peer-reviewedLactobacillus paracasei strains are common members of the nonstarter
microbiota present in various types of cheeses. The draft genome sequences of
three strains isolated from mature cheddar cheeses are reported here

Fitzgerald, Gerald F

McAuliffe, Olivia

Stefanovic, Ewelina

ABSTRACT
          
            Lactobacillus paracasei
            strains are common members of the nonstarter microbiota present in various types of cheeses. The draft genome sequences of three strains isolated from mature cheddar cheeses are reported here.
          </jats:p

Ewelina Stefanovic

Gerald Fitzgerald

Olivia McAuliffe

Crossref

Genome Announcements

Draft Genome Sequences of Three Lactobacillus paracasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese

Lactobacillus paracasei strains are common members of the nonstarter microbiota present in various types of cheeses. The draft genome sequences of three strains isolated from mature cheddar cheeses are reported here

Fitzgerald, Gerald F.

Irish Universities

Draft genome sequences of three Lactobacillus paracasei strains, members of the nonstarter microbiota of mature cheddar cheese

T-Stór

Draft Genome Sequences of ThreeLactobacillus paracasei Strains, Membersof the Nonstarter Microbiota of MatureCheddar CheeseEwelina Stefanovic,a,b Gerald Fitzgerald,b Olivia McAuliffeaTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Irelanda; School of Microbiology, UniversityCollege Cork, Cork, IrelandbABSTRACT Lactobacillus paracasei strains are common members of the nonstartermicrobiota present in various types of cheeses. The draft genome sequences ofthree strains isolated from mature cheddar cheeses are reported here.Lactic acid bacteria (LAB) are Gram-positive aerotolerant bacteria with a wide spec-trum of practical applications, including food production, biotechnology, andmedicine-related ﬁelds (1). Strains of the genus Lactobacillus have been isolated fromdiverse habitats, such as fermented products, plant materials, and human and animalgastrointestinal tracts (2). In cheese, Lactobacillus paracasei forms part of the nonstartermicrobiota and is considered to have an important role in the ripening process andﬂavor development (3). The three Lactobacillus paracasei strains (DPC2071, DPC4206,and DPC4536) analyzed in this study were isolated from mature cheddar cheeses aspart of the nonstarter LAB population.Bacterial DNA was isolated from all three strains, and genomic libraries wereprepared with the Nextera XT DNA library preparation kit (Illumina, Inc., USA). The 2 250-bp paired-end read sequencing was performed on an Illumina MiSeq platform(MicrobesNG, University of Birmingham, United Kingdom). The assembly of each ge-nome was performed using the SeqMan NGen application of the DNAStar LasergeneGenomics Suite (DNAStar, Inc., Madison, WI, USA). Glimmer version 3.02 (4) and RAST (5)were used to predict open reading frames (ORFs). Initially, the RAST server was used toannotate each genome, and the annotations were veriﬁed and manually curated usingBLASTp (6) and Artemis (7).Sequence assemblies for the three strains indicated coverages of 88, 70, and101 for DPC2071, DPC4206, and DPC4536, respectively. The length of the DPC2071genome was 2,936,872 bp, consisting of 41 nonoverlapping contigs, with a contig N50of 300,051 bp, a maximum contig size of 536,232 bp, and a total of 2,827 protein-coding genes. In the case of strain DPC4206, the assembly yielded a genome sequenceof 3,095,268 bp, consisting of 49 contigs. The maximum contig size was 322,047 bp, andthe contig N50 was 142,300 bp, while a total of 2,951 protein-coding genes wereidentiﬁed. The draft genome sequence of strain DPC4536 was 3,078,575 bp long, andit consisted of 35 contigs and 2,931 genes encoding proteins. The maximum contig sizewas 426,277 bp, and the contig N50 was 191,696 bp. The GC content of all threegenomes was 46.3%, which corresponds to the usual GC content of L. paracaseigenomes.These sequencing data will contribute to the pool of available Lactobacillus para-casei genomes and enable further comparative genome analysis of strains of thisspecies.Received 30 May 2017 Accepted 31 May2017 Published 20 July 2017Citation Stefanovic E, Fitzgerald G, McAuliffeO. 2017. Draft genome sequences of threeLactobacillus paracasei strains, members of thenonstarter microbiota of mature cheddarcheese. Genome Announc 5:e00655-17.https://doi.org/10.1128/genomeA.00655-17.Copyright © 2017 Stefanovic et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Ewelina Stefanovic,ewelina.stefanovic@teagasc.ie.PROKARYOTEScrossmVolume 5 Issue 29 e00655-17 genomea.asm.org 1 on July 31, 2017 by TEAGASChttp://genomea.asm.org/Downloaded from Accession number(s). The whole-genome shotgun projects have been deposited atDDBJ/EMBL/GenBank under the accession numbers NCSN00000000, NCSO00000000,and NCSP00000000, while the versions described in this paper are versionsNCSN01000000, NCSO01000000, and NCSP01000000 for strains DPC2071, DPC4206,and DPC4536, respectively.ACKNOWLEDGMENTSE. Stefanovic is the recipient of the Teagasc Walsh Fellowship. This work was fundedby Teagasc (grant 6224).REFERENCES1. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A,Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y,Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V,Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I,Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E,Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F,Broadbent J, Hutkins R, O’Sullivan D, Steele J, Unlu G, Saier M, Klaenham-mer T, Richardson P, Kozyavkin S, Weimer B, Mills D. 2006. Comparativegenomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103:15611–15616. https://doi.org/10.1073/pnas.0607117103.2. Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, vanHylckama Vlieg JE, Siezen RJ. 2013. Lactobacillus paracasei comparativegenomics: towards species pan-genome deﬁnition and exploitation ofdiversity. PLoS One 8:e68731. https://doi.org/10.1371/journal.pone.0068731.3. Gobbetti M, De Angelis M, Di Cagno R, Mancini L, Fox PF. 2015. Pros andcons for using non-starter lactic acid bacteria (NSLAB) as secondary/adjunct starters for cheese ripening. Trends Food Sci Technol 45:167–178.https://doi.org/10.1016/j.tifs.2015.07.016.4. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterialgenes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679.https://doi.org/10.1093/bioinformatics/btm009.5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. TheRAST server: rapid annotations using subsystems technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic LocalAlignment Search Tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2.7. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, BarrellB. 2000. Artemis: sequence visualization and annotation. Bioinformatics16:944–945. https://doi.org/10.1093/bioinformatics/16.10.944.Stefanovic et al.Volume 5 Issue 29 e00655-17 genomea.asm.org 2 on July 31, 2017 by TEAGASChttp://genomea.asm.org/Downloaded from 

Cork Open Research Archive

Title Draft genome sequences of three Lactobacillus paracasei strains,members of the nonstarter microbiota of mature cheddar cheeseAuthor(s) Stefanovic, Ewelina; Fitzgerald, Gerald F.; McAuliffe, OliviaPublication date 2017Original citation Stefanovic, E., Fitzgerald, G. and McAuliffe, O. (2017) 'Draft genomesequences of three Lactobacillus paracasei strains, members of thenonstarter microbiota of mature cheddar cheese', GenomeAnnouncements, 5(29), e00655-17 (2pp). doi: 10.1128/genomeA.00655-17Type of publication Article (peer-reviewed)Link to publisher'sversionhttp://genomea.asm.org/content/5/29/e00655-17http://dx.doi.org/10.1128/genomeA.00655-17Access to the full text of the published version may require asubscription.Rights © 2017, Stefanovic et al. This is an open-access article distributedunder the terms of the Creative Commons Attribution 4.0International license.https://creativecommons.org/licenses/by/4.0/Item downloadedfromhttp://hdl.handle.net/10468/4883Downloaded on 2018-08-23T19:19:28ZDraft Genome Sequences of ThreeLactobacillus paracasei Strains, Membersof the Nonstarter Microbiota of MatureCheddar CheeseEwelina Stefanovic,a,b Gerald Fitzgerald,b Olivia McAuliffeaTeagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Irelanda; School of Microbiology, UniversityCollege Cork, Cork, IrelandbABSTRACT Lactobacillus paracasei strains are common members of the nonstartermicrobiota present in various types of cheeses. The draft genome sequences ofthree strains isolated from mature cheddar cheeses are reported here.Lactic acid bacteria (LAB) are Gram-positive aerotolerant bacteria with a wide spec-trum of practical applications, including food production, biotechnology, andmedicine-related ﬁelds (1). Strains of the genus Lactobacillus have been isolated fromdiverse habitats, such as fermented products, plant materials, and human and animalgastrointestinal tracts (2). In cheese, Lactobacillus paracasei forms part of the nonstartermicrobiota and is considered to have an important role in the ripening process andﬂavor development (3). The three Lactobacillus paracasei strains (DPC2071, DPC4206,and DPC4536) analyzed in this study were isolated from mature cheddar cheeses aspart of the nonstarter LAB population.Bacterial DNA was isolated from all three strains, and genomic libraries wereprepared with the Nextera XT DNA library preparation kit (Illumina, Inc., USA). The 2 250-bp paired-end read sequencing was performed on an Illumina MiSeq platform(MicrobesNG, University of Birmingham, United Kingdom). The assembly of each ge-nome was performed using the SeqMan NGen application of the DNAStar LasergeneGenomics Suite (DNAStar, Inc., Madison, WI, USA). Glimmer version 3.02 (4) and RAST (5)were used to predict open reading frames (ORFs). Initially, the RAST server was used toannotate each genome, and the annotations were veriﬁed and manually curated usingBLASTp (6) and Artemis (7).Sequence assemblies for the three strains indicated coverages of 88, 70, and101 for DPC2071, DPC4206, and DPC4536, respectively. The length of the DPC2071genome was 2,936,872 bp, consisting of 41 nonoverlapping contigs, with a contig N50of 300,051 bp, a maximum contig size of 536,232 bp, and a total of 2,827 protein-coding genes. In the case of strain DPC4206, the assembly yielded a genome sequenceof 3,095,268 bp, consisting of 49 contigs. The maximum contig size was 322,047 bp, andthe contig N50 was 142,300 bp, while a total of 2,951 protein-coding genes wereidentiﬁed. The draft genome sequence of strain DPC4536 was 3,078,575 bp long, andit consisted of 35 contigs and 2,931 genes encoding proteins. The maximum contig sizewas 426,277 bp, and the contig N50 was 191,696 bp. The GC content of all threegenomes was 46.3%, which corresponds to the usual GC content of L. paracaseigenomes.These sequencing data will contribute to the pool of available Lactobacillus para-casei genomes and enable further comparative genome analysis of strains of thisspecies.Received 30 May 2017 Accepted 31 May2017 Published 20 July 2017Citation Stefanovic E, Fitzgerald G, McAuliffeO. 2017. Draft genome sequences of threeLactobacillus paracasei strains, members of thenonstarter microbiota of mature cheddarcheese. Genome Announc 5:e00655-17.https://doi.org/10.1128/genomeA.00655-17.Copyright © 2017 Stefanovic et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Ewelina Stefanovic,ewelina.stefanovic@teagasc.ie.PROKARYOTEScrossmVolume 5 Issue 29 e00655-17 genomea.asm.org 1 on October 5, 2017 by IRIShttp://genomea.asm.org/Downloaded from Accession number(s). The whole-genome shotgun projects have been deposited atDDBJ/EMBL/GenBank under the accession numbers NCSN00000000, NCSO00000000,and NCSP00000000, while the versions described in this paper are versionsNCSN01000000, NCSO01000000, and NCSP01000000 for strains DPC2071, DPC4206,and DPC4536, respectively.ACKNOWLEDGMENTSE. Stefanovic is the recipient of the Teagasc Walsh Fellowship. This work was fundedby Teagasc (grant 6224).REFERENCES1. Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, Pavlov A,Pavlova N, Karamychev V, Polouchine N, Shakhova V, Grigoriev I, Lou Y,Rohksar D, Lucas S, Huang K, Goodstein DM, Hawkins T, Plengvidhya V,Welker D, Hughes J, Goh Y, Benson A, Baldwin K, Lee JH, Díaz-Muñiz I,Dosti B, Smeianov V, Wechter W, Barabote R, Lorca G, Altermann E,Barrangou R, Ganesan B, Xie Y, Rawsthorne H, Tamir D, Parker C, Breidt F,Broadbent J, Hutkins R, O’Sullivan D, Steele J, Unlu G, Saier M, Klaenham-mer T, Richardson P, Kozyavkin S, Weimer B, Mills D. 2006. Comparativegenomics of the lactic acid bacteria. Proc Natl Acad Sci U S A 103:15611–15616. https://doi.org/10.1073/pnas.0607117103.2. Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, vanHylckama Vlieg JE, Siezen RJ. 2013. Lactobacillus paracasei comparativegenomics: towards species pan-genome deﬁnition and exploitation ofdiversity. PLoS One 8:e68731. https://doi.org/10.1371/journal.pone.0068731.3. Gobbetti M, De Angelis M, Di Cagno R, Mancini L, Fox PF. 2015. Pros andcons for using non-starter lactic acid bacteria (NSLAB) as secondary/adjunct starters for cheese ripening. Trends Food Sci Technol 45:167–178.https://doi.org/10.1016/j.tifs.2015.07.016.4. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterialgenes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679.https://doi.org/10.1093/bioinformatics/btm009.5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. TheRAST server: rapid annotations using subsystems technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic LocalAlignment Search Tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2.7. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, BarrellB. 2000. Artemis: sequence visualization and annotation. Bioinformatics16:944–945. https://doi.org/10.1093/bioinformatics/16.10.944.Stefanovic et al.Volume 5 Issue 29 e00655-17 genomea.asm.org 2 on October 5, 2017 by IRIShttp://genomea.asm.org/Downloaded from 

Lactobacillus paracasei strains are common members of the nonstarter
microbiota present in various types of cheeses. The draft genome sequences of
three strains isolated from mature cheddar cheeses are reported here

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Draft Genome Sequences of Three Lactobacillus paracasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese

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