Journal Article Review Ppublish
PubMed: 40619813 DOI: 10.1093/bib/bbaf323
Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.
Brief Bioinform 26(4)
Authors: Syed Sabih Ur Rehman, Muhammad Ibtisam Nasar, Cristina S Mesquita, Souhaila Al Khodor, Richard A Notebaart, Sascha Ott, Sunil Mundra, Ramesh P Arasardanam, Khalid Muhammad, Mohammad Tauqeer Alam
Affiliations
- Department of Biology, United Arab Emirates University, Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
- Bioinformatics & Digital Health Services (RTP), University of Warwick, CV4 7AL, Coventry, United Kingdom.
- Reproductive and Perinatal Health Division, Research Department, Sidra Medicine, Doha, Qatar.
- Food Microbiology, Wageningen University and Research, 6700 AA, Wageningen, The Netherlands.
- Warwick Medical School, University of Warwick, CV4 7AL, Coventry, United Kingdom.
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Khalifa Bin Zayed Street, P.O. Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
- Warwick Medical School, University of Warwick, CV4 7AL, Coventry, United Kingdom. Institute of Precision Diagnostics & Translational Medicine, University Hospitals Coventry & Warwickshire NHS Trust, Clifford Bridge Road, Coventry CV2 2DX, United Kingdom. Leicester Cancer Research Centre, University of Leicester, LE1 7RH, Leicester, United Kingdom.
Abstract
Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.
MeSH
Dysbiosis, Multiple Chronic Conditions, Systems Biology, Metagenomics, Research, Therapeutics, Gastrointestinal Microbiome