@article {pmid41705261,
year = {2026},
author = {Fentie, EG and Lim, K and Andargie, YE and Park, S and Shin, JH},
title = {Preserving fermented-foods microbial diversity through systematic culturomics for the discovery of multi-strain probiotic candidates.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101318},
pmid = {41705261},
issn = {2665-9271},
abstract = {Fermented foods (FFs) represent complex living ecosystems that deliver viable microbes and bioactive metabolites linked to human health benefits. However, many probiotic strains isolated from FFs fail to reproduce these effects in vivo, likely due to the disruption of their natural ecological synergy during isolation. Here, we employed a systematic, ecology-aware culturomics framework to transform the Kimchi microbiome into genome-vetted, multi-species probiotic candidates while preserving ecological fidelity. Specifically, 56 distinct enrichment culture conditions were established using six liquid media (In-situ, MRS, NB, TSB, BHI, BB) across varied redox states (aerobic, anaerobic, microaerophilic), incubation periods (12 h, 66 h), and selective suppressants (CHIR-090, nalidixic acid). Results indicated that In-situ and MRS media under microaerophilic conditions effectively preserved the lactobacilli core, whereas generalist media and aeration expanded taxonomic breadth to include rare taxa. Furthermore, extended incubation (66h) successfully unlocked 107 unique taxa compared to the limited diversity of short incubation (12h). Shotgun metagenomic mining further revealed promising functional properties, including acid tolerance, adhesion modules, and diverse bacteriocin-skewed biosynthetic gene clusters. Crucially, the collection exhibited a strong safety profile: only 1 % of identified risk factors were antibiotic resistance genes (ARGs) on mobile genetic elements (MGEs), and only 4 % represented colocalized ARGs, virulence factors, and MGEs. Systematic-culturomic isolation later yielded over 90 strains, including Weissella, Bacillus, and Lactococcus, significantly expanding beyond standard lactobacilli-centric portfolios. Overall, this study confirms that ecology-aware culturomics captures the functional diversity of the Kimchi microbiome, providing a scalable model for realizing the full therapeutic potential of FFs.},
}

@article {pmid41705163,
year = {2026},
author = {},
title = {Correction to: Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag020},
doi = {10.1093/ismeco/ycag020},
pmid = {41705163},
issn = {2730-6151},
abstract = {[This corrects the article DOI: 10.1093/ismeco/ycaf183.].},
}

@article {pmid41704957,
year = {2026},
author = {Zhu, J and Xia, T and Wang, L and Yin, X and Ma, Y and Shen, J},
title = {Investigating the benefits of metagenomic next-generation sequencing for patients experiencing infections after total hip replacement surgery: a retrospective cohort study with a minimum of one year of follow-up.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1735867},
pmid = {41704957},
issn = {2235-2988},
mesh = {Humans ; Male ; Middle Aged ; *Arthroplasty, Replacement, Hip/adverse effects ; Female ; Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Prosthesis-Related Infections/microbiology/diagnosis/drug therapy ; Aged, 80 and over ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Follow-Up Studies ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {OBJECTIVE: To explore the clinical significance of metagenomic next-generation sequencing (mNGS) technology in diagnosing and treating periprosthetic joint infection (PJI) following total hip arthroplasty (THA).

METHODS: From September 2018 to September 2024, 15 patients with periprosthetic infection after total hip arthroplasty were admitted. There were 11 males and 4 females; ages ranged from 28 to 87 years old, with an average of 63 years old. Infection occurred 6 to 42 months after total hip arthroplasty, with an average of 22.7 months. The infection lasted between 15 and 115 days, averaging 37.6 days. After being admitted to the hospital, joint fluid was collected for bacterial culture and mNGS. Following admission, joint fluid was collected for bacterial culture and mNGS, and antibiotics were adjusted based on the results, with surgery used to control the infection if needed.

RESULTS: Bacterial culture method was positive in 10 cases (66.7%), with a total of 12 pathogenic bacteria types detected. MNGS was positive in 15 cases (100.0%), with a total of 19 pathogenic bacteria types detected. There was a statistically significant difference in the positive rate between the two methods (P < 0.05). Out of the 10 patients, 5 who tested positive using both the bacterial culture method and mNGS test showed identical pathogenic bacterial types, resulting in a 50.0% compliance rate. The testing time (from sample delivery to results) was (3.07 ± 0.96) days for bacterial culture method and (1.67 ± 0.49) days for mNGS test, and the difference was statistically significant (t=5.03, P<0.001). The patients were followed up for 13 to 82 months, with a mean of 40.7 months. In one patient, the infection returned three months after undergoing one-stage revision surgery, while the other 14 patients showed no signs of infection, resulting in an infection control rate of 93.3%.

CONCLUSION: MNGS can detect the pathogenic bacteria of postoperative PJI after THA more quickly and accurately than the bacterial culture method, which is crucial for guiding antibiotic and surgical treatment combinations for patients with postoperative PJI after THA.},
}

Humans
Male
Middle Aged
*Arthroplasty, Replacement, Hip/adverse effects
Female
Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Prosthesis-Related Infections/microbiology/diagnosis/drug therapy
Aged, 80 and over
*Metagenomics/methods
Adult
*Bacteria/genetics/classification/isolation & purification
Follow-Up Studies
Anti-Bacterial Agents/therapeutic use

@article {pmid41704904,
year = {2025},
author = {Av, EZ and Greenberg, A and Knaan, T and Melanson, EL and Youngster, I and Dubnov-Raz, G and Borenstein, E and Gepner, Y},
title = {The associations between physical activity, microbiome and metabolic adaptation in sedentary overweight adults.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1722274},
pmid = {41704904},
issn = {2296-861X},
abstract = {Despite well-established benefits of exercise on metabolic regulation and the gut microbiome (GM), its impact on body composition is inconsistent and often attenuated by metabolic adaptation. This compensation mechanism adjusts energy expenditure including total daily energy expenditure (TDEE) and resting metabolic rate (RMR). Intra-individual variation in exercise response remains unclear, but might be explained by the GM. In this well-controlled study, we investigated the relationship between aerobic exercise, GM composition, and metabolic adaptation in a cohort of 16 sedentary overweight adults (ages 21-45, 50% female) over a 12-week moderate-intensity intervention (65-75% HRmax; 20 kcal/kg/week). Pre- and post-intervention RMR was measured via whole-room calorimetry, TDEE by doubly labeled water, and GM composition via shotgun metagenomics. While body composition did not change at the group-level, a subset of participants ("responders") showed improved body composition and aerobic capacity. Using machine learning, we identified bacterial species, including Faecalibacterium prausnitzii species, whose abundance pre-training is predictive of response. Additionally, we found that responder GM communities are more compositionally cohesive and post-training increases in GM diversity are associated with higher TDEE and RMR. These findings highlight the complex interaction between exercise, metabolism and the GM, and suggest that baseline GM characteristics may contribute to individual variability in metabolic adaptation. This insight may help guide microbiome-informed strategies to enhance exercise efficacy. Clinical trial registration: ClinicalTrials.gov, identifier NCT04460040.},
}

@article {pmid41704848,
year = {2025},
author = {Nayak, D and Behera, P and Singh, S and Tripathy, PS and Dash, SS and Dasgupta, M and Mohanty, S and Sahoo, MR and Satapathy, CR and Sasmal, A and Sahu, S},
title = {Sucrose supplementation influences gut microbial diversity and functional shifts in Apis cerana indica.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733283},
pmid = {41704848},
issn = {1664-302X},
abstract = {Honeybee colonies are increasingly threatened by nutritional scarcity and biotic stressors, underscoring the need to understand the role of gut microbiota in mitigating these challenges. This study examined the gut microbial composition of Apis cerana indica under two dietary regimes: sucrose-fed and sucrose-unfed, to assess how nutrition influences microbial diversity and metabolic potential following metagenomics. Metagenomic sequencing of gut samples revealed 147,146 contigs, with the longest and shortest contigs measuring 615,154 kb and 200 kb, respectively. Comparative analysis indicated a higher relative abundance of Bacillus spp. in sucrose-fed bees, whereas Enterococcus was more dominant in unfed populations. Sucrose feeding significantly enhanced gut microbial diversity (Shannon index: 2.59; Simpson's index: 0.87) compared to unfed bees (Shannon: 1.91; Simpson: 0.68). Key genera, including Gilliamella, Bacillus, and Lactobacillus, were consistently present but showed varying relative abundances. Functional annotation via KEGG pathway analysis revealed elevated activity of glycolysis and the pentose phosphate pathway in sucrose-fed bees, with exclusive detection of key metabolic enzymes, hexokinase and enolase. Additionally, elevated sucrose metabolism and proteolytic enzyme activity were noted, reflecting enhanced metabolic versatility. Our findings highlight the importance of sucrose dietary supplementation in shaping gut microbial structure and function, their diversity, and metabolic capacity, suggesting its potential as a practical nutritional intervention to sustain honeybee health during a period of floral dearth. The outcome of the study encourages exploring the long-term ecological and physiological impacts of dietary strategies on colony resilience and productivity.},
}

@article {pmid41704809,
year = {2026},
author = {Zhang, M and Jiao, T and Li, W},
title = {Allergic bronchopulmonary aspergillosis in a patient without history of asthma: a case report.},
journal = {Medical mycology case reports},
volume = {51},
number = {},
pages = {100770},
pmid = {41704809},
issn = {2211-7539},
abstract = {Allergic bronchopulmonary aspergillosis (ABPA) is a pulmonary hypersensitivity disease triggered by Aspergillus fumigatus. While the standard first-line therapy per International Society for Human and Animal Mycology (ISHAM) guidelines is glucocorticoids or itraconazole alone, combination therapy may be used briefly for rapid symptom control. We present a 39-year-old man without asthma who presented with cough and sputum. Chest computed tomography (CT) revealed diagnostic findings of central bronchiectasis and high-attenuation mucus, later confirmed as mucus plugs by bronchoscopy. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) detected a high load of A. fumigatus. Markedly elevated total IgE, A. fumigatus-specific IgE, and eosinophils confirmed ABPA. Although initial voriconazole monotherapy failed, adding oral glucocorticoids led to rapid clinical and radiographic improvement. No recurrence was observed on CT 7 months post-treatment, reinforcing that asthma is not a prerequisite for ABPA diagnosis.},
}

@article {pmid41704794,
year = {2025},
author = {Basu, U and Ahanger, SA and Gai, X and Hu, X},
title = {Longitudinal metagenomics reveals continuous restructuring of soil pathobiome under persistent Phytophthora pressure.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1749879},
pmid = {41704794},
issn = {1664-462X},
abstract = {Soil borne pathogen, Phytophthora nicotianae causes black shank disease in tobacco, present a pervasive threat to global agriculture, with conventional control strategies often proving inadequate. A critical gap exists in our understanding of the long-term, dynamic interplay between the pathogen and the soil microbiome. To address this, we conducted a six-year longitudinal metagenomic study in a monocultured tobacco field, revealing a pathobiome in constant, non-equilibrium adaptation. Our analysis uncovered profound microbial restructuring, beginning with cumulative transcriptional reprogramming of highly significant genes. Functional profiling showed a critical metabolic shift toward anabolic capacity, with a 66.7% increase in KEGG orthologs and enrichment of amino acid biosynthesis (+8.9%), ribosomes (+13.0%), and quorum sensing (+11.0%). The soil resistome underwent dramatic succession, featuring an initial coordinated defense (R[2]=0.825), a comprehensive collapse in Year 3-4 (917 downregulated genes), and a resilient recovery that drove a net increase in antibiotic resistance, indicating a lasting ecosystem alteration. Virulence factor evolution revealed strategic trade-offs, with flagella systems dominating (2,583 occurrences) while more costly energy consuming secretion systems declined, and 87 core virulence factors persisted across time. Crucially, we observed a widespread decoupling between genetic potential and functional expression; key categories for defense and signal transduction declined in abundance (slopes of -150.4 and -264.9, respectively) despite stable gene counts, suggesting a systemic, energy conserving survival strategy. Concurrently, the community experienced progressive diversity loss (Shannon index slope = -0.0464/yr at genus level) despite maintained species richness (717 species), indicating restructuring was driven by shifting evenness rather than species loss. Our findings exhibit that persistent pathogen pressure drives the soil microbiome into a continuous state of adaptive restructuring, prioritizing coordinated defensiveness and metabolic efficiency over stability. This time resolved framework challenges static views of soil ecosystems and provides a foundational dataset for developing predictive, microbiome informed strategies to manage soil borne diseases sustainably.},
}

@article {pmid41704740,
year = {2026},
author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C},
title = {Integrated metagenomic and metabolomic analysis reveals regional style differences in Maotai-flavour Baijiu.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100558},
pmid = {41704740},
issn = {2666-5174},
abstract = {This research focused on Maotai-flavour Baijiu from three representative production regions in the Chishui River Basin, namely Maotai Town (MT), Jinsha (JS), and Renhuai (RH). By integrating metabolomics and macrogenomics techniques, the study analyzed the differences in volatile flavor compounds and microbial community structures in the fourth-round fermented grains and base liquor. Additionally, it explored the associative mechanism between microorganisms and flavor metabolism. The findings indicate that the microbial community compositions of fermented grains vary significantly across different production areas. The production area of Maotai Town mainly consists of Saccharomyces and Lactobacillus, with the highest content of ester substances. The fungal community in Jinsha is extremely stochastic, abundant in Mucoromycota, and has elevated contents of aldehydes and phenols. The distribution of microorganisms and flavor substances in the Renhuai production area lies between the two. The sensory evaluation of the base liquor indicates that the Jinsha production area features prominent floral and fruity aromas, the Maotai Town exhibits significant sour and sauce aromas, and the Renhuai production area has a well-balanced flavor. The correlation analysis shows that yeasts such as Saccharomyces and Pichia are positively correlated with esters such as ethyl acetate, while bacteria such as Limosilactobacillus are closely associated with short-chain fatty acid metabolism. This research reveals the microbiological basis for the differences in the Maotai style among different production regions and provides a theoretical foundation for regional characteristic production and process optimization.},
}

@article {pmid41704508,
year = {2026},
author = {Sidiq, Y and Rahayu, T and Indrayudha, P and Tyastuti, EM and Althaf, AZW and Sari, BK},
title = {Metabarcoding data: Full-length 16S rRNA sequence of endophytic bacteria in the root of asymptomatic and blast-symptomatic rice plants (Oryza sativa, L.).},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112522},
pmid = {41704508},
issn = {2352-3409},
abstract = {There is a sustained demand for biofertilizers to enhance crop productivity. Endophytic bacteria associated with disease-tolerant rice varieties offer significant potential as biofertilizers; however, the bacteriome diversity within these plants remains underexplored. This dataset presents full-length 16S metagenomic sequences of endophytic bacteria isolated from the roots of blast-infected and uninfected rice plants. Root samples were processed and subjected to surface sterilisation. Following total genomic DNA extraction, sequencing was performed using 16S ribosomal RNA primers via the high-throughput Oxford Nanopore Technologies platform. The raw sequence data were filtered for quality control using NanoFilt. Subsequently, the sequences were aligned against the National Center for Biotechnology Information (NCBI) 16S RefSeq database to identify the species of the endophytic root bacteria. The data associated with this project have been registered in the NCBI BioProject database under accession number PRJNA992961. The dataset comprises two distinct sample groups, each analysed in duplicate, with sequencing yields ranging from 17.7 to 20.3 Mb. Consequently, this dataset provides valuable insights regarding the comparative composition of endophytic bacteria inhabiting healthy roots versus those found in blast-infected rice. Characterizing this diversity, particularly within healthy rice plants, is essential for foundational research underpinning the future development of biofertilizers.},
}

@article {pmid41704501,
year = {2026},
author = {Yoshioka, Y and Ando, C and Yamashita, H and Kawamitsu, M and Kawachi, M and Tsunematsu, Y and Shoguchi, E},
title = {A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112499},
pmid = {41704501},
issn = {2352-3409},
abstract = {Increasing occurrences of toxic dinoflagellate blooms are a growing concern under climate change. The benthic dinoflagellate Ostreopsis blooms through mechanisms that remain poorly understood and is assumed to produce palytoxin-like compounds such as ovatoxins. Recent studies have highlighted the diversity of bacterial communities associated with Ostreopsis and suggested a possible role for these bacteria in toxin biosynthesis. However, genome information on potential bacterial toxin producers remains limited. Here, we report a dataset of bacterial metagenome-assembled genomes (MAGs) obtained from the culture of the toxic dinoflagellate Ostreopsis cf. ovata strain (NIES-3351). HiFi long reads from PacBio Revio system were assembled with hifiasm-meta. We identified forty complete bacterial MAGs, each with an estimated completeness of 93-100%. These MAGs span a wide range of genome sizes (1.5 Mb to 6.7 Mb) and GC contents (36% to 67%). The dataset is available at DDBJ/ENA/GenBank under accession number PRJDB37958.},
}

@article {pmid41704314,
year = {2026},
author = {Liu, Y and Xu, H and Cao, J and He, Q and Wang, N and Du, M and Zhao, Y and Dugarjaviin, M and Zhang, X},
title = {Effect of equine-derived Lactobacillus M11 on the reproductive performance of KM pregnant female mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741988},
pmid = {41704314},
issn = {1664-302X},
abstract = {INTRODUCTION: This study aimed to evaluate the effects of equine-derived Lactobacillus M11 on reproductive performance and metabolic profiles in pregnant Kunming (KM) mice. The objective was to explore the potential of M11 as a safe and effective alternative to antibiotics in antibiotic-free farming systems.

METHODS: Specific pathogen-free (SPF) female KM mice were randomly assigned to a blank control group (BC) and three intervention groups (M11-L, M11-M, M11-H). The intervention groups received daily gavage of M11 at low (1.0 × 10[7] CFU/mL), medium (1.0 × 10[8] CFU/mL), and high (1.0 × 10[9] CFU/mL) concentrations for 21 days. Host physiological parameters, metagenomic profiles, and metabolomic signatures were analyzed to assess the impact of M11 supplementation.

RESULTS: (1) Host Physiology and Biochemistry: The M11-H group exhibited a significant elevation in albumin (ALB; 40.30 ± 1.75 g/L), suggesting enhanced nutritional status or hepatic protein synthesis. The M11-L group showed transient increases in alanine aminotransferase (ALT; 59.57 ± 10.34 U/L) and total cholesterol (TC; 2.90 ± 0.24 mmol/L), indicative of adaptive hepatic lipid metabolism. (2) Microbial Community Reconfiguration: Metagenomic analysis revealed significant structural shifts in the gut microbiota between the BC and M11-H groups. Notably, the M11-H group showed enrichment of Bacillota, which correlated with "O-antigen nucleotide sugar biosynthesis," while differences in Pseudomonadota were associated with immune regulation. (3) Metabolomic Profiling: Partial Least Squares Discriminant Analysis (PLS-DA) demonstrated clear separation in the cecal metabolome space. KEGG pathway enrichment analysis highlighted significant alterations in "glycine/serine/threonine metabolism" and "arginine/proline metabolism" pathways. (4) Integrated Multi-Omics Analysis: Correlation analysis identified a significant positive association between s_Clostridiaceae_bacterium (Bacillota) and specific metabolites (3-hydroxy-4-aminopyridine sulfate), suggesting the formation of a regulatory "gut-reproductive axis."

DISCUSSION: The results demonstrate that Lactobacillus M11 improves metabolic support during pregnancy through three primary mechanisms: modulation of the gut microbiota, activation of key metabolic pathways, and enhancement of antioxidant capacity. These findings provide a theoretical basis for the application of probiotic-mediated reproductive support in antibiotic-free farming, highlighting M11 as a promising candidate for improving livestock health and productivity.},
}

@article {pmid41704313,
year = {2026},
author = {Ramzan, F and Vassiliou, L and Tsaltas, D},
title = {Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1697953},
pmid = {41704313},
issn = {1664-302X},
abstract = {Orchids, one of the most diverse and ecologically important plant families, form complex associations with endophytic microorganisms that are vital for their survival, growth, and adaptation. These endophytes, including both fungi and bacteria, inhabit orchid tissues without causing harm and contribute to key physiological processes such as nutrient acquisition, stress tolerance, and disease resistance. This review explores the diversity and ecological roles of orchid-associated endophytes, emphasizing their significance in promoting germination, biomass production, and resilience to environmental stressors. Plant Growth-Promoting Bacteria (PGPB) such as Pseudomonas, Bacillus, and Burkholderia enhance nutrient uptake and plant defense, offering eco-friendly alternatives to chemical fertilizers and pesticides. Beyond ecological functions, endophytes show potential in biotechnology for sustainable agriculture, conservation, and novel bioactive compound discovery. Despite advances in molecular tools like metagenomics and next-generation sequencing, challenges persist in fully understanding and utilizing these microbes. This review highlights the need for multidisciplinary collaboration to optimize microbial inoculants, elucidate symbiotic mechanisms, and develop practical applications for conservation and sustainable horticulture. By integrating fundamental research with applied strategies, this work aims to unlock the full potential of orchid-associated endophytes in ecological and commercial domains.},
}

@article {pmid41704276,
year = {2026},
author = {Zhang, Y and Chen, W and Yu, X and Feng, J and Sammad, A and Wang, Z and Yin, K},
title = {Leonurine ameliorates experimental type 2 diabetes through gut microbiota remodeling, enhanced butyrate production, and MPC2 activation to restore GLP-1 secretion.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1747267},
pmid = {41704276},
issn = {1663-9812},
abstract = {The core pathophysiological mechanism of type 2 diabetes mellitus (T2DM) is closely associated with gut microbiota dysbiosis and its consequential impairment of enteroendocrine glucagon-like peptide-1 (GLP-1) secretion. T2DM mouse model was established using high-fat diet (HFD) feeding combined with streptozotocin (STZ) administration. Diabetic mice received 30 or 60 mg/kg of leonurine (LEO) via daily gavage for 12 weeks. Gut microbiota composition was profiled by metagenomic sequencing, fecal short chain fatty acids (SCFAs) concentrations were quantified via enzyme-linked immunosorbent assay (ELISA), and GLP-1 expression was assessed using oral glucose tolerance tests (OGTT), ELISA, and immunofluorescence. In vitro, high-glucose (25 mM)-challenged GLUTag enteroendocrine cells were employed to delineate the butyrate-mitochondrial pyruvate carrier 2 (MPC2) regulatory network using qPCR and Western blotting. LEO intervention significantly ameliorated glucose intolerance in diabetic mice and elevated GLP-1 levels in serum and colonic tissues. Metagenomic analysis revealed that LEO (60 mg/kg) remodeled gut microbiota structure, markedly enhancing α-diversity and specifically enriching butyrate-producing Alistipes. Mechanistically, butyrate activated MPC2 expression, effectively restoring cristae architecture defects observed by transmission electron microscopy, thereby promoting GLP-1 secretion. Crucially, MPC2 knockdown abrogated the secretagogue effect of butyrate on GLP-1 in GLUTag cells. LEO alleviates T2DM by remodeling the gut microbiota ecosystem, enhancing butyrate biosynthesis, and activating an MPC2-dependent mitochondrial energy metabolism pathway to reverse GLP-1 secretory dysfunction in intestinal L cells. This study establishes MPC2-mediated mitochondrial functional repair as a core mechanism through which microbial metabolites regulate enteroendocrine hormone secretion, identifying a novel therapeutic target within the "gut-islet axis" for diabetes intervention. Future studies should identify its active constituents, elucidate downstream effectors, and validate this mechanism in germ-free models.},
}

@article {pmid41703832,
year = {2026},
author = {Yao, X and Chen, X and Niu, J and Li, J and Li, W and Zhu, H and Li, X and Sun, B},
title = {Storage time drives divergent microbial functions and flavor metabolism in high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118363},
doi = {10.1016/j.foodres.2026.118363},
pmid = {41703832},
issn = {1873-7145},
mesh = {*Food Storage/methods ; *Taste ; *Hot Temperature ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Metagenomics ; Metabolomics ; Time Factors ; Bacteria/metabolism/classification ; *Flavoring Agents/metabolism ; },
abstract = {Baijiu is a traditional Chinese distilled liquor, whose unique flavor highly relies on the synergistic metabolism of diverse microbial communities during the brewing process. The high-temperature Daqu (HTD) used in sauce-flavor Baijiu plays a crucial role in flavor synthesis due to its enrichment of heat-resistant functional microbiota. However, traditional techniques have limited understanding of microbial community succession and functional dynamics during Daqu storage, hindering precise quality and flavor regulation. This study systematically investigated the dynamic evolution of physicochemical indexes, microbial community structure, metabolic functions, and flavor compounds in HTD during different storage periods (1st, 3rd, and 6th months) through integrated metagenomics and GC-MS metabolomics. Results showed continuous decreases in moisture, starch, and pH during storage, while aminopeptide nitrogen and acidity peaked at the 3rd month. Esters reached their highest levels at the 1st month (YQ), alcohols peaked at the 3rd month (EQ), and aldehydes dominated at the 6th month (SQ). LEfSe analysis identified Kroppenstedtia eburnea and Paecilomyces variotii as biomarkers for YQ, Saccharopolyspora rectivirgula and Aspergillus chevalieri for EQ, and Rasamsonia emersonii for SQ. Metagenomic analysis revealed differential carbohydrate and amino acid metabolism pathways: YQ showed highest enzyme abundance for phenethyl alcohol metabolism, EQ exhibited peak enzymes for pyrazine synthesis and ethanol metabolism, while SQ demonstrated superior glucoamylase activity. In addition, maximum tetramethylpyrazine at the 3rd month and highest microbial diversity in later storage (6th month).},
}

*Food Storage/methods
*Taste
*Hot Temperature
*Alcoholic Beverages/microbiology/analysis
*Microbiota
*Food Microbiology
Gas Chromatography-Mass Spectrometry
Metagenomics
Metabolomics
Time Factors
Bacteria/metabolism/classification
*Flavoring Agents/metabolism

@article {pmid41703795,
year = {2026},
author = {Pais, ACS and Ribeiro, TB and Coscueta, ER and Salsinha, AS and Pintado, MM and Silvestre, AJD and Santos, SAO},
title = {Phenolic compounds' impact on gut microbiota: Insights from in vitro batch fecal fermentation for composition modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118167},
doi = {10.1016/j.foodres.2025.118167},
pmid = {41703795},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Feces/microbiology ; *Fermentation ; Fatty Acids, Volatile/metabolism/analysis ; *Phenols/pharmacology/metabolism ; Prebiotics ; Flavanones/pharmacology/metabolism ; Ellagic Acid/pharmacology/metabolism ; Bacteria/drug effects/genetics/metabolism ; Male ; Adult ; Female ; },
abstract = {The relationship between phenolic compounds and gut microbiota (has been widely studied to explore the health benefits of these bioactive dietary compounds. Phenolic compounds are metabolized by gut microbiota, while also modulating its composition. However, the individual effects of these compounds on human gut microbiota remain underexplored. To address this, three phenolic compouds-ellagic acid, naringenin, and phloroglucinol-underwent in vitro batch fermentation with fecal samples from healthy donors. Samples were analyzed through 16S metagenomics sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography. Results showed that ellagic acid and phloroglucinol had prebiotic properties, producing SCFAs like acetic, propanoic, and butyric acids and promoting the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium. In contrast, naringenin was linked to the growth of pathogenic genera like Escherichia and Salmonella. This study provides valuable insights into how specific phenolic compounds influence gut microbiota composition, contributing to potential pharmaceutical or nutraceutical developments.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Feces/microbiology
*Fermentation
Fatty Acids, Volatile/metabolism/analysis
*Phenols/pharmacology/metabolism
Prebiotics
Flavanones/pharmacology/metabolism
Ellagic Acid/pharmacology/metabolism
Bacteria/drug effects/genetics/metabolism
Male
Adult
Female

@article {pmid41703237,
year = {2026},
author = {Ariyo, S and Sanusi, IO and Veerabhadrappa, K and Tenywa, MG and Olutona, GO and Onohuean, H},
title = {Deterministic and probabilistic health risk assessment of heavy metals in liquid herbal cough formulations from Western Uganda.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40622-3},
pmid = {41703237},
issn = {2045-2322},
abstract = {This study investigated the concentrations and human health risks (carcinogenic and non-carcinogenic) associated with heavy metals in liquid herbal cough formulations obtained from the Western Region of Uganda. Twelve brands of registered (government authority) herbal cough formulations from reputable pharmacies were obtained and analysed. The mixtures were acid digested prior to Atomic Absorption Spectroscopy (AAS) analysis to quantify cadmium (Cd), copper (Cu), iron (Fe), lead (Pb), nickel (Ni), and zinc (Zn) in the herbal formulations, followed by human health risk assessment, using two different approaches: deterministic and probabilistic (Monte Carlo simulation). The results showed significant variations in heavy metal concentrations, with Cu, Fe, Ni, Cd, Pb, and Zn ranging from 0.020 to 1.272, not detected (ND) to 6.734, ND to 0.129, 0.002 to 0.051, ND to 0.190, and 0.043 to 0.527 mg/L, respectively, within the World Health Organization limit (WHO). Multivariate statistical analysis revealed that anthropogenic activities were the major source of heavy metal contamination. The hazard index (HI) values obtained ranged from 7.0 × 10[-4] to 2.59 × 10[-2] in children and 6.0 × 10[-4] to 2.49 × 10[-2] in adults, indicating extremely low non-carcinogenic risk (HI < 1) of exposure to heavy metals. Similarly, the incremental lifetime carcinogenic risks (ILCRs) of Ni, Pb, and Cd for both the children and adults were below the acceptable limit of 1.0 × 10[-4], indicating no carcinogenic health risk. Moreover, the probabilistic risk assessment revealed that Pb and Cd had less than a 0.01% chance of exceeding the WHO limit (negligible risk). Findings from this study indicate that heavy metal concentrations in the brands of herbal cough formulations from Western Uganda are below the safety thresholds and are safe for consumption under realistic exposure conditions.},
}

@article {pmid41702980,
year = {2026},
author = {Paoli, JE and Aung, O and Lilak, AA and Maw, MT and Cleary, NG and Watto, E and Hassell, J and Win, YT and Thein, WZ and Evans, TS and Valitutto, M and Goldstein, T and Johnson, CK and Mazet, JA and Fleischer, R and VanTassel, N and Subramaniam, K and Anderson, BD and von Fricken, ME and Mavian, CN and Murray, S},
title = {Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38406-w},
pmid = {41702980},
issn = {2045-2322},
support = {AID-OAA-A-14-00102 , GHN-A-OO-09-0001000//United States Agency for International Development/ ; },
}

@article {pmid41702865,
year = {2026},
author = {Zhang, Z and Li, Z and Chen, X and Zu, Y and Li, S and Liang, B and Ho, SH and Wang, A},
title = {Simultaneous Trichloroacetate Dechlorination Metabolism and Nitrogen Fixation in Nitrogen-Limited Aquifers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c16767},
pmid = {41702865},
issn = {1520-5851},
abstract = {Haloacetates, particularly trichloroacetate (TCAA), are pervasive contaminants, yet their biotransformation in anoxic, nutrient-limited environments remains poorly understood. Here, we elucidate a geographically widespread attenuation of haloacetates in nutrient-limited aquifers by field surveys across six Chinese provinces. Enrichment cultures metabolized TCAA as the sole carbon and energy source. Major metabolites (oxalate, acetate, CO2) indicated complete hydrolytic dechlorination accompanied by fermentation and mineralization. Isotope labeling and chemical probe studies confirmed the simultaneous occurrence of TCAA dechlorination and nitrogen fixation under fixed nitrogen-limited conditions. Integrated metagenomic, metabolomic, and transcriptional analyses demonstrated nitrogen-regulated metabolic reconfiguration. Acetyl-CoA potentially associated with TCAA metabolism may enter the TCA cycle under nitrogen-limited conditions. Dehalogenase gene (had) homologues extensively co-occurred with homologues of nitrogenase genes (nifHDK) in oligotrophic environments. Potential cross-feeding interactions among unclassified Azospira sp., Ralstonia pickettii, and Azospira inquinata mediated carbon-nitrogen intermediate exchange. This study identifies a previously unrecognized process that enables simultaneous TCAA detoxification and nitrogen acquisition in oligotrophic aquifers, thereby proposing an energy-conserving and ecologically adaptive strategy for haloacetate bioremediation.},
}

@article {pmid41702524,
year = {2026},
author = {Lips, S and Schmitt-Jansen, M and Borchert, E},
title = {Metagenomic analyses of the plastisphere reveals a common functional potential across oceans.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {395},
number = {},
pages = {127830},
doi = {10.1016/j.envpol.2026.127830},
pmid = {41702524},
issn = {1873-6424},
abstract = {Trillions of plastic particles have accumulated in the oceans, covered by microbial biofilms (termed 'plastisphere') whose functional potential remains underexplored. We evaluated as one of the first of its kind genome-resolved bacterial metagenomes of the plastisphere from the North Atlantic and North Pacific garbage patches and compared their structure and functional potential to ambient plankton. Our data revealed a characteristic genetic potential of the plastisphere with functionally equivalent traits across both oceans. We found more coding genes, bigger genomes and higher GC-content in the plastisphere in comparison to the surrounding plankton community, despite residing in the same environment, reflecting an increased metabolic capacity in the plastisphere. An analysis of 340 functional genes confirmed that the plastisphere consists of microorganisms with a higher potential for nutrient metabolism, metabolize a wider range of carbon sources, attenuate radicals, fix their own nitrogen and use alternative energy sources like anoxygenic photosynthesis. Our results suggest that the overriding factor for the high functional similarity of the plastisphere in both oceans is the habitat for biofilm formation with the potential to support mutualism and nutrient sharing making genomic streamlining as found in plankton, unnecessary. Consequently, increasing plastic pollution promotes the expansion of a new functional unit at the surface of the oligotrophic oceans with various roles in biogeochemical cycles.},
}

@article {pmid41702518,
year = {2026},
author = {Wang, X and Huo, X and Hu, H and Wang, Y and Cheng, W and Wang, Y and Sun, C and Wu, X and Chen, Y},
title = {Metagenomic mining and functional reconstitution of hexanoic acid biosynthetic enzymes from Baijiu pit bottom.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134231},
doi = {10.1016/j.biortech.2026.134231},
pmid = {41702518},
issn = {1873-2976},
abstract = {Hexanoic acid is a key flavor compound in Baijiu and a valuable platform chemical, yet its efficient biosynthesis remains challenging. To overcome the carbon chain elongation bottleneck in the reverse β-oxidation (RBO) pathway in Saccharomyces cerevisiae, this study explored the metagenomic resource of a hexanoic acid-producing microbial community from the bottom of Jiang-flavor Baijiu pit. Three enriched hexanoic acid-producing consortia were obtained, all co-producing butanoic, hexanoic, and octanoic acids. Metagenomic analysis showed that while microbial compositions differed, the consortia shared similar core functional enzymes. Further correlation analysis identified 3-hydroxyacyl-CoA dehydrogenase (HBD) and acetate CoA-transferase (CAT) as key enzymes positively correlated with hexanoic acid synthesis. These enzymes were then expressed in an engineered RBO-pathway yeast strain. Expression of CAT-1 increased butanoic and hexanoic acid production by 25% and 34%, respectively, marking the first application of CAT in enhancing chain elongation in yeast. In summary, this study innovatively identified the key enzyme CAT from the microbiota of Jiang-flavor Baijiu pit bottom and achieved efficient hexanoic acid synthesis through heterologous expression. This work not only offers a strategy for mining high-performance enzymes but also provides theoretical support and technical references for the efficient biosynthesis of hexanoic acid.},
}

@article {pmid41702480,
year = {2026},
author = {Wang, B and Jiang, Y and Li, D and Wang, C},
title = {Enhancing the diagnosis accuracy of Chlamydia psittaci infection via metagenomic next-generation sequencing.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105895},
doi = {10.1016/j.meegid.2026.105895},
pmid = {41702480},
issn = {1567-7257},
abstract = {Metagenomic next-generation sequencing (mNGS) is an innovative diagnostic technique that integrates high-throughput sequencing with bioinformatics analysis. Recently, its unbiased approach, broad pathogen coverage, and rapid turnaround have led to its expanded use in diagnosing infectious diseases. This is particularly true for atypical bacterial pathogens such as Chlamydia psittaci, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Legionella spp., for which mNGS has demonstrated significant diagnostic utility. C. psittaci, a highly pathogenic obligate intracellular bacterium, can cause severe community-acquired pneumonia (CAP). Its virulence is attributed to unique genomic pathogenicity islands, which encode both a specialized secretion system (such as the Type III Secretion System) and effector proteins like the Chlamydial Protease-like Activity Factor (CPAF), coupled with its capacity for rapid intracellular replication. Furthermore, its close genetic similarity to C. pneumoniae complicates differentiation by standard Polymerase Chain Reaction (PCR) assays. This review examines the advancements in using mNGS to diagnose C. psittaci infections in clinical settings and discusses the remaining challenges. The excessive use of antibiotics in clinical practice is still a common problem. Through its unbiased detection, mNGS can accurately identify mixed infections, thereby providing a microbiological basis for targeted antibiotic therapy. Our compilation of case reports and studies from the last five years indicates that mNGS effectively assists clinicians in promptly adjusting antibiotic regimens and holds great potential for the clinical identification of chlamydial co-infections.},
}

@article {pmid41702469,
year = {2026},
author = {Qin, L and Wu, D and Yang, J and Song, Y and Shen, C},
title = {Macro-scale resuspension governs gene-scale mechanisms of phosphorus cycling in a shallow lake.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124040},
doi = {10.1016/j.envres.2026.124040},
pmid = {41702469},
issn = {1096-0953},
abstract = {Internal phosphorus loading from sediments is becoming a major barrier to lake restoration, yet the mechanisms governing phosphorus dynamics under sediment resuspension remain poorly understood. Using controlled laboratory experiments with sediments collected from Lake Yangcheng, we examined how disturbance intensity, frequency, and duration regulate phosphorus fractions, alkaline phosphatase activity (APA), microbial community composition, and functional gene expression. Our results revealed that low-intensity disturbance, especially under high-frequency intermittent disturbance, enhanced organic phosphorus mineralization, characterized by elevated phosphate, increased APA and strong upregulation of phoB and phoX genes. Metagenomic sequencing results further showed that these conditions supported high richness of phosphorus-solubilizing bacteria (PSB), sustaining biologically mediated conversion of organic phosphorus to bioavailable phosphate. In contrast, high-intensity disturbance shifted phosphorus dynamics toward particulate dominance, rapidly satisfying microbial phosphate demand and suppressing phosphatase expression and enzymatic mineralization. Across all disturbance treatments, Pseudomonadota remained the dominant PSB phylum, and phoB consistently exhibited the highest abundance among functional genes, underscoring their central roles in phosphorus cycling. In all, our experiments demonstrate that disturbance intensity determines whether internal phosphorus loading is governed primarily by microbial or physical processes. This study highlights that optimizing resuspension patterns, rather than simply minimizing total disturbance, may provide a more effective strategy for controlling internal loading and reducing algal bloom risk in shallow urban lakes.},
}

@article {pmid41702430,
year = {2026},
author = {Nozaki, T and Kobayashi, Y and Ikeda, M and Shigenobu, S},
title = {Symbiont replacement and subsequent genome erosion reshape a dual obligate aphid symbiosis.},
journal = {Proceedings. Biological sciences},
volume = {293},
number = {2065},
pages = {},
doi = {10.1098/rspb.2025.2484},
pmid = {41702430},
issn = {1471-2954},
support = {//Japan Society for the Promotion of Science/ ; },
mesh = {*Symbiosis ; Animals ; *Aphids/microbiology/physiology ; *Buchnera/genetics/physiology ; *Serratia/genetics/physiology ; *Genome, Bacterial ; Phylogeny ; },
abstract = {Many insects rely on obligate microbial symbioses, often involving multiple partners. Although symbiont replacement is well-documented, how newly acquired and resident obligate symbionts adapt after such events remains unclear. Here, we investigate the dual obligate symbiosis of the aphid Lachnus tropicalis, where an ancestral Serratia lineage was replaced by a newly acquired Serratia lineage while the primary symbiont Buchnera remained. Our metagenomic sequencing yielded complete genomes of Buchnera (0.42 Mb) and Serratia (2.8 Mb), revealing developing metabolic complementarity. Although the Serratia genome retained abundant gene sets for amino acid synthesis, it also contained pseudogenes in leucine and methionine pathways, which would be compensated for by Buchnera or the host. Comparison with Lachnus roboris, which harbours the ancestral Serratia lineage, showed that the newly acquired Serratia in L. tropicalis exhibits identical tissue localization and vertical transmission pattern, suggesting the smooth succession of the prior microniche. Notably, Buchnera in L. tropicalis exhibited a slightly more degenerated genome than its counterpart in L. roboris, indicating that symbiont replacement can accelerate gene loss even in ancient symbionts. Overall, our findings provide new insights into the dynamics of novel mutualism establishment and highlight symbiont replacement as a driver of host-symbiont co-evolution.},
}

*Symbiosis
Animals
*Aphids/microbiology/physiology
*Buchnera/genetics/physiology
*Serratia/genetics/physiology
*Genome, Bacterial
Phylogeny

@article {pmid41702408,
year = {2026},
author = {Hernández-Vázquez, A and Garcia-Arellano, H and González-Cervantes, RM and López-Pérez, M and Soto, LMH and Meza, JAC and Aguirre-Garrido, JF},
title = {Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70279},
doi = {10.1111/1758-2229.70279},
pmid = {41702408},
issn = {1758-2229},
mesh = {*Lakes/microbiology ; Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; *Hydroxybutyrates/metabolism ; Mexico ; Metagenome ; Bacterial Proteins/genetics/metabolism ; *Polyesters/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Carboxylic Ester Hydrolases/genetics/metabolism ; Polyhydroxybutyrates ; },
abstract = {Crater Lake (Isabel Island, Mexico) is a meromictic, stratified, haloalkaline system. To identify and characterise PHB depolymerases across the vertical physicochemical gradients of the lake, we analysed seven metagenomes from the water column (0-23 m), one sediment metagenome, and the genomes of two organisms (HB105m and VN105m) isolated from 5 m. Taxonomic profiles revealed vertical stratification: Actinobacteriota and Cyanobacteriota dominated surface waters, while Pseudomonadota, Bacillota, and Bacteroidota prevailed in deeper layers and sediments. Alpha-diversity indices peaked at 5 and 20 m and declined at 23 m. We identified 16 putative PHB depolymerases spanning a broader phylogenetic range than previously documented for haloalkaline ecosystems. These included homologues affiliated with Vreelandella, Thiomicrorhabdus, Chloroflexota, Candidatus Cloacimonadota, and Desulfobacterales. The structural variation observed in lipase-box motifs and signal peptides suggests functional differentiation linked to redox and oxygen gradients across depths. Phylogenetic analysis of predicted and reference enzymes showed depth-specific clustering, with extracellular depolymerases predominant in oxic layers and intracellular forms more common in microoxic-anoxic zones. Overall, our results expand the known diversity of PHB-degrading lineages in extreme environments and highlight several candidate enzymes with potential biotechnological relevance for future experimental characterisation.},
}

*Lakes/microbiology
Phylogeny
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
*Hydroxybutyrates/metabolism
Mexico
Metagenome
Bacterial Proteins/genetics/metabolism
*Polyesters/metabolism
*Microbiota
Geologic Sediments/microbiology
*Carboxylic Ester Hydrolases/genetics/metabolism
Polyhydroxybutyrates

@article {pmid41700856,
year = {2026},
author = {Zhang, R and Poulain, AJ and Pu, Q and Liu, J and Abdelhafiz, MA and Feng, X and Meng, B and Grégoire, DS},
title = {Methane cycling microbes are important predictors of methylmercury accumulation in rice paddies.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0202825},
doi = {10.1128/aem.02028-25},
pmid = {41700856},
issn = {1098-5336},
abstract = {Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice-growing season to identify microbial and environmental factors influencing methylmercury dynamics. We show that hgcA gene abundance, the key gene required for methylation, was not a significant predictor of methylmercury concentration in paddy soils. We also show that the merB gene abundance correlated with methylmercury in mercury-polluted rhizosphere samples. Methane cycling genes were actively expressed, and their beta-diversity was significantly associated with methylmercury levels. Methanogen abundance correlated with higher methylmercury under elevated total mercury concentrations. Analysis of the methanotroph-associated mbnT gene, implicated in demethylation, revealed an unexpected positive correlation with methylmercury. Multiple regression and machine learning models converged on mercury bioavailability and methanogen/methanotroph abundances as key predictors of methylmercury, with methanogen-associated hgcA gene abundance and methanogen-methanotroph interactions highlighted under flooded, low-redox conditions. These findings suggest that methane-cycling microbes play key roles in methylmercury cycling dynamics and point to management strategies that could simultaneously mitigate mercury pollution and greenhouse gas emissions.IMPORTANCEMethylmercury is a microbially derived neurotoxin that accumulates in the food staple rice (Oryza sativa). Mitigating the health effects of methylmercury exposure requires predicting mercury cycling dynamics in rice paddies. This task is challenging because of the complex interplay of microbial and environmental factors. Our study coupled genomic and geochemical measurements with machine learning models to identify the key biological indicators of methylmercury accumulation. We demonstrated that the abundance of methanogens and methanotrophs is a major microbial predictor of methylmercury variability. This predictive framework, which considers the interactions between these coupled microbial guilds, offers greater power than methods relying only on mercury methylation genes. These findings inform better management and remediation strategies for rice paddies, offering a path to reduce methylmercury exposure and mitigate greenhouse gas emissions.},
}

@article {pmid41700755,
year = {2026},
author = {You, C and Ren, P and Guan, Y and Gong, K and Hua, Z and Zhou, W and Mei, X and Wang, Y and Wang, X and Xu, Y and Shen, Q and Wei, Z},
title = {Forecasting Root Rot Disease through Predictive Microbial Functional Profiling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e22628},
doi = {10.1002/advs.202522628},
pmid = {41700755},
issn = {2198-3844},
support = {2022YFC3501501//National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; KJYQ2025034//Fundamental Research Funds for the Central Universities/ ; BK20240194//Natural Science Foundation of Jiangsu Province/ ; 42377118//National Natural Science Foundation of China/ ; 42277113//National Natural Science Foundation of China/ ; BE2022423//Jiangsu Carbon Peak & Carbon Neutrality Science and Technology Innovation Special Fund/ ; 2024M760612//China Postdoctoral Science Foundation/ ; },
abstract = {Early diagnosis of soil-borne diseases like root rot is a long-standing challenge in agriculture. While microbial functional genes are recognized as potent indicators of soil healthy, their application has been primarily limited to current or past soil conditions. Here, we demonstrate that microbial functional genes can transition from descriptive indicators to reliable predictive biomarkers. By analyzing 199 paired metagenomes from healthy and diseased medicinal plants rhizosphere soil samples, we identified a conserved core set of functional genes, specifically those governing biofilm formation, stress response, and plant-microbe mutualism that are robustly associated with root rot disease. To bridge the gap between discovery and field application, we developed a framework that integrates cost-effective qPCR assay for these key genes and fused their abundance data with machine learning. This model achieved over 80% accuracy in predicting disease onset from independent, pre-symptomatic soil samples, identifying risks long before visible symptoms of infection appeared. Our findings suggest a practical path for moving beyond simple microbial correlations toward an active forecasting tool. By positioning microbial functional genes at the core of disease management, this framework provides a targeted approach for mitigating soil-borne risks and supporting sustainable agricultural practices.},
}

@article {pmid41700136,
year = {2026},
author = {Hubot, N and Giering, SLC and Orel, N and Klun, K and Herndl, GJ and Hohaus, F and Lucas, CH and Tinta, T},
title = {Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20784},
pmid = {41700136},
issn = {2167-8359},
mesh = {*Scyphozoa/chemistry/metabolism ; Animals ; *Microbiota ; *Mucus/chemistry/metabolism ; Seawater/microbiology/chemistry ; Nitrogen/metabolism/analysis ; *Nutrients/metabolism ; Ecosystem ; Amino Acids/metabolism ; },
abstract = {Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish-primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)-remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h[-1] until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findings highlight that live jellyfish, through the release of OM, play an active and previously underappreciated role in shaping ambient microbial community dynamics and nutrient fluxes in marine systems affected by jellyfish blooms.},
}

*Scyphozoa/chemistry/metabolism
Animals
*Microbiota
*Mucus/chemistry/metabolism
Seawater/microbiology/chemistry
Nitrogen/metabolism/analysis
*Nutrients/metabolism
Ecosystem
Amino Acids/metabolism

@article {pmid41699596,
year = {2026},
author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X},
title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-07744-8},
pmid = {41699596},
issn = {1479-5876},
support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; },
}

@article {pmid41699578,
year = {2026},
author = {Wu, H and Li, N and Yang, S and Qiu, J and Zhang, M and Wang, L and Gao, R and Wu, L and Yu, Q and Cheng, X},
title = {Prevotella denticola promotes caries by inducing oral microbial dysbiosis.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-07876-9},
pmid = {41699578},
issn = {1472-6831},
support = {82170937//the National Nature Science Foundation of China/ ; 81800955//the National Nature Science Foundation of China/ ; (No. 2025GH-YBXM-033)//External Cooperation Areas of the Key Research and Development (R&D) Program of Shaanxi Province/ ; LCB202408//the Special Project of the National Clinical Research Center for Oral Diseases/ ; },
}

@article {pmid41699270,
year = {2026},
author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E},
title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41699270},
issn = {2058-5276},
abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.},
}

@article {pmid41699049,
year = {2026},
author = {Wu, LL and Liao, YJ and Peng, WH and Chen, LK and Huang, YC and Chen, CY and Juan, CC},
title = {FK506-binding protein-5 in high-fat diet-induced metabolic dysfunction-associated steatotic liver disease.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38549-w},
pmid = {41699049},
issn = {2045-2322},
support = {108-2320-B-010-045-MY3, 110-2320-B-002-080-MY3, MOST 111-2314-B-A49-072, NSTC 112-2314-B-A49-028-MY3, NSTC 112-2740-B-A49-002, NSTC 113-2740-B-A49-003, NSTC 113-2321-B-A49-014-, NSTC 114-2321-B-A49-004 -, NSTC 114-2740-B-A49-003//Ministry of Science and Technology, Taiwan/ ; MOST 106-2320-B-010-009-MY3//Ministry of Science and Technology, Taiwan/ ; CI-110-22 and CI-111-24//Yen Tjing Ling Medical Foundation/ ; },
abstract = {A high-fat diet (HFD) alters the gut microbiota (GM), impairs metabolic efficiency, and increases gut permeability and inflammation. Obesity and insulin resistance are associated with GM dysbiosis. The GM is strongly associated with metabolic disorders and fatty liver disease. The co-chaperone protein FK506-binding protein-5 (FKBP5) regulates several vital cellular processes. Although FKBP5 has been implicated in stress-related disorders, it has not been directly linked to HFD-induced metabolic fatty liver disease. This study aimed to elucidate how FK506 binding protein 5 impairment affects the GM in HFD-induced metabolic dysfunction-associated fatty liver disease and metabolic dysfunction-associated steatotic liver disease (MASLD). Wild-type and FKBP5-knockout (FKKO) mice were fed a normal chow diet or a high-fat diet for 16 weeks. Mouse GM was examined using 16 S rRNA metagenomic analysis. The number of gut-liver immune cells was measured using flow cytometry. HFD-induced hepatic steatosis and inflammation were prevented in FKBP5-deficient mice. FKKO animals showed higher butyric acid levels and GM resistance to diet-induced obesity alterations according to 16 S ribosomal rRNA gene analysis and displayed an HFD-specific gut-liver immunological response that maintained gut barrier failure and mucosal immunity, which are important for GM homeostasis. FKBP5 helps the GM address inadequate immunological responses, including lower gut and liver CD11b[+]Ly6C[+] monocytes and neutrophils, and protects against obesity by improving the GM response to HFD-induced MASLD. FKBP5 protects against HFD-induced MASLD through metabolic coordination between the gut barrier and intrahepatic immunity.},
}

@article {pmid41698961,
year = {2026},
author = {Mascarenhas, AC and Kantor, RS and Thissen, J and Kok, CR and Borucki, M and Morales, C and Messenger, S and Jaing, C and Wadford, DA},
title = {Metagenomic sequencing identifies potential respiratory pathogens in PCR-negative subset of surveillance samples.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33917-4},
pmid = {41698961},
issn = {2045-2322},
support = {grant 6 Nu50CK000539//Centers for Disease Control and Prevention Epidemiology and Laboratory Capacity for Community Surveillance/ ; },
abstract = {Respiratory pathogens are a significant source of global morbidity, mortality, and economic burden, with the COVID-19 pandemic driving increased interest in and funding for respiratory disease surveillance. Syndromic panel multiplex nucleic acid amplification tests (NAATs) such as the BioFire Respiratory Panel (RP) are designed to identify the most common etiologic agents of respiratory illness. Untargeted metagenomic sequencing is a powerful tool for pathogen-agnostic detection, enabling the recovery of complete genomes for genomic epidemiology and variant tracking. In this study, we performed untargeted metagenomic sequencing of 305 samples previously negative by BioFire RP and SARS-CoV-2 testing and 26 samples that were previously positive by either of the diagnostic tests. A subset of 78 samples underwent probe-capture enrichment sequencing targeting human viruses. Using these methods, we identified human respiratory viruses in 16 of the 305 previously negative samples (5%). The most common viruses identified were Influenza C virus, Human Bocavirus, Rhinovirus A and C, and SARS-CoV-2. Consensus genomes were recovered for 14 viruses with > 90% coverage breadth, revealing closely related Bocavirus strains from neighboring counties and distinct Rhinovirus strains across samples. We also identified 21 samples with a single predominant bacterial or fungal species in the previous negative cohort. These findings underscore the challenges of identifying causal agents from multiplex NAAT-negative cases and highlight the utility of metagenomics for expanding the scope of pathogen surveillance.},
}

@article {pmid41698575,
year = {2026},
author = {Du, Y and Zhao, S and Hu, Y and Wang, X and Zhang, L and Lin, B and Wang, M and Xu, Q},
title = {Dietary selection of starters drives changes of growth performance, fermentation, hindgut microbiome, and metabolism in preweaning calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27473},
pmid = {41698575},
issn = {1525-3198},
abstract = {Early feeding of starter is an effective strategy for modulating gastrointestinal microbiota in newborn calves. However, the effects of starter nutrient composition on calf gut microbiota vary significantly. Although both fiber and starch are essential for early calf nutrition, each has distinct advantages and disadvantages. This study investigated how high-starch and high-fiber diets influence growth performance, hindgut health, and microbiota in calves. Two groups of calves were fed experimental starters with distinct nutrient compositions: a high-starch (HS, n = 8) diet containing 40.4% starch and 13.3% NDF, and a high-fiber (HF, n = 7) diet containing 18.8% starch and 30.5% NDF (DM basis). The experiment spanned calf ages 14 to 63 d, with weekly BW and body size measurements using calibrated scales and measuring tape. Serum was collected via jugular venipuncture for metabolic marker analysis. At trial end, animals were slaughtered to collect hindgut tissues and contents for immunoblotting, metagenomic sequencing, and metabolite analysis. We identified a fundamental trade-off that HS feeding shaped a Bifidobacterium-dominated enterotype, correlating with superior growth performance. In contrast, HF feeding selected for a Bacteroides-dominated, more mature microbiota and significantly enhanced gut barrier integrity by upregulating key tight junction proteins (ZO-1, Claudin-1, and E-cadherin). Multiomics integration revealed that this trade-off was underpinned by different microbial metabolic pathways. The HS hindgut was enriched in enzymes and metabolites for carbohydrate and AA fermentation, driving growth. Conversely, the HF hindgut exhibited enhanced enzymatic capacity for fiber degradation (e.g., starch phosphorylase) and a metabolic profile favoring arginine biosynthesis and acetate production, which supported barrier function. This functional divergence was further evidenced in distinct short-chain fatty acid (SCFA) profiles. The HF group exhibited significantly elevated acetate and a trend for higher total SCFA concentration, whereas the HS group showed increased branched-chain fatty acids (isovalerate) and a trend toward higher butyrate and valerate proportions. Our findings provide a mechanistic model linking dietary carbohydrate source to a fundamental choice between growth optimization and gastrointestinal health in preweaning calves, offering novel insights for targeted nutritional strategies.},
}

@article {pmid41698537,
year = {2026},
author = {Wang, D and Ren, Z and Fu, W},
title = {Research on performance differences and mechanisms of sulfur-iron composite packing materials prepared from different iron sources in nitrogen and phosphorus removal from wastewater.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134220},
doi = {10.1016/j.biortech.2026.134220},
pmid = {41698537},
issn = {1873-2976},
abstract = {To address the structural instability and limited nutrient removal of traditional fillers, this study fabricated four novel composite fillers-incorporating zero-valent iron (Fe[0]), siderite (FeCO3), pyrite (FeS2), and calcium carbonate-via a melt-encapsulation method. Batch and continuous experiments systematically revealed distinct nitrogen and phosphorus removal mechanisms and microbial architectures among these fillers. While all exhibited denitrification potential, S-FeCO3 demonstrated superior shock resistance, maintaining 78.36-94.71 % nitrogen removal and reducing sulfate accumulation by 30.92 %. Conversely, S-Fe[0] caused significant nitrite accumulation (2.83 mg/L). For phosphorus, S-FeCO3 (80.53-84.49 %) significantly outperformed S-FeS2 (70.84-78.57 %) and S-Fe[0]. Microbial analysis showed a transition from Thiobacillus dominance in S-CaCO3 to Thiobacillus-Ferritrophicum co-dominance in iron-coupled systems. At the molecular level, sulfur-iron coupling up-regulated key denitrification genes (narG, nirS, nirK, nosZ) by accelerating electron transfer and relieving Fur-mediated repression, providing a systematic strategy for filler optimization in simultaneous nutrient removal processes.},
}

@article {pmid41698498,
year = {2026},
author = {Song, Y and Li, X and Li, C and Xu, J and Liu, F and Zhao, Z and Zhong, X},
title = {A Case Study of Delayed-Diagnosed Leprosy: Advancing Diagnosis through MetaPath.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108490},
doi = {10.1016/j.ijid.2026.108490},
pmid = {41698498},
issn = {1878-3511},
abstract = {BACKGROUND: Leprosy, a chronic infectious disease caused by Mycobacterium leprae, can lead to sensory deficits, motor impairment, disability, and social stigma, imposing a dual physical and psychological burden on patients. Early diagnosis and standardized treatment are therefore crucial. Metagenomic Capture Technology for Pathology (MetaPath) is a probe-capture-based high-throughput sequencing technology for pathogen nucleic acids, which holds promise for the early detection of Mycobacterium leprae in pathological specimens.

CASE SUMMARY: A 78-year-old male presented with erythematous, scaly and pruritic plaques on his trunk and extremities for over six months, worsening in the last two months. Initial differential diagnoses, including dermatomyositis, psoriasis, and mycosis fungoides, were not confirmed by laboratory or histopathological examinations. Subsequent, MetaPath revealed the presence of Mycobacterium leprae. Further history-taking revealed a prior contact with a leprosy patient and similar, undiagnosed symptoms dating back five years. The patient was finally diagnosed with paucibacillary leprosy (borderline tuberculoid type). Following isolation, referral, and initiation of standardized multidrug therapy (rifampicin and dapsone), the patient entered a long-term follow-up phase.

CONCLUSION: MetaPath successfully detected Mycobacterium leprae, providing a definitive molecular etiological evidence for this long-term undiagnosed case. This demonstrates the key advantage of MetaPath in the early diagnosis of challenging infectious diseases.},
}

@article {pmid41698031,
year = {2026},
author = {Meng, Q and An, X and Hu, W and Ma, M and Chen, Z and Wei, G and Chen, C},
title = {Nanopriming with Silicon Quantum Dots Strengthens Wheat Drought Tolerance through Physiological Regulation and Microbial Functions.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11900},
pmid = {41698031},
issn = {1520-5118},
abstract = {Seed priming offers a promising approach to strengthening drought resilience in wheat. In this study, seeds were primed with silicon quantum dots (SiQDs) at concentrations of 0, 250, 500, 750, and 1000 mg L[-1]. Under drought stress induced by 15% PEG-6000, 500 mg L[-1] SiQDs increased the level of germination by 18.2%. In a 30 day pot experiment conducted under drought conditions at 40% field capacity, 500 mg L[-1] SiQDs significantly enhanced shoot biomass (157.1%) and the relative water content (26.7%), reduced root malondialdehyde (24.7%), and increased root proline (76.7%) and soluble sugar (68.7%). 16S rRNA gene and metagenomic sequencing analyses revealed that SiQDs enriched Proteobacteria in the rhizosphere, including the genera Sphingomonas, Lysobacter, and Variovorax, and activated functional pathways associated with biofilm formation and bacterial colonization. These results demonstrate that SiQD priming enhances drought tolerance by improving plant physiological responses and modulating rhizosphere microbial communities.},
}

@article {pmid41697419,
year = {2026},
author = {Ni, W and Huang, H and Wang, X and Yu, A and Ren, J and Li, H},
title = {Metagenomic Analysis Reveals Alterations in the Gut Microbiome of Preterm Infants with Extrauterine Growth Restriction.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {177},
pmid = {41697419},
issn = {1432-0991},
support = {No. 82101811//National Natural Science Foundation of China/ ; No. RCJC20231211085923029//Shenzhen Science and Technology Program/ ; No. SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; Guangdong High-level Hospital Construction Fund//Guangdong High-level Hospital Construction Fund/ ; Clinical key specialty construction project of Guangdong Province//Clinical key specialty construction project of Guangdong Province/ ; No. 20232011//Project of Guangdong Provincial Administration of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature/growth & development ; Infant, Newborn ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Female ; Feces/microbiology ; Male ; },
abstract = {Extrauterine growth restriction (EUGR) is a pervasive clinical issue in preterm infants, affecting neonatal development and their long-term health. This study aimed to characterize the gut microbiome and its derived genes in preterm neonates with EUGR using metagenomic sequencing. Sixty-two preterm infants hospitalized in the neonatal intensive care unit at Guangdong Women and Children Hospital were enrolled in this study. Participants were divided into two groups: the EUGR group (n = 34) and the normal growth group (AGA, n = 28). Fecal samples were collected at one month postnatally. Total bacterial DNA was extracted and sequenced using the Illumina HiSeq X Ten system. Significant differences in the gut microbial community between the EUGR and AGA groups were observed, as evidenced by the Bray-Curtis dissimilarity index. The EUGR group exhibited a notable increase in Klebsiella pneumoniae and Enterococcus faecalis, along with a significant decrease in Streptococcus raffinosi, Rothia mucilaginosa, Parabacteroides merdae and Eggerthella lenta compared to the AGA group. Functional annotation of metagenomic genes identified 415 genes with significantly different relative abundances between the groups. A classification model incorporating five discriminatory genes achieved effective separation of EUGR from AGA infants. Additionally, the EUGR group exhibited a higher relative abundance of antibiotic resistance genes. This study elucidates the alterations in the gut microbiome and its derived genes in preterm neonates with EUGR. These findings provide new insights into the potential microbial signatures associated with impaired growth, although further mechanistic studies are needed to clarify causal relationships.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Infant, Premature/growth & development
Infant, Newborn
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Female
Feces/microbiology
Male

@article {pmid41697418,
year = {2026},
author = {Hossain, A and Haque, I and Al Mamun, A and Al-Din, SMS and Ara, H and Das, TK and Rahman, MM},
title = {Physicochemical and metagenomic characterization of drinking water: Public health implications in Kushtia Municipality, Bangladesh.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {3},
pages = {224},
pmid = {41697418},
issn = {1573-2959},
mesh = {Bangladesh ; *Drinking Water/microbiology/chemistry ; *Water Microbiology ; *Environmental Monitoring ; Water Quality ; Metagenomics ; Public Health ; RNA, Ribosomal, 16S ; Bacteria ; Water Purification ; },
abstract = {Physicochemical and bacterial contamination pose a significant threat to drinking water quality in Bangladesh, requiring comprehensive analysis. This study investigates the physicochemical and metagenomic quality of drinking water from one of four water treatment plants (WTPs) in Kushtia Municipality, Bangladesh. Water samples (n = 3) from untreated, treated, and supplied water were collected between March 1 and 7, 2025. Thirteen physicochemical parameters were analyzed using traditional methods, while bacterial load was assessed using Plate Count Agar. Microbial diversity was analyzed through metagenomic sequencing of DNA extracted using the DNeasy PowerWater Kit, targeting the 16S rRNA gene (V3-V4 region) on the Illumina MiSeq platform. Alpha and beta diversity were evaluated with Chao1, Shannon, and Simpson indices, and taxonomic and pathway analysis were performed on the Kaiju and Nephele platforms. Water quality was assessed using treatment efficiency metrics, the Water Quality Index (WQI), and the Nemerow Pollution Index (NPI). Results reveal that only three of the physicochemical parameters meet the water quality standards of Bangladesh. The WTP's cumulative efficiency metric was found to be 30.76%. The WQI indicated that all water samples were unfit for drinking. The NPI showed that eight out of thirteen physicochemical parameters significantly contribute to poor water quality. Microbial evaluations revealed high bacterial levels in untreated and supplied water samples. Alpha diversity analysis, using Shannon and Simpson indices, showed no significant differences in bacterial abundance across water types. Beta diversity analysis indicated minimal dissimilarity. Functional profiling suggested the presence of antibiotic resistance-associated pathways, with predicted beta-lactam resistance representing 24.1% in treated water and 25.0% in supplied water. The dominant phyla include Proteobacteria (38% in untreated, 39% in treated, and 42% in supplied). About 75%, 83%, and 67% of the identified bacterial species were found to be pathogenic, antibiotic-resistant, and biofilm-forming, respectively, while 58% were classified as opportunistic pathogens. These results underscore the need for improved water treatment practices and more robust monitoring systems to ensure the population can access safe drinking water.},
}

Bangladesh
*Drinking Water/microbiology/chemistry
*Water Microbiology
*Environmental Monitoring
Water Quality
Metagenomics
Public Health
RNA, Ribosomal, 16S
Bacteria
Water Purification

@article {pmid41697296,
year = {2026},
author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W},
title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
pmid = {41697296},
issn = {1615-6102},
}

@article {pmid41697036,
year = {2026},
author = {Reva, ON and Sifuna, A and Orata, F and Omolo, C and Iramiot, JS and Enright, MC and Mutshembele, A and Zhou, J and Shivoga, WA},
title = {From Lake Victoria to the Tap: Antibiotic Resistance and Pathogenic Contamination of Kisumu City Water Supply and Wastewater Network.},
journal = {Tropical medicine & international health : TM & IH},
volume = {},
number = {},
pages = {},
doi = {10.1111/tmi.70105},
pmid = {41697036},
issn = {1365-3156},
support = {GCRFNGR8\1143//UK Global Challenges Research Fund Networking/ ; NIHR163838//UK National Institute for Health and Care Research/ ; },
abstract = {Waterborne diseases and antimicrobial resistance (AMR) pose mounting public health threats across sub-Saharan Africa, particularly in rapidly urbanising regions dependent on untreated or poorly treated surface waters. This study applied shotgun metagenomic sequencing to characterise microbial communities, virulence factors and antibiotic resistance genes (ARGs) in water samples collected from Lake Victoria, River Wigwa, Dunga Water Treatment Plant, Nyalenda Wastewater Stabilisation Ponds and the tap water outlet in post-treatment supply pipe in Kisumu city (Kenya). Bacterial taxa dominated all metagenomes, with 121 classes represented. Cyanobacteria, particularly Planktothrix, were highly abundant in lake and tap water, whereas wastewater and river samples exhibited greater taxonomic diversity. Major human pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Bacillus cereus/anthracis, were detected in nearly all samples, with unexpectedly high prevalence in tap water. Viral indicators of faecal contamination (adenoviruses, enteroviruses and torque teno viruses) corroborated widespread wastewater influence. Functional gene profiling revealed a rich resistome comprising aminoglycoside-modifying enzymes, β-lactamases, vancomycin-resistance operons and disinfectant-resistance determinants. The highest ARG and virulence gene frequencies occurred in tap and treatment-plant water, suggesting that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa. In contrast, Lake Victoria water exhibited lower ARG abundance, reflecting natural self-purification processes. These findings underscore the inadequate water treatment and open wastewater systems create ecological 'hotspots' for ARG selection and horizontal gene transfer. Metagenomic surveillance integrated into One Health frameworks can enhance risk forecasting and guide interventions to mitigate AMR emergence and dissemination in freshwater systems serving over 35 million people across the Lake Victoria basin.},
}

@article {pmid41697021,
year = {2026},
author = {Han, B and Wen, H and Li, Y and Wang, Y and Lv, X and Kang, M and Huang, W and Lan, Y and Tong, S and Zhang, M and Chen, D and Zhu, C and Jiang, Y and Tang, D},
title = {Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR-NF-κB axis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag028},
pmid = {41697021},
issn = {1751-7370},
abstract = {Crohn's disease (CD) is a complex chronic transmural inflammatory bowel disease. Although vedolizumab (VDZ) markedly improves clinical outcomes in CD, treatment non-response remains a significant limitation, constraining its broader utility. Elucidating the mechanisms underlying VDZ responsiveness is thus critically needed. In this research, we employed a humanized mouse model of 2,4,6-trinitrobenzene sulfonic acid-induced colitis to investigate VDZ treatment response in CD. Our findings indicate that VDZ significantly alleviated disease phenotypes in a portion of CD mice. Integrated metagenomic and metabolomic profiling identified baseline gut microbiota-derived secondary bile acids as potential predictors of VDZ efficacy. Subsequent fecal microbiota transplantation from clinical donors into pseudo-germ-free mice confirmed that gut microbial composition critically influences VDZ responsiveness. Targeted metabolomics further pinpointed lithocholic acid (LCA) as a key microbially derived metabolite correlated with therapeutic remission. Single-cell RNA sequencing also revealed that intestinal macrophages serve as pivotal mediators of LCA-driven modulation of treatment outcomes. Furthermore, transcriptomic analyses demonstrated that LCA polarizes macrophages toward an M2-resolutive phenotype via concurrent engagement of the TGR5/FXR and their downstream NF-κB pathways. Ultimately, using a conditioned medium co-culture system, we established that the regulatory effects of pro-resolutive macrophage niche on treatment response in a manner dependent on the TGR5/FXR-NF-κB axis. Taken together, our study elucidates a microbiota-immune circuit in which gut microbial metabolite LCA augments VDZ responsiveness in CD by reprogramming macrophages toward a pro-resolutive phenotype via the TGR5/FXR-NF-κB signaling network. These insights provide a mechanistic foundation for biomarker development and personalized therapeutic strategies in inflammatory bowel disease.},
}

@article {pmid41696869,
year = {2026},
author = {Ju, Y and Lin, S and Hu, S and Jin, X and Xiao, L and Zhang, T and Zhang, Y and Zhang, L and Ma, X and Zhu, F and Guo, R},
title = {GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630563},
doi = {10.1080/19490976.2026.2630563},
pmid = {41696869},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; *Mental Disorders/microbiology ; *Brain ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics ; Female ; *Brain-Gut Axis ; Biomarkers ; },
abstract = {Emerging evidence underscores bidirectional communication along the microbiota-gut-brain axis in neuropsychiatric disorders. However, the field lacks dedicated metagenomic resources with standardized phenotyping for these conditions. Existing single-cohort studies face inherent limitations due to restricted sample sizes, confounding heterogeneity, and methodological fragmentation, compromising reproducibility and mechanistic insights. To overcome these challenges, we constructed the Gut Microbiome in Multinational Integrated Neuropsychiatric Disorders (GutMIND) database, a comprehensive resource integrating shotgun metagenomic data with harmonized metadata. Adhering to a standardized preprocessing protocol and rigorous quality control workflow, this dataset represents the largest gut-brain microbiome repository to date, encompassing 31 studies across 12 countries (n = 3,492) spanning 14 neuropsychiatric conditions. Utilizing this dataset, we characterized microbial community heterogeneity, which was significantly elevated in patients compared to healthy controls. Subsequently, we developed a computational framework, MetaClassifier, enabling the diagnosis of neuropsychiatric disorders and the identification of microbial biomarkers. Employing a comprehensive two-stage validation strategy, we first assessed the model utilizing taxonomic abundance profiles via nested cross-validation in the high-quality discovery cohort (n = 2,734), achieving a mean AUROC of 0.69 (range: 0.55-0.78) across 8 disorders. Its robustness was further confirmed in an independent platform-extended validation cohort (n = 400), yielding a mean AUROC of 0.71 (range: 0.60-0.76). We also developed the Microbial Gut-Brain Axis Health Index (MGBA-HI), which effectively distinguished neuropsychiatric status in both the high-quality cohort and the platform-extended cohort. Furthermore, integrative analysis of health-abundant species, index-derived biomarkers, and ecological prevalence, we identified 9 core neuropsychiatric-protective microbiota. These species predominantly exhibited metabolic capacities linked to glutamate synthesis and acetate production. Building upon this, the GutMIND framework ensures robust cross-cohort comparability while minimizing technical heterogeneity, thereby enhancing inferential rigor in gut microbiome-neuropsychiatry research. Notably, the MetaClassifier, MGBA-HI, and core microbiota hold translational potential for developing microbiome-based prognostic tools and personalized therapeutic strategies in neuropsychiatric disorders. The source code and usage instructions for MetaClassifier are accessible at https://github.com/juyanmei/MetaClassifier.},
}

Humans
*Gastrointestinal Microbiome
*Machine Learning
*Mental Disorders/microbiology
*Brain
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Male
Metagenomics
Female
*Brain-Gut Axis
Biomarkers

@article {pmid41696622,
year = {2026},
author = {Zhu, Z and Miao, X},
title = {Research progress of metagenomic next-generation sequencing in infectious diseases of the spine: a systematic review.},
journal = {Therapeutic advances in infectious disease},
volume = {13},
number = {},
pages = {20499361251412789},
pmid = {41696622},
issn = {2049-9361},
abstract = {BACKGROUND: Infectious diseases of the spine (IDS) cause structural destruction and abscess formation, requiring precise early diagnosis. While conventional culture methods show limited sensitivity and slow turnaround, metagenomic next-generation sequencing (mNGS) offers a promising alternative with its broader pathogen spectrum, rapid turnaround time, high detection rate, and sensitivity, showing significant advantages in the diagnosis of IDS.

OBJECTIVES: This systematic review aims to synthesize the current evidence on the advantages and clinical utility of mNGS in diagnosing and managing IDS, focusing on pyogenic and granulomatous spinal infections.

DESIGN: The systematic review conducted in accordance with PRISMA guidelines.

DATA SOURCES AND METHODS: A comprehensive literature search was performed across nine electronic databases (including PubMed, Web of Science, and Embase) from 2010 to April 2025. Studies reporting on mNGS for pathogen detection in patients with suspected or confirmed spinal infections were included. The quality of included observational studies was assessed using the STROBE checklist. Data on detection spectrum, rate, sensitivity, turnaround time, and clinical impact were extracted and synthesized narratively due to high heterogeneity.

RESULTS: Twenty-nine studies (25 retrospective studies and 4 case reports) from China were included. mNGS demonstrated a significantly broader detection spectrum, identifying common pathogens (e.g., Staphylococcus aureus, Mycobacterium tuberculosis) as well as rare and fastidious organisms that were missed by conventional methods. The pooled detection rate of mNGS (36.8%-95.5%) was consistently and significantly higher than that of culture (5.9%-59.2%). mNGS also showed superior sensitivity (39%-94.7%) compared to culture. The average turnaround time for mNGS (29-53 h) was substantially faster than for culture (2-10 days). mNGS-guided therapy was associated with improved clinical outcomes, including significant reductions in inflammatory markers.

CONCLUSION: mNGS represents a powerful diagnostic tool for IDS, offering broader detection spectrum, higher detection rate, faster turnaround time, and greater sensitivity compared to conventional methods. This enables more targeted antimicrobial therapy and improves clinical management. Challenges including high costs and difficulty in distinguishing colonization from infection remain. Future efforts should focus on technical optimization, workflow automation, protocol standardization, and outcome validation in larger prospective studies.

TRIAL REGISTRATION: CRD420251170912.},
}

@article {pmid41696361,
year = {2026},
author = {Yin, L and Xu, L and Shan, YN and He, Z and Li, Y and Chen, W},
title = {Microbiota-driven therapeutic efficacy of Hyperoside in ulcerative colitis and associated anxiety.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1734356},
pmid = {41696361},
issn = {2235-2988},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology/complications ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Anxiety/drug therapy ; Disease Models, Animal ; *Quercetin/analogs & derivatives/pharmacology/therapeutic use ; Male ; Cytokines/metabolism ; Colon/pathology/drug effects ; Mice, Inbred C57BL ; Molecular Docking Simulation ; Signal Transduction/drug effects ; Metabolomics ; Brain-Derived Neurotrophic Factor/metabolism ; Anti-Inflammatory Agents/pharmacology ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is subtype of inflammatory bowel disease that is frequently comorbid with anxiety disorders. However, effective dual-targeting therapies are still lacking. Hyperoside (HYP), a natural flavonoid, exhibits anti-inflammatory and neuroprotective properties, yet its potential therapeutic effects on UC and associated anxiety, as well as the underlying mechanisms, remain largely unexplored.

METHODS: A murine model of DSS-induced colitis was established and treated with HYP. Disease activity was assessed through body weight, colon length, and histopathology. Anxiety-like behaviors were evaluated using open field and elevated plus maze tests. Neuroinflammation was examined through immunohistochemistry of BDNF expression and microglial activation. Gut microbiota composition was profiled by metagenomic sequencing, and metabolomic profiling was conducted using the Q300 Kit. Network pharmacology and molecular docking were employed to predict signaling pathways, which were further validated by Western blotting. Additionally, antibiotic depletion experiments were conducted to determine microbiota dependency.

RESULTS: HYP administration significantly ameliorated DSS-induced colitis, as evidenced by attenuated weight loss, restored colon length, and improved histopathology. It suppressed pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and restored intestinal barrier integrity by upregulating Mucin-2 and ZO-1. Furthermore, HYP also alleviated anxiety-like behaviors and mitigated neuroinflammation by increasing BDNF levels and suppressing microglial activation. HYP treatment also restored gut microbial homeostasis, enriching beneficial bacteria such as Enterobacter ludwigii while reducing the abundance of Enterobacter hormaechei, Escherichia coli, and Acinetobacter baumannii. Metabolomic analysis revealed that HYP significantly promoted arginine biosynthesis. Network pharmacology and molecular docking identified the MAPK, PI3K-Akt, and NF-κB pathways as potential targets, with HYP showing strong binding affinity to MAPK3, AKT1, and NFκB1. Importantly, the therapeutic effects of HYP were abolished in microbiota-depleted mice.

CONCLUSION: Our findings demonstrate that HYP effectively alleviates DSS-induced colitis and comorbid anxiety-like behaviors. Its efficacy is dependent on the gut microbiota and is associated with the restoration of microbial homeostasis, enhancement of arginine metabolism, and modulation of the MAPK/PI3K-Akt/NF-κB signaling pathways. HYP represents a promising microbiota-targeting therapeutic candidate for UC and its neuropsychiatric comorbidities.},
}

Animals
*Colitis, Ulcerative/drug therapy/microbiology/complications
Mice
*Gastrointestinal Microbiome/drug effects
*Anxiety/drug therapy
Disease Models, Animal
*Quercetin/analogs & derivatives/pharmacology/therapeutic use
Male
Cytokines/metabolism
Colon/pathology/drug effects
Mice, Inbred C57BL
Molecular Docking Simulation
Signal Transduction/drug effects
Metabolomics
Brain-Derived Neurotrophic Factor/metabolism
Anti-Inflammatory Agents/pharmacology

@article {pmid41696071,
year = {2025},
author = {Forbrigger, Z and MacDonald, T and Kulkarni, K and Stadnyk, AW},
title = {Investigating diet to control asparagine uptake as an adjunct to asparaginase treatment.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1634113},
pmid = {41696071},
issn = {2234-943X},
abstract = {Ongoing refinements of multidrug regimens, and particularly the addition of L-asparaginase, resulted in an immediate gain in survival for pediatric acute lymphoblastic leukemia patients. Yet L-asparaginase has substantial side effects which may require dose reductions or delays in subsequent doses. There are at least 3 possible sources of L-asparagine to consider when balancing blood levels with asparaginase dosing, diet, cell synthesis and bacterial synthesis. To date, there is one precedent, in mice, in which blood L-asparagine levels are reduced as a consequence of reducing consumed levels. We build on that approach in experiments aimed at testing whether long-term dietary restriction of L-asparagine and possibly gut bacteria can impact blood levels. In our experiment, 2 groups of mice received food pellets with either 4% or 0% L-asparagine. Blood and fecal metabolites and fecal bacteria were sampled over 72 days. After this accommodation period, all mice continued their diet and received a single injection of pegylated E. coli recombinant L-asparaginase. Samples for bacteria and metabolites were collected 4 and 5 days later, respectively. Neither diet had adverse effects on the general health of the mice nor did diet alone change blood L-asparagine levels. Both diets led to changes in gut bacteria. L-asparaginase depleted blood L-asparagine in mice consuming either diet. Bacteria identified in fecal pellets revealed that the microbiomes of mice in the 2 cages were different (cage effect) and remained different although metagenomic analyses of day 72 feces indicated there were no diet-dependent differences in bacterial asparaginase or asparagine synthetase. These outcomes indicate that mice recover from any short-term down regulation of blood L-asparagine due to diet and consequently the metabolic controls become complex, and the gut microbes seem to not be a great influence. Further research should include approaches to determine the source of L-asparagine in the blood while ingesting diets with no/low or high amounts of L-asparagine.},
}

@article {pmid41696028,
year = {2026},
author = {Tian, W and Petrová, E and Sakai, S and Nweze, JE and Daebeler, A and Angel, R},
title = {Cultivation and genomic characterization of novel methanogens from arid desert biocrust.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag013},
pmid = {41696028},
issn = {2730-6151},
abstract = {Methanogens are strictly anaerobic archaea capable of energy conservation by methane production, yet their presence in oxic and arid environments challenges existing paradigms. In this study, we enriched and genomically characterized seven methanogenic cultures from desert biocrusts, affiliated with the genera Methanobacterium, Methanosarcina, and Methanocella. Six of these new enrichment cultures represent new species. Nonetheless, phylogenomic analyses revealed close genetic relationships with organisms from anoxic environments, indicating the absence of an evolutionary distinction. Comparative genomics exposed diverse though non-unique repertories of antioxidant (e.g. catalase, superoxide dismutase and desulfoferrodoxin), and desiccation-resistance genes (including genes for maintaining osmotic pressure and repair of cell wall and membrane), with Methanobacterium spp possessing the lowest gene abundance and diversity for oxygen and desiccation tolerance. Nevertheless, the occurrence of a Class I methanogen such as Methanobacterium in arid soils challenges the notion that members of this class are less oxygen tolerant than Class II. Pangenome analysis further uncovered unique genes enriched in membrane-associated functions and potentially non-functional stress-related genes. Via a global metagenomic survey we find that methanogens are underdetected in dryland soils, likely due to sequencing depth limitations. Our findings highlight previously overlooked methanogen diversity and ecological plasticity in oxic and desiccated habitats, and emphasize the need for further studies to elucidate their survival strategies.},
}

@article {pmid41696023,
year = {2026},
author = {Chen, G and Jing, H and Liu, B and Zhang, J and Ou, Y and Liu, W and Tian, X and Wang, R and Yan, J and Mao, T and Yang, S and Zheng, Y and Hou, L and Dong, H},
title = {Unique phylogenies and metabolic adaptations of novel lineage III and comammox Nitrospira species from deep-sea sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag003},
pmid = {41696023},
issn = {2730-6151},
abstract = {The genus Nitrospira, which includes canonical nitrite-oxidizing bacteria (NOB) and species capable of complete ammonia oxidation (comammox), plays an important role in the global biogeochemical nitrogen cycle. Typically, lineage IV Nitrospira predominate in marine environments, and other lineages are thought to be less abundant and remain poorly characterized in oceanic systems. Here, we recovered five novel metagenome-assembled genomes (MAGs) affiliated with Nitrospira lineage II-IV from deep-sea sediments. Notably, two of these MAGs represent members of lineage III and comammox Nitrospira, respectively, suggesting the presence of previously uncharacterized lineages in the deep sea. Phylogenetic and gene locus analyses indicated that deep-sea lineage III and comammox Nitrospira form distinct evolutionary clades that diverge from their terrestrial and coastal relatives, and we therefore designate these two marine-derived groups as "lineage III clade B" and "comammox clade A4", respectively. Comparative read recruitment analyses revealed that these lineages exhibit potential pan-oceanic distribution in deep-sea sediments and waters, albeit at very low abundances. Furthermore, the identification of genes encoding amtB-type ammonium transporters (amtB), the ABC-type glycerol-3-phosphate transport system (ugpABCE), a multi-subunit Na[+]/H[+] antiporter (mnh), and betaine transporters (BetT, opuABC) suggests that these newly discovered Nitrospira species possess adaptive capabilities to thrive in oligotrophic and saline marine environments. These findings provide novel insights into the occurrence, metabolic features, and adaptation strategies of lineage III and comammox Nitrospira, expand our understanding of Nitrospira diversity in the deep sea, and offer valuable perspectives on the evolutionary history of various Nitrospira lineages.},
}

@article {pmid41696020,
year = {2026},
author = {Kim, J and Murakami, T and Toyoda, A and Mori, H},
title = {Behavioural phase transitions in the migratory locust, Locusta migratoria, are related to changes in the gut bacterial composition.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag009},
pmid = {41696020},
issn = {2730-6151},
abstract = {Locusta migratoria is a grasshopper species that can change its behaviour from solitary to gregarious. Previous studies have implicated metabolites such as serotonin and dopamine in the regulation of behavioural transition in this species. While many studies using cultured microbes have demonstrated that some microbes harbor the neuroactive metabolic potential of these neurotransmitters, the association between microbial community composition and phase transition remains poorly understood. Here, we employed 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing analyses to compare the composition of gut microbial communities of L. migratoria in different behavioural phases. We found that Serratia ureilytica was enriched in the gut of gregarious individuals in contrast to the decreased presence of Klebsiella aerogenes, one of the most abundant taxa in wild individuals. The gut microbiome of gregarious individuals was functionally characterised by enriched kynurenine and tryptophan synthesis pathways, and by reduced representation of GABA, indole, and dopamine metabolism pathways compared with that of solitary individuals. These compositional changes were consistent with the enrichment of S. ureilytica and depletion of K. aerogenes, which possess the corresponding genes. In particular, the genes for kynurenine synthesis encoded by S. ureilytica specific to the gregarious phase, are known to be involved in the tryptophan production and are associated with reduced serotonin synthesis. These results highlight a distinct shift in both the taxonomic and functional composition of the gut microbiome across behavioural phases and suggest a potential microbial contribution to the behavioural changes of L. migratoria.},
}

@article {pmid41695957,
year = {2026},
author = {Dobrzyński, J and Gradowski, M and Radkowski, A and Bujak, H},
title = {Chloroflexota in agricultural soils: current knowledge and future research directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705889},
pmid = {41695957},
issn = {1664-302X},
abstract = {The review organizes current knowledge on the biofunctions, life-history strategies, and environmental responses of Chloroflexota in agricultural soils. Members of this phylum play key roles in carbon, nitrogen, and phosphorus cycling through a high degree of metabolic versatility, including photosynthesis, redox reactions, and the degradation of complex organic compounds such as cellulose and lignin. Chloroflexota contribute to major soil processes, including nitrification, denitrification, and nitrogen fixation. In agricultural soils, the predominant classes are Anaerolineae and Ktedonobacteria, each exhibiting distinct ecological strategies. Anaerolineae members, such as Leptolinea, Bellilinea, and Anaerolinea, are often associated with nutrient-enriched conditions, suggesting copiotrophic or competitor- and ruderal-like traits. In contrast, Ktedonobacteria show negative responses to increased soil carbon and nitrogen, suggesting that its members are oligotrophic. Despite these trends, responses to soil organic carbon, nitrogen, phosphorus, and pH vary substantially across studies, likely due to functional heterogeneity within the phylum and insufficient taxonomic resolution in metataxonomic datasets. Emerging evidence from metagenome-assembled genomes (MAGs) reveals that Chloroflexota harbor genes involved in carbon fixation, nitrogen transformations, and phosphorus solubilization, highlighting their previously underestimated ecological significance. However, most Chloroflexota remain uncultured, and available genomic data are still limited. Future research integrating high-resolution taxonomic profiling, metagenomics, and cultivation-based approaches is needed to clarify the ecological roles and life-history strategies of Chloroflexota members. Such advances may ultimately establish this phylum as an important microbial indicator of soil fertility and environmental change in agricultural soils.},
}

@article {pmid41695945,
year = {2026},
author = {Kothe, CI and Mak, T and Julienne, A and Okazaki, K and Jahn, LJ and Evans, JD},
title = {Miso without kōji: nesashi miso ecology driven by spontaneous fermentation with Mucor plumbeus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759987},
pmid = {41695945},
issn = {1664-302X},
abstract = {Nesashi miso is a rare, traditionally fermented soybean paste from Japan, and unlike most misos is produced through spontaneous fermentation without the use of a kōji starter. Here we analyzed a nesashi miso alongside two other misos from the same producer (rice and black soybean) as well as a hatchō miso from another producer which, like the nesashi, is based only on soybeans. Shotgun metagenomics confirmed that while Aspergillus oryzae dominated the three kōji-based misos, nesashi miso lacked this starter culture, and revealed that it was instead dominated by other filamentous fungi, mainly Mucor spp. and Penicillium spp., and contained typical yeast and bacterial genera found in traditional misos such as Zygosaccharomyces and Tetragenococcus. Principal component analysis (PCA) of 65 publicly available metagenomes showed that the nesashi miso sample clustered with other spontaneous solid-state fermentations like Chinese qu rather than with traditional kōji-based misos. To further characterize this unique fermentation, we isolated the Mucor sp. from nesashi miso, and sequenced it using long-read genomic sequencing. Pangenomic analysis confirmed its identity as M. plumbeus, and revealed close relationships between food- and environment-derived strains, suggesting that some Mucor species may already be naturally equipped to grow, establish and function in food fermentation niches. The nesashi strain specifically shared a large core genome with M. racemosus C, a strain patented for use in food, suggesting the former's potential for use in and potentially even adaptation to food environments. Functional annotation highlighted unique genes in the food strain group associated with amino acid metabolism, which may contribute to flavor formation. Together, these findings bridge traditional fermentation practices with meta/genomic insights, highlighting the built fermentation environment as a reservoir of potential starter cultures and the genus Mucor as a worthy candidate for future food fermentation research and innovation.},
}

@article {pmid41695690,
year = {2026},
author = {Zhang, W and Zheng, Y and Han, G and He, X},
title = {A novel analysis workflow for simultaneous parsing prokaryotic and eukaryotic microbial genes from metagenomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20769},
pmid = {41695690},
issn = {2167-8359},
mesh = {*Metagenome/genetics ; Workflow ; *Prokaryotic Cells ; *Eukaryota/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; *Genes, Microbial ; },
abstract = {Accurately predicting coding genes from metagenomic samples containing a high proportion of eukaryotic content remains a significant challenge. Novel and reliable methods for the simultaneous prediction of prokaryotic and eukaryotic microbial genes are crucial to address this. We evaluated gene prediction accuracy of MetaGeneMark and MetaEuk using representative genomes from diverse organisms. Based on these findings, we developed an innovative analytical workflow. This approach involves an initial prediction of eukaryotic genes using MetaEuk, followed by the masking of these predicted eukaryotic genes and any co-identified partial prokaryotic genes using a custom Perl script. Remaining prokaryotic genes are then predicted from the masked metagenome using MetaGeneMark or metaProdigal. This integrated strategy achieved similar quantities and average lengths of eukaryotic genes compared to using MetaEuk alone. Notably, the quantity of predicted prokaryotic genes and viral genes using the new workflow was 14-18% higher than that obtained with standalone prokaryotic predictors. Furthermore, validation on a mixed prokaryotic-eukaryotic metagenome demonstrated that our workflow yielded genes with significantly higher average lengths, indicating reduced fragmentation and improved gene integrity. This novel workflow effectively enables the rapid and comprehensive retrieval of high-quality prokaryotic and eukaryotic coding sequences from diverse metagenomes.},
}

*Metagenome/genetics
Workflow
*Prokaryotic Cells
*Eukaryota/genetics
*Metagenomics/methods
*Computational Biology/methods
*Genes, Microbial

@article {pmid41695450,
year = {2026},
author = {Rusiñol, M and Martínez-Puchol, S and Ribeiro, D and Verdaguer, J and Torrejón-Llorens, O and Itarte, M and Estarlich-Landajo, I and Mejías-Molina, C and Juliachs-Torroella, G and Girones, R and Ramírez, GA and Baliellas, J and Bofill-Mas, S and Fernández-Cassi, X},
title = {Livestock aggregated samples for monitoring viruses infecting animals and potentially zoonotic viral pathogens.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101340},
pmid = {41695450},
issn = {2352-7714},
abstract = {Active surveillance of livestock pathogens is essential to prevent animal health losses and zoonotic spillover. This study evaluted aggregated environmental sampling as a non-invasive approach for monitoring swine- and cattle-associated viruses across farms and slaughterhouses, bridging the gap between agricultural biosecurity and public health. Over eleven months, 105 samples, including swine slurry, cattle manure, farm air, and slaughterhouse wastewater, were collected and analyzed using pathogen-specific (RT) qPCR and targeted viral metagenomics. Seasonal and sample patterns were evident, with higher detection of rotavirus A (RoV-A) and bovine coronavirus (BCoV) in slurry and wastewater during winter, and porcine reproductive and respiratory syndrome virus (PRRSV), porcine epidemic diarrhea virus (PEDV) and transmissible gastroenteritis virus (TGEV) sporadicly in slaughterhouse wastewater. Farm slurry or manure were optimal for enteric viruses such as RoV-A or hepatitis E virus (HEV), and farm air proved valuable for respiratory viruses like BCoV. Targeted sequencing identified a broader viral community, revealing up to 80% of total detected viral species in slaughterhouse wastewater alone. Frequent detection of porcine bocavirus, circoviruses and astrovirus, alongside zoonotic viruses such as HEV and porcine bufavirus (PBuV), underscored the environmental transmission risk at the human-animal interface. Sequencing also uncovered viruses of unclear pathogenicity, including kobuvirus and copiparvovirus, underscoring the complexity of the livestock virome and the potential for emerging viral threats. Slaughterhouse wastewater consistently captured the highest viral richness, integrating inputs from multiple farms and regions, while farm air samples yielded lower diversity but detected respiratory (astrovirus, caliciviruses) and persistent viruses (papillomaviruses, polyomaviruses). Aggregated sampling proved particularly efficient in swine systems, while cattle surveillance may require adapted strategies due to lower stocking densities and greater ventilation. This work demonstrates the novelty and value of aggregated environmental samples, collected at different points in the production chain, as strategic One Health sentinels. This scalable, practical approach supports early warning and control of animal and zoonotic diseases, directly contributing to One Health surveillance.},
}

@article {pmid41695017,
year = {2026},
author = {Galdamez, IA and Jimenez, K and Cira, M and Osborn, K and Ayad, M and Lee, CM and Patel, K and Galdamez, BA and Sloan, A and Shenkiryk, A and Cason, T and Gomez, NA and Phillips, M and Rosado, S and Rosado, A and Mishra, DR and Cherrington, EA and Griffin, R and Jay, JA},
title = {Evaluating Antibiotic Resistance in Urban Rivers and Coral Reefs of Belize: Evidence for Hotspots and a Potential Screening Tool.},
journal = {GeoHealth},
volume = {10},
number = {2},
pages = {e2025GH001427},
pmid = {41695017},
issn = {2471-1403},
abstract = {Antibiotic resistance is a significant threat to global public health and can disproportionately affect low- and middle- income countries (LMICs). There is a lack of studies focusing on antibiotic resistance in coral reef regions and environmental reservoirs in Central America. This study followed modified World Health Organization (WHO)'s Global Tricycle Surveillance protocols for the environmental sector to address these gaps. Water samples were collected from key areas in the lower Belize River, including above and below the Belize City, an open fish market, and sewage lagoon outfall, and coral reefs. Water samples underwent qPCR analysis for a suite of antibiotic resistance gene classes (sul1, sul2, ermF, tetA, and blaSHV), intI1, and 16S rRNA. Additionally, a subset of samples were tested for extended-spectrum β-lactamase (ESBL) E. coli and underwent shotgun sequencing. Results show that antibiotic resistance genes (ARGs) were highest and most diverse near Belize City, particularly near the treatment lagoons and open fish market. The coral reef regions had lower levels of antibiotic resistance though not void of their presence. This study is an application of a modified Global Tricycle Surveillance protocol integrated with qPCR- and metagenomics-based characterization of environmental antibiotic resistance in understudied areas. Notably, data from this study indicated that ESBL-E. coli could potentially be used as a screening tool for environmental antibiotic resistance, as it was only present at sites that had the highest levels of ARGs.},
}

@article {pmid41694529,
year = {2026},
author = {Vivarelli, S and De Francesco, C and Paba, E and Giambò, F and Fenga, C},
title = {The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1746385},
pmid = {41694529},
issn = {2296-2565},
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Occupational Exposure ; One Health ; },
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, driven by the extensive use of antibiotics in both human medicine and livestock production. In the context of the One Health framework, this review investigates the role of the gut microbiome and resistome, which represents the collection of antimicrobial resistance genes (ARGs), within livestock and among occupationally exposed workers. Intensive farming practices often involve routine, subtherapeutic antibiotic use, fostering antibiotic-resistant bacteria (ARB) in the gastrointestinal tract of animals. These ARB and ARGs are excreted into the environment, contributing to resistance spread through mobile genetic elements. From a Planetary Health perspective, this environmental dissemination reflects how human-driven livestock practices can perturb ecosystems, creating global health risks that link animal, human, and environmental well-being. Human exposure, particularly among farm workers and veterinarians, raises significant concerns about zoonotic transmission of pathogens and, potentially, ARB. Novel advances in metagenomic and metatranscriptomic technologies enhanced our understanding of gut microbial communities and their resistomes, revealing overlaps in ARG profiles between animals and livestock workers. These technologies also support the development of novel microbiome-targeted strategies, including prebiotics, probiotics, food supplementation and workplace-improvement strategies, aimed at reducing antimicrobial use and restoring healthy microbiome balance. The review also highlights the importance of integrated surveillance and cross-sectoral collaboration to monitor and control AMR transmission. Understanding the ecological dynamics of the gut resistome in livestock systems is essential for designing effective interventions that safeguard both animal and human health.},
}

Animals
*Livestock/microbiology
Humans
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
*Occupational Exposure
One Health

@article {pmid41694517,
year = {2026},
author = {Song, Z and Huang, Y and Gu, Y and Che, L and Zhang, K and Liu, Q and Guan, Q and Sui, L},
title = {Correction: Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1788645},
doi = {10.3389/fpubh.2026.1788645},
pmid = {41694517},
issn = {2296-2565},
abstract = {[This corrects the article DOI: 10.3389/fpubh.2025.1756127.].},
}

@article {pmid41694508,
year = {2026},
author = {Scaglione, G and Mastroianni, N and Rizzo, A and Palomba, E and Carcione, D and Brigante, G and Principe, L and Colaneri, M and Gori, A and Borgonovo, F},
title = {Integrating artificial intelligence with genome sequencing against antimicrobial resistance: a narrative review.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1757161},
pmid = {41694508},
issn = {2296-2565},
mesh = {Humans ; *Artificial Intelligence ; *Whole Genome Sequencing/methods ; Machine Learning ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial resistance (AMR) represents an escalating global health threat, demanding diagnostic strategies capable of rapid, accurate, and comprehensive pathogen characterization. Genomic sequencing has transformed our ability to elucidate resistance mechanisms and track their evolution, yet its routine clinical adoption remains limited by cost, workflow constraints, and extended turnaround times. This narrative review examines how artificial intelligence (AI) and machine learning (ML) can enhance and operationalize sequencing-based diagnostics across the clinical microbiology continuum. We summarize current AI applications in whole-genome sequencing for AMR prediction, pan-genome feature extraction, and multicenter model generalizability, including emerging approaches such as federated learning. We then explore AI-driven metagenomic analytics for pathogen detection, resistome profiling, outbreak investigation, and prognostic modeling. Complementary non-genomic technologies, Raman spectroscopy and MALDI-TOF MS, are also evaluated for their potential to deliver rapid resistance profiling when integrated with ML. Finally, we discuss practical barriers, including cost, dataset standardization, interpretability, and regulatory challenges, while outlining future directions toward scalable, explainable, and equitable AI-guided diagnostics. Integrating AI with genomic and rapid phenotypic tools offers a pathway to real-time surveillance, optimized antimicrobial stewardship, and strengthened preparedness against emerging infectious threats.},
}

Humans
*Artificial Intelligence
*Whole Genome Sequencing/methods
Machine Learning
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid41694087,
year = {2026},
author = {Hu, Q and Sardi, MI and Naqvi, SA and Paton, ND and Hackenhaar, L and Pluk, P and de Laat, J and Chakrabarti, A and Khafipour, E},
title = {Effects of processed soybean meal on growth performance and gut microbiome composition in pigs in regular nursery and enterotoxigenic Escherichia coli challenged conditions.},
journal = {Translational animal science},
volume = {10},
number = {},
pages = {txag004},
pmid = {41694087},
issn = {2573-2102},
abstract = {Hydrothermal-mechanical (HTM) processing of soybean meal (SBM) has been shown to enhance intestinal health and growth in post-weaning pig compared to conventional SBM. It was hypothesized that HTM processing improves protein utilization, particularly under enterotoxigenic Escherichia coli (ETEC) challenge, resulting in better growth and a more resilient hindgut microbiome. A total of 268 weaned pigs (6.82 ± 0.85 kg body weight) were allotted to regular nursery (5 pigs/pen, 10-11 pens/treatment) or ETEC challenge (3 pigs/pen, 12 pens/treatment) and fed one of three isocaloric diets with equal standardized ileal digestible lysine: SBM, HTM SBM, or enzyme-treated (Enz Trt) SBM. Test soy products replaced SBM in a wheat-barley-SBM base diet for the first 3 wk, followed by a common diet for 3 wk. On d 14 post-weaning, ileal digesta and feces were collected for crude protein (CP) digestibility, short-chain fatty acid (SCFA), and microbiome analysis. Growth performance, digestibility, and SCFA data were analyzed using general linear models and microbiome data from Nanopore shotgun sequencing were center-log-ratio transformed for statistical analysis in R. No diet × challenge interaction was observed on ADG, ADFI or BW. Pigs in regular nursery conditions had higher ADG (P < 0.01) and ADFI (P < 0.05) than ETEC challenged pigs during d 0-7. HTM SBM and Enz Trt SBM improved ADG (P < 0.05) with similar ADFI compared to SBM across conditions. From d 7-12, pigs fed HTM SBM or Enz Trt SBM had greater ADG (P < 0.05) and ADFI (P < 0.01) than SBM-fed pigs. BW remained lower (P < 0.05) in SBM-fed pigs from d 12-21 and during the final 3 wk. Under regular nursery conditions, HTM SBM improved apparent total tract digestibility of CP (P < 0.01) compared SBM, but with no difference from Enz Trt SBM. Microbiome composition was affected by diet (P < 0.01) and ETEC challenge (P < 0.01). HTM SBM and Enz Trt SBM tended to increase α-diversity (P = 0.10) of the microbiome compared to SBM, with no difference between the two treatments. HTM SBM and Enz Trt SBM increased abundance of species positively correlated with growth and beneficial SCFA, such as caproate (P < 0.05) and valerate (P < 0.05). In conclusion, HTM SBM and Enz Trt improved ADFI, ADG resulting higher BW and promoted beneficial microbes linked to performance in nursery pigs under both regular nursery and ETEC-challenged conditions.},
}

@article {pmid41693971,
year = {2026},
author = {Xu, T and Hou, WX and Yang, ST and Shao, YP and Wang, J and Han, TT and Li, JN},
title = {Danggui-Baishao herb pair protects against dextran sulfate sodium-induced colitis by modulating the Wnt/β-catenin pathway.},
journal = {World journal of gastroenterology},
volume = {32},
number = {5},
pages = {113024},
pmid = {41693971},
issn = {2219-2840},
mesh = {Animals ; Dextran Sulfate/toxicity ; *Wnt Signaling Pathway/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Disease Models, Animal ; Mice ; Humans ; Molecular Docking Simulation ; *Colitis/chemically induced/drug therapy/pathology/prevention & control ; Colon/pathology/drug effects ; Male ; beta Catenin/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Intestinal Mucosa/drug effects/pathology ; Glucosides/pharmacology ; Metabolomics ; Pyrimidinones ; Bridged Bicyclo Compounds, Heterocyclic ; },
abstract = {BACKGROUND: The Danggui-Baishao herb pair is the foundation of a traditional Chinese medicine formula known as Shaoyao decoction, which is widely used in the treatment of colitis.

AIM: To uncover the mechanisms underlying the anti-colitis effects of the Danggui-Baishao herb pair.

METHODS: The chemical composition of the herb pair was characterized by high performance liquid chromatography-quadrupole/time of flight mass spectrometry analysis. A mouse model of colitis was induced by administering 2.5% dextran sulfate sodium. The therapeutic effects of the herb pair were evaluated based on body weight changes, colon length, histopathological, intestinal inflammation, and barrier function. To investigate the underlying mechanisms, RNA sequencing, metabolomics, 16S rRNA sequencing, metagenomics, and the β-catenin inhibitor ICG-001 were utilized. Furthermore, molecular docking and dextran sulfate sodium-treated HCT 116 cells were conducted to explore the protective mechanisms of benzoylpaeoniflorin.

RESULTS: The herb pair improved body weight, colon length, intestinal inflammation, and barrier function. Additionally, the herb pair upregulated the expression of intestinal stem cells marker leucine-rich repeat-containing G-protein coupled receptor 5 and proliferation-related proteins. RNA sequencing analysis showed that the herb pair activated the Wnt/β-catenin signaling pathway. Metabolomic analysis revealed changes in bile acids composition. Through 16S rRNA and metagenomic sequencing, it was observed that the herb pair modulated the gut microbiota, with an enrichment of probiotics and a depletion of pathogenic bacteria. Following intraperitoneal injection of antagonist ICG-001, the therapeutic efficacy was diminished. Molecular docking showed that benzoylpaeoniflorin can bind to β-catenin. Furthermore, benzoylpaeoniflorin can activated the Wnt/β-catenin signaling pathway and the therapeutic efficacy was also diminished by the ICG-001 in vitro.

CONCLUSION: The herb pair effectively reduces colonic inflammation and maintains the integrity of the intestinal barrier. Moreover, the anti-colitis efficacy of the herb pair is closely associated with activation of the Wnt/β-catenin pathway.},
}

Animals
Dextran Sulfate/toxicity
*Wnt Signaling Pathway/drug effects
*Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry
Disease Models, Animal
Mice
Humans
Molecular Docking Simulation
*Colitis/chemically induced/drug therapy/pathology/prevention & control
Colon/pathology/drug effects
Male
beta Catenin/metabolism
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Intestinal Mucosa/drug effects/pathology
Glucosides/pharmacology
Metabolomics
Pyrimidinones
Bridged Bicyclo Compounds, Heterocyclic

@article {pmid41693862,
year = {2025},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1726935},
pmid = {41693862},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology ; Mycobacterium tuberculosis/genetics ; Male ; Female ; Gene Expression Profiling ; Biomarkers/analysis ; Metagenomics ; Prospective Studies ; Middle Aged ; Adult ; Microbiota ; Transcriptome ; Bacteriophages/genetics ; Lung/microbiology ; },
abstract = {BACKGROUND: Drug-resistant tuberculosis (DR-TB) undermines global TB control, yet how resistant Mycobacterium tuberculosis strains interact with the lung microbiome, phage communities, and local host immunity remains poorly defined.

METHODS: In a prospective cohort of 130 pulmonary TB patients (49 DR-TB, 81 drug-susceptible TB [DS-TB] patients), bronchoalveolar lavage fluid (BALF) was subjected to paired metagenomic and transcriptomic profiling. Microbial and bacteriophage community structures were assessed by diversity metrics and differential abundance testing, whereas host responses were characterized by gene expression, pathway enrichment, and immune cell deconvolution. A Random Forest model was trained to evaluate the diagnostic potential of host transcriptional signatures.

RESULTS: DR-TB airways presented distinct microbial beta diversity, with enrichment of Streptococcus spp. and streptococcal-targeting phages (e.g., Javan variants, phi-Ssu5SJ28rum). Transcriptomic analysis revealed 494 differentially expressed genes, which were associated with increased oxidative phosphorylation, suppressed ion channel and transporter activity, and enrichment of extracellular matrix remodeling pathways. Immune profiling demonstrated a significant reduction in γδ T cells in DR-TB patients (P = 0.0059). An 8-gene host-derived signature (ARHGEF5, PTGES3L, GAL3ST1, RANBP17, ACTA2_AS1, CBY3, MAMSTR, and LOC102031319) discriminated DR-TB from DS-TB with high accuracy (AUC = 0.837).

CONCLUSION: This dual-omics study defines the airway niche of DR-TB as a convergence of microbial dysbiosis, phage imbalance, and host immune-metabolic dysfunction. By uncovering DR-TB-specific microbial and transcriptional signatures, and deriving a predictive host-based classifier, our findings provide mechanistic insights and highlight novel opportunities for microbiome- and host-directed interventions in drug-resistant tuberculosis.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology
Mycobacterium tuberculosis/genetics
Male
Female
Gene Expression Profiling
Biomarkers/analysis
Metagenomics
Prospective Studies
Middle Aged
Adult
Microbiota
Transcriptome
Bacteriophages/genetics
Lung/microbiology

@article {pmid41693402,
year = {2026},
author = {Parveen, S and Shafi, Z and Shahid, M and Iqbal, MZ and Naznine, F and Ansari, MI},
title = {Omics-Driven Insights Into Soil Microbial Diversity and Phytopathogen Interactions for Sustainable Agriculture and Food Security.},
journal = {Journal of basic microbiology},
volume = {66},
number = {2},
pages = {e70155},
doi = {10.1002/jobm.70155},
pmid = {41693402},
issn = {1521-4028},
support = {//The authors are thankful for the support received from the Department of Science and Technology-Funds for Improvement of Science and Technology Infrastructure (DST-FIST), with grant acknowledgment and sanction number (SR/FST/LS-1/2017/13(C)). The authors express their deep gratitude to Integral University, Lucknow-226026, India, for their generous support of this work and for providing the manuscript communication number (IU/R&D/2025-MCN0003515)./ ; //Department of Science and Technology-Funds/ ; },
mesh = {*Soil Microbiology ; *Food Security ; *Agriculture/methods ; Biodiversity ; Metabolomics/methods ; Crops, Agricultural/microbiology/growth & development ; Proteomics ; Metagenomics ; Microbiota ; Plant Diseases/microbiology ; Bacteria/genetics/metabolism ; Ecosystem ; },
abstract = {Soil microbial diversity plays a pivotal role in sustainable agriculture by regulating nutrient cycling, organic matter turnover, and natural suppression of phytopathogens, thereby supporting crop productivity and ecosystem resilience. However, intensive agricultural practices and environmental stressors have led to a decline in soil biodiversity, compromising soil functionality and food security. Recent advances in omics technologies-including metagenomics, transcriptomics, proteomics, and metabolomics offer powerful tools to unravel the complexity, of soil microbial communities and their interactions with plants and pathogens. These integrated approaches provide high-resolution insights into microbial structure, functional dynamics, metabolic pathways, and the mechanisms underpinning plant-microbe-pathogen interactions. Furthermore, omics-driven understanding supports the development of sustainable strategies such as organic farming, conservation practices, and microbial bioinoculants, which restore microbial diversity, enhance nutrient use efficiency, reduce chemical inputs, and mitigate disease pressure. By linking soil health to crop nutritional quality and broader food system sustainability, this review highlights the potential of omics-guided approaches to optimize soil microbial ecosystems for resilient agriculture and global food security.},
}

*Soil Microbiology
*Food Security
*Agriculture/methods
Biodiversity
Metabolomics/methods
Crops, Agricultural/microbiology/growth & development
Proteomics
Metagenomics
Microbiota
Plant Diseases/microbiology
Bacteria/genetics/metabolism
Ecosystem

@article {pmid41693232,
year = {2026},
author = {Morsli, M and Magnan, C and Salipante, F and Dubois, A and Schuldiner, S and Cellier, N and Sotto, A and Lavigne, JP and Dunyach-Remy, C},
title = {Enhancing diabetic foot osteomyelitis diagnosis with metagenomics next-generation sequencing, proof of concept.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {},
number = {},
pages = {e70235},
doi = {10.1111/dme.70235},
pmid = {41693232},
issn = {1464-5491},
abstract = {Diabetic foot osteomyelitis (DFOM) is a serious medical condition that necessitates robust diagnostic tools for effective clinical management. Conventional diagnostic methods for DFOM rely heavily on bacterial culture, which is time-consuming and may fail to capture the full microbial diversity present in infections. This pilot study explored the utility of metagenomics next-generation sequencing (mNGS) as a complementary diagnostic tool for DFOM. We retrospectively analysed ten bone biopsies from nine diabetic persons using both routine microbiological culture and mNGS. Routine culture identified 11 bacterial species across seven biopsies, while mNGS detected 84 species, including all those found by culture. High microbial diversity (Shannon index = 1.10) was associated with severe osteomyelitis, leading to amputation in three of seven DFOM cases. Interestingly, one culture-negative biopsy revealed high bacterial diversity by mNGS and progressed to a severe infection within 7 days. mNGS also identified resistance genes, providing additional insights for targeted therapy. Integrating mNGS into routine clinical microbiology may serve as a complementary method to conventional diagnostics, particularly for distinguishing infection from colonization and predicting clinical outcomes. However, challenges such as human DNA contamination and limited sequencing depth must be addressed to optimize its clinical application. These findings support the integration of mNGS into diagnostic workflows for bone biopsies for improved management of DFOM.},
}

@article {pmid41692940,
year = {2026},
author = {Le, B and Jia, L and Pang, T and Han, S and Duan, Y and Zhao, XM},
title = {A review of computational approaches for metagenomics by long-read sequencing.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41692940},
issn = {1869-1889},
abstract = {The metagenomic next-generation sequencing (mNGS), also known as short-read sequencing (SRS), is widely used to explore microbial composition and function. However, short reads, due to their difficulty in crossing repetitive regions, can lead to fragmented assemblies, hampering the comprehensive characterization of microbial genomes. In contrast, long-read sequencing (LRS) technologies, such as those from Pacific Biosciences (PacBio) and Oxford Nanopore, can span these complex repetitive regions and reconstruct continuous genomes, which enables high-resolution taxonomic classification and the precise recovery of essential genetic elements. This review provides a systematic overview of the computational approaches for long-read metagenomics, highlighting the progress in taxonomic profiling strategies, assembly and binning methods, and the detection of genetic elements. Furthermore, the review discusses the application of LRS in detecting structural variations (SVs), identifying methylation patterns, and characterizing strains. By combining advanced technologies and computational improvements, this review indicates the transformative potential of LRS in enhancing our understanding of microbial diversity, functions, and interactions within microbial communities.},
}

@article {pmid41692795,
year = {2026},
author = {Vega, L and Birchenall-Jiménez, CI and Aponte, A and Durán, D and López, C and Moreno-Matson, MC and Perilla, C and Pinilla, D and Rodríguez-Leguizamón, G and Sánchez, E and Santana, A and Herrera, G and Ramírez, JD and Muñoz, M},
title = {Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00809-5},
pmid = {41692795},
issn = {1757-4749},
abstract = {BACKGROUND: Diarrhea remains a major cause of morbidity worldwide, particularly in low- and middle-income countries. Hospital environments impose strong selective pressures on the gut microbiome through antimicrobial exposure, invasive procedures, and pathogen transmission, yet differences between hospital-onset and community-onset diarrhea remain poorly characterized at the microbiome level. This study aimed to compare the taxonomic and functional profiles of the gut microbiome in hospitalized (Hosp) and emergency room (ER) patients with diarrhea using shotgun metagenomics.

RESULTS: Fecal samples from 41 patients (Hosp = 24; ER = 17) attending the Hospital Universitario Mayor-Méderi (Bogotá, Colombia) were analyzed. The gut microbiomes were dominated by Enterobacteriaceae, particularly Klebsiella pneumoniae and Escherichia coli, together with abundant bacteriophages from the families Myoviridae, Siphoviridae, Podoviridae, and crAss-like phages. Phages predicted to infect Escherichia and Klebsiella were significantly depleted in Hosp patients (p < 0.05). Read-based functional profiling revealed the presence of virulence factors associated with K. pneumoniae capsule biosynthesis, secretion systems, and toxins from Clostridioides difficile and Clostridium perfringens. In parallel, Hosp patients showed a higher diversity of antimicrobial resistance markers, with a marked increase in glycopeptide resistance determinants. A total of 492 high-quality metagenome-assembled genomes were reconstructed, including multiple diarrhea-associated taxa. Hosp patients exclusively harbored genomes of K. pneumoniae, Enterococcus faecium, and most reconstructed Clostridium species (C. symbiosum, C. saccharolyticum_A, C. innocuum, C. scindens, C. leptum, and Clostridium sp000435835). In contrast, ER patients harbored genomes classified as Escherichia coli, Escherichia flexneri, and Enterococcus faecalis. Genomes associated with hospitalization carried higher loads of antimicrobial resistance markers (e.g., oqxA and aac(6')-Ii) and virulence factors (e.g., iutA and traT), whereas ER genomes, particularly E. coli and E. flexneri, encoded diverse aminoglycoside resistance and adhesion traits.

CONCLUSIONS: Hospital-onset diarrhea was associated with distinct microbiome features, including differences in phage-bacteria dynamics involving key diarrhea-associated taxa, as well as a higher abundance of virulence factors and antimicrobial resistance markers. These findings underscore the potential value of shotgun metagenomics as a complementary approach for infection surveillance and the development of precision diagnostic strategies in hospital settings.},
}

@article {pmid41691988,
year = {2026},
author = {Pan, Y and Zong, G and Liu, M and Wang, Z and Zhu, H and Wei, Z and Shan, Y and Lu, Y},
title = {Restoring gut microbiota homeostasis to ameliorate colitis via Huangqin decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {153},
number = {},
pages = {157929},
doi = {10.1016/j.phymed.2026.157929},
pmid = {41691988},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory gut disorder involving dysregulated host-microbiota interactions. Huangqin decoction (HQD) is an herbal formula with known anti-inflammatory and microbiota-modulating effects, but its protective mechanism in ulcerative colitis remains unclear.

PURPOSE: To investigate whether HQD ameliorates colitis by rebalancing gut microbiota homeostasis and to elucidate the underlying immunological and regenerative mechanisms involved.

METHODS: A DSS-induced colitis mouse model was used to evaluate the effects of HQD. Colitis severity and inflammation were evaluated by the clinical disease index, histological analysis, and cytokine levels, and the gut microbiota profiles were analyzed via metagenomic sequencing. We used mechanistic assays to evaluate the effects of specific bacterial strains on intestinal organoids and neutrophil NETosis.

RESULTS: HQD significantly alleviated colitis symptoms and inflammation. It remodelled the gut microbiota, suppressing Desulfovibrionaceae while enriching Lachnospiraceae. This microbiota shift drove reduced NETosis and activated Wnt/β-catenin signaling to enhance intestinal stem cell (ISC) proliferation, thereby promoting mucosal repair. In organoid cultures, Lachnospiraceae promoted organoid growth, whereas Desulfovibrionaceae caused epithelial damage and, independently, triggered NETosis in immune contexts. Notably, administration of the Lachnospiraceae bacterium ameliorated colitis and increased colonic Wnt/β-catenin signaling, confirming its regenerative role.

CONCLUSION: HQD ameliorates colitis by rebalancing the gut microbiota, thereby suppressing harmful inflammation and promoting epithelial regeneration. These findings provide mechanistic support for HQD as a microbiota-mediated therapeutic strategy in colitis.},
}

@article {pmid41691957,
year = {2026},
author = {Jiang, W and Pu, J and Wang, F and Yan, J and Yang, Q and Yang, S and Bian, D},
title = {Study on the degradation performance and toxicity reduction mechanism of electroplating wash wastewater by a hydrolysis-acidification-MPR synergistic system.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128990},
doi = {10.1016/j.jenvman.2026.128990},
pmid = {41691957},
issn = {1095-8630},
abstract = {This study focuses on high-strength, low-biodegradability electroplating wash wastewater (COD ≥20,000 mg/L, BOD5/COD ≤0.1). A laboratory-scale hydrolysis-acidification (HA)-micro-pressure internal circulation multiphase reactor (MPR) combined treatment process was constructed. In the HA stage, wastewater biodegradability was significantly improved, with the BOD5/COD ratio being increased from 0.03 to 0.31. The MPR stage then further deepened degradation, enabling the system to maintain a COD removal rate above 97% during stable operation, linear alkylbenzene sulfonate (LAS) and TN removal rates were achieved at over 99% and 96.8%, respectively. Vibrio fischeri luminescence inhibition was reduced from >95% in the influent to approximately 65% in the HA effluent and <10% in the MPR effluent. GC-MS analysis revealed that the HA stage cleaved high-molecular-weight pollutants such as long-chain alkanes and esters into mid- and small-molecule products (e.g., 3-methylcyclohexanone and 2,5-dimethylnonane), while the MPR stage further converted these intermediates into low-toxicity small molecules (e.g., trimethylsilanol and hexamethylcyclotrisiloxane). Metagenomic analysis showed that facultative anaerobic fermenters (Aminivibrio, Alcaligenes) were enriched in the HA stage, whereas aerobic bacteria (Pseudomonas, Brevundimonas) predominated in the MPR stage. Key functional genes (alkB, cyp450, gpmB) were significantly enriched during the stable period, promoting carbon metabolism and stress resistance. This study elucidated that the HA-MPR synergistic system achieved efficient and stable degradation and toxicity mitigation of electroplating wash wastewater through a multi-stage cooperative mechanism of acidification cleavage and aerobic deep mineralization, providing theoretical and technical support for the engineering application of this process.},
}

@article {pmid41691930,
year = {2026},
author = {Liu, Q and Chen, S and Wang, Y and Wang, S and Zhou, R and Kou, G},
title = {Prunus persica (L.) Batsch root enriched Pseudomonas for enhanced saline-alkali tolerance by inducing fatty acid and flavonoid biosynthesis.},
journal = {Plant physiology and biochemistry : PPB},
volume = {232},
number = {},
pages = {111134},
doi = {10.1016/j.plaphy.2026.111134},
pmid = {41691930},
issn = {1873-2690},
abstract = {Peach (Prunus persica (L.) Batsch) is one of the most widely cultivated economic fruit crops worldwide. However, saline-alkali stress poses substantial challenges to its cultivation and production. This study investigated the synergistic response of peach roots and their rhizosphere microbiota to saline-alkali stress. We examined alterations in the rhizosphere bacterial community and its functional characteristics under such stress using 16S rRNA and metagenomic sequencing. The results indicated a significant enrichment of the genus Pseudomonas in the rhizosphere, accompanied by enhanced functional potential related to cell motility, biofilm formation, and signal transduction. Nine Pseudomonas strains were isolated from the stressed rhizosphere, all of which exhibited plant growth-promoting (PGP) traits in vitro, among which strains R8 showed the most comprehensive PGP profile and most significantly enhanced plant growth in pot experiments. Physiological and transcriptomic analyses demonstrated that R8 inoculation upregulates key genes involved in fatty acid (e.g., FAD, KCS, PAS) and flavonoid biosynthesis (e.g., CHS, CHI, F3H, FLS). This transcriptional reprogramming enhanced membrane stability (increased proline content) and antioxidant capacity (higher flavonoid levels), leading to systemic improvement in saline-alkali tolerance. This study reveals the adaptive strategy of peach to saline-alkali stress mediated by rhizobacteria and highlights the potential of R8 as a microbial inoculant for sustainable cultivation.},
}

@article {pmid41691882,
year = {2026},
author = {Xie, Y and Xu, Y and Ma, C and Chen, L and Cai, Y and Wu, S and Fan, Y and Zhang, C and Tian, Y and Tian, Y and Zhang, Y and Li, X and He, D},
title = {Cerebral sparganosis caused by spirometra sp.: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {1},
pages = {117311},
doi = {10.1016/j.diagmicrobio.2026.117311},
pmid = {41691882},
issn = {1879-0070},
abstract = {Cerebral sparganosis is a rare parasitic infection caused by plerocercoid larvae of the genus Spirometra. Due to its nonspecific clinical manifestations, diagnosis remains challenging in clinical practice. Here, we report a case of a 72-year-old female who presented with intermittent fever and migratory intracranial mass lesions over a seven-year period, accompanied by progressive cognitive decline and right homonymous hemianopia. Metagenomic next-generation sequencing (mNGS) analysis of cerebrospinal fluid identified Spirometra sp. The diagnosis was further confirmed through brain lesion biopsy and tissue mNGS analysis. Following treatment with praziquantel and albendazole, the patient showed clinical improvement with no evidence of recurrence during 1-year follow-up. This case report highlights the diagnostic value of mNGS in identifying rare parasitic infections, particularly in cases of cerebral sparganosis where clinical presentation may be non-specific.},
}

@article {pmid41691872,
year = {2026},
author = {Zhang, XR and Hou, J and Rong, Z and Wu, YH and Cui, HL},
title = {Haladaptatus marinus sp. nov., Haladaptatus rarus sp. nov., Haladaptatus ordinarius sp. nov., and Halomicrococcus pelagicus sp. nov., halophilic archaea from diverse coastal tidal flats.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126698},
doi = {10.1016/j.syapm.2026.126698},
pmid = {41691872},
issn = {1618-0984},
abstract = {Six novel halophilic archaeal strains, DFWS20[T], NG-SE-30[T], NG-WS-4[T], HHT-WS-8, NG-SE-24[T], and SG-WS-1, were isolated from different coastal regions of China. Metagenome and amplicon analyses showed that the abundance of archaea in the corresponding samples was very low. Strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 were found to cluster with current Haladaptatus species, while strains NG-SE-24[T] and SG-WS-1 with those of Halomicrococcus based on 16S rRNA and rpoB' gene phylogenies. The overall-genome related indexes (OGRIs), average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values, between strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], HHT-WS-8, and Haladaptatus species were 77.0-83.1%, 22.2-28.3%, and 74.7-84.8%, while those between strains NG-SE-24[T], SG-WS-1, and Halomicrococcus species were 79.6-94.9%, 26.0-63.9%, and 76.5-94.1%, respectively. These values were lower than the threshold of species classification. In contrast, the OGRIs between strains NG-WS-4[T] and HHT-WS-8, as well as those between strains NG-SE-24[T] and SG-WS-1, were above the threshold of species classification. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, and antibiotic sensitivity, were determined in these six strains and the existing species of the corresponding genera. The most abundant pathways in the genera Haladaptatus and Halomicrococcus were related to carbohydrate metabolism and amino acid metabolism. Based on the natural habitat analysis of the 16S rRNA genes of the strains, their target sequences were primarily found in habitats such as aquatic, soil, sediments, plant, and marine environments. The major polar lipids of strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol sulfate (PGS), and sulfated mannosyl glucosyl diether (S-DGD-1), while those of strains NG-SE-24[T] and SG-WS-1 were PG, PGP-Me, S-DGD-1, and galactosyl mannosyl glucosyl diether (TGD-2). Based on these polyphasic classification, strains DFWS20[T], NG-SE-30[T], NG-WS-4[T], and HHT-WS-8 represent three novel species of the genus Haladaptatus while NG-SE-24[T] and SG-WS-1 represent a novel species of the genus Halomicrococcus.},
}

@article {pmid41691815,
year = {2026},
author = {Xia, J and Han, J and Hong, L and Qiu, YY and Xie, Y and Xu, H and Zhang, L and Jiang, F},
title = {Resilient sulfur-driven treatment of real acid mine drainage enabled by reorganization of core sulfidogenic microorganisms.},
journal = {Water research},
volume = {294},
number = {},
pages = {125521},
doi = {10.1016/j.watres.2026.125521},
pmid = {41691815},
issn = {1879-2448},
abstract = {Elemental sulfur-driven sulfidogenic processes offer a promising alternative to conventional sulfate reduction for acid mine drainage (AMD) treatment, with advantages in lower operation cost induced by lower organic demand. However, their long-term performance and microbial stability under real AMD conditions, where high acidity and metal concentrations impose strong environmental stress, remain poorly understood. Here, we operated a laboratory-scale sulfur-driven bioreactor for 258 days to evaluate the long-term sulfide production, metal removal efficiency, and microbial succession when treating real AMD. The system maintained stable sulfide production (68.3 ± 12.1 mg S/L-h) under acidic conditions (pH 4.1 ± 0.2) with a carbon-to-sulfur ratio (∼0.23, mg TOC per mg sulfide) consistent with the theoretical value for sulfur reduction. Over 99.9% of Zn[2+], Cu[2+], Ni[2+], Cd[2+], and Co[2+] in AMD were effectively removed via in-situ precipitation with biogenic sulfide. Even exposed to high metal concentrations (e.g., ∼400 mg/L Zn[2+], ∼51 mg/L Cu[2+]), the sulfidogenic bacteria exhibited strong resilience and robustness. Microbial analyses revealed a substantial shift from diverse fermenters under synthetic wastewater to specialized, metal-tolerant sulfur reducers (e.g., Desulfurella, Athalassotoga) under AMD conditions. Metagenome-assembled genomes of these taxa revealed distinct metabolic strategies, including sulfur respiration, acid resistance, and metal detoxification, supporting their dominance under metal-rich and low-pH environments. Notably, the community exhibited strong structural resilience to both long-term metal exposure and acute metal shocks, maintaining sulfidogenic functionality through internal community reorganization rather than taxonomic turnover. These findings demonstrated the feasibility, robustness, and ecological adaptability of sulfur-driven sulfidogenic systems for cost-effective treatment of real-world AMD.},
}

@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}

@article {pmid41691450,
year = {2026},
author = {Chen, S and Gu, Y and Bahadur, A and Liu, E and Wu, T and Zhu, X and Zou, Y and Liang, H and Wei, P and Wu, L and Wu, Q and Yang, P and Yu, H and Yang, Y},
title = {Divergent Responses of Bacterial Communities to Permafrost Degradation and Their Associations With Carbon Across Vertical Profiles.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e10516},
doi = {10.1002/advs.202510516},
pmid = {41691450},
issn = {2198-3844},
support = {2022YFF0801903//National Key R&D Program of China/ ; xbzg-zdsys-202214//"Light of the West" Cross-team Project of the Chinese Academy of Sciences/ ; U23A2062//National Natural Science Foundation of China/ ; U24A20586//National Natural Science Foundation of China/ ; 23ZDFA017//Science and Technology Program of Gansu Province/ ; CSFSE-FX-2505//Freedom Project of the State Key Laboratory of Cryospheric Science and Frozen Soil Engineering, Northwest Institute of Eco-Environment and Resources, CAS/ ; },
abstract = {Permafrost degradation poses a significant threat to the organic carbon (C) pool primarily through regulating microorganisms. However, microbial responses and their associations with C loss across vertical profiles remain unclear. Here, we use metagenomic sequencing to investigate bacterial communities in 125 samples from five 15 m-depth permafrost cores, spanning from the active layer to the permafrost layer along a degradation gradient on the Qinghai-Tibet Plateau. We find that α-diversity decreases, while stochastic processes and community stability increase from the active layer to the permafrost layer. Along permafrost degradation, these community attributes follow similar variations within the active layer but remain constant within the permafrost layer. The relative abundance and interaction of core taxa play important roles in maintaining community stability in the active and permafrost layers, respectively. As permafrost degrades, the negative relationships between community stability and C storage become more intense, especially in the active layer. These findings demonstrate that degradation induces microbial responses that potentially amplify C release, supporting a positive feedback loop to climate warming. Our work provides novel insights into the vertical heterogeneity of this mechanism and is crucial for modeling future permafrost C dynamics.},
}

@article {pmid41691253,
year = {2026},
author = {Daryani, NE and Jazayeri, SM and Izadi, N and Ahmadi, H and Baghi, HB and Shirmohammadi, M and Sabbaghian, M and Shekarchi, AA and Marvi, SS and Azadi, A and Poortahmasebi, V},
title = {Characterizing the gut virome in ulcerative colitis and crohn's disease: signatures of disease severity.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03091-8},
pmid = {41691253},
issn = {1743-422X},
support = {979157//National Institute for Medical Research Development/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic disorder marked by intestinal inflammation and immune dysregulation. While bacterial dysbiosis has been widely investigated, the gut virome remains less explored. Altered viral communities, particularly bacteriophages, may destabilize microbial balance and amplify host inflammation.

METHODS: To characterize virome alterations, we conducted a cross-sectional observational study in Tabriz, Iran, involving fifty participants divided into five groups: mild UC, severe UC, mild CD, severe CD, and healthy controls. Stool samples were processed for viral nucleic acid extraction and analyzed using metagenomic next-generation sequencing. Bioinformatics pipelines included diversity assessment, taxonomic profiling, functional annotation, and discriminant analysis (LEfSe). Predictive modeling was performed with random forest classifiers.

RESULTS: Virome richness and diversity were reduced in severe UC and CD compared with controls, whereas mild cases showed values closer to healthy individuals. Taxonomic profiling revealed depletion of crAss-like phages and microviridae in IBD, along with enrichment of Caudovirales families such as siphoviridae and myoviridae. Among eukaryotic viruses, anelloviridae were prominent in severe IBD, and herpesviridae were enriched specifically in severe UC. Functional annotation highlighted enrichment of structural and lytic phage proteins in severe groups, whereas lysogeny-associated domains were more abundant in healthy controls. Random forest models based on viral features achieved appropriate accuracy, with an AUC of 0.89 for distinguishing IBD from controls and 0.83 for classifying mild versus severe disease.

CONCLUSION: Thus, IBD is associated with reduced virome diversity, loss of core protective phages, and selective enrichment of bacteriophages and eukaryotic viruses. These findings suggest that virome features may have potential as biomarkers for non-invasive diagnosis and severity stratification in IBD, requiring validation in larger and longitudinal cohorts.},
}

@article {pmid41691172,
year = {2026},
author = {Motta, H and Perin, APA and Rosin, GF and Reuwsaat, JCV and Mocelin, I and Lopes, FC and Mayer, FQ and de Medeiros, VP and Brum, IS and Baethgen, LF and Gregianini, TS and Staats, CC and Vainstein, MH and Kmetzsch, L},
title = {SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04828-9},
pmid = {41691172},
issn = {1471-2180},
support = {405934/2022-0//Instituto Nacional de Ciência e Tecnologia (INCT FUNVIR)/ ; 408717/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/2551-0000396-6//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; },
}

@article {pmid41691170,
year = {2026},
author = {Zhou, W and Zou, X and Li, J and Alhaskawi, A and Abdalbary, SA and Lu, H},
title = {Chronic osteomyelitis of the right thumb caused by Actinomyces radingae and Finegoldia magna: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12860-3},
pmid = {41691170},
issn = {1471-2334},
abstract = {BACKGROUND: Osteomyelitis of the hand is relatively uncommon and often results from penetrating trauma or postoperative infection. Rare pathogens such as Actinomyces radingae and Finegoldia magna pose diagnostic and therapeutic challenges due to their slow growth, frequent involvement in polymicrobial infections, and limited antibiotic susceptibility data.

CASE PRESENTATION: A 66-year-old male sustained a crush injury being caught in a door to his right thumb over two years prior, leading to repeated episodes of redness, swelling, pain, and restricted motion. Despite undergoing surgical intervention three months earlier at another hospital, his symptoms persisted. Radiography revealed cortical irregularity and surrounding soft tissue swelling of the distal phalanx. Magnetic resonance imaging revealed bone marrow edema of the distal phalanx and adjacent soft tissue inflammation, raising suspicion for underlying osteomyelitis in the appropriate clinical context. Laboratory markers of infection were within normal limits. The patient underwent surgery including necrotic bone removal, extensor tendon reconstruction with muscle transposition, and nail bed debridement. Intraoperative findings included purulent drainage, nail deformity, and tendon necrosis. Metagenomic next-generation sequencing (mNGS)of bone tissue identified Actinomyces radingae (8,019 reads) and Finegoldia magna (4,223 reads). Based on the chronic clinical course, imaging findings, intraoperative evidence of necrotic bone, and pathogen identification by metagenomic next-generation sequencing, a diagnosis of chronic osteomyelitis of the distal phalanx was established. Postoperatively, the patient received ertapenem (1 g QD) with good clinical response.

CONCLUSION: This case highlights the importance of considering uncommon pathogens in chronic post-traumatic hand infections and demonstrates the utility of mNGS in identifying atypical bacteria, enabling targeted therapy and improved outcomes.},
}

@article {pmid41690672,
year = {2026},
author = {Zhang, Y and Bai, Y and Ni, J and Shi, J and Zhang, Y and Bell-Sakyi, L and Wu, X and He, C and Deng, F and Yin, F and Shen, S and Fang, Y},
title = {Evidence of human exposure to tick-borne viruses based on viromes of ticks and presence of specific antibodies among patients in Hainan Island, Southern China.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.02.008},
pmid = {41690672},
issn = {1995-820X},
abstract = {Hainan Island, located in the South China Sea, is known as an area with diseases related to Rickettsia spp. or spirochete infection; however, the potential threat there from infection with tick-borne viruses (TBVs) remains obscure. In the present study, the dominant tick species, including Rhipicephalus sanguineus and Rhipicephalus microplus, were collected in Hainan Island, and tick viromes were investigated by metagenomic sequencing. In total, 27 viral species were identified belonging to the families Orthomyxoviridae, Flaviviridae, Nairoviridae, Phenuiviridae, Totiviridae, Chuviridae, Rhabdoviridae, and Parvoviridae, amongst which one novel virus and 13 new strains were discovered. Subsequently, individual ticks were screened for seven TBVs, Huanggang Rhabd tick virus 1 (HRTV1), Lihan tick virus (LHTV), Mivirus (MIV), Guangdong tick quaranjavirus (GTQV), Wenchang Ephemerovirus (WEPMV), Jingmen tick virus (JMTV), and brown dog tick phlebovirus (BDPTV), resulting in high prevalence rates of 16.97%, 9.59%, 10.33%, 7.38%, 7.01%, 6.27%, and 3.69%, respectively. While co-infection with multiple viruses was more frequent in R. sanguineus, R. microplus ticks generally had higher viral loads. Four febrile patients showed antibody responses to three TBVs, one each to LHTV and JMTV, and two to GTQV; the patient with antibodies to JMTV also showed neutralizing activity against this virus. This study promoted our understanding of the diversity and complexity of the TBV community in Hainan Island. The results provide serological evidence that human exposure to TBVs like JMTV may have occurred in Hainan, raising concern about potential risks from TBVs and the need to perform further surveys of TBVs among ticks, animals and humans.},
}

@article {pmid41690272,
year = {2026},
author = {Bao, M and Liu, X and Chang, N and Wang, M and Zuo, S and Yin, G and Li, W and Zhang, S and Zhang, Y and Shen, W},
title = {Seasonal variation and co-occurrence of metal resistance and virulence genes in landfill leachate pathogens: Implications for environmental risk management.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141460},
doi = {10.1016/j.jhazmat.2026.141460},
pmid = {41690272},
issn = {1873-3336},
abstract = {The co-dissemination of metal resistance genes (MRGs) and virulence factor genes (VFGs) in landfill leachate pathogens poses a significant yet underquantified public health risk. To address this gap, this study used metagenomic analysis to assess MRG/VFG occurrence and removal efficiency, and proposed a novel metal resistance index (MRI)-virulence risk index (RVI) framework to quantify microbial risks across raw, ultrafiltered, reverse-osmosis-treated leachate and adjacent groundwater in Hohhot, China. Metagenomic analyses identified 175 MRGs and 1024 VFGs, highlighting significant co-occurrence patterns (Spearman R > 0.6, P < 0.05) among dominant pathogens, including Pseudomonas aeruginosa and Escherichia coli. The results of PCoA analysis showed that the leachate treatment process could significantly change the spectrum of virulence gene and heavy metal resistance gene in the leachate. Linear regression analysis (all P < 0.001) revealed significant positive correlations between treated leachate and groundwater microbial VFGs/MRGs across seasons. Summer showed the strongest associations (R[2]: 0.733-0.892), followed by moderate correlations in spring (R[2]: 0.364-0.698) and autumn (R[2]: 0.349-0.642), with spatial heterogeneity in BG3 and marked seasonal impacts overall. MRI, RVI, and the MRI/RVI ratio increased sequentially after treated, indicating that high-risk microbial traits persist post-treatment. Importantly, this elevated MRI/RVI ratio is attributable to the relative proportional increase of high-risk genes rather than an absolute rise in their abundance. Our results demonstrate the leachate treatment partially mitigates heavy metal resistance/virulence loads but fails to eliminate all high-risk genes, revealing seasonal MRG-VFG co-enrichment and treatment efficacy. The MRI-RVI framework guides leachate management optimization for environmental and public health.},
}

@article {pmid41690221,
year = {2026},
author = {Jiang, Y and Shu, W and Wan, J and Yan, J and Liu, Q and Jiang, Y},
title = {Impacts of co-exposure to nanoplastics and ofloxacin on marine planktonic microbial communities and DMSP dynamics.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107908},
doi = {10.1016/j.marenvres.2026.107908},
pmid = {41690221},
issn = {1879-0291},
abstract = {Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound in marine food webs and the main precursor of the climate-active gas dimethyl sulfide (DMS), yet its water-column cycling under the joint influence of emerging pollutants remains poorly constrained. A 19-day microcosm experiment was conducted to examine the long-term effects of single and combined exposure to nanoplastics (NPs) and the antibiotic ofloxacin on planktonic microbial communities and DMSP cycling in coastal seawater. Combined exposure induced much stronger inhibitory effects than either single pollutant, markedly weakening the late-phase biomass recovery observed under the antibiotic-only treatment. DMSP dynamics exhibited a biphasic disruption pattern: an initial transient accumulation was followed by persistently low concentrations later in the experiment, coinciding with pronounced declines in microeukaryotic and total biomass. Combined metagenomic and flow cytometric analyses revealed a "functional decoupling" scenario, in which the surviving community displayed elevated relative abundances of DMSP biosynthesis- and degradation-related genes, while the sharp reduction in microeukaryotic biomass and overall community size constrained the maintenance and renewal of the water-column DMSP pool. Co-occurrence network analysis further showed that co-exposure simplified the microbial network from a more distributed, complex structure to a highly centralized one, with fewer nodes and keystone taxa and decreased robustness indices along the pollution gradient. Together, these findings indicate that the co-occurrence of nanoplastics and antibiotics can disturb DMSP-related functions by eroding community structural stability and functional redundancy, providing experimental evidence for the vulnerability of coastal DMSP cycling to mixed-pollutant stress.},
}

@article {pmid41689625,
year = {2026},
author = {Hayashi, T and Iida, N and Yasuda, K and Yoshio, T and Terashima, T and Takatori, H and Moriyama, H and Takeshita, Y and Takamura, T and Yamashita, T},
title = {Escherichia coli as a gut microbial marker of obesity and its reduction following bariatric treatment.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {41689625},
issn = {1435-5922},
support = {19K17394//Japan Society for the Promotion of Science/ ; 23K15036//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Alterations in the gut microbiota have been implicated in obesity-related metabolic disorders; however, the disease-relevant microbial features that link gut dysbiosis to metabolic risk remain incompletely defined. In particular, whether quantitative expansion or strain-level divergence of specific taxa underlie metabolic dysfunction is unclear.

METHODS: We performed cross-sectional and longitudinal metagenomic analyses of fecal samples from 19 patients with severe obesity undergoing bariatric intervention and 30 healthy donors. Whole-genome shotgun sequencing was combined with quantitative PCR to assess both relative and absolute bacterial abundance. Cultured Escherichia coli isolates were further examined by whole-genome sequencing to evaluate strain-level diversity. Associations between microbial features and metabolic parameters were analyzed.

RESULTS: The gut microbiota of patients with severe obesity was taxonomically and functionally distinct from that of healthy donors. Among altered taxa, E. coli was significantly enriched in obesity and showed a consistent and marked reduction at 6 months post-intervention, irrespective of procedure type. Absolute E. coli abundance quantified by qPCR decreased significantly following intervention. In contrast, whole-genome analysis revealed no clear genotypic clustering of E. coli strains by host phenotype. Notably, E. coli abundance correlated positively with HbA1c and systolic blood pressure and negatively with serum albumin levels, whereas global microbial diversity and KEGG-based metabolic pathways showed limited longitudinal change.

CONCLUSIONS: Quantitative expansion of gut E. coli, rather than strain-specific genomic divergence, is associated with metabolic risk in severe obesity and is consistently reduced at 6 months after bariatric intervention. These findings suggest that microbial load-dependent effects of E. coli may be associated with obesity-related metabolic dysfunction and represent a potential biomarker. This exploratory, single-center study is hypothesis-generating and warrants further validation in larger, multi-center cohorts as well as interventional studies using preclinical animal models.},
}

@article {pmid41689511,
year = {2026},
author = {Xu, R and Mayer, MJ and Philo, M and Gall, GL and Mulaw, G and Ponsero, A and Narbad, A},
title = {Combining Lactiplantibacillus plantarum and Bifidobacterium adolescentis can improve GABA production in faecal fermentations.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag047},
pmid = {41689511},
issn = {1365-2672},
abstract = {AIMS: This project aimed to investigate production of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) from potential probiotic strains. We studied production in co-cultures and faecal fermentations and examined the effect of selected strains on the faecal microbiome composition and metabolome in vitro.

METHODS AND RESULTS: Strains of intestinally-derived Bifidobacterium adolescentis and Lactiplantibacillus plantarum from fermented cereals were grown singly, in co-culture and in faecal fermentations designed to simulate colonic conditions.Isolates synthesised varing amounts of GABA in vitro; GABA production could be increased by co-culture, lactic acid or reduced pH but was decreased in the presence of high buffering. In faecal fermentations, selected strains inoculated singly or in combination persisted over 24 hours and increased the GABA concentration without causing major disruptions in the microbiome or metabolome. B. adolescentis supplementation increased short chain fatty acids acetate and propionate and L. plantarum was associated with increased succinate levels, while all treatments exhibited a reduction in Escherichia compared to the controls.

CONCLUSIONS: GABA production from these lactic acid bacteria is strain-specific and the combination of these two species shows potential for future next-generation probiotic development.},
}

@article {pmid41688638,
year = {2026},
author = {Dekkers, KF and Pertiwi, K and Baldanzi, G and Lundmark, P and Hammar, U and Moksnes, MR and Coward, E and Nethander, M and Salih, GA and Miari, M and Nguyen, D and Sayols-Baixeras, S and Eklund, AC and Holm, JB and Nielsen, HB and Volpiano, CG and Méric, G and Thangam, M and Hakaste, L and Tuomi, T and Ahlqvist, E and Smith, CA and Allen, M and Reimann, F and Gribble, FM and Ohlsson, C and Hveem, K and Melander, O and Nilsson, PM and Engström, G and Smith, JG and Michaëlsson, K and Ärnlöv, J and Orho-Melander, M and Fall, T},
title = {Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {41688638},
issn = {1546-1718},
support = {2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 2020-02191//Vetenskapsrådet (Swedish Research Council)/ ; 2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; 521-2013-2756//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01236//Vetenskapsrådet (Swedish Research Council)/ ; 2021-02273//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01291//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01015, 2020-00243//Vetenskapsrådet (Swedish Research Council)/ ; 2018-02784, 2018-02837, EXODIAB 2009-1039//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20200173//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2022-0344//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2020-0711//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//Lars Erik Lundbergs Stiftelse för Forskning och Utbildning (Lundberg Foundation for Research and Education)/ ; CKFUU-1025348, 987986, 976460, 963488, 936407, 695401, and 797891//Centrum fÖr Klinisk Forskning Dalarna (Center for Clinical Research Dalarna)/ ; },
abstract = {Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 × 10[-11]) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.},
}

@article {pmid41688119,
year = {2026},
author = {Akpulu, CP and Maikudi Sada, H and Ahmed, H and Idris, HB and Yakubu, R and Aminu, A and Iregbu, K and Oduwo, J and Owinoh, E and Lankapalli, AK and De Nies, L and Achi, CR and Thomson, K and Stracy, M and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Nigeria (INBUGS-NG).},
journal = {BMJ open},
volume = {16},
number = {2},
pages = {e111007},
doi = {10.1136/bmjopen-2025-111007},
pmid = {41688119},
issn = {2044-6055},
mesh = {Humans ; Nigeria ; *Gastrointestinal Microbiome ; Female ; Infant ; *Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; Male ; Infant, Newborn ; Longitudinal Studies ; Feces/microbiology ; Adult ; Breast Feeding/statistics & numerical data ; Milk, Human/microbiology ; Delivery, Obstetric ; Pregnancy ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Nigeria (INBUGS-NG) investigates how delivery mode, antibiotic exposure, feeding practices and environmental factors shape gut microbiome development and acquisition of antibiotic resistance genes (ARGs) during the first year of life in northern Nigeria.

PARTICIPANTS: Between February and July 2024, 90 mother-infant dyads were enrolled at a tertiary hospital in Kano city, Nigeria. This was a prospective longitudinal cohort with follow-ups at 10 scheduled time points: days 0, 1, 3, 5, 7, 14, 28, 90, 180 and 365. We also intensified stool sampling after infant antibiotic administration, enabling dense early-life sampling. To date, the cohort has contributed 480 infant stool samples, 232 maternal rectal swabs, 254 breast milk samples and 806 environmental samples (total 1772). In parallel, socio-demographic, clinical and cultural data were collected using Research Electronic Data Capture (REDCap) and household visit diaries.

FINDINGS TO DATE: Baseline data show that 84/90 mothers (93.3%) received postpartum antibiotics, and 26/90 infants (28.9%) received antibiotics within the first 3 months of life. Only 8% of infants were exclusively breastfed, with early water supplementation common. Caesarean deliveries accounted for 25% of births, and the mean gestational age was 38.5 weeks. Across the cohort, high retention was achieved, and the study has generated a unique long-read metagenomic resource from an African infant population, with analyses ongoing.

FUTURE PLANS: Shotgun long-read metagenomic sequencing (Oxford Nanopore) will enable strain-level and plasmid-level profiling of microbial communities and ARGs. Planned analyses include associations between early-life exposures and resistome dynamics, as well as cross-cohort comparisons with a parallel study in Pakistan. Follow-up will continue through 12 months.},
}

Humans
Nigeria
*Gastrointestinal Microbiome
Female
Infant
*Anti-Bacterial Agents/therapeutic use
Prospective Studies
Male
Infant, Newborn
Longitudinal Studies
Feces/microbiology
Adult
Breast Feeding/statistics & numerical data
Milk, Human/microbiology
Delivery, Obstetric
Pregnancy

@article {pmid41687886,
year = {2026},
author = {Jin, B and Yan, Y and Bai, Z and He, H and Du, J and Xu, Y and Ma, C and Wang, L and Ji, J},
title = {Metagenomics reveals the mechanisms of endogenous partial denitrification (EPD) driven by different valence iron states:Nitrite accumulation, microbial adaptation, functional gene and metabolic pathways.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134209},
doi = {10.1016/j.biortech.2026.134209},
pmid = {41687886},
issn = {1873-2976},
abstract = {To enhance the performance of endogenous partial denitrification (EPD) systems, different iron valence states (nano-zero-valent iron (nZVI), Fe(II), and Fe(III)) were introduced, and their effects on microbial communities and metabolic pathways were investigated using metagenomics. The results indicated that iron supplementation significantly improved the removal of COD, NO3[-]-N, and PO4[3-]-P, as well as NO2[-]-N accumulation. Notably, Fe(III) proved most effective, achieving a NO2[-]-N accumulation of 27.7 ± 3.7 mg/L and a PO4[3-]-P removal efficiency of 64.7 ± 7.5%, whereas excessive Fe(II) and Fe(III) (40 mg/L) inhibited NO2[-]-N accumulation. While the overall microbial community structure remained stable, iron addition enriched specific denitrifying and phosphorus-accumulating genera such as Candidatus Competibacteraceae (1.36%, 2.40%, 2.30%), Candidatus Competibacter (0.40%, 0.65%, 0.62%), and Thauera (3.02%, 1.76%, 3.00%). nZVI promoted carbon utilization and denitrification gene expression, enhanced the including endogenous carbon transformation and nitrogen metabolism. In contrast, Fe(II) and Fe(III) enhanced NO2[-]-N accumulation by suppressing key genes (nirS/nirK, norB, nosZ) and shifted phosphorus metabolism toward chemical removal as the dominant pathway. Exogenous iron optimizes the performance of the EPD system by downregulating iron metabolism genes (afuA, fbpA, and afu) to mitigate iron toxicity stress. These findings provide theoretical support for optimizing EPD systems and improving nutrient removal in wastewater treatment.},
}

@article {pmid41687847,
year = {2026},
author = {Wang, N and Kang, Z and Wang, X and Zhang, Y and Li, X and Sun, Y and Xi, J and Shen, L},
title = {Sewage-sludge-derived biostimulant enables fertilizer reduction while maintaining rice yield through microbiome-mediated nutrient cycling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124020},
doi = {10.1016/j.envres.2026.124020},
pmid = {41687847},
issn = {1096-0953},
abstract = {Modern agriculture relies heavily on chemical fertilizers to sustain high yields, yet excessive inputs contribute to soil acidification, water eutrophication, greenhouse gas emissions, and biodiversity loss. Sewage-sludge-derived biostimulants (SS-BS) may help reduce fertilizer dependency while sustaining crop performance through plant-soil-microbiome interactions. Here, we evaluated SS-BS in a paddy rice field trial conducted during a single growing season (2024) under conventional management. Three fertilization regimes were compared: low-fertilizer control (CK), conventional fertilization (FP), and reduced mineral fertilization supplemented with SS-BS (BS). Across the 2024 season, rice yield and key yield components in BS were comparable to, or approached, those in FP with reduced mineral fertilizer input. Shotgun metagenomic profiling indicated that BS was associated with shifts in microbial functional pathways related to nitrogen, phosphorus, and potassium cycling, and with changes in the relative abundance of taxa linked to nutrient transformation processes. Partial least squares path modeling (PLS-PM) further suggested that microbial functional attributes were associated with the relationships among fertilization regime, soil properties, and yield outcomes. Collectively, these results from a single-season field experiment indicate that SS-BS has the potential to support fertilizer-reduction strategies in rice systems and motivate multi-season validation of its agronomic performance and microbiome- associated effects.},
}

@article {pmid41648108,
year = {2026},
author = {Martinez, NAP and Arnaldi, MR and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Microbiota-Based Interventions Differentially Rescue Gut and Social Behavior Phenotypes in a Drosophila Autism-like Model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41648108},
issn = {2692-8205},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a lifelong neurological and developmental disorder that has no cure and is often accompanied by gastrointestinal (GI) issues. The bidirectional communication system known as the gut microbiota-brain axis may help explain how GI dysfunction contributes to neurological symptoms. Loss-of-function mutations in the histone demethylases KDM5A, KDM5B or KDM5C are found in patients with intellectual disability and ASD. Previous studies using a Drosophila Kdm5 loss-of-function (Kdm5 [LOF]) ASD-like model revealed gut microbial dysbiosis, reduced abundance of Lactiplantibacillus plantarum, and impaired social behavior. While L. plantarum supplementation rescued intestinal abnormalities, it did not restore social behavior.

METHODS: Here, we evaluated multiple microbiota-based interventions, including probiotic supplementation with Lactiplantibacillus plantarum, Lactobacillus helveticus, their combination, and fecal microbiota transplantation (FMT), to determine their capacity to modulate gut microbial composition and behavior in Kdm5 [LOF] flies. Gut bacterial abundance was quantified using colony-forming unit (CFU) assays and full-length 16S rRNA gene sequencing. Social behavior was assessed using the social distance assay, while anxiety-like behavior and locomotion were evaluated using the open field test. Gut-specific Kdm5 knockdown was used to assess tissue-specific contributions to microbiota and behavioral phenotypes.

RESULTS: Kdm5 deficiency resulted in reduced abundance of culturable Lactobacillus, Acetobacter, and Enterobacter species, accompanied by impaired social behavior. L. plantarum supplementation restored gut microbial abundance in both whole-body Kdm5 [LOF] and gut-specific Kdm5 knockdown models but did not significantly rescue social behavior. In contrast, L. helveticus significantly improved social interaction in Kdm5 [LOF] flies despite minimal effects on gut bacterial abundance, revealing a dissociation between microbial restoration and behavioral outcomes. Gut-specific Kdm5 knockdown phenocopied both microbial and social defects observed in Kdm5 [LOF] mutants. Notably, FMT from healthy donors partially restored Lactobacillus abundance, reshaped gut microbial community structure, and partially improved social behavior in Kdm5 [LOF] recipient flies.

CONCLUSIONS: Together, these findings identify Kdm5 as a key regulator of gut microbial viability and social behavior and demonstrate that microbiota-based interventions exert strain- and phenotype-specific effects. Our results reveal that restoration of microbial abundance alone is insufficient to rescue social behavior and highlight the importance of functional host-microbe interactions in gut-brain communication. This work establishes Drosophila as a tractable platform for dissecting epigenetic regulation of microbiota-behavior relationships relevant to ASD and for evaluating targeted probiotic and microbiota-transfer strategies.},
}

@article {pmid41687784,
year = {2026},
author = {Thriene, K and Stanislas, V and Huang, KD and Strowig, T and Michels, KB},
title = {Impact of Yogurt and Rolled Oats Consumption on the Gut Microbiome: A Randomized Crossover Study displaying Individual Responses and General Resilience.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101408},
doi = {10.1016/j.tjnut.2026.101408},
pmid = {41687784},
issn = {1541-6100},
abstract = {BACKGROUND: Yogurt and rolled oats are commonly linked to gut health through pro- and prebiotic effects, but these benefits remain understudied, especially in healthy individuals eating a regular diet.

OBJECTIVE: This study primarily aimed to investigate the effects of daily yogurt and rolled-oats consumption on gut microbial composition. Secondary outcomes included stool metabolites and blood-based health markers.

METHODS: In this randomized, open-label, two-period crossover trial, 110 healthy participants were randomly assigned to one of two sequences: 250 g of yogurt daily followed by 250 g of yogurt with 50 g of rolled oats, or the reverse with a washout period in between. Stool and blood samples were collected at baseline and post-intervention. Metagenomic sequencing and metabolomic analysis were conducted on stool samples, while health markers related to metabolic control, inflammation, immune response, oxidative stress, and gut permeability were assessed in the participants' blood.

RESULTS: Of the 119 randomized participants, 110 completed the study (53 yogurt first, 57 yogurt and rolled oat first). Yogurt consumption transiently increased yogurt-associated bacteria, with Streptococcus thermophilus rising from absent to 0.97% (95% CI 0.71-1.26) in the yogurt intervention and 0.79% (0.58-1.03) in the yogurt with oats intervention. In a small Prevotella-predominant subgroup (n = 8), adding rolled oats increased microbial evenness (q < 0.001) and reduced inter-individual divergence (q < 0.05), suggesting a temporary slight homogenization. No additional effects on fecal short-chain fatty acids (SCFAs) concentrations or human health markers were identified. Functional metagenomic changes were mainly driven by yogurt-derived bacterial enrichment.

CONCLUSION: A healthy gut microbiota is largely stable and resilient to short-term diet changes, yet individual differences in small changes highlight the importance of personalized dietary recommendations.

CLINICAL TRIAL REGISTRATION: German register for clinical studies, identifier: DRKS00023146 https://drks.de/search/en/trial/DRKS00023146/details.},
}

@article {pmid41687589,
year = {2026},
author = {Luo, S and Tang, C and Shan, Y and Wan, C and Mo, Y and Huang, Y and Wu, R and Yu, F and Li, Y},
title = {Phosphate-solubilizing bacteria enhance cadmium phytoremediation by Solanum nigrum L. through improved phosphorus availability and cycling in contaminated soil.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141422},
doi = {10.1016/j.jhazmat.2026.141422},
pmid = {41687589},
issn = {1873-3336},
abstract = {Phosphate-solubilizing bacteria (PSB)-assisted phytoremediation has been recognized as an effective strategy for remediating cadmium (Cd)-contaminated soils, yet species-specific physiological and ecological traits among hyperaccumulators result in distinct Cd uptake mechanisms. Although the pivotal role of phosphorus (P) cycling in promoting Cd uptake is established, its mechanistic linkage with PSB-mediated phytoremediation remains poorly understood. This study employed Enterobacter sp. FM-1 and the Cd hyperaccumulator Solanum nigrum L. (S. nigrum L.) to elucidate how PSB regulate Cd accumulation through P cycling. Enterobacter inoculation significantly decreased soil pH and increased bioavailable Cd by 43.4 %-104.3 % relative to the control. The pH-driven mineralization of organic P was the primary process enhancing soil available P (AP), which rose by 12.1-32.2 %. Soil AP content was positively correlated with Cd concentrations in S. nigrum tissues, indicating a close association between enhanced phosphorus availability and plant Cd accumulation, accompanied by strengthened antioxidant defense related responses. Furthermore, PSB inoculation elevated phytochelatin levels via P-starvation response pathways, mitigating oxidative stress. Enhanced polyphosphate synthesis and phosphatase activity further promoted plant growth and P turnover. Metagenomic analysis revealed that Proteobacteria were the predominant carriers of P-cycling genes in the S. nigrum L. rhizosphere. Overall, Enterobacter sp. inoculation reshaped rhizosphere microbial communities, increased P bioavailability and improved Cd tolerance. These findings provide mechanistic insight into the coupling between microbial P activation and Cd uptake, offering a sustainable, microbially driven strategy for Cd-contaminated soil phytoremediation.},
}

@article {pmid41687586,
year = {2026},
author = {Xu, L and Xu, W and Yang, Y and Wu, J and Su, X and Dong, F and Xiao, X and Chen, C and Zheng, X and Sun, F},
title = {Single-stage bioreactor integrating anammox and sulfur-driven autotrophic denitrification for nitrogen removal from landfill leachate.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141444},
doi = {10.1016/j.jhazmat.2026.141444},
pmid = {41687586},
issn = {1873-3336},
abstract = {An integrated anaerobic ammonium oxidation-sulfur autotrophic denitrification (Anammox-SAD) bioreactor was developed for nitrogen removal from real landfill leachate without external organic carbon. The system was operated continuously for 105 days under stepwise-decreasing hydraulic retention time (HRT), with a stable influent NO2[-]-N/NH4[+]-N ratio of 1.2-1.5 provided by partial nitrification. The anammox zone maintained robust performance, yielding average effluent NH4[+]-N, NO2[-]-N and NO3[-]-N of 18 ± 5, 6 ± 9, and 110 ± 16 mg/L, respectively. At an HRT as low as 0.5 d, the maximum nitrogen removal rate reached 2.04 kg N/(m[3] d). Despite influent fluctuations (total nitrogen of 600-840 mg/L), the integrated reactor achieved a stable total nitrogen removal of 85-89 %. The downstream SAD zone effectively polished anammox-derived nitrate, reducing NO3[-]-N from 80-150 to 35-60 mg/L. Sulfur oxidation was confirmed by elevated sulfate concentrations, while anammox-associated alkalinity generation provided intrinsic pH buffering, sustaining favorable conditions for SAD. Metagenomic analyses revealed coordinated nitrogen-sulfur metabolic networks, showing that shortening HRT enhanced microbial diversity and functional redundancy but revealed kinetic limitations in substrate reduction. Overall, the integrated anammox-SAD system provides a robust and low-carbon strategy for treating high-strength landfill leachate.},
}

@article {pmid41687578,
year = {2026},
author = {Zhou, Q and Liang, H and Huang, J and Klümper, U and Fang, P and Yu, Z and Wang, Y and Berendonk, TU and Lin, L and Li, X and Li, B},
title = {Impact of sulfonamides on microbial community and antibiotic resistome profiles in anaerobic digestion of swine wastewater.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141426},
doi = {10.1016/j.jhazmat.2026.141426},
pmid = {41687578},
issn = {1873-3336},
abstract = {Residual antibiotics in swine wastewater promote the proliferation of the antibiotic resistome, posing significant threats to environmental and human health. Although anaerobic digestion (AD) is widely applied for treating swine wastewater, the effects of antibiotics on the microbial community and resistome during AD remain unclear. This study employed amplicon and metagenomic sequencing, combined with long- and short-read hybrid assembly, to comprehensively investigate the impact of sulfonamides on the microbiome and resistome during AD. Enterococcus, a genus capable of utilizing exogenous folate, was identified as the dominant genus under sulfonamide stress. A total of 24 antibiotic resistance gene (ARG) types and 440 subtypes were identified. Sulfonamide stress selectively enriched sulfonamide resistance genes, with no notable co-selective effects on ARGs for other antibiotic classes. Short-term exposure significantly enriched sul2 (3.8-fold) and sul3 (4.0-fold), while long-term exposure enriched sul1 (1.6-fold). Sulfonamides especially promoted the proliferation of sulfonamide resistance genes on both mobilizable and non-mobilizable plasmids. The co-occurrence of multiple categories of mobile genetic elements and ARGs on contigs was inferred to play a critical role in driving ARG dissemination. Whereas a strain belonging to Enterococcus_I emerged as the dominant resistant bacterium in the AD system, a particular multidrug-resistance risk was identified for a strain belonging to the Filifactoraceae family. This work provides a new perspective on the impact of antibiotics on microbial community and antibiotic resistome composition and dynamics during the AD treatment process of swine wastewater.},
}

@article {pmid41687577,
year = {2026},
author = {Feng, Y and Zhang, X and Lai, S and Chen, F and Hu, J and Li, M and Sun, W},
title = {Nontarget screening uncovers the overlooked impact of antibiotic transformation products on riverine resistomes.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141425},
doi = {10.1016/j.jhazmat.2026.141425},
pmid = {41687577},
issn = {1873-3336},
abstract = {Antibiotics, their transformation products (TPs), and antibiotic resistance genes (ARGs) pose a major environmental threat, yet the influence of TPs on ARGs remains poorly understood. This study combined target, suspect and nontarget analysis via high-resolution mass spectrometry with metagenomic analysis to systematically profile the occurrence of antibiotics, TPs, and ARGs in an urban river. A total of 32 parent antibiotics and 49 TPs were identified, with concentrations ranging from 0.002193 ng/L and not detected145 ng/L, respectively. TPs accounted for a substantial portion of total antibiotic loads (41.3 % in spring and 31.9 % in summer). Metagenomic sequencing revealed 1599 ARG subtypes conferring resistance to 28 classes of antibiotics. TPs can drive antimicrobial resistance directly by exerting selective pressure through their residual antibacterial activity, and indirectly through reverting to parent compounds, thereby reintroducing bioactive antibiotics into the environment. Therefore, the inclusion of TPs improved ARG-antibiotic correlations. Multivariate analyses revealed that TPs exerted comparable or greater influence on ARG profiles than parent antibiotics. Specific TPs, particularly β-lactams, macrolides, and quinolones, significantly affected the abundance of multiple ARGs, underscoring their substantial and non-negligible impact. This study highlights the previously underestimated role of antibiotic TPs in shaping ARG profiles and calls for an urgent update of risk assessment frameworks to incorporate TPs for comprehensive environmental and public health evaluation.},
}

@article {pmid41687496,
year = {2026},
author = {Shyam, S and Sarma, H},
title = {Microbial community shifts and nutrient alteration in rice rhizospheres induced by Fe functionalized magnetic nanocarbon derived from rice husk.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128840},
doi = {10.1016/j.jenvman.2026.128840},
pmid = {41687496},
issn = {1095-8630},
abstract = {Soil fertility degradation and low nutrient-use efficiency remain major constraints in sustainable rice cultivation, especially in acidic soils. Biochar-based nanocomposites have emerged as advanced tools to improve nutrient bioavailability and soil health. This study examines the influence of rice husk biochar (HB) and its Fe-functionalized nanoscale variant, magnetic nanocarbon husk biochar (MNHB), on soil physicochemical properties, early growth of Oryza sativa (rice), and rhizosphere microbial dynamics. MNHB exhibited a fixed carbon content of 49.6%, ash content of 17.4%, and strong thermal stability above 400 °C. Dynamic light scattering and zeta potential analyses confirmed nanoscale particle size (<100 nm) with a surface charge of -25 mV, indicating good colloidal stability. FE-SEM imaging verified nanoscale morphology (81.58 ± 17.22 nm). Application of MNHB (5%) significantly enhanced root length (15.7 ± 0.49 cm), shoot length (46.41 ± 1.89 cm), and biomass (48.9% above Control, 25.3% above HB; p < 0.05). Soil pH, electrical conductivity, organic carbon, and macronutrients (N, P, K) increased substantially, demonstrating improved nutrient cycling and bioavailability. Metagenomic sequencing revealed reduced microbial alpha diversity but a marked community shift favoring Pseudomonadota (∼20% increase) and enrichment of beneficial genera such as Streptomyces, Micromonospora, and Neurospora tetrasperma. This work lies in establishing that Fe-functionalization in biochar nanosystems not only enhances nutrient transformation and uptake efficiency but also selectively restructures the rhizosphere microbiome, thereby coupling nutrient enrichment with microbial modulation for sustainable soil fertility restoration and crop productivity improvement.},
}

@article {pmid41687486,
year = {2026},
author = {Wang, H and Tian, Z and Jiang, Q and Feng, L and Tian, Z and Cheng, J and Jiang, S and Li, B},
title = {Enhancing sulfide-based denitrification under dual high-salinity and sulfide stress: Metabolic adaptation via compatible solutes in functional microbes.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128858},
doi = {10.1016/j.jenvman.2026.128858},
pmid = {41687486},
issn = {1095-8630},
abstract = {This study demonstrated enhanced sulfur autotrophic denitrification (SAD) under dual high-salinity (3% Na2SO4) and sulfide (142.5 mg L[-1] S[2-]) stress using biostimulants. Screening of ten biostimulants (1 mg L[-1]) revealed compatible solutes (glycine betaine, trehalose, and mannitol) as optimal enhancers. At a higher level of 100 mg L[-1], the addition of all compatible solutes significantly boosted TN removal rates >3-fold, with mannitol achieving the highest (9.38 mg L[-1] h[-1]) (p < 0.05). Short term of dosage tests further showed better TN removal at higher trehalose/mannitol concentrations (10-100 mg L[-1]), while glycine betaine peaked at 50 mg L[-1]. Furthermore, metagenomic analysis revealed potential mechanisms for resisting the dual stress of high salinity and sulfide. Those mechanisms act through osmotic protection (via specific transporter genes and elevated extracellular polymeric substances), carbon provision boosting TN removal via heterotrophic denitrification (nirS), and enzymatic antioxidant defense (SOD1/NQO1). The addition of exogenous compatible solutes critically mitigates dual stress from high salinity and sulfide toxicity, demonstrating significant potential for SAD system enhancement.},
}

@article {pmid41687314,
year = {2026},
author = {He, J and Duan, Y and Yang, S and Toldrá, F and Zheng, J and Du, M and Wang, L and Ndraha, N and Wang, S and Chen, J},
title = {Insights into the mechanism of nutty aroma formation by Staphylococcus saprophyticus in fermented sausages.},
journal = {International journal of food microbiology},
volume = {451},
number = {},
pages = {111669},
doi = {10.1016/j.ijfoodmicro.2026.111669},
pmid = {41687314},
issn = {1879-3460},
abstract = {To achieve a starter culture with the ability of improving nutty aroma in the formulation of fermented sausage, this study evaluated sixteen staphylococci strains first, then demonstrated the function of the strain in sausage fermentation using volatolomics and metagenomics. Within sixteen tested strains, S. saprophyticus 108 presented superior safety and technological properties and produced the highest amounts of 3-methylbutanal. With spontaneously fermented sausage as control, S108 group distinctly enhanced the production of 3-methylbutanal, 3-methylbutanoic acid and its ethyl ester, and nutty note of S108 group was obviously perceivable. The relative abundance of S. saprophyticus in both control and S108 groups increased throughout the fermentation process and such increase was more dramatic in S108 group. Although the differences in the number of functional genes predicted by control and S108 group in CAZy, eggNOG, and KEGG databases were comparatively small, the contribution of S. saprophyticus to major nutrient metabolisms was the main difference. Both S. saprophyticus and L. mesenteroides were annotated with predominant abundances in main metabolic pathways, while S. saprophyticus abundance involved in the metabolic pathways was higher in S108 group than in control. Specifically, branched-chain amino acid degradation, phenylalanine metabolism, glycolysis, pyruvate metabolism, butanoate and propanoate metabolism, glycerolipid and glycerophospholipid metabolism were mainly driven by S. saprophyticus, linked to the higher generation of volatile compounds in S108 group compared to control. The results provided scientific support for developing a functional starter culture through clarifying the mechanism of nutty aroma formation by S. saprophyticus in the production of fermented sausages.},
}

@article {pmid41687166,
year = {2026},
author = {Wang, P and Wang, J and Zhang, P and Jiao, Z and Bai, X and Zhao, Z and Fan, J and Zhang, S and Zhao, B and Ren, X and Dou, H and Bai, W},
title = {Temperature-dependent effects of lanthanum-modified bentonite on sediment nitrogen removal processes and the underlying microbial mechanisms.},
journal = {Water research},
volume = {294},
number = {},
pages = {125514},
doi = {10.1016/j.watres.2026.125514},
pmid = {41687166},
issn = {1879-2448},
abstract = {Lanthanum-modified bentonite (LMB) is widely used for phosphorus control in eutrophic lakes, but its effects on sediment nitrogen removal remains unclear. This study investigated the effects of LMB on denitrification and anammox, and underlying microbial mechanisms, under different dissolved oxygen (DO) and temperature (T) conditions using isotope tracing and metagenomics. The results demonstrated that the influence of LMB on sediment nitrogen removal was highly temperature-dependent. At 15 °C, LMB significantly enhanced both processes: denitrification increased by an average of 67.75 % under aerobic conditions, while anammox increased by 163.52 % and 93.47 % under aerobic and anaerobic conditions, respectively. Conversely, at 30 °C, LMB inhibited both processes. The denitrification decreased by average reductions of 57.36 % and 79.46 %, and anammox decreased by 32.51 % and 54.46 % under aerobic and anaerobic conditions, respectively. Microbial results revealed that LMB regulated denitrification in a temperature-dependent manner by modulating the key functional gene nosZ. In contrast, LMB generally suppressed anammox genes (hzsA, hzsB, and hdh), particularly under anaerobic conditions. Redundancy analysis (RDA) and structural equation modeling (SEM) identified pH, moisture content (MC), electrical conductivity (EC), total carbon (TC), total nitrogen (TN), NO3[-]-N, and NH4[+]-N as the key environmental factors driving variations in functional gene abundances. Our findings reveal that the temperature-dependent effects are primarily driven by the regulation of the nosZ gene and synergistic interactions among key physicochemical factors. Therefore, for remediating of eutrophic lakes with severe nitrogen pollution, the addition of LMB should be strategically adjusted to low-temperature seasons to maximize its ecological benefits in promoting nitrogen removal.},
}

@article {pmid41687083,
year = {2026},
author = {Olaniyi, KS and Moodley, J and Moodley, R and Mackraj, I},
title = {Assessment of human placental microbial signatures in pre-eclampsia using shotgun metagenomics.},
journal = {Canadian journal of physiology and pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjpp-2025-0274},
pmid = {41687083},
issn = {1205-7541},
abstract = {This study evaluated the presence of bacterial species in the placenta of women with pre-eclampsia and compared with that of normotensive women. One hundred and twenty participants, comprising 60 pre-eclamptic (30 early- and late-onset, respectively) and 60 age-matched normotensive women (30 early and late-gestation normotensive, respectively) were recruited. After informed consent was obtained, the placenta were obtained through caesarean section with sterile and standardized clinical procedures. DNA was extracted from each tissue, and the samples were pooled into six libraries and sequenced on Illumina NextSeq500 using a shotgun metagenomic approach. Bioinformatics was used to analyse the reads with the implementation of Kraken2/MetaPhlAn classification methods and complemented by multi-layered contamination assessment strategy that included frequency-based decontam filtering. Most reads were classified as belonging to the phyla Cutibacterium acnes, Staphylococcus epidermidis, and various Bradyrhizobium species. PE samples showed notable Corynebacterium tuberculostearicum and Pseudomonas species, while Bradyrhizobium and Cutibacterium acnes dominated normotensive samples. Further analysis showed no significant difference between bacterial species of pre-eclamptic and normotensive placental samples. The results show very low levels of bacteria in the placental samples. In addition, a little difference was observed between the bacterial compositions of pre-eclamptic and age-matched normotensive placental tissues, but not statistically significant.},
}

@article {pmid41686700,
year = {2026},
author = {Ierardi, RA and Ericsson, AC and Lahmers, KK and Shen, Z and Raghavan, RK},
title = {Detection of Anaplasma marginale (Rickettsiales: Anaplasmataceae) in host-seeking adult Dermacentor variabilis (Acari: Ixodidae) on cattle pastures, Missouri, United States.},
journal = {Journal of medical entomology},
volume = {63},
number = {1},
pages = {},
doi = {10.1093/jme/tjag014},
pmid = {41686700},
issn = {1938-2928},
support = {00081722//Taylor Geospatial Institute/ ; 7003929 and 7006485//USDA National Institute of Food and Agriculture, Animal Health projects/ ; //University of Missouri College of Veterinary Medicine Veterinary Research Scholars Program/ ; 58-2090-2-020//USDA Agricultural Research Service/ ; },
mesh = {Animals ; *Anaplasma marginale/isolation & purification ; Missouri ; *Dermacentor/microbiology ; Male ; Cattle ; Cattle Diseases/microbiology ; Anaplasmosis ; },
abstract = {Bovine anaplasmosis is an economically important and globally distributed disease of cattle caused by a rickettsia, Anaplasma marginale Theiler, which infects bovine red blood cells. In the United States, A. marginale is transmitted by adult male Dermacentor spp. ticks. Our objectives were to estimate the prevalence of A. marginale among host-seeking D. variabilis Say males and describe tick activity on beef cow-calf grazing operations in Missouri. Ticks were collected by dragging a total of 348 750-meter transects on 5 field sites from May 2022 to August 2024. In total, 29,132 ticks were collected: 27,502 Amblyomma americanum Linnaeus, 1,504 D. variabilis, 101 Haemaphysalis longicornis Neumann, and 25 individuals of uncommonly encountered species. A total of 692 adult male D. variabilis were divided into 154 pools of ≤5 ticks/pool for analysis. Anaplasma marginale was detected by quantitative polymerase chain reaction (qPCR) in 1 pool of 5 adult males (0.6%). Illumina sequencing detected an Anaplasma bovis (Donatien and Lestoquard 1936)-like sequence in 38 pools (24.7%). The endosymbionts Francisella spp. and Rickettsia spp. were detected in 100% and 32.5% of pools, respectively. To the best of our knowledge, this is the first study to detect A. marginale in host-seeking D. variabilis collected in the field. Our findings also represent the first reports of H. longicornis, an invasive species, in 4 Missouri counties.},
}

Animals
*Anaplasma marginale/isolation & purification
Missouri
*Dermacentor/microbiology
Male
Cattle
Cattle Diseases/microbiology
Anaplasmosis

@article {pmid41686580,
year = {2026},
author = {Zhang, H},
title = {Diagnostic value of mNGS in patients with suspected tumor: An observational study.},
journal = {Medicine},
volume = {105},
number = {7},
pages = {e47379},
doi = {10.1097/MD.0000000000047379},
pmid = {41686580},
issn = {1536-5964},
mesh = {Humans ; *DNA Copy Number Variations ; Female ; Male ; Retrospective Studies ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Neoplasms/genetics/diagnosis ; Adult ; Aged ; *Metagenomics/methods ; Chromosome Aberrations ; *Infections/diagnosis/genetics ; },
abstract = {Some patients suspected of infection may have potential causes, such as tumors, but conventional examination methods are negative. Copy number variation (CNV) analysis based on metagenomics next generation sequencing (mNGS) can simultaneously detect pathogenic microorganisms and tumors signals. Patients with suspected infection in our department were retrospectively analyzed, and mNGS and chromosomal CNV analysis were performed simultaneously. A total of 9 patients with positive tumor signal were included in the study. This study was divided into 2 parts: in the first part, patients suspected of infection were finally diagnosed with a tumor by CNV assisted analysis; in the second part, the accuracy of this analysis was verified again by patients with a history of cancer. Three of five patients without a history of tumor were diagnosed with hematological malignancy. All patients with active tumor had obvious abnormal CNV signals. The chromosomal abnormalities mainly included multiple chromosome duplication and deletion, arm level duplication and deletion, and chromosome aneuploidy. mNGS-based CNV analysis had clinical value for patients with underlying tumor.},
}

Humans
*DNA Copy Number Variations
Female
Male
Retrospective Studies
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Neoplasms/genetics/diagnosis
Adult
Aged
*Metagenomics/methods
Chromosome Aberrations
*Infections/diagnosis/genetics

@article {pmid41686420,
year = {2026},
author = {Senthilkumar, K and Muthiah, P},
title = {A Comprehensive Review of Kombucha Fermentation and Probiotic Functional Mechanisms: Microbial Dynamics, Bioactive Compounds and Health Effects.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41686420},
issn = {1867-1314},
abstract = {The rising demand for health-promoting beverages, kombucha presents significant opportunities for scientific innovation and commercial growth. Symbiotic culture of bacteria and yeast (SCOBY), which includes acetic acid bacteria (AAB), lactic acid bacteria (LAB), and several yeast species, plays a major role in kombucha fermentation. During fermentation, kombucha produces bioactive compounds mainly catechins, theaflavins, tannins, and organic acids that enhance health efficacy and probiotic properties, supporting gut health and non-communicable disease prevention. The present study emphasizes, nutritional qualities of kombucha through different Komagataeibacter starter cultures and alternative substrates such as herbal infusions and fruit extracts. This review also highlights the role of AAB, LAB, and Yeast in the production mechanism of the kombucha beverage by the different microbial strains of microbial species and the fibril network of bacterial cellulose. This study further explains the bioactivities in the human body, especially mechanisms of action in the intestine through fundamental signaling pathways such as PIK3-AKT, MAPK, NFκB, PPARγ, and JAK-STAT. Therapeutic efficacy of kombucha, including various substrate-based antioxidants, antimicrobials, synergistic impact, delivery mechanism of anticancer, anti-diabetic insulin, and glycaemic responses, regulations of inflammatory markers (ILs) in anti-obese properties, has also been reviewed. Further, it is necessary to develop the advanced kombucha beverage qualities through metagenomics, metabolomics. Future studies should address these research gaps to ensure controlled microbial and probiotic stability, validate metabolites availability, and explore innovative applications for improved functionality and shelf-life.},
}

@article {pmid41686173,
year = {2026},
author = {Yang, Z and Zhang, F and Li, H and Liu, B and Liu, P and Wu, Z and Li, Y and Miao, J and Li, X and Liang, H and Zhong, Y and Xiao, L and Zou, Y and He, N and Li, S},
title = {Gut Commensal Phocaeicola vulgatus AF107-22 Alleviates Obesity-Induced Metabolic Syndrome via Promoting Gut Microbiota-Derived Spermidine Synthesis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14443},
pmid = {41686173},
issn = {1520-5118},
abstract = {Obesity-induced metabolic syndrome (MetS) is a prevalent metabolic disorder, and therapeutic strategies targeting the gut microbiota hold considerable promise. Phocaeicola vulgatus (P. vulgatus) is a gut commensal bacterium that plays an important role in modulating the composition and metabolism of gut microbiota. This study demonstrated that the abundance of P. vulgatus is significantly negatively correlated to obesity-induced MetS and complications in human metagenomic data. Oral gavage of P. vulgatus significantly ameliorated high-fat-diet (HFD)-induced MetS symptoms in mice, reducing body weight, systemic inflammation, and hepatic steatosis. Furthermore, multiomics analyses indicated that P. vulgatus treatment significantly enhanced the production of gut microbiota-derived spermidine and spermine. Subsequently, population-based analysis confirmed a strong negative correlation between plasma spermidine levels and MetS progression, supporting that such parameters may serve as potential biomarkers for MetS. This study reveals a potential mechanism, bridging commensal probiotic and spermidine metabolism, with implications for treating obesity-induced MetS.},
}

@article {pmid41685655,
year = {2026},
author = {Zhai, Y and Wang, X and Deng, X and Li, X and Hu, B and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M},
title = {Sequential Oxidizing-Reducing Degradation of Organic Micropollutants in Simulated Riverbank Filtration.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18277},
pmid = {41685655},
issn = {1520-5851},
abstract = {Riverbank filtration is a nature-based water treatment strategy known for its effective removal of organic micropollutants. Yet, the mechanisms governing their biodegradation, especially the role of redox transitions in mediating biotransformation, remain insufficiently understood. Here, we integrate metagenomic profiling with chemical analytics in a 10 m simulated riverbank filtration system to demonstrate how sequential oxidizing-reducing degradation enhances organic micropollutant transformation. Oxygen stratification structured distinct microbial and enzymatic pathways: oxidizing zones (>+200 mV redox potential) facilitated cytochrome P450-mediated oxidation (oxidizing condition, OXD), while subsequent redox shifts to reducing conditions (←400 mV, sequential oxidizing-reducing (SOR) conditions) activated reductive transformations (e.g., via nitronate monooxygenase and aldehyde dehydrogenase) and conjugation pathways. These SOR conditions significantly enhanced the removal of recalcitrant compounds, including irbesartan (+25.3%), benzotriazole (13.4%), and gabapentin (+9.7%). Metagenomic analysis revealed redox-driven microbial specialization, with Pseudomonadota and Nitrospirota dominating in oxidizing zones and reducing microzones enriched in pathways associated with nitrotoluene and ethylbenzene degradation, providing genomic evidence for sequential organic micropollutant breakdown. These findings establish a mechanistic framework for harnessing oxidizing-reducing microbial partnerships to amplify organic micropollutant removal in nature-based water treatment systems, which can be used for riverbank filtration site selection and well field construction and optimization.},
}

@article {pmid41685543,
year = {2026},
author = {Mwakibete, L and Hoarau, AOG and Ahyong, V and Waltari, E and Bender, SJ and Davison, S and Niedringhaus, KD and Gibison, ML and Gagne, RB and Miller, EA and Murphy, LA and Kistler, AL and Tato, CM},
title = {Discovery of a novel bandavirus using metagenomic sequencing in a retrospective analysis of an unresolved 2020 mortality event involving wild black vultures in the northeastern United States.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {10406387261418632},
doi = {10.1177/10406387261418632},
pmid = {41685543},
issn = {1943-4936},
abstract = {Investigations of wildlife diseases and mortality events can sometimes lead to inconclusive results because of limitations in testing combined with an ever-increasing number of emerging viruses. The use of tools such as unbiased metagenomic next-generation sequencing (mNGS) can facilitate the identification of causative agents when conventional investigation methods fail. We performed a retrospective mNGS analysis on RNA isolated from postmortem samples collected during a mortality event in free-ranging, wild black vultures (Coragyps atratus) that occurred in eastern Pennsylvania and western New Jersey in 2020. We describe the discovery and identification of a novel species of bandavirus (family Phenuiviridae) in case specimens from this die-off, as well as some of the associated pathology findings. The Bandavirus genus comprises tickborne viral species that have been reported across 5 continents. These viruses have been implicated in outbreaks in a variety of mammalian hosts, including humans, and in avian species, making them important potential sources of zoonotic spillover events. Genomic and phylogenetic analyses of the bandavirus that we detected indicate that its closest relative is Hunter Island virus, a bandavirus previously implicated in albatross mortality events off the coast of Tasmania, Australia. Follow-up PCR testing of samples from 16 additional vultures from the same cohort indicate that this new bandavirus was the likely cause of death.},
}