TY - JOUR

T1 - MetaFX: Feature extraction from whole-genome metagenomic sequencing data

AU - Ivanov, A.

AU - Popov, V.

AU - Morozov, M.

AU - Olekhnovich, E.

AU - Ulyantsev, V.

N1 - Export Date: 29 March 2026; Cited By: 0; Correspondence Address: A. Ivanov; Information Technology and Programming Department, ITMO University, St. Petersburg, Kronverksky Pr. 49, 197101, Russian Federation; email: abivanov@itmo.ru; CODEN: BOINF

PY - 2026/2/3

Y1 - 2026/2/3

N2 - Motivation Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers. Results Here we present MetaFX - an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average. Availability and implementation MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369. © 2026 The Author(s). Published by Oxford University Press.

AB - Motivation Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers. Results Here we present MetaFX - an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9±10% on average. Availability and implementation MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369. © 2026 The Author(s). Published by Oxford University Press.

KW - Databases, Genetic

KW - Gastrointestinal Microbiome

KW - Humans

KW - Inflammatory Bowel Diseases

KW - Machine Learning

KW - Metagenome

KW - Metagenomics

KW - Software

KW - Whole Genome Sequencing

KW - genetic database

KW - genetics

KW - human

KW - inflammatory bowel disease

KW - intestine flora

KW - machine learning

KW - metagenome

KW - metagenomics

KW - microbiology

KW - procedures

KW - software

KW - whole genome sequencing

KW - Gastrointestinal Microbiome/genetics

KW - Whole Genome Sequencing/methods

KW - Inflammatory Bowel Diseases/microbiology

KW - Metagenomics/methods

UR - https://www.mendeley.com/catalogue/a092e068-0f94-33c1-b1ea-f82265c64f92/

U2 - 10.1093/bioinformatics/btag018

DO - 10.1093/bioinformatics/btag018

M3 - Article

C2 - 41557465

VL - 42

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 2

ER -