genomecentric

Genomecentric, often written as genome-centric, describes an approach or perspective that treats the genome as the primary unit of analysis. In microbial ecology and metagenomics, a genome-centric or genome-resolved approach seeks to reconstruct, study, and compare individual genomes recovered from complex communities rather than analyzing genes or markers in isolation.

This approach typically relies on shotgun sequencing of environmental DNA, followed by assembly and binning to produce metagenome-assembled genomes (MAGs). MAGs are assessed for quality in terms of completeness and contamination, then dereplicated to remove redundancy and annotated to infer metabolic potential, ecological roles, and evolutionary relationships. The genome-centric view enables direct links between phylogeny, physiology, and ecology at the organism level, supporting investigations into population structure, biogeography, microbial interactions, and evolution, including horizontal gene transfer and pangenome dynamics.

Beyond metagenomics, a genome-centric emphasis appears in population and comparative genomics, where the focus is on whole-genome variation, synteny, and structural differences rather than single-gene analyses. The approach supports integration of multi-omics data by associating functional signals with specific genomes, facilitating holistic interpretations of community function and organismal diversity.

Limitations include incomplete or chimeric genome reconstructions, gaps from assembly challenges, and biases arising from uneven coverage or reference databases. The genome-centric paradigm is complementary to gene-centric methods and is often used alongside them to achieve a comprehensive view of microbial communities and genomic diversity in sequencing studies.