Comparative genomics of the lactic acid bacteria.
Open accessAbstract
Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.
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Strains of L. lactis are typically auxotrophic for several amino acids and need an extracellular protease to grow to high cell densities in milk.
“Strains of L. lactis are typically auxotrophic for several amino acids and in order to grow to high cell densities in milk they need an extracellular protease.”
From Modeled Structure of the Cell Envelope Proteinase of Lactococcus lactis (2020) · cites this paper as Makarova et al., 2006
The Introduction (page unavailable) describes both prototrophic and auxotrophic pathways across lactic acid bacteria, but does not establish that L. lactis strains are typically auxotrophic for several amino acids. The phyletic-patterns section says L. lactis retains many biosynthetic reactions; searches for an extracellular protease and growth to high cell densities in milk found no passage addressing that requirement. (LLM, conf=0.72)
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- Authors
- 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, D. M., Hawkins, T., Plengvidhya, V., Welker, D., Hughes, J., Goh, Y., Benson, A., Baldwin, K., Lee, J.-H., 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., Klaenhammer, T., Richardson, P., Kozyavkin, S., Weimer, B., & Mills, D.
- Affiliations
- National Institutes of Health (US)
- Fidelity Systems (United States) (US)
- Birkbeck, University of London (GB)
- Joint Genome Institute (US)
- Agricultural Research Service (US)
- Biology and
- University of Nebraska–Lincoln (US)
- University of Minnesota (US)
- Department of Food Science, University of Wisconsin, Madison, WI 53706;
- University of Wisconsin–Madison (US)
- University of California San Diego (US)
- North Carolina State University (US)
- Utah State University (US)
- University of California, Davis (US)
- Nutrition and Food Science and
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN 55108;
- Department of Food Science and Toxicology, University of Idaho, Moscow, ID 83844
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2006-10-17
- Volume
- 103
- Issue
- 42
- Pages
- 15611-15616
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1622870
- OpenAlex
- W2098686923
- Cited by
- 1,391
- References
- 59
- Citations by year
- 2026: 26 · 2025: 44 · 2024: 30 · 2023: 54 · 2022: 59 · 2021: 70 · 2020: 66 · 2019: 64 · 2018: 59 · 2017: 85 · 2016: 76 · 2015: 78 · 2014: 117 · 2013: 76 · 2012: 88
- FWCI
- 118.64
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, DE-AC03-?, AC03-76SF00098, W-7405, 05CH11231, -7405-ENG-48, W‐7405‐ENG‐48, W-7405-ENG-36, DE-AC02-)
- U.S. Department of Agriculture (DE-AC02-05CH11231)
- Utah State University
- Utah Agricultural Experiment Station
- Dairy Management
- American Vineyard Foundation
- Pickle Packers International
- Joint Genome Institute (AC02-05CH11231, DE–AC02–05CH11231)
- National Institutes of Health (DE-AC02–05CH11231, DE-AC03- 76SF00098)
- Office of Science (DEAC03-76SF00098, DEAC02–05CH11231, AC02-05CH11231, DE-AC02)
- Agricultural Research Service
- National Institute of General Medical Sciences (R01GM055434, R01 GM55434)
- Biological and Environmental Research (05CH11231, DE-AC02 − 05CH11231, AC02-05CH11231)
- Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48, DE-AC03-76SF00098, W-7405-ENG-36, DE-AC02-05CH11231)
- Lawrence Berkeley National Laboratory (AC02‐05CH11231, DE AC03 76SF00098, 05CH11231)
- Los Alamos National Laboratory (W‐7405‐ENG‐36, DE-AC02-05CH11231)
- 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
- lactic acid bacteria, comparative genomics, genome sequence, phylogenetic diversity, transporters, prototrophy, auxotrophy, gene loss, horizontal gene transfer, fermented foods, fermented beverages
- MeSH terms
- Animals, Bacterial Proteins, Biological Evolution, Food Microbiology, Lactobacillus, Phylogeny, Streptococcaceae, Genome, Bacterial, Lactic Acid, Gene Transfer, Horizontal, Genomics
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.
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