With the success
of the Human Genome Project, large-scale systemic projects became
a reality that enabled rapid development of the systems biology field.
Systems biology approaches to host–pathogen interactions have
been instrumental in the discovery of some specifics of Gram-negative
bacterial recognition, host signal transduction, and immune tolerance.
However, further research, particularly using multi-omics approaches,
is essential to untangle the genetic, immunologic, (post)transcriptional,
(post)translational, and metabolic mechanisms underlying progression
from infection to clearance of microbes. The key to understanding
host–pathogen interactions lies in acquiring, analyzing, and
modeling multimodal data obtained through integrative multi-omics
experiments. In this article, we will discuss how multi-omics analyses
are adding to our understanding of the molecular basis of host–pathogen
interactions and systemic maladaptive immune response of the host
to microbes and microbial products.