Innovating Works

Metagenome binning

Financiado
Accurate reconstruction of microbial genomes from the environment
Metagenome-assembled genomes (MAGs) obtained from metagenomics are of fundamental value to understanding diverse ecological niches of microbes such as the human gut, with applications in medicine, biotechnology, and climate scienc... Metagenome-assembled genomes (MAGs) obtained from metagenomics are of fundamental value to understanding diverse ecological niches of microbes such as the human gut, with applications in medicine, biotechnology, and climate science. However, the quality of MAGs constructed with state-of-the-art tools is often unsatisfactory and worse than the self-reported quality. The main source of error is binning, a computational step that groups sequences assembled from short sequencing reads (contigs) into species-wise bins. The two chief challenges are accurately binning (1) genomes with low abundance and (2) highly conserved regions. Due to cross-mapping of reads, the contigs from conserved regions appear to have abundances equal to the sum of the abundances of the related species or strains. As conventional binning tools all rely on clustering contigs according to their abundances across samples, conserved regions end up forming separate bins. Besides, most existing methods optimise quality measures (purity and completeness based on conserved marker genes) and assess the final quality on these very measures, leading to highly optimistic results. I aim to solve these problems by developing a binning algorithm that applies i) linear mixture models using non-negative matrix factorization to account for cross-mapping, ii) Poisson statistics to accurately model low abundance, and iii) Bayesian statistics-based multinomial clustering to calculate bin numbers. Importantly, it does not require marker gene-based quality measures for binning. By improving the binning of low-abundance and highly conserved contigs, this approach should yield more high-quality MAGs, thereby enhancing a multitude of downstream metagenomic analyses for all areas of microbiome research. ver más
31/07/2025
MPG
190K€
Duración del proyecto: 25 meses Fecha Inicio: 2023-06-19
Fecha Fin: 2025-07-31

Línea de financiación: concedida

El organismo HORIZON EUROPE notifico la concesión del proyecto el día 2023-06-19
Línea de financiación objetivo El proyecto se financió a través de la siguiente ayuda:
Presupuesto El presupuesto total del proyecto asciende a 190K€
Líder del proyecto
MAXPLANCKGESELLSCHAFT ZUR FORDERUNG DER WISSE... No se ha especificado una descripción o un objeto social para esta compañía.
Perfil tecnológico TRL 4-5