Genome Sequence of Lactobacillus helveticus , an Organism Distinguished by Selective Gene Loss and Insertion Sequence Element Expansion
Open accessAbstract
Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species, considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the L. helveticus genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Strain DPC4571 possesses three peptide transport systems: the oligopeptide Opp transport system and the di- and tri-peptide transport systems Dpp and DtpT.
“it was determined that strain DPC4571 possesses three peptide transport systems, the oligopeptide Opp transport system and the di- and tri-peptide transport system, Dpp and DtpT, respectively.”
From Lactobacillus helveticus: the proteolytic system (2013) · cites this paper as Callanan et al., 2008
Cites
Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., Thomson, N., Harris, D. E., Holden, M. T. G., Churcher, C. M., Bentley, S. D., Mungall, K. L., et al. (2003) · Nature Genetics · doi:10.1038/ng1227 · Cited by 1,037 · see citing works
Use of autolytic starter systems to accelerate the ripening of Cheddar cheese
Hannon, J. A., Wilkinson, M. G., Delahunty, C. M., Wallace, J. M., Morrissey, P. A., & Beresford, T. P. (2003) · International Dairy Journal · doi:10.1016/s0958-6946(02)00178-4 · Cited by 141 · cited 1× · see citing works
“terness, and increased flavor notes (19, 20, 23).”
BackgroundSelf-citationGrowth phase and growth medium effects on the peptidase activities of Lactobacillus helveticus
Kenny, O., FitzGerald, R. J., O’Cuinn, G., Beresford, T., & Jordan, K. (2003) · International Dairy Journal · doi:10.1016/s0958-6946(03)00073-6 · Cited by 47 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Genes and Molecules of Lactobacilli Supporting Probiotic Action
Lebeer, S., Vanderleyden, J., & De Keersmaecker, S. C. J. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00017-08 · Cited by 1,013 · see citing works
The Complex Microbiota of Raw Milk
Quigley, L., O'Sullivan, O., Stanton, C., Beresford, T. P., Ross, R. P., Fitzgerald, G. F., & Cotter, P. D. (2013) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12030 · Cited by 919 · see citing works
Self-citationGenome-scale analyses of health-promoting bacteria: probiogenomics
Ventura, M., O'Flaherty, S., Claesson, M. J., Turroni, F., Klaenhammer, T. R., van Sinderen, D., & O'Toole, P. W. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2047 · Cited by 471 · see citing works
Lactobacillus surface layer proteins: Structure, function and applications
Hynönen, U., & Palva, A. (2013) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-013-4962-2 · Cited by 283 · see citing works
Lactobacillus helveticus: the proteolytic system
Griffiths, M. W., & Tellez, A. M. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00030 · Cited by 241 · see citing works
“Consumer interest in functional food has motivated researchers to focus on the bioactive compounds formed during fermentation of dairy products by lactic acid bacteria (LAB) such as L. helveticus (Matar et al., 2003; Vinderola et al., 2007b; Rattanachaikunsopon and Phumkhachorn, 2010; Wakai and…”
BackgroundInfluentialThe <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation
O’Flaherty, S., Briner Crawley, A., Theriot, C. M., & Barrangou, R. (2018) · mSphere · doi:10.1128/msphere.00140-18 · Cited by 118 · see citing works
Updates in the Metabolism of Lactic Acid Bacteria
Mayo, B., Aleksandrzak‐Piekarczyk, T., Fernández, M., Kowalczyk, M., Álvarez‐Martín, P., & Bardowski, J. (2010) · Biotechnology of Lactic Acid Bacteria · doi:10.1002/9780813820866.ch1 · Cited by 125 · see citing works
Biochemistry of Cheese Ripening: Proteolysis
Ardö, Y., McSweeney, P. L. H., Magboul, A. A. A., Upadhyay, V. K., & Fox, P. F. (2017) · Cheese · doi:10.1016/b978-0-12-417012-4.00018-1 · Cited by 121 · see citing works
Rong, J., Zheng, H., Liu, M., Hu, X., Wang, T., Zhang, X., Jin, F., & Wang, L. (2015) · BMC Microbiology · doi:10.1186/s12866-015-0525-2 · Cited by 99 · see citing works
Genay, M., Sadat, L., Gagnaire, V., & Lortal, S. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02395-08 · Cited by 66 · see citing works
Heme proteins in lactic acid bacteria
Baureder, M., & Hederstedt, L. (2013) · Advances in Microbial Physiology · doi:10.1016/b978-0-12-410515-7.00001-9 · Cited by 45 · see citing works
Senan, S., Prajapati, J. B., & Joshi, C. G. (2015) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-015-9199-1 · Cited by 46 · see citing works
Matta, T., Agrawal, K., Datta, P., Kumari, L., Bishnoi, M., Chopra, K., & Kondepudi, K. K. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10628-w · Cited by 4 · see citing works
- Authors
- Callanan, M., Kaleta, P., O'Callaghan, J., O'Sullivan, O., Jordan, K., McAuliffe, O., Sangrador-Vegas, A., Slattery, L., Fitzgerald, G. F., Beresford, T., & Ross, R. P.
- Affiliations
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute (IE)
- Corresponding author
- Beresford, Tom
- Venue
- Journal of Bacteriology
- Publisher
- American Society for Microbiology
- Published
- 2008-01-15
- Volume
- 190
- Issue
- 2
- Pages
- 727-735
- ISSN
- 0021-9193 (ISSN-L)
- 1098-5530
- PMC
- PMC2223680
- OpenAlex
- W2119255453
- Cited by
- 204
- References
- 3
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 3 · 2023: 7 · 2022: 8 · 2021: 3 · 2020: 4 · 2019: 2 · 2018: 7 · 2017: 12 · 2016: 4 · 2015: 14 · 2014: 22 · 2013: 19 · 2012: 15
- FWCI
- 28.76
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Bacteriology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Food Institutional Research Measure
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Lactobacillus helveticus, insertion sequences, mobile genetic elements, cheese cultures, gene loss, niche adaptation, comparative genomics, genome stability, sequence diversity, Lactobacillus
- MeSH terms
- Base Sequence, Chromosomes, Bacterial, DNA Transposable Elements, DNA, Bacterial, Genes, Bacterial, Molecular Sequence Data, Polymorphism, Genetic, Genome, Bacterial, Conserved Sequence, Gene Deletion, Sequence Analysis, DNA, Synteny, Lactobacillus helveticus
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
