@article {pmid42437837,
year = {2026},
author = {Devi, U and Ramadass, B and Pullattayil, AK and Vishnu Bhat, B},
title = {Gut Microbiome in Neonatal Necrotizing Enterocolitis - A Comprehensive Review of Evidence.},
journal = {Indian journal of pediatrics},
volume = {},
number = {},
pages = {},
pmid = {42437837},
issn = {0973-7693},
abstract = {Necrotizing enterocolitis (NEC) is one of the most catastrophic gastrointestinal emergency occurring predominantly in preterm neonates. It contributes to substantial neonatal morbidity and mortality. Disturbances in the intestinal microbiome are crucial to disease pathogenesis. In preterm infants, an immature intestinal barrier, dysregulated immune responses, and environmental exposures altogether predispose to alteration in microbial colonization and intestinal inflammation. This review was done to present the current evidence on gut microbiome alterations associated with NEC in preterm infants. A systematic search of the MEDLINE and EMBASE databases was performed using search strategy related to prematurity, intestinal microbiota, and necrotizing enterocolitis. A total of 42 studies assessing microbial composition, microbial progression, or microbial functional patterns in relation to NEC were included. Across the included studies, NEC was commonly preceded by reduced microbial diversity, delayed maturation of anerobic communities, and expansion of Proteobacteria, particularly Enterobacteriaceae family such as Klebsiella and Escherichia. Longitudinal studies further showed that these microbial changes may become evident days to weeks before clinical disease, suggesting a potential window for early risk identification. Functional analyses also showed alterations in microbial metabolic pathways, including short-chain fatty acids, tricarboxylic acid intermediates, volatile compounds, and viral signatures that may lead to epithelial injury and inflammatory signaling. Clinical and environmental factors including antibiotic exposure, mode of delivery, feeding practices, and NICU microbial ecosystem are important determinants of neonatal gut microbiome development. Thus, the current evidence supports a reproducible pattern of intestinal dysbiosis preceding NEC. Better understanding of microbiome dynamics may aid early risk stratification and support microbiome-targeted preventive strategies in vulnerable preterm populations.},
}

@article {pmid42437892,
year = {2026},
author = {Chen, Y and Lu, S and Zhao, A and Li, M and Gan, X and Wang, Y and Yang, Y and Huang, M and Wang, Q and Niu, T and Zhou, Y},
title = {Blood mNGS: an effective non-invasive diagnostic tool for Pneumocystis jirovecii pneumonia.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05408-7},
pmid = {42437892},
issn = {1471-2180},
support = {2024J0304//the Scientific Research Fund of Yunnan Provincial Department of Education/ ; 202401AY070001-295//the Kunming Medical Joint Special Project of Yunnan Provincial Science and Technology Plan Project/ ; 82370192//National Natural Science Foundation of China/ ; GYYX24003//1.3.5 Project of High Altitude Medicine/ ; 2024NSFSC1746//West China Hospital, Sichuan University, the Natural Science Foundation of Sichuan Province/ ; 2022YFC2406804//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening opportunistic infection. Colonization is prevalent but cannot be reliably distinguished from active infection by conventional methods. Metagenomic next-generation sequencing (mNGS) is a promising diagnostic tool, but the value of blood mNGS for diagnosis, microbial community comparison, and outcome-related associations in PJP remains unclear.

METHODS: We analyzed 73 suspected PJP patients with paired BALF and blood mNGS. Using strict diagnostic criteria, patients were classified as: PJP (n = 50) and P. jirovecii colonization (PJC, n = 23). Bioinformatic analyses compared compartment-specific microbiota. BALF-blood concordance and associations between P. jirovecii load and outcomes were evaluated.

RESULTS: BALF showed higher α-diversity than blood (both Shannon and Simpson, P < 0.001), whereas β-diversity showed no compartmental segregation. BALF identified 216 species versus 43 in blood; however, the top-10 species were concordantly ranked (90% concordance). Blood mNGS distinguished PJP from PJC with an AUC of 0.80 (specificity 95.7%, sensitivity 62.0% at RPM > 4.8), outperforming BALF mNGS (AUC 0.76), blood PCR (AUC 0.64) and BALF PCR (AUC 0.73). Gram-negative bacteria accounted for a large proportion of blood taxa (75% of top 20 taxa), while BALF showed additional fungal taxa including Aspergillus fumigatus. LEfSe identified matrix-specific taxa: oral commensals in PJC-BALF. Blood P. jirovecii load correlated positively with LDH (r = 0.34, P = 0.0035), CRP (r = 0.34, P = 0.0031), and BDG (r = 0.26, P = 0.025), and was higher in non-survivors (P < 0.05).

CONCLUSION: Blood mNGS may serve as a non-invasive, highly specific complementary tool for PJP diagnosis and broader microbiological assessment.},
}

@article {pmid42437920,
year = {2026},
author = {Diaz-Canestro, C and Cheung, K and Roche, E and Sarabia, JM and Tse, MA and Xu, A},
title = {Multi-omics signatures of circulating factors associated with cardiorespiratory fitness adaptations in individuals with prediabetes.},
journal = {Cardiovascular diabetology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12933-026-03286-x},
pmid = {42437920},
issn = {1475-2840},
abstract = {BACKGROUND: Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO2peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO2peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO2peak to HIIT in individuals with prediabetes.

METHODS: Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles.

RESULTS: After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO.

CONCLUSIONS: Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.},
}

@article {pmid42437978,
year = {2026},
author = {Xia, J and Meng, L and Fang, Y and Ban, H and Okazaki, Y and Yoshida, T and Endo, H and Nagasaki, K and Ogata, H},
title = {Rapid Diversification of a Natural Heterosigma akashiwo Virus Population during a Host Bloom.},
journal = {Microbes and environments},
volume = {41},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME26018},
pmid = {42437978},
issn = {1347-4405},
mesh = {Japan ; *Genetic Variation ; *Giant Viruses/genetics/classification/isolation & purification ; *Eutrophication ; Phylogeny ; Genome, Viral ; Metagenomics ; Seawater/virology ; Biodiversity ; },
abstract = {Despite the ecological importance of viruses, our understanding of their evolutionary dynamics in natural environments remains limited. This gap is particularly pronounced for giant dsDNA viruses of the phyla Nucleocytoviricota and Mirusviricota. Knowledge on their population genetic dynamics is mostly derived from a small number of laboratory-based experiments, while patterns in nature are rarely observed. To overcome this limitation, we traced the genetic structure and transcription status of Heterosigma akashiwo virus (HaV) using high-frequency, time-resolved sampling during a host bloom in a coastal area of Japan by integrating cell counting, metabarcoding, and metagenomic and metatranscriptomic sequencing. The results obtained revealed that HaV dominated the giant virus community in most samples, with relative abundance up to 56%. Despite its high abundance, the HaV population exhibited a low level of microdiversity, but had a higher pN/pS ratio than other giant viruses in the study site. Microdiversity increased during the early sampling period, peaked mid-sampling, and decreased during the later period, consistent with rapid diversification during viral expansion, which may be driven by both in situ mutations and the succession of pre-existing minor variants. Several accessory genes, including a glycosyltransferase and an endonuclease, were highly expressed, providing functional evidence consistent with host interaction-driven selective pressure during the bloom. Collectively, these results indicate that HaV population dynamics during algal blooms are shaped by host-driven selection acting on standing genetic variations.},
}

Japan
*Genetic Variation
*Giant Viruses/genetics/classification/isolation & purification
*Eutrophication
Phylogeny
Genome, Viral
Metagenomics
Seawater/virology
Biodiversity

@article {pmid42438180,
year = {2026},
author = {Castells-Ballester, J and Taron, A and Smith, M and Gawron, R and Beaulieu, J and Papa, O and Buss, J and Ong, J and Chen, M},
title = {Development of a Microdroplet-Based Functional Genomic Screening Pipeline by Combination of DNA Nanoflowers and PURExpress Cell-Free Expression.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.6c00061},
pmid = {42438180},
issn = {2161-5063},
abstract = {We present a microfluidic workflow that couples reconstituted in vitro transcription-translation (IVTT) with ultrahigh-throughput droplet screening to directly link genotype and phenotype within complex, heterogeneous DNA pools. The approach employs DNA nanoflowers as clonal, high-copy templates, enabling robust protein expression from single DNA molecules encapsulated in picoliter droplets. When integrated with fluorescence-assisted microdroplet sorting (FADS) and a DNA recovery pipeline that reconstituted selected libraries for subsequent iterative rounds, the platform achieves approximately 400-600-fold enrichment per selection cycle and supports functional discovery and directed evolution entirely independent of host cell expression. As a proof of principle, we demonstrate recovery of the recombinase RecA from an E. coli genomic library screened for single-stranded DNA binders, highlighting the platform's capability to identify DNA-interacting and DNA-modifying enzymes. By eliminating host-derived background activity and toxicity constraints that often complicate lysate- or cell-based metagenomic screens, this method potentially expands access to enzyme classes that have historically been difficult to assay.},
}

@article {pmid42438386,
year = {2026},
author = {Yuan, D and Cui, X and Zhang, S and Wang, Y and Sun, Y and Xiao, M and Zhang, M and Zheng, L},
title = {Nitrifiers Drive Different N2O Production Patterns in Tropical River Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c01501},
pmid = {42438386},
issn = {1520-5851},
abstract = {Since the 20th century, global riverine nitrous oxide (N2O) emissions have increased 4-fold; however, the N2O emissions of tropical rivers are still unclear. Here, we employed a series of techniques (closed chamber, biological inhibitor, [15]N-[18]O double tracer, metagenomic sequencing, and reverse transcription qPCR) to analyze in situ N2O flux, potential N2O production rate, and N2O production mechanism of China's tropical rivers. In the 82 sediment samples from the top 10 Hainan rivers, high levels of in situ N2O flux and potential N2O production rate were detected in all samples, indicating that Hainan rivers are significant hotspots of N2O emissions. The higher values were observed in estuary samples (avg: 4.48 ± 0.25 mg m[-2] d[-1], 39.17 ± 3.28 ng N g[-1] d[-1]) compared to nonestuary samples (avg: 1.98 ± 0.16 mg m[-2] d[-1], 21.29 ± 4.68 ng N g[-1] d[-1]). Nitrifier denitrification (ND) dominates the N2O production, and its contribution to estuary samples (avg. 49.31-78.90%) is higher than that for nonestuary samples (avg. 32.27-66.19%). We found that complete ammonia-oxidizing bacteria (comammox) Nitrospira nitrificans and ammonia-oxidizing bacteria (AOB) Nitrosomonas marina cooperate to produce N2O via the ND pathway in estuary samples, and AOB Nitrosomonas europaea produces N2O via the ND pathway in nonestuary samples. Salinity, NH4[+], pH, and total organic matter (TOM) affect N2O production via three key species. Our findings advance the mechanistic understanding of tropical rivers in the tropical N-cycle and global climate change. Ammonium fertilizer management and estuary ecological restoration should be prioritized in tropical river basins.},
}

@article {pmid42438737,
year = {2026},
author = {Faleiros, CA and Gonçalves, OS and Nunes, AT and Pires, CS and Poleti, MD and Fukumasu, H},
title = {Host breed and geography shape the antiviral defense landscape of the bovine rumen microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag162},
pmid = {42438737},
issn = {2730-6151},
abstract = {The rumen microbiome represents a complex, phage-rich ecosystem where microbial survival depends on both metabolic cooperation and antiviral defense. However, global and breed-associated variations in rumen prokaryotic immune systems remain poorly understood. Here, we performed the most comprehensive profile to date of antiviral defense systems (DS) in the rumen, analyzing 6530 microbial genomes and metagenome-assembled genomes (MAGs) from diverse cattle breeds and geographic regions. In this global dataset, we identified >90 000 DS, the most abundant of which were restriction-modification, PDC-S01, deoxyribonucleic acid modification systems (DMS_other), AbiE and SoFic, with variations influenced by both host the lineage and geographic region. A more in-depth analysis was performed using two complementary antiviral annotation frameworks for Nellore cattle (Bos indicus) from Brazil. Data exhibited a remarkably enriched antiviral defense repertoire, with over 15 632 DS encoded across 547 high-quality MAGs. These systems were densely clustered in dominant rumen lineages, such as Prevotella, and positively correlated with prophage abundance, consistent with virus-host coevolution. Notably, we also detected viral contigs encoding both antiviral defense and anti-defense genes, underscoring the arms race between the phages and their microbial hosts. Metatranscriptomic data from North America and Oceania revealed high expression levels of toxin-antitoxin modules, clustered regularly interspaced short palindromic repeats components, and restriction enzymes, suggesting a basal level of antiviral activity. These findings reveal the rumen as an antiviral innovation hotspot, highlighting microbiome resilience with implications for ecology, adaptation, and phage-based interventions.},
}

@article {pmid42439467,
year = {2026},
author = {Luo, Y and Kang, FL and Li, QM and Yang, WC},
title = {Metagenomic Association Uncovers Host Genotype-Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76373},
doi = {10.1002/advs.76373},
pmid = {42439467},
issn = {2198-3844},
support = {YSBR-011//CAS project for Young Scientists in Basic Research/ ; 2023YFD1200600//National Key Research and Development Program of China/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2016QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
abstract = {Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth-promoting function, and systematic approaches to uncover salt-tolerance-enhancing plant growth-promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co-occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter. Correlation analyses identified bacterial taxa positively associated with STI, including documented salt-tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis, enhances soybean salt tolerance and reshapes host ion-transport and oxidative-stress gene expression under salinity, validating our screening strategy. Our culture-independent metagenomic association approach reveals host genotype-structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor-saving means for high-throughput identification of salt-tolerant PGPR.},
}

@article {pmid42439510,
year = {2026},
author = {Hertramph, TL and Dorda, M and Pallenberg, ST and Sauer-Heilborn, A and Ringshausen, FC and Steglich, M and Hansen, G and Tümmler, B and Wiehlmann, L and Rosenboom, I and Dittrich, A-M},
title = {Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0060126},
doi = {10.1128/spectrum.00601-26},
pmid = {42439510},
issn = {2165-0497},
abstract = {Mutation-specific cystic fibrosis (CF) transmembrane conductance regulator (CFTR) modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has dramatically improved clinical outcomes for people with CF (pwCF), yet its impact on the nasal microbial metagenome remains insufficiently understood. This prospective, post-approval study investigated the impact of 15-week ETI therapy on sinonasal microbiota of pwCF aged 12 years and older. Whole-genome shotgun sequencing was performed on total DNA from 24 paired nasal lavage samples, with synthetic spike-in controls enabling absolute abundance normalization. Taxonomic profiling was conducted using the Wochenende pipeline. ETI did not induce major shifts in alpha or beta diversity. Instead, the overall microbial community became further dominated by the skin commensals Staphylococcus epidermidis and Cutibacterium acnes, accompanied by a more than twofold increase in total bacterial load. Classical CF pathogens showed divergent trajectories: Pseudomonas aeruginosa tended to decrease, whereas Staphylococcus aureus exhibited a tendency toward increased abundance. Co-occurrence network analysis revealed a transition from a dense, multicomponent baseline network to a single, fully connected, but less densely integrated network following treatment initiation.IMPORTANCEThe nasal cavity represents the primary entry point of microorganisms into the respiratory tract and a potential reservoir for lower airway infection, the major cause of CF disease progression. Using shotgun metagenomics with spike-in controls, this study provides the first genome-wide characterization of how ETI alters microbial load and pathogen dynamics in CF nasal airways. Treatment with ETI strengthened the dominance of skin commensals in the nares while reducing P. aeruginosa. Given the observed increase in S. aureus, further work is needed to determine whether this represents expansion of a typical nasal colonizer or a clinically relevant rise of a key CF pathogen that could act as a reservoir for future lower airway infection.},
}

@article {pmid42439573,
year = {2026},
author = {van Haren, MHI and Have, Lt and Koopman, PD and Buil, JB and Maat, I and Rahamat-Langendoen, JC and Martens, L and Moorlag, SJCFM and van den Bosch, B and Koenraad, E and Wertheim, HFL and Melchers, WJG and Pas, SD},
title = {Clinical impact of 16S rRNA RC-PCR NGS on infectious disease management.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0002326},
doi = {10.1128/spectrum.00023-26},
pmid = {42439573},
issn = {2165-0497},
abstract = {16S rRNA metagenomics provides a culture-independent method for diagnosing infections with fastidious or uncultivable organisms, guiding targeted therapy, and detecting polymicrobial communities. This study utilizes reverse complement (RC)-PCR next-generation sequencing (NGS) to accurately identify bacterial pathogens from clinical specimens and assess its impact on clinical decision-making, setting it apart from conventional 16S sequencing approaches. A retrospective analysis of an ISO 15189 accredited 16S RC-PCR NGS diagnostic workflow targeting the V1-6 and V9 regions of the 16S rRNA gene was conducted over a 2-year period, including 390 clinical specimens from 316 patients. 16S RC-PCR NGS results were discussed in a multidisciplinary consultation and subsequently reported to the clinic. In total, 1,283 RC-PCR results were analyzed, of which 517 were from clinical specimens, 284 were negative controls, 66 were positive controls, and 416 were from wet lab and bioinformatic pipeline validation. 16S RC-PCR NGS assay detected bacterial taxa in 179/390 (45.9%) of clinical specimens, while 201/390 (51.5%) were negative, and 10/390 (2.6%) yielded uninterpretable results. The specimen types pus, pleural fluid, and heart valves exhibited the highest positivity rate (68% to 70%). Overall, 16S RC-PCR NGS influenced diagnostic decision making in 145/282 (51.4%) clinical cases and guided therapeutic management in 77/282 (27.3%) cases. Results providing definite evidence for either the presence or absence of bacterial infection were considered clinically valuable. Integration of 16S RC-PCR NGS pathogen detection with multidisciplinary consultation markedly improved clinical management, directly impacting diagnosis and treatment of complex clinical cases in a tertiary care setting. The effect was most pronounced in brain abscess patients, where RC-PCR results guided treatment decisions in 9/13 (69.2%) of cases.IMPORTANCETimely and accurate diagnosis is essential for managing serious infections, yet clinicians often face situations where routine laboratory tests do not provide clear answers. This study demonstrates that next-generation sequencing (NGS) of the bacterial 16S rRNA gene can decisively resolve these uncertainties. By revealing whether bacteria are present in clinical specimens, this approach influenced clinical reasoning and supported treatment decisions across a variety of challenging cases. 16S reverse-complement PCR was especially powerful for brain abscesses and infections where the causative microorganism was unclear, providing clarity that directly improved patient care. These findings show that integrating advanced sequencing with expert clinical interpretation can enhance the management of complex infections and support more confident, evidence-based therapy.},
}

@article {pmid42440035,
year = {2026},
author = {Mathiyazhagan, S and Balu, B and Gunaseelan, RJ and Piliyan, R and Perumal, S and Natesan, M},
title = {Discovery of novel bio-resources from the hidden biodiversity of marine mangrove ecosystems.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {10},
pages = {},
pmid = {42440035},
issn = {1573-2983},
mesh = {*Wetlands ; *Biodiversity ; Animals ; Biological Products ; Fungi/metabolism ; Bacteria/metabolism ; Biotechnology ; Invertebrates/metabolism ; },
abstract = {Marine mangrove wetlands are ecologically complex ecosystems that serve as rich reservoirs of biologically active compounds with significant biotechnological potential. This review synthesizes current knowledge on mangrove-associated microorganisms and biota, including bacteria, fungi, algae, and invertebrates, with emphasis on their bioassay activities and derived bioactive metabolites. Various analytical approaches, including chromatographic techniques, LC-MS/NMR analysis, and in silico tools, have been employed to identify and characterize compounds such as enzymes, polysaccharides, biosurfactants, and antimicrobial peptides. These biomolecules exhibit diverse functional applications in medicine, environmental management, and industrial processes, including nitrogen fixation, bioremediation, and hydrocarbon degradation. The review highlights that mangrove-derived bioactive compounds are influenced by both ecological interactions and environmental conditions. Furthermore, recent advances indicate a shift toward genome-guided discovery using multi-omics and metagenomic approaches, enabling the identification of novel biosynthetic pathways, particularly from unculturable microorganisms. This integrated approach enhances the efficiency of bioactive compound discovery and supports scalable production through synthetic biology. Overall, mangrove ecosystems represent promising platforms for sustainable biotechnological innovation, underscoring the need for their conservation and the development of integrated validation strategies.},
}

*Wetlands
*Biodiversity
Animals
Biological Products
Fungi/metabolism
Bacteria/metabolism
Biotechnology
Invertebrates/metabolism

@article {pmid42440756,
year = {2026},
author = {Kraiselburd, I and Susenburger-Lange, R and Balzer, M and Magin, S and Block, K and Consten, L and Dörr, A and Dörr, AK and Gosch, J and Nishad, S and Sachse, S and Thomas, A and Triebs, A and Welling, J and Wilhelm, A and Widera, M and Schmithausen, R and Meyer, F},
title = {Wastewater-based epidemiology for public health - benefits and trade-offs of different molecular methods for the generation of actionable data in a small-town context.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1828355},
doi = {10.3389/fpubh.2026.1828355},
pmid = {42440756},
issn = {2296-2565},
mesh = {*Wastewater/microbiology ; Humans ; Germany/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; *Public Health ; Metagenomics ; },
abstract = {BACKGROUND: Wastewater-based epidemiology (WBE) is a promising complement to traditional surveillance systems, yet its practical utility and performance in real-world public health settings remain insufficiently characterized. This study aims to evaluate the feasibility and added value of WBE for monitoring infectious disease dynamics at the regional level, with a particular focus on jointly identifying, together with public health authorities, actionable and scalable methodological strategies based on cost, applicability, and the relevance and timeliness of the information generated.

METHODS: Composite influent wastewater samples were collected over 6 weeks from a treatment plant serving a defined district in western Germany. Samples were analyzed using quantitative PCR and both targeted and shotgun metagenomic sequencing. WBE findings were compared with routine case-based surveillance data from the corresponding catchment area.

RESULTS: All pathogens reported through routine public health surveillance during the study period were also detected in wastewater. In addition, WBE identified signals from clinically relevant pathogens not captured by case-based surveillance. Sequencing approaches provided further resolution on pathogen diversity and resistance profiles. The combined use of targeted and untargeted methods revealed differences in sensitivity and resolution, with complementary strengths across approaches, and enabled the definition of a practical, tiered approach to support actionable surveillance at the regional level.

CONCLUSION: This study describes the operational integration of WBE into a regional public health workflow, providing timely, population-level data that complements routine surveillance and can reveal pathogen circulation not captured by reported cases. Building on the established advantages of WBE, our results highlight its practical value when jointly implemented with public health authorities, enabling context-specific, actionable insights that enhance situational awareness, guide targeted local responses and support earlier detection of emerging threats.},
}

*Wastewater/microbiology
Humans
Germany/epidemiology
*Wastewater-Based Epidemiological Monitoring
*Public Health
Metagenomics

@article {pmid42441076,
year = {2026},
author = {Mohammadzadeh, P and Pilvaieh, A and Dousti, A and Bahrami, MRS and Ziaee, F},
title = {Multimodal characterisation of spontaneous Merkel cell carcinoma in the endangered Caucasian squirrel (Sciurus anomalus pallescens): integrating spatial transcriptomics, imaging mass cytometry and metagenomic sequencing.},
journal = {Journal of veterinary research},
volume = {70},
number = {2},
pages = {321-334},
doi = {10.2478/jvetres-2026-0034},
pmid = {42441076},
issn = {2450-7393},
abstract = {INTRODUCTION: Merkel cell carcinoma is an aggressive neuroendocrine skin malignancy rarely reported in non-domestic species.

MATERIAL AND METHODS: A cutaneous nodule from an endangered Caucasian squirrel (Sciurus anomalus pallescens) was examined using histopathology, immunohistochemistry, imaging mass cytometry, spatial transcriptomics (10× Visium) and metagenomic sequencing.

RESULTS: Histology revealed a high-grade neuroendocrine carcinoma with frequent mitoses (52 per 2.37 mm[2]) and necrosis. Tumour cells were positive for cytokeratin 20 (paranuclear dot pattern), synaptophysin and chromogranin A, with a high Ki-67 index (68%). Spatial analyses delineated a distinct tumour core and combined invasive front and stromal compartments, revealing upregulation of neuroendocrine (atonal basic helix-loop-helix transcription factor 1 and neurogenic differentiation factor 1) and proliferative (marker of proliferation Ki-67) programmes, and activation of phosphoinositide 3-kinase-AKT serine/threonine kinase 1-mechanistic target of rapamycin and mitogen-activated protein kinase pathways. No evidence of Merkel cell polyomavirus was found. The tumour microenvironment was immune-excluded, with programmed-death ligand 1 expression on ~22% of tumour cells and CD8[+] T cells restricted to the stroma.

CONCLUSION: This study provides a comprehensive methodological framework for high-resolution tumour profiling in conservation pathology and highlights the emergence of neoplasia in threatened wildlife.},
}

@article {pmid42441094,
year = {2026},
author = {Dal, GE and Çelik, B and Sabuncu, A and Yılmaz, M and Kekeç, AI and Dümen, E and İkiz, S and Diker, KS},
title = {Metagenomic analysis of the vaginal microbiota in cows with ovarian cysts.},
journal = {Journal of veterinary research},
volume = {70},
number = {2},
pages = {215-225},
doi = {10.2478/jvetres-2026-0028},
pmid = {42441094},
issn = {2450-7393},
abstract = {INTRODUCTION: This study compared the vaginal microbiota composition of dairy cows with follicular and luteal ovarian cysts using metagenomic analysis.

MATERIAL AND METHODS: Ovarian cysts, which impair reproductive performance through endocrine disruption, were diagnosed by ultrasonography and serum hormone evaluation in Holstein cows 30-60 d postpartum. Forty-five cows were initially included and divided into follicular cyst, luteal cyst and control groups. Vaginal lavage samples were analysed using third-generation sequencing, and taxonomic classification was performed through 16S rRNA gene analysis.

RESULTS: A total of 258 operational taxonomic units (OTUs) were identified, with the highest diversity observed in the control group (mean of 56.8 OTUs) and the lowest in the luteal cyst group (mean of 49.0 OTUs). Proteobacteria was the dominant phylum across all groups (93.4%), followed by Tenericutes (5.9%). Firmicutes, Bacteroidetes and Fusobacteria accounted for less than 1%. At the family level, Burkholderiaceae (62.7%) and Pasteurellaceae (24.0%) were predominant, while of the genera, Ralstonia was the most abundant (62.2%). The luteal group had the highest relative abundance of Burkholderiaceae, whereas Pasteurellaceae was most abundant in the control group.

CONCLUSION: These results indicate that cystic cows exhibit reduced microbial diversity and altered bacterial composition in comparison with healthy animals. The predominance of Proteobacteria and Ralstonia suggests a potential link between endocrine imbalance and changes in the vaginal microenvironment. Hormonal analyses supported the classification of cyst types, with follicular cyst cows showing low progesterone (0.31 ± 0.05 ng/mL) and high oestradiol-17β concentrations (55.57 ± 7.91 pg/mL), whereas luteal cyst cows exhibited higher progesterone (2.89 ± 0.74 ng/mL) and lower oestradiol-17β concentrations (6.19 ± 0.56 pg/mL) (P < 0.001). These results may support future studies evaluating vaginal microbial profiles as complementary indicators of ovarian status in dairy cows.},
}

@article {pmid42442076,
year = {2026},
author = {Ma, L and Zhang, J and He, X and Wang, Z and Zhao, M},
title = {Hemophagocytic lymphohistiocytosis secondary to disseminated histoplasmosis diagnosed by bone marrow smear microscopy and metagenomic next-generation sequencing: A case report and review of literature.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117542},
doi = {10.1016/j.diagmicrobio.2026.117542},
pmid = {42442076},
issn = {1879-0070},
abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Histoplasma capsulatum infection is rare in immunocompetent individuals but is associated with an extremely high mortality rate. Here, we report a case of disseminated histoplasmosis (DHP) in an immunocompetent patient. The pathogen was confirmed by bone marrow smear microscopy and metagenomic next-generation sequencing (mNGS). The patient experienced rapid clinical deterioration and was subsequently diagnosed with HLH secondary to DHP. Following targeted antimicrobial therapy with amphotericin B and immunomodulatory treatment involving etoposide and ruxolitinib, the patient's clinical condition improved. Early clinical manifestations of DHP are often atypical, while conventional diagnostic methods frequently yield negative results in the early stage. This case indicates that bone marrow examination combined with mNGS facilitates early definitive diagnosis. Furthermore, this report rarely describes the sequential morphological changes of Histoplasma capsulatum in bone marrow tissue.},
}

@article {pmid42442081,
year = {2026},
author = {Shayo, MJ and Kuchaka, D and Beti, M and Kimu, P and Wadugu, B and Jensen, EEB and Kumburu, H and Kazyoba, P and Ali, M and , and Clausen, PTLC and Muro, F and Mmbaga, BT and Kiwelu, I and Alifrangis, M and Aarestrup, FM and Sonda, T},
title = {Identification of enteric viral pathogens in Tanzanian children under the age of five with diarrhea using nanopore-based metagenomic sequencing.},
journal = {Virology},
volume = {623},
number = {},
pages = {111024},
doi = {10.1016/j.virol.2026.111024},
pmid = {42442081},
issn = {1096-0341},
abstract = {Diarrhea continues to be a significant contributor to illness and death among children, especially in low-income settings. In Tanzania, diarrheal disease remains a public health concern with many minors under five seeking healthcare despite the wide coverage of rotavirus vaccine. The diagnosis of pediatric diarrhea in Tanzania primarily focuses on specific viral diseases, which may overlook the broad-spectrum of viral pathogens. In this study, Oxford Nanopore-based metagenomic sequencing was applied to characterize viral pathogens in 200 stool samples from children under the age of five presented with diarrhea. Samples were collected from April 2023 to April 2024 at health facilities in six regions across mainland Tanzania and Zanzibar. At least one known diarrhea linked virus was detected in 31% of the participants. Although no statistical difference could be observed across different age categories, a slightly higher detection was observed in children aged 6-23 months. Human adenovirus was the most frequently detected 16% (32/200) in this study. Rotavirus was the second most frequently detected virus 9.5% (19/200) despite participant vaccination status. Other enteric viruses detected was astrovirus, norovirus, human bocavirus and Aichi virus were detected in 2.5% (5/200), 2% (4/200), 0.5% (1/200) and 0.5% (1/200) of the study participants respectively. Rotavirus showed negative correlation with temperature and relative humidity while human adenovirus was positively correlated to relative humidity. Metagenomics also revealed the presence of non-enteric viral pathogens, including measles and HAdV-C and HAdV-B, within this cohort. This study identified a range of viral pathogens associated with pediatric diarrhea in this cohort, including agents not typically targeted by routine diagnostic assays by using untargeted metagenomic technique direct to the clinical samples. These findings contribute baseline data that could inform future, larger-scale surveillance efforts in Tanzania.},
}

@article {pmid42442149,
year = {2026},
author = {Hong, M and Ji, L and Gao, J and Zhang, H and Ge, S and Yuan, C},
title = {Granulomatous inflammation in lung and lymph node specimens: A molecularly enhanced pathology-based algorithm for etiologic differential diagnosis.},
journal = {Annals of diagnostic pathology},
volume = {85},
number = {},
pages = {152684},
doi = {10.1016/j.anndiagpath.2026.152684},
pmid = {42442149},
issn = {1532-8198},
abstract = {Granulomatous inflammation is frequently encountered in lung and lymph node specimens and represents a diagnostic challenge because diverse infectious, immune-mediated, exposure-related, and neoplastic conditions may produce overlapping histologic patterns. Necrotizing, non-necrotizing, suppurative, foreign body-type, vasculitic, and malignancy-associated granulomas provide important diagnostic clues but are rarely disease-specific. Conventional pathology-based evaluation, including hematoxylin and eosin assessment, special stains, immunohistochemistry, culture, and serologic or antigen testing, remains the foundation of etiologic diagnosis. However, these methods may be limited by low organism burden, prior antimicrobial therapy, small tissue samples, formalin fixation, and broad etiologic heterogeneity. Molecular methods, including targeted polymerase chain reaction, 16S ribosomal RNA sequencing, internal transcribed spacer sequencing, targeted next-generation sequencing, and metagenomic next-generation sequencing, provide complementary tools for pathogen detection and species-level identification. This review summarizes the major histopathologic patterns and etiologic categories of granulomatous inflammation in lung and lymph node specimens and proposes a molecularly enhanced pathology-based algorithm for diagnostic workup. The goal is not to replace morphology with molecular testing, but to use histopathology to guide molecular assay selection and to interpret molecular findings within the appropriate tissue, microbiologic, radiologic, and clinical context.},
}

@article {pmid42442277,
year = {2026},
author = {Zhang, X and Han, S and Zhao, A and Wei, B and Chang, X and Song, S and Zhao, Y and Zhao, Z and Zhang, X and Chen, J},
title = {Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120488},
doi = {10.1016/j.ecoenv.2026.120488},
pmid = {42442277},
issn = {1090-2414},
abstract = {Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.},
}

@article {pmid42442278,
year = {2026},
author = {Li, X and Chen, Y and Wang, J and Shu, Y and Lv, G},
title = {Phytotoxic effects and rhizosphere microecological responses of peanut to oxytetracycline and microplastic co-exposure.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120498},
doi = {10.1016/j.ecoenv.2026.120498},
pmid = {42442278},
issn = {1090-2414},
abstract = {Microplastics (MPs) and antibiotics represent escalating emerging contaminants in global agricultural soils, posing substantial threats to crop health and ecosystem functionality worldwide. However, a comprehensive understanding of their joint toxicity and the underlying rhizosphere mechanisms under co-contamination remains elusive, leaving a critical knowledge gap. This study conducted a pot experiment using the globally cultivated peanut (Arachis hypogaea) exposed to polystyrene (PS) or polylactic acid (PLA) MPs (0.25 and 2% w/w) and oxytetracycline (OTC, 10 mg·kg[-1]), integrating metagenomic sequencing and untargeted metabolomics to elucidate root-zone microecological responses. High-concentration co-exposures significantly suppressed peanut shoot biomass, and OTC was identified as the primary contributor to reduced leaf catalase activity (CAT) (p < 0.01). Metagenomic profiling revealed that co-exposure significantly reshaped the rhizosphere microbiota (R[2] = 0.939, p = 0.001), enriching Pseudomonadota while inhibiting Actinobacteriota. Untargeted metabolomics detected 3789 metabolites, revealing that co-exposure significantly regulated the accumulation of defensive flavonoids (taxifolin and daidzin) and stress-responsive steroids (ponasterone A). Particularly, the combined exposure of PLA MPs and OTC induced the most severe metabolic disruption in the rhizosphere, generating 374 differential metabolites compared to the PLA-alone treatment. Procrustes analysis confirmed a tight coupling between microbial communities and metabolomes (M[2] = 0.619, p = 0.004). Network analysis further identified key regulatory nodes (Nocardioides and taxifolin) that bridge the associations between the rhizosphere microenvironment and plant growth traits. This study demonstrates that microbial shifts and metabolic adjustments are essential in mediating plant responses to multi-pollutant stress, providing crucial theoretical and mechanistic insights for global agricultural environmental risk assessment under co-contamination scenarios.},
}

@article {pmid42442320,
year = {2026},
author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A},
title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111939},
doi = {10.1016/j.ijfoodmicro.2026.111939},
pmid = {42442320},
issn = {1879-3460},
abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.},
}

@article {pmid42442424,
year = {2026},
author = {Luo, Z and Zhang, K and Wang, L and Zhang, J and Huang, Y and Lu, X and Zhao, F and Cao, S and Li, J},
title = {Astragalus polysaccharides reshape gut resistome of postpartum dairy cows.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135399},
doi = {10.1016/j.biortech.2026.135399},
pmid = {42442424},
issn = {1873-2976},
abstract = {Antibiotic resistance genes (ARGs) in livestock feces represent an important environmental reservoir of antimicrobial resistance. Natural product intervention is a potential strategy for regulating the gut microbiome of livestock; however, its effects on the gut resistome of postpartum dairy cows remain poorly understood. In this study, we investigated the effects of Astragalus polysaccharides (APS) supplementation on the fecal microbiome, ARGs, mobile genetic elements (MGEs), virulence factors (VFs), and ARG-carrying metagenome-assembled genomes (MAGs) in dairy cows during postpartum period. Alpha and beta diversity analyses showed that APS supplementation did not significantly alter the global resistome, mobilome, or virulome structure. The content of several ARGs and VFs, including AAC(6')-Iw, qacEdelta1, ast, PM_RS00425, and sdrF, significantly decreased in the APS group, and several plasmid-associated MGEs genes showed group-specific changes. Co-occurrence network analysis revealed complex associations between ARGs, VFs, and core bacterial taxa, with Paludibacter and Parabacteroides identified as potential microbial reservoirs of resistance- and virulence-associated genes. Furthermore, 101 metagenome-assembled genomes (MAGs) were recovered, 42 of which carried multiple ARGs. Bin.1, assigned to Scatovivens, had the highest ARG count. APS supplementation reduced the overall ARG load, particularly the ARG contribution in bin.1. However, APS utilization potential was not significantly correlated with ARG density or ARG load across MAGs. Thus, this study provides new insights into APS supplementation and nutritional strategies that can mitigate the fecal ARG burden in dairy production.},
}

@article {pmid42442443,
year = {2026},
author = {Umair, M and Jamal, Z and Ali, Q and Hakim, R and Rana, MS and Javed, Y and Bugti, AR and Ayub, A and Sabeen, F and Waheed, Y and Salman, M},
title = {Emergence of Reassortant Crimean-Congo Hemorrhagic fever virus lineages, Pakistan, 2023-2024.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105988},
doi = {10.1016/j.meegid.2026.105988},
pmid = {42442443},
issn = {1567-7257},
abstract = {Crimean-Congo hemorrhagic fever virus (CCHFV) remains endemic in Pakistan, yet whole-genome data are limited. During 2023-2024 national surveillance, 151 suspected cases were screened by qRT-PCR; 23 were confirmed at the NIH, Islamabad. Shotgun metagenomic sequencing of 17 cases (15 Pakistan, 2 Afghanistan) generated high-quality genomes, with 65% classified as Asia-1 genotype, while 35% showed segment reassortment involving Asia-2-derived S and/or M segments. Reassortment involved primarily S and M segments, while L segments remained conserved. Phylogenetic analysis revealed Asia-1 sequences closely related to strains from India, Afghanistan, Iran, and the Middle East, whereas Asia-2 sequences clustered with Indian and Central Asian strains, suggesting cross-border and regional viral exchange. S-segment phylogeography indicated northern Punjab (Rawalpindi, Islamabad, Chakwal, Attock) as a region potential involved in viral connectivity. Region-specific mutations (S: G185S, D186N; M: P90L, T122I, M35L, L443S, I1597V) may reflect localized viral evolution. These findings underscore ongoing viral diversification, reassortment, and regional connectivity, highlighting the need for integrated genomic surveillance to guide public health interventions.},
}

@article {pmid42442450,
year = {2026},
author = {Zhang, Z and Xia, Y and Liu, Y and Tao, L and Ju, F},
title = {Future Climate Scenarios Reduce Antibiotic Resistome-associated Risk but Enrich Specific Soil-borne Pathogens.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125248},
doi = {10.1016/j.envres.2026.125248},
pmid = {42442450},
issn = {1096-0953},
abstract = {Understanding how climate change reshapes the soil resistome, i.e., the collection of antibiotic resistance genes (ARGs), is critical for environmental and public health. Using a representative six-year (2014-2019) metagenomic dataset from a long-term climate manipulation experiment, this study investigated the impacts of future climate scenarios on cropland and grassland soil resistomes. Both simulated climate warming (+0.6°C) and extreme summers (+2.2°C during 2018-2019) significantly altered soil resistome structures, reducing ARG richness by 4.4%-12.5% while increasing the abundance of specific ARG types predominantly carried by gram-positive bacteria by 31.5%-72.8%. Simulated climate and extreme summer also reduced the abundance of high-risk ARGs by 10.0% and 27.2%, respectively, and concomitantly lowered the estimated resistome-associated risk by 18.3% and 36.4%, primarily through selectively filtering their bacterial hosts (e.g., Pseudomonadota). At the same time, future climate scenarios confer a competitive advantage for specific soil-dwelling antibiotic-resistant phytopathogens (e.g., Rhodococcus fascians) and human pathogens (e.g., Mycobacterium spp.), potentially increasing their prevalence and public health relevance in soil ecosystems. These findings highlight the contrasting responses of soil resistomes and pathogen communities under future climate scenarios and underscore the importance of long-term monitoring of soil ARGs and pathogens under the context of on-going global change within a One-Health framework.},
}

@article {pmid42442462,
year = {2026},
author = {Fukada, A and Suda, K and Watayo, H and Motooka, D and Shinoda, T and Tohya, M and Ishiyama, A and Nishimura, Y and Fujiwara, K and Ochi, T and Goto, H and Nikai, K and Ishii, J and Yamamoto, Y and Okazaki, T and Nakamura, S and Kirikae, T and Yamataka, A and Watanabe, S and Miyano, G},
title = {Characteristics and environmental susceptibility of first-pass meconium microbiota in neonates with congenital intestinal atresia.},
journal = {Journal of pediatric surgery},
volume = {},
number = {},
pages = {163290},
doi = {10.1016/j.jpedsurg.2026.163290},
pmid = {42442462},
issn = {1531-5037},
abstract = {PURPOSE: Whether congenital gastrointestinal atresia (atresia) specifically affects the meconium microbiota because of an altered intrauterine intestinal environment remains unclear. Therefore, we aimed to characterize the meconium microbiota of neonates with congenital anomalies, specifically atresia.

METHODS: Meconium samples were collected from healthy term neonates (control), neonates with congenital malformations other than atresia (other anomalies), and those with atresia who were admitted to the growing care unit or obstetrics ward. Alpha-diversity (Shannon index and observed features) and beta-diversity (principal coordinate analysis) were assessed through 16S rRNA gene sequencing. The microbial composition was examined at the phylum and genus levels, and stratified by delivery mode and mother's antibiotic exposure.

RESULTS: The study included 20 controls, 37 neonates with other anomalies, and 11 with atresia, including esophageal, duodenal, small intestinal, and colonic atresia. Alpha-diversity was the lowest in atresia, particularly with cesarean delivery or maternal antibiotic exposure (p<0.05). Beta-diversity analysis demonstrated that the distribution of microbial profiles significantly differed between the control and atresia groups (p<0.05). At the phylum level, atresia had a high proportion of Bacteroidetes, whereas Firmicutes and Proteobacteria were reduced. Several genera that were abundant in the control were markedly reduced in atresia (p<0.001 vs. control; p<0.01, among 3 groups), with higher Pseudomonas but lower Staphylococcus (p<0.05, vs. control and other anomalies) and Escherichia (p<0.05 vs. other anomalies).

CONCLUSION: Congenital gastrointestinal atresia demonstrated unique meconium microbiota profiles compared with those of healthy neonates and other congenital anomalies. This suggests differences in the intraintestinal environment during the fetal period.

LEVEL OF EVIDENCE: Ⅱ.},
}

@article {pmid42442593,
year = {2026},
author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W},
title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121232},
doi = {10.1016/j.cca.2026.121232},
pmid = {42442593},
issn = {1873-3492},
abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.

METHODS: This prospective study enrolled 105 patients aged ≥60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.

RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1β, IL-6, IL-8, TNF-α, IFN-γ), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).

CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.},
}

@article {pmid42443172,
year = {2026},
author = {Mühlberg, L and Ruta, J and Mikirtumov, V and Burton-Smith, R and Murata, K and Kudryashev, M and Okamoto, K and Bogdanow, B and Liu, F},
title = {Integrative structural interactomics reveals protein organization and structure in a giant virus.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42443172},
issn = {2041-1723},
support = {LI 3260/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KU 3222/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC-STG-2020 No. 949184//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Leibniz-Wettbewerb P70/2018//Leibniz-Gemeinschaft (Leibniz Association)/ ; 24ama121005j0003//Japan Agency for Medical Research and Development (AMED)/ ; 2018-03387 and 2023-01857//Vetenskapsrådet (Swedish Research Council)/ ; CTS23:2703//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; },
abstract = {Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrate cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocate 88 viral proteins to different virion sub-compartments and propose topologies of 25 inner membrane proteins. We assign eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.},
}

@article {pmid42130477,
year = {2026},
author = {Molano, LG and Hirsch, P and Keller, A and Dolejska, M and Palkovicova, J},
title = {HERA: a web server for host element reference-based aligner.},
journal = {Nucleic acids research},
volume = {54},
number = {W1},
pages = {W154-W159},
pmid = {42130477},
issn = {1362-4962},
support = {469073465//Deutsche Forschungsgemeinschaft/ ; //European Commission/ ; 205/2025/FVHE//University of Veterinary Sciences in Brno/ ; 24-12527S//Czech Science Foundation/ ; },
mesh = {*Software ; Internet ; *Plasmids/genetics/chemistry ; Genome, Bacterial ; Sequence Alignment ; Genomics/methods ; },
abstract = {Plasmids play a central role in bacterial adaptation and in the dissemination of antimicrobial resistance, driving a growing need for accessible tools that support their comparative analysis without requiring local computational infrastructure. Although several circular genome visualization platforms exist, most are designed for general bacterial genome analysis rather than focused on plasmid comparison. Host element reference-based aligner (HERA) is a web server for intuitive visualization and comparison of plasmids and other circular molecules through BLAST alignment against reference sequences. Built on interactive circular genome visualization, HERA simplifies comparative genomics by providing an accessible interface for exploring sequence similarity, identifying conserved regions, and analyzing genetic elements without the complexity of traditional local tools. HERA includes a plasmid-oriented annotation pipeline covering replicon and mobility typing, antimicrobial resistance detection, mobile element identification, and homology search against the PLSDB plasmid database. HERA also provides an automatic selection of the reference which is the most appropriate from the uploaded sequences. The web server is available without login or any restriction at https://web.ccb.uni-saarland.de/hera/.},
}

*Software
Internet
*Plasmids/genetics/chemistry
Genome, Bacterial
Sequence Alignment
Genomics/methods

@article {pmid42436166,
year = {2026},
author = {Chen, Y and Ma, J and Guo, Z and Chen, J and Wang, X and Xiao, J and Hu, D and Yan, J and Deng, W and Nu, Z and He, H and He, W and Luo, J and Zhang, YP and Li, Y},
title = {A rugged life: how host-microbiome adaptations associated with the semi-feral lifestyle of gayal (Bos frontalis).},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01095-4},
pmid = {42436166},
issn = {2055-5008},
support = {CY22624109//Yunnan Provincial Universities Service Key Industry Technology Project - Doctoral Student Industry-Oriented Scientific Research Innovation Training Project/ ; KC-242410789//Graduate Research and Innovation Project of Yunnan University/ ; 2021YFD1200904//National Key Research and Development Program of China/ ; 32470654//National Natural Science Foundation of China/ ; 202407AA110003//Special funds for central guidance of local scientific and technological development/ ; 202601BC070001//Major Program of Yunnan Fundamental Research Projects/ ; XDYC-QNRC-2023-0371//"Xingdian Talent Support Program" Grant of Yunnan Province/ ; },
abstract = {The semi-domesticated gayal (Bos frontalis) is an endangered browsing ruminant inhabiting the rugged Eastern Himalayan foothills, and maintains an energy-intensive lifestyle on nutrient-poor, fiber-rich feed. However, the dietary, microbial, and host physiological features underlying this adaptation remain poorly understood. Here, we analyzed fecal metagenomes from ten bovine populations (n = 334) to characterize dietary composition. Then we profiled the four-chambered (FC) stomach microbiome in adult gayal (Bos frontalis), yak (Bos grunniens), and taurine cattle (Bos taurus). Host transcriptomes were profiled across the FC stomach in adult individuals from gayal, yak and cattle. Dietary analysis revealed a woody plant-dominated, bamboo-rich dietary pattern in gayal. Gastric metagenomes in gayal showed high population-level microbial diversity, pronounced individual-associated community structure, and functional potentials related to aromatic compound transformation, nitrogen metabolism, and metabolic flexibility. Transcriptomes revealed compartment-specific specialization in the gayal stomach, including rumen immune signatures and reticulum contractile/electrophysiological features. Exploratory compartment-level integration further suggested possible consistency between host transcriptomic features and microbial functional potential. Together, these multi-omics findings suggest a host-microbiome system potentially associated with the utilization of chemically complex, low-quality forage, providing a framework for understanding digestive features of browsing ruminants and for conserving host-associated gastrointestinal microbiomes.},
}

@article {pmid42436177,
year = {2026},
author = {Eriksson, D and Righetti, D and Benedetti, F and Gruber, N and Paoli, L and Salazar, G and Sunagawa, S and Vogt, M},
title = {Nitrogen fixation rates increase with diazotroph richness in the global ocean.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61132-2},
pmid = {42436177},
issn = {2045-2322},
abstract = {Marine nitrogen fixation is a key process to support and maintain the ocean's primary production, yet our knowledge of the distribution and diversity of the diazotrophic microbes that are capable of fixing nitrogen is very limited. Here, integrating microscopic and metagenomic data, we determine the biogeography and richness of the main diazotrophic taxa across the global ocean. Analyzing 22,000 records and 15 species, we deduce a latitudinal gradient in diazotroph richness, with higher richness to the tropics driven by temperature and nutrient levels. Cyanobacteria dominate in nutrient-poor gyres, while non-cyanobacterial diazotrophs thrive in nutrient-rich zones. Across the global ocean, diazotroph richness is found to correlate positively with nitrogen fixation rates, suggesting a positive biodiversity-ecosystem function relationship. While this relationship is robust to spatial autocorrelation and confounding environmental drivers, spatial dependence in the global datasets and potential unmeasured covariates may influence local-scale inferences. The findings suggest that positive biodiversity-ecosystem functioning relationships with implications for global biogeochemical cycling exist in marine plankton.},
}

@article {pmid42436183,
year = {2026},
author = {Liu, Z and Wu, H and Howe, S and Zuo, B and Tian, Y and Wang, X and Assress, HA and Shang-Lun Lan, R and Mu, C and Xiao, Y and Huang, Y and Looper, M and Tsai, T and Zhao, J},
title = {Lactiplantibacillus plantarum promotes intestinal goblet cell differentiation via indole-3-lactic acid-AHR signaling in pigs.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01085-6},
pmid = {42436183},
issn = {2055-5008},
support = {Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 32573234//the National Natural Science Foundation of China/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; Grant No. 2023B10564001//Double First-Class Discipline Promotion Project/ ; USDA-ARS 6026-10700-001-000D//USDA/ ; USDA-ARS 6026-10700-001-000D//Food and Nutrition Service/ ; 2023YFE0124400//National Key Research and Development Program of China/ ; 2025-WPY-00-001//the Guangdong Provincial Special Fund Project for Seed Industry Revitalization/ ; },
abstract = {The swine intestinal microbiota dynamically remodels during development and supports gut homeostasis. However, whether stage-specific microbial shifts, are associated with epithelial development remains poorly understood. Here, longitudinal metagenomic profiling of the swine gut microbiome identified Lactiplantibacillus plantarum as a transiently enriched nursery-stage bacterium positively associated with goblet cell numbers. Dietary supplementation with L. plantarum validated this association, showing increased goblet cell numbers and MUC2 expression in the ileum of nursery piglets. Co-culture with porcine ileum organoids further demonstrated that L. plantarum cell-free supernatant promoted ileal organoid growth and goblet cell differentiation. Integrated untargeted metabolomic analyses of ileal samples and bacterial culture supernatants identified indole-3-lactic acid (ILA) as a potential key microbial metabolite from L. plantarum. Mechanistically, ILA promoted intestinal stem cell proliferation and MUC2 expression, accompanied by increased expression of aryl hydrocarbon receptor (AHR) and its downstream target CYP1A1 in ileal organoids. Consistently, activation of AHR using FICZ increased MUC2 expression, whereas inhibition with CH-223191 suppressed MUC2 expression in ileal organoids. Collectively, these findings uncover a L. plantarum-ILA-AHR signaling axis that promotes intestinal goblet cell differentiation, providing mechanistic insight into microbial metabolite-mediated regulation of epithelial homeostasis during post-weaning period in pigs.},
}

@article {pmid42436393,
year = {2026},
author = {Zhao, Y and Wang, H and Duan, J},
title = {A rare presentation of clinically diagnosed lyme disease with probable neuroborreliosis, septic shock, and bone marrow suppression: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13899-y},
pmid = {42436393},
issn = {1471-2334},
support = {2025-HX-27//Evaluation of the effects of acupuncture intervention on central nervous system regulation in septic patients/ ; },
abstract = {BACKGROUND: Lyme disease is rarely considered in critically ill patients from regions not routinely recognised as endemic. Severe presentations including septic shock, central nervous system involvement, and bone marrow suppression may therefore be difficult to recognise, particularly when laboratory confirmation is incomplete.

CASE PRESENTATION: A 60-year-old man from an inland province of northern China was admitted to the intensive care unit with four months of relapsing fever, acute delirium, respiratory distress, and septic shock. During admission, he developed recurrent high-grade fever with migratory erythematous rashes. Collateral history revealed a tick bite approximately 15 months earlier, followed by an expanding erythematous lesion compatible with erythema migrans. Cerebrospinal fluid showed markedly elevated opening pressure (>30 cmH2O), lymphocytic pleocytosis, elevated protein, and a normal CSF-to-serum glucose ratio, consistent with aseptic meningitis. Bone marrow aspiration showed pure red cell aplasia and megakaryocyte maturation arrest. Blood, urine, and cerebrospinal fluid cultures were negative, and metagenomic next-generation sequencing did not identify alternative pathogens. Lyme serology showed isolated IgM positivity with IgG negativity. Confirmatory two-tier testing and CSF Borrelia antibody testing were unavailable in our centre. This patient was therefore classified as clinically diagnosed Lyme disease with probable neuroborreliosis. Treatment with ceftriaxone and doxycycline was followed by defervescence and haematological recovery. At follow-up several weeks after discharge, the patient was afebrile, fully alert, and oriented.

CONCLUSIONS: This case highlights an unusual severe presentation of clinically diagnosed Lyme disease with probable neuroborreliosis, intracranial hypertension, septic shock, and bone marrow suppression. Geographic origin should not preclude diagnostic consideration. In critically ill patients with unexplained fever, cytopenias, and dynamic cutaneous lesions, careful tick exposure history and bedside dermatological assessment may prove decisive where laboratory testing is inconclusive.},
}

@article {pmid42437026,
year = {2026},
author = {Mohidin, AF and Neshat, SA and Santillan, E and Wuertz, S},
title = {Disturbance intensity shapes universal and context-dependent functional traits in anaerobic microbiomes.},
journal = {Environmental science and ecotechnology},
volume = {32},
number = {},
pages = {100729},
pmid = {42437026},
issn = {2666-4984},
abstract = {Trait-based frameworks, notably Grime's competitor-stress-tolerant-ruderal theory, offer a powerful lens for predicting how environmental fluctuations govern community structure. Yet, classical ecological models assume environments combining extreme stress and intense disturbance are non-viable for sustained colonisation, leaving a critical bottleneck in our ability to predict how microbial systems withstand compounded operational pressures. This gap severely hinders the predictive management of engineered microbiomes critical for global waste-to-energy conversion. Here we extend the application of classic ecological frameworks by demonstrating that anaerobic digester microbiomes deploy distinct, predictable life-history strategies across a 182-day compounded gradient of biomass turnover and organic loading. High-intensity single-event disturbances drive severe volatile fatty acid accumulation (propionate reaching 2,955 mg L[-1]), selectively shifting the microbiome toward stress-tolerant and stress-tolerant-ruderal strategies. Traits associated with ribosome function, molecular chaperones, and enzymatic reactive oxygen species detoxification were particularly enriched under highly disturbed conditions. Conversely, intermediate regimes were associated with ruderal strategies that prioritise rapid growth over resource-uptake efficiency, dropping total chemical oxygen demand removal to 41%. Cross-system comparisons encompassing anaerobic digestion, activated sludge, and soil ecosystems, revealed both universal and context-dependent ecological traits. Survival-associated traits linked to cell maintenance and repair, protective mechanisms, and cell motility were universally associated with stress-tolerant or ruderal strategies across ecosystems, whereas nutrient transport and metabolic traits exhibited greater context dependency. These insights establish a gene-resolved framework that reconciles microbial trait selection with ecological theory, providing a roadmap to engineer microbiome resilience against process failures.},
}

@article {pmid42437039,
year = {2026},
author = {Goraya, MU and Fatima, G and Hayat, K and Raza, A and Yong, D},
title = {The evolution of diagnostic microbiology: integrating culture-based methods and genomic advances.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21411},
pmid = {42437039},
issn = {2167-8359},
mesh = {Humans ; *Genomics/methods ; *Microbiological Techniques/methods/trends ; Bacteria/genetics/isolation & purification ; *Molecular Diagnostic Techniques/methods ; Machine Learning ; },
abstract = {Over the past several decades, diagnostic microbiology has progressed from traditional culture methods to include modern, culture-independent molecular and metagenomic approaches for diagnosing infectious diseases and guiding antimicrobial therapy. Since the beginning of the twenty-first century, clinical diagnostic microbiology has made considerable strides in optimizing pathogen identification. This progress has been driven by the introduction of optimized sampling methods, advanced diagnostic kits, and new technologies like mass spectrometry for bacterial identification, real-time genomics, and adaptable culture systems. However, the costs of advanced molecular methods are very high, and they require massive instrumentation to reach a clinical diagnosis. Conventional cultures remain cost-effective and can be performed with minimal resource requirements compared to advanced laboratory equipment. However, the most significant challenge with conventional methods is the reporting time of results (several days). Since the newer molecular and genomic methods do not meet all the diagnostic demands, strategies have shifted toward employing techniques with higher precision, sensitivity, and better time efficiency. The integration of artificial intelligence and machine learning is set to redefine diagnostic paradigms, facilitating not only rapid and precise pathogen identification but also addressing foundational limitations in data analysis and interpretation. This review evaluates the synergy between conventional and emerging diagnostic technologies, emphasizing their clinical utility, limitations, and future trajectories for diverse audiences in microbiology and healthcare.},
}

Humans
*Genomics/methods
*Microbiological Techniques/methods/trends
Bacteria/genetics/isolation & purification
*Molecular Diagnostic Techniques/methods
Machine Learning

@article {pmid42437291,
year = {2026},
author = {Griffin, NG and Hughes, AE and Erdody, DS and Berlemont, E and Sweeney, S and Fareghbal, T and Hagedorn, KB and Berlemont, R},
title = {Annotation of glycoside hydrolases in unassembled metagenomes using CAZyOGH.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag137},
pmid = {42437291},
issn = {2635-0041},
abstract = {MOTIVATION: Functional characterization of microbiomes often relies on the sequencing of metagenomic DNA extracted from environmental samples, with current approaches using metagenome-assembled genomes (MAGs). Although glycoside hydrolases (GHs) are central to carbon cycling, accurate annotation of GHs in metagenomic datasets remains challenging due to the multidomain architecture of carbohydrate-active enzymes and the prevalence of unassembled short reads due to limitations in the MAG-generation process.

RESULTS: Here, we present CAZyOGH (CAZymes Open-source GH annotation), a curated reference database for the domain-specific identification of 135 protein domains spanning 99 GH families with well-defined catalytic domain signatures. CAZyOGH focuses on individual GH domains, enabling robust annotation of both assembled and unassembled metagenomic data. We validated CAZyOGH by reanalyzing genomes listed in CAZy db, where predicted GH profiles closely matched reported values. Next, we used CAZyOGH to analyze 12 human gut metagenomes and 12 newly sequenced soil microbiomes to reveal environment-specific GH repertoires. By accurately detecting catalytic domains independent of the genomic context, CAZyOGH improves sensitivity and specificity in short-read metagenomic annotation. This framework provides a scalable and reproducible approach to investigate carbohydrate-active enzymes across ecosystems, advancing our capacity to characterize microbial functional potential in global carbon cycling.

CAZyOGH data is available on figshare (https://figshare.com/projects/CAZyO_GH/267770).},
}

@article {pmid42437307,
year = {2026},
author = {Guo, Y and Liang, Y and Liu, L and Zhou, Y and Yang, X and Ming, X and Hu, P and Wu, J and Li, D and Hou, D and Xia, S and Wang, X and Zuo, Y},
title = {Decoding preeclampsia: A fusion of multi-view machine learning and multi-omics to identify putative inflammation-related mechanisms.},
journal = {Molecular therapy. Nucleic acids},
volume = {37},
number = {3},
pages = {102992},
pmid = {42437307},
issn = {2162-2531},
abstract = {Preeclampsia (PE) is a leading cause of maternal and fetal morbidity and mortality worldwide, with placental inflammation recognized as a central pathogenic feature, yet the upstream triggers and inflammatory mechanisms remain incompletely understood. Here, we combined placental single-cell transcriptomics with gut metagenomic and metabolomic profiling to characterize inflammatory signatures in PE. Stratified analyses across clinical subgroups-defined by fetal number, onset timing, and fetal sex-revealed that placental single-cell transcriptomics coupled with multi-view machine learning consistently prioritized bacteria-associated inflammatory features across all subgroups. Superimposed on this shared foundation, we identified subgroup-specific trajectories: twin PE exhibited IL-1-dominant inflammation with compensatory antioxidant metabolic shifts, while singleton PE showed IFN-II-associated immune activation. Early-onset PE displayed sexual dimorphism-male fetuses featured bacterial defense pathways, lipid metabolic programs, and trophoblast-confined glycolysis, while female fetuses exhibited angiogenesis, chemotaxis, nitric oxide signaling pathways, and glycolytic reprogramming in immune cells, whereas late-onset PE exhibited comparatively attenuated inflammatory activity. Gut metagenomic profiling revealed enrichment of lipopolysaccharide (LPS)-producing taxa and depletion of beneficial commensals in PE, accompanied by metabolomic alterations that aligned with inflammatory pathways also highlighted in placental analyses. Collectively, these findings reveal a conserved bacteria-associated inflammatory program in PE that is modulated by clinical context and linked to gut microbial dysbiosis.},
}

@article {pmid42437513,
year = {2026},
author = {Dhande, SS and Mankoskar, NA and Panakkal, HP and Gupta, IR and Bhagat, RP},
title = {Critical Review on Microbial Inulinase Production: Emerging Strategies, AI-Driven Optimization, and Applications.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70306},
pmid = {42437513},
issn = {1097-0290},
support = {Plan & Stat/RDC/2024-25/1018-21//Dr. Babasaheb Ambedkar Marathwada University/ ; },
abstract = {Microbial inulinases are increasingly recognized as valuable biocatalysts for the sustainable production of high-value products, including fructooligosaccharides, fructose, bioethanol, and organic acids in industries, such as food, pharmaceuticals, and bioenergy. In the last few decades, microbial inulinase research has advanced significantly, from strain selection and fermentation optimization to advanced enzyme engineering and immobilization, improving yields, stability, and reusability. There are still some final bottlenecks, such as low yields, poor thermostability, and high purification costs. This review examines strategies to innovate and overcome these bottlenecks, including novel immobilization strategies that utilize nanomaterials, system-scale bioprocess optimization using artificial intelligence (AI), and bioprospecting extremophiles using metagenomics. The present review discusses how statistical and computational modeling (RSM, ANN, and AI) significantly increases yield and process efficiency, with comments on their relevance to contemporary biorefinery applications. The advanced immobilization approaches significantly enhance operational stability and reusability, allowing for continuous processing. This review situates the development of inulinase as not just an enzymological effort but a multidisciplinary effort involving process engineering and sustainability science. Overall, emphasize is given toward the thought that advancements leaning toward the future will require a synthesis of AI-designed enzyme systems; economical immobilization supports; and incorporation of circular bioeconomy principles through the valorization of agro-wastes. These barriers to knowledge transfer must be resolved if we are to unlock the full bioeconomic potential of microbial inulinase systems.},
}

@article {pmid42437546,
year = {2026},
author = {Fregolente, LG and Roth, FN and Warncke, JD and Macpherson, AJ and Yilmaz, B and Bassetti, CLA},
title = {The gut-sleep connection: a scoping review into microbiome alterations in sleep-wake and circadian disorders.},
journal = {Sleep medicine},
volume = {147},
number = {},
pages = {109136},
doi = {10.1016/j.sleep.2026.109136},
pmid = {42437546},
issn = {1878-5506},
abstract = {Sleep is fundamental to brain, body, mental, and social health. In parallel, the gut microbiome is increasingly recognized as a key regulator of immune, metabolic, endocrine, and neurophysiological processes. This scoping review explored current evidence on gut microbiome alterations in relation to sleep duration and sleep loss, sleep-wake disorders, and circadian rhythm-related phenotypes. Searches of MEDLINE, Embase, and Cochrane were conducted up to February 2024. Of 2059 records identified, 54 studies met the eligibility criteria. Thirty-eight studies were observational, nine interventional, and seven genome-wide association or Mendelian-randomization studies. The most frequently investigated phenotypes were insomnia (15 studies, 28%), obstructive sleep apnea (12 studies, 22%), circadian rhythm or circadian-misalignment phenotypes (10 studies, 19%), and sleep duration or sleep loss/deprivation (9 studies, 17%). Most studies used 16S rRNA gene sequencing to assess gut microbiota composition and diversity, while shotgun metagenomic sequencing and functional analyses were less common. Across disorders, studies reported alterations in microbial diversity, taxonomic composition, short-chain fatty acid-producing taxa, bile acid-related pathways, inflammatory markers, and cardiometabolic or neurophysiological correlates. However, findings were limited by heterogeneous sleep phenotyping, small sample sizes, cross-sectional designs, variable microbiome methods, and inconsistent control of diet, medication use, body mass index, comorbidities, and stool sampling protocols. Current evidence supports an association between sleep-wake and circadian disturbances and gut microbiome alterations, but causality and disorder-specific microbial signatures remain unresolved. Standardized longitudinal and multi-omics studies are needed to clarify mechanisms and therapeutic potential.},
}

@article {pmid42437625,
year = {2026},
author = {Souto, LCDS and Ubaid, FK and Hernández, LHA and da Silva, SP and Barbosa, BB and Farias, LDSS and Coelho, TFSB and Cruz, ACR and Mascarenhas, JDP},
title = {New Iflavirus identified in Chiroxiphia pareola birds from an ecotone area in northeast Brazil.},
journal = {Virus research},
volume = {},
number = {},
pages = {199776},
doi = {10.1016/j.virusres.2026.199776},
pmid = {42437625},
issn = {1872-7492},
abstract = {Avian species play a key role in the ecology of viruses, acting as reservoirs, sentinels, and biological carriers across diverse environments. Here, we describe the detection and genomic characterization of a novel iflavirus identified in fecal samples from the Chiroxiphiapareola("blue-backed manakin") collected in areas of the Middle North region of Brazil, Maranhão state. Viral RNA was extracted from pool fecal samples and subjected to next-generation sequencing. De novo assembly and comparative analyses enabled the recovery of a complete picorna-like viral genome of 9,043 nucleotides, comprising a single open reading frame encoding a polyprotein of 2,896 amino acids. Phylogenetic analyses based on the RNA-dependent RNA polymerase (RdRp) domain and the translated polyprotein consistently clustered the virus within the family Iflaviridae, forming a specific clade with reference sequences previously reported in arthropods. Functional domain analysis revealed conserved motifs characteristic of positive-sense single-stranded RNA viruses, including helicase superfamily 3 and RdRp domains. Although iflaviruses are classically associated with arthropod hosts, their detection in avian fecal samples is likely related to dietary intake, suggesting the presence of a transient virome rather than active infection. The sampling area is characterized by increasing environmental degradation, which may favor interactions between wildlife and anthropogenic environments, highlighting the importance of viral surveillance. This study reports, for the first time, the genome of an iflavirus detected in C. pareola, expanding current knowledge on iflavirus diversity and reinforcing the relevance of wildlife-based surveillance in ecologically altered regions under anthropogenic pressure.},
}

@article {pmid42430137,
year = {2026},
author = {Allen, L and Sheneman, A and Morrow, MA},
title = {Post-wildfire soil bacterial MAGs and metagenome analysis.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0044426},
doi = {10.1128/mra.00444-26},
pmid = {42430137},
issn = {2576-098X},
abstract = {We compare the differences between bacteria in soil affected by a wildfire to an unaffected area from Minnewaska State Park, NY, located in the biodiverse northern Shawangunk Ridge. We detail our metagenomic sequencing data, relative abundance of bacterial phyla, and the taxonomic classification of three MAGs.},
}

@article {pmid42430408,
year = {2026},
author = {Khan, N and Nasir, MM and Aziz, U and Manzoor, H and Raziq, MF and Hussain, Z and Jabeen, I and Kayani, MUR},
title = {Integrative metagenomics and structural bioinformatics identify explainable gut microbial variants associated with Crohn's disease.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0340748},
doi = {10.1371/journal.pone.0340748},
pmid = {42430408},
issn = {1932-6203},
mesh = {*Crohn Disease/microbiology/genetics ; Humans ; *Metagenomics/methods ; *Computational Biology/methods ; Polymorphism, Single Nucleotide ; Molecular Dynamics Simulation ; Bacteroides/genetics ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/chemistry/metabolism ; Colitis, Ulcerative/microbiology/genetics ; },
abstract = {Metagenomics has revealed disease-associated shifts in microbial taxa and functions in inflammatory bowel disease (IBD) patients. However, the role of genomic variation in gut commensals remains poorly understood. Here, we integrated metagenomic profiling, variant calling, and structural bioinformatics to identify disease-associated variants in the gut microbes. Crohn's disease (CD) and ulcerative colitis (UC) showed significant negative associations with Bacteroides uniformis, Bacteroides vulgatus, and Eubacterium rectale. These bacteria exhibited 190,712 single-nucleotide polymorphisms, including 479 CD-specific and 235 UC-specific variants. Variant prioritization identified a CD-specific Val170Leu substitution in the conserved starch-binding domain of the Starch Utilization System D (SusD) protein in B. uniformis. Structural modeling and cyclodextrin docking indicated reduced binding affinity in the mutant, while 200-ns molecular dynamics simulations showed stable ligand retention only in the wild type. These findings suggest that impaired starch metabolism driven by SusD variation may contribute to B. uniformis depletion in CD and demonstrate the value of integrating metagenomics with structural analyses to identify functionally relevant microbial variants.},
}

*Crohn Disease/microbiology/genetics
Humans
*Metagenomics/methods
*Computational Biology/methods
Polymorphism, Single Nucleotide
Molecular Dynamics Simulation
Bacteroides/genetics
*Gastrointestinal Microbiome/genetics
Bacterial Proteins/genetics/chemistry/metabolism
Colitis, Ulcerative/microbiology/genetics

@article {pmid42430554,
year = {2026},
author = {Penzotti, P and Gutkind, G and Powers, RA and Power, P},
title = {Environmental species from theTelluria group as the putative origin of bifunctionalβ-lactamases.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0342825},
doi = {10.1128/spectrum.03428-25},
pmid = {42430554},
issn = {2165-0497},
abstract = {β-Lactamases comprise two structurally and evolutionarily well-defined groups: serine- (SBL) and metallo-β-lactamases (MBL). To date, clinically relevant β-lactamases are typically monofunctional DD-peptidases, containing a single active site cavity per molecule. Recently, several genes encoding putative β-lactamases from the four molecular classes (named as LRA) were identified through functional metagenomics in Alaskan soil samples. blaLRA-13 encoded a 609-amino acid protein encompassing a class D and a class C-like β-lactamase fused as a single polypeptide, translated from a single open reading frame (ORF). Furthermore, we identified 20 LRA-13 homologs, one of them found in a Duganella hordei isolate, sharing 91.3% amino acid identity. Predicted structures generated with AlphaFold 3 showed similar conserved architectures encompassing an N-terminal and C-terminal domains compatible with class D and class C β-lactamases, respectively, connected by a short peptide as a linker and containing their characteristic structural features. A maximum likelihood (ML) evolutionary tree showed a close relationship between LRA-13 and the putative β-lactamase from Duganella hordei, a species belonging to the Telluria group, indicating that bifunctional enzymes likely evolved from a common remote ancestor and that their diversification may provide an evolutionary advantage in certain environmental niches. The genetic content of blaLRA-13 and related genes appears to have a conserved synteny. The description of β-lactamases with two catalytic sites constitutes a novel finding and provides a basis for exploring new evolutionary mechanisms.IMPORTANCEβ-Lactamases are enzymes able to destroy β-lactam antibiotics and are divided into two main groups according to their structural and mechanistic features: serine- (SBL) and metallo-β-lactamases (MBL). To date, β-lactamases that represent a threat and are produced by bacterial pathogens contain a unique catalytic "pocket,"i.e., only a single β-lactam molecule is bound and cleaved at a time. LRA-13 and other related proteins seem to contain two different catalytic sites of different kinds (one of them is related to class C β-lactamases and the other to class D enzymes). In this study, we analyzed if these enzymes can represent a different evolutionary path for the β-lactamases.},
}

@article {pmid42430840,
year = {2026},
author = {Li, QD and Wang, YY and Nwankwo, C and Hu, Y and Dong, XY and Hou, J and Chen, XD and Cui, HL},
title = {Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov., halophilic archaea from coastal tidal flats, a saline lake, and a marine solar saltern.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {5},
pages = {126750},
doi = {10.1016/j.syapm.2026.126750},
pmid = {42430840},
issn = {1618-0984},
abstract = {Five novel halophilic archaeal strains, designated DTA46[T], DTA98[T], HHNYT27[T], N11[T], and SY-15[T], were isolated from diverse saline environments across various regions of China. Amplicon and metagenome analyses revealed that three amplicon reads were affiliated with strains DTA46[T], HHNYT27[T], and N11[T] while two MAGs related to strains N11[T] and SY-15[T]. The sequence similarities among these five strains and current species of the genus Halorubrum were 93.1%-99.1% and 86.0%-95.9% judged by 16S rRNA and rpoB' genes, respectively. Phylogenomic and comparative genomic analyses revealed their close affiliation with Halorubrum. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values between these strains and existing Halorubrum species ranged from 74.9%-93.6%, 22.3%-58.3%, and 68.3%-93.7%, respectively. All are below the recommended thresholds for species delineation, which supports their classification as novel taxa. The growth characteristics of strains DTA46[T], DTA98[T], HHNYT27[T], N11[T], and SY-15[T] were determined as follows: temperature range 20-60 °C (optima: 35, 37-42, 37, 35, and 42 °C), NaCl concentration 1.4-5.5 M (optima: 2.6, 3.1, 3.1, 3.1, and 5.1 M), and pH range 5.5-9.5 (optima: 8.0, 8.0, 7.0, 7.5, and 7.0). Based on the polyphasic characterization integrating phenotypic, chemotaxonomic, phylogenetic, and phylogenomic evidence, strains DTA46[T], DTA98[T], HHNYT27[T], N11[T], and SY-15[T] are proposed to represent five novel species of the genus Halorubrum, for which the names Halorubrum marinum sp. nov., Halorubrum rarum sp. nov., Halorubrum wangae sp. nov., Halorubrum shenae sp. nov., and Halorubrum zhoui sp. nov. are designated, respectively.},
}

@article {pmid42430921,
year = {2026},
author = {Li, Z and Xie, R and Zhang, W and Cheng, J and Jia, P and Liu, C and Guo, X and Zhuang, L and Chen, T},
title = {Lead fraction transformation drives microbial functional recovery and coupled nutrient cycling-metal resistance networks in Pb-Zn tailings.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142947},
doi = {10.1016/j.jhazmat.2026.142947},
pmid = {42430921},
issn = {1873-3336},
abstract = {Ecological remediation of lead-zinc (Pb-Zn) mine tailings, characterized by nutrient deficiency and high concentrations of toxic metals, represents a significant environmental challenge. While revegetation is a promising strategy, the underlying microbial functional responses, particularly the coupling between nutrient cycling and heavy metal detoxification, remain insufficiently understood. This study investigated the geochemical evolution and microbial functional succession of a Pb-Zn tailings pond, encompassing fresh tailings, weathering, and revegetation areas. Geochemical analysis, metagenomic sequencing, and the cultivation of the dominant bacterial strain were employed. Results demonstrated that revegetation significantly enhanced microbial α-diversity and shifted community assembly toward stochasticity. Metagenomic analysis revealed a substantial increase in the abundance and diversity of functional genes related to carbon, nitrogen, phosphorus, and sulfur (C/N/P/S) cycling, concurrent with the enrichment of metal resistance genes. The transformation of Pb fraction, specifically a decrease in bioavailable (exchangeable) fractions and an increase in stable (organic-bound, residual) fractions, was identified as the key driver of microbial functional recovery. Co-occurrence network analysis demonstrated a strong synergy between the Pb resistance gene zntA/yhhO and core nutrient-cycling genes. Furthermore, the dominant isolated strain, Pseudomonas aeruginosa QPBII-1, exhibited high Pb(Ⅱ) removal efficiency (98.5%). Multi-faceted characterization indicated its removal mechanism involves extracellular immobilization and intracellular reduction of Pb(Ⅱ) to less toxic Pb(0)/PbO, supported by genomic evidence (e.g., pbrA, narB). This study demonstrates that revegetation fosters an integrated microbial network that couples biogeochemical cycling with metal resistance, providing a mechanistic basis for developing sustainable bioremediation strategies for metalliferous tailings.},
}

@article {pmid42431026,
year = {2026},
author = {Guhanraj, R and Matharasi, AP},
title = {Integrated anaerobic culture and molecular approaches for periodontal pathogens: Advancements in microbial detection and characterization.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {3},
pages = {117540},
doi = {10.1016/j.diagmicrobio.2026.117540},
pmid = {42431026},
issn = {1879-0070},
abstract = {Periodontal diseases are polymicrobial infections driven by complex interactions between anaerobic pathogens and host immune responses within the periodontal pocket. Accurate detection and characterization of these pathogens are critical for early diagnosis, disease risk assessment, and effective therapeutic intervention. This review aims to critically evaluate conventional anaerobic culture and advanced molecular diagnostic techniques for the detection and characterization of periodontal pathogens, highlighting their respective advantages, limitations, and clinical relevance. A comprehensive analysis of existing literature was conducted focusing on traditional culture-based approaches and emerging molecular technologies, including polymerase chain reaction (PCR), quantitative PCR (qPCR), 16S rRNA gene sequencing, next-generation sequencing (NGS), and multi-omics strategies such as metagenomics, metatranscriptomics, proteomics, and metabolomics. Anaerobic culture remains the gold standard for microbial isolation, enabling phenotypic characterization, antimicrobial susceptibility testing, and functional studies. However, it is labor-intensive, time-consuming, and limited in detecting fastidious, slow-growing, or viable-but-non-culturable microorganisms. In contrast, molecular techniques offer rapid, sensitive, and comprehensive detection of key periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Advanced omics approaches further provide insights into microbial functionality, virulence, and host-microbe interactions. Nevertheless, molecular methods are limited in assessing microbial viability and antimicrobial susceptibility. The integration of culture-based and molecular diagnostic approaches enhances diagnostic accuracy and supports early, targeted therapeutic interventions. This combined strategy facilitates personalized treatment planning, improves clinical outcomes, and helps reduce inappropriate antimicrobial use in periodontal therapy. Both anaerobic culture and molecular diagnostics possess distinct yet complementary strengths. An integrated diagnostic approach combining phenotypic and high-resolution molecular techniques is essential for improving diagnostic accuracy, enabling personalized treatment strategies, advancing precision periodontal care, and contributing to Good Health and Well-Being through improved oral health outcomes and responsible antimicrobial stewardship.},
}

@article {pmid42431120,
year = {2026},
author = {Osborne, CJ and Deakins, AG and Ergunay, K and Bourke, BP and Linton, YM and Jiang, L and Grieco, JP and Achee, NL and McDermott, EG},
title = {Metagenomic sequencing provides insight into pathogenic and related benign microbes in ticks collected from pastured cattle.},
journal = {Veterinary microbiology},
volume = {320},
number = {},
pages = {111135},
doi = {10.1016/j.vetmic.2026.111135},
pmid = {42431120},
issn = {1873-2542},
abstract = {Biting arthropods (e.g., ticks and mosquitoes) feed on pastured cattle and may serve as sentinels for certain pathogens present in the environment, including those with the capacity to spillover from wildlife into managed herds and humans. Metagenomic next generation sequencing (mNGS)-enabled by applications such as Oxford Nanopore Technologies (ONT)-allows samples to be screened for a diverse array of known and unknown pathogens compared to traditional targeted methods reliant on polymerase chain reaction (PCR). This study examined the utility of mNGS to identify potential pathogens relevant to animal and human health in samples collected from pastured cattle in Arkansas. Twenty Angus calves (Bos taurus) were sampled by collecting whole blood, swabbing the nose, mouth, and peri-anal region, and collecting ticks during a three-minute search. Each sample type was processed according to published procedures, and samples were sequenced using ONT MinION flow cells. mNGS analysis identified potentially pathogenic Theileria, Ehrlichia, and Borrelia species in tick samples. Downstream PCR identified Theileria cervi in 28.89% (13/45) of tick pools and 5.00% (1/20) of blood samples, a Babesia sp. in 6.67% (3/45) tick pools, three Ehrlichia species (E. chaffeensis, E. ewingii, and Panola Mountain Ehrlichia) in 6.61% (8/121) of ticks, and Borrelia lonestari in 2.48% (3/121) of ticks. In conclusion, the mNGS approach illuminated a wide spectrum of suspected microorganisms down to the genus-level, which were further characterized and confirmed as pathogenic species with conventional molecular detection approaches, thereby demonstrating a rigorous approach for a broad-spectrum screen and confirmation framework for pathogen identification.},
}

@article {pmid42431299,
year = {2026},
author = {Zhang, X and Cai, M and Lin, J and Feng, Z and Wang, W and Jiao, Y and Lu, L},
title = {Multi-year glyphosate exposure impairs soil fertility, microbial communities, nutrient cycling genes, and tea quality in tea plantations.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128689},
doi = {10.1016/j.envpol.2026.128689},
pmid = {42431299},
issn = {1873-6424},
abstract = {Although glyphosate is highly effective for weed control, its potential risks to tea agroecosystems remain a significant concern. Previous studies have shown inhibitory effects on soil microbial communities in tea plantations, yet the multi-year impacts of glyphosate on microbially mediated nutrient cycling remain poorly understood. To address this gap, we conducted a three-year controlled field experiment, applying glyphosate at 0 kg a.i. ha[-1] (CK), 2.3 kg a.i. ha[-1] (G1), and 6.9 kg a.i. ha[-1] (G2), and used metagenomic sequencing to evaluate its effects on soil fertility, microbial communities, nutrient cycling genes, and tea quality. The results showed that glyphosate application significantly increased soil pH but reduced the contents of total organic carbon, total nitrogen, total potassium, available nutrients, and enzyme activities, leading to marked declines in soil fertility. Relative to CK, G2 reduced microbial alpha diversity, with Chao1, Shannon, and Pielou indices decreasing by 33.22%, 14.97%, and 11.50%, respectively. Tea quality was also affected, with free amino acids and caffeine decreasing by 22.67% and 11.30%, respectively, whereas tea polyphenols and the phenol/ammonia ratio increased by 12.16% and 45.08%, respectively. G2 also restructured bacterial communities, including depletion of Actinobacteria and Planctomycetota and more than 70-fold enrichment of Candidatus Rokubacteria. Metagenomic analysis revealed broad suppression of carbon, nitrogen, and phosphorus cycling genes under G2. Overall, these results suggest that repeated glyphosate exposure over three years may alter soil ecological processes and compromise tea quality, highlighting the need for more sustainable weed management strategies and reduced reliance on glyphosate in tea plantations.},
}

@article {pmid42431300,
year = {2026},
author = {Zou, Y and Wang, D and Chen, W and Jin, Z and Xie, Y and Li, Y and Wang, L},
title = {Shifts of antibiotic resistance genes across an estuarine meandering bend and dissemination risks to offshore oceans.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128757},
doi = {10.1016/j.envpol.2026.128757},
pmid = {42431300},
issn = {1873-6424},
abstract = {Meandering is a fundamental geomorphic feature of rivers that plays a critical role in regulating pollutant attenuation. To elucidate its impact on antibiotic resistance genes (ARGs) distribution in estuarine intertidal sediments, samples were collected from both the landward side (freshwater-dominated) and the seaward side (tide-dominated) of a meander bend during ebb and flood tides. The total relative abundance of ARGs was approximately 2.7 times higher on the landward side, peaking during the ebb tide. Microbial composition analysis showed that genera Acinetobacter and Pseudomonas were dominant at the landward sites, while halophilic genera such as Marinobacter and Exiguobacterium were abundant at the seaward sites. Further analysis of metagenome-assembled genomes (MAGs) demonstrated that the dominant landward genus Acinetobacter acted as a key host of ARGs, with two of four MAGs encoding more than ten ARGs. Notably, the total relative abundance of mobile genetic elements was high but consistent between sides and tidal cycles (p > 0.05). Given this high dissemination risk, we further forecasted the ARGs transfer scenarios to oceanic settings based on a set of offshore MAGs (n = 3626). Three ARGs, i.e., acrA, vanSL, and AAC(2')-Ia, were inferred to have transfer potential, supported by neighboring MGEs detected in marine microorganisms. Analysis of the genomes of predicted recipients in the SRA database confirmed the predicted mobilizations. Together, this study highlights that the meandering planform may serve as a significant barrier, attenuating the discharge of ARGs from terrestrial sources into the marine environment.},
}

@article {pmid42431420,
year = {2026},
author = {Yang, M and Li, Y and Chen, Y and Zhang, Y and Wang, Y and Liu, Q and Lu, S and Wang, X},
title = {Low-dose sodium acetate-mediated energy compensation stabilizes oxygen-limited urea hydrolysis coupled with partial nitritation/anammox for high-strength urea wastewater treatment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135374},
doi = {10.1016/j.biortech.2026.135374},
pmid = {42431420},
issn = {1873-2976},
abstract = {The high free ammonia (FA) environment generated during high-strength urea wastewater hydrolysis can impair biological nitrogen removal, while insufficient energy supply under inorganic influent conditions may limit long-term high-load urea hydrolysis. In this study, a continuous-flow two-stage system coupling an up-flow anaerobic filter reactor (UAFR) with a partial nitritation/anammox (PN/A) reactor was developed, and the role of low-dose sodium acetate in stabilizing UAFR urea hydrolysis was investigated. The UAFR showed hydrolysis deterioration under inorganic feeding, whereas hydrolysis performance rapidly recovered after anhydrous sodium acetate equivalent to 100 mg/L chemical oxygen demand was added on day 53. When the influent urea concentration increased to 2000 mg/L, the UAFR maintained a urea removal efficiency above 99.5%, with a urea removal rate of 8.0 kg urea/(m[3]·d). Acetate withdrawal caused a marked increase in effluent urea, indicating that high-load hydrolysis stability was closely associated with continuous acetate supply. Microbial community and metagenomic analyses showed enrichment of fermentative bacteria such as Tissierella and community-level increases in ackA-pta and urease-related genes, suggesting enhanced acetate-associated energy metabolism and urea hydrolysis potential under high-FA stress. After PN/A treatment, the overall total nitrogen removal efficiency reached 73.4%. This study demonstrates that low-dose acetate can stabilize UAFR urea hydrolysis and enable its coupling with autotrophic PN/A for high-strength urea wastewater treatment.},
}

@article {pmid42431426,
year = {2026},
author = {Tian, Y and Sun, J and Shu, Q and Sun, H and Yang, X and Liu, Y and Zhang, Y and Ding, J and Lan, L and Gong, P and Wang, G},
title = {Spiramycin fermentation residue-derived biochar regulates soil nutrient cycling, microbial communities, and antibiotic resistance gene dynamics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135372},
doi = {10.1016/j.biortech.2026.135372},
pmid = {42431426},
issn = {1873-2976},
abstract = {Spiramycin fermentation residues (SFR) are hazardous wastes enriched with residual antibiotics, yet they can serve as potential feedstocks for resource recovery after appropriate treatment. In this study, SFR-derived biochar (SFR-BC) was produced by pyrolysis and applied to agricultural soil to evaluate its effects on soil properties, microbial communities, potential pathogenic bacteria, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). A 60-day soil incubation experiment was conducted with one control and three SFR-BC application rates of 0.5%, 1.0%, and 2.0%. SFR-BC improved soil physicochemical properties, nutrient status, enzyme activities, and microbial alpha diversity. Metagenomic analysis showed that SFR-BC altered the abundance of functional genes associated with carbon and nitrogen cycling, indicating shifts in microbial functional potential. SFR-BC also changed bacterial co-occurrence patterns, with the high-dose treatment showing a more complex and highly connected network structure during incubation. In addition, high-dose SFR-BC reduced several potential pathogenic bacteria, including major plant pathogenic taxa. SFR-BC decreased soil ARG abundance by 9.38%-33.67% and MGE abundance by 6.49%-27.89% relative to the control, showing a dose-dependent reduction in antibiotic resistance-related genetic elements. Network and PLS-PM analyses further indicated that ARG variation was statistically associated with soil physicochemical properties, microbial diversity, potential bacterial hosts, and MGEs. Overall, these results suggest that SFR-BC can improve short-term soil nutrient status and reduce ARGs, MGEs, and several potential pathogenic taxa under controlled incubation conditions, providing useful evidence for the potential valorization of antibiotic fermentation residues through pyrolysis.},
}

@article {pmid42431948,
year = {2026},
author = {Neshat, SA and Santillan, E and Wuertz, S},
title = {Uncovering microbial life-history strategies under disturbance: a trait-based computational analysis of anaerobic systems.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01067-8},
pmid = {42431948},
issn = {2055-5008},
abstract = {Trait-based approaches are helpful in simplifying ecosystem complexity to explore disturbance-diversity-function relationships. These frameworks classify organisms based on their functional characteristics-traits that influence growth, survival and reproduction-providing a mechanistic basis to understand how communities respond to changes in their environment. The application of these approaches has been successful in ecology, but to date has only been tested in a few microbial ecosystems, namely, soil microbial communities and aerobic bioreactors treating wastewater. Here, we employed Grime's competitor-stress-tolerant-ruderal framework in replicated mesophilic anaerobic bioreactors exposed to a disturbance (biomass removal) with varied frequencies at a constant number of disturbance events for 90 days. Bioreactors were inoculated with sludge from full-scale anaerobic digesters and fed with a mixture of primary and waste activated sludge. A genome-resolved metagenomics approach was utilised to assess the microbial communities in terms of composition and functional potential. We found that communities across the disturbance range were clustered into three groups, suggesting the adoption of a three-way life-history strategy. This study demonstrates, for the first time, the applicability of trait-based life-history strategies in anaerobic microbial systems under disturbance using genome-resolved techniques, providing a new perspective for understanding and managing microbial ecosystems under disturbance conditions.},
}

@article {pmid42431976,
year = {2026},
author = {Chattaraj, S and Chatterjee, I and Nandi, R and Mohapatra, PKD and Mitra, P and Mandal, A and Mitra, D and Ganguly, A},
title = {Effect of probiotic Bacillus cereus PKA18 on the overall growth, gut microbiome, and immunity in Clarias magur (Hamilton, 1822).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57479-1},
pmid = {42431976},
issn = {2045-2322},
abstract = {The current study evaluated the probiotic potential of Bacillus cereus PKA18, isolated from indigenous Clarias batrachus, as a dietary supplement for the cultivation of Clarias magur fingerlings (In India, the species Clarias batrachus was reclassified as the neotype Clarias magur). Prior to application in fish, Bacillus cereus PKA18 was subjected to safety evaluation, which confirmed negative enterotoxin production, non-hemolytic (γ-hemolysis) behavior on sheep, fish, and human blood agar, and the absence of pathogenic effects or adverse impacts on fish growth following intraperitoneal administration. A total of 240 fingerlings (average weight: 4.96 ± 0.06 g) were randomly assigned to four dietary groups (Control, C1, C2, and C3), each in triplicate, and reared for 60 days in continuous-flow chambers (92 × 61 × 92 cm[3]; 516 L; 5 cm bottom mud). The control group received basal feed without any probiotic additives, while treatment groups were administered feed supplemented with increasing concentrations of B. cereus PKA18: C1 (2 × 10[4] CFU), C2 (2 × 10[5] CFU), and C3 (2 × 10[6] CFU) per 100 g of feed. Fish in the C2 group exhibited significantly (p < 0.05) superior performance in terms of specific growth rate (3.14 ± 0.05), protein efficiency ratio (2.15 ± 0.12), and live weight gain (27.77 ± 1.24 g), along with the lowest feed conversion ratio (1.29 ± 0.11). Serum biochemical analyses showed notable enhancement in total proteins and reduction in hepatic enzymes (ALT, ALP, AST) in C2-fed fish. Antioxidant enzyme activities were significantly higher in the C2 group. These included superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-PX). Malondialdehyde (MDA) levels were lowest in this group. Digestive enzyme activities (protease, amylase, cellulase, xylanase, and lipase) were also significantly higher in the C2 group compared to control. Species-level 16 S rRNA gene analysis demonstrated that probiotic-fed Clarias magur exhibited a marked shift in intestinal microbiota, characterized by dominance of beneficial Cetobacterium spp., enrichment of Bacillus spp., and a significant reduction of opportunistic and pathogenic bacteria compared to the control group. Functional profiling further revealed that probiotic supplementation promoted a more metabolically efficient microbial community, with targeted enrichment of core metabolic and genetic information processing pathways despite lower overall functional abundance. Following a pathogenic challenge with Vibrio vulnificus (MTCC 1145), fish in the control and C2 groups were assessed for immune response. Fish fed C2 have demonstrated enhanced activity of respiratory burst, myeloperoxidase, α2-macroglobulin and antiprotease. Additionally, a significant upregulation of immune-related genes (IL-6 and C3a) was observed in the liver, muscle, and intestinal tissues of fish fed with C2. Post-challenge survivability was found to be highest in the C2 group, indicating improved resistance to vibriosis. Overall, the study identifies 2 × 10[5] CFU/100 g feed of B. cereus PKA18 (C2 feed) as the optimal probiotic dose for promoting growth performance, digestive activity, immune functions and disease resistance in Clarias magur. These findings support its potential application in the conservation-oriented aquaculture of this endangered species.},
}

@article {pmid42432469,
year = {2026},
author = {Liu, L and Fu, M and Peng, J and Duan, T and Ma, X and Liu, H and Sha, R and Yang, Y and Yan, H and Jia, R and Li, X and An, X and Liu, Y and Lu, Q},
title = {Bio-valorization of Caragana korshinskii forage via a synthetic microbial community.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05353-5},
pmid = {42432469},
issn = {1471-2180},
abstract = {Caragana korshinskii represents a critical ecological and feed resource in arid regions, yet its utilization is severely impeded by the recalcitrant lignocellulose barrier. This study established a cross-kingdom synthetic microbial community (SynCom) to synergistically overcome this bottleneck, integrating Lactobacillus plantarum for rapid acidification with the fibrolytic enzyme secretion of Bacillus subtilis and the oxidative delignification potential of Aspergillus niger. We integrated microbiome profiling and functional prediction to decode the fermentation dynamics and metabolic mechanisms. Results demonstrated that the SynCom (LBA) treatment engineered a robust fermentation system, achieving a significantly higher in vitro dry matter digestibility (49.68%) and neutral detergent fiber digestibility (25.65%) compared to the control (P < 0.05). This enhancement was driven by a directed shift in the microbiome, where Lactobacillus abundance surged to > 95%, effectively suppressing spoilage genera like Staphylococcus and Weissella via competitive exclusion. Metagenomic prediction revealed that the SynCom upregulated key metabolic modules, specifically pyruvate metabolism and amino acid biosynthesis pathways, facilitating rapid acidification and protein preservation. These findings delineate a coordinated degradation-fermentation-preservation process driven by a rationally assembled synthetic consortium, offering a promising and sustainable bio-valorization strategy for converting high-fiber woody biomass into high-quality livestock feed.},
}

@article {pmid42432510,
year = {2026},
author = {Feng, J and Zhang, B and Lu, W and Liu, H and Liu, Y and Zou, Y and Ma, H},
title = {Streptococcus anginosus group brain abscesses and subdural empyemas: exploratory compartment-specific phenotypes and discharge outcomes in a single-center retrospective cohort study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13998-w},
pmid = {42432510},
issn = {1471-2334},
abstract = {BACKGROUND: Intracranial suppuration caused by the Streptococcus anginosus group (SAG) includes brain abscess and subdural empyema, but compartment-specific phenotypes and short-term outcomes remain incompletely described. We characterized clinical, radiological, and microbiological features and explored factors associated with poor discharge outcome.

METHODS: We conducted a single-center retrospective cohort study of patients with imaging-confirmed intracranial suppuration and SAG identified by culture and/or metagenomic next-generation sequencing from October 2020 to October 2025. Cases were classified as intracerebral (n = 39), subdural (n = 6), or mixed (n = 7). The primary outcome was Glasgow Outcome Scale (GOS) at discharge; GOS 1-3 defined poor discharge outcome. Analyses were descriptive, with exploratory univariable logistic regression.

RESULTS: A total of 52 patients were included. Patients with subdural empyema were younger and had numerically lower admission functional status than those with intracerebral infection, whereas subdural and mixed-compartment infections showed higher inflammatory-marker levels. Ventricular involvement was uncommon (5/52, 9.6%) and was observed more frequently among patients with poor discharge outcomes in unadjusted comparisons (5/12 vs. 0/40). Complete ring enhancement was confined to intracerebral cases, and S. intermedius was the predominant species. At discharge, 12 patients (23.1%) had poor outcomes, including six in-hospital deaths (11.5%). Lower admission KPS and fever were exploratory univariable associations with poor discharge outcome.

CONCLUSIONS: This study describes compartment-specific clinical, imaging, and microbiological features of Streptococcus anginosus group brain abscesses and subdural empyemas. Ventricular involvement may be a marker of severe disease, but all findings should be interpreted as exploratory and require validation in larger multicenter studies.},
}

@article {pmid42432696,
year = {2026},
author = {Clarke, MD and Falcione, S and Boghozian, R and Todoran, R and Zhang, Y and Real, MGC and StPierre, A and Joy, T and Jickling, GC},
title = {Metagenomic analysis of blood virome in ischemic stroke reveals an increase in herpesvirus transcripts and host immune activation.},
journal = {Genome medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13073-026-01707-w},
pmid = {42432696},
issn = {1756-994X},
abstract = {BACKGROUND: Viral infections may influence stroke pathophysiology. Several infections have been linked to increased risk of stroke, however our understanding of these viral interactions with immune and host tissue is limited. We performed a transcriptomic analysis of the blood virome following ischemic stroke to study these interactions.

METHODS: Viruses were measured by RNA sequencing of blood from 37 patients with ischemic stroke and 32 matched controls. RNA reads are aligned against a human reference genome, as well as a comprehensive database of human virus genomes. Host gene expression following stroke is examined in relation to the presence of viral transcripts.

RESULTS: Viral RNAs were detected in the blood samples of both ischemic stroke and control groups. Viral reads with a prevalence > 3% and raw counts > 2 were from a total of 6 viral families. This included several human herpesviruses (HHVs), adenoviruses, and papillomaviruses, as well as human pegivirus, respiratory syncytial virus, and human endogenous retrovirus K (HERV-K). Combined, counts from HHVs were higher in stroke compared to control by a fold change of 2.13. Coinfection with multiple HHVs was more common in stroke, with a 1.23 fold increase in the number of detected herpesviruses. Reads from two viral genes were increased in stroke, UL95 from cytomegalovirus (CMV), and EBNA2 from Epstein-Barr virus (EBV). Genes associated with stroke, including APOE, C3, PDGF, and CXCL2 were differentially expressed in stroke samples which contained high counts of one or both of UL95 and EBNA2.

CONCLUSION: Viral RNAs from multiple families can be detected within the human blood virome. HHV transcripts were the most abundant of viral RNAs detected. Among stroke patients, HHV transcripts were more prevalent, with higher counts, and indicated a higher rate of coinfection with multiple HHV species. Expression of the EBV gene EBNA2 and the CMV gene UL95 may relate to changes in immune gene expression following stroke. Further evaluation is needed to determine the effects that the human virome have on stroke risk, immune response to stroke, and long-term outcome.},
}

@article {pmid42432805,
year = {2026},
author = {He, B and Liu, B and Wang, X and Xia, M and Ding, C and Nazar, M and Cheng, Y and Xiao, D},
title = {Rumen-derived Prevotella and Megasphaera elsdenii mitigate methane production through functional modulation of rumen microbial metabolism.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42432805},
issn = {1674-9782},
support = {2023YFD1300903//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) production represents a major energy loss in ruminant systems and contributes substantially to agricultural greenhouse gas emissions. Increasing ruminal propionate production has been proposed as a strategy to redirect metabolic hydrogen away from methanogenesis, although the underlying microbial mechanisms remain incompletely understood.

RESULTS: Four rumen-derived Prevotella strains and one Megasphaera elsdenii strain were isolated, genomically characterized, and evaluated using an in vitro rumen fermentation model. Distinct strain-specific responses were observed. Compared with the control, Prevotella strains RH14 and RH35 significantly reduced CH4 accumulation at 48 h (P < 0.05), coinciding with lower total gas and carbon dioxide (CO2) production, whereas RH3, RH27, and RH19 showed CH4 production comparable to the control. Volatile fatty acid (VFA) profiles showed comparatively smaller differences among treatments, although RH14 maintained relatively greater total VFA and propionate concentrations at later incubation stages. Metagenomic analysis indicated that methane mitigation was associated with reduced relative abundance of methanogenesis-related pathways, particularly hydrogenotrophic methanogenesis (P < 0.05), whereas archaeal community composition remained largely unchanged. However, metagenomic data reflect gene abundance rather than activity and do not directly indicate functional regulation.

CONCLUSIONS: These findings demonstrate strain-specific effects of rumen-derived bacteria on rumen fermentation and methane production. In particular, Prevotella strains RH14 and RH35 showed potential to mitigate methane formation through functional modulation of microbial metabolism, partially displacing rather than completely eliminating methanogens. These results provide a functional basis for the future development of rumen microbial interventions aimed at improving rumen fermentation efficiency and mitigating enteric methane emissions.},
}

@article {pmid42433691,
year = {2026},
author = {Hasan, M and Schirtzinger, EE and Stancic, S and Affonso, P and Lu, A and Souza-Neto, JA and Klenda, KL and Ferreyra, FM and Noll, LW and Hanzlicek, GA and Retallick, J and Miller, LC},
title = {A targeted PCR approach for the detection of IOLA in canine infectious respiratory disease samples during an atypical CIRD outbreak in winter 2023.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1849862},
pmid = {42433691},
issn = {2297-1769},
abstract = {BACKGROUND: During winter 2023, an atypical canine infectious respiratory disease (aCIRD) outbreak was associated with high case-fatality rates and poor antibiotic response. Preliminary metagenomics investigations claimed partial sequences resembling Infectious Organism Lurking in Human Airways (IOLA), a poorly characterized bacterium first described in humans, in canine respiratory samples. However, its detectability remained uncertain and required systematic molecular investigation.

METHODS: We screened 777 veterinarian-submitted canine respiratory samples from the United States using 16S targeted sequencing for samples positive for Rickettsiales, the lowest taxonomic classification for IOLA. Samples containing sequencing reads classified as for Rickettsiales were tested by PCR assay targeting two IOLA genes (16S rRNA and PrfA). Assays were optimized at 58 °C with 500 nM primers, and products visualized by agarose gel and capillary electrophoresis. Analytical sensitivity was 10[4] copies/μl and 10[4] copies/μl for 16S and PrfA assay, respectively. Candidate amplicons were verified by Sanger sequencing and BLAST analysis.

RESULTS: Of the 777 samples screened, 55 contained sequencing reads classified as Rickettsiales. Forty-five of the 55 samples were negative by 16S rRNA PCR, while 10 samples produced amplicons near the expected size. The PrfA PCR assay was negative across all samples. Sequencing representative samples from those that produced 16S amplicons confirmed nonspecific amplification. Therefore, all 55 samples were negative for IOLA.

CONCLUSION: Dual-target PCR identified no evidence of IOLA in respiratory samples from the 2023 aCIRD outbreak. Non-specific amplification in the 16S PCR assay highlights the need for multi-target validation in novel pathogen detection and supports prioritization of established CIRD pathogens over unverified organisms.},
}

@article {pmid42434089,
year = {2026},
author = {Őrsi, Á and Laczkó, L and Bőkényné Tóth, R and Freytag, C and Tóth, P and Simay, G and Szabó, N and Kardos, G and Lovas-Kiss, Á},
title = {Microbiota shows major difference in case of two shorebird species with different feeding strategy.},
journal = {Veterinary and animal science},
volume = {34},
number = {},
pages = {100754},
pmid = {42434089},
issn = {2451-943X},
abstract = {Despite the well-known effects of the gut microbiota on mammals, other vertebrates have only recently begun receiving attention in research. Our study focused on describing the cloacal microbiome of Common Snipe (Gallinago gallinago) and Wood Sandpiper (Tringa glareola), using 16S rRNA metabarcoding, to understand how different foraging methods can affect their microbiome. Assessing the host microbial diversity, we found that Shannon- (W = 253, p = 0.099), Simpson- (W = 268, p = 0.168) and inverse Simpson- diversities (W = 268, p = 0.168) did not differ significantly, however, there was a tendency towards the Wood Sandpiper having the higher values. SIMPER analysis revealed that the differences were caused by several bacterial taxa, the biggest contributor being Catellicoccus marimammalinum (mean contribution = 2.76%, p = 0.003) which had greater abundances in Common Snipe (mean relative abundance = 22.76%) than in the Wood Sandpiper (8.27%). We found great differences in Fusobacteria abundances between the hosts, as this phylum had an average abundance of 29.4% in Wood Sandpiper and 8.8% in Common Snipe samples. This difference in their microbiome may be explained by the higher chitin consumption of Wood Sandpiper which is associated with higher Fusobacteria abundance. We found multiple important animal (Mycoplasma iowae, Brachyspira hyodysenteriae) and human pathogens (Campylobacter jejuni, Aeromonas veronii, Vibrio cholerae), some of which are also associated with the growing problem of antimicrobial resistance (Escherichia coli, Enterococcus faecalis). The high prevalence of these pathogens in wild waterbirds should be considered important when assessing human and environmental health hazards.},
}

@article {pmid42434393,
year = {2026},
author = {Wang, B and Yu, Y and Huang, S and He, Y and Chen, Y and Dong, S and Tang, D and Cheng, Z and Cao, L},
title = {Metabolomic and Metagenomic Correlation Reveals the Network Regulatory Mechanism of Cecal Microbiota Structural Changes Induced by Eimeria tenella.},
journal = {International journal of veterinary science and medicine},
volume = {14},
number = {},
pages = {8},
pmid = {42434393},
issn = {2314-4599},
abstract = {BACKGROUND: Eimeria tenella poses a significant threat to the poultry industry, and understanding the correlation between metabolic changes in cecal tissues and microbial community alterations is crucial for studying parasite-host interactions.

AIMS AND OBJECTIVES: To investigate the associations among dominant bacterial populations, key functional genes, and altered metabolites in cecal tissues and contents during E. tenella infection.

MATERIALS AND METHODS: Metagenomic analysis was first performed on cecal contents to identify the dominant bacterial communities, followed by metabolomic analysis of cecal tissues and contents. Correlation analysis was then conducted to evaluate the relationships among microbial communities, functional genes, and differential metabolites.

RESULTS: Correlation analysis showed that increased potentially pathogenic genera were generally positively associated with upregulated metabolites and negatively associated with downregulated metabolites, whereas reduced commensal genera showed the opposite trend. Shared KEGG pathways co-enriched by differential metabolites and microbial functional genes were identified, mainly involving amino acid metabolism, transport systems, membrane-associated metabolism, and nucleotide metabolism. The metabolites linked to dominant bacterial communities were primarily enriched in pathways such as amino sugar metabolism, sialic acid metabolism, and glycerophospholipid metabolism. These findings reflected complex metabolic reprogramming and interactions between the host and pathogen, especially in cecal tissue repair, immune regulation, and metabolic competition with the pathogen.

CONCLUSION: This study provided valuable insights into parasite-host interactions and laid a foundation for understanding the role of bacterial community-associated metabolites in cecal coccidiosis.},
}

@article {pmid42434420,
year = {2026},
author = {Al-Maleki, AR and Flores-Treviño, S and Cheah, CW and Abdelhafiz, YA},
title = {Editorial: Microbiota, antibiotic resistance, and host-microbe interactions: a comprehensive exploration of infectious disease dynamics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1899262},
pmid = {42434420},
issn = {2235-2988},
}

@article {pmid42434557,
year = {2026},
author = {Hossen, N and Mascellino, MT},
title = {Molecular insights into antimicrobial resistance in human bacterial pathogens: mechanisms, resistance genes, and translational diagnostic applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1842688},
pmid = {42434557},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) represents one of the most critical global public health challenges. This review provides a comprehensive overview of the molecular foundation of AMR in human bacterial pathogens, including the biology of resistance genes and the importance of the mobile genetic elements-plasmids, transposons, and integrons-in facilitating the rapid horizontal transfer of resistance determinates across the populations. We critically evaluate current and emerging molecular diagnostic platforms - including targeted polymerase chain reaction (PCR), whole-genome sequencing (WGS), clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies, and metagenomics - emphasizing their comparative performance, limitations, and suitability for point-of-care deployment. The review addresses the translational integration of molecular diagnostics into antimicrobial stewardship programmes and real-time AMR surveillance, with particular attention to the persistent gap between laboratory-generated genomic data and actionable clinical decision-making. Emerging evidence suggests that artificial intelligence (AI) and machine learning hold considerable promise for improving resistance phenotype prediction from genomic data and informing personalized antibiotic therapy, although widespread clinical implementation remains in its early stages. The transition from phenotypic to genotypic strategies represents a significant paradigm shift in AMR, with the potential to substantially improve surveillance, diagnostic accuracy, and therapeutic outcomes, provided that outstanding barriers in infrastructure, standardization, and equity are addressed.},
}

@article {pmid42434559,
year = {2026},
author = {Saraiva, M and Gerilovych, A and Ay, H},
title = {Editorial: Harnessing aquatic microbial symbioses for sustainable aquaculture: unveiling biodiversity and ecosystem dynamics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1897215},
doi = {10.3389/fmicb.2026.1897215},
pmid = {42434559},
issn = {1664-302X},
}

@article {pmid42434564,
year = {2026},
author = {Diaz, B and House, T and Padala, M and Schoeniger, JS and Mageeney, CM},
title = {HtPIP: High-throughput phage isolation platform increases diversity and reduces isolation time using multiple bacteria.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1845440},
pmid = {42434564},
issn = {1664-302X},
abstract = {Bacteriophages are ubiquitous in nature, but relatively few have been isolated and characterized compared to the number of bacterial strains. Phage biotechnology applications benefit from a diverse library of isolated phages to kill or transfer genetic material to a bacterium of interest. However, scaling up phage discovery for diverse bacterial hosts can be time-consuming and costly. We developed an approach to capture novel phages for multiple bacterial strains in parallel from an environmental sample using commercially available 0.2-μM filter plates. Using this High-throughput Phage Isolation Platform (HtPIP), 12 novel phages were isolated spanning 9 diverse bacterial host genera. Eleven of the isolated phages define new phage species, with nine also defining new genera. The HtPIP was used to discover both DNA and RNA phages, including a Tectiviridae infecting Pseudomonas putida mt-2 and a Leviviricetes infecting a Microbacterium isolate, which represents the first cultured RNA phage infecting a host outside of Proteobacteria. Using a metagenomic approach, we demonstrate that the HtPIP captures a higher proportion of novel phages compared to traditional low-throughput methods.},
}

@article {pmid42434567,
year = {2026},
author = {Huang, J and Bol, R and Liu, D and Kiladze, E and Lou, X and Wang, H and Zhang, J and Ge, Z and Wang, T},
title = {Multi-omics reveal soil microbial dysbiosis and metabolite toxicity as drivers of blueberry continuous cropping obstacles.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1880203},
pmid = {42434567},
issn = {1664-302X},
abstract = {Blueberry (Vaccinium spp.) are one of the most economically important fruit trees globally. However, due to continuous cropping have limited the industry's ability to produce consistently over the long term, and the mechanism underlying the development of this continuous cropping problem is not yet fully understood. In this study, we applied metagenomic and metabolomic to systematically detect changes in microbial community structure, function and metabolic profiles in rhizosphere and non-rhizosphere soils after different years of continuous blueberry cultivation (0, 2, 4, and 6 years) in Dalian (China). The results showed that continuous cultivation significantly reduced overall microbial diversity and the bacterial and fungal Shannon index, with the decrease being more significant in the rhizosphere soils (P < 0.05). The β diversity analysis showed that the microbial community structure was distinctly separated between cultivation periods, with the most prominent differences in the rhizosphere soils (PERMANOVA, P < 0.01). The increased cultivation duration led to a decrease in the relative abundance of beneficial functional taxa in the microbial community, while the depletion-tolerant and stress-adapted taxa were gradually enriched. Functional annotation analysis showed that KEGG pathways related to stress response, amino acid degradation, and energy metabolism significantly increased, while functions related to nutrient transformation and plant-microbe interactions were weakened (FDR < 0.05). The metabolomic results further showed that 6 years of continuous cultivation significantly reshaped the rhizosphere metabolite composition. This was evidenced by the accumulation of various secondary metabolites in the rhizosphere soil, including metabolites related to potential self-toxicity (e.g., ferulic acid, 3-hydroxyphenylacetic acid, and 2-hydroxycinnamic acid), mainly involved in the pathways of amino acid metabolism, lipid metabolism, and secondary metabolite synthesis. In conclusion, continuous cultivation of blueberry induced pronounced shifts in rhizosphere microbial community structure, function, and metabolite composition, suggesting that these changes may contribute to the development of continuous cropping obstacles (CCO).},
}

@article {pmid42434987,
year = {2026},
author = {Cusi, MG and Savellini, GG and Cassol, C and Nencioni, C and Bernini, L and Tacconi, D and Alessandri, G and Rizzo, L and Anichini, G and Smura, T and Vapalahti, O},
title = {Molecular evidence of neuroinvasive Sindbis virus infection in humans: detection in cerebrospinal fluid by next generation sequencing.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2703397},
doi = {10.1080/22221751.2026.2703397},
pmid = {42434987},
issn = {2222-1751},
abstract = {Sindbis virus (SINV) is a mosquito borne alphavirus causing seasonal outbreaks in northern Europe, Africa and Russia. Neurological involvement in humans is poorly documented, and detection in cerebrospinal fluid (CSF) has not previously been reported. This study provides the first unequivocal evidence of human CNS involvement by detecting SINV RNA directly in the cerebrospinal fluid of four autochthonous patients presenting with acute neurological symptoms in south eastern Tuscany, Italy, July-August 2025. Utilizing metagenomic Next Generation Sequencing (mNGS), we reconstructed complete viral genomes, strongly supporting a causal relationship between SINV and neurological manifestations. Phylogenetic analysis revealed a complex epidemiological landscape in Italy characterized by the co-circulation of Clade D lineages. Our findings fundamentally expand the clinical spectrum of SINV, demonstrating that it is not merely an arthritogenic pathogen, but a neuroinvasive threat to humans. This highlights the critical need to include SINV in the differential diagnosis of viral CNS infections in endemic areas and underscores the urgency for enhanced European laboratory surveillance.},
}

@article {pmid42435095,
year = {2026},
author = {Aziz, U and Akhoon, RH and Gani, KM},
title = {Wastewater-associated antibiotic resistance in Western Himalayas: prevalence and diversity in a north Indian city of Srinagar, Jammu and Kashmir.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {8},
pages = {},
pmid = {42435095},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; India ; Himalayas ; Anti-Bacterial Agents/pharmacology ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Cities ; Bacteria/genetics/classification/drug effects ; Escherichia coli ; },
abstract = {Antibiotic-resistant bacteria (ARB) in wastewater have emerged as a major environmental and public health concern, particularly in areas with high urbanization and limited wastewater treatment efficiency. Despite this, limited data exist on the distribution and diversity of ARB in the Western Himalayan region of India. This study addresses this gap by assessing the prevalence, antibiotic resistance patterns, and antibiotic-resistant genes (ARG) diversity of wastewater-associated bacteria in Srinagar, Jammu and Kashmir. A total of 18 influent and effluent wastewater samples were collected from nine wastewater treatment plants (WWTPs) in Srinagar, Jammu and Kashmir, and were examined to investigate antibiotic-resistant bacteria (ARBs). Enterococcus faecium and Escherichia coli were isolated using selective media, identified through Gram staining and 16S rDNA PCR, and assessed for antibiotic susceptibility. Both bacterial species exhibited higher resistance in influent samples compared to effluent samples. Enterococcus faecium showed notable resistance to ampicillin, minocycline, and linezolid, whereas Escherichia coli showed greater resistance to minocycline and nitrofurantoin. Metagenomic analysis revealed that bacteria accounted for 99.98% of the taxonomic composition, with shotgun sequencing identifying diverse antibiotic resistance genes (ARGs), including tet(B), tet36, adeF, adeG, emrK, and acrB, associated with resistance to tetracyclines, fluoroquinolones, and β-lactams. This highlights the urgent need for strengthened antibiotic management practices and enhanced wastewater treatment technologies to limit the spread of resistance elements into aquatic environments.},
}

*Wastewater/microbiology
India
Himalayas
Anti-Bacterial Agents/pharmacology
*Environmental Monitoring
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Waste Disposal, Fluid
Cities
Bacteria/genetics/classification/drug effects
Escherichia coli

@article {pmid42435326,
year = {2026},
author = {Garcia, A and Trivedi, D and Anthony, DC and Swann, JR and Burnet, PWJ},
title = {Glycodeoxycholic and deoxycholic bile acids impair recognition and spatial memory in adult mice, and reduce central CREB-BDNF signaling and cytokine expression with neuroanatomical specificity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2701471},
doi = {10.1080/19490976.2026.2701471},
pmid = {42435326},
issn = {1949-0984},
mesh = {Animals ; Male ; *Cyclic AMP Response Element-Binding Protein/metabolism/genetics ; Mice ; Female ; Signal Transduction/drug effects ; *Spatial Memory/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism/genetics ; *Deoxycholic Acid/metabolism/administration & dosage ; *Cytokines/metabolism/genetics ; Receptors, N-Methyl-D-Aspartate/genetics/metabolism ; Mice, Inbred C57BL ; Hippocampus/metabolism/drug effects ; Brain/metabolism/drug effects ; Bile Acids and Salts ; },
abstract = {Emerging evidence suggests that bile acids, traditionally recognized for their role in digestion, also influence brain function and memory. This study examined the effects of two microbiota-derived secondary bile acids, deoxycholic acid (DCA) and glycodeoxycholic acid (GDCA), on memory in mice and the associated molecular mechanisms. Male and female mice received daily oral administration of DCA, GDCA, or vehicle, and spatial working and reference memory (Y-maze) and recognition memory (novel object recognition task) were assessed. After testing, gene expression and signaling activity were measured in the frontal cortex and hippocampus. Administration of GDCA after 10 d disrupted recognition memory, whereas DCA intake for 12 d impaired spatial reference memory. Neither bile acid administered for 5 d affected spatial working memory. GDCA reduced NMDA receptor subunit (GluN1, GluN2A) mRNAs and encoded protein and brain-derived neurotrophic factor (BDNF) mRNA expression and attenuated CREB signaling in the frontal cortex, which is consistent with the observed recognition memory deficit. GDCA did not alter the abundance of transcripts encoding bile acid receptors (FXR or TGR5) or their corresponding protein levels. In contrast, DCA modified the FXR and TGR5 mRNAs and proteins in a region-specific manner and decreased CREB signaling in the hippocampus, likely contributing to spatial memory deficits. In the frontal cortex, DCA increased GluA1 phosphorylation and reduced IL-1β and IL-6 expression, which may have helped preserve recognition memory. Exploratory metagenomic analysis of fecal samples showed no significant microbial differences, though subtle, non-significant functional gene changes suggested early adaptations. These findings reveal that DCA and GDCA exert distinct, receptor- and region-specific effects on cognition, identifying bile acids as modulators of microbiome-gut-brain communication.},
}

Animals
Male
*Cyclic AMP Response Element-Binding Protein/metabolism/genetics
Mice
Female
Signal Transduction/drug effects
*Spatial Memory/drug effects
*Brain-Derived Neurotrophic Factor/metabolism/genetics
*Deoxycholic Acid/metabolism/administration & dosage
*Cytokines/metabolism/genetics
Receptors, N-Methyl-D-Aspartate/genetics/metabolism
Mice, Inbred C57BL
Hippocampus/metabolism/drug effects
Brain/metabolism/drug effects
Bile Acids and Salts

@article {pmid42435590,
year = {2026},
author = {Yan, Y and Yang, B and Bao, P and Chen, B and Jia, Y and Lu, H},
title = {Polyethylene microplastics impose reversible redox suppression in sulfur-driven wastewater treatment systems under antibiotic co-stress.},
journal = {Water research},
volume = {305},
number = {},
pages = {126399},
doi = {10.1016/j.watres.2026.126399},
pmid = {42435590},
issn = {1879-2448},
abstract = {Microplastics and antibiotics frequently co-occur in wastewater treatment systems, yet their combined effect on sulfur-driven bioprocesses and the subsequent post-stress recovery remains poorly resolved. In this study, the long-term response of a sulfate-reducing bacteria (SRB) sludge system treating sulfamethoxazole (SMX)-laden wastewater to polyethylene microplastics (PE MPs; 100 - 800 particles/L) was investigated by combining parallel continuous-flow reactors, batch physiological assays, and metagenomic analysis. PE MPs exerted a concentration-dependent but function-differentiated inhibition, in which SMX removal was more sensitive than chemical oxygen demand (COD) removal and sulfate reduction. At 800 particles/L, SMX removal declined from 37.1 ± 4.1% to 30.5 ± 5.2%, accompanied by elevated intracellular reactive oxygen species (ROS; 138.2 ± 4.0%), increased lactate dehydrogenase (LDH) leakage (122.0 ± 7.1% of the control), weakened antioxidant capacity, and a higher dead-cell fraction (29.7 ± 2.0%). Metagenomic analysis further revealed suppression of central carbon metabolism, dissimilatory sulfate reduction, lipid metabolism, and antioxidant defense, indicating that PE MPs disrupted redox homeostasis and thereby constrained energy supply, sulfur-related electron transfer, membrane maintenance, and stress-response capacity. Notably, after PE MPs withdrawal, SMX removal recovered to 37.8 ± 4.0%, and ROS declined to 107.8 ± 2.8% despite continued SMX loading, together with partial restoration of sulfur-related functional potential. These findings support a reversible, redox-mediated metabolic suppression model rather than irreversible functional collapse, providing an engineering basis for the stable application and functional resilience evaluation of sulfur-driven biotechnologies under fluctuating microplastic exposure, while highlighting the need for future enzyme-level verification of ROS-dependent causal mechanisms.},
}

@article {pmid42435593,
year = {2026},
author = {Zhang, Y and Li, YT and Zhang, Q and Wang, XT and Wang, W and Wang, A and Ma, J and Lee, DJ and Ren, N and Chen, C},
title = {Thiocyanate-driven denitrification with mixotrophic flexibility for real coking wastewater treatment: Novel insights into nitrogen cycling.},
journal = {Water research},
volume = {305},
number = {},
pages = {126438},
doi = {10.1016/j.watres.2026.126438},
pmid = {42435593},
issn = {1879-2448},
abstract = {Industrial coking wastewater, characterized by high thiocyanate (SCN[-]), nitrate, and complex toxic organics, challenges conventional biological nitrogen removal and impedes resource recovery. To shift the treatment objective from mere detoxification to predictable nitrogen partitioning, a SCN[-]-driven biological nitrogen removal (SCN[-]-BNR) bioreactor was operated for 200 days, comprising a 160-day synthetic stoichiometric optimization phase and a 40-day validation phase with undiluted real coking wastewater. We identified the influent SCN[-]-S/NO3[-]-N mass ratio (S/N) as the primary operational lever governing nitrogen fate. Increasing this ratio to ∼4.0 drove >99% nitrate removal, with DNRA contributing 49.1% of the total nitrate reduction. Crucially, [15]N stable isotope tracing and metagenomics elucidated a synergistic cross-feeding mechanism: Chlorobium sp. likely initiates SCN[-] cleavage, followed by cyanate hydrolysis (cynS) and dissimilatory nitrate reduction to ammonium (DNRA, nrfA) driven by distinct populations (SpSt-501 sp. And JADFDR01 sp.). DNRA was highly activated under electron-donor-surplus conditions, directly contributing up to 22.8% of the generated effluent ammonium. This metabolic division of labor proved exceptionally resilient; the mixotrophic consortium maintained stable >95% SCN[-] and >90% NO3[-] removal during real wastewater validation, demonstrating strong tolerance to phenol, quinoline, and salinity. This study provides a verifiable operational-mechanistic framework for engineering next-generation SCN[-]-driven bioreactors, integrating robust complex wastewater detoxification with circular nitrogen management.},
}

@article {pmid42435595,
year = {2026},
author = {Ma, B and Zhang, C and Li, F and Adamovich, B and Huang, T and Zhang, H},
title = {Iron-manganese co-mediated electron shuttling rewires mixotrophic aerobic denitrification metabolism: Unraveling metabolic complementarity and functional regulation.},
journal = {Water research},
volume = {305},
number = {},
pages = {126447},
doi = {10.1016/j.watres.2026.126447},
pmid = {42435595},
issn = {1879-2448},
abstract = {Electron donor scarcity is the primary bottleneck limiting the biological reduction of elevated nitrate (NO3[-]-N) in eutrophic reservoir water. However, simultaneous microbial aerobic denitrification mediated by iron-manganese redox offers a viable strategy for mitigating nitrogen pollution in such organic electron donor-limited natural aquatic systems. Here, we constructed four bioreactors to investigate the functional regulation and metabolic complementarity underlying the bioremediation of NO3[-]-N via iron-manganese coupling in eutrophic reservoir water. The iron-manganese co-doped reactor system exhibited NO3[-]-N reduction rate of 0.82523-1.01249 mg/L/d, which was higher than that of the other reactors. Furthermore, iron-manganese synergy significantly enhanced phosphorus and organic matter removal in aquatic systems, combining biochemical degradation and physical sedimentation. We also detected the simultaneous occurrence of NO3[-]-N reduction (napA/B, narB/G/H/I, nirS/K, norB/C, and nosZ), aerobic respiration (Cyo, Cyd, Cco, and Cox), and quorum sensing (cciR, expR, lasR, mqsR, solR, sdiA, rpaR, and raiR) via functional gene analysis using a metagenomic database in iron-manganese synergy reactors. Furthermore, functional genes involved in iron redox cycling (korA/B/C/D and fhuF) and manganese oxidation (moxA, mcoA, cotA, and mnxG) were encoded by Nitrospirota, Thermoproteota, Desulfobacterota, and Halobacteriota, potentially facilitating a sustained supply of iron-based electron donors during the operation of iron-only and iron-manganese coupling reactors. Meanwhile, the microbial community exhibited complementary metabolic profiles and higher electron transport chain activity in the iron-manganese synergy reactors. Knowledge of the effects of functional regulation and metabolic complementarity in iron-manganese coupling systems can broaden our grasp of the scientific basis for applying water quality improvement strategies in reservoirs.},
}

@article {pmid42435639,
year = {2026},
author = {Neofytos, D and Muñoz, P and Averbuch, D and Mikulska, M and Vanbiervliet, Y and Baccelli, F and Vidal, CG and Aguilar-Guisado, M and Blijlevens, N and Akova, M and Calandra, T and Cordonnier, C},
title = {Non-culture based diagnostic tests for detection of bacterial infections in hematology patients with febrile neutropenia: A review by the European Conference on Infections in Leukemia (ECIL-10).},
journal = {Current research in translational medicine},
volume = {74},
number = {3},
pages = {103600},
doi = {10.1016/j.retram.2026.103600},
pmid = {42435639},
issn = {2452-3186},
abstract = {BACKGROUND: Limited data are available on the performance of non-culture-based diagnostics in hematology patients with febrile neutropenia (FN).

METHODS: The European Conference on Infections in Leukaemia (ECIL) 10 group performed a review (2011-2024) on the performance of available in Europe non-culture-based diagnostic methods on blood samples in hematology patients with FN, focusing on bacterial infections. The following tests were included: direct matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), multiplex/specific polymerase chain reaction (PCR), T2-magnetic resonance (T2MR), and metagenomic next generation sequencing (mNGS). A list of 6 predefined pertinent questions was assessed for the performance of each test.

RESULTS: For MALDI-TOF-MS, 4/16 (25%) articles were retained, including 475 hematology patients (98 with FN), with sensitivity ranging from 63 to 92.6%. For multiplex-PCR, 8/293 (2.7%) articles were retained, including 509 hematology patients (209 with FN), with a sensitivity of 80.5% and 100% (2 studies) and one study reporting a specificity of 88.5%. For T2MR, 1/18 (5.6%) article was retained including 648 hematology patients (309 with FN) and sensitivity and specificity of 84.2 and 85.9%, respectively. For mNGS, 6/35 (17%) articles were retained: 459 hematology patients (335 with FN), sensitivity (40-100%) and specificity (40-84%) reported in 3 studies. No articles were found on specific PCR in hematology patients. Improved microbiological documentation was reported in 5, 1, and 5 studies on multiplex-PCR, T2MR, and mNGS, respectively. Faster time to diagnosis was reported in 1, 5, and 1 studies on MALDI-TOF-MS, multiplex-PCR, and T2MR, respectively. Treatment choice was affected by the results of MALDI-TOF-MS, multiplex-PCR, mNGS in 1, 6, and 2 studies, respectively. No significant impact on overall survival or length of stay was reported for any of the tests reviewed.

CONCLUSIONS: Limited evidence exists on the performance of non-culture-based diagnostics in hematology patients. Blood cultures should be routinely used, even if new tests are available, which should be used in conjunction with the routine microbiological techniques, until more quality data are available.},
}

@article {pmid42435910,
year = {2026},
author = {Almeida, L and Alexandrino, DAM and Lilienthal, T and Karpe, NV and Ribeiro, N and Oliveira, RS and Carvalho, MF and Freitas, M},
title = {Compost microbiomes as reservoirs of cellulolytic microorganisms for cellulosic textile degradation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135373},
doi = {10.1016/j.biortech.2026.135373},
pmid = {42435910},
issn = {1873-2976},
abstract = {Cellulosic textiles, constituting over 30% of global fibre production, are biodegradable but remain challenging to recycle at scale owing to their high crystallinity, chemical finishes, and heterogeneous waste streams. Although microorganisms drive cellulose turnover in natural ecosystems, their potential for transforming anthropogenic cellulosic waste remains largely unexplored. In this study, composting was evaluated both as a sustainable approach to textile biodegradation and a reservoir of cellulolytic microorganisms with biotechnological potential. Biodegradation assays of cotton and lyocell were integrated with shotgun metagenomics and targeted cultivation to identify microbial taxa and enzymes involved in cellulose degradation. Composting trials showed that degradation was strongly influenced by both composting system and fibre composition. Community composting achieved near-complete textile disintegration, while shredded textiles exhibited the highest degradation rates, reaching up to 97%. Shotgun metagenomic revealed a bacterial-dominated community enriched in Actinomycetota and Bacillota and characterised by an abundance of glycoside hydrolases. Culture-based screening recovered 62 microbial isolates, of which Neurospora and Aspergillus exhibited the highest cellulolytic activity (>60%). In vitro assays further showed that cotton was more readily degraded than lyocell, with several isolates achieving >70% mass loss. Metagenomic approach revealed a predominantly bacterial composting community at the sampled stage, whereas cultivation preferentially recovered fungi that, despite their low relative abundance in situ, exhibited strong cellulolytic potential. These findings highlight the potential of composting as a sustainable end-of-life strategy for cellulosic textiles and identify compost microbiomes as valuable reservoirs of cellulolytic microorganisms for the development of sustainable bioprocesses for textile waste treatment.},
}

@article {pmid42436017,
year = {2026},
author = {Wang, Q and Zhong, W and Huang, H and Yang, X and Liu, X and Ren, Y and He, F and Li, J},
title = {Harnessing microbial modulators to mitigate antibiotic-induced gut dysbiosis: from phytochemicals to faecal microbiota transplantation.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-28},
doi = {10.1163/18762891-bja00123},
pmid = {42436017},
issn = {1876-2891},
abstract = {Antibiotics remain indispensable for the management of infectious diseases; however, their use inevitably perturbs the gut microbiota. Advances in metagenomics and multiomics approaches have demonstrated that antibiotic exposure profoundly disrupts microbial diversity and community structure, leading to the depletion of key commensals, the expansion of opportunistic pathogens, metabolic dysfunction, and the emergence of antimicrobial resistance. These alterations are increasingly associated with a broad spectrum of dysbiosis-related diseases (DRDs), encompassing metabolic, neuropsychiatric, and immune-mediated disorders. To mitigate or reverse antibiotic-induced microbial imbalances, various microbiota-targeted interventions have emerged as promising alternatives or complementary approaches. These include dietary phytochemicals (such as polyphenols, alkaloids, and organosulfur compounds), probiotics, prebiotics, synbiotics, postbiotics, bacteriophage therapy, and faecal microbiota transplantation (FMT). Evidence from in vitro and animal studies has provided mechanistic insights into how these interventions modulate microbial composition and function; however, clinical evidence varies across intervention type. This review summarizes the composition and functional roles of the gut microbiota, outlines the consequences of antibiotic exposure, and provides an overview of the underlying mechanisms, recent evidence, and potential applications of microbiota-targeted interventions in preserving intestinal homeostasis. This review aims to provide a theoretical basis and reference framework for the development of safer and more effective alternatives or adjuncts to antibiotic therapy.},
}

@article {pmid42426176,
year = {2026},
author = {Latorre, F and Jaillon, O and Sieracki, ME and Cruaud, C and Massana, R and Logares, R},
title = {Global population structure in MAST-4 unicellular marine predators.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10607-z},
pmid = {42426176},
issn = {2399-3642},
support = {CTM2015-69936-P//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; PID2022-137508NB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; RYC-2013-12554//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; CEX2019-000928-S//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; 240904//Norges Forskningsråd (Research Council of Norway)/ ; },
abstract = {Marine heterotrophic flagellates (HFs) are key unicellular predators in marine food webs. Understanding their diversity and distributions is crucial for comprehending ocean ecosystems. MAST-4, an uncultured clade of Marine Stramenopiles, comprises a key group of bacterivorous heterotrophic flagellates (HFs) in the ocean microbiome. While we know that temperature is a major driver of MAST-4's biogeography, the population structure of MAST-4 species remains poorly known, limiting our ability to understand their ecology and adaptations. Here, we investigate the global population diversity and structure of MAST-4 species A, B, C, and E using metagenomics and single-cell genomics data from the Tara Oceans expedition. We find substantial population divergence in MAST-4A and C, with lower divergence in species B and E. Temperature and salinity are the primary factors structuring these populations. Analyses of positively selected genes reveal genomic regions likely involved in population adaptation to different environments. Our findings enhance the understanding of the population diversity and structure of these critical unicellular predators, providing insights into their ecological roles and adaptations in the global ocean. They also contribute to our general understanding of microbial populations, a largely unexplored dimension of biodiversity that plays a crucial role in grasping the impacts of global change.},
}

@article {pmid42426205,
year = {2026},
author = {Wang, RH and Pan, G and Wang, S and Wang, J and Li, SC},
title = {High-quality phage assembly from metagenomes with PALACE.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42426205},
issn = {1546-1696},
abstract = {Millions of phage genomes have been mined from metagenomic data recently but the genome completeness remains poor because of the limitations of existing phage detection methods, which rely on metagenomic contigs that fragment phage genomes. Here, we present PALACE, a conjugate-graph-based framework for assembling high-quality phage genomes from metagenomes. PALACE incorporates homology-based and deep-learning-based methods to detect phage signals and constructs a conjugate graph from the metagenomic sample. On simulated data, PALACE generates accurate and complete phage genomes, achieving an F1 score of 0.92-1.00 across simulation settings, outperforming the second-best method by 0.21-0.48. Applying PALACE to 914 gut metagenomic samples from healthy controls and participants with colorectal cancer (CRC) yielded 5,306 high-quality phage genomes, outperforming the second-best benchmark method by 55.98% in median genome completeness. We observed a high degree of functional organization for genes within phage genomes. Phages from participants with CRC exhibited a notable enrichment of metabolic factors, suggesting their adaptation to nutrient availability in the CRC gut environment.},
}

@article {pmid42426353,
year = {2026},
author = {Marszałek, K and Kowalski, MB and Jagiełło, A and Woźniak, A and Herda, K and Płoski, R and Ossowski, A and Oliveira, M and Zbieć-Piekarska, R and Łabaj, PP and Branicki, W},
title = {Evaluation of targeted Massively Parallel Sequencing methods for forensic metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13944-5},
pmid = {42426353},
issn = {1432-0614},
abstract = {Massively Parallel Sequencing (MPS) is effective for monitoring the microbial composition of environmental samples. Soil microbial signatures are critical for pinpointing the geographic location of forensic evidence, but standard 16S rRNA methods lack species-level resolution. Targeted sequencing panels, consisting of informative DNA fragments, can overcome this shortcoming and are highly desirable for forensic investigations. To address this, we evaluated three target enrichment methods for metagenomic analysis. First, we used Whole Metagenome Sequencing (WMS) data from 134 soil samples across 46 locations in Poland to extract a set of 200 markers. Using these markers, we created prototype targeted sequencing panels to compare two amplicon capture-based methods (Thermo Fisher AmpliSeq™ and Integrated DNA Technologies xGen™) and one hybridization capture-based method (Roche KAPA HyperPlus). The comparison of the technologies was guided by the results of classification of sample origin by machine learning classifier trained on feature profiles from WMS. The methods were assessed on technical parameters including data quality, reproducibility, sensitivity, and practical implementation for forensic laboratories. The performance and precision varied depending on technology and DNA concentration. The Roche KAPA HyperPlus hybridization capture-based method consistently demonstrated superior performance. Across various DNA input quantities, it showed the highest correlation with WMS data and achieved an exceptional F1 score of 0.94 at 5 ng, significantly outperforming the amplicon-based methods. This indicates that hybridization capture is a more robust and accurate approach for forensic soil microbiome profiling, particularly for low-template evidence, providing a highly reliable tool for predicting geographic origin. KEY POINTS: • Targeted Massively Parallel Sequencing methods for forensic soil microbial analysis • Targeted sequencing allowed the determination of the place of origin of soil samples • Roche KAPA HyperPlus: the most accurate classification of the soil samples origin.},
}

@article {pmid42426489,
year = {2026},
author = {Dimri, A and Sharma, P and Vishvakarma, R and Sharma, S},
title = {Effect of Probiotics on the Gut-Mammary Pathway: Implications on Infant Microbiota Transfer and Development.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {42426489},
issn = {2161-3311},
mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; Female ; *Gastrointestinal Microbiome ; Infant, Newborn ; Milk, Human/microbiology ; Lactobacillus ; Bifidobacterium ; Pregnancy ; Infant ; *Gastrointestinal Tract/microbiology ; Lactation ; *Mammary Glands, Human/microbiology ; },
abstract = {PURPOSE OF REVIEW: Transfer of microbiota from the maternal gut, during lactation, takes place via breastmilk, which establishes an intricate beneficial microbial ecosystem in the gut of the newborn. A healthy gut microbiota influences and enhances the neonatal health, and aids in multidimensional development-metabolically, immunologically, neurologically, and hormonally. Several microorganisms like Lactobacillus and Bifidobacterium get transferred to the infant gut and play a key role in its colonization and programming. Administration of such microbes, or probiotics, to the mother can assist in improving the benefits imparted by breastmilk to the infant, and can also provide health benefits to the mother. In recent years, there has been a focus on related metagenomic studies and the immunological effects of individual genera have also been studied in detail. In this review, we observe the gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios. We also analyze the level of evidence of potential of some promising probiotic strains in the transfer, establishment, and development of infant gut microbiota based on recently conducted studies.

RECENT FINDINGS: The analysis of recent metagenomic studies proved that strains like Bifidobacterium infantis, Lactobacillus rhamnosus, and Limosilactobacillus reuteri exibit a high level of evidence in benefitting the microbiota transfer as well as establishment, diversification, and development of the infant gut ecosystem. Hence, these strains in particular, can be given as supplements to mothers during pregnancy and lactation, in order to improve their inherent immunity and the overall health of the mother-infant dyad. With the advent of metagenomics, the roles, functions and effects of microbes in the gut-mammary pathway have been re-examined. This review, critically evaluates the recent studies related to gut-mammary pathway and the different roles played by probiotics in prenatal and postnatal scenarios with particular emphasis on the strength and quality of their evidence.},
}

Humans
*Probiotics/administration & dosage/pharmacology
Female
*Gastrointestinal Microbiome
Infant, Newborn
Milk, Human/microbiology
Lactobacillus
Bifidobacterium
Pregnancy
Infant
*Gastrointestinal Tract/microbiology
Lactation
*Mammary Glands, Human/microbiology

@article {pmid42426596,
year = {2026},
author = {Bunga, S and Tan, A and Roos, M and Kuersten, S},
title = {RiboZAP: a species-agnostic pipeline for rRNA depletion probe design in metatranscriptomics.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06533-w},
pmid = {42426596},
issn = {1471-2105},
abstract = {BACKGROUND: Metatranscriptomic (MetaT) sequencing provides insights into gene expression and functional activity within microbial communities, but its utility is limited by the high abundance of ribosomal RNA (rRNA), which often accounts for ≥ 90% of total RNA. Efficient rRNA depletion is therefore essential to maximize mRNA coverage and sequencing efficiency. Commercial rRNA depletion kits can effectively reduce rRNA content; they are typically optimized for specific host microbiomes and often underperform in others. For example, probes designed for the human gut microbiome frequently show reduced efficiency when applied to non-human samples such as mouse cecal donor samples-a common model in microbiome research. Regardless of the depletion strategy used, designing rRNA removal probes solely based on a microbiome's taxonomic composition often requires an extensive number of probes, making the approach expensive and difficult to manufacture. To address these challenges, we developed RiboZAP, a species-agnostic computational pipeline that designs custom RNase H depletion probes directly from MetaT sequencing data without prior knowledge of sample composition.

RESULTS: RiboZAP-designed probe sets achieved 43-62% predicted rRNA depletion across both design and independent mouse cecal MetaT samples. Probes performed effectively on non-design samples, with depletion performance consistent with those observed in the design samples. Read composition and taxonomic diversity of residual rRNA, calculated using Shannon diversity indices, showed no evidence of probe-induced bias following depletion. In silico predictions were consistent with previously reported experimental depletion results [1-3], where RiboZAP designed probes improved mRNA recovery up to ~ 75% (P < 0.01). Comprehensive downstream validation demonstrated no bias in differential gene expression (R[2] = 0.96), metabolic pathway profiling (ρ = ~0.92-0.95), or taxonomic composition.

CONCLUSION: In this study, we demonstrate a data-driven, in silico approach for designing additional rRNA depletion probes that perform consistently across samples of the same sample type. Probe sets designed from a subset of samples can be applied to independent samples of the same type. This approach enables estimation of rRNA depletion prior to synthesis, reducing experimental costs, and improving the efficiency of MetaT profiling from complex microbial communities.},
}

@article {pmid42426749,
year = {2026},
author = {Zhan, S and Zheng, Y and Wu, T and Hou, X and Li, J and Ma, S and Gai, W and Shen, N and Zheng, J},
title = {Nucleosome-targeted host DNA depletion enables automated plasma metagenomic sequencing for sensitive detection of bloodstream pathogens.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08597-x},
pmid = {42426749},
issn = {1479-5876},
support = {F252052//Beijing Natural Science Foundation/ ; BYSYJC2023005//Peking University Third Hospital Fund for Interdisciplinary Research/ ; 2025-VHR-O-SY-21//State Key Laboratory of Vascular Homeostasis and Remodeling Open Research Fund/ ; 2025YFC2609702 and 2025YFC2609700//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Bloodstream infections (BSIs) are leading causes of sepsis-related mortality. Although metagenomic next-generation sequencing (mNGS) enables culture-independent pathogen detection, its clinical utility in plasma is limited by the overwhelming abundance of host cell-free DNA (cfDNA) and labor-intensive manual workflows.

METHODS: A plasma host DNA depletion mNGS (HD-mNGS) assay was developed which integrated nucleosome-targeted host DNA depletion with automated DNA extraction and library preparation. Analytical performance was evaluated through limit of detection, linearity, precision, and contamination control. Clinical performance was assessed in a cohort of 107 patients with suspected BSI and benchmarked against blood culture (BC), conventional microbiological testing (CMT), and standard mNGS without host depletion, using a composite clinical reference standard.

RESULTS: Nucleosome depletion markedly reduced host DNA background by an average of 66-fold, consequently enriching microbial reads by approximately 46.73-fold. The automated HD-mNGS assay exhibited robust analytical sensitivity, with limits of detection (LoD) ranging from 9.1 to 38 genome equivalents (GE) /mL for bacteria and fungi, and from 283 to 321 GE/mL for viruses and excellent linearity across tested concentrations (R[2] = 0.915-0.989). Furthermore, the automated workflow maintained strong quantitative correlation with manual protocols while significantly reducing common skin and environmental contaminants by 71.7% and 83.7%, respectively. In a cohort of 107 patients, HD-mNGS demonstrates improved diagnostic performance for BSI, achieving a significantly higher pathogen detection rate (64.49%) and clinical positive percent agreement (PPA: 95.24%) than standard mNGS, BC, and CMT (P < 0.001). Crucially, HD-mNGS demonstrates enhanced performance in detecting rare, fastidious, and intracellular pathogens (such as Mycobacterium tuberculosis and Rickettsia) that yield extremely low concentrations of circulating DNA, overcoming the limitations of traditional methods while maintaining high overall diagnostic total percent agreement (TPA: 88.79%).

CONCLUSIONS: Nucleosome-targeted host DNA depletion integrated with a fully automated mNGS platform significantly enhances microbial detection in plasma and provides a scalable approach for standardized BSI diagnostics.},
}

@article {pmid42426884,
year = {2026},
author = {Lei, Y and Xu, Y and Yan, Y and Zhang, J and Zhang, T and Huang, J and Huang, Y and Zhong, J and Wang, X and Zhang, K and Chen, Y},
title = {Multi-omics and functional validation reveal that Methanobrevibacter-derived L-3-aminoisobutyrate alleviates subclinical mastitis in dairy goats via the HSPA1B-p65 signaling pathway.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02464-z},
pmid = {42426884},
issn = {2049-2618},
abstract = {BACKGROUND: Subclinical mastitis (SCM) is prevalent in dairy livestock and compromises milk quality and lactation performance. Although often attributed to bacterial infection, many cases lack identifiable pathogens, suggesting alternative mechanisms. While evidence supports a gut-mammary gland axis, the microbial drivers and microbiota-derived metabolites linking gut dysbiosis to SCM remain unclear. Here, we aimed to identify SCM-associated gut microbial markers, prioritize candidate therapeutic metabolites and define the underlying mechanism.

RESULTS: Based on differences in somatic cell count (SCC) and inflammatory phenotypes across a cohort of 167 mid-lactation Saanen dairy goats, we selected 6 healthy and 6 SCM goats for downstream analyses. By integrating metagenomics, metabolomics, cross-species fecal microbiota transplantation (FMT) and functional validation in vitro and in vivo, we found that SCM was accompanied by reduced milk yield and heightened inflammatory signatures. Compared with the Healthy group, SCM goats exhibited marked remodelling of the gut microbiota, with enrichment of opportunistic taxa (Eubacterium and Blautia) and a pronounced depletion of archaeal Methanobrevibacter spp. Notably, FMT from SCM donors recapitulated mammary inflammatory phenotypes in mice, supporting a causal contribution of gut dysbiosis to mammary inflammation. Joint metagenomic functional profiling and metabolomics further identified the branched-chain amino-acid-derived metabolite L-3-aminoisobutyrate (BAIBA) as significantly enriched in the gut of healthy goats. Moreover, Methanobrevibacter spp. harboured key enzyme genes (vorA, vorB and vorD) implicated in BAIBA biosynthesis. In an LPS-challenged MAC-T model, BAIBA attenuated mammary epithelial inflammation by activating endoplasmic reticulum protein quality control programmes and restoring HSPA1B expression, thereby suppressing NF-κB activation and reducing pro-inflammatory cytokine production. Finally, in naturally infected goats, intramammary administration of BAIBA lowered SCC, highlighting translational potential.

CONCLUSIONS: This study identifies BAIBA as a microbiota-derived metabolite that protects against SCM by restraining mammary inflammation via the HSPA1B-NF-κB axis, establishing a mechanistic gut-mammary link and highlighting a potential non-antibiotic intervention strategy. Video Abstract.},
}

@article {pmid42426896,
year = {2026},
author = {Tóth, GE and Nagy, A and Costales, JA and Camacho, MA and Burneo, SF and Petersen, M and Bialonski, A and Baum, H and Horváth, B and Heitmann, A and Lühken, R and Schmidt, M and Schmidt-Chanasit, J and Tauber, Z and Cadar, D},
title = {A highly sensitive amplicon sequencing workflow for genomic surveillance of Usutu virus.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
doi = {10.1186/s12985-026-03251-w},
pmid = {42426896},
issn = {1743-422X},
mesh = {Humans ; *Flavivirus/genetics/isolation & purification/classification ; Germany ; *High-Throughput Nucleotide Sequencing/methods ; *Genome, Viral ; *Flavivirus Infections/virology ; Workflow ; Blood Donors ; RNA, Viral/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Genomic surveillance of Usutu virus (USUV) in blood donors is hampered by extremely low viral loads, which usually prevent reliable genome sequencing. We developed and validated a tiled amplicon-based sequencing protocol optimized for low-titer samples. Serial dilutions of four phylogenetically distinct USUV lineages showed ≥ 95% genome recovery above 100 RNA copies/µL and 65-98% recovery between 3 and 100 copies/µL. We applied the method to 27 USUV-positive blood donors from Germany (median 1.70 copies/µL), achieving lineage assignment in 74% and ≥ 70% genome coverage in 63% of samples. This approach enables routine genomic surveillance of USUV in blood donors.},
}

Humans
*Flavivirus/genetics/isolation & purification/classification
Germany
*High-Throughput Nucleotide Sequencing/methods
*Genome, Viral
*Flavivirus Infections/virology
Workflow
Blood Donors
RNA, Viral/genetics
Phylogeny
Genomics/methods
Sequence Analysis, DNA/methods

@article {pmid42427046,
year = {2026},
author = {Guo, YF and Zhan, QY and Huang, LN},
title = {[Clinical characteristics, diagnosis and treatment strategies, and prognostic factors in 47 patients with pulmonary mucormycosis].},
journal = {Zhonghua nei ke za zhi},
volume = {65},
number = {7},
pages = {734-742},
doi = {10.3760/cma.j.cn112138-20260201-00069},
pmid = {42427046},
issn = {0578-1426},
support = {2025ZD01902400//National Science and Technology Major Project/ ; },
mesh = {Humans ; *Mucormycosis/diagnosis ; Male ; Prognosis ; *Lung Diseases, Fungal/diagnosis ; Middle Aged ; Retrospective Studies ; Female ; Antifungal Agents ; Risk Factors ; Adult ; Voriconazole ; },
abstract = {Objective: To summarize the clinical characteristics, diagnostic and therapeutic strategies, and prognostic factors in patients with pulmonary mucormycosis. Methods: The patients with pulmonary mucormycosis admitted to the Department of Respiratory and Critical Care Medicine and the Lung Transplantation Department of China-Japan Friendship Hospital from January 2016 to March 2023 were retrospectively evaluated. High-risk factors, clinical manifestations, imaging findings, microbiological tests, therapeutic interventions, and clinical outcomes were analyzed, and variables were compared between survivors and non-survivors. Intergroup statistical analyses were performed using the chi-squared test, or Fisher's exact test, etc. Results: Of the 47 patients (21 confirmed, 26 clinically diagnosed), 32 (68.1%) were male, and the mean age of the cohort was (48±17) years. High-risk factors were present in 87.2% (41/47) of patients, primarily diabetes mellitus (53.2%, 25/47) and immunosuppression (42.6%, 20/47); 53.2% (25/47) had a history of voriconazole exposure. Hemoptysis occurred in 57.4% (27/47) of patients, of whom 17.0% (8/47) experienced massive hemoptysis; 48.9%(23/47) required interventional or surgical management. Chest CT scans revealed large consolidative opacities (70.2%, 33/47) and thick-walled cavities (48.9%, 23/47), and contrast-enhanced CT identified vascular involvement. The positive rate for lower respiratory tract fungal culture was only 17.1% (6/35), and that of smear microscopy was 18.2% (6/33), whereas the positive rate of metagenomic next-generation sequencing (mNGS) reached 76.0% (19/25), with mNGS of bronchoalveolar lavage fluid reaching 85.0% (17/20). Overall, 34.0% (16/47) of patients were diagnosed exclusively via mNGS. Conventional amphotericin B formulations were administered to 68.1% (32/47) of patients (including 10 who received liposomal amphotericin B); these formulations were associated with an adverse drug reaction rate of 86.7% (26/30), which contributed to only 40.7% (11/27) of these treated patients receiving a full therapeutic dose. Azoles were administered to 91.5% (43/47) of patients (15 received azoles alone), and among those treated with posaconazole, 88.0% (22/25) achieved target plasma concentrations; 48.9% (23/47) received combination therapy consisting of an amphotericin B formulation plus an azole. The survival rate among patients who underwent surgical intervention combined with antifungal therapy was 11/12, which was higher than that of patients who received antifungal therapy alone (28/35). Compared with survivors, non-survivors demonstrated significantly higher incidences of dyspnea (8/8 vs. 14/39, P=0.001), uncontrolled fever (6/8 vs. 12/39, P=0.027), pleural effusion (8/8 vs. 17/39, P=0.003), atelectasis (5/8 vs. 6/39, P=0.016), and severe complications (7/8 vs. 13/39, P=0.015). Furthermore, a significantly lower proportion of non-survivors received adequate antifungal dosing (1/8 vs. 21/39, P=0.037). Conclusions: Pulmonary mucormycosis predominantly occurs in high-risk populations such as those with diabetes mellitus or immunosuppression. Hemoptysis is a prominent clinical manifestation, while imaging findings commonly include large areas of consolidation, thick-walled cavities, and signs of vascular invasion. Early execution of contrast-enhanced chest CT, along with bronchoscopy with bronchoalveolar lavage fluid mNGS, improves the diagnostic yield. Adequate antifungal therapy combined with aggressive surgical intervention may contribute to improved prognosis. Severe complications, dyspnea, uncontrolled fever, pleural effusion, atelectasis, and inadequate antifungal treatment are associated with a poor prognosis, underscoring the need for early recognition and management.},
}

Humans
*Mucormycosis/diagnosis
Male
Prognosis
*Lung Diseases, Fungal/diagnosis
Middle Aged
Retrospective Studies
Female
Antifungal Agents
Risk Factors
Adult
Voriconazole

@article {pmid42427959,
year = {2026},
author = {Wang, L and Ding, K and Yu, S and Guo, Z and Wang, Y and Zeng, L and Yuan, W},
title = {Atypical congenital toxoplasmosis presenting with neonatal jaundice and central nervous system involvement: a case report and therapeutic challenges to limited access to first-line anti-toxoplasma medications.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1874973},
pmid = {42427959},
issn = {2296-2360},
abstract = {BACKGROUND: Congenital toxoplasmosis (CT) is a vertically transmitted infection with a variable clinical spectrum, ranging from asymptomatic infection at birth to severe neurological and ocular sequelae. While the classic triad of hydrocephalus, intracranial calcifications, and chorioretinitis is well characterized, isolated neonatal hyperbilirubinemia as the initial presenting feature is uncommon and may delay diagnosis. We report a case of CT in a Chinese neonate who presented with jaundice and was subsequently found to have subclinical active chorioretinitis, cerebral edema, and bilateral central auditory pathway dysfunction. The case also illustrates therapeutic challenges related to the availability of first-line anti-parasitic agents.

CASE PRESENTATION: A 9-day-old term male infant was admitted for persistent jaundice. He was born at 39 [+] [4] weeks' gestation, with a prenatal history notable only for maternal cat exposure and treated hypothyroidism. Initial serological testing at the referring hospital revealed positive Toxoplasma gondii IgM and IgG. After transfer, two consecutive blood metagenomic next-generation sequencing (mNGS) tests detected T. gondii DNA (reads: 6 and 7). The combination of negative first-trimester maternal serology, postpartum maternal IgM/IgG positivity, neonatal IgM positivity, and repeated detection of T. gondii DNA in neonatal blood strongly supported congenital toxoplasmosis. Cerebrospinal fluid (CSF) analysis showed pleocytosis and elevated protein, while CSF mNGS was negative, possibly reflecting low pathogen burden or compartmentalized infection. Further evaluation demonstrated bilateral active chorioretinitis on fundoscopic examination, abnormal brainstem auditory evoked potentials consistent with bilateral central auditory pathway dysfunction, and brain MRI showing cerebral edema with punctate hemorrhages. Due to initial unavailability of pyrimethamine, azithromycin followed by trimethoprim-sulfamethoxazole was administered; however, no clear improvement in CSF inflammatory indices was observed during this period. After initiation of standard therapy with pyrimethamine, sulfadiazine, and folinic acid, the patient demonstrated rapid clinical improvement and radiological resolution of brain lesions on follow-up MRI, with marked improvement of chorioretinal scars.

CONCLUSIONS: Clinicians should consider congenital toxoplasmosis in neonates with unexplained jaundice, even in the absence of classic clinical manifestations. Comprehensive multi-organ evaluation, including neuroimaging, ophthalmologic examination, and auditory testing, is essential for early disease characterization. Standard pyrimethamine-sulfadiazine-folinic acid therapy may be associated with better clinical and radiological outcomes and should be used when available. Long-term multidisciplinary follow-up is necessary to monitor potential sequelae.},
}

@article {pmid42428097,
year = {2026},
author = {Hanze Villavicencio, KL and Tanes, C and Malekshahi, C and Cutillo, D and Knoll, MD and Prosperi, C and Kalaycioglu, M and Harris, M and Utz, PJ and Mattei, LM and Beiting, DP},
title = {Microbial and immune determinants of disease severity and death in pediatric pneumonia.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.02.26356561},
pmid = {42428097},
abstract = {Pneumonia is a leading cause of death globally and disproportionately affects children in lower- and middle-income countries. To explore microbial and immune correlates of disease and death, we performed metagenomic sequencing of upper respiratory tract (URT) microbiome in 309 children in Mali with pneumonia and 150 age- and season- and site-matched controls. We show that the URT microbiome matures throughout early life and is influenced by breastfeeding. URT microbiome maturation was disrupted during pneumonia resulting in loss of commensal species and expansion of pathobionts, which was linked to disease severity and death. Analysis of serum antibody levels revealed that low levels of passively acquired antibody from mothers, deficient antibody responses to RSV, and persistent autoantibody to cytokines were associated with pneumonia mortality in an age-dependent manner. These findings underscore the complex nature of pneumonia and identify microbial and immune factors for risk stratification and therapeutic interventions in pediatric pneumonia.},
}

@article {pmid42428114,
year = {2026},
author = {Wang, Q and Wang, BY and Wilus, D and Xie, H},
title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {42428114},
abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced bleeding on probing and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of microbial community. Established periodontal pathogens, including Porphyromonas gingivalis and Tannerella forsythia , as well as the emerging pathogen Escherichia coli , decreased following treatment, whereas health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus , increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified treatment-associated differences in several carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.},
}

@article {pmid42428252,
year = {2026},
author = {Qi, W and Kong, M and Meng, X and Sun, Z and Mei, Z and Pu, Y and Zhou, X and Wang, Q and Qiu, JG and Jiang, BH and Shen, J and Yuan, C and Ji, JS and Wang, X and Kan, H and Zheng, Y},
title = {The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.},
journal = {Environmental health perspectives},
volume = {134},
number = {3},
pages = {335-350},
pmid = {42428252},
issn = {1552-9924},
mesh = {Humans ; *Air Pollution/adverse effects/statistics & numerical data ; *Gastrointestinal Microbiome/drug effects ; Aged ; Particulate Matter/adverse effects ; Ozone ; Male ; Female ; *Cognition/drug effects ; *Cognitive Dysfunction/epidemiology ; *Air Pollutants ; *Environmental Exposure/statistics & numerical data ; },
abstract = {BACKGROUND: Growing evidence links air pollution to cognitive dysfunction in older adults. The gut microbiome and circulating metabolites present an important yet unexplored pathway given their crucial role in the gut-brain axis. OBJECTIVES: We aimed to explore the potential roles of gut bacteria, fungi, microbial functional potentials, and circulating metabolites in the association of residential PM2.5 and O3 exposure with cognitive dysfunction. METHODS: We analyzed gut microbiome data from 1,027 older adults using metagenome and internal transcribed spacer sequencing to profile bacterial and fungal taxa, functional pathways, and enzyme abundances. Targeted metabolomics quantified 195 circulating metabolites, such as amino acids and organic acids. Annual average ambient PM2.5 and O3 exposures were estimated by using satellite-based models. Cognitive outcomes, including mild cognitive impairment and cognitive decline, were assessed using the Mini-Mental State Examination and Hasegawa Dementia Scale. Statistical analyses included Microbiome Multivariable Association with Linear Models (with a false discovery rate threshold of 0.25) for microbial associations and multivariate regression for metabolites and cognitive outcomes. RESULTS: Higher PM2.5 and O3 exposures were associated with disturbances in microbial composition, altered taxonomic profiles (e.g., decreased abundances of Blautia obeum and Gordonibacter pamelaeae), and disrupted functional pathways, particularly those regulating 2-oxoglutarate. These findings were partially replicated in an independent population. Higher air pollution levels were associated with increased circulating levels of 2-oxoglutarate and l-glutamine (key metabolites in neurodegenerative progression), which were further linked to higher odds of concurrent mild cognitive impairment (OR: 1.39-1.56) and an increased 2-year risk of cognitive decline (OR: 1.26-1.37). These associations were partially mediated by air pollution-related changes in microbial anaerobic energy metabolism pathways, especially involving 2-oxoglutarate metabolism and the enzyme aspartate transaminase. CONCLUSIONS: Our findings highlight the role of the gut microbiome and microbial metabolites in mediating the detrimental impact of air pollution on cognitive health in older adults, providing new insights into the underlying etiology for future hypothesis generation.},
}

Humans
*Air Pollution/adverse effects/statistics & numerical data
*Gastrointestinal Microbiome/drug effects
Aged
Particulate Matter/adverse effects
Ozone
Male
Female
*Cognition/drug effects
*Cognitive Dysfunction/epidemiology
*Air Pollutants
*Environmental Exposure/statistics & numerical data

@article {pmid42429397,
year = {2026},
author = {Romo Bechara, N and Bardeskar, N and Hopkins, HA and Bobay, L-M and Raymann, K},
title = {Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0121326},
doi = {10.1128/spectrum.01213-26},
pmid = {42429397},
issn = {2165-0497},
abstract = {UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits.

IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.},
}

@article {pmid42429454,
year = {2026},
author = {Di Leo, D and Nilsson, E and Westmeijer, G and Pinhassi, J and Lundin, D},
title = {nf-core/magmap: Map metatranscriptomes to large collections of genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag501},
pmid = {42429454},
issn = {1367-4811},
abstract = {SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes.

The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

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

@article {pmid42429456,
year = {2026},
author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K},
title = {Exploring life's hidden majority: microbial dark matter symposium highlights.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0058725},
doi = {10.1128/msphere.00587-25},
pmid = {42429456},
issn = {2379-5042},
abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.},
}

@article {pmid42429485,
year = {2026},
author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW},
title = {Multi-omics Analysis Identify Novel Microbiome-Metabolome Signatures Associated with Obesity.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag172},
pmid = {42429485},
issn = {1365-2672},
abstract = {AIMS: Explore the potential microbiome and serum metabolome factors and their interactions associated with obesity.

METHODS AND RESULTS: We performed a systematic multi-omics analysis using paired metagenomic and metabolomic profiles-including untargeted serum metabolomics, lipidomics, and short-chain fatty acids (SCFAs) with body mass index (BMI) from a cohort of 495 US men. Single omics analysis identified 52 gut bacteria species and 31 serum metabolites for potential associations with BMI. Among the identified bacteria, Collinsella stercoris (C.stercoris) (Coef.=-0.147, P=0.015) was negatively associated, whereas Bacteroides fragilis (B.fragilis) (Coef.=0.294, P=1.22E-04) and Veillonella dispar (V.dispar) (Coef.=0.135, P=0.001) were positively associated, these results were further validated by an independent Chinese cohort. Several of the identified metabolites including gamma-glutamylglycine (Coef.=-0.713, P=4.53E-06), asparagine (Coef.=-0.629, P=3.53E-05), glycine (Coef.=-0.952, P=5.28E-09) and serotonin (Coef.=0.566, P=1.78E-04) were associated with these significant bacteria (P<0.05).

CONCLUSION: This multi-omics study identifies key gut bacteria and serum metabolites that interact to associate with host obesity, providing systemic insight into microbiome-host metabolic interactions.},
}

@article {pmid42429570,
year = {2026},
author = {Sánchez-Nieto, E and Martínez-Abarca, F and Millán, V and Molina-Sánchez, MD and García-Rodríguez, FM and Toro, N},
title = {A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0038126},
doi = {10.1128/spectrum.00381-26},
pmid = {42429570},
issn = {2165-0497},
abstract = {Bacteriophages exert strong selective pressure on soil- and rhizosphere-associated bacteria, including plant-associated symbionts. Reverse transcriptase-associated defense systems of the UG family are widespread across bacterial lineages, yet their ecological roles remain largely undefined. Within this family, UG5 systems are distinguished by reverse transcriptases fused to or associated with a nitrilase domain. Here, we combine phylogenetic, metagenomic, and functional analyses to investigate the evolutionary context and antiviral activity of UG5-associated systems. Phylogenetic analysis of 728 nitrilase domains places UG5-associated nitrilases within a well-supported UG-related radiation encompassing the UG1, UG5, and UG6 families, with UG1 nested within a broader UG5 lineage. Metagenomic analysis further revealed UG5-associated reverse transcriptases in soil- and rhizosphere-derived metagenomes. Based on this observation, we characterized a UG5-large reverse transcriptase (RT)-associated system, here designated DRT11, encoded on the pSymA megaplasmid of Sinorhizobium meliloti RMO17, a nitrogen-fixing symbiont of Medicago sativa. Despite lacking the transmembrane protein typical of canonical UG5-large architectures, DRT11 confers protection against naturally occurring M. sativa rhizosphere phages with podovirus-like morphology. Phage infection assays reveal protection at low multiplicities of infection, consistent with an abortive-infection-like mechanism. Moreover, mutational analyses demonstrate that antiviral activity requires only the RT and its fused C-terminal nitrilase domain, establishing DRT11 as a minimal UG5-associated antiviral system.IMPORTANCEIn this study, we report the functional characterization of a UG5-large reverse transcriptase-associated defense system (DRT11) encoded on the pSymA megaplasmid of the nitrogen-fixing plant symbiont Sinorhizobium meliloti. Using a combination of phylogenetic, metagenomic, genomic, and experimental approaches, we demonstrate that DRT11 functions as a bona fide antiviral defense module, providing protection against naturally occurring rhizosphere phages through a minimal reverse transcriptase-nitrilase architecture. This work establishes direct functional evidence for antiviral activity within the UG5 family and clarifies the evolutionary placement of UG5-associated systems within the broader UG radiation.},
}

@article {pmid42429609,
year = {2026},
author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA},
title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0002726},
doi = {10.1128/msphere.00027-26},
pmid = {42429609},
issn = {2379-5042},
abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS vaginal carriage is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokines at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences, with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to eight pro-inflammatory cytokines post-GBS infection. Diabetic mice exhibited decreased proportions of uterine neutrophils and, following GBS exposure, also displayed an expanded vaginal γδ T cell compartment compared with controls. Pairing cytokine observations with GBS colonization revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS phenotypes. Intravaginal supplementation with rIL-1α resolved GBS burden differences between diabetic mice and controls, confirming that deficient vaginal cytokines contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention.IMPORTANCEPeople with T2D are more susceptible to microbial infections, but there is limited understanding of the mechanisms that drive this vulnerability. One possibility is that T2D enhances the colonization of opportunistic pathogens, like GBS, in mucosal reservoirs as a precursor to infection. In this study, we used a diabetic mouse model to test whether diabetes alters the vaginal mucosa to promote GBS colonization. We found that increased vaginal GBS colonization in diabetic mice was not linked to tissue glucose availability or changes in the vaginal microbiome but instead was associated with impaired vaginal immune responses. These findings provide a foundation for translational approaches to reduce GBS persistence and dissemination in at-risk individuals.},
}

@article {pmid42429615,
year = {2026},
author = {Jiang, K and Xiong, F and Peng, Y and Meng, L and Wang, X and Xu, Y and Tang, T and Gao, H},
title = {Intermittent Fasting Restores Cardiac Lipid Homeostasis in Diabetic Cardiomyopathy in Association With Akkermansia Muciniphila and 1-methyl-L-histidine.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76528},
doi = {10.1002/advs.76528},
pmid = {42429615},
issn = {2198-3844},
support = {22274115//National Natural Science Foundation of China/ ; 21974096//National Natural Science Foundation of China/ ; LZ26C010002//Zhejiang Provincial Natural Science Foundation of China/ ; LQN26C010004//Zhejiang Provincial Natural Science Foundation of China/ ; },
abstract = {Diabetic cardiomyopathy (DCM) is a major cardiovascular complication of diabetes with limited effective interventions. Using a streptozotocin-induced insulin-deficient, type 1 diabetes-like DCM mouse model, we show that intermittent fasting (IF) improves cardiac function and attenuates myocardial remodeling. Antibiotic-mediated microbiota depletion largely abolished these benefits, whereas fecal microbiota transplantation from IF-treated donors recapitulated cardioprotection, supporting a causal role of the gut microbiota. Metagenomic profiling identified Akkermansia muciniphila (A. muciniphila) as a prominent IF-responsive taxon, and A. muciniphila supplementation alleviated cardiac injury without obvious improvement in glycaemia. Integrated serum and heart metabolomics identified 1-methyl-L-histidine as a microbiota-associated metabolite reduced in diabetes but restored by IF and A. muciniphila. In vitro and ex vivo assays further supported an L-anserine-linked microbial route for 1-methyl-L-histidine generation. Importantly, oral 1-methyl-L-histidine supplementation recapitulated key cardioprotective effects, remodeled cardiac lipid homeostasis, and reduced lipid peroxidation and oxidative injury. Together, these findings support a gut microbiota-metabolite-lipid axis associated with IF-related cardioprotection in DCM and highlight microbial metabolites as tractable targets to complement dietary intervention.},
}

@article {pmid42429677,
year = {2026},
author = {Sarkar, M and Maddheshiya, A and Tailor, P and Nath, S and Makkar, N and , and Misra, S and Desiraju, BK and Wadhwa, N and Bhatnagar, S and Kshetrapal, P and Mukherjee, S},
title = {Longitudinal shifts in oral microbiome composition and metabolic pathways associated with preterm birth.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0018426},
doi = {10.1128/msystems.00184-26},
pmid = {42429677},
issn = {2379-5077},
abstract = {Oral dysbiosis in pregnant women with oral diseases has been associated with adverse pregnancy outcomes. However, the inter-individual variability in oral microbiome composition of pregnant women without any oral disease, and its role in preterm birth, has not been studied yet. Here, we have collected saliva from 20 term birth (TB) and 20 preterm birth (PTB) delivering women without any self-reported oral disease at three trimesters (n = 120). Microbial DNA was subjected to 16S rRNA gene sequencing for taxonomic classification, and microbial pathways were investigated by PICRUSt2. In a subset of samples, shotgun metagenomic sequencing was done to identify microbial species, their gene families, and their pathways. TB and PTB women were distributed into three distinct oral community types (OCTs). Haemophilus parainfluenzae and Rothia mucilaginosa were associated with TB and PTB, respectively. The chorismate biosynthesis pathway, essential for folic acid biosynthesis, was significantly enriched in TB, whereas the enterobactin biosynthesis pathway that produces iron chelators (siderophores) was significantly enriched in PTB. The heterolactic fermentation pathway that reduces oral pH was enriched in PTB. Our data suggest that oral microbiome changes might have an impact on birth outcomes in women even without any history of self-reported oral disease during the pregnancy period.IMPORTANCEThe importance of this study lies in demonstrating that compositional and functional shifts in the oral microbiome are associated with pregnancy outcomes. Using a longitudinal design across three trimesters in an Indian cohort, we show that pregnant women segregate into distinct oral community types with consistent associations to term birth (TB) and preterm birth (PTB). Importantly, the TB-associated microbiome was enriched in taxa and pathways linked to vitamin and amino acid biosynthesis, including chorismate and threonine metabolism, which are critical for fetal growth. In contrast, PTB was associated with pathways related to iron scavenging and acidification of the oral environment, suggesting a metabolically stressed and dysbiotic state. These findings highlight the oral microbiome as a previously underappreciated, modifiable factor in pregnancy outcomes and underscore its potential relevance for early risk stratification and preventive strategies against PTB.},
}

@article {pmid42429741,
year = {2026},
author = {Koraimann, G and Hölzl, N and Koller, M and Zarfel, G and Treiber, F},
title = {A complete Candidatus walczuchella monophlebidarum genome assembled from citrus leaf metagenomic sequences.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0062026},
doi = {10.1128/mra.00620-26},
pmid = {42429741},
issn = {2576-098X},
abstract = {We present the complete de novo assembly of a Candidatus Walczuchella monophlebidarum genome (286,606 bp), a flavobacterial endosymbiont of the giant-scale insect Icerya purchasi. The genome was assembled from metagenomic short read Illumina sequences obtained from DNA of citrus leaves collected in Carinthia, Austria in November 2024.},
}

@article {pmid42429749,
year = {2026},
author = {Cluett, H and Chandler, JC and Bisha, B},
title = {A coding-complete genome sequence of bovine-like coronavirus identified in white-tailed deer (Odocoileus virginianus) in the United States.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0050026},
doi = {10.1128/mra.00500-26},
pmid = {42429749},
issn = {2576-098X},
abstract = {Bovine coronavirus within the Embecovirus subgenus causes respiratory and enteric diseases in domestic cattle. We report a coding-complete genome of bovine-like coronavirus from a white-tailed deer (Odocoileus virginianus) in New Jersey, USA. This genome is 30,988 bp with a guanine-cytosine content of 37%.},
}

@article {pmid42429762,
year = {2026},
author = {Putman, T and Abdel-Hamid, AM and Galbraith, E and Schimmel, P and Kim, H and Yasuma, T and Alhawsawi, MAB and Boateng, KA and Holmes, J and Duersteler, M and D'Alessandro-Gabazza, CN and Fujimoto, H and Kobayashi, T and Walden, KKO and Rendon, G and Fields, CJ and Zuckermann, FA and Mackie, RI and Son, S and Leistikow, KR and Gabazza, EC and King, MR and Cann, I},
title = {A Bacillus-based direct-fed microbial mixture remodels the gut microbiome to augment the respiratory health of Salmonella-infected pigs.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0097226},
doi = {10.1128/aem.00972-26},
pmid = {42429762},
issn = {1098-5336},
abstract = {Commercial pork production is practiced worldwide and represents a major source of protein for global populations. Pigs, however, are plagued by various diseases that affect their productivity. A common practice is to administer antibiotics in the feed to reduce infections and promote growth. However, antibiotic utilization in pig production has been identified as a source of spread of antibiotic resistance genes, prompting the need for antibiotic alternatives in swine production. Salmonella enterica serotype Choleraesuis and porcine reproductive and respiratory syndrome virus (PRRSV) are two disease agents with a significant impact on the pork industry. In this study, we designed experiments to test the hypothesis that a Bacillus-based direct-fed microbial (DFM) cocktail will alleviate the impact of Salmonella infection alone or in combination with PRRSV. Both single and dual infections resulted in shifts in the cecal microbiota from that of the Control group, with administration of the DFM dampening this effect, especially in the Salmonella-infected group. In the absence of the DFM, the infected pigs exhibited gross changes in the lungs, including tissue hepatization. Significantly, the DFM application suppressed the lesions in the lungs of Salmonella-only infected pigs. Using metagenome-assembled genomes, we found that DFM administration to Salmonella-only infected pigs led to cecal microbiota enriched in the potential to produce immune-stimulating short-chain fatty acids and naturally occurring antimicrobials, including peptides. The putative antimicrobial peptides derived from this study, upon biochemical characterization, could lead to their application as novel antimicrobials in animal agriculture and health.IMPORTANCEAntibiotics, as feed additives, have been integral to commercial pork production. Their use, however, has fostered the spread of antibiotic resistance genes in the environment. In this study, we explored the use of a mixture of naturally occurring bacteria, comprising species of the genus Bacillus, as an alternative to antibiotics in the pig diet. The bacterial mixture reversed disease lesions in the lungs of pigs infected with Salmonella enterica serotype Choleraesuis, a bacterium that causes severe disease in commercial pigs. Our findings suggest that applying the bacterial mixture to the Salmonella-infected pigs shifts the microbes in the gut to a community that is endowed with antimicrobials that mitigate the effects of Salmonella infection. We present data showing the novelty of putative antimicrobials discovered in the present study and postulate that their characterization will yield new antimicrobials that can be used in different sectors of animal production and health. PRRSV was included in the study to model a common bacterial-viral co-infection in swine, as it exacerbates disease severity. This design allowed assessment of whether Bacillus-based DFM could improve outcomes along the gut-lung axis under realistic co-infection conditions.},
}

@article {pmid42429885,
year = {2026},
author = {Delik, A and Ülger, Y and Albayrak, F and Orhan, U and Unal, U and Gov, E and Dinçer, S},
title = {Machine learning integration of tissue-specific metagenomic signatures for colorectal cancer diagnosis.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {42429885},
issn = {2190-3883},
abstract = {Colorectal cancer (CRC) represents a significant global health burden. Leveraging machine learning (ML) with metagenomic and tissue-specific data presents new opportunities for improving diagnostic accuracy and understanding the microbiome's role in CRC. This study was conducted to enhance diagnostic efficiency and identify crucial bacterial biomarkers in CRC using various ML models applied to metagenomic data. A total of 33 samples were analyzed, comprising 20 healthy controls and 13 CRC patients. Each sample included demographic data (age, gender) and bacterial information (Bacteroides, Enterococcus, Faecalibacterium, Proteobacteria, Gammaproteobacteria, Firmicutes, Enterobacteriaceae, Clostridia). Six models: Logistic Regression, Naive Bayes, Decision Tree, Support Vector Machine (SVM) with both linear and polynomial kernels and Multilayer Perceptron (MLP) were employed. Performance was evaluated using leave-one-out cross-validation (LOOCV). To address the class imbalance, F1-score was utilized as the primary metric for feature selection. A consensus-based feature elimination strategy, where bacterial features were iteratively removed only if their exclusion improved or maintained the F1-score across the majority of the models was implemented. For the MLP, a grid search was integrated into each iteration to optimize hidden layer architectures and solvers, thereby ensuring that robust performance was achieved for each feature subset. The analysis was conducted using a 10-feature initial set consisting of 2 demographic and 8 microbial features. Model performances were optimized through a consensus-based feature elimination strategy, and it was determined that diagnostic success increased with the exclusion of the Faecalibacterium, Age, and Enterobacteriaceae features during the process. The highest performance was achieved with the SVM model with Linear kernel when Bacteroides was excluded from the 9-feature subset (Table 4), reaching an accuracy of 87.88% and an F1-score of 83.33%. Within the final biomarker set, Enterococcus and Firmicutes were identified as the most critical predictive features due to the sharpest declines in F1-score observed in their absence. This study demonstrates that the systematic elimination of initial clinical and metagenomic features maximizes CRC diagnostic accuracy and model stability. The process, initiated with a 10-feature baseline set was subsequently refined to establish a high-precision diagnostic mechanism with an F1-score of 83.33%. The identified final microbial signatures, consisting of 5-6 taxa, provide a clinically applicable, non-invasive diagnostic foundation with low input requirements.},
}

@article {pmid42429927,
year = {2026},
author = {Lirio, CPT and Albino, EED and Nisnisan, KKS and Castro, AE},
title = {Gut bacterial community profile of the endemic catfish Arius manillensis from Pasig River, Philippines.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0037026},
doi = {10.1128/mra.00370-26},
pmid = {42429927},
issn = {2576-098X},
abstract = {The Pasig River is a highly urbanized waterway, yet the microbial ecology of its native fauna remains poorly understood. This study provides the first report of the gut bacterial community of the catfish Arius manillensis, revealing bacterial taxa and underscoring the need to study host-associated microbiomes in urban aquatic ecosystems.},
}

@article {pmid42430134,
year = {2026},
author = {Laureano, G and Lal, V and Mitchell, L and Santillan Olea, E and Tovar, J and Scoles, A and Arun, A},
title = {Meta-genome assembled genome of Agrobacterium oryzihabitans associated with the cultivated yellow-green alga Vaucheria bursata.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0047325},
doi = {10.1128/mra.00473-25},
pmid = {42430134},
issn = {2576-098X},
abstract = {We report a draft metagenome-assembled genome (MAG) of an Agrobacterium species from Vaucheria bursata. The MAG is 89% complete (CheckM2 v1.1.0) with 3,281 predicted genes, providing a basis to explore bacteria-algae interactions and their role in the Vaucheria microbiome.},
}

@article {pmid42430136,
year = {2026},
author = {Aoki, M and Wakui, N and Hayashi, K and Syutsubo, K},
title = {High-quality metagenome-assembled genome sequences of Bacteroidota and Pseudomonadota bacteria, assembled from a manganese(II)-oxidizing biofilm reactor.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0058826},
doi = {10.1128/mra.00588-26},
pmid = {42430136},
issn = {2576-098X},
abstract = {We report five high-quality, potentially novel metagenome-assembled genomes (MAGs) recovered from a manganese(II)-oxidizing biofilm reactor. Affiliated with Bacteroidota and Pseudomonadota, these MAGs provide a genomic basis for understanding the ecology and metabolic potential of Mn(II)-oxidizing systems and represent a valuable resource for future functional studies of biofilm-mediated metal cycling.},
}