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Background  Fresh sprouted seeds have been associated with a number of large outbreaks caused by  Salmonella  and Shiga toxin-producing  E. coli . However, the high number of commensal bacteria found on sprouted seeds hampers the detection of these pathogens. Knowledge about the composition of the sprout microbiome is limited. In this study, the microbiome of mungo bean sprouts and the impact of buffered peptone water (BPW) and Enterobacteriaceae enrichment broth (EE-broth)-based enrichment protocols on this microbiome were investigated.    Results  Assessments based on aerobic mesophilic colony counts showed similar increases in mungo bean sprout background flora levels independent of the enrichment protocol used. 16S rRNA sequencing revealed a mungo bean sprout microbiome dominated by  Proteobacteria  and  Bacteroidetes . EE-broth enrichment of such samples preserved and increased  Proteobacteria  dominance while reducing  Bacteroidetes  and  Firmicutes  relative abundances. BPW enrichment, however, increased  Firmicutes  relative abundance while decreasing  Proteobacteria  and  Bacteroidetes  levels. Both enrichments also lead to various genus level changes within the  Protobacteria  and  Firmicutes  phyla.    Conclusions  New insights into the microbiome associated with mungo bean sprout and how it is influenced through BPW and EE-broth-based enrichment strategies used for detecting Gram-negative pathogens were generated. BPW enrichment leads to  Firmicutes  and  Proteobacteria  dominance, whereas EE-broth enrichment preserves  Proteobacteria  dominance in the mungo bean sprout samples. By increasing the relative abundance of  Firmicutes , BPW also increases the abundance of Gram-positive organisms including some that might inhibit recovery of Gram-negative pathogens. The use of EE-broth, although preserving and increasing the dominance of  Proteobacteria , can also hamper the detection of lowly abundant Gram-negative target pathogens due to outgrowth of such organisms by the highly abundant non-target  Proteobacteria  genera comprising the mungo bean sprout associated background flora.

Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens