Complete Resequencing and Reannotation of the Lactobacillus Plantarum WCFS1 Genome

Overview

Journal J Bacteriol

Publisher American Society for Microbiology

Specialty Microbiology

Date 2011 Dec 14

PMID 22156394

Citations 59

Authors

Roland J Siezen

Christof Francke

Bernadet Renckens

Jos Boekhorst

Michiel Wels

Michiel Kleerebezem

Sacha A F T van Hijum

Affiliations

Soon will be listed here.

Abstract

There is growing interest in the beneficial effects of Lactobacillus plantarum on human health. The genome of L. plantarum WCFS1, first sequenced in 2001, was resequenced using Solexa technology. We identified 116 nucleotide corrections and improved function prediction for nearly 1,200 proteins, with a focus on metabolic functions and cell surface-associated proteins.

Citing Articles

Directional and Strain-Specific Interaction Between and .

Kondakala S, Yoon S, Daddy Gaoh S, Kweon O, Kim S, Hart M Microorganisms. 2025; 12(12.

PMID: 39770635 PMC: 11677646. DOI: 10.3390/microorganisms12122432.

Genomic Characterization of Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese.

Gizachew S, Engidawork E Genes (Basel). 2024; 15(11).

PMID: 39596588 PMC: 11593849. DOI: 10.3390/genes15111389.

Strategies to enhance stress tolerance in lactic acid bacteria across diverse stress conditions.

Derunets A, Selimzyanova A, Rykov S, Kuznetsov A, Berezina O World J Microbiol Biotechnol. 2024; 40(4):126.

PMID: 38446232 DOI: 10.1007/s11274-024-03905-3.

Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade-off between secondary and primary metabolism.

Qiu S, Huang Y, Liang S, Zeng H, Yang A Microb Biotechnol. 2024; 17(2):e14425.

PMID: 38393514 PMC: 10886434. DOI: 10.1111/1751-7915.14425.

The biocontrol agent AMBP214 is dispersible to plants via bumblebees.

Temmermans J, Legein M, Zhao Y, Kiekens F, Smagghe G, De Coninck B Appl Environ Microbiol. 2023; 89(11):e0095023.

PMID: 37882529 PMC: 10686056. DOI: 10.1128/aem.00950-23.

References

Finn R, Mistry J, Tate J, Coggill P, Heger A, Pollington J . The Pfam protein families database. Nucleic Acids Res. 2009; 38(Database issue):D211-22. PMC: 2808889. DOI: 10.1093/nar/gkp985. View

Gross G, Snel J, Boekhorst J, Smits M, Kleerebezem M . Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin. Benef Microbes. 2011; 1(1):61-6. DOI: 10.3920/BM2008.1006. View

Ganzle M, Vermeulen N, Vogel R . Carbohydrate, peptide and lipid metabolism of lactic acid bacteria in sourdough. Food Microbiol. 2006; 24(2):128-38. DOI: 10.1016/j.fm.2006.07.006. View

Aymerich T, Martin B, Garriga M, Hugas M . Microbial quality and direct PCR identification of lactic acid bacteria and nonpathogenic Staphylococci from artisanal low-acid sausages. Appl Environ Microbiol. 2003; 69(8):4583-94. PMC: 169148. DOI: 10.1128/AEM.69.8.4583-4594.2003. View

Wels M, Bongers R, Boekhorst J, Molenaar D, Sturme M, de Vos W . Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome. J Bacteriol. 2009; 191(10):3420-3. PMC: 2687170. DOI: 10.1128/JB.01672-08. View

Kleerebezem M, Hols P, Bernard E, Rolain T, Zhou M, Siezen R . The extracellular biology of the lactobacilli. FEMS Microbiol Rev. 2010; 34(2):199-230. DOI: 10.1111/j.1574-6976.2010.00208.x. View

Finn R, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T . Pfam: clans, web tools and services. Nucleic Acids Res. 2005; 34(Database issue):D247-51. PMC: 1347511. DOI: 10.1093/nar/gkj149. View

Francke C, Siezen R, Teusink B . Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol. 2005; 13(11):550-8. DOI: 10.1016/j.tim.2005.09.001. View

Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M . Artemis: sequence visualization and annotation. Bioinformatics. 2000; 16(10):944-5. DOI: 10.1093/bioinformatics/16.10.944. View

10.

Mundt J, Hammer J . Lactobacilli on plants. Appl Microbiol. 1968; 16(9):1326-30. PMC: 547649. DOI: 10.1128/am.16.9.1326-1330.1968. View

11.

Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen R . Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups. Nucleic Acids Res. 2006; 34(7):1947-58. PMC: 1435977. DOI: 10.1093/nar/gkl138. View

12.

Marco M, Bongers R, de Vos W, Kleerebezem M . Spatial and temporal expression of Lactobacillus plantarum genes in the gastrointestinal tracts of mice. Appl Environ Microbiol. 2006; 73(1):124-32. PMC: 1797133. DOI: 10.1128/AEM.01475-06. View

13.

Siezen R, Tzeneva V, Castioni A, Wels M, Phan H, Rademaker J . Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ Microbiol. 2009; 12(3):758-73. DOI: 10.1111/j.1462-2920.2009.02119.x. View

14.

Bron P, Marco M, Hoffer S, Van Mullekom E, de Vos W, Kleerebezem M . Genetic characterization of the bile salt response in Lactobacillus plantarum and analysis of responsive promoters in vitro and in situ in the gastrointestinal tract. J Bacteriol. 2004; 186(23):7829-35. PMC: 529069. DOI: 10.1128/JB.186.23.7829-7835.2004. View

15.

Marco M, Peters T, Bongers R, Molenaar D, van Hemert S, Sonnenburg J . Lifestyle of Lactobacillus plantarum in the mouse caecum. Environ Microbiol. 2009; 11(10):2747-57. PMC: 2978903. DOI: 10.1111/j.1462-2920.2009.02001.x. View

16.

Boekhorst J, Wels M, Kleerebezem M, Siezen R . The predicted secretome of Lactobacillus plantarum WCFS1 sheds light on interactions with its environment. Microbiology (Reading). 2006; 152(Pt 11):3175-3183. DOI: 10.1099/mic.0.29217-0. View

17.

Troost F, van Baarlen P, Lindsey P, Kodde A, de Vos W, Kleerebezem M . Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1 in vivo. BMC Genomics. 2008; 9:374. PMC: 2519092. DOI: 10.1186/1471-2164-9-374. View

18.

Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell B . Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics. 2008; 24(23):2672-6. PMC: 2606163. DOI: 10.1093/bioinformatics/btn529. View

19.

Overbeek R, Larsen N, Walunas T, DSouza M, Pusch G, Selkov Jr E . The ERGO genome analysis and discovery system. Nucleic Acids Res. 2003; 31(1):164-71. PMC: 165577. DOI: 10.1093/nar/gkg148. View

20.

Aryanta R, Fleet G, Buckle K . The occurrence and growth of microorganisms during the fermentation of fish sausage. Int J Food Microbiol. 1991; 13(2):143-55. DOI: 10.1016/0168-1605(91)90056-u. View