High levels of gums such as dextran, produced by
Leuconostoc
and
Lactobacillus
spp., have a severe impact on factory throughput and sugar quality. This study aimed to determine the phylogenetic relationships between gum‐producing
Leuconostoc
and
Lactobacillus
bacteria which were isolated from various locations in a sugarcane processing factory at times when low‐ and high‐dextran raw sugar, respectively, were produced. Phylogenetic analysis of 16S rRNA gene sequences grouped 81 isolates with the type strains of
Leuconostoc mesenteroides
(subspp.
mesenteroides
,
dextranicum,
and
cremoris
),
Leuconostoc pseudomesenteroides, Leuconostoc lactis,
and
Leuconostoc citreum
, respectively. Forty‐three isolates clustered with the type strain of
Lactobacillus fermentum
. The phylogenetic relatedness of the isolates was determined by sequencing and analysis of the housekeeping genes
rpoA
and
dnaA
for
Leuconostoc
spp. and the
pheS
and
tuf
genes for the
Lactobacillus
spp. The
rpoA
gene proved discriminatory for the phylogenetic resolution of all of the isolated
Leuconostoc
spp. and the
dnaA
housekeeping gene was shown to be effective for isolates clustering with the type strains of
Leuc. mesenteroides
and
Leuc. citreum
. None of the loci examined permitted differentiation at the subspecies level of
Leuc. mesenteroides
. Single‐locus analysis, as well as the concatenation of the
pheS
and
tuf
housekeeping gene sequences, yielded identical phylogenies for the
Lactobacillus
isolates corresponding to
L. fermentum
.
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