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Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis

Karlsen ST, Vesth TC, Oregaard G, Poulsen VK, Lund O, Henderson G, et al. (2021) Machine learning predicts and provides insights into milk acidification rates of Lactococcus lactis. PLoS ONE 16(3): e0246287

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Regulation and distinct physiological roles of manganese in bacteria

Elleke F Bosma, Martin H Rau, Lieke A van Gijtenbeek, Solvej Siedler, Regulation and distinct physiological roles of manganese in bacteria, FEMS Microbiology Reviews, Volume 45, Issue 6, November 2021, fuab028.

Lacticaseibacillus rhamnosus Impedes Growth of Listeria spp. in Cottage Cheese through Manganese Limitation

van Gijtenbeek, L.A.; Singer, Q.; Steffensen, L.E.; Neuens, S.; Guldager, H.S.; Bidstrup, S.; Høgholm, T.; Madsen, M.G.; Glass, K.; Siedler, S. Lacticaseibacillus rhamnosus Impedes Growth of Listeria spp. in Cottage Cheese through Manganese Limitation. Foods 2021, 10, 1353.

Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12^®

Jensen K, Al-Nakeeb K, Koza A, Zeidan AA. 2021. Updated genome sequence for the probiotic bacterium Bifidobacterium animalis subsp. lactis BB-12^®. Microbiol Resour Announc 10:e00078-21.

Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling

Schöpping, M., Gaspar, P., Neves, A.R. et al. Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling. npj Syst Biol Appl 7, 47 (2021).

Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis

van Gijtenbeek LA, Eckhardt TH, Herrera-Domínguez L, Brockmann E, Jensen K, Geppel A, Nielsen KF, Vindeloev J, Neves AR, Oregaard G. Gene-Trait Matching and Prevalence of Nisin Tolerance Systems in Lactococus lactis. Front Bioeng Biotechnol. 2021 Mar 3;9:622835.

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Use of Cell Envelope Targeting Antibiotics and Antimicrobial Agents as a Powerful Tool to Select for Lactic Acid Bacteria Strains With Improved Texturizing Ability in Milk Fermentations

Sørensen K., Kjærbølling I., Neves A., Machielsen R., Johansen E. Use of Cell Envelope Targeting Antibiotics and Antimicrobial Agents as a Powerful Tool to Select for Lactic Acid Bacteria Strains With Improved Texturizing Ability in Milk Fermentations. 2021 Mar.

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Respiratory physiology of Lactococcus lactis in chemostat cultures and its effect on cellular robustness in frozen and freeze-dried starter cultures

Johanson A, Goel A, Olsson L, Franzén CJ. 2020. Respiratory physiology of Lactococcus lactis in chemostat cultures and its effect on cellular robustness in frozen and freeze-dried starter cultures. Appl Environ Microbiol 86:e02785-19.

Competitive exclusion is a major bioprotective mechanism of lactobacilli against fungal spoilage in fermented milk products

Siedler S, Rau MH, Bidstrup S, Vento JM, Aunsbjerg SD, Bosma EF, McNair LM, Beisel CL, Neves AR. 2020. Competitive exclusion is a major bioprotective mechanism of lactobacilli against fungal spoilage in fermented milk products. Appl Environ Microbiol 86:e02312-19

Complete Genome Sequences of 28 Lactococcal Bacteriophages Isolated from Failed Dairy Fermentation Processes

Marcelli B, de Jong A, Janzen T, Serrano M, Kok J, Kuipers OP. 2020. Complete genome sequences of 28 lactococcal bacteriophages isolated from failed dairy fermentation processes. Microbiology Resource Announcements 9:e01535-19.

Towards the reconstruction of the genome-scale metabolic model of Lactobacillus acidophilus La-14

Cunha E., Zeidan A., Dias O. (2021) Towards the Reconstruction of the Genome-Scale Metabolic Model of Lactobacillus acidophilus La-14. In: Panuccio G., Rocha M., Fdez-Riverola F., Mohamad M., Casado-Vara R. (eds) Practical Applications of Computational Biology & Bioinformatics, 14th International Conference (PACBB 2020). PACBB 2020. Advances in Intelligent Systems and Computing, vol 1240. Springer, Cham.

Criteria to Qualify Microorganisms as “Probiotic” in Foods and Dietary Supplements

Binda S, Hill C, Johansen E, Obis D, Pot B, Sanders ME, Tremblay A and Ouwehand AC (2020) Criteria to Qualify Microorganisms as “Probiotic” in Foods and Dietary Supplements. Front. Microbiol. 11:1662

Screening for texturing Leuconostoc and genomics behind polysaccharide production

Vera Kuzina Poulsen, Anna Koza, Kosai Al-Nakeeb, Gunnar Oeregaard, Screening for texturing Leuconostoc and genomics behind polysaccharide production, FEMS Microbiology Letters, Volume 367, Issue 20, October 2020.

Harnessing the metabolic potential of Streptococcus thermophilus for new biotechnological applications

Markakiou, S., Gaspar, P., Johansen, E., Zeidan, A., and A.R. Neves. (2020). Harnessing the metabolic potential of Streptococcus thermophilus for new biotechnological applications. Curr. Opin. Biotech. 61:142-152.

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Bifidobacterium breve Bif195 Protects Against Small-Intestinal Damage Caused by Acetylsalicylic Acid in Healthy Volunteers

Mortensen, B., Murphy, C., O’Grady, J., Lucey, M., Elsafi, G., Barry, L., Westphal, V., Wellejus, A., Lukjancenko, O., C. Eklund, A., Bjørn Nielsen, H., Baker, A., Damholt, A., E.T. van Hylckama Vlieg, J., Shanahan, F., Buckley, M.

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Putative antibiotic resistance genes present in extant Bacillus licheniformis and Bacillus paralicheniformis strains are probably intrinsic and part of the ancient resistome

Agersø, Y., Bjerre, K., Brockmann, E. Johansen, E., Nielsen, B., Siezen, R., Stuer-Lauridsen, B., Wels, M. and A. Zeidan. (2019). Putative antibiotic resistance genes present in extant Bacillus licheniformis and Bacillus paralicheniformis strains are probably intrinsic and part of the ancient resistome. PLoS ONE 14: e0210363.

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Editorial overview: Microbial solutions in food biotechnology: fermentation, cell factories and beneficial microbes

Bachmann, H. and A. R. Neves. (2019). Editorial overview: Microbial solutions in food biotechnology: fermentation, cell factories and beneficial microbes. Current Opin. Biotechnol. 56:vi-viii.

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Improving End-User Trust in the Quality of Commercial Probiotic Products

Jackson, S.A., Schoeni, J.L., Vegge, C., Pane, M., Stahl, B., Bradley, M., Goldman, V.S., Burguière, P., Atwater, J.B. and M.E. Sanders. (2019). Improving End-User Trust in the Quality of Commercial Probiotic Products. Front. Microbiol. 10: fmicb.2019.00739.

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A specific sugar moiety in the Lactococcus lactis cell wall pellicle is required for infection by CHPC971, a member of the rare 1706 phage species

Marcelli, B., de Jong, A., Karsens, H., Janzen, T., Kok, J. and O.P. Kuipers. (2019). A specific sugar moiety in the Lactococcus lactis cell wall pellicle is required for infection by CHPC971, a member of the rare 1706 phage species. Appl. Environ. Microbiol. 85:e01224-19.

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High-throughput screening for texturing Lactococcus strains

Poulsen, V.K., Derkx, P. and G. Øregaard. (2019). High-throughput screening for texturing Lactococcus strains. FEMS Microbiol. Lett. 366: fnz001.

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Microbiota of sliced cooked ham packaged in modified atmosphere throughout the shelf life

Raimondi, S., Luciani, R.,  Sirangelo, T., Amaretti, A., Leonardi, A., Ulrici, A., Foca, G., D’Auria, G., Moya, A., Zuliani, V., Seibert, T., Soeltoft-Jensen, J. and M. Rossi. (2019). Microbiota of sliced cooked ham packaged in modified atmosphere throughout the shelf life. Int. J. Food Microbiol. 289:200-208.

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Bioprotective mechanisms of lactic acid bacteria against spoilage organisms in food

Siedler, S., Balti, R. and A.R. Neves. (2019). Bioprotective mechanisms of lactic acid bacteria against spoilage organisms in food. Curr. Opin. Biotechnol. 56:138-146.

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Post hatch recovery of a probiotic Enterococcus faecium strain in the yolk sac and intestinal tract of broiler chickens after in ovo injection

Skjøt-Rasmussen, L., Sandvang, D., Blanch, A., Nielsen J.M., Styrishave, T., Schnabl, J., Brockmann, E., Beck, C.N. and A.S. Kiess. (2019). Post hatch recovery of a probiotic Enterococcus faecium strain in the yolk sac and intestinal tract of broiler chickens after in ovo injection. FEMS Microbiol. Lett. 366: fnz078.

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CFD predicted pH gradients in lactic acid bacteria cultivations

Spann, R., Glibstrup, J., Pellicer‐Alborch, K., Junne, S., Neubauer, P., Roca, C., Kold, D., Eliasson Lantz, A., Sin, G., Gernaey, K. V. and U. Krühne. (2019). CFD predicted pH gradients in lactic acid bacteria cultivations. Biotech. Bioeng. 116:769-780.

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Novel isolates of Streptococcus thermophilus bacteriophages from group 5093 identified with an improved multiplex PCR typing method

Szymczak, P., Vogensen, F.K. and T. Janzen. (2019). Novel isolates of Streptococcus thermophilus bacteriophages from group 5093 identified with an improved multiplex PCR typing method. Int. Dairy J. 91:18-24.

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A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages

Szymczak, P., Rau, M.H., Monteiro, J.M., Pinho, M.G., Filipe, S.R., Vogensen, F.K., Zeidan, A.A. and T. Janzen. (2019). A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages. Sci. Rep. 9:7991(2019).

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Encapsulation of Aspartic Protease in Nonlamellar Lipid Liquid Crystalline Phases

Valldeperas, M., Talaikis, N., Dhayal, S.K., Velička, M., Barauskas, J., Niaura, G. and T. Nylander. (2019). Encapsulation of Aspartic Protease in Nonlamellar Lipid Liquid Crystalline Phases. Biophys. J. 5:829-843.

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Hybrid coating of alginate microbeads based on protein‐biopolymer multilayers for encapsulation of probiotics

Yucel Falco, C., Amadei, F., Dhayal, S.K., Cárdenas, M., Tanaka, M. and J. Risbo. (2019). Hybrid coating of alginate microbeads based on protein‐biopolymer multilayers for encapsulation of probiotics. Biotechnol Progress. 35:e2806. 

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Antimicrobial susceptibility testing and tentative epidemiological cut-off values of five Bacillus species relevant for use as animal feed additives or for plant protection

Agersø, Y., Stuer-Lauridsen, B., Bjerre, K., Jensen, M., Johansen, E., Bennedsen, M., Brockmann, E. and B. Nielsen. (2018). Antimicrobial susceptibility testing and tentative epidemiological cut-off values of five Bacillus species relevant for use as animal feed additives or for plant protection. Appl. Environ. Microbiol. 84: e01108-18.

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Transport of valine across the small intestinal epithelium in pigs fed different valine levels and Bacillus subtilis

Blaabjerg, K., Nørgaard, J.V., Nielsen, B., Cantor, M.D., Derkx, P., Sehested, J. and H. D. Poulsen. (2018). Transport of valine across the small intestinal epithelium in pigs fed different valine levels and Bacillus subtilis. J. Anim. Physiol. Anim. Nutr.102:e856–e863.

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MARSI: metabolite analogues for rational strain improvement

Cardoso, J.G.R., Zeidan, A.A, Jensen, K., Sonnenschein, N., Neves, A.R and M.J. Herrgård. (2018). MARSI: metabolite analogues for rational strain improvement. Bioinformatics2018:1-3.

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The possible causal relationship between fragmentation of genomic DNA and formation of viable, but non-culturable probiotic bacteria upon storage in dry state

Hansen, M.-L.R.W., Ramsussen, M.A., Skov, T., Clausen, A. and J. Risbo. (2018). The possible causal relationship between fragmentation of genomic DNA and formation of viable, but non-culturable probiotic bacteria upon storage in dry state. Biotechnol. Progress.34:231- 242.

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Use of natural selection and evolution to develop new starter cultures for fermented foods

Johansen, E. (2018). Use of natural selection and evolution to develop new starter cultures for fermented foods. Ann. Rev. Food Sci. Technol.9:411-428.

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Adaptive evolution of industrial Lactococcus lactis under cell envelope stress provides strain-dependent phenotypic diversity

López-González, M.J., Escobedo, S., Rodriguez, A., Neves, A.R., Janzen, T. and B. Martínez. (2018). Adaptive evolution of industrial Lactococcus lactis under cell envelope stress provides strain-dependent phenotypic diversity. Front. Microbiol. 9:2654-2671.

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Presence of galactose in precultures induces lacS and leads to short lag phase in lactose‑grown Lactococcus lactis cultures

Lorántfy, B., Johanson, A., Faria Oliveira, F., Franzén, C.J., Mapelli, V. and L. Olsson. (2018). Presence of galactose in precultures induces lacS and leads to short lag phase in lactose‑grown Lactococcus lactis cultures. J.Industr. Microbiol. & Biotech. 46:33-43.

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Identification and characterization of a novel antifungal peptide in fermented milk product containing bioprotective Lactobacillus cultures

McNair, L.F., Siedler, S., Vinther, J.M., Hansen, A.M., Neves, A.R., Garrigues, C., Jäger, A.K., Franzyk, H. and D. Staerk. (2018). Identification and characterization of a novel antifungal peptide in fermented milk product containing bioprotective Lactobacillus cultures. FEMS Yeast Res., 18: foy094.

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Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches

Muhammed, M.K., Olsen, M.L., Kot, W., Neve, H., Castro-Mejía, J.L., Janzen, T., Hansen, L.H., Nielsen, D.S., Sørensen, S.J., Heller, K.J. and F.K. Vogensen. (2018). Investigation of the bacteriophage community in induced lysates of undefined mesophilic mixed-strain DL-cultures using classical and metagenomic approaches. Int. J. Food Microbiol. 272:61-72.

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Antimicrobial susceptibility of bifidobacteria from probiotic fermented milk products and determination of the genetic basis of the occurrence of tetracycline resistance in Enterococcus species after in vitro conjugation with Bifidobacterium animalis subsp. lactis

Naghizadeh Raeisi, S., Ghoddusi, H., Boll, E., Farahmand, N., Stuer-Lauridsen, B., Johansen, E., Sutherland, J. and I. Ouoba. (2018). Antimicrobial susceptibility of bifidobacteria from probiotic fermented milk products and determination of the genetic basis of the occurrence of tetracycline resistance in Enterococcus species after in vitro conjugation with Bifidobacterium animalis subsp. lactis. Food Control. 94:205-211.

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Constraint-based modeling in microbial food biotechnology

Rau, M.H and A.A. Zeidan. (2018). Constraint-based modeling in microbial food biotechnology. Biochem. Soc. Trans.46:249-260.

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A probabilistic model-based soft sensor to monitor lactic acid bacteria fermentations

Spann, R., Roca, C., Kold, D., Eliasson Lantz, A., Gernaey, K.V. and G. Sin. (2018). A probabilistic model-based soft sensor to monitor lactic acid bacteria fermentations. Biochem. Eng. J. 135:49-60.

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Cell wall glycans mediate recognition of the dairy bacterium Streptococcus thermophilus by bacteriophages

Szymczak, P., Filipe, S.R., Covas, G., Vogensen, F.K, Neves, A.R. and T. Janzen. (2018). Cell wall glycans mediate recognition of the dairy bacterium Streptococcus thermophilus by bacteriophages. Appl. Environ. Microbiol. e01847-18.

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Influence of Oenococcus oeni and Brettanomyces bruxellensis on Wine Microbial Taxonomic and Functional Potential Profile

Zepeda-Mendoza, M.L., Edwards, N.K., Madsen, M.G., Abel-Kistrup, M., Puetz, L., Sicheritz-Ponten, T. and J.H. Swiegers. (2018). Influence of Oenococcus oeni and Brettanomyces bruxellensis on Wine Microbial Taxonomic and Functional Potential Profile. Am J Enol Vitic. 69:321-333.

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Development of Tyrosine Decarboxylase–Negative Strains of Lactobacillus curvatus by Classical Strain Improvement 

Strøman, P., Sørensen K. I., Derkx, P. m. F. Neves, A. R. (2018) Development of Tyrosine Decarboxylase–Negative Strains of Lactobacillus curvatus by Classical Strain Improvement. Journal of Food Protection 81:4, 628-635.

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Future access and improvement of industrial lactic acid bacteria cultures

Johansen, E. (2017). Future access and improvement of industrial lactic acid bacteria cultures. Microbial Cell Factories.16:230.

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Regulatory and safety requirements for food cultures

Laulund, S., Wind, A., Derkx, P.M.F., and V. Zuliani. (2017). Regulatory and safety requirements for food cultures. Microorganisms5:28.

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Characterization of a membrane-bound C-glucosyltransferase responsible for carminic acid biosynthesis in Dactylopius coccus Costa

Kannangara, R.M., Siukstaite, L., Borch-Jensen, J., Madsen, B., Kongstad, K.T., Stærk, D., Bennedsen, M., Okkels, F.T., Rasmussen, S.A., Larsen, T.O., Frandsen, R.J.N. and B.L. Møller. (2017). Characterization of a membrane-bound C-glucosyltransferase responsible for carminic acid biosynthesis in Dactylopius coccus Costa. Nature Communications 8:1987.

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Untargeted GC-MS metabolomics reveals changes in the metabolite dynamics of industrial scale batch fermentations of Streptococcus thermophilus broth

Khakimov, B., Christiansen, L.D., Heins, A.-L., Sørensen, K.M., Schöller, C., Clausen, A., Skov, T., Gernaey, K.V. and S.B. Engelsen. (2017), Untargeted GC-MS metabolomics reveals changes in the metabolite dynamics of industrial scale batch fermentations of Streptococcus thermophilus broth. Biotechnol. J.12:1700400.

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Evidence for nitric oxide synthase activity in Staphylococcus xylosus mediating nitrosoheme formation

Ras, G., Zuliani, V., Derkx, P., Seibert, T.M., Leroy, S. and R. Talon. (2017). Evidence for nitric oxide synthase activity in Staphylococcus xylosus mediating nitrosoheme formation. Front. Microbiol.

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Polysaccharide production by LAB: from genes to industrial application

Zeidan, A.A., Poulsen, V.K., Janzen, T., Buldo, P., Derkx, P.M.F., Øregard, G. and A.R. Neves. (2017). Polysaccharide production by LAB: from genes to industrial application. FEMS Microbiol. Rev.41(Suppl. 1):SS168-200.

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Enhancing the sweetness of yoghurt through metabolic remodeling of carbohydrate metabolism in Streptococcus thermophilus and Lactobacillus delbrueckii

Sørensen, K., Curic-Bawden, M., Junge, M. P., Janzen, T. and E. Johansen. (2016). Enhancing the sweetness of yoghurt through metabolic remodeling of carbohydrate metabolism in Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. Appl. Environ. Microbiol.82:3683-3692.

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The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology

Derkx, P.M.F., Janzen, T., Sørensen, K.I., Christensen, J.E., Stuer-Lauridsen, B. and E. Johansen. (2014). The art of strain improvement of industrial lactic acid bacteria without the use of recombinant DNA technology. Microbial Cell Factories. 13 (Suppl 1):S5.

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The Science behind the Probiotic Strain Bifidobacterium animalis subsp. lactis BB-12^®

Jungersen, M., Wind, A., Johansen, E., Christensen, J., Stuer-Lauridsen, B. and D. Eskesen. (2014). The Science behind the Probiotic Strain Bifidobacterium animalis subsp. lactis BB-12^®. Microorganisms.2:92-110.

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Effects of genetic, processing or product formulation changes on efficacy and safety of probiotics

Sanders, M.E., Klaenhammer, T.R., Ouwehand, A.C., Pot, B., Johansen, E., Heimbach, J.T., Marco, M.L., Tennilä, J., Ross, R.P., Franz, C., Pagé, N., Pridmore, R.D., Leyer, G., Salminen, S., Charbonneau, D., Call, E. and I. Lenoir-Wijnkoop. (2014). Effects of genetic, processing or product formulation changes on efficacy and safety of probiotics. Annals NY Acad. Sci.1309:1-18.

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