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Background   Lactobacillus fermentum  is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize  L. fermentum  at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments ( clpX ,  dnaA ,  dnaK ,  groEL ,  murC, murE ,  pepX ,  pyrG ,  recA ,  rpoB , and  uvrC ).    Results  MLST analysis of 203 isolates of  L. fermentum  from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the  L. fermentum  isolates analyzed belonged to two major groups. A standardized index of association ( I   A   S ) indicated a weak clonal population structure in  L. fermentum . Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in  L. fermentum . The results from the minimum spanning tree strongly suggested that evolution of  L. fermentum  STs was not correlated with geography or food-type.    Conclusions  The MLST scheme developed will be valuable for further studies on the evolution and population structure of  L. fermentum  isolates used in food products.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0447-z) contains supplementary material, which is available to authorized users.

bmc microbiology

The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST)