Skip to main content
SpringerLink
Log in

Fixing the Damage: The Evolution of Probiotics from Fermented Food to Biotherapeutic Products

  • Chapter
  • First Online:
A Sustainable Green Future

  • 626 Accesses

Abstract

Microbiomes live in symbiosis with their hosts at all stages of their life cycles, forming holobionts. The gut microbiome contributes to absorbing energy and affects the immune system and provides intense chemical communication and coordination of host physiological functions, characterizing the gut-brain axis. The human lifestyle promotes alterations in ecological relationships between the host and microbiome, as the non-rational use of antibiotics, biocides, and processed food, decreasing microbiome diversity and affecting gut homeostasis. This dysbiosis leads to disease development, as colitis, obesity, metabolic syndromes, diabetes mellitus, cancer, and liver, cardiovascular, and neurodegenerative diseases. Probiotic bacterial strains have been used in different dairy products to modulate the structure of the intestinal microbiome and recover a part of the lost functional balance, but a deep scientifical background is necessary to shift the focus of this product consumption, from food to pharmaceutical industry. Next-generation probiotic species have been sought with preventive and therapeutic characteristics; the main concern is efficiency and safety, which is the reason for the new category of live biotherapeutic products need to be standardized as drugs to be commercially viable, to search for intestinal homeostasis recovery and reducing dysbiosis and a chain of adverse effects that could culminate in severe and chronic diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. K. Aagaard, J. Ma, K.M. Antony, R. Ganu, J. Petrosino, J. Versalovic, The placenta harbors a unique microbiome. Sci. Transl. Med. 21, 237–265 (2014). https://doi.org/10.1126/scitranslmed.3008599

    Article  CAS  Google Scholar 

  2. Abbas AK, Lichtman AH, Pillai S, Imunologia celular e molecular. (Elsevier, Rio de Janeiro, 2019)

    Google Scholar 

  3. A. Adak, M.R. Khan, An insight into gut microbiota and its functionalities. Cell. Mol. Life Sci. 76, 473–493 (2019). https://doi.org/10.1007/s00018-018-2943-4

    Article  CAS  Google Scholar 

  4. R. Aerts, O. Honnay, A.V. Nieuwenhuyse, Biodiversity and human health: Mechanisms and evidence of the positive health effects of diversity in nature and green spaces. Br. Med. Bull. 127, 5–22 (2018). https://doi.org/10.1093/bmb/ldy021

    Article  Google Scholar 

  5. A. Ait-Belgnaoui, W. Han, F. Lamine, H. Eutamene, J. Fioramonti, L. Bueno, V. Theodorou, Lactobacillus farciminis treatment suppresses stress-induced visceral hypersensitivity: A possible action through interaction with epithelial cells cytoskeleton contraction. Gut 55, 1090–1094 (2006). https://doi.org/10.1136/gut.2005.084194

    Article  CAS  Google Scholar 

  6. C. Alcon-Giner, M.J. Dalby, S. Caim, J. Ketskemety, A. Shaw, K. Sim, M.A.E. Lawson, R. Kiu, C. Leclaire, L. Chalklen, M. Kujawska, S. Mitra, F. Fardus-Reid, G. Belteki, K. McColl, J.S. Kroll, P. Clarke, L.J. Hall, Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome: An observational study. Cell Rep. Med. 1, 1–15 (2020). https://doi.org/10.1016/j.xcrm.2020.100077

    Article  CAS  Google Scholar 

  7. C.V. Almeida, M.R. Camargo, E. Russo, A. Amedei, Role of diet and gut microbiota on colorectal cancer immunomodulation. World J. Gastroenterol. 25(2), 151–162 (2019). https://doi.org/10.3748/wjg.v25.i2.151

    Article  CAS  Google Scholar 

  8. A. Almeida, A.L. Mitchell, M. Boland, S.C. Forster, G.B. Gloor, A. Tarkowska, T.D. Lawley, R.D. Finn, A new genomic blueprint of the human gut microbiota. Nature 568, 499–504 (2019). https://doi.org/10.1038/s41586-019-0965-1

    Article  CAS  Google Scholar 

  9. A. Alok, I.D. Singh, S. Singh, M. Kishore, P.C. Jha, M.A. Iqubal, Probiotics: A new era of biotherapy. Adv. Biomed. Res. 6, 31 (2017). https://doi.org/10.4103/2277-9175.192625

    Article  CAS  Google Scholar 

  10. K.R. Amato, M.C. Arrieta, M.B. Azad, C.W. Kuzawa, The human gut microbiome and health inequities. Proc Natl Acad Sci U S A 118, e2017947118 (2021). https://doi.org/10.1073/pnas.2017947118

    Article  CAS  Google Scholar 

  11. A.N. Ardissone, D.M. Cruz, A.G. Davis-Richardson, K.T. Rechigl, N. Li, J.C. Drew, R. Murgas-Torrazza, R. Sharma, M.L. Hudak, E.W. Triplett, J. Neu, Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One 9, 1–8 (2014). https://doi.org/10.1371/journal.pone.0090784

    Article  Google Scholar 

  12. A. Banik, S.K. Halder, C. Ghosh, K.C. Mondal, Fungal probiotics: Opportunity, challenge, and prospects, in Recent Advancement in White Biotechnology Through Fungi. Fungal Biology, ed. by A. Yadav, S. Singh, S. Mishra, A. Gupta, (Springer, Cham, 2019), pp. 101–117. https://doi.org/10.1007/978-3-030-14846-1_3

    Chapter  Google Scholar 

  13. G. Berg, D. Rybakova, D. Fischer, et al., Microbiome definition re-visited: Old concepts and new challenges. Microbiome 8, 103 (2020). https://doi.org/10.1186/S40168-020-00875-0

    Article  Google Scholar 

  14. P. Brinker, M.C. Fontaine, L.W. Beukeboom, J. Falcao Salles, Host, symbionts, and the microbiome: The missing tripartite interaction. Trends Microbiol. 27, 480–488 (2019). https://doi.org/10.1016/j.tim.2019.02.002

    Article  CAS  Google Scholar 

  15. J.L. Brito Alves, Y. de Oliveira, N.N.C. Carvalho, R.G.S. Cavalcante, M.M. Pereira Lira, L.C.P.D. Nascimento, M. Magnani, H. Vidal, V.A. Braga, E.L. de Souza, Gut microbiota and probiotic intervention as a promising therapeutic for pregnant women with cardiometabolic disorders: Present and future directions. Pharmacol. Res. 145, 104252 (2019). https://doi.org/10.1016/j.phrs.2019.104252

    Article  Google Scholar 

  16. J. Cai, Z. Chen, W. Wu, Q. Lin, Y. Liang, High animal protein diet and gut microbiota in human health. Crit. Rev. Food Sci. Nutr., 1–13 (2021). https://doi.org/10.1080/10408398.2021.1898336

  17. P.D. Cani, W.M. de Vos, Next-generation beneficial microbes: The case of Akkermansia muciniphila. Front. Microbiol. 8, 1765 (2017). https://doi.org/10.3389/fmicb.2017.01765

    Article  Google Scholar 

  18. I. Castigliuolo, M.F. Riegler, L. Valenick, J.T. LaMont, C. Pothoulakis, Saccharomyces boulardii protease inhibits the effects of Clostridium difficile toxins A and B in human colonic mucosa. Infect. Immun. 67, 302–307 (1999). https://doi.org/10.1128/IAI.67.1.302-307.1999

    Article  Google Scholar 

  19. T. Cerdó, A. Ruiz, I. Acuña, et al., Gut microbial functional maturation and succession during human early life. Environ. Micobiol. 20, 2160–2177 (2018). https://doi.org/10.1111/1462-2920.14235

    Article  CAS  Google Scholar 

  20. A. Chavira, P. Belda-Ferre, T. Kosciolek, F. Ali, P.C. Dorrestein, R. Knight, The microbiome and its potential for pharmacology. Handb. Exp. Pharmacol. 260, 301–326 (2019). https://doi.org/10.1007/164_2019_317

    Article  CAS  Google Scholar 

  21. P. Chen, X. Tang, Gut microbiota as regulators of Th17/Treg balance in patients with myasthenia gravis. Front. Immunol. 12, 1–12 (2021). https://doi.org/10.3389/fimmu.2021.803101

    Article  CAS  Google Scholar 

  22. H. Chung The, S.H. Le, Dynamic of the human gut microbiome under infectious diarrhea. Curr. Opin. Microbiol. 66, 79–85 (2022). https://doi.org/10.1016/j.mib.2022.01.006

    Article  CAS  Google Scholar 

  23. O.O. Coker, W.K.K. Wu, S.H. Wong, J.J. Sung, J. Yu, Altered gut archaea composition and interaction with bacteria are associated with colorectal cancer. Gastroenterology 159, 1459–1470 (2020). https://doi.org/10.1053/j.gastro.2020.06.042

    Article  CAS  Google Scholar 

  24. M.C. Collado, S. Rautava, J. Aakko, et al., Human gut colonisation may be initiated in utero by distinct microbial communities in the placenta and amniotic fluid. Sci. Rep. 61(6), 1–13 (2016). https://doi.org/10.1038/srep23129

    Article  CAS  Google Scholar 

  25. V. Coman, D.C. Vodnar, Gut microbiota and old age: Modulating factors and interventions for healthy longevity. Exp. Gerontol. 141, 111095 (2020). https://doi.org/10.1016/J.EXGER.2020.111095

    Article  CAS  Google Scholar 

  26. A.V. Contreras, B. Cocom-Chan, G. Hernandez-Montes, T. Portillo-Bobadilla, O. Resendis-Antonio, Host-microbiome interaction and cancer: Potential application in precision medicine. Front. Physiol. 7, 606 (2016). https://doi.org/10.3389/fphys.2016.00606

    Article  Google Scholar 

  27. A.Y. Coqueiro, R. Raizel, A. Bonvini, J. Tirapegui, M.M. Rogero, Probiotics for inflammatory bowel diseases: A promising adjuvant treatment. Int. J. Food Sci. Nutr. 70(1), 20–29 (2019). https://doi.org/10.1080/09637486.2018.1477123

    Article  Google Scholar 

  28. M. Cordaillat-Simmons, A. Rouanet, B. Pot, Live biotherapeutic products: The importance of a defined regulatory framework. Exp. Mol. Med. 52(9), 1397–1406 (2020). https://doi.org/10.1038/s12276-020-0437-6

    Article  CAS  Google Scholar 

  29. P.D. Cotter, C. Hill, R.P. Ross, Bacteriocins: Developing innate immunity for food. Nat. Rev. Microbiol. 3, 777–788 (2005). https://doi.org/10.1038/nrmicro1273

    Article  CAS  Google Scholar 

  30. F. Cristofori, F. Indrio, V.L. Miniello, M. De Angelis, R. Francavilla, Probiotics in celiac disease. Nutrients 10(12), 1824 (2018). https://doi.org/10.3390/nu10121824

    Article  CAS  Google Scholar 

  31. K. D’hoe, S. Vet, K. Faust, F. Moens, G. Falony, D. Gonze, V. Lloréns-Rico, L. Gelens, J. Danckaert, L. De Vuyst, J. Raes, Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community. elife 7, e37090 (2018). https://doi.org/10.7554/eLife.37090.001

    Article  Google Scholar 

  32. E.B.M. Daliri, F.K. Ofosu, R. Chelliah, B.H. Lee, D.H. Oh, Health impact and therapeutic manipulation of the gut microbiome. High Throughput 9, 17 (2020). https://doi.org/10.3390/ht9030017

    Article  CAS  Google Scholar 

  33. E.B.M. Daliri, F.K. Ofosu, R. Chelliah, B.H. Lee, D.H. Oh, Challenges and perspective in integrated multi-omics in gut microbiota studies. Biomol. Ther. 11, 300 (2021). https://doi.org/10.3390/biom11020300

    Article  CAS  Google Scholar 

  34. U. Daniluk, J. Daniluk, R. Kucharski, T. Kowalczyk, K. Pietrowska, P. Samczuk, A. Filimoniuk, A. Kretowski, D. Lebensztejn, M. Ciborowski, Untargeted metabolomics and inflammatory markers profiling in children with crohn’s disease and ulcerative colitis-A preliminary study. Inflamm. Bowel Dis. 25, 1120–1128 (2019). https://doi.org/10.1093/ibd/izy402

    Article  Google Scholar 

  35. C. Dausset, S. Patrier, P. Gajer, C. Thoral, Y. Lenglet, J.M. Cardot, P. Judlin, J. Ravel, A. Nivoliez, Comparative phase I randomized open-label pilot clinical trial of Gynophilus® (Lcr regenerans®) immediate release capsules versus slow release muco-adhesive tablets. Eur. J. Clin. Microbiol. Infect. Dis. 37(10), 1869–1880 (2018). https://doi.org/10.1007/s10096-018-3321-8

    Article  CAS  Google Scholar 

  36. C. Depommier, A. Everard, C. Druart, H. Plovier, M. Van Hul, S. Vieira-Silva, G. Falony, J. Raes, D. Maiter, N.M. Delzenne, M. de Barsy, A. Loumaye, M.P. Hermans, J.P. Thissen, W.M. de Vos, P.D. Cani, Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: A proof-of-concept exploratory study. Nat. Med. 25(7), 1096–1103 (2019). https://doi.org/10.1038/s41591-019-0495-2

    Article  CAS  Google Scholar 

  37. M. Derrien, A.-S. Alvarez, W.M. de Vos, The gut microbiota in the first decade of life. Trends Microbiol. 27, 997–1010 (2019). https://doi.org/10.1016/J.TIM.2019.08.001

    Article  CAS  Google Scholar 

  38. M.G. Dominguez-Bello, F. Godoy-Vitorino, R. Knight, M.J. Blaser, Role of the microbiome in human development. Gut 68, 1108 (2019). https://doi.org/10.1136/GUTJNL-2018-317503

    Article  CAS  Google Scholar 

  39. C. Duvallet, S.M. Gibbons, T. Gurry, R.A. Irizarry, E.J. Alm, Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat. Commun. 8, 1–10 (2017). https://doi.org/10.1038/s41467-017-01973-8

    Article  CAS  Google Scholar 

  40. K. Fadhlaoui, M.E. Arnal, M. Martineau, P. Camponova, B. Ollivier, P.W. O’Toole, J.F. Brugère, Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: Another face of next-generation probiotics. Appl. Microbiol. Biotechnol. 104(11), 4705–4716 (2020). https://doi.org/10.1007/s00253-020-10599-8

    Article  CAS  Google Scholar 

  41. FAO, IFAD, UNICEF, WFP, WHO, The State of Food Security and Nutrition in the World 2019. Safeguarding Against Economic Slowdowns and Downturns (FAO, Rome, 2019). Licence: CC BY-NC-SA 3.0 IGO

    Google Scholar 

  42. O. Fiehn, Metabolomics – The link between genotypes and phenotypes, in Functional Genomics, ed. by C. Town, (Springer, Dordrecht, 2002), pp. 155–171. https://doi.org/10.1007/978-94-010-0448-0_11

    Chapter  Google Scholar 

  43. L. Flandroy, T. Poutahidis, G. Berg, G. Clarke, M. Dao, E. Decaestecker, E. Furman, T. Haahtela, S. Massart, H. Plovier, Y. Sanz, G. Rook, The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Sci. Total Environ. 627, 1018–1038 (2018). https://doi.org/10.1016/j.scitotenv.2018.01.288

    Article  CAS  Google Scholar 

  44. W. Fong, Q. Li, J. Yu, Gut microbiota modulation: A novel strategy for prevention and treatment of colorectal cancer. Oncogene 39(26), 4925–4943 (2020). https://doi.org/10.1038/s41388-020-1341-1

    Article  CAS  Google Scholar 

  45. R. Francavilla, M. Piccolo, A. Francavilla, L. Polimeno, F. Semeraro, F. Cristofori, S. Castellaneta, M. Barone, F. Indrio, M. Gobbetti, M. De Angelis, Clinical and microbiological effect of a multispecies probiotic supplementation in celiac patients with persistent IBS-type symptoms: A randomized, double-blind, placebo-controlled, multicenter trial. J. Clin. Gastroenterol. 53(3), e117–e125 (2019). https://doi.org/10.1097/MCG.0000000000001023

    Article  CAS  Google Scholar 

  46. R. Fuller, Probiotics in man and animals. J. Appl. Bacteriol. 66, 365–378 (1989)

    Article  CAS  Google Scholar 

  47. V.T. George, M.M. Varghese, M.S. Vaseem, A. Thomas, P.G. Ittycheria, C.K. Sreejith, The promising future of probiotics: A new era in periodontal therapy. J. Int. Oral Health 8, 404 (2016). https://doi.org/10.2047/jioh-08-03-21

    Article  Google Scholar 

  48. C. Gil-Cruz, C. Perez-Shibayama, A.D. Martin, F. Ronchi, K. van der Borght, R. Niederer, L. Onder, M. Lütge, M. Novkovic, V. Nindl, G. Ramos, M. Arnoldini, E.M.C. Slack, V. Boivin-Jahns, R. Jahns, M. Wyss, C. Mooser, B.N. Lambrecht, M.T. Maeder, H. Rickli, L. Flatz, U. Eriksson, M.B. Geuking, K.D. McCoy, B. Ludewig, Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy. Science 366, 881–886 (2019). https://doi.org/10.1126/science.aav3487

    Article  CAS  Google Scholar 

  49. V. Gopalakrishnan, C.N. Spencer, L. Nezi, A. Reuben, M.C. Andrews, T.V. Karpinets, P.A. Prieto, D. Vicente, K. Hoffman, S.C. Wei, A.P. Cogdill, L. Zhao, C.W. Hudgens, D.S. Hutchinson, T. Manzo, M.M. de Petraccia, T. Cotechini, T. Kumar, W.S. Chen, S.M. Reddy, R.S. Sloane, J. Galloway-Pena, H. Jiang, P.L. Chen, E.J. Shpall, K. Rezvani, V.B. Jensen, A.G. Swennes, F. McAllister, E.M.R. Sanchez, Y. Zhang, E. Le Chatelier, L. Zitvogel, N. Pons, J.L. Austin-Breneman, L.E. Haydu, E.M. Burton, J.M. Gardner, E. Sirmans, J. Hu, A.J. Lazar, T. Tsujikawa, A. Diab, H. Tawbi, I.C. Glitza, W.J. Hwu, S.P. Patel, S.E. Woodman, R.N. Armaria, M.A. Davies, J.E. Gershenwald, P. Hwu, J.E. Lee, J. Zhang, L.M. Coussens, Z.A. Cooper, P.A. Futreal, C.R. Daniel, N.J. Ajami, J.F. Petrosino, M.T. Tetzlaff, P. Sharma, J.P. Alisson, R.R. Jenq, J.A. Wargo, Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359, 97–103 (2018). https://doi.org/10.1126/science.aan4236

    Article  CAS  Google Scholar 

  50. F. Graziani, A. Pujol, C. Nicoletti, S. Dou, M. Maresca, T. Giardina, M. Fons, J. Perrier, Ruminococcus gnavus E1 modulates mucin expression and intestinal glycosylation. J. Appl. Microbiol. 120, 1403–1417 (2016). https://doi.org/10.1111/jam.13095

    Article  CAS  Google Scholar 

  51. A.C. Gregory, O. Zablocki, A.A. Zayed, A. Howell, B. Bolduc, M.B. Sullivan, The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe 28, 724–740 (2020). https://doi.org/10.1016/j.chom.2020.08.003

    Article  CAS  Google Scholar 

  52. A. Gupta, I.M. Reizman, C.R. Reisch, K.L. Prather, Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat. Biotechnol. 35(3), 273–279 (2017). https://doi.org/10.1038/nbt.3796

    Article  CAS  Google Scholar 

  53. R. Hansen, I.R. Sanderson, R. Muhammed, S. Allen, C. Tzivinikos, P. Henderson, L. Gervais, I.B. Jeffery, D.P. Mullins, E.A. O’Herlihy, J.D. Weinberg, G. Kitson, R.K. Russell, D.C. Wilson, A double-blind, placebo-controlled trial to assess safety and tolerability of (Thetanix) Bacteroides thetaiotaomicron in adolescent Crohn’s disease. Clin. Transl. Gastroenterol. 12(1), e00287 (2020). https://doi.org/10.14309/ctg.0000000000000287

    Article  Google Scholar 

  54. M.K. Heavey, D. Durmusoglu, N. Crook, A.C. Anselmo, Discovery and delivery strategies for engineered live biotherapeutic products. Trends Biotechnol. 1, S0167-7799(21)00176-1 (2021). https://doi.org/10.1016/j.tibtech.2021.08.002

    Article  CAS  Google Scholar 

  55. A. Heintz-Buschart, P. Wilmes, Human gut microbiome: Function matters. Trends Microbiol. 26, 563–574 (2018). https://doi.org/10.1016/J.TIM.2017.11.002

    Article  CAS  Google Scholar 

  56. P. Herd, A. Palloni, F. Rey, J.B. Dowd, Social and population health science approaches to understand the human microbiome. Nat. Hum. Behav. 2, 808–815 (2018). https://doi.org/10.1038/s41562-018-0452-y

    Article  Google Scholar 

  57. M. Jabczyk, J. Nowak, B. Hudzik, B. Zubelewicz-Szkodzińska, Diet, probiotics and their impact on the gut microbiota during the COVID-19 pandemic. Nutrients 13(9), 3172 (2021). https://doi.org/10.3390/nu13093172

    Article  CAS  Google Scholar 

  58. H.E. Jakobsson, T.R. Abrahamsson, M.C. Jenmalm, K. Harris, C. Quince, C. Jernberg, B. Björkstén, L. Engstrand, A.F. Andersson, Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section. Gut 63, 559–566 (2014). https://doi.org/10.1136/gutjnl-2012-303249

    Article  CAS  Google Scholar 

  59. J. Jiang, B. Yang, R.P. Ross, C. Stanton, J. Zhao, H. Zhang, W. Chen, Comparative genomics of Pediococcus pentosaceus isolated from different niches reveals genetic diversity in carbohydrate metabolism and immune system. Front. Microbiol. 11, 253 (2020). https://doi.org/10.3389/fmicb.2020.00253

    Article  Google Scholar 

  60. A. Joly, F. Leulier, F. De Vadder, Microbial modulation of the development and physiology of the enteric nervous system. Trends Microbiol. 29, 686–699 (2021). https://doi.org/10.1016/j.tim.2020.11.007

    Article  CAS  Google Scholar 

  61. M. Kamada, S. Hase, K. Sato, A. Toyoda, A. Fujiyama, Y. Sakakibara, Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. PLoS One 9, e109999 (2014). https://doi.org/10.1371/journal.pone.0109999

    Article  CAS  Google Scholar 

  62. T. Kamiya, L. Wang, P. Forsythe, G. Goettsche, Y. Mao, Y. Wang, G. Tougas, J. Bienenstock, Inhibitory effects of Lactobacillus reuteri on visceral pain induced by colorectal distension in Sprague-Dawley rats. Gut 55, 191–196 (2006). https://doi.org/10.1136/gut.2005.070987

    Article  CAS  Google Scholar 

  63. E.R. Kim, H.N. Kwon, H. Nam, J.J. Kim, S. Park, Y.H. Kim, Urine-NMR metabolomics for screening of advanced colorectal adenoma and early stage colorectal cancer. Sci. Rep. 9, 4786–4796 (2019). https://doi.org/10.1038/s41598-019-41216-y

    Article  CAS  Google Scholar 

  64. E.Y. Klein, T.P. Van Boeckel, E.M. Martinez, R. Laxminarayan, Global increase and geographic convergence in antibiotic consumption between 2000 and 2015. Proc Natl Acad Sci U S A 115, E3463–E3470 (2018). https://doi.org/10.1073/pnas.1717295115

    Article  CAS  Google Scholar 

  65. R. Knight, A. Vrbanac, B.C. Taylor, A. Aksenov, C. Callewaert, J. Debelius, A. Gonzalez, T. Kosciolek, L.I. McCall, D. McDonald, A.V. Melnik, J.T. Morton, J. Navas, R.A. Quinn, J.G. Sanders, A.D. Swafford, L.R. Thompson, A. Tripathi, Z.Z. Xu, J.R. Zaneveld, Q. Zhu, J.G. Caporaso, P.C. Dorrestein, Best practices for analysing microbiomes. Nat. Rev. Microbiol. 16, 410–422 (2018). https://doi.org/10.1038/s41579-018-0029-9

    Article  CAS  Google Scholar 

  66. A.A. Kolodziejczyk, D. Zheng, E. Elinav, Diet–microbiota interactions and personalized nutrition. Nat. Rev. Microbiol. 17, 742–753 (2019). https://doi.org/10.1038/s41579-019-0256-8

    Article  CAS  Google Scholar 

  67. K. Korpela, A. Salonen, B. Hickman, C. Kunz, N. Sprenger, K. Kukkonen, E. Savilahti, M. Kuitunen, W.M. Vos, Fucosylated oligosaccharides in mother’s milk alleviate the effects of caesarean birth on infant gut microbiota. Sci. Rep. 8, 1–7 (2017). https://doi.org/10.1038/s41598-018-32037-6

    Article  CAS  Google Scholar 

  68. K.A. Krautkramer, J. Fan, F. Bäckhed, Gut microbial metabolites as multi-kingdom intermediates. Nat. Rev. Microbiol. 19(2), 77–94 (2021). https://doi.org/10.1038/s41579-020-0438-4

    Article  CAS  Google Scholar 

  69. P. Kundu, E. Blacher, E. Elinav, S. Pettersson, Our gut microbiome: The evolving inner self. Cell 171, 1481–1493 (2017). https://doi.org/10.1016/J.CELL.2017.11.024

    Article  CAS  Google Scholar 

  70. A.J. La Reau, G. Suen, The Ruminococci: Key symbionts of the gut ecosystem. J. Microbiol. 56, 199–208 (2018). https://doi.org/10.1007/s12275-018-8024-4

    Article  CAS  Google Scholar 

  71. E. Lamousé-Smith, D. Kelly, I. De Cremoux, Designing bugs as drugs: Exploiting the gut microbiome. Am. J. Physiol. Gastrointest. Liver Physiol. 320, G295–G303 (2020). https://doi.org/10.1152/ajpgi.00381.2019

    Article  Google Scholar 

  72. S.H. Lee, Y. Yun, S.J. Kim, E.J. Lee, Y. Chang, S. Ryu, H. Shin, H.L. Kim, H.N. Kim, J.H. Lee, Association between cigarette smoking status and composition of gut microbiota: Population-based cross-sectional study. J. Clin. Med. 7, 282 (2018). https://doi.org/10.3390/jcm7090282

    Article  CAS  Google Scholar 

  73. T. Legesse Bedada, T.K. Feto, K.S. Awoke, A.D. Garedew, F.T. Yifat, D.J. Birri, Probiotics for cancer alternative prevention and treatment. Biomed. Pharmacother. 129, 110409 (2020). https://doi.org/10.1016/j.biopha.2020.110409

    Article  CAS  Google Scholar 

  74. L.C. Lew, S.B. Choi, B.Y. Khoo, S. Sreenivasan, K.L. Ong, M.T. Liong, Lactobacillus plantarum DR7 reduces cholesterol via phosphorylation of AMPK that down-regulated the mRNA expression of HMG-CoA reductase. Korean J. Food Sci. Anim. Resour. 38(2), 350–361 (2018). https://doi.org/10.5851/kosfa.2018.38.2.350

    Article  Google Scholar 

  75. M. Li, J. Wen, Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb. Cell Fact. 20, 178 (2021). https://doi.org/10.1186/s12934-021-01671-7

  76. E.C. Lindsay, N.B. Metcalfe, M.S. Llewellyn, The potential role of the gut microbiota in shaping host energetics and metabolic rate. J. Anim. Ecol. 89, 2415–2426 (2020). https://doi.org/10.1111/1365-2656.13327

    Article  Google Scholar 

  77. P. Littlejohn, B.B. Finlay, When a pandemic and an epidemic collide: COVID-19, gut microbiota, and the double burden of malnutrition. BMC Med. 19(1), 31 (2021). https://doi.org/10.1186/s12916-021-01910-z

    Article  CAS  Google Scholar 

  78. X. Liu, B. Mao, J. Gu, J. Wu, S. Cui, G. Wang, J. Zhao, H. Zhang, W. Chen, Blautia—A new functional genus with potential probiotic properties? Gut Microbes 13, 1875796 (2021). https://doi.org/10.1080/19490976.2021.1875796

    Article  CAS  Google Scholar 

  79. S. Long, Y. Yang, C. Shen, Y. Wang, A. Deng, Q. Qin, L. Qiao, Metaproteomics characterizes human gut microbiome function in colorectal cancer. npj Biofilms Microbiomes 6, 14–24 (2020). https://doi.org/10.1038/s41522-020-0123-4

    Article  Google Scholar 

  80. C. Long-Smith, K.J. O’Riordan, G. Clarke, C. Stanton, T.G. Dinan, J.F. Cryan, Microbiota-gut-brain axis: New therapeutic opportunities. Annu. Rev. Pharmacol. Toxicol. 60, 477–502 (2020). https://doi.org/10.1146/annurev-pharmtox-010919-023628

    Article  CAS  Google Scholar 

  81. A.C. Luissint, C.A. Parkos, A. Nusrat, Inflammation and the intestinal barrier: Leukocyte–epithelial cell interactions, cell junction remodeling, and mucosal repair. Gastroenterology 151, 616–632 (2016). https://doi.org/10.1053/j.gastro.2016.07.008

    Article  CAS  Google Scholar 

  82. P. Markowiak, K. Śliżewska, Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients 9(9), 1021 (2017). https://doi.org/10.3390/nu9091021

    Article  CAS  Google Scholar 

  83. P.I. Megat Mohd Azlan, S.F. Chin, T.Y. Low, H.M. Neoh, R. Jamal, Analyzing the Secretome of gut microbiota as the next strategy for early detection of colorectal cancer. Proteomics 19(10), e1800176 (2019). https://doi.org/10.1002/pmic.201800176

    Article  CAS  Google Scholar 

  84. A. Mejía-Caballero, V.A. Salas-Villagrán, A. Jiménez-Serna, A. Farrés, Challenges in the production and use of probiotics as therapeuticals in cancer treatment or prevention. J. Ind. Microbiol. Biotechnol. 48(9–10), kuab052 (2021). https://doi.org/10.1093/jimb/kuab052

    Article  CAS  Google Scholar 

  85. C. Milani, S. Duranti, F. Bottacini, E. Casey, F. Turroni, J. Mahony, C. Belzer, S.D. Palacio, S.A. Montes, L. Mancabelli, G.A. Lugli, J.M. Rodriguez, L. Bode, W. de Vos, M. Gueimonde, A. Margolles, D. van Sinderen, M. Ventura, The first microbial colonizers of the human gut: Composition, activities, and health implications of the infant gut microbiota. Microbiol. Mol. Biol. Rev. 81, 1–67 (2017). https://doi.org/10.1128/MMBR00036-17

    Article  Google Scholar 

  86. G.E. Miller, P.A. Engen, P.M. Gillevet, M. Shaikh, M. Sikaroodi, C.B. Forsyth, E. Mutlu, A. Keshavarzian, Lower neighborhood socioeconomic status associated with reduced diversity of the colonic microbiota in healthy adults. PLoS One 11, e0148952 (2016). https://doi.org/10.1371/journal.pone.0148952

    Article  CAS  Google Scholar 

  87. J. Mishra, M. Stubbs, L. Kuang, N. Vara, P. Kumar, N. Kumar, Inflammatory bowel disease therapeutics: A focus on probiotic engineering. Mediat. Inflamm. 2022, 1–15 (2022). https://doi.org/10.1155/2022/9621668

    Article  CAS  Google Scholar 

  88. J.A. Molina-Tijeras, J. Gálvez, M.E. Rodríguez-Cabezas, The immunomodulatory properties of extracellular vesicles derived from probiotics: A novel approach for the management of gastrointestinal diseases. Nutrients 11(5), 1038 (2019). https://doi.org/10.3390/nu11051038

    Article  CAS  Google Scholar 

  89. M. Moreno-Paz, M.J. Gómez, A. Arcas, V. Parro, Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community. BMC Genom. 11, 404 (2010). https://doi.org/10.1186/1471-2164-11-404

    Article  CAS  Google Scholar 

  90. M.E.F. Nader-Macías, P.R. De Gregorio, J.A. Silva, Probiotic lactobacilli in formulas and hygiene products for the health of the urogenital tract. Pharmacol. Res. Perspect. 9(5), e00787 (2021). https://doi.org/10.1002/prp2.787

    Article  CAS  Google Scholar 

  91. R. Nagpal, B.J. Neth, S. Wang, S.P. Mishra, S. Craft, H. Yadav, Gut mycobiome and its interaction with diet, gut bacteria and Alzheimer’s disease markers in subjects with mild cognitive impairment: A pilot study. EBioMedicine 59, 102950 (2020). https://doi.org/10.1016/j.ebiom.2020.102950

    Article  CAS  Google Scholar 

  92. K. Nishida, D. Sawada, Y. Kuwano, H. Tanaka, K. Rokutan, Health benefits of Lactobacillus gasseri CP2305 tablets in young adults exposed to chronic stress: A randomized, double-blind, placebo-controlled study. Nutrients 11(8), 1859 (2019). https://doi.org/10.3390/nu11081859

    Article  CAS  Google Scholar 

  93. M.P. O’Donnell, B.W. Fox, P.H. Chao, F.C. Schroeder, P. Sengupta, A neurotransmitter produced by gut bacteria modulates host sensory behaviour. Nature 583(7816), 415–420 (2020). https://doi.org/10.1038/s41586-020-2395-5

    Article  CAS  Google Scholar 

  94. A. Oka, R.B. Sartor, Microbial-based and microbial-targeted therapies for inflammatory bowel diseases. Dig. Dis. Sci. 65(3), 757–788 (2020). https://doi.org/10.1007/s10620-020-06090-z

    Article  CAS  Google Scholar 

  95. B. Olas, Probiotics, prebiotics and synbiotics-A promising strategy in prevention and treatment of cardiovascular diseases? Int. J. Mol. Sci. 21(24), 9737 (2020). https://doi.org/10.3390/ijms21249737

    Article  CAS  Google Scholar 

  96. A. Oniszczuk, T. Oniszczuk, M. Gancarz, J. Szymańska, Role of gut microbiota, probiotics and prebiotics in the cardiovascular diseases. Molecules 26(4), 1172 (2021). https://doi.org/10.3390/molecules26041172

    Article  CAS  Google Scholar 

  97. B. Peng, H. Li, X.X. Peng, Functional metabolomics: From biomarker discovery to metabolome reprogramming. Protein Cell 6, 628–637 (2015). https://doi.org/10.1007/s13238-015-0185-x

    Article  CAS  Google Scholar 

  98. J. Plaza-Díaz, F.J. Ruiz-Ojeda, L.M. Vilchez-Padial, A. Gil, Evidence of the anti-inflammatory effects of probiotics and synbiotics in intestinal chronic diseases. Nutrients 9(6), 555 (2017). https://doi.org/10.3390/nu9060555

    Article  CAS  Google Scholar 

  99. E.L. Plummer, D.M. Bulach, G.L. Murray, S.E. Jacobs, S.N. Tabrizi, S.M. Garland, ProPrems Study Group, Gut microbiota of preterm infants supplemented with probiotics: Sub-study of the ProPrems trial. BMC Microbiol. 18, 1–8 (2018). https://doi.org/10.1186/s12866-018-1326-1

    Article  CAS  Google Scholar 

  100. B. Pot, Y. Vandenplas, Factors that influence clinical efficacy of live biotherapeutic products. Eur. J. Med. Res. 26(1), 40 (2021). https://doi.org/10.1186/s40001-021-00509-7

    Article  Google Scholar 

  101. M. Primec, M. Klemenak, D. Di Gioia, I. Aloisio, N. Bozzi Cionci, A. Quagliariello, M. Gorenjak, D. Mičetić-Turk, T. Langerholc, Clinical intervention using Bifidobacterium strains in celiac disease children reveals novel microbial modulators of TNF-α and short-chain fatty acids. Clin. Nutr. 38(3), 1373–1381 (2019). https://doi.org/10.1016/j.clnu.2018.06.931

    Article  CAS  Google Scholar 

  102. E.M. Quigley, The efficacy of probiotics in IBS. J. Clin. Gastroenterol. 42, S85–S90 (2008). https://doi.org/10.1097/MCG.0b013e31816244ca

    Article  Google Scholar 

  103. S. Rampelli, S. Turroni, C. Mallol, C. Hernandez, B. Galván, A. Sistiaga, E. Biagi, A. Astolfi, P. Brigidi, S. Benazzi, C.M. Lewis Jr., C. Warinner, C.A. Hofman, S.L. Schnorr, M. Candela, Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Commun. Biol. 4 (2021). https://doi.org/10.1038/s42003-021-01689-y

  104. A. Ray, A. Khare, N. Krishnamoorthy, Z. Qi, P. Ray, Regulatory T cells in many flavors control asthma. Mucosal Immunol. 3, 216–229 (2010). https://doi.org/10.1038/mi.2010.4

    Article  CAS  Google Scholar 

  105. G. Reid, R. Kort, S. Alvarez, R. Bourdet-Sicard, V. Benoit, M. Cunningham, D.M. Saulnier, J.E.T. van Hylckama Vlieg, H. Verstraelen, W. Sybesma, Expanding the reach of probiotics through social enterprises. Benef. Microbes 9(5), 707–715 (2018). https://doi.org/10.3920/BM2018.0015. Wageningen Academic Publishers

    Article  CAS  Google Scholar 

  106. M.A.M. Rogers, M.T. Greene, S. Saint, C.E. Chenoweth, P.N. Malani, I. Trivedi, D.M. Aronoff, Higher rates of Clostridium difficile infection among smokers. PLoS One 7, e42091 (2012). https://doi.org/10.1371/journal.pone.0042091

    Article  CAS  Google Scholar 

  107. G.A.W. Rook, 99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: Darwinian medicine and the ‘hygiene’ or ‘old friends’ hypothesis. Clin. Exp. Immunol. 160, 70–79 (2010). https://doi.org/10.1111/j.1365-2249.2010.04133.x

    Article  CAS  Google Scholar 

  108. G.A.W. Rook, C.L. Raison, C.A. Lowry, Microbiota, immunoregulatory old friends and psychiatric disorders, in Microbial Endocrinology: The Microbiota-Gut-Brain Axis in Health and Disease, ed. by M. Lyte, J.F. Cryan, (Springer, New York, 2014), pp. 319–356

    Chapter  Google Scholar 

  109. A. Rouanet, S. Bolca, A. Bru, I. Claes, H. Cvejic, H. Girgis, A. Harper, S.N. Lavergne, S. Mathys, M. Pane, B. Pot, C. Shortt, W. Alkema, C. Bezulowsky, S. Blanquet-Diot, C. Chassard, S.P. Claus, B. Hadida, C. Hemmingsen, C. Jeune, B. Lindman, G. Midzi, L. Mogna, C. Movitz, N. Nasir, M. Oberreither, J.F.M.L. Seegers, L. Sterkman, A. Valo, F. Vieville, M. Cordaillat-Simmons, Live Biotherapeutic Products, a road map for safety assessment. Front. Med. (Lausanne) 7, 237 (2020). https://doi.org/10.3389/fmed.2020.00237

    Article  Google Scholar 

  110. C. Rousseaux, X. Thuru, A. Gelot, N. Barnich, C. Neut, L. Dubuquoy, C. Dubuquoy, E. Merour, K. Geboes, M. Chamaillard, A. Ouwehand, G. Leyer, D. Carcano, J.F. Colombel, D. Ardid, P. Desreumaux, Lactobacillus acidophilus modulates intestinal pain and induces opioid and cannabinoid receptors. Nat. Med. 13, 35–37 (2007). https://doi.org/10.1038/nm1521

    Article  CAS  Google Scholar 

  111. L. Rueda-Ruzafa, F. Cruz, P. Roman, D. Cardona, Gut microbiota and neurological effects of glyphosate. Neurotoxicology 75, 1–8 (2019). https://doi.org/10.1016/j.neuro.2019.08.006

    Article  CAS  Google Scholar 

  112. E. Rutayisire, K. Huang, Y. Liu, F. Tao, The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: A systematic review. BMC Gastroenterol. 16, 1–12 (2016). https://doi.org/10.1186/s12876-016-0498-0

    Article  Google Scholar 

  113. A. Rutsch, J.B. Kantsjö, F. Ronchi, The gut-brain axis: How microbiota and host inflammasome influence brain physiology and pathology. Front. Immunol. 11, 1–24 (2020). https://doi.org/10.3389/fimmu.2020.604179

    Article  CAS  Google Scholar 

  114. R. Satokari, Modulation of gut microbiota for health by current and next-generation probiotics. Nutrients 11(8), 1921 (2019). https://doi.org/10.3390/nu11081921

    Article  Google Scholar 

  115. B. Shan, Z. Ai, S. Zeng, Y. Song, J. Song, Q. Zeng, Z. Liao, T. Wang, C. Huang, D. Su, Gut microbiome-derived lactate promotes to anxiety-like behaviors through GPR81 receptor-mediated lipid metabolism pathway. Psychoneuroendocrinology 117, 104699 (2020). https://doi.org/10.1016/j.psyneuen.2020.104699

    Article  CAS  Google Scholar 

  116. F. Shanahan, T.S. Ghosh, P.W. O’Toole, The healthy microbiome—What is the definition of a healthy gut microbiome? Gastroenterology 160, 483–494 (2021). https://doi.org/10.1053/j.gastro.2020.09.057

    Article  Google Scholar 

  117. M. Shapira, Gut microbiotas and host evolution: Scaling up symbiosis. Trends Ecol. Evol. 31, 539–549 (2016). https://doi.org/10.1016/J.TREE.2016.03.006

    Article  Google Scholar 

  118. A. Sharma, S.-H. In, Special issue on the human microbiome: From symbiosis to therapy. Exp. Mol. Med. 52, 1361 (2020). https://doi.org/10.1038/S12276-020-00488-5

  119. C.C. Silva, M.A. Monteil, E.M. Davis, Overweight and obesity in children are associated with an abundance of Firmicutes and reduction of Bifidobacterium in their gastrointestinal microbiota. Child. Obes. 16, 204–210 (2020). https://doi.org/10.1089/chi.2019.0280

    Article  Google Scholar 

  120. A. Sivan, L. Corrales, N. Hubert, J.B. Williams, K. Aquino-Michaels, Z.M. Early, F.W. Benyamin, Y.M. Lei, B. Jabri, M.L. Alegre, E.B. Chang, T.F. Gajewski, Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science 350, 1084–1089 (2015). https://doi.org/10.1126/science.aac4255

    Article  CAS  Google Scholar 

  121. K. Skonieczna-Żydecka, K. Jakubczyk, D. Maciejewska-Markiewicz, K. Janda, K. Kaźmierczak-Siedlecka, M. Kaczmarczyk, I. Łoniewski, W. Marlicz, Gut biofactory-neurocompetent metabolites within the gastrointestinal tract. A scoping review. Nutrients 12(11), 3369 (2020). https://doi.org/10.3390/nu12113369

    Article  CAS  Google Scholar 

  122. K.S. Smirnov, T.V. Maier, A. Walker, S.S. Heinzmann, S. Forcisi, I. Martinez, J. Walter, P. Schmitt-Kopplin, Challenges of metabolomics in human gut microbiota research. Int. J. Med. Microbiol. 306, 266–279 (2016). https://doi.org/10.1016/j.ijmm.2016.03.006

    Article  CAS  Google Scholar 

  123. B. Stecher, The roles of inflammation, nutrient availability and the commensal microbiota in enteric pathogen infection. Microbiol. Spectr. 3, 297–320 (2015). https://doi.org/10.1128/microbiolspec.MBP-0008-2014

    Article  CAS  Google Scholar 

  124. Y. Su, D. Chen, D. Yuan, C. Lausted, J. Choi, C.L. Dai, V. Voillet, V.R. Duvvuri, K. Scherler, P. Troisch, P. Baloni, G. Qin, B. Smith, S.A. Kornilov, C. Rostomily, A. Xu, J. Li, S. Dong, A. Rothchild, J. Zhou, K. Murray, R. Edmark, S. Hong, J.E. Heath, J. Earls, R. Zhang, J. Xie, S. Li, R. Roper, L. Jones, Y. Zhou, L. Rowen, R. Liu, S. Mackay, D.S. O’Mahony, C.R. Dale, J.A. Wallick, H.A. Algren, M.A. Zager, ISB-Swedish COVID19 Biobanking Unit, W. Wei, N.D. Price, S. Huang, N. Subramanian, K. Wang, A.T. Magis, J.J. Hadlock, L. Hood, A. Aderem, J.A. Bluestone, L.L. Lanier, P.D. Greenberg, R. Gottardo, M.M. Davis, J.D. Goldman, J.R. Heath, Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19. Cell 183(6), 1479–1495.e20 (2020). https://doi.org/10.1016/j.cell.2020.10.037

    Article  CAS  Google Scholar 

  125. A.C. Tadrowski, M.R. Evans, B. Waclaw, Phenotypic switching can speed up microbial evolution. Sci. Rep. 8, 8941 (2018). https://doi.org/10.1038/s41598-018-27095-9

    Article  CAS  Google Scholar 

  126. H. Tamaki, H. Nakase, S. Inoue, C. Kawanami, T. Itani, M. Ohana, T. Kusaka, S. Uose, H. Hisatsune, M. Tojo, T. Noda, S. Arasawa, M. Izuta, A. Kubo, C. Ogawa, T. Matsunaka, M. Shibatouge, Efficacy of probiotic treatment with Bifidobacterium longum 536 for induction of remission in active ulcerative colitis: A randomized, double-blinded, placebo-controlled multicenter trial. Dig. Endosc. 28(1), 67–74 (2016). https://doi.org/10.1111/den.12553

    Article  Google Scholar 

  127. O.R. Tamtaji, M. Taghizadeh, R. Daneshvar Kakhaki, E. Kouchaki, F. Bahmani, S. Borzabadi, S. Oryan, A. Mafi, Z. Asemi, Clinical and metabolic response to probiotic administration in people with Parkinson’s disease: A randomized, double-blind, placebo-controlled trial. Clin. Nutr. 38(3), 1031–1035 (2019). https://doi.org/10.1016/j.clnu.2018.05.018

    Article  CAS  Google Scholar 

  128. G. Tang, L. Zhang, Update on strategies of probiotics for the prevention and treatment of colorectal cancer. Nutr. Cancer 74(1), 27–38 (2022). https://doi.org/10.1080/01635581.2020.1865420

    Article  CAS  Google Scholar 

  129. T. Thomas, J. Gilbert, F. Meyer, Metagenomics – A guide from sampling to data analysis. Microb. Inform. Exp. 9, 3 (2012). https://doi.org/10.1186/2042-5783-2-3

    Article  CAS  Google Scholar 

  130. L. Tipton, J.L. Darcy, N.A. Hynson, A developing symbiosis: Enabling cross-talk between ecologists and microbiome scientists. Front. Microbiol. 10 (2019). https://doi.org/10.3389/FMICB.2019.00292

  131. A.S. Torson, Y.W. Dong, B.J. Sinclair, Help, there are “omics” in my comparative physiology! J. Exp. Biol. 223, jeb191262 (2020). https://doi.org/10.1242/jeb.191262

    Article  Google Scholar 

  132. S. Uroz, P.E. Courty, P. Oger, Plant symbionts are engineers of the plant-associated microbiome. Trends Plant Sci. 24, 905–916 (2019). https://doi.org/10.1016/j.tplants.2019.06.008

    Article  CAS  Google Scholar 

  133. L. Valdés-Varela, M. Gueimonde, P. Ruas-Madiedo, Probiotics for prevention and treatment of Clostridium difficile infection. Adv. Exp. Med. Biol. 1050, 161–176 (2018). https://doi.org/10.1007/978-3-319-72799-8_10

    Article  Google Scholar 

  134. A.M. Vargason, A.C. Anselmo, Evaluation of surface modified live biotherapeutic products for oral delivery. ACS Biomater Sci. Eng. (2020). https://doi.org/10.1021/acsbiomaterials.0c01405

  135. N.C. Verberkmoes, A.L. Russell, M. Shah, A. Godzik, M. Rosenquist, J. Halfvarson, M.G. Lefsrud, J. Apajalahti, C. Tysk, R.L. Hettich, J.K. Jansson, Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179–189 (2009). https://doi.org/10.1038/ismej.2008.108

    Article  CAS  Google Scholar 

  136. E.F. Verdu, P. Bercik, G.E. Bergonzelli, X.-X. Huang, P. Blennerhasset, F. Rochat, M. Fiaux, R. Mansourian, I. Corthésy-Theulaz, S.M. Collins, Lactobacillus paracasei normalizes muscle hypercontractility in a murine model of postinfective gut dysfunction. Gastroenterology 127, 826–837 (2004). https://doi.org/10.1053/j.gastro.2004.06.007

    Article  CAS  Google Scholar 

  137. E.F. Verdu, P. Bercik, M. Verma-Gandhu, X.-X. Huang, P. Blennerhassett, W. Jackson, Y. Mao, L. Wang, F. Rochat, S.M. Collins, Specific probiotic therapy attenuates antibiotic induced visceral hypersensitivity in mice. Gut 55, 182–190 (2006). https://doi.org/10.1136/gut.2005.066100

    Article  CAS  Google Scholar 

  138. S. Verheijden, G.E. Boeckxstaens, Neuroimmune interaction and the regulation of intestinal immune homeostasis. Am. J. Physiol. Gastrointest. Liver Physiol. 314, G75–G80 (2018). https://doi.org/10.1152/ajpgi.00425.2016

    Article  CAS  Google Scholar 

  139. A. Vrieze, F. Holleman, E.G. Zoetendal, W.M. De Vos, J.B.L. Hoekstra, M. Nieuwdorp, The environment within: How gut microbiota may influence metabolism and body composition. Diabetologia 53, 606–613 (2010). https://doi.org/10.1007/s00125-010-1662-7

    Article  CAS  Google Scholar 

  140. A.W. Walker, S.H. Duncan, P. Louis, H.J. Flint, Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol. 22, 267–274 (2014). https://doi.org/10.1016/j.tim.2014.03.001

    Article  CAS  Google Scholar 

  141. M. Wang, M. Li, S. Wu, C.B. Lebrilla, R.S. Chapkin, I. Ivanov, S.M. Donovan, Fecal microbiota composition of breast-fed infants is correlated with human milk oligosaccharides consumed. J. Pediatr. Gastroenterol. Nutr. 60, 825–833 (2015). https://doi.org/10.1097/MPG.0000000000000752

    Article  CAS  Google Scholar 

  142. D.Z. Wang, L.F. Kong, Y.Y. Li, Z.X. Xie, Environmental microbial community proteomics: Status, challenges and perspectives. Int. J. Mol. Sci. 17, 1275 (2016). https://doi.org/10.3390/ijms17081275

    Article  Google Scholar 

  143. N. Wang, F. Zhu, L. Chen, K. Chen, Proteomics, metabolomics and metagenomics for type 2 diabetes and its complications. Life Sci. 212, 194–202 (2018). https://doi.org/10.1016/j.lfs.2018.09.035

    Article  CAS  Google Scholar 

  144. Z. Wang, Z. Lai, X. Zhang, P. Huang, J. Xie, Q. Jiang, Q. Zhang, K.F. Chung, Altered gut microbiome compositions are associated with the severity of asthma. J. Thorac. Dis. 13, 4322–4338 (2021). https://doi.org/10.21037/jtd-20-2189

    Article  Google Scholar 

  145. J.C. Wells, A.L. Sawaya, R. Wibaek, M. Mwangome, M.S. Poullas, C.S. Yajnik, A. Demaio, The double burden of malnutrition: Aetiological pathways and consequences for health. Lancet 395(10217), 75–88 (2020). https://doi.org/10.1016/S0140-6736(19)32472-9

    Article  Google Scholar 

  146. World Health Organization, Global Nutrition Targets 2025 Breastfeeding Policy Brief (2014). https://apps.who.int/iris/handle/10665/149022. Accessed 29 Jan 2022

  147. T. Yang, H. Li, A.C. Oliveira, R. Goel, E.M. Richards, C.J. Pepine, M.K. Raizada, Transcriptomic signature of gut microbiome-contacting cells in colon of spontaneously hypertensive rats. Physiol. Genomics 52, 121–132 (2020). https://doi.org/10.1152/physiolgenomics.00087.2019

    Article  CAS  Google Scholar 

  148. Z.T. Yu, C. Chen, D.E. Kling, B. Liu, J.M. McCoy, M. Merighi, M. Heidtman, D.S. Newburg, The principal fucosylated oligosaccharides of human milk exhibit prebiotic properties on cultured infant microbiota. Glycobiology 23, 169–177 (2013). https://doi.org/10.1093/glycob/cws138

    Article  CAS  Google Scholar 

  149. R. Yu, F. Zuo, H. Ma, S. Chen, Exopolysaccharide-producing bifidobacterium adolescentis strains with similar adhesion property induce differential regulation of inflammatory immune response in Treg/Th17 axis of DSS-colitis mice. Nutrients 11, 1–20 (2019). https://doi.org/10.3390/nu11040782

    Article  CAS  Google Scholar 

  150. L. Zhang, H. Yi, Potential antitumor and anti-inflammatory activities of an extracellular polymeric substance (EPS) from Bacillus subtilis isolated from a housefly. Sci. Rep. 12, 1–10 (2022). https://doi.org/10.1038/s41598-022-05143-9

    Article  CAS  Google Scholar 

  151. X. Zhang, S.A. Deeke, Z. Ning, A.E. Starr, J. Butcher, J. Li, J. Mayne, K. Cheng, B. Liao, L. Li, R. Singleton, D. Mack, A. Stintzi, D. Figeys, Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Nat. Commun. 9, 2873–2887 (2018). https://doi.org/10.1038/s41467-018-05357-4

    Article  CAS  Google Scholar 

  152. M.A.C. Zijlmans, K. Korpela, J.M. Riksen-Walraven, W.M. de Vos, C. Weerth, Maternal prenatal stress is associated with the infant intestinal microbiota. Psychoneuroendocrinology 53, 233–245 (2015). https://doi.org/10.1016/j.psyneuen.2015.01.006

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Luiz de Queiroz College of Agriculture and Centre for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil

    Paloma Nathane Nunes de Freitas

  2. Department of Biotechnology, Genetics and Cell Biology, State University of Maringá, Maringa, Brazil

    Caroline Rosa Silva & Paola Pereira Constantin

  3. Department of Structural and Molecular Biology, and Genetics, Ponta Grossa State University, Ponta Grossa, Brazil

    Sônia Alvim Veiga Pileggi, Marcelo Ricardo Vicari & Marcos Pileggi

Authors
  1. Paloma Nathane Nunes de Freitas
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Caroline Rosa Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Paola Pereira Constantin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sônia Alvim Veiga Pileggi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Marcelo Ricardo Vicari
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Marcos Pileggi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marcos Pileggi .

Editor information

Editors and Affiliations

  1. Department of Bioengineering, Ege University, Bornova, Izmir, Türkiye

    Suphi S. Oncel

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

de Freitas, P.N.N., Silva, C.R., Constantin, P.P., Pileggi, S.A.V., Vicari, M.R., Pileggi, M. (2023). Fixing the Damage: The Evolution of Probiotics from Fermented Food to Biotherapeutic Products. In: Oncel, S.S. (eds) A Sustainable Green Future. Springer, Cham. https://doi.org/10.1007/978-3-031-24942-6_12

Download citation

Publish with us

Policies and ethics

Search

Navigation