Journal article
Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?
Frontiers in microbiology, Vol.17, 1884628
2026
Abstract
Introduction
Metagenome-assembled genomes (MAGs) have transformed microbiology by enabling genome-resolved characterization of uncultivated organisms directly from complex environmental sequence data. From the early reconstruction of acid mine drainage communities to large-scale global genome catalogs, MAGs have expanded the bacterial and archaeal tree of life and enabled ecological and evolutionary investigations at the genomic scale (Tyson et al., 2004; Parks et al., 2017; Nayfach et al., 2021). As MAG-based analyses have become increasingly widespread, however, genome quality scores are gradually repurposed in ways that extended beyond their original intent. In practice, MAGs classified as highly complete are frequently treated as close approximations of biological genomes, even when assembly fragmentation, strain heterogeneity, uneven coverage, and selective sequence loss remain considerable.
The issue lies not with completeness metrics themselves, but with the biological meaning often attached to them. Estimated completeness is commonly interpreted as broadly reflecting genomic recovery, even though the regions most difficult to reconstruct are frequently those most relevant to ecological and evolutionary inference. Regions associated with accessory and adaptive functions, including ribosomal operons, plasmids, genomic islands, and biosynthetic gene clusters (BGCs), are disproportionately vulnerable to assembly collapse, coverage filtering, and binning exclusion (Sczyrba et al., 2017; Shaiber and Eren, 2019; Maguire et al., 2020; Meziti et al., 2021). Consequently, a MAG may retain the genomic features required to satisfy quality thresholds while simultaneously losing regions associated with horizontal gene transfer (HGT), ecological specialization, host interaction, or adaptive metabolism.
This distinction becomes increasingly important as genome-resolved metagenomics moves beyond taxonomic cataloging toward ecological, functional, and evolutionary inference. A completeness score may summarize expected recovery of conserved genomic features, but it does not directly measure how much of the biologically informative genome has been reconstructed. As a result, downstream interpretations can carry a level of confidence that exceeds the underlying genomic evidence.
In this article, marker-based completeness refers to the inferred recovery of expected conserved markers or model-predicted genomic features used for quality assessment. Structural completeness refers to the physical reconstruction of genome architecture, including chromosome continuity, contig fragmentation, operons, repeats, plasmids, and mobile regions. Biological completeness refers to the recovery of the genome fraction needed to support a given ecological, functional, or evolutionary inference. These dimensions are related, but they are not equivalent.
Details
- Title
- Rethinking metagenome-assembled genome completeness: are we truly recovering complete genomes?
- Authors/Creators
- Thierry Alexandre Pellegrinetti - Ministère de l'Agriculture, des Pêcheries et de l'AlimentationJoshua Molligan - Ministère de l'Agriculture, des Pêcheries et de l'AlimentationLucas William Mendes - Universidade de São PauloAlexandre Pedrinho - Murdoch UniversityEdel Pérez-López - Ministère de l'Agriculture, des Pêcheries et de l'Alimentation
- Publication Details
- Frontiers in microbiology, Vol.17, 1884628
- Identifiers
- 991005903581007891
- Copyright
- © 2026 Pellegrinetti, Molligan, Mendes, Pedrinho and Perez-Lopez.
- Murdoch Affiliation
- School of Environmental and Conservation Sciences
- Language
- English
- Resource Type
- Journal article
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