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Gene editing and genetic engineering approaches for advanced probiotics: A review

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  • Ai, L., Zhang, H., Guo, B., Chen, W., Wu, Z. and Wang, Y. (2008). Preparation, partial characterization and bioactivity of exopolysaccharides from Lactobacillus casei LC2W. Carbohydr. Polym. 74:353–357.
  • Aires, J., Anglade, P., Baraige, F., Zagorec, M., Champomier-Verges, M. C. and Butel, M. J. (2010). Proteomic comparison of the cytosolic proteins of three Bifidobacterium longum human isolates and B. longum NCC2705. BMC Microbiol. 10:1–29.
  • Argyri, A. A., Zoumpopoulou, G., Karatzas, K. A., Tsakalidou, E., Nychas, G. J., Panagou, E. Z. and Tassou, C. C. (2013). Selection of potential probiotic lactic acid bacteria from fermented olives by in vitro tests. Food Microbiol. 33:282–291.
  • Auer, T. O., Duroure, K., Cian, A. D., Concordet, J. P. and Bene, F. D. (2014). Highly efficient CRISPR/Cas9- mediated knock-in in zebrafish by homology independent DNA repair. Genome Res. 24:142–153.
  • Botta, C., Langerholc, T., Cencic, A. and Cocolin, L. (2014). In vitro selection and characterization of new probiotic candidates from table olive microbiota. PLoS ONE. 9:944–957.
  • Bottacini, F., Medini, D., Pavesi, A., Turroni, F., Foroni, E., Riley, D., Giubellini, V., Tettelin, H., van Sinderen, D. and Ventura, M. (2010). Comparative genomics of the genus Bifidobacterium. Microbiol. 156:3243–3254.
  • Braff, D., Shis, D. and Collins, J. J. (2016). Synthetic biology platform technologies for antimicrobial applications. Adv. Drug Deliv. Rev. 105:35–43. doi: 10.1016/j.addr.2016.04.006.
  • Burgard, A. P., Pharkya, P. and Maranas, C. D. (2003). Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84:647–657.
  • Celedon, J. C. and Weiss, S. T. (2004). Use of antibacterials in infancy: clinical implications for childhood asthma and allergies. Treat. Respir. Med. 3:291–294.
  • Collado, M. C., Meriluoto, J. and Salminen, S. (2007). Measurement of aggregation properties between probiotics and pathogens: in vitro evaluation of different methods. J. Microbiol. Methods. 71:71–74.
  • Collado, M., Meriluoto, J. and Salminen, S. (2008). Adhesion and aggregation properties of probiotic and pathogen strains. Eur. Food Res. Technol. 226:1065–1073.
  • Coman, M. M., Verdenelli, M. C., Cecchini, C., Silvi, S., Orpianesi, C., Boyko, N. and Cresai, A. (2014). In vitro evaluation of antimicrobial activity of Lactobacillus rhamnosus IMC 501®, Lactobacillus paracasei IMC 502® and SYNBIO® against pathogens. J. Appl. Microbiol. 117:518–527.
  • Dave, R. I. and Shah, N. P. (1998). Ingredient supplementation effects on viability of probiotic bacteria in yogurt. J. Dairy Sci. 81:2804–2816.
  • De Angelis, M., Calasso, M., Cavallo, N., Cagno, R. D. and Gobbetti, M. (2016). Functional proteomics within the genus Lactobacillus. Proteom. 16:946–962.
  • Di Cagno, R., De Angelis, M., Calasso, M. and Gobbetti, M. (2011). Proteomics of the bacterial cross-talk by quorum sensing. J. Proteomics. 74:19–34.
  • Diaz-Torres, M. L., Villedieu, A., Hunt, N., McNab, R., Spratt, D. A., Allan, E., Mullany, P. and Wilson, M. (2006). Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using a metagenomic approach. FEMS Microbiol. Lett. 258:257–262.
  • Dimitrov, D. V. (2011). The human gutome: Nutrigenomics of the host-microbiome interactions. OMICS. 15:419–430.
  • Eck, P. and Friel, J. (2013). Should probiotics be considered as vitamin supplements? Vitam. Miner. 3:124.
  • Fijan, S. (2014). Microorganism with claimed probiotic properties: An overview of recent literature. Int. J. Environ. Res. Public Health. 11:4745–4767.
  • Gorbach, S. L. and Goldin, B. R. (1992). Nutrition and the gastrointestinal microflora. Nutr. Rev. 50:378–381.
  • Goyal, S., Raj, T., Banerjee, C., Imam, J. and Shukla, P. (2013). Isolation and ecological screening of indigenous probiotic microorganisms from curd and chili sauce samples. Int. J. Probiotics Prebiotics. 8:91–94.
  • Gronlund, M. M., Lehtonen, O. P., Eerola, E. and Kero, P. (1999). Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. J. Pediatr. Gastroenterol. Nutr. 28:19–25.
  • Gueimonde, M. and Collado, M. C. (2012). Metagenomics and probiotics. Clin. Microbiol. Infect. 18:32–34.
  • Gupta, S. K. and Shukla, P. (2015). Advanced technologies for improved expression of recombinant proteins in bacteria: perspectives and applications. Crit. Rev. Biotechnol. 18:1–10.
  • Hale, C. R., Majumdar, S., Elmore, J., Pfister, N., Compton, M., Olson, S., Resch, A. M., Glover, C. V. 3rd, Graveley, B. R., Terns, R. M. and Terns, M. P. (2012). Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs. Mol. Cell. 45:292–302.
  • Harmsen, H. J., Wildeboer-Veloo, A. C., Raangs, G. C., Wagendorp, A. A., Klijn, N., Bindels, J. G. et al. (2000). Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J. Pediatr. Gastroenterol. Nutr. 30:61–67.
  • Hickson, M. (2011). Probiotics in the prevention of antibiotic-associated diarrhea and Clostridium difficile infection. Therap. Adv. Gastroenterol. 4:185–197.
  • Imura, K. and Okada, A. (1998). Amino acid metabolism in pediatric patients. Nutr. 14:143–148.
  • Ivanov, I. I. and Honda, K. (2012). Intestinal commensal microbes as immune modulators. Cell Host Microbe. 12:496–508.
  • Jena, P. K., Trivedi, D., Thakore, K., Chaudhary, H., Giri, S. S., and Seshadri, S. (2013). Isolation and characterization of probiotic properties of lactobacilli isolated from rat fecal microbiota. Microbiol. Immunol. 57:407–416.
  • Jones, M. L., Martoni, C. J. and Prakash, S. (2012). Cholesterol lowering and inhibition of sterol absorption by Lactobacillus reuteri NCIMB 30242: a randomized controlled trial. Eur. J. Clin. Nutr. 66:1234–1241.
  • Kailasapathy, K. and Chin, J. (2000). Survival and therapeutic potential of probiotic organisms with reference to Lactobacillus acidophilus and Bifidobacterium spp. Immunol. Cell Biol. 78:80–88.
  • Kailasapathy, K. and Rybka, S. (1997). Lactobacillus acidophilus and Bifidobacterium spp.-their therapeutic potential and survival in yoghurt. Aust. J. Dairy Technol. 52:28–35.
  • Kanchiswamy, C. N., Maffei, M., Malnoy, M., Velasco, R. and Kim, J. S. (2016). Fine-tuning next-generation genome editing tools. Trends Biotechnol. 34:562–574.
  • Kekkonen, R. A., Sysi-Aho, M., Seppanen-Laakso, T., Julkunen, I., Vapaatalo, H., Oresic, M. and Korpela, R. (2008). Effect of probiotic Lactobacillus rhamnosus GG intervention on global serum lipidomic profiles in healthy adults. World J. Gastroenterol. 14:3188–3194.
  • Khoroshkin, M. S., Leyn, S. A., Sinderen, D. V. and Rodionov, D. A. (2016). Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus. Front. Microbiol. 2016; 7:120.
  • Kim, H., Kim, T. and Lee, S. Y. (2008). Metabolic flux analysis and metabolic engineering of microorganisms. Mol. BioSyst. 4:113–120.
  • Kinoshita, H., Imoto, S., Suda, Y., Ishida, M., Watanabe, M., Kawai, Y., Kitazawa, H., Miura, K., Horii, A. and Saito, T. (2013). Proposal of screening method for intestinal mucus adhesive lactobacilli using the enzymatic activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Anim. Sci. J. 84:150–158.
  • Kleerebezem, M., Hols, P., Bernard, E., Rolain, T., Zhou, M., Siezen, R. J. and Bron, P. A. (2010). The extracellular biology of the lactobacilli. FEMS Microbiol. Rev. 34:199–230.
  • Kullisaar, T., Zilmer, M., Mikelsaar, M., Vihalemm, T., Annuk, H., Kairane, C. and Kilk, A. (2002). Two antioxidative lactobacilli strains as promising probiotics. Int. J. Food Microbiol. 72:215–224.
  • Kumar, V., Baweja, M., Singh, P. K. and Shukla, P. (2016). Recent developments in systems biology and metabolic engineering of plant–microbe interactions. Front. Plant Sci. 7:1421.
  • Kwon, S. K., Kwak, M. J., Seo, J. G., Chung, M. J. and Kim, J. F. (2015). Complete genome sequence of Bifidobacterium longum KCTC 12200BP, a probiotic strain promoting the intestinal health. J. Biotechnol. 214:169–170.
  • Lahteinen, T., Malinen, E., Koort, J. M., Mertaniemi-Hannus, U., Hankimo, T., Karikoski, N., Pakkanen, S., Laine, H., Sillanpaa, H., Soderholm, H. and Palva, A. (2010). Probiotic properties of Lactobacillus isolates originating from porcine intestine and feces. Anaerobe. 16:293–300.
  • Lahtinen, S. J., Jalonen, L., Ouwehand, A. C. and Salminen, S. J. (2007). Specific Bifidobacterium strains isolated from elderly subjects inhibit growth of Staphylococcus aureus. Int. J. Food Microbiol. 117:125–128.
  • Laparra, J. M. and Sanz, Y. (2009). Comparison of in vitro models to study bacterial adhesion to the intestinal epithelium. Lett. Appl. Microbiol. 49:695–701.
  • Lavermicocca, P., Valerio, F., Lonigro, S. L., Di Leo, A. and Visconti, A. (2008). Antagonistic activity of potential probiotic lactobacilli against the ureolytic pathogen Yersinia enterocolitica. Curr. Microbiol. 56:175–181.
  • Lee, J. H. and O'Sullivan, D. J. (2010). Genomic insights into bifidobacteria. Microbiol. Mol. Biol. Rev. 74:378–416.
  • Lee, J. H. and O'Sullivan, D. J. (2008). Metabolic engineering of Lactococcus lactis for the development of a one-step bioconversion of lactose into tagatose. ASM Annual Meeting, Boston, MA.
  • Lee, S. Y., Park, J. M. and Kim, T. Y. (2011). Application of metabolic flux analysis in metabolic engineering. Meth. Enzymol. 498:67–93.
  • Lepage, P., Leclerc, M. C., Joossens, M., Mondot, S., Blottière, H. M., Raes, J., Ehrlich, D. and Doré, J. (2013). A metagenomic insight into our gut's microbiome. Gut. 62:146–158.
  • Lew, L. C. and Liong, M. T. (2013). Bioactives from probiotics for dermal health: functions and benefits. J. Appl. Microbiol. 114:1241–1253.
  • Li, B., Liu, F., Tang, Y., Luo, G., Evivie, S., Zhang, D., Wang, N., Li, W. and Huo, G. (2015). Complete genome sequence of Lactobacillus helveticus KLDS1.8701, a probiotic strain producing bacteriocin. J. Biotechnol. 212:90–91.
  • Li, H. and O'Sullivan, D. J. (2003). Altered growing conditions can inhibit nisin production in lactic cultures by disrupting the signal transduction pathway. J. Dairy Sci. 86:1–30.
  • Li, P., and Gu, Q. (2016). Complete genome sequence of Lactobacillus plantarum LZ95, a potential probiotic strain producing bacteriocins and B-group vitamin riboflavin. J. Biotechnol. 229:1–2.
  • Li, P., Zhou, Q. and Gu, Q. (2016). Complete genome sequence of Lactobacillus plantarum LZ227, a potential probiotic strain producing B-group vitamins. J. Biotechnol. 234:66–70.
  • Li, W., Xia, X., Chen, X., Rui, X., Jiang, M., Zhang, Q., Zhou, J. and Dong, M. (2015). Complete genome sequence of Lactobacillus helveticus MB2-1, a probiotic bacterium producing exopolysaccharides. J. Biotechnol. 209:14–15.
  • Li, N., Wang, Y., Zhu, P., Liu, Z., Guo, B. and Ren, J. (2015). Improvement of exopolysaccharide production in Lactobacillus casei LC2W by overexpression of NADH oxidase gene. Microbiol. Res. 171:73–77.
  • Lin, Z. H., Long, H. X., Bo, Z. and Wu, Y. (2008). New descriptors of amino acids and their application to peptide QSAR study. Peptides. 29:1798–1805.
  • Liu, F., Li, B., Du, J., Yu, S., Li, W., Evivie, S. E., Guo, L., Ding, X., Xu, M. and Huo, G. (2016). Complete genome sequence of Enterococcus durans KLDS6.0930, a strain with probiotic properties. J. Biotechnol. 217:49–50.
  • Liu, J. K., Wei, C. H., Hou, X. L. and Yu, L. Y. (2014). Passive protection of mice pups through oral or intranasal immunization of dams with recombinant Lactobacillus casei vaccine against ETEC F41. Res. Vet. Sci. 96:283–287.
  • Liu, L. and Li, P. (2016). Complete genome sequence of Lactobacillus paraplantarum L-ZS9, a probiotic starter producing class II bacteriocins. J. Biotechnol. 222:15–16.
  • Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F. J., Wolf, Y. I., Yakunin, A. F., van der Oost, J. and Koonin, E. V. (2011). Evolution and classification of the CRISPR–Cas systems. Nat. Rev. Microbiol. 9:467–477.
  • Manichanh, C., Rigottier‐Gois, L., Bonnaud, E., Gloux, K., Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P., Roca, J. and Dore, J. (2006). Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut. 55:205–211.
  • Marco, M. L., de Vries, M. C., Wels, M., Molenaar, D., Mangell, P., Ahrne, S., de Vos, W. M., Vaughan, E. E. and Kleerebezem, M. (2010). Convergence in probiotic Lactobacillus gut- adaptive responses in humans and mice. ISME J. 4:1481–1484.
  • Marteau, P. R., de Vrese, M., Cellier, C. J. and Schrezenmeir, J. (2001). Protection from gastrointestinal diseases with the use of probiotics. Am. J. Clin. Nutr. 73:430–436.
  • Martin, J. H. (1996). Technical considerations for incorporating Bifidobacteria and bifidogenic factors into dairy products. Bull. IDF 313:49–51.
  • Martin, F. P., Sprenger, N., Montoliu, I., Rezzi, S., Kochhar, S. and Nicholson, J. K. (2010). Dietary modulation of gut functional ecology studied by fecal metabonomics. J. Proteome. Res. 9:5284–5295.
  • Matvei, S., Khoroshkin, S. A., Leyn, D. V. S. and Dmitry, A. R. (2016). Transcriptional regulation of carbohydrate utilization pathways in the Bifidobacterium genus. Front. Microbiol. 7:1–14. doi: 10.3389/fmicb.2016.00120.
  • McConnell, E. L., Fadda, H. M. and Basit, A. W. (2008). Gut instincts: explorations in intestinal physiology and drug delivery. Int. J. Pharm. 364:213–226.
  • Molenaar, D., Bringel, F., Schuren, F. H., Vos, W. M., Siezen, R. J. and Kleerebezem, M. (2005). Exploring Lactobacillus plantarum genome diversity by using microarrays. J. Bacteriol. 187:6119–6127.
  • Oh, J. H. and van Pijkeren, J. P. (2014). CRISPR–Cas9-assisted recombineering in Lactobacillus reuteri. Nucleic Acids Res. 42:e131.
  • O'Sullivan, D. (2012). Lactic acid bacteria and bifidobacteria: current progress in advanced research a book review. Microb. 7:287–288.
  • O'Sullivan, O., O'Callaghan, J., Vegas, A. S., McAuliffe, O., Slattery, L., Kaleta, P., Callanan, M., Fitzgerald, G. F., Ross, R. P. and Beresford, T. (2009). Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol. 9:1–9.
  • Ouwehand, A. C. and Salminen, S. J. (1998). The health effect of cultured milk products with viable and non-viable bacteria. Int. Dairy J. 8:749–758.
  • Patro, J. N., Ramachandran, P., Barnaba, T., Mammel, M. K., Lewis, J. L. and Elkins, C. A. (2016). Culture-independent metagenomic surveillance of commercially available probiotics with high-throughput next-generation sequencing. mSphere 1(2):e00057–16. doi:10.1128/mSphere.00057-16.
  • Penders, J., Thijs, C., Vink, C., Stelma, F. F., Snijders, B., Kummeling, I. et al. (2006). Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 118:511–521.
  • Pharkya, P. and Maranas, C. D. (2006). An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab. Eng. 8:1–13.
  • Pharkya, P., Burgard, A. P. and Maranas, C. D. (2004). Optstrain: a computational framework for redesign of microbial production systems. Genome Res. 14:2367–2376.
  • Pisano, M. B., Viale, S., Conti, S., Fadda, M. E., Deplano, M., Melis, M. P., Deiana, M, and Cosentino, S. (2014). Preliminary evaluation of probiotic properties of Lactobacillus strains isolated from Sardinian dairy products. Biomed. Res. Int. 2014:286390.
  • Pistiner, M., Gold, D. R., Abdulkerim, H., Hoffman, E. and Celedon, J. C. (2008). Birth by cesarean section, allergic rhinitis, and allergic sensitization among children with a parental history of atopy. J. Allergy Clin. Immunol. 122:274–279.
  • Preidis, G. A., Hill, C., Guerrant, R. L., Ramakrishna, B. S. and Tannock, G. W. (2011). Probiotics, enteric, and diarrheal diseases, and global health. Gastroenterology. 140:8–14. In press.
  • Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C. et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464:59–65.
  • Qiu, Z. B., Chen, J., Chen, J. J., Rong, L., Ding, W. Q., Yang, H. J. and Zhong, L. (2013). Effect of recombinant Lactobacillus casei expressing interleukin-10 in dextran sulfate sodium-induced colitis mice. J. Dig. Dis. 14:76–83.
  • Rebollar, E. A., Antwis, R. E., Becker, M. H., Belden, L. K., Bletz, M. C., Brucker, R. M., Harrison, X. A., Hughey, M. C., Kueneman, J. G., Loudon, A. H., McKenzie, V., Medina, D., Minbiole, K. P. C., Rollins-Smith, L. A., Walke, J. B., Weiss, S., Woodhams, D. C. and Harris, R. N. (2016). Using “omics” and integrated multi-omics approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases. Front. Microbiol. 7:68. doi: 10.3389/fmicb.2016.00068.
  • Reister, M., Hoffmeier, K., Krezdorn, N., Rotter, B., Liang, C., Rund, S., Dandekar, T., Sonnenborn, U. and Oelschlaeger, T. A. (2014). Complete genome sequence of the gram-negative probiotic Escherichia coli strain Nissle 1917. J. Biotechnol. 187:106–107.
  • Ruiz, L., Hidalgo, C., Blanco-Míguez, A., Lourenço, A., Sánchez, B. and Margolles, A. (2016). Tackling probiotic and gut microbiota functionality through proteomics. J. Proteom. 147:28–39.
  • Saha, R., Chowdhury, A. and Maranas, C. D. (2014). Recent advances in the construction of metabolic models and integration of omics data. Curr. Opin. Biotechnol. 29:39–45.
  • Saulnier, D. M., Santos, F., Roos, S., Mistretta, T. A., Spinler, J. K., Molenaar, D., Teusink, Bas. and Versalovic, J. (2011). Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS ONE. 6:1–14.
  • Saulnier, D. M., Santos, F., Roos, S., Mistretta, T. A., Spinler, J. K., Molenaar, D., Teusink, B. and Versalovic, J. (2011). Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS ONE. 6:18783.
  • Schaeffer, S. M. and Nakata, P. A. (2015). CRISPR/Cas9-mediated genome editing and gene replacement in plants: transitioning from lab to field. Plant Sci. 240:130–142.
  • Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C. and Izard, J. (2012). Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 13:42.
  • Selle, K., Klaenhammer, T. R. and Barrangou, R. (2015). CRISPR-based screening of genomic island excision events in bacteria. Proc. Natl. Acad. Sci. 112:8076–8081.
  • Serban, D. E. (2011). The gut microbiota in the metagenomics era: sometimes a friend, sometimes a foe. Roum. Arch. Microbiol. Immunol. 70:134–140.
  • Serban, D. E. (2014). Gastrointestinal cancers: Influence of gut microbiota, probiotics and Prebiotics. Cancer Lett. 345:258–270.
  • Shah, N. P. (2000). Probiotic bacteria: selective enumeration and survival in dairy foods. J. Dairy Sci. 83:894–907.
  • Shima, T., Fukushima, K., Setoyama, H., Imaoka, A., Matsumoto, S., Hara, T., Suda, K. and Umesaki, Y. (2008). Differential effects of two probiotic strains with different bacteriological properties on intestinal gene expression, with special reference to indigenous bacteria. FEMS Immunol. Med. Microbiol. 52:69–77.
  • Singh, P. K. and Shukla, P. (2011). Molecular modeling and docking of microbial inulinases towards perceptive enzyme-substrate interactions. Indian J. Microbiol. 52:373–380.
  • Singh, P. K. and Shukla, P. (2015). Systems biology as an approach for deciphering microbial interactions. Brief. Funct. Genomics. 14:166–168.
  • Singh, P. K., Joseph, J., Goyal, S., Grover, A. and Shukla, P. (2016). Functional analysis of the binding model of microbial inulinases using docking and molecular dynamics simulation. J. Mol. Model. 22:1–7.
  • Sontheimer, E. and Barrangou, R. (2015). The bacterial origins of the CRISPR genome editing revolution. Hum. Gene Ther. 26:413–424.
  • Spor, A., Koren, O. and Ley, R. (2011). Unravelling the effects of the environment and host genotype on the gut microbiome. Nat. Rev. Microbiol. 9:279–290.
  • Suebwongsa, N., Lulitanon, V., Mayo, B., Yotpanya, P. and Panya, M. (2016). Development of an Escherichia coli–Lactobacillus casei shuttle vector for heterologous protein expression in Lactobacillus casei. SpringerPlus 5:169, doi:10.1186/s40064-016-1760-1.
  • Suebwongsa, N., Panya, M., Namwat, W., Sookprasert, S., Redruello, B., Mayo, B., Alvarez, M. A. and Lulitanond, V. (2013). Cloning and expression of a codon-optimized gene encoding the influenza A virus nucleocapsid protein in Lactobacillus casei. Int. Microbiol. 16:93–101.
  • Sun, Z., Zhang, W., Bilige, M. and Zhang, H. (2014). Complete genome sequence of the probiotic Lactobacillus fermentum F-6 isolated from raw milk. J. Biotechnol. 194:110–111.
  • Tan, P. L. and Liong, M. T. (2014). In silico approaches for probiotic-derived bioactives. Trends Biotechnol. 32:599–601.
  • Tan, Q., Xu, H., Aguilar, Z. P., Peng, S., Dong, S., Wang, B., Li, P., Chen, T., Xu, F. and Wei, H. (2013). Safety assessment and probiotic evaluation of Enterococcus faecium YF5 isolated from sourdough. J. Food Sci. 78:587–593.
  • Tang, W. H., Wang, Z., Levison, B. S., Koeth, R. A., Britt, E. B., Fu, X., Wu, Y. and Hazen, S. L. (2013). Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. New Engl. J. Med. 368:1575–1584.
  • Tap, J., Mondot, S., Levenez, F., Pelletier, E. et al. (2009). Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11:2574–2584.
  • Upadrasta, A., Stanton, C., Hill, C., Fitzgerald, G. and Ross, R. P. (2011). Improving the stress tolerance of probiotic cultures: recent trends and future directions, in Stress Responses of Lactic Acid Bacteria, eds E. Tsakalidou and K. Papadimitriou, New York: Springer, 395–438.
  • Van, P. J. P. and Britton, R. A. (2014). Precision genome engineering in lactic acid bacteria. Microb. Cell Factor. 13:1–10.
  • Vanamee, E. S., Santagata, S. and Aggarwal, A. K. (2001). FokI requires two specific DNA sites for cleavage. J. Mol. Biol. 309:69–78.
  • Ventura, M., O'Flaherty, S., Claesson, M. J., Turroni, F., Klaenhammer, T. R., van Sinderen, D. and O'Toole, P. W. (2009). Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat. Rev. Microbiol. 7:61–71.
  • Wang, H., O'Sullivan, D. J., Baldwin, K. and Mckay, L. L. (1999). Cloning, sequencing and expression of the pyruvate carboxylase gene in Lactococcus lactis subsp. lactis C2 and characterization of a pyc mutant. Appl. Environ. Microbiol. 66:1223–1227. In press.
  • Wilson, S. A. and Roberts, S. C. (2014). Metabolic engineering approaches for production of biochemicals in food and medicinal plants. Curr. Opin. Biotechnol. 26:174–182.
  • Wu, Q. and Shah, N. P. (2017). The potential of species-specific tagatose-6-phosphate (T6P) pathway in Lactobacillus casei group for galactose reduction in fermented dairy foods. Food Microbiol. 62:178–187.
  • Yadav, R. and Shukla, P. (2015). An overview of advanced technologies for selection of probiotics and their expediency: a review. Crit. Rev. Food Sci. Nutr. doi: 10.1080/10408398.2015.1108957.
  • Yadav, R., Singh, P. K. and Shukla, P. (2017). Metabolic engineering for probiotics and their genome-wide expression profiling: areview. Curr. Protein. Pept. Sci. 18:1–7.
  • Yang, B., Chen, H., Tian, F., Zhao, J., Gu, Z., Zhang, H., Chen, Y. Q. and Chen, W. (2015). Complete genome sequence of Lactobacillus plantarum ZS2058, a probiotic strain with high conjugated linoleic acid production ability. J. Biotechnol. 214:212–213.
  • Yang, Y., An, H., Zhai, Z., Wang, G., Li, J. and Hao, Y. (2016). Complete genome sequence of Lactobacillus helveticus CAUH18, a potential probiotic strain originated from koumiss. J. Biotechnol. 224:18–19.
  • Yao, G., Gao, P. and Zhang, W. (2016). Complete genome sequence of probiotic Bacillus coagulans HM-08: a potential lactic acid producer. J. Biotechnol. 228:71–72.
  • Zhang, D., Ji, H., Liu, H., Wang, S., Wang, J. and Wang, Y. (2016). Complete genome sequence of probiotic Lactobacillus reuteri ZLR003 isolated from healthy weaned pig. J. Biotechnol. 228:69–70.
  • Zhang, W., Sun, Z., Bilige, M. and Zhang, H. (2015). Complete genome sequence of probiotic Lactobacillus plantarum P-8 with antibacterial activity. J. Biotechnol. 193:41–42.
  • Zheng, B., Jiang, X., Cheng, H., Xu, Z., Li, A., Hu, X. and Xiao, Y. (2015). Complete genome sequence of Lactobacillus heilongjiangensis DSM 28069(T): insight into its probiotic potential. J. Biotechnol. 216:65–66.
  • Zhou, M., Theunissen, D., Wels, M. and Siezen, R. J. (2010). LAB-Secretome: genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of lactic acid bacteria. BMC Genom. 11:1–16.
  • Zhu, D., Sun, Y., Huo, G. C., Yang, L., Liu, F., Li, A. and Meng, X. C. (2016). Complete genome sequence of Bifidobacterium animalis subsp. lactis KLDS 2.0603, a probiotic strain with digestive tract resistance and adhesion to the intestinal epithelial cells. J. Biotechnol. 220:49–50.
  • Zoetendal, E. G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C. C. G. M., Troost, F. J., Bork, P., Wels, M., Vos, W. M., and Kleerebezem, M. (2012). The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 6:1415–1426.

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