Table 1.

Summary of selected tools and resources used in microbe–host interaction research.

Resource/Tool	Standalone Version?	Description	Can User-Provided Datasets Be Handled?	Nonpathogenic Species Included/Handling?	Protein–Protein Interactions?	Inferring Downstream Effects?	Microorganisms Supported	Host Organisms Supported
PHISTO [24]	online	Web-tool for mining and retrieving host–pathogen interactions	no	no	yes	no	Viral, bacterial, fungal, and protozoan pathogens	Human
PATRIC [25]	online	Genome-focussed infectious disease research database	yes	no	yes	no	Bacterial pathogens	Actinoptergii, Arachnida, Chromadorea, Insecta, and Mammalia
Proteopathogen2 [26]	online	Database and web application to store and display fungal pathogen proteomics data	no	no	no	no	Fungal pathogens	Mammalian species
VirBase [27]	online	Database of virus–host ncRNA-associated interactions and interaction networks during viral infections	no	yes	no	no	Virus	Vertebrates, plants, and arthropods
NetCoperate [31]	python module	Web-based tool and software package for determining host–microbe and microbe–microbe cooperative potential from metabolic networks	yes	yes	no	yes	Any microorganism	Any host species
Kbase [32]	Online, python, and java	Software and data platform that enables data sharing, integration, and analysis of microbes, plants, and their communities by creating workflows consisting of a series of analysis tool runs and code blocks	yes	yes	no	yes	Any microorganism	Any host
M²IA [79]	web-based server	Statistical analysis methods for microbiome and metabolome data integration, including correlation analysis and functional network analysis	yes	yes	no	yes	Any microorganism	Any host species
COMETS [80]	Matlab and a python toolbox	Modelling framework that integrates dynamic flux balance analysis with diffusion to communities	yes	yes	no	yes	Any microorganism	Any host species
MicrobioLink (this paper)	Python and Docker	Integrated evaluation of microbe–host interaction networks	yes	yes	yes	yes	Any microorganism	Any host species