@article {pmid42104558,
year = {2026},
author = {Luo, X and Lei, Z and Fang, D and Chen, H and Qian, L and Jin, C and Wang, X and Liu, X and Liu, H and Wang, Y},
title = {Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71234},
pmid = {42104558},
issn = {1469-8137},
support = {32300265//Young Scientists Fund of the National Natural Science Foundation of China/ ; },
abstract = {Actinorhizal plants are ecologically important pioneer species in temperate regions, capable of nitrogen-fixing root nodule symbiosis with Frankiaceae bacteria. Despite their significance within the nitrogen-fixing clades (NFC), multi-omics studies of actinorhizal symbiosis remain scarce. We profiled prokaryotic communities in the rhizosphere, root, and/or nodule compartments from five phylogenetically representative actinorhizal species, three legumes, and four nonnodulated NFC species using 16S rDNA sequencing. Transcriptomic and metagenomic analyses were performed on actinorhizal roots and nodules, respectively. Metagenome-assembled genomes revealed four novel Frankiaceae species. Frankiae relative abundance levels in nodules were generally lower than rhizobia in legumes. Actinorhizal nodules harbour diverse bacterial taxa, which exhibit predominantly positive interactions, with Frankiae forming a tightly interacting subgroup. Actinorhizal plants engage actively with soil microbiota, recruiting a specific rhizosphere community enriched with beneficial microbes, including ammonia-oxidising archaea. Many symbiotic mechanisms in nodulating host plants are conserved and derived from pre-existing molecular modules. Our analysis suggests the phosphoinositide signalling likely functions in actinorhizal symbiotic signal transduction. However, Frankiae exhibit fundamentally different symbiotic functional characteristics compared to rhizobia, reflecting less intimate symbiosis, which might favour the life-history strategies of temperate perennial actinorhizal plants.},
}

@article {pmid42104576,
year = {2026},
author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R},
title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70246},
doi = {10.1111/aji.70246},
pmid = {42104576},
issn = {1600-0897},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; },
abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.

METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.

RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.

CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).},
}

Humans
Female
Pregnancy
*Placenta/microbiology
*Premature Birth/microbiology/immunology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics

@article {pmid42104663,
year = {2026},
author = {Yang, KL and Zhai, JN and Ye, JW and Zhang, XN and Wei, QC and Wang, H and Wang, HM and Chu, LL and Yang, J},
title = {Dysbiosis of Gut Archaea is Associated with Obesity and Could be Recovered after Bariatric Surgery.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {4},
pages = {437-446},
doi = {10.3967/bes2026.019},
pmid = {42104663},
issn = {2214-0190},
mesh = {Humans ; *Bariatric Surgery ; *Gastrointestinal Microbiome ; *Obesity/microbiology/surgery ; Male ; Female ; *Archaea/physiology/genetics/classification ; Adult ; Middle Aged ; *Dysbiosis/microbiology ; },
abstract = {OBJECTIVE: Obesity is closely associated with an altered gut microbiota; however, the role of archaea in obesity remains unknown. We aimed to delineate the alterations in gut archaea in obese subjects and explore the changes in bariatric surgery-associated gut archaeal composition.

METHODS: Metagenomic sequencing data from 191 obese subjects and 184 lean controls were retrieved from three public cohorts. Of these, 23 obese patients who underwent bariatric surgery were followed up for 3 months.

RESULTS: The gut archaea of obese subjects showed significantly lower Shannon diversity index than those of lean controls. Principal component analysis of the gut archaea revealed distinct clusters in obese subjects and lean controls. A model using the 20 top archaeal genera discriminated obese from lean controls with an area under the receiver operating characteristic curve (AUC) of 0.79, 0.83, and 0.86 in three cohorts. Ecological analysis showed decreased trans-kingdom correlations between archaea and bacteria in obese subjects compared to those in lean controls, with partial restoration observed after bariatric surgery.

CONCLUSION: This is the first study to demonstrate that obesity is characterized by gut archaeal dysbiosis across multiple cohorts. Bariatric surgery-induced weight loss is associated with significant changes in the gut archaea.},
}

Humans
*Bariatric Surgery
*Gastrointestinal Microbiome
*Obesity/microbiology/surgery
Male
Female
*Archaea/physiology/genetics/classification
Adult
Middle Aged
*Dysbiosis/microbiology

@article {pmid42104937,
year = {2026},
author = {Kang, X and Hu, L and Song, J and Zhang, Z and Li, Y and Zhang, Q and Luo, C and Pang, Y and Guo, P and Yue, B and Li, P and Fan, Z},
title = {Snake Gut Microbiota as a Source of Anti-Inflammatory Probiotics: Isolation and Functional Characterization of Two Novel Strains.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70118},
pmid = {42104937},
issn = {1749-4877},
support = {2023NSFSC1935//Sichuan Science and Technology Program/ ; },
abstract = {The intestinal microbiome is fundamental to host physiological homeostasis, while deviations from its balanced state have been linked to inflammatory bowel diseases (IBD). To address the limitations of conventional antibiotic therapies, this study explored snake gut microbiota as a novel source of anti-inflammatory probiotics. We explored the gut microbiota of five snake species (Deinagkistrodon acutus, Trimerodytes annularis, Trimerodytes percarinatus, Lycodon rufozonatus, and Trimeresurus stejnegeri) through metagenomic sequencing. Community composition analysis revealed that the phylum-level composition was mainly Proteobacteria, Bacteroidetes, Actinomycetota, and Firmicutes. We further detected some potential probiotic species, such as Enterococcus, Lactobacillus, and Limosilactobacillus. From 196 isolated strains, Lactobacillus johnsonii DA0116 and Limosilactobacillus reuteri DA0218 were selected through rigorous safety and functional assessments, including acid/bile tolerance, pathogen inhibition, and adhesion capacity. In a DSS-induced murine colitis model, both strains significantly reduced disease activity index (DAI), pro-inflammatory cytokines (TNF-α, IL-6, and IL-8), and restored gut microbiota diversity. Additionally, whole-genome analysis identified bacteriocin synthesis clusters (gassericin-S/T) and carbohydrate metabolism genes, explaining their antimicrobial and immunomodulatory properties. This study not only emphasizes the untapped latent value of reptilian gut microbiota for probiotic discovery but also provides two candidate strains with therapeutic promise for IBD and functional food applications.},
}

@article {pmid42105239,
year = {2026},
author = {Minich, JJ},
title = {Protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing using PacBio HiFi or Oxford Nanopore Technologies.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104526},
doi = {10.1016/j.xpro.2026.104526},
pmid = {42105239},
issn = {2666-1667},
abstract = {Long-read sequencing, whether using PacBio (PB) or Oxford Nanopore Technologies (ONT), requires high-molecular-weight (HMW) DNA at high purity and free of contaminants. Here, we present a protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing. We describe steps for microbial inactivation, nucleic acid stabilization, and HMW DNA extraction. We then detail procedures for DNA cleanup, shearing, library preparation, and DNA sequencing. For complete details on the use and execution of this protocol, please refer to Minich et al.[1].},
}

@article {pmid42105544,
year = {2026},
author = {Li, T and Feng, K and Wang, S and Du, X and Li, J and Gu, S and Zhao, B and Yang, X and Peng, X and He, Q and Wang, Y and Wang, D and Wang, J and Wang, Z and Liu, M and Xiao, J and Men, J and Jin, D and Zhang, J and Deng, Y},
title = {Integrating digital PCR and metagenomics to quantify potential soilborne bacterial pathogens in urban ecosystem.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142312},
doi = {10.1016/j.jhazmat.2026.142312},
pmid = {42105544},
issn = {1873-3336},
abstract = {Understanding the environmental occurrence patterns of soilborne pathogens is essential for public health, yet a comprehensive and accurate assessment remains challenging. This study presents an innovative technical framework integrating metagenomic pathogen screening with quantitative validation using chip-based digital PCR (dPCR) targeting the overall bacteria community as well as three dominant species-Ralstonia pickettii, Saccharomonospora viridis, and Gordonia terrae. This approach enabled a comprehensive quantification of potential human-, plant-, and zoonotic pathogens and elucidation of their environmental drivers across urban soil habitats in Beijing. Farmland and hospital greenspaces exhibited higher potential pathogen richness (15.55 ± 5.87 and 10.70 ± 4.52) and abundance (22,475.52 ± 15,559.92 and 26,217.62 ± 19,299.90 copies g[-1] soil) compared with forests and campus greenspaces. The composition of potential pathogens varied among habitats, with farmlands containing the highest number of unique species, and four taxa were detected across all habitats, showing strong adaptive capacity. Pathogen diversity was positively correlated with total and available phosphorus and with total bacterial α- and β-diversity, while negatively associated with soil organic carbon, reflecting limited pathogen inputs in carbon-rich forest soils and the key role of phosphorus in pathogen enrichment. Climatic and soil physicochemical factors indirectly influenced pathogen diversity by modulating bacterial communities, whereas human activities directly increased pathogen abundance. Molecular ecological network analysis demonstrated that 81% of the associations between pathogenic and non-pathogenic taxa were significantly negative, suggesting competitive exclusion as a key regulatory mechanism. Collectively, these findings provide a precise monitoring framework and new insights into cross-species interactions, contributing to improved risk assessment and One Health strategies for the prevention of soilborne diseases.},
}

@article {pmid42105734,
year = {2026},
author = {Zhang, J and Zeng, W and Meng, Q and Gong, Q and Lu, Y and Bi, Z and Peng, Y},
title = {Efficient amino acid capture from sludge fermentation by Tetrasphaera enhances simultaneous nitrification, endogenous denitrification and phosphorus removal.},
journal = {Water research},
volume = {301},
number = {},
pages = {126061},
doi = {10.1016/j.watres.2026.126061},
pmid = {42105734},
issn = {1879-2448},
abstract = {The simultaneous nitrification endogenous denitrification and phosphorus removal (SNDPR) process shows great potential for carbon, nitrogen, and phosphorus removal. However, its application is challenged by limited carbon availability and the strong reliance of glycogen-accumulating organisms (GAOs) and traditional polyphosphate-accumulating organisms (PAOs) on volatile fatty acids. This study first established a fermentative PAO Tetrasphaera-dominated SNDPR coupled with in-situ sludge fermentation process, achieving stable and efficient nitrogen (95.7 ± 0.6%) and phosphorus (92.6 ± 1.6%) removal using complex organics (e.g., amino acids and proteins) from wastewater and sludge as carbon sources. Extending the anaerobic duration (from 5 h to 17 h) regulated the phosphorus removal and fermentation capacity of Tetrasphaera, promoting its dominance at the genomic (10.89%), transcriptional (6.24%), and translational (24.0%) levels. For phosphorus removal, the denitrifying phosphorus removal (DPR) rate using nitrite increased from 0.98 ± 0.05 mgN/gVSS·h at 5 h to 2.70 ± 0.07 mgN/gVSS·h at 17 h, shifting the system from aerobic phosphorus uptake dominance to a cooperative pattern with DPR, effectively lowering carbon demand. For fermentation, metagenomic analysis revealed that efficient amino acid capture by Tetrasphaera facilitated the retention of substantial sludge hydrolysates for intracellular amino acid storage, improving nutrient removal and mitigating NH4[+]-N and PO4[3-]-P release. Additionally, anammox bacteria (Candidatus Brocadia, 2.67%) self-enriched and synergistically contributed to nitrogen removal. Overall, this study provides new insights into the metabolic shift between fermentation and phosphorus removal in Tetrasphaera, demonstrating the feasibility of stable and efficient carbon, nitrogen and phosphorus removal by the SNDPR process in VFA-limited wastewater.},
}

@article {pmid42106331,
year = {2026},
author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P},
title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72762-5},
pmid = {42106331},
issn = {2041-1723},
support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; },
abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.},
}

@article {pmid42106335,
year = {2026},
author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I},
title = {Population-scale characterization of the oral microbiome and associations with metabolic health.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72748-3},
pmid = {42106335},
issn = {2041-1723},
abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.},
}

@article {pmid42106361,
year = {2026},
author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X},
title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01001-y},
pmid = {42106361},
issn = {2055-5008},
support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&D Programme/ ; },
abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.},
}

@article {pmid42106412,
year = {2026},
author = {Guo, L and Holyoak, GR and DeSilva, U},
title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49532-w},
pmid = {42106412},
issn = {2045-2322},
abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.},
}

@article {pmid42106682,
year = {2026},
author = {Wang, Y and Ma, Y and Yi, J and Li, X and Shao, Y and Cao, L},
title = {A case report of post-arthroscopic knee infection caused by Capnocytophaga sputigena in an anemic patient.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13507-z},
pmid = {42106682},
issn = {1471-2334},
support = {23ZR1480300//Science and Technology Innovation Action Program of the Shanghai Science and Technology Commission/ ; },
abstract = {BACKGROUND: Capnocytophaga sputigena (C. sputigena), a species of bacteria resident in the human oral cavity. Here, to the best of our knowledge, this is the first reported case of a post-arthroscopic knee infection caused by this organism in an anemic patient. We described the clinical characteristics, therapeutic intervention and outcome associated with knee joint infection induced by this bacterium. Furthermore, the treatment approaches and challenges in managing this particular pathogen were explored.

CASE PRESENTATION: A 58-year-old female patient presented with a knee infection following arthroscopy, caused by C. sputigena. The species C. sputigena was confirmed on the basis of the results of the joint fluid culture and metagenomics next-generation sequencing (mNGS). The infection was treated with arthroscopic debridement, in addition to intravenous and intra-articular meropenem irrigation. The initial therapy with meropenem resulted in clinical improvement, and was subsequently de-escalated to amoxicillin-clavulanate potassium. Following a period of observation, the patient was discharged, as her condition was stable.

CONCLUSIONS: The case of a post-arthroscopic knee infection caused by C. sputigena in an anemic patient resulted in surgeons developing a more profound clinical understanding of infections induced by the bacterium. The combination of arthroscopic debridement with meropenem therapy (subsequently followed by de-escalation to amoxicillin-clavulanate potassium) yielded favourable clinical outcomes, thereby establishing a practical reference point for the management and prognosis of such infections.},
}

@article {pmid42106812,
year = {2026},
author = {Ottesen, A and Kocurek, B and Mammel, MK and Charles, SJ and Dietrich, J and Pauley, S and Cole, SD and Rankin, S and Ceric, O},
title = {Breaking the culture habit: Complementing culture-based veterinary diagnostics with metagenomic data -A case study of feline and canine skin infections.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05476-x},
pmid = {42106812},
issn = {1746-6148},
abstract = {BACKGROUND: Skin infections have been described as the primary cause for veterinary small animal practice visits, frequently requiring topical and systemic antibiotics. These infections often represent secondary complications of underlying pathologies, that can lead to recurrent infections and multiple antibiotic exposures. This creates selection pressure toward antibiotic resistance at the intersection of skin, bloodstream, and shared human-animal environments. This case study integrates Veterinary Diagnostic Laboratory (VDL) aerobic culture results with metagenomic (MGX) data to evaluate the combined utility of these approaches in advancing One Health veterinary diagnostics. Simultaneous reporting of culture-recovered pathogens alongside infection microbiomes and resistomes could strengthen pathogen epidemiology, illuminate polymicrobial etiologies, and inform antimicrobial stewardship.

RESULTS: One feline and eight canine skin swabs were analyzed with aerobic culture and traditional antimicrobial susceptibility testing (AST) and compared with MGX profiles. VDL aerobic culture and AST identified Staphylococcus aureus, S. pseudintermedius, S. schleiferi, methicillin resistant (MR) S. schleiferi (MRSS), MR S. pseudintermedius (MRSP) and Pseudomonas aeruginosa. MGX data detected the identical bacterial pathogens and identified methicillin resistance genes (mecA, mecI, mecR1) in samples where AST had confirmed MRSP and MRSS. MGX data also detected mec genes in samples without culture confirmed MR phenotypes as well as describing multi-domain microbiota (bacteria, fungi, protists, viruses, phages), antimicrobial resistance genes (ARGs), plasmids, and metabolic features associated with the skin infection samples.

CONCLUSIONS: MGX data detected the identical VDL recovered pathogens and genes that confer the AMR phenotypes recovered by VDL AST. MGX data also detected additional uncultured pathogens, ARGs, multi-domain microbiota, mobile AMR elements, and metabolic features. Future applications for these methods used simultaneously could support monitoring programs, advance pathogen epidemiology, inform treatment strategy, advance judicious antimicrobial administration, and provide data for machine learning (ML) models to improve precision veterinary diagnosis and treatment.},
}

@article {pmid42106836,
year = {2026},
author = {Navazesh, SE and Ter Horst, A and Wen, W and Liu, Y and Kiang, D and Li, Z and Yu, A and Brown, CT and Ji, P},
title = {Dietary iron and metal-based growth promoters differentially modulate the gut resistome and Escherichia coli virulome in weaned pigs.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42106836},
issn = {1674-9782},
support = {NNFSA210073688//Novo Nordisk Foundation/ ; NNFSA210073688//Novo Nordisk Fonden/ ; },
abstract = {BACKGROUND: High levels of zinc oxide (ZnO) and copper sulfate are widely used as alternative growth promoters in postweaning pig diet. However, excessive exposure to these metals may drive co-selection for heavy metal (HMR) and antibiotic resistance (AMR). Nursery diets also contain abundant iron to offset the low bioavailability of plant-derived iron, yet how dietary iron influence gut dysbiosis and microbial resistance in postweaning pigs remains unclear. This exploratory study examined the effects of dietary iron and metal-based growth promoters on the fecal resistome of postweaning pigs using shotgun metagenomics and whole-genome sequencing (WGS).

METHODS: Fifty weanling pigs were stratified and randomly assigned to five dietary treatments for 24 d. Experimental diets included a control diet (Con) containing 25, 139, and 141 mg/kg of Cu, Fe, and Zn, respectively, a low-iron diet (LFe, 19 mg Fe/kg), a high-iron diet (HFe, 1,219 mg Fe/kg), a high-copper diet (HCu, 257 mg Cu/kg), and a high-zinc diet (HZn, 2,631 mg Zn/kg, including 2,490 mg Zn/kg from ZnO). All pigs were orally administered with F18 enterotoxigenic Escherichia coli (ETEC) on d 13-16. Metagenome sequencing were performed on d 24 fecal DNA (n = 24) to identify HMR genes (BacMet Predicted database) and AMR genes (CARD database). Functional annotation was performed using HUMAnN3. Whole genome sequencing (WGS) was conducted on 120 E. coli isolates from fecal cultures on d 1, 12, and 24, and AMR and virulence genes were identified from contig assemblies using ABRicate.

RESULTS: Dietary metal treatments significantly altered β-diversity of HMR genes compared with Con, with HZn differing from both HCu and LFe (P < 0.05). Fecal iron levels correlated with sodB (ρ = 0.64, P = 0.075), an iron-containing superoxide dismutase, while fecal copper levels correlated with pcoC (ρ = 0.66, P = 0.075), a plasmid-mediated copper resistance gene. Across metagenomes, 172 AMR genes were identified, dominated by glycopeptide and tetracycline resistance. While dietary iron had minimal effects on fecal AMR profile, HZn induced the largest shifts in resistome, including increases of ant(9)-la, conferring aminoglycoside resistance on mobile genetic elements, and adeF, encoding a multidrug efflux pump (P < 0.05). Functional profiling revealed enrichment of carbohydrate metabolism pathways in HZn group (P < 0.05). WGS of E. coli isolates showed distinct AMR profiles under HZn on d 24 and distinct virulence profile under LFe on d 12, exhibiting increased prevalence of exotoxin and T3SS genes (P < 0.05).

CONCLUSION: Dietary iron restriction enhanced E. coli virulence genes, whereas excessive ZnO induced the most pronounced changes in the gut resistome and microbial metabolism, highlighting a risk for AMR co-selection and marked influence on gut microbiota.},
}

@article {pmid42107247,
year = {2026},
author = {Tan, T and Hu, T and Chen, B and Kuang, W and Yu, H and Xie, Y and Zhang, Z and Wang, H and Deng, Z and Zhang, C},
title = {Boosting anaerobic reductive dehalogenation with natural protein amendments to unlock cryptic organohalide-reducing bacteria.},
journal = {Marine environmental research},
volume = {219},
number = {},
pages = {108100},
doi = {10.1016/j.marenvres.2026.108100},
pmid = {42107247},
issn = {1879-0291},
abstract = {Deep-sea sediments host a rich yet largely unexplored reservoir of microorganisms capable of reductive dehalogenation. However, the activity of dehalogenating consortia is often limited even under carbon-rich conditions, impeding the identification of key functional players. In this study, we report that the addition of natural protein materials can dramatically stimulate reductive dehalogenation in an enrichment culture derived from deep-sea cold seep sediments. This stimulatory effect was clearly demonstrated by supplementation with bovine serum albumin (BSA), which significantly enhanced the degradation rates of 2,4,6-tribromophenol (2,4,6-TBP) and tetrachloroethene (PCE). Integrated metagenomic and metatranscriptomic analyses revealed that two candidate novel clostridial lineages-Romboutsia and Oxobacteraceae-present in BSA-amended cultures harbored distinct reductive dehalogenase (RDase) genes. Romboutsia harbored three RDase genes, with one being upregulated during the degradation of 2,4,6-TBP intermediates and another specifically responding to PCE, suggesting a substrate-dependent regulatory strategy. Oxobacteraceae encoded a cytosolic RDase that was highly expressed during 2,4,6-TBP transformation. Metabolic reconstruction further indicated that both lineages could utilize BSA-derived amino acids for growth. This work establishes an effective biostimulation strategy to activate dehalogenation in deep-sea microbial communities and expands the known diversity and functional versatility of candidate organohalide-reducing bacteria.},
}

@article {pmid42107339,
year = {2026},
author = {Zhang, X and Lu, J and Bao, Q and Xu, K},
title = {Renal mucormycosis caused by Apophysomyces species: case report and literature review.},
journal = {Journal de mycologie medicale},
volume = {36},
number = {2},
pages = {101627},
doi = {10.1016/j.mycmed.2026.101627},
pmid = {42107339},
issn = {1773-0449},
abstract = {INTRODUCTION: Mucormycosis represents an uncommon yet aggressive and life-threatening fungal infection, typically occurring in immunocompromised individuals. Unlike most Mucorales infections, Apophysomyces frequently infects otherwise healthy hosts, raising significant clinical concern. Alarmingly its atypical manifestation, necrotizing fasciitis, is often misdiagnosed as a bacterial infection due to overlapping clinical features.

CLINICAL CASE: Herein we present a case of Apophysomyces infection in kidney in an immunocompetent 52-year-old man, whose condition deteriorated swiftly, leading to failure of several organs, culminating in death. All laboratory results, including serological assays and microbial cultures from blood, respiratory secretions, urine, and stool, showed no abnormalities. The diagnosis was confirmed through metagenomic next-generation sequencing (mNGS) which was highlighted as valuable for early diagnosis. We conducted a literature review of 13 cases previously reported from 1994 to 2025, implying a higher prevalence among immunocompetent individuals. Patients of Indian constituted the majority across all reported cases. PCR, fungal culture and histopathological examination served as the primary diagnostic methods. Systemic antifungal agents were administered to 13 individuals, while surgical intervention was performed in 8 cases. Complete recovery was achieved in 7 patients.

CONCLUSIONS: Therefore our report highlights Apophysomyces variabilis as a novel pathogen of clinical importance in China, emphasizing that mortality rates escalate substantially without timely detection and appropriate management.},
}

@article {pmid42107405,
year = {2026},
author = {Guo, Y and Zhou, W and Dong, M and Qiu, W and Gao, X and Ahmad, T and Farid, B and Lyu, W and Sun, L},
title = {Root-secreted aminosalicylic acid and 4,6-dioxoheptanoic acid: Dual roles in enhancing 4-nonylphenol bioavailability and regulating rhizospheric microbiota community.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142282},
doi = {10.1016/j.jhazmat.2026.142282},
pmid = {42107405},
issn = {1873-3336},
abstract = {Root exudates and rhizospheric microorganisms are key drivers of organic pollutant degradation in soil. However, the mechanisms underlying their coordinated effects are not yet fully understood. This paper analyzes the changes in the composition of Astragalus sinicus root exudates induced by 4-nonylphenol (4-NP) exposure and investigates the effects of key exudate components on 4-NP sorption-desorption, rhizospheric degradation, and soil microbial community. Metabolomic analysis indicated significant alterations in profile composition induced by 4-NP exposure, with organic acids representing the major responsive category. Specifically, aminosalicylic acid and 4,6-dioxoheptanoic acid-two pivotal organic acids-markedly enhanced 4-NP desorption from soil at a concentration of 50 μmol/L. Their addition reduced the desorption coefficient by 6.4-fold and 3.2-fold, respectively, compared to the control. A pot experiment further validated that application of the two organic acids significantly increased rhizospheric dissipation of 4-NP by 20.0-23.0% compared to soils planted with A. sinicus alone. Metagenomic analysis demonstrated that the key root exudates selectively enriched pollutant-degrading microorganisms (Pseudoxanthomonas sp. A, Cupriavidus, Rhodococcus, and Penicillium), and increased the abundance of functional genes (Cox1, ligB, ligI, and pcaF) and pathways associated with xenobiotic biodegradation. These findings indicate that specific root exudates enhance microbial degradation capacity by improving 4-NP bioavailability, providing a mechanistic basis for the targeted optimization of phytoremediation strategies for 4-NP-contaminated soils.},
}

@article {pmid42107727,
year = {2026},
author = {Ramesh, K and Chellam, PV},
title = {Comparative genomic surveillance of fluoroquinolone resistance markers across major riverine hotspots by leveraging public metagenomes.},
journal = {International journal of antimicrobial agents},
volume = {},
number = {},
pages = {107839},
doi = {10.1016/j.ijantimicag.2026.107839},
pmid = {42107727},
issn = {1872-7913},
abstract = {The global surge in fluoroquinolone resistance (FQR) underscores the urgent need for robust environmental surveillance. From a One Health perspective, rivers serve as critical conduits and hotspots for antimicrobial resistance (AMR) dissemination. To address this, we conducted a systematic metagenomic surveillance of FQR across spatially prioritized freshwater ecosystems using distribution data of five major markers (gyr, par, qnr, aac, qep) retrieved from the National Center for Biotechnology Information (NCBI) Pathogen Detection Isolate Browser. Among 164 riverine metagenomic datasets, 31 high-quality datasets from the Mississippi, Yukon, Saint Lawrence, Yangtze, and Pearl rivers were analyzed. FQR genes were detected in 12 datasets, with normalized abundances ranging from 0.01 to 1.22 copies per bacterial cell. Plasmid-mediated qnrS2 and efflux pump genes (qepA2, AbaQ) emerged as the most prevalent determinants. Multivariate analyses revealed river-specific clustering patterns and strong correlations with metal resistance genes, highlighting co-selection pressures. The predominance of conjugative mobile genetic elements indicated an elevated potential for horizontal gene transfer. Taxonomic profiling further revealed enrichment of clinically important and World Health Organization (WHO) priority pathogens. Community structure analyses (Permutational Multivariate Analysis, R[2] = 0.7598, p = 0.003) confirmed significant microbial variations across rivers. Collectively, this integrative approach identifies environmental reservoirs of FQR genes, supporting river-based AMR surveillance. These insights are pivotal for shaping evidence-driven mitigation strategies and informing both national and global AMR policies.},
}

@article {pmid42107869,
year = {2026},
author = {Wang, L and Lin, F and Yuhan, Y and Li, S and Pan, Z and Wu, Y and Gao, Y and Zhu, L and Wang, J and Wang, J},
title = {Humic substances with different molecular weights independently increased antibiotic resistance in agricultural soils contaminated with sulfamethazine.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128302},
doi = {10.1016/j.envpol.2026.128302},
pmid = {42107869},
issn = {1873-6424},
abstract = {Humic substances (HS) are known to enhance soil structure, but their effects on the antibiotic resistance distribution in agricultural soils, especially under sulfonamide contamination, remain poorly understood. This study employed an indoor soil microcosm experiment combined with metagenomic sequencing to examine the effects of high molecular weight humic acid (HA) and low molecular weight fulvic acid (FA) on the dynamics of the antibiotic resistance in sulfamethazine (SM2) contaminated agricultural soil, with the aim of identifying key driving factors. The results revealed that both HA and FA, especially at 1 g/kg, increased the total abundance of antibiotic resistance genes (ARGs), including dominant genes, such as Sul1, Cmx, VanR, Sul2 and FloR. Additionally, HS application led to increased abundance of mobile genetic elements (MGEs) and potential ARG hosts, such as Actinobacteria. Notably, HA inhibited the growth of cultivable sulfonamide-resistant bacteria (SRB), while FA promoted their growth. However, the antibiotic resistance ratio of cultivable bacteria remained relatively high under both HS treatments, consistent with the elevated ARG abundance. This may be attributed to the enhanced competitiveness of Pseudomonas within the SRB community under HS exposure. Variance partitioning analysis (VPA) indicated that MGEs and microbial communities jointly contributed to ARG variation and were closely associated with the antibiotic resistome. This study provides new insights into the ecological risks associated with HS application in agricultural soils.},
}

@article {pmid42107880,
year = {2026},
author = {Yao, L and Shen, L and Liu, X and Fu, J and Pan, D},
title = {Ventriculo-Abdominal Subcutaneous Tunnelled External Drainage as a Transition Therapy to Reduce Shunt Failure Rate in Post-infection Hydrocephalus Patients: A single-center retrospective cohort study.},
journal = {World neurosurgery},
volume = {},
number = {},
pages = {125037},
doi = {10.1016/j.wneu.2026.125037},
pmid = {42107880},
issn = {1878-8769},
abstract = {OBJECTIVE: Assess the clinical efficacy of Ventriculo-Abdominal Subcutaneous Tunnelled External Drainage (VASTED) as a transition treatment before ventriculoperitoneal shunting(VPS) in the management of post-infection hydrocephalus(PIH).

METHODS: This study enrolled 384 patients who developed PIH after craniotomy. Following external ventricular drainage(EVD) and combined intravenous antibiotic therapy, patients underwent VASTED as a transitional treatment measure before definitive VPS placement when they achieved three consecutive negative cerebrospinal fluid(CSF) bacterial cultures within two weeks and no pathogen detection by metagenomic next-generation sequencing (mNGS). The primary endpoint of the study was the shunt failure rate after one year of follow-up, with infection and catheter blockage as the evaluation criteria.

RESULTS: A total of 378 cases underwent VPS surgery, with 6 cases refusing or abandoning treatment. During a one-year follow-up period, 9 shunt failures occurred (2.38%, 95% CI: 0.43-3.05). Among these, 5 failures were infection-related (1.3%) and 4 were due to pure mechanical obstruction (1.1%). The shortest duration of VASTED was 14 days, while the longest was 387 days, with a median drainage time of 69 days (95% CI: 28-112 days).

CONCLUSION: In patients with PIH, implementing VASTED as a transitional surgical treatment approach is closely associated with an extremely low one-year failure rate of VPS. This transitional strategy can significantly reduce the high failure rate following VPS.},
}

@article {pmid42108251,
year = {2026},
author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J},
title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52077-7},
pmid = {42108251},
issn = {2045-2322},
support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; },
abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.},
}

@article {pmid42108276,
year = {2026},
author = {Saha, PK and Sar, P and Sarkar, S and Mukherjee, D and Kazy, SK},
title = {Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential CO2 assimilation and bioconversion potential under varying oxygen level.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51641-5},
pmid = {42108276},
issn = {2045-2322},
support = {MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022//Ministry of Earth Sciences (MoES), Government of India/ ; },
abstract = {Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO2/H2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO2 utilization and possible bioconversion to valuable biomolecules.},
}

@article {pmid42108288,
year = {2026},
author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L},
title = {A Brief Review of Microbial Omics: Methods and Perspectives.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {1-20},
pmid = {42108288},
issn = {1940-6029},
mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; },
abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.},
}

*Genomics/methods
*Metabolomics/methods
*Proteomics/methods
*Microbiota/genetics
*Computational Biology/methods
Single-Cell Analysis/methods
Artificial Intelligence
Transcriptome
Metagenomics/methods

@article {pmid42108290,
year = {2026},
author = {Li, B and Xu, J and Zhao, T and Yang, X and Yin, Q and Zou, Y},
title = {Metagenomic Data Preprocessing and Quality Control.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {43-61},
pmid = {42108290},
issn = {1940-6029},
mesh = {*Metagenomics/methods/standards ; Quality Control ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; Workflow ; *Metagenome ; *Computational Biology/methods ; },
abstract = {Accurate metagenomic analysis relies on clean and well-processed sequencing reads. This chapter presents a concise four-step workflow for preprocessing: raw data assessment, adapter and quality filtering, host DNA removal, and final clean-read evaluation. By standardizing these essential procedures, researchers can minimize contamination, reduce technical bias, and ensure reliable inputs for assembly and downstream metagenomic analyses.},
}

*Metagenomics/methods/standards
Quality Control
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Software
Workflow
*Metagenome
*Computational Biology/methods

@article {pmid42108291,
year = {2026},
author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y},
title = {Metagenomic Assembly and Gene Prediction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3033},
number = {},
pages = {63-89},
pmid = {42108291},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.},
}

*Metagenomics/methods
*Metagenome
*Computational Biology/methods
Molecular Sequence Annotation
Contig Mapping/methods
Software
Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid42103932,
year = {2026},
author = {Wang, F and Zeng, W and Zhang, Z and Li, N and Cui, Z and Bai, J and Yan, J and Zhang, Y and Miao, Y and Gu, L and Xiong, B},
title = {Gut microbiota-modulated glutamic acid rejuvenates the quality of oocytes deteriorated by advanced reproductive age.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42103932},
issn = {1757-4684},
support = {2023YFD1300502//MOST | National Key Research and Development Program of China (NKPs)/ ; BYSYSZKF2023029//State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital/ ; KYCX25_1007//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
abstract = {The gut microbiota plays a vital role in maintaining the physiological function of host health and the pathogenesis of various diseases. However, its relationship with maternal age-associated decline in oocyte quality remains elusive. Here, we report that establishment of gut microbiota from young donors in aged mice by fecal microbiota transplantation (FMT) is an effective method to rejuvenate the quality of maternally aged oocytes. Specifically, young gut microbiota promoted the ovulation and maturation of aged oocytes, and inhibited occurrence of cytoplasm fragmentation and spindle/chromosome abnormalities, hence enhancing the oocyte quality and female fertility. By integrating metagenome and untargeted metabolome of intestinal digesta, as well as targeted metabolome of ovaries and micro-transcriptome of oocytes, we identified that Bacteroides_caecimuris-modulated glutamic acid levels mediated the restorative effects of young gut microbiota on the aged oocytes through strengthening the mitochondria function. In addition, we demonstrated that in vivo supplementation of glutamic acid also enhanced the quality of aged oocytes, and the improvement of oocyte quality by glutamic acid was conserved across species. Altogether, our findings highlight the importance of gut microbiota in the oocyte aging and provide potential improvement strategies for age-related decline in oocyte quality and female fertility.},
}

@article {pmid42104156,
year = {2026},
author = {Minnaar, LS and Inokuma, K and Hasunuma, T and den Haan, R},
title = {Engineering natural Saccharomyces cerevisiae isolates for enhanced one-step cellulosic ethanol production.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13830-0},
pmid = {42104156},
issn = {1432-0614},
abstract = {Engineering yeast strains for use as chassis organisms in second-generation (2G) bioethanol is a promising strategy to improve process economics. Natural isolates of Saccharomyces cerevisiae offer strain backgrounds with greater genetic diversity and enhanced robustness, with the potential for improved heterologous protein production capabilities. In this study, heterologous cellulase production using different expression strategies was evaluated in various process-relevant conditions. Enhanced cellulolytic activity was clearly demonstrated in a cell-tethered enzyme system, compared to a free enzyme system, across identical strain backgrounds. Superior secretory capacity was obtained for YI59_V2 for all individual enzymes across all process-relevant conditions tested. In addition, this strain exhibited improved hydrolysis efficiency and ethanol production from crystalline cellulose, achieving ~10 g/L after 96 h (~88% of the maximum theoretical yield) without the need for exogenous cellulase supplementation. Interestingly, enhanced strain robustness against process-relevant, secretion, and cell wall stresses was also observed in transformants with cell-tethered cellulase systems compared to those with free enzyme systems. This study highlights that the expression design strategy for cellulase-encoding genes in this natural isolate was pivotal for increasing protein titres and for influencing strain robustness. Strains exhibiting elevated cellulase activity and increased robustness represent a key step toward the industrial deployment of consolidated bioprocessing (CBP). KEY POINTS: • Cell-tethered expression greatly boosted cellulase activity and cellulose breakdown. • YI59_V2 yielded ~ 10 g/L ethanol from crystalline cellulose without added enzymes. • Tethered enzymes reshaped cell walls and altered stress tolerance.},
}

@article {pmid42104260,
year = {2026},
author = {Nguyen, TT and Steen, IH and Bøe, MH and Otterlei, M and Stokke, R},
title = {Arctic deep-sea hydrothermal microbiomes as a natural niche for novel antimicrobial peptides.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05098-1},
pmid = {42104260},
issn = {1471-2180},
abstract = {BACKGROUND: The escalating threat of antimicrobial resistance (AMR) has created an urgent need for new antimicrobial agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics due to their broad-spectrum activity and reduced risk of resistance development. While most AMP discovery efforts have focused on terrestrial microbes, extreme environments remain largely untapped. Deep-sea hydrothermal vent biofilms, such as those from the Arctic Mid-Ocean Ridges (AMOR), are unique ecosystems characterized by high pressure, temperature gradients, and chemical extremes. These conditions select for microorganisms with specialized adaptations, including the production of bioactive compounds that confer survival advantages. Such peptides may exhibit enhanced stability and novel mechanisms of action, making hydrothermal biofilms an exceptional resource for next-generation antimicrobials.

RESULTS: Using metagenomic and metatranscriptomic datasets from nine recently published AMOR biofilms, we predicted 961 AMP sequences with Macrel, of which 873 were unique and showed no identity to entries in the Antimicrobial Peptide Database (APD). AMPs were distributed across 51 microbial phyla, including underrepresented archaeal groups such as Asgardarchaeota, Nanoarchaeota, and Micrarchaeota. Transcriptomic profiling detected AMP expression in 25 phyla, including low-abundance candidate taxa, highlighting active AMP production. In silico minimum inhibitory concentration (MIC) prediction using APEX 1.1 suggested that 16.7% of AMPs may inhibit at least one clinically relevant pathogen, with Acinetobacter baumannii emerging as the most susceptible. Four peptides were synthesized for experimental validation; AMP OLKFNNDA_52_10 exhibited moderate in vitro activity against Staphylococcus aureus and weak activity against Escherichia coli, while showing low cytotoxicity toward human HEK293 cells. Other tested peptides displayed weak or no activity, underscoring discrepancies between computational predictions and biological outcomes.

CONCLUSIONS: Our study reveals extensive taxonomic and structural diversity of AMPs in Arctic hydrothermal vent biofilms and identifies novel candidates withbioactive potential. These findings emphasize the importance of integrating metagenomics, transcriptomics, machine learning, and experimental validation to uncover bioactive compounds from underexplored microbial ecosystems. Overall, AMOR biofilms represent a rich and untapped source of AMPs, offering new opportunities for antimicrobial drug discovery in the fight against AMR.},
}

@article {pmid42098851,
year = {2026},
author = {Dong, J and Cao, Y and Chen, X and Xie, T and Zhang, X and Zhao, Q and Shi, C and Miao, Q and Xu, Z and Yan, L and Dong, L},
title = {Buyang Huanwu Decoction promotes neurorepair after spinal cord injury through a Lactobacillus johnsonii-indole-3-lactic acid-AhR-PI3K/Akt axis.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {42098851},
issn = {1749-8546},
support = {YSJ2025009//Postgraduate Research & Practice Innovation Program of Yan'an University/ ; 22XYJ0002//Xi'an Innovation Capability Strong Foundation Plan - Medical Research Project/ ; 2025PT-01//Platform Construction Project of Shaanxi Province's Health and Wellness Scientific Research and Innovation Capacity Enhancement Program/ ; },
abstract = {BACKGROUND: Spinal cord injury (SCI) induces gut microbiota dysbiosis, which significantly affects recovery. Buyang Huanwu Decoction (BHD), a traditional Chinese medicine formula, has shown therapeutic effects on SCI. Although BHD is known to modulate gut microbiota, whether its benefits are mediated through the gut-spinal cord axis remains unclear.

METHODS: A rat SCI model was established. BHD was administered orally, and fecal microbiota transplantation (FMT) from BHD-treated rats (BHD-FMT) was performed to assess neuroprotective and gut-protective effects. Behavioral testing, histology, and immunofluorescence evaluated motor recovery, inflammation, and neuroregeneration. Gut microbiota profiling was performed using 16S rDNA sequencing and metagenomics, while targeted metabolomics quantified tryptophan metabolites. Transcriptomics validated key pathways, and a microbiota-metabolite-signaling network was constructed.

RESULTS: BHD significantly improved motor function, reduced spinal inflammation, and promoted neuronal survival and axonal regeneration. It restored gut function, reduced colonic inflammation, and enhanced ZO-1 and Occludin expression, which were further confirmed by FMT. BHD-FMT reshaped the gut microbiota and enriched Lactobacillus johnsonii, which correlated positively with recovery. Metabolomics showed increased tryptophan metabolites, including indole-3-lactic acid (ILA) and indole-3-propionic acid (IPA), with ILA strongly associated with functional improvement. Transcriptomic analysis and Western blot validation demonstrated that BHD-FMT activated the AhR-PI3K/Akt pathway, which was suppressed by an AhR antagonist.

CONCLUSION: BHD promotes neuroregeneration after SCI by reshaping gut microbiota and enhancing tryptophan metabolism, potentially exerting its effects through the L. johnsonii-ILA-AhR-PI3K/Akt network. These findings reveal a gut-spinal cord axis-mediated mechanism of BHD and highlight microecological targets for SCI therapy.},
}

@article {pmid42098871,
year = {2026},
author = {Biswas, P and Ahmed, S and Mondal, S and Oladokun, S and Gundogdu, O and Mallick, AI},
title = {Recombinant LAB vector-based multicomponent vaccine against Campylobacter jejuni potentially promoting a healthier microbial balance in the poultry gut.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02421-w},
pmid = {42098871},
issn = {2049-2618},
support = {BB/Y007115/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P409/2023-24//BactiVac, University of Birmingham, UK/ ; IC-12047(12)/2/2024-BP-IUCA//Indo-UK (DBT-BBSRC)/ ; },
abstract = {BACKGROUND: Diarrheal diseases remain the second leading cause of preventable death globally, particularly among children under the age of 5 in developing countries, accounting for an estimated 2-3 million deaths annually. Among bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains a major contributor, particularly in low- and middle-income countries (LMICs). As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonization proteins (SECPs), namely haemolysin co-regulated protein (Hcp), valine glycine repeats G (VgrG), Campylobacter adhesion to fibronectin (CadF), fibronectin-like protein A (FlpA), and jejuni lipoprotein A (JlpA). Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion of avian and non-avian hosts. To minimize C. jejuni adhesion and subsequent colonization in the avian gut, we explored the potential of a multicomponent mucosal vaccine composed of CadF, Hcp, and JlpA protein of C. jejuni.

RESULTS: For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits of C. jejuni, CadF, Hcp, and JlpA. Utilizing this live vector-based multicomponent mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonizing, we used chitosan, a natural mucoadhesive, biodegradable polymer, to microencapsulate the engineered bacteria and increase their gut retention time for optimal interaction with local immune cells. Our in vivo immunization study demonstrated that oral administration of this multicomponent vaccine formulation elicited a strong local antibody response (sIgA) (p < 0.0001) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection (~ 1.54 log10 reduction) against the cecal colonization of C. jejuni. Beyond targeting C. jejuni, we hypothesized that the vaccine may influence the overall gut microbiota, potentially promoting a healthier microbial balance in the poultry gut. To this end, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota (~ 2-fold), accompanied by increased abundance of the phyla Bacteroidota, as part of a beneficial microbial community.

CONCLUSIONS: Together, this study underscores the potential of a live vector-based, multicomponent mucosal vaccine as a promising, cost-effective strategy to reduce the cecal load of C. jejuni, potentially limiting the risk of foodborne transmission in poultry production systems.},
}

@article {pmid42098876,
year = {2026},
author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B},
title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02406-9},
pmid = {42098876},
issn = {2049-2618},
support = {2023YFD2000703//National Key R&D Program of China/ ; 2023YFD2000701//National Key R&D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.

RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150 kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20 g/kg dry matter) decreased daily CH4 emissions by ~ 8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.

CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.},
}

@article {pmid42099457,
year = {2026},
author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y},
title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70123},
pmid = {42099457},
issn = {2770-596X},
abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.},
}

@article {pmid42099461,
year = {2026},
author = {Wu, R and Wen, T and Shang, N and Xie, P and Wang, Z and Li, H and Li, S and Zhang, D},
title = {Chondroitin sulfate restores muscle mass via gut-muscle axis remodeling through sugar-bile acid metabolism reprogramming.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70118},
pmid = {42099461},
issn = {2770-596X},
abstract = {Glucocorticoid-induced myopathy is characterized by progressive muscle atrophy and impaired regeneration, yet effective microbiota-oriented interventions for preserving muscle homeostasis remain largely unexplored. Here, we demonstrate that dietary chondroitin sulfate (DCS) restores muscle mass and function through a microbiota-dependent gut-muscle metabolic axis. DCS failed to confer protection in germ-free or antibiotic-treated mice, establishing gut microbiota as a prerequisite for its efficacy. Microbiota transplantation and mono-colonization experiments identified Lactobacillus johnsonii Z-RW as a functionally relevant mediator capable of recapitulating muscle protection under controlled microbial conditions. Integrated metagenomic, metabolomic, and proteomic analyses revealed coordinated reprogramming of intestinal sugar utilization and bile acid metabolism following DCS administration. Notably, DCS promoted bile acid deconjugation and enrichment of secondary bile acids, coinciding with restoration of muscle regenerative and energetic programs, including upregulation of NMRK2, PAX7, and SIRT1. Metabolite supplementation further implicated bile acids as candidate mediators linking microbial metabolism to muscle phenotypes. To quantitatively integrate these shifts, we introduce the sugar-bile acid ratio as a systems-level descriptor of microbiota-driven metabolic remodeling. Our findings delineate a microbiota-dependent metabolic framework through which a functional polysaccharide reshapes intestinal biochemistry to influence distal muscle physiology. This work highlights bile acid-associated signaling as a central relay within the gut-muscle axis and provides a conceptual foundation for microbiota-targeted strategies to mitigate muscle wasting.},
}

@article {pmid42099660,
year = {2026},
author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF},
title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.},
journal = {BJUI compass},
volume = {7},
number = {5},
pages = {e70186},
pmid = {42099660},
issn = {2688-4526},
abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.

SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12 weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.

RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p = 0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p = 0.001), Bray-Curtis (p = 0.008), and nonweighted UniFrac metrics (p = 0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p = 0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p = 0.043) but not of treatment response.

CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.},
}

@article {pmid42100218,
year = {2026},
author = {Hussain, N and Muccee, F and Mirza, AF and Ashraf, NM and Al Haddad, AHI},
title = {Genomic insights into Solea solea gut-borne Enterococcus faecalis for the development of new probiotics in aquaculture.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1778532},
pmid = {42100218},
issn = {2297-1769},
abstract = {Dietary manipulations using probiotics may contribute to the sustainable development of aquaculture. For probiotic applications, their traits, safety profiles, and functional characteristics should be explored. Whole genome sequencing (WGS) can be an informative tool in this regard. We initiated this study to obtain genomic insights into S. solea gut-associated bacteria. Bacteria (n = 20) exhibiting probiotic characteristics were subjected to DNA extraction. A mixture comprising equimolar concentrations of each bacterial DNA was prepared and analyzed through WGS. BV-BRC, metaSPAdes, MetaBAT2, DAS Tool, and PATRIC were used for taxonomic profiling, metagenome assembly, genome binning, comprehensive genome annotation, and subsystem analysis, respectively. For tree construction, MUSCLE and RaxML were employed. Fourteen bins comprising Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota were generated. Among these, the bin comprising the genome of Enterococcus faecium was selected. Its genome comprises 129 contigs with 2,944 coding sequences (CDSs). Genes associated with metabolism, protein processing, stress response, defense and virulence, cellular processes, and cell envelope were identified. Pathways identified included fatty acid and ketone body biosynthesis, glycerolipid and glycerophospholipid metabolism, linoleic acid metabolism, and self-defense mechanisms. This study confirmed the probiotic efficiencies of E. faecium. Hence, this bacterium might be employed as a fish feed supplement in aquaculture.},
}

@article {pmid42100351,
year = {2026},
author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z},
title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100600},
pmid = {42100351},
issn = {2666-5174},
abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.},
}

@article {pmid42100652,
year = {2026},
author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C},
title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799729},
pmid = {42100652},
issn = {2235-2988},
mesh = {Animals ; *Probiotics/administration & dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; },
abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.

METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 μg/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1×10⁸ CFU/day) and high (1×10⁹ CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.

RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6±6.8 to 512.4±48.9 U/L), AST (78.3±9.5 to 684.7±62.1 U/L), and plasma ammonia (38.9±5.2 to 128.6±14.3 μmol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7±41.6 U/L (low dose) and 248.9±32.4 U/L (high dose). Ammonia levels decreased to 86.4±9.7 μmol/L and 59.8±7.6 μmol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8±4.2 to 63.9±6.4 mM), lower ammonia (8.9±1.1 to 3.7±0.5 mM), improved intestinal barrier integrity (TEER: 462±38 to 721±44 Ω·cm²), and reduced TNF-α (214.6±22.8 to 74.9±12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.},
}

Animals
*Probiotics/administration & dosage
Rats, Wistar
Male
Metagenomics
Rats
Feces/microbiology/chemistry
Disease Models, Animal
*Gastrointestinal Microbiome
*Liver Failure
Cytokines
Ammonia/blood
Dysbiosis
Galactosamine

@article {pmid42100656,
year = {2026},
author = {Li, T and Liu, J and Wang, X},
title = {Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: a comparative study stratified by immune status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1812778},
pmid = {42100656},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; *Respiratory Tract Infections/diagnosis/microbiology/immunology ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Fungi/genetics/isolation & purification/classification ; Aged, 80 and over ; Molecular Diagnostic Techniques/methods ; },
abstract = {BACKGROUND: Pulmonary infections represent a significant global health concern, contributing substantially to morbidity and mortality worldwide. Metagenomic next-generation sequencing (mNGS) represents an advanced, comprehensive, and unbiased diagnostic approach for pathogen identification, effectively overcoming many limitations inherent in conventional diagnostic methods. This study aimed to systematically evaluate the clinical performance of mNGS in the etiological diagnosis of pulmonary infections, with a particular emphasis on its utility across diverse immune statuses.

METHODS: This retrospective study included 136 patients with suspected pulmonary infections admitted to the Department of Respiratory Medicine at Shandong Provincial Hospital from June 2023 to April 2025. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and concurrently subjected to mNGS and conventional microbiological testing (CMT). The pathogen detection spectrum and diagnostic performance of mNGS were systematically compared against those of CMT.

RESULTS: mNGS exhibited a significantly higher overall pathogen detection rate compared to CMT (77.2% vs. 50.0%, P < 0.001). Regarding the pathogen spectrum, mNGS identified a broader array of microorganisms, encompassing 19 bacterial, 9 fungal, and 2 mycobacterial species, in contrast to the 11 bacterial, 5 fungal, and 1 mycobacterial species detected by CMT. Diagnostic performance analysis further revealed that mNGS sensitivity was significantly superior to that of CMT (74.6% vs. 46.7%, P < 0.001). Furthermore, mNGS demonstrated a distinct advantage in detecting mixed infections, with a detection rate of 19.1%, significantly exceeding that of CMT (8.8%, P < 0.05). Subgroup analysis indicated a significantly higher incidence of mixed infections in immunocompromised patients compared to immunocompetent patients (35.1% vs. 13.1%, P < 0.05). Additionally, immunocompromised patients were more frequently subjected to adjustments in antimicrobial therapy guided by mNGS results (56.8% vs. 35.4%, χ² = 5.094, P < 0.05).

CONCLUSIONS: In conclusion, mNGS offers superior sensitivity and broader pathogen coverage for the etiological diagnosis of pulmonary infections compared to conventional microbiological testing. Its enhanced capability to detect mixed infections significantly improves diagnostic accuracy in immunocompromised patients and effectively facilitates the dynamic optimization of antimicrobial therapy. Serving as a powerful complement to traditional diagnostic methods, mNGS holds particular value for the rapid diagnosis of complex and immunosuppression-associated pulmonary infections.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Male
Female
*Metagenomics/methods
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
Adult
*Respiratory Tract Infections/diagnosis/microbiology/immunology
Sensitivity and Specificity
Bacteria/genetics/isolation & purification/classification
Fungi/genetics/isolation & purification/classification
Aged, 80 and over
Molecular Diagnostic Techniques/methods

@article {pmid42100705,
year = {2026},
author = {Li, J and Liu, M and Yang, C and Fan, Z and Su, J and Hu, Y and Yang, Y and Li, J and Pu, Y and Ma, E and Deng, X and Sun, J},
title = {Preceding crops may reduce denitrification potential and enhance ammonium assimilation pathways.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1808894},
pmid = {42100705},
issn = {1664-302X},
abstract = {BACKGROUND: Soil microorganisms are pivotal to nitrogen (N) cycling in croplands, yet how preceding crops modulate their functional profiles remains unclear.

OBJECTIVE: This field study aimed to quantify the effects of barley (BT) and rapeseed (RT) preceding crops (vs. no preceding crop, CK) on soil microbial functions and N-metabolic pathways in tobacco fields.

RESULTS: High-throughput metagenomics revealed that BT and RT significantly increased soil microbial richness (Chao1 index) compared to CK. At the genus level, CK contained 64% and 24% fewer unique taxa than BT and RT, respectively. While the top five KEGG functional pathways (e.g., Metabolic pathways, Biosynthesis of secondary metabolites) were conserved across treatments, their relative abundances differed. Critically, preceding crops reduced soil denitrification rates and increased glutamine dehydrogenase activity. Redundancy analysis confirmed that ammonium-N concentration was the key edaphic factor strongly correlated with microbial community structure and function (P < 0.01).

CONCLUSION: Our findings demonstrate that barley and rapeseed preceding crops enhance microbial richness and activity, thereby inhibiting denitrification and promoting N fixation via altered ammonium-N dynamics.},
}

@article {pmid42100978,
year = {2026},
author = {Ranade, AV and Hegde, PS and Agni, MB and Rai, P and Upadhyay, SS and Aravind, A and Keshava Prasad, TS and Gowda, KMD},
title = {Cardiometabolomic signatures and gut microbiota dynamics in perinatally undernourished F1 offspring: Decoding the metabolic footprint.},
journal = {Journal of biosciences},
volume = {51},
number = {},
pages = {},
pmid = {42100978},
issn = {0973-7138},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Female ; Rats ; Pregnancy ; Rats, Wistar ; *Malnutrition/metabolism/microbiology ; Docosahexaenoic Acids/administration & dosage/pharmacology ; Metabolome ; Fetal Development ; Male ; Metabolomics ; Maternal Nutritional Physiological Phenomena ; Dietary Supplements ; *Prenatal Exposure Delayed Effects/metabolism ; Xanthophylls ; },
abstract = {The Developmental Origins of Health and Disease (DOHaD) hypothesis asserts that detrimental prenatal conditions, such as dietary deficiencies, may lead to enduring health consequences. Perinatal undernutrition, an important concern during fetal development, may affect growth and metabolic programming, resulting in lasting health implications. Maternal nutrition is crucial in modulating fetal endocrine systems and metabolic functions, influencing the development, blood circulation, and nutrient absorption. The present study examines the impact of perinatal undernutrition on the composition of gut microbiota and metabolite levels in offspring of undernourished dams, using an Albino Wistar rat model. Furthermore, we investigated the combined impact of astaxanthin (AsX) and docosahexaenoic acid (DHA) supplementation on cardiometabolic outcomes in these progenies. Astaxanthin, a powerful antioxidant, and DHA, an omega-3 fatty acid, have shown the ability to favorably alter the gut flora and metabolic pathways. The direct influence of AsX on gut microbiota remains unexplored, whereas DHA's role in fostering beneficial microbes and regulating metabolite production is well documented. The current study used metabolomics and metagenomics to investigate the intricate relationship between metabolites and gut microbiota in health and disease, offering insights into fetal programming and possible strategies to improve offspring health. The results highlight the need to address perinatal undernutrition and enhance gut health through targeted dietary interventions to improve long-term health outcomes.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
Female
Rats
Pregnancy
Rats, Wistar
*Malnutrition/metabolism/microbiology
Docosahexaenoic Acids/administration & dosage/pharmacology
Metabolome
Fetal Development
Male
Metabolomics
Maternal Nutritional Physiological Phenomena
Dietary Supplements
*Prenatal Exposure Delayed Effects/metabolism
Xanthophylls

@article {pmid42100992,
year = {2026},
author = {Xu, X and Chen, D and Luo, N and Zhang, W and Lou, L},
title = {Metagenomic next-generation sequencing for pathology-suspected fungal infections at rare anatomical sites: a case series.},
journal = {Future science OA},
volume = {12},
number = {1},
pages = {2669032},
doi = {10.1080/20565623.2026.2669032},
pmid = {42100992},
issn = {2056-5623},
abstract = {OBJECTIVE: Histopathology for suspected fungal infections lacks species-level identification and is prone to morphological mimics. The utility of metagenomic next-generation sequencing (mNGS) at rare anatomical sites is underexplored.

METHODS: We retrospectively analyzed 10 cases with histopathology suggestive of fungal infection at rare sites (brain, cardiac valve, bone, etc.). All underwent mNGS testing on formalin-fixed paraffin-embedded samples.

RESULTS: mNGS detected fungal DNA in 8/10 cases (80%), providing species-level identification (e.g., Cryptococcus, Candida, Fusarium, Rhizopus, Histoplasma). Polymicrobial infections were identified in 70%. mNGS corrected two misdiagnoses: one confirmed neurocysticercosis; another revealed only bacteria in a suspected fungal lesion. Antimicrobial resistance genes (ErmB) were identified in two cases.

CONCLUSION: mNGS enhances diagnostic precision at rare sites by enabling species identification, uncovering polymicrobial infections, and correcting morphological misdiagnoses, supporting targeted therapy.},
}

@article {pmid42101034,
year = {2026},
author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM},
title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70354},
doi = {10.1111/1758-2229.70354},
pmid = {42101034},
issn = {1758-2229},
support = {NA19NOS4190106//Texas General Land Office/ ; },
mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Ecosystem ; },
abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.},
}

*Estuaries
*Fresh Water/chemistry/microbiology/virology
Salinity
*Viruses/genetics/classification/isolation & purification
Bacteria/genetics/classification/isolation & purification
Temperature
Metagenomics
Ecosystem

@article {pmid42101202,
year = {2026},
author = {Yashar, M and Thigale, UY and Karakus, S},
title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000001228},
pmid = {42101202},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.

RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced α-diversity and shifts in dominant taxa. Genera such as Staphylococcus, Corynebacterium, and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.

SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.},
}

@article {pmid42101460,
year = {2026},
author = {Colmant, AMG and Parry, RH and Charrel, R and Coutard, B},
title = {Benchmarks for taxonomic classification of jingmenviruses and closely related viruses using newly identified genomic sequences.},
journal = {The Journal of general virology},
volume = {107},
number = {5},
pages = {},
doi = {10.1099/jgv.0.002254},
pmid = {42101460},
issn = {1465-2099},
mesh = {*Genome, Viral ; Phylogeny ; *Flaviviridae/classification/genetics/isolation & purification ; Genomics ; Metagenomics ; },
abstract = {Jingmenviruses are a group of viruses related to orthoflaviviruses characterized by a segmented genome and multipartite organization that have been detected worldwide in a wide range of hosts. With the growing number of new jingmenvirus sequences identified in metagenomics data, it can be difficult to assess whether a new sequence is associated with a new virus species or with a strain of an existing species. The ICTV is about to ratify the reclassification of the Flaviviridae family, recognizing segmented viruses previously designated jingmenviruses as part of that family and proposing two genera to classify them: Jingmenvirus and Guaicovirus. These proposals do not include clear criteria to classify jingmenviruses and related sequences into species or genera. In order to determine such criteria, we generated a large sequence database from published and newly assembled sequences. Indeed, we screened public raw sequencing data from studies that did not search for or report jingmenvirus or related sequences, looking for new strains of previously described viruses. We then performed multiple sequence alignments and used the inferred percentage identity values to determine demarcation criteria based on the distribution of evolutionary distances upon pairwise comparisons. We report the identification of almost 60 libraries containing jingmenvirus and related sequences, in a wide range of sample types and geographical locations. Using these data and published sequences, we have determined that to be classified as a virus species, at least four segments are required, on which eight cut-off values in percentage identity (nucleotide and amino acid) are used for demarcation. The use of these criteria would enhance consistency in jingmenvirus taxonomy and provide a standardized framework for comparative genomics studies of these viruses, as they are still under-characterized.},
}

*Genome, Viral
Phylogeny
*Flaviviridae/classification/genetics/isolation & purification
Genomics
Metagenomics

@article {pmid42101522,
year = {2026},
author = {Yuan, C and Zhang, T and Huo, J and Liang, W and Wang, L},
title = {Comparative analysis of next-generation versus third-generation sequencing for pathogen detection in clinical samples: a diagnostic accuracy study.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42101522},
issn = {1573-0972},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Prospective Studies ; *Communicable Diseases/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification ; Viruses/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Fungi/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; },
abstract = {BACKGROUND: The rapid and accurate identification of pathogens is crucial for clinical management of infectious diseases. While Next-generation sequencing (NGS) has transformed pathogen detection, Third-generation sequencing (TGS) offers advantages in real-time analysis and long-read capabilities. This study comprehensively compares the diagnostic performance of NGS and TGS across diverse clinical samples.

METHODS: We conducted a prospective diagnostic accuracy study involving 105 clinical samples (58 bronchoalveolar lavage fluid, 28 whole blood, 19 other body fluids) from patients with suspected infections. All samples were analyzed using both NGS (BGI platform) and TGS (Nanopore platform). Diagnostic performance was evaluated against a composite reference standard incorporating clinical diagnosis, microbiological culture, and laboratory findings.

RESULTS: NGS demonstrated significantly higher sensitivity compared to TGS (95.9% vs. 82.4%, p < 0.001), while TGS showed superior specificity (87.1% vs. 64.5%, p = 0.012). The overall agreement between platforms was 85.7% (Kappa = 0.702). NGS exhibited particular advantages in viral detection (32 vs. 8 detections, p < 0.001) and fungal identification (28 vs. 18 detections, p = 0.023), whereas both technologies showed comparable bacterial detection capabilities. The area under the ROC curve was 0.92 for NGS and 0.85 for TGS. Turnaround time was significantly shorter for TGS (median 8 h vs. 30 h, p < 0.001).

CONCLUSION: NGS and TGS demonstrate complementary strengths in clinical pathogen detection. NGS offers superior sensitivity and enhanced detection of viral and fungal pathogens, making it suitable for comprehensive diagnostic evaluation. TGS provides rapid results with higher specificity, advantageous for time-critical clinical decisions. A combined or scenario-specific approach may optimize pathogen detection in clinical practice.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
Prospective Studies
*Communicable Diseases/diagnosis/microbiology
*Bacteria/genetics/isolation & purification/classification
Viruses/genetics/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology/virology
Fungi/genetics/isolation & purification
*Molecular Diagnostic Techniques/methods

@article {pmid42101699,
year = {2026},
author = {Bharsakale, RD and Gubyad, MG and Jagannadham, PTK and Kokane, SB and Warghane, AJ and Kokane, AD and Ghosh, DK},
title = {Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42101699},
issn = {1573-0972},
support = {Grant No. F.No. 16-11/PP/ICAR-CRP/25-26//ICAR- Consortium Research Platform on Vaccine and Diagnostics/ ; },
mesh = {*Citrus/microbiology ; India ; *Genome, Bacterial ; *Plant Diseases/microbiology ; *Rhizobiaceae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Whole Genome Sequencing ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Base Composition ; Liberibacter ; },
abstract = {Huanglongbing (HLB, 'Candidatus Liberibacter asiaticus') is one of the most devastating pathogens in citrus domain. Here, we present the nearly complete genome sequence of a CR-NGP1 strain obtained a from symptomatic Nagpur Mandarin (Citrus reticulata) tree in the Nagpur region of Central India. High-throughput sequencing on the Illumina NovaSeq 6000 platform generated ~ 85.7 million paired-end reads, 63.5 million paired-end reads and 14.8 million paired-end reads for sample CLas_001, CLas_002 and CLas_003 each with 150 bp read length, respectively. Two assembly strategies were used: (i) reference-based assembly with SPAdes produced a draft genome of ~ 1.19 Mb with assembly comprised 149 contigs, with an N50 of 14,173 bp, longest contig of 39,711 bp, and an overall GC content of 36.27%. (ii) KBase CONCOCT binning v1.1 applied to all 3 samples produced a nearly complete CR-NGP1 genome of ~ 1,156,009 bases with assembly of 93 contig, with an N50 of 17,668 bp, a longest contig of 39,711 bp, and an overall GC content of 36.4%. This resource of a CLas genome from Central India provides important insights to understand genetic diversity of CLas strains and will facilitate comparative genomics and epidemiological studies of Huanglongbing.},
}

*Citrus/microbiology
India
*Genome, Bacterial
*Plant Diseases/microbiology
*Rhizobiaceae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing
Phylogeny
Whole Genome Sequencing
DNA, Bacterial/genetics
Sequence Analysis, DNA
Base Composition
Liberibacter

@article {pmid42101805,
year = {2026},
author = {Li, Q and Yang, X and Zhu, H and Yang, S and Yin, G},
title = {A rare case of long-standing lupus vulgaris with psoriasiform manifestations diagnosed by mNGS: a case report.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42101805},
issn = {1435-4373},
abstract = {This report describes a rare case of lupus vulgaris mimicking psoriasis, undiagnosed for over 40 years. Conventional diagnostics, including histopathology and mycobacterial culture, failed to yield a definitive diagnosis. Ultimately, metagenomic next-generation sequencing (mNGS) of the skin tissue detected the Mycobacterium tuberculosis complex, confirming the infection. The patient showed marked clinical improvement following two months of dual-drug anti-tuberculosis therapy. This case highlights the clinical utility of mNGS for diagnosing atypical, long-standing cutaneous tuberculosis when conventional methods are negative, thereby preventing prolonged misdiagnosis and ensuring timely treatment.},
}

@article {pmid42102564,
year = {2026},
author = {Long, Z and Zhang, B and Bing, H and Wu, Y},
title = {Identifying microbial candidates for assisted phytoremediation through long-term microbial succession and functional gene shifts across a 50-year chronosequence of vanadium-titanium magnetite tailings.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142304},
doi = {10.1016/j.jhazmat.2026.142304},
pmid = {42102564},
issn = {1873-3336},
abstract = {Soil microorganisms are central to vegetation restoration in metalliferous wastes. However, within mine tailings restoration chronosequences, particularly those enriched with vanadium (V), the long-term successional dynamics of microbial communities, their functional potentials, and the functional partitioning between key microbial taxa and lower-abundance microbial lineages remain poorly understood. Here, we utilized metagenomic sequencing across a 50-year restoration chronosequence to investigate changes in the microbial community and functional genes related to plant growth-promotion (phosphorus, nitrogen, and iron acquisition) and V tolerance/bioreduction. The results demonstrated significant shifts in the microbial community after five years of restoration. At the phylum level, Actinobacteria, Acidobacteria, Pseudomonadota, and Gemmatimonadota were dominant. In early stages (< 15 years), nitrogen and phosphorus acquisition genes (e.g., nif, fix, phoD) were 1.3-2.5 times more prevalent than in later stages, whereas functional genes associated with V (e.g., napA, narG, nirS) increased 1.5- to 2-fold over time. Vanadium and nitrogen were the primary environmental factors regulating both community structure and the relative abundance of critical functional genes. Keystone taxa possessed more nitrogen and phosphorus acquisition genes (65% and 45%, respectively), while metagenome-assembled genomes (MAGs) were enriched in genes related to siderophore biosynthesis (71%) and denitrification (potential V bioreduction) (65%). Based on functional gene profiles, Bradyrhizobium, Allosphingosinicella, Baekduia, Sphingomicrobium, and Hylemonella were identified as promising microbial candidates for enhancing restoration in V-contaminated sites. This study enables the development of targeted microbial consortia to mitigate nutrient deficiency and V toxicity, directly informing the design of more efficient, stage-specific phytoremediation strategies in V-rich tailings.},
}

@article {pmid42102590,
year = {2026},
author = {Feng, R and Wang, X and Zhang, X and Li, L and Gao, X and Li, J and Kang, J and Yu, X and Jia, S and Zheng, G and Shi, P},
title = {Hidden antibiotic resistance risks and key drivers during tertiary wastewater treatment deciphered by an integrated metagenomic framework.},
journal = {Environment international},
volume = {212},
number = {},
pages = {110281},
doi = {10.1016/j.envint.2026.110281},
pmid = {42102590},
issn = {1873-6750},
abstract = {Potential high-risk antibiotic resistance genes (ARGs) were considered as higher public health threats in wastewater treatment systems. While tertiary wastewater treatment processes (TWTPs) effectively remove conventional and emerging pollutants, their impact on ARGs with potential higher risk remains unclear. In this study, metagenomic assembly and binning were applied to profile potential-risk ARGs and identify key factors shaping their distribution during TWTPs. Results showed that potential-risk ARGs accounted for 34.32 ± 1.98% to 59.71 ± 1.55% of total ARGs, indicating their widespread persistence. Notably, DB significantly increased the relative abundance of potential-risk ARGs, particularly those conferring resistance to multidrug, bacitracin, and aminoglycoside. In parallel, DB treatment elevated the abundance of mobile genetic elements (MGEs), primarily transposase-related. DB treatment facilitated the co-occurrence of potential-risk ARGs and MGEs, especially multidrug and transposase/recombinase. Key bacterial hosts carrying potential-risk ARGs, such as Pseudomonas and Acinetobacter, were highly enriched after DB treatment, contributing substantially to the proliferation of these ARGs. In contrast, UV disinfection and CW treatment continuously reduced the abundance and risk levels of potential-risk ARGs, highlighting their complementary roles in mitigating antibiotic resistance risks during TWTPs. Variation partitioning analysis showed that bacterial community composition explained 36.15% of the variation in potential-risk ARG profiles, underscoring its primary role in ARG dynamics. Overall, this study provides genome-resolved insights into the hidden risks of ARGs and key drivers during TWTPs, highlights the necessity of optimizing operational parameters to mitigate antibiotic resistance dissemination.},
}

@article {pmid42102689,
year = {2026},
author = {Wang, W and Jiang, H and Liang, C and Yang, Y and She, D and Cheng, G and Wang, H},
title = {Soil functional carbon fraction accrual in temperate forests is linked to understory herbs, soil nutrients and microbial alterations.},
journal = {Journal of environmental management},
volume = {407},
number = {},
pages = {129886},
doi = {10.1016/j.jenvman.2026.129886},
pmid = {42102689},
issn = {1095-8630},
abstract = {Enhancing stable soil organic carbon (SOC) storage is vital for climate change mitigation. This study challenges the tree-centric paradigm in forest carbon management by investigating the relative roles of trees and understory herbs in driving SOC sequestration in temperate forests of Northeast China. Analyzing 720 soil samples from a 7.2 ha experimental forest, we measured oxidizable SOC fractions and tested the hypothesis that the understory herb layer is a primary driver of SOC accrual, mediated by soil properties and microbial communities. Results strongly supported our hypotheses. Plots with dense, tall herbs exhibited significantly higher levels of active and passive carbon fractions (increases of 7%-16%, amplified to 21%-45% when accounting for soil nutrients, physiochemistry, and water-holding capacity), whereas tree size showed no significant effect. Soil nitrogen was the strongest predictor of SOC variation. Herbs intensified the positive SOC-nitrogen relationship and were positively associated with beneficial soil conditions (e.g., near-neutral pH), contrary to the weak or negative correlations observed for trees. Structural equation modeling revealed that herbs exerted significant direct and indirect positive effects on carbon fractions, while the effects of trees were nonsignificant. Metagenomic analysis identified two contrasting microbial phyla groups: "positive-SOC" phyla (e.g., Thaumarchaeota, Planctomycetes) associated with herbs and high SOC, and "negative-SOC" phyla (e.g., Chloroflexi, Gemmatimonadetes). These findings underscore the critical, underappreciated role of the understory herb layer in SOC sequestration, mediated through soil nutrient enhancement, soil acidity, water retention, and shifts in microbial communities. Forest management strategies aiming to maximize carbon storage should prioritize herb layer conservation alongside tree layer considerations.},
}

@article {pmid42102934,
year = {2026},
author = {Chen, Y and Li, Y and Cheng, S and Ma, Y and Zhang, Y and Zhang, W and Xu, X and Liu, Z and Duan, X and Duan, H and Zhou, A and Li, X and Makinia, J},
title = {Brief aerobic pretreatment for stabilizing long-term caproate production from food waste via fungi-bacteria chain-elongating consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134810},
doi = {10.1016/j.biortech.2026.134810},
pmid = {42102934},
issn = {1873-2976},
abstract = {Recovery of medium-chain carboxylic acids (MCCA) from food waste is constrained by low efficiency and instability. This study validated a short-term aerobic pretreatment (AP) strategy to enhance fungi-bacteria synergy. In batch tests, AP (0.2 vvm) achieved optimal caproate titers of 22.32 ± 1.56 g COD/L. The pretreatment enriched ethanol-producing yeasts and lactate-producing bacteria, establishing a robust co-electron donor pool. Metagenomic analysis revealed that this synergy suppressed the competing tricarboxylic acid cycle, redirecting carbon flux towards reverse β-oxidation (RBO) pathway and providing essential precursors for Clostridium_sensu_stricto_12. In a 134-day semi-continuous operation, AP sustained high titers (17.2-22.1 g COD/L) through a specialized guild dominated by the Ruminococcaceae bacterium BL-6, avoiding the systemic performance deterioration observed in controls. Life cycle assessment (LCA) confirmed a >60% carbon footprint reduction compared to conventional routes. Short-term aerobic pretreatment effectively regulates microbial succession to stabilize low-carbon MCCA production from food waste.},
}

@article {pmid42102935,
year = {2026},
author = {Li, J and Wu, Y and Li, X and Gao, R and Chen, X and Zhang, S and Zhang, J and Zhang, L and Zhang, S and Peng, Y},
title = {Partial Denitrification-Mediated anammox Evolution in anoxic Compartments: Deciphering metabolic activity and microbial community.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134812},
doi = {10.1016/j.biortech.2026.134812},
pmid = {42102935},
issn = {1873-2976},
abstract = {The integration of partial denitrification (PD, NO3[-]→NO2[-]) with anaerobic ammonium oxidation (Anammox) in anoxic biofilm systems presents a transformative approach for enhanced nitrogen removal from municipal wastewater. Through a 7-month comparative analysis of spatially stratified anoxic zones in an anaerobic-anoxic-oxic bioreactor treating real wastewater (NH4[+]: 47.6 ± 4.7 mg N/L; COD: 154.8 ± 29.6 mg/L), this study achieved 71.8 ± 5.8% total nitrogen removal (effluent TN: 12.9 ± 3.9 mg N/L), aiming to propose optimization frameworks targeting biofilm carrier deployment in the anoxic zone. Test results showed that functional dominance partitioning emerged as a key determinant: the first anoxic zone (A1) exhibited peak anammox activity (0.034 kg N/m[3]/d) via rapid acetate-driven nitrate reduction, while the third zone (A3) sustained maximum Ca. Brocadia abundance (1.7%). Metagenomic sequencing further revealed that the highest ratio of NO3[-] reductase gene (narG) to NO2[-] reductase genes (nirS, nirK) was 2.06 in A3 compared to 1.39-1.68 in the other biofilms, indicating a stronger ability to supply NO2[-] to anammox. Carbon metabolic gene distribution revealed A1's acetate/glucose preference versus A3's endogenous metabolism dominance (elevated TCA cycle genes). This study proposes an innovative biofilm management framework for energy-efficient municipal wastewater treatment: front-positioned carriers maximize anammox nitrogen removal under moderate carbon-to-nitrogen ratios (3-5), while rear-positioned units secure anammox biomass retention during carbon surges.},
}

@article {pmid42102938,
year = {2026},
author = {Wu, Y and Yang, X and Deng, Y and Zhao, S and Wang, D and Zhang, W},
title = {Performance of microbial deodorization on anaerobically digested biosolids and odor rebound under rewetting conditions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134809},
doi = {10.1016/j.biortech.2026.134809},
pmid = {42102938},
issn = {1873-2976},
abstract = {Odor control is a critical bottleneck in the quality upgrade of anaerobically digested biosolids for land application. The efficacy of microbial deodorization on biosolids has been scarcely evaluated and the mechanisms behind remain unclear. This study applied a sensory-instrumental combined analysis approach to evaluate the deodorization efficiency of two microbial agents on biosolids and odor recurrence upon rewetting. Results show that treatment with microbial agent could reduce the odor intensity and mitigate ammonia emission, yet it failed to completely eliminate the odor. The volatile profile of biosolids is complex, including various N-, S-, O-containing organic and inorganic compounds that collectively contribute to the malodor of biosolids. Rewetting of biosolids induced a rapid odor rebound to varying degrees depending on the maturity of biosolids. Deodorization treatment enhanced the solubility, transformation of biosolids organic matter and increased the humic-like characteristics of WEOM and reshaped the bacterial community showing enrichment of functional taxa (e.g., Actinobacteriota and Chloroflexi). Metagenomic analysis revealed that the key nitrogen-cycling genes (ureC, narG) were suppressed, thereby limiting the generation of NH3 and other related odorants. These findings elucidate a mechanistic linkage between microbial dynamics and the odor generation potential of biosolids, and highlight the critical role of moisture management in governing odor generation and post-deodorization biological stability of biosolids.},
}

@article {pmid42102997,
year = {2026},
author = {Li, Y and Yu, T and Li, Z and Peng, J and Zhang, Y and Wang, Q and Xie, S},
title = {From high- to low-risk resistomes: Dynamic shifts in antibiotic resistance during biofilm development in a full-scale biological activated carbon fluidized bed.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128291},
doi = {10.1016/j.envpol.2026.128291},
pmid = {42102997},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) in drinking water bioreactor biofilms pose significant public health risks, yet existing studies focus on mature biological activated carbon (BAC) biofilms, overlooking the early colonization stage critical for ARG origin and dissemination. This gap hinders understanding of ARG dynamics and resistance mechanisms during drinking water BAC biofilm development. Using metagenomics, we first systematically investigated ARG risk dynamics in a full-scale biological activated carbon fluidized bed (BACFB)-a state-of-the-art drinking water technology-across operational days 7-187. Microbial communities and ARG profiles clustered distinctively into early (days 7-37) and late (days 82-187) stages. Upon biofilm stabilization, total ARG abundance significantly decreased (P< 0.05), with high-mobility/high-risk ARGs (sulfonamide-, florfenicol-, aminoglycoside-type) replaced by low-mobility types (rifamycin-, fosfomycin-type). These shifts were correlated with reduced abundance of Pseudomonadota (P < 0.05), increasing trends in the abundance of Bacillota and Actinomycetota (P < 0.1), and decreased abundance of mobile genetic elements, particularly plasmids (P < 0.01). Pathogenic ARGs shifted from aminoglycoside/tetracycline to rifamycin, with Bacillus thuringiensis/Streptococcus pneumoniae (rphB-carrying) as key late-stage risks. Rank I/II and emerging ARGs (mcr, tet(X)) also declined. Our findings uncover the dynamics of ARG risks during BAC biofilm development and highlight the underlying ecological drivers, providing a robust scientific basis for targeted risk mitigation in drinking water treatment systems.},
}

@article {pmid42103024,
year = {2026},
author = {Zhang, T and Li, S and Wu, Y and Leung, J and Jiang, H and Xu, Z and Ng, SC and Kwok, T},
title = {Gut microbial signatures for aging-related sarcopenia and dietary links among community-dwelling old-old adults: A metagenomic study.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {113161},
doi = {10.1016/j.exger.2026.113161},
pmid = {42103024},
issn = {1873-6815},
abstract = {BACKGROUND AND OBJECTIVES: Sarcopenia, characterized by progressive loss of muscle mass, strength and function, poses a major aging-related health challenge. While a gut-muscle axis is implicated, microbiota-sarcopenia associations in the old-old (≥80 years) remain unexplored.

METHODS: This cross-sectional analysis included 315 community-dwelling adults aged ≥80 years from a longitudinal cohort at the 20-year follow-up timepoint, of whom 180 met the inclusion criteria. Gut microbiota was profiled by shotgun metagenomic sequencing alongside sarcopenia assessment. Microbial taxa associated with sarcopenia were identified using MaAsLin2, and dietary associations were assessed by partial Spearman correlation.

RESULTS: The prevalence of sarcopenia in this old-old cohort (mean age 86.8 ± 4.3 years) was 51.7%. Sarcopenic individuals showed lower nutrition scores, reduced microbial richness and altered β-diversity (all P < 0.05). Multivariable analysis identified six differentially abundant species associated with sarcopenia (FDR < 0.10), including two positively associated (Ruthenibacterium lactatiformans and Catenibacillus scindens), and four negatively associated (Phascolarctobacterium faecium, Pyramidobacter piscolens, Lacrimispora saccharolytica and Limosilactobacillus mucosae). Random forest and LEfSe analysis validated R. lactatiformans and P. faecium as the most discriminative signatures for sarcopenia. After adjusting for obesity, these signatures remained significant (P < 0.05). These alterations were linked to functional dysregulation, including increased purine degradation and reduced biotin biosynthesis potential. R. lactatiformans abundance negatively correlated with dietary maltose intake (P < 0.05).

CONCLUSION: In old-old adults, we identified distinct gut microbiota signatures associated with sarcopenia. R. lactatiformans and P. faecium emerged as candidate features. The dietary-microbiota correlations suggest potential nutrition strategies. These findings provide a basis for exploring microbiota-based approaches in advanced aging.},
}

@article {pmid42103277,
year = {2026},
author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X},
title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.015},
pmid = {42103277},
issn = {2090-1224},
abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.

METHODS: Here, we enrolled 206 young chest pain patients (18-45 years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.

RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.

CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.},
}

@article {pmid42103708,
year = {2026},
author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J},
title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72757-2},
pmid = {42103708},
issn = {2041-1723},
support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.},
}

@article {pmid42103726,
year = {2026},
author = {Goulet, L and Plaza Oñate, F and Famechon, A and Quinquis, B and Belda, E and Prifti, E and Le Chatelier, E and Gautreau, G},
title = {CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72637-9},
pmid = {42103726},
issn = {2041-1723},
support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Metagenomic sequencing provides insights into microbial communities, but it can be compromised by technical biases, including cross-sample contamination. This phenomenon arises when microbial content is inadvertently exchanged among concurrently processed samples, distorting microbial profiles and compromising the reliability of metagenomic data and downstream analyses. Existing detection methods rely on negative controls, which are insufficiently used and do not detect cross-contamination within non-control samples. Meanwhile, strain-level bioinformatics approaches do not distinguish contamination from natural strain sharing and lack sensitivity. To fill this gap, we introduce CroCoDeEL, a decision-support tool for detecting and quantifying cross-sample contamination. Leveraging linear modeling and a pre-trained supervised model, CroCoDeEL identifies specific contamination patterns in species abundance profiles. It requires no negative controls or prior knowledge of sample processing positions, offering improved accuracy and versatility. Benchmarks across three public datasets demonstrate that CroCoDeEL can detect contaminated samples and identify their contamination sources, even at low rates (<0.1%), provided sufficient sequencing depth. Application of CroCoDeEL to several existing studies reveals previously undetected contamination.},
}

@article {pmid42103925,
year = {2026},
author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S},
title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52250-y},
pmid = {42103925},
issn = {2045-2322},
abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.},
}

@article {pmid41866358,
year = {2026},
author = {Deepthi, M and Vadakkadath Meethal, K},
title = {Bacterially expressed recombinant TMOF induces mortality and gut microbial alterations in Aedes albopictus larvae.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41866358},
issn = {2045-2322},
abstract = {UNLABELLED: Mosquitoes, as vectors of numerous diseases, pose significant threat to human health. Aedes mosquitoes transmit diseases such as dengue, yellow fever and chikungunya, with dengue fever alone responsible for approximately 40,000 deaths and more than 96 million symptomatic cases annually. Current mosquito control methods are inadequate and results in environmental health hazards and development of resistance. Therefore, targeted control strategies are essential. In this context, we cloned and expressed the Trypsin Modulating Oostatic Factor (TMOF), a decapeptide that inhibits trypsin biosynthesis in mosquitoes by binding to a receptor. The codon-optimized gene for the TMOF peptide was synthesised and cloned in to pFN29AHis6Halo vector and expressed in Escherichia coli. The supernatant from the bacterial lysate containing recombinant TMOF peptide exhibited larvicidal activity against Aedes albopictus mosquito larvae, with an LC50 (48 h) of 242.1 ± 6.04 µg/mL. However, lysate from BL21 cells alone or recombinant peptide expressed with a single base shift in reading frame did not cause any mortality. The recombinant TMOF peptide was purified using nickel affinity chromatography and showed an LC50 of 2.13 ± 0.02 µg/mL, exhibiting 113.6 times more efficacy than the bacterial lysate supernatant. The LC90 (48 h) for bacterial lysate and affinity purified TMOF was 340.41 ± 6.04 µg/mL and 4.39 ± 0.20 µg/mL, respectively. TMOF peptide released from the recombinant protein by trypsin digestion also showed larvicidal activity. Exposure of larvae to TMOF fusion protein resulted in inhibition of trypsin biosynthesis in-vivo. Metagenomic analysis of the gut microbiota from TMOF-treated larvae resulted in reduction in abundance of bacteria belonging to Pseudomonadota and Bacillota compared to that of untreated larvae. Recombinant TMOF is also effective against Culex mosquito larvae, but shows no effects on non-target organisms such as Drosophila melanogaster, Luprops tristis, and Aplocheilus lineatus. Thus, the use of TMOF expressed in E. coli offers a promising eco-friendly method of mosquito control. (Patent number: 554267).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41440-3.},
}

@article {pmid41902972,
year = {2026},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S},
title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41902972},
issn = {1432-184X},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Autónoma del Estado de Morelos, Secretaría de Educación Pública/ ; },
abstract = {UNLABELLED: The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus Methanonatronarchaeum, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02712-7.},
}

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48529-9},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

@article {pmid42092044,
year = {2026},
author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E},
title = {CCMRI: a classification and curated database of climate change-related microbiome studies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51914-z},
pmid = {42092044},
issn = {2045-2322},
support = {2772//Hellenic Foundation for Research and Innovation/ ; },
abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.},
}

@article {pmid42092708,
year = {2026},
author = {Ye, Y and Miao, H and Fang, W and Ni, J and Yang, K and Gu, P and Ren, X and Zhang, Z},
title = {Deciphering dual effects of humic substrates on anaerobic ammonium oxidation: from metabolic facilitation to systemic nitrogen flux interference.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134791},
doi = {10.1016/j.biortech.2026.134791},
pmid = {42092708},
issn = {1873-2976},
abstract = {Anaerobic Ammonium Oxidation (Anammox) is a promising strategy for nitrogen removal from landfill leachate due to its energy efficiency and independence from external carbon sources. However, continuous changes in recalcitrant organic compounds (i.e., fulvic acid (FA) and humic acid (HA)) at different landfill stages have potential effect on stability of anammox process. The present study systematically investigated the successive change of FA/HA concentrations and ratio that induced by different landfill age on anammox process in a laboratory-scale moving bed biofilm reactor operated over 200 days. Results showed a distinct dual-effect transition of FA and HA on the anammox process. 50-100 mg/L FA significantly improved nitrogen removal, achieving a peak total nitrogen removal efficiency (TNRE) of 91%. In contrast, the introduction of HA (100-200 mg/L) triggered a decline in TNRE to 80% and caused substantial nitrate (NO3[-]-N) accumulation. Microbial analysis revealed that FA-driven carbon abundance stimulated Candidatus Kuenenia and DNRA-functional Paracoccus and Bacillus, whereas HA suppressed DNRA bacteria in favor of nitrification. Metagenomic analysis showed that the electron shuttle and carbon source characteristics of FA enriched the relative abundance of energy metabolism genes (i.e., F-type ATPase) and quorum sensing genes (i.e., lamB), accelerating the anammox and denitrification process. However, HA interfered with the nitrogen metabolic flux via suppressing denitrification process (i.e., napA/B and nirS) and promoting nitrification genes (i.e., amoA and nxrA/B), leading to the accumulation of NO3[-]-N. These findings provide a mechanistic basis for optimizing anammox processes under varying humic substance conditions in landfill leachate treatment.},
}

@article {pmid42092716,
year = {2026},
author = {Chai, Z and Chen, H and Cui, J and Song, C and Zheng, Y and Li, Y and Gao, T and Zheng, M},
title = {Micromolar chlorate sensitivity of wastewater-associated comammox Nitrospira: Endogenous toxification mechanism and implications for nitrification management.},
journal = {Bioresource technology},
volume = {454},
number = {},
pages = {134789},
doi = {10.1016/j.biortech.2026.134789},
pmid = {42092716},
issn = {1873-2976},
abstract = {Chlorate (ClO3[-]) is widely employed as a specific inhibitor of nitrite-oxidizing bacteria (NOB) to differentiate the contributions of ammonia-oxidizing microorganisms (AOMs). However, the discovery of completed ammonia oxidizing (comammox) Nitrospira, which performs both ammonia and nitrite oxidation, challenges the assumed specificity of chlorate, raising the question of whether it also inadvertently inhibits the ammonia oxidation activity of comammox Nitrospira, potentially leading to an underestimation of total ammonia oxidation activity in mixed communities. This study investigates the inhibitory kinetics and mechanisms of chlorate on wastewater-associated comammox Nitrospira. Batch assays revealed that comammox ammonia oxidation was hypersensitive to chlorate, with a half-maximal inhibitory concentration (IC50) of 9.11 µM, orders of magnitude lower than canonical NOB inhibition levels. Metabolic assays showed that 10 μM chlorate reduced ammonia oxidation activity to 49.1% during exposure, with recovery requiring multiple cultivation cycles. Integrated metagenomic and meta-transcriptomic analyses uncovered an endogenous toxification mechanism: chlorate is reduced by nitrite oxidoreductase (NXR) to cytotoxic chlorite, which triggers the upregulation of chlorite dismutase (CLD) and reactive chlorine species (RCS) defense genes, ultimately leading to metabolic arrest. This study confirms the inhibitory effect of chlorate on comammox Nitrospira and deciphers its RCS-mediated mechanism, emphasizing the need for caution when using chlorate-based assays to assess ammonia oxidation activity and providing a theoretical basis for selectively suppressing comammox Nitrospira in WWTPs.},
}

@article {pmid42092717,
year = {2026},
author = {Fu, D and Ma, H and Zhang, J and Wang, H and Wu, Y and Ge, L and Fan, C and Wu, S and Zhang, S and Gao, H and Chen, Z},
title = {Interplay of quorum-sensing signals (homoserine lactone/penicillic acid) and nitrate in regulating microbial processes: As(III) immobilization, CH4 and N2O emission in constructed wetlands.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134788},
doi = {10.1016/j.biortech.2026.134788},
pmid = {42092717},
issn = {1873-2976},
abstract = {The concurrent mitigation of arsenic (As) pollution and greenhouse gas (GHG) emissions in constructed wetlands represents a significant challenge, largely due to the complex interactions within microbial-driven elemental cycles. This study investigated the regulatory roles of distinct quorum-sensing (QS) signals, i.e., C4-homoserine lactone (C4-HSL, a promoter) and penicillic acid (PA, a quencher), in concert with nitrate on the microbial-mediated transformation of As and GHGs (CH4 and N2O) in flooded paddy soil microcosms. The results revealed that the nitrate + C4-HSL treatment concurrently enhanced As(III) immobilization (increased by 8%) while suppressing CH4 and N2O emissions (by 7% and 56%) over a 24-day incubation period, compared to nitrate alone. Conversely, the nitrate + PA treatment inhibited As(III) oxidation (∼17.6 µM residual As(III) leaching) and promoted the accumulation of GHGs (increasing CH4 and N2O emissions by 8% and 77%). Mechanistically, C4-HSL activated the complete QS signaling network under nitrate amendment. This activation led to the enrichment of key functional microbial consortia (e.g., Pseudogulbenkiania, Streptomyces and Alicyclobacillus), an increase in relative abundance of critical metabolic genes (e.g., aox, pmo, nosZ, cpaF, tadA and cco), stimulated the secretion of protein-rich extracellular polymeric substances, and enhanced overall electron transfer system activity. These coordinated changes fostered coupled biogeochemical processes such as Fe(II)/Mn(II)-coupled denitrification and denitrifying AOM. In contrast, PA disrupted native QS communication, suppressed the aforementioned functional microbial groups and altered biofilm composition. Overall, the application of specific QS signals with nitrate exhibits the potential to directionally steer microbial community function, thereby highlighting a promising microbial-level strategy for the co-management of As and GHGs in engineered wetland systems.},
}

@article {pmid42092753,
year = {2026},
author = {Palanisamy, M and Babalola, OO and Ramalingam, S},
title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42092753},
issn = {2730-6844},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; },
abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.

DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.},
}

*Salvia officinalis/microbiology
*Plant Leaves/microbiology
*Metagenomics
*Endophytes/genetics/classification
*Microbiota
*Metagenome
Bacteria/genetics/classification
Fungi/genetics

@article {pmid42093069,
year = {2026},
author = {Yuan, J and Li, J and Jin, L and Ye, J and Zhang, Z},
title = {Human herpesvirus-6B infection leading to hemophagocytic lymphohistiocytosis in an adult: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-026-06071-2},
pmid = {42093069},
issn = {1752-1947},
abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) secondary to human herpesvirus-6B (HHV-6B) infection is rare in immunocompetent adults.

CASE PRESENTATION: We report the case of a 43-year-old East Asian (Chinese) woman who developed HLH, presenting with persistent fever, jaundice, and cytopenias. Metagenomic next-generation sequencing (mNGS) identified HHV-6B in both peripheral blood and liver tissue, thereby establishing the etiologic diagnosis. Prompt initiation of antiviral therapy with ganciclovir, combined with corticosteroids and intravenous immunoglobulin, resulted in rapid clinical remission.

CONCLUSIONS: This case highlights the critical importance of early pathogen identification using mNGS and timely immunomodulatory treatment for improving outcomes in adult patients with virus-associated HLH.},
}

@article {pmid42093272,
year = {2026},
author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q},
title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0652},
pmid = {42093272},
issn = {2095-3941},
support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; },
abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.

METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.

RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.

CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.},
}

@article {pmid42093327,
year = {2026},
author = {Wang, S and Li, S and Lyu, H and Zhi, W and Dang, Z and Guo, R and Zhu, X and Ji, G},
title = {Quantifying the Contribution of Cryptic Sulfide-Driven Autotrophic Denitrification to N2O Production in a Seasonally Hypoxic River-Reservoir System.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c03313},
pmid = {42093327},
issn = {1520-5851},
abstract = {Sulfur-autotrophic denitrification (S-ADN) has been frequently reported in inland waters, yet its quantitative contribution to nitrous oxide (N2O) productions remains poorly constrained. By combining field sampling, enrichment cultures, stable isotopes, and metagenomic analysis, we quantified S-ADN-derived N2O productions in an oligotrophic river-reservoir system and validated the universality of our approach across diverse aquatic ecosystems. A Thiobacillus-dominated S-ADN enrichment culture was successfully established over 218 days of continuous supplementation with reduced sulfur compounds, yielding critical isotopic signatures for source partitioning (δ[15]N[Bulk], average N isotopic composition; δ[18]O; and δ[15]N[SP], site preference). Then, the multi-isotope Bayesian model revealed that S-ADN (14.8%) and nitrifier denitrification (NDN, 21.1%) rapidly occupied the ecological niche of heterotrophic denitrification (HDN, 8.6%) to total microbial N2O sources under organic carbon-limited conditions. The cryptic sulfur cycle supplies a considerable pool of electron donors for S-ADN under low-sulfide conditions. Autotrophic denitrifiers (e.g., Thiobacillus, Sulfuritalea) exhibited significant synergistic interactions with ammonia-oxidizing archaea (AOA, Nitrosarchaeum), while ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira) jointly completed nitrification─with Nitrosomonas further competing for nitrite to drive NDN. This study advances the quantitative assessment of S-ADN's role in N2O production and provides novel insights into microbial community interactions in oligotrophic aquatic systems.},
}

@article {pmid42093770,
year = {2026},
author = {Niu, S and Guo, L and Li, Z and Liu, Y and Zhao, L},
title = {Clinical utility of metagenomic next-generation sequencing in the diagnosis of severe influenza complicated by invasive pulmonary aspergillosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1746504},
pmid = {42093770},
issn = {2235-2988},
mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/complications ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Influenza, Human/complications/diagnosis ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Mannans/blood ; Galactose/analogs & derivatives ; Aged ; ROC Curve ; Adult ; China ; },
abstract = {OBJECTIVE: The incidence and mortality of severe influenza complicated by invasive pulmonary aspergillosis (IPA) have risen markedly in recent years. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) for detecting IPA in patients with severe influenza.

METHODS: Severe influenza patients with suspected of having IPA admitted to Xinxiang Central Hospital, Henan Province, China, from March 2020 to September 2025 were retrospectively enrolled. Bronchoalveolar lavage fluid (BALF) and blood were collected for fungal culture, galactomannan (GM) assay, and mNGS. Final classification into IPA and non-IPA groups was based on composite clinical and microbiological criteria. Sensitivity, specificity, and receiver operating characteristic curves were used to compare the diagnostic performance of the three methods.

RESULTS: Comparison with traditional fungal culture and GM testing, mNGS provided significantly faster results. Among 189 patients suspected of severe influenza-associated IPA, mNGS demonstrated a sensitivity of 72.1% and a specificity of 80.2%. Its sensitivity was higher than that of fungal culture (28.6%), serum GM testing (37.6%), and BALF GM testing (44.1%); however, its specificity was slightly lower than that of fungal culture (89.5%), serum GM testing (84.3%), and BALF GM testing (81.3%). The area under the ROC curve (AUC) for mNGS was 0.76, which is higher than that for BALF GM testing (0.63), serum GM testing (0.61), and fungal culture (0.59). The combined diagnostic approach yielded an AUC of 0.83.

CONCLUSION: mNGS offers a rapid, sensitive and accurate solution for invasive pulmonary aspergillosis in severe influenza patients. It outperforms conventional fungal culture and galactomannan assays. Integrating mNGS with traditional diagnostic methods could substantially improve early detection and overall yield of IPA.},
}

Humans
*Invasive Pulmonary Aspergillosis/diagnosis/microbiology/complications
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Influenza, Human/complications/diagnosis
Retrospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity
*Metagenomics/methods
Mannans/blood
Galactose/analogs & derivatives
Aged
ROC Curve
Adult
China

@article {pmid42094492,
year = {2026},
author = {Shan, Y and Pucci, N and Berns, C and Hoogendijk, R and Beijnvoort, M and Li, S and Sánchez-Cano, A and Kramer, G and Du, W and Mende, DR and Jan van Dijk, AD and Wortel, M and Zhang, J},
title = {A bifidobacterial enzyme orchestrates ecology and function of infant gut bacterial community.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.718440},
pmid = {42094492},
issn = {2692-8205},
abstract = {Human milk oligosaccharides (HMOs) are abundant and structurally diverse glycans that shape the development of infant gut microbiota. Yet, how individual HMOs and bacterial genes drive the community assembly remain elusive. Here, we reconstructed an eight-member infant Bacterial Community (iBaCo) from representing dominant taxa in human infant feces. When individual HMOs were the sole carbohydrate source, they showed deterministic effects on the iBaCo composition and metabolic output. Notably, the tetramer HMO lacto-N-tetraose (LNT), in spite of its identical monomer composition as lacto-N-neotetraose (LNnT), showed a strong effect on maintaining Bifidobacterium breve abundance in iBaCo, whereas LNnT did not. Monoculture growth profiling, proteomics, enzymatic kinetic assay, and molecular docking revealed that β -galactosidase D4BMY8 and the relevant downstream pathways are induced by LNT and that D4BMY8 has substrate preference on LNT over LNnT, enabling a faster growth of Bi. breve and accumulation of acetate and lactate in LNT compared to LNnT. Metabolic flux analysis indicated that the substrate-preference of β -galactosidase D4BMY8 drives the skewed energy cost toward lactate/acetate metabolic output. Finally, the D4BMY8-encoding gene lacZ5 is widely spread in all isolated Bi. breve genomes, but divergently distributed in infant metagenome-assembled Bi. breve genomes. Together, we demonstrated that a single enzyme-substrate interaction could orchestrate the composition and metabolic function of an infant bacterial community, which may contribute to the assembly of dynamic infant gut microbiota. Our integrative approach provides a mechanistic framework for understanding the interaction between diet, microbial community, and infant gut health.},
}

@article {pmid42094499,
year = {2026},
author = {Majidian, S and Chalco, A and Zheng, X and Webby, RJ and Bowman, AS and Poulson, RL and Nemeth, NM and Sedlazeck, FJ and Agustinho, DP},
title = {Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.29.721707},
pmid = {42094499},
issn = {2692-8205},
abstract = {Phylogenomic surveillance is limited not by sequencing throughput, but by the difficulty of converting heterogeneous raw data into reliable evolutionary inference, particularly for low-titer and contaminated viral field samples. Here we present Omni2Tree, an assembly-free framework that reconstructs viral phylogenies directly from raw sequencing reads and generates easily shareable interactive reports and genome-wide entropy profiles to identify diversification. In H5N1 benchmark analyses, Omni2Tree maintained accurate placement and topological stability even under low coverage, unlike assembly or reference based methods. Omni2Tree generated an annotated phylogeny for 64-sample H5N1 field surveillance dataset from the eastern USA in under 3 hours. Omni2Tree recovered known phylogenetic structure and key variability insights across 1,328 hepatitis C virus and 707 human cytomegalovirus datasets, and resolved co-infecting respiratory viruses in clinical metagenomic samples. By enabling direct analysis from raw reads, Omni2Tree supports faster, more portable, and more decentralized phylogenomic surveillance across outbreak, clinical, and resource-limited settings.},
}

@article {pmid42094537,
year = {2026},
author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J},
title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.29.721577},
pmid = {42094537},
issn = {2692-8205},
abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.},
}

@article {pmid42094770,
year = {2026},
author = {Tekere, M and Kalu, CM},
title = {Relative abundance of heavy metal resistance genes of three drinking water treatment plants unveiled through shotgun metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822428},
pmid = {42094770},
issn = {1664-302X},
abstract = {INTRODUCTION: The occurrence and abundance of heavy metal resistance genes (HMRGs) in drinking water treatment plants (DWTPs) and the stages at which they occur are a global challenge due to the risk of consuming contaminated water.

METHODS: The present study identified HMRGs associated with raw water sources, treatment stages (disinfection and filtration), final treated water, and produced sludge in three DWTPs across three provinces (Gauteng, Limpopo, and Mpumalanga) in South Africa, using a shotgun metagenomic approach.

RESULTS: In total, five classes of heavy metals (copper, arsenic, mercury, chromate, silver) and 50 resistance genes were identified across the three DWTPs. Most of the genes were obtained from the disinfection stages of the DWTPs.

DISCUSSION: This genomic dataset provides valuable information on the impact of disinfection stages on the relative abundance of HMRGs in drinking water treatment processes. Additionally, the transfer of genes into the final treated water consumed by the populace is a significant human health concern.},
}

@article {pmid42094845,
year = {2026},
author = {Olson, N and Thystrup, CAN and Smith, F and Mucache, H and Fafetine, J and Saíde, J and Mondlane-Milisse, A and Brito, DRA and Jesser, KJ and Brown, J and Hald, T and Freeman, M and Levy, K and Nadimpalli, ML},
title = {Strain-level analyses of public sequencing data to characterize Escherichia coli strain sharing between children and chickens in Mozambique.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101429},
pmid = {42094845},
issn = {2352-7714},
abstract = {Escherichia coli causes diarrhea in children and can be transmitted from animals. Characterizing the scope of human-animal strain sharing is crucial for assessing potential health risks; however, conventional methods that assess single isolates are resource-intensive and lack sensitivity. Strain-level metagenomic analyses can reveal within-host strain diversity and between-host strain sharing. In this study, we aimed to determine whether E. coli strains we previously detected among chickens in Mozambique might pose meaningful risks to local children. To achieve this, we compared E. coli strains in chicken metagenomes to E. coli strains reported by others in children's stool in the same community during the same period (2014-2022) using the Strain Genome Explorer toolkit. At least one E. coli strain was shared between 37/23,937 (0.15%) chicken-human pairs. This approach represents a novel method for assessing the scope of bacterial strain sharing between human and animal populations within a community.},
}

@article {pmid42094906,
year = {2026},
author = {Zeng, Q and Xie, L and Dai, W and Xu, F and Dai, Y},
title = {Extracorporeal Membrane Oxygenation Haemoperfusion for Leptospirosis Pulmonary Hemorrhagic Disease: Report of 1 Case.},
journal = {Respirology case reports},
volume = {14},
number = {},
pages = {e70565},
pmid = {42094906},
issn = {2051-3380},
abstract = {Severe pulmonary leptospirosis (SPFL), characterized by diffuse alveolar haemorrhage (DAH) and acute respiratory distress syndrome (ARDS), carries a high mortality, often due to diagnostic delays and complex management. We report a case of a 42-year-old male with outdoor occupational exposure who presented with fever and hemoptysis, rapidly progressing to severe respiratory failure and thrombocytopenia. Chest imaging confirmed DAH/ARDS. For refractory hypoxemia, veno-venous extracorporeal membrane oxygenation (VV-ECMO) was initiated without systemic anticoagulation due to active pulmonary haemorrhage. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid rapidly identified Leptospira interrogans, enabling targeted antimicrobial therapy alongside multidisciplinary support. The patient gradually improved, was successfully weaned from ECMO and ventilator support, and was discharged without residual organ dysfunction. This case demonstrates that early application of anticoagulation-free VV-ECMO combined with mNGS-based rapid diagnosis and multidisciplinary care can improve outcomes in SPFL, highlighting the importance of considering this diagnosis in febrile patients with DAH and environmental exposure.},
}

@article {pmid42094994,
year = {2026},
author = {Vasselin, A and Scavazzin, V and Talarmin, JP and Lamoureux, C and Pérès, M and Le Bars, H and Fangous, MS and Beauruelle, C and Ansart, S and Héry-Arnaud, G},
title = {Granulicatella adiacens infective endocarditis in pregnancy: diagnostic contribution of metagenomic sequencing-a case report.},
journal = {ASM case reports},
volume = {2},
number = {3},
pages = {},
pmid = {42094994},
issn = {2996-2684},
abstract = {BACKGROUND: Granulicatella adiacens is a fastidious Gram-positive coccus and is a rare but recognized cause of infective endocarditis. Infective endocarditis during pregnancy is uncommon but carries substantial maternal and fetal risk. Plasma metagenomic analysis of microbial cell-free DNA has emerged as a complementary diagnostic tool in culture-negative infections.

CASE SUMMARY: We describe a 35-year-old pregnant woman with known mitral valve prolapse who presented at 21 weeks of gestation with an acute ischemic stroke. Initial etiological work-up, including transesophageal echocardiography, was unremarkable. Ten days later, she re-presented with left-arm pain and neurologic symptoms. Repeat echocardiography revealed multiple mitral vegetations compatible with infective endocarditis. Despite multiple sets of prolonged-incubation blood cultures and extensive serological testing, all microbiological investigations remained negative. Empirical intravenous ceftriaxone was initiated based on the working diagnosis of HACEK endocarditis. A plasma metagenomic cell-free DNA test ultimately identified G. adiacens, which was suspected to have entered the body through dental treatment received a few weeks earlier. Ceftriaxone was continued given the favorable clinical response, with vegetation resolution, troponin decline, and uncomplicated term delivery of a healthy infant.

CONCLUSION: This case illustrates the diagnostic challenges of culture-negative infective endocarditis in pregnancy and underscores the value of plasma microbial cell-free DNA sequencing as a complementary tool when conventional methods fail. It also emphasizes the need to repeat echocardiography when clinical suspicion remains high and raises the question of antibiotic prophylaxis for high-risk dental procedures in pregnant women with underlying valvular heart disease.},
}

@article {pmid42095002,
year = {2026},
author = {de Araújo Butarelli, AC and Peres, FV and Pellizari, VH and Bendia, AG},
title = {Hot life in Antarctica: a novel metabolically versatile Pyrodictiaceae genus thriving at a volcanic-cryosphere-marine interface.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag080},
pmid = {42095002},
issn = {2730-6151},
abstract = {Deception Island fumaroles in Antarctica represent rare environments where extreme heat intersects with cryospheric and marine conditions, creating remarkable environmental gradients. From the near-boiling sediments, we reconstructed a high-quality metagenome-assembled genome affiliated with the Pyrodictiaceae. Phylogenomic analyses revealed that this genome, proposed to represent Ca. Pyroantarcticum pellizari, forms a distinct lineage separated from known genera in the family. Functional annotation uncovered a versatile metabolic repertoire, including pathways for sulfur and nitrogen cycling, peptide and amino acid transport, and mixotrophic energy conservation. Stress-response systems such as reverse gyrase, thermosome, and small heat-shock proteins were complemented by lineage-specific genes related to membrane stability, metal detoxification, and Pyrodictiaceae-specific cannulae. These adaptations likely support survival under sharp temperature gradients, hydrogen sulfide emissions, and high metal concentrations at the volcanic-cryosphere-marine interface. Our findings expand the phylogenetic and ecological scope of Pyrodictiaceae, highlighting Antarctic marine volcanoes as unique refuges for hyperthermophiles and as valuable models for investigating life's habitability under extreme temperatures.},
}

@article {pmid42095017,
year = {2026},
author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X},
title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1768985},
pmid = {42095017},
issn = {2297-1769},
abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.},
}

@article {pmid42095439,
year = {2026},
author = {Williams, TGS and Umpleby, H and Fisayo, T and Rampling, T and Houlihan, CF},
title = {Clinician perspectives on patient consent for metagenomic next-generation sequencing of blood samples for the diagnosis of infection in clinical practice.},
journal = {Journal of medical microbiology},
volume = {75},
number = {5},
pages = {},
doi = {10.1099/jmm.0.002164},
pmid = {42095439},
issn = {1473-5644},
mesh = {Humans ; *Metagenomics ; *High-Throughput Nucleotide Sequencing ; *Informed Consent ; Surveys and Questionnaires ; United Kingdom ; *Communicable Diseases/diagnosis/blood ; },
abstract = {Introduction. Pathogen diagnostics based on metagenomic next-generation sequencing (mNGS) are now in clinical use. mNGS can identify unexpected pathogens or organisms of unclear significance and generate human genomic data. Given these features, it has been suggested that patients should provide specific informed consent for mNGS.Gap Statement. There is limited published guidance on the appropriate form of consent for clinical infectious disease mNGS to guide clinical implementation and current practice varies.Aim. To inform a pilot of mNGS for returning travellers delivered at a reference laboratory for use by specialist infection clinicians, we sought clinician perspectives on the form of consent required for mNGS and the information patients require to make an informed decision.Methodology. A national survey of infection specialists provided clinicians' opinions.Results. If consent for an infection screen including blood-borne virus testing had already been provided, only a minority of surveyed clinicians (22 out of 124, 18%) thought that mNGS should be discussed before it was performed on pre-existing blood samples.Conclusion. Most of the UK infection clinicians surveyed did not think that mNGS of blood from returning travellers required discussion before being performed when patients had already consented for infection diagnostics to find the cause of their illness. However, clinicians felt that patients should be aware of the potential for additional testing and wanted information on mNGS to be readily available.With the increasing availability of clinical infectious disease mNGS, engagement of non-specialist clinicians and patients is required to confirm the generalizability of these perspectives. The model of consent used for clinical infectious disease mNGS should be ethically adequate in addition to being acceptable to patients and clinicians.},
}

Humans
*Metagenomics
*High-Throughput Nucleotide Sequencing
*Informed Consent
Surveys and Questionnaires
United Kingdom
*Communicable Diseases/diagnosis/blood

@article {pmid42095681,
year = {2026},
author = {Muthamilselvi Sivabalan, SK and Vijayakumar, V and Sengupta, P and Palmal, S and Krishnamurthi, S and Kumar Singh, N and Kyrpides, NC and Raman, K and Venkateswaran, K},
title = {Unveiling hidden microbial diversity in Mars 2020 mission assembly cleanrooms with molecular insights into the persistence and perseverance of novel species defying metagenome sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0127325},
doi = {10.1128/spectrum.01273-25},
pmid = {42095681},
issn = {2165-0497},
abstract = {NASA cleanrooms, which are critical for assembling space mission components, are maintained under stringent decontamination protocols to minimize biological contamination. These environments are characterized by nutrient-poor and oligotrophic conditions, leading to low microbial loads. Despite extensive cleaning, oligotrophs capable of surviving in such conditions continue to persist, often remaining undetected due to their low abundance, resistance to environmental stresses, and difficulties in biomolecule extraction. Even with shotgun metagenome sequencing technologies, these microbes may go undetected or be underrepresented due to their robust cell walls and the absence of reference genomes in publicly available databases. Over a 6-month study of Mars 2020 mission cleanrooms, 182 bacterial strains belonging to 19 families were identified using a whole-genome sequencing (WGS) approach. Among these, 14 novel Gram-positive species were discovered, including eight spore formers. Though the novel species comprised only 0.001% of the sequencing data, their successful cultivation allowed for functional characterization. Through WGS data mining, genomic traits associated with resilience in extreme conditions were revealed. These species were found to be involved in nitrogen cycling, carbohydrate metabolism, and radiation resistance, traits essential for survival in extreme environments. Furthermore, 12 biosynthetic gene clusters were identified, including those linked to ectoine and [Formula: see text]-poly-L-lysine production, suggesting potential biotechnological applications. These findings highlight the hidden microbial diversity within cleanrooms and emphasize the necessity of advanced detection strategies. A better understanding of these microbes will provide insights into extremophiles with applications in biotechnology, medical research, and life support systems for future space exploration missions.IMPORTANCEDespite strict decontamination protocols, NASA cleanrooms harbor low-biomass microbial communities adapted to nutrient-poor environments. These oligotrophic microbes often go undetected in shotgun metagenomics methods due to their low abundance, resistance to lysis, and lack of reference genomes. Standard shotgun metagenome sequencing methods fail to retrieve them, as dominant microbial DNA overshadows rare species. Over 6 months of monitoring Mars 2020 mission cleanrooms, 182 bacterial strains from 19 families were identified, including 14 novel Gram-positive species, 8 of which were spore formers. Though present at 0.001% abundance in sequencing data, we successfully cultured them, enabling functional characterization. These microbes exhibited roles in nitrogen cycling, carbohydrate metabolism, and radiation resistance, with 12 biosynthetic gene clusters linked to ectoine and [Formula: see text]-poly-L-lysine production. These findings highlight the previously underestimated microbial diversity in cleanrooms and emphasize the need for advanced detection strategies to explore extremophiles with applications in biotechnology and space exploration.},
}

@article {pmid42096004,
year = {2026},
author = {Huang, YJ and Shen, ZQ and Hu, DP and Huang, YY and Chen, GY and Lin, Y and Hu, BM and Yuan, XX and Deng, GP and Li, X},
title = {Multi-Omics Analysis Reveals Inflammatory Activation and Maternal-Fetal Interface Remodeling in Spontaneous Abortion.},
journal = {Current medical science},
volume = {},
number = {},
pages = {},
pmid = {42096004},
issn = {2523-899X},
abstract = {BACKGROUND: Spontaneous abortion (SA) is a common adverse outcome of early pregnancy, yet its underlying pathophysiological mechanisms remain incompletely understood. Accumulating evidence suggests that dysregulated inflammatory responses at the maternal-fetal interface play a critical role in pregnancy loss. However, the potential associations between alterations in gut microbiota, metabolic disturbances, and localized decidual inflammation in patients with SA have not been systematically characterized.

METHODS: Women with SA (n = 30) and those with normal early pregnancy (NP, n = 28) were enrolled in this study. Proinflammatory cytokines were quantified in decidual tissue homogenates, and histopathological and molecular analyses were performed to evaluate inflammatory activation at the maternal-fetal interface. The gut microbiota composition was profiled using shotgun metagenomic sequencing, while metabolic alterations in the feces were assessed by untargeted metabolomics. Integrated multi-omics analyses were conducted to explore associations among gut microbial dysbiosis, metabolic perturbations, decidual inflammatory signaling, and molecular alterations.

RESULTS: Compared with those from the NP group, the decidual tissues from the SA group exhibited significantly elevated levels of IL-1β and TNF-α (1.49-fold and 1.51-fold, both P < 0.0001), accompanied by pronounced histopathological abnormalities. Enhanced activation of the NF-κB signaling pathway was observed at the maternal-fetal interface in SA patients. Metagenomic analyses revealed distinct differences in the gut microbiota composition and community structure between the two groups, with differentially abundant bacterial taxa identified (LDA score > 2.0). Consistent with these findings, fecal metabolomic profiling clearly revealed differences between SA and NP patients, with differentially abundant metabolites (VIP > 1.0, adjusted P < 0.05) predominantly enriched in lipid metabolism, amino acid metabolism, and immune-related pathways. In addition, the expression of leucine-rich repeat-containing G protein-coupled receptor 6 was significantly upregulated (P < 0.0001) in the decidual tissue of SA patients.

CONCLUSIONS: These findings indicate that SA is associated with localized inflammatory activation at the maternal-fetal interface, dysregulation of decidual molecular activity, gut microbiota dysbiosis, and metabolic perturbations. Integrated multi-omics analyses suggest potential interactions among these factors that may be linked to decidual dysfunction during early pregnancy, providing new insights into the complex pathophysiology of SA.},
}

@article {pmid42096148,
year = {2026},
author = {Zhu, D and Wang, S and Sun, X and Britton, RA},
title = {CRISPR-AsCas12a and dAsCas12a-Mediated Gene Knockout and Knockdown in Clostridioides difficile.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3046},
number = {},
pages = {47-55},
pmid = {42096148},
issn = {1940-6029},
mesh = {*Clostridioides difficile/genetics ; *CRISPR-Cas Systems/genetics ; Gene Editing/methods ; *Gene Knockout Techniques/methods ; *Gene Knockdown Techniques/methods ; Bacterial Proteins/genetics ; CRISPR-Associated Proteins/genetics ; },
abstract = {Clostridioides difficile (C. difficile) is a leading cause of antibiotic-associated diarrhea and severe colitis, yet its genetic manipulation has long been constrained by low DNA transfer efficiency and limited recombination systems. Recent advances in CRISPR-based technologies have revolutionized the genetic toolkit for this pathogen, enabling precise genome editing and transcriptional regulation. Among CRISPR nucleases, Cas12a offers distinct advantages over Cas9 for bacterial applications, including a smaller size, T-rich PAM recognition, single-crRNA requirement, and reduced toxicity, which enhances conjugation efficiency in genetically recalcitrant organisms. AsCas12a-based platforms have enabled large fragment deletions, multiplex editing, and rapid generation of marker-free mutants in C. difficile. Complementing these nuclease-active systems, nuclease-deactivated variants (dCas9 or dAsCas12a) support CRISPR interference (CRISPRi)-a reversible, tunable approach for transcriptional repression without altering genomic sequences. Compared to traditional mutagenesis, CRISPRi greatly accelerates functional genomics by enabling high-throughput screening and drug target discovery. Together, our lab has independently developed CRISPR-AsCas12a-mediated genome editing and dAsCas12a-based CRISPRi tools, providing complementary strategies to overcome longstanding genetic barriers in C. difficile. These tools open new avenues for system-level interrogation of virulence, antibiotic resistance, and host-pathogen interactions.},
}

*Clostridioides difficile/genetics
*CRISPR-Cas Systems/genetics
Gene Editing/methods
*Gene Knockout Techniques/methods
*Gene Knockdown Techniques/methods
Bacterial Proteins/genetics
CRISPR-Associated Proteins/genetics

@article {pmid42096157,
year = {2026},
author = {Pizzini, J and McCullough, HC and Sidner, BS and Britton, RA and Piepenbrink, KH and Auchtung, JM},
title = {An In Vitro Model for Studying Interactions Between Gastrointestinal Microbes and Planktonic and Sessile Clostridioides difficile Populations.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3046},
number = {},
pages = {171-187},
pmid = {42096157},
issn = {1940-6029},
mesh = {*Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism/chemistry ; Bacterial Adhesion ; Bioreactors/microbiology ; *Plankton ; Intestinal Mucosa/microbiology ; Hydrogels/chemistry ; Biofilms/growth & development ; },
abstract = {Interactions between Clostridioides difficile, the gastrointestinal microbiota, and the host mucosal epithelium play important roles in governing the ability of C. difficile to colonize and cause disease. Several in vitro tools have been developed to investigate C. difficile physiology in the presence of microbial communities. In this chapter, we describe a model for studying C. difficile-mucin interactions in the presence of a complex microbiota using continuous flow bioreactors. This model can facilitate mechanistic studies of specific microbes and mucin structures important for C. difficile colonization, complementing findings from animal models. The approach presented here builds upon the preceding chapter's protocol for generating mucin hydrogels on glass slides and extends it to examine C. difficile adhesion to mucosal surfaces.},
}

*Clostridioides difficile/physiology
*Gastrointestinal Microbiome
Humans
Mucins/metabolism/chemistry
Bacterial Adhesion
Bioreactors/microbiology
*Plankton
Intestinal Mucosa/microbiology
Hydrogels/chemistry
Biofilms/growth & development

@article {pmid42096470,
year = {2026},
author = {Hardick, J and Anantharam, R and Lu, J and Salzberg, SL and Rothman, RE and Fenstermacher, KZJ and Pekosz, A and Onzia, A and Nakiyingi, L and Manabe, YC and Kandathil, AJ},
title = {Comparison of unbiased metagenomic next generation sequencing to targeted multiplex diagnostic assays for the detection of respiratory viruses.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0347750},
doi = {10.1371/journal.pone.0347750},
pmid = {42096470},
issn = {1932-6203},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Respiratory Tract Infections/virology/diagnosis ; Male ; Female ; Adult ; Nasopharynx/virology ; Middle Aged ; Multiplex Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics/isolation & purification ; *RNA Viruses/genetics/isolation & purification ; Aged ; Child, Preschool ; Adolescent ; Child ; Young Adult ; },
abstract = {OBJECTIVES: Accurate diagnosis of existing and emerging respiratory pathogens is important. We evaluated the capability of unbiased metagenomic next generation sequencing (mNGS) to identify pathogenic RNA viruses from two cohorts of nasopharyngeal (NP) swabs previously tested by commercial multiplex respiratory diagnostics.

METHODS: NP swabs (N = 100) in viral transport media (VTM) were assessed using mNGS for this study. Cohort 1 (N = 52) consisted of symptomatic individuals who tested negative for SARS-CoV-2, influenza A/B, and RSV by the Xpert Xpress CoV-2/Flu/RSV Plus multiplex respiratory virus panel and were tested by mNGS for undetected pathogens. Cohort 2 (N = 48) included symptomatic individuals who were positive (N = 26) or negative (N = 22) by the ePlex RP2 multiplex respiratory pathogen panel. Samples were positive for influenza A (N = 8), rhinovirus/enterovirus (N = 5), RSV (N = 4), adenovirus (N = 3), parainfluenza (N = 2), seasonal coronaviruses (N = 2), and human metapneumovirus (N = 1), as well as a rhinovirus/enterovirus/human metapneumovirus co-infected sample (N = 1). mNGS results were compared with ePlex RP2 findings, and symptomatic negative samples were evaluated for additional pathogen detection.

RESULTS: Cohort 1 contained 8% (4/52) viral and 19% (10/52) bacterial reads. In cohort 2, positive concordance between ePlex RP2 and mNGS was 31% (8/26). mNGS did not identify any viral reads in ePlex RP2-negative samples. However, it detected other microbial reads, such as Acanthamoeba castellanii, in 21% (10/48) of samples.

CONCLUSION: In this study, targeted multiplex amplification methods demonstrated better overall sensitivity in NPs of symptomatic respiratory individuals than mNGS. Other mNGS approaches may produce different results. This study suggests that mNGS may offer adjunctive information, including the detection of rare pathogens, which may be helpful in some clinical contexts.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Respiratory Tract Infections/virology/diagnosis
Male
Female
Adult
Nasopharynx/virology
Middle Aged
Multiplex Polymerase Chain Reaction/methods
SARS-CoV-2/genetics/isolation & purification
*RNA Viruses/genetics/isolation & purification
Aged
Child, Preschool
Adolescent
Child
Young Adult

@article {pmid42096522,
year = {2026},
author = {Zhao, D and Zhang, C and Li, M and Li, H and Su, S and Zhang, X},
title = {Characteristics of carbon-fixing microbial communities and pathways across different aquatic systems in the Tianjin Binhai region.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag112},
pmid = {42096522},
issn = {1365-2672},
abstract = {AIMS: Microbial carbon fixation is central to carbon cycling and carbon sink functioning in coastal aquatic ecosystems. Although carbon fixation pathways have been increasingly investigated across diverse aquatic environments, comparative evidence remains limited for hydrologically connected yet hydrochemically contrasting coastal groundwater and surface water systems. This study aimed to compare carbon-fixation-associated microbial communities and major carbon fixation pathways across groundwater, river water and reservoir water in the Tianjin coastal region.

METHODS AND RESULTS: We integrated metagenomic sequencing with hydrochemical analyses to characterise carbon-fixation-associated microbial communities and six representative carbon fixation pathways. Surface waters were dominated by bacteria and showed relatively stable community composition, whereas groundwater communities comprised both bacteria and archaea and displayed pronounced spatial heterogeneity. The Calvin-Benson-Bassham cycle was prevalent across all water types, and the reductive tricarboxylic acid (rTCA) cycle was also widely distributed. Groundwater showed higher contributions of the Wood-Ljungdahl pathway, the archaeal 3-hydroxypropionate/4-hydroxybutyrate and dicarboxylate/4-hydroxybutyrate cycles, together with the rTCA cycle, indicating coexisting carbon fixation strategies. Pathway abundance and module completeness further suggested differences in pathway integrity among water types. Total dissolved solids, HCO3⁻, CO32⁻ and dissolved organic carbon were key correlates of carbon fixation gene distribution.

CONCLUSIONS: Carbon-fixation-associated microbial communities, pathway distributions, and pathway integrity differed markedly between coastal groundwater and surface waters. Groundwater exhibited enhanced non-CBB cycle potentials and more diversified carbon fixation strategies, highlighting the importance of groundwater processes in evaluating carbon sequestration potential and carbon cycling in hydrochemically heterogeneous coastal aquatic systems.},
}

@article {pmid42096753,
year = {2026},
author = {Jin, B and Bai, Z and Yan, Y and He, H and Du, J and Xu, Y and Wang, L and Ji, J},
title = {Antibiotic-driven mechanisms in endogenous partial denitrification (EPD): Nitrite accumulation, microbial adaptation, functional gene responses and resistance gene proliferation.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142257},
doi = {10.1016/j.jhazmat.2026.142257},
pmid = {42096753},
issn = {1873-3336},
abstract = {The mechanisms by which antibiotics affect Endogenous Partial Denitrification (EPD) systems remain unclear. This study investigated the relationships between antibiotic type and pollutant removal, along with the underlying microbial metabolic mechanisms in an EPD system exposed to three antibiotics. The results showed that sulfadiazine (SD) and sulfamethoxazole (SMZ) exhibited higher chemical oxygen demand removal efficiency than tetracycline (TC). In the SD system, NO3[-]-N removal was 84.13%, whereas other systems achieved 97%, which was associated with a higher abundance of the n arG and nirS. Proteobacteria and Chloroflexi demonstrated strong adaptability to the antibiotics. TC inhibited the tricarboxylic acid cycle and organic matter degradation may be related to the reduced mdh. SD induced microorganisms to convert carbon sources into polyhydroxybutyrate instead of utilizing them directly, while SMZ optimized nitrogen metabolism by increasing the abundance of nirS and nirK, leading to higher NO2[-]-N accumulation in these two EPD systems. SD stress reduced the abundance of ppk2/ppx gene, inhibited the energy production and internal carbon reserve of denitrifying polyphosphate-accumulating organisms in anaerobic stage. Although the microorganisms had stronger phosphorus uptake potential by up-regulating ppk1 gene, the lack of ATP necessary to drive this process eventually led to the reduction of PO4[3] [-]-P removal ability. The abundance of resistance genes peaked in the SD system, significantly increasing the risk of antibiotic resistance. This study deciphers the metabolic mechanisms of the EPD system in response to three types of antibiotics and provides a scientific basis for its application in environments with fluctuating antibiotic stress.},
}

@article {pmid42096819,
year = {2026},
author = {Kumar, K and Dutta, P},
title = {Integration of mass spectrometry and molecular biotechnology to study bioaerosols.},
journal = {Chemosphere},
volume = {405},
number = {},
pages = {144949},
doi = {10.1016/j.chemosphere.2026.144949},
pmid = {42096819},
issn = {1879-1298},
abstract = {Conventional culture-based and microscopic approaches yield limited information about the diversity, content, and real-time behaviour of biological aerosols. In recent years, mass spectrometry (MS) and molecular biotechnology have evolved as powerful and complementary analytical methods for detecting, identifying, and characterising air biological particles. This study critically reviews recent improvements in MS-based techniques for analysing bioaerosol chemical markers, proteins, metabolites, and toxins, including MALDI-TOF MS, GC-MS, LC-MS/MS, and real-time aerosol mass spectrometry. In parallel, contemporary advances in molecular biotechnology, including as PCR-based assays, metagenomics, and MS-driven proteomics and metabolomics, are described, with a focus on atmospheric applications. Special emphasis is placed on integrated analytical workflows that combine MS with molecular techniques to improve specificity, sensitivity, and source attribution. The current issues of low biomass concentrations, sampling artefacts, data interpretation, and standardisation are discussed, and future perspectives on portable MS systems, multi-omics integration, and AI-assisted data processing are presented. This study offers a thorough analytical chemistry viewpoint on next-generation methodologies for monitoring bioaerosols and promotes the development of enhanced instruments for assessing air quality and protecting human health.},
}

@article {pmid42097292,
year = {2026},
author = {Hennecart, B and Belda, E and de Lahondès, R and Zucker, JD and Prifti, E},
title = {StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag212},
pmid = {42097292},
issn = {1367-4811},
abstract = {SUMMARY: Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. We present StrainMake, a Snakemake-based workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data. StrainMake integrates widely used tools across all major steps-quality control, assembly, binning, dereplication, taxonomic and functional annotation-while also providing non-redundant gene catalogues, community-scale metabolic models, and strain-level microdiversity metrics. The modular design enables the use of alternative tools, scalable execution on HPC systems, and full reproducibility through Snakemake and Conda.

RESULTS: Applied to the CAMI II strain-madness dataset, StrainMake   produced high-quality assemblies and metagenome-assembled genomes (MAGs), while enabling strain-resolved comparisons across samples. Hybrid assemblies improved contiguity, whereas short-read assemblies offered faster runtimes, illustrating the workflow's benchmarking capacity.

StrainMake is open source and available at https://github.com/UMMISCO/strainmake, together with comprehensive documentation. Generated data are deposited in Zenodo (doi : 10.5281/zenodo.16950162).},
}

@article {pmid42097342,
year = {2026},
author = {Yin, D and Chen, M and Chen, X and Feng, Y and Zhou, X and Guan, Y and Zhang, Y and Bai, S and Li, L and Ouyang, H and Cheng, J and Zhu, W},
title = {Integrative multi-omics reveals that Pueraria thomsonii Radix alleviates dyslipidemia by remodeling gut microbiota and regulating arachidonic acid metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121816},
doi = {10.1016/j.jep.2026.121816},
pmid = {42097342},
issn = {1872-7573},
abstract = {Pueraria thomsonii Radix (PTR, "Fen-ge") is a food-medicine herb widely used in China for metabolic complaints. Its putative lipid-modulating effects are supported by traditional practice, but the molecular basis remains incompletely understood.

AIM OF THE STUDY: To elucidate the active constituents and mechanisms by which PTR mitigates dyslipidemia.

MATERIALS AND METHODS: Chemical profiling and plasma exposure of PTR constituents were characterized by UPLC-Q-TOF-MS/MS. A high-fat-diet rat model was used to assess pharmacodynamic endpoints including serum lipid panel, hepatic histopathology, liver injury markers and inflammatory cytokines. Untargeted plasma metabolomics was performed in rats and patients; rat fecal 16S rRNA gene sequencing and hepatic transcriptomics complemented mechanism inference. Multivariate models were cross-validated and FDR-controlled; pathway and multi-omics correlation analyses integrated metabolite-microbe-gene relationships.

RESULTS: PTR significantly ameliorated dyslipidemia in high-fat diet-fed rats, as evidenced by improved serum lipid profiles, reduced ALT/AST levels, and alleviated hepatic steatosis and inflammation in histopathological examination. Integrated metabolomic analysis across rats and patients revealed that the restored metabolic pathways were primarily concentrated in arachidonic acid and unsaturated fatty acid metabolism. Gut microbiota analysis indicated that PTR remodeled microbial taxa correlated with arachidonic acid-related lipid metabolism. Meanwhile, hepatic transcriptomics data showed that differentially expressed genes were functionally enriched in biological processes such as lipid oxidation and were bioinformatically linked to the AMPK signaling pathway.

CONCLUSIONS: PTR may ameliorate dyslipidemia through coordinated modulation of the gut microbiota and arachidonic acid metabolic network. Based on integrated omics analysis, the hepatic AMPK signaling pathway may potentially be involved in this regulatory process; however, its direct mechanistic role requires further experimental validation. Future investigations employing targeted lipid-omics, protein phosphorylation assays, and microbiota-transfer experiments are warranted to elucidate the causal relationships.},
}

@article {pmid42097354,
year = {2026},
author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S},
title = {Integrative Machine Learning Models to Unravel Gut Microbial Dysbiosis and Functional Disruption in Polycystic Ovary Syndrome.},
journal = {F&S science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.xfss.2026.04.005},
pmid = {42097354},
issn = {2666-335X},
abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared to healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.

DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PolyCystic Ovary Syndrome (PCOS) MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.

RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of pro-inflammatory taxa such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals including Roseburia hominis and Prevotella copri. These compositional shifts indicate a pro-inflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome based machine learning models achieved a diagnostic accuracy of 84.25% (AUC 0.93), underscoring their predictive potential.

CONCLUSION: The gut microbiome in PCOS is characterized by a pro-inflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.},
}

@article {pmid42097759,
year = {2026},
author = {Li, Z and Zhang, Q and Wang, H and Zhang, Z and Liu, J and Li, L and Lin, Y and Wang, Y and Yin, C and Wang, W and Shen, F and Han, Z and Hao, S and Cong, P and Tian, T and Liu, Q and Chen, X and Zhan, H and Peng, T and Yu, X and Pu, X and Lian, X and Wang, T},
title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Suspected Native Spinal Brucella Infection: A Multicenter Study.},
journal = {Neurospine},
volume = {23},
number = {2},
pages = {487-499},
doi = {10.14245/ns.2551698.849},
pmid = {42097759},
issn = {2586-6583},
support = {2023YFC2812004//National Key Research and Development Program/ ; 24-4-4-zrjj-154-jch//Qingdao Natural Science Foundation/ ; //Qingdao City Healthcare Key Discipline Construction Project/ ; 2023TSGC051l//Technological Innovation Capability Improvement Project/ ; ZR2024MH251//Shandong Provincial Natural Science Foundation General Project/ ; 202404070869//Shandong Province Medical and Health Science Project/ ; },
abstract = {OBJECTIVE: The aim is to study the diagnostic positive rates of metagenomic next-generation sequencing (mNGS), microbial culture, and serologic testing in suspected native spinal brucellosis, and to evaluate the clinical value of their combined application.

METHODS: In this multicenter, retrospective observational study, 128 patients with suspected native spinal brucellosis from 6 medical centers (February 2020 to February 2025) were enrolled. Specimens from infection sites were subjected to microbial culture, mNGS, and serological testing (agglutination test).

RESULTS: Of the 128 patients with suspected native spinal Brucella infections, 118 patients were diagnosed with Brucella spondylitis. Among the 118 confirmed Brucella spondylitis cases, mNGS demonstrated a positivity rate of 92.37% (109 of 118), significantly higher than that of culture (26.27%, 31 of 118) and agglutination test (83.05%, 98 of 118). In the 87 culture-negative samples, mNGS detected Brucella in 91.95% (80 of 87), compared to 82.76% (72 of 87) by agglutination test. mNGS confirmed Brucella infection in all 16 cases that were agglutination test negative. mNGS combined with agglutination tests can effectively complement each other, improving the sensitivity of diagnosis and thereby minimizing missed diagnoses to the greatest extent. Among the 10 nonbrucellar spinal pathologies, agglutination test showed a high false-positive rate of 90% (9 of 10), whereas mNGS had a 10% (1 of 10) false-positive rate. Therefore, the agglutination test has a relatively high rate of false positives.

CONCLUSION: mNGS detection represents an effective adjunct to microbial culture and the agglutination test. The concurrent use of all 3 methods enhances diagnostic accuracy and reduces the likelihood of missed and incorrect diagnoses, significantly improving patient prognosis and guiding personalized clinical treatment.},
}

@article {pmid42098163,
year = {2026},
author = {Weng, Y and He, S and Luo, Z and Sun, J and Cheng, Q and Chen, Y and Tong, H},
title = {Keystone microbial taxa in the formation of stale aroma during pile fermentation of ripened Pu-erh tea.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00794-8},
pmid = {42098163},
issn = {2396-8370},
support = {CYB23127//Chongqing Graduate Student Research Innovation Project/ ; 2024J1110//Yunnan Provincial Department of Education/ ; 32272764//National Natural Science Foundation of China/ ; },
abstract = {Ripened Pu-erh tea is prized for its distinctive stale aroma. Methoxy-phenolic compounds, key contributors to this aroma, are produced during pile fermentation; however, the specific microorganisms responsible for their synthesis remain unclear. In this study, we identified the dominant taxa (Aspergillus luchuensis, A. fumigatus, Staphylococcus gallinarum, and S. kloosii) during pile fermentation through morphological analysis and metagenomic profiling. Gas Chromatography-Mass Spectrometry (GC-MS) analysis demonstrated the pivotal role of methoxy-phenolic compounds in the stale aroma. Moreover, using a metagenomic-based Weighted Gene Co-expression Network Analysis (WGCNA) combined with bivariate correlation network analysis, we identified key microbial taxa (Trichomonascus ciferrii, Heyndrickxia coagulans and Enterococcus sp.) involved in the generation of these compounds. Finally, we found that solid-state fermentation involving both dominant and keystone microbial taxa produced the highest levels of methoxy-phenolic compounds. Our findings reveal an inconsistency between dominant high-abundance taxa and keystone microbial taxa responsible for methoxy-phenolic compound synthesis during pile fermentation.},
}

@article {pmid42098310,
year = {2026},
author = {Li, W and Ni, P and Xu, J and Zhao, X and Dou, A and Wang, Y and Peng, L and Huang, S and Chen, Y and Shi, Q and Xie, Y and Zhang, W and Pan, S and Zhou, C},
title = {HIV-driven virome dysbiosis unveils distinct virome features and inter-viral correlations in blood and respiratory niches.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10221-z},
pmid = {42098310},
issn = {2399-3642},
support = {No. 82550118//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {While systemic immune dysregulation is well-documented in HIV infection, its impact on blood and respiratory tract viromes remains poorly understood. This study characterizes HIV-associated alterations in viral communities and examines their clinical relevance. Using viral metagenomics, we compare 203 ART-treated HIV-positive individuals and 120 healthy controls. HIV infection significantly restructures the blood virome, shifting from bacteriophage dominance (96.2% in controls) to eukaryotic virus predominance (69.1%). Increased alpha diversity, significant β-diversity divergence, and heightened dispersion heterogeneity are observed in HIV cases. Consistent enrichment of Flaviviridae, Parvoviridae, and Anelloviridae is detected. Throat viromes maintain phage dominance (>90%) but exhibit strain-level diversification, including Microviridae proliferation. Network analysis reveals Retroviridae-Anelloviridae co-dynamics (r = +0.562) and identifies Picobirnaviridae as a key interactor. Functional analysis shows enriched viral replication and host modulation genes. Compartment-specific disruption patterns nominate Pegivirus C, parvovirus B19, and Anelloviruses as potential biomarkers. Cross-kingdom viral interactions suggest novel mechanisms influencing disease progression and support future virome-targeting adjunct therapies.},
}

@article {pmid42098386,
year = {2026},
author = {Wei, X and Bashir, K and Tian, X and Farooq, A and Olimi, E and Cernava, T and Zhang, L and Yu, X and Chen, Q and Penttinen, P and Gu, Y},
title = {Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10162-7},
pmid = {42098386},
issn = {2399-3642},
support = {41201256//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Biodegradable microplastics and heavy metals increasingly co-occur in soils through plastic mulching, organic amendments, and legacy metal contamination. Yet, their combined effects on soil-plant-microbiota interactions remain unclear, particularly for the virus. Here we evaluated the impacts of bio-MPs, polylactic acid (PLA), lead (Pb), and their combination on buckwheat and rhizosphere bacterial-viral communities. Co-contamination reduced soil pH and nutrient availability, increased Pb accumulation in plant tissues and suppressed buckwheat growth. Metagenomic analyses revealed that both bacterial and viral communities were altered under Pb-containing treatments. Bacterial genes associated with carbon and phosphorus metabolism were suppressed, while viral auxiliary metabolic genes (AMGs) related to carbon utilization were enriched, especially carbohydrate esterases that hydrolyze PLA ester bonds. A putative AMG-associated carbohydrate esterase gene (P9222_28545) was identified and the esterase activity confirmed via heterologous expression in E. coli. These findings highlight a potential role of viruses in mediating microplastic degradation in soils.},
}

@article {pmid42098439,
year = {2026},
author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ},
title = {Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01627-1},
pmid = {42098439},
issn = {2730-664X},
abstract = {BACKGROUND: Celiac disease affects ~1-2% of people and remains incurable, requiring lifelong dietary restriction. The gut microbiome is thought to contribute to the development and progression of celiac disease. However, findings across previous studies are fragmented, making it difficult to understand exactly how the gut microbiome is involved.

METHODS: We integrate over 900 samples from global datasets spanning different disease stages (before onset, during active disease, and after treatment), body sites, and research methods. Datasets produced using both 16S rRNA gene sequencing and shotgun metagenomics profile the gut microbiome. Alpha and beta diversity analyses and differential abundance testing identify consistent changes in bacterial communities linked to celiac disease. Machine learning tests how well microbiome data predicts disease status.

RESULTS: Here, we show that celiac disease is not marked by large changes in gut microbiome diversity. Instead, there are subtle, consistent changes in specific bacteria, including a reduction in beneficial butyrate producers (Faecalibacterium, Prevotella, Agathobacter, Gemmiger), changes in mucin-associated microbes (Akkermansia muciniphila), and an increase in potentially harmful bacteria (Helicobacter, Campylobacter, Haemophilus parainfluenzae). These changes are seen before and during active disease and persist on a gluten-free diet. Microbiome-based disease prediction is moderately accurate for active disease and weaker for prospective performance, likely constrained by training data.

CONCLUSIONS: Our findings suggest that celiac disease is linked to specific changes in gut bacteria that are not fully resolved by diet alone. Future treatments may need to focus on restoring healthy gut bacteria, not just avoiding gluten, to better manage the disease.},
}

@article {pmid42098757,
year = {2026},
author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J},
title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42098757},
issn = {1674-9782},
support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; },
abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.

RESULTS: Fifty‑six lactating Holstein cows (28 high‑yield cows, HY; 28 low‑yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high‑yield control (HCON), high‑yield SIF (HSIF), low‑yield control (LCON), and low‑yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.

CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.},
}

@article {pmid42098796,
year = {2026},
author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V},
title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02420-x},
pmid = {42098796},
issn = {2049-2618},
support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Università e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; },
abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.

RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.

CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.},
}

@article {pmid42086823,
year = {2026},
author = {Ismaeil, M and Saeed, AM and Donia, SA and El-Sayed, WS},
title = {Predictive functional profiling of 16S rRNA genes amplicons reveals bioremediation and sulfur metabolism capacity in thermophilic hot spring bacteriomes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42086823},
issn = {2045-2322},
mesh = {*Hot Springs/microbiology ; *Sulfur/metabolism ; *RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Soil Microbiology ; Hot Temperature ; Proteobacteria/genetics/metabolism ; },
abstract = {Thermophilic hot springs host highly specialized microbial communities critical for biogeochemical cycling and novel biotechnological applications. This study investigated the structure of the bacterial communities (bacteriomes) and predicted functional potential related to bioremediation and sulfur metabolism across three geochemically diverse soil sites within the Pharaoh's Bath Hot Springs ecosystem in South Sinai, Egypt. These sites were categorized by distinct thermal profiles: 70 °C (HS1), 75 °C (HS2), and 80 °C (HS3). Using 16 S rRNA gene amplicon sequencing and PICRUSt functional prediction, sequence analysis via the EzBioCloud server revealed that the HS2 site harbored the highest evenness and overall microbial diversity. Taxonomically, the HS1 and HS3 sites were dominated by Proteobacteria; in contrast, the HS2 site exhibited a more diverse profile, characterized by a reduced Proteobacteria presence and a high abundance of Rhodothermaeota. Predictive functional profiling identified 13 genes associated with biodegradation pathways (e.g., catechol and xylene degradation), suggesting an intrinsic genetic capacity to degrade complex aromatics and halogenated compounds across these thermal gradients. Regarding sulfur metabolism, functional predictions indicated that the HS2 site possessed the highest potential for dissimilatory sulfate reduction. Meanwhile, the HS1 site specialized in assimilatory sulfate reduction and, alongside the HS2 site, demonstrated a higher predicted capacity for sulfide oxidation. The distribution of heat-response genes varied by location: HspQ and Hsp33 were most prominent at the HS1 site, while HSP20 and DnaK reached their maximum abundance at the HS2 site. Overall, this study demonstrates the substantial intrinsic bioremediation potential of the studied bacteriomes and provides a predictive framework for understanding microbial functional potential in this system, with future studies offering opportunities to refine in situ functional validation and application.},
}

*Hot Springs/microbiology
*Sulfur/metabolism
*RNA, Ribosomal, 16S/genetics
Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
Microbiota
Phylogeny
Soil Microbiology
Hot Temperature
Proteobacteria/genetics/metabolism