Probiotics are live nonpathogenic microorganisms extensively used in food, pharmaceutical and medicinal industries. Recently, attention has focused on specific features of probiotics and on the abilities of some long known and recently described species of this group. In general, desired features of probiotics include resistance to acid and bile salts to avoid dysbiosis and induction of immune system development. The advent of next-generation sequencing technology has propelled the genomic area, allowing a search for probiotic features in a wide range of probiotic species, especially bacteria. In this context, functional genomics analyses can help interpret big data, correlating the findings with comparative genomics analyses, in a search for direct applications. To select the articles in this review, we used the following indexing terms: (probiotics OR probiosis) AND (genomics OR transcriptomics OR proteomics OR metabolomics OR culturomics) AND bacteria. Proteomics and transcriptomics methodologies reveal important information about proteins and transcripts differentially expressed under specific conditions that mimic host environments in health and disease. In addition, new research approaches have been developed for probiotics, such as metabiotic and metagenomic analyses of host microbiota. Also, we examined probiotic related features, including bacterial safety aspects; tolerance towards digestive constraints, such as gastric juice and bile salts; bacterial pathogen exclusion mechanisms; adhesion-related genes; antimicrobial peptides; immune development and function; omics; metagenomics; culturomics; functional genomics; transcriptomics; proteomics; metabiotics and metabolomics. In summary, currently there is considerable interest in probiotic bacteria, and structural and functional genomics analyses have potential to help research in this area.