Taxonomy bias in metagenome-assembled genome recovery.

Daniel J Nebauer, Tiffanie Nelson, Caitlin Romanis, Brett A Neilan, Verlaine J Timms

Abstract read

In one paragraph

Article in Microbial genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Daniel J NebauerSchool of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.

Tiffanie NelsonSchool of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.

Caitlin RomanisSchool of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.

Brett A NeilanSchool of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.

Verlaine J TimmsSchool of Environmental and Life Sciences, The University of Newcastle, Callaghan, New South Wales, Australia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing is rapidly expanding the availability of representative genomes. However, this practice may skew the representation of specific taxa in real-world datasets. This bias is attributed primarily to the known inefficiencies of sequence-by-synthesis platforms in amplifying GC-rich and AT-rich sequence fragments. Here, we recover 216 medium- and high-quality MAGs from an Australian wetland site. Notably, no MAGs were recovered for some dominant cyanobacterial and proteobacterial species known to be present. A new protocol involving read-based classification and alignment to the MAG dataset demonstrated the highly efficient recovery of low-GC organisms in the

Indexed as

BacteriaMetagenomeMetagenomicsBase CompositionGenome, BacterialPhylogenySequence Analysis, DNAShotgun SequencingGC biasmetagenome-assembled genomes (MAGs)microbial diversityshotgun metagenomicstaxonomic bias

Identifiers

PMID42257696

DOI10.1099/mgen.0.001736

PMCPMC13245658

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.