From cultures to communities: exploring microbes with Oxford Nanopore sequencing
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Join our webinar where we examine the diverse applications of Oxford Nanopore sequencing across the microbial research spectrum; from individual bacterial isolates to complex microbial communities. The speakers will showcase how real-time, long-read sequencing is transforming clinical microbiology, utilising automated workflows for rapid pathogen identification and surveillance. The session will also explore human microbiome studies, metagenome-assembled genomes (MAGs) as well as the cutting-edge bioinformatic tools and software for microbiome analysis.
Whether you're working with cultures in the lab or diverse communities in the gut, this session offers a comprehensive look at how Oxford Nanopore is advancing microbial genomics.
The webinar will be broadcast at 4:30 pm (BST) / 11:30 am (EDT) / 08:30 am (PDT).
Webinar agenda
Estimated webinar timings | Talk title | Speaker |
|---|---|---|
4:30 pm (BST) / 11:30 am (EDT) | Welcome and introduction | Anna Niewiadomska, Oxford Nanopore Technologies |
4:35 pm (BST) / 11:35 am (EDT) | Clinical use of WGS: Cost-effective in-house approach | Jose Alexander, AdventHealth Orlando |
4:50 pm (BST) / 11:50 am (EDT) | Oxford Nanopore sequencing enables strain-level metagenomics and reveals the structure and function of a mature compost microbiome | Christine He, Oxford Nanopore Technologies |
5:05 pm (BST) / 12:05 pm (EDT) | Discovering broader host ranges and an IS-bound prophage class through long-read metagenomics | Angela Hickey, Stanford University |
5:20 pm (BST) / 12:20 pm (EDT) | Minimizer-space ONT read error correction enables efficient construction of hundreds of high-quality metagenome assembled genomes from challenging and complex sample types | Robert James, Quadram Institute Bioscience |
5:35 pm (BST) / 2:35pm (EDT) | Live Q & A with our speakers |
Meet the speakers
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Anna Niewiadomska, Market Segment Manager - Public Health, Oxford Nanopore TechnologiesWith over 15 years in the field of microbiology, Anna Maria Niewiadomska combines a deep knowledge of experimental and in silico methods for the generation and analysis of genomic and bioinformatic data, with wide-ranging experience in scientific communication and outreach.
Dr Niewiadomska has worked on multiple projects focusing on innate immunology, host/virus interactions, viral phylogenetics, mathematical modeling of antimicrobial resistance, and emerging infectious disease outbreaks. More recently, she has worked on pandemic response to multiple viral outbreaks such as SARS-CoV-2 and Mpox virus and collaborated with the SAVE and SPHERES consortia to identify emerging SARS-CoV-2 viral variants of concern.
In-house Whole-Genome Sequencing (WGS) has been proven to significantly reduce costs and improve operational efficiency compared to reference laboratory services for bacterial and mycobacterial identification. At AdventHealth Orlando, a 12-month cost analysis was conducted following the implementation of an in-house WGS protocol designed to replace send-out services for organism identification.
Long-read sequencing was selected for its simplicity, customization, and minimal instrumentation needs. WGS provides broader genomic coverage. The workflow employed the ZymoBIOMICS MagBead 96 DNA Kit (Zymo Research) for DNA extraction, followed by library preparation using the Rapid Ligation Kit, and sequencing on the Flongle flow-cell and MK1C sequencer (Oxford Nanopore). The in-house protocol, colony-to-result, enables multiplexing of six isolates per flow-cell. Samples were sequenced on Tuesdays and Thursdays. The standardized protocol ensures scalability and adaptability, accounting reagents, instruments, and labor costs.
From October-2022 to September-2023, 93 bacterial and 667 mycobacterial isolates were sent to reference laboratories, costing $364 and $369 per isolate, respectively, including shipping. Post-implementation (October-2023 to September-2024), 78 bacterial and 705 mycobacterial isolates were processed in-house at $63 per isolate, saving $230,646. Return on investment was achieved within one month. Turnaround time improved from an average of 9 days to 48 hours.
Following these results, we transitioned to the GridION sequencer (Oxford Nanopore) while maintaining the same workflow and enabling expanded capabilities. Additionally, clinically significant mold identification, has been implemented using a similar protocol. This study highlights the cost-effectiveness, scalability, and operational improvements of in-house WGS, offering a model for other clinical laboratories seeking efficiency and broader identification capabilities.
In-house Whole-Genome Sequencing (WGS) has been proven to significantly reduce costs and improve operational efficiency compared to reference laboratory services for bacterial and mycobacterial identification. At AdventHealth Orlando, a 12-month cost analysis was conducted following the implementation of an in-house WGS protocol designed to replace send-out services for organism identification.
Long-read sequencing was selected for its simplicity, customization, and minimal instrumentation needs. WGS provides broader genomic coverage. The workflow employed the ZymoBIOMICS MagBead 96 DNA Kit (Zymo Research) for DNA extraction, followed by library preparation using the Rapid Ligation Kit, and sequencing on the Flongle flow-cell and MK1C sequencer (Oxford Nanopore). The in-house protocol, colony-to-result, enables multiplexing of six isolates per flow-cell. Samples were sequenced on Tuesdays and Thursdays. The standardized protocol ensures scalability and adaptability, accounting reagents, instruments, and labor costs.
From October-2022 to September-2023, 93 bacterial and 667 mycobacterial isolates were sent to reference laboratories, costing $364 and $369 per isolate, respectively, including shipping. Post-implementation (October-2023 to September-2024), 78 bacterial and 705 mycobacterial isolates were processed in-house at $63 per isolate, saving $230,646. Return on investment was achieved within one month. Turnaround time improved from an average of 9 days to 48 hours.
Following these results, we transitioned to the GridION sequencer (Oxford Nanopore) while maintaining the same workflow and enabling expanded capabilities. Additionally, clinically significant mold identification, has been implemented using a similar protocol. This study highlights the cost-effectiveness, scalability, and operational improvements of in-house WGS, offering a model for other clinical laboratories seeking efficiency and broader identification capabilities.
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Jose Alexander, Director - Clinical Microbiologist, AdventHealth Orlando)
Christine He, Genomic Applications Bioinformatician, Oxford Nanopore TechnologiesChristine has extensive work experience in the field of bioinformatics and genomics. Christine is currently working as a Bioinformatics Scientist (Genomic Applications) at Oxford Nanopore Technologies since September 2022. Prior to this, she worked at Invitae as a Bioinformatics Scientist (Metagenomics) from February 2021 to September 2022. Before transitioning into industry, Christine was a Postdoctoral Fellow at the University of California, Berkeley from April 2017 to December 2020. Christine conducted her PhD research as a student at the Georgia Institute of Technology from August 2011 to April 2017, focusing on prebiotic chemistry and the RNA World hypothesis. She completed her Bachelor of Science (B.S.) degree in Chemical & Biomolecular Engineering from the University of Maryland between 2007 and 2011.
Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ~5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name “IScream phages”. These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.
Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ~5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name “IScream phages”. These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.
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Angela Hickey, Graduate Student, Stanford UniversityWe present nanoMDBG, an evolution of the metaMDBG HiFi assembler, designed to support kit 14, R10 ONT sequencing data through scalability and a novel pre-processing step that performs fast and accurate error correction in minimizer-space. NanoMDBG reconstructs more high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. This paradigm holds true across a range of large metagenomic ONT datasets, including a ~650 Gbp soil sample and ~250 gbp human faecal sample sequenced specifically for this study. As a result of these advances, we show that the latest ONT technology, combined with adequate long-read metagenomic library preparation, can now produce results comparable to those obtained using PacBio HiFi sequencing at equivalent sequencing depths.
We present nanoMDBG, an evolution of the metaMDBG HiFi assembler, designed to support kit 14, R10 ONT sequencing data through scalability and a novel pre-processing step that performs fast and accurate error correction in minimizer-space. NanoMDBG reconstructs more high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. This paradigm holds true across a range of large metagenomic ONT datasets, including a ~650 Gbp soil sample and ~250 gbp human faecal sample sequenced specifically for this study. As a result of these advances, we show that the latest ONT technology, combined with adequate long-read metagenomic library preparation, can now produce results comparable to those obtained using PacBio HiFi sequencing at equivalent sequencing depths.
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Robert James, Research Scientist, Quadram Institute Bioscience
