Subspecies-level genome comparison of Lactobacillus delbrueckii
Open accessAbstract
Lactobacillus delbrueckii comprises six subspecies, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. delbrueckii subsp. jakobsenii, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. sunkii, and L. delbrueckii subsp. indicus. We investigated the evolution of the six subspecies of L. delbrueckii using comparative genomics. While the defining feature of the species was the gene number increment driven by mobile elements and gene fragmentation, the repertoire of subspecies-specific gene gains and losses differed among the six subspecies. The horizontal gene transfer analyses indicated that frequent gene transfers between different subspecies had occurred when the six subspecies first diverged from the common ancestor, but recent gene exchange was confined to a subspecies implying independent evolution of the six subspecies. The subspecies bulgaricus is a homogeneous group that diverged from the other subspecies a long time ago and underwent convergent evolution. The subspecies lactis, jakobsenii, delbrueckii, and sunkii were more closely related to each other than to other subspecies. The four subspecies commonly show increasing genetic variability with increasing genome size. However, the four subspecies were distinguished by specific gene contents. The subspecies indicus forms a branch distant from the other subspecies and shows an independent evolutionary trend. These results could explain the differences in the habitat and nutritional requirements of the subspecies of L. delbrueckii.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
L. delbrueckii exhibited six main subspecies in accordance with literature.
“L. delbrueckii , widely employed in the dairy industry, exhibited six main subspecies (subsp.) in accordance with literature 106 (Figure 6B).”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [106]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662 · see citing works
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,426 · see citing works
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
Castresana, J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026334 · Cited by 10,447 · see citing works
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707 · see citing works
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410 · see citing works
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C., Alexander, D., Marks, P., Klammer, A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,008 · see citing works
PHASTER: a better, faster version of the PHAST phage search tool
Arndt, D., Grant, J. R., Marcu, A., Sajed, T., Pon, A., Liang, Y., & Wishart, D. S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw387 · Cited by 3,496 · see citing works
Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313 · see citing works
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
Lee, I., Kim, Y. O., Park, S., & Chun, J. (2015) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.000760 · Cited by 3,187 · see citing works
ProtTest: selection of best-fit models of protein evolution
Abascal, F., Zardoya, R., & Posada, D. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti263 · Cited by 3,063 · see citing works
Dendroscope: An interactive viewer for large phylogenetic trees
Huson, D. H., Richter, D. C., Rausch, C. R., Dezulian, T., Franz, M., & Rupp, R. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-460 · Cited by 1,240 · see citing works
The Universal Protein Resource (UniProt): an expanding universe of protein information
Wu, C. H. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj161 · Cited by 1,116 · see citing works
FASconCAT: Convenient handling of data matrices
Kück, P., & Meusemann, K. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2010.04.024 · Cited by 539 · see citing works
van de Guchte, M., Penaud, S., Grimaldi, C., Barbe, V., Bryson, K., Nicolas, P., Robert, C., Oztas, S., Mangenot, S., Couloux, A., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603024103 · Cited by 417 · see citing works
Comparative genomic structure of prokaryotes.
Bentley, S., & Parkhill, J. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.38.072902.094318 · Cited by 352 · see citing works
PanGP: A tool for quickly analyzing bacterial pan-genome profile
Zhao, Y., Jia, X., Yang, J., Ling, Y., Zhang, Z., Yu, J. M., Wu, J., & Xiao, J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu017 · Cited by 248 · see citing works
Metagenomic reconstructions of gut microbial metabolism in weanling pigs
Wang, W., Hu, H., Zijlstra, R. T., Zheng, J., & Gänzle, M. G. (2019) · Microbiome · doi:10.1186/s40168-019-0662-1 · Cited by 134 · see citing works
Comparative genomics of lactic acid bacteria reveals a niche-specific gene set
O’Sullivan, Ó., O’Callaghan, J., Sangrador‐Vegas, A., McAuliffe, O. E., Slattery, L., Kaleta, P., Callanan, M. J., Fitzgerald, G. F., Ross, R. P., & Beresford, T. P. J. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-50 · Cited by 129 · see citing works
BadiRate: estimating family turnover rates by likelihood-based methods
Librado, P., Vieira, F. G., & Rozas, J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr623 · Cited by 120 · see citing works
Drawing explicit phylogenetic networks and their integration into SplitsTree
Kloepper, T. H., & Huson, D. H. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-22 · Cited by 112 · see citing works
Weiss, N., Schillinger, U., & Kandler, O. (1983) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(83)80012-5 · Cited by 104 · see citing works
Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action
Kafsi, H. E., Binesse, J., Loux, V., Buratti, J., Boudebbouze, S., Dervyn, R., Kennedy, S., Galleron, N., Quinquis, B., Batto, J.-M., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-407 · Cited by 90 · see citing works
Germond, J.-E., Lapierre, L., Delley, M., Mollet, B., Felis, G. E., & Dellaglio, F. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg012 · Cited by 73 · see citing works
Lactobacillus delbrueckii subsp. indicus subsp. nov., isolated from Indian dairy products
Dellaglio, F., Felis, G. E., Castioni, A., Torriani, S., & Germond, J. (2005) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.63067-0 · Cited by 73 · see citing works
Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii
Tanigawa, K., & Watanabe, K. (2010) · Microbiology · doi:10.1099/mic.0.043240-0 · Cited by 67 · see citing works
Ghosh, T. S., Arnoux, J., & O’Toole, P. W. (2020) · Gut Microbes · doi:10.1080/19490976.2020.1822729 · Cited by 62 · see citing works
Kudo, Y., Oki, K., & Watanabe, K. (2011) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.037051-0 · Cited by 36 · see citing works
Adimpong, D. B., Nielsen, D. S., Sørensen, K. I., Vogensen, F. K., Sawadogo‐Lingani, H., Derkx, P. M. F., & Jespersen, L. (2013) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.048769-0 · Cited by 33 · see citing works
LACTOBACILLUS spp. | Lactobacillus delbrueckii Group
Crow, V. L., & Curry, B. (2002) · Encyclopedia of Dairy Sciences · doi:10.1016/b0-12-227235-8/00243-1 · Cited by 4 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146 · see citing works
Health-Promoting Effects and Safety Aspects of Lactobacillus delbrueckii: A Food Industry Species
de Jesus, L. C. L., Santos, R. C. V., Quaresma, L. S., Américo, M. F., Rodrigues, T. V., Freitas, A. D. S., Campos, G. M., Dutra, J. D. C. F., Barroso, F. A. L., Laguna, J. G., et al. (2024) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2024.104605 · Cited by 28 · see citing works
Pham, V. D., Xu, Z. S., Simpson, D. J. W., Zhang, J. S., & Gänzle, M. G. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01892-24 · Cited by 18 · see citing works
Genomic and phenotypic imprints of microbial domestication on cheese starter cultures
Somerville, V., Thierer, N., Schmidt, R. S., Roetschi, A., Braillard, L., Haueter, M., Berthoud, H., Shani, N., von Ah, U., Mazel, F., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52687-7 · Cited by 17 · see citing works
Bae, W., Lee, Y. J., Jung, W., Shin, S. L., Kim, T., & Sohn, M. (2023) · Scientific Reports · doi:10.1038/s41598-023-39454-2 · Cited by 12 · see citing works
Gunathunga, C. J., Undugoda, L. J. S., Manage, P. M., Nugara, R. N., Nilmini, A. H. L. R., Udayanga, D., & Sandaruwan, C. (2023) · Food Bioscience · doi:10.1016/j.fbio.2023.103544 · Cited by 11 · see citing works
Dias, S. R., Batista, N. N., Bressani, A. P. P., Dias, D. R., & Schwan, R. F. (2025) · Journal of Agriculture and Food Research · doi:10.1016/j.jafr.2025.101717 · Cited by 12 · see citing works
Al-Mujahidy, S. M. J., Kryukov, K. A., Ikeo, K., Saito, K., Uddin, M. E., & Sina, A. A. I. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03470-23 · Cited by 11 · see citing works
Magossi, G., Gzyl, K. E., Holman, D. B., Nagaraja, T. G., Amachawadi, R. G. G., & Amat, S. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01725-24 · Cited by 10 · see citing works
Grizon, A., Theil, S., Hélinck, S., Gerber, P., Bonnarme, P., & Chassard, C. (2024) · Microorganisms · doi:10.3390/microorganisms12030512 · Cited by 8 · see citing works
Sun, Y., Zhao, Q., Li, W., Kwok, L., & Zhang, H. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1732127 · Cited by 9 · see citing works
Zhao, K., Qiu, L., Tao, X., Zhang, Z., & Wei, H. (2024) · Microorganisms · doi:10.3390/microorganisms12010181 · Cited by 7 · see citing works
Quaresma, L. S., Santos, R. C. V., Gomes, G. C., Américo, M. F., Campos, G. M., Laguna, J. G., Barroso, F. A. L., Azevedo, V., & de Jesus, L. C. L. (2024) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-024-04046-3 · Cited by 6 · see citing works
Yamane, K., Tanizawa, Y., Kobayashi, H., Kamizono, T., Kojima, Y., Takagi, H., & Tohno, M. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006517 · Cited by 5 · see citing works
Tan, Y., Qin, S., Sun, L., Wang, Z., Li, X., Liu, L., Zhu, H., Wang, Q., Cai, Y., & Gao, M. (2025) · Food Bioscience · doi:10.1016/j.fbio.2025.105987 · Cited by 4 · see citing works
Harlé, O., Niay, J., Parayre, S., Nicolas, A., Henry, G., Maillard, M.-B., Valence, F., Thierry, A., Guédon, É., Falentin, H., et al. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01936-23 · Cited by 4 · see citing works
Guérin, F., Sassi, M., Gravey, F., Zouari, A., Quenet, B., Lecourt, M., Ract, P., Michaux, C., Auzou, M., Isnard, C., et al. (2025) · Journal of Clinical Microbiology · doi:10.1128/jcm.02072-24 · Cited by 3 · see citing works
Zang, J., Xiao, L., Zhao, X., Shi, Y., Ma, K., Zhang, C., Geng, S., Rui, X., Lin, T., & Li, W. (2026) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2026.2631641 · Cited by 3 · see citing works
Chaudhari, D. N., Ahire, J. J., Devkatte, A. N., & Kulthe, A. A. (2024) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-024-10385-2 · Cited by 3 · see citing works
Hassan, A. S. I., Henawy, A. R., Saied, Y. A., Garas, K. A., Shahat, O. M., & Halema, A. A. (2025) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10618-y · Cited by 2 · see citing works
Bazukyan, I. L., Miteva, D., Velikova, T. V., & Dimov, S. (2023) · Insects · doi:10.3390/insects14060540 · Cited by 2 · see citing works
Özcan, A., Kiraz, D., Yeniyiğit, Ç., & Gül, İ. (2025) · Current Microbiology · doi:10.1007/s00284-025-04373-0 · Cited by 2 · see citing works
Tursi, A., D’Avino, A., Brandimarte, G., Mocci, G., Pellegrino, R., Federico, A., Savarino, E. V., Gravina, A. G., & the HERICIUM-COLON Study Group (2025) · Nutrients · doi:10.3390/nu17193152 · Cited by 1 · see citing works
Exploring New Species of Lactic Acid Bacteria in Fermented Foods: A Case Study of Zha‐Chili
Qu, D., Wang, Y., Yan, L., Hou, Q., Zhao, H., & Guo, Z. (2025) · Food Science & Nutrition · doi:10.1002/fsn3.71090 · Cited by 1 · see citing works
Widenmann, A., Dhadda, K., Chen, Y., Low, K. E., Abbott, D. W., Guan, L. L., & Gänzle, M. G. (2026) · Journal of Dairy Science · doi:10.3168/jds.2025-28214 · Cited by 1 · see citing works
Bakhtiyarov, K. R., Игнатко, И. В., Siniakova, E. V., Zueva, A. S., & Дмитриевна, К. Т. (2024) · Meditsinskiy sovet = Medical Council · doi:10.21518/ms2024-466
Sedano-Juaréz, C. O., Vichi-Lozada, J., Quintanilla, R. E. L., Dávila-Delgado, R., & Molina, A. I. B. (2024) · BIOtecnia · doi:10.18633/biotecnia.v26.2423
Genetics of Lactic Acid Bacteria
McAuliffe, O. E. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15956-5.00004-x
Cristofolini, M., Ronsivalle, M. A., Pramazzoni, M., Zaccarini, G., Pizzamiglio, V., & Solieri, L. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1755652
Temporal response patterns of swine gut microbiota to arabinoxylan
Wei, S., Zhang, H., Liu, Y., Chen, N., Li, S., Zhu, S., Zong, X., Wang, Y., & Jin, M. (2026) · Journal of Advanced Research · doi:10.1016/j.jare.2026.07.021
Slow-growing and fastidious uropathogens in hospitalized patients: an up-to-date review
Reissier, S., & Cattoir, V. (2026) · Future Microbiology · doi:10.1080/17460913.2026.2700895
Oliveira, Á. R., Bressani, A. P. P., Ramos, C. L., Dias, D. R., & Schwan, R. F. (2026) · Food Research International · doi:10.1016/j.foodres.2026.119960
Tan, H.-L., Huang, F., Li, H., He, M.-Q., Wang, L., Zeng, X. Y., Huang, Y., & Ma, Y.-L. (2026) · Food Reviews International · doi:10.1080/87559129.2026.2705408
Sharma, P., Sharma, A., & Lee, H. (2026) · 3 Biotech · doi:10.1007/s13205-026-04978-7
- Authors
- Baek, M.-G., Kim, K. W., & Yi, H.
- Affiliations
- Korea University (KR)
- Corresponding author
- Yi, Hana
- Venue
- Scientific Reports
- Published
- 2023-02-23
- Volume
- 13
- Issue
- 1
- Pages
- 3171-3171
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC9950072
- OpenAlex
- W4321616888
- Cited by
- 35
- References
- 30
- Citations by year
- 2026: 8 · 2025: 9 · 2024: 15 · 2023: 3
- FWCI
- 5.05
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Research Foundation
- National Research Foundation of Korea
- Ministry of Science and ICT, South Korea
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Lactobacillus delbrueckii, comparative genomics, horizontal gene transfer, transposable elements, gene fragmentation, gene gain and loss, convergent evolution, subspecies differentiation, genome size, Lactobacillus bulgaricus, Lactobacillus delbrueckii subsp. lactis, bacterial evolution
- MeSH terms
- Biological Evolution, Genome, Bacterial, Gene Transfer, Horizontal, Lactobacillus delbrueckii
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
