@article {pmid41965542,
year = {2026},
author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R},
title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.},
journal = {International journal of emergency medicine},
volume = {19},
number = {1},
pages = {},
pmid = {41965542},
issn = {1865-1372},
abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches.

METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised.

RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm.

CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.},
}

@article {pmid41973308,
year = {2026},
author = {Aydin, F and Çek, Ş},
title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {41973308},
issn = {1573-7446},
abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.},
}

@article {pmid41981860,
year = {2026},
author = {Liu, B and Yang, J and Wang, J and Zhang, J and Wang, L and Qu, B and Guo, L and Zhang, X and Yang, X and Jiang, Y},
title = {Application of Whole-Genome Sequencing and Metagenomic Sequencing in Microbial Analysis of Milk Powder and Its Processing Environment: Current Findings and Challenges.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {3},
pages = {e70478},
doi = {10.1111/1541-4337.70478},
pmid = {41981860},
issn = {1541-4337},
support = {//Danone Asia-Pacific Management Co. Ltd./ ; },
mesh = {*Whole Genome Sequencing ; *Milk/microbiology ; Animals ; *Metagenomics ; *Food Microbiology ; Food Handling ; Powders ; Food Contamination/analysis ; },
abstract = {As dairy enterprises increasingly focus on microbial contamination, traditional detection technologies are gradually showing limitations in terms of detection capability, accurate source tracking, and rapid response, especially when dealing with microbial communities in complex processing environments. Fortunately, whole-genome sequencing (WGS) and metagenomic sequencing provide innovative alternative solutions. These technologies significantly improve the detection of harmful microbes by offering strain-level resolution, detecting low-abundance organisms, and uncovering previously undetectable microbes. This review discusses the application of WGS and metagenomic sequencing in microbial monitoring, contamination source tracking, and quality control across the entire milk powder production chain. In particular, it highlights the progress made in microbial typing and source tracking, as well as in the detection of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). This review also compares microbial control standards for milk powder and its processing environment across different countries and international organizations, providing a regulatory perspective. Furthermore, the integration of emerging technologies is also discussed, particularly machine learning (ML) and deep learning (DL). Artificial intelligence (AI) enables more efficient, predictive, and accurate microbial monitoring, improving contamination control and contributing to safer and higher-quality milk powder production processes. This review provides critical insights that contribute to improving microbial safety management and control strategies in milk powder production.},
}

*Whole Genome Sequencing
*Milk/microbiology
Animals
*Metagenomics
*Food Microbiology
Food Handling
Powders
Food Contamination/analysis

@article {pmid41982876,
year = {2026},
author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X},
title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799474},
pmid = {41982876},
issn = {1664-302X},
}

@article {pmid41982885,
year = {2026},
author = {Santiago-Rodriguez, TM and Toranzos, GA},
title = {Editorial: Advances in phage applications: deciphering phage biological and ecological mechanisms through metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822387},
doi = {10.3389/fmicb.2026.1822387},
pmid = {41982885},
issn = {1664-302X},
}

@article {pmid41982959,
year = {2026},
author = {Zhang, K and Zheng, J and Wei, A and Qin, M and Zhu, G},
title = {Pulmonary infection caused by Tropheryma whipplei in a child before hematopoietic stem cell transplantation: a case report.},
journal = {Translational pediatrics},
volume = {15},
number = {3},
pages = {91},
pmid = {41982959},
issn = {2224-4344},
abstract = {BACKGROUND: Tropheryma whipplei (TW) triggers Whipple's disease (WD), a rare, chronic multisystemic infection with heterogeneous clinical presentations that can be easily overlooked, particularly Whipple's pneumonia. The advent of metagenomic next-generation sequencing (mNGS) technology applied to bronchoalveolar lavage fluid (BALF) analysis has enabled the identification of an increasing number of patients with acute pneumonia due to TW. Most reports describe symptomatic middle-aged males with cough, while asymptomatic pediatric cases remain exceptionally rare. Without adequate antibiotic therapy, WD is invariably fatal, especially in patients undergoing hematopoietic stem cell transplantation (HSCT). There is no established consensus on the optimal treatment regimen or duration, particularly for pediatric patients.

CASE DESCRIPTION: An 8-year-old boy with primary immunodeficiency due to a genetic mutation presented without respiratory symptoms. Yet, high-resolution computed tomography (HRCT) revealed nodular lesions. Initially misdiagnosed as a fungal infection, subsequent mNGS analysis of BALF identified TW as the sole pathogen, leading to a diagnosis of TW-associated pneumonia. Following a combined anti-infective therapy regimen, the patient successfully underwent the myeloablative conditioning (MAC) regimen. Neutrophil and platelet engraftment occurred promptly, with no severe transplant-related complications.

CONCLUSIONS: This retrospective analysis describes a clinical scenario involving a pediatric patient who exhibited no respiratory symptoms prior to transplantation but showed characteristic nodular lesions on imaging studies, ultimately confirming acute pneumonia caused by TW. Under a combination anti-infection regimen consisting of intravenous ceftriaxone, oral doxycycline, and oral hydroxychloroquine, the child tolerated the MAC regimen well. Neutrophil and platelet engraftment proceeded without delay, and follow-up imaging confirmed complete resolution of the pulmonary lesions.},
}

@article {pmid41983569,
year = {2026},
author = {Vogel, MA and Machairas, F and Ferchiou, S and Osvatic, J and Alzubaidy, H and Séneca, J and Hausmann, B and Klun, K and Petersen, JM},
title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag094},
pmid = {41983569},
issn = {1751-7370},
abstract = {Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a 'three-way' facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca. Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.},
}

@article {pmid41983714,
year = {2026},
author = {Viguier, C and Mansuy, JM and Martin-Blondel, G},
title = {Recent advances in flavivirus encephalitis.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
pmid = {41983714},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Flaviviruses are an increasing public health concern, responsible for a broad spectrum of human disease ranging from asymptomatic or mild febrile illness to severe neuroinvasive infections such as encephalitis. Flavivirus encephalitis is associated with substantial mortality and long-term neurological sequelae, yet no specific antiviral therapy is currently available. Diagnosis remains challenging because of transient viremia and serological cross-reactivity, and preventive strategies are unevenly implemented. This review summarizes recent advances in the diagnosis, prognostic assessment, treatment, and prevention of flavivirus-associated encephalitis.

RECENT FINDINGS: Recent studies have reshaped diagnostic strategies through improved viral detection, including multimatrix molecular testing and metagenomic approaches, alongside better characterization of host-response markers in cerebrospinal fluid. Recent work has substantially refined understanding of host susceptibility, highlighting preexisting antitype I interferon autoantibodies as a major driver of severe disease across neurotropic flaviviruses, and identifying several biomarkers with potential prognostic value. Neuroimaging work has refined MRI pattern recognition across flaviviral encephalitis, with limited but evolving prognostic implications. While management remains largely supportive, the therapeutic pipeline is increasingly diverse, with growing interest in host-directed strategies.

SUMMARY: Flavivirus encephalitis represents a major clinical challenge driven by host vulnerability, diagnostic complexity, and the absence of validated therapies. Integrating recent advances in diagnostics, risk stratification, and prevention is essential, while ongoing therapeutic development offers cautious optimism for future management.},
}

@article {pmid41983840,
year = {2026},
author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K},
title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e299936},
doi = {10.1590/1519-6984.299936},
pmid = {41983840},
issn = {1678-4375},
mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; },
abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.},
}

Animals
Cattle/microbiology
*Livestock/microbiology
Camelus/microbiology
Sheep/microbiology
*Microbiota/genetics/physiology
Chickens/microbiology
Horses/microbiology

@article {pmid41983925,
year = {2026},
author = {El Zibaoui, R and Venkatesan, A},
title = {An update on infectious encephalitis: from epidemiology to management.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
pmid = {41983925},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Infectious encephalitis (IE) is a serious neurological condition that poses a major global health threat. This review summarizes emerging pathogens, particularly arboviruses, updated diagnostic strategies, and evolving treatment approaches, emphasizing ongoing gaps in diagnosis and management.

RECENT FINDINGS: Established arboviruses such as West Nile virus, Japanese encephalitis virus, Powassan virus, and Eastern Equine virus have regained attention due to their geographic expansion and the appearance of distinct genotypes. In parallel, increasing reports of encephalitis by newly emerging pathogens such as Oropouche virus and scrub typhus speak to the evolving nature of the epidemiology of IE. Advances in diagnostics, including multiplex PCR and metagenomic next-generation sequencing, have enhanced the breadth and accuracy of pathogen identification. As treatment options remain scarce, the role of immunomodulatory agents and novel antiviral molecules in the management of IE is actively being investigated.

SUMMARY: The emergence of novel and reemerging pathogens highlights the need for rapid, accurate diagnostics. Advanced molecular techniques and the identification of novel therapeutic targets have the potential to change the landscape of IE. However, strengthening surveillance and vaccination strategies, along with ongoing efforts in vaccine development, remain crucial for optimizing patient outcomes, increasing public health preparedness, and mitigating future outbreaks.},
}

@article {pmid41984378,
year = {2026},
author = {Tao, X and Du, Z and Wang, X and Lv, L and Zhang, G and Liang, J and Zou, W},
title = {Volatile Fatty Acid Production from Baijiu Distillers' Grains Via Anaerobic Fermentation with Rumen Microbes: Performance and Mechanism.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41984378},
issn = {1559-0291},
support = {52400160//National Natural Science Foundation of China/ ; 52360020//National Natural Science Foundation of China/ ; E2024202030//Natural Science Foundation of Hebei Province/ ; RKJH[2025]26//Renhuai Municipal Science and Technology Program/ ; Qiankehe Jichu QN [2025] 292//Youth Science and Technology Talent Project of the Guizhou Provincial Basic Research Program/ ; },
}

@article {pmid41984912,
year = {2026},
author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , },
title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e86058},
doi = {10.2196/86058},
pmid = {41984912},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.

OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.

METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.

RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.

CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Infant, Newborn
Female
Infant
Longitudinal Studies
Prospective Studies
Birth Cohort
South Africa
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Observational Studies as Topic
Rural Population
Milk, Human/microbiology/chemistry
Male
Risk Factors

@article {pmid41985067,
year = {2026},
author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR},
title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {4},
pages = {e70159},
doi = {10.1002/arch.70159},
pmid = {41985067},
issn = {1520-6327},
support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science & Technology, New Delhi, India (INSPIRE-JRF)/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth & development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.},
}

Animals
Larva/microbiology/growth & development
*Microbiota
Metagenomics
*Culicidae/microbiology/growth & development
*Metamorphosis, Biological
Bacteria/genetics/classification
Metagenome

@article {pmid41985316,
year = {2026},
author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P},
title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.},
journal = {Biomaterials advances},
volume = {185},
number = {},
pages = {214878},
doi = {10.1016/j.bioadv.2026.214878},
pmid = {41985316},
issn = {2772-9508},
abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.},
}

@article {pmid41985330,
year = {2026},
author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K},
title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {198},
number = {},
pages = {119370},
doi = {10.1016/j.biopha.2026.119370},
pmid = {41985330},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.

METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).

RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.

CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.},
}

@article {pmid41985671,
year = {2026},
author = {Wang, Y and Liu, X and Li, Z and Kang, A and Bai, Y and Wang, Y and Liu, Y and Zhang, C and Yang, J and Cai, Q and Feng, Y and Yi, H and Zhang, M and Zhang, F and Liu, H and Xu, C},
title = {Oligofructose alleviates hyperandrogenism in polycystic ovary syndrome through gut microbiota-derived bile acids.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.036},
pmid = {41985671},
issn = {2090-1224},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common endocrine disorder in reproductive-age women, characterized by hyperandrogenism and metabolic dysfunction. Dietary interventions are recommended as one of the first-line therapies. Oligofructose (OFS), a prebiotic fiber, has demonstrated clinical benefits in PCOS; however, its underlying mechanism remains unclear.

OBJECTIVES: To determine whether OFS alleviates PCOS-like phenotypes through bile acid-dependent mechanisms and to identify downstream ovarian steroidogenic responses.

METHODS: Letrozole-induced PCOS-like mice received OFS supplementation. Microbiota dependence was assessed using antibiotic depletion and fecal microbiota transplantation (FMT). Bile acid involvement was evaluated using cholestyramine. Gut microbial composition and function were profiled by 16S rRNA and metagenomic sequencing, and bile acids were quantified by UHPLC-MS/MS. Ovarian transcriptomics, ex vivo ovarian explants, and primary granulosa cells were used to examine steroidogenic changes, with pharmacological inhibition applied to assess TGR5-related signaling.

RESULTS: OFS improved reproductive and metabolic abnormalities in PCOS-like mice. These benefits were abolished by microbiota depletion and bile acid sequestration, indicating microbiota- and bile acid-dependent effects. OFS was associated with increased circulating hyodeoxycholic acid (HDCA), which negatively correlated with serum testosterone. HDCA supplementation partially reproduced endocrine improvements under microbiota-depleted conditions. Ovarian transcriptomic and functional analyses demonstrated enhanced aromatization following OFS treatment. In ex vivo ovarian explants and primary granulosa cells, HDCA increased estradiol production, reduced testosterone, and upregulated CYP19A1 (encoding aromatase). Under androgen stimulation, pharmacological inhibition of TGR5 attenuated HDCA-associated increases in estradiol and aromatase activity, supporting involvement of TGR5-related signaling.

CONCLUSION: OFS alleviates PCOS-like phenotypes in a microbiota- and bile acid-dependent manner and enhances ovarian aromatization. These findings move beyond descriptive bile acid alterations in PCOS by providing functional evidence that dietary fiber-induced bile acid remodeling is associated with modulation of ovarian steroidogenic regulation.},
}

@article {pmid41986005,
year = {2026},
author = {Ansari, A and Shete, O and Ghosh, TS},
title = {Artificial intelligence in microbial metagenomics.},
journal = {Progress in molecular biology and translational science},
volume = {221},
number = {},
pages = {255-276},
doi = {10.1016/bs.pmbts.2026.01.009},
pmid = {41986005},
issn = {1878-0814},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; Microbiota/genetics ; Machine Learning ; },
abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.},
}

*Metagenomics/methods
*Artificial Intelligence
Humans
Microbiota/genetics
Machine Learning

@article {pmid41986051,
year = {2026},
author = {},
title = {Correction to 'Clinical Value of Metagenomic Next-Generation Sequencing in Early Diagnosis of Peritoneal Dialysis-Associated Peritonitis: A Randomised Controlled Observational Trial'.},
journal = {Nephrology (Carlton, Vic.)},
volume = {31},
number = {4},
pages = {e70203},
doi = {10.1111/nep.70203},
pmid = {41986051},
issn = {1440-1797},
}

@article {pmid41986605,
year = {2026},
author = {Sumithra, TG and Gayathri, S and Mannur, VS and Neethu, N and Ratheesh Kumar, R and Nair, AV and Ratheesh, L and Zainul Abid, PM and Sundari, BKR and Dharani, G and Krupesha Sharma, SR},
title = {Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48651-8},
pmid = {41986605},
issn = {2045-2322},
support = {Deep-sea Metagenomics for enhanced next-generation bioethanol production' under Deep Ocean Mission (DOM) [MoES/PAMC/DOM/176/2023 (E-14624)]//Ministry of Earth Sciences/ ; },
}

@article {pmid41986657,
year = {2026},
author = {Luchen, CC and Piedade, GJ and Chibuye, M and Simuyandi, M and Chisenga, CC and Chilengi, R and Bosomprah, S and Schultsz, C and Mende, DR and Harris, VC},
title = {Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {},
pmid = {41986657},
issn = {2731-8745},
support = {2023159//Amsterdam University Medical Center Amsterdam Public Health Research Institute/ ; LSHM23007//Track-AMR/ ; LSHM23007//Track-AMR/ ; 09150161810022//Netherlands Organisation for Health Research and Development (ZonMw) VENI/ ; 219775/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; LSHM21033//Co-funding by PPP Allowance awarded by Health~Holland, Top Sector Life Sciences & Health GLORIA/ ; AI173360/NH/NIH HHS/United States ; },
abstract = {Antimicrobial resistance (AMR) costs lives, diminishes antimicrobial effectiveness and increases health care costs. We conducted a re-analysis of pooled fecal metagenomes from individual participants to characterise AMR gene (ARG) distributions in 0-2 year-old healthy infants across income and geography. From 2275 screened studies, we included nine datasets and 1944 fecal metagenomes. Resistome gene identifier (RGI) was used to identify ARGs, and gut microbiomes were profiled using Sylph. We assessed associations between ARGs, Escherichia coli abundance, and national-level indicators. In the first 3 months of life, ARG abundance patterns were not significantly different across income groups; however, by 6 months of age, infants in LICs had higher ARG abundance, associated with increased E. coli carriage. Caesarean section rates, antibiotic use, and income inequality positively correlated with ARG abundance in younger infants; physician density negatively correlated with ARG abundance in older children. These descriptive age- and context-specific associations may inform interventions to mitigate the carriage and spread of ARGs and the rise of AMR in vulnerable pediatric populations.},
}

@article {pmid41986663,
year = {2026},
author = {Luiken, REC and Prinsen, H and Dasari, SN and Zweerus, H and Timmerman, AJ and Speksnijder, DC and Dohmen, W and Wagenaar, JA and Heederik, DJJ and Zomer, AL},
title = {Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {},
pmid = {41986663},
issn = {2731-8745},
abstract = {The use of antimicrobials in livestock farming drives selection and dissemination of antimicrobial resistance (AMR), prompting implementation of veterinary stewardship programs to reduce antimicrobial usage (AMU). We evaluated changes in AMR on 45 Dutch pig farms before and after tailored, coaching-based interventions using phenotypic testing of Escherichia coli and metagenomic profiling of pooled faeces. Post-weaning pig farms, including nursery and fattening units, entered the intervention in a stepped-wedge design, with intervention periods ranging from 10 to 27 months. Across farms, AMU and abundances of several antimicrobial resistance gene classes declined over time, alongside reductions in overall resistome levels. Proportions of phenotypic AMR in E. coli were more variable, although decreased AMU was associated with lower resistance for specific antimicrobial classes, such as tetracyclines and beta-lactams. While longer follow-up is required to fully assess long-term impacts, these findings indicate that veterinary antimicrobial stewardship programs can yield measurable short-term reductions in AMR at farm level.},
}

@article {pmid41986664,
year = {2026},
author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J},
title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10050-0},
pmid = {41986664},
issn = {2399-3642},
abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.},
}

@article {pmid41986859,
year = {2026},
author = {Iñiguez-Luna, MI and Gómez-Godínez, LJ and Cadena-Zamudio, JD and Cadena-Zamudio, DA and Aguirre-Noyola, JL and Barrera-Guzmán, LA},
title = {Omics Sciences: Driving the Conservation and Characterization of Plant Genetic Resources.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3011},
number = {},
pages = {345-364},
pmid = {41986859},
issn = {1940-6029},
abstract = {Omics sciences have revolutionized the conservation and characterization of plant genetic resources by enabling a comprehensive understanding of genetic diversity, molecular mechanisms, and adaptive traits. Advances in genomics, transcriptomics, proteomics, metabolomics, and metagenomics have facilitated the identification of genes and metabolic pathways associated with stress tolerance, nutritional value, and agronomic performance. These technologies have enhanced the efficiency of germplasm banks by improving genetic resource characterization, optimizing conservation strategies, and accelerating breeding programs for climate-resilient crops. Additionally, omics approaches contribute to biodiversity conservation by revealing evolutionary relationships, ecosystem dynamics, and the functional roles of microbial communities in plant health. The integration of multi-omics data with bioinformatics and artificial intelligence further enhances predictive capabilities, enabling targeted conservation and breeding efforts. This review highlights the pivotal role of omics sciences in securing plant genetic resources for sustainable agriculture and global food security.},
}

@article {pmid41975427,
year = {2026},
author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P},
title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05460-5},
pmid = {41975427},
issn = {1746-6148},
support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; },
}

@article {pmid41975703,
year = {2026},
author = {Rong, R and Long, Y and Li, Y and Lin, L and Yang, J and Hu, Z and Liu, D and Chen, P},
title = {Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {7},
pages = {},
pmid = {41975703},
issn = {2075-4418},
support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; P12220011-230148//Undergraduate teachingquality and teaching reform licensing project SYSU/ ; },
abstract = {Metagenomic and targeted next-generation sequencing (NGS) technologies are rapidly transforming diagnosis and management for infectious diseases. This review comprehensively examines the current applications of metagenomic NGS (mNGS) and targeted NGS (tNGS) in clinical microbiology, highlighting their roles in pathogen detection, antimicrobial resistance profiling, virulence characterization, and outbreak investigation-particularly in complex cases such as pneumonia, critical illness with pulmonary infections, and pediatric acute respiratory illnesses. We discuss the diagnostic performance, advantages, and limitations of these approaches, including challenges related to sensitivity, specificity, standardization, bioinformatic complexity, and cost-effectiveness. Furthermore, we explore emerging opportunities for integrating NGS-based surveillance with public health strategies, such as wastewater epidemiology, to monitor healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) at the population level. Finally, we outline key steps needed to translate these powerful genomic tools from research settings into routine clinical and public health practice.},
}

@article {pmid41975975,
year = {2026},
author = {Szala, Ł and Staninska-Pięta, J and Piotrowska-Cyplik, A},
title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41975975},
issn = {2076-2615},
support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; },
abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.},
}

@article {pmid41976452,
year = {2026},
author = {Li, X and Li, Y and Li, Q and Jin, Y and Chen, Y},
title = {Rumen Metagenomic and Muscle Metabolomic Characterization of Meat Quality in Duolang Sheep at Different Ages.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976452},
issn = {2304-8158},
support = {2022TSYCLJ0014//Program for Science and Technology Innovation Talents/ ; 2023B02015//Key Research and Development Program Project of Xinjiang Uygur Autonomous Region/ ; },
abstract = {This study aimed to investigate the changes in the meat quality characteristics of Duolang sheep using rumen metagenomic and muscle metabolomic analyses across different age groups. A total of 24 three-month-old male Duolang sheep were selected and reared, and samples of longissimus thoracis muscle and rumen contents were collected at 4, 6, and 8 months of age to evaluate meat quality, metabolites, rumen metagenome, and volatile fatty acids (VFAs). The results indicated that the lightness (L*45min) and yellowness (b*45min) of the longissimus thoracis muscle at 45 min post-slaughter were significantly higher at 4 and 6 months than at 8 months of age (p < 0.05). In terms of ruminal VFAs, butyrate concentration was significantly higher at 6 months than at 4 months (p < 0.05), and valerate concentration exhibited a quadratic relationship with age (p = 0.02). With increasing age, the relative abundances of Prevotella and Fibrobacter increased, whereas those of Methanobrevibacter and Bacteroides decreased (p < 0.05), leading to shifts in functional pathways related to amino acid, lipid, and carbohydrate and energy metabolism. Untargeted metabolomics revealed that muscle betaine and inosine peaked at 4 months of age, whereas L-arginine, L-proline, and inosinic acid were most abundant at 6 months of age (p < 0.05). Correlation analysis revealed that the b*45min was positively associated with ruminal concentrations of propionate, butyrate, and valerate, as well as with the relative abundances of key Selenomonadales taxa (p < 0.05). Inosinic acid exhibited a positive correlation with the abundance of the genus Sodaliphilus and ruminal butyrate concentration (p < 0.05), while Sodaliphilus abundance was negatively correlated with inosine (p < 0.05). In summary, this study demonstrates that age-related variations in the meat quality of Duolang sheep are closely associated with rumen microbial ecology and muscle metabolites, offering novel insights into the molecular mechanisms underlying meat quality formation and identifying potential biomarkers.},
}

@article {pmid41976454,
year = {2026},
author = {Olupot, CK and Sheehan, O and Kampff, Z and McDonnell, B and Woods, DF and Lugli, GA and Ventura, M and Reen, FJ and Sinderen, DV and Mahony, J},
title = {Raw Milk Cheese Microbiomes: A Paradigm for Interactions of Lactic Acid Bacteria in Food Ecosystems.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976454},
issn = {2304-8158},
abstract = {While industrial-scale dairy fermentations often employ pasteurized milk as the substrate, many farmhouse and traditional production practices apply raw milk derived from a variety of mammals. Certain artisanal production systems rely on the autochthonous microbiota of the milk, fermentation vessels, equipment and/or environment to initiate milk coagulation. While the technological properties of lactic acid bacteria associated with dairy fermentations are well described, their interactions with other organisms during fermentation and cheese ripening are poorly investigated. This study presents an overview of the microbial ecology of raw and pasteurized milk used in the production of Irish farmhouse cheeses using metagenomic and culture-based approaches. Metagenomic analysis of four raw milk-derived cheeses established the dominant presence of either lactococci or Streptococcus spp. and with a secondary population of various lactobacilli. Interestingly, the Brie sample was also demonstrated to possess significant proportion of Hafnia spp. This was corroborated in culture-based analysis where Hafnia isolates were also identified. Furthermore, we report on the motility phenotype, lactose utilization ability and metabolic products of isolates of Hafnia paralvei and Hafnia alvei, and determine that these strains could grow in a non-antagonistic manner on plates with strains of Lactococcus lactis and Streptococcus thermophilus. As artisanal and farmhouse production systems are often associated with protected or regionally significant products, it is essential to develop a clear understanding of the microbial communities within and the complex relationships between the community members.},
}

@article {pmid41976504,
year = {2026},
author = {Buranavanitvong, N and Thanthithum, C and Kanyakam, K and Azzout-Marniche, D and Jouan-Rimbaud Bouveresse, D and Chotechuang, N and Prakitchaiwattana, C},
title = {Diet-Associated Gut Bacterial Microbiota and Metabolome Signatures Linked to Fermented Food Intake in Healthy Postmenopausal Women.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976504},
issn = {2304-8158},
support = {FOOD_FF_68_290_2300_073//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; GCUGR1125671022D//the 90th Anniversary of Chulalongkorn University Scholarship under the Ratchadapisek Somphot Endowment Fund/ ; NA//the Second Century Fund (C2F), Chulalongkorn University/ ; },
abstract = {Long-term adherence to plant-based diets can modify gut bacterial microbiota composition and metabolite profiles, which may be particularly relevant for postmenopausal women who frequently adopt such diets and experience age-related changes in nutrient absorption and metabolism. Fermented foods, commonly consumed in vegetarian diets, enhance dietary diversity and nutritional quality. This study compared gut bacterial microbiota and fecal metabolomes between vegetarians (VGs) and omnivores (OMs) and evaluated the contribution of fermented food intake. Thirty-two healthy postmenopausal Thai women (>55 years; 16 VGs, 16 OMs) were enrolled. Gut bacterial microbiota and fecal metabolites were analyzed using 16S rRNA metagenomic and untargeted [1]H-NMR metabolomics. The five most frequently consumed fermented foods were microbiologically characterized. Fermented food consumption was found to be significantly different between groups. OM participants reported infrequent consumption (<10% per week), whereas VG participants consumed fermented foods daily, often in multiple forms (>60% of weekly meals). VG participants exhibited enrichment of Prevotella, Faecalibacterium, and Blautia, while OM participants showed higher abundances of Bacteroides and Escherichia-Shigella. LEfSe identified Weissella as a bacterial taxon associated with the VG group. Functional prediction and metabolomic analyses indicated enhanced carbohydrate fermentation and increased short-chain fatty acid (SCFA) production in VGs, whereas OM profiles reflected greater protein catabolism. Fermented foods consumed by VGs shared microbial biomarkers with the VG gut bacterial microbiota and were rich in SCFAs and essential amino acids, supporting their potential role as microbial and metabolic contributors within the gut ecosystem and nutritional adequacy in postmenopausal vegetarians.},
}

@article {pmid41977149,
year = {2026},
author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J},
title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
doi = {10.3390/ijms27072960},
pmid = {41977149},
issn = {1422-0067},
mesh = {*Malus/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Fermentation ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics ; },
abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.},
}

*Malus/metabolism/chemistry
*Gastrointestinal Microbiome
*Fermentation
Humans
*Yeasts/metabolism
Fatty Acids, Volatile/metabolism
Bacteria/classification/genetics

@article {pmid41977414,
year = {2026},
author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J},
title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
doi = {10.3390/ijms27073233},
pmid = {41977414},
issn = {1422-0067},
support = {2024YFF0907700//National Key R&D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; },
mesh = {*Wood/microbiology/metabolism ; *Microbiota ; Lignin/metabolism ; *Penicillium/metabolism/genetics ; Metagenomics/methods ; },
abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.},
}

*Wood/microbiology/metabolism
*Microbiota
Lignin/metabolism
*Penicillium/metabolism/genetics
Metagenomics/methods

@article {pmid41978025,
year = {2026},
author = {De Nat, M and Boscolo, S and Gallo, SP and Nanni, L and Fusaro, D},
title = {Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {7},
pages = {},
doi = {10.3390/s26072238},
pmid = {41978025},
issn = {1424-8220},
mesh = {*Deep Learning ; Humans ; *Genome, Viral/genetics ; Neural Networks, Computer ; *Sequence Analysis, DNA/methods ; Metagenomics/methods ; Base Sequence ; *Viruses/genetics ; },
abstract = {Detecting highly divergent or previously unknown viruses is a critical bottleneck in clinical diagnostics and pathogen surveillance. While alignment-based methods often fail to classify sequences lacking homology to known references, deep learning offers a powerful alternative for signal extraction from 'viral dark matter.' In this work, we present a high-performance ensemble of deep convolutional neural networks specifically designed to identify viral contigs in complex human metagenomic datasets. Our framework processes sequences acquired from high-throughput biological sensors and integrates complementary architectures to capture both local motifs and global genomic signatures. The proposed ensemble achieves state-of-the-art performance, reaching an AUROC of 0.939 on 300 bp contigs and significantly outperforming existing models such as transformer-based approaches, ViraMiner, and DeepVirFinder. Crucially, our results demonstrate high robustness to data degradation, maintaining stable predictive power even with a 10% random nucleotide substitution rate, a common challenge in degraded clinical samples. Furthermore, the model generalizes to 'unseen' viral families not present during training, demonstrating its utility for emerging threat detection. To ensure full reproducibility and facilitate further research in clinical sensing, the complete code and datasets are publicly available on Github.},
}

*Deep Learning
Humans
*Genome, Viral/genetics
Neural Networks, Computer
*Sequence Analysis, DNA/methods
Metagenomics/methods
Base Sequence
*Viruses/genetics

@article {pmid41979145,
year = {2026},
author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA},
title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.},
journal = {Research report (Health Effects Institute)},
volume = {},
number = {237},
pages = {1-58},
pmid = {41979145},
issn = {1041-5505},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Feces/chemistry/microbiology ; Female ; *Metabolome/drug effects ; Infant ; Male ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; Particulate Matter/adverse effects/analysis ; *Environmental Exposure/adverse effects ; California ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; },
abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.

METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter ≤2.5 µm and ≤10 µm in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.

RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.

CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Feces/chemistry/microbiology
Female
*Metabolome/drug effects
Infant
Male
*Air Pollution/adverse effects/analysis
*Air Pollutants/adverse effects/analysis
Pregnancy
Particulate Matter/adverse effects/analysis
*Environmental Exposure/adverse effects
California
Prenatal Exposure Delayed Effects
Infant, Newborn

@article {pmid41979617,
year = {2026},
author = {Li, G and Dan, N and Lu, T},
title = {Two Cases of Severe Chlamydia psittaci Pneumonia with Respiratory Failure and Literature Review.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250675},
pmid = {41979617},
issn = {1433-6510},
mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation & purification ; *Respiratory Insufficiency/microbiology/diagnosis/etiology ; *Psittacosis/diagnosis/drug therapy/microbiology/complications ; Male ; Anti-Bacterial Agents/therapeutic use ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Female ; Treatment Outcome ; },
abstract = {BACKGROUND: Chlamydia psittaci pneumonia is a zoonotic disease with non-specific clinical manifestations, often leading to delayed diagnosis. Metagenomic next-generation sequencing (mNGS) can help us identify pathogens in a timely manner and quickly adjust treatment strategies.

METHODS: We reported two cases of severe Chlamydia psittaci pneumonia with respiratory failure and reviewed relevant literature.

RESULTS: Both patients were diagnosed with Chlamydia psittaci infection through mNGS after routine pathogen testing failed. After using Omadacycline based treatment, the patients' clinical and radiological characteristics improved significantly and were successfully cured.

CONCLUSIONS: For patients infected with Chlamydia psittaci pneumonia, timely identification of the pathogen is crucial. mNGS can quickly detect Chlamydia psittaci in critically ill patients, guide clinical timely targeted treatment, and improve patient symptoms.},
}

Humans
*Chlamydophila psittaci/genetics/isolation & purification
*Respiratory Insufficiency/microbiology/diagnosis/etiology
*Psittacosis/diagnosis/drug therapy/microbiology/complications
Male
Anti-Bacterial Agents/therapeutic use
Middle Aged
High-Throughput Nucleotide Sequencing
Female
Treatment Outcome

@article {pmid41979623,
year = {2026},
author = {Xie, BX and Chen, Y and Tan, YR and Jiang, T and Huang, MH and Zhu, YM and Chen, S},
title = {Challenges in the Diagnosis of Hematogenous Disseminated Pulmonary Tuberculosis with Multiple Organ Involvement.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250640},
pmid = {41979623},
issn = {1433-6510},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Pericardial Effusion/microbiology ; Male ; Tomography, X-Ray Computed ; High-Throughput Nucleotide Sequencing ; Middle Aged ; *Tuberculosis, Miliary/diagnosis/microbiology ; Antitubercular Agents/therapeutic use ; },
abstract = {BACKGROUND: Tuberculosis is a public health problem worldwide, and China is a high-burden country. Hematogenous disseminated pulmonary tuberculosis is one of the most serious forms of tuberculosis, and diagnosing hematogenous pulmonary tuberculosis is a challenge, even for the most experienced clinicians, who may also feel perplexed. We report a case of hematogenous disseminated tuberculosis involving multiple organs that was initially misdiagnosed as metastatic malignancy. The diagnosis was finally confirmed by metagenomic Next-Generation Sequencing (m-NGS) of peritoneal and pericardial effusions, which detected Mycobacterium tuberculosis complex.

METHODS: Appropriate laboratory tests, m-NGS, Chest and abdominal CT, Pericardiocentesis, and Peritoneal puncture.

RESULTS: Chest and abdominal CT showed diffuse nodules in both lungs, pericardial effusion, bilateral pleural effusion, and abdominal pelvic effusion. Tuberculosis bacillus antibody was negative, erythrocyte sedimentation rate increased to 42 mm/H, and the carcinoembryonic antigen (CEA) increased to 7.1 ng/mL, peritoneal effusion adenosine deaminase increased to 65.17 U/L, pericardial effusion adenosine deaminase increased to 142.39 U/L. m-NGS of pericardial effusion and peritoneal effusion detected 886,963 M. tuberculosis complex.

CONCLUSIONS: Miliary tuberculosis is a severe and rare form of tuberculosis. Delayed diagnosis may be the most important factor leading to death from miliary tuberculosis. We report a case where Mycobacterium tuberculosis was identified through mNGS of pericardial and peritoneal effusions, enabling rapid diagnosis of disseminated tuberculosis. This case provides a new approach for the rapid diagnosis of disseminated tuberculosis.},
}

Humans
*Mycobacterium tuberculosis/genetics/isolation & purification
*Tuberculosis, Pulmonary/diagnosis/microbiology
Pericardial Effusion/microbiology
Male
Tomography, X-Ray Computed
High-Throughput Nucleotide Sequencing
Middle Aged
*Tuberculosis, Miliary/diagnosis/microbiology
Antitubercular Agents/therapeutic use

@article {pmid41980062,
year = {2026},
author = {Zhan, J and Yang, W and Guo, J and Yu, Y and Lai, S and Liu, X and Zhou, S},
title = {Iron plaques as terminal electron acceptors optimize clostridial fermentation and nitrogen fixation in rice rhizospheres.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag088},
pmid = {41980062},
issn = {1751-7370},
abstract = {Fermentative Clostridium species associated with rice roots can contribute substantially to biological nitrogen fixation in anoxic paddy soils, yet whether their biological nitrogen fixation is regulated by the redox chemistry of rhizosphere remains unclear. Here we show that iron plaques on rice roots function as terminal electron acceptors that reprogram Clostridium fermentation and thereby enhance biological nitrogen fixation. In nitrogen-fixation microcosms, Clostridium sensu stricto I was selectively enriched under plaque-associated Fe(III)-reducing conditions, coinciding with elevated nitrogen fixation. Metabolomic profiling coupled with metabolic flux analysis revealed that Fe(III) reduction redirects a portion of carbon and electron flow from low-energy-yield solventogenesis toward high-energy-yield acidogenesis. This shift increases cellular ATP generation and expands the reductant pool, thereby benefiting the energetic and reductant demands of nitrogenase. Integrated transcriptomic and metagenomic analyses further identified NosR, a flavin mononucleotide-binding protein that is upregulated during Fe(III) reduction and may facilitate electron delivery to plaque-associated Fe(III). Our findings establish a mechanism in which iron plaque reduction optimizes fermentation for biological nitrogen fixation, providing fundamental insights into coupled Fe-N cycling in rice rhizospheres and suggesting potential strategies for sustainable nitrogen management in flooded agroecosystems.},
}

@article {pmid41980294,
year = {2026},
author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Glucose metabolism's impact on Blastocystis presence in the human gut.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106647},
doi = {10.1016/j.clnu.2026.106647},
pmid = {41980294},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.

METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.

RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.

CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.},
}

@article {pmid41980639,
year = {2026},
author = {Li, R and Li, S and Yan, Y and Xie, Y and Liu, L and Zhao, J and Zhang, J and Cai, Z and Huang, X},
title = {Reductive soil disinfestation and hydrothermal biochar regulate antibiotic resistance mechanisms by reshaping soil bacterial functional traits and interaction patterns.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134622},
doi = {10.1016/j.biortech.2026.134622},
pmid = {41980639},
issn = {1873-2976},
abstract = {The health risk posed by antibiotic resistance genes (ARGs) in agricultural soils has become a growing concern. However, a systematic understanding of how microbial life history strategies, functional traits, and community interactions jointly shape ARG dynamics remains lacking. This knowledge gap not only constrains our ability to elucidate the evolutionary mechanisms underlying microbial resistance but also hampers the precise prediction and effective management of soil ARG risks. Here, we established distinct soil habitats through diverse soil managements, including control (CK), reductive soil disinfestation (RSD), and RSD combined with hydrothermal biochar application (HCR), to investigate how microbial traits and interactions shape ARG resistance mechanisms using metagenomic analyses. Our results showed that RSD and HCR treatments significantly reduced the overall abundance and ecological risk of ARGs compared to CK. In CK soils, microbial communities characterized by intensive interactions, high metabolic activity, and rapid growth efficiency promoted the enrichment of ARGs conferring resistance via antibiotic target alteration, protection, or replacement. In contrast, RSD/HCR treatments favored slow-growing, functionally complex, and competition-dominated communities, which were enriched in ARGs associated with antibiotic efflux mechanisms. Moreover, ARGs exhibited pronounced co-occurrence patterns with antimicrobial biosynthetic gene clusters in highly competitive environments. Collectively, this study reveals the selective responses of ARG resistance mechanisms to distinct microbial ecological strategies and provides new insights for the precise management of environmental antibiotic resistance risks.},
}

@article {pmid41980640,
year = {2026},
author = {Yang, H and Peng, N and Fan, Y and Huang, J and Zhang, J and Li, L and Ding, J and Tang, Z and Song, J and Liu, D and Hu, R and He, Z and Wang, C},
title = {Genome-Resolved insights into significance of DNRA Microbes in N2O production during manure composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134617},
doi = {10.1016/j.biortech.2026.134617},
pmid = {41980640},
issn = {1873-2976},
abstract = {Nitrous oxide (N2O) production during manure composting has traditionally been attributed primarily to heterotrophic denitrification (HD), while the roles of alternative pathways remain poorly resolved. Using time-resolved multi-omics across 37 samples from various manure sources, our study investigated the transcriptional landscape of N2O-producing pathways during composting. Microorganisms associated with dissimilatory nitrate reduction to ammonium (DNRA), including Fermentimonas and JAHWKS01 lineages, accounted for 21.2-33.1% of N2O-producing gene expression-comparable to HD-revealing DNRA as a previously underappreciated source. DNRA-associated gene expression was regulated by viral factors, predominantly through lytic Caudoviricetes phages. Expanding our analysis to 174 public metagenomic datasets revealed that DNRA-derived N2O-producing gene abundance peaked under static and hyperthermophilic conditions, highlighting aeration and temperature as critical mitigation controls. Furthermore, our study identified a substantial proportion of microorganisms harboring both DNRA and HD pathways. These findings refine mechanistic understanding of composting N2O emissions and inform multi-pathway mitigation strategies.},
}

@article {pmid41980647,
year = {2026},
author = {Song, M and Jiang, L and Lin, Z and Li, J and Luo, C and Qiu, R},
title = {Size-dependent effect of microplastics on sulfamethoxazole degraders in soil as revealed by integration of SIP and metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134620},
doi = {10.1016/j.biortech.2026.134620},
pmid = {41980647},
issn = {1873-2976},
abstract = {Microbes related to antibiotic degradation in situ in agricultural soil with MPs and their response to different sizes of MPs are ambiguity. This study investigated the microbes participating in antibiotic degradation in soils with 4.5 mm and 0.1 mm MPs by using DNA-SIP with metagenomics, Raman-activated cell sorting (RACS) with sulfamethoxazole (SMX) and polyethylene as the model compound and MPs. The 4.5 mm MPs enhanced SMX degradation by promoting diversity and abundance of degraders benefiting from improved soil properties, relation between degraders and SMX, and bacteria with positive co-occurrence relationship with degraders. The 0.1 mm MPs inhibited SMX degradation by decreasing diversity, abundance of degraders, and intensifying bacteria mutually exclusive with degraders due to harsher soil conditions. Furthermore, DNA-SIP-RACS successfully acquired cells of SIP-identified putative degraders, and directly linked SMX degradation potential with metC1, metF1and luxS1, proving possibility of applying this approach in antibiotic-degrading microbes in soil.},
}

@article {pmid41980652,
year = {2026},
author = {Back, JP and Klain, V and Pintro, VO and Lopes, FC and Marques, AL and Kray, J and Beys-da-Silva, WO and Santi, L and Schrank, A and Mayer, FQ and Vainstein, MH},
title = {Viral Diversity of Coastal Restinga Soils From Southern Brazil.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70343},
doi = {10.1111/1758-2229.70343},
pmid = {41980652},
issn = {1758-2229},
support = {441167/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 382064/2025-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 383394/2024-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 314485/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305705/2025-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303971/2025-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313620/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303945/2025-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Viruses/classification/genetics/isolation & purification ; Phylogeny ; Metagenomics ; Soil/chemistry ; },
abstract = {Coastal ecotones are highly dynamic environments for viral studies due to their extreme abiotic conditions, transitional nature between marine and terrestrial domains and high biodiversity. In Brazil, the Restinga is a coastal ecotone along the shoreline, characterized by nutrient-poor sandy soils, high salinity, strong winds and intense solar radiation, hosting poorly explored microbial communities essential for ecological balance. This exploratory study provides a preliminary characterization of viral diversity across three Restinga localities in southern Brazil (Imbé, Cidreira and Mostardas) using metagenomics. We identified 261 viral families, 2023 genera and 6064 species, with 'Unknown' representing 44%-46% of families and ~9% of genera. Among known taxa, Mimiviridae was most frequent (15%-16%), followed by Phycodnaviridae (9%), Peduoviridae (5%) and Kyanoviridae (4%-5%). Genera such as Tupanvirus and Fadolivirus were abundant (~5%), with Fadolivirus algeromassiliense and Donellivirus gee among the most frequent species. Although alpha diversity and composition did not differ significantly among sites, landscape features influenced viral communities. Viral richness and abundance increased with urban land cover and isolation but decreased with Restinga cover and patch fragmentation.},
}

Brazil
*Soil Microbiology
*Biodiversity
*Viruses/classification/genetics/isolation & purification
Phylogeny
Metagenomics
Soil/chemistry

@article {pmid41980940,
year = {2026},
author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z},
title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00986-w},
pmid = {41980940},
issn = {2055-5008},
support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.},
}

@article {pmid41980943,
year = {2026},
author = {Kim, J and Kim, N and Cha, JH and Ma, J and Lee, I},
title = {Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41980943},
issn = {2041-1723},
support = {2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; RS-2025-18362970//National Research Foundation of Korea (NRF)/ ; 2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Benchmarking ; Humans ; Neural Networks, Computer ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Metagenomic binning is essential for reconstructing prokaryotic genomes from metagenomic samples. We benchmarked various binning tools using Critical Assessment of Metagenome Interpretation (CAMI)-simulated, custom-simulated, and real metagenomic datasets, primarily focusing on short-read sequencing data. Our analysis highlights critical factors influencing binning efficacy: (i) Sequencing depth and taxonomic complexity strongly impact binning performance, while CAMI-simulated benchmarking datasets exhibit substantially lower complexity than human gut and environmental metagenomes, (ii) Chimeric genome rates vary widely across tools, (iii) Multi-sample binning is most effective with about 20 samples, as using too few or too many samples can reduce its benefits, and (iv) Binning efficacy was lower for single-end sequencing samples due to reduced contig quality and assembly fragmentation. Neural network-based tools consistently outperformed others in genome recovery from both real samples and simulated samples with realistic taxonomic complexity, though at higher computational cost. By integrating and refining genome bins from the top three binning tools, we recovered >30% more high-quality genomes than previous methods. This study provides practical guidance for improving metagenomic binning to facilitate the reconstruction of prokaryotic genomes.},
}

*Metagenomics/methods
*Metagenome/genetics
Benchmarking
Humans
Neural Networks, Computer
Computational Biology/methods
High-Throughput Nucleotide Sequencing

@article {pmid41980953,
year = {2026},
author = {Luo, E and Pham, ND and Rogers, TJ and Sheam, MM and Benner, BE and Vallino, JJ and Trubl, G and Huber, JA},
title = {Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71833-x},
pmid = {41980953},
issn = {2041-1723},
abstract = {Aquatic environments absorb ~2.5 gigatonnes of atmospheric carbon each year[1], more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this dissolved inorganic carbon into biomass that can subsequently flow into other trophic levels, or be released back into the environment through viral lysis. While there is substantial knowledge about the diversity and activity of viruses infecting photoautotrophic primary producers and the ecosystem impact, little is known about viruses infecting chemoautotrophs, representing a gap in our understanding of key processes driving microbial carbon cycling. Here, we combine metagenomics with quantitative [12/13]C stable isotopic probing (qSIP) mesocosm experiments in a marine-derived meromictic pond to quantify population-specific isotopic enrichment, identify key chemoautotrophic primary producers, and virus-host dynamics. Isotopically enriched carbon is tracked from the genomes of chemoautotrophs to putative viruses, showing that active populations of hydrogen/sulfur-oxidizing chemoautotrophs (Thiomicrorhabdus, Hydrogenovibrio, Sulfurimonas, Sulfurovum) are targeted by viruses. This work provides the foundation for revealing the diversity and activity of viruses infecting globally-widespread chemoautotrophs. Our study sheds light on trophic interactions that impact microbial carbon cycling in aphotic environments and builds toward biogeochemical models that incorporate viral impacts on chemoautotrophic microbial communities.},
}

@article {pmid41981035,
year = {2026},
author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA},
title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46295-2},
pmid = {41981035},
issn = {2045-2322},
support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; },
}

@article {pmid41981202,
year = {2026},
author = {Benedicenti, O and Strand, DA and Mohammad, SN and Gulla, S and Amundsen, MM and Sindre, H and Vrålstad, T},
title = {Integrated approaches for pathogen monitoring and shotgun metagenomic analysis in Atlantic salmon farming.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48791-x},
pmid = {41981202},
issn = {2045-2322},
support = {328724//Norges Forskningsråd/ ; 328724//Norges Forskningsråd/ ; 328724//Norges Forskningsråd/ ; 328724//Norges Forskningsråd/ ; 328724//Norges Forskningsråd/ ; 328724//Norges Forskningsråd/ ; 328724//Norges Forskningsråd/ ; 101136346//European Commission/ ; 101136346//European Commission/ ; 901674//Fiskeri - og havbruksnæringens forskningsfond/ ; },
abstract = {Specific tools for detecting waterborne pathogens are essential for limiting disease spread in aquaculture. We evaluated a field-deployable workflow combining filtration of eDNA/eRNA with targeted (RT-)qPCR and complementary shotgun metagenomics to monitor pathogens and microbial community dynamics in a single-farm study following one Atlantic salmon production cohort from hatchery to slaughter. The primary aim was to assess workflow feasibility and performance under real farm conditions, while secondarily examining whether metagenomic profiles could contextualise microbial shifts associated with pathogen presence. ISAV was consistently detected in hatchery water at ~ 4 × 10[3]-9 × 10[3] copies/L, whereas PRV1 was detected only inside sea pens from August onward (~ 4 × 10[2]-1.5 × 10[4] copies/L) and increased by more than two orders of magnitude after wellboat delousing. Shotgun metagenomics yielded a median of ~ 1.5 × 10[5] reads per sample (mean read length ~ 2.5 kb; N50 > 2 kb), enabling broad taxonomic screening. PRV1-positive seawater samples showed modest decreases in richness and shifts in viral taxa, though patterns were subtle and should be interpreted cautiously given low pathogen loads. The workflow was practical for trained farm personnel, and this integrated approach offers a scalable system for routine pathogen surveillance and supports earlier, evidence-based biosecurity actions, providing broader microbial information than qPCR alone.},
}

@article {pmid41981426,
year = {2026},
author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L},
title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].},
journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery},
volume = {40},
number = {4},
pages = {548-556},
doi = {10.7507/1002-1892.202601002},
pmid = {41981426},
issn = {1002-1892},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Prosthesis-Related Infections/microbiology ; Female ; Middle Aged ; Aged ; *Osteoarthritis/microbiology ; Dysbiosis/microbiology ; Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.

METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7±1) and (14±1); for the AF group, preoperatively and on postoperative day (7±1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).

RESULTS: Analysis of gut microbiota diversity showed that the preoperative α-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7±1), the α-diversity indices in the PJI group on postoperative day (7±1) were lower, but the difference was not significant (P>0.05); by postoperative day (14±1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the α-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.

CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.},
}

Humans
Male
*Gastrointestinal Microbiome
*Prosthesis-Related Infections/microbiology
Female
Middle Aged
Aged
*Osteoarthritis/microbiology
Dysbiosis/microbiology
Prosthesis Failure
Arthroplasty, Replacement, Knee/adverse effects

@article {pmid41981681,
year = {2026},
author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD},
title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00896-6},
pmid = {41981681},
issn = {2524-6372},
support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; },
abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.

METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63 years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.

RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.

CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.},
}

@article {pmid41981684,
year = {2026},
author = {Clough, J and Mikac, KM},
title = {Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00564-7},
pmid = {41981684},
issn = {2524-4671},
}

@article {pmid41968748,
year = {2026},
author = {Hilpert, K},
title = {Peptidomics: A New Dimension in Microbiome Research.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665436241260327111926},
pmid = {41968748},
issn = {1875-5305},
abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research, which needs to be changed. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.},
}

@article {pmid41969349,
year = {2026},
author = {Cheng, L and Wang, J and Sun, J and Xu, S and Zhao, G and Li, M},
title = {Integrated multi-omics of the ruminal microbiome and host metabolome reveals compensatory growth in response to dietary energy restriction and re-alimentation in growing beef bulls.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {265-281},
pmid = {41969349},
issn = {2405-6383},
abstract = {Understanding the mechanisms of dietary energy on compensatory growth in beef cattle is crucial for improving feed efficiency and mitigating the environmental footprint of beef production. The objectives of the study were to investigate the effects of dietary energy restriction and subsequent re-alimentation on growth performance, nutrient digestibility, ruminal microbiome, plasma metabolites, and nitrogen metabolism in growing beef bulls. Twelve 6-8-month-old Simmental crossbred bulls (initial body weight: 226 ± 24 kg) were randomly allocated to two groups (n = 6 per group): the dietary energy restriction group (REC) was fed a diet containing 9.25 MJ/kg metabolizable energy (ME) for 4 weeks (energy restriction period), followed by a 2-week re-alimentation period with a 10.29 MJ/kg ME diet, while the control group (CON) was fed the 10.29 MJ/kg ME diet consistently throughout the experimental period. Dietary energy restriction significantly decreased body weight and average daily gain (ADG) compared to CON (P < 0.05). However, no significant differences were observed by the end of the re-alimentation period (P > 0.05), demonstrating successful compensatory growth through dietary energy modulation. Ruminal propionate, total volatile fatty acids, ammonium nitrogen, and microbial crude protein (MCP) concentrations significantly decreased in the energy restriction treatment compared to CON (P < 0.05), but MCP exceeded the levels in CON after dietary energy re-alimentation (P < 0.05). Energy restriction also significantly increased urinary nitrogen excretion (P = 0.002), driven by imbalanced amino acid metabolism and significantly increased urinary urea (P = 0.038), which significantly reduced protein synthesis and nitrogen retention (P = 0.017). Metagenomics analysis revealed that energy restriction significantly increased the relative abundances of Limosilactobacillus, Enterococcus, and Aliarcobacter (P < 0.05), while decreasing those of Gemmatirosa and Mesorhizobium (P < 0.05). Dietary energy re-alimentation significantly increased the relative abundance of Gramella, Acetobacter, Phaeobacter, and Flammeovirga (P < 0.05). These bacteria are associated with pathways related to amination, transamination, and microbial protein synthesis. Integrated multi-omics revealed shifts in the ruminal microbiome and host metabolome, particularly in pathways related to ruminal urea hydrolysis, biosynthesis of glutamate, glutamine, and alanine, and post-absorptive amino acid metabolism, which collectively enhanced protein synthesis and compensatory growth. These findings establish a practical feeding strategy to optimize feed efficiency and enhance compensatory growth in beef bulls via short-term dietary energy manipulation.},
}

@article {pmid41969354,
year = {2026},
author = {Dayan, J and De Cesare, A and Soglia, F and Zampiga, M and Indio, V and Antenucci, EL and Petracci, M and Sirri, F},
title = {Nutritional alternatives to commercial lipid sources: Impact of the dietary inclusion of black soldier fly (Hermetia illucens) larvae oil on broiler chicken productivity, breast meat quality traits and caeca microbiome.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {255-264},
pmid = {41969354},
issn = {2405-6383},
abstract = {Protein production from poultry, particularly broiler chickens, is considered a key component of future global food security, due to its relatively high sustainability. However, the use of resources such as soybean oil remains a concern. Black soldier fly (Hermetia illucens [HI]) larvae oil represents a promising alternative due to a relatively rapid rearing cycle and ability to utilize organic waste as growth substrates. This study investigated how replacing a commercial lipid source such as soybean oil, with HI larvae oil affects broiler growth performance, meat quality traits, fatty acid (FA) profile, and caeca microbiome. A total of 552 one-d-old male Ross 308 broilers, with equal initial weights (48.89 ± 0.18 g; P = 0.597), were allocated to three dietary treatments with 8 replicate pens per group (23 birds/pen). All birds received the same commercial basal diet, formulated to be isoenergetic and with the same amino acid profile, differing only in the source of the supplemented oil: 100% soybean oil group (CON), 50% soybean oil + 50% HI larvae oil group (MIX), or 100% HI larvae oil group (HIO). Growth performance parameters were recorded at the end of each feeding phase (14, 28, and 42 d). At slaughter (42 d), 10 breasts (pectoralis-major muscle) and thighs (extensor-iliotibialis muscle) samples per group were collected for meat quality assessment, and caecal content samples were obtained from 8 birds/group for microbiome analysis. Growth performance metrics showed an improvement in feed conversion ratio during the starter phase for HI larvae oil-fed groups (1.54 vs. 1.45 vs. 1.46 for CON, MIX, and HIO, respectively; P < 0.001) and comparable performance across the trial. Meat quality traits remained within commercially acceptable ranges, with minimal effects observed, apart from variations in breast fillet redness and thigh protein oxidation. FA analysis indicated higher levels of saturated FAs in the HI groups, with a concurrent reduction in omega (n)-6 levels and a more balanced n-6 to n-3 ratio (16.47 vs. 15.18 vs. 11.60 for CON, MIX, and HIO, respectively; P < 0.001). The caecal microbiome revealed stable diversity across groups, with only minor shifts in relative abundance. Overall, the findings showed that HI larvae oil is an effective alternative to conventional vegetable lipid sources in poultry nutrition, with added potential to enhance growth performance during the early growth stages.},
}

@article {pmid41969371,
year = {2026},
author = {Ramos Peña, DE and Boussetta-Charfi, O and Antezack, A and Amroune, N and Colson, P and Monnet-Corti, V and Saia, RS and Guillemot, J and Pozzetto, B and Pillet, S and La Scola, B and Bourlet, T and Fragoso Motta, AC},
title = {Interplay Between Oral Microbiota and Mouth Health in People Living With HIV Under Antiretroviral Therapy With or Without Periodontitis.},
journal = {International journal of dentistry},
volume = {2026},
number = {},
pages = {8794149},
pmid = {41969371},
issn = {1687-8728},
abstract = {People living with HIV (PLWH) in combined antiretroviral therapy (cART) face microbiota shifts linked to immune status, ART regimen, and periodontal diseases, which are capable of inducing local and systemic inflammation. This study aimed to analyze the oral microbial community composition in PLWH under cART with (n = 24) or without (n = 25) periodontitis using shotgun metagenomic sequence analysis, and describe the interaction between bacterial species, clinical and immunological parameters, and the response to nonsurgical periodontal therapy (NSPT). Saliva samples were collected at baseline for both groups, and 30 days after NSPT for the periodontitis group. Within the periodontitis group, all periodontal parameters presented highly significant improvement after NSPT when compared to baseline. The gingival microbiota did not differ significantly between patients with periodontitis and controls; however, a wider range of bacterial species was found in the microbiota of the periodontitis group compared to the control group, while post-treatment the periodontitis group presented an alpha diversity intermediate between the two former groups. Regarding the distribution of the different bacterial species, Porphyromonas gingivalis was found significantly enriched in the periodontitis group, along with different Treponema sp., Fretibacterium fastidiosum, Campylobacter rectus, Bacteroides zoogleoformans, Tannerella forsythia, and Porphyromonas endodontalis. Correlations between seven inflammatory markers and seven periodontitis-related bacterial taxa were found for saliva in the group of periodontitis patients, which was not the case in controls; interestingly, the profiles after NSPT showed intermediate results. By contrast to saliva, the inflammatory markers of periodontitis patients showed no marked differences in blood plasma, except for TNF-alpha and partly IL-4. In view of the fact that oral microbial imbalance may contribute not only to local disease but also to systemic immune activation in the course of HIV-1 infection, reinforcing the importance of maintaining periodontal health represents a part not to be neglected for an optimal management of PLWH.},
}

@article {pmid41969565,
year = {2026},
author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH},
title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.},
journal = {PNAS nexus},
volume = {5},
number = {4},
pages = {pgag073},
pmid = {41969565},
issn = {2752-6542},
abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.},
}

@article {pmid41969652,
year = {2026},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Correction: Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1826950},
doi = {10.3389/fcimb.2026.1826950},
pmid = {41969652},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1726935.].},
}

@article {pmid41969653,
year = {2026},
author = {Dai, Z and Hu, Y and Tai, A and Lu, Y and Hu, S and Pan, J and Xiao, Y and Ma, X and Fu, Q and Zhao, H and Su, Z and Tong, P and Hao, Z and Yao, G and Wang, J},
title = {Characterization of a Klebsiella pneumoniae mutant strain wGF 1-2 with attenuated virulence, altered morphology, and reduced biofilm formation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1761564},
pmid = {41969653},
issn = {2235-2988},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/virology/physiology ; *Biofilms/growth & development ; Animals ; Mice ; Virulence ; Klebsiella Infections/microbiology/pathology ; Disease Models, Animal ; Mutation ; Proteomics ; Host-Pathogen Interactions ; Bacteriophages ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Female ; Metagenomics ; },
abstract = {INTRODUCTION: The global rise of antimicrobial resistance has positioned multidrug-resistant Klebsiella pneumoniae as a critical health threat, necessitating alternative therapeutic strategies such as phage therapy. However, the long-term evolutionary consequences of phage-bacteria interactions remain poorly understood. This study characterizes a unique attenuated mutant, wGF 1-2, derived from a hypervirulent K. pneumoniae strain (GF) during phage isolation efforts.

METHODS: The wGF 1-2 mutant was serendipitously isolated during attempts to obtain lytic phages against the parental GF strain. We performed an integrated multi-omics and phenotypic characterization, including genomic sequencing, proteomic profiling, and transcriptomic analysis. Host-pathogen interactions were assessed using a murine infection model (evaluating survival and tissue colonization), and the impact on the gut microbiota was analyzed via metagenomics.

RESULTS: Compared to the parental strain, wGF 1-2 exhibited a significant reduction in biofilm formation and distinct morphological alterations. In a murine model, the mutant was avirulent, resulting in 100% survival even at a high challenge dose (10⁶ CFU), with minimal tissue colonization. Multi-omics analysis revealed extensive genomic structural variations (81 insertions and 64 deletions). Proteomic shifts included the downregulation of proteins involved in metal ion binding and metabolic pathways. Furthermore, infection with wGF 1-2 led to host inflammatory suppression and a restructuring of the gut microbiota characterized by an increase in beneficial Bacteroidota.

DISCUSSION: This study provides a comprehensive characterization of an attenuated K. pneumoniae mutant, wGF 1-2. The extensive genomic and phenotypic alterations observed highlight the significant evolutionary potential of bacterial pathogens during phage interactions. These findings underscore the necessity of thorough safety assessments, including evolutionary risk evaluations, for the future development of phage-based therapies.},
}

*Klebsiella pneumoniae/genetics/pathogenicity/virology/physiology
*Biofilms/growth & development
Animals
Mice
Virulence
Klebsiella Infections/microbiology/pathology
Disease Models, Animal
Mutation
Proteomics
Host-Pathogen Interactions
Bacteriophages
Gene Expression Profiling
Gastrointestinal Microbiome
Female
Metagenomics

@article {pmid41970373,
year = {2026},
author = {Duan, Y and Wang, L and Cui, H and Fang, Z and Lu, Y and Sun, Z},
title = {The effect of elastic-band resistance training on fecal microbiota and derived metabolites of aged individuals with possible sarcopenia.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1762454},
pmid = {41970373},
issn = {2296-858X},
abstract = {BACKGROUND: Individuals with possible sarcopenia exhibit altered microbiota profiles and poor intestinal metabolism. Exercise training is linked to changes in gut microbiota and has been proposed to enhance the quality of aging skeletal muscle.

AIMS: In older adults with possible sarcopenia, the study aimed to determine if elastic-band resistance training modulates gut microbiota and its generated metabolites and investigate the underlying relationships with physical function.

METHODS: Thirty-one volunteers with possible sarcopenia were randomly assigned to either the control group (CG, n = 17) or the intervention group (RG, n = 14), which underwent 24 weeks of elastic-band resistance training. Physical function, body composition, and blood and fecal samples were collected from each patient at baseline and 24 weeks. Enzyme-linked immunosorbent assay (ELISA) was used to evaluate protein metabolism regulatory factors, targeted metabolomics was used to quantify short-chain fatty acid (SCFA) levels, and metagenomic sequencing was used to analyze the composition of the fecal microbiota.

RESULTS: The gait speed (GS), arm curl test (ACT), 2-min step test (2MST), and timed up-and-go test (TUGT) all showed notable improvements in the RG. The RG also showed lower serum levels of tumor necrosis factor-α (TNF-α) and higher plasma concentrations of acetate and propionate. Following the intervention, the RG displayed decreased abundances of Eisenbergiella and Eggerthella and increased abundances of the genus Bacillus. Eggerthella abundance was inversely connected with 2MST performance, whereas the change in propionate level was positively correlated with 2MST, TUGT, GS, and appendicular skeletal muscle index (ASMI).

CONCLUSION: The elastic-band resistance training effectively improved physical function, modulates gut microbiota and SCFAs. The results revealed the physiological mechanisms by which gut microbiota and SCFAs regulate aging muscle health, providing scientific support for possible sarcopenia prevention and treatment via gut-muscle axis bidirectional crosstalk.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/index.html.},
}

@article {pmid41971320,
year = {2026},
author = {Wu, Y and Deng, L and He, X and Zhou, D and Ling, S and He, M and Wang, Q and Wang, C and Wang, M and Wu, H and Li, L and Li, D and Yun, L},
title = {Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1737792},
pmid = {41971320},
issn = {1664-302X},
abstract = {INTRODUCTION: The world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.

METHODS: In this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.

RESULTS AND DISCUSSION: The predominant Escherichia-Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.},
}

@article {pmid41971325,
year = {2026},
author = {Qi, L and Kang, H and Li, X and Wang, L and Lin, Y and Zhan, M and Zeng, F and Xiao, Z and Liu, X and Chen, Z and Liu, L},
title = {Multi-omics profiling implicates gut microbiota-sphingolipid interplay in the neuroprotective effects of semaglutide on diabetic cognitive impairment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1705784},
pmid = {41971325},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome is a critical regulator of host health, but how it mediates the therapeutic effects of drugs targeting neurodegenerative diseases like diabetic cognitive impairment (DCI) is unclear. Here, we investigated whether the neuroprotective effects of the GLP-1 agonist semaglutide (SE) are linked to its modulation of the gut-brain axis.

METHODS: We used an integrative multi-omics approach in a mouse model of DCI. We combined fecal shotgun metagenomics and targeted bile acid profiling with cerebral proteomics and metabolomics to characterize the gut-brain crosstalk following a 12-week SE treatment. Animal behavior, neuronal survival and synaptic integrity were assessed to confirm therapeutic efficacy.

RESULTS: SE treatment reversed cognitive deficits, rescued hippocampal neuronal loss, and restored synaptic integrity in diabetic mice. At the ecosystem level, metagenomics revealed that SE treatment profoundly remodeled the gut microbiota, enhancing microbial α-diversity, enriched beneficial genera (Bacteroides, Barnesiella), and depleted the pro-inflammatory genus Desulfovibrio. This microbial shift was associated with normalized fecal and cerebral bile acid profiles. Mechanistically, our analysis implicated a dysregulated sphingolipid pathway in the DCI brain, characterized by the upregulation of the transporter ATP-binding cassette transporter A2 (ABCA2) and the enzymes sphingosine-1-phosphate phosphatase 1 (SGPP1) and ceramide synthase 2 (CERS2). SE treatment dynamically modulated this pathway: it downregulated ABCA2 in a potentially weight-independent manner and SGPP1 in a weight-dependent fashion, linked to the normalization of cerebral bile acid profiles. In contrast, CERS2, a robust marker of disease severity, was not altered by SE.

CONCLUSION: Our study uncovers a novel "gut microbiota-bile acid-sphingolipid" axis in DCI and suggests that SE acts via a dual mechanism. It drives a weight-dependent restoration of the gut-brain axis, normalizing microbial and bile acid profiles to regulate SGPP1, while also exerting weight-independent effects, potentially through direct modulation of targets like ABCA2. This work highlights the gut microbiome as a key component in the therapeutic action of SE and reveals the multifaceted nature of its neuroprotective effects.},
}

@article {pmid41971343,
year = {2026},
author = {Qiao, YC and Jiang, XX and Zhan, JP and Cheng, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG},
title = {Correction: Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1832275},
doi = {10.3389/fmicb.2026.1832275},
pmid = {41971343},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1691984.].},
}

@article {pmid41971525,
year = {2026},
author = {Adekoya, AE and Boggs, TE and Ibberson, CB},
title = {Revealing community dynamics in polymicrobial infections through a quantitative framework.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag061},
pmid = {41971525},
issn = {2730-6151},
abstract = {Laboratory models provide tractable, reproducible systems that have long served as foundational tools in microbiology. However, the extent to which these models accurately mimic the biological environments they represent remains poorly understood. A quantitative framework was recently introduced to assess how well laboratory models capture microbial physiology in situ. However, applications of this framework have been limited to characterizing the physiology of a single species in human infections, leaving a gap in our understanding of overall microbial community physiology in polymicrobial contexts. Here, we extended this framework to evaluate the accuracy of laboratory model systems in capturing community-level functions in polymicrobial infection. As a proof of concept, we applied the extended framework to a polymicrobial model of human chronic wound (CW) infection. CWs harbor metabolically diverse bacterial species that engage in a range of microbe-microbe interactions, ultimately impacting community dynamics and disease progression. However, studies on the mechanistic drivers of chronic wound infection have relied on single species or pairwise approaches. Here, we demonstrate that our adapted framework can be used to develop accurate polymicrobial models. Further, we demonstrate that this extended framework can evaluate the occurrence of known microbe-microbe interactions. Building on our prior work in large-scale metagenomic and metatranscriptomic analysis, we propose a highly accurate 6-member synthetic bacterial community model i.e. representative of the taxonomic and functional complexity of human CW infections. This approach will support the development of ecologically relevant polymicrobial models and better treatment strategies.},
}

@article {pmid41971531,
year = {2026},
author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B},
title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag046},
pmid = {41971531},
issn = {2730-6151},
abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.},
}

@article {pmid41971738,
year = {2026},
author = {Ji, HL and Liu, CH and Nie, CX and Luo, JF and Li, XR and Fu, AS and Ge, YL},
title = {Metagenomic next-generation sequencing unveils invasive aspergillosis masquerading as miliary tuberculosis in a neutropenic leukemia patient: a case report.},
journal = {Frontiers in fungal biology},
volume = {7},
number = {},
pages = {1751760},
pmid = {41971738},
issn = {2673-6128},
abstract = {BACKGROUND: Empirical anti-tuberculosis therapy is a common strategy when patients with acute leukemia chemotherapy-induced neutropenia develop diffuse pulmonary small nodular and subsolid lesions. However, the absence of pathogenetic verification may lead to catastrophic consequences.

METHODS: Following negative conventional microbiological cultures (bronchoalveolar lavage bacterial culture, Gram/Gram-negative test) and ineffective anti-infective therapy, a second bronchoscopy revealed caseous obstructive lesions in the right upper lobe bronchus. Metagenomic Next-Generation Sequencing (mNGS) analysis of lavage fluid ultimately confirmed invasive pulmonary fungal disease.

RESULTS: The mNGS analysis of the bronchoalveolar lavage fluid (BALF) reported 6,750 Aspergillus fumigatus sequences, 43 Aspergillus complex sequences, and 81 Candida albicans sequences (considered airway colonization with no pathogenic significance), confirming probable invasive pulmonary aspergillosis (IPA) in line with the 2023 revised EORTC/MSGERC consensus criteria for invasive fungal diseases. Following discontinuation of anti-tuberculosis therapy, targeted antifungal treatment with amphotericin B (40 mg daily) was initiated. Post-treatment, the patient's temperature normalized. Follow-up CT demonstrated improved absorption of lesions in the left lung and right lower lobe, with stable cavitary nodules in the right upper lobe.

CONCLUSION: This case demonstrates that invasive pulmonary fungal infection can perfectly mimic the typical radiographic features of hematogenous disseminated pulmonary tuberculosis, including diffuse small nodular and subsolid lesions with a miliary distribution pattern predominantly in the upper lobes and extrapulmonary manifestations such as erythema nodosum. For unexplained pulmonary infections in immunocompromised hosts where conventional diagnosis and empirical treatment fail, the timely application of bronchoscopy combined with mNGS technology represents a critical breakthrough for achieving precise diagnosis.},
}

@article {pmid41971837,
year = {2026},
author = {Du, S and Lin, D and Zhang, TL and Chu, HY and Zhu, D},
title = {Earthworm gut's potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size.},
journal = {Fundamental research},
volume = {6},
number = {2},
pages = {837-846},
pmid = {41971837},
issn = {2667-3258},
abstract = {The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm-soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle.},
}

@article {pmid41971922,
year = {2026},
author = {Zhu, W and Li, Y and Xu, Q and Lin, D and Zhou, T and Yang, F and Shi, M},
title = {Late-onset fungal infection of the bronchial stump post-lung resection: a report of two rare cases of Aspergillus flavus and mixed Candida/Cryptococcus coinfection diagnosed via metagenomic next-generation sequencing.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {63},
pmid = {41971922},
issn = {2523-1995},
abstract = {BACKGROUND: Fungal infection of the bronchial stump is rare, characterized by insidious clinical manifestations and often misdiagnosed as bacterial infection or tumor recurrence. Most reported cases involve Aspergillus fumigatus, with Aspergillus flavus encountered far less frequently. Importantly, fungal colonization of the bronchial stump by Cryptococcus species has not been previously documented, nor has a mixed infection involving Cryptococcus and other fungi at this site. These rare presentations highlight diagnostic blind spots in postoperative airway management and underscore the need for heightened clinical awareness.

CASE DESCRIPTION: Case 1: A 53-year-old man underwent left upper lobectomy for adenocarcinoma four years prior. In 2024, he presented with hoarseness and chest tightness. Positron emission tomography-computed tomography (PET-CT) revealed a metabolically active soft-tissue nodule adjacent to the surgical suture line. Bronchoscopic biopsy combined with metagenomic next-generation sequencing (mNGS) confirmed the diagnosis of bronchial stump aspergillosis (BSA). The patient received posaconazole therapy for 7 months. Case 2: A 77-year-old woman underwent right lower lobectomy for adenocarcinoma six years earlier. In 2025, she developed cough with sputum production. CT demonstrated bilateral pneumonia with focal consolidation/atelectasis and bilateral pleural effusions. Bronchoscopy and mNGS identified a mixed infection with Candida albicans and Cryptococcus neoformans at the bronchial stump. Following treatment with caspofungin and fluconazole, her clinical symptoms improved, and follow-up CT imaging showed resolution of inflammatory changes.

CONCLUSIONS: Although fungal infection of the bronchial stump is rare, it warrants early consideration when post-lobectomy patients develop persistent symptoms unresponsive to antibiotics. Early radiological clues-such as unexpected metabolic activity around suture granulomas or localized nodular thickening at the stump-should prompt further evaluation. When conventional cultures remain negative and clinical deterioration continues, early initiation of mNGS can facilitate timely pathogen identification and guide targeted antifungal therapy.},
}

@article {pmid41972094,
year = {2026},
author = {Yoshioka, I and Hayashi, C and Endo, Y and Sawada, A and Mori, Y and Ban, S and Yaguchi, T},
title = {Detection of fungal contamination on museum books stored under controlled environmental conditions: A discrepancy between culture-based and metagenomic analysis approaches.},
journal = {Mycoscience},
volume = {67},
number = {1},
pages = {20-26},
pmid = {41972094},
issn = {1618-2545},
abstract = {Mold contamination in library and museum collections poses risks to both cultural heritage and human health. This study examined fungal flora on books stored under controlled environmental conditions (temperature <20 °C, relative humidity <50%) in The University Museum, The University of Tokyo. Both culture-dependent methods and DNA-based metabarcoding targeting the internal transcribed spacer 2 region were used. DNA analysis revealed that Aspergillus halophilicus accounted for over 90% of the sequences from six books. In contrast, culture-based methods using standard media (e.g., PDA, DG18, M40Y) primarily isolated species such as Aspergillus, Penicillium, and Cladosporium, but not A. halophilicus. However, cultivation on CzA supplemented with 70% sucrose at lower temperatures enabled successful isolation of A. halophilicus from one sample. The strain was identified based on morphological features and β-tubulin gene analysis. These findings demonstrate a notable discrepancy between molecular and culture-based results, underscoring the limitations of conventional media for detecting xerophilic fungi in dry environments. The study suggests that desiccation-tolerant species like A. halophilicus can thrive even under strict storage controls and may evade standard integrated pest management (IPM) protocols. To better assess fungal risks in preservation settings, combining improved media with DNA-based methods is essential.},
}

@article {pmid41972101,
year = {2026},
author = {Tong, W and Qiao, L and Yang, Y and Li, X and Zhang, Y and Huang, Z and Luo, H and Zhao, L and Zhang, S},
title = {Cross-kingdom metabolic cooperation drives vanillic acid biosynthesis: A spatiotemporal dissection of microbial functional networks in solid-state fermentation.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101394},
pmid = {41972101},
issn = {2665-9271},
abstract = {Microbial self-organization into spatiotemporally structured consortia is key to metabolic specialization in natural environments, yet the principles governing this process in food fermentation are poorly understood. Here, we elucidate how cross-kingdom microbial cooperation drives the biosynthesis of vanillic acid (VA), a critical flavor and bioactive phenolic compound, during the solid-state fermentation of strong-flavor baijiu (SFB). Integrated metagenomic and network analyses across stratified pit layers and fermentation stages revealed a defined three-phase succession model. Early phase (D0-D12) was dominated by filamentous fungi (Aspergillus, Paecilomyces) in upper layers, initiating starch hydrolysis and phenylpropane precursor synthesis (e.g., contributing 22.6% to phenylalanine ammonia-lyase). A transitional bacterial-fungal consortium (Pichia, Klebsiella) then mediated intermediate conversion (D12-D45), with enzymatic hotspots shifting downward. The maturation phase (D45-D85) was defined by the dominance of acidophilic Acetilactobacillus (>80% relative abundance) in the lower layer, which executed the final synthesis steps (contributing 31.5% to caffeic acid O-methyltransferase) and concurrently suppressed vanillic acid degradation via downregulation of vanillate O-demethylase. Network analysis confirmed a spatial metabolic division of labor: fungi specialized in upper-layer lignin deconstruction, while bacteria dominated the completion of phenylpropanoid pathways in the lower layer. Critically, peak VA accumulation (0.375 mg/L at D45) coincided with synchronized enzyme expression across layers, demonstrating active metabolic coordination rather than passive environmental filtering. Our findings establish that functional succession and spatial compartmentalization are fundamental ecological principles enabling efficient biosynthesis in solid-state fermentation, demonstrating that flavor outcomes can be programmed through targeted microbial consortium design.},
}

@article {pmid41972180,
year = {2026},
author = {Zhai, Y and Yu, M and Cheng, L and Liu, X and Yan, J},
title = {Orientia tsutsugamushi and Epstein-Barr Virus coinfection presenting with transient fluctuating hearing loss: a case report.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1750100},
pmid = {41972180},
issn = {1664-3224},
mesh = {Humans ; Female ; Middle Aged ; *Epstein-Barr Virus Infections/diagnosis/complications/drug therapy/virology ; *Scrub Typhus/diagnosis/complications/drug therapy/microbiology ; *Coinfection/diagnosis ; *Orientia tsutsugamushi/immunology ; *Herpesvirus 4, Human/immunology ; *Hearing Loss/diagnosis/etiology ; },
abstract = {Scrub typhus, caused by the obligate intracellular bacterium Orientia tsutsugamushi(O. tsutsugamushi), is an acute febrile illness. While neurological complications are known, hearing loss is an uncommon manifestation, and coinfection with Epstein-Barr virus(EBV) presents unique diagnostic and pathophysiological challenges. A 58-year-old woman presented with a 5-day history of high fever, severe headache, and constitutional symptoms. She reported transient, fluctuating bilateral hearing loss. Examination revealed characteristic eschars on her legs. Laboratory findings indicated hepatic impairment and systemic inflammation. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid detected O. tsutsugamushi and EBV. EBV serology profile (VCA-IgG+, VCA-IgM-, EBNA-IgG+) suggested viral reactivation. The patient failed to respond to initial beta-lactam antibiotic therapy but showed rapid and complete resolution of symptoms, including hearing loss, after initiation of doxycycline. At the 1-month and 3-month follow-up, audiological assessment confirmed normal hearing. This case highlights a rare presentation of scrub typhus with EBV coinfection involving fluctuating hearing loss. The dramatic response to doxycycline suggests this auditory symptom may be a reversible, immune-mediated complication of O. tsutsugamushi infection. Physicians should be aware of this potential manifestation in endemic areas. The immunological interplay between these pathogens warrants further investigation.},
}

Humans
Female
Middle Aged
*Epstein-Barr Virus Infections/diagnosis/complications/drug therapy/virology
*Scrub Typhus/diagnosis/complications/drug therapy/microbiology
*Coinfection/diagnosis
*Orientia tsutsugamushi/immunology
*Herpesvirus 4, Human/immunology
*Hearing Loss/diagnosis/etiology

@article {pmid41972428,
year = {2026},
author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG},
title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18849},
doi = {10.1002/advs.202518849},
pmid = {41972428},
issn = {2198-3844},
support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; },
abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.},
}

@article {pmid41972755,
year = {2026},
author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB},
title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0011326},
doi = {10.1128/msphere.00113-26},
pmid = {41972755},
issn = {2379-5042},
abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.},
}

@article {pmid41972785,
year = {2026},
author = {He, X and Liu, J and Cheng, H and Zhu, X and Lin, H and Li, D-W and Yang, Y and Liu, R and Song, D and Zheng, Y and Lea-Smith, DJ and Pedentchouk, N and Todd, JD and Zhao, M and Zhang, X-H},
title = {Metabolically diverse microorganisms mediating hydrocarbon cycling in the subseafloor sediment of the Challenger Deep.},
journal = {mBio},
volume = {},
number = {},
pages = {e0394325},
doi = {10.1128/mbio.03943-25},
pmid = {41972785},
issn = {2150-7511},
abstract = {Hadal subseafloor sediments host abundant and active microbial biosphere with considerable heterotrophic activity. However, carbon and nutrient cycling processes and mechanisms driven by hadal subsurface microorganisms remain poorly understood. Using culture-dependent and culture-independent methods, we characterized the diversity, metabolism, and vertical dynamics of hydrocarbon-degrading (HYD) bacteria in a subsurface sediment core (MT20-750, ~750 cm below seafloor [cmbsf]) collected from the Challenger Deep (10,816 m below sea level) in the Mariana Trench. The sediment core contained high concentrations of mid- and long-chain n-alkanes (310-8,724 ng/g), although no }

@article {pmid41973542,
year = {2026},
author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S},
title = {Functional gut microbiomes enhance performance in house fly larvae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0001126},
doi = {10.1128/aem.00011-26},
pmid = {41973542},
issn = {1098-5336},
abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.

IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.},
}

@article {pmid41973723,
year = {2026},
author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB},
title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {229},
pages = {},
doi = {10.3791/70187},
pmid = {41973723},
issn = {1940-087X},
mesh = {Humans ; *Feces/virology ; *Metagenomics/methods ; *DNA, Viral/genetics/isolation & purification/chemistry ; *DNA Viruses/genetics/isolation & purification ; },
abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.},
}

Humans
*Feces/virology
*Metagenomics/methods
*DNA, Viral/genetics/isolation & purification/chemistry
*DNA Viruses/genetics/isolation & purification

@article {pmid41974680,
year = {2026},
author = {Valverde, G and Sarhan, MS and Cook, R and Rota-Stabelli, O and Adriaenssens, EM and Zink, A and Maixner, F},
title = {An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71603-9},
pmid = {41974680},
issn = {2041-1723},
abstract = {Streptococcus pyogenes, or Group A Streptococcus (GAS), is a human pathogen responsible for a range of diseases, from mild infections to severe illnesses. Despite its significance in modern clinical settings, little is known about the pathogen's evolutionary history or its presence in ancient human populations. Here, we present genomic evidence of S. pyogenes in the pre-Columbian Americas. We analysed a tooth from a naturally mummified individual dating to the Late Intermediate Period (1283-1383 cal AD), housed in the National Museum of Archeology (MUNARQ) in La Paz, Bolivia. Mitochondrial DNA analysis confirmed the host's Native American ancestry. Shotgun metagenomic sequencing and de-novo assembly enabled the near-complete reconstruction of an ancient S. pyogenes genome displaying close similarity to contemporary strains linked to pharyngitis. The genome contains core virulence genes, but prophages lack streptococcal pyrogenic exotoxins. Phylogenetic analyses place the strain at the base of modern S. pyogenes diversity, and Bayesian analyses indicate that most extant lineages diversified globally within the past ~5,500 years. Our results push back the confirmed presence of S. pyogenes in the Americas by several centuries and suggest that the pathogen circulated among Indigenous populations prior to the European contact.},
}

@article {pmid41974697,
year = {2026},
author = {Espinosa, CA and Njunge, JM and Tickell, KD and Diallo, AH and Sayeem Bin Shahid, ASM and Gazi, MA and Kazi, Z and Yoshioka, E and Tigoi, C and Mburu, M and Ngari, M and Ngao, N and Omer, E and Gumbi, W and Gichuki, BM and Mitchel, A and Williams, J and Gogain, J and Janjic, N and Mandal, R and Jenkins, B and Browne, HP and Shao, Y and Rozday, T and Stares, MD and Dawson, NJR and Berson, E and Chang, A and Kim, Y and Mataraso, SJ and Shu, CH and Phongpreecha, T and Xue, L and Saleem, A and Singa, B and Ahmed, T and Voskuijl, WP and Wishart, DS and Houpt, ER and Liu, J and Ali, A and Mupere, E and Chisti, MJ and Bandsma, RHJ and Lawley, TD and Koulman, A and Lancioni, CL and Aghaeepour, N and Berkley, JA and Walson, JL and , },
title = {Multiomics characterization of acute child illness and mortality in Africa and South Asia.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69754-w},
pmid = {41974697},
issn = {2041-1723},
abstract = {Childhood illnesses from infectious diseases in low- and middle-income countries contribute substantially to the global under-five mortality. Many hospitalized children experience incomplete recovery, readmission, and post-discharge mortality despite guideline-directed care. However, targeted interventions remain elusive due to limited understanding of underlying mechanisms. In this work, we employ multiomic profiling and multivariate modeling to investigate biological drivers of inpatient and post-discharge mortality in 3,101 acutely ill children across nine sites in sub-Saharan Africa and South Asia. In a nested case-cohort (N = 1008), we generate plasma proteomics, serum metabolomics and lipidomics, stool metagenomics, and fecal pathogen data at admission and discharge. Additionally, we profile 270 geographically matched community children for biological baselines. We identify a generalizable mortality signature marked by immune, inflammatory, and metabolic dysregulation with gut dysbiosis. We show that mortality-associated signals persist from admission through discharge, indicating unresolved disease and that malnourished children show greater baseline perturbations, explaining elevated risk. We also find some children with low clinical severity display high predicted mortality risk from targeted biomarkers. Finally, we distill predictive models to a clinically feasible biomarker panel and validate our findings in an independent cohort (N = 100). By linking inpatient and post-discharge mortality to specific biological mechanisms, our findings highlight why current care can fail and demonstrate how biomarker-guided risk stratification can identify vulnerable children currently missed by clinical assessments, enabling targeted interventions to reduce mortality in low- and middle-income countries.},
}

@article {pmid41974712,
year = {2026},
author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y},
title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71718-z},
pmid = {41974712},
issn = {2041-1723},
support = {R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI143313//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.},
}

@article {pmid41975031,
year = {2026},
author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE},
title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10048-8},
pmid = {41975031},
issn = {2399-3642},
support = {DairyBio//Dairy Australia/ ; },
abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.},
}

@article {pmid41975041,
year = {2026},
author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , },
title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41975041},
issn = {1532-1827},
support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).

METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.

RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa -notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.

CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.

PROSPERO: CRD42023433704.},
}

@article {pmid41975095,
year = {2026},
author = {Guan, K and Ocampo, RF and Matheus Carnevali, PB and Castelle, CJ and Gonzalez-Osorio, L and Castanzo, DT and Thomas, NC and Brothers, M and Dangerfield, TL and Hooper, MM and West, MS and Appleby, NM and Krudop, I and Lamothe, RC and Aliaga Goltsman, DS and Alexander, LM and Butterfield, CN and Johnson, KA and Brown, CT and Taylor, DW},
title = {Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency.},
journal = {Nature structural & molecular biology},
volume = {},
number = {},
pages = {},
pmid = {41975095},
issn = {1545-9985},
abstract = {Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing because of their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here we identify and characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Alistipes sp. Cas12f (Al3Cas12f), which supports robust genome editing in human cells. Through structural, biochemical and kinetic analyses, we compare Al3Cas12f to two recently described orthologs, Oscillibacter sp. Cas12f and Ruminiclostridium herbifermentans Cas12f. These orthologs present divergent architectures and regulatory features governing protospacer-adjacent motif recognition, guide RNA (gRNA) binding, dimerization and DNA cleavage. Notably, Al3Cas12f achieves efficient R-loop formation through a stable dimer interface and a naturally optimized gRNA. Leveraging these structural insights, we generate an engineered Al3Cas12f variant (RKK) that increases editing and improves activity across several tested genomic loci. By overcoming locus-dependent variability and an apparent potency threshold, this engineered compact editor seems to expand the feasibility of low-dose, AAV-compatible therapeutic genome editing. Our results elucidate mechanistic determinants of Cas12f activity and offer a framework for engineering compact genome editors that may bear therapeutic potential.},
}

@article {pmid41975182,
year = {2026},
author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A},
title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47528-0},
pmid = {41975182},
issn = {2045-2322},
support = {818431//Horizon 2020 Framework Programme/ ; },
abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.},
}

@article {pmid41975253,
year = {2026},
author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V},
title = {Decoding the microbial landscape of endometrial cancer: a case-control study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05017-4},
pmid = {41975253},
issn = {1471-2180},
support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; },
}

@article {pmid41975274,
year = {2026},
author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN},
title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655793},
doi = {10.1080/19490976.2026.2655793},
pmid = {41975274},
issn = {1949-0984},
abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.},
}

@article {pmid41964456,
year = {2026},
author = {Lefebvre, CS and Salmona, M and Hamane, S and Dellière, S and Charlier, V and Huguenin, A and Bonnal, C and Legoff, J and Feghoul, L and Dutkiewicz, M and Caméléna, F and Berçot, B and Charvet, E and Battistella, M and Alanio, A and Ghelfenstein-Ferreira, T},
title = {Shotgun metagenomic sequencing improves cross-kingdom diagnosis of mycetoma.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70450},
pmid = {41964456},
issn = {1468-3083},
}

@article {pmid41964564,
year = {2026},
author = {Zhao, S and Lin, S and Chen, M and Yan, J and Yang, D and Guo, F and Qu, H and Chen, Y},
title = {Iron-Cycling-Constructed Wetland-Microbial Fuel Cell-Enhanced Removal of Sartans: The Overlooked Singlet Oxygen and Functional Microorganisms.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c00492},
pmid = {41964564},
issn = {1520-5851},
abstract = {The global challenge of population aging has led to an increase in the utilization of cardiovascular drugs such as sartans, which are frequently detected in aquatic environments and necessitate advanced treatment. Current sartan removal technologies are limited by their requirement for strict reaction conditions and the potential formation of toxic byproducts. This study presents a novel iron-cycling-constructed wetland-microbial fuel cell (Fe-CWMFC) that combines biotic and abiotic processes to effectively degrade sartans (94.4 ± 3.5%-95.9% ± 3.3%). Mass balance analysis revealed that direct microbial degradation pathways made the highest contribution (40.7-44.5%), followed by ROS-driven degradation (20.3-21.8%), substrate adsorption (26.1-29.7%), and plant uptake (2.3-2.5%). Iron cycling enhanced ROS-driven degradation, with 11.3-13.3% derived from biotic [1]O2 and 7.0-9.3% derived from abiotic [1]O2. Metagenomic binning analysis identified 60 MAGs (e.g., Thiobacillus, Nitrosomonas) with sartan degradation potential, which harbor genes encoding functional enzymes (e.g., decarboxylase, dehydroxylase, and demethylase). By combining biodegradation and ROS-driven degradation to target functional groups (e.g., -COOH, -OH, and -CH3) in sartans, the toxicity was significantly reduced. This research enhances our understanding of the combined role of ROS and microorganisms in micropollutant removal and highlights Fe-CWMFC as a high-efficiency, sustainable, and low-toxicity treatment technology for complex environmental applications.},
}

@article {pmid41964658,
year = {2026},
author = {Liu, H and Wang, C and Huang, Z and Wang, J and Cai, F and Tian, C and Feng, J and Shen, J and Wang, X},
title = {Progressive Decomposition of Algal Organic Matter Decouples Nitrogen Transformations in Lake Sediments: Evidence from Short-Term Incubation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08386},
pmid = {41964658},
issn = {1520-5851},
abstract = {Against the backdrop of global lake eutrophication, algal bloom decay is increasingly affecting ecosystems. Algal organic matter (AOM), a natural complex mixture, undergoes multiple release and transformation stages, yet its composition and pathways remain unclear. This study used spectroscopic, mass spectrometric, and metagenomic analyses to monitor a time-compressed algal decay experiment. Results showed that AOM release and transformation can be divided into three stages. Within 1 day, labile AOM consisting mainly of proteins (8.36%), lipids (8.22%), and unsaturated carbohydrates (7.72%) was rapidly released, reshaping nitrogen (N) cycling. Its high bioavailability promoted sediment mineralization and a positive priming effect, while anaerobic conditions reduced nitrification and denitrification rates by 88.7% and 34.5%. Within 3-7 days, semilabile AOM rich in tannins (19.2%) and carbohydrates (9.41%) was gradually decomposed, maintaining anaerobic conditions. The imbalance of excessive NH4[+] and depleted NO3[-] led to the decoupling of nitrification-denitrification. After 7 days, humic-like AOM dominated by lignins (56.8%) prevailed, reducing oxygen consumption and enabling rapid recovery of nitrification and slow rebound of denitrification. These findings clarify the phased transformations of AOM and their microbial interactions, providing mechanistic insights into the short-term fluctuations of lake water quality and microbial processes during bloom decay.},
}

@article {pmid41965517,
year = {2026},
author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H},
title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05023-6},
pmid = {41965517},
issn = {1471-2180},
support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.

RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.

CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.},
}

@article {pmid41965741,
year = {2026},
author = {Khangarot, R and Kumari, V and Mishra, R and Singh, A},
title = {Artificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance.},
journal = {Biomedical engineering online},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12938-026-01568-9},
pmid = {41965741},
issn = {1475-925X},
abstract = {Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in deep learning, transformer-based sequence models, graph neural networks, and multimodal architectures have greatly improved microbial classification accuracy, antibiotic resistance gene (ARG) detection, and resistance prediction. Taking metagenomic sequencing into consideration, these advancements have contributed to the development of sensitive, scalable, and non-invasive methods to profile microbiomes, determine novel resistance, and monitor AMR trends at the population level. This review summarizes recent advances in AI-aided microbiology, with a particular emphasis on AMR surveillance. Specific topics include deep learning frameworks for ARG annotation, emerging approaches to identifying new resistance genes, and multimodal applications (genomic and clinical metadata) aimed at improving phenotype prediction. The role of metagenome-assembled genomes (MAGs) to enhance AMR surveillance efforts is noted, along with their noted limitations relative to isolate genomes. The discussion includes the examination of explainable AI (XAI) techniques including SHAP, attention mechanism approaches, and gradient-based attribution approaches, with the aim of increasing transparency and clinical explainability. We also cover potential applications including AI-enabled non-invasive fecal microbiome diagnostics, laboratory automation, and environmental surveillance. While there has been significant progress, unresolved issues exist relating to dataset variations, liability of models to datasets, interpretability, and regulatory approval. Overcoming these barriers, however, will require standardized frameworks for these workflows, privacy-preserving federated learning methods, and interpretable AI frameworks for clinical and public health tools. AI could fundamentally change AMR surveillance by allowing for earlier resistance detection, advanced risk assessment recommendation, and improved monitoring strategies globally.},
}

@article {pmid41965996,
year = {2026},
author = {Wang, C and Shen, J and Liu, H and Huang, Z and Wang, J and Tian, C and Cai, F and Feng, J and Sha, F and Wang, X},
title = {DNRA dominates over denitrification during algal blooms in a mesotrophic lake: Implications for nitrogen retention and eutrophication risk.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129621},
doi = {10.1016/j.jenvman.2026.129621},
pmid = {41965996},
issn = {1095-8630},
abstract = {Nitrogen (N) overloading threatens global lake ecosystems. However, how algal blooms affect the N balance in mesotrophic lakes by shaping N-cycling biogeographic patterns remains a critical knowledge gap. This study systematically elucidated N cycling patterns and microbial mechanisms driving N retention during algal blooms in Erhai Lake by integrating field monitoring,[15]N isotope pairing technique ([15]N-IPT), and absolute quantitative metagenomics. Results revealed that algal blooms shaped a N-cycling functional pattern in Erhai Lake characterized by organic degradation and synthesis (ODAS) dominance and dissimilatory nitrate reduction (DNR) as a key process. Notably, algal blooms disrupted traditional nitrification-denitrification coupling, shifting N cycling towards a retention mode dominated by dissimilatory nitrate reduction to ammonium (DNRA). Sedimentary DNRA contributed 69% (14.69 ± 5.57 μmol N L[-1] h[-1]) of total dissimilatory nitrate reduction (DNR) process, supported by significantly elevated NrfA (602.49 ± 121.04 μmol d[-1] g[-1]) and NirBD (361.29 ± 138.39 μmol d[-1] g[-1]) enzyme activities. Partial Least Squares Path Modeling (PLS-PM) identified the nitrogen retention index (NRI) as co-regulated by water depth and algal-mediated microbial activity/rates. High-NRI sediments were dominated by Bacteroidota (mainly orders Marinilabiliales and families Prolixibacteraceae) and Myxococcota (primarily families Anaeromyxobacteraceae), while low-NRI sediments were characterized by enrichment of Pseudomonadota (Thioalkalivibrio nitratireducens and Gallionellaceae) and Campylobacterota (Campylobacter sp. BCW_8712). DNRA outcompeted denitrification, diverting nitrate to ammonium rather than N2 gas and resulting in an internal N loading that was an order of magnitude higher than external inputs. This work challenges the denitrification-centric paradigm, revealing the microbial mechanisms of endogenous N accumulation under algal bloom conditions and providing a theoretical basis for the management of plateau lakes.},
}

@article {pmid41966291,
year = {2026},
author = {Ashango, ZA and Seyum, EG and Nwogha, JS},
title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105941},
doi = {10.1016/j.meegid.2026.105941},
pmid = {41966291},
issn = {1567-7257},
abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.},
}

@article {pmid41966300,
year = {2026},
author = {Bojko, J and Abd-Alla, A},
title = {'Invertebrate-virome sequence detection: implications for invertebrate products trading and regulations' - An editorial for the special issue.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108623},
doi = {10.1016/j.jip.2026.108623},
pmid = {41966300},
issn = {1096-0805},
abstract = {Invertebrates can be infected by many viruses that may either cause disease (invertebrate‑pathogenic viruses) or be transmitted to vertebrates or plants. Viral infections may occur in natural invertebrate populations as well as in mass‑reared colonies. The significant recent advances in genome‑sequencing technologies have provided fast and relatively inexpensive tools for detecting invertebrate viruses in both wild and mass‑rearing settings, even at very low levels. The presence of such viruses raises important questions regarding the impact of covert infections on invertebrate health, sanitation, and overall colony performance. The articles in this special issue address viral sequence detection, viral sequence diversity, the impact of viruses on invertebrates, and the relationship between food and feed, and policy.},
}

@article {pmid41966314,
year = {2026},
author = {Liu, S and Qin, Y and Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H},
title = {Genomic Characterization, Antimicrobial Resistance and Virulence Profiles of Klebsiella pneumoniae Isolated from Mink in Northern China.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108485},
doi = {10.1016/j.micpath.2026.108485},
pmid = {41966314},
issn = {1096-1208},
abstract = {Klebsiella pneumoniae is an important opportunistic pathogen of One Health concern, and its multidrug-resistant (MDR) and hypervirulent strains pose serious threats to public health. However, the epidemiological characteristics, antimicrobial resistance profiles, and virulence potential of K. pneumoniae circulating in farmed minks remain poorly understood. In this study, we integrated phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis to investigate the epidemiology, resistance determinants, and virulence characteristics of K. pneumoniae isolated from farmed minks in northern China. A total of 41 K. pneumoniae strains from 325 fecal samples (isolation rate: 12.62%), including three hypervirulent strains. All isolates exhibited multidrug resistance, with complete resistance to florfenicol, azithromycin, and sulfisoxazole, but remained highly susceptible to carbapenems and polymyxin B. Whole-genome sequencing revealed that the isolates harbored 241 antibiotic resistance genes (ARGs), including ESBL-associated genes and the plasmid-mediated mcr-1.1, along with 7,111 virulence factor genes (VFGs) and 135 mobile genetic elements (MGEs). Metagenomic analysis further revealed a complex resistome and virulome, with 7,259 ARGs and 6,701 virulence-related genes identified across samples. Antibiotic target alteration and efflux were the dominant resistance mechanisms, while effector delivery systems, metabolic functions, and adherence were the major virulence categories. MGEs were abundant, especially transposases, indicating active genetic mobility within the microbial community. Overall, this study provides a comprehensive characterization of antimicrobial resistance and virulence features of mink-derived K. pneumoniae and highlights the potential role of farmed minks as reservoirs of multidrug-resistant bacteria within the One Health framework, offering important insights for antimicrobial resistance surveillance and public health risk assessment.},
}

@article {pmid41966472,
year = {2026},
author = {Merkhan, K and Chaudhry, AS},
title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.},
journal = {Anaerobe},
volume = {98},
number = {},
pages = {103046},
doi = {10.1016/j.anaerobe.2026.103046},
pmid = {41966472},
issn = {1095-8274},
abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.

METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72 h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20 g kg[-1] DM) for each PFA.

RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20 g kg[-1] DM, followed by GBL with a 28.5% reduction at 10 g kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.

CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.},
}

@article {pmid41966559,
year = {2026},
author = {Jordán, M and Bustos-Caparros, E and Gago, JF and Zhang, Z and Tian, Z and Singleton, DR and Rossello-Mora, R and Grifoll, M and Vila, J},
title = {Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142004},
doi = {10.1016/j.jhazmat.2026.142004},
pmid = {41966559},
issn = {1873-3336},
abstract = {Polycyclic aromatic nitrogen heterocycles (PANHs), also known as azaarenes, are common co-contaminants at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Recent non-target analysis of PAH-contaminated soil samples has revealed an unexpected abundance and diversity of PANHs, with acridine standing out as a predominant compound within this group. Despite its known toxicity and prevalence in contaminated soils, the microbial communities and biochemical mechanisms responsible for acridine degradation remain poorly understood. We conducted DNA-stable isotope probing (DNA-SIP) using newly synthesized uniformly labeled [13]C-acridine to comprehensively assess the bacterial taxa and functional genes involved in acridine biodegradation in a creosote-contaminated soil. Metagenomic analysis of [13]C-enriched DNA from soil incubations identified a member of the genus Sphingobium as the primary acridine degrader. Transcriptomic analysis based on its 16S rRNA gene expression demonstrated a strong correlation with acridine removal from the soil. Shotgun metagenomic sequencing enabled the reconstruction of one metagenome-assembled genome (MAG). Functional annotation of this MAG revealed five gene clusters potentially involved in acridine biodegradation, and their actual contribution was assessed by gene expression analysis in soil incubations. Based on these findings, we reconstructed the metabolic pathway for putative acridine degradation in PAH-contaminated soil.},
}

@article {pmid41966829,
year = {2026},
author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, SÁ and Ferenczi, S and Szőke, Z},
title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104498},
doi = {10.1016/j.xpro.2026.104498},
pmid = {41966829},
issn = {2666-1667},
abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].},
}

@article {pmid41967167,
year = {2026},
author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB},
title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101830},
doi = {10.1016/j.cbd.2026.101830},
pmid = {41967167},
issn = {1878-0407},
abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.},
}

@article {pmid41967206,
year = {2026},
author = {Moletta-Denat, M and Azam, O and Pourcher, AM and Manno, M and Zennaro, B and Bonin, E and Bonnafous, A and Chenon, P and Leboucher, A and Alvarez-Fraga, L and Godon, JJ and Wéry, N},
title = {Fate of pathogenic bacteria in five full-scale biogas plants monitored using cultivation, dPCR, and shotgun metagenomics: Insights from each approach.},
journal = {Waste management (New York, N.Y.)},
volume = {218},
number = {},
pages = {115505},
doi = {10.1016/j.wasman.2026.115505},
pmid = {41967206},
issn = {1879-2456},
abstract = {Current global standards for quantification of pathogenic or indicator bacteria in biogas plants primarily rely on culture-based methods using specific media. However, molecular techniques such as quantitative PCR, digital PCR (dPCR), and shotgun metagenomics are increasingly employed in research and may offer more effective pathogen monitoring for industrial applications. This study analyzed samples from five full-scale biogas plants using traditional culture-based methods, dPCR and shotgun metagenomics to monitor indicator bacteria (Escherichia coli, Enterococcus spp. and Clostridium perfringens) and pathogenic species (Salmonella enterica, Listeria monocytogenes, Staphylococcus aureus and Clostridium botulinum). The DNA extraction protocol was optimized to achieve quantification limits of 1.1 copies of gene g[-1] wet weight, compatible with regulatory thresholds. Comparing the three methods revealed that shotgun metagenomics detected a greater diversity of pathogenic species in biowaste, including S. aureus and C. botulinum. Acidophilic conditions in hydrolysis tank effectively hygienized the biowaste. In contrast, the four agricultural biogas plants showed limited effect on the three indicator bacteria, as indicated by dPCR. This study demonstrates, for the first time, the added value of combining dPCR and shotgun metagenomics to assess pathogen dynamics in biogas plants. Together, these methods provide a more comprehensive and specific view of microbial contaminants, as illustrated by the detection of Enterococcus cecorum in digestates.},
}

@article {pmid41967340,
year = {2026},
author = {Li, M and Yao, K and Harindintwali, JD and Qian, M and Wu, N and Kan, Y and Song, Z and Xiao, X and Liu, P and Zhao, Y},
title = {Alkali-organic synergy rewires microbial acid tolerance to restore nitrogen cycling in acidic soils.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129619},
doi = {10.1016/j.jenvman.2026.129619},
pmid = {41967340},
issn = {1095-8630},
abstract = {Soil acidification in global croplands is intensifying, yet the microbial mechanisms by which amendments restore soil nitrogen (N) cycling remain poorly understood. Here, we used a decade-long field experiment in strongly acidic soils to elucidate how alkali slag and organic manure, alone and in combination, regulate acid-tolerant microbial functions and N transformation processes. By integrating soil physicochemical analyses, 16 S rRNA gene sequencing, and shotgun metagenomics, we show that the combined application of organic manure and alkali slag (OM + AS) most effectively increased soil pH (from 4.18 to 5.42) and reduced inorganic N accumulation relative to single amendments (Ammonium nitrogen, nitrate nitrogen, and total organic nitrogen decreased by 15.66 mg/kg, 12.56 mg/kg, and 46.09 mg/kg respectively). Metagenomic profiling revealed that OM + AS consistently up-regulated acid-tolerance pathways (proton pump increased by 6.12%, alkali production increased by 9.75%, acid consumption increased by 5.12%) together with key N cycling genes, with the strongest enhancement observed for nitrification (increased by 84.54%). Network analysis demonstrated significant positive co-occurrence between acid-tolerance and nitrification genes across the microbial community. Correspondingly, bacterial taxa harboring these functions, including Sphingomonas and Nitrospira, were most abundant under OM + AS. We propose that alkali slag and organic manure act synergistically to elevate soil pH, relieve acid stress on microbes, and promote a community with dual capacities for acid tolerance and active N transformation. These findings mechanistically link soil acidity amelioration with enhanced microbial-mediated N cycling and offer a functional basis for designing targeted soil remediation strategies.},
}

@article {pmid41967439,
year = {2026},
author = {Tang, C and Wan, C and Gan, J and He, Z and Wei, C and Tan, H and Wu, R and Yu, F and Li, Y},
title = {Rhizosphere phosphorus and iron cycling accelerates manganese phytoextraction by Polygonum lapathifolium.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142033},
doi = {10.1016/j.jhazmat.2026.142033},
pmid = {41967439},
issn = {1873-3336},
abstract = {Manganese (Mn) contamination in mining soils poses persistent ecological risks due to its high mobility and potential accumulation in plants. Although exogenous microbial inoculation is increasingly used to improve phytoremediation, the mechanisms by which it regulates rhizosphere phosphorus (P) and iron (Fe) cycling, and thereby influences Mn bioavailability, remain poorly understood. We hypothesized that Enterobacter sp. inoculation would enhance Mn phytoextraction by stimulating rhizosphere P activation and Fe speciation transformation, thereby promoting nutrient acquisition and Mn mobilization. To test this hypothesis, we investigated the effects of Enterobacter sp. inoculation on rhizosphere P/Fe fractions, functional genes, and Mn phytoextraction. Enterobacter sp. significantly decreased rhizosphere soil pH and enhanced P-releasing enzyme activities, increasing available P by 26.7% under the C1.0 (3.8 ×10[7] CFU·g[-1] (soil)) treatment compared with the control (p < 0.05). Concurrently, Fe(II) and amorphous Fe increased by 11.9% and 15.1%, respectively (p < 0.05), indicating enhanced Fe transformation in the rhizosphere. These shifts facilitated plant P and Fe acquisition, promoted biomass production, enhanced Mn phytoextraction in Polygonum lapathifolium L. by strengthening rhizosphere redox conditions and mineral interfacial processes. Metagenomic analysis revealed that Enterobacter sp. inoculation increased the functional potential of genes related to P activation (e.g., gcd, phnP) and Fe biosynthesis/uptake (e.g., hemH, pchB), mainly associated with Pseudomonadota and Actinomycetota. Partial least squares path modeling further confirmed positive associations among P/Fe cycling genes, rhizosphere P/Fe fractions, enzymatic activities, and plant growth. Overall, microbial inoculation enhanced Mn phytoremediation by coordinating rhizosphere nutrient cycling processes, providing a promising strategy for the remediation of HMs-contaminated mining soils.},
}

@article {pmid41967476,
year = {2026},
author = {Wang, H and Di, D and Du, S and Tateno, R and Peñuelas, J and Migliavacca, M and Chen, Q and Guan, J and Song, Y and Shi, W},
title = {Plant functional trait differentiation and microbial life-history strategy shifts drive soil respiration under long-term forest restoration.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag042},
pmid = {41967476},
issn = {1758-4469},
abstract = {Soil respiration (Rs) represents a major carbon (C) flux linking plant productivity with microbial decomposition; however, the mechanisms by which contrasting forest restoration pathways regulate Rs and its components remain insufficiently understood. We conducted a six-year field observation (2017-2022) across abandoned farmland (AF), Quercus liaotungensis forest (QF), and Robinia pseudoacacia plantation (RP) on the Loess Plateau, China, integrating measurements of Rs, autotrophic (Ra), heterotrophic (Rh), plant functional traits, soil physicochemical properties, and microbial C metabolic potential. Afforestation significantly increased Rs, with a stronger enhancement observed in QF than in RP. Although Ra did not differ significantly between the two forest types, Rh accounted for approximately 70% of Rs and primarily explained the significant differences in Rs between restoration pathways. Elevated Rh in QF was strongly associated with greater abundances of microbial functional genes involved in the degradation of C substrates. Integrated analyses further revealed that differentiation in plant functional traits between QF (conservative strategy) and RP (acquisitive strategy) indirectly amplified Rh contributions to Rs by reshaping soil substrate availability and coordinating shifts in microbial life-history strategies. Collectively, our findings identify plant functional trait differentiation as a key driver of long-term Rs dynamics, mediated by shifts in microbial life-history strategies.},
}

@article {pmid41967488,
year = {2026},
author = {Du, M and Xue, P and Minasny, B and Jang, HJ and McBratney, A},
title = {Macroecological processes impact Australian soil resistomes and climatically stable regions with anthropogenic activities serve as ARG hotspots.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag079},
pmid = {41967488},
issn = {1751-7370},
abstract = {Soil antibiotic resistance genes (ARGs) pose a global health threat, but a critical knowledge gap remains regarding how macro-scale pedoclimatic constraints interact with land-use intensification to determine the spatial distribution of the soil resistome. To address this, we conducted a continental-scale survey of Australian topsoils and used metagenomic analysis to reveal the hierarchy of drivers shaping the soil resistome. Machine learning was applied to predict the spatial ARG distribution across Australia. We found that, at the continental scale, climatic variability acts as the dominant filter on ARG distribution, overriding local soil properties and human disturbance. Unexpectedly, climatically stable regions, characterised by sandy and low-carbon soils in Southwestern Australia, emerged as ARG hotspots. We also demonstrated that anthropogenic land use amplifies ARG abundance within these climatically stable regions. Furthermore, spatial modelling revealed distinct geographical patterns: although total ARG abundance was enriched in coastal regions, specific resistance mechanisms showed unique distributions. As a continental-scale investigation of soil ARGs in Australia, this study provides a framework to identify high-risk regions where lower climatic variability and intensive farming interact to enhance antimicrobial resistance.},
}