Single-cell analysis (SCA) has been increasingly recognized as the key 
technology for the elucidation of cellular functions, which are not accessible 
from bulk measurements on the population level. Thus far, SCA has been achieved 
by miniaturization of established engineering concepts to match the dimensions 
of a single cell. However, SCA requires procedures beyond the classical approach 
of upstream processing, fermentation, and downstream processing because the 
biological system itself defines the technical demands. This review 
characterizes currently available microfluidics and microreactors for invasive 
(i.e., chemical) and noninvasive (i.e., biological) SCA. We describe the recent 
SCA omics approaches as tools for systems biology and discuss the role of SCA in 
genomics, transcriptomics, proteomics, metabolomics, and fluxomics. Furthermore, 
we discuss applications of SCA for biocatalysis and metabolic engineering as 
well as its potential for bioprocess optimization. Finally, we define present 
and future challenges for SCA and propose strategies to overcome current 
limitations.