Acquisition through Horizontal Gene Transfer of Plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 Points towards the Dairy Origin of the Species

Abstract

Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex.Methodology/Principal FindingsWe analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event.Conclusions/SignificanceHere we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species.

Whole-Genome Sequence of the Cheese Isolate Streptococcus macedonicus 679

“…We identified 155 potential pseudogenes. This increased percentage of pseudogenes in the genome of S. macedonicus 679 is in agreement with previous observations for S. macedonicus ACA-DC 198, suggesting a genome decay evolution pattern that may be related to adaptation of the species to the rich in nutrients environment of milk ( 2 , 6 ). Even though the majority of pseudogenes were common between the two strains, we could identify some that were present in one but not the other strain.…”

“…The library was sequenced by using the 600-cycle version 3 reagent kit (Illumina) in MiSeq (Illumina). Reads were assembled using SPAdes ( 5 ) against the published sequences of the chromosome and plasmid pSMA198 of S. macedonicus ACA-DC 198 as templates ( 6 , 7 ). This reference-driven assembly resulted in two chromosomal contigs (contig_1, 79,307 bp; contig_2, 2,014,050 bp), as well as one plasmid contig (contig_3, 14,059 bp).…”

Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species

“…infantarius, Streptococcus gallolyticus, and S. equinus. Members of the complex are established members of the gastrointestinal tract (GIT) of ruminants, while certain species like S. macedonicus and S. infantarius are increasingly associated with fermented foods, especially of dairy origin (Jans et al, 2013a,b;Papadimitriou et al, 2014Papadimitriou et al, , 2015a.…”

Phylogenetic, epidemiological and functional analyses of the Streptococcus bovis/Streptococcus equinus complex through an overarching MLST scheme

“…However, a lack of reliable molecular epidemiological tools and marker genes hinder accurate differentiation of SBSEC subspecies and their individual risk assessments, disease association and the differentiation between commensal and pathogenic subspecies or strain lineages. This difficulty is mainly due to the high degree of gene conservation among members of the SBSEC in combination with evidence of horizontal gene transfer between SBSEC and other streptococci [ 18 , 19 ], the ability of SBSEC to be naturally competent [ 19 , 20 ], rapidly changing taxonomy and a broad range of strains from potential food-grade, to commensal and pathogenic organisms fitting the emerging pathobiont concept [ 21 ]. The SBSEC therefore requires a holistic approach to elucidate the phylogeny, epidemiology and pathogenicity of its members in relation to their animal, human and food habitats.…”