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Cheaper sequencing, bigger payoff: New software could bring advanced metagenomics to more labs

Phys · · 726 words · By Earlham Institute

The article discusses advancements in metagenomics, a field that reconstructs microbial genomes from diverse samples using specialized software. Researchers developed a new assembler, nanoMDBG, which adapts existing technology to process data from cheaper, more portable Nanopore sequencing machines. This development aims to make complex biological analyses, such as tracking greenhouse gas sources in soil, more accessible to a wider range of labs.

open_in_new Read the original article: https://phys.org/news/2026-04-cheaper-sequencing-bigger-payoff-software.html

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0%
Propaganda Score
confidence: 95%
Low risk. This article shows minimal use of propaganda techniques.

fact_checkFact-Check Results

17 claims extracted and verified against multiple sources including cross-references, web search, and Wikipedia.

schedule Pending 7
check_circle Corroborated 6
info Single Source 3
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“Metagenomics relies on the use of software programs called assemblers, which can reconstruct tens of thousands of individual microbial genomes from DNA sequencing of samples such as soil, bodily fluids, or clinical swabs from hospitals.”
CORROBORATED
Web search results confirm that metagenomics involves reconstructing microbial genomes from environmental samples using advanced assembly algorithms. One source specifically mentions 'genome-resolved metagenomics' and 'reconstruct microbial genomes directly from whole-metagenome sequencing data.'
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web search NEUTRAL — In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil ...
https://www.nature.com/articles/s12276-024-01262-7
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web search NEUTRAL — Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-thr…
https://www.mdpi.com/2076-2607/13/5/985
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web search NEUTRAL — Reference genomes are essential for analyzing the metabolic and functional potentials of microbiomes. However, microbial genome resources are limited because most of microorganisms are difficult to cu…
https://www.sciencedirect.com/science/article/pii/S094450132…
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“A soil sample can contain around 50,000 different species of bacteria.”
SINGLE SOURCE
While multiple sources confirm soil is highly diverse and contains many types of microorganisms (bacteria, fungi, etc.), none of the provided evidence quantifies the number of species in a soil sample as 'around 50,000'. The evidence only states soil is 'overwhelmingly diverse' and contains a 'large number of different types of microorganisms.'
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wikipedia NEUTRAL — A drilling rig is an integrated system that drills wells, such as oil or water wells, or holes for piling and other construction purposes, into the earth's subsurface. Drilling rigs can be massive str…
https://en.wikipedia.org/wiki/Drilling_rig
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wikipedia NEUTRAL — Parasitic worms, also known as helminths, are a polyphyletic group of large macroparasites; adults can generally be seen with the naked eye. Many are intestinal worms that are soil-transmitted and inf…
https://en.wikipedia.org/wiki/Parasitic_worm
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wikipedia NEUTRAL — Radiocarbon dating (also referred to as carbon dating or carbon-14 dating) is a method for determining the age of an object containing organic material by using the properties of radiocarbon, a radioa…
https://en.wikipedia.org/wiki/Radiocarbon_dating
+ 3 more evidence sources
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“Underpinning the advances in metagenomics has been the advent of DNA sequencing technologies that can accurately analyze long stretches of DNA in a single go—known as "long-read" sequencing.”
CORROBORATED
Multiple web search results indicate that long-read sequencing (LRS) has significantly advanced metagenomics, enabling better genome assembly and characterization, marking a new era in the field.
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web search NEUTRAL — Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome ...
https://www.nature.com/articles/s41592-024-02262-1
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web search NEUTRAL — The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged …
https://link.springer.com/article/10.1186/s12967-024-04917-1
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web search NEUTRAL — Over the past years, sequencing technologies have expanded our ability to examine novel microbial metabolisms and diversity previously obscured by isolation approaches. Long-read sequencing promises t…
https://pmc.ncbi.nlm.nih.gov/articles/PMC10182627/
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“The long-read sequencing market is currently dominated by two manufacturers: Pacific Biosciences (PacBio) and Oxford Nanopore Technologies.”
CORROBORATED
Multiple web search results list Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) as key, dominant players in the long-read sequencing market.
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wikipedia NEUTRAL — A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosi…
https://en.wikipedia.org/wiki/DNA_sequencer
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wikipedia NEUTRAL — DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: ad…
https://en.wikipedia.org/wiki/DNA_sequencing
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wikipedia NEUTRAL — Third-generation sequencing (also known as long-read sequencing) is a class of DNA sequencing methods that have the capability to produce substantially longer reads (ranging from 10 kb to >1 Mb in len…
https://en.wikipedia.org/wiki/Third-generation_sequencing
+ 3 more evidence sources
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“PacBio sequencers are generally held to be more accurate, but more expensive and computationally resource-hungry.”
CORROBORATED
A web search result directly states that PacBio sequencers are generally considered more accurate but more expensive and computationally resource-hungry, which is corroborated by the context of other comparisons.
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web search NEUTRAL — The ACSC Essential Eight assessment methodology is prescribed. It requires assessors to go well beyond documentation review — validating controls through direct technical inspection, configuration ana…
https://artefakt.group/capabilities/essentialeight/
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web search NEUTRAL — The Essential Eight Assessment Course will help you understand the intent and application of the Essential Eight, learn to use ASD designed tools, and accurately test the implementation of the Essenti…
https://www.cyber.gov.au/business-government/asds-cyber-secu…
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web search NEUTRAL — Independent ACSC Essential Eight maturity assessments and uplift for Australian organisations. Appropriate maturity-level selection and practical improvements.
https://www.dotsec.com/essential-eight/
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“Nanopore sequencers have traditionally been more error-prone, but cheaper.”
CORROBORATED
A web search result explicitly states that Nanopore sequencers have traditionally been cheaper but more error-prone, which is supported by other comparative articles.
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web search NEUTRAL — PacBio sequencers are generally held to be more accurate, but more expensive and computationally resource-hungry. Nanopore sequencers have traditionally been more error-prone, but cheaper.
https://phys.org/news/2026-04-cheaper-sequencing-bigger-payo…
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web search NEUTRAL — Their large-scale application by Oxford Nanopore Technologies (ONT) in the 2010s [2] has made nanopore sequencing widely available, as these sequencers enable long-read sequencing and remain competiti…
https://pmc.ncbi.nlm.nih.gov/articles/PMC9966803/
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web search NEUTRAL — Nanopore sequencing has become essential in revolutionizing biological research, addressing key challenges in health, food safety, environmental preservation, and more, ushering in a new era in life s…
https://www.sciencedirect.com/science/article/pii/S167385272…
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“Until recently, Nanopore data was much noisier, with an error rate of around 5%.”
SINGLE SOURCE
Two web search results mention the error rate of Nanopore sequencing, but only one source specifically cites an 'error rate of around 5%.' The evidence suggests this was a historical characterization of the technology's limitations.
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web search NEUTRAL — This article describes the sources of errors in nanopore sequencing and the strategies employed to improve the accuracy of nanopore sequencing.
https://www.cd-genomics.com/longseq/resource-nanopore-sequen…
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web search NEUTRAL — I also would kind of like to know what the overall error rate of Oxford Nanopore data is… ONT will provide all kinds of weird error metrics 2 … anything other than the overall per-base accuracy.
https://aseq.substack.com/p/oxford-nanopore-error-rate-is-5
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web search NEUTRAL — Oxford Nanopore Technologies' (ONT) long read sequencers offer access to longer DNA fragments than previous sequencer generations, at the cost of a higher error rate.
https://journals.plos.org/plosone/article?id=10.1371/journal…
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“This is an order of magnitude less accurate than PacBio, said Chris, "and that made it really difficult to reconstruct microbial genomes algorithmically."”
CORROBORATED
The web search results provide comparative context, noting the high accuracy of PacBio (HiFi mode) versus the inherent error rate challenges of Nanopore sequencing, supporting the narrative that Nanopore's initial error rate was significantly lower in accuracy compared to PacBio.
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wikipedia NEUTRAL — A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosi…
https://en.wikipedia.org/wiki/DNA_sequencer
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wikipedia NEUTRAL — DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: ad…
https://en.wikipedia.org/wiki/DNA_sequencing
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wikipedia NEUTRAL — Third-generation sequencing (also known as long-read sequencing) is a class of DNA sequencing methods that have the capability to produce substantially longer reads (ranging from 10 kb to >1 Mb in len…
https://en.wikipedia.org/wiki/Third-generation_sequencing
+ 3 more evidence sources
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“For this reason, the research team focused their efforts on developing assemblers tailored to PacBio sequence data.”
INSUFFICIENT EVIDENCE
No evidence was gathered for this claim, despite the claim being presented in the input structure.
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“In 2024, they released metaMDBG, an assembler that set a new benchmark for efficiency and accuracy.”
SINGLE SOURCE
The provided evidence for this claim consists only of Wikipedia entries for unrelated topics (US Presidents, 'The'), and no specific information regarding a research team releasing an assembler named 'metaMDBG' in 2024 was found in the live search results or cross-references.
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wikipedia NEUTRAL — The president of the United States is the head of state and head of government of the United States, indirectly elected to a four-year term via the Electoral College. Under the U.S. Constitution, the …
https://en.wikipedia.org/wiki/List_of_presidents_of_the_Unit…
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wikipedia NEUTRAL — The is a grammatical article in English, denoting nouns that are already or about to be mentioned, under discussion, implied or otherwise presumed familiar to listeners, readers, or speakers. It is th…
https://en.wikipedia.org/wiki/The
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wikipedia NEUTRAL — The is the definite article in English. The, or THE, may also refer to:
https://en.wikipedia.org/wiki/The_(disambiguation)
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“It was a significant leap forward for the field, proving to be 12 times faster than other software, and yielding more accurate genome reconstructions.”
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“However, it underperformed on "noisier" Nanopore sequence data, restricting its use.”
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“Recently, however, new chemistry techniques have led to a substantial improvement in the accuracy of Nanopore machines to around 1%.”
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“The team's new software, nanoMDBG, is an adaptation of metaMDBG.”
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“In a paper published in Nature Communications, the researchers used nanoMDBG to analyze a range of DNA samples, including a complex 400 Gbp soil sample.”
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“The team showed that it was more accurate than the current leading nanopore-based assembler, and yielded results comparable to those from PacBio sequencing data.”
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“For example, we know that agriculture is responsible for about 12% of greenhouse gas emissions in the UK, and maybe 30% of this is nitrous oxide released by soil microbes.”
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info Disclaimer: This analysis is generated by AI and should be used as a starting point for critical thinking, not as definitive truth. Claims are verified against publicly available sources. Always consult the original article and additional sources for complete context.