TY - BOOK
T1 - Lactococcus lactis SK1virus Taxonomy and Development of High-Throughput qPCR Methods to Evaluate SK1virus Development in Dairies Using Undefined Starter Cultures
AU - Liu, Cong
PY - 2018
Y1 - 2018
N2 - Bacteriophages attacking the Lactic acid bacteria (LAB), used as starter cultures in
the dairy industry, produce many problems due to increased processing time, low
quality or even failure of fermentation, as well as huge economic burden
worldwide.
In the first part of this study, we dealt with taxonomy of SK1virus in genomic
level. We collected 60 fully sequenced phages (11 phages were from public
database; the rest were from our own collection) from the lactococcal Sk1virus
genus (former known as the 936 phage group or 936 species), and analyzed the
effect of using >95% ANI for species differentiation based on whole genome
sequence and based on core genome sequence. The results showed that, if a
simple >95 % ANI was used, a 35 new species of SK1virus would be generated
almost, whenever a new phage genome was sequenced giving a very unstable
taxonomy. Most of core genes from SK1virus phages were located in the
conserved late-expressed region and a small part was located in the early- and
middle- expressed regions. Using a >95% ANI for the core genes for designation
of species still results in an unmanageable number of species. So both methods
generated on average a new species almost for every second new sequence.
This will mean generating an useless taxonomy below genus level, and we
suggest that no species is assigned to the SK1virus genus based on whole
genome or whole core genome using >95 % ANIb or that the 936 group
should be assigned to the 936species.
In the second part, we further investigated the abundance in the diversity of L.
lactis and Leuconostoc phages in whey samples in a Danish dairy using named
TK5 starter culture over 12 years. L. lactis phage from 936 species and P335
species were both appeared frequently in the whey samples. Based on receptor
binding protein analysis, most of the 936 subgroups were predicted to attack the
strains of L. lactis subsp. cremoris. The control sample (without any whey sample
added) was dominated by 936 phage species, suggesting the possibility of
evolution among these phages at any point during the 12-year period. Furthermore,
the emergences of new phages were found over time indicating that they probably
have developed from already existing phages or from lysogenic strains.
In the last part, we finally present a high-throughput qPCR system to detect
different groups of lactococcal bacteriophages in 936 species by their RBP. We
compared the DNA sequences of RBP genes from a large number of recently
sequenced phages belonging to the 936-species and correlated sequences with
host-range. The host-range related groups were identified, and the groups a pair of
qPCR specific primers were designed targeting the region of RBP genes.
AB - Bacteriophages attacking the Lactic acid bacteria (LAB), used as starter cultures in
the dairy industry, produce many problems due to increased processing time, low
quality or even failure of fermentation, as well as huge economic burden
worldwide.
In the first part of this study, we dealt with taxonomy of SK1virus in genomic
level. We collected 60 fully sequenced phages (11 phages were from public
database; the rest were from our own collection) from the lactococcal Sk1virus
genus (former known as the 936 phage group or 936 species), and analyzed the
effect of using >95% ANI for species differentiation based on whole genome
sequence and based on core genome sequence. The results showed that, if a
simple >95 % ANI was used, a 35 new species of SK1virus would be generated
almost, whenever a new phage genome was sequenced giving a very unstable
taxonomy. Most of core genes from SK1virus phages were located in the
conserved late-expressed region and a small part was located in the early- and
middle- expressed regions. Using a >95% ANI for the core genes for designation
of species still results in an unmanageable number of species. So both methods
generated on average a new species almost for every second new sequence.
This will mean generating an useless taxonomy below genus level, and we
suggest that no species is assigned to the SK1virus genus based on whole
genome or whole core genome using >95 % ANIb or that the 936 group
should be assigned to the 936species.
In the second part, we further investigated the abundance in the diversity of L.
lactis and Leuconostoc phages in whey samples in a Danish dairy using named
TK5 starter culture over 12 years. L. lactis phage from 936 species and P335
species were both appeared frequently in the whey samples. Based on receptor
binding protein analysis, most of the 936 subgroups were predicted to attack the
strains of L. lactis subsp. cremoris. The control sample (without any whey sample
added) was dominated by 936 phage species, suggesting the possibility of
evolution among these phages at any point during the 12-year period. Furthermore,
the emergences of new phages were found over time indicating that they probably
have developed from already existing phages or from lysogenic strains.
In the last part, we finally present a high-throughput qPCR system to detect
different groups of lactococcal bacteriophages in 936 species by their RBP. We
compared the DNA sequences of RBP genes from a large number of recently
sequenced phages belonging to the 936-species and correlated sequences with
host-range. The host-range related groups were identified, and the groups a pair of
qPCR specific primers were designed targeting the region of RBP genes.
UR - https://rex.kb.dk/primo-explore/fulldisplay?docid=KGL01011893296&context=L&vid=NUI&search_scope=KGL&tab=default_tab&lang=da_DK
M3 - Ph.D. thesis
BT - Lactococcus lactis SK1virus Taxonomy and Development of High-Throughput qPCR Methods to Evaluate SK1virus Development in Dairies Using Undefined Starter Cultures
PB - Department of Food Science, Faculty of Science, University of Copenhagen
ER -