beds: implications for biogeochemical function.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125118},
doi = {10.1016/j.envres.2026.125118},
pmid = {42361879},
issn = {1096-0953},
abstract = {Ecological floating beds (EFBs), plant-substrate floating treatment systems, have been widely implemented in aquatic ecological restoration, where microbes play crucial roles in nutrient cycling and material transformation. However, the ecology of viruses in EFBs remains poorly understood. Here, prokaryotic and metagenome-derived viral communities in a full-scale EFB were analyzed over 12 months utilizing 84 samples from biofilms, plant roots, and surrounding water. Viral communities, dominantly by Caudoviricetes (96.7%), exhibited temporal and habitat-dependent responses that contrasted with their prokaryotic hosts. Deterministic processes, primarily temperature and total organic carbon, shaped viral community composition and auxiliary metabolic gene (AMG) repertoires. Temperate viruses were enriched in biofilms and roots (8.91%-13.45%) compared to water (7.75%), indicating distinct interactions with attached prokaryotes and highlighting these niches as potential metabolic hotspots. Virus-host linkage analyses connected viruses to dominant prokaryotes and revealed abundant AMGs (n = 3,703; 238 types), including genes implicated in carbon, phosphorus and sulfur transformations. Furthermore, prokaryotic C/N/P/S-cycling gene repertoires showed stronger coupling in attached habitats, whereas viruses carrying element-cycling AMGs were relatively more abundant in water. These findings provide a genome-resolved view of habitat-dependent viral community structure and auxiliary metabolic potential in EFBs, identifying attached habitats as important compartments for future validation of virus-host interactions and their possible links to restoration-related biogeochemical processes.},
}

@article {pmid42361932,
year = {2026},
author = {Ying, Y and Zheng, X and Yang, J and Ye, H and Dong, Z and Ji, Y and Li, S and Tan, X and Zhang, W},
title = {Tong-Xie-Yao-Fang Ameliorates IBS-D: Potential Role of Alistipes finegoldii-associated Gut Tryptophan Indole Metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {122061},
doi = {10.1016/j.jep.2026.122061},
pmid = {42361932},
issn = {1872-7573},
abstract = {Irritable bowel syndrome with diarrhea (IBS-D) is a prevalent chronic gastrointestinal condition characterized by visceral hypersensitivity, low-grade mucosal inflammation, and impaired epithelial barrier integrity. Current therapies remain limited, highlighting the need for more alternative strategies. Tong-Xie-Yao-Fang (TXYF), a classical Chinese herbal formula, has shown clinical efficacy in IBS-D, however, the mechanisms underlying its therapeutic effects remain unclear.

AIM OF THE STUDY: This study aimed to investigate whether and how TXYF exerts therapeutic effects by modulating colonic tryptophan metabolism, with a particular focus on the gut microbiota.

MATERIALS AND METHODS: IBS-D model was induced by combining chemical irritation and wrap restraint stress in C57BL/6J mice, and multi-omics approaches were employed to identify specific microbiota and metabolites modulated by TXYF. The multi-omics findings were further verified in vivo and in vitro.

RESULTS: TXYF treatment significantly alleviated IBS-D symptoms in our model. Non-targeted metabolomics identified the tryptophan-indole pathway as a key axis modulated by TXYF, with indole-3-acetic acid (IAA) emerging as a prominent differential metabolite in colonic tissue. Western blot analysis showed that TXYF activated the aryl hydrocarbon receptor (AhR) in the colon. Integrative metagenomic and metabolomic analyses revealed a strong association between Alistipes finegoldii and colonic indole and IAA levels. Consistent with these findings, transplantation of A. finegoldii combined with tryptophan supplementation, or administration of IAA alone, recapitulated the therapeutic effects of TXYF against IBS-D. In vitro, both IAA and faecal supernatant from TXYF-treated mice protected against tumour necrosis factor-induced epithelial barrier disruption in an AhR-dependent manner.

CONCLUSION: Collectively, the present study suggests that the therapeutic efficiency of TXYF against IBS-D is closely associated with its ability to modify microbiota-derived colonic IAA production, with gut microbiota member Alistipes finegoldii playing a key role in this effect.},
}

@article {pmid42361963,
year = {2026},
author = {Loc, DH and Sulesco, T and Tóth, GE and Lühken, R and Schmidt-Chanasit, J and Velavan, TP},
title = {First Mosquito-Based Molecular Evidence of Tembusu Virus in Vietnam.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108927},
doi = {10.1016/j.ijid.2026.108927},
pmid = {42361963},
issn = {1878-3511},
abstract = {BACKGROUND: Mosquito borne flavivirus diversity in Vietnam remains incompletely characterized. Tembusu virus (TMUV), an emerging flavivirus associated with ducks and other avian hosts, has been reported in poultry in Vietnam, but molecular evidence from field-caught mosquitoes has been lacking.

METHODS: We screened 10,658 mosquitoes representing four major arbovirus vector species including Aedes aegypti, Ae. albopictus, Culex quinquefaciatus, Cx. tritarniorhynchus, collected across multiple ecological settings in Vietnam. Mosquitoes were grouped into 586 pools and tested using broad range RT-PCR assays targeting flaviviruses and alphaviruses. Positive flavivirus amplicons were subjected to sequencing, and one TMUV positive pool underwent deeper sequencing and phylogenetic analysis.

RESULTS: The Cx. tritaeniorhynchus pool (25 specimens) collected in rural southern Vietnam yielded a TMUV draft genome. In the complete genome phylogeny, the Vietnamese mosquito derived sequence clustered within a distinct monophyletic clade comprising strains from China, Thailand, Taiwan, and Vietnam.

CONCLUSIONS: These findings provide the first mosquito-based molecular evidence of a TMUV related virus in Vietnam and suggest that mosquito surveillance can reveal previously unrecognized viral diversity and transmission patterns.},
}

@article {pmid42362546,
year = {2026},
author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74744-z},
pmid = {42362546},
issn = {2041-1723},
abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.},
}

@article {pmid42362550,
year = {2026},
author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R},
title = {Remodelling of the gut virome after long-term fasting.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42362550},
issn = {2055-5008},
abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.},
}

@article {pmid42362787,
year = {2026},
author = {Sinha, B and Khandeparker, L},
title = {Seasonal variation in plastic-associated biofilm microbial assemblages: a microcosm approach.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42362787},
issn = {1573-2959},
abstract = {Plastic pollution in natural ecosystems creates novel niches, known as the "Plastisphere", that host heterogeneous microbial communities shaped by substrate type and environmental conditions. This study explored the effects of seasonal variation on the plastisphere evolution on different plastic substrates, oxo-degradable carrier bags (Oxo), oxo-degradable garbage bags (Oxo-G), normal plastics (N), and snack packets (Sn) for 30 days in a microcosm experiment using ambient water from the monsoon-influenced Zuari estuary. The results indicated that the early-stage (day 5) plastisphere was dominated by fast-growing r-strategists, such as Alpha- and Gamma-proteobacteria as well as Campylobacterota-related lineages, whereas mature biofilms (day 30) showed increased abundance of secondary colonisers, including Planctomycetota, Actinomycetota, and Bacteroidota. The oxo-degradable plastics emerged as preferred substrates, likely due to their prooxidant-mediated abiotic degradation and the novel nature of the conditioning film. Salinity, in conjunction with nutrient concentrations, emerged as a major driver of microbial abundance in the plastisphere. Though the putative pathogens, such as Vibrio spp. and total coliforms, were present at very low abundance in the aged plastisphere during the SW-Mon and PostM seasons, their persistence indicates their resilience even under nutrient-limited conditions. Although a closed microcosm system probably introduced bottle effects, influencing temporal changes in nutrient levels and microbial abundance, the study provides baseline insights into substrate- and season-driven patterns of plastisphere development. Overall, these findings underscore the dynamic interplay among various factors, including plastic types and seasonal environmental shifts, in shaping plastisphere maturation. This has potential implications for public health and ecosystem functioning in the natural marine environment. Employing functional metagenomics analysis in future in situ studies of plastisphere communities can provide further insights and is a way forward for predicting associated ecological risks.},
}

@article {pmid41499025,
year = {2026},
author = {Cunanan, DJ and Carandang, THDC and Pilapil, JD and Cunanan, DJ and Mollasgo, AG and Manalo, GNS and Co, GS and Rosch, J and Carroll, K and Notarte, KI},
title = {Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {45},
number = {4},
pages = {1077-1091},
pmid = {41499025},
issn = {1435-4373},
abstract = {PURPOSE: Accurate and timely diagnosis is essential to ensure effective management of bacterial pneumonia to improve patient outcomes. This study aims to evaluate the use of metagenomic nanopore sequencing in the microbiological diagnosis of pneumonia compared to standard diagnostic procedures. METHODS: A comprehensive literature search across multiple databases was performed. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy 2 (QUADAS-2) tool. Pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and area under the curve (AUC) were determined. RESULTS: Thirteen studies were included in the systematic review, with eight eligible for meta-analysis. In the microbiological diagnosis of bacterial pneumonia, the overall sensitivity of nanopore sequencing using both MinION and GridION platforms is 86.08% (95% CI 75.96–92.37) while specificity is 84.97% (95% CI 75.94–91.02). Results show a high PPV (85.13%; 95% CI 77.72–90.38) and high NPV (85.27%; 95% CI 76.79–91.01). Nanopore sequencing also has a high diagnostic value based on the computed AUC (0.922) and DOR (40.68; 95% CI 11.22–147.48). Sensitivity analyses suggest a trend toward higher diagnostic accuracy for bacterial pneumonia with the MinION device and lower accuracy with the GridION platform. We also found that accuracy is higher when the focus of diagnosis is ventilator-associated pneumonia (VAP) and when endotracheal aspirate alone is utilized as the sample type. CONCLUSIONS: Nanopore sequencing offers faster, real-time results compared to traditional culture. It also shows higher specificity than short-read metagenomic next-generation sequencing (mNGS), particularly in ventilator-associated pneumonia. Further research is warranted for subgroup analyses to optimize the use of nanopore sequencing in detecting bacterial pneumonia.},
}

@article {pmid41511674,
year = {2026},
author = {Yin, Q and Mei, X and Ma, Y and Zheng, M},
title = {Central nervous system infections caused by carbapenem-resistant klebsiella pneumoniae after CAR T-cell therapy in a patient with preexisting colonization: a case report and literature review.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {45},
number = {5},
pages = {1491-1499},
pmid = {41511674},
issn = {1435-4373},
support = {81974005//National Natural Science Foundation of China/ ; Y-SYBLD2022MS-0055//the Beijing Xisike Clinical Oncology Research Foundation/ ; 2025AFD777//the Joint Fund for Innovation and Development of Natural 205 Science Foundation of Hubei Province/ ; },
abstract = {OBJECTIVE: To investigate the risk factors for corresponding infections following chimeric antigen receptor (CAR) T-cell infusion in Carbapenem-resistant Enterobacteriaceae (CRE) carriers and to provide insights for managing such cases. METHODS: A retrospective analysis was performed on the clinical presentation, laboratory findings, treatment, and prognosis of a patient with preexisting colonization who developed CRE intracranial infection after CAR T-cell therapy. A systematic review of the literature was conducted to explore optimal antibiotic strategies for CRE-associated central nervous system infections. RESULTS: Carbapenem-resistant Klebsiella pneumoniae was detected in perianal swabs before preconditioning chemotherapy, and the patient subsequently received high-dose corticosteroids for cytokine release syndrome and immune effector cell-associated neurotoxicity syndrome following CAR T-cell infusion. Despite broad-spectrum coverage, recurrent fevers and convulsions ensued. Metagenomic next-generation sequencing of cerebrospinal fluid on day +14 confirmed Kbsiella pneumoniae infection, later identified as a multidrug-resistant strain. Clinical and microbiological clearance was achieved following combination therapy centered on intravenous ceftazidime-avibactam, supplemented with intrathecal polymyxin B, guided by antibiotic susceptibility testing. The patient ultimately died three months later due to lymphoma progression. CONCLUSION: Defining optimal management strategies for CRE carriers is essential to integrate infection risk mitigation into the personalized framework of CAR T-cell therapy.},
}

@article {pmid41654923,
year = {2026},
author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY},
title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41654923},
issn = {1479-5876},
support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.},
}

@article {pmid41779333,
year = {2026},
author = {Hu, Y and Li, A and Qiu, S and Zhu, T and Guo, J and Zhang, W and Zhao, C and Lyu, Y},
title = {Characteristics of Multispecies Bacterial Cocultures for the Removal of Ammonia, Nitrate, and Nitrite from Water.},
journal = {Applied biochemistry and biotechnology},
volume = {198},
number = {5},
pages = {3811-3830},
pmid = {41779333},
issn = {1559-0291},
support = {2025AFD305//Hubei Provincial Natural Science Foundation - Yichang Innovation and Development Joint Fund/ ; },
abstract = {The removal of ammonia, nitrate, and nitrite from wastewater is essential for controlling nitrogen pollution. However, the efficiency of biological nitrogen removal is often limited by the scarcity of highly active bacterial strains. In this study, a coculture system, designated YEM003, was constructed using eight nitrogen-metabolizing bacterial strains isolated from the same activated sludge. YEM003 exhibited robust nitrogen removal performance, effectively eliminating ammonia, nitrate, and nitrite from wastewater under varying oxygen conditions. Metagenomic analysis revealed enrichment of key genes involved in nitrogen metabolism and elucidated nitrogen removal pathways of YEM003. Due to the unbalanced abundance distribution of the eight strains in YEM003, the contributions of each strain to the nitrogen removal metabolism in different wastewaters differed significantly. Overall, YEM003 exhibits comprehensive and efficient biological nitrogen removal capabilities and shows strong potential for application in wastewater nitrogen removal processes.},
}

@article {pmid41803286,
year = {2026},
author = {Zhu, C and Zhu, Y and Gao, H and Wang, X and Guo, Y and Sun, H and Qi, M and Zhang, B and Hu, Y},
title = {Long-Term Preservation of Humid Earthen Sites: Shelter Efficacy, Essential Oil Dynamics, and Microbial Adaptation.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41803286},
issn = {1432-0991},
support = {2023C03G1752302//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
abstract = {This study evaluates the long-term conservation of humid earthen archaeological sites using protective shelters and plant essential oil treatments at the Laohuling Dam (Liangzhu, China), a UNESCO World Heritage site. Over seven years (2017–2024), structural deterioration, biological colonization, and microbial community dynamics were monitored through field surveys, amplicon sequencing (16 S rRNA and ITS), and shotgun metagenomics. Protective shelters effectively reduced large-scale structural damage and higher-plant colonization; however, enclosed and climate-controlled conditions promoted persistent microbial biofilms in high-humidity zones. Oregano essential oil treatments rapidly eliminated visible biofilms and suppressed recolonization for approximately 6–8 months, but did not prevent long-term microbial recovery. Post-treatment communities shifted from phototrophic and biofilm-forming taxa toward fast-growing, opportunistic heterotrophs, predominantly affiliated with Pseudomonadota. Metagenomic analyses revealed a stable resistome across consecutive treatment years. The high abundance of multidrug resistance genes (e.g., adeF, β-lactam- and CAMP-associated genes) primarily reflected the dominance of Pseudomonadota-related taxa rather than evidence of resistance evolution driven by essential oil application. No significant increase in resistance gene diversity or abundance was detected. These findings demonstrate that sheltering and essential oil treatments are effective short-term conservation tools but reshape microbial succession rather than eliminating biological risks. Long-term preservation of humid earthen sites therefore requires integrated strategies combining microclimate control, low-bioreceptivity materials, and continuous microbial monitoring.},
}

@article {pmid41998050,
year = {2026},
author = {Gao, Y and Kim, J and Wu, R and Chowdhury, NB and Lee, JY and Nicora, CD and Moore, RJ and Monroe, ME and Jansson, JK and Burnum-Johnson, KE},
title = {Metaproteomics uncovers the functional capacity of a soil microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47816-9},
pmid = {41998050},
issn = {2045-2322},
support = {Early Career Research Program//U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research/ ; },
abstract = {The soil microbiome plays a vital role in key ecosystem processes, but its functional capacity remains poorly understood. Microbial activities underpin many applications in environmental biotechnology, such as nutrient cycling, contaminant degradation, and the recovery and transformation of minerals and elements. However, analyzing the complex soil metaproteome is challenging. Here, we propose an approach to explore soil metaproteomes, which will improve our understanding of the metabolic potential within the soil microbiome. As a proof of concept, we generated high-quality metaproteomes from native prairie soil using high-resolution tandem mass spectrometry. Over 15,000 peptides were identified using paired metagenomes. By using lowest common ancestor method, the peptides were conservatively assigned to 21 bacterial, fungal, and archaeal phyla or superphyla, including rare soil bacterial phyla such as Candidatus Tectomicrobia, as well as viruses. Functional analysis at the pathway level was performed using complementary KEGG and MetaCyc databases, revealing essential biogeochemical cycles, such as carbon and sulfur cycling. By combining taxonomic and functional analyses, we disentangled the relative contributions of individual soil microbial phylum-level taxon to community metabolic functions. This study highlights the importance of taxon-resolved functional analysis enabled by soil metaproteomics, surpassing the capabilities of other single-omics methods. It offers new insights into how individual microbes function within complex soil microbiomes, paving the way for more targeted microbial strategies to improve system performance in bioeconomy applications.},
}

@article {pmid42029951,
year = {2026},
author = {Kallistova, A and Savvichev, A and Toshchakov, S and Tutubalina, N and Rusanov, I and Petrova, K and Kadnikov, V and Beletsky, A and Zakharova, E and Ravin, N and Pimenov, N},
title = {Structure and Metabolic Potential of Microbial Communities in High-altitude Lake Enriched with Dissolved Organic Carbon.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42029951},
issn = {1432-0991},
support = {22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; 22-14-00038-C//Russian Science Foundation/ ; },
abstract = {It is evident that climate change is causing glaciers to melt at an accelerated rate. This has a noticeable impact on the hydrological regime of high-altitude lakes, as well as the activity of microbial communities. However, the impact of climate change on microbial processes, abundance and diversity of microbial communities in high-altitude lakes remains to be elucidated. The objective of the study was to evaluate the structure, activity and metabolic capacity of microbial communities inhabiting the high-altitude Caucasus lake. Analytical and radiotracer methods were used together with 16S rRNA profiling, and metagenome analyses. Elevated concentrations of dissolved organic carbon (DOC) were observed in both the water column of the lake (12.2–19.4 mg/l) and the pore water of the sediments (6.3–15.8 mg/l). The intensity of photosynthesis in water column was very low. The bulk of phototrophs concentrated on the sediment surface where we suggest they produce organic matter due to sufficient light penetration and warming of the overlying water. The elevated DOC concentrations facilitated the activity of diverse heterotrophic microorganisms, resulting in oxygen depletion and activation of anaerobic processes in sediments. In case of an increase in the average annual temperature of the region, it is possible to predict the transformation of the lake into a eutrophic meromictic reservoir with constantly anoxic water layers, where sulfate reduction and methanogenesis would assume a pivotal role.},
}

@article {pmid42047869,
year = {2026},
author = {Gloanec, N and Huré, M and Bailly, L and Petit, É and Loutelier-Bourhis, C and Goux, D and Coëffier, M and Ribet, D},
title = {Pilosibacter rotomagensis sp. nov., a Butyrate-Producing Bacterium Isolated from Human Faeces.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42047869},
issn = {1432-0991},
support = {SUMONING ANR-22-CE14-0064-01//Agence Nationale de la Recherche/ ; Labex SynOrg ANR-11-LABX-0029//Agence Nationale de la Recherche/ ; ANR-18-EURE-0020 XL CHEM//Agence Nationale de la Recherche (FR)/ ; },
abstract = {Isolating bacteria from the human gut microbiota and analyzing their phenotypes is essential for complementing the data obtained by metagenomics and for characterizing the functions of these microorganisms in human physiology. In this study, we isolated bacteria from the gut microbiota of healthy individuals and identified an uncharacterized bacterial strain that we designated HC1M1C21T. Phylogenetic analyses based on 16S rRNA and whole genome sequences indicated that this strain belongs to the family Lachnospiraceae. The closest relative of strain HC1M1C21T is Pilosibacter fragilis CSJ-4T (97.0% 16S rRNA gene sequence identity). P. fragilis was initially classified in the family Clostridiaceae. Based on our phylogenetic analyses, we propose to transfer the genus Pilosibacter from the family Clostridiaceae to the family Lachnospiraceae. HC1M1C21T has a DNA G + C content of 48.7%. This strain is anaerobic, Gram-stain-positive, non-motile and non-spore-forming. HC1M1C21T cells appear as single rods or chained rods with tapered ends. Optimal growth was observed at 37°C, at pH between 5.7 and 7.0 and at salinity below 10 g/L. HC1M1C21T is a potent butyrate producer. On the basis of these data, HC1M1C21T represents a novel species from the genus Pilosibacter, for which the name Pilosibacter rotomagensis sp. nov. is proposed. The type strain of P. rotomagensis is HC1M1C21T (= DSM 119410T=LMG 33828T).},
}

@article {pmid42062386,
year = {2026},
author = {Szklenarik, G and Dora, D and Szincsak, S and Acquah, CK and Biswas, A and Horváth, M and Galffy, G and Lohinai, Z},
title = {The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47296-x},
pmid = {42062386},
issn = {2045-2322},
abstract = {Chronic obstructive pulmonary disease (COPD) is increasingly recognized as a systemic disorder affecting host–microbiome interactions beyond the airways. Although bacterial alterations in COPD have been documented, the gut mycobiome and its ecological integration with bacterial communities remain unexplored. In this study, we profiled the gut mycobiome of 61 non-small-cell lung cancer (NSCLC) patients stratified by COPD severity using ITS2 sequencing and analyzed 47 overlapping patients with available metagenomic data to construct cross-kingdom bacterial–fungal networks. Alpha diversity, assessed by Shannon, Simpson, and Chao1 indices, did not differ significantly between patients with and without severe COPD. Partial least squares discriminant analysis (PLS-DA) revealed partial separation of the two groups, with COPD severity explaining 6% of overall compositional variance (R[2]=0.06, p = 0.058). COPD-severe patients exhibited a significantly reduced Ascomycota/Basidiomycota ratio (p = 0.039) and lower relative abundance of Mucoromycota. Analysis of compositions of microbiomes (ANCOM) identified Myrothecium and Lasiodiplodia crassispora enriched in severe COPD, while Helotiales_unclassified and Phallus atrovolvatus were more abundant in non-severe cases. Fungal co-occurrence networks demonstrated reduced connectivity and modularity in severe COPD compared with non-severe COPD. Cross-kingdom analyses integrating bacterial genera revealed strengthened Candida–Enterococcus/Clostridium hubs and weakened Faecalibacterium/Roseburia–yeast associations in severe disease. Keystone analysis showed increased centrality for Candida, Aspergillus, Enterococcus, and Clostridium, and decreased centrality for Akkermansia and Roseburia. A compositional balance classifier achieved high discriminatory power (AUC = 0.88) in distinguishing COPD-severe from non-severe patients. These findings indicate that COPD severity is not characterized by major diversity loss but by guild-specific compositional shifts and extensive network rewiring, favoring oxygen-tolerant, opportunistic taxa over short-chain fatty acid–associated commensals.},
}

@article {pmid42343068,
year = {2026},
author = {He, G and Liu, T and Xing, J and Rao, L and Chen, S and Xie, C and Wei, G and Quan, X},
title = {In Situ Quorum Quenching Effect Induced by Negative Potential on Electro-Conductive Membranes for Membrane Fouling Control in Membrane Bioreactors.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04557},
pmid = {42343068},
issn = {1520-5851},
abstract = {Membrane fouling is a major impediment to the widespread application of membrane bioreactors (MBRs) for water treatment. In recent years, the electro-conductive membrane bioreactor (E-MBR) has demonstrated efficacy in mitigating membrane fouling. The application of a negative potential to the electro-conductive membrane promotes electrostatic repulsion, effectively displacing negatively charged extracellular polymeric substances (EPS) away from the membrane surface. However, given the established vital role of quorum sensing (QS) in membrane fouling development, the interference of the negative potential on QS-mediated EPS secretion and biofilm formation has been largely overlooked. Herein, we found that the negative potential applied to the electro-conductive membrane could effectively suppress the QS process, thereby inducing the in situ quorum quenching (QQ) effect. The application of negative potential significantly reduced the levels of the signal molecule C14-HSL as well as EPS. Metagenomic analysis indicated that the relative abundance of the "signal transduction mechanism" pathway was suppressed, and the functional genes encoding C14-HSL receptor proteins belonging to "LuxR family" was downregulated in the cake layer of E-MBR. Density functional theory calculations and molecular dynamics simulation results revealed that the application of negative potential enhanced the electrostatic repulsion between the membrane and C14-HSL and induced the conformational changes of the LuxR protein, which synergistically induced the in situ QQ effect. This study provides a novel perspective on the antifouling mechanism in E-MBR.},
}

@article {pmid42343220,
year = {2026},
author = {Nichols, H and Molokin, A and Davies, CP and Maloney, JG},
title = {Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05298-9},
pmid = {42343220},
issn = {1471-2180},
support = {8042-32000-112-00-D//USDA, ARS/ ; },
abstract = {BACKGROUND: Microeukaryotic parasites of the intestinal tract are an understudied group of organisms that infect humans and many other animals. Targeted sequencing methods focused on individual loci are usually employed for detection of these parasites, making comprehensive studies of microeukaryotic parasite diversity within hosts or other systems difficult. Exploratory approaches such as shotgun metagenomic sequencing to survey the diversity of microeukaryotic parasites in new and existing datasets are not well developed.

RESULTS: Utilizing existing datasets from 12 goose fecal samples, we explored some of the benefits and challenges of using shotgun metagenome sequencing to detect microeukaryotic parasites. We demonstrated the importance of careful curation of read classification data to avoid erroneously linking pathogens to hosts or environments as unsupported classifications were common in the data and varied widely depending on analysis parameters. However, we were able to establish strong support for the presence of sequences of Eimeria and Enterocytozoon bieneusi. In addition, examination of trichomonad reads indicated that parasite reads mapping to human pathogens unlikely to colonize geese may in fact represent cryptic microeukaryotic species that are not included in existing curated databases opening new potential avenues of study.

CONCLUSIONS: Taken together these findings support the idea that exploring microeukaryotic parasite diversity within shotgun metagenomic datasets can be beneficial to our understanding of the presence and diversity of these organisms in wildlife hosts.},
}

@article {pmid42343233,
year = {2026},
author = {Suenaert, P and Segers, A and Rymenans, L and Devroye, H and Moll, JM and Cani, PD and de Vos, WM},
title = {Effect of pasteurized Akkermansia muciniphila MucT on insulin sensitivity, body composition, and GLP-1 production in subjects with metabolic syndrome: impact of low baseline gut Akkermansia levels.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690689},
doi = {10.1080/19490976.2026.2690689},
pmid = {42343233},
issn = {1949-0984},
mesh = {Humans ; *Metabolic Syndrome/metabolism/microbiology/therapy ; Female ; Middle Aged ; *Glucagon-Like Peptide 1/metabolism ; Male ; *Insulin Resistance ; Double-Blind Method ; *Probiotics/administration & dosage ; *Body Composition ; Adult ; Akkermansia ; *Verrucomicrobia ; Gastrointestinal Microbiome ; Pasteurization ; Prediabetic State/metabolism ; Aged ; },
abstract = {Pasteurized Akkermansia muciniphila MucT was found to improve barrier function in preclinical models and a proof-of-concept study in obese and prediabetic adults. Here, we describe the results of a double-blind placebo-controlled multicenter (Ireland and Germany) trial in 142 adults with metabolic syndrome, with or without prediabetes. The primary endpoint of whole-body insulin sensitivity (Matsuda index) did not differ after 4-months of daily administration of capsules containing 30 billion cells of pasteurized A. muciniphila MucT compared to placebo in the intention-to-treat subjects. Subsequent exploratory analyses showed that 3-months intake of pasteurized A. muciniphila MucT already improved HOMA-based hepatic insulin sensitivity in prediabetic (12%; p = 0.05) and 63-y-or-older-age subgroups (p = 0.05) while increasing post-OGTT excursion of the insulinotropic hormone glucagon-like peptide 1 (GLP-1) over placebo (p < 0.01). Further analysis of the gut microbiota by deep metagenomic analysis showed minor effects of the intervention but revealed that the baseline microbial composition differed from that in matched healthy adults. We found that participants with low baseline Akkermansia gene counts experienced significant health improvements and GLP-1 excursion after 3-months of treatment with pasteurized A. muciniphila MucT over the placebo. These benefits included improved insulin sensitivity (as shown by Matsuda and HOMA-S indices) and GLP-1 excursion (post-OGTT) (p < 0.05), reductions in body weight (p = 0.06) and decreased trunk fat (p < 0.05). In conclusion, daily supplementation with pasteurized A. muciniphila MucT has the potential to improve health markers in overweight or obese normo- or dysglycemic adults with the most significant improvements in subjects with low baseline intestinal Akkermansia levels, who are apparently truly in need of this intervention. Clinical trial registration no.: NCT05114018 clinicaltrials.gov.},
}

Humans
*Metabolic Syndrome/metabolism/microbiology/therapy
Female
Middle Aged
*Glucagon-Like Peptide 1/metabolism
Male
*Insulin Resistance
Double-Blind Method
*Probiotics/administration & dosage
*Body Composition
Adult
Akkermansia
*Verrucomicrobia
Gastrointestinal Microbiome
Pasteurization
Prediabetic State/metabolism
Aged

@article {pmid42343345,
year = {2026},
author = {Huang, H and Ye, X and Gu, D and Huang, E and Yu, X and Ai, L and Deng, J and Guo, P and Liu, H and Chen, Y and Wang, R and Luo, Y and Chen, P},
title = {Blood-based targeted sequencing of microbial cell-free DNA in severe pneumonia-associated sepsis.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03786-0},
pmid = {42343345},
issn = {1465-993X},
support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2022B1111020003//2021 Guangdong Province Key Areas Research and Development Plan "Biosafety Technology" Key Project/ ; 2023P-TS46//Featured Clinical Technique of Guangzhou/ ; 0720240122//Guangdong Provincial Center for Disease Control and Prevention Supports Talent Projects/ ; },
abstract = {BACKGROUND: Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) improves pathogen detection in severe pneumonia-related sepsis, but sampling is invasive and prone to false-positive results. Blood is easier to obtain, and broad-spectrum targeted NGS (tNGS) of microbial cell-free DNA may offer a practical alternative to BALF-based testing. We evaluated the diagnostic and prognostic value of blood-based bstNGS.

METHODS: In this retrospective cohort, 122 adults with suspected severe pneumonia-related sepsis and paired BALF and blood samples underwent BALF-mNGS, blood-bstNGS and blood-mNGS. Pathogens were adjudicated using a composite clinical reference. We assessed blood-BALF concordance, compared diagnostic performance across methods, and examined whether blood-bstNGS could down-weight likely false-positive BALF-only detections and stratify prognosis.

RESULTS: BALF-mNGS identified 414 microorganisms; 51% were adjudicated as causative or possibly causative, corresponding to 85.24% of patients. Among these pathogenic microorganisms, blood-bstNGS detected 45.02%, significantly more than blood-mNGS (22.27%), and nearly all pathogens detected by blood-mNGS were also detected by blood-bstNGS. Against the clinical reference, blood-bstNGS showed higher sensitivity (63.46%) than blood-mNGS (35.58%), conventional microbiological tests (CMTs) (49.04%), and blood culture (9.62%). Organisms detected only in BALF but not in blood were less likely to be classified as causative. Patients with concordant blood-bstNGS and BALF-mNGS profiles had significantly lower 30-day and 90-day mortality.

CONCLUSIONS: In severe pneumonia-related sepsis, blood-bstNGS provides sensitive, non-invasive pathogen detection. It acts as a complementary tool rather than a replacement for BALF-mNGS, offering an important diagnostic alternative when BALF is unavailable and improving specificity and prognostic utility when used in combination.},
}

@article {pmid42343457,
year = {2026},
author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X},
title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02453-2},
pmid = {42343457},
issn = {2049-2618},
abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.

RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.

CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.},
}

@article {pmid42343580,
year = {2026},
author = {Cuau, M and Avalon, NE and Ryu, B and Glukhov, E and Almaliti, J and Rego, A and Teixeira, TR and Shingyoji, M and L De Souza, M and Trinidad-Javier, A and Kumpornsin, K and Chen, J and McNamara, CW and Caffrey, CR and Winzeler, EA and Vasconcelos, VM and Leão, PN and Gerwick, WH},
title = {AI-Accelerated Structure Elucidation of Boavistamides A-C, Cyclic Depsipeptides from a Marine Filamentous Cyanobacterium Collected in Cabo Verde.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.6c00391},
pmid = {42343580},
issn = {1520-6025},
abstract = {Boavistamide A (1), a new alkyne-containing cyclic depsipeptide featuring the rare 3-amino-2-methyl-7-octynoic acid (AMOYA) moiety, was discovered along with two structurally related analogs, boavistamides B and C (2 and 3), from a filamentous marine cyanobacterium collected on Boa Vista Island, Cabo Verde. Their isolation was guided by antiplasmodial activity, GNPS MS/MS molecular networking, LC-MS profiling, and dereplication using the MarinLit database. The planar structures of boavistamides A-C (1-3) were elucidated through comprehensive HRMS and 1D/2D NMR analyses, with annotation support from AI-based tools SMART-NMR 2.1 and DeepSAT. The absolute configurations were established using Marfey's analysis and l-Phe-OMe coupling, complemented by NMR-based conformational studies. Boavistamides A and B exhibited moderate antiplasmodial activity with no mammalian cell cytotoxicity. Microscopic observations and metagenomic binning identified the producer strain as belonging to the genus Okeania (Microcoleaceae). These results expand the chemical diversity of AMOYA-containing cyanobacterial metabolites and highlight the utility of integrated metabolomics and AI-assisted workflows for natural product discovery from environmental samples.},
}

@article {pmid42343765,
year = {2026},
author = {Qiu, X and Lei, Z and Wang, J},
title = {[Effects of graphene sol on the root growth of tomato seedlings and the rhizosphere soil microbiota].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {42},
number = {5},
pages = {2103-2113},
doi = {10.13345/j.cjb.250783},
pmid = {42343765},
issn = {1872-2075},
support = {Y2022036//the Youth Innovation Promotion Association CAS/ ; },
mesh = {*Solanum lycopersicum/growth & development/drug effects ; *Plant Roots/growth & development/drug effects ; *Seedlings/growth & development/drug effects ; *Rhizosphere ; *Soil Microbiology ; *Graphite/pharmacology ; *Microbiota/drug effects ; Soil/chemistry ; Nitrogen/metabolism ; },
abstract = {Graphene exhibits broad application potential in agriculture due to its unique physical and chemical properties. In home gardening, low survival rates of seedlings during the early transplanting stage represent a common challenge, yet whether graphene can ameliorate this problem remains underexplored. This study analyzed the root growth rate, soil nutrients, and soil microbiota of tomato seedlings in response to graphene sol treatment. The results revealed that graphene sol at concentrations of 50 mg/L and 100 mg/L promoted root growth, while that at higher concentrations exhibited inhibitory effects. Furthermore, all tested concentrations of graphene sol led to a decrease in soil organic matter content and an increase in available nitrogen content. Metagenomic sequencing revealed that 50 mg/L and 100 mg/L graphene sol treatments enhanced the abundance of soil microorganisms that promote humus and organic matter decomposition, participate in soil nitrogen cycling, and mediate heavy metal metabolism. In conclusion, appropriate concentrations of graphene sol can improve the root growth, increase the soil nitrogen availability, and enrich specific beneficial microorganisms of tomato seedlings during the early transplanting stage. These findings provide a theoretical reference for the rational application of graphene-based materials in home gardening.},
}

*Solanum lycopersicum/growth & development/drug effects
*Plant Roots/growth & development/drug effects
*Seedlings/growth & development/drug effects
*Rhizosphere
*Soil Microbiology
*Graphite/pharmacology
*Microbiota/drug effects
Soil/chemistry
Nitrogen/metabolism

@article {pmid42343869,
year = {2026},
author = {Liang, P and Zhang, X and Cai, S and Hu, Z and Dong, L},
title = {Invasive aspergillosis in autoimmune inflammatory rheumatic diseases: epidemiology, risk factors, diagnosis, management and challenges.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2685285},
doi = {10.1080/07853890.2026.2685285},
pmid = {42343869},
issn = {1365-2060},
mesh = {Humans ; *Rheumatic Diseases/immunology/complications/drug therapy/epidemiology ; Risk Factors ; *Autoimmune Diseases/immunology/complications/drug therapy/epidemiology ; Aspergillus/immunology/isolation & purification ; Immunosuppressive Agents/adverse effects ; Immunocompromised Host ; *Opportunistic Infections/epidemiology/diagnosis/immunology ; Antifungal Agents/therapeutic use ; *Invasive Pulmonary Aspergillosis/epidemiology/diagnosis ; Aspergillosis/diagnosis/epidemiology ; },
abstract = {BACKGROUND: Invasive aspergillosis (IA) is a life-threatening opportunistic fungal infection caused by Aspergillus species. In recent years, IA appears to have become more frequently reported among patients with autoimmune inflammatory rheumatic diseases (AIIRD), likely reflecting the broader use of immunosuppressive therapies, with incidence in high-risk AIIRD subgroups reported to reach approximately 6.7% in selected cohorts.

OBJECTIVE: This review aims to summarize the current evidence on the epidemiology, susceptibility mechanisms, risk factors, clinical presentation, diagnosis, and management of IA in AIIRD, and to outline the clinical practical challenges in this population.

METHODS: This narrative review was informed by a structured literature search of PubMed, Embase, Web of Science, and Google Scholar for studies on IA in AIIRD published up to August 2025.

RESULTS: IA in AIIRD patients generally appears to arise from multiple interacting factors, including compromised host immunity, immunosuppressive therapy, the underlying rheumatic disease itself, comorbidities, and environmental exposures. Aspergillus infection and the resulting anti-Aspergillus immunity may also induce or exacerbate autoimmune inflammation. Invasive pulmonary aspergillosis is the most commonly reported manifestation, typically presenting with nonspecific respiratory symptoms, and disseminated infection tends to occur in the setting of profound immunosuppression. Early, integrated microbiologic testing (e.g. serum or bronchoalveolar lavage galactomannan, culture, polymerase chain reaction, and next-generation sequencing) together with serial imaging examination may facilitate earlier detection and guides care. Although robust AIIRD-specific evidence remains limited, current practice generally favour a multidisciplinary, individualized approach incorporating timely antifungal therapy and careful modulation of immunosuppression. Reported mortality remains high, ranging from 25% to 85% across AIIRD cohorts, particularly when diagnosis and treatment are delayed.

CONCLUSIONS: IA is a serious and likely under-recognized infection in AIIRD patients. Multiple determinants appear to increase infection risk, and symptoms and imaging manifestations can mimic rheumatic disease activity, potentially contributing to diagnostic delay. Current epidemiological and clinical data on AIIRD-IA remain limited, and further studies are needed to refine risk stratification, establish diagnostic criteria tailored to AIIRD patients, and inform more evidence-based management strategies.},
}

Humans
*Rheumatic Diseases/immunology/complications/drug therapy/epidemiology
Risk Factors
*Autoimmune Diseases/immunology/complications/drug therapy/epidemiology
Aspergillus/immunology/isolation & purification
Immunosuppressive Agents/adverse effects
Immunocompromised Host
*Opportunistic Infections/epidemiology/diagnosis/immunology
Antifungal Agents/therapeutic use
*Invasive Pulmonary Aspergillosis/epidemiology/diagnosis
Aspergillosis/diagnosis/epidemiology

@article {pmid42343917,
year = {2026},
author = {Krasaesin, A and Wongbanthit, Y and Chaiboonyarak, T and Wang, DH and Alinejad-Rokny, H and Samaranayake, L and Pongpanich, M and Porntaveetus, T},
title = {Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687219},
pmid = {42343917},
issn = {2000-2297},
abstract = {OBJECTIVE: To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.

METHODS: Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6-17 years) were performed, following by bioinformatics evaluation.

RESULTS: Beta diversity demonstrated significant differences between groups (p < 0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.

CONCLUSION: These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.},
}

@article {pmid42343927,
year = {2026},
author = {González-Ramírez, IS and Song, MJ and Mehlferber, EC and Mishler, BD},
title = {Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica.},
journal = {Applications in plant sciences},
volume = {14},
number = {3},
pages = {e70064},
pmid = {42343927},
issn = {2168-0450},
abstract = {PREMISE: The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.

METHODS: We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.

RESULTS: The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.

DISCUSSION: Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.},
}

@article {pmid42343969,
year = {2026},
author = {Schaerer, LG and Anderson, RS and Chan, J and De Long, SK},
title = {Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag035},
pmid = {42343969},
issn = {2633-6685},
abstract = {Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable product profiles resulting from an inability to control the microbial communities underlying waste decomposition and product biosynthesis. Over time, lactic acid bacteria (LAB) often dominate AAD bioreactors and overproduce shorter chain acids causing acidosis. Here an AAD bioreactor where caproic acid production increased from an average of 3.9 g/l to an average of 12.3 g/l when the feedstock was switched from manure and paperboard to food waste. Time series shotgun metagenomics is used to investigate how microbial dynamics drive performance shifts. The dominant LAB shifted from Lactobacillus amylovorus spp. to Lactiplantibacillus pentosus spp. following the feedstock switch, corresponding with increased diversity and relative abundance (26.2%) of Caproicibacter spp. (putative chain elongator). Additionally, L. amylovorus MAGs encoded biosynthesis genes to produce the bacteriocin helveticin often produced by LAB to target closely related species. Lactiplantibacillus pentosus MAG.84 encodes bacteriocin-degrading enzymes and helveticin resistance genes, suggesting putitive mechanisms for bacteriocin resistance. These results suggest that bacteriocins may be an underappreciated mechanism for shaping microbial community dynamics in AAD.},
}

@article {pmid42343970,
year = {2026},
author = {Das, R and Kumar, R and Tamang, B},
title = {Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag032},
pmid = {42343970},
issn = {2633-6685},
abstract = {Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus, and Pediococcus, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in Mesu (Sikkim), Tuaithar (Manipur), Lung-Seij (Meghalaya), and Bastenga (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with Lactiplantibacillus plantarum, Lactobacillus acetotolerans, and Pediococcus pentosaceus exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with mesu samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.},
}

@article {pmid42343982,
year = {2026},
author = {van Mourik, DJM and Balvers, M and Jansen, VLBI and de Jonge, PA and Coppens, M and Nieuwdorp, M and Middeldorp, S and Eikenboom, JCJ and Voorberg, J and van Mens, TE},
title = {Cross-Reactivity of Antiphospholipid Antibodies with Gut Commensal Proteins in Antiphospholipid Syndrome.},
journal = {TH open : companion journal to thrombosis and haemostasis},
volume = {10},
number = {},
pages = {a28685248},
pmid = {42343982},
issn = {2512-9465},
abstract = {BACKGROUND: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the persistent presence of antiphospholipid antibodies (aPL), mainly targeted against β2 glycoprotein 1 (β2GP1). The autoimmune response to β2GP1 is aimed at several B-cell and T-cell epitopes. Molecular mimicry of these epitopes by gut commensal proteins, so-called mimotopes, causing cross-immunization, might contribute to the formation of aPL.

OBJECTIVE: To study the potential role of gut microbiome cross-immunization in APS by examining cross-reactivity of aPL with gut commensal mimotope-containing proteins.

METHODS: Fecal microbial metagenome of APS patients was determined using shotgun sequencing. An in-house developed in silico pipeline was used to identify gut commensal proteins that show sequence homology with known β2GP1 B and T cell epitopes in the metagenomic data. An enzyme-linked immunosorbent assay was used to test the identified microbial proteins for IgG cross-reactivity, with plasma of 21 APS patients and 17 control participants.

RESULTS: The in silico pipeline resulted in the identification of six gut commensals with a B cell and T cell β2GP1 epitope homologue. Of these, YjjG family noncanonical pyrimidine nucleotidase, one of the candidate-β2GP1 B cell mimicking proteins, showed significantly increased IgG reactivity in APS patients compared to control participants, as well as higher binding of a specific anti-β2GP1 monoclonal antibody than a negative control.

CONCLUSION: Our study shows reactivity of IgG antibodies to YjjG family noncanonical pyrimidine nucleotidase from Roseburia amylophila in APS patients. Insights into the origins of antibody formation may yield new therapeutic targets for improvement of APS treatment.},
}