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Publications tagged "Metagenomics"

Blog: Ruminating on the rumen microbiome

In this blog, Beatriz Delgado Corrales, Óscar González Recio, and Mónica Gutiérrez Rivas describe their work on classifying rumen microbiomes, comparing long-read and short-read sequencing platforms...

Blog: Metagenomic sequencing: which assembly method is best?

In this blog, Adriel Latorre-Perez shares his work on comparing methods for assembling metagenomes from nanopore sequencing data, and he provides recommendations on the best tools to use for the job...

Interview: Generating microbial insights from nanopore metagenomic data using an open-source, cloud-based metagenomics tool for researchers

Sara Simmonds is a computational biologist at the Chan Zuckerberg Initiative (CZI), where she works closely with scientists, engineers, and the product team to develop open-source software for met...

Oxford Nanopore releases a novel protocol for the rapid metagenomic characterisation of DNA and RNA viruses

This protocol describes a simple metagenomic workflow that can be used to identify DNA and RNA viruses. This method has been applied in human clinical samples to characterise the pathogen currently ...

Systematic dissection of a complex gut bacterial community

Efforts to model the gut microbiome have yielded important insights into the mechanisms of interspecies interactions, the impact of priority effects on ecosystem dynamics, and the role of diet and n...

In vivo augmentation of a complex gut bacterial community

Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or...

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

Background Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks. Quasimetagenomics can substantial...

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Fast and accurate identification of pathogens is an essential task in healthcare settings. Next generation sequencing platforms such as Illumina have greatly expanded the capacity with which differe...

Novel canine high-quality metagenome-assembled genomes, prophages, and host-associated plasmids by long-read metagenomics together with Hi-C proximity ligation

Long-read metagenomics facilitates the assembly of high-quality metagenome-assembled genomes (HQ MAGs) out of complex microbiomes. It provides highly contiguous assemblies by spanning repetitive reg...

Mapping the microbial diversity and natural resistome of north Antarctica soils

The rising of multi-resistant bacterial pathogens is currently one of the most critical threats to global health and requires urgent actions for its control and a better understanding of the origin,...

MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses

New advances in sequencing technology and bioinformatics analysis tools have significantly supported the culture-independent analysis of complex microbial communities associated with environmental, ...

BugSeq 16S: NanoCLUST with improved consensus sequence classification

NanoCLUST has enabled species-level taxonomic classification from noisy nanopore 16S sequencing data for BugSeq’s users and the broader nanopore sequencing community. We noticed a high misclassifica...

Haemophilus influenzae meningitis direct diagnosis by metagenomic next-generation sequencing: a case report

Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influen...

Linking carbohydrate structure with function in the human gut microbiome using hybrid metagenome assemblies

Complex carbohydrates that escape digestion in the small intestine, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between particul...

Anatomy promotes neutral coexistence of strains in the human skin microbiome

What enables strains of the same species to coexist in a microbiome? Here, we investigate if host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human s...

Nanopore sequencing and its application to the study of microbial communities

Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable tec...

MMMVI: Detecting SARS-CoV-2 Variants of Concern in Metagenomic Samples

Motivation SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Variants of Concern (VOCs) and Variants of Interest (VOIs) are lineages that represent a greater risk to public health, and can...

The food additive xanthan gum drives adaptation of the human gut microbiota

The diets of industrialized countries reflect the increasing use of processed foods, often with the introduction of novel food additives. Xanthan gum is a complex polysaccharide with unique rheologi...

Inferring species compositions of complex fungal communities from long- and short-read sequence data

Background The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in ...

Linked machine learning classifiers improve species classification of fungi when using error-prone long-reads on extended metabarcodes

The increased usage of long-read sequencing for metabarcoding has not been matched with public databases suited for error-prone long-reads. We address this gap and present a proof-of-concept study f...

Phylodynamic modelling of bacterial outbreaks using nanopore sequencing

Nanopore sequencing and phylodynamic modelling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Here...

Soil disturbance affects plant productivity via soil microbial community shifts

Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is u...

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Background: Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms recently implemented in Oxford Nanopore's own control software. By examining the f...

Synergistic effect of short- and long-read sequencing on functional meta-omics

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts from genes and proteins present in situ. Here, we evaluate short-read-only, long-read-...

Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbi...

16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis

Research question: Full-length 16S rRNA gene sequencing using nanopore technology is a fast alternative to conventional short-read 16S rRNA gene sequencing with low initial investment costs that ha...

Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read data (ONT MinION) obtained from an e...

What’s under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits

pH has been identified as a master regulator of the soil environment, controlling the solubility and availability of nutrients. As such, soil pH exerts a strong influence on indigenous microbial com...

A peek into the plasmidome of global sewage

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impac...

High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes

By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long-read sequencing strategies offer comprehensive insights into the organization of genetic inf...

A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

Metagenomic next-generation sequencing (mNGS) holds promise as a diagnostic tool for unbiased pathogen identification and precision medicine. However, its medical utility depends largely on assay si...

Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis

Background Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative...

Automated strain separation in low-complexity metagenomes using long reads

High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the sam...

Microbial population dynamics and evolutionary outcomes under extreme energy-limitation

As the most abundant and diverse form of life on Earth, microorganisms commonly inhabit energy-limited environments where cellular maintenance and growth is highly constrained. To gain insight into ...

Hybrid clustering of long and short-read for improved metagenome assembly

Next-generation sequencing has enabled metagenomics, the study of the genomes of microorganisms sampled directly from the environment without cultivation. We previously developed a proof-of-concept,...

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system

Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure–function relationships in complex environments. To compare the recovery of genomes ...

Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions

The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses timely makes it a powerful tool for public health emergency response. Third-generation sequencing (TGS) ...

Is oxford nanopore sequencing ready for analyzing complex microbiomes?

This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the ...

Precision long-read metagenomics sequencing for food safety by detection and assembly of Shiga toxin-producing Escherichia coli in irrigation water

Shiga toxin-producing Escherichia coli (STEC) contamination of agricultural water might be an important factor to recent foodborne illness and outbreaks involving leafy greens. Closed bacterial geno...

Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by re...

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

Long-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length and are therefore particularly relevant for microbiome studies. Howev...

The microbiome of Leonardo da Vinci’s drawings: a bio-archive of their history

Seven emblematic Leonardo da Vinci’s drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic document...

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification

The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be...

Complete, high-quality genomes from long-read metagenomic sequencing of two wolf lichen thalli reveals enigmatic genome architecture

Fungal genomes display incredible levels of complexity and diversity, and are exceptional study systems for genome evolution. Here we used the Oxford Nanopore MinION sequencing platform to generate ...

Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

Background The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Becau...

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant

Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production. To avoid their accumulation, raw water in the Netherlands, and many other c...

Preliminary assessment of nanopore-based metagenomic sequencing for the diagnosis of prosthetic joint infection

Objectives Pathogen identification is crucial for the diagnosis and management of periprosthetic joint infection (PJI). Although culturing methods are the foundation of pathogen detection in PJI, f...

Detection of astrovirus in a cow with neurological signs by Nanopore technology, Italy

In this study, starting from nucleic acids purified from the brain tissue, Nanopore technology was used to identify the etiological agent of severe neurological signs observed in a cow which was imm...

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

Species-level genetic characterization of complex bacterial communities has important clinical applications. In the present study, we assessed the performance of full-length 16S rRNA gene analysis o...

Abundance and diversity of phages, microbial taxa and antibiotic resistance genes in the sediments of the river Ganges through metagenomic approach

In the present study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community and antibiotic re...

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial resistant organisms on the Illumina Miseq and Oxford MinION platforms

Purpose Antimicrobial resistance (AMR) is a public health threat where efficient surveillance is needed to prevent outbreaks. Existing methods for detection of gastrointestinal colonization of multi...

Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America

The cricetine rodent Peromyscus leucopus is an important reservoir for several human zoonoses, including Lyme disease, in North America. Akin to hamsters, the white-footed deermouse has been unevenl...

MetaGenomic analysis of short and long reads

Identifying single organisms in environmental samples is one of the key tasks of metagenomics. During the last few years, third generation sequencing technologies have enabled researchers to sequenc...

Rhizomicrobiomics of Caesalpinia bonducella, a wonder plant for PCOS treatment

Plant and rhizobacterial interactions contribute partly to a plant’s medicinal properties and are well studied through metagenomics. In this study, 16S rDNA, 18S rDNA, and ITS meta-sequencing were p...

Rapid diagnostics of orthopaedic-implant-associated infections using Nanopore shotgun metagenomic sequencing on tissue biopsies

Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diag...

New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

Background Using metagenomics to determine animal diet offers a new and promising alternative to current methods. Here we show that rapid and inexpensive diet quantification is possible through meta...

Capturing in situ virus-host range and interaction dynamics through gene fusion with epicPCR

Viruses impact microbial diversity, phenotype, and gene flow through virus-host interactions that in turn alter ecology and biogeochemistry. Though metagenomics surveys are rapidly cataloging viral ...

Identifying taxonomic units in metagenomic DNA streams

With the emergence of portable DNA sequencers, such as Oxford Nanopore Technology MinION, metagenomic DNA sequencing can be performed in real-time and directly in the field. However, because metagen...

Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

Food processing environments can harbor microorganisms responsible for food spoilage or foodborne disease. Efficient and accurate identification of microorganisms throughout the food chain can allow...

Tripartite holobiont system in a vent snail broadens the concept of chemosymbiosis

Many animals inhabiting deep-sea vents are energetically dependent on chemosynthetic endosymbionts, but how such symbiont community interacts with host, and whether other nutritional sources are ava...

Microbiome dataset analysis from a shrimp pond in Ninh Thuan, Vietnam using shotgun metagenomics

Vietnam is one of the top shrimp producing and exporting countries in the world. However, viral and bacterial epidemic diseases cause severe damages to shrimp farming, resulting in millions of US do...

Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)

Middle East Respiratory Syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastroint...

Genome evolution in bacteria isolated from million-year-old subseafloor sediments

Deep below the seafloor, microbial life subsists in isolation from the surface world under perpetual energy limitation. The extent to which subsurface microbes evolve and adapt to their subseafloor ...

Truncated denitrifiers dominate the denitrification pathway in tundra soil metagenomes

In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved i...

Characterization of fecal microbiota with clinical specimen using long-read and short-read sequencing platform

Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS...

Soil disturbance affects plant growth via soil microbial community shifts

Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is u...

The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described in association with the Drosophilidae. This has limited the opport...

High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS

Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment. To better understand microbial communities and...

Comparison of ultrafiltration and iron chloride flocculation in the preparation of aquatic viromes from contrasting sample types

Viral metagenomes (viromes) are a valuable untargeted tool for studying viral diversity and the central roles viruses play in host disease, ecology, and evolution. Establishing effective methods to ...

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challe...

Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

Life in Movile Cave (Romania) relies entirely on primary carbon fixation by bacteria oxidizing sulfide, methane and ammonia with oxygen, nitrate, sulfate, and ferric iron. There, large spherical-ovo...

Metagenomic characterization of a harmful algal bloom using nanopore sequencing

Water bodies around the world are increasingly threatened by harmful algal blooms (HABs) under current trends of rising water temperature and nutrient load. Metagenomic characterization of HABs can...

Classification of changes in the fecal microbiota associated with colonic adenomatous polyps using a long-read sequencing platform

The microbiota is the community of microorganisms that colonizes the oral cavity, respiratory tract, and gut of multicellular organisms. The microbiota exerts manifold physiological and pathological...

Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics

Microbial communities in their natural habitats consist of closely related populations that may exhibit phenotypic differences and inhabit distinct niches. However, connecting genetic diversity to e...

Benchmarking metagenomic classification tools for long-read sequencing data

In recent years, both long-read sequencing and metagenomic analysis have been significantly advanced. Although long-read sequencing technologies have been primarily used for de novo genome assembly,...

Detection of plasmid contigs in draft genome assemblies using customized Kraken databases

Plasmids play an important role in bacterial evolution and mediate horizontal transfer of genes including virulence and antimicrobial resistance genes. Although short-read sequencing technologies ha...

Assessment of viral targeted sequence capture using nanopore sequencing directly from clinical samples

Shotgun metagenomic sequencing (SMg) enables the simultaneous detection and characterization of viruses in human, animal and environmental samples. However, lack of sensitivity still poses a challen...

Application of respiratory metagenomics for COVID-19 patients on the intensive care unit to inform appropriate initial antimicrobial treatment and rapid detection of nosocomial transmission

Background Clinical metagenomics (CMg) is being evaluated for translation from a research tool into routine diagnostic service, but its potential to significantly improve management of acutely unwel...

Metagenomic next-generation sequencing of nasopharyngeal specimens collected from confirmed and suspect COVID-19 patients

Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuab...

Unearthing the boreal soil resistome associated with permafrost thaw

Understanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antib...

The wastewater microbiome: A novel insight for COVID-19 surveillance

Wastewater-Based Epidemiology is a tool to face and mitigate COVID-19 outbreaks by evaluating conditions in a specific community. This study aimed to analyze the microbiome profiles using nanopore ...

Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION

Plastic debris in the ocean form a new ecosystem, termed ‘plastisphere’, which hosts a variety of marine organisms. Recent studies implemented DNA metabarcoding to characterize the taxonomic composi...

Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens

Background Viruses are the most abundant biological entities on Earth, known to be crucial components of microbial ecosystems. However, there is little information on the viral community within agri...

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses

As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification in a fast and accurate manner are needed. Existing tools were eit...

Bac-PULCE: Bacterial Strain and AMR Profiling Using Long Reads via CRISPR Enrichment

Rapid identification of bacterial pathogens and their antimicrobial resistance (AMR) profiles is critical for minimising patient morbidity and mortality. While many sequencing methods allow deep gen...

Strand-wise and bait-assisted assembly of nearly-full rrn operons applied to assess species engraftment after faecal microbiota transplantation

Background Effective methodologies to accurately identify members of the gut microbiota at the species and strain levels are necessary to unveiling more specific and detailed host-microbe interacti...

Metagenomics Strain Resolution on Assembly Graphs

We introduce a novel bioinformatics pipeline, STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, when multiple metagenome samples from the same community are available....

Long-Read Metagenomics to Retrieve High-Quality Metagenome-Assembled Genomes from Canine Feces

Background Metagenomics is a powerful and rapidly developing approach that provides new biological insights into the microbes inhabiting underexplored environments, such as canine fecal microbiome....

nPhase: An accurate and contiguous phasing method for polyploids

While genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes, i.e. deducing haplotypes from genomic data, remains...

Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador.

SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. Th...

Using SPAdes de novo assembler

SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. ...

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characteriz...

Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function

Background Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic ...

NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline

Metagenomic sequencing combined with Oxford Nanopore Technology has the potential to become a point-of-care test for infectious disease in public health and clinical settings, providing rapid diagn...

Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa

To date, human gut microbiome research in adults has focused on western populations, with an additional minority of studies examining nonwestern populations including agriculturalist or hunter-gathe...

Interview: Nanopore sequencing: the missing puzzle piece in molecular identification

Ahmed Abd El Wahed is a scientist at the Institute of Animal Hygiene, University of Leipzig, and established a mobile suitcase laboratory for the rapid detection of viruses, bacteria and parasites...

Limited SARS-CoV-2 diversity within hosts and following passage in cell culture

Since the first reports of pneumonia associated with a novel coronavirus (COVID-19) emerged in Wuhan, Hubei province, China, there have been considerable efforts to sequence the causative virus, SAR...

Species-level evaluation of the human respiratory microbiome

Background Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of m...

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

COVID-19 is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China’s most populous province, during early 2020 ...

Blog: PuntSeq - Portable nanopore sequencing of freshwater metagenomes

In this blog, Lara Urban discusses the importance of freshwater microbial monitoring, and the founding of PuntSeq – a citizen science effort centred around using nanopore sequencing technology to ga...

Complete and validated genomes from a metagenome

The assembly and binning of metagenomically-assembled genomes (MAGs) using Illumina sequencing has improved the genomic characterization of unculturable communities. However, short-read-only metagen...

Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria

Bacteriophages (phages), or bacterial viruses, are very diverse and highly abundant worldwide, including as a part of the human microbiomes. Although a few metagenomic studies have focused on oral ...

Amplicon-based detection and sequencing of SARS-CoV-2 in nasopharyngeal swabs from patients with COVID-19 and identification of deletions in the viral genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, parti...

Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom

Background Human metapneumovirus (HMPV) infection causes a spectrum of respiratory tract disease, and may be a significant pathogen in the context of immunocompromise. Here, we report direct-from-sa...

DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing

Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods. Performing shotgun metagenomi...

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

There is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing tech...

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of vi...

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

Nanopore sequencing provides a great opportunity for direct detection of chemical DNA modification. However, existing computational methods were either trained for detecting a specific form of DNA m...

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms

Background Metagenomic sequencing is a well-established tool in the modern biosciences. While it promises unparalleled insights into the genetic content of the biological samples studied, conclusion...

Computational methods for 16S metabarcoding studies using Nanopore sequencing data

Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throu...

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements. Correct assignment of genomic...

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur ...

Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read s...

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

The rise of antimicrobial resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prev...

Performance of metagenomic next-generation sequencing for the diagnosis of viral meningoencephalitis in a resource limited setting

Background Meningoencephalitis is a devastating disease worldwide. Current diagnosis fails to establish the cause in ≥50% of patients. Metagenomic next-generation sequencing (mNGS) has emerged as pa...

Freshwater monitoring by nanopore sequencing

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a...

Rapid and real-time identification of fungi up to the species level with long amplicon nanopore sequencing from clinical samples

The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-2...

Profiling of human gut virome with Oxford Nanopore technology

The human gut virome plays critical roles in maintaining gut microbial composition and functionality, as well as host physiology and immunology. Yet, there are insufficient amount of studies on this...

The limits, capabilities, and potential for life detection with MinION sequencing in a paleochannel Mars analog

No instrument capable of direct life detection has been included on a mission payload to Mars since NASA's Viking missions in the 1970s. This prevents us from discovering whether life is or ever was...

Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health. Here we report the application of several complementary whole-genome sequencing (WGS) technologies to chara...

Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital

Background Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety. Objectives To investigate the genomic dynamics...

Metagenome dataset of wheat rhizosphere from Ghazipur region of Eastern Uttar Pradesh

Wheat is the major crop in India and like other crops also subjected to influence by microbial communities of the rhizospheric region which are extremely diverse and undoubtedly play a central role ...

Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing

Currently, the majority of non-culturable microbes in sea water are yet to be discovered. Nanopore sequencing offers a solution to overcome the challenge of identifying the genomes and complex compo...

Adding insult to injury: Effects of chronic oxybenzone exposure and elevated temperature on two reef-building corals

We studied the effect of chronic oxybenzone exposure and elevated temperature on coral health. Microcolonies of Stylophora pistillata and Acropora tenuis were cultured in 20 flow-through aquaria, of...

Long reads from Nanopore sequencing as a tool for animal microbiome studies

In the era of bioinformatics and metagenomics, the study of the ruminal microbiome has gained considerable relevance in the field of animal breeding, since the composition of the rumen microbiota si...

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system

Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure‐function relationships in complex environments. To compare the recovery of genomes...

Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing

Human papillomavirus (HPV) is a major pathogen that causes cervical cancer and many other related diseases. The HPV infection-related cervical microbiome could be an inducing factor of cervical canc...

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Asgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota. Members of this group...

Randomly primed, strand-switching MinION-based sequencing for the detection and characterization of cultured RNA viruses

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false negative detection results. Targeted detection methods have a limited ability...

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens

The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled t...

Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study

Background Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibilit...

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignmen...

Direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION – promising strategies for multiplex identification of viable pathogens in food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in...

Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens: A paradigm shift in mycological diagnostics

The advent of next generation sequencing technologies has enabled the characterization of the genetic content of entire communities of organisms, including those in clinical specimens, without prior...

Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

River confluences are a hub of biodiversity with limited information with respect to the structure and the functions of the microbial communities. The River Ganges is the national river of India, ha...

Evaluating the potential of direct RNA nanopore sequencing: Metatranscriptomics highlights possible seasonal differences in a marine pelagic crustacean zooplankton community

The implementation of cost-effective monitoring programs for zooplankton remains challenging due to the requirements of taxonomical expertise and the high costs of sampling and species identificatio...

Comprehensive analysis of horizontal gene transfer among multidrug-resistant bacterial pathogens in a single hospital

Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this thr...

Unlinked rRNA genes are widespread among bacteria and archaea

Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into...

Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids

Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes a...

Entirely off-grid and solar-powered DNA sequencing of microbial communities during an ice cap traverse expedition

Microbial communities in remote locations remain under-studied. This is particularly true on glaciers and icecaps, which cover approximately 11% of the Earth’s surface. The principal reason for this...

Rapid sequencing‐based diagnosis of infectious bacterial species from meningitis patients in Zambia

Objectives We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology‐based seq...

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares...

Complete microbial genomes for public health in Australia and Southwest Pacific

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strain...

Genetic biomonitoring and biodiversity assessment using portable sequencing technologies: current uses and future directions

We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatl...

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around th...

Optimizing DNA extraction methods for Nanopore sequencing of Neisseria gonorrhoeae direct from urine samples

Background Empirical gonorrhoea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnosti...

An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: a pilot study of head and neck cancer patients

Gut metagenome profiling using the Oxford Nanopore Technology (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was compa...

Genomics of aerobic photoheterotrophs in wheat phyllosphere reveals divergent evolutionary patterns of photosynthetic genes in Methylobacterium spp.

Phyllosphere is a habitat to a variety of viruses, bacteria, fungi, and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between ...

Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, length o...

Structural equation models to disentangle the biological relationship between microbiota and complex traits: methane production in dairy cattle as a case of study

The advent of metagenomics in animal breeding poses the challenge of statistically modelling the relationship between the microbiome, the host genetics and relevant complex traits. A set of structur...

DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the probl...

Strain-level identification of bacterial tomato pathogens directly from metagenomic sequences

Routine strain-level identification of plant pathogens directly from symptomatic tissue could significantly improve plant disease control and prevention. Here we tested the Oxford Nanopore Technolog...

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes

When bacterial symbionts become associated with their hosts, their genomes are thought to decay inexorably towards an organelle-like fate due to decreased recombination and inefficient selection. De...

Detection of atypical porcine Pestivirus genome in newborn piglets affected by congenital tremor and high pre-weaning mortality

Recently, piglets from a high-health status farm began exhibiting congenital tremors, high pre-weaning mortality and incidence of splayed legs. Postmortem histological examination identified a small...

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach that is adapted to the breakdown of plant-derived complex polysaccharides. The genomes of t...

Offline next generation metagenomics sequence analysis using MinION Detection Software (MINDS)

Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstre...

Assembly methods for nanopore-based metagenomic sequencing: a comparative study

Background Metagenomic sequencing has lead to the recovery of previously unexplored microbial genomes. In this sense, short-reads sequencing platforms often result in highly fragmented metagenomes, ...

kASA: Taxonomic Analysis of Metagenomic Data on a Notebook

The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available software tools for that purpose either consume large amounts of RAM or yie...

Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN

Metagenomics has become a part of the standard toolkit for scientists interested in studying microbes in the environment. Compared to 16S rDNA sequencing, which allows coarse taxonomic profiling of ...

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

Influenza is a major global public health threat as a result of its highly pathogenic variants, large zoonotic reservoir, and pandemic potential. Metagenomic viral sequencing offers the potential of...

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metag...

Metagenomic insights to understand transient influence of Yamuna River on taxonomic and functional aspects of bacterial and archaeal communities of River Ganges

River confluences are interesting ecosystems to investigate for their microbial community structure and functional potentials. River Ganges is one of the most important and holy rivers of India with...

Assembly-free single-molecule nanopore sequencing recovers complete virus genomes from natural microbial communities

Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, and horizontal gene transfer. Despite recent progress in viral metagenomics, the inherent ge...

Metagenomic profiling of microbial pathogens in the Little Bighorn River, Montana

Metagenomic sequencing and analysis were performed to identify potential microbial pathogens in the Little Bighorn River. Rapid, real-time sequencing was achieved using the portable MinION platform,...

Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

The complexity of microbial communities, combined with technical biases in next-generation sequencing, pose a challenge to metagenomic analysis. Here, we develop a set of internal DNA standards, ter...

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epi...

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

Background Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathoge...

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

Background Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best...

Improving recovery of member genomes from enrichment reactor microbial communities using MinION-based long read metagenomics

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes. While much progress has been made on cultured isolates, the ability of these methods to...

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies. We pre...

Genetic repertoires of anaerobic microbiomes driving generation of biogas

Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limi...

New tools for diet analyses: nanopore sequencing of metagenomic DNA from stomach contents to quantify diet in an invasive population of rats

Introduced species of mammals in New Zealand have had catastrophic effects on populations of diverse native species. Quantifying the diets of these omnivorous and predatory species is critical for u...

Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus

Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigat...

Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples

Background The recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both ...

Long-read metagenomics reveals cryptic and abundant marine viruses

Marine bacteriophages impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in cultur...

In Situ Field Sequencing and Life Detection in Remote (79°26′N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities

Significant progress is being made in the development of the next generation of low cost life detection instrumentation with much smaller size, mass and energy requirements. Here, we describe in sit...

Culture-independent analysis of liver abscess using nanopore sequencing

The identification of microbial species has depended predominantly upon culture-based techniques. However, the difficulty with which types of organisms are cultured implies that the grown species ma...

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

Background Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gol...

Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics

Background We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agent...

Metagenomic arbovirus detection using MinION nanopore sequencing

With its small size and low cost, the hand-held MinION sequencer is a powerful tool for in-field surveillance. Using a metagenomic approach, it allows non-targeted detection of viruses in a sample w...

A world of opportunities with nanopore sequencing

Oxford Nanopore Technologies' MinION sequencer was launched in pre-release form in 2014 and represents an exciting new sequencing paradigm. The device offers multi-kilobase reads and a streamed m...

Measuring Soil Health With Nanopore Sequencing

If a farmer wants to understand the health and fertility of their soil, they could send a sample to a lab for chemical analysis. This produces useful data, including levels of: 1) nitrogen, 2) phosp...

Deep Sequencing: Intra-Terrestrial Metagenomics Illustrates The Potential Of Off-Grid Nanopore DNA Sequencing

Genetic and genomic analysis of nucleic acids from environmental samples has helped transform our perception of the subsurface as a major reservoir of microbial novelty. Many of the microbial taxa l...

Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer

The ability to sequence DNA outside of the laboratory setting has enabled novel research questions to be addressed in the field in diverse areas, ranging from environmental microbiology to viral epi...

The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We ...

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

Objectives: The introduction of metagenomic sequencing to diagnostic microbiology has been hampered by slowness, cost and complexity. We explored whether MinION nanopore sequencing could accelerate ...

In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third Golden Age. However, conventional metagenomics st...

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-...

Mash: fast genome and metagenome distance estimation using MinHash

Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence co...

What’s in my pot? Real-time species identification on the MinION

Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted becaus...

Nanopore sequencing for metagenomic diagnosis of infectious diseases

Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer tu...

Oxford Nanopore MinION Applications: Kits and Tools, Genetics and Metagenomics

The Applications team at Oxford Nanopore has two overarching responsibilities: creation and development of sample and library preparation protocols for a wide variety of sample types, and undertakin...

Centrifuge: rapid and sensitive classification of metagenomic sequences

Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing sch...

Species level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

Background: The miniaturised and portable DNA sequencer MinION has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide ...

INC-Seq: Accurate single molecule reads using nanopore sequencing

Background Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relative...

Nanopore Sequencing in Microgravity

Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close m...

Complete nitrification by Nitrospira bacteria

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidising either ammonia or nitr...