Journal
CELLS
Volume 9, Issue 5, Pages -Publisher
MDPI
DOI: 10.3390/cells9051278
Keywords
microbiota-host interactions; protein-protein interactions; systems biology; networks; network diffusion; computational pipeline
Categories
Funding
- CAPES-the Brazilian Federal Agency for Support and Evaluation of Graduate Education within the Ministry of Education of Brazil
- CNPq-Brazilian National Council for Scientific and Technological Development
- UKRI Biotechnological and Biosciences Research Council (BBSRC) UK [BB/J004529/1, BB/P016774/1, BB/CSP17270/1]
- BBSRC [BB/R012490/1, BBS/E/F/000PR10353, BBS/E/F/000PR10355]
- European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme [694679]
- Earlham Institute (Norwich, UK)
- Quadram Institute (Norwich, UK)
- BBSRC [BBS/E/F/000PR10353, BBS/E/T/000PR9819, BBS/E/F/00044500, BBS/E/F/000PR10355] Funding Source: UKRI
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Microbiome-host interactions play significant roles in health and in various diseases including autoimmune disorders. Uncovering these inter-kingdom cross-talks propels our understanding of disease pathogenesis and provides useful leads on potential therapeutic targets. Despite the biological significance of microbe-host interactions, there is a big gap in understanding the downstream effects of these interactions on host processes. Computational methods are expected to fill this gap by generating, integrating, and prioritizing predictions-as experimental detection remains challenging due to feasibility issues. Here, we present MicrobioLink, a computational pipeline to integrate predicted interactions between microbial and host proteins together with host molecular networks. Using the concept of network diffusion, MicrobioLink can analyse how microbial proteins in a certain context are influencing cellular processes by modulating gene or protein expression. We demonstrated the applicability of the pipeline using a case study. We used gut metaproteomic data from Crohn's disease patients and healthy controls to uncover the mechanisms by which the microbial proteins can modulate host genes which belong to biological processes implicated in disease pathogenesis. MicrobioLink, which is agnostic of the microbial protein sources (bacterial, viral, etc.), is freely available on GitHub.
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