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...

Full description

Bibliographic Details
Published in:	STAR Protocols
Main Authors:	Lejla Gul, Anna Julia Elias, Tanvi Tambaku, Marton Olbei, Emily Watters, Balazs Bohar, Dezso Modos, Matthew Madgwick, Tamas Korcsmaros
Format:	Article
Language:	English
Published:	Elsevier 2025-03-01
Subjects:	Bioinformatics Cell Biology Microbiology Systems biology
Online Access:	http://www.sciencedirect.com/science/article/pii/S2666166724007354

Similar Items

MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome–Host Interactions
by: Tahila Andrighetti, et al.
Published: (2020-05-01)

CytokineLink: A Cytokine Communication Map to Analyse Immune Responses—Case Studies in Inflammatory Bowel Disease and COVID-19
by: Marton Olbei, et al.
Published: (2021-08-01)

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways.
by: Agatha Treveil, et al.
Published: (2021-02-01)

Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell‐type specific manner that are altered in inflammatory bowel disease
by: Lejla Gul, et al.
Published: (2022-01-01)

Trópicos, microbios y vectores The tropics, microbes, and vectors
by: Sandra Caponi
Published: (2002-01-01)

Host-associated microbes mitigate the negative impacts of aquatic pollution
by: Rachel E. Diner, et al.
Published: (2024-10-01)

Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level
by: Marton Olbei, et al.
Published: (2022-08-01)

Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease
by: Yiran Zhang, et al.
Published: (2024-09-01)

Integrated intra‐ and intercellular signaling knowledge for multicellular omics analysis
by: Dénes Türei, et al.
Published: (2021-03-01)

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology
by: Monica C. Gestal, et al.
Published: (2024-07-01)

RNA editing in host lncRNAs as potential modulator in SARS-CoV-2 variants-host immune response dynamics
by: Partha Chattopadhyay, et al.
Published: (2024-06-01)

Protocol for efficient germination of Castilleja (Orobanchaceae) for chemical haustorium induction and parasite-host interaction studies
by: Sagar Bashyal, et al.
Published: (2025-06-01)

The vitellogenin receptor gene contributes to mating and host-searching behaviors in parasitoid wasps
by: Yifeng Sheng, et al.
Published: (2023-04-01)

An effector of Phthorimaea absoluta oral secretions inhibits host plant defense
by: Xiaodi Wang, et al.
Published: (2024-07-01)

Nest desertion as an anti-parasitism strategy in hosts selects for late egg-laying behavior in cuckoos
by: Guo Zhong, et al.
Published: (2023-11-01)

Importance of cooperation: How host nest defenses effectively prevent brood parasitism from the cuckoos
by: Longwu Wang, et al.
Published: (2023-04-01)

Transcriptomic response of wetland microbes to root influence
by: Luise Grüterich, et al.
Published: (2024-11-01)

Host defense peptides human β defensin 2 and LL-37 ameliorate murine necrotizing enterocolitis
by: Shiloh R. Lueschow-Guijosa, et al.
Published: (2024-06-01)

Conformational Dynamics of Nonenveloped Circovirus Capsid to the Host Cell Receptor
by: Jiarong Li, et al.
Published: (2020-10-01)

Microbiota-derived β carotene is required for strobilation of Aurelia aurita by impacting host retinoic acid signaling
by: Nadin Jensen, et al.
Published: (2025-02-01)

Visual and thermal stimuli modulate mosquito-host contact with implications for improving malaria vector control tools
by: Manuela Carnaghi, et al.
Published: (2024-01-01)

A programmable, selection-free CRISPR interference system in Staphylococcus aureus for long-term host interaction studies
by: Roni Miah, et al.
Published: (2025-09-01)

Genome-scale CRISPR-Cas9 screen identifies host factors as potential therapeutic targets for SARS-CoV-2 infection
by: Madoka Sakai, et al.
Published: (2024-08-01)

Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions
by: Mary Hongying Cheng, et al.
Published: (2022-03-01)

The branched receptor-binding complex of Ackermannviridae phages promotes adaptive host recognition
by: Anders Nørgaard Sørensen, et al.
Published: (2024-09-01)

Economic microbiology: exploring microbes as agents in economic systems
by: Nicola Luigi Bragazzi, et al.
Published: (2024-02-01)

Systems biology of virus-host signaling network interactions
by: Qiong Xue, et al.
Published: (2012-04-01)

Omics Approaches to Identify Potential Biomarkers of Inflammatory Diseases in the Focal Adhesion Complex
by: Johanne Brooks, et al.
Published: (2017-04-01)

Drosophila parasitoids go to space: Unexpected effects of spaceflight on hosts and their parasitoids
by: Jennifer Chou, et al.
Published: (2024-01-01)

Differential RNA editing landscapes in host cell versus the SARS-CoV-2 genome
by: Małgorzata Kurkowiak, et al.
Published: (2023-11-01)

Profiling of ERBB receptors and downstream pathways reveals selectivity and hidden properties of ERBB4 antagonists
by: Lukša Popović, et al.
Published: (2024-02-01)

Microbial diversity in mountain-dwelling amphibians: The combined effects of host and climatic factors
by: Wei Zhu, et al.
Published: (2024-06-01)

Editorial: Host Manipulation by Parasites
by: Marta I. Sánchez, et al.
Published: (2019-10-01)

Induction of host genes by nested genes during C. elegans development
by: Fabien Soulavie, et al.
Published: (2025-08-01)

Fibromodulin overexpression drives oral squamous cell carcinoma via activating downstream EGFR signaling
by: Lingyun Xia, et al.
Published: (2023-11-01)

Targeted disruption of the cls gene in Buchnera aphidicola impairs membrane integrity and host symbiont dynamics
by: Kathrine Xin Yee Tan, et al.
Published: (2025-08-01)

Inhibition of host cell division by T5 protein 008 (Hdi)
by: Tridib Mahata, et al.
Published: (2023-12-01)

Host ZCCHC3 blocks HIV-1 infection and production through a dual mechanism
by: Binbin Yi, et al.
Published: (2024-03-01)

Exploring host-commensal-pathogen dynamics in cell line and organotypic human intestinal epithelial models
by: Nening M. Nanlohy, et al.
Published: (2024-05-01)

Selective protein aggregation confines and inhibits endotoxins in wounds: Linking host defense to amyloid formation
by: Jitka Petrlova, et al.
Published: (2023-10-01)