Frontiers in Microbiology (Nov 2023)
A toolbox of machine learning software to support microbiome analysis
- Laura Judith Marcos-Zambrano,
- Víctor Manuel López-Molina,
- Burcu Bakir-Gungor,
- Marcus Frohme,
- Kanita Karaduzovic-Hadziabdic,
- Thomas Klammsteiner,
- Eliana Ibrahimi,
- Leo Lahti,
- Tatjana Loncar-Turukalo,
- Xhilda Dhamo,
- Andrea Simeon,
- Alina Nechyporenko,
- Alina Nechyporenko,
- Gianvito Pio,
- Gianvito Pio,
- Piotr Przymus,
- Alexia Sampri,
- Vladimir Trajkovik,
- Blanca Lacruz-Pleguezuelos,
- Oliver Aasmets,
- Oliver Aasmets,
- Ricardo Araujo,
- Ioannis Anagnostopoulos,
- Ioannis Anagnostopoulos,
- Önder Aydemir,
- Magali Berland,
- M. Luz Calle,
- M. Luz Calle,
- Michelangelo Ceci,
- Michelangelo Ceci,
- Hatice Duman,
- Aycan Gündoğdu,
- Aycan Gündoğdu,
- Aki S. Havulinna,
- Aki S. Havulinna,
- Kardokh Hama Najib Kaka Bra,
- Eglantina Kalluci,
- Sercan Karav,
- Daniel Lode,
- Marta B. Lopes,
- Marta B. Lopes,
- Patrick May,
- Bram Nap,
- Miroslava Nedyalkova,
- Inês Paciência,
- Inês Paciência,
- Lejla Pasic,
- Meritxell Pujolassos,
- Rajesh Shigdel,
- Antonio Susín,
- Ines Thiele,
- Ines Thiele,
- Ciprian-Octavian Truică,
- Paul Wilmes,
- Paul Wilmes,
- Ercument Yilmaz,
- Malik Yousef,
- Malik Yousef,
- Marcus Joakim Claesson,
- Marcus Joakim Claesson,
- Jaak Truu,
- Enrique Carrillo de Santa Pau
Affiliations
- Laura Judith Marcos-Zambrano
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
- Víctor Manuel López-Molina
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
- Burcu Bakir-Gungor
- Department of Computer Engineering, Abdullah Gül University, Kayseri, Türkiye
- Marcus Frohme
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
- Kanita Karaduzovic-Hadziabdic
- Faculty of Engineering and Natural Sciences, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
- Thomas Klammsteiner
- Department of Microbiology and Department of Ecology, University of Innsbruck, Innsbruck, Austria
- Eliana Ibrahimi
- Department of Biology, University of Tirana, Tirana, Albania
- Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
- Tatjana Loncar-Turukalo
- Faculty of Technical Sciences, University of Novi Sad, Novi Sad, Serbia
- Xhilda Dhamo
- Department of Applied Mathematics, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
- Andrea Simeon
- 0BioSense Institute, University of Novi Sad, Novi Sad, Serbia
- Alina Nechyporenko
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
- Alina Nechyporenko
- 1Department of Systems Engineering, Kharkiv National University of Radioelectronics, Kharkiv, Ukraine
- Gianvito Pio
- 2Department of Computer Science, University of Bari Aldo Moro, Bari, Italy
- Gianvito Pio
- 3Big Data Lab, National Interuniversity Consortium for Informatics, Rome, Italy
- Piotr Przymus
- 4Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruń, Poland
- Alexia Sampri
- 5Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, United Kingdom
- Vladimir Trajkovik
- 6Faculty of Computer Science and Engineering, Ss. Cyril and Methodius University, Skopje, North Macedonia
- Blanca Lacruz-Pleguezuelos
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
- Oliver Aasmets
- 7Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
- Oliver Aasmets
- 8Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Ricardo Araujo
- 9Nephrology and Infectious Diseases R & D Group, i3S—Instituto de Investigação e Inovação em Saúde; INEB—Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- Ioannis Anagnostopoulos
- 0Department of Informatics, University of Piraeus, Piraeus, Greece
- Ioannis Anagnostopoulos
- 1Computer Science and Biomedical Informatics Department, University of Thessaly, Lamia, Greece
- Önder Aydemir
- 2Department of Electrical and Electronics Engineering, Karadeniz Technical University, Trabzon, Türkiye
- Magali Berland
- 3INRAE, MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas, France
- M. Luz Calle
- 4Faculty of Sciences, Technology and Engineering, University of Vic – Central University of Catalonia, Vic, Barcelona, Spain
- M. Luz Calle
- 5IRIS-CC, Fundació Institut de Recerca i Innovació en Ciències de la Vida i la Salut a la Catalunya Central, Vic, Barcelona, Spain
- Michelangelo Ceci
- 2Department of Computer Science, University of Bari Aldo Moro, Bari, Italy
- Michelangelo Ceci
- 3Big Data Lab, National Interuniversity Consortium for Informatics, Rome, Italy
- Hatice Duman
- 6Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale, Türkiye
- Aycan Gündoğdu
- 7Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri, Türkiye
- Aycan Gündoğdu
- 8Metagenomics Laboratory, Genome and Stem Cell Center (GenKök), Erciyes University, Kayseri, Türkiye
- Aki S. Havulinna
- 9Finnish Institute for Health and Welfare - THL, Helsinki, Finland
- Aki S. Havulinna
- 0Institute for Molecular Medicine Finland, FIMM-HiLIFE, Helsinki, Finland
- Kardokh Hama Najib Kaka Bra
- 1Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Eglantina Kalluci
- Department of Applied Mathematics, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
- Sercan Karav
- 2Department of Molecular Biology and Genetics, Çanakkale Onsekiz Mart University, Çanakkale, Türkiye
- Daniel Lode
- Division Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
- Marta B. Lopes
- 3Department of Mathematics, Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Marta B. Lopes
- 4UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
- Patrick May
- 5Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Bram Nap
- 6School of Medicine, University of Galway, Galway, Ireland
- Miroslava Nedyalkova
- 7Department of Inorganic Chemistry, Faculty of Chemistry and Pharmacy, University of Sofia, Sofia, Bulgaria
- Inês Paciência
- 8Center for Environmental and Respiratory Health Research (CERH), Research Unit of Population Health, University of Oulu, Oulu, Finland
- Inês Paciência
- 9Biocenter Oulu, University of Oulu, Oulu, Finland
- Lejla Pasic
- 0Sarajevo Medical School, University Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
- Meritxell Pujolassos
- 4Faculty of Sciences, Technology and Engineering, University of Vic – Central University of Catalonia, Vic, Barcelona, Spain
- Rajesh Shigdel
- 1Department of Clinical Science, University of Bergen, Bergen, Norway
- Antonio Susín
- 2Mathematical Department, UPC-Barcelona Tech, Barcelona, Spain
- Ines Thiele
- 6School of Medicine, University of Galway, Galway, Ireland
- Ines Thiele
- 3APC Microbiome Ireland, University College Cork, Cork, Ireland
- Ciprian-Octavian Truică
- 4Computer Science and Engineering Department, Faculty of Automatic Control and Computers, National University of Science and Technology Politehnica, Bucharest, Romania
- Paul Wilmes
- 5Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, Esch-sur-Alzette, Luxembourg
- Paul Wilmes
- 6Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Belvaux, Luxembourg
- Ercument Yilmaz
- 7Department of Computer Technologies, Karadeniz Technical University, Trabzon, Türkiye
- Malik Yousef
- 8Department of Information Systems, Zefat Academic College, Zefat, Israel
- Malik Yousef
- 9Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel
- Marcus Joakim Claesson
- 3APC Microbiome Ireland, University College Cork, Cork, Ireland
- Marcus Joakim Claesson
- 0School of Microbiology, University College Cork, Cork, Ireland
- Jaak Truu
- 1Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Enrique Carrillo de Santa Pau
- Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
- DOI
- https://doi.org/10.3389/fmicb.2023.1250806
- Journal volume & issue
-
Vol. 14
Abstract
The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.
Keywords