Browse Papers

Search the literature by keyword, topic, or author. Filter to articles with full text available.

Full text All articles Nanopore Basecalling

1201 results

Full text 2026

Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women

Kozhakhmetov S, Kushugulova A, Vinogradova E, et al.

Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in …

Read PDF

Metagenomics

Full text 2025

Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource

Tang H, Liu H, Yuan L, et al.

Metagenomic Next-Generation Sequencing (mNGS) enables simultaneous sequencing of both microbial and host nucleic acids in clinical samples. However, analytical approaches for interpreting complex mNGS datasets are seldom disclosed, limiting advancements in multimodal analysis and omics-driven …

Read PDF

Metagenomics

Full text 2025

Editorial: Targeted metagenomics in pathogen detection

Zhou J, Kamau E, Wei Q.

No abstract available.

Read PDF

Metagenomics

Full text 2026

Long-Read Metagenomics Profiling for Identification of Key Microorganisms Affected by Heavy Metals at Technogenic Zones

Isgandarov I, Abilda Z, Kanat R, et al.

Heavy metal pollution poses a serious threat to soil ecosystems worldwide, as long-term exposure can alter microbial community functioning and reduce overall ecosystem resilience. This study investigated the impact of heavy metal contamination in technogenic …

Read PDF

Metagenomics

Full text 2026

In silico performance of a targeted enriched metagenomics approach to infer Mycoplasma bovis strains in milk

Biesheuvel MM, Barkema HW, Morley PS, et al.

Strain variation plays a key role in the microbial epidemiology of Mycoplasma bovis, yet its true diversity remains incompletely characterized, partly due to limitations of culture-based methods. This study evaluated the in silico suitability of …

Read PDF

Metagenomics

Full text 2026

Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer

Abuah CY, Sipes K, Buongiorno J, et al.

The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on …

Read PDF

Metagenomics

Full text 2026

Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor

Schaerer LG, Anderson RS, Chan J, et al.

Methane-arrested anaerobic digestion (AAD) is a waste management strategy that produces carboxylic acid precursors to industrial products (fuels, bio-based polymers, and pharmaceuticals) from organic wastes. A major challenge preventing application of AAD is highly variable …

Read PDF

Metagenomics

Full text 2026

Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest

Abagnale V, Palacin-Lizarbe C, Paul D, et al.

The nitrous oxide (N2O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N2O dynamics of the lichen Platismatia glauca in boreal …

Read PDF

Metagenomics

Full text 2025

Genome-Resolved Metagenomics of Rice Straw Degradation Experiments in Colombian Fields

Yepes-García J, Novoa-Montenegro N, Otero-Jiménez V, et al.

Extensive rice harvesting yields more than 800 million tons of rice straw (RS) per year globally, generating a byproduct that is often difficult for farmers to manage efficiently without burning it. In the quest for …

Read PDF

Metagenomics

Full text 2026

A comparison of methods for the optimal recovery of the human fecal virome

De Chiara L, Doughty R, Estévez-Gómez N, et al.

Human virome research is gaining increasing attention as viruses are recognized as critical modulators of microbial communities and human health. Viral metagenomics, however, faces unique challenges, including the low abundance and diversity of viruses in …

Read PDF

Bioinformatics Metagenomics

Full text 2026

CAMP: a modular metagenomics analysis system for integrated multistep data exploration

Mak L, Tierney B, Wei W, et al.

Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring …

Read PDF

Metagenomics

Full text 2025

Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements

Cifuentes SG, Graham J, Trueba G, et al.

Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) …

Read PDF

Metagenomics

Full text 2026

Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India

Sumithra TG, Gayathri S, Mannur VS, et al.

Mesopelagic sediments represent a critical yet understudied component of marine ecosystems, where environmental gradients strongly influence microbial community structure and function. This study profiles prokaryotic and fungal communities in the sediments along a bathymetric transect …

Read PDF

Metagenomics

Full text 2026

Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study

Harshvardhan, Kaur M, Grover V, et al.

<h4>Introduction</h4>Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have …

Read PDF

Metagenomics

Full text 2026

Advancing Plant Microbiome Research Through Host DNA Depletion Techniques

Wang Y, Yang J, Hou H, et al.

Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant …

Read PDF

Metagenomics

Full text 2026

Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings

Peddle SD, Cando-Dumancela C, Costin S, et al.

Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function …

Read PDF

Metagenomics

Full text 2025

Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus

Rodriguez-Fernandez IA, Santiago-Rodriguez TM, Figueroa-Pratts PG, et al.

Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns …

Read PDF

Metagenomics

Full text 2025

Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing

Russell JN, Kos D, Yacoub E, et al.

Bovine respiratory disease (BRD) is the primary disease of cattle and is responsible for most of the antibiotic use in the beef industry, both for metaphylaxis and treatment. Infection prevention and targeted treatments would benefit …

Read PDF

Metagenomics

Full text 2025

Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis

Haugum K, Ravi A, Afset JE, et al.

Infectious gastroenteritis is a significant health issue globally. Identifying the causative pathogen is crucial for treatment, infection control and epidemiological surveillance. While PCR-based analyses are fast and sensitive, they only detect known pathogens. Clinical metagenomics …

Read PDF

Metagenomics

Full text 2025

Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study

Sanjrambam B, Sharma D, Bakshi RK, et al.

<h4>Introduction</h4>Recent research highlights that the gut microbiota of pregnant women undergoes significant changes throughout pregnancy, influenced by factors such as diet, environment, and sociocultural practices. A diverse gut microbiome during pregnancy is linked to improved …

Read PDF

Metagenomics

Browse Papers

Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: <i>Lactobacillus iners</i> as a <i>Candida</i>-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women

Bronchoalveolar lavage fluid metagenomic datasets: a multidimensional clinical biomolecular resource

Editorial: Targeted metagenomics in pathogen detection

Long-Read Metagenomics Profiling for Identification of Key Microorganisms Affected by Heavy Metals at Technogenic Zones

<i>In silico</i> performance of a targeted enriched metagenomics approach to infer <i>Mycoplasma bovis</i> strains in milk

Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer

Acetate to caproate: metagenomic insights into functional shifts in a methane-arrested anaerobic bioreactor

Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest

Genome-Resolved Metagenomics of Rice Straw Degradation Experiments in Colombian Fields

A comparison of methods for the optimal recovery of the human fecal virome

CAMP: a modular metagenomics analysis system for integrated multistep data exploration

Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements

Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India

Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study

Advancing Plant Microbiome Research Through Host DNA Depletion Techniques

Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings

Gut microbial community structure of the adult citrus root weevil <i>Diaprepes abbreviatus</i>

Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing

Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis

Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study