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Systems solutions by lactic acid bacteria: from paradigms to practice
Open accessAbstract
Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications.
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![Figure 1 Development of genome sequencing in the last two decades. The number of entries in the NCBI database were scored and summed for the plasmids and bacteriophages [phages] as well as the genomes from Lactobacillus or Lactococcus and Streptrococcus spp. that are considered as LAB.](/paper-figures/c47a8b4198ce4e8d8099ffb6bfdd17a3/systems-solutions-by-lactic-acid-bacteria-from-paradigms-to-practice-figure-1.jpg)
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“Mixed-strain undefined cultures result in more resilience and robustness in dairy processes as compared with selected ones, characterized by a low strain diversity [53,113].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [113]
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CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 5,947
CRISPR/Cas, the Immune System of Bacteria and Archaea
Horvath, P., & Barrangou, R. (2010) · Science · doi:10.1126/science.1179555 · Cited by 2,471
Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
Brouns, S. J. J., Jore, M. M., Lundgren, M., Westra, E. R., Slijkhuis, R. J. H., Snijders, A. P. L., Dickman, M. J., Makarova, K. S., Koonin, E. V., & van der Oost, J. (2008) · Science · doi:10.1126/science.1159689 · Cited by 2,460
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
Garneau, J. E., Dupuis, M.-È., Villion, M., Romero, D. A., Barrangou, R., Boyaval, P., Fremaux, C., Horvath, P., Magadán, A. H., & Moineau, S. (2010) · Nature · doi:10.1038/nature09523 · Cited by 2,336
Complete genome sequence of Lactobacillus plantarum WCFS1
Kleerebezem, M., Boekhorst, J., van Kranenburg, R., Molenaar, D., Kuipers, O. P., Leer, R., Tarchini, R., Peters, S. A., Sandbrink, H. M., Fiers, M. W. E. J., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0337704100 · Cited by 1,472
Comparative genomics of the lactic acid bacteria.
Makarova, K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607117103 · Cited by 1,391
Gasson, M. J. (1983) · Journal of Bacteriology · doi:10.1128/jb.154.1.1-9.1983 · Cited by 1,313
The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403Preprint
Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D., & Sorokin, A. (2001) · Genome Research · doi:10.1101/gr.169701 · Cited by 1,161
The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403
Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D., & Sorokin, A. (2001) · Genome Research · doi:10.1101/gr.gr-1697r · Cited by 1,139
Host interactions of probiotic bacterial surface molecules: comparison with commensals and pathogens
Lebeer, S., Vanderleyden, J., & De Keersmaecker, S. C. J. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2297 · Cited by 1,062
Research works printed but not linked: 1
- 10.1016/j.fmrre.2005.04.009 · DOI
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Solà, L., Quadu, E., Bortolazzo, E., Bertoldi, L., Randazzo, C. L., Pizzamiglio, V., & Solieri, L. (2022) · Research Square · doi:10.21203/rs.3.rs-1873227/v1
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Metadata
- Authors
- de Vos, W. M.
- Venue
- Microbial Cell Factories
- Published
- 2011
- Volume
- 10
- Issue
- Suppl 1
- Pages
- S2
- ISSN
- 1475-2859 (ISSN-L)
- PMC
- PMC3231926
- OpenAlex
- W2097603527
- Cited by
- 134
- References
- 131
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 4 · 2023: 6 · 2022: 10 · 2021: 5 · 2020: 8 · 2019: 9 · 2018: 12 · 2017: 7 · 2016: 8 · 2015: 12 · 2014: 18 · 2013: 12 · 2012: 9
- Type
- conference abstract
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Microbial Cell Factories (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- Academy of Finland
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- lactic acid bacteria, probiotics, starter cultures, metagenomics, comparative genomics, synthetic biology, industrial applications, self-learning systems
- MeSH terms
- Animals, Bifidobacterium, Biotechnology, Fermentation, Food-Processing Industry, Humans, Lactic Acid, Probiotics, Lactobacillales
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