Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink
Summary: Analyzing host-microbe interactions is essential for understanding how microbiota changes disrupt host homeostasis. Here, we present a protocol for predicting host-microbe protein-protein interactions and their downstream effects using MicrobioLink. We describe steps for setting up the envi...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-03-01
|
| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166724007354 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832595764651491328 |
|---|---|
| author | Lejla Gul Anna Julia Elias Tanvi Tambaku Marton Olbei Emily Watters Balazs Bohar Dezso Modos Matthew Madgwick Tamas Korcsmaros |
| author_facet | Lejla Gul Anna Julia Elias Tanvi Tambaku Marton Olbei Emily Watters Balazs Bohar Dezso Modos Matthew Madgwick Tamas Korcsmaros |
| author_sort | Lejla Gul |
| collection | DOAJ |
| description | Summary: Analyzing host-microbe interactions is essential for understanding how microbiota changes disrupt host homeostasis. Here, we present a protocol for predicting host-microbe protein-protein interactions and their downstream effects using MicrobioLink. We describe steps for setting up the environment, installing software, and preparing human transcriptomic and bacterial proteomic data. The protocol outlines procedures for predicting protein-protein interactions through domain-motif interactions, integrating multi-omic datasets to map downstream effects, performing network analyses to identify key regulatory pathways, and visualizing multi-layered networks for systems-level data interpretation.For complete details on the use and execution of this protocol, please refer to Gul et al.1 and Poletti et al.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-787f73fcca024d5e9beda9cc6d0daedf |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-787f73fcca024d5e9beda9cc6d0daedf2025-01-18T05:05:13ZengElsevierSTAR Protocols2666-16672025-03-0161103570Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLinkLejla Gul0Anna Julia Elias1Tanvi Tambaku2Marton Olbei3Emily Watters4Balazs Bohar5Dezso Modos6Matthew Madgwick7Tamas Korcsmaros8Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK; Corresponding authorQuadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK; Department of Morphology and Physiology, Faculty of Health Sciences, Semmelweis University, 1086 Budapest, HungaryDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UKDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UKDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UKDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UKDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UKQuadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK; Earlham Institute, Norwich, Norfolk NR4 7UZ, UKDepartment of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London W12 0NN, UK; Quadram Institute Bioscience, Norwich, Norfolk NR4 7UQ, UK; Earlham Institute, Norwich, Norfolk NR4 7UZ, UK; Corresponding authorSummary: Analyzing host-microbe interactions is essential for understanding how microbiota changes disrupt host homeostasis. Here, we present a protocol for predicting host-microbe protein-protein interactions and their downstream effects using MicrobioLink. We describe steps for setting up the environment, installing software, and preparing human transcriptomic and bacterial proteomic data. The protocol outlines procedures for predicting protein-protein interactions through domain-motif interactions, integrating multi-omic datasets to map downstream effects, performing network analyses to identify key regulatory pathways, and visualizing multi-layered networks for systems-level data interpretation.For complete details on the use and execution of this protocol, please refer to Gul et al.1 and Poletti et al.2 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166724007354BioinformaticsCell BiologyMicrobiologySystems biology |
| spellingShingle | Lejla Gul Anna Julia Elias Tanvi Tambaku Marton Olbei Emily Watters Balazs Bohar Dezso Modos Matthew Madgwick Tamas Korcsmaros Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink STAR Protocols Bioinformatics Cell Biology Microbiology Systems biology |
| title | Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink |
| title_full | Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink |
| title_fullStr | Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink |
| title_full_unstemmed | Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink |
| title_short | Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink |
| title_sort | protocol for predicting host microbe interactions and their downstream effect on host cells using microbiolink |
| topic | Bioinformatics Cell Biology Microbiology Systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166724007354 |
| work_keys_str_mv | AT lejlagul protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT annajuliaelias protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT tanvitambaku protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT martonolbei protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT emilywatters protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT balazsbohar protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT dezsomodos protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT matthewmadgwick protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink AT tamaskorcsmaros protocolforpredictinghostmicrobeinteractionsandtheirdownstreameffectonhostcellsusingmicrobiolink |