@article {pmid42082982,
year = {2026},
author = {Li, J and Guo, S and Yu, H and Hong, X and Nie, J and Sun, H},
title = {Thyroid functional state-dependent dysbiosis of gut microbiota in Hashimoto's thyroiditis: a cross-sectional metagenomic profiling study.},
journal = {Thyroid research},
volume = {19},
number = {1},
pages = {},
pmid = {42082982},
issn = {1756-6614},
abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is a prevalent autoimmune thyroid disease (AITD) closely linked to genetic predisposition and environmental factors. Gut microbiota dysbiosis has recently been implicated as a critical contributor to AITDs' pathogenesis. Our study aims to systematically investigate the dynamic alterations in gut microbial communities under varying thyroid functional statuses and elucidate their underlying mechanisms.

METHODS: 67 HT patients with varying thyroid functional statuses and 23 healthy controls were enrolled. Fecal 16 S rDNA sequencing and analyses (alpha diversity, LEfSe, correlation, functional pathways) assessed microbiota-thyroid function links.

RESULTS: HT patients with hypo/hyperthyroidism had lower gut microbiota richness than euthyroid patients (more reduced in hyperthyroidism). The hyperthyroid group exhibited enrichment of Fusobacterium, the hypothyroid group was dominated by Clostridium sensu stricto_1, and the euthyroid group showed a predominance of short-chain fatty acid (SCFA)-producing bacteria (e.g., Lactobacillus). Clostridium sensu stricto_1 positively correlated with TPO-Ab levels but negatively correlated with FT3.Pro-inflammatory genera(e.g., Escherichia-Shigella, Streptococcus) demonstrated negative correlations with FT3.Functional prediction analysis revealed potential associations with L-tyrosine degradation in the hyperthyroid group, reduced proportions of bile acid metabolism pathways in the hypothyroid group, and enriched proportions of fatty acid metabolism pathways in the euthyroid group.

CONCLUSIONS: This study revealed that gut microbiota dysbiosis is closely associated with thyroid functional statuses in HT. Specific bacterial genera, such as Clostridium sensu stricto_1 and Fusobacterium, may contribute to immune regulation and disease progression. The dynamic alterations in gut microbial profiles provide potential biomarkers for precision diagnosis and treatment of HT.},
}

@article {pmid42083021,
year = {2026},
author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S},
title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00898-4},
pmid = {42083021},
issn = {2524-6372},
support = {2022YFD1500600//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.

RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding α-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.

CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.},
}

@article {pmid42083059,
year = {2026},
author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B},
title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02419-4},
pmid = {42083059},
issn = {2049-2618},
support = {284894//Fonds de recherche du Québec/ ; },
abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.

RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade ≥ 2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade ≥ 2 irAE had a lower alpha diversity compared to those who did not develop grade ≥ 2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade ≥ 2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin immunofluorescence signal and increased TNF-α and IL-1β expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also maintained after treatment with P. bifermentans < 3 kDa filtered supernatant.

CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.},
}

@article {pmid42083116,
year = {2026},
author = {Onohuean, FE and Onohuean, M and Olot, H and Onohuean, H},
title = {Poor Glycemic Control in East Africa: Prevalence, Risk Factors and Public Health Implications in Diabetes Management.},
journal = {Endocrinology, diabetes & metabolism},
volume = {9},
number = {3},
pages = {e70233},
doi = {10.1002/edm2.70233},
pmid = {42083116},
issn = {2398-9238},
mesh = {Humans ; *Glycemic Control/statistics & numerical data ; Africa, Eastern/epidemiology ; Risk Factors ; Prevalence ; *Public Health ; *Diabetes Mellitus/epidemiology/therapy/blood ; Cross-Sectional Studies ; Blood Glucose/analysis ; Glycated Hemoglobin/analysis ; *Diabetes Mellitus, Type 2/epidemiology/blood/therapy ; },
abstract = {BACKGROUND: Diabetes mellitus remains a major public health concern in East Africa, and poor glycaemic control continues to drive avoidable complications, deaths and pressure on already stretched health systems.

OBJECTIVE: To estimate the prevalence of poor glycemic control and describe the main factors associated with it among people living with diabetes in East Africa.

METHODS: This review synthesized evidence from observational studies, cross-sectional surveys and regional health databases identified through PubMed, Scopus and Web of Science, following PRISMA guidance. Sociodemographic, clinical and behavioural indicators were examined to identify common patterns and predictors of poor glycaemic control. The review also considered how measurement approaches shaped reported estimates.

RESULTS: Fifty records were identified across PubMed (10), Scopus (23) and Web of Science (17). After screening, 37 records were eligible for full-text review, and 15 studies met the inclusion criteria for evidence synthesis. Across the region, poor glycemic control was consistently high, ranging from 60% to 85%. Most studies were facility-based and cross-sectional. Glycemic control was assessed mainly using HbA1c, commonly defined as ≥ 7% or > 7.5%, and less frequently by fasting blood glucose, typically ≥ 7.2 mmol/L or > 130 mg/dL. Type 2 diabetes was the dominant population studied, with fewer mixed cohorts and only one study focused on type 1 diabetes. Factors repeatedly linked to poor control included older age, longer duration of diabetes, poor medication adherence, limited access to care, low health literacy, inadequate diabetes education, insulin use, comorbidities, diabetic complications, unhealthy diet, physical inactivity, sedentary behaviour, substance use and limited self-management support.

CONCLUSION: Poor glycemic control is alarmingly common among people with diabetes in East Africa and reflects intertwined clinical, behavioural and health-system challenges. Region-specific strategies are needed to strengthen primary care, improve diabetes education, expand affordable monitoring and treatment and enhance surveillance to guide policy and resource allocation.},
}

Humans
*Glycemic Control/statistics & numerical data
Africa, Eastern/epidemiology
Risk Factors
Prevalence
*Public Health
*Diabetes Mellitus/epidemiology/therapy/blood
Cross-Sectional Studies
Blood Glucose/analysis
Glycated Hemoglobin/analysis
*Diabetes Mellitus, Type 2/epidemiology/blood/therapy

@article {pmid42083299,
year = {2026},
author = {Qin, R and Wang, C and Cong, M and Tian, L and Li, N},
title = {Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.},
journal = {Cancer medicine},
volume = {15},
number = {5},
pages = {e71915},
doi = {10.1002/cam4.71915},
pmid = {42083299},
issn = {2045-7634},
support = {JYKY2024-0050409022//Beijing Vlove Charity Foundation/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Neoplasms/complications ; Aged ; *Pneumonia/diagnosis/microbiology ; Sputum/microbiology ; Adult ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: With the development of new sequencing technologies, metagenomic next-generation sequencing (mNGS) has become a diagnostic tool for respiratory tract infections. Patients with cancer may develop pneumonia caused by infections or antitumor therapy. Therefore, pneumonia in patients with cancer is more complex than that in healthy individuals. Currently, few reports are available on the use of mNGS for diagnosing pneumonia in patients with cancer.

METHODS: In this retrospective study, 14 patients with cancer diagnosed with pneumonia in March 2023 were enrolled from the Emergency Department of the Chinese Academy of Medical Sciences Cancer Hospital. Sputum samples from the patients were examined using conventional tests and mNGS to identify pathogens. The mNGS and conventional test results were compared to assess the diagnostic yield in patients with cancer.

RESULTS: The overall pathogen detection rate of mNGS was 64.29% (9/14), with corresponding diagnostic sensitivity, specificity, false-negative rate and false-positive rate of 90.00%, 25.00%, 10.00% and 75.00%, respectively. Among 13 paired sputum specimens, mNGS exhibited a numerically higher pathogen detection rate (61.54%, 8/13) than conventional diagnostic assays (38.46%, 5/13). McNemar's paired chi-square test demonstrated no statistically significant difference between the two detection methods (p = 0.37), and Kappa concordance analysis generated a coefficient of 0.27 (p = 0.23), suggesting poor inter-method consistency. Compared with conventional tests, mNGS detected additional pathogens in 8 specimens and identified a greater number of pathogens in 9/14 (64%) samples. Moreover, mNGS results led to diagnostic revisions and subsequent antimicrobial therapy adjustments in 64% (9/14) of enrolled patients. Additionally, mNGS detected antibiotic resistance genes in five patients, which provided guidance for antibiotic selection.

CONCLUSIONS: Metagenomic next-generation sequencing (mNGS) showed potential value in pathogen detection, as it appeared to identify pathogens more rapidly and comprehensively than conventional methods. It may provide auxiliary support for the diagnosis and treatment of pneumonia in this vulnerable population.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Middle Aged
*Metagenomics/methods
Retrospective Studies
*Neoplasms/complications
Aged
*Pneumonia/diagnosis/microbiology
Sputum/microbiology
Adult
Sensitivity and Specificity

@article {pmid42083599,
year = {2026},
author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV},
title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.},
journal = {Acta naturae},
volume = {18},
number = {1},
pages = {55-63},
pmid = {42083599},
issn = {2075-8251},
abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.},
}

@article {pmid42084116,
year = {2026},
author = {Qi, J and Liang, C and Zhang, C and Wang, M and Wei, G and Jiao, S},
title = {Intensifying Aridity Undermines the Role of Soil Biodiversity in Supporting Ecosystem Stability.},
journal = {Global change biology},
volume = {32},
number = {5},
pages = {e70903},
doi = {10.1111/gcb.70903},
pmid = {42084116},
issn = {1365-2486},
support = {42477129//National Science Foundation of China/ ; JYB2025XDXM706//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Biodiversity ; *Soil Microbiology ; *Climate Change ; China ; *Soil/chemistry ; *Ecosystem ; *Desert Climate ; },
abstract = {Biodiversity is widely recognized for enhancing ecosystem stability, yet its contribution is highly sensitive to climate change. However, whether and how climatic factors, particularly aridity, modulate the role of soil biodiversity in stabilizing ecosystems remains poorly understood. Here, we integrated a comprehensive soil survey of 265 dryland agricultural fields along a 3800 km east-west transect in China with a global meta-dataset encompassing 996 sites across six continents. Our analysis revealed a positive association between soil biodiversity and ecosystem stability, quantified using 11-year Normalized Difference Vegetation Index (NDVI) data (2012-2022). Critically, both our field data and global synthesis revealed that increasing aridity significantly weakened this biodiversity-stability relationship. The decline in soil microbial network complexity with increasing aridity partially explains this decoupling. Metagenomic analyses further showed that as aridity increased, microbial life history strategies shifted toward greater investment in stress tolerance at the expense of growth yield and resource acquisition. Together, our findings represent a substantial advance in revealing how intensifying aridity undermines the role of soil biodiversity in supporting ecosystem stability, and highlight the importance of microbial network complexity and life history strategies as key predictors of biodiversity-stability relationships under global change.},
}

*Biodiversity
*Soil Microbiology
*Climate Change
China
*Soil/chemistry
*Ecosystem
*Desert Climate

@article {pmid42084385,
year = {2026},
author = {Rodríguez, P and Simon, SA and Probst, AJ and Magnabosco, C},
title = {Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0150025},
doi = {10.1128/msystems.01500-25},
pmid = {42084385},
issn = {2379-5077},
abstract = {Cosmopolitan microbial lineages are found in anoxic sediments worldwide, but the details about their ecology and evolution remain underexplored. In this study, we identified persistent populations from these cosmopolitan lineages belonging to Planctomycetes, Chloroflexi Atribacteria, and Candidatus Bathyarchaeia from an ~8,000-year sedimentary sequence. To investigate the genomic variations within these persistent populations, a pangenome of each population was constructed using all non-redundant metagenome-assembled genomes (MAGs) recovered from the sedimentary sequence and was screened for enriched functional genes, single-nucleotide polymorphism (SNP) density, dN/DS ratios, and pseudogene content. Our results show that the majority of persistent populations studied possess large variable genomes enriched for energy conservation and transcriptional regulation functions with increasing depth, whereas Planctomycetes retain a highly conserved, SNP-poor core genome. Analysis of SNPs across depths indicates progressive isolation with burial, while a subset of core genes shows signatures of positive selection. Collectively, the data support depth-associated selection acting alongside drift across Lake Cadagno's persistent sedimentary lineages.IMPORTANCEThroughout the subsurface, multiple examples of "evolutionary stasis" have been reported in microbial lineages that exhibit lower rates of metabolic activity and cellular turnover. This study uses an ~8,000-year sedimentary record of Lake Cadagno to evaluate how persistent populations of cosmopolitan bacteria and archaea have changed with burial and identifies signals of progressive genetic isolation along with positive selection of population-specific subsets of core genes with depth. Together, these changes show that Lake Cadagno's persistent populations are not in stasis but diverge over time and burial.},
}

@article {pmid42084478,
year = {2026},
author = {Wang, C and Dou, P and Wang, Y and Li, X and Zhang, Y and Ma, X},
title = {A wolf in sheep's clothing: An unusual zoonotic pathogen in peritoneal dialysis effluent and an important diagnostic strategy.},
journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis},
volume = {},
number = {},
pages = {8968608261448060},
doi = {10.1177/08968608261448060},
pmid = {42084478},
issn = {1718-4304},
abstract = {Brucellosis is an infectious disease characterized by a natural foci, caused by Brucella, a genus of Gram-negative bacilli known for its obligate aerobic growth and capability for intracellular parasitism. This pathogen can be transmitted zoonotically between animals and humans. Due to its mechanism of intracellular survival, monotherapy with a single antibiotic often proves ineffective in eradicating Brucella. Therefore, clinical management necessitates the implementation of multidrug combination therapy alongside extended therapeutic regimens to achieve optimal bacteriological clearance. Conventional diagnostic methods, such as bacterial culture and serological testing, are frequently hindered by the fastidious growth requirements of the pathogen and the risk of false-positive serological cross-reactivity. These limitations may result in delayed diagnosis or unnecessary interventions. Recent advancements in molecular biology-particularly genomic analysis technologies-have revolutionized pathogen detection by facilitating rapid and precise identification of elusive pathogens. This study reports the first documented case of refractory peritoneal dialysis-associated peritonitis caused by Brucella diagnosed via metagenomic next-generation sequencing (mNGS). By employing mNGS to identify the pathogen, we summarize the clinical characteristics of this case and highlight the diagnostic advantages of this technology. Our findings aim to guide clinicians in selecting appropriate diagnostic approaches for similar cases, avoiding unnecessary delays and optimizing resource utilization in clinical practice.},
}

@article {pmid42084497,
year = {2026},
author = {Leech, J and Obafemi, YD and Breselge, S and Aremu, T and Obadina, AO and Itohan, ME and Ezekiel, CN and Parkouda, C and Tankoano, A and Traoré, K and Banwo, K and Kunadu, AP and Madilo, FK and Sanni, AI and Ogunremi, OR and Onipede, G and Odeny, DA and Otieno, C and Claesson, MJ and Cotter, PD},
title = {Characterizing microbiomes of African fermented foods in a global context.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
doi = {10.1099/mic.0.001695},
pmid = {42084497},
issn = {1465-2080},
mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Food Microbiology ; Metagenome ; Fermentation ; Africa ; Kenya ; Burkina Faso ; Ghana ; },
abstract = {Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.},
}

*Fermented Foods/microbiology
*Microbiota/genetics
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
*Food Microbiology
Metagenome
Fermentation
Africa
Kenya
Burkina Faso
Ghana

@article {pmid42084683,
year = {2026},
author = {Maurya, S and Shukla, AK and Reddy, B and Singh, AK and Singh, VK and Tripathi, M},
title = {Metagenomic insights into microbial community, antibiotic resistance genes, and virulence factor in Saryu River water, India.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42084683},
issn = {1614-7499},
abstract = {A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.},
}

@article {pmid42084764,
year = {2026},
author = {Joshi, G and Khannam, KS},
title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42084764},
issn = {1432-072X},
mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Biodegradation, Environmental ; },
abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.},
}

*Microbiota
*Biotechnology
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Biodegradation, Environmental

@article {pmid42085791,
year = {2026},
author = {Besharati Fard, M and Ahmadi, N and Chen, Y and How, SW and De Vrieze, J and Wu, D},
title = {Tetracycline and ciprofloxacin reduce nitrification and denitrification activity and alter microbial community composition and activity in microalgal-bacterial aerobic granular sludge.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142255},
doi = {10.1016/j.jhazmat.2026.142255},
pmid = {42085791},
issn = {1873-3336},
abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) systems offer promising potential for wastewater treatment under chemical stress. However, their performance in the presence of antibiotics remains poorly understood. This study evaluated the response of MB-AGS to 1000 µg/L of tetracycline and ciprofloxacin in two separate bioreactors operated under alternating dark (60 min) and light (170 min) cycles at 20 °C. Chemical oxygen demand (COD) removal remained stable at 90 ± 4% (tetracycline) and 91 ± 6% (ciprofloxacin) over 80 days, suggesting that COD conversion was not impacted by antibiotic exposure. However, phosphate removal declined from ∼63% (antibiotic-free bioreactors) to 45 ± 6% (under tetracycline exposure) and 38 ± 8% (under ciprofloxacin exposure) after addition of antibiotics. Ciprofloxacin inhibited nitrification (declined to ∼50% NH4[+] removal), associated with reduced abundance of Nitrosomonas, while tetracycline impacted denitrification, evidenced by a lower Thauera abundance. Despite these impacts, the system removed 88.3 ± 5.6% of tetracycline and 69.5 ± 12.4% of ciprofloxacin, primarily through biosorption (for both antibiotics were more than 80%). Extracellular polymeric substances content increased by ∼19% under antibiotics exposure. Metagenomic analysis indicated changes in microbial community composition and function, while the overall antibiotic resistance gene profile remained relatively stable despite dynamic changes in individual resistance genes under antibiotic exposure. These findings demonstrate the strong potential of MB-AGS systems for effective organic carbon removal, while also highlighting opportunities to further enhance nutrient removal and mitigate antibiotic resistance genes under antibiotic stress.},
}

@article {pmid42085838,
year = {2026},
author = {ElHefnawi, M and Amin, DH and Elfiky, AM and Tamam, FMM and Elabiad, MA and Zada, S and Abu-Shahba, N},
title = {From culture to metagenomics: A paradigm shift in diagnosing infective endocarditis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {1},
pages = {117449},
doi = {10.1016/j.diagmicrobio.2026.117449},
pmid = {42085838},
issn = {1879-0070},
abstract = {Infective endocarditis (IE) is a severe disease that damages heart valves and can lead to major complications, including heart failure, embolic events, and stroke. It is the third most common fatal infection worldwide. This review examines the clinical burden of IE, its microbial causes, and the ongoing challenges in diagnosis. Particular attention is given to the limitations of traditional blood cultures, especially in detecting culture-negative and fastidious organisms, and to the emerging role of metagenomic approaches. A comprehensive review of the literature was conducted, focusing on diagnostic methods such as blood cultures, molecular assays, and metagenomic sequencing. The role of bacterial biofilms in treatment failure and antibiotic resistance was also explored. Metagenomics, especially cell-free metagenomic DNA (cf-mDNA), shows promise as a non-invasive diagnostic tool that can overcome culture-based limitations. However, standardized protocols and prospective studies are needed to validate its routine clinical application in IE diagnosis and management.},
}

@article {pmid42085875,
year = {2026},
author = {Amin, H and Šantl-Temkiv, T and M Wouters, I and Johannesen, A and Sigsgaard, T and Schlünssen, V and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ},
title = {Urban indoor airborne antibiotic resistance genes: Role of antibiotic use and outdoor air pollution.},
journal = {The Science of the total environment},
volume = {1034},
number = {},
pages = {181854},
doi = {10.1016/j.scitotenv.2026.181854},
pmid = {42085875},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) in airborne dust represent an emerging concern for public health, particularly in indoor environments where human exposure is prolonged. While external environmental pressures are known to shape the abundance and diversity of microorganisms in indoor dust, their role in ARG dynamics remains underexplored. This study assessed the temporal and spatial patterns of airborne ARGs in indoor dust across four Nordic cities (Aarhus, Bergen, Reykjavik, and Uppsala) using electrostatic dust collectors (EDCs) in the same households at two time points: 2012 and 2022. Shotgun metagenomic sequencing was performed to profile ARGs. National antibiotic consumption data were obtained from the European Surveillance of Antimicrobial Consumption (ESAC-Net), outdoor air pollution data (PM2.5 and PM10) from the Copernicus Atmosphere Monitoring Service (CAMS), and meteorological parameters from the NASA POWER database. Beta diversity analysis revealed city-specific differences in ARG composition (PERMANOVA, R[2] = 0.18, P = 0.03), but no consistent temporal shift over the 10-year period. Macrolide, tetracycline, and aminoglycoside resistance genes were among the most abundant and persistent classes. A previously undetected macrolide resistance sequence was identified across all cities in 2022. Although national antibiotic consumption declined, cross-sectional correlations between national antibiotic consumption and ARG abundance strengthened from 2012 (Spearman's ρ = 0.25) to 2022 (ρ = 0.37), suggesting sustained ARG presence despite reduced antibiotic consumption. Several ARG classes showed associations with outdoor particulate matter, and these relationships were influenced by local meteorological conditions. For example, higher absolute humidity was associated with a weaker relationship between PM and polymyxin resistance genes, whereas stronger wind speeds were associated with stronger relationships between PM and Sulfonamide resistance genes. These findings highlight the complex environmental interplay between antibiotic consumption, air pollution, meteorological factors, and ARG dynamics in indoor air, emphasizing the need for integrated environmental and AMR surveillance, especially in the context of climate change.},
}

@article {pmid42085931,
year = {2026},
author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB},
title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.},
journal = {EBioMedicine},
volume = {127},
number = {},
pages = {106281},
doi = {10.1016/j.ebiom.2026.106281},
pmid = {42085931},
issn = {2352-3964},
abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.

METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).

FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.

INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.

FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).},
}

@article {pmid42086548,
year = {2026},
author = {Lu, M and Jiao, JJ and Luo, X and Feng, X and Liang, W and Yu, S and Qi, Y and Wang, Z and Li, H and Li, M},
title = {Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72058-8},
pmid = {42086548},
issn = {2041-1723},
support = {32225003, 32393970, 32393971, 92251306//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42407109//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42130702//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Elevated ammonium concentrations in deltaic groundwater pose a widespread environmental challenge, yet the microbial mechanisms linking depositional history to ammonium dynamics remain poorly understood. The Pearl River Delta, with the highest naturally occurring groundwater ammonium concentrations documented globally, provides a unique natural system to investigate these processes. Here, by integrating geochemical and metagenomic data, we show that fermentation-related genes are the most prevalent across all depositional zones, suggesting fermentation as the potential primary pathway for ammonium production, with the functional potential declining as sedimentary organic matter becomes increasingly recalcitrant with sediment age. Secondary mechanisms shift from nitrate reduction to nitrite ammonification across terrestrial-to-marine-dominated zones, reflecting salinity-driven metabolic partitioning. Notably, the marine-derived genus Brevirhabdus emerges as a key taxon linking depositional history to present-day biogeochemistry, demonstrating remarkable metabolic versatility. These findings demonstrate that paleo-depositional and hydrogeological evolution fundamentally shape microbial landscapes and dictate groundwater quality in deltaic systems worldwide.},
}

@article {pmid42086631,
year = {2026},
author = {Moon, K and Kang, I and Cho, JC},
title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-07383-0},
pmid = {42086631},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; },
abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.},
}

@article {pmid42071227,
year = {2026},
author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z},
title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.},
journal = {Clinical and translational medicine},
volume = {16},
number = {5},
pages = {e70667},
doi = {10.1002/ctm2.70667},
pmid = {42071227},
issn = {2001-1326},
support = {2022YFA1304000//National Key R&D Program of China/ ; 2024B1111150001//Guangdong S&T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/genetics/pathology/etiology ; Humans ; Animals ; *DNA Damage/drug effects ; Mice ; Male ; *Lactates/metabolism/adverse effects ; Gastrointestinal Microbiome ; *Carcinogenesis ; Female ; Feces/microbiology ; Middle Aged ; },
abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.},
}

*Colorectal Neoplasms/microbiology/genetics/pathology/etiology
Humans
Animals
*DNA Damage/drug effects
Mice
Male
*Lactates/metabolism/adverse effects
Gastrointestinal Microbiome
*Carcinogenesis
Female
Feces/microbiology
Middle Aged

@article {pmid42071909,
year = {2026},
author = {Corrigan, A and Stockdale, S and Mackenzie, AM and Wilkinson, RG and Warren, H and Taylor-Pickard, J and Murphy, R},
title = {Rumen Microbiome Development in Lambs Following Maternal and Early-Life Prebiotic Mannan-Rich Fraction (MRF) Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/ani16081137},
pmid = {42071909},
issn = {2076-2615},
support = {NA//Alltech (Ireland)/ ; },
abstract = {The early-life rumen microbiome is highly dynamic, shaped by dietary transitions and maternal influences. Several dietary additives have been studied during the pre- and post-weaning periods to improve animal welfare, growth performance, and farming efficiencies. This study investigated microbial community assembly and growth performance of lambs provided with a mannan-rich fraction (MRF) supplement, either through maternal supplementation, directly, or via a combination of both. Using metagenomic sequencing and gas chromatography, we found differences in rumen microbial alpha and beta diversity related to both sampling time point and MRF supplementation (p < 0.05). At week 8, lamb microbiomes showed greater variance in their Shannon alpha diversity, with direct MRF supplementation only to the lamb resulting in a significantly greater diversity (p < 0.05). At week 20, combined maternal and lamb supplementation resulted in the highest Shannon diversity and was different compared to all other groups (p < 0.05). Beta diversity analyses combined with differential abundance analyses revealed that microbial community structures are driven by both diet and time, with maternal MRF supplementation associated with enrichment of taxa involved in carbohydrate fermentation and succinate metabolism, including Succiniclasticum ruminis, Succinovibrio dextrinosolvens, and Fibrobacter succinogenes. Generalized linear modeling identified significant associations between microbial alpha diversity metrics and total volatile fatty acids in lambs, particularly butyrate and valerate. Furthermore, at week 8, there was a significant positive correlation between alpha diversity metrics and propionate and valerate. In this study, lambs receiving MRF through maternal and direct supplementation had the highest growth performance, measured as the median average daily gains (kg) and final weights (kg) of lambs. These findings suggest that MRF supplementation, especially when provided both maternally and directly, may influence the lamb rumen microbiome and alter its metabolic potential with potential implications for optimizing early-life nutrition strategies in ruminant production systems.},
}

@article {pmid42072313,
year = {2026},
author = {Alamri, A and Almutairi, AK and AlSinan, F and Alramadhan, A and Aldehalan, F and Almutairi, H and Alghuraybi, M and AlHarbi, NM and Alghannam, SF and Alotaibi, SS and AlOmary, M and AlKhater, S},
title = {Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.},
journal = {Biomedicines},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biomedicines14040772},
pmid = {42072313},
issn = {2227-9059},
support = {IF-2020-016-CAMS//This work was funded by the Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia (IF-2020-016-CAMS) and approved by the deanship of scientific research (DSR) at Imam Abdulrahman bin Faisal University (IAU)./ ; },
abstract = {Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma.},
}

@article {pmid42073328,
year = {2026},
author = {Indio, V and Mekonnen, YT and Oliveri, C and Rubboli, S and Candela, M and Seguino, A and Serraino, A and De Cesare, A},
title = {Reducing Antimicrobial Resistance in Poultry Carcasses Extends Beyond Farm-Level Interventions.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/foods15081440},
pmid = {42073328},
issn = {2304-8158},
support = {Horizon 2020 "Controlling Microbiomes Circulations for Better Food Systems" (CIRCLES) no. 818290.//European Union/ ; },
abstract = {The aim of this study was to assess how raising chickens without the use of antimicrobials affects the microbiome of poultry carcasses. A total of 151 caeca and neck skin samples from chickens raised without antimicrobials were collected in the same slaughterhouse and submitted to shotgun metagenomic sequencing. Caeca were dominated by Bacillota and Bacteroidota, while carcasses by Pseudomonadota. The caeca microbiome was enriched in genes related to a proliferating and metabolically active microbial community. Carcass-associated microbiomes were enriched in functional genes linked to adaptation to nutritionally limited and oxidative environments. A significantly higher cumulative antimicrobial resistance gene abundance was detected in carcasses compared to caeca. Specifically, carcasses exhibited approximately 1.5 times more AMR genes, reflecting an increase of nearly 49%. While caeca showed enrichment of resistance determinants associated with Gram-positive anaerobic gut commensals, carcasses were characterized by a predominance of multidrug efflux systems and clinically relevant β-lactam resistance genes, commonly associated with environmental and opportunistic Gram-negative bacteria. In carcasses, carbapenem-associated genes, such as OXA-58-like and CphA, were detected. However, these genes have not been associated with carbapenemase-producing Enterobacterales. Overall, the findings of this study indicate that reducing antimicrobial resistance in food animal production systems extends beyond farm-level intervention. At present, the benefits of the interventions aimed at reducing antimicrobial resistance at farm level seem to be compromised during the post-harvest stages.},
}

@article {pmid42073366,
year = {2026},
author = {Brasileiro, CG and Moreno, MTDC and Santos, EO and Saranraj, P and Cardoso, AM and Vieira, JMBD},
title = {Assessing Food Safety Risks in Homemade Fermented Beverages: A Case Study with Quinoa Rejuvelac.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040556},
pmid = {42073366},
issn = {2075-1729},
support = {E2023//FAPERJ, CNPq, and CAPES/ ; },
abstract = {Spontaneous fermentation processes can promote uncontrolled microbial growth and increase the risk of foodborne contamination, making the characterization of artisanal beverages essential for consumer safety. This study investigated the microbial composition of quinoa-based rejuvelac, a homemade fermented drink often perceived as a functional food, with the objective of identifying potential microbiological hazards associated with its preparation. High-throughput sequencing of the 16S rRNA V3-V4 region was combined with shotgun metagenomics to profile bacterial communities and recover metagenome-assembled genomes. The analysis revealed a strong dominance of Pseudomonadales, mainly Pseudomonas, Acinetobacter, Enterobacter and Burkholderiales, while lactic acid bacteria typically responsible for stable and safe fermentations were not detected. Shotgun metagenomics recovered medium- to high-quality genomes from Burkholderiaceae and Clostridiales, supporting the overrepresentation of non-beneficial taxa and indicating deviations from expected fermentation microbiota. These results show that the spontaneous preparation of rejuvelac may favor bacterial groups associated with environmental contamination rather than fermentative pathways, underscoring the importance of hygiene practices, controlled starter cultures and monitoring strategies to mitigate microbiological risk. The study highlights the need for improved safety standards in artisanal fermented foods to prevent unintended microbial contamination and protect consumers.},
}

@article {pmid42073451,
year = {2026},
author = {Cerreto, M and Maestri, M and Pallozzi, M and Cerrito, L and Stella, L and Ianiro, G and Gasbarrini, A and Ponziani, FR},
title = {Gut Microbiota Biomarkers in Patients with Hepatocellular Carcinoma in the Era of Immune Checkpoint Inhibitors.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040641},
pmid = {42073451},
issn = {2075-1729},
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the therapeutic landscape for hepatocellular carcinoma (HCC); however, a considerable proportion of patients do not achieve durable clinical benefits. This highlights the need for reliable predictive biomarkers, which are currently lacking. The accumulated evidence supports a relevant role of the gut-liver axis in modulating immunotherapy outcomes, and several studies have identified distinct microbial features associated with either responders or non-responders. Responders to immunotherapy frequently present with higher microbial diversity and enrichment of beneficial taxa, whereas the expansion of pro-inflammatory and pathogenic bacteria has been associated with primary resistance and increased treatment-related toxicity in non-responders. However, the available findings remain heterogeneous across cohorts, likely owing to differences in geography, diet, liver disease etiology, treatment regimens, and microbiome analytical methods. Machine-learning models integrating metagenomic and metabolomic data have shown encouraging results in defining microbial signatures associated with treatment outcomes, although variability among cohorts currently limits their clinical applicability and generalizability. Beyond microbial taxonomic composition, microbiota-derived metabolites-such as short-chain fatty acids, bile acids, inosine, and tryptophan catabolites-appear to play a crucial role in shaping the tumor microenvironment and host immune responses, thus representing additional candidate biomarkers, also due to the relative ease of their measurement. Finally, microbiota-targeted interventions are emerging as potential strategies to enhance immunotherapy efficacy. Overall, the gut microbiome and its metabolic activity represent promising tools, albeit still under investigation, for patient stratification and personalized management in HCC treated with ICIs. Therefore, this review aims to summarize and critically discuss the current evidence on gut microbiota-derived biomarkers of response and resistance to ICIs in HCC, with particular focus on microbial composition, microbiota-related metabolites, and emerging microbiome-based therapeutic strategies. This narrative review provides an updated overview of the role of gut microbiota as both a biomarker and a therapeutic target in patients with hepatocellular carcinoma (HCC) receiving immune checkpoint inhibitor (ICI) therapy.},
}

@article {pmid42073497,
year = {2026},
author = {Carraturo, F and Salamone, M and Annunziata, M and Di Brizzi, EV and Giorgio, CM and Petrillo, A and Fedi, L and Maione, A and Guida, M and Galdiero, E},
title = {Preliminary Characterization of Skin Microbiota and Mycobiota in Atopic Dermatitis by Metagenomic and Culture-Based Analyses.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/life16040690},
pmid = {42073497},
issn = {2075-1729},
support = {PRIN2022//European Union-Next Generation EU location/ ; 2022HC3FRM//Serum metabolomics in atopic dermatitis (MetabAD)/ ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease influenced by several factors, including immune system imbalance, impairment of the epidermal barrier, and alterations in the composition of the gut and skin bacterial and fungal microbiota. This study combines metagenomic sequencing and culture-based methods to explore the impact of probiotic supplementation on the cutaneous microbiota and mycobiota of AD patients. Twenty-five adults diagnosed with AD were enrolled, and skin swabs were analyzed to characterize microbial diversity and load. Culturomic analyses identified 42 bacterial and 6 fungal species, confirming Staphylococcus aureus and Candida parapsilosis as predominant taxa. High-throughput sequencing revealed Staphylococcus spp. and Malassezia spp. as dominant genera, with notable interindividual variability. While probiotic use did not significantly influence bacterial diversity, it was associated with higher richness and evenness in fungal communities, as shown by alpha and beta diversity metrics. Malassezia restricta was more prevalent among probiotic users, whereas Candida parapsilosis and Rhodotorula mucilaginosa were enriched in non-users. These findings indicate an association between probiotic use and differences in the composition and diversity of the skin mycobiota compared with the bacterial microbiota, suggesting that fungal communities may be more responsive to probiotic-associated factors. Integrating metagenomic and culturomic approaches offers valuable insights into the complex interactions among host factors, microbial communities, and probiotic use in AD, paving the way for targeted microbiome-based therapeutic strategies.},
}

@article {pmid42073729,
year = {2026},
author = {Ren, L and Zhang, X and Xu, X and Qin, Q and Fan, H and Wang, Z and Wang, W},
title = {Enhancing Duck Manure Anaerobic Digestion with Hydrochar: Exploring Green Material Potential via Bidirectional AD-HTC Coupling.},
journal = {Materials (Basel, Switzerland)},
volume = {19},
number = {8},
pages = {},
doi = {10.3390/ma19081563},
pmid = {42073729},
issn = {1996-1944},
support = {Grant No. 52300163//National Natural Science Foundation of China/ ; Grant No. ZR2024QE099//Shandong Provincial Natural Science Foundation/ ; },
abstract = {The efficient resource utilization of duck manure and agricultural/forestry wastes (AFW) plays a significant role in environmental protection and promoting the sustainable development of the economy and society. This study examined the effects of hydrochar derived from AFW in the anaerobic digestion (AD) process, determining the optimal addition ratio. This research systematically investigated the impact of hydrochar on methane yield, as well as changes of short-chain fatty acids, microbial community dynamics, and metabolic pathways during AD of duck manure. The underlying mechanisms were clarified by metagenomic and metabolomic analyses. This experiment used duck manure as substrate and added hydrochar of four different dosage levels. Laboratory batch tests ran for 32 days at 37 ± 0.5 °C, with three parallel samples for each group. The results indicated that hydrochar additive significantly improved methane yield (p < 0.05), with a maximum increase of 27.13% at an optimal dosage of 10.91 g·L[-1]. This amendment enhanced the abundance of Firmicutes, Bacteroidota, Chloroflexota, Halobacteriota, and Methanosarcina significantly. Compared to the control group, the abundances of functional genes involved in hydrolysis, acidogenesis, and acetogenesis pathways increased by 28-254% in the optimal treatment group, with methanogenesis-related genes showing a 16-155% enhancement (p < 0.05).},
}

@article {pmid42074337,
year = {2026},
author = {Liu, X and Chen, Y and Zhou, X and Xiao, Y and Yuan, X and Su, N and Chen, C and Yan, Q and Chen, X},
title = {Bacillus subtilis and Trichoderma harzianum Reshape Rhizosphere Microbiome and Reprogram Root Transcriptome to Promote Mungbean Growth Under Continuous-Cropping Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {8},
pages = {},
doi = {10.3390/ijms27083699},
pmid = {42074337},
issn = {1422-0067},
support = {2025YFE0121200//National Key R&D Program of China/ ; CARS-08//China Agriculture Research System of MOF and MARA-Food Legumes/ ; JBGS[2021]004//Jiangsu Seed Industry Revitalization Project/ ; },
mesh = {*Bacillus subtilis/physiology ; *Rhizosphere ; *Vigna/growth & development/microbiology/genetics ; *Plant Roots/microbiology/genetics/growth & development ; *Transcriptome ; *Microbiota ; Soil Microbiology ; Metagenomics ; *Hypocreales/physiology ; Gene Expression Profiling ; },
abstract = {Mungbean (Vigna radiata) is an important cash crop, yet the production is significantly compromised by continuous cropping. Beneficial microbial inoculation offers a promising strategy to alleviate the stresses through rhizosphere modulation and host physiological reprogramming. This study evaluated the efficacy of two biological control agents, Bacillus subtilis (B. subtilis) and Trichoderma harzianum (T. harzianum), in promoting mungbean growth under continuous-cropping conditions. Both individual applications of B. subtilis and T. harzianum significantly improved plant biomass, root system architecture, and yield. Combined metagenomic and transcriptomic analyses were conducted to unravel the underlying mechanisms. According to metagenomic analysis, both B. subtilis and T. harzianum were responsible for significant changes in beta diversity without significantly affecting the alpha diversity of the rhizosphere microbial community. T. harzianum recruited Chitinophagaceae unclassified, Abditibacterium, Hydrogenophilaceae unclassified, Methylophilaceae unclassified, and Chimaeribacter, while Bs recruited Candidatus Saccharibacteria unclassified. Transcriptomic analysis indicated that T. harzianum induced more extensive transcriptional reprogramming than B. subtilis. The enrichment analysis revealed both shared and distinct responses triggered by the two treatments. These findings suggest that B. subtilis and T. harzianum alleviate continuous-cropping stress through distinct yet complementary mechanisms involving rhizosphere microbiome modulation and mungbean transcriptional reprogramming. This study provides a sustainable strategy for legume cultivation.},
}

*Bacillus subtilis/physiology
*Rhizosphere
*Vigna/growth & development/microbiology/genetics
*Plant Roots/microbiology/genetics/growth & development
*Transcriptome
*Microbiota
Soil Microbiology
Metagenomics
*Hypocreales/physiology
Gene Expression Profiling

@article {pmid42075183,
year = {2026},
author = {van Essen, RRT and Kaur, J and Li, T and Sawbridge, TI},
title = {Isolation of N-Fixing Bacteria from Warm-Season Pasture Grasses and the Evaluation of Nitrogen Effects on the Bacterial Communities Present in Cenchrus clandestinus.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040786},
pmid = {42075183},
issn = {2076-2607},
support = {DB F.2//DairyBio 21-26, Future Forages Program/ ; },
abstract = {Nitrogen is essential for plant growth. Reliance on synthetic nitrogen fertilisers, however, is costly and contributes to soil degradation. Utilising nitrogen-fixing bacteria as biofertilisers may offer a sustainable alternative, reducing fertiliser costs and environmental impact. In this study, we attempted to isolate nitrogen-fixing bacteria from 14 seed batches of warm-season pasture grasses and successfully isolated bacteria from three of these batches. Whole genome sequencing confirmed the presence of the nif operon within all three isolates. Two seed batches of Cenchrus clandestinus (Hochst. ex Chiov.) Morrone from which nif-containing bacteria were isolated, along with two 'nif'-negative C. clandestinus seed batches, were used in nitrogen-limiting growth assays. This was done to evaluate the effect of the presence of seed-associated nitrogen-fixing bacteria within a seed batch on nitrogen-limited plant growth and the associated plant microbiome composition, using 16S amplicon sequencing of root and shoot samples. Initial plant growth assays revealed significantly reduced root length between plants grown from seed batches harbouring nitrogen-fixing bacteria and those without, under limiting nitrogen availability, but no resulting shoot biomass reduction was observed. The plant microbiomes of these nif-positive seed batches were also statistically similar to each other, compared to the nif-negative seed batch plants. Plant microbiomes of all four C. clandestinus seed batches were significantly different from their original seed microbiomes, showing shifts in community composition. This study demonstrates the presence of potential nitrogen-fixing bacteria associated with warm-season pasture grass seeds at low abundance and reveals differences in plant-associated bacterial community composition between seed batches harbouring and lacking these bacteria.},
}

@article {pmid42075229,
year = {2026},
author = {Lai, R and Wang, Z and Liu, P and Tong, J and Ahmed, Z and Cui, R and Gu, Y and Luo, G},
title = {Environmental Altitude and Host Genetics Shape Divergent Microbiota and a Conserved Resistome in Porcine Intestinal Niches.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040832},
pmid = {42075229},
issn = {2076-2607},
support = {Grant No. RQD2025005//Southwest Minzu University Research Startup Funds/ ; 32472888//National Natural Science Foundation of China/ ; XZ202501ZY0147//Science and Technology Projects of Xizang Autonomous Region/ ; 2024YFHZ0373//Sichuan Science and Technology Program/ ; sccxtd-2026-08//Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; 2024MS150//he Sichuan Provincial Administration of Traditional Chinese Medicine Science and Technology Research Special Project/ ; },
abstract = {Environmental stressors and host genetics influence gut microbiota and antimicrobial resistance, but their combined effects across intestinal niches remain poorly unexplored. We conducted a metagenomic analysis of 60 jejunal and cecal samples from 30 native Chinese pigs across three altitudes (500 m, 1400 m, and 3850 m). The aim was to disentangle the interactive impacts of altitude, breed, and intestinal site on microbiome structure and antibiotic resistome dynamics. The cecal microbiota was taxonomically conserved and strongly associated with breed. Conversely, while jejunal communities exhibited structural variations among the sampled cohorts, differences in alpha diversity (Shannon index, p < 0.01) appeared to be primarily associated with breed differences rather than an independent altitudinal effect. High-altitude Tibetan pigs showed an enrichment of Bifidobacterium and Pseudomonas, which may be linked to hypoxia adaptation. Despite a shared core resistome (88 ARG types), the cecum harbored significantly higher ARG abundance than the jejunum within-breed comparisons of Tibetan pigs across altitudes; this revealed stable ARG profiles (p > 0.05) suggesting that, although some descriptive differences were observed, the independent effect of altitude weakens when the genetic effect is taken into account. Furthermore, carbohydrate-active enzymes (e.g., CBM13, GH33) correlated positively with ARG abundance. In conclusion, the jejunum appears to act as an environmentally responsive niche, while the cecum exhibits a higher ARG abundance that is closely associated with the host breed.},
}

@article {pmid42075233,
year = {2026},
author = {Mousa, WK and AlShami, R and Ghemrawi, R},
title = {Shared Microbial Blueprints Underlying Symbiotic Plasticity in Desert Plant Endophytes.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040836},
pmid = {42075233},
issn = {2076-2607},
support = {SWARD-F23-020.//Sandooq Al Watan/ ; },
abstract = {The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments.},
}

@article {pmid42075236,
year = {2026},
author = {Wang, Z and Ma, C and Huang, H and Ke, S and Lv, J and Hu, J and Wang, S and Bao, Z},
title = {Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040840},
pmid = {42075236},
issn = {2076-2607},
support = {2025B1111180001//Guangdong S&T Program/ ; 2025A04J3824//GCI Science & Technology (China)/ ; SOLZSKY2025013//Department of Science and Technology of Hainan Province/ ; },
abstract = {Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont-the host and its associated microbiota-remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies.},
}

@article {pmid42075252,
year = {2026},
author = {Amin, H and Šantl-Temkiv, T and Finster, K and Schlünssen, V and Sigsgaard, T and Wouters, IM and Sørensen, MT and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ},
title = {Airborne Movement of Antibiotic Resistance Genes Between Livestock Stables and Farmers' Homes.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040855},
pmid = {42075252},
issn = {2076-2607},
support = {TMS2021TMT03//Trond Mohn stiftelse/ ; No. 137087//NordForsk/ ; },
abstract = {Antibiotic resistance genes (ARGs) are prevalent in livestock environments due to antimicrobial use, yet their airborne dispersal into human-occupied indoor spaces remains poorly characterized. We investigated whether airborne ARGs disperse from livestock stables into farmers' homes and surrounding outdoor environments. Electrostatic dust collectors were deployed in paired pig and cow stables and their associated homes in Jutland, Denmark, to collect settled airborne dust. Pooled samples were analyzed using shotgun metagenomic sequencing. ARG dispersal patterns were assessed using FEAST source tracking and ecological similarity metrics, including shared ARG ratios and Jaccard indices. Pig production systems exhibited higher antibiotic use and stronger resistome continuity with farmers' homes than cow systems, reflected by greater FEAST contributions (P = 0.029) and Jaccard similarity (P = 0.029). Beta-diversity analysis supported higher compositional similarity between pig stables and homes (PERMANOVA R[2] = 0.23, p = 0.052), whereas cow environments showed greater divergence (R[2] = 0.41, P = 0.035). Across environments, tetracycline, macrolide-lincosamide-streptogramin B, and aminoglycoside resistance genes dominated, consistent with livestock-specific antibiotic use patterns. Supplementary indoor-outdoor comparisons across cow, pig, and chicken stables (from an independent 2024 sampling campaign not directly comparable to the 2008 EDC-based survey) revealed contrasting dispersal dynamics, with higher bacterial species spillover from cow stables but stronger ARG overlap from pig stables. Collectively, these findings are consistent with airborne ARG connectivity across occupational and environmental interfaces and support consideration of air as a potential pathway in One Health AMR surveillance.},
}

@article {pmid42075269,
year = {2026},
author = {Yang, J and Yue, Y and Li, X and Lv, R},
title = {Dynamics of Microbial Carbon Metabolism During Vegetation Restoration in Sandy Ecosystems.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040873},
pmid = {42075269},
issn = {2076-2607},
support = {2024B04031-2//Research and Development of Efficient Utilization Technology for Brackish Water in Desert Photovoltaic Power Stations/ ; 2024AAC03102//Natural Science Foundation of Ningxia/ ; },
abstract = {Understanding the succession of soil microbial carbon metabolism functions is crucial for elucidating carbon cycling mechanisms during ecosystem restoration in sandy lands. Soils were collected from Caragana korshinskii shrubland sites across a restoration chronosequence (0, 10, 30, 50, and 70 years) in the Mu Us Sandy Land. Biolog carbon source utilization analysis and metagenomic sequencing were employed to characterize the successional patterns of microbial carbon metabolism functions-a shift in carbon metabolism strategies from acquisition to conservation, and a transition in functional diversity from generalism to specialization. The results indicated that microbial communities exhibited two associated successional shifts in functional characteristics: carbon source utilization tended to transition from simple to complex substrates, while functional gene expression showed a progressive shift from broad multi-pathway patterns toward pathway-specific specialization. AWCD values increased continuously with restoration duration, and carbon source utilization patterns diverged significantly around 30 years. Early-stage sites (0-30 years) primarily utilized simple carbon sources, whereas late-stage sites (50-70 years) shifted toward more complex and diverse substrates. Principal component analysis revealed that 27 carbon sources contributed 91.3% of the variance to PC1. Microbial community structure succession revealed that Actinobacteria peaked at 10 years (43.63%), Proteobacteria peaked at 30 years (45.66%), and taxa such as Bacilli and Solirubrobacter dominated at 50-70 years. Carbon metabolism pathways exhibited stage-specific succession: glycolysis and the ED pathway were active in early stages, acetate metabolism dominated with the 3HB cycle peaking in intermediate stages, and the CBB cycle increased in later stages while methane metabolism shifted from high to low contribution. These two associated successional shifts occurred along the same restoration chronosequence, with the progressive transition in substrate utilization accompanying the development of specialist functional characteristics. These findings provide insights into the successional dynamics of microbial carbon metabolism during vegetation restoration, offering a microbiological basis for optimizing ecological restoration practices and enhancing soil carbon sequestration in sandy lands.},
}

@article {pmid42075270,
year = {2026},
author = {Oladipo, P and Kade, A and Onohuean, H and Ram, JL},
title = {From Cryptic Clade to Emerging Pathogen: Exploring the Evolutionary Divergence and Clinical Relevance of Escherichia marmotae.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040869},
pmid = {42075270},
issn = {2076-2607},
abstract = {The Escherichia genus includes both commensal and pathogenic species and is characterized by its diversity and adaptability to the mammalian gut and other environments. Among these species, E. coli has facilitated many scientific advances as a model organism. Recently, a new member of the Escherichia genus, Escherichia marmotae, has been described as a phylogenetically distinct clade that shows the greatest genetic divergence from E. coli. This review explores E. marmotae, its cryptic evolution, distinct characteristics, and ecological niches. E. marmotae has recently gained scientific prominence due to its association with animal feces, environmental occurrence, human clinical samples, and emerging as a potential pathogen. While its pathogenicity remains understudied, growing evidence from clinical, environmental, and animal sources suggests the need for heightened surveillance. This review highlights current knowledge gaps, underscores the need for improved diagnostic tools, and proposes future research directions to elucidate the clinical and ecological implications of this emerging pathogen.},
}

@article {pmid42075274,
year = {2026},
author = {Chen, L and Chen, Y and Peng, Q and Zhou, D and Feng, S},
title = {Metagenomics and Metagenome-Assembled Genomes Analysis of Highland Barley Baijiu Daqu.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040877},
pmid = {42075274},
issn = {2076-2607},
abstract = {Highland barley Baijiu is a kind of fermented liquor with national characteristics produced in the Qinghai-Tibet Plateau, and its quality largely depends on the highland barley Baijiu Daqu (HBQ). HBQ contains abundant microbial resources and embedded unknown genomes that have not yet been decoded. In order to deeply understand the key contribution of microorganisms in HBQ, this study analyzed the microbial community structure of HBQ, inferred predicted functions and recovered high-quality metagenome-assembled genomes (MAGs) based on Metagenomics. The results indicated that Pantoea agglomerans was the most abundant species in HBQ, followed by Lichtheimia ramosa, Pichia kudriavzevii, Saccharomycopsis fibuligera and Wickerhamomyces anomalus. The predictive function of the HBQ was focused on annotating carbohydrate metabolism and amino acid metabolism. Meanwhile, six high-quality MAG strains were recovered and identified as Unclassified Kroppenstedtia, Erwinia persicina, Leuconostoc citreum, Saccharopolyspora rectivirgula, Levilactobacillus brevis, and Pantoea agglomerans. Genome annotation of the recovered genomes showed eggNOG predicted function as well as primary and secondary metabolites. The metabolic network diagram of the functional microorganisms in HBQ related to flavor compounds was also predicted. The results can help to understand the formation mechanism of flavor profiles in highland barley Baijiu.},
}

@article {pmid42075297,
year = {2026},
author = {Li, X and Qin, Z and Wang, H and Tao, X and Xia, J and Zhao, Y and Yi, P and Ma, Y and Wang, X and Ma, X and Li, N and Zhong, Q and Yao, G},
title = {Seasonal Dynamics of Skin Microbiota and Metabolites in Transhumant-Grazed Altay Sheep.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040901},
pmid = {42075297},
issn = {2076-2607},
support = {2022TSYCJC0026//the "Tianshan Talent" Youth Science and Technology Top Talent Project of Xinjiang Uygur Autonomous Region/ ; },
abstract = {To explore the seasonal variation patterns of the skin microecology of Altay sheep under transhumant grazing conditions, skin swabs were collected from 60 free-grazing Altay sheep at seasonal transition nodes in the Altay region. Metagenomic sequencing combined with untargeted metabolomics was used to characterize their bacterial community structure, functional pathways, and metabolite profiles. The results showed that the skin microecology of Altay sheep presented obvious seasonal variation patterns. In spring, 35 of the 39 highly abundant bacteria were environmentally derived, five proliferation-related pathways were significantly enriched, and the levels of five metabolites associated with microbial community regulation and skin barrier defense were elevated. In summer, the abundance of three skin symbiotic bacteria increased, the activities of eight pathways mainly related to biofilm formation were significantly enhanced, and the contents of five metabolites primarily associated with membrane lipid homeostasis and selective bacteriostasis increased. In autumn, the abundances of nine radiation-resistant and cold-tolerant strains increased, together with the elevated abundance of two opportunistic pathogens; five repair-related pathways were active, and the levels of four anti-inflammatory and repair-associated metabolites were synchronously increased. In winter, the abundance of two cold-tolerant strains increased, the activities of pathways related to nitrogen metabolism and energy synthesis were enhanced, and one lignan compound was identified as the key metabolite. These findings elucidate the seasonal dynamic patterns of the skin microecology of Altay sheep and provide a theoretical basis for research on the adaptive mechanisms and seasonal health management of Altay sheep and other sheep in alpine regions.},
}

@article {pmid42075311,
year = {2026},
author = {Cruells, A and Eguren, C and Robainas Barcia, A and Martínez, H and Sharaf, M and Ruiz, C and Sánchez-Baos, A and Carrón, N and Bou, L and Pérez, M and De Lucas, R and Guerra-Tapia, A},
title = {Shotgun Metagenomic Characterization of Acne Microbiota Before and After Treatment with a Topical Biotechnological Phytocomplex: Understanding Skin Dysbiosis.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040915},
pmid = {42075311},
issn = {2076-2607},
abstract = {This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris.},
}

@article {pmid42075321,
year = {2026},
author = {Wang, W and Wang, Z and Zhang, P and Zhang, J},
title = {Environmental Regulation of Gut Microbial Networks Links to Growth Variation in Schizopygopsis younghusbandi Across Contrasting Aquaculture Systems.},
journal = {Microorganisms},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/microorganisms14040925},
pmid = {42075321},
issn = {2076-2607},
support = {XZ202501JD0019; XZ202402ZD0005; XZ202401ZY0059//Science and Technology Program of Tibet Autonomous Region/ ; XZ202501JD0019//the Base and Talent Program Projects of Science and Technology Program of Tibet Autonomous Region/ ; 42371170//National Natural Science Foundation of China/ ; //the Agricultural and Animal Husbandry Science and Technology Innovation Project/ ; },
abstract = {Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host-microbiome-environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development.},
}

@article {pmid42075340,
year = {2026},
author = {Cheng, L and Shen, Q and Wang, Y},
title = {Root-Zone Nitrogen Fertilization Increases Oilseed Rape Yield: Reprogramming Rhizosphere N-Cycling and Strengthening Soil-Plant Coupling.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081137},
pmid = {42075340},
issn = {2223-7747},
support = {2024J0487//Scientific Research Fund Project of the Education Department of Yunnan Province/ ; 202304BQ040005//Project of Science and Technology Department of Yunnan Province/ ; },
abstract = {Root-zone nitrogen fertilization (RZF) can increase crop N uptake and yield, yet the underlying rhizosphere N-cycling functional mechanisms remain insufficiently resolved. In a field experiment with winter oilseed rape (Brassica napus L.), RZF was compared with conventional fertilization (CF) under the same N input rates, alongside a zero-N control (N0). Compared with CF, RZF significantly increased seed yield (by 0.44 t ha[-1]) and aboveground N uptake (by 20.45 kg ha[-1]), while simultaneously enriching rhizosphere mineral N pools (NH4[+]-N and NO3[-]-N by 54.50% and 56.02%, respectively). Shotgun metagenomics revealed that RZF reprogrammed rhizosphere N-cycling functional potential, characterized by enhanced nitrogen fixation, reduced nitrification and denitrification, and a tendency toward increased assimilatory nitrate reduction. These module-level shifts were supported by concordant changes in key functional genes, indicating greater genetic potential for N retention and assimilation (nifD, glnA, gltB, nasA, napB, nrfA) and reduced potential for nitrification- and denitrification-driven N losses (amoB/C, narI, nirK, norB). Taxonomic composition analysis showed enrichment of Bradyrhizobium and suppression of key nitrifier taxa (Nitrosospira and a Nitrososphaeraceae-affiliated taxon) under RZF. Rhizosphere pH exhibited the strongest Mantel correlation with multiple N-cycling modules, and rhizosphere available N (AN; sum of NH4[+]-N and NO3[-]-N) was positively associated with plant N traits and yield. Structural equation modeling supported a pathway in which a functional balance index (retention/assimilation vs. loss/oxidation) increased AN (0.22), and AN strongly promoted yield (0.90). Collectively, these results elucidate a rhizosphere-centered mechanism whereby localized N placement strengthens soil-plant N coupling and enhances crop productivity through reprogramming microbial N-cycling functional potentials, positioning rhizosphere N processes as a key mechanistic bridge for microbiome-informed optimization of root-zone fertilization.},
}

@article {pmid42075353,
year = {2026},
author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV},
title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081151},
pmid = {42075353},
issn = {2223-7747},
support = {22-74-10001-П//the Russian Science Foundation/ ; },
abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.},
}

@article {pmid42076876,
year = {2026},
author = {Krupa, Ł and Schmarz, GP and Staroń, R and Schmidt, HH and Rehner, J and Becker, SL and Krawczyk, M},
title = {Metagenomic profiling of bile in malignant cholestasis: Analysis of samples collected during EUS-guided biliary drainage.},
journal = {European journal of clinical investigation},
volume = {56},
number = {5},
pages = {e70200},
doi = {10.1111/eci.70200},
pmid = {42076876},
issn = {1365-2362},
support = {Precision-BTC-Network CA22125//European Cooperation in Science and Technology/ ; //Saarland University and the UdS-HIPS TANDEM initiative/ ; 469073465//Deutsche Forschungsgemeinschaft/ ; 2022-784-024//European Union Horizon 2020 Transcan project/ ; 2024-040//Dr. Rolf M. Schwiete Stiftung/ ; },
}

@article {pmid42076937,
year = {2026},
author = {Lundtorp-Olsen, CM and Andersen, SVR and Massarenti, L and Gürsoy, M and Splunter, AV and Bikker, FJ and Gursoy, UK and Markvart, M and Damgaard, C and Belstrøm, D},
title = {Probiotics Augment the Effect of Non-Surgical Periodontal Treatment-A Randomised, Double-Blinded, Placebo-Controlled Trial.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70136},
pmid = {42076937},
issn = {1600-051X},
support = {1044-00093B//Innovationsfonden/ ; //Archer Daniels Midland/ ; },
abstract = {AIM: To determine the effect of probiotic lozenges containing Lacticaseibacillus rhamnosus PB01, Latilactobacillus curvatus EB10 and xylitol after non-surgical periodontal treatment (NSPT) on changes in microbial composition. The secondary aims were to assess the clinical and immunological impact of probiotic consumption.

MATERIALS AND METHODS: Eighty adults with stage II or III periodontitis were enrolled and received NSPT at baseline, followed by a 12-week consumption of probiotics or placebo. Microbial sampling and clinical examination were performed at baseline, Week 6 and Week 12. The subgingival microbiota was analysed using 16S sequencing, the salivary microbiota by metagenomic sequencing and selected cytokines and proteases in saliva by bead-based immunoassay.

RESULTS: Sixty-one participants completed the trial (probiotics n = 32, placebo n = 29). At Week 12, Treponema socranskii, Selenomonas sputigena, Dialister pneumosintes, Dialister invisus, Anaeroglobus geminatus and Fusobacterium nucleatum were significantly associated with the placebo group, while Streptococcus sanguinis, Neisseria elongata and Neisseria oralis were associated with the probiotic group. Bleeding on probing percentage (BoP%) and number of periodontal pockets (PPD) ≥ 5 mm decreased significantly more in the probiotic group compared to the placebo group (p < 0.05).

CONCLUSION: The tested probiotic supplement resulted in an additional short-term decrease in periodontitis-associated species along with greater improvements in BoP% and PPD ≥ 5 mm 12 weeks post-NSPT, compared to the placebo group.},
}

@article {pmid42077846,
year = {2026},
author = {Pinheiro, GL and Lin, NJ and Parratt, KH and Hines, I and Hack, HR and Servetas, SL and Iyer, H and Da Silva, SM},
title = {The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {23885-23899},
pmid = {42077846},
issn = {2470-1343},
abstract = {Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.},
}

@article {pmid42078366,
year = {2026},
author = {Sy, M and Ndiaye, T and Thakur, R and Gaye, A and Levine, ZC and Ngom, B and Bellavia, KL and Firer, D and Toure, M and Ndiaye, IM and Diedhiou, Y and Mbaye, AM and Gomis, JF and DeRuff, KC and Deme, AB and Ndiaye, M and Badiane, AS and Paye, MF and Sabeti, PC and Ndiaye, D and Siddle, KJ},
title = {Oral and plasma microbiome in the context of acute febrile illness.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.26351042},
pmid = {42078366},
abstract = {Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.},
}

@article {pmid42078431,
year = {2026},
author = {Tang, J and Luo, Z and Li, Y and Jiang, W and Weng, Y and Zhang, G and Li, C and Liu, Y and Sun, X and Chen, L},
title = {Invasive pericardial and pulmonary aspergillosis by uncommon Aspergillus species in anti-interferon-γ autoantibody-associated immunodeficiency: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1760017},
pmid = {42078431},
issn = {2296-858X},
abstract = {This case report describes a 51-year-old female patient who presented with dyspnea and was diagnosed with invasive aspergillosis affecting the pericardium and lungs, secondary to immunodeficiency syndrome caused by anti-interferon-γ autoantibodies. Diagnosis was established by pericardial tissue metagenomic next-generation sequencing (mNGS) identifying Aspergillus udagawae and serum anti-interferon-γ autoantibody testing (titer 1:2,500). Despite sequential antifungal therapy with voriconazole, isavuconazole, and amphotericin B, the patient developed progressive multifocal infection, including an abdominal wall abscess and mediastinal infection caused by Aspergillus siamensis, and ultimately died of multiple organ failure. This case highlights the diagnostic challenges and poor prognosis associated with this rare immunodeficiency syndrome and emphasizes the importance of early recognition, precise pathogen identification, and consideration of immunomodulatory therapy.},
}

@article {pmid42078521,
year = {2026},
author = {Meng, T and Shi, J and Zhang, X and Zhao, X and Liu, Y and Rong, M and Chen, L and Dai, Y and Wei, S and Liu, J and Lu, Z},
title = {Mechanistic insights into nitrogen fertilizer regulation of carbon-nitrogen cycling and greenhouse gas emissions: a metagenomics-based investigation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1808047},
pmid = {42078521},
issn = {1664-302X},
abstract = {Nitrogen (N) fertilizer application can regulate the structure of soil microbial community and influence the abundance of functional genes involved in carbon (C) and N cycling, thereby affecting greenhouse gas (GHG) emissions. This study was conducted in 2023-2024, setting up six nitrogen application rates: N0 (0 kg·ha[-1]), N120 (0 kg·ha[-1]), N180 (0 kg·ha[-1]), N240 (0 kg·ha[-1]), N300 (0 kg·ha[-1]), and N360 (0 kg·ha[-1]). Using 16S amplicon sequencing technology and metagenomic sequencing, the study analyzed the abundance of carbon and nitrogen cycling functional genes. Combined with measurements of CH4, N2O, and CO2 emission fluxes, the research elucidated the mechanism by which nitrogen fertilizer regulates microbial modulation of greenhouse gas emissions. The results indicated that nitrogen application significantly increased greenhouse gas (CH4, N2O, CO2) emissions, with the highest emissions observed under the N300 treatment. Nitrogen application regulated soil nutrients, increasing soil total nitrogen, nitrate nitrogen, and microbial biomass carbon content. Reasonable nitrogen application (N240) increased bacterial α-diversity (Shannon index, Chao index, PD index) in the soil by 10.82, 14.65, and 1.92%, respectively, compared to N0. It also increased the abundance of dominant nitrogen-fixing bacterial phyla, including Actinobacteria, Proteobacteria, and Nitrospirota. Furthermore, it regulated the abundance of microbial-mediated functional genes involved in dissimilatory nitrate reduction (nirB), assimilatory nitrate reduction (nasA), denitrification (narG, narH, nirS), nitrification (norC, nxrA, nxrB, hao, amoC), as well as those in the carbon cycle related to methane metabolism (pmoA, pmoC, mttC), carbon fixation (por/nifj, rbcl/cbbl), and hydrogenotrophic methanogenesis (mch, hdrA, frdE). This regulation further modulated greenhouse gas emissions. Therefore, this study clarifies the microbe-associated mechanisms underlying the N fertilizer-driven coupling of C and N cycles with GHG emissions through an integrated analysis of microbial diversity and metagenomics. Furthermore, it offers new insights for sustainable N fertilizer management and emission mitigation strategies in agricultural systems.},
}

@article {pmid42078528,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R and Han, Y},
title = {Identification of novel CRESS-DNA viruses in the human vaginal microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790643},
pmid = {42078528},
issn = {1664-302X},
abstract = {INTRODUCTION: Circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses are widely distributed across diverse hosts and environments, yet their diversity within the human vaginal virome remains poorly characterized. This study aimed to investigate the presence, diversity, and evolutionary relationships of CRESS-DNA viruses in the human vaginal niche.

METHODS: Viral metagenomic sequencing was performed on 24 pooled vaginal swab libraries derived from women with and without vaginitis. After host sequence removal and quality control, de novo assembly and viral identification were conducted. Candidate viral genomes were curated based on genomic features, followed by functional annotation, phylogenetic analysis using Rep protein sequences, and genome-wide pairwise nucleotide identity comparisons.

RESULTS: A total of five CRESS-DNA viral genomes were identified, including four complete and one nearly complete circular genomes. All genomes exhibited canonical architectures, encoding Rep and Cap proteins and containing conserved HUH endonuclease and superfamily 3 helicase motifs. Phylogenetic analysis placed these viruses within the orders Rohanvirales, Ringavirales, Cirlivirales, and Cremevirales, representing multiple distinct evolutionary lineages. Genome-wide pairwise identity analysis showed that all identified viruses fell below established species- and genus-level thresholds, indicating that they represent novel taxa. Comparative analyses further revealed substantial divergence from known environmental and vertebrate-associated viruses.

DISCUSSION: These findings expand the known diversity of CRESS-DNA viruses in the human vaginal virome and highlight their broad evolutionary diversity. The detected viruses likely represent diverse ecological origins rather than stable host-specific infections, and no clear association with vaginitis was observed. This study provides new insights into the evolutionary landscape of CRESS-DNA viruses in the human reproductive tract and underscores the need for further investigation into their biological roles and potential health implications.},
}

@article {pmid42078532,
year = {2026},
author = {Padmanabhan, C and Puig, A},
title = {Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844864},
pmid = {42078532},
issn = {1664-302X},
}

@article {pmid42078537,
year = {2026},
author = {Shen, T and Zhou, Y and Gao, J and Xiong, X and Chen, C},
title = {Gut microbiota regulates growth retardation in pigs through their metabolites of taurine and butyric acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811659},
pmid = {42078537},
issn = {1664-302X},
abstract = {Growth retardation of piglets has always been observed in current pig production system. Here we defined these pigs as stunted pigs. Stunted pigs show normal feed intake, but exhibit extremely slow growth speed. This brings a big economic loss to pig industry. Many factors can lead to growth retardation, including gut microbiota which has been reported to play important roles in growth retardation of children. However, whether and which gut microbial taxa are associated with growth retardation of piglets are largely unknown. Here we used 16S rRNA gene and shotgun metagenomic sequencing to identify bacterial taxa associated with growth retardation in 126 pigs including stunted pigs and their pairwise littermates showing normal growth. We identified several Clostridium spp. significantly enriched in the gut of normal growing pigs, including Clostridium symbiosum which was the key biomarker distinguishing stunted pigs and normal growing pigs, while several Bacteroides spp. had higher abundances in stunted pigs. Clostridium spp. was significantly associated with the shifts of functional capacities of the gut microbiome between normal and stunted pigs, e.g., biosynthesis of unsaturated fatty acids. Untargeted serum metabolome analysis found that normal growing pigs had higher concentration of taurine in serum. Increased concentration of serum taurine was associated with increased abundance of Clostridium symbiosum. Furthermore, all metabolites having higher abundances in normal growing pigs were enriched in the pathway of taurine and hypotaurine metabolism. Short-chain fatty acids (SCFAs) analysis identified butyric acid having higher concentration in feces of normal growing pigs in both discovery and validation cohorts, and the changes in the abundances of Clostridium symbiosum was correlated with the shifts of the concentrations of fecal SCFAs. These results suggested that Clostridium spp., especially Clostridium symbiosum improved pig growth by increasing the concentrations of serum taurine and fecal butyric acid, and was an important biomarker associated with pig growth. This study provided important insights into the effect of the gut microbiome on pig growth retardation.},
}

@article {pmid42078542,
year = {2026},
author = {Mao, Y and Lv, Q and Chen, S and Wang, L and Li, K and Xie, Z and Yin, F and Xu, L and Wang, Q and Zhao, C},
title = {Case Report: An imported severe case of paediatric scrub typhus with Karp B subgenotype in non-endemic Northern China, Beijing.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1733143},
pmid = {42078542},
issn = {2296-2360},
abstract = {Scrub typhus, a zoonosis caused by Orientia tsutsugamushi (O. tsutsugamushi), remains a significant public health threat in the Asia-Pacific region. This disease is transmitted through the bite of infected trombiculid mite larvae (chiggers) and typically manifests as acute undifferentiated fever during the early stage. Despite the availability of targeted antibiotic therapies, delayed diagnosis frequently leads to severe complications and fatal outcomes. Here, we report a severe imported paediatric case in Beijing, a city in China's temperate zone, involving a 12-year-old girl with a recent travel history to Yunnan Province. The patient presented with fever, characteristic eschar, regional lymphadenopathy, and septic shock, ultimately progressing to multiorgan dysfunction syndrome. Whole-genome metagenomic next-generation sequencing (mNGS) of blood, cerebrospinal fluid (CSF), and sputum samples revealed O. tsutsugamushi with high sequence read counts, whereas blood cultures remained negative for other bacterial pathogens. Subsequent PCR amplification and Sanger sequencing confirmed the mNGS findings. Phylogenetic analysis of the TSA56 gene classified the strain within the Karp cluster. Serological analysis revealed the presence of O. tsutsugamushi-specific IgM and IgG antibodies. This severe paediatric case highlights the importance of considering travel-associated scrub typhus in the differential diagnosis of febrile illnesses in non-endemic regions. This is particularly relevant for patients with a history of insect bites in areas known to be endemic for O. tsutsugamushi.},
}

@article {pmid42079098,
year = {2026},
author = {Wucher, BR and Pardo-De la Hoz, CJ and Stamper, I and Sharma, S and Kaune, D and Bendale, P and Peled, J and Xavier, JB},
title = {Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.716137},
pmid = {42079098},
issn = {2692-8205},
abstract = {The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa , typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides- a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis . Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patient's microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.},
}

@article {pmid42079121,
year = {2026},
author = {Qian, K and Abhyankar, V and Keo, D and Zarceno, P and Toy, T and Eskin, E and Arboleda, VA},
title = {Systematic evaluation of 24 extraction and library preparation combinations for metagenomic sequencing of SARS-CoV-2 in saliva.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.719115},
pmid = {42079121},
issn = {2692-8205},
abstract = {UNLABELLED: Sequencing the respiratory tract transcriptome has the potential to provide insights into infectious pathogens and the host's immune response. While DNA-based sequencing is more standard in clinical laboratories due to its stability, RNA assays offer unique advantages. RNA reflects dynamic physiological changes, and for RNA viruses, viral RNA particles directly represent copies of the viral genome, enabling greater diagnostic sensitivity. However, RNA's susceptibility to degradation remains a significant challenge, particularly in RNase-rich specimens like saliva. To address this, we conducted a systematic, combinatorial evaluation of 24 distinct mNGS workflows, crossing eight nucleic acid extraction methods with three RNA-Seq library preparation protocols. Remnant saliva samples (n = 6) were pooled and spiked with MS2 phage as a control. The SARS-CoV-2 virus was spiked into half of the samples, which were extracted using the eight different extraction methods (n = 3) and compared using RNA Integrity Number equivalent (RINe) scores and RNA concentration. The extracted RNA was then processed across the three library construction methods and subjected to short-read sequencing to assess all 24 combinations head-to-head. We compared methods based on viral read recovery and found that RINe and concentration did not correlate with viral detection. The Zymo Quick-RNA Magbead kit and the Tecan Revelo RNA-Seq High-Sensitivity RNA library kit were the extraction and library-preparation kits that yielded the most SARS-CoV-2 reads, respectively. Importantly, our combinatorial analysis revealed that any small variability attributable to different nucleic acid extraction methods was heavily overshadowed by differences in quality attributable to the RNA-Seq library preparation methods. These findings challenge the reliance on conventional RNA quality metrics for clinical metagenomics and underscore the need to redefine extraction quality standards for mNGS applications.

IMPORTANCE: mNGS is a powerful and unbiased approach towards pathogen detection that has mostly been applied to blood and cerebrospinal fluid samples. However mNGS has recently been applied to more areas including the respiratory pathogen detection space, with potential applications in both in-patient diagnostics and public health surveillance. Saliva samples are an ideal sample type for these use cases since they can be collected non-invasively. However, saliva is also a challenging sample type due to its high RNase activity and often yields low-quality nucleic acid. This study explores the feasibility of using saliva specimens in mNGS with contrived SARS-CoV-2 samples to optimize the combination of two factors: nucleic acid extraction and RNA-seq library preparation. Exploration in this area could enhance the sensitivity of saliva-based mNGS assays, with the goal of future expansion of this specimen type in clinical diagnostics and public health surveillance.

KEY POINTS: The choice of RNA-Seq library preparation kit has a greater impact on pathogen detection than the nucleic acid extraction method.The combination of Zymo Quick-RNA Magbead extraction kit and TECAN Revelo RNA-Seq High Sensitivity RNA library kit recovered the highest percentage of total SARS-CoV-2 reads.RNA quantity and RINe score do not correlate with viral read capture, indicating a need for an alternative metric to assess RNA quality for downstream mNGS clinical diagnostics.},
}

@article {pmid42079283,
year = {2026},
author = {Brenner, E and Vang, C and Johnson, C and Ravi, J},
title = {Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.13.678797},
pmid = {42079283},
issn = {2692-8205},
abstract = {UNLABELLED: Prochlorococcus species are the most abundant marine photosynthetic bacteria. Despite broadly shared phenotypic traits and marine habitats, they exhibit remarkable genomic diversity. We ask what genomic signatures underlie its ecotypic divergence into high- and low-light adapted lineages, and whether these signatures can still be recovered from incomplete assemblies. From ∼1,000 publicly available Prochlorococcus genomes, we focused on those with information on their light adaptation ecotype (high-light/low-light), phylogenetic clades, and depth of isolation. Across these divisions, we calculated average nucleotide identity and constructed pangenomes to assess cyanobacterial core genes vs. those that separate ecotypes. Despite scant conservation, we observe a sharp taxon separation by light ecotypes. Classical machine learning models trained to predict ecotype achieve near-perfect binary classification accuracy even when predicting on partial genomes (Matthews Correlation Coefficient = 0.86 - 1.00), while regression models trained to predict the depth of isolation performed poorly, with high root mean square error values (37.6 - 42.0m). For ecotype prediction, we analyzed top gene features across model runs and classes; these features included photosynthesis-associated genes and pathways, as well as many novel markers of unknown function. When separating ecotypes further by previously described phylogenetic clades, genomic content and composition show even clearer separation among clades, supporting the taxonomic breadth of the Prochlorococcus collective. These results emphasize the genomic specialization underlying ecotypic divergence and support the utility of ML approaches for cyanobacterial ecotype prediction from metagenomic data. Expanded sampling will yield novel clade-specific biology. All data, models, and results are available on GitHub: https://github.com/JRaviLab/cyano_adaptation .

IMPORTANCE: Prochlorococcus are common aquatic cyanobacteria that can derive energy from light. They can be classified into high-/low-light ecotypes depending on how they use light. Prochlorococcus have small genomes compared to other bacteria, but the gene sets they carry are also remarkably flexible, which may help them survive and adapt to their harsh oceanic environment. We studied hundreds of Prochlorococcus genomes from around the world in an effort to predict ecotypes from partial genome sequences. We used comparative genomics, machine learning, and other statistical methods to identify genomic features associated with ecotypes. These statistical approaches predicted ecotypes accurately, reliably, and according to large differences in gene content and genome structure. Our results support that Prochlorococcus can be divided into different species or genera based on clades, and provide many gene targets for further research to understand cyanobacterial circadian rhythms or improve their bioengineering potential as chassis organisms.},
}

@article {pmid42079297,
year = {2026},
author = {Cornman-Homonoff, J and Rajendran, KM and Kolandaivelu, S and Coon, SD and Kupec, JT and Wang, L and Hu, G and Jala, VR and Sandle, GI and Rajendran, VM},
title = {Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.20.719706},
pmid = {42079297},
issn = {2692-8205},
abstract = {Diet is a major determinant of gut microbiome structure and function, yet the role of dietary electrolytes-particularly sodium-remains poorly defined. Here, we identify dietary sodium availability as a key regulator of gut microbial fermentation and host energy harvest. Using a controlled sodium-sufficient versus sodium-deprived dietary intervention in rats, we integrated shotgun metagenomic sequencing, functional pathway analysis, targeted short-chain fatty acid (SCFA) quantification, and host physiological phenotyping. Sodium deprivation induced a coordinated restructuring of the gut microbiome, characterized by depletion of classical saccharolytic Firmicutes, including multiple Lactobacillus species, and enrichment of stress-tolerant, metabolically flexible taxa. Functional profiling revealed a shift away from growth-associated metabolic programs toward stress-adaptive and nutrient-scavenging pathways. Consistent with these changes, fecal concentrations of key SCFAs-including acetate, butyrate, hexanoate, and valerate-were significantly reduced, indicating impaired microbial fermentative capacity. These microbiome-level alterations translated into measurable host phenotypes, including reduced cecal mass and attenuated weight gain, consistent with decreased microbial energy harvest. Together, these findings establish a functional link between luminal sodium availability, microbial metabolic efficiency, and host energy balance, extending the framework of diet-microbiome interactions beyond macronutrients to include dietary electrolytes. This work identifies sodium as a previously underappreciated ecological constraint shaping gut microbial metabolism and suggests that modulation of dietary sodium intake may influence host metabolic outcomes through microbiome-mediated mechanisms.},
}

@article {pmid42079427,
year = {2026},
author = {Xolalpa-Aroche, A and Contreras-Peruyero, H and Delgado-Suárez, EJ and Hernández-Mena, DI and Moguel-Chin, WI and Rivero-Cruz, JF and Velarde, RA and Ortiz-Vázquez, E and Rivero-Cruz, BE and Lovaco-Flores, JA and Rodríguez Orduña, L and Licona-Cassani, C and Barona-Gómez, F and Sélem-Mojica, N},
title = {Genome-resolved metagenomics reveals a phylogenetically cohesive Acetilactobacillus-like species complex dominating stingless bee pot honey.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag063},
pmid = {42079427},
issn = {2730-6151},
abstract = {Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing [Formula: see text]81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI [Formula: see text], interclade ANI [Formula: see text]), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.},
}

@article {pmid42079429,
year = {2026},
author = {Christensen, R and Wang, YHD and Arnoldini, M and Cremer, J},
title = {Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag075},
pmid = {42079429},
issn = {2730-6151},
abstract = {Fermentation products released by bacteria in the large intestine, such as butyrate and propionate, play central roles in host physiology and health. While the metabolic pathways producing these short-chain fatty acids (SCFAs) are well-characterized, less is known about their relative prevalence across hosts and gut conditions. Here, we introduce a genome-resolved, abundance-weighted bioinformatics framework that integrates pathway-based gene identification with extensive literature validation to systematically quantify the potential for butyrate and propionate production across bacterial species and human gut microbiomes. By comparing pathway predictions against over 700 experimentally characterized strains, we demonstrate high concordance with reported metabolic phenotypes, validating our approach beyond prior purely computational studies. Weighted by species abundance across ~18 000 metagenomic samples, we find that dominant gut taxa disproportionately drive SCFA production, with butyrate pathways enriched in Bacillota and propionate pathways in Bacteroidota. This abundance-weighted analysis reveals that pathway presence is well conserved at the family level, highlighting the ecological relevance of dominant taxa for community-level fermentation potential. Our results further show pronounced inter-individual variation and associations with age, birthing method, and inflammatory bowel disease, emphasizing how shifts in microbiota composition influence SCFA availability. By combining pathway-level resolution, abundance-weighted inference, and literature-based validation, our framework provides a robust, scalable approach to link microbial functional potential with host-relevant outcomes.},
}

@article {pmid42079433,
year = {2026},
author = {Batilong, LS and Traifalgar, RFM and Del Castillo, CS and Jore, KAG and Fantonalgo, IRL and Huervana, FH and Javellana, TF and Pagapulan, MJBB and Failaman, AN and Gayosa, VED},
title = {Gut-Derived Lactic Acid Bacteria, Pediococcus pentosaceus, Enhances Growth Performance and Resistance to Pathogenic Vibrio harveyi of Hatchery-Bred Milkfish (Chanos chanos) in Nursery Culture.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {6489487},
pmid = {42079433},
issn = {1687-918X},
abstract = {Hatchery-bred milkfish (Chanos chanos) fry continue to face stocking challenges due to inferior growth performance and reduced resilience compared with wild-caught fry. Recent metagenomic studies have shown that wild fry harbor a higher relative abundance of bacterial taxa belonging to the phylum Bacillota. These include lactic acid bacteria (LAB), which are widely recognized for their probiotic potential in aquaculture. Building on this metagenomic insight, the present study adopted a targeted approach to isolate LAB with anti-Vibrio activity and evaluate its probiotic potential in hatchery-bred C. chanos nursery culture. Screening identified Pediococcus pentosaceus HLAB22 as a promising LAB candidate, which was subsequently assessed through in vivo probiotic trials. Probiotic supplementation significantly improved growth performance, survival, and reduced the incidence of opercular deformities in early juveniles. The most pronounced effects observed at 10[6] CFU, followed by 10[3] CFU g[-1] feed compared with the control group. Gut colonization experiment demonstrated that dietary supplementation with P. pentosaceus HLAB22 at 10[6] CFU g[-1] feed enabled intestinal colonization within 12 days. This also resulted in near-complete suppression of Vibrio populations, supporting the significant decrease in water and C. chanos gut Vibrio load during the feeding trial. Furthermore, during immersion challenge with pathogenic V. harveyi, the in vitro anti-Vibrio activity of P. pentosaceus HLAB22 was translated into enhanced in vivo protection, yielding a survival rate of 83.33% in treated fish compared with 33.33% in the control group. Collectively, these findings indicate that oral application of P. pentosaceus HLAB22 at 10[6] CFU g[-1] feed is an effective strategy for promoting growth and enhancing resilience in C. chanos nursery culture. This study supports the use of targeted, host-associated probiotics to improve the performance of hatchery-bred milkfish fry and mitigate key challenges in nursery production systems.},
}

@article {pmid42079444,
year = {2026},
author = {Fang, T and Yuan, F and Chen, Y and Li, N and Zhang, Y and Liu, H and Liu, X and Miao, Q and Hu, B},
title = {Emerging role of metagenomic next-generation sequencing in infectious disease diagnostics: Clinical integration and future directions.},
journal = {mLife},
volume = {5},
number = {2},
pages = {148-163},
pmid = {42079444},
issn = {2770-100X},
abstract = {Infectious disease diagnostics has been transformed by metagenomic next-generation sequencing (mNGS), an unbiased approach that detects bacteria, viruses, fungi, and parasites in a single assay. By sequencing all nucleic acids in a sample, mNGS overcomes the narrow detection scope and slow turnaround of conventional tests, substantially improving pathogen detection. In conditions such as meningitis/encephalitis, sepsis, and pneumonia, mNGS frequently identifies etiologies missed by routine diagnostic tests, thereby facilitating earlier pathogen-directed therapy and, in selected settings, improving clinical management and outcomes. This approach is particularly valuable for immunocompromised, pediatric, and intensive care unit (ICU) patients with atypical infections. Currently, clinical mNGS workflows primarily rely on short-read sequencing platforms (e.g., Illumina), whereas long-read platforms (e.g., Nanopore, PacBio) offer advantages for rapid or high-resolution applications. Optimized bioinformatics and stringent quality control are essential for reliable results. Beyond clinical diagnostics, mNGS provides valuable genetic data on antimicrobial resistance (AMR) and pathogen phylogeny, supporting public health and outbreak surveillance (e.g., wastewater monitoring and variant tracking). Current challenges include distinguishing colonization from infection, interpreting sequencing data quantitatively, and reducing cost and turnaround time. Looking ahead, emerging strategies such as targeted panels, rapid automated workflows, and host‑response integration are expected to further shorten time‑to‑result and improve diagnostic specificity. Parallel progress in ethical and regulatory frameworks remains essential to ensure responsible implementation. To support clinical adoption, a standardized framework for clinical interpretation of mNGS results, together with associated training, has been developed and implemented. Overall, mNGS is likely to become an increasingly important component of infectious disease diagnostics, with ongoing innovations expected to broaden its clinical and epidemiological impact.},
}

@article {pmid42079557,
year = {2026},
author = {Kujala, K and Kinnunen, V},
title = {Lactic acid bacteria dominate urban Bokashi: a participatory, culture-independent pilot study of microbial diversity and functional potential in household-scale food waste fermentation.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag018},
pmid = {42079557},
issn = {2633-6685},
abstract = {In recent years, concerns over declining biodiversity in urban spaces have increased. Urban Bokashi composting (i.e. microaerobic or anaerobic fermentation of food waste indoors) has been suggested as a possibility to promote microbial diversity in the domestic environment. However, studies on microbial communities in household-scale Bokashi and their potential impacts on health and environment are lacking. Thus, the present pilot study investigated microbial communities in different stages of the Bokashi composting process in collaboration with six Bokashi practitioners by looking into physicochemical characteristics as well as microbial community composition (16S amplicon sequencing, 34 samples) and functional potential (shotgun metagenome sequencing, 11 samples). The collective results indicate that i) microbial communities in Bokashi compost differed between stages, but also between households, ii) microbial communities were dominated by lactic acid bacteria like Lentilactobacillus or Lacticaseibacillus, iii) metabolic pathways for the production of diverse organic acids were detected, iv) application of Bokashi ferment or leachate to soil can supply nutrients and organic acids to promote plant growth but does not substantially affect soil microbial community composition, and v) potentially pathogenic organisms were detected in extremely low abundances. Thus, urban Bokashi is likely not associated with increased health risks and positive impacts are feasible.},
}

@article {pmid42079638,
year = {2026},
author = {Han, X and Zang, D and Lin, M and Yin, Y and Liu, D and Sun, Q and Chen, J},
title = {Dynamic changes in gut microbiota and metabolites in advanced lung cancer patients with immune-related adverse events.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1731931},
pmid = {42079638},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lung Neoplasms/drug therapy/immunology/metabolism ; Aged ; *Immune Checkpoint Inhibitors/adverse effects ; *Metabolome ; Metabolomics/methods ; *Drug-Related Side Effects and Adverse Reactions/metabolism/etiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Immune-related adverse events (irAEs) represent an urgent clinical challenge. Although accumulating evidence suggests that irAEs are associated with the gut microbiota and its metabolites, our understanding of the dynamic alterations in the gut microbiota and related metabolic profiles throughout the onset and progression of irAEs remains limited.

METHODS: A total of 48 fecal samples were collected from 32 lung cancer patients treated with immune checkpoint inhibitors, including 16 patients who developed irAEs and 16 who did not. Fecal samples were collected at baseline and, in patients with irAEs, at the time of irAEs onset. Metagenomic sequencing and untargeted metabolomics analyses were performed to identify baseline differences in gut microbiota and metabolites, characterize longitudinal dynamic changes in gut microbiota and metabolite profiles in patients with irAEs, and construct a machine learning based random forest model to predict the occurrence of irAEs.

RESULTS: There were baseline differences in microbial communities and metabolites between the two groups. In the non-irAEs group, Phocaeicola coprocola was enriched and Micrococales decreased. At baseline, viomycin was positively correlated with irAEs, while metabolites such as calcitriol and L-isoleucine were negatively correlated with irAEs. The roles of valine, leucine and isoleucine metabolism and vitamin B6 metabolism pathways were downregulated in the irAEs group. Compared to baseline, there were significant changes in gut microbiota and metabolites during the onset of irAEs, and the abundance of Veillonella increased during irAEs onset. Dynamic monitoring of metabolic changes in irAEs revealed decreased levels of trypsin butylester, BQ 123, DL-o-tyrosine, and nicotinamide-beta-riboside during irAEs attacks. Lysine degradation, arachidonic acid metabolism, folate biosynthesis, nicotinate and nicotinamide metabolism, and C5-branched dibasic acid metabolism were downregulated during the progression of irAEs. A model for predicting the occurrence of irAEs based on differential microbiota and metabolites was constructed, and after robust validation, the model showed good performance and excellent discriminative power.

CONCLUSIONS: The occurrence and development of irAEs are associated with the composition of the gut microbiota and metabolites, as well as their dynamic changes over time. These findings highlight the potential of gut microbiota and metabolites as biomarkers for predicting the occurrence and progression of irAEs.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
Male
Female
Middle Aged
*Lung Neoplasms/drug therapy/immunology/metabolism
Aged
*Immune Checkpoint Inhibitors/adverse effects
*Metabolome
Metabolomics/methods
*Drug-Related Side Effects and Adverse Reactions/metabolism/etiology
Feces/microbiology

@article {pmid42080299,
year = {2026},
author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J},
title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.},
journal = {Molecular ecology},
volume = {35},
number = {9},
pages = {e70367},
doi = {10.1111/mec.70367},
pmid = {42080299},
issn = {1365-294X},
support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; },
mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; },
abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.},
}

*Lakes/virology/microbiology
*Viruses/genetics/classification
Metagenomics
Fresh Water/virology
Microbiota/genetics
Ecosystem
Geologic Sediments/virology
Biodiversity
Metagenome

@article {pmid42080548,
year = {2026},
author = {Zhang, X and Zhong, A and Liu, Y and Zou, J and Gu, M and Zhu, X and Xu, H and Yin, S},
title = {Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016326},
doi = {10.1128/msystems.00163-26},
pmid = {42080548},
issn = {2379-5077},
abstract = {Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of Bacteroides uniformis, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with Bacteroides uniformis abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of Bacteroides uniformis and elevation of deoxycholic acid were linked to CIH-induced hepatic phenotypes and were sensitive to antibiotic intervention, supporting a contributory role of gut microbiota-bile acid interactions in this process. Together, these findings underscore the potential importance of gut microbiota-host metabolic crosstalk in OSA-associated hepatic steatosis and suggest that microbiota- or bile acid-targeted strategies may warrant further investigation as adjunctive approaches for risk stratification and therapeutic intervention in OSA-related liver disease.},
}

@article {pmid42080847,
year = {2026},
author = {Terzi, I and Akinosoglou, K},
title = {More Detection, Better Decisions? Rethinking Pathogen-Driven Therapy in Diabetic Foot Infections.},
journal = {The international journal of lower extremity wounds},
volume = {},
number = {},
pages = {15347346261447707},
doi = {10.1177/15347346261447707},
pmid = {42080847},
issn = {1552-6941},
abstract = {Pathogen-driven therapy is central to the management of diabetic foot infections (DFIs), where antimicrobial selection relies on microbiological identification. Over the past decade, diagnostic capabilities have expanded from conventional cultures to high-resolution molecular sequencing, substantially increasing pathogen detection. Whether this expansion translates into better therapeutic decisions, however, remains uncertain. This narrative review examines the roles and limitations of culture-based methods, antimicrobial susceptibility testing, targeted polymerase chain reaction panels, 16S rRNA gene sequencing, and shotgun metagenomics in DFIs. Culture remains the cornerstone of pathogen-directed therapy because it identifies viable organisms and provides phenotypic susceptibility data that inform antibiotic selection and de-escalation. Molecular techniques broaden detection and reveal polymicrobial complexity and resistance genes, yet increased analytical sensitivity does not consistently clarify pathogen prioritization, distinguish colonization from infection, or improve patient-centered outcomes. Intensified diagnostic strategies often lead to antimicrobial modification without clear gains in healing or cost-effectiveness. These findings underscore a persistent interpretative gap: detection capacity has advanced more rapidly than frameworks linking microbiological data to meaningful therapeutic action. Microbiology is indispensable but insufficient in isolation. Improved outcomes will depend less on detecting additional organisms and more on integrating microbiological findings with surgical management, vascular status, and multidisciplinary care.},
}

@article {pmid42081091,
year = {2026},
author = {Gui, C and Li, J and Wang, Q and Chen, L and Shao, Q},
title = {Robot-Assisted Incision and Drainage for a Polymicrobial Brain Abscess.},
journal = {The Journal of craniofacial surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/SCS.0000000000012848},
pmid = {42081091},
issn = {1536-3732},
abstract = {OBJECTIVE: To evaluate the clinical utility of robot-assisted incision and drainage in the management of a polymicrobial brain abscess located in the central region.

METHODS: We retrospectively analyzed a case of polymicrobial odontogenic brain abscess in a 71-year-old male who presented with stroke-like symptoms. The patient was admitted due to progressive right-sided weakness, initially mimicking an acute ischemic stroke. Gadolinium-enhanced T1-weighted magnetic resonance imaging (MRI) revealed ring-enhancing lesions in the left precentral gyrus and the right temporal lobe, with corresponding high signal on diffusion-weighted imaging (DWI), highly suggestive of a brain abscess. Following empirical antibiotic therapy (vancomycin and meropenem), the patient clinically deteriorated, and a repeat MRI demonstrated enlargement of the left central abscess. During the Remebot robotic navigation, the abscess was incised and drained, yielding thick, yellowish-white purulent material. Postoperative metagenomic next-generation sequencing (mNGS) of the pus identified a polymicrobial infection comprising Fusobacterium nucleatum, Streptococcus constellatus, Parvimonas micra, and Porphyromonas gingivalis.

RESULTS: Based on the microbiological findings, the antibiotic regimen was tailored to a triple combination of vancomycin, meropenem, and metronidazole for 2 weeks, followed by vancomycin plus meropenem for an additional 4 weeks, complemented by rehabilitation and hyperbaric oxygen therapy. The patient demonstrated remarkable neurological recovery. One month post-surgery, right limb muscle strength had returned to grade 5, with only mild residual impairment in fine-motor coordination of the right hand. Three-month follow-up MRI revealed complete resolution of the previously observed intracranial ring-enhancing lesions.

CONCLUSION: For eloquent-area brain abscesses that progress despite medical management, robot-assisted incision and drainage offers a safe, precise, and efficacious minimally invasive surgical option. Integration of mNGS technology for pathogen identification enables targeted antimicrobial therapy, a pivotal step toward achieving favorable outcomes in complex infections.},
}

@article {pmid42081443,
year = {2026},
author = {Reddy, SP and Morgenroth-Rebin, J and Wang, S and Wilson, MR},
title = {Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {230},
pages = {},
doi = {10.3791/70075},
pmid = {42081443},
issn = {1940-087X},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/cerebrospinal fluid/microbiology ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for unbiased pathogen detection and host transcriptional profiling in clinical and research settings. While its utility in diagnosing central nervous system (CNS) infections is increasingly recognized, cerebrospinal fluid (CSF) samples pose unique challenges due to low nucleic acid abundance and susceptibility to degradation. This study presents an optimized research-based protocol for Illumina sequencing platforms tailored to CSF mNGS, spanning sample handling, nucleic acid extraction, library preparation, sequencing, and bioinformatic analysis. Quality control approaches adaptable to both high and low-resource settings are also provided, including alternatives to capillary electrophoresis. This study demonstrates the protocol's robustness through two representative cohorts: a high-depth, NovaSeq-based workflow and a cost-conscious NextSeq-based workflow. Across these cohorts, pathogens were detected in over 50% of cases, underscoring the method's diagnostic potential even with resource-constrained adaptations. This protocol facilitates reproducible CSF mNGS, providing a foundation for diverse applications in neuroinfectious disease research and diagnostics.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Central Nervous System Infections/cerebrospinal fluid/microbiology

@article {pmid42081609,
year = {2026},
author = {Wang, Y and Zhang, B and Shen, C and Cao, M and Wang, N and Chen, T and He, G and Sun, G and Li, C and Li, Y and Yin, X and Sun, Y and Li, C and Zhou, X},
title = {N- Carbamoylglutamate enhances bull spermatogenesis via Paraprevotella-Mediated vitamin B6 biosynthesis in rumen microbiota.},
journal = {Reproduction (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/reprod/xaag049},
pmid = {42081609},
issn = {1741-7899},
abstract = {N-carbamoylglutamate (NCG), a functional analog of the arginine precursor, shows strong potential in enhancing spermatogenesis in bulls. In this study, dietary NCG supplementation significantly increased sperm density and motility in XiangXi yellow bulls, the local beef cattle. Metagenomic and serum metabolomic analyses revealed that NCG altered the composition of rumen microbiota, notably increasing the abundance of Paraprevotella and elevating serum vitamin B6 levels (p < .05), suggesting a possible microbiota-associated metabolic modulation underlying its reproductive benefits. To explore this mechanism, a busulfan-induced mouse model of impaired spermatogenesis was established. Mice received transplants of either rumen microbiota from NCG-treated bulls or the differential genus Paraprevotella. Both treatments alleviated reproductive damage and increased vitamin B6 levels in serum and testis. Mechanistic investigation indicated that Paraprevotella was associated with upregulated expression of 3-phosphoserine aminotransferase (SerC), a key enzyme involved in vitamin B6 biosynthesis. Subsequent vitamin B6 supplementation experiments showed increased testicular glutathione levels and reduced thiobarbituric acid-reactive substances level (TBARS, expressed as MDA equivalents). These experiments supported a contributory role of vitamin B6 in promoting spermatogenesis, including increased sperm count and enhanced expression of spermatogenic cell markers. In summary, this study demonstrated that NCG enhanced spermatogenesis in bulls by reshaping the rumen microbiota, particularly through enrichment of Paraprevotella, which was associated with increased systemic vitamin B6 levels and contributed to reproductive improvement. These findings provide further insights into the application of NCG in improving fertility in ruminants.},
}

@article {pmid42082028,
year = {2026},
author = {Zhang, Q and Hu, Y and Wang, G and Kong, L and Xu, Z and Ma, X and Chen, R},
title = {Deciphering the impact of chlortetracycline on methanogenesis, microbial properties and antibiotic resistance genes in an anaerobic ceramic membrane bioreactor treating swine wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134760},
doi = {10.1016/j.biortech.2026.134760},
pmid = {42082028},
issn = {1873-2976},
abstract = {The presence of chlortetracycline (CTC) in swine wastewater poses a threat to anaerobic treatment and ecological safety. This study investigated the concentration-dependent effects of CTC on methanogenesis, microbial properties, and antibiotic resistance genes in an anaerobic ceramic membrane bioreactor (AnCMBR). Batch assays identified a biological inhibition threshold at 50 mg/L CTC. During long-term operation, CTC at 10 mg/L (after a brief adaptation) increased methane yield by 28%, while 50 mg/L CTC inhibited methanogenesis and reduced COD removal from 97% to 86%. High-level CTC raised antibiotic resistance gene abundance and decreased acute toxicity removal from 68% to 46%. Biodegradation dominated CTC removal, but its contribution declined from 42% to 19% as CTC increased, lowering overall removal from 60% to 30%. Metagenomic analysis revealed that low-level CTC upregulated hydrolysis/fermentation-related genes (e.g., enolase, phosphoglycerate mutase, pyruvate kinase), enhancing substrate supply for methanogenesis. In contrast, high-level CTC markedly enriched Spirochaetes (from 3% to 66%), suppressed key methanogenic genes involved in methyl-CoM reductase and downstream acetyl-CoA metabolism, while preserving acetoclastic pathway genes (acsS1.2, ackA, pta), collectively shifting the pathway toward acetoclastic methanogenesis. Notably, the AnCMBR maintained stable filtration performance, with the transmembrane pressure remaining below 6.5 kPa over 160 days. These findings demonstrate that low CTC levels can be tolerated after acclimation, whereas high CTC stress severely impairs methanogenesis, detoxification, and biosafety.},
}

@article {pmid42082029,
year = {2026},
author = {Hou, Y and Ren, B and Song, J and Li, P and Xue, Z and Zhao, Y and Dzakpasu, M},
title = {Antibiotics removal and nutrient transformation in constructed wetlands using novel aluminum Sludge-Derived Substrates.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134779},
doi = {10.1016/j.biortech.2026.134779},
pmid = {42082029},
issn = {1873-2976},
abstract = {The widespread use and environmental persistence of norfloxacin (NOR) and sulfamerazine (SMR) have raised concerns over their impacts on aquatic systems and biological nutrient removal. Constructed wetlands (CWs) offer a sustainable, low-cost approach for antibiotic abatement, yet the mechanisms by which NOR and SMR influence microbial nutrient transformation in CWs remain unclear. Here, alum sludge was repurposed as a novel substrate (NALS) in vertical flow CWs, providing a dual pathway for valorizing waste while targeting simultaneous antibiotic and nutrient removal. The systems effectively removed both NOR and SMR (70-77%) under environmentally relevant concentrations (3 and 10 mg/L) and maintained robust nutrient elimination, with COD removal of 75-81%, TP > 90%, and peak NH4[+]-N and NO3[-]-N removals of 93% and 88%, respectively. High antibiotic levels inhibited COD and TP removal, whereas low concentrations stimulated TP removal. Notably, elevated NOR impaired NH4[+]-N and TN removal, while SMR showed negligible effects on ammonium dynamics. Metagenomic analysis revealed that both antibiotics distinctly suppressed microbial communities across taxonomic levels and disrupted functional genes related to nitrification, denitrification, and nitrogen fixation. This work demonstrates the efficacy of NALS-based CWs in co-removing antibiotics and nutrients, while offering mechanistic insights into how antibiotic exposure reshapes microbial structure and function-advancing the design of sustainable treatment systems for antibiotic-laden wastewater.},
}

@article {pmid42082030,
year = {2026},
author = {Li, D and Zhao, Z and Li, H},
title = {Achieving nitrogen removal in the integrated upper fixed-biofilm activated sludge reactor without recirculation: Differential protein and metagenomic analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134774},
doi = {10.1016/j.biortech.2026.134774},
pmid = {42082030},
issn = {1873-2976},
abstract = {The Integrated Fixed-film Activated Sludge (IFAS) system emerges as an advanced nitrogen removal technology, particularly effective for treating high-nitrogen wastewater due to its sophisticated configuration. This research introduces an enhanced Integrated Upper Fixed-film Activated Sludge (IUFAS) reactor featuring a two-stage series design. By strategically positioning carrier media in the upper compartment and implementing controlled influent distribution with aeration in the lower section, the system achieves functional compartmentalization within a single reactor without liquid and sludge recirculation. Experimental results under influent conditions of chemical oxygen demand/total nitrogen (C/N) ratio (4-5) and hydraulic retention time (10 h) confirmed effective nitrogen removal, evidenced by effluent total nitrogen consistently below 7 mg N/L and removal efficiency exceeding 87%. Notably, the optimized IUFAS configuration achieved functional zoning by establishing a pronounced dissolved oxygen gradient between the upper (0.1 ∼ 0.7 mg/L) and bottom compartments (0.3 ∼ 3.6 mg/L). This oxygen stratification facilitated distinct nitrogen removal pathways, including stable anaerobic ammonium oxidation (Anammox) as evidenced by successful Candidatus Brocadia enrichment in the secondary reactor's upper zone. Microbial analysis further indicated potential modulation of electron flow by sulfate-reducing bacteria and sulfur-driven denitrifying bacteria, whose synergistic activity optimized electron transfer pathways and enhanced denitrification efficiency. Additionally, microalgae reduced aeration demand, lowering energy consumption. These findings propose novel strategies for optimizing carbon source allocation in nitrogen removal processes, supporting the development of energy-efficient wastewater treatment systems.},
}

@article {pmid42082383,
year = {2026},
author = {Asthana, S and Bhat, AD and Mahadevan, G and Kothegala, L and Negi, S and Yadav, S and Sudhakaran, A and Roy, A and Makwana, M and Patel, R and Rao B, H and George, CE and Gayen, S and Shukla, S and Jhunjhunwala, S and Sen, P and Kaur, P and Bhat, R and Saini, DK and , and , },
title = {The BHARAT study: a multi-modal, multi-omics investigation of aging signatures in the Indian population.},
journal = {Aging},
volume = {18},
number = {1},
pages = {380-396},
doi = {10.18632/aging.206373},
pmid = {42082383},
issn = {1945-4589},
mesh = {Humans ; India ; Male ; *Aging/genetics/metabolism ; Cross-Sectional Studies ; Female ; Middle Aged ; Aged ; Adult ; Biomarkers ; Adolescent ; Young Adult ; Metabolomics ; Proteomics ; *Healthy Aging ; Life Style ; Multiomics ; },
abstract = {India is undergoing a rapid demographic transition, with its elderly population projected to exceed 347 million by 2050. Although aging is the primary risk factor for multiple chronic diseases, most biological age (BA) models have been developed for Western populations, with limited applicability to Indian demographics. The BHARAT study (Biomarkers of Healthy Aging, Resilience, Adversity, and Transitions) aims to develop and validate composite signatures of aging in the Indian population by integrating multi-omics, biochemical, clinical, and lifestyle data. The BHARAT study is a multi-center, cross-sectional observational study designed using a hub-and-spoke model, with the Indian Institute of Science (IISc) serving as the central hub for omics analyses, biobanking, and data integration. Participants are stratified into five age groups (18-29, 30-44, 45-59, 60-74, ≥75 years) with balanced rural-urban and gender representation. The study primarily includes healthy participants, excluding those with chronic diseases that are not resolved by medication. Data collection encompasses comprehensive clinical and cognitive assessments, lifestyle and quality-of-life questionnaires, and biological sampling (including blood, urine, stool, cheek swabs, and hair). Multi-omics profiling spans epigenomics, proteomics, metabolomics, lipidomics, metagenomics, and immune phenotyping, integrating untargeted discovery-based Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) with targeted assays under harmonized protocols and quality-controlled biobanking standards. As the first large-scale, discovery-driven aging cohort in India, BHARAT will generate population-specific reference datasets, (re)train and calibrate biological clocks, develop a data-driven framework for organ-specific clocks, and identify biomarkers of physiological resilience and decline. Given that presently this study is cross-sectional in design, it will help establish a scalable framework for subsequent longitudinal and translational research to develop context-specific diagnostics, predictive models, and therapeutic targets for healthy aging in India.},
}

Humans
India
Male
*Aging/genetics/metabolism
Cross-Sectional Studies
Female
Middle Aged
Aged
Adult
Biomarkers
Adolescent
Young Adult
Metabolomics
Proteomics
*Healthy Aging
Life Style
Multiomics

@article {pmid42082531,
year = {2026},
author = {An, K and Wang, D and Qu, Y and Yu, H and Liang, H and Mao, Z and Xue, Z and Li, J},
title = {Branched-chain amino acids ameliorate CD4[+] T-cell-associated gut immune inflammation in Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01375-y},
pmid = {42082531},
issn = {2373-8057},
support = {81901303//National Natural Scientific Foundation of China/ ; 82471273//National Natural Scientific Foundation of China/ ; 82301621//National Natural Scientific Foundation of China/ ; },
abstract = {Previous studies have shown that alterations in the gut microbiota and its derived metabolites, branched-chain amino acids (BCAAs), are correlated with T-cell-associated immune imbalance and Parkinson's disease (PD). However, the associations among BCAAs, gastrointestinal dysfunction and T-cell-related gut inflammation remain unclear. This study showed that the constipation symptoms in the PD mice persisted after chronic MPTP treatment. An imbalance in the CD4[+] T-cell subtypes was observed in the colonic lamina propria (cLP), mesenteric lymph nodes (mLNs), and spleen. Metagenomic and metabolomic analyses showed that microbial dysbiosis promoted BCAA degradation rather than biosynthesis, and reduced BCAA levels were confirmed in the serum. BCAA supplementation alleviated constipation symptoms and increased Th1 and Th17 cell infiltration in the cLP, mLNs and spleen were significantly attenuated after BCAA treatment. This study highlights the therapeutic value of BCAAs in mitigating gut immune inflammation-associated constipation symptoms in PD.},
}

@article {pmid42082533,
year = {2026},
author = {Tamang, S and Sherpa, MT and Najar, IN and Kumar, S and Das, S and Sharma, P and Das, N and Chowdhury, R and Thousen, R and Ranjan, RK and Pandey, P and Thakur, N},
title = {Metagenomic analysis of bacterial diversity, antibiotic resistance, and functional profiles in the ice core samples from two glaciers of Sikkim Himalaya.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40915-7},
pmid = {42082533},
issn = {2045-2322},
support = {BT/PR41644/NER/95/1718/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR41644/NER/95/1718/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Glaciers cover a substantial portion of the world and are home to various biological populations. The Himalayas constitute the largest glaciated region outside the poles; hence, they are regarded as "The Third Pole" of the World. There are around 84 glaciers in the Teesta basin (Sikkim Himalaya). There is substantially less data available on the microbial diversity embedded in the glacial ice core samples of the Sikkim Himalaya, as well as their physico-chemistry and potential geomorphological hazards related to their retreat or decrease in snow-line cover. The present study aims to evaluate the microbial diversity in the glacier ice core region and the study area; therefore, two glaciers in the Sikkim Himalaya were chosen: Frey-Peak and Rathong Glacier. The bacterial diversity analysis reveals the prevalence of various phyla, including Pseudomonadota, Actinomycetota, Bacillota, and Bacteroidota. The random forest model reveals the significant contributions of various elements, including Na, Mg, K, Ca, and Zn, to the alpha diversity of the studied glaciers. Among physicochemical parameters, pH was found to contribute the most in shaping bacterial diversity. Cluster of Orthologous Groups (COG) analysis underscored a predominance of genes associated with amino acids (23.5%), carbohydrates (18.93%), lipids (10.88%), energy (17.26%), coenzymes (9.38%), and ion transport/metabolism (14.71%). KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology (KO) analysis revealed the presence of 4,915 to 96,954 genes. Interestingly, the metagenomic analysis revealed the presence of specific species of Bradyrhizobium, Beijerinckia, Burkholderia, and Corynebacterium, which are associated with nitrogen metabolism, suggesting their potential involvement in biogeochemical processes. Additionally, a total of 59 to 419 bacterial genes related to sulphur metabolism were deduced through the KEGG functional analysis. The study detected the presence of various antibiotic resistance genes corresponding to different classes of antibiotics, including aminoglycoside, tetracycline, fluoroquinolone, macrolide, and erythromycin. Network analysis reveals that antibiotic resistance genes primarily interact with the phyla Pseudomonadota, Bacillota, and Actinomycetota. The melting of glaciers, a significant effect of climate change, may release contaminants, antibiotic resistance genes, and pathogenic bacteria into free-flowing rivers, potentially impacting human health.},
}

@article {pmid42068031,
year = {2026},
author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y},
title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2665870},
doi = {10.1080/19490976.2026.2665870},
pmid = {42068031},
issn = {1949-0984},
mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth & development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth & development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; },
abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.},
}

Animals
*Syndecan-1/genetics/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Mice
*Intestinal Mucosa/microbiology/metabolism
Gastrointestinal Microbiome
*Biofilms/growth & development
Mice, Knockout
Humans
*Faecalibacterium prausnitzii/physiology/genetics/growth & development
Mice, Inbred C57BL
Homeostasis
Disease Models, Animal
Dextran Sulfate
Colitis/microbiology/chemically induced
Male
Fecal Microbiota Transplantation

@article {pmid42068598,
year = {2026},
author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J},
title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128530},
doi = {10.1016/j.micres.2026.128530},
pmid = {42068598},
issn = {1618-0623},
abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.},
}

@article {pmid42068877,
year = {2026},
author = {Liao, W and Gao, J and Zhang, J and Wu, Y and Jiang, Y and Liu, H and Chen, S and Xiu, L and Zhong, G},
title = {Haizao Yuhu Decoction alleviates goiter via the gut-thyroid axis: Microbiota-derived SCFAs promote hormone synthesis and restore apoptosis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158256},
doi = {10.1016/j.phymed.2026.158256},
pmid = {42068877},
issn = {1618-095X},
abstract = {BACKGROUND AND PURPOSE: Haizao Yuhu Decoction (HYD) is a classic Traditional Chinese Medicine for goiter, but its mechanism related to the "gut-thyroid axis" remains unknown. This study investigates whether HYD treats goiter via this axis and elucidates the underlying mechanisms.

METHODS: A rat goiter model was induced with propylthiouracil (PTU), followed by two weeks of HYD treatment. Gut microbiota was analyzed by metagenomic sequencing; fecal and serum short-chain fatty acids (SCFAs) were quantified by targeted LC-MS/MS analysis. Thyroid function was assessed via iodine content and hormone levels. Key proteins in hormone synthesis and apoptosis were evaluated by Western blot and immunohistochemistry. Fecal microbiota transplantation (FMT) supported microbiota causality.

RESULTS: HYD alleviated goiter and hypothyroidism. It restored gut microbiota diversity and enriched SCFA-producing bacteria (e.g., Bifidobacterium pseudolongum), coincident with increased SCFAs including butyrate. These SCFA changes correlated with reduced HDAC1/2/3/8 in thyroid tissue, consistent with enhanced histone acetylation, and were accompanied by upregulation of NIS, TG, TPO, and DUOX2. Concurrently, elevated SCFAs were associated with AKT/Mdm2 pathway inhibition, p53 stabilization, downstream activation of P21 and Caspase-3, and suppression of Bcl-2, supporting a model of promoted thyroid cell apoptosis. FMT supported that HYD-modulated microbiota alone reproduced these effects.

CONCLUSION: HYD alleviates PTU-induced goiter in rats in a manner associated with gut microbiota remodeling and increased SCFA production, which correlate with enhanced thyroid hormone synthesis and restored apoptosis-a relationship supported by FMT experiments. However, direct interactions between HYD and PTU cannot be fully excluded. These findings are consistent with a model in which HYD acts through the gut-thyroid axis, providing mechanistic insights into its therapeutic effects.},
}

@article {pmid42069091,
year = {2026},
author = {Jin, H and Meng, L and Yulug, B and Altay, O and Li, X and Cankaya, S and Hanoglu, L and Ji, B and Coskun, E and Idil, E and Nogaylar, R and Oktem, EO and Sayman, D and Karaca, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Borén, J and Zhang, C and Uhlén, M and Mardinoglu, A},
title = {Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {107424},
doi = {10.1016/j.nbd.2026.107424},
pmid = {42069091},
issn = {1095-953X},
abstract = {While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.},
}

@article {pmid42069117,
year = {2026},
author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA},
title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128242},
doi = {10.1016/j.envpol.2026.128242},
pmid = {42069117},
issn = {1873-6424},
abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detect high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.},
}

@article {pmid42069315,
year = {2026},
author = {Wu, G and Du, J and Li, H and Dong, Y and Wang, Q and Hu, F and Ji, J},
title = {Synergistic integration of sustainable wastewater treatment and agricultural waste valorization: Rapid in-situ enrichment of anammox bacteria via corncob biocarriers.},
journal = {Bioresource technology},
volume = {454},
number = {},
pages = {134769},
doi = {10.1016/j.biortech.2026.134769},
pmid = {42069315},
issn = {1873-2976},
abstract = {The slow proliferation of anammox bacteria (AnAOB) limits the large-scale application of anammox technology in mainstream wastewater treatment. Here, an innovative strategy was proposed in which agricultural waste corncob was utilized as biocarriers for the rapid enrichment of AnAOB. This study systematically validated the feasibility of using corncob as biocarriers to enhance the self-enrichment of AnAOB. Results showed that corncob addition shortened the anammox startup time by approximately 64.0% and increased total inorganic nitrogen (TIN) removal efficiency by 28.4%. The anammox activity of the corncob biofilm and flocs was 3.2- and 1.1-fold higher, respectively, than that of the control. The microbial community analysis indicated that corncob biofilm harbored the highest relative abundance of AnAOB (23.9%). Within the corncob biofilm, lignocellulolytic microbes degraded macromolecular organics to provide electron donors for denitrifiers, which facilitated nitrogen metabolic couplingbetween denitrifiers and AnAOB, therebyestablishing favorable microenvironment for the enrichment of AnAOB. Furthermore, metagenomic revealed NO cross-feeding between AnAOB and their symbionts further offered an ideal niche for AnAOB. Concurrently, the upregulation of key carbon metabolism genes indicated heightened microbial activity within the biofilm, while quorum sensing (QS) mechanisms also played a significant role in maintaining the dynamic stability of microbial community. This work established a natural and highly efficient pathway for the self-enrichment of AnAOB, simultaneously providing a synergistic solution for agricultural wastes (AWs) valorization, advanced wastewater nitrogen removal, and carbon neutrality, demonstrating broad application prospects and significant ecological value.},
}

@article {pmid42069316,
year = {2026},
author = {Zhao, X and Tian, X and Zhang, H and Dang, Y and Ma, J},
title = {Metagenomic understanding of the performance enhancement in anaerobic digestion by granular activated carbon coupled with riboflavin under high organic loading.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134752},
doi = {10.1016/j.biortech.2026.134752},
pmid = {42069316},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) often suffers operation failure from ammonia inhibition and volatile fatty acids (VFAs) accumulation under high organic loading rates (OLRs). To overcome these limitations, this study employed granular activated carbon coupled with riboflavin (RFGAC) by stimulating direct interspecies electron transfer (DIET). A semi-continuous AD experiment was conducted for 145 days with OLRs ranging from 2.25 to 11.25 kg COD/(m[3]·d). The results showed that the RFGAC group achieved the highest methane content of 78%, and maintained a COD removal rate above 95%, outperforming the GAC group and the control. At an OLR of 6.75 kg COD/(m[3]·d), the control collapsed due to severe acidification when the pH dropped lower than 6.5, while the RFGAC group stably operated with effluent COD of 2200-5300 mg/L and seldom VFAs accumulation. Microbial community analysis revealed that RFGAC selectively shifted microbial community composition especially at high OLR, promoting Methanosarcina to form a synergistic consortium. The Pearson correlation analysis of digestion performance and metagenome revealed that Methanosarcina had a stronger correlation with methanogenesis than Methanothrix, which was enriched in the presence of GAC alone. Metabolic pathway analysis confirmed key DIET-related functional genes, hdrA2 and methyl transfer-associated mtrH, were respectively upregulated by 7-fold and 5-fold. This study offers a viable strategy to improve chicken manure AD, and provides deep mechanistic insights on RFGAC modulation of microbial community succession and functional gene expression.},
}

@article {pmid42069539,
year = {2026},
author = {Hagenbeek, A and Masukagami, Y and Palanichamy, P and Husnik, F},
title = {Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12881-x},
pmid = {42069539},
issn = {1471-2164},
support = {RGEC29/2024;DOI:https://doi.org/10.52044/HFSP.RGEC292024.pc.gr.194160//Human Frontier Science Program/ ; },
abstract = {The intracellular endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. Despite its prevalence, little is known about the biology of Ca. Lariskella, nor do we grasp the full extent of its host range. Here, we report the first known occurrence of Ca. Lariskella infecting a population of free-living marine nematodes (Enoplida, Thoracostomopsideae). This novel nematode-infecting Ca. Lariskella was found to be closely related to insect-infecting strains, despite the drastic shift in both host taxonomy and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both the nematode somatic cells and developing oocytes, confirming its status as a nematode endosymbiont and strongly suggesting maternal transmission. This finding led us to reassess the host range of Ca. Lariskella. We screened the SRA database for Ca. Lariskella sequences and performed genome-resolved metagenomics on SRA entries positive for Ca. Lariskella. We recovered 16 novel Ca. Lariskella metagenome-assembled genomes from SRA entries, including from novel hosts such as ants and treehoppers. However, we did not encounter further instances of Ca. Lariskella within nematodes or marine invertebrates, which we attribute to the relatively poor sampling of these groups. Overall, our findings illustrate the ability of Ca. Lariskella to infect both arthropods and nematodes as well as hosts from both terrestrial and marine environments.},
}

@article {pmid42069617,
year = {2026},
author = {Yuan, H and Song, Y and Nie, L and Yang, Z and Yang, L and Yang, K and Yang, Y and Li, W and Wang, X and Zhang, XX and Hua, Y and Yuan, ZG},
title = {The gut metabolite arachidonic acid alleviates intestinal injury induced by a Toxoplasma gondii strain isolated from a wild rodent.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07389-y},
pmid = {42069617},
issn = {1756-3305},
support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; },
abstract = {BACKGROUND: Wild isolates of Toxoplasma gondii may exhibit different virulence characteristics and host adaptability compared with those of laboratory strains. In this study, we isolated a novel rodent-derived T. gondii strain, denoted TgRodGz1, and evaluated its pathogenic features.

METHODS: TgRodGz1 was isolated from T. gondii-positive wild rodents in Guangdong Province and compared with the RH and Me49 strains in C57BL/6 mice. Virulence and intestinal injury were evaluated by survival analysis, brain cyst quantification, histopathology, tight junction assessment and qPCR. Gut microbiota and metabolic alterations were analyzed by metagenomic sequencing and LC-MS/MS-based metabolomics.

RESULTS: Compared with theT. gondii laboratory strains RH and Me49, TgRodGz1 was associated with more pronounced intestinal injury, including villus atrophy, barrier disruption and downregulation of tight junction proteins and increased gut permeability and inflammation. Metagenomic analysis revealed significant intestinal flora dysbiosis, with a marked reduction in beneficial bacteria and expansion of pathogenic bacteria. Metabolomic analysis revealed suppression of arachidonic acid (ARA) metabolism during TgRodGz1 infection. Supplementation with ARA did not directly inhibit parasite growth but significantly alleviated intestinal lesions, reduced brain cyst burden and attenuated inflammatory responses, including microglial activation.

CONCLUSIONS: These findings suggest that TgRodGz1 represents a distinct T. gondii genotype associated with pronounced intestinal pathology and suggest that ARA supplementation may alleviate intestinal and neuroinflammatory changes associated with T. gondii infection.},
}

@article {pmid42069941,
year = {2026},
author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I},
title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.},
journal = {Current microbiology},
volume = {83},
number = {6},
pages = {},
pmid = {42069941},
issn = {1432-0991},
mesh = {Humans ; *Prebiotics/administration & dosage ; Animals ; *Gastrointestinal Microbiome/drug effects ; Probiotics ; *Microbiota ; },
abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.},
}

Humans
*Prebiotics/administration & dosage
Animals
*Gastrointestinal Microbiome/drug effects
Probiotics
*Microbiota

@article {pmid42070641,
year = {2026},
author = {Wu, M and Liao, H and Luo, Y and Yao, Y and Yang, D and Hu, Z and Gao, L and Xia, X},
title = {Moisture transfer-driven quality enhancement in solid-state fermented Daqu: Synergistic effects of microbial community adaptation and functional enzyme metabolism.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134771},
doi = {10.1016/j.biortech.2026.134771},
pmid = {42070641},
issn = {1873-2976},
abstract = {Solid-state fermented Daqu exhibits a typical heterogeneous structure, where moisture regulates the microbial activity by driving gas diffusion in the pores and nutrient enrichment, playing a crucial role in the quality of the final product. However, there is a lack of clarity regarding how moisture transfer affects Daqu microbial assembly and metabolic flux. This study pioneered a real-time controllable fermentation platform, employing stoichiometry, nuclear magnetic resonance, and metagenomics to investigate microbial saccharifying metabolic functions under moisture transfer regulation. Comparing representative low (LM: 34%, 36%) and high (HM: 38%, 40%) moisture groups, we found that porosity exhibited a strong positive correlation with water activity (coefficient > 0.9, p < 0.01), serving as the primary physicochemical contributor governing moisture transfer priority. Furthermore, steady-state mass transfer in the HM group (≥ 38%) enhanced the transfer rate from free water (T23) to capillary water (T22: 10-100 ms), shaping a saccharifying functional microbial community dominated by Rhizopus and Bacillus. Weighted network and functional gene predictions indicated that this process strengthened the substrate preference of core microorganisms toward starch, significantly reinforcing the metabolic synergy between glucoamylase and α-amylase. Conversely, transient mass transfer in the LM group (< 38%) triggered microbial functional differentiation, promoting the redistribution of non-starch polysaccharide hydrolases. Our research revealed the effects of moisture transfer on nutrient availability, microbial adaptation, and metabolic functions in stack-fermented Daqu. This work ensures Daqu stability and presents novel strategies to optimize solid-state fermentation efficiency through moisture-driven microbial metabolic trade-offs.},
}

@article {pmid42070688,
year = {2026},
author = {Shurigin, V and Lu, X and Khan, AR and Muhammad, M and Ullah, I and Egamberdieva, D and Yu, Y and Li, L},
title = {Unveiling the Plant Growth-Promoting and Antifungal Potential of Melissa officinalis Endophytes: the Integrative Culture-Dependent and Metagenomic Approaches.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {},
number = {},
pages = {113182},
doi = {10.1016/j.plantsci.2026.113182},
pmid = {42070688},
issn = {1873-2259},
abstract = {Endophytic bacteria play a central role in plant health, yet their diversity and functions in medicinal plants remain poorly characterized. In this study, we integrated high-throughput sequencing, culture-based isolation, functional assays, and greenhouse validation to characterize the endophytic microbiome of Melissa officinalis L. High-throughput sequencing revealed 347 species with strong tissue-specific structuring. Paucibacter and Pseudomonas genera related to phylum Pseudomonadota dominated in all plant tissues. Nineteen culture-dependent strains representing Pseudomonas, Microbacterium, Plantibacter, Agreia, and Kocuria demonstrated various plant growth-promoting traits, including phosphate solubilization, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-related compounds (IRC) production, siderophore secretion, and hydrolytic enzyme activities (chitinase, protease, and lipase). Pseudomonas fluorescens XIEG-4RS14 showed antifungal activity against Fusarium graminearum (50%) and F. moniliforme (37%), P. marginalis XIEG-4RS15 showed 100 and 62%, P. baetica XIEG-4RS18 showed 28 and 42%, P. fluorescens XIEG-4RS32 showed 45 and 39%, and P. rhodesiae XIEG-4RS37 showed 58 and 27% respectively. Greenhouse assays demonstrated that strains Pseudomonas fluorescens XIEG-4RS14, P. fluorescens XIEG-4RS32, P. taetrolens XIEG-4RS19, and P. poae XIEG-4RS27 increased wheat root and shoot dry weight by up to 113% to 60% respectively. These findings revealed that M. officinalis harbors highly cooperative and functionally effective endophytes with strong potential as next-generation bioinoculants for sustainable crop production.},
}

@article {pmid42070841,
year = {2026},
author = {Li, S and Yan, X and Ndayishimiye, JC and Smirnov, A and Tsyganov, AN and Nassonova, E and Mazei, NG and Mazei, YA and Yang, J},
title = {Urban park metagenomics highlights sediments as a potential hotspot for CH4 and N2O emission across diverse habitats.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {481-491},
doi = {10.1016/j.jes.2025.07.053},
pmid = {42070841},
issn = {1001-0742},
mesh = {*Methane/analysis ; Metagenomics ; *Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; *Nitrous Oxide/analysis ; Ecosystem ; *Environmental Monitoring ; *Air Pollutants/analysis ; Greenhouse Gases/analysis ; Microbiota ; },
abstract = {Urban areas contribute the vast majority of greenhouse gas (GHG) emissions, and urban greenspaces, including urban parks, are being established to promote environmental health by mitigating GHG emissions. However, the diversity of CH4 and N2O cycling genes and microbiomes in urban park ecosystems remains poorly understood. Here, we sampled five types of habitats in subtropical urban parks, including moss, sediment, soil, tree hole, and water, to explore the microbial communities and microbially mediated CH4 and N2O cycling processes using metagenomic sequencing. We found strongly positive biodiversity-ecosystem-functioning (BEF) relationships in nitrogen cycling functions, as well as in CH4 cycling, except in sediment, indicating the microbial community in the sediment had reached function saturation for CH4 cycling. CH4 cycling was driven by a few specific microbial genera, whereas many microorganisms participated in the denitrification process. Microbes in sediment exhibited the highest CH4 and N2O metabolic potential among the five habitats, especially for methanogenesis and N2O production processes. Significant positive correlations were observed between the mcrA and N2O cycling genes, suggesting methanogenesis could be coupled with denitrification. Environmental factors, such as dissolved oxygen, total nitrogen, and total carbon greatly affected microbial community composition and functional gene families. These results highlight that pond sediments are an overlooked potential source of CH4 and N2O emissions, which may undermine the role of urban greenspace in reducing GHG emissions. Reducing nitrogen pollution and eutrophication is recommended to mitigate CH4 and N2O emissions from pond sediments in urban environments.},
}

*Methane/analysis
Metagenomics
*Geologic Sediments/microbiology/chemistry
Parks, Recreational
*Nitrous Oxide/analysis
Ecosystem
*Environmental Monitoring
*Air Pollutants/analysis
Greenhouse Gases/analysis
Microbiota

@article {pmid42070844,
year = {2026},
author = {Wu, C and Wu, Y and Pan, J and Lv, Y and Li, W and Hu, M and Wang, J and Su, S and Zou, Q and Xue, S},
title = {Evolution and role of manganese-transforming bacterial microorganisms during natural manganese-tailing succession.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {516-525},
doi = {10.1016/j.jes.2026.01.018},
pmid = {42070844},
issn = {1001-0742},
mesh = {*Manganese/metabolism ; *Bacteria/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Mining ; },
abstract = {The natural succession of tailings is critical for reducing their adverse environmental impacts. However, the current knowledge of the Mn-transforming microorganisms involved in the natural vegetation succession of Mn tailings is very limited. This study reveals for the first time the evolution of Mn-transforming microorganisms during vegetation succession in Mn tailing. The results revealed that the amount of reducible Mn increased during the succession process (divided into nake-land, bryophyte, herb and woody-plant stages), which is the most important geochemical property driving bacterial community diversity. Metagenomic functional profile analysis revealed that the abundance of genes involved in nutrient uptake, metal tolerance, and metal detoxification increased during succession. A total of 51 metagenome-assembled genomes (MAGs) were reconstructed, in which 6 encoding multicopper oxidase (cotA)-containing MAGs were identified. The relative abundance of these cotA-containing MAGs first increased but then decreased during succession. Notably, genes associated with carbon fixation and denitrification were also identified in these cotA-containing MAGs, indicating their roles in coupling the cycling of manganese, carbon and nitrogen. These results suggest that Mn(II)- oxidizing bacteria could be crucial for lowering Mn toxicity, obtaining nutrients, and potentially contributing to the ecological succession of Mn tailings. The investigation of Mn-transforming microorganisms (cotA-MAGs) has also contributed to understanding the succession mechanisms and restoration of Mn tailing ecosystems.},
}

*Manganese/metabolism
*Bacteria/metabolism
Biodegradation, Environmental
*Soil Microbiology
*Soil Pollutants/metabolism
Mining

@article {pmid42070845,
year = {2026},
author = {Yan, S and Li, R and Shen, X and Zhu, Y and Li, Y and Xu, M and Xie, S},
title = {Unveiling the role of bacterial communities in carbon fixation of mangrove wetlands: Insights into the redox potential and biogeochemical interactions.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {526-537},
doi = {10.1016/j.jes.2025.08.024},
pmid = {42070845},
issn = {1001-0742},
mesh = {*Wetlands ; *Carbon Cycle ; Oxidation-Reduction ; *Soil Microbiology ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mangrove wetlands are crucial for carbon sequestration, however, the contributions of bacterial carbon fixation in these ecosystems are often overlooked, and the predominant pathways remains unknown. This gap seriously hinders the understanding and precise assessment of carbon sequestration. This study systematically investigates the pathways, rates, and influential factors of bacterial carbon fixation in mangrove wetlands, utilizing soils from various tidal zones and depths. Through an integrated approach that combines in situ metagenome sequencing, [13]CO2 tagging experiment, functional gene abundance measurement, and 16S rRNA sequencing, we provide the first evidence that the reverse tricarboxylic acid cycle is the predominant pathway for carbon (C) fixation in mangrove soils. The mangrove ecosystem was identified as a significant hotspot for bacterial carbon fixation, with rates in topsoil ranging from 15 to 63 mmol C/(m[2]·day), significantly influenced by environmental variables such as oxidation-reduction potential, and ammonium and nitrate concentrations. In deep soils, high carbon fixation rates were detected in low tidal zones but not in middle and high tidal zones, which did not align with the abundance of carbon fixation functional genes. Notably, we found a strong correlation between carbon fixation rates and nitrogen metabolism processes, underscoring the ecological interactions between these biogeochemical cycles. These findings greatly enhance our understanding of microbial contributions to carbon cycling in mangrove ecosystems and offer novel insights into blue carbon sequestration and the management of coastal wetlands under varying environmental conditions.},
}

*Wetlands
*Carbon Cycle
Oxidation-Reduction
*Soil Microbiology
*Bacteria/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42070879,
year = {2026},
author = {Xin, Y and Liu, L and Chen, SH and Zhao, QB and Zheng, YM},
title = {Enhancing urban river self-purification through riverbed substrates configuration: A nature-based solution for nutrient removal and restoration planning.},
journal = {Journal of environmental sciences (China)},
volume = {164},
number = {},
pages = {95-108},
doi = {10.1016/j.jes.2026.01.038},
pmid = {42070879},
issn = {1001-0742},
mesh = {*Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; Nitrogen/analysis ; *Environmental Restoration and Remediation/methods ; Nutrients ; Phosphorus/analysis ; },
abstract = {Appropriate riverbed substrates, as nature-based engineering components, are critical for enhancing nutrient mitigation and ecosystem sustainability in urban rivers. However, their role in regulating hydrologically mediated nutrient fluxes and biofilm functions remains unclear, limiting substrate-optimized design for urban river restoration. This study integrated machine learning modeling, scenario simulations, and metagenomic analysis to quantify substrate-driven interfacial nutrient removal efficiencies and uncover microbial regulation mechanisms. A back propagation neural network could accurately predict interfacial ammonium and total organic carbon removal efficiencies (RMSE: 0.59-6.92 mg/(L·h·m[2]), R[2]: 0.66-0.97), with retention time, temperature, dissolved oxygen, and nutrient load identified as key predictors. Building upon the model-predicted scenario results, analysis of similarity tests confirmed that substrate type significantly influenced interfacial nutrient removal efficiencies (R > 0.05, P < 0.001). Scoring metrics demonstrated fine sand (1295) and gravel (1281) gained higher total scores than other substrates (1110-1182), indicating higher interfacial nutrient removal capacities. Metagenomic analyses revealed that these differences were driven by divergence in microbial functional potential. Substrate type selectively enriched functional genes related to nitrogen and carbon cycling (R > 0.18, P < 0.05), with gravel microcosms showing significantly higher gene abundance (8.00 × 10[-4]-2.08 × 10[-3]), despite similar community compositions governed by stochastic assembly (R[2] > 0.84). Topological analysis revealed that redundancy of functional gene network significantly influenced ammonium removal efficiency (P < 0.05), with fine sand and gravel enhancing ammonium removal, while lower clustering coefficients in artificial filler and gravel microcosms significantly promoted total organic carbon removal. This study suggested that fine sand and gravel should be more effective riverbed substrates for enhancing interfacial nutrient removal in urban river restoration.},
}

*Rivers/chemistry
*Water Pollutants, Chemical/analysis
Nitrogen/analysis
*Environmental Restoration and Remediation/methods
Nutrients
Phosphorus/analysis

@article {pmid42071059,
year = {2026},
author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D},
title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50831-5},
pmid = {42071059},
issn = {2045-2322},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; },
abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.},
}

@article {pmid41877145,
year = {2026},
author = {Zhang, QN and Zhang, XH and Shi, SS},
title = {Tacrolimus-induced interstitial lung injury in a pediatric cardiac transplant recipient: a case report and literature review.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41877145},
issn = {1471-2431},
abstract = {BACKGROUND: Tacrolimus-induced interstitial lung injury (TI-ILI) is a rare but potentially fatal adverse effect of calcineurin-inhibitor therapy. To our knowledge, TI-ILI has not previously been reported in a paediatric heart-transplant recipient.

CASE PRESENTATION: A 6-year-old boy with PLN-related dilated cardiomyopathy underwent orthotopic heart transplantation. Maintenance immunosuppression comprised tacrolimus, mycophenolate mofetil and prednisone. On post-operative day 13 he developed bilateral ground-glass opacities with interlobular septal thickening on chest CT. Broncho-alveolar lavage metagenomics showed only low-abundance Pseudomonas aeruginosa and Acinetobacter baumannii; extensive microbiological, cardiac work-up was negative. Infiltrates progressed despite targeted antibiotics, but resolved within 4 weeks after tacrolimus was replaced by cyclosporine and corticosteroids were doubled. No relapse occurred during 6 months of follow-up.

CONCLUSIONS: TI-ILI should be considered in any heart transplant recipient with unexplained progressive bilateral pulmonary infiltrates. Early tacrolimus withdrawal and prompt corticosteroid therapy are associated with complete recovery; re-exposure to tacrolimus is contraindicated.},
}

@article {pmid42067917,
year = {2026},
author = {Fang, Q and Huang, S and Zhang, C and Li, M and Ye, Z and Guo, H and Xiao, M and Wang, S and Yu, L and Zhang, H and Zhao, J and Tian, F and Chen, W and Zhai, Q},
title = {Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02415-8},
pmid = {42067917},
issn = {2049-2618},
support = {BX20250339//Postdoctoral Fellowship Program and China Postdoctoral Science Foundation/ ; U23A20259//National Natural Science Foundation of China/ ; JUSRP622013//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.

RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.

CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.},
}

@article {pmid42062664,
year = {2026},
author = {Kieliszek, M},
title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
pmid = {42062664},
issn = {1559-0720},
abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.},
}

@article {pmid42062918,
year = {2026},
author = {Guo, P and Zhang, S and Huang, Z and Zhu, J and Zhang, W},
title = {Potential drug-drug interactions and 30-day mortality in ICU patients with bloodstream infection: a single-center retrospective study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13426-z},
pmid = {42062918},
issn = {1471-2334},
abstract = {BACKGROUND: Patients in intensive care units (ICUs) with bloodstream infection (BSI) commonly receive multiple antimicrobials and supportive drugs, which increases the likelihood of potential drug-drug interactions (pDDIs). Evidence focused specifically on ICU patients with BSI remains limited.

OBJECTIVES: To describe the prevalence and severity of pDDIs in ICU patients with BSI and to examine whether pDDI exposure was associated with 30-day mortality.

METHODS: We performed a single-center retrospective cohort study of 90 adult ICU patients with an index episode of BSI between January 2019 and December 2024. Time zero was defined as the sampling time of the first qualifying positive blood culture or a clinically accepted positive blood metagenomic next-generation sequencing result for the index episode. Medication administration records, rather than prescription orders alone, were used for pDDI ascertainment. pDDIs were screened with the Micromedex Drug Interactions database (Merative, web-based version updated daily; accessed January 15, 2025). Exposure was defined within a fixed 48-hour window after time zero; a pDDI required actual administration of both interacting agents within the same 24-hour period during this window. Severity was standardized as mild, moderate, or severe. The primary outcome was 30-day all-cause in-hospital mortality. Because only 18 deaths occurred, the primary multivariable model included any pDDI exposure and SOFA score.

RESULTS: Seventy of 90 patients (77.8%) had at least one pDDI within the fixed exposure window. Based on the highest patient-level severity, 13/70 (18.6%) had mild, 22/70 (31.4%) moderate, and 35/70 (50.0%) severe pDDIs. The most frequent combinations were vancomycin plus amikacin (18/90, 20.0%) and piperacillin/tazobactam plus vancomycin (15/90, 16.7%). The clinical consequences listed for common pairs were reference-predicted interaction consequences rather than adjudicated observed toxicities. In the parsimonious multivariable model, any pDDI exposure was associated with higher observed 30-day mortality (adjusted OR 4.23, 95% CI 1.27-14.09; P = 0.02), and each 1-point increase in SOFA score was also associated with mortality (adjusted OR 1.32, 95% CI 1.07-1.64; P = 0.01).

CONCLUSIONS: pDDIs were common in this ICU BSI cohort and were associated with higher observed 30-day mortality. These findings should be interpreted cautiously given the retrospective single-center design, limited event count, residual confounding, and incomplete control of time-dependent exposure. Structured pDDI screening may still support medication safety in critically ill patients.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42063196,
year = {2026},
author = {Liu, Z and Meng, C and Shen, J and Wang, H and Guo, J and Zhao, J and Mu, C and Zhu, W},
title = {Dietary regulation on gut resistome linked with microbial amino acid metabolism in pigs.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42063196},
issn = {2524-4671},
support = {National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; },
}

@article {pmid42063256,
year = {2026},
author = {Liu, Y and Wu, J and Yang, Y and He, Y and Zhou, R and Li, Y and Sun, J and Gong, M and Mei, X and Li, Y and Huang, H and Du, F and Deng, W and Ye, C and He, X and Li, L and Hao, J and Yang, M and Zhu, Y and Zhu, S},
title = {Decoupling the 'Attract-and-Kill' Strategy: Independent Functions for Zoospore Attraction and ROS-Executed Killing Synergize in Disease-Suppressive Intercropping.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101876},
doi = {10.1016/j.xplc.2026.101876},
pmid = {42063256},
issn = {2590-3462},
abstract = {Soilborne Phytophthora diseases pose a major threat to agricultural sustainability. How non-host roots disrupt the transmission of soilborne Phytophthora pathogens without relying on classical antimicrobial exudates remains unknown. Through a decade-long field study, we demonstrate that strip intercropping achieves sustainable disease suppression (up to 46.85%) by leveraging non-host roots as ecological barriers that intercept zoospore transmission. Moving beyond the conventional focus on antimicrobial exudates, we decouple the 'attract-and-kill' strategy into two discrete functions: a broad-spectrum attraction function widespread among non-host plants (13 of 15 genera), which alone reduces disease by 9.2-24.4%; and a specialized killing function restricted to few species (e.g., garlic), where elevated root-interface concentrations of sulfur compounds induce cystospore rupture and germination inhibition, delivering 42.9-49.3% field suppression. The synergy of universal attraction and targeted killing intensifies efficacy at the rhizosphere interface. Mechanistically, killing is executed through a conserved ROS-PCD pathway, with pathogen sensitivity determined by intrinsic redox-buffering capacity. Metagenomic profiling further revealed that garlic roots and sulfur compounds enrich microbial motility genes and apoptosis pathways, adding a complementary mechanistic layer to the 'attract and kill'framework. We thus propose this two-component, ecology-based strategy for sustainable Phytophthora management in diversified cropping systems.},
}

@article {pmid42063433,
year = {2026},
author = {Chen, L and Li, J and Liu, X and Chen, X and Li, H and Xie, D and Chen, Y and Yuan, J and Tao, E},
title = {Case Report: Beyond commensal: Staphylococcus epidermidis as a novel cause of NARDS.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1631683},
pmid = {42063433},
issn = {2296-2360},
abstract = {Staphylococcus epidermidis (S. epidermidis), usually a harmless skin bacterium, can become an opportunistic pathogen in newborns, particularly those with risk factors like premature membrane rupture. Although it commonly causes late-onset sepsis, its association with neonatal acute respiratory distress syndrome (NARDS) is rare. This report describes a unique case of NARDS in a full-term newborn caused by S. epidermidis. The infant, born via cesarean at 40 2/7 weeks with a 30.5-hour membrane rupture, developed severe respiratory failure shortly after birth, necessitating mechanical ventilation. Initial treatment with penicillin and cefotaxime was ineffective, and by day 3, the infant's condition worsened, showing respiratory distress, petechial rashes, and high inflammatory markers. Treatment was changed to vancomycin and meropenem, with the addition of intravenous immunoglobulin and two doses of pulmonary surfactant. Metagenomic next-generation sequencing (mNGS) confirmed S. epidermidis in the airway secretions. The patient was discharged after 19 days with a diagnosis of NARDS, intrauterine infectious pneumonia, neonatal air leak syndrome, type II respiratory failure, neonatal sepsis, and congenital heart defects. In conclusion, S. epidermidis is a novel pathogen capable of causing NARDS in high-risk infants with prolonged membrane rupture. The proposed mechanisms-including surfactant dysfunction and biofilm-associated virulence-are supported by experimental literature and are consistent with the clinical phenotype observed in our patient, though direct confirmation requires further study. Notably, skin symptoms like erythematous rash and petechiae may indicate invasive S. epidermidis infection, especially in cases of respiratory distress with skin symptoms following premature rupture of membranes. Moreover, mNGS is vital for pathogen identification when traditional cultures fail.},
}

@article {pmid42063498,
year = {2026},
author = {Xiang, L and Wang, X and Wen, M and Wang, X and Zhang, Y and Tian, W and Liu, M and Zhang, W},
title = {Metagenomic insights into the rhizosphere microbiome dysbiosis associated with tobacco bacterial wilt.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809980},
pmid = {42063498},
issn = {1664-302X},
abstract = {Tobacco bacterial wilt, caused by Ralstonia solanacearum, threatens global tobacco production. While the rhizosphere microbiome defends against soil-borne pathogens, mechanisms underlying how bacterial wilt reshapes microbial community structure, function, and ecological interactions remain poorly understood. Here, we employed metagenomic sequencing to investigate taxonomic and functional alterations in the rhizosphere microbiome of symptomatic (S) and asymptomatic (A) tobacco plants across two locations (Fenggang and Bozhou), establishing four groups: FA, FS, BA, and BS. Quality control of sequencing data showed no technical bias between groups (p > 0.05). Contrary to the paradigm that pathogen invasion reduced microbial diversity, alpha diversity analysis revealed higher species richness (Sobs) in symptomatic soils, whereas community evenness (Shannon and Simpson indices) remained unchanged, suggesting selective reshuffling rather than microbiome collapse. Beta-diversity analysis revealed significant compositional shifts associated with disease status (PERMANOVA, R [2] = 0.713, p = 0.001), with symptomatic communities displaying greater heterogeneity. Taxonomic profiling revealed consistent enrichment of the pathogen R. solanacearum and opportunistic bacteria (including Stenotrophomonas and Pseudomonas) in symptomatic rhizospheres, concomitant with depletion of putative beneficial taxa (Candidatus_Solibacter, Luteitalea, and Metarhizium). Functional annotation indicated a metabolic shift from homeostatic maintenance to stress adaptation and pathogenicity. Symptomatic soils exhibited significant enrichment of virulence factors, including motility and secretion system genes, microbial defense mechanism genes (COG), and antibiotic resistance genes (CARD). Additionally, increased abundance of carbohydrate-active enzymes (CAZy)-particularly glycoside hydrolases-suggested intensive nutrient acquisition from decaying tissues. Co-occurrence network analysis revealed that asymptomatic communities formed denser, competition-driven networks characterized by a higher proportion of negative correlations. Disease destabilized these networks by reducing connectivity and, crucially, rewired interactions of R. solanacearum from negative to positive associations with taxa such as Sphingobium, thereby reflecting erosion of competitive constraints and pathogen incorporation into cooperative networks. Our findings revealed that bacterial wilt drove multi-layered dysbiosis, encompassing pathogen-driven taxonomic selection, functional shifts toward stress adaptation and intensified competition, and collapse of stable antagonistic networks associated with plant health. This study provided mechanistic insights into microbiome-mediated disease progression and identified specific microbial taxa and network properties as candidate targets for ecological disease management and early diagnostic indicators.},
}

@article {pmid42063509,
year = {2026},
author = {González de Figueras, C and Gómez, S and Lamprecht-Grandío, M and Mirete, S and Díaz-Rullo, J and Martínez-Rodríguez, P and Sánchez-Costa, M and González-Pastor, JE},
title = {Enhancing UV-C and perchlorate resistance in Arabidopsis thaliana through the introduction of microbial genes from hypersaline environment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1789302},
pmid = {42063509},
issn = {1664-302X},
abstract = {Ultraviolet (UV) radiation reaching the Earth's surface affects all living organisms. Recent reports show a trend of increasing exposure levels due to stratospheric ozone depletion and contamination. UV-B radiation (280-315 nm), previously largely absorbed by the ozone layer, now reaches the surface in higher doses, posing a particular threat to plants, which are sessile organisms and cannot escape adverse conditions. The intrinsic protective and repair mechanisms in plants may be insufficient to counteract this increase, potentially impacting crop productivity, distribution, and quality, with serious implications for agriculture and ecological stability. This study aims to enhance plant resistance to UV radiation by introducing genes derived from extremophilic microorganism, which have previously shown to confer UV-protective effects in UV resistance to a radiation-sensitive Escherichia coli strain (recA mutant). Extremophile microorganisms have been discovered in high-irradiation environments, such as hypersaline lakes, where survival relies on unique genetic adaptations. In our laboratory, four genes were selected from metagenomic libraries derived from high-altitude hypersaline lakes in Argentina (Diamante and Ojo Seco, at 4,589 m and 3,200 m respectively) and from the Es Trenc salt flat (Mallorca, Spain). Based on these promising results, the genes were introduced into Arabidopsis thaliana to evaluate their potential to enhance UV-B tolerance in plants. The selected genes included one encoding a TATA-box binding protein, and three hypothetical proteins. Each gene was independently transformed into Arabidopsis thaliana lines and subjected to UV-B and UV-C irradiation (4.5 kJ·m[-2]), with UV-C (100-280 nm) ultimately chosen for its higher damaging potential to test the limits of plant tolerance. Additionally, cross-resistance was evaluated using sodium perchlorate, a common soil contaminant and oxidative stressor. Plants were exposed to concentrations between 3.67 and 7.34 g/L, exceeding those used in previous studies. As a result, the plants obtained were more resistant to UV radiation and were also capable of growing in environments containing higher levels of perchlorate in the growth medium. Thus, the expression of these genes in the plant appears to contribute to enhanced stress resistance.},
}

@article {pmid42063777,
year = {2026},
author = {Zhu, M and Sun, C and Zhang, Y and Na, Y and Wang, Y and Zhao, Q and Gu, Y},
title = {Blepharitis driven by microbiome dysbiosis and Demodex infestation: possible pathogenic mechanisms.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1801375},
pmid = {42063777},
issn = {2296-858X},
abstract = {Blepharitis is a chronic inflammation of the eyelid margin that is mediated by the immune system. It is one of the common ocular surface diseases and often leads to serious sequelae that threaten vision, such as dry eye syndrome due to insufficient tear secretion, corneal neovascularization, and stubborn chalazion. Elucidating its precise etiology is therefore imperative. Emerging high-throughput sequencing and metagenomic analyses have unveiled a quantitative and qualitative disruption of the periocular microbiome (dysbiosis), characterized by the expansion of specific bacterial species such as Staphylococcus aureus, coupled with episodic blooms of Demodex. These perturbations are no longer considered epiphenomena. In this review, we reveal the possible mechanisms of the role of blepharitis and microbiota dysbiosis.},
}

@article {pmid42063778,
year = {2026},
author = {Wu, S and Wu, M and Li, W and Zhang, C and Bi, Y and Fan, Y and Xu, Y and He, D},
title = {Case Report: Diagnosis of leptospirosis presenting as aseptic meningitis using metagenomics CAPture sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1734396},
pmid = {42063778},
issn = {2296-858X},
abstract = {BACKGROUND: Leptospirosis is a globally prevalent zoonotic disease caused by pathogenic Leptospira species. The manifestation of leptospirosis can range widely, from being asymptomatic to causing severe multi-organ failure with a high mortality rate. It is uncommon for leptospirosis to present primarily with neurological complications. In this context, we discuss a notable case of Leptospira borgpetersenii infection manifesting as aseptic meningitis in China.

CASE PRESENTATION: In this study, we describe a primary case of neuroleptospirosis leading to symptomatic aseptic meningitis following exposure to Leptospira borgpetersenii. Initially managed for viral meningitis, the diagnosis of leptospirosis was subsequently confirmed through cerebrospinal fluid (CSF) analysis using metagenomic next-generation sequencing (mNGS) and Metagenomics CAPture Sequencing (MetaCAP), both of which identified Leptospira borgpetersenii. Following a course of antibiotics and methylprednisolone therapy, the patient fully recovered.

CONCLUSION: This case underscores the importance of considering leptospirosis in differential diagnoses for aseptic meningitis, especially in individuals with occupational risks related to water or animal exposure. MetaCAP's extensive coverage, sensitivity, and early pathogen detection capabilities can significantly enhance patient outcomes.},
}