Supplementary material
Fig S1 MALDI-TOF MS profiles of the Lactobacillus bombicola (a), Convivina intestini (b), and Weissella
bombi (c) isolates and their closest neighbours (Lactobacillus apis LMG 26964T, Leuconostoc mesenteroides
subsp. mesenteroides LMG 6893T and Weissella hellenica LMG 15125T, respectively). Cluster analysis was
performed by Pearson correlation and the hierarchical clustering method UPGMA.
Fig S2 Phylogenetic tree based on the 16S rRNA gene sequences of intestinal Lactobacillus species.
The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time
Reversible model (Nei et al., 2000). The bootstrap consensus tree inferred from 100 replicates (Felsenstein,
1985) is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The percentage of
replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the
branches (Felsenstein, 1985) if the percentage was 50% or higher. Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances
estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with
superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.2353)). The rate variation model allowed for some sites to be
evolutionarily invariable ([+I], 50.1753% sites). The tree is drawn to scale, with branch lengths measured in the
number of substitutions per site. The analysis involved 45 nucleotide sequences with Leuconostoc
mesenteroides subsp. mesenteroides JCM 6124T as the outgroup. There were a total of 1629 positions in the
final dataset. Evolutionary analyses were conducted in MEGA5 (Tamura et al., 2011).
Fig S3 Phylogenetic tree based on the 16S rRNA gene sequences of all Weissella species.
The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time
Reversible model (Nei et al., 2000). The bootstrap consensus tree inferred from 100 replicates (Felsenstein,
1985) is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The percentage of
replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the
branches if the percentage was 50% or higher (Felsenstein, 1985). Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances
estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with
superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.1474)). The rate variation model allowed for some sites to be
evolutionarily invariable ([+I], 61.6388% sites). The tree is drawn to scale, with branch lengths measured in the
number of substitutions per site. The analysis involved 20 nucleotide sequences with Leuconostoc
mesenteroides subsp. mesenteroides JCM 6124T as the outgroup. There were a total of 1593 positions in the
final dataset. Evolutionary analyses were conducted in MEGA5 (Tamura et al., 2011).
Fig S4 Phylogenetic tree based on the 16S rRNA gene sequences of all Leuconostoc and Fructobacillus species.
The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time
Reversible model (Nei et al., 2000). The bootstrap consensus tree inferred from 100 replicates (Felsenstein,
1985) is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The percentage of
replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the
branches if the percentage was 50% or higher (Felsenstein, 1985). Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances
estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with
superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.1379)). The rate variation model allowed for some sites to be
evolutionarily invariable ([+I], 66.0191% sites). The tree is drawn to scale, with branch lengths measured in the
number of substitutions per site. The analysis involved 25 nucleotide sequences with Weissella hellenica LMG
15125T as the outgroup. There were a total of 1596 positions in the final dataset. Evolutionary analyses were
conducted in MEGA5 (Tamura et al., 2011).
Fig S5 Phylogenetic tree based on the pheS sequences of intestinal Lactobacillus species
The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time
Reversible model (Nei et al., 2000). The bootstrap consensus tree inferred from 100 replicates (Felsenstein,
1985) is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The percentage of
replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the
branches if the percentage was 50% or higher (Felsenstein, 1985). Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances
estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with
superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.7529)). The rate variation model allowed for some sites to be
evolutionarily invariable ([+I], 24.5718% sites). The tree is drawn to scale, with branch lengths measured in the
number of substitutions per site. The analysis involved 41 nucleotide sequences with Weissella hellenica LMG
15125T as the outgroup. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 475
positions in the final dataset. Evolutionary analyses were conducted in MEGA5 (Tamura et al., 2011).
Fig S6 Phylogenetic tree based on the pheS sequences of all Weissella species.
The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time
Reversible model (Nei et al., 2000). The bootstrap consensus tree inferred from 100 replicates (Felsenstein,
1985) is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The percentage of
replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the
branches if the percentage was 50% or higher (Felsenstein, 1985). Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances
estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with
superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.3810)). The rate variation model allowed for some sites to be
evolutionarily invariable ([+I], 38.8491% sites). The tree is drawn to scale, with branch lengths measured in the
number of substitutions per site. The analysis involved 18 nucleotide sequences with Leuconostoc
mesenteroides subsp. mesenteroides LMG 6893T as the outgroup. Codon positions included were
1st+2nd+3rd+Noncoding. There were a total of 459 positions in the final dataset. Evolutionary analyses were
conducted in MEGA5 (Tamura et al., 2011).
Fig S7 Phylogenetic tree based on the pheS sequences of all Leuconostoc and Fructobacillus species.
The evolutionary history was inferred by using the Maximum Likelihood method based on the General Time
Reversible model (Nei et al., 2000). The bootstrap consensus tree inferred from 100 replicates (Felsenstein,
1985) is taken to represent the evolutionary history of the taxa analyzed (Felsenstein, 1985). The percentage of
replicate trees in which the associated taxa clustered together in the bootstrap test are shown next to the
branches if the percentage was 50% or higher (Felsenstein, 1985). Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances
estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with
superior log likelihood value. A discrete Gamma distribution was used to model evolutionary rate differences
among sites (5 categories (+G, parameter = 0.4716)). The rate variation model allowed for some sites to be
evolutionarily invariable ([+I], 32.3665% sites). The tree is drawn to scale, with branch lengths measured in the
number of substitutions per site. The analysis involved 22 nucleotide sequences with Weissella hellenica LMG
15125T as the outgroup. Codon positions included were 1st+2nd+3rd+Noncoding. There were a total of 471
positions in the final dataset. Evolutionary analyses were conducted in MEGA5 (Tamura et al., 2011).
Fig S8 (GTG)5-PCR profiles of different Lactobacillus bombicola (a), Weissella bombi (b) and Convivina
intestini (c) isolates and their closest neighbours (Lactobacillus apis LMG 26964T, Leuconostoc mesenteroides
subsp. mesenteroides LMG 6893T and Weissella hellenica LMG 15125T, respectively). Cluster analysis was
performed by Pearson correlation and the hierarchical clustering method UPGMA.