References
-
Larsen, I. S. et al. Experimental diets dictate the metabolic benefits of probiotics in obesity. Gut Microbes 15, (2023).
-
Nicola, T. et al. A lactobacilli-based inhaled live biotherapeutic product attenuates pulmonary neutrophilic inflammation. Nat. Commun. 15, (2024).
-
Leroy, F. & De Vuyst, L. Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends Food Sci. Technol. 15, 67–78 (2004).
-
Legein, M. et al. Modes of Action of Microbial Biocontrol in the Phyllosphere. Front. Microbiol. 11, 544057 (2020).
-
Backer, R. et al. Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture. Front. Plant. Sci. 9, 402666 (2018).
-
Lebeer, S. et al. Functional analysis of lactobacillus rhamnosus GG pili in relation to adhesion and immunomodulatory interactions with intestinal epithelial cells. Appl. Environ. Microbiol. 78, 185–193 (2012).
-
de Vries, M. C., Vaughan, E. E., Kleerebezem, M. & de Vos, W. M. Lactobacillus plantarum—survival, functional and potential probiotic properties in the human intestinal tract. Int. Dairy. J. 16, 1018–1028 (2006).
-
FDA. Early Clinical Trials with Live Biotherapeutic Products: Chemistry, Manufacturing, and Control Information; Guidance for Industry. (2016).
-
Vargason, A. M. & Anselmo, A. C. Live Biotherapeutic Products and Probiotics for the Skin. Adv. NanoBiomed Res. 1, 1–6 (2021).
-
Hemmerling, A. et al. Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomised, placebo-controlled trial. Lancet Microbe. 6, 1–12 (2025).
-
Smillie, C. S. et al. Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell. Host Microbe. 23, 229–240e5 (2018).
-
Kumar, R. et al. Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile. NPJ Biofilms Microbiomes 3, (2017).
-
Lebeer, S. et al. Selective targeting of skin pathobionts and inflammation with topically applied lactobacilli. Cell. Rep. Med. 3, 100521 (2022).
-
Cohen, C. R. et al. Randomized Trial of Lactin-V to Prevent Recurrence of Bacterial Vaginosis. N Engl. J. Med. 382, 1906–1915 (2020).
-
Van Holm, W. et al. Antimicrobial potential of known and novel probiotics on in vitro periodontitis biofilms. npj Biofilms Microbiomes. 9, 1–12 (2023).
-
De Boeck, I. et al. Lacticaseibacillus rhamnosus GG in a chewable colonizes the nose and facilitates local immune benefits in allergic rhinoconjunctivitis patients. Microbiol Spectr 0, (2025).
-
Wendel, U. Assessing Viability and Stress Tolerance of Probiotics—A Review. Front. Microbiol. 12, 818468 (2022).
-
Capozzi, V., Fragasso, M. & Russo, P. Microbiological Safety and the management of microbial resources in artisanal foods and beverages: The need for a transdisciplinary assessment to conciliate actual trends and risks avoidance. Microorganisms 8, (2020).
-
Ashaolu, T. J. Safety and quality of bacterially fermented functional foods and beverages: a mini review. Food Qual. Saf. 4, 123–127 (2020).
-
Bron, P. A., Grangette, C., Mercenier, A., De Vos, W. M. & Kleerebezem, M. Identification of Lactobacillus plantarum Genes That Are Induced in the Gastrointestinal Tract of Mice. J. Bacteriol. 186, 5721 (2004).
-
Spacova, I. et al. Expression of fluorescent proteins in Lactobacillus rhamnosus to study host–microbe and microbe–microbe interactions. Microb. Biotechnol. 11, 317–331 (2018).
-
Turpin, P. E., Maycroft, K. A., Bedford, J., Rowlands, C. L. & Wellington, E. M. H. A rapid luminescent-phage based MPN method for the enumeration of Salmonella typhimurium in environmental samples. Lett. Appl. Microbiol. 16, 24–27 (1993).
-
Fasanello, V. J., Liu, P., Botero, C. A. & Fay, J. C. High-throughput analysis of adaptation using barcoded strains of Saccharomyces cerevisiae. PeerJ 8, e10118 (2020).
-
Fleischmann, R. D. et al. Whole-Genome Random Sequencing and Assembly of Haemophilus influenzae Rd. Sci. (80-). 269, 496–512 (1995).
-
Parks, D. H. et al. An ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50, D785–D794 (2022).
-
Anderson, B. D. & Bisanz, J. E. Challenges and opportunities of strain diversity in gut microbiome research. Front. Microbiol. 14, 1–8 (2023).
-
Dijkshoorn, L., Ursing, B. M. & Ursing, J. B. Strain, clone and species: Comments on three basic concepts of bacteriology. J. Med. Microbiol. 49, 397–401 (2000).
-
Hill, C. & International Scientific Association for Probiotics and Prebiotics (ISAPP). What is a strain in microbiology and why does it matter? ISAPP Sci. Blog (2022).
-
Van Rossum, T., Ferretti, P., Maistrenko, O. M. & Bork, P. Diversity within species: interpreting strains in microbiomes. Nat. Rev. Microbiol. 18, 491–506 (2020).
-
Pasolli, E. et al. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat. Commun. 11, 1–12 (2020).
-
De Boeck, I. et al. Randomized, double-blind, placebo-controlled trial of a throat spray with selected Lactobacilli in COVID-19 outpatients. Microbiol. Spectr. 10, (2022).
-
De Boeck, I. et al. Lactobacilli Have a Niche in the Human Nose. Cell. Rep. 31, 107674 (2020).
-
Lebeer, S. et al. A citizen-science-enabled catalogue of the vaginal microbiome and associated factors. Nat. Microbiol. 8, 2183–2195 (2022).
-
Wuyts, S. et al. Carrot juice fermentations as man-made microbial ecosystems dominated by lactic acid bacteria. Appl. Environ. Microbiol. 84, e00134–e00118 (2018).
-
Alimolaei, M. & Golchin, M. A comparison of methods for extracting plasmids from a difficult to lyse bacterium: Lactobacillus casei. Biologicals 45, 47–51 (2017).
-
Wuyts, S. et al. Comparative genome analysis of lactobacillus mudanjiangensis, an understudied member of the lactobacillus plantarum group. Microb. Genomics 5, (2019).
-
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
-
Orakov, A. et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 22, 1–19 (2021).
-
Kankainen, M. et al. Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human- mucus binding protein. Proc. Natl. Acad. Sci. 106, 17193–17198 (2009).
-
Petrova, M. I. et al. Comparative genomic and phenotypic analysis of the vaginal probiotic lactobacillus rhamnosus GR-1. Front. Microbiol 9, (2018).
-
Kleerebezem, M. et al. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. 100, 1990–1995 (2003).
-
Malik, S. et al. High mannose-specific lectin Msl mediates key interactions of the vaginal Lactobacillus plantarum isolate CMPG5300. Sci. Rep. 2016 61 (6), 1–16 (2016).
-
Danielsen, M. Characterization of the tetracycline resistance plasmid pMD5057 from Lactobacillus plantarum 5057 reveals a composite structure. Plasmid 48, 98–103 (2002).
-
Leer, R. J., van Luijk, N., Posno, M. & Pouwels, P. H. Structural and functional analysis of two cryptic plasmids from Lactobacillus pentosus MD353 and Lactobacillus plantarum ATCC 8014. MGG Mol. Gen. Genet. 234, 265–274 (1992).
-
Allonsius, C. N. et al. Inhibition of Candida albicans morphogenesis by chitinase from Lactobacillus rhamnosus GG. Sci. Rep. 9, 2900 (2019).
-
Reid, G., Cook, R. L. & Bruce, A. W. Examination of strains of lactobacilli for properties that may influence bacterial interference in the urinary tract. J. Urol. 138, 330–335 (1987).
-
Sriramulu, D. D. et al. Lactobacillus reuteri DSM 20016 produces cobalamin-dependent diol dehydratase in metabolosomes and metabolizes 1,2-propanediol by disproportionation. J. Bacteriol. 190, 4559–4567 (2008).
-
Jörissen, J. et al. Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species. mSystems 6, (2021).
-
Mignolet, J., Fontaine, L., Kleerebezem, M. & Hols, P. Complete genome sequence of Streptococcus salivarius HSISS4, a human commensal bacterium highly prevalent in the digestive tract. Genome Announc 4, (2016).
-
Butler, R. R., Soomer-James, J. T. A., Frenette, M. & Pombert, J. F. Complete genome sequences of two human oral microbiome commensals, Streptococcus salivarius ATCC 25975 and S. salivarius ATCC 27945. Genome Announc 5, (2017).
-
Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50, D785–D794 (2022).
-
Hyatt, D. et al. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 11, 1–11 (2010).
-
Wittouck, S., Eilers, T., van Noort, V. & Lebeer, S. SCARAP: scalable cross-species comparative genomics of prokaryotes. Bioinformatics btae735 https://doi.org/10.1093/bioinformatics/btae735 (2024).
-
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T. & Aluru, S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 2018. 91 9, 1–8 (2018).
-
Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7, 203–214 (2000).
-
Bustin, S. A. et al. The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611–622 (2009).
-
Lebeer, S. et al. Selective targeting of skin pathobionts and inflammation with topically applied lactobacilli. Cell Rep. Med 3, (2022).
-
Wuyts, S. et al. Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features. mSystems 2, (2017).
-
Vander Donck, L. et al. Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli. Cell Rep 44, (2025).
