@article {pmid41998666,
year = {2026},
author = {Yang, F and Du, Y and Ji, J and Zhang, P},
title = {Eosinophilic granulomatous inflammation and multi-organ involvement probable caused by Paragonimus heterotremus infection in a pediatric patient: a rare case report.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41998666},
issn = {1471-2431},
abstract = {BACKGROUND: Paragonimus heterotremus is a parasitic flatworm endemic to Southeast Asia that causes pulmonary and extrapulmonary infections. While more common in adults, pediatric cases are rare and often present atypically, posing diagnostic challenges. Eosinophilic granulomatous inflammation due to parasitic infection is especially difficult to identify in children.

CASE PRESENTATION: A 9-year-old female child initially exhibited subcutaneous swelling and notable peripheral blood eosinophilia, resulting in two hospital stays without a conclusive diagnosis. Upon admission to our center, laboratory results showed increased white blood cell count, hemoglobin, platelets, and persistent eosinophilia, along with a significantly increased total IgE levels. Imaging revealed granulomatous inflammation in the skin and lungs with mild pleural effusion. Despite negative parasitic serology, a newly developed umbilical mass during hospitalization was surgically excised. Anatomopathological examination and metagenomic next-generation sequencing (mNGS) supported a probable diagnosis of P. heterotremus infection.

CONCLUSIONS: This case highlights the diagnostic challenges of pediatric eosinophilic granulomatous inflammation due to rare parasitic infections, particularly in non-endemic areas. It highlights the need for heightened clinical awareness, thorough evaluation, and advanced diagnostic tools for timely and accurate identification of uncommon parasitic diseases in children.},
}

@article {pmid42206864,
year = {2026},
author = {Zhao, R and Biddle, JF},
title = {Community structure and methylation of microbes in an artificially forced sediment core.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0353325},
doi = {10.1128/spectrum.03533-25},
pmid = {42206864},
issn = {2165-0497},
abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.},
}

@article {pmid42207030,
year = {2026},
author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S},
title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01620k},
pmid = {42207030},
issn = {2042-650X},
abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.},
}

@article {pmid42207032,
year = {2026},
author = {Giani, N and John, J and Campbell, B},
title = {Shotgun metagenomics and metatranscriptomics of soil microbial communities under monoculture and polyculture cover crops.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0030926},
doi = {10.1128/mra.00309-26},
pmid = {42207032},
issn = {2576-098X},
abstract = {Here, we present 30 metagenomes, 21 metatranscriptomes, and 334 metagenome-assembled genomes collected from soils under different cover crop species. This data set will be useful for studying microbial interactions, especially functional redundancy, with relevance to agricultural management and sustainability.},
}

@article {pmid42207051,
year = {2026},
author = {Sutanto, TPW and Pratama, A and Ishii, E and Iida, T and Matsuda, S},
title = {TsrA modulates type III secretion system 2 expression as a co-regulator of H-NS in Vibrio parahaemolyticus.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0055625},
doi = {10.1128/jb.00556-25},
pmid = {42207051},
issn = {1098-5530},
abstract = {Vibrio parahaemolyticus, a gram-negative marine bacterium, is a major cause of seafood-borne gastroenteritis worldwide. This pathogen relies on type III secretion system 2 (T3SS2), which is encoded on a pathogenicity island, for its enteropathogenicity. Expression of T3SS2 is activated by a regulatory pathway centered on the transcriptional activator VtrB, which is antagonized by the xenogeneic silencer, histone-like nucleoid-structuring protein (H-NS). However, the complete transcriptional network is not yet fully understood. In this study, we identified TsrA as a negative regulator of T3SS2 gene expression. TsrA is a small protein conserved among Vibrio species that lacks a putative DNA-binding motif but has been implicated in the regulation of virulence genes in Vibrio cholerae. In V. parahaemolyticus, deletion of tsrA increased VtrB production and T3SS2 secretion, thereby enhancing T3SS2-dependent pathogenicity. Transcription of vtrB occurs via a two-step activation process, in which TsrA affects the primary activation step, thereby modulating VtrB production. We further provide experimental evidence that TsrA physically interacts with H-NS via its C-terminal region, which correlates with its regulatory activity on vtrB expression. A systematic mutational analysis of the C-terminal 26 residues revealed several residues critical for TsrA regulatory activity. Moreover, the regulatory effect of TsrA on T3SS2 gene expression was dependent on H-NS, demonstrating that TsrA functions in concert with H-NS. Thus, our findings provide new insights into the regulatory mechanisms of virulence gene expression in V. parahaemolyticus by defining the role of TsrA in this network, while also placing TsrA among H-NS co-regulators.IMPORTANCENucleoid-associated proteins (NAPs) play key roles in virulence gene regulation in bacteria. The best-studied NAP is H-NS, which often functions with co-regulators to fine-tune gene expression. TsrA, a small protein lacking a DNA-binding motif conserved among Vibrio species, has been suggested to be functionally related to H-NS in Vibrio cholerae, although its mechanism remains unknown. Here, we demonstrate that TsrA negatively regulates the expression of type III secretion system 2 (T3SS2), a major virulence determinant of Vibrio parahaemolyticus, an important seafood-borne pathogen. TsrA modulates the transcription of vtrB, which encodes the essential activator for T3SS2 expression, through direct physical interaction with H-NS. Our findings reveal a molecular link between TsrA and H-NS, providing mechanistic insights into NAP- and TsrA-mediated regulation of virulence in Vibrio.},
}

@article {pmid42207344,
year = {2026},
author = {Cagirgan, OY and Korkmaz, S and Diker, KS},
title = {Intestinal microbiome in necrotic enteritis infection of broiler and comparison of treatment alternatives.},
journal = {Tropical animal health and production},
volume = {58},
number = {5},
pages = {},
pmid = {42207344},
issn = {1573-7438},
support = {VTF-190002//Bilimsel Araştırma Projeleri Birimi, Aydın Adnan Menderes Üniversitesi/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Clostridium Infections/veterinary/microbiology/drug therapy ; *Poultry Diseases/microbiology/drug therapy ; *Enteritis/veterinary/microbiology/drug therapy ; Clostridium perfringens/physiology ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/physiology ; *Probiotics/administration & dosage ; Amoxicillin/therapeutic use/administration & dosage ; Necrosis/veterinary/microbiology ; Male ; },
abstract = {Clostridium perfringens is the primary causative agent of necrotic enteritis (NE), a gastrointestinal disease that leads to substantial economic losses in poultry. This study aims to characterize the intestinal microbiome of chickens and assess the effects of Bacillus velezensis on gut microbiota and recovery from necrotic enteritis, comparing its efficacy to antibiotic treatment. The experiment involved five groups, each consisting of 16 chickens. The first group, the start-of-challenge (DB) group, included day-old chicks. The second group, the post-challenge control (DS) group, was reared until the end of the trial. The third group was infected with C. perfringens (NE group). The fourth group received both C. perfringens and B. velezensis (BV group), while the fifth group was treated with C. perfringens and amoxicillin (AB group). All chickens were euthanized via cervical dislocation following the experimental infection. Fecal samples collected from the cecum underwent 16 S rRNA gene-based metagenomic analysis, and the resulting data were statistically evaluated. Macroscopic examination after euthanasia revealed pathological changes in the intestines of chickens in the NE group, which had received only C. perfringens. Their intestines appeared swollen, with slight mild mucosal hemorrhage. In contrast, no macroscopic lesions were observed in the DB, DS, BV, or AB groups. Microbiome analysis showed a decline in microbial diversity within the NE group. The BV group exhibited a microbial composition most similar to that of healthy animals, followed by the AB group. The study concludes that B. velezensis could serve as an alternative to prophylactic antibiotics in mitigating the adverse effects of necrotic enteritis on the gut microbiome.},
}

Animals
*Chickens/microbiology
*Clostridium Infections/veterinary/microbiology/drug therapy
*Poultry Diseases/microbiology/drug therapy
*Enteritis/veterinary/microbiology/drug therapy
Clostridium perfringens/physiology
Anti-Bacterial Agents/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Bacillus/physiology
*Probiotics/administration & dosage
Amoxicillin/therapeutic use/administration & dosage
Necrosis/veterinary/microbiology
Male

@article {pmid42207373,
year = {2026},
author = {Shao, C and Li, J and Huang, C and Tang, M and Zeng, J and Zhou, W and Zhang, D and Zeng, G and Wang, J and Hua, T and Zhong, C and Hu, J and Xu, X},
title = {Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42207373},
issn = {1435-4373},
support = {20170522160421261//Bao'an District Science and Technology Program/ ; 2023B110008//Guangdong Provincial Clinical Research Center for Laboratory Medicine/ ; },
abstract = {RESEARCH BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a culture-independent pathogen identification method, which can directly sequence all nucleic acids present in clinical samples, and has shown transformative potential in the diagnostic field of complex, critical and emerging infectious diseases, but its clinical application value has not been fully evaluated. This study aims to compare the diagnostic efficacy of mNGS and traditional microbiological testing (TMT), and evaluate its impact on clinical decision-making.

RESEARCH METHODS: This retrospective study analyzed the data of the laboratory information system (LIS) of patients who received both mNGS and TMT testing.

RESEARCH RESULTS: In samples of bronchoalveolar lavage fluid (BALF), blood and cerebrospinal fluid (CSF), the positive rates of mNGS were 86.70%, 77.17% and 53.57% respectively, which were significantly higher than the corresponding positive rates of TMT (41.38%, 14.13%, 17.86%). Clinical correlation analysis showed that 77.84%, 66.20% and 73.33% of the positive mNGS results of the three types of samples were of clinical significance respectively. 15.34%~29.58% of the cases adjusted their treatment regimens according to the positive mNGS results, and 33.33%~61.54% of the cases adjusted their treatment regimens according to the negative mNGS results. Most patients who had their treatment adjusted showed improvement or relief of symptoms. Overall, various pathogenic microorganisms were detected in more than 60% of the samples.

RESEARCH CONCLUSION: This study confirms the significant advantages of mNGS in the precise diagnosis of infectious diseases, as well as its value in guiding individualized treatment strategies.},
}

@article {pmid42208188,
year = {2026},
author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S},
title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.},
journal = {Water research},
volume = {302},
number = {},
pages = {126138},
doi = {10.1016/j.watres.2026.126138},
pmid = {42208188},
issn = {1879-2448},
abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.},
}

@article {pmid42208292,
year = {2026},
author = {Majumdar, A and Bagchi, D and Kotta-Loizou, I and Buck, M},
title = {The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142431},
doi = {10.1016/j.jhazmat.2026.142431},
pmid = {42208292},
issn = {1873-3336},
abstract = {Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.},
}

@article {pmid42208296,
year = {2026},
author = {Wang, Q and Ma, Y and Niu, J and Liu, Y and Chao, C and Zhao, Y},
title = {Enhanced anti-toxicity memory of Cr(VI)-4-CP stressed denitrification by bio-promoter: Microbial cooperation and multi-path electron transfer drive toxics transformation-migration.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142497},
doi = {10.1016/j.jhazmat.2026.142497},
pmid = {42208296},
issn = {1873-3336},
abstract = {Coexisting heavy metals and organic pollutants in industrial wastewaters posed synergistic inhibition to denitrification by activating dissimilatory nitrate reduction and disrupting electron supply-consumption balance. Taking Cr(VI) and 4-chlorophenol (4-CP) as representative pollutants, this study proposed a combined bio-promoter composed of growth factors and phosphomolybdic acid (PMo12) to accelerate recovery and establish anti-toxicity memory under compound stress. The promoter restored over 90% nitrogen removal within 9 T and maintained 63.6% nitrogen removal under Cr(VI)-4-CP re-stress. Compared to first-stress, the recovered system reduced 37.44 mg/L more Cr(VI) and kept 4-CP below 5 mg/L, thus rapidly relieving Cr(VI)-4-CP toxicity and increasing the supply of direct electron donor nicotinamide adenine dinucleotide (NADH, 65.5%) and energy source adenosine triphosphate (ATP, 27.8%). Meanwhile, the enhanced extracellular polymeric substance (EPS) ensured 11.15 mg/g mixed liquid suspended solids (MLSS) more chromium immobilization with 97.9% distributed intercellularly, preventing Cr(VI) from invading cells and minimizing intracellular oxidative damage. The biofilm-fixed Mo (4.28 mg/g MLSS) shortened electron transfer distance to NO3[-]-N, which, combined with a 17.3% increase in cytochrome (cyt.c), formed a new mode of multi-path electron transfer. Microbacterium with glucose-4-CP co-metabolism and denitrification functions contributed 13.0% of the recovered community, transforming glucose and 4-CP competitive metabolism into collaborative metabolism, further enhancing the anti-toxicity memory, and ensuring efficient denitrification performance.},
}

@article {pmid42208547,
year = {2026},
author = {Goldberg, H and Dyhrman, ST and DeMers, MA and Braakman, R and Hennon, GMM},
title = {Forces Shaping Diversity of Hydrogen Peroxide Detoxification Potential in Ocean Microbial Ecosystems.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70315},
doi = {10.1111/1462-2920.70315},
pmid = {42208547},
issn = {1462-2920},
support = {OCE-1937715//National Science Foundation/ ; OCE-2019589//National Science Foundation/ ; },
mesh = {*Hydrogen Peroxide/metabolism ; *Seawater/microbiology ; *Catalase/genetics/metabolism ; Ecosystem ; Oceans and Seas ; *Bacteria/genetics/metabolism/classification ; Bacterial Proteins/genetics/metabolism ; Metagenome ; *Microbiota ; Genome, Bacterial ; },
abstract = {Microbial communities have evolved interactions to support growth and essential ecosystem functions. For example, marine cyanobacteria like Prochlorococcus lack the catalase genes (katE, katG and manganese catalase) required for detoxifying freely-diffusible hydrogen peroxide, relying on co-occurring catalase-carrying 'helper' microbes for this function. However, the eco-evolutionary forces shaping catalase distribution are not well understood. We examined genomes, metagenome-assembled genomes (MAGs), and metagenomes to assess catalase gene distributions across diverse marine prokaryotes-including within the known 'helper' genus Alteromonas-and across surface ocean ecosystems. Within Alteromonas, most genomes contain two katE copies, while katG copy number varies across species. Across ecosystems, the Altermonadaceae family is the predominant katE carrier. Some taxa (e.g., SAR202) lack all catalases, highlighting their dependence on 'helpers'. Overall, streamlined genomes, including from SAR11, generally have one katG copy and lack katE, while larger genomes with higher GC content characteristic of copiotrophs have more copies of both catalases. Finally, in free-living communities, katG gene frequency increases with decreased particulate organic carbon (POC) concentrations, whereas in particle-associated communities, katE gene frequency increases with elevated POC. Together, these observations suggest that hydrogen peroxide detoxification capabilities are widespread and shaped by the contributions of particle-associated microbes to total community metabolism.},
}

*Hydrogen Peroxide/metabolism
*Seawater/microbiology
*Catalase/genetics/metabolism
Ecosystem
Oceans and Seas
*Bacteria/genetics/metabolism/classification
Bacterial Proteins/genetics/metabolism
Metagenome
*Microbiota
Genome, Bacterial

@article {pmid42208809,
year = {2026},
author = {Korva, M and Bogovič, P and Knap, N and Kogoj, R and Slunečko, J and Zakotnik, S and Suljič, A and Resman Rus, K and Pozvek, P and Strle, F and Avšič-Županc, T and Petrovec, M},
title = {Emerging human pathogen: Identifying Spiroplasma ixodetis as a frequent cause of unlocalised febrile illness.},
journal = {The Journal of infection},
volume = {93},
number = {1},
pages = {106776},
doi = {10.1016/j.jinf.2026.106776},
pmid = {42208809},
issn = {1532-2742},
abstract = {OBJECTIVES: Febrile illness without clear localisation presents a significant diagnostic challenge due to non-specific symptoms and diverse aetiologies. Spiroplasma ixodetis, an emerging tick-associated pathogen previously linked mainly to congenital cataracts, has not been well characterised in adults. We investigated the prevalence and clinical features of S. ixodetis infection in adults with acute febrile illness without localisation.

METHODS: Shotgun metagenomic sequencing identified S. ixodetis in the initial 209 patient cohort and the sequences were used to developed a novel real-time PCR assay targeting the 23S rRNA gene. Initial cohort screening was followed by testing 128 patients from an additionally selected targeted cohort. Positive results were confirmed by sequencing of 16S and 23S rRNA genes.

RESULTS: S. ixodetis DNA was confirmed in 7.2% patients from the initial and in 35.2% patients from the additional cohort (60 in total). All were identified in the period from April to October and 57% reported a recent tick-bite. Clinical presentation was homogenous, characterised by fever, headache, bicytopenia and liver enzyme abnormalities. Outcomes were favourable, with 15% requiring hospitalisation.

CONCLUSION: This study identifies S. ixodetis as a previously unrecognised cause of adult febrile illness without localisation, bridging the gap between previously published data between tick studies and isolated human case reports.},
}

@article {pmid42208810,
year = {2026},
author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB},
title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106774},
doi = {10.1016/j.jinf.2026.106774},
pmid = {42208810},
issn = {1532-2742},
abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.

METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.

RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (β=1.36, P=0.010) and higher overall pathobiont relative abundance (β=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (β=1.60, P=0.007) and relative abundance (β=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.

CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.},
}

@article {pmid42208932,
year = {2026},
author = {Lv, H and Jin, S and Li, L and Ma, S and Wang, Y and Zhang, Y and Guo, K},
title = {Diagnostic Accuracy of Metagenomic Next-Generation Sequencing for Invasive Pulmonary Aspergillosis: A Systematic Review and Meta-Analysis.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108827},
doi = {10.1016/j.ijid.2026.108827},
pmid = {42208932},
issn = {1878-3511},
abstract = {OBJECTIVES: To systematically evaluate the diagnostic accuracy of metagenomic next‑generation sequencing (mNGS) for invasive pulmonary aspergillosis (IPA), and to compare its sensitivity and specificity with conventional methods.

METHODS: Meta‑analysis was performed to pool sensitivity, specificity, and diagnostic odds ratio (DOR). The comparison test between mNGS and conventional diagnostic methods was conducted through pairwise comparisons, and effect size was expressed using the risk difference (RD) and 95% confidence interval.

RESULTS: Twelve studies were included, the pooled sensitivity of mNGS was 0.75 (95% CI: 0.65-0.84), specificity 0.93 (95% CI: 0.84-0.97), DOR 35.69 (95% CI: 13.70-92.97). The comparative analysis showed mNGS had higher sensitivity compared with galactomannan (RD = 0.22, 95% CI: 0.16-0.29), culture (RD = 0.40, 95% CI: 0.26-0.55), and (1→3)-β-D-glucan (BDG) (RD = 0.23, 95% CI: 0.09-0.37). For BDG assay, mNGS also demonstrated superior specificity (RD = 0.12, 95% CI: 0.04-0.20).

CONCLUSION: mNGS demonstrates promising diagnostic accuracy for IPA, with favorable sensitivity and specificity, and shows higher sensitivity than several conventional methods. BALF is the preferred specimen, and combined testing with multiple sample types improves diagnostic yield.},
}

@article {pmid42208954,
year = {2026},
author = {Baker, B and Baz Lomba, JA and Bitilinyu-Bangoh, J and Berglöf, A and Bombaywala, S and Calvert-Joshua, T and Kaboré, B and Kingpriest, P and Lang, T and Levy, JI and Lompo, P and Lyimo, E and Martens, L and Mavoko, HM and Mesuere, B and Moremi, N and Mulder, N and Ndure, SL and Rameto, MA and Rinke de Wit, TF and Sebukoto, H and Smith, E and Tahita, MC and Tevuzula, VM and Tippett Barr, BA and Tiwari, A and Tran, T and Ubomba-Jaswa, E and Van Den Bossche, T and Wolday, D and Krolicka, A and Baraka, V and Pitkänen, T and Lood, R},
title = {Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101426},
doi = {10.1016/j.lanmic.2026.101426},
pmid = {42208954},
issn = {2666-5247},
abstract = {Persistent SARS-CoV-2 transmission, ongoing mpox outbreaks, and the continued spread of endemic diseases such as typhoid fever and cholera underscore the urgent need for global, multiomics surveillance. In this Personal View, we present Project ODIN, a consortium of European and African partners launched in 2023 that aims to meet this challenge by deploying innovative systems for near real-time pathogen detection and actionable public health insights. The project is a collaboration between high-income and low-income countries in northern Europe and sub-Saharan Africa. Focusing on low-income and middle-income countries, ODIN integrates metagenomics with mobile laboratory systems for comprehensive pathogen monitoring across diverse environments. ODIN emphasises standardised sampling, bioinformatics pipelines, and data-sharing protocols to ensure reliable, interoperable results while addressing infrastructure and resource limitations. By bridging gaps in genomic surveillance, these initiatives seek to strengthen outbreak preparedness, improve pathogen detection, monitor antimicrobial resistance, and provide a holistic approach to One Health challenges. Together, these innovations could advance global surveillance capacity-particularly in under-resourced regions-paving the way for effective disease control and evidence-based policy making.},
}

@article {pmid42209028,
year = {2026},
author = {Hoeter, K and Marriott, L and Neuberger, EWI and Dagwadordsch, U and Kumar, RS and Simon, P and Bodenstein, M and Kersaudy-Kerhoas, M},
title = {Plasma metagenomic cfDNA sequencing identifies pathogens in culture-negative sepsis following urinary pouch rupture.},
journal = {BMJ case reports},
volume = {19},
number = {5},
pages = {},
doi = {10.1136/bcr-2025-267878},
pmid = {42209028},
issn = {1757-790X},
mesh = {Humans ; Female ; *Sepsis/microbiology/diagnosis/drug therapy/blood ; Anti-Bacterial Agents/therapeutic use ; *Cell-Free Nucleic Acids/blood ; *Pseudomonas Infections/diagnosis/drug therapy/blood ; Metagenomics/methods ; *Klebsiella Infections/diagnosis/drug therapy/blood ; Rupture, Spontaneous ; Klebsiella/isolation & purification/genetics ; },
abstract = {A patient with a complex urological history presented with abdominal pain and respiratory distress after catheter dysfunction. She underwent emergency surgery for a ruptured urinary pouch. Sepsis was later diagnosed based on clinical deterioration, including tachycardia, fever, an elevated respiratory rate and raised inflammatory markers, but blood cultures remained negative. A metagenomic microbial cell-free DNA (cfDNA) assay (iSEP-SEQ), performed early from plasma as part of a research protocol, identified Klebsiella and Pseudomonas at the genus level. Results were obtained retrospectively and were not available in real time; therefore, they did not alter immediate management. These findings were confirmed by cultures from drainage fluid and urine. Broad-spectrum antibiotic treatment led to clinical improvement. This case highlights the limitations of conventional microbiological methods in culture-negative sepsis and illustrates the role of cfDNA-based metagenomic testing as an adjunctive and complementary diagnostic tool for early, accurate pathogen detection. Early use of such tools may support timely and targeted management in complex infectious disease presentations.},
}

Humans
Female
*Sepsis/microbiology/diagnosis/drug therapy/blood
Anti-Bacterial Agents/therapeutic use
*Cell-Free Nucleic Acids/blood
*Pseudomonas Infections/diagnosis/drug therapy/blood
Metagenomics/methods
*Klebsiella Infections/diagnosis/drug therapy/blood
Rupture, Spontaneous
Klebsiella/isolation & purification/genetics

@article {pmid42209192,
year = {2026},
author = {Leggio, M and Schramm, S and Dietz, L and Ocón, B and Wirtz, S and Puertolas Balint, F and Yilmaz, B and Petzold, J and Liu, LJ and Dedden, M and Ekici, A and , and Meng, X and Bingham, D and Ullrich, KA and Heltmann-Meyer, S and Günther, C and Hildner, K and Atreya, R and Atreya, I and Müller, TM and Gerlach, RG and Schroeder, BO and Macpherson, A and Butcher, EC and Neurath, MF and Zundler, S and , },
title = {The endogenous peptide GPR15L shapes the intestinal microbiota to counteract colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337619},
pmid = {42209192},
issn = {1468-3288},
abstract = {BACKGROUND: The peptide GPR15L is produced by colonic epithelial cells and has been implicated in T cell recruitment to the large intestine. However, its role in chronic colitis has been unclear so far.

OBJECTIVE: To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD.

DESIGN: We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alters the course of acute dextran sodium sulfate colitis and T cell transfer colitis. The impact of GPR15L on microbiota was explored with co-housing, littermate and faecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival.

RESULTS: GPR15L clearly mitigated experimental colitis, but this was independent of T cell recruitment and GPR15. Instead, we observed that the effects of GPR15L were mediated by altered microbiomes in the large intestine and, consistently, showed that GPR15L acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of GPR15L counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival.

CONCLUSIONS: GPR15L is a host-defence peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.},
}

@article {pmid42209465,
year = {2026},
author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L},
title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73084-2},
pmid = {42209465},
issn = {2041-1723},
abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.},
}

@article {pmid42209510,
year = {2026},
author = {Dommann, J and Sprecher, VP and Beisel, C and Ballmer, D and Hürlimann, E and Coulibaly, JT and Keiser, J and Schneeberger, PHH},
title = {Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01018-3},
pmid = {42209510},
issn = {2055-5008},
support = {101019223/ERC_/European Research Council/International ; 101019223/ERC_/European Research Council/International ; },
abstract = {Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight (≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.},
}

@article {pmid42209552,
year = {2026},
author = {Olszyński, RM and Mann, DG and Zakrzewski, PK and Peszek, Ł and Ács, É and Shemesh, S and Trobajo, R},
title = {Nitzschia excavata sp. nov. (Bacillariaceae), a new diatom species from a post-mining reservoir revealed by morphology, molecular phylogeny, and metabarcoding-based biogeography.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42209552},
issn = {2045-2322},
support = {RRF 2.3.1 21 2022 00008//Széchenyi Plan Plus programme/ ; RRF 2.3.1 21 2022 00008//Széchenyi Plan Plus programme/ ; },
mesh = {*Diatoms/genetics/classification/ultrastructure ; *Phylogeny ; *DNA Barcoding, Taxonomic ; Phylogeography ; Mining ; DNA, Ribosomal/genetics ; Poland ; },
abstract = {The Bogdałów post-mining reservoir (Poland) represents a slightly alkaline, moderately mineralised ecosystem formed by flooding a former lignite pit. Its anthropogenic origin and stable physicochemical conditions have enabled the development of species-rich diatom assemblages, particularly numerous Nitzschia (Bacillariaceae) species. To explore this diversity, an integrative approach combining microscopy and DNA-based analyses was employed. Morphological examinations were performed using light and scanning electron microscopy, as well as confocal laser scanning microscopy. Molecular phylogenetic analyses were based on the sequencing of the nuclear SSU rDNA and the chloroplast rbcL and psbC gene markers. This comprehensive study led to the discovery and formal description of Nitzschia excavata sp. nov., distinguishable by unique morphological features and a phylogenetically distinct lineage. Furthermore, environmental DNA metabarcoding and metagenomic database searches revealed sequences identical or closely related to the N. excavata sp. nov. lineage in freshwater habitats across Europe and China, indicating that this taxon has an unexpectedly broad distribution. These findings underscore the value of integrating classical morphological analysis with multi-marker molecular data in diatom taxonomy and demonstrate that anthropogenic habitats may support taxa with broader distributions than previously recognized. The study highlights the important role of metabarcoding and metagenomics in revealing cryptic diversity and clarifying the biogeographic patterns of newly described species.},
}

*Diatoms/genetics/classification/ultrastructure
*Phylogeny
*DNA Barcoding, Taxonomic
Phylogeography
Mining
DNA, Ribosomal/genetics
Poland

@article {pmid42209868,
year = {2026},
author = {Ajeh, IJ and Ikukpla'si, OSI},
title = {The non-bacterial oncobiome: the role of the mycobiome and virome in tumor plasticity.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {38},
number = {1},
pages = {},
pmid = {42209868},
issn = {2589-0409},
mesh = {Humans ; Tumor Microenvironment ; *Neoplasms/pathology/microbiology/virology ; *Mycobiome ; *Virome ; Epithelial-Mesenchymal Transition ; Cell Plasticity ; },
abstract = {Tumor plasticity, the capacity of malignant cells to undergo reversible phenotypic switching, is a fundamental driver of lineage diversion and therapeutic resistance. While the bacterial microbiome is a recognized modulator of the tumor microenvironment (TME), the non-bacterial oncobiome, comprising the mycobiome (fungi) and virome (viruses), represents a critical but under-explored frontier in cellular adaptability. This review synthesizes current evidence regarding the mechanistic contributions of fungal and viral constituents to tumor plasticity and characterizes the molecular cross-talk that facilitates host cell reprogramming. We conducted a structured narrative synthesis of literature indexed in PubMed, Scopus, and Web of Science (2020-2026), focusing on high-throughput studies such as ITS sequencing, metagenomics NGS (mNGS), and single-cell network analyses. We specifically evaluated evidence concerning the activation of host pattern recognition receptors and the subsequent transcriptional rewiring of lineage-defining markers. Emerging data indicate that fungal dysbiosis, particularly involving Candida and Malassezia species, triggers the Dectin-1/STAT3 signaling axis, a known inducer of epithelial-mesenchymal transition (EMT). Concurrently, the virome, ranging from integrated oncoviruses to reactivated endogenous retroviruses (ERVs), is shown to hijack the Wnt/ β-catenin pathway, enforcing a progenitor-like stemness state. This inter-kingdom synergy promotes an immune-excluded niche, effectively shielding plastic sub-populations from cytotoxic stress and targeted therapies. The non-bacterial oncobiome provides genomic momentum and inflammatory cues necessary to lower the threshold for phenotypic switching. This review highlights that stabilizing the TME ecosystem through ecologically targeted therapy may be a prerequisite for overcoming drug resistance and improving clinical outcomes in refractory cancers.},
}

Humans
Tumor Microenvironment
*Neoplasms/pathology/microbiology/virology
*Mycobiome
*Virome
Epithelial-Mesenchymal Transition
Cell Plasticity

@article {pmid42210135,
year = {2026},
author = {Feng, W and Xiao, H and Hu, B and Chen, T and Hu, H and Guo, L and Guo, X and Zhu, L and Liu, G},
title = {Clinical characteristics, diagnosis, and management of central nervous system aspergillosis in children: a single-center experience.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13675-y},
pmid = {42210135},
issn = {1471-2334},
support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; PX2024042//Beijing Municipal Administration of Hospitals Incubating Program/ ; },
abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is a severe and frequently misdiagnosed infection in pediatric patients. Systematic pediatric data on its clinical, radiological, diagnostic, and therapeutic features remain limited.

METHODS: We retrospectively identified children aged 0-18 years with proven or probable CNS aspergillosis admitted to Beijing Children's Hospital between January 2010 and December 2024. Demographic, clinical, laboratory, and imaging data were collected. Treatment regimens and clinical outcomes were systematically evaluated.

RESULTS: Sixteen patients were included (12 males), with a median age of 5 years. Hematological malignancies were the most common predisposing factor. Notably, 25% (4/16) of patients lacked identifiable predisposing conditions. Clinical presentations were nonspecific, with fever, seizures, and impaired consciousness being the most common features, and an initial misdiagnosis occurred in 56.3% (9/16) of cases. In contrast to the low yield of cerebrospinal fluid (CSF) cultures, CSF metagenomic next-generation sequencing (mNGS) detected Aspergillus nucleic acids in all tested patients (7/7). Magnetic resonance imaging (MRI) most commonly revealed irregular cerebral abscesses (14/16), frequently accompanied by meningeal enhancement (14/16) and obstructive hydrocephalus (10/16). Among evaluable patients receiving initial voriconazole monotherapy, a partial response was observed in 22.2% (2/9). Conversely, higher response rates were observed with regimens containing liposomal amphotericin B (L-AmB), including initial combination therapy (75.0%) and salvage treatment (80.0%). The all-cause mortality rate was 37.5% (6/16), and moderate-to-severe disability was present in 30.0% (3/10) of survivors.

CONCLUSIONS: Pediatric CNS aspergillosis can occur across a broad risk spectrum, often with nonspecific symptoms, leading to frequent misdiagnosis. Our findings support the early incorporation of CSF mNGS and comprehensive neuroimaging (including whole-neuraxis MRI when clinically indicated) to facilitate timely diagnosis and assess dissemination. The observed high rate of progression with initial voriconazole monotherapy and the relatively favorable responses associated with regimens containing L-AmB highlight the need for prospective pediatric studies to refine initial treatment strategies in severe disease.

CLINICAL TRIAL REGISTRATION: Not applicable.},
}

@article {pmid42210369,
year = {2026},
author = {Pangestu, HS and Yang, I and Natasha, A and Rajoriya, S and Hennisa, H and Park, J and Park, K and Kim, J and Kim, SG and Klein, TA and Kim, HC and Oh, Y and Song, JW and Kim, WK},
title = {Molecular prevalence, genomic characterization, and zoonotic potential of novel paramyxovirus and hepacivirus in Alexandromys fortis, Republic of Korea.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {},
pmid = {42210369},
issn = {1297-9716},
support = {ProMIS ID C0039-09-ME//Global Emerging Infections Surveillance Branch (GEIS)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion/ ; RS-2023-KH140418//Government-wide R&D to Advance Infectious Disease Prevention and Control, Republic of Korea/ ; 2024-ER2502-00//Korea National Institute of Health Research Project/ ; RS-202300249142//Basic Science Research Program through the NRF by the Ministry of Education/ ; NF22SA0082041//Novo Nordisk Foundation PAD award to CBL/ ; U01 AI151810/AI/NIAID NIH HHS/United States ; 2023R1A2C2006105//Basic Research Program through the NRF grant funded by the Korean government (MSIT)/ ; RS-2024-00400152//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through High-Risk Animal Infectious Disease Control Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs/ ; },
mesh = {Animals ; Republic of Korea/epidemiology ; *Genome, Viral ; Phylogeny ; *Arvicolinae/virology ; *Paramyxoviridae Infections/veterinary/epidemiology/virology ; *Rodent Diseases/virology/epidemiology ; *Zoonoses/virology/epidemiology ; Prevalence ; *Paramyxoviridae/genetics/isolation & purification ; *Hepatitis C/virology/epidemiology/veterinary ; },
abstract = {Rodents are substantial reservoirs of zoonotic viruses with regular human exposure restricted to a limited number of species. Numerous rodent species have been shown to harbor emerging viruses, including paramyxoviruses and hepaciviruses. Reed voles (Alexandromys fortis), a rodent species that inhabits grasslands and riparian environments throughout East Asia, remain poorly characterized in terms of their viral diversity. In this study, 258 A. fortis specimens collected from rural areas in Gyeonggi Province, Republic of Korea (ROK) were screened for paramyxoviruses and subjected to metagenomic next-generation sequencing. Genome characterization, phylogenetic and cophylogenetic assessments, and prediction of signal peptidase cleavage sites were performed to analyze the molecular features of the identified viruses. Zoonotic potential was evaluated using a genome-based machine-learning model. A nearly complete genome of a novel paramyxovirus, designated as Pyeongtaek Alexandromys paramyxovirus (PyAPV), was identified in six A. fortis specimens, with all sequences clustering within the genus Jeilongvirus. A nearly complete genome of a rodent-associated hepacivirus was also obtained from four specimens and classified as a distinct lineage within the species Hepacivirus J. These findings demonstrate the role of A. fortis as a natural reservoir of emerging viruses and expand current knowledge of rodent-associated viral diversity in the ROK.},
}

Animals
Republic of Korea/epidemiology
*Genome, Viral
Phylogeny
*Arvicolinae/virology
*Paramyxoviridae Infections/veterinary/epidemiology/virology
*Rodent Diseases/virology/epidemiology
*Zoonoses/virology/epidemiology
Prevalence
*Paramyxoviridae/genetics/isolation & purification
*Hepatitis C/virology/epidemiology/veterinary

@article {pmid42210378,
year = {2026},
author = {Han, J and Liu, J and Wang, T and Dong, B and Zhang, F and Li, S and Zou, Q and Li, D},
title = {Temporal variations in the gut microbiota of François' langur (Trachypithecus francoisi): implications for adaptation to seasonal dietary change and conservation.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00580-7},
pmid = {42210378},
issn = {2524-4671},
abstract = {Despite growing research on gut microbiota in wild primates, seasonal functional dynamics of the gut microbiota in this endangered folivorous species remain poorly understood. This study investigates the seasonal variations in the gut microbiota of François' langur (Trachypithecus francoisi) and their implications for dietary adaptation and conservation. Using shotgun metagenomic sequencing, fecal samples were collected across four seasons within the Mayanghe National Nature Reserve in China (n = 24). The study identified significant seasonal shifts in microbial diversity and composition. While alpha diversity metrics reflecting community evenness (Shannon and Simpson equivalents) remained stable (Padj > 0.05), species richness (Hill number, q = 0) was significantly lower in Fall compared to Spring and Winter (Padj = 0.013). Results revealed that dominant phyla included Bacillota and Bacteroidota, with a significant enrichment of Faecalibacterium during Fall. Functional analysis showed a predominance of carbohydrate metabolism, which remained stable at broad metabolic levels; however, fine-scale functional units (KOs and CAZy families) exhibited distinct seasonal signatures. A moderate correlation between taxonomic and functional profiles (Mantel r = 0.43, P = 0.001) suggests a partial decoupling. These findings highlight the ecological plasticity of the gut microbiota and underscore how taxonomic flexibility enables functional homeostasis, aiding the physiological resilience of endangered primates in fluctuating environments.},
}

@article {pmid42210496,
year = {2026},
author = {Gourabi, MJR and Kargar, M and Kamali, A and Sharahi, JY},
title = {Fungal-Bacterial Interactions in Polymicrobial Infections: Hidden Threats.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70320},
doi = {10.1002/mbo3.70320},
pmid = {42210496},
issn = {2045-8827},
mesh = {Humans ; *Coinfection/microbiology/drug therapy ; Biofilms/growth & development ; *Microbial Interactions ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Candida albicans/physiology ; *Bacteria/drug effects ; *Fungi/physiology/drug effects ; *Mycoses/microbiology ; *Bacterial Infections/microbiology ; },
abstract = {Polymicrobial infections involving fungi and bacteria represent a major and increasingly recognized clinical challenge, in which interkingdom interactions significantly amplify disease severity, antimicrobial resistance, and treatment failure. Rather than passive co-existence, fungal-bacterial communities form highly coordinated systems driven by physical adhesion, quorum sensing, metabolic interdependence, and biofilm-mediated structural reinforcement. These cooperative interactions, exemplified by pairs such as Candida albicans-Staphylococcus aureus and Pseudomonas aeruginosa-Aspergillus fumigatus, promote the development of treatment-recalcitrant biofilms with enhanced immune evasion and multidrug tolerance. The global rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has further intensified this burden, with polymicrobial biofilms now representing a post-antibiotic clinical scenario in which therapeutic failure is driven not by individual resistant organisms but by emergent, cooperative resistance architectures. Conventional diagnostic approaches remain insufficient, as culture-based methods frequently fail to capture the complexity of mixed microbial communities. Emerging technologies such as MALDI-TOF mass spectrometry, metagenomic sequencing, and fluorescence in situ hybridization offer improved resolution but are not yet fully integrated into routine clinical practice. Therapeutically, increasing evidence indicates that monotherapy is inherently inadequate in polymicrobial infections due to the emergent nature of microbial cooperation. Effective management therefore requires combination strategies that simultaneously target multiple pathogens and their shared biofilm infrastructure. These include antibiotic-antifungal combinations, phage therapy, enzymatic and nanoparticle-mediated biofilm disruption, metabolic interference, and host-directed immunomodulation. Importantly, recent advances also highlight the role of biophysical properties such as biofilm viscoelasticity and matrix stiffness as critical and previously underappreciated therapeutic targets. This review uniquely integrates biochemical, biophysical, and therapeutic dimensions of polymicrobial infections into a unified systems-level framework in which microbial cooperation is the central driver of pathogenesis, resistance, and treatment failure. Fungal-bacterial interactions are thereby positioned along a dynamic continuum from commensalism to pathogenesis, shaped by host susceptibility and environmental perturbations. Future progress will depend on interdisciplinary strategies combining multi-omics technologies, precision diagnostics, and microbiome-informed therapeutic design to effectively disrupt these complex microbial networks.},
}

Humans
*Coinfection/microbiology/drug therapy
Biofilms/growth & development
*Microbial Interactions
Anti-Bacterial Agents/therapeutic use/pharmacology
Candida albicans/physiology
*Bacteria/drug effects
*Fungi/physiology/drug effects
*Mycoses/microbiology
*Bacterial Infections/microbiology

@article {pmid42210528,
year = {2026},
author = {Zhou, X and Zhang, M and Zhou, J and Han, J},
title = {Multi-target effects of Limosilactobacillus reuteri RE225 on hyperuricemia through xanthine oxidase inhibition, nucleoside degradation, gut microbiota modulation, and renal TLR4-NF-κB suppression.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70749},
pmid = {42210528},
issn = {1097-0010},
support = {2024S138//Ningbo Public Welfare Research Program/ ; //K.C. Wong Magna Fund of Ningbo University/ ; },
abstract = {BACKGROUND: Hyperuricemia, a major risk factor for gout and kidney disease, requires safe and effective dietary strategies beyond conventional pharmacotherapy. This study investigated the multi-target effects of the food-grade probiotic Limosilactobacillus reuteri RE225 on hyperuricemia. It was evaluated in vitro for xanthine oxidase (XOD) inhibition and nucleoside degradation, and in vivo in hyperuricemic mice gavaged daily with low or high doses of RE225 (1 × 10[6] or 1 × 10[9] CFU). Serum uric acid (UA), XOD activity, inflammatory cytokines, intestinal permeability markers - fluorescein isothiocyanate-dextran (FITC-dextran), lipopolysaccharide (LPS), and d-lactate - and renal TLR4/NF-κB signaling were quantified. Fecal metagenomics and Kyoto Encyclopedia of Genes and Genomes ortholog (KO) profiling were used to assess microbiota structure and function.

RESULTS: Limosilactobacillus reuteri RE225 dose-dependently inhibited XOD and degraded more than 50% of nucleosides in vitro. In vivo, RE225 reduced serum urate, restored intestinal barrier function, suppressed inflammation, and downregulated renal TLR4/NF-κB signaling. Metagenomic analysis showed that L. reuteri RE225 reversed UA-induced loss of microbial richness and evenness, enriched Faecalibaculum and Erysipelotrichaceae, and shifted functional profiles from proliferation- and inflammation-related modules (K02315, K02970, and K03496) toward carbohydrate utilization and genetic stability pathways (K01784 and K07491).

CONCLUSION: Limosilactobacillus reuteri RE225 shows promise as a dietary intervention for the management of hyperuricemia. © 2026 Society of Chemical Industry.},
}

@article {pmid42210827,
year = {2026},
author = {Syatrawati, and Kuswinanti, T and Nasruddin, A and Rosmana, A and Hikmahwati, },
title = {Metagenomic Insights into Rhizosphere Fungal Communities Across Different Rice Cultivation Systems.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {29},
number = {3},
pages = {147-159},
doi = {10.3923/pjbs.2026.147.159},
pmid = {42210827},
issn = {1812-5735},
mesh = {*Oryza/microbiology/growth & development ; *Rhizosphere ; *Metagenomics/methods ; *Fungi/genetics/classification ; Soil Microbiology ; Agriculture/methods ; },
abstract = {Background and Objective: Rhizosphere fungi play a crucial role in nutrient cycling and plant protection, yet most are difficult to cultivate using conventional methods. Consequently, their ecological functions remain largely unknown. Therefore, metagenomic approaches allow for comprehensive and accurate mapping of fungal taxonomic profiles without the need for cultivation and this study investigated the variation of rhizosphere fungi across different rice cultivation systems to elucidate their diverse potentials. Materials and Methods: A metagenomic approach was employed to identify fungi originating from the rhizosphere of rice cultivated in various field conditions, including irrigated, rainfed and organic rice fields. The diversity of fungi from rhizosphere samples was assessed to comprehend the relationships and metrics within the rice cropping systems utilized by farmers. Results: The findings indicated that the rhizosphere fungal index from organic rice fields exhibited the highest Shannon and Simpson index values compared to those from irrigated and rainfed rice fields. Conclusion: Metagenomic analysis revealed that the most dominant fungal diversity at the family level was Trichocomaceae, at the genus level was Talaromyces and at the species level was Talaromyces wortmannii.},
}

*Oryza/microbiology/growth & development
*Rhizosphere
*Metagenomics/methods
*Fungi/genetics/classification
Soil Microbiology
Agriculture/methods

@article {pmid42211404,
year = {2026},
author = {Su, L and Zhang, Y and Xie, Y and Wu, J and Yang, Y and Li, Y and Huang, Y and Liu, X and Wei, X and Chen, Q},
title = {Integrated metabolomics and gut microbiota analyses reveal the protective effects of matrine in ulcerative colitis.},
journal = {Frontiers in chemistry},
volume = {14},
number = {},
pages = {1826894},
pmid = {42211404},
issn = {2296-2646},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by gut microbial dysbiosis and metabolic dysfunction. Matrine, a natural alkaloid with anti-inflammatory properties, shows therapeutic potential; however, its mechanisms involving the coordinated modulation of bacteria, fungi, and host intestinal luminal metabolism remain unclear.

METHODS: We evaluated the therapeutic efficacy of matrine using a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis. Disease severity was assessed via the disease activity index, colon length, and histopathology. Integrated multi-omics approaches, including metagenomics, ITS fungal sequencing, and untargeted metabolomics of intestinal luminal contents, were employed to systematically characterize the regulatory effects of matrine on gut bacteria, fungi, and metabolic profiles.

RESULTS: Here, we demonstrated that oral matrine significantly alleviated disease severity in a DSS-induced UC mouse model, as evidenced by improved disease activity index, colon length, histopathology, and restoration of tight junction proteins. Integrated multiomics revealed that matrine restored bacterial homeostasis-suppressing Escherichia while enriching SCFAs-producing taxa (Muribaculum, Paramuribaculum, Clostridium). Metagenomic predictions revealed that matrine treatment reversed the model-induced suppression of carbohydrate metabolism and bile acid biosynthesis while upregulating depleted CAZy enzyme families, thereby correcting dysregulated metabolic functions in colitis. Furthermore, matrine rebalanced the mycobiota by normalizing the Ascomycota/Basidiomycota ratio. Intestinal luminal contents untargeted metabolomics identified 43 matrine-responsive metabolites, implicating correction of bile acid metabolism, attenuation of leukotriene-mediated inflammation, and reversal of acylcarnitine-driven epithelial energy disruption. Critically, pro-inflammatory metabolites correlated positively with Escherichia and negatively with beneficial symbionts.

CONCLUSION: Our findings established that matrine exerted protective effects in UC through a unified "microbiota-metabolism" axis, highlighting its promise as a multi-target therapeutic agent for UC.},
}

@article {pmid42211783,
year = {2026},
author = {Ding, F and Li, Y and He, T and Wang, Y and Li, Y and Huang, Y and Yin, G and Yang, J and Liu, Y and Li, Y and Li, T and Hou, L and Liu, M},
title = {Deciphering the drivers of antibiotic resistance gene transmission in the megacity: Co-occurring contaminants and bacterial community.},
journal = {Eco-Environment & Health},
volume = {5},
number = {2},
pages = {100242},
pmid = {42211783},
issn = {2772-9850},
abstract = {Urban waters are widely contaminated with co-occurring microplastics and antibiotics. Human-land interactions (e.g., wastewater discharge, stormwater runoff, and land use) drive contaminant distribution and antimicrobial resistance. Nevertheless, there is a lack of systematic research evaluating the role of co-occurring contaminants in shaping the spread of antibiotic resistance genes (ARGs). In this study, a metagenomic approach was used to characterize the diversity and distribution of ARGs based on contaminant co-occurring patterns. The random forests and partial least squares path model (PLS-PM) were used to identify and prioritize the factors impacting ARGs, leading to a thorough environmental health ecological risk evaluation. Industrial waters, especially pharmaceutical factories, were significant reservoirs and hotspots for the development of ARGs. Urban estuaries further gathered and amplified the effects of co-occurring contaminants, thereby enhancing the prevalence of ARGs. The potential spread of ARGs was dominated by contaminant co-occurring patterns in urban waters, whereas microbial communities dominated in sediments. Urban zoning comprehensively affected environmental health risks, indicating that environmental management strategies, such as controlling pollution sources and implementing remediation, should prioritize water bodies in agricultural areas and sediments in commercial/residential areas.},
}

@article {pmid42211787,
year = {2026},
author = {Zhang, R and Chen, YK and Zhu, QY and Feng, RY and Liu, H and Ma, MM and Wang, XJ},
title = {Metagenomic profiling of ocular surface microbiome alterations in patients with progressive supranuclear palsy-Richardson's syndrome.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100605},
pmid = {42211787},
issn = {2666-5174},
abstract = {This study employed shotgun metagenomic sequencing to characterize the ocular surface microbiome in 20 progressive supranuclear palsy-Richardson's syndrome (PSP-RS) patients, 17 Parkinson's disease (PD) patients, and 30 healthy controls (HC). Comparative analysis revealed that PSP-RS patients exhibited significantly altered microbial β-diversity compared to HC, while PD patients showed no such significant changes. Both patient groups demonstrated decreased abundance of g_Vibrio, with PSP-RS patients additionally showing marked increases in g_Acinetobacter and g_Anaerococcus. Importantly, correlation analyses identified that increased g_Acinetobacter abundance was positively associated with ocular motor impairment severity, while elevated g_Anaerococcus levels correlated with both freezing of gait severity and longer disease duration in PSP-RS patients. This is the first shotgun metagenomic investigation of the ocular surface microbiome in PSP-RS and these findings provide evidence that specific alterations in the ocular surface microbiome may contribute to PSP-RS pathogenesis and disease progression.},
}

@article {pmid42211840,
year = {2026},
author = {Pesantes, N and Barberá, A and Pérez-Rocher, B and Artacho, A and Vargas, SL and Moya, A and Ruiz-Ruiz, S},
title = {Correction: Influence of mental health medication on microbiota in the elderly population in the Valencian region.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1861757},
doi = {10.3389/fmicb.2026.1861757},
pmid = {42211840},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1094071.].},
}

@article {pmid42211849,
year = {2026},
author = {Du, R and Xu, C and Zhao, D and Zeng, H and Cheng, Y and Tang, K and Cai, P and Zhang, Y},
title = {Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1824768},
pmid = {42211849},
issn = {1664-302X},
abstract = {Estuarine sediments are pivotal zones for iron (Fe) cycling, mediated by microbial communities and coupled to carbon, nitrogen, sulfur and phosphorus transformations. However, the microbial iron metabolic processes in estuarine sediments remain poorly characterized, particularly under hypoxia. This study compared metagenomes from the Oujiang River Estuary, an oxic estuary, and the Yangtze River Estuary, a seasonally hypoxic estuary, complemented by sediment core incubations to assess geochemical responses to deoxygenation. The taxonomic affiliations of iron metabolism-related genes in the oxic estuary were homogeneous with depth, dominated by Proteobacteria and Thermodesulfobacteriota. In contrast, the hypoxic estuary exhibited strong stratification, with the surface enriched in Proteobacteria and deeper horizons dominated by Chloroflexota and Candidatus Bathyarchaeota. The surface sediments of the hypoxic estuary at 0-8 centimeters below the seafloor showed a hotspot with co-enrichment of dissimilatory iron reduction (e.g., mtrABC) and iron oxidation genes (e.g., mtoA) relative to both deeper layers in the same estuary and the oxic estuary, consistent with elevated genetic potential for Fe redox turnover. This hotspot also harbored high-affinity Fe acquisition systems (siderophores, inorganic Fe transporters, and heme uptake), suggesting the potential for microbial competition for iron. Co-occurrence networks connecting Fe metabolism with carbon, nitrogen, sulfur and phosphorus cycling were more complex in the hypoxic estuary than in the oxic estuary, revealing strong associations between Fe acquisition/redox cycling and organic matter turnover. A 16-day incubation of sediment cores from the oxic estuary showed that short-term deoxygenation enhanced dissolved Fe, phosphate, and ammonium release. Overall, our results suggest that bottom-water hypoxia is associated with major shifts in microbial iron metabolism potential, with implications for iron-organic matter interactions and nutrient regeneration under coastal deoxygenation.},
}

@article {pmid42211850,
year = {2026},
author = {Li, L and Liu, R and Yang, H and Zhao, Y},
title = {Metagenomic sequencing reveals structural and functional differentiation of rhizosphere bacterial communities driven by nitrogen and potassium deficiency associated with root rot of Schisandra chinensis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1827096},
pmid = {42211850},
issn = {1664-302X},
abstract = {BACKGROUND: Frequent incidence of root rot in Schisandra chinensis impairs its yield and quality, yet the rhizosphere microecological mechanism driving this incidence remains unclear.

METHODS: To clarify this mechanism, healthy and root rot-infected S. chinensis plants were analyzed in this study. The plant growth, rhizosphere soil physicochemical properties, and the structural and functional differences in rhizosphere bacterial communities under both conditions were analyzed.

RESULTS: Our results showed that root rot significantly inhibited S. chinensis growth and pathogen colonization-induced rhizosphere acidification, with reduced hydrolyzable nitrogen (HN) and available potassium (AK). Analysis of the intergroup differences in bacterial species revealed that the healthy rhizosphere was enriched with Acidobacteriota, Luteitalea, Pseudomonadota, Pseudolabrys, and Methylomirabilota, whereas infected rhizosphere was dominated by Gaiella (Actinomycetota), Gemmatimonas (Gemmatimonadota), Bradyrhizobium, and Sphingomicrobium (Pseudomonadota). Functional annotation based on COG, KEGG, and CAZy databases revealed that the bacteria of the healthy rhizosphere were enriched in defensive-cooperative functions (synergistic metabolism, secondary metabolite synthesis, complex carbon metabolism), while those of the infected rhizosphere exhibited simplified survival functions (individual metabolism, ABC transport, simple carbohydrate metabolism). Redundancy analysis identified HN and AK as key nutrients driving community differentiation in the rhizosphere.

CONCLUSION: This study revealed that root rot in S. chinensis is closely associated with an imbalance in the rhizosphere environment-bacterial community-function system, with healthy plants exhibiting specific core bacterial biomarkers and more complex synergistic metabolic networks, while HN and AK are key nutrients influencing rhizosphere bacterial communities. This study clarifies the rhizosphere microecological mechanism associated with S. chinensis root rot, providing a theoretical basis for its control.},
}

@article {pmid42212564,
year = {2026},
author = {Kim, Y and Kim, JK and Her, M and Kong, HS and Moon, JS and Yun, CS},
title = {Shotgun Metagenomic Diagnosis of Unidentified Pathogens in Hepatic Necrosis Samples from Samgye Chickens.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-235},
doi = {10.1080/03079457.2026.2674233},
pmid = {42212564},
issn = {1465-3338},
abstract = {Chicken infectious anemia virus (CIAV), infectious bursal disease virus (IBDV), and Eimeria spp. are major immunosuppressive pathogens in chickens that predispose host to secondary infections, including Clostridium septicum-associated hepatic necrosis. In this case, shotgun metagenomic sequencing was applied to identify C. septicum that could not be isolated by traditional bacterial culture in Samgye chickens. Six 35-day-old Samgye chicken carcasses were submitted for disease diagnosis, histopathological examination, and bacterial and viral isolation/identification were performed. Pooled liver samples were subjected to shotgun metagenomic sequencing to identify microbial composition, virulence factors, and antimicrobial resistance genes. Samgye chickens exhibited dorsal dermatitis, hepatic necrosis, and splenomegaly. Histopathology revealed hepatic necrosis with bacterial colonies and lymphoid depletion. PCR detected CIAV, antigenic variant IBDV, chicken astrovirus, and Eimeria, whereas bacterial culture yielded no growth. Shotgun metagenomic analysis identified C. septicum as predominant bacterium, and CIAV as dominant viral pathogen. The α-toxin and the antimicrobial resistance tetA(P) genes were detected from liver samples. This is the first report of concurrent CIAV, avIBDV, Eimeria spp., and C. septicum infection from Samgye chickens in South Korea, suggesting that immunosuppressive infections may predispose chickens to C. septicum-associated hepatic necrosis and highlight the diagnostic utility of shotgun metagenomic sequencing.},
}

@article {pmid42212611,
year = {2026},
author = {Sauer, P},
title = {[Current trends in sepsis diagnosis - from classic culture to advanced molecular identification].},
journal = {Klinicka mikrobiologie a infekcni lekarstvi},
volume = {32},
number = {1},
pages = {24-29},
pmid = {42212611},
issn = {1211-264X},
mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture ; *Molecular Diagnostic Techniques/trends ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Sepsis is a critical condition characterized by life-threatening organ dysfunction caused by a dysregulated host response to infection, where each hour of delay in initiating adequate therapy increases mortality by 7-10%. This paper summarizes current trends in microbiological diagnostics, moving from the gold standard of blood culture toward advanced molecular identification. The traditional culture-based process is limited by a time lag of 12-48 hours. Modern approaches include accelerating identification from positive blood cultures using MALDI-TOF MS and RAST methods, which reduce the time to targeted treatment. Significant innovation is represented by culture-independent technologies such as T2MR, SepsiTest-UMD, Cube Dx, and InfectID-BSI, enabling pathogen detection directly from whole blood within a few hours. The future of sepsis diagnosis is further enhanced by digital PCR for absolute quantification of bacterial load, metagenomic sequencing (mNGS) for identifying unexpected pathogens, and transcriptomics for assessing the host immune response. Integrating these technologies with artificial intelligence (AI) predictive models paves the way for precision medicine and personalized care for septic patients. Keywords: sepsis, blood culture, molecular diagnostics, PCR, mNGS, MALDI-TOF MS, artificial intelligence.},
}

Humans
*Sepsis/diagnosis/microbiology
Blood Culture
*Molecular Diagnostic Techniques/trends
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid42212684,
year = {2026},
author = {Liu, J and Zhao, P and Jiang, D and Li, S and Jin, C and Xu, D and Wang, X and Chen, Y and Tang, B and Qu, X},
title = {Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2672791},
doi = {10.1080/19490976.2026.2672791},
pmid = {42212684},
issn = {1949-0984},
mesh = {Humans ; *Precision Medicine/methods ; *Artificial Intelligence ; *Gastrointestinal Microbiome ; *Tumor Microenvironment ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; Multiomics ; Animals ; },
abstract = {The gut microbiome functions as a key regulator of tumorigenesis and progression, thereby modulating tumor development and treatment outcomes (including chemoresistance, immunotherapy efficacy, and adverse effects) through its influence on the immune microenvironment and metabolite-mediated signaling pathways. Recent advances in multiomics technologies (metagenomics, metabolomics, and transcriptomics) have generated large-scale, comprehensive, and heterogeneous datasets whose complexity exceeds the capabilities of manual analysis, thus necessitating the implementation of artificial intelligence-based approaches. This review systematically examines the crucial role of the gut microbiome in tumorigenesis, with particular emphasis on colorectal cancer (CRC), specifically addressing its utility as a diagnostic and prognostic biomarker. Furthermore, building upon existing applications of artificial intelligence (AI) in microbiome research and cancer diagnosis and treatment, this review presents an AI-driven precision intervention framework and delineates personalized treatment strategies.},
}

Humans
*Precision Medicine/methods
*Artificial Intelligence
*Gastrointestinal Microbiome
*Tumor Microenvironment
*Colorectal Neoplasms/microbiology/therapy/diagnosis
Multiomics
Animals

@article {pmid42212786,
year = {2026},
author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E},
title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0171425},
doi = {10.1128/msystems.01714-25},
pmid = {42212786},
issn = {2379-5077},
abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.

IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.},
}

@article {pmid42212790,
year = {2026},
author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T},
title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0014426},
doi = {10.1128/msystems.00144-26},
pmid = {42212790},
issn = {2379-5077},
abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.},
}

@article {pmid42212800,
year = {2026},
author = {Yabe, S and Zheng, Y and Takahashi, S and Yang, C and Nose, Y and Yamazaki, S and Okuma, N and Rachmania, MK and Ningsih, F and Sjamsuridzal, W and Sato, M and Toyooka, K and Ichihashi, Y},
title = {Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters in Ktedonobacteria.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019726},
doi = {10.1128/msystems.00197-26},
pmid = {42212800},
issn = {2379-5077},
abstract = {UNLABELLED: Soils harbor immense biosynthetic gene cluster (BGC) diversity that mediates microbial interactions, yet this potential remains unevenly mapped and poorly characterized across diverse bacterial lineages. Ktedonobacteria (phylum Chloroflexota) are an actinomycete-like lineage widely distributed in terrestrial soils, including oligotrophic volcanic deposits; however, their secondary metabolism and genome architecture remain poorly characterized. Here, we integrate targeted cultivation from volcanic soils at Mount Zao (Japan) with genome-resolved metagenomics and comparative analysis of public genomes to examine biosynthetic potential across 183 ktedonobacterial genomes. We identified 1,546 BGCs and grouped them into 1,162 non-redundant gene-cluster families (GCFs) using antiSMASH and BiG-SLiCE. Nearly one quarter of genomes encoded ≥10 distinct GCFs, and several family-level clades exhibited high GCF richness that approached that of Streptomyces within our data set, highlighting a putatively biosynthetically rich yet underexplored soil bacterial lineage. Most ktedonobacterial BGCs were highly divergent from current reference collections and exhibited unusually low intra-genomic redundancy, suggesting broad putative chemical diversity. Long-read assemblies from 10 cultured strains revealed recurrent 1.6-3.5 Mb ECE-like contigs with chromid-like features, but distinct maintenance features. These replicons were consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the phylogenetic landscape of soil biosynthetic diversity and highlight ECE-like contigs as major genomic reservoirs for secondary metabolism in Ktedonobacteria.

IMPORTANCE: Soil bacteria produce many of the small molecules that become medicines and help microbes interact with each other. Yet most of this chemical diversity remains unexplored because many soil lineages are difficult to cultivate and remain genomically underrepresented. Much of what we know comes from well-studied groups such as actinomycetes, leaving many soil lineages largely unexplored. We analyzed 183 genomes from Ktedonobacteria, an actinomycete-like group within the phylum Chloroflexota that is widespread in terrestrial soils, including nutrient-poor volcanic deposits. We uncovered a large and diverse set of gene clusters predicted to produce secondary metabolites, many of which lack close counterparts in current reference collections. We also show that these clusters are concentrated on large ECE-like contigs with chromid-like features, pointing to a dedicated genomic reservoir that can accumulate and reshuffle biosynthetic traits. Our results expand the known sources of soil biosynthetic diversity and provide a foundation for future cultivation and functional characterization of Ktedonobacteria metabolites.},
}

@article {pmid42213267,
year = {2026},
author = {Gulnihol, S and Abdukhamid, N and Rustam, T and Firdavs, U and Gholami, AA},
title = {Methodological concerns in the association between gut microbiota and sarcopenia: from cross‑sectional associations to statistical fragility.},
journal = {Aging clinical and experimental research},
volume = {38},
number = {1},
pages = {},
pmid = {42213267},
issn = {1720-8319},
mesh = {Humans ; *Sarcopenia/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Aged ; Iran ; },
abstract = {This commentary critically appraises the cross‑sectional study by Nasrollahizadeh et al. on gut microbiota and sarcopenia in Iranian older adults. Key limitations include; after FDR correction for twelve bacterial genera, no significant differences remained between groups; Akkermansia lost significance in sensitivity analyses; Lactobacillus showed a confidence interval including 1.00; four primer pairs lacked validation with no MIQE‑compliant efficiency data; the cross‑sectional design precludes causal inference; and no sample size justification was reported. The study offers valuable hypothesis‑generating data, but evidence remains preliminary. Future longitudinal studies with metagenomic approaches are essential.},
}

Humans
*Sarcopenia/microbiology
Cross-Sectional Studies
*Gastrointestinal Microbiome
Aged
Iran

@article {pmid42213269,
year = {2026},
author = {Song, X and Cai, D and Yu, X and Zhang, X and Zhu, W},
title = {Effects of different cultivation methods on microbial community structure of lettuce based on metagenomic analysis.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42213269},
issn = {1678-4405},
support = {Z2021067//Tianjin Municipal Transportation Commission Science and Technology Development Plan Project/ ; Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)//Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)/ ; },
mesh = {*Lactuca/microbiology/growth & development ; Soil Microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Hydroponics/methods ; *Microbiota ; Metagenome ; Biodiversity ; },
abstract = {BACKGROUND: Lettuce cultivation primarily involves two methods: traditional soil-based cultivation and modern hydroponic systems. However, research on the microbial community structure of lettuce under these distinct cultivation approache is still limited.

METHOD: This study employed whole-genome shotgun metagenomic sequencing (metagenomic sequencing) to analyze the impact of soil-based and hydroponic cultivation systems on the microbial community structure and functional profiles of lettuce.

RESULTS: The microbial diversity index of soil samples was significantly higher than that of hydroponic samples, indicating a more diverse and complex microbial community in the soil environment. Key functional phylum, including Acidobacteriota and Actinomycetota, were more abundant in soil samples, supporting nutrient cycling and plant-microbe interactions through pathways involved in carbon metabolism, organic matter decomposition, and antibiotic biosynthesis. In contrast, hydroponic samples were dominated by Cyanobacteriota and Verrucomicrobiota, with enrichment of pathways associated with stress response, including quorum sensing, ABC transporters, and oxidative phosphorylation. Although α-diversity did not differ significantly between cultivation systems, their microbial community composition and functional profiles were markedly distinct: soil-grown lettuce exhibited enrichment in sugar catabolism and synergistic prokaryotic metabolic functions, whereas hydroponic lettuce showed a predominance of energy metabolism and enrichment of viral-related pathways. Furthermore, differential distribution of antibiotic resistance genes underscores the role of environmental selective pressures in shaping microbial functional adaptations.

CONCLUSION: This study demonstrates that different cultivation methods significantly influence the microbial community structure and function in lettuce. These findings provide a theoretical foundation for optimizing cultivation systems and offer scientific guidance for precisely modulating microbial functions to promote lettuce growth and health.},
}

*Lactuca/microbiology/growth & development
Soil Microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Hydroponics/methods
*Microbiota
Metagenome
Biodiversity

@article {pmid42213733,
year = {2026},
author = {Wheelahan, JW and Vaz, PK and Legione, AR and Hartley, CA and Rourke, NL and Lynch, M and McMeekin, B and Dobson, EC and Devlin, JM},
title = {Virological investigation and comparative genomic analysis of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus).},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0345964},
doi = {10.1371/journal.pone.0345964},
pmid = {42213733},
issn = {1932-6203},
mesh = {Animals ; *Elephants/virology ; *Herpesviridae Infections/veterinary/virology ; *Genome, Viral ; Australia ; Phylogeny ; Viral Load ; *Herpesviridae/genetics ; Genomics ; },
abstract = {Elephant endotheliotropic herpesviruses (EEHV) pose a significant threat to the conservation of Asian elephants (Elephas maximus) worldwide, with a high mortality rate in young elephants. However, several components of EEHV virology remain underexplored, particularly for EEHV1B. This study describes a fatal case of EEHV1B infection in a nine-year-old Asian elephant from an ex situ conservation herd, examining herd viral dynamics, tissue viral loads and comparative genomics. This elephant succumbed to haemorrhagic disease within three days of developing clinical signs, despite therapeutic intervention. Quantitative PCR (qPCR) was performed on serial trunk washes and whole-blood surveillance samples collected before and after the clinical event, as well as on post-mortem tissues preserved in different storage media (DNA/RNA Shield, RNALater, and viral transport medium). Metagenomic next-generation sequencing of infected tissues was performed to characterise the complete viral genome, analyse variation from other published EEHV genomes and assess for evidence of viral recombination between EEHV subspecies. The affected elephant demonstrated a marked viraemia at onset of clinical disease, with viral load peaking at 5.47 x 106 viral genome equivalents per mL of blood, one day after the onset of clinical signs. Samples stored in viral transport medium yielded the greatest viral and host DNA recovery by qPCR, although tissues stored at -80 °C without media were still suitable for molecular detection. Whole genome sequencing demonstrated 96.0% pairwise nucleotide identity between the assembled genome (EEHV1B_AUP_01_2023, GenBank accession: PX651398) and the previously reported EEHV1B sequence (KC462164), and a maximum of 90.9% identity to published EEHV1A genomes, with evidence of recombination between the viral subspecies at several genomic regions. Viral recombination between EEHV subspecies may have significant implications for the pathogenesis of EEHV disease, the reliability of molecular diagnostics and the efficacy of vaccinations and anti-viral therapy.},
}

Animals
*Elephants/virology
*Herpesviridae Infections/veterinary/virology
*Genome, Viral
Australia
Phylogeny
Viral Load
*Herpesviridae/genetics
Genomics

@article {pmid42213849,
year = {2026},
author = {Meijer, J and Skiadas, P and Rainey, PB and Hogeweg, P and Dutilh, BE},
title = {Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.},
journal = {Science advances},
volume = {12},
number = {22},
pages = {eaeb8246},
doi = {10.1126/sciadv.aeb8246},
pmid = {42213849},
issn = {2375-2548},
mesh = {*Bacteriophages/genetics/physiology ; *Soil Microbiology ; *Evolution, Molecular ; Ecosystem ; *Composting ; Metagenomics ; Phylogeny ; Genome, Viral ; },
abstract = {Bacteriophages play critical roles in microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. Here, we tracked viral dynamics in 20 compost-derived microbial communities over 1 year. Communities formed two alternative stable types, each dominated by distinct cellulose degraders and comprising hundreds of genera. In one community type, we observed massive, parallel outbreaks of Theomophage, a previously uncharacterized member of the Schitoviridae, reaching up to 74% of metagenomic reads-the largest bacteriophage outbreak documented to date. Despite extensive replication, Theomophage displayed notable genetic stability during outbreaks and over time. In contrast, the experimental migration of viral communities triggered rapid evolution driven by recombination and the accumulation of newly arising mutations, particularly after colonization of communities of the alternative type in which the phage was initially absent. These results reveal the spatial and temporal scales at which bacteriophage microdiversity evolves in complex ecosystems and show that viral mixing, likely common in nature, can rapidly accelerate phage evolution.},
}

*Bacteriophages/genetics/physiology
*Soil Microbiology
*Evolution, Molecular
Ecosystem
*Composting
Metagenomics
Phylogeny
Genome, Viral

@article {pmid42214271,
year = {2026},
author = {Lin, Y and Roy, S and Hagedoorn, PL},
title = {Microbial melanin-like material: A factor beyond influencing the brown color of activated sludge.},
journal = {Water research},
volume = {303},
number = {},
pages = {126195},
doi = {10.1016/j.watres.2026.126195},
pmid = {42214271},
issn = {1879-2448},
abstract = {Melanin is a group of phenolic-quinone pigments. Natural melanin is nearly ubiquitous; found in all types of living organisms, ranging from mammals to bacteria. However, its presence and biosynthesis genomic potential in activated sludge have not been investigated. To explore this potential, melanin-like material was extracted from activated sludge collected from a municipal wastewater treatment plant. The extracted melanin-like material was characterized through biochemical analyses in comparison to synthetic melanin and humic acids that are commercially available. Metagenomic analysis of microbial community members in activated sludge and detection of tyrosine-derived melanin synthesis genes was performed. Additionally, the potential application of the extracted melanin-like material as a natural pigment was evaluated by testing its ability to color wool yarn. It was found that melanin-like material extracted from activated sludge accounted for around 11% of sludge dry mass. The isolated material displayed intrinsic autofluorescence, strong UV absorption, high oxidative stability, and free radical-rich EPR signal. FTIR analysis indicated a mixed polymer dominated by pyomelanin-like structures with eumelanin features, distinguishing it from synthetic melanin and humic acid. Metagenomic screening of the sludge community revealed widespread genomic potential for pyomelanin monomeric precursors biosynthesis across key functional genera (e.g. genera Zoogloea, Nitrotoga, Nitrosomonas, Ca. Accumulibacter, Azonexus, Ca. Competibacter, Propionivibrio, and Rhodoferax). These results suggest that microbial melanin-like material is an overlooked contributor to sludge coloration. Furthermore, the extracted pigment exhibited high affinity and wash fastness on wool fibers, demonstrating its potential for valorization as a sustainable biobased colorant.},
}

@article {pmid42214309,
year = {2026},
author = {Guo, N and Chen, J and Lei, Z and Qu, L and Xie, W and Yin, K and Yang, Y},
title = {Evidence for the connectivity of antibiotic resistance genes between seamount and coastal environments.},
journal = {Ecotoxicology and environmental safety},
volume = {319},
number = {},
pages = {120325},
doi = {10.1016/j.ecoenv.2026.120325},
pmid = {42214309},
issn = {1090-2414},
abstract = {Antibiotic resistance genes (ARGs) have drawn global attention and are ubiquitously detected in marine environments. Seamounts, prominent seafloor features with high biodiversity, may be hotspots for ARG proliferation and transfer. However, little is known about the existence, microbial associations, or connectivity with terrestrial sources of ARGs in seamounts. In this study, high-throughput sequencing approaches were employed to investigate the distribution, hosts, mobility, and coastal connectivity of ARGs in sediments from the Zhongnan Seamount, South China Sea. The most abundant ARG types were elfamycin, aminoglycoside, and tetracycline. ARG abundance was significantly higher in abyssopelagic zone sediments, suggesting the seamount acts as a sink and deep-sea regions are a major ARG reservoir. Results indicated high horizontal gene transfer potential, with key genes EF-Tu, rpsJ, parC, and parE as predominant mediators. Metagenome-assembled genomes identified 36 bacterial genera as ARG hosts, dominated by Methylomirabilota and Pseudomonadota. The source tracking and genetic connectivity analysis revealed a clear input of coastal ARGs to the seamount, emphasizing the need to investigate global ARG dissemination and its potential ecological effects. Overall, these findings identify the seamount environment as a deep-sea ARG hotspot, providing valuable insights into the prevalence, hosts, and sources of ARGs in the marine ecosystem.},
}

@article {pmid42214347,
year = {2026},
author = {Peredo, EL and Kulp, R and Rodriguez, F and Weintraub, MN and Anand, M and Bixler, S and Koller, J and Lee, C and Mathai, D and Tuytschaevers, S and Kumar, G},
title = {Metagenome-assembled genomes from biological soil crusts in sandy sediments of Kitty Todd Nature Preserve, OH, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0038026},
doi = {10.1128/mra.00380-26},
pmid = {42214347},
issn = {2576-098X},
abstract = {Biological soil crusts (BSCs) are complex structures composed of prokaryotes, green microalgae, fungi, and small mosses that bind soil particles together. To further understand the microbial composition and interactions among members of these consortia, we investigated the microbial diversity of BSCs found in a xeric patch in northwestern Ohio.},
}

@article {pmid42214368,
year = {2026},
author = {Karmarkar, B and Dhotre, D},
title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0321425},
doi = {10.1128/spectrum.03214-25},
pmid = {42214368},
issn = {2165-0497},
abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.

IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.},
}

@article {pmid42214386,
year = {2026},
author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG},
title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.},
journal = {mBio},
volume = {},
number = {},
pages = {e0071126},
doi = {10.1128/mbio.00711-26},
pmid = {42214386},
issn = {2150-7511},
abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.

IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.

CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.},
}

@article {pmid42214591,
year = {2026},
author = {Zhu, Y and Li, D and Ma, B and Zhang, T and Zeng, H and Zhang, J and Li, S and Ding, F},
title = {Effluent-released sludge in granular anammox systems: nitrogen transformation potential and potential biosafety concerns.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124887},
doi = {10.1016/j.envres.2026.124887},
pmid = {42214591},
issn = {1096-0953},
abstract = {Granular anaerobic ammonium oxidation (anammox) sludge enables effective biomass retention and supports the stable operation of anammox reactors. During long-term operation, however, effluent-released sludge (ERS) is continuously washed out with the effluent, exhibiting physicochemical and microbial characteristics that differ markedly from those of retained sludge (RS). The functional role and biosafety implications of ERS remain poorly understood. In this study, RS and ERS from the same granular anammox reactor were systematically compared in terms of nitrogen removal performance, microbial community composition, functional gene profiles, and biosafety-related features. RS maintained high anammox activity, whereas ERS showed reduced anammox performance but was characterized by a pronounced enrichment of comammox Nitrospira, supporting more diverse nitrogen transformation pathways. Metagenomic and 16S rRNA analyses further indicated the co-occurrence of comammox Nitrospira and heterotrophic denitrifiers in ERS, suggesting a potential metabolic linkage involving nitrate production and partial reduction to nitrite that may complement anammox activity. Functional pathway analysis revealed diminished autotrophic carbon fixation in ERS, alongside enhanced heterotrophic metabolism and cobalamin biosynthesis. In parallel, ERS exhibited elevated abundances of antibiotic resistance genes and pathogenic taxa. Collectively, these results demonstrate that ERS represents a functionally distinct biomass fraction with unique microbial and metabolic characteristics, as well as potential biosafety implications, warranting further consideration in the evaluation and management of granular anammox systems.},
}

@article {pmid42214592,
year = {2026},
author = {Zhu, Y and Liu, H and Yi, Y and Li, Z and Ye, J},
title = {Agricultural allochthonous dissolved organic matter is associated with microbial functional differentiation in methane- and nitrogen-related gene profiles in rural rivers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124865},
doi = {10.1016/j.envres.2026.124865},
pmid = {42214592},
issn = {1096-0953},
abstract = {Agricultural non-point source (ANPS) pollution introduces chemically complex dissolved organic matter (DOM) into rural rivers, yet how different agricultural practices structure DOM-microbial differentiation at the molecular scale remains unclear. Here, we compared rivers polluted by three dominant ANPS subtypes-aquaculture (AQ), livestock and poultry farming (LP), and crop farming (CF)-across winter and summer in Shanghai, China, by integrating Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) with 16S rRNA gene sequencing and metagenomics. Distinct DOM-microbial differentiation patterns were identified among ANPS subtypes. AQ was characterized by higher proportions of heteroatom-rich compounds (30.6%) and higher-molecular-weight compounds, LP by more aromatic and lignin-/tannin-associated molecular features (AI_mod = 0.261), and CF by CHOS-enriched (26.8%) but overall lower DOM chemodiversity. These molecular fingerprints co-occurred with differences in microbial diversity, community assembly (βNTI), and co-occurrence network topology, indicating relatively stable DOM-microbial templates shaped by long-term agricultural inputs. Seasonal variability further modified DOM composition and microbial differentiation, but responses differed among ANPS subtypes. Event-driven systems (AQ and LP) exhibited pronounced winter-summer shifts, whereas the background-dominated system (CF) showed weaker temporal variability but more persistent DOM-microbial coupling patterns. Low- to medium-molecular-weight (m/z 100-550) DOM fractions showed the strongest co-variation with nitrogen- and methane-related functional gene potentials, suggesting molecular-weight-dependent associations between DOM composition and microbial functional gene profiles. Overall, these findings suggest that ANPS pollution comprises source- and season-specific DOM-microbial templates that can be distinguished using molecular and functional indicators, providing a basis for source-oriented monitoring and targeted management of agriculturally impacted rural river systems.},
}

@article {pmid42214594,
year = {2026},
author = {Zhang, Y and Zhang, L and Zhang, S and Yang, C and Wang, Z and Si, G and Peng, Y},
title = {Synergistic Antibiotic-Laden Wastewater Treatment Doubles Denitrification Rate in a Pilot Mineral-Based Autotrophic Biofilter by Breaking Microbial Spatial-Metabolic Constraints.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124860},
doi = {10.1016/j.envres.2026.124860},
pmid = {42214594},
issn = {1096-0953},
abstract = {The practical application of pyrite-based autotrophic denitrification biofilters (PADB) is limited by their low nitrogen removal rate (NRR). This study demonstrates that in a pilot-scale PADB (750 L) treating NO3[-]-N wastewater, heterotrophic bacterial consortia (HBs) severely impair the denitrification activity of autotrophic denitrifying bacteria (ADB) through network encapsulation and metabolic shunting. However, after switching to treating composite wastewater containing antibiotics, the system achieved an antibiotic removal rate of 95.12%. And it's NRR from 32.37 to 63.15 mg N/(L·d), representing a 0.95-fold enhancement. Integrated co-occurrence network and metagenomic analyses revealed a three-stage cascade reaction underlying this improvement: (i) The antibiotic stress halted carbon-feeding from ADB and hydrolytic-acidifying bacteria to HBs (fermentation gene abundance decreased by 1.89-58.45%), depriving HBs of energetic and substrate support and resulting in their selective elimination (0.63-fold decrease in relative abundance). This relieved ADB's metabolic burden and shortened their physical distance to pyrite; (ii) Elevated electron and energy demand in ADB activated dormant genes for electron shuttle synthesis (menC/E: 0 to 342/402 TPM) and upregulated sulfur metabolism genes (∼3.9-fold), enhancing pyrite dissolution and electron harvesting; (iii) This augmented electron flow stimulated ADB's carbon fixation pathway (Calvin-Benson-Bassham cycle genes upregulated 14.89-fold) and amplified energy metabolism (1.33-1.55-fold enhancement in glycolysis and Tricarboxylic Acid cycle), supplying ample material and energy for ADB proliferation and denitrification. Consequently, ADB enrichment accelerated 509-fold, while the abundance of key denitrification genes (napA/B, nosZ) increased by 2.1-11.04-fold. These molecular and population-level changes doubled the system's NRR compared to its original level.},
}

@article {pmid42214595,
year = {2026},
author = {Pan, W and Zhang, L and Liang, L and Du, L and Guo, X},
title = {Nanoplastics Reshape Nitrogen Cycling in Submerged Macrophyte Systems: A Metagenomic Perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124885},
doi = {10.1016/j.envres.2026.124885},
pmid = {42214595},
issn = {1096-0953},
abstract = {Nanoplastics (NPs) pose a potential risk to aquatic ecosystems. Submerged macrophytes are critical for nitrogen removal, but how nitrogen cycling responds to NP-induced stress remains unclear. This study used Myriophyllum aquaticum to evaluate nitrogen cycling in submerged macrophyte-sediment systems exposed to 100 nm polystyrene (PS) NPs at 10, 100, and 1000 μg/L, integrating stable isotope tracing and metagenomic profiling to explore microbial community and nitrogen-cycling gene responses across rhizosphere and non-rhizosphere compartments. Low PS-NP exposure (10 μg/L) slightly increased the NH4[+]-N removal efficiency to 81.5%, whereas medium and high PS-NP exposures (100 and 1000 μg/L) reduced the NH4[+]-N removal efficiency, with values around 70.9%. Low doses stimulated nitrification (NO3[-]-N accumulation) and high doses inhibited N2O emissions; δ[15]N tracing showed disrupted NH4[+]-N to N2 reduction. Plant-only microcosms had the highest N2O release (1.37 mg, 1.5% of total N). Metagenomics revealed concentration-dependent, spatially distinct microbial community shifts: low PS-NPs increased rhizosphere α-diversity, while high concentrations depleted Proteobacteria, enriched Acidobacteria/Bacteroidetes, and reduced key nitrogen-cycling genera (e.g., Dechloromonas, Accumulibacter). In the rhizosphere, denitrification genes (nirK/S,nosZ) were upregulated by 2.5- and 3-fold, respectively, while DNRA (nrfA) and nitrogen fixation (nifH) genes were downregulated by 1.7- and 2.3-fold. Network and canonical correspondence analyses indicated stronger environmental filtering in bulk sediments (explaining 52.0% of variance) and spatially structured nitrogen metabolic pathway reorganization. These findings show concentration-dependent PS-NP exposure differentially shapes microbial community composition and nitrogen-cycling functions in rhizosphere and bulk sediments.},
}

@article {pmid42214685,
year = {2026},
author = {Jiang, T and Prioult, G and Quann, E},
title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101621},
doi = {10.1016/j.tjnut.2026.101621},
pmid = {42214685},
issn = {1541-6100},
abstract = {Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health, but are constrained by poor bioavailability. Only 5-10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract; the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits, owing to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways. Production of these metabolites varies markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes-termed metabotypes-that strongly influence clinical and nutritional responsiveness. This review synthesizes recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and examines how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes. We further evaluate emerging evidence supporting synergistic synbiotics-targeted combinations of probiotics with specific polyphenol or bioactive precursors-as a strategy to standardize and enhance the generation of beneficial microbial metabolites. These synbiotic strategies demonstrate capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging. Together, these findings position metabolite-guided synbiotics as a promising paradigm for precision nutrition. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate translation of microbiota-targeted interventions.},
}

@article {pmid42214867,
year = {2026},
author = {Lu, J and Zhang, S and Guo, Y and Wu, H and Hu, Z and Kong, Q and Zhang, J},
title = {Magnetite-facilitated AHL-mediated quorum sensing enhances nitrate removal and mitigates nitrous oxide emissions in constructed wetlands under polycyclic aromatic hydrocarbons stress.},
journal = {Journal of hazardous materials},
volume = {513},
number = {},
pages = {142523},
doi = {10.1016/j.jhazmat.2026.142523},
pmid = {42214867},
issn = {1873-3336},
abstract = {The performance of constructed wetlands (CWs) in removing nitrate (NO3[-]-N) and mitigating nitrous oxide (N2O) emissions can be impaired by trace organic pollutants like polycyclic aromatic hydrocarbons (PAHs). Magnetite has been widely applied as a substrate to regulate nitrogen transformation in CWs; however, its potential role in mediating quorum sensing (QS) to alleviate PAH-induced inhibition remains unclear. In this study, conventional CWs (CW-A) and magnetite-amended CWs (CW-B) were established to evaluate NO3[-]-N removal and N2O emissions and the associated mechanisms under PAH-stress conditions. Results indicated that CW-B maintained a high NO3[-]-N removal efficiency (90.14%), whereas CW-A exhibited a marked decline from 65.06% to 47.32%. Magnetite amendment reduced N2O emissions by 68.97% compared with CW-A. Furthermore, the enhanced performance of CW‑B was closely linked to the strengthening of QS. CW-B sustained elevated levels of acyl-homoserine lactone (AHL) signaling molecules (e.g., C8-HSL) under PAH stress, while these signals were suppressed in CW-A. Metagenomic analysis revealed enrichment of key functional genera (e.g., Tessaracoccus and Pseudomonas) and genes associated with QS and nitrogen transformation (e.g., luxI, nirS, and nosZ) in CW-B, supporting enhanced NO3[-]-N removal and reduced N2O emissions. The reinforced QS further promoted interspecies electron transfer and enhanced microbial network robustness and resilience. Additionally, PAHs stimulated the DNRA process and enhanced the abundance of DNRA-related genes (i.e., nrfA and nrfH) in both CWs, leading to increased effluent total nitrogen. Overall, this study elucidates a magnetite-mediated QS mechanism that enhances nitrogen transformation and microbial metabolic stability in CWs under PAH stress.},
}

@article {pmid42215097,
year = {2026},
author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L},
title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {238},
number = {},
pages = {119428},
doi = {10.1016/j.foodres.2026.119428},
pmid = {42215097},
issn = {1873-7145},
mesh = {Multiomics ; *Microbiota/physiology ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis/metabolism ; China ; Metabolomics/methods ; *Food Microbiology ; *Taste ; *Flavoring Agents/metabolism ; Metagenomics ; Bacteria/metabolism/classification ; Temperature ; Fungi/metabolism/classification/genetics ; },
abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.},
}

Multiomics
*Microbiota/physiology
Fermentation
*Alcoholic Beverages/microbiology/analysis
Gas Chromatography-Mass Spectrometry
Volatile Organic Compounds/analysis/metabolism
China
Metabolomics/methods
*Food Microbiology
*Taste
*Flavoring Agents/metabolism
Metagenomics
Bacteria/metabolism/classification
Temperature
Fungi/metabolism/classification/genetics

@article {pmid42215200,
year = {2026},
author = {Jones, RC and Visger, CJ and Lopez, CA},
title = {The microbiota of wild fermented cider from U.S. west coast apples.},
journal = {Food microbiology},
volume = {139},
number = {},
pages = {105120},
doi = {10.1016/j.fm.2026.105120},
pmid = {42215200},
issn = {1095-9998},
mesh = {*Malus/microbiology ; Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Yeasts/isolation & purification/classification/genetics/metabolism ; United States ; Food Microbiology ; Fruit/microbiology ; },
abstract = {Traditional methods to produce apple cider rely on wild fermentations, where the indigenous microbes present on the fruit and environment transform the pressed apple juice, or must, to cider. The identification of the diverse bacteria and yeast responsible for wild fermentations is an important step in designing practices that promote desired microbes while preventing expansion of spoilage microbes. Here, we sought to survey the microbial communities found in wild fermented ciders from the western United States using shotgun metagenomics sequencing in packaged cider. There, we found a substantial diversity of bacteria and yeast genomic sequences; however, despite variation in apple origin and cidery, there was consistent identification of Oenococcus oeni, Lentilactobacillus hilgardii, and Brettanomyces bruxellensis. Additionally, Tatumella ptyseos, a member of the plant-associated Erwiniaceae, was identified in all cider batches, with T. ptyseos representing one of the most abundant observed taxa in some batches. Analysis of the identified T. ptyseos strains suggests the presence of adaptations to a cider environment that include carbohydrate fermentation, methionine salvage, and nutrient iron and zinc scavenging. These results provide preliminary support that the microbial communities established in fermenting cider contain core constituents that may stratify based on key metabolic characteristics or adaptations to a low nutrient, high competition environment.},
}

*Malus/microbiology
Fermentation
*Microbiota
*Bacteria/classification/genetics/isolation & purification/metabolism
*Alcoholic Beverages/microbiology/analysis
*Yeasts/isolation & purification/classification/genetics/metabolism
United States
Food Microbiology
Fruit/microbiology

@article {pmid41998770,
year = {2026},
author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH},
title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {41998770},
issn = {1756-994X},
support = {NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Emerging evidence suggests that maternal-prenatal gut microbiome disturbances shape offspring allergic outcomes through modulation of the in utero immune environment. Yet, no comprehensive clinical studies in human mother–offspring dyads have deconvoluted the maternal-prenatal gut microbiome and systemic immune-metabolome signatures underlying offspring allergic predisposition.

METHODS: We performed a longitudinal nested case–control study involving 128 well-characterized mother–offspring dyads from defined cases (offspring with atopic dermatitis (AD); n = 64) and controls (offspring without AD; n = 64). Maternal stool and blood samples were collected at multiple time points during gestation for multi-omic profiling. Structural and functional gut microbiome composition was characterized via metagenomic sequencing, while systemic metabolome and serum immune milieu were profiled using targeted plasma metabolomics and Olink proximity extension assays, respectively. In offspring early-life, stool samples were collected longitudinally up to 6 months of age for gut microbiome and metabolome analyses.

RESULTS: Mothers of AD infants exhibited longitudinal enrichments of gut Klebsiella pneumoniae, Roseburia intestinalis, Clostridioides difficile and Bilophila sp. 4_1_30, alongside depletions in gut Clostridium sp. CAG:678, Romboutsia timonensis, Akkermansia muciniphila, Blautia hansenii and Alistipes ihumii during pregnancy. These taxonomic shifts were associated with systemic metabolomic alterations, including elevated branched-chain amino acids and immune-related metabolites (e.g., creatine, ornithine), and a concurrent pro-inflammatory TH2-skewed immunological milieu marked by increased interleukin-4 (IL-4) and IL-5 and decreased CXCL11. In early life, AD infants harbored a dysbiotic gut microbiome characterized by persistent enrichments of potentially pathogenic Escherichia coli and K. pneumoniae, along with depletion of short chain fatty acid-producing Bacteroides species and beneficial colonizers. Integrated multi-omic analyses across the prenatal-postnatal axis indicated that the impaired establishment of gut microbiome in AD infants may, in part, be attributed to the (1) potential transmission of maternally originated Klebsiella and (2) immunomodulatory effects of a maternal-prenatal pro-inflammatory, TH2-skewed milieu during gestation.

CONCLUSIONS: Our study uncovers a distinct maternal-prenatal gut microbiome and systemic metabolome–immune signature that predisposes offspring to AD by disrupting early-life gut microbial establishment. These findings highlight the gestational period as a critical window for preventive strategies targeting the maternal microbiome or systemic immune-metabolic axes to mitigate allergic disease susceptibility in offspring.

TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov (NCT 03531658).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01655-5.},
}

@article {pmid42202790,
year = {2026},
author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R},
title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102835},
doi = {10.1016/j.xcrm.2026.102835},
pmid = {42202790},
issn = {2666-3791},
abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.},
}

@article {pmid42203111,
year = {2026},
author = {Wang, L and Bai, L and Li, H and Zhang, P and He, F},
title = {A Case of Imported Infection in China: Initially Treatment-unresponsive Schistosomiasis Coinfection with Bladder Tuberculosis.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {101157},
doi = {10.1016/j.ijmmb.2026.101157},
pmid = {42203111},
issn = {1998-3646},
abstract = {Schistosoma haematobium, endemic to sub-Saharan Africa, causes urogenital disease, differing from Schistosoma japonicum, which affects the hepatointestinal system and is the only endemic schistosome in China. A Chinese male with persistent hematuria after prolonged occupational exposure in Angola was initially attributed to S. japonicum. Following failed treatment, metagenomic sequencing confirmed S. haematobium infection, and subsequent urethral resection detected Mycobacterium tuberculosis DNA, establishing concurrent bladder tuberculosis. This case highlights the need for molecular diagnostics in patients with hematuria after sub-Saharan exposure and the immunomodulatory risks posed by helminth infections.},
}

@article {pmid42203372,
year = {2026},
author = {McCann, P and Megaw, J and Gobert, GN},
title = {Parasite-associated microbiomes: An unseen microenvironment.},
journal = {Advances in parasitology},
volume = {131},
number = {},
pages = {31-70},
doi = {10.1016/bs.apar.2026.03.001},
pmid = {42203372},
issn = {2163-6079},
mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; },
abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.},
}

Animals
Humans
*Microbiota
*Host-Parasite Interactions
*Parasites/microbiology/physiology
Symbiosis

@article {pmid42203690,
year = {2026},
author = {Fullam, A and Prasoodanan Pk, V and Kuhn, M and Bork, P and Schmidt, TSB},
title = {microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag343},
pmid = {42203690},
issn = {1367-4811},
abstract = {MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.

RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories.

AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305,626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42203770,
year = {2026},
author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M},
title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73297-5},
pmid = {42203770},
issn = {2041-1723},
support = {1026-00386B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; },
abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.},
}

@article {pmid42203854,
year = {2026},
author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I},
title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42203854},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; },
abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.},
}

Humans
Female
Pregnancy
*Saliva/microbiology
*Microbiota/genetics
*Metagenomics/methods
Adult
*Mouth/microbiology
Shotgun Sequencing
Cross-Sectional Studies
Metagenome
Bacteria/genetics/classification

@article {pmid42204574,
year = {2026},
author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N},
title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.},
journal = {Annals of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ana.78243},
pmid = {42204574},
issn = {1531-8249},
support = {RF1AG075922/GF/NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; R01NS097723/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; },
abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026.},
}

@article {pmid42204631,
year = {2026},
author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH},
title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07471-5},
pmid = {42204631},
issn = {1756-3305},
support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.

METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples (n = 46) was investigated by metagenomic shotgun sequencing and comparatively analysed at the phylum, genus, and species levels. In addition, the prevalence of potential pathogen DNA in head lice samples (n = 204) was assessed using real-time PCR with stringent negative controls.

RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722 genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level, DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial DNA from these taxa.

CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB microbiome in head lice. The high proportion of unannotated genes (>95%) underscores the limited representation of louse-associated microbial genomes in public databases and suggests  substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may suggest prior exposure, mechanical carriage, or residual DNA from blood meals. These exploratory findings contribute new insights into the microbiota associated with human lice.},
}

@article {pmid42204733,
year = {2026},
author = {Fang, Q and Liu, J and Xuan, C and Li, C and Jiang, X and Zhang, S and Li, Q and Liu, X and Liu, Q and Zhang, L and Wang, Y and Cui, J and Qu, Y and Zhang, J and Li, P and Chen, X},
title = {Targeting the gut‒kidney axis for lupus nephritis treatment: multimechanism regulatory strategies and evidence from Traditional Chinese medicine.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {42204733},
issn = {1749-8546},
support = {2022YFC3602000//the National Key Research and Development Program of China/ ; 82274327//the National Natural Science Foundation of China/ ; 32141005//the National Natural Science Foundation of China/ ; },
abstract = {Lupus nephritis (LN) treatment remains challenging because of the limited efficacy and substantial side effects of conventional immunosuppressive therapies. Traditional Chinese medicine (TCM), with its holistic and multitarget approach, offers unique therapeutic potential. The emerging gut-kidney axis theory provides a new framework for understanding LN pathogenesis by linking gut dysbiosis and intestinal barrier injury to renal inflammation. This review systematically examines the role of gut-kidney axis dysregulation in LN progression and establishes connections between the TCM spleen-kidney correlation theory and this modern concept. Accumulating evidence suggests that TCM compounds and active ingredients alleviate renal injury and improve LN through multiple mechanisms. TCM compounds modulate the gut microbiota composition, enhance intestinal barrier integrity, reduce endotoxin translocation, and suppress systemic inflammation. These findings position the gut-kidney axis as a critical target for TCM intervention. Through multicomponent synergy, TCM restores gut homeostasis and inhibits aberrant immune responses. Future studies should integrate multiomics approaches, including metagenomics and metabolomics, and prospective clinical trials should dynamically track the gut microbiota and metabolite profiles in LN patients. Such investigations will clarify the precise mechanisms by which TCM modulates the gut-kidney axis and facilitate the development of personalized TCM-based therapeutic strategies.},
}

@article {pmid42204882,
year = {2026},
author = {Jiang, Y and Zhao, J and Chen, Z and Jiang, N and Lu, C and Zhang, Y and Chen, H},
title = {Long-Term Effects of Straw-Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote-Fungus-Protist Interactions and Metagenomic-Metabolite Linkages.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70339},
doi = {10.1111/1462-2920.70339},
pmid = {42204882},
issn = {1462-2920},
support = {2022YFD1500302//National Key Research and Development Program of China/ ; 42277282//National Natural Science Foundation of China/ ; 2022A1515010861//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20250604174440054//Shenzhen Natural Science Foundation in Basic Research Fund/ ; JCYJ20220530150201003//Shenzhen Natural Science Foundation in Basic Research Fund/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism/genetics/physiology ; Metagenomics ; *Charcoal ; *Carbon Sequestration ; Bacteria/metabolism/genetics/classification ; *Fertilizers/analysis ; China ; Microbiota ; Carbon/metabolism ; Metagenome ; },
abstract = {Here, we conducted a seven-year field experiment in black soils of Northeast China to evaluate the effects of carbon (C) management, that is, control, straw return (SD), straw-biochar (BC), and a combined amendment (SDBC), with three fertilization levels (N0: unfertilized control, N60: 60% of conventional rates, N100: conventional rates) on soil microbiomes, metagenomics, and metabolomics. Results showed that BC significantly elevated soil total C (+15%), total N (+10%), and NH 4 + $$ {\mathrm{NH}}
_4^{+}
$$ (+63%) relative to controls. Microbial community analyses revealed that SD increased prokaryotic richness but reduced protist diversity, whereas BC and SDBC suppressed fungal diversity. Integrated metagenomic and metabolomic profiling uncovered microbial functional adaptations to rich-C conditions under BC and SDBC, characterized by downregulated C metabolism-related genes and concurrent accumulation of lipid-associated metabolites. Crucially, BC decreased the abundance of bacterial virulence factors, contrasting with SD elevating pathogenic potentials. Among three fertilization levels, the reduced rates of N60 optimized microbial network complexity and minimized pathogen invasion risks more effectively than conventional rates of N100 without compromising soil fertility. Collectively, by deciphering prokaryote-fungus-protist interactions and metagenomic-metabolite linkages, our research highlights that straw-derived biochar application and optimized fertilization offers a sustainable strategy to foster beneficial microbial associations, suppresses pathogenic potential, and enhances carbon storage.},
}

*Soil Microbiology
*Soil/chemistry
*Fungi/metabolism/genetics/physiology
Metagenomics
*Charcoal
*Carbon Sequestration
Bacteria/metabolism/genetics/classification
*Fertilizers/analysis
China
Microbiota
Carbon/metabolism
Metagenome

@article {pmid42205184,
year = {2026},
author = {Wang, X and Wang, H and Liu, J and Zhang, H and Zhou, XJ},
title = {Gut Virome Characteristics and Network Alterations in IgA Nephropathy.},
journal = {Kidney international reports},
volume = {11},
number = {7},
pages = {106550},
pmid = {42205184},
issn = {2468-0249},
abstract = {INTRODUCTION: Emerging evidence implicates gut microbiota dysbiosis in the pathogenesis of IgA nephropathy (IgAN), yet the contribution of the gut virome remains unexplored. This study aimed to characterize virome signatures and virus-microbiota interactions in IgAN.

METHODS: We performed a rigorously matched case-control study including 32 patients with biopsy-proven IgAN and 32 healthy controls. Fecal viral-like particles and bacterial communities were profiled using metagenomic sequencing and full-length 16S ribosomal RNA (rRNA) sequencing. Statistical analysis included diversity, differential abundance, network analysis, and correlation with clinical indices.

RESULTS: IgAN subjects displayed significant reductions in gut virome richness (severe IgAN vs. healthy controls, P = 0.03), with a lower relative abundance of Caudoviricetes in severe IgAN (P = 0.045) and enrichment of Tectiliviricetes in mild disease (P = 0.03). We identified 113 differentially abundant bacteriophage contigs (82 up, 31 down; false discovery rate < 0.05); key predicted hosts shifted toward Bacteroides, Clostridium, and Roseburia in IgAN, whereas Faecalibacterium and Alistipes prevailed in controls. Viral and bacterial alpha diversity correlated in healthy controls but not in IgAN (r = 0.38, P = 0.03 vs. r = 0.04, P = 0.81). IgAN virome encoded more glyco-modifying enzymes (P < 0.05), with strong correlations to estimated glomerular filtration rate (eGFR) (r = 0.65, P = 0.001). Viral and bacterial alpha diversity were significantly correlated with proteinuria and gross hematuria (r = 0.18-0.25, - < 0.05).

CONCLUSION: This study describes potential alterations in gut virome diversity, bacteriophage composition, bacteriome-virome relationships, and predicted functional profiles in IgAN, suggesting potential relevance of the gut virome to intestinal ecological alterations.},
}

@article {pmid42205574,
year = {2026},
author = {Liao, G and Xiao, J and Zhang, B and Wang, S and Wan, X and Zhang, C and Lyu, C and Yan, B and Zhao, Y and Kang, C and Zhang, Y and Yuan, F and Zhao, Z and Chen, Y and Guo, L and Zhang, Y},
title = {Enhancement of genetic potential for soil carbon and nitrogen cycling by organic fertilizer substitution improves the ecological environment for licorice cultivation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1758116},
pmid = {42205574},
issn = {1664-302X},
abstract = {BACKGROUND: Excessive chemical fertilizer application has become a core bottleneck restricting the green and sustainable cultivation of Glycyrrhiza uralensis (licorice). Partial organic fertilizer substitution can improve soil microecology and licorice growth traits, yet its regulatory effects on microbial functional genes mediating soil carbon (C) and nitrogen (N) cycling remain unclear.

RESULTS: Using metagenomic sequencing, we investigated the effects of six fertilization regimes [100% organic fertilizer (OF100), 100% chemical fertilizer (OF0), and organic-inorganic combinations (OF25, OF50, OF75)] on the genetic potential of soil C and N cycling, as well as soil properties and licorice growth traits in bulk and rhizosphere soils of licorice. Organic substitution significantly altered the abundance of C and N cycling-related functional genes: OF100 significantly increased the abundance of genes associated with methane oxidation (pmoA/amoA), carbon degradation (pel, cbh) and nitrification (pmoB/amoB), while OF0 significantly upregulated the methanogenesis-related gene mttA and downregulated nitrogen degradation genes; optimized fertilization (OF50) significantly reduced the abundance of genes linked to excessive carbon degradation (malZ) and nitrogen loss genetic potential (nirK), and markedly increased the abundance of genes for carbon fixation (pccA) and nitrogen mineralization (GDH). PERMANOVA revealed that soil compartment (bulk vs. rhizosphere) explained 62.87% of the total variation in functional gene profiles, which was 5.67 times higher than the contribution of fertilization regime (11.10%).

CONCLUSION: Rational organic-inorganic fertilization effectively regulates soil microbial functional genes related to C and N cycling, optimizes soil nutrient cycling potential, reduces nutrient loss risk, and enhances nutrient supply efficiency for licorice growth. These findings provide a scientific basis for fertilizer management optimization and sustainable cultivation of licorice.},
}

@article {pmid42205899,
year = {2026},
author = {Patil, BL and Shanmugaraj, C and Madhusudan, M},
title = {Metagenomic profiling of endophytic microbiomes associated with fruit pulp and seed kernels of different mango varieties reveals conservation of bacterial communities in seed kernels.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {222},
pmid = {42205899},
issn = {2190-572X},
abstract = {UNLABELLED: Bacterial and fungal communities associated with mango pulp and seed kernels from eight Indian mango varieties were profiled using 16 S rRNA and ITS amplicon sequencing. Bacterial diversity was consistently higher in seed kernels (647 ± 238 OTUs) than in pulp tissues (196 ± 112 OTUs). Seed kernel-associated bacterial communities were dominated by Firmicutes (35.8-44.0%) and Bacteroidota (16.8-35.8%) and showed high compositional consistency across varieties, with core genera including Prevotella, Ruminiclostridium, and Lachnoclostridium. In contrast, pulp-associated bacterial communities were enriched in Proteobacteria (6.5-88.5%) and Actinobacteria (4.4-34.6%) and exhibited pronounced inter-varietal variability, particularly in the relative abundance of Bacteroidota (0.8-53.8%). Fungal communities displayed lower richness (14-72 OTUs) and higher variability, with Candida kruisii (15-67%) and Hanseniaspora uvarum (up to 86%) as dominant taxa. Non-metric multidimensional scaling and hierarchical clustering revealed clear tissue-driven segregation of bacterial communities, whereas fungal assemblages showed weaker tissue-associated structuring. Seed kernels harbored approximately 3.3-fold more unique bacterial OTUs than pulp tissues, with the Amrapali seedkernel exhibiting the highest richness (789 OTUs). Across varieties, 82% of kernel-associated bacterial OTUs were shared, compared with 31% in pulp, indicating a conserved kernel microbiome and a more variable, cultivar-specific pulp microbiome. These results highlight strong tissue-level compartmentalization of mango-associated bacterial communities across cultivars.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04848-2.},
}

@article {pmid42205903,
year = {2026},
author = {Hameed, A and Ghate, SD and Shastry, RP},
title = {Fecal functional metagenomics reveals increased gut Bacillota/Pseudomonadota (Firmicutes/Proteobacteria) ratio and altered bacterial CAZyme profile in human colorectal cancer.},
journal = {3 Biotech},
volume = {16},
number = {6},
pages = {230},
pmid = {42205903},
issn = {2190-572X},
abstract = {UNLABELLED: Gut microbial dysbiosis has been implicated in the onset and/or progression of colorectal cancer (CC). We recently identified the emergence of low-abundance bacterial taxa affiliated with the phylum Bacillota in the gut microbiome of CC patients, as revealed by 16S rRNA gene amplicon sequencing. Here, we subjected the fecal samples from CC (n = 4) and healthy control (HC, n = 4) participants to functional metagenomics using the Illumina Novaseq 6000 platform. Metagenome-assembled genomes (MAGs) showed compositional differences among bacterial phylotypes in CC and HC. Species observed, richness (Chao1), and diversity (Shannon's) were high in CC, whereas species abundance peaked in HC. The Bacillota to Pseudomonadota ratio was high (> 3-fold) in CC (2.45) as compared to HC (0.70). MAGs revealed a decline in the distribution frequency of COGs involved in carbohydrate transport and metabolism (G), inorganic ion transport and metabolism (P), and unknown function (S) in CC. However, CC and HC samples exhibited marginal variations in terms of G/P (1.29 and 1.18, respectively) and G/S (0.35 and 0.40, respectively) ratios. Analysis further revealed a significant increment in glycosyltransferases GT1, GT2 and GT4, particularly in CC. In contrast, the glycoside hydrolases GH5 and GH9 declined in CC. GT/GH ratios were found to increase > 2-fold in CC (3.94) compared with HC (1.37). The present pilot-scale dataset-specific work reflects perseverance of Bacillota, significant decline in Pseudomonadota, a stable G/P and G/S ratios and enrichment of glycosyltransfererases in CC. Further transcriptomic-based studies in larger cohorts are warranted to gain insights into the implications of dysbiosis and its pathophysiological relevance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04882-0.},
}

@article {pmid42206066,
year = {2026},
author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R},
title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.},
journal = {Infectious medicine},
volume = {5},
number = {2},
pages = {100260},
pmid = {42206066},
issn = {2772-431X},
abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.

METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.

RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 × 10⁻⁵ and 1.2 × 10⁻⁵, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 × 10⁻⁵ and 1.1 × 10⁻⁴ in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid‑mediated ARGs and Cr, and between transposon‑mediated ARGs and Cr/V. The MP of transposon‑mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid‑mediated ARGs but positively with insertion sequence‑mediated ARGs. Ni concentration was positively associated with the MP of IS‑mediated VFGs.

CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.},
}

@article {pmid42206150,
year = {2026},
author = {Sun, K and Wang, F and Niu, T and Wang, H and Liu, Y and Guo, L and Wang, X and Hou, X},
title = {Metagenomic and metabolomic insights into the rhizosphere of Paeonia suffruticosa 'Luoyang Hong' across a continuous cropping chronosequence.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1754999},
pmid = {42206150},
issn = {1664-462X},
abstract = {The cultivation of Paeonia suffruticosa 'Luoyang Hong', a valuable ornamental crop, faces significant challenges due to replanting issues. However, the dynamics of its rhizosphere micro-ecosystem under continuous cropping remain poorly understood. This study systematically investigates the successional patterns of the rhizosphere micro-ecosystem over a 12- to 42-year chronosequence to identify the underlying drivers of these issues. Using an integrated multi-omics approach combining metagenomics and non-targeted metabolomics, we deciphered the rhizosphere mechanisms associated with replanting issues in Paeonia suffruticosa 'Luoyang Hong'. Based on differential changes in metabolites within the soil and root systems, key substances such as succinic acid, trans-ferulic acid, vanillic acid, and Leu-Val-Arg-Lys were identified. The microbial succession demonstrated a distinct temporal progression. Initially, at the 12-year stage, the rhizosphere was enriched with beneficial bacterial genera. However, around the 20-year stage, the abundance of these beneficial genera significantly declined. Subsequently, at the 34-year stage, the community shifted to a dominance of genera associated with organic matter degradation. Finally, at the 42-year stage, a partial recovery of certain beneficial genera and their functions was observed. Despite this recovery, the overall system continued to exhibit signs of continuous degradation. Integrated multi-omics analysis further revealed significant positive correlations, such as that between N,N-dimethyldodecylamine N-oxide and several differential microbial genera, underscoring the complex interactions between metabolites and microbes. Our findings provide a systematic perspective on the micro-ecological dynamics in the rhizosphere of Paeonia suffruticosa 'Luoyang Hong', offering deeper insights into replanting issues and supporting future mitigation strategies.},
}

@article {pmid42206286,
year = {2026},
author = {Oladejo, OA and Ibiwoye, DO and Faniyi, AA and Ayoola, MO and Oguntunji, AO and Ayansina, AD and Dahunsi, SO},
title = {Dynamics of enzyme and metabolic profile of broilers fed black soldier fly (Hermetiailucens) larvae-based diets.},
journal = {Biochemistry and biophysics reports},
volume = {46},
number = {},
pages = {102618},
pmid = {42206286},
issn = {2405-5808},
abstract = {This study investigated the impact of replacing fishmeal with black soldier fly larvae meal (BSFLM) on growth performance, microbial enzyme activity, and metabolic functions in broiler chickens. A total of fifty Arbor Acre Plus chicks were distributed across five dietary groups, including a control (100% fishmeal) and four diets containing increasing levels of BSFLM (25%, 50%, 75%, and 100%) in a completely randomized design. Broilers were reared over eight weeks, and cecal samples were subjected to 16S rRNA metagenomic sequencing to profile gut microbial enzyme activities and metabolic functions. Results revealed a progressive increase in microbial enzyme abundance and functional metabolic pathways with higher BSFLM inclusion, particularly in the 50% (T3) and 100% (T5) groups. Key enzymes, including ABC-2-type ATP-binding proteins, RNA polymerase sigma factors, and carbohydrate-active enzymes, were significantly upregulated, supporting enhanced carbohydrate fermentation, amino acid biosynthesis, and central carbon metabolism. Metabolic pathway analysis indicated a dietary shift from carbohydrate-driven fermentation in the control group to a more protein- and lipid-centered metabolism in BSFL-fed birds, with T3 showing a balanced metabolic profile and T5 exhibiting hyper-metabolic activity. These findings demonstrate that BSFLM can replace fishmeal without compromising gut health and may even enhance microbial functionality, with a 50% replacement emerging as an optimal inclusion level to sustain balanced microbial metabolism.},
}

@article {pmid42206340,
year = {2026},
author = {Huerta, AI and Joglekar, P and Totsline, N and D'Amico-Willman, KM and Ritchie, DF},
title = {Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1951},
pages = {},
doi = {10.1098/rstb.2025.0124},
pmid = {42206340},
issn = {1471-2970},
support = {//National Institute of Food and Agriculture/ ; //Foundation for Food and Agriculture Research/ ; },
mesh = {*Bacteriophages/physiology/genetics ; *Plants/virology/microbiology ; *Microbiota ; *Biological Evolution ; },
abstract = {Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.},
}

*Bacteriophages/physiology/genetics
*Plants/virology/microbiology
*Microbiota
*Biological Evolution

@article {pmid42206370,
year = {2026},
author = {Chen, L and Lin, L and Wang, Z and Yu, L and Ren, B and Zhou, S and Wang, P and Li, Y and Lu, E and Dong, Z},
title = {Fusobacterium nucleatum-Derived Isoleucine Exacerbates Aneurysm by Inducing Ferroptosis in Vascular Smooth Muscle Cells.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.126.324050},
pmid = {42206370},
issn = {1524-4636},
abstract = {BACKGROUND: Bacterial communities and their metabolites are increasingly recognized as key contributors to cardiovascular disease, yet their role and mechanistic involvement in abdominal aortic aneurysm (AAA) pathogenesis remain insufficiently defined.

METHODS: Dental plaques from patients with AAA and matched healthy controls were subjected to metagenomic sequencing, and corresponding plasma samples underwent untargeted metabolomic profiling. In vivo, mice were topically exposed in the oral cavity to Fusobacterium nucleatum (Fn) followed by AngII (angiotensin II) infusion to evaluate its impact on AAA progression. A homologous recombination-based ilvE deletion strategy was used to confirm the role of Fn in isoleucine biosynthesis. Molecular assays were performed to assess ferroptosis-related signatures and histone acetylation in smooth muscle cells, while chromatin immunoprecipitation-quantitative polymerase chain reaction verified the specific acetylation target. In addition, dietary restriction of isoleucine was introduced in the AAA murine model to explore therapeutic relevance.

RESULTS: Patients with AAA showed a marked enrichment of Fn in dental plaque, and topical application of Fn aggravated AngII-induced AAA in mice. Elevated plasma isoleucine concentrations were observed in both human AAA and experimental models. Genetic deletion of ilvE in Fn diminished bacterial isoleucine release and mitigated AAA development in mice. Mechanistic analyses revealed that Fn-derived isoleucine promoted ferroptosis in smooth muscle cells through H3K9ac (histone H3 lysine 9 acetylation)-dependent transcriptional activation of ACSL4 (acyl-CoA [coenzyme A] synthetase long-chain family member 4), a core regulator of ferroptosis. Dietary isoleucine restriction in the AngII-induced model reduced H3K9ac, suppressed ferroptosis, and alleviated aneurysmal progression.

CONCLUSIONS: Fn-derived isoleucine drives ferroptosis in smooth muscle cells via H3K9ac-mediated activation of ACSL4, delineating a microbiota-metabolite-epigenetic axis in AAA pathogenesis and nominating dental plaque Fn abundance and circulating isoleucine as exploratory biomarker candidates requiring larger, independent validation.},
}

@article {pmid42206586,
year = {2026},
author = {Yeo, S and Park, H},
title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2681840},
doi = {10.1080/19490976.2026.2681840},
pmid = {42206586},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation & purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation & purification/classification/genetics ; },
abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.},
}

Humans
*Gastrointestinal Microbiome
Feces/microbiology
*Enterococcus faecium/isolation & purification/classification/genetics
Metagenomics/methods
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Bifidobacterium/isolation & purification/classification/genetics

@article {pmid42190464,
year = {2026},
author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A},
title = {Age, strain, and gut section shape the microbiome of commercial laying hens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107152},
doi = {10.1016/j.psj.2026.107152},
pmid = {42190464},
issn = {1525-3171},
abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.},
}

@article {pmid42190784,
year = {2026},
author = {Qadeer, A and Nazir, MJ and Muhammad, S and Azim, R and Wang, Q and Hussain, MM},
title = {Decoding heavy metal tolerance in rice: Nucleic acid-based technologies shaping global food security.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152693},
doi = {10.1016/j.ijbiomac.2026.152693},
pmid = {42190784},
issn = {1879-0003},
abstract = {Global rice production is critically threatened by heavy metal contamination, particularly cadmium (Cd) and arsenic (As), which compromises yield, diminishes grain nutritional quality, and exposes billions of consumers to nephrotoxic and carcinogenic risks. Conventional remediation strategies (soil amendments, water management, phytoremediation) are prohibitively expensive, temporally protracted, and fundamentally reactive, while conventional breeding is constrained by linkage drag, polygenic trait architecture, and absence of natural alleles that restrict toxic metal uptake from essential mineral nutrition. This review critically examines how nucleic acid-based technologies have fundamentally reconfigured the discovery-to-deployment pipeline for heavy metal tolerance in rice. We trace the progression from early QTL mapping and positional cloning of transporters through population-scale GWAS and pan-genomics, which have resolved the full allelic series at these loci, to contemporary CRISPR-mediated genome editing, that generated transgene-free, field-validated low-accumulating lines. Transcriptomic, epigenomic, and metagenomic tools have further illuminated the dynamic stress response, non-coding regulatory networks, and rhizosphere microbiome contributions to metal exclusion. Translational case studies including Japan's marker-assisted deployment of OsHMA3 for Cd mitigation and South Asia's development of OsLsi2-edited low-As lines demonstrate that these technologies are not merely academic instruments but operational solutions. However, specificity-versus-essentiality dilemma, multi-metal antagonism (Cd/As redox conflict), and profound regulatory divergence (SDN-1 exemption in the Americas, Japan, and India versus GMO classification in the EU) remain formidable barriers. We conclude that nucleic acid technologies constitute the cornerstone of a second Green Revolution focused on grain quality and safety, contingent upon sustained investment in synthetic biology, digital integration, and internationally harmonized governance frameworks.},
}

@article {pmid42190825,
year = {2026},
author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J},
title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124845},
doi = {10.1016/j.envres.2026.124845},
pmid = {42190825},
issn = {1096-0953},
abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.},
}

@article {pmid42190956,
year = {2026},
author = {Xia, R and Cui, B and Li, G and Zhou, H and Luo, W and Xu, Z},
title = {Integrated metagenomics unravels the microbial mechanisms driving greenhouse gas and odor emissions during composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134984},
doi = {10.1016/j.biortech.2026.134984},
pmid = {42190956},
issn = {1873-2976},
abstract = {While composting is widely used for the resource recovery of organic waste, it is complicated by greenhouse gas and odor emissions. An integrated analysis of emission characteristics and elemental metabolism mechanisms is essential for targeted control strategies. Using integrated metagenomics and modular network analysis, this study identified the biotic and abiotic factors driving gaseous emissions. Results showed that methane (CH4) and nitrous oxide (N2O) emissions mainly occurred during the mesophilic and cooling stages, whereas ammonia (NH3) and hydrogen sulfide (H2S) peaked at the thermophilic stage. Initially, acidogens (e.g. Klebsiella) and methanogens (e.g. Methanobacterium) promoted CH4 production via aceticlastic (e.g. ackA gene) and hydrogenotrophic (e.g. frhB gene) pathways. Meanwhile, nitrate-reducing bacteria and denitrifiers converted nitrate nitrogen to N2O via assimilatory/dissimilatory reduction and denitrification pathways, respectively. As temperature increased into the thermophilic stage, CH4 and N2O production decreased due to the thermal inhibition of acidogens and nitrate-reducing bacteria. However, intense mineralization of organic nitrogen/sulfur compounds released ammonium and sulfate ions, leading to NH3 volatilization and microbial H2S production by sulfate-reducing bacteria (e.g. Desulfitibacter) via synergistic assimilatory/dissimilatory sulfate reduction pathways. Reduced thermal inhibition at the cooling stage restored activity of acidogens and methanogens, which drove CH4 emission via all four pathways. Denitrifiers (e.g. Pusillimonas) with nirS and norC genes and nitrifiers (e.g. Devosia) with hao genes were also enriched, increasing N2O production. Nevertheless, N2O was ultimately reduced to N2 by denitrifiers carrying nosZ at the mature stage. These findings provide fundamental insights for developing targeted strategies to mitigate gaseous emissions during composting.},
}

@article {pmid42191017,
year = {2026},
author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Caracciolo, AB and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V},
title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2026.05.013},
pmid = {42191017},
issn = {1876-4347},
abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7,959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.},
}

@article {pmid42192344,
year = {2026},
author = {Liu, L and Su, P and Gong, F and Wang, A and Wang, X and Yang, L and Mo, W and Jiang, T},
title = {Diagnosis and management of mixed Chlamydia abortus and psittaci pneumonia guided by metagenomic next-generation sequencing: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13691-y},
pmid = {42192344},
issn = {1471-2334},
support = {2023SK4077//the China Hunan Provincial Clinical Medical Technology Demonstration Base for Cardiac Arrest Diseases/ ; },
abstract = {BACKGROUND: Chlamydia abortus primarily causes abortion and stillbirth in animals and is associated with pregnancy-related complications in humans. However, it is an extremely rare cause of pneumonia in humans. While Chlamydia psittaci is a well-established respiratory pathogen, pneumonia resulting from a co-infection with both species has not been previously reported.

CASE PRESENTATION: A 57-year-old male presented with fever, cough, and shortness of breath. Imaging revealed extensive pulmonary inflammation and consolidation, which rapidly progressed to respiratory failure. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) confirmed a mixed infection with Chlamydia abortus and Chlamydia psittaci. Following the early initiation of targeted doxycycline therapy, the patient's clinical symptoms and pulmonary imaging showed significant improvement, leading to a full recovery and hospital discharge.

CONCLUSIONS: To our knowledge, this study reports the first case of atypical pneumonia caused by a mixed Chlamydia abortus and Chlamydia psittaci infection in a male patient, thereby expanding the clinical spectrum of these zoonotic pathogens. The case exhibited a "clinical-imaging dissociation," characterized by severe radiographic changes alongside relatively mild clinical symptoms. When conventional diagnostic methods failed to identify the pathogens, mNGS provided a rapid and precise diagnosis. Guided by this result, early targeted therapy with doxycycline achieved a marked therapeutic effect, preventing progression to severe disease and an adverse outcome.

TRIAL REGISTRATION: Not applicable.},
}

@article {pmid42192666,
year = {2026},
author = {Liu, L and Wang, M and Wang, X and Liu, Y and Li, Z},
title = {Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050444},
pmid = {42192666},
issn = {2079-6382},
support = {242300420230//Natural Science Foundation of Henan Province/ ; },
abstract = {Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation.},
}

@article {pmid42192676,
year = {2026},
author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW},
title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050456},
pmid = {42192676},
issn = {2079-6382},
support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; },
abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.},
}

@article {pmid42192677,
year = {2026},
author = {Carneiro, PAM and Santos, LRD and Jardim, R and Silva, CBDGE and Araújo, FR and Dávila, AMR},
title = {Resistome and Mobilome Profiling of Raw Cow and Buffalo Milk from the Brazilian Amazon via Shotgun Metagenomics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050454},
pmid = {42192677},
issn = {2079-6382},
support = {408696/2024-9//Beef Cattle National Science and Technology Institute/CNPq/ ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a global health threat, with raw milk serving as a potential reservoir for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). This study characterized the resistome and mobilome of raw milk from cows (Bos taurus) and water buffalo (Bubalus bubalis) in the Brazilian Amazon, a region where unpasteurized dairy consumption is culturally ingrained. Methods: Using shotgun metagenomic sequencing, we analyzed 32 pooled milk samples from extensive and semi-intensive farms in the Manaus Metropolitan Region. Results: Sequencing yielded over 3.1 million contigs. While cow milk showed a higher prevalence of positive samples (80%), buffalo milk exhibited a significantly higher abundance and diversity of ARG-associated contigs (301 contigs vs. 85 in cows). Clinically relevant genes were identified, including AbaQ, ArnT, and KpnF, alongside complex multi-AMR cassettes co-occurring with plasmids and widespread viral sequences (dominated by Caudoviricetes). Integrons were ubiquitous in cattle and highly prevalent in buffalo samples. Conclusions: These findings indicate that raw milk in the Amazon harbors a rich reservoir of resistance determinants and MGEs, likely driven by farm-level antibiotic usage. This underscores a critical food safety risk and highlights the need for One Health-based surveillance in the region.},
}

@article {pmid42192724,
year = {2026},
author = {Skotareva, AE and Sokolova, EA and Voronina, EN},
title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antibiotics15050502},
pmid = {42192724},
issn = {2079-6382},
support = {125012300671-8//Russian state-funded project/ ; },
abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.},
}

@article {pmid42193165,
year = {2026},
author = {Liang, Y and Wang, H and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y},
title = {High-Fiber Diet Supplemented with N-Carbamylglutamate Modulates Uterine Microbiota, Metabolites, and Transcriptome to Improve Reproductive Efficiency in Sows.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antiox15050542},
pmid = {42193165},
issn = {2076-3921},
support = {No.2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025M780240//China Postdoctoral Science Foundation/ ; NO.2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; },
abstract = {Uterine microbiome homeostasis and antioxidant capacity are critical for sow fertility. While high-fiber diets and N-carbamylglutamate (NCG) individually enhance sow fertility, their synergistic effects on the antioxidant status, microbiota, metabolites, and transcriptome remain unclear. Here, sows were assigned to the low-fiber (3.73%) or high-fiber (7.46% crude fiber) group, each without or with 0.05% NCG, throughout the 114-day gestation. Sex hormones and antioxidants in serum were detected. Multi-omics approaches were employed to investigate the impact of a high-fiber diet supplemented with NCG (H + N) on uterine microbiota, metabolites, and gene expression profiles. The study revealed that H + N significantly increased total antioxidant capacity (T-AOC) level in serum. Metagenomic analysis revealed an increased abundance of Clostridium disporicum in the uterine microbiota. Plasma metabolomics identified hydroxylysine as a key metabolite mediating this effect, and this metabolite was positively correlated with elevated abundance of Clostridium disporicum. Subsequent transcriptomic profiling revealed activation of the PI3K-Akt signaling pathway, closely linked to improved T-AOC level. Overall, these findings demonstrated that H + N could modulate the uterine microbiota (specifically Clostridium disporicum), increase hydroxylysine production, and activate the PI3K-Akt signaling pathway. These effects further enhanced hormonal activity and antioxidant capacity, ultimately improving sow reproductive efficiency.},
}

@article {pmid42193259,
year = {2026},
author = {Zhang, MY and Ke, ZZ and Deng, PL and Qin, YY and Mo, SL and Qiu, LT and Xu, JJ and Tong, CX and Song, JL},
title = {Rhamnocitrin Ameliorates the Intestinal Fibrosis in DSS-Induced Colitis Mice by Modulating Host-Metabolites and Remodeling the Gut Microbiome.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/antiox15050639},
pmid = {42193259},
issn = {2076-3921},
support = {82273630//National Natural Science Foundation of China/ ; 81960590//National Natural Science Foundation of China/ ; 81760589//National Natural Science Foundation of China/ ; 81560530//National Natural Science Foundation of China/ ; },
abstract = {Ulcerative colitis (UC) is characterized by barrier disruption, microbiota dysbiosis, fibrosis, and impaired autophagy. We investigated the effects of Rhamnocitrin (Rha) in dextran sulfate sodium (DSS)-induced chronic UC mice using histological analysis, molecular assays, and multiomics profiling. Rha alleviated weight loss and colon shortening; improved mucus secretion and tight junction protein expression; suppressed NLRP3 inflammasome activation; activated autophagy via AMPK activation and consequent Akt/mTOR inhibition; and attenuated colonic fibrosis. Multiomics analysis integrating 16S rRNA sequencing, metagenomics, and metabolomics revealed that Rha remodels the gut microbiota and is associated with elevated levels of beneficial metabolites, including butyrate in the colon, glutamate and γ-aminobutyric acid in the liver, and α-linolenic acid in the serum. Correlation analysis revealed close associations between microbiota and metabolite alterations, and improved barrier integrity, reduced inflammation, and attenuated fibrosis. These findings suggest that Rha ameliorates chronic UC by modulating autophagy, microbiota composition, and host metabolism across the gut-liver axis.},
}

@article {pmid42193752,
year = {2026},
author = {Guo, T and Wan, B and Ye, Y and Zhang, Y and Mao, M and Li, R and Fang, Y and Lu, Y and Shao, R and Wu, Y and Wang, Y and Wu, J and Yang, H},
title = {A Prevotella-Rich Gut Microbiota and Microbial CAZymes Are Associated with Half-Diving Length in Ducks.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/ani16101460},
pmid = {42193752},
issn = {2076-2615},
support = {2024YFF1000900//National Key Research and Development Program of China/ ; 32302739//National Natural Science Foundation of China/ ; 32360830//National Natural Science Foundation of China/ ; 20243BCE51147//Ganpo Juncai Support Program/ ; QN2023015//Ganpo Juncai Support Program/ ; 20232ACB215003//Natural Science Foundation of Jiangxi Province/ ; },
abstract = {The gut microbiota is closely associated with host growth by nutritional metabolism and immune homeostasis. Half-diving length, a key indicator of duck development and production efficiency, correlates with economic traits like body weight and slaughter yield, yet its link to gut microbiota remains unclear. This study combined metagenomic and metabolomic analyses to explore the association between gut microbiota and duck half-diving length. We found distinct microbial communities between ducks with high (H) and low (L) half-diving lengths: the H group had more carbohydrate-active enzymes (CAZymes) genes (p < 0.05), especially glycoside hydrolases (GHs), and was enriched in MAG3173 (Prevotella sp000431975), which features complete carbohydrate and amino acid metabolic pathways and key CAZymes. Metabolomics revealed slightly higher short-chain fatty acids (SCFAs) levels in the H group, but glycerophospholipids, particularly phosphatidylinositol (PI), were significantly upregulated (p < 0.05). The Prevotella-rich microbial structure in the H group is potentially linked to enhanced polysaccharide degradation capacity and altered SCFAs abundance. This metabolic shift may be associated with host energy supply and lipid metabolic profiles, thereby influencing duck growth. Collectively, this study found significant correlations between duck half-diving length and gut microbial composition, functional capacity, and intestinal metabolic signatures. The study proposes the hypothesis of a potential Prevotella-CAZymes-glycerophospholipid metabolism axis, which might offer a theoretical reference and candidate microbial targets for understanding the microbe-phenotype association in waterfowl.},
}

@article {pmid42193766,
year = {2026},
author = {Qiu, G and Bai, H and Shi, J and Xue, Y and Wang, T and Qin, S and Zhou, X and He, K},
title = {Metagenomic and Metabolomic Analysis of Intestinal Excrement Differences Between Natural Hatching and Artificial Peeling out of the Shell in Nipponia nippon.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/ani16101472},
pmid = {42193766},
issn = {2076-2615},
support = {ZJXRDQ-2025-JC28//the Project for Enhancing the Reproductive Capacity of the Red-crowned Crane/ ; },
abstract = {The Nipponia nippon is a critically endangered species, and its breeding efforts are of vital importance for its conservation. Although artificial shell removal is sometimes employed in current breeding programs to increase survival rates, it may also have unknown impacts on chicks' development. To investigate the influence of artificial shell removal on the gut microbiota composition in Nipponia nippon, metagenomic sequencing and untargeted LC-MS/MS analyses were performed. Samples from the early, mid, and late stages of natural hatching (ZE, ZM, ZL) and artificial shell removal (RE, RM, RL) were compared. Results indicated that the natural hatching groups formed a unique, highly diverse, and stable community by the late stage (ZL). Conversely, artificial peeling caused the microbial community succession to stagnate at an intermediate state. The RL group experienced a sharp decline in alpha diversity and a significant enrichment of opportunistic pathogens, such as Edwardsiella, Clostridium, and Fusobacterium. Functionally, the microbial community in the RL group remained in a stage of expanding basic functions rather than reaching an advanced equilibrium state. Metabolomic analysis confirmed this developmental arrest, revealing abnormal accumulations of organic acids, such as citric acid, and indole derivatives in the RL group. This indicates metabolic dysregulation, stress, and altered microbial-host chemical signaling. Furthermore, the significant biomarker Edwardsiella was strongly correlated with multiple differential metabolites in the RL group. Ultimately, these results indicate that artificial peeling intervention disrupts environmental adaptation and induces metabolic alterations in the intestinal development of the Nipponia nippon chicks.},
}

@article {pmid42193830,
year = {2026},
author = {Zhou, K and Shi, H and Kong, X and Ma, W and Kang, J and Che, H and Hua, Y},
title = {Wuwei Jianpi San Improves Growth Performance and Immune Status in Yaks Through Modulation of Rumen Microbiota and Host Metabolism.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/ani16101539},
pmid = {42193830},
issn = {2076-2615},
support = {CARS-37, CARS-07G-13//China Agriculture Research System of MOF and MARA/ ; No. Gaufx-03J01//Fuxi Foundation of Gansu Agricultural University/ ; 24YFNA016//Gansu Provincial Key Research and Development Program - Agriculture Field/ ; KJZC-2025-14//Modern Cold and Drought Characteristic Agricultural Science and Technology Sup-port Project of Gansu Province/ ; },
abstract = {To investigate the effects of Wuwei Jianpi San (WJPS), a Chinese herbal compound feed additive, on rumen microecology, host metabolism, and immune function in healthy yaks (Bos grunniens), and to determine the optimal supplementation level, 32 yaks with similar initial body weight were randomly assigned to four groups: a control group and three groups receiving 0.5%, 1.0%, or 2.0% WJPS for 90 days. Growth performance, hematological indices, serum antioxidant and immune parameters, tryptophan metabolites, ruminal short-chain fatty acids (SCFAs), and rumen microbiota were analyzed. WJPS supplementation improved growth performance, as shown by a reduced feed-to-gain ratio in all treated groups and tended to increase average daily gain in the 2.0% group. It also enhanced hematological, antioxidant, and immune status, evidenced by increased white blood cell (WBC) and lymphocyte (Lym) counts and elevated interleukin-2 (IL-2), immunoglobulin G (IgG), and superoxide dismutase (SOD) levels. Moreover, 2.0% WJPS increased total SCFAs, acetate, and n-butyrate, while WJPS reduced kynurenine pathway metabolites, including kynurenine, 3-hydroxykynurenine, and quinolinic acid. Metagenomic analysis showed that WJPS tended to shape rumen microbial composition by increasing Bacillota and decreasing Bacteroidota, and these microbial changes were associated with host immune indices and tryptophan metabolism. Overall, 2.0% WJPS showed the best comprehensive effect.},
}

@article {pmid42195821,
year = {2026},
author = {Wang, X and Liu, X and Han, G and Erdene, K and Bai, C and Cao, Q and Zheng, Y and Hai, L and Ao, C},
title = {Allium mongolicum Regel-Mediated Rumen Microbiota Intervention Modulates Hepatic Metabolome to Reduce 4-Alkyl Branched-Chain Fatty Acids in Lamb Longissimus Thoracis Muscle.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101617},
pmid = {42195821},
issn = {2304-8158},
support = {32260839//National Natural Science Foundation of China/ ; },
abstract = {Deposition of three key 4-alkyl branched-chain fatty acids (KBCFA), including 4-methyloctanoic acid (MOA), 4-ethyloctanoic acid (EOA), and 4-methylnonanoic acid (MNA), causes the gamey flavor in sheep meat. This study integrated metagenomics and metabolomics to evaluate how Allium mongolicum Regel (AMR) supplementation (15 g/d) and rumen fluid transplantation (RFT) modulate rumen microbiota and hepatic metabolism to reduce KBCFA in lamb longissimus thoracis muscle. The experiment consisted of two phases. In Phase I, twelve 3-month-old male Dorper × Small Tailed Han sheep (25 ± 1 kg) were selected as the rumen donor group. These sheep were supplemented with 15 g/d/head of AMR powder in their basal diet until the end of the experiment. In Phase II, thirty 3-month-old male Dorper × Small Tailed Han sheep (23 ± 2 kg) were randomly assigned to one of three groups (n = 10 per group): the control group (STG), which was fed the basal diet and received a physiological saline transplant; the AMR group, which was fed the basal diet supplemented with 15 g/d/head of AMR powder and received a physiological saline transplant; and the rumen fluid transplant group (RTG), which was fed the basal diet and received a rumen fluid transplant from the donor group. Compared to the STG, results showed that the MOA, EOA, and MNA in the AMG decreased by 64.51%, 54.72%, and 49.34%, respectively. Similarly, the MOA, EOA, and MNA in the RTG were reduced by 63.13%, 56.17%, and 49.60%, respectively (p < 0.001). For the rumen metagenome, AMR enriched the genus Prevotella, while RFT increased Butyrivibrio. Hepatic metabolomics revealed a distinct shift where AMR elevated amino acid derivatives and RFT enhanced carnitine-related metabolites. These alterations indicate a potential metabolic shift associated with amino acid metabolism and mitochondrial β-oxidation, rather than lipid elongation. We postulate that this coordinated regulation across the rumen-liver-muscle axis may alter the availability of lipogenic precursors for KBCFA synthesis, ultimately contributing to improved meat flavor.},
}

@article {pmid42195847,
year = {2026},
author = {Song, D and Yang, L and Zhang, C},
title = {Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101643},
pmid = {42195847},
issn = {2304-8158},
support = {32460269//National Natural Science Foundation of China/ ; MTXYTD202501//The Science and Technology Innovation Team of Moutai Institute/ ; Qiankehe Platform Talent-ZDSYS [2023] 007//Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation industry/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Industry Group Co., Ltd./ ; },
abstract = {Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems.},
}

@article {pmid42195939,
year = {2026},
author = {Chen, P and Du, G and Chen, J and Fang, F},
title = {Construction of Synthetic Microbial Community with Core Microorganisms for Soy Sauce Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101736},
pmid = {42195939},
issn = {2304-8158},
support = {32172182//National Natural Science Foundation of China/ ; },
abstract = {Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce.},
}

@article {pmid42196007,
year = {2026},
author = {Duo, Q and Zhao, Y and Osman, H and Shao, W and Zhao, Y},
title = {Correlation Between Microbial Communities and Volatile Organic Compounds in Camel Milk at Different Lactation Stages in Xinjiang, China.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/foods15101804},
pmid = {42196007},
issn = {2304-8158},
support = {2023B02034-1//Xinjiang Academy of Agricultural Sciences/ ; XJARS-11-09//Xinjiang Academy of Agricultural Sciences/ ; xjnkywdzc-2026002-10//Xinjiang Academy of Agricultural Sciences/ ; },
abstract = {The aroma of camel milk is a key sensory indicator for evaluating its quality and flavor. Camel milk collected at different lactation stages exhibits unique flavor characteristics. However, no systematic study has yet explored the aroma characteristics and variation patterns of camel milk across these stages. This study employs HS-SPME-GC-MS, multivariate statistical analysis, and metagenomics to systematically reveal differences in aroma formation in camel milk across lactation periods and their interactions with microbial communities. A total of 577 metabolites is detected. Through OPLS-DA screening, 24 key differential flavor compounds are identified. ROAV analysis indicates that 2,4-undecadienal and (E)-2-undecenal are the main contributors to the fatty, creamy, fresh green, and citrus aromas of camel milk. Some compounds are more abundant in colostrum, while others are richer in mature milk. For microbiota, colostrum is dominated by Proteobacteria, Psychrobacter, and Janthinobacterium, whereas mature milk is dominated by Acinetobacter and Moraxella. Mature milk shows significantly higher alpha diversity and species richness. Spearman correlation analysis shows that core bacterial groups such as Enterococcus and Lactococcus are significantly positively correlated with characteristic flavor compounds, including aldehydes and lactones. This finding suggests that HS-SPME-GC-MS, combined with multivariate analysis, effectively distinguishes patterns associated with microbes and flavor metabolites in camel milk at different lactation stages, which provides a theoretical basis for quality control and further processing of camel milk.},
}

@article {pmid42196140,
year = {2026},
author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL},
title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104155},
pmid = {42196140},
issn = {1422-0067},
support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; },
mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth & development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; },
abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.},
}

Animals
*Biofouling
*Microbiota
Larva/microbiology
Biofilms/growth & development
Quorum Sensing
Ecosystem
*Aquatic Organisms/microbiology

@article {pmid42196196,
year = {2026},
author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L},
title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104213},
pmid = {42196196},
issn = {1422-0067},
support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; },
abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/metabolism
*Metagenomics/methods
*Metabolomics/methods
Male
*Gastrointestinal Microbiome/genetics
Female
Aged
Middle Aged
Feces/microbiology
Multiomics
Metabolome
Biomarkers
RNA, Ribosomal, 16S/genetics
China
Case-Control Studies

@article {pmid42196214,
year = {2026},
author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT},
title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104232},
pmid = {42196214},
issn = {1422-0067},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; },
abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/genetics
*Protein Interaction Maps
*Deep Learning
Phenotype
*Gastrointestinal Microbiome
*Protein Interaction Mapping/methods
*Host Microbial Interactions

@article {pmid42196222,
year = {2026},
author = {Zhang, X and Cai, L and Bai, Y and Peng, F},
title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {10},
pages = {},
doi = {10.3390/ijms27104238},
pmid = {42196222},
issn = {1422-0067},
support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; },
abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.},
}

*Metagenomics/methods
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
Nutrients