Frontiers in Microbiology (Feb 2021)
Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions
- Isabel Moreno-Indias,
- Isabel Moreno-Indias,
- Leo Lahti,
- Miroslava Nedyalkova,
- Ilze Elbere,
- Gennady Roshchupkin,
- Muhamed Adilovic,
- Onder Aydemir,
- Burcu Bakir-Gungor,
- Enrique Carrillo-de Santa Pau,
- Domenica D’Elia,
- Mahesh S. Desai,
- Mahesh S. Desai,
- Laurent Falquet,
- Laurent Falquet,
- Aycan Gundogdu,
- Aycan Gundogdu,
- Karel Hron,
- Thomas Klammsteiner,
- Marta B. Lopes,
- Marta B. Lopes,
- Laura Judith Marcos-Zambrano,
- Cláudia Marques,
- Michael Mason,
- Patrick May,
- Lejla Pašić,
- Gianvito Pio,
- Sándor Pongor,
- Vasilis J. Promponas,
- Piotr Przymus,
- Julio Saez-Rodriguez,
- Alexia Sampri,
- Rajesh Shigdel,
- Blaz Stres,
- Blaz Stres,
- Blaz Stres,
- Ramona Suharoschi,
- Jaak Truu,
- Ciprian-Octavian Truică,
- Baiba Vilne,
- Dimitrios Vlachakis,
- Ercument Yilmaz,
- Georg Zeller,
- Aldert L. Zomer,
- David Gómez-Cabrero,
- Marcus J. Claesson
Affiliations
- Isabel Moreno-Indias
- Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clìnica de Endocrinologìa y Nutrición, Hospital Clìnico Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
- Isabel Moreno-Indias
- Centro de Investigación Biomeìdica en Red de Fisiopatologtìa de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
- Miroslava Nedyalkova
- Human Genetics and Disease Mechanisms, Latvian Biomedical Research and Study Centre, Riga, Latvia
- Ilze Elbere
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Gennady Roshchupkin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
- Muhamed Adilovic
- Department of Genetics and Bioengineering, International University of Sarajevo, Sarajevo, Bosnia and Herzegovina
- Onder Aydemir
- Department of Electrical and Electronics Engineering, Karadeniz Technical University, Trabzon, Turkey
- Burcu Bakir-Gungor
- Department of Computer Engineering, Abdullah Gul University, Kayseri, Turkey
- Enrique Carrillo-de Santa Pau
- 0Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
- Domenica D’Elia
- 1Department for Biomedical Sciences, Institute for Biomedical Technologies, National Research Council, Bari, Italy
- Mahesh S. Desai
- 2Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Mahesh S. Desai
- 3Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
- Laurent Falquet
- 4Department of Biology, University of Fribourg, Fribourg, Switzerland
- Laurent Falquet
- 5Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Aycan Gundogdu
- 6Department of Microbiology and Clinical Microbiology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
- Aycan Gundogdu
- 7Metagenomics Laboratory, Genome and Stem Cell Center (GenKök), Erciyes University, Kayseri, Turkey
- Karel Hron
- 8Department of Mathematical Analysis and Applications of Mathematics, Palacký University, Olomouc, Czechia
- Thomas Klammsteiner
- 9Department of Microbiology, University of Innsbruck, Innsbruck, Austria
- Marta B. Lopes
- 0NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), FCT, UNL, Caparica, Portugal
- Marta B. Lopes
- 1Centro de Matemática e Aplicações (CMA), FCT, UNL, Caparica, Portugal
- Laura Judith Marcos-Zambrano
- 0Computational Biology Group, Precision Nutrition and Cancer Research Program, IMDEA Food Institute, Madrid, Spain
- Cláudia Marques
- 2CINTESIS, NOVA Medical School, NMS, Universidade Nova de Lisboa, Lisbon, Portugal
- Michael Mason
- 3Computational Oncology, Sage Bionetworks, Seattle, WA, United States
- Patrick May
- 4Bioinformatics Core, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Lejla Pašić
- 5Sarajevo Medical School, University Sarajevo School of Science and Technology, Sarajevo, Bosnia and Herzegovina
- Gianvito Pio
- 6Department of Computer Science, University of Bari Aldo Moro, Bari, Italy
- Sándor Pongor
- 7Faculty of Information Tehnology and Bionics, Pázmány University, Budapest, Hungary
- Vasilis J. Promponas
- 8Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- Piotr Przymus
- 9Faculty of Mathematics and Computer Science, Nicolaus Copernicus University, Toruñ, Poland
- Julio Saez-Rodriguez
- 0Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Heidelberg, Germany
- Alexia Sampri
- 1Division of Informatics, Imaging and Data Sciences, School of Health Sciences, University of Manchester, Manchester, United Kingdom
- Rajesh Shigdel
- 2Department of Clinical Science, University of Bergen, Bergen, Norway
- Blaz Stres
- 3Jozef Stefan Institute, Ljubljana, Slovenia
- Blaz Stres
- 4Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
- Blaz Stres
- 5Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Ramona Suharoschi
- 6Molecular Nutrition and Proteomics Lab, Faculty of the Food Science and Technology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
- Jaak Truu
- 7Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Ciprian-Octavian Truică
- 8Department of Computer Science and Engineering, Faculty of Automatic Control and Computers, University Politehnica of Bucharest, Bucharest, Romania
- Baiba Vilne
- 9Bioinformatics Research Unit, Riga Stradins University, Riga, Latvia
- Dimitrios Vlachakis
- 0Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Athens, Greece
- Ercument Yilmaz
- 1Department of Computer Technologies, Karadeniz Technical University, Trabzon, Turkey
- Georg Zeller
- 2European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Aldert L. Zomer
- 3Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- David Gómez-Cabrero
- 4Navarrabiomed, Complejo Hospitalario de Navarra (CHN), IdiSNA, Universidad Pública de Navarra (UPNA), Pamplona, Spain
- Marcus J. Claesson
- 5School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
- DOI
- https://doi.org/10.3389/fmicb.2021.635781
- Journal volume & issue
-
Vol. 12
Abstract
The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 “ML4Microbiome” that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.
Keywords
