Next-generation probiotics: the spectrum from probiotics to live biotherapeutics


The leading probiotics currently available to consumers are generally drawn from a narrow range of organisms. Knowledge of the gut microbiota and its constituent actors is changing this paradigm, particularly given the phylogenetic range and relatively unknown characteristics of the organisms under investigation as novel therapeutics. For this reason, and because their development is likely to be more amenable to a pharmaceutical than a food delivery route, these organisms are often operationally referred to as next-generation probiotics, a concept that overlaps with the emerging concept of live biotherapeutic products. The latter is a class of organisms developed exclusively for pharmaceutical application. In this Perspective, we discuss what lessons have been learned from working with traditional probiotics, explore the kinds of organisms that are likely to be used as novel microbial therapeutics, discuss the regulatory framework required, and propose how scientists may meet this challenge.

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Figure 1: Timeline of selected milestones in the history of probiotics and next-generation probiotics.
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  1. 1

    Hill, C. et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat. Rev. Gastroenterol. Hepatol. 11, 506–514 (2014).

    Article  PubMed  Google Scholar 

  2. 2

    EFSA. Statement on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA. 2: suitability of taxonomic units notified to EFSA until March 2015. EFSA J. 13, 4138 (2015).

    Article  Google Scholar 

  3. 3

    Sun, X., Fiala, J. L. & Lowery, D. Patent watch: modulating the human microbiome with live biotherapeutic products: intellectual property landscape. Nat. Rev. Drug. Discov. 15, 224–225 (2016).

    CAS  Article  PubMed  Google Scholar 

  4. 4

    Deng, H. M. et al. A novel strain of Bacteroides fragilis enhances phagocytosis and polarises M1 macrophages. Sci. Rep. 6, 29401 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. 5

    Moncrief, J. S., Duncan, A. J., Wright, R. L., Barroso, L. A. & Wilkins, T. D. Molecular characterization of the fragilysin pathogenicity islet of enterotoxigenic Bacteroides fragilis. Infect. Immun. 66, 1735–1739 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6

    Obiso, R. J. Jr., Azghani, A. O. & Wilkins, T. D. The Bacteroides fragilis toxin fragilysin disrupts the paracellular barrier of epithelial cells. Infect. Immun. 65, 1431–1439 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Shiryaev, S. A. et al. Substrate cleavage profiling suggests a distinct function of Bacteroides fragilis metalloproteinases (fragilysin and metalloproteinase II) at the microbiome-inflammation-cancer interface. J. Biol. Chem. 288, 34956–34967 (2013).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8

    Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & Kasper, D. L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107–118 (2005).

    CAS  Article  Google Scholar 

  9. 9

    Ulsemer, P., Toutounian, K., Schmidt, J., Karsten, U. & Goletz, S. Preliminary safety evaluation of a new Bacteroides xylanisolvens isolate. Appl. Environ. Microbiol. 78, 528–535 (2012).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. 10

    Ulsemer, P. et al. Impact of oral consumption of heat-treated Bacteroides xylanisolvens DSM 23964 on the level of natural TFα-specific antibodies in human adults. Benef. Microbes 7, 485–500 (2016).

    CAS  Article  PubMed  Google Scholar 

  11. 11

    Yanagibashi, T. et al. IgA production in the large intestine is modulated by a different mechanism than in the small intestine: Bacteroides acidifaciens promotes IgA production in the large intestine by inducing germinal center formation and increasing the number of IgA+ B cells. Immunobiology 218, 645–651 (2013).

    CAS  Article  PubMed  Google Scholar 

  12. 12

    Woo, T. D. et al. Inhibition of the cytotoxic effect of Clostridium difficile in vitro by Clostridium butyricum MIYAIRI 588 strain. J. Med. Microbiol. 60, 1617–1625 (2011).

    CAS  Article  PubMed  Google Scholar 

  13. 13

    Shimbo, I. et al. Effect of Clostridium butyricum on fecal flora in Helicobacter pylori eradication therapy. World J. Gastroenterol. 11, 7520–7524 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  14. 14

    Kobashi, K., Takeda, Y., Itoh, H. & Hase, J. Cholesterol-lowering effect of Clostridium butyricum in cholesterol-fed rats. Digestion 26, 173–178 (1983).

    CAS  Article  PubMed  Google Scholar 

  15. 15

    Takeda, Y., Itoh, H. & Kobashi, K. Effect of Clostridium butyricum on the formation and dissolution of gallstones in experimental cholesterol cholelithiasis. Life Sci. 32, 541–546 (1983).

    CAS  Article  PubMed  Google Scholar 

  16. 16

    Shinnoh, M. et al. Clostridium butyricum MIYAIRI 588 shows antitumor effects by enhancing the release of TRAIL from neutrophils through MMP-8. Int. J. Oncol. 42, 903–911 (2013).

    CAS  Article  PubMed  Google Scholar 

  17. 17

    Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. USA 105, 16731–16736 (2008).

    CAS  Article  PubMed  Google Scholar 

  18. 18

    Rossi, O. et al. Faecalibacterium prausnitzii A2–165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses. Sci. Rep. 6, 18507 (2016).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  19. 19

    Zhang, M. et al. Faecalibacterium prausnitzii inhibits interleukin-17 to ameliorate colorectal colitis in rats. PLoS ONE 9, e109146 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  20. 20

    Motta, J. P. et al. Food-grade bacteria expressing elafin protect against inflammation and restore colon homeostasis. Sci. Transl. Med. 4, 158ra144 (2012).

    Article  PubMed  Google Scholar 

  21. 21

    Frossard, C. P., Steidler, L. & Eigenmann, P. A. Oral administration of an IL-10-secreting Lactococcus lactis strain prevents food-induced IgE sensitization. J. Allergy Clin. Immunol. 119, 952–959 (2007).

    CAS  Article  PubMed  Google Scholar 

  22. 22

    Caluwaerts, S. et al. AG013, a mouth rinse formulation of Lactococcus lactis secreting human trefoil factor 1, provides a safe and efficacious therapeutic tool for treating oral mucositis. Oral Oncol. 46, 564–570 (2010).

    CAS  Article  PubMed  Google Scholar 

  23. 23

    Robert, S. & Steidler, L. Recombinant Lactococcus lactis can make the difference in antigen-specific immune tolerance induction, the type 1 diabetes case. Microb. Cell Fact. 13, (Suppl 1), S11 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  24. 24

    Farrar, M. D. et al. Engineering of the gut commensal bacterium Bacteroides ovatus to produce and secrete biologically active murine interleukin-2 in response to xylan. J. Appl. Microbiol. 98, 1191–1197 (2005).

    CAS  Article  PubMed  Google Scholar 

  25. 25

    Hamady, Z. Z. et al. Xylan-regulated delivery of human keratinocyte growth factor-2 to the inflamed colon by the human anaerobic commensal bacterium Bacteroides ovatus. Gut 59, 461–469 (2010).

    CAS  Article  PubMed  Google Scholar 

  26. 26

    Hamady, Z. Z. et al. Treatment of colitis with a commensal gut bacterium engineered to secrete human TGF-β1 under the control of dietary xylan 1. Inflamm. Bowel Dis. 17, 1925–1935 (2011).

    Article  PubMed  Google Scholar 

  27. 27

    Hamady, Z. Z. et al. Identification and use of the putative Bacteroides ovatus xylanase promoter for the inducible production of recombinant human proteins. Microbiology 154, 3165–3174 (2008).

    CAS  Article  PubMed  Google Scholar 

  28. 28

    EC. Regulation (EC) no 1924/2006 of the European Parliament and of the Council of 20 December 2006 on nutrition and health claims made on foods. OJ L. 404, 9–25 (2013).

    Google Scholar 

  29. 29

    Substantiation for Structure/Function Claims Made in Infant Formula Labels and Labeling: Guidance for Industry (FDA, 2016).

  30. 30

    Dietary Supplements: New Dietary Ingredient Notifications and Related Issues: Guidance for Industry (FDA, 2016).

  31. 31

    Early Clinical Trials with Live Biotherapeutic Products: Chemistry, Manufacturing, and Control Information: Guidance for Industry (FDA, 2016).

  32. 32

    Sanders, M. E., Shane, A. L. & Merenstein, D. J. Advancing probiotic research in humans in the United States: challenges and strategies. Gut Microbes 7, 97–100 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  33. 33

    Investigational New Drug Applications — Determining Whether Human Research Studies Can Be Conducted Without an Investigational New Drug Application: Guidance for Clinical Investigators, Sponsors, and Institutional Review Boards; Partial Stay and Republication of Guidance (FDA, 2015).

  34. 34

    Olle, B. Medicines from microbiota. Nat. Biotechnol. 31, 309–315 (2013).

    CAS  Article  PubMed  Google Scholar 

  35. 35

    van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N. Engl. J. Med. 368, 407–415 (2013).

    CAS  Article  PubMed  Google Scholar 

  36. 36

    Petrof, E. O. & Khoruts, A. From stool transplants to next-generation microbiota therapeutics. Gastroenterol. 146, 1573–1582 (2014).

    Article  Google Scholar 

  37. 37

    Ulsemer, P. et al. Specific humoral immune response to the Thomsen-Friedenreich tumor antigen (CD176) in mice after vaccination with the commensal bacterium Bacteroides ovatus D-6. Cancer Immunol. Immunother. 62, 875–887 (2013).

    CAS  Article  PubMed  Google Scholar 

  38. 38

    Gerard, P. et al. Bacteroides sp. strain D8, the first cholesterol-reducing bacterium isolated from human feces. Appl. Environ. Microbiol. 73, 5742–5749 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. 39

    Chen, J. C., Lee, W. J., Tsou, J. J., Liu, T. P. & Tsai, P. L. Effect of probiotics on postoperative quality of gastric bypass surgeries: a prospective randomized trial. Surg. Obes. Relat. Dis. 12, 57–61 (2016).

    Article  PubMed  Google Scholar 

  40. 40

    Hosomi, M., Tanida, N. & Shimoyama, T. The role of intestinal bacteria in gallstone formation in animal model. A study on biliary lipid composition and bile acid profiles in bile, small intestinal contents and feces of clostridium butyricum MIYAIRI no. 588 monocontaminated mice. Gastroenterol. Jpn. 17, 316–323 (1982).

    CAS  Article  PubMed  Google Scholar 

  41. 41

    Isa, K. et al. Safety assessment of the Clostridium butyricum MIYAIRI 588(R) probiotic strain including evaluation of antimicrobial sensitivity and presence of Clostridium toxin genes in vitro and teratogenicity in vivo. Hum. Exp. Toxicol. 35, 818–832 (2016).

    CAS  Article  PubMed  Google Scholar 

  42. 42

    Kohiruimaki, M. et al. Effects of active egg white product/Clostridium butyricum MIYAIRI 588 additive on peripheral leukocyte populations in periparturient dairy cows. J. Vet. Med. Sci. 70, 321–323 (2008).

    Article  PubMed  Google Scholar 

  43. 43

    Kuroiwa, T., Kobari, K. & Iwanaga, M. Inhibition of enteropathogens by Clostridium butyricum MIYAIRI 588. Kansenshogaku Zasshi 64, 257–263 (1990).

    CAS  Article  PubMed  Google Scholar 

  44. 44

    Murayama, T. et al. Effects of orally administered Clostridium butyricum MIYAIRI 588 on mucosal immunity in mice. Vet. Immunol. Immunopathol. 48, 333–342 (1995).

    CAS  Article  PubMed  Google Scholar 

  45. 45

    Nakanishi, S. & Tanaka, M. Sequence analysis of a bacteriocinogenic plasmid of Clostridium butyricum and expression of the bacteriocin gene in Escherichia coli. Anaerobe 16, 253–257 (2010).

    CAS  Article  PubMed  Google Scholar 

  46. 46

    Sato, S., Nagai, H. & Igarashi, Y. Effect of probiotics on serum bile acids in patients with ulcerative colitis. Hepatogastroenterology 59, 1804–1808 (2012).

    PubMed  Google Scholar 

  47. 47

    Seki, H. et al. Prevention of antibiotic-associated diarrhea in children by Clostridium butyricum MIYAIRI. Pediatr. Int. 45, 86–90 (2003).

    Article  PubMed  Google Scholar 

  48. 48

    Seo, M. et al. Clostridium butyricum MIYAIRI 588 improves high-fat diet-induced non-alcoholic fatty liver disease in rats. Dig. Dis. Sci. 58, 3534–3544 (2013).

    Article  PubMed  Google Scholar 

  49. 49

    Takahashi, M. et al. The effect of probiotic treatment with Clostridium butyricum on enterohemorrhagic Escherichia coli O157:H7 infection in mice. FEMS Immunol. Med. Microbiol. 41, 219–226 (2004).

    CAS  Article  PubMed  Google Scholar 

  50. 50

    Weng, H., Endo, K., Li, J., Kito, N. & Iwai, N. Induction of peroxisomes by butyrate-producing probiotics. PLoS ONE 10, e0117851 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  51. 51

    Yasueda, A. et al. The effect of Clostridium butyricum MIYAIRI on the prevention of pouchitis and alteration of the microbiota profile in patients with ulcerative colitis. Surg. Today 46, 939–949 (2016).

    Article  PubMed  Google Scholar 

  52. 52

    Simonyte Sjodin, K., Vidman, L., Ryden, P. & West, C. E. Emerging evidence of the role of gut microbiota in the development of allergic diseases. Curr. Opin. Allergy Clin. Immunol. 16, 390–395 (2016).

    Article  PubMed  Google Scholar 

  53. 53

    Song, H., Yoo, Y., Hwang, J., Na, Y. C. & Kim, H. S. Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis. J. Allergy Clin. Immunol. 137, 852–860 (2016)

    CAS  Article  PubMed  Google Scholar 

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We thank the panel members of the ISAPP 2016 meeting for stimulating discussions, and M. E. Sanders for reviewing the section on regulations. The opinions in this article are those of the authors only, and do not represent a consensus of the ISAPP convened panel.

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P.W.O.T. and C.H. are funded in part by Science Foundation Ireland (APC/SFI/12/RC/2273) in the form of a research centre which is/has recently been in receipt of research grants from the following companies: Cremo, Mead Johnson Nutrition, Kerry, General Mills, GE Healthcare, Friesland Campina, Sigmoid, Alimentary Health, Second Genome, Nutricia, Danone, Janssen, AbbVie, Suntory Morinaga Milk Industry Ltd, Pfizer Consumer Health, Radisens, 4D Pharma, Crucell, Adare Pharma, Artugen Therapeutics, Caelus. P.W.O.T. is a founder shareholder of Tucana Health Ltd. C.H. is a founder shareholder in Artugen therapeutics. These relationships with industry have no bearing on the present work and neither influenced nor constrained it. J.R.M. has consulted and received payment from Cultech Ltd, Takeda Pharmaceuticals and Unilever.

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Correspondence to Paul W. O’Toole.

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O’Toole, P., Marchesi, J. & Hill, C. Next-generation probiotics: the spectrum from probiotics to live biotherapeutics. Nat Microbiol 2, 17057 (2017).

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