The Clash of Microbiomes: From the Food Matrix to the Host Gut
Abstract
:1. The Advent of Fermented Foods and Their Functional Applications
2. Breaking Down the Fermentation Process
3. Fermented Foods Harbor a Stable, Yet Dynamic, Microbial Ecosystem
4. The Clash of Microbiomes
5. Newcomers in Action
6. The Dawn of a New Era
7. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
- Tamang, J.P.; Cotter, P.D.; Endo, A.; Han, N.S.; Kort, R.; Liu, S.Q.; Mayo, B.; Westerik, N.; Hutkins, R. Fermented foods in a global age: East meets West. Compr. Rev. Food Sci. Food Saf. 2020, 19, 184–217. [Google Scholar] [CrossRef] [Green Version]
- Marco, M.L.; Heeney, D.; Binda, S.; Cifelli, C.J.; Cotter, P.D.; Foligné, B.; Gänzle, M.; Kort, R.; Pasin, G.; Pihlanto, A.; et al. Health benefits of fermented foods: Microbiota and beyond. Curr. Opin. Biotechnol. 2017, 44, 94–102. [Google Scholar] [CrossRef] [PubMed]
- Lorenzo, J.M.; Munekata, P.E.; Gómez, B.; Barba, F.J.; Mora, L.; Pérez-Santaescolástica, C.; Toldrá, F. Bioactive peptides as natural antioxidants in food products—A review. Trends Food Sci. Technol. 2018, 79, 136–147. [Google Scholar] [CrossRef]
- Nataraj, B.H.; Ali, S.A.; Behare, P.V.; Yadav, H. Postbiotics-parabiotics: The new horizons in microbial biotherapy and functional foods. Microb. Cell Fact. 2020, 19, 168. [Google Scholar] [CrossRef] [PubMed]
- Gille, D.; Schmid, A.; Walther, B.; Vergères, G. Fermented food and non-communicable chronic diseases: A review. Nutrients 2018, 10, 448. [Google Scholar] [CrossRef] [Green Version]
- Iwatani, S.; Yamamoto, N. Functional food products in Japan: A review. Food Sci. Hum. Wellness 2019, 8, 96–101. [Google Scholar] [CrossRef]
- Number of Products Certified as ‘Foods for Specified Health Uses’ (FOSHU) in Japan in 2011 to 2020. Available online: https://www.statista.com/statistics/1196260/japan-number-foshu-products/ (accessed on 3 December 2021).
- EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA). Scientific Opinion on the substantiation of health claims related to live yoghurt cultures and improved lactose digestion (ID 1143, 2976) pursuant to Article 13(1) of Regulation (EC) No 1924/2006. EFSA J. 2010, 8, 1763. [Google Scholar] [CrossRef]
- Solomons, N.W. Fermentation, fermented foods and lactose intolerance. Eur. J. Clin. Nutr. 2002, 4, S50–S55. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Balaguer, F.; Enrique, M.; Llopis, S.; Barrena, M.; Navarro, V.; Álvarez, B.; Chenoll, E.; Ramón, D.; Tortajada, M.; Martorell, P. Lipoteichoic acid from Bifidobacterium animalis subsp. lactis BPL1: A novel postbiotic that reduces fat deposition via IGF-1 pathway. Microb. Biotechnol. 2021. [Google Scholar] [CrossRef]
- Şanlier, N.; Gökcen, B.B.; Sezgin, A.C. Health benefits of fermented foods. Crit. Rev. Food Sci. Nutr. 2019, 59, 506–527. [Google Scholar] [CrossRef]
- Wang, Y.; Wu, J.; Lv, M.; Shao, Z.; Hungwe, M.; Wang, J.; Bai, X.; Xie, J.; Wang, Y.; Geng, W. Metabolism Characteristics of lactic acid bacteria and the expanding applications in food industry. Front. Bioeng. Biotechnol. 2021, 9, 612285. [Google Scholar] [CrossRef]
- El Sheikha, A.F.; Hu, D.M. Molecular techniques reveal more secrets of fermented foods. Crit. Rev. Food Sci. Nutr. 2020, 60, 11–32. [Google Scholar] [CrossRef] [PubMed]
- Food and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO). Guidelines for the Evaluation of Probiotics in Food. 2021. Available online: https://www.who.int/foodsafety/fs_management/en/probiotic_guidelines.pdf (accessed on 3 December 2021).
- Hill, C.; Guarner, F.; Reid, G.; Gibson, G.R.; Merenstein, D.J.; Pot, B.; Morelli, L.; Canani, R.B.; Flint, H.J.; Salminen, S.; 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. 2014, 11, 506–514. [Google Scholar] [CrossRef] [Green Version]
- De Filippis, F.; Parente, E.; Ercolini, D. Recent past, present, and future of the food microbiome. Annu. Rev. Food Sci. Technol. 2018, 9, 589–608. [Google Scholar] [CrossRef] [Green Version]
- Arias-Sánchez, F.I.; Vessman, B.; Mitri, S. Artificially selecting microbial communities: If we can breed dogs, why not microbiomes? PLoS Biol. 2019, 17, e3000356. [Google Scholar] [CrossRef] [Green Version]
- Dourou, D.; Spyrelli, E.D.; Doulgeraki, A.I.; Argyri, A.A.; Grounta, A.; Nychas, G.E.; Chorianopoulos, N.G.; Tassou, C.C. Microbiota of chicken breast and thigh fillets stored under different refrigeration temperatures assessed by next-generation sequencing. Foods. 2021, 10, 765. [Google Scholar] [CrossRef]
- Wieërs, G.; Belkhir, L.; Enaud, R.; Leclercq, S.; Philippart de Foy, J.M.; Dequenne, I.; de Timary, P.; Cani, P.D. How Probiotics Affect the Microbiota. Front. Cell Infect. Microbiol. 2020, 9, 454. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Ashraf, R.; Shah, N.P. Immune system stimulation by probiotic microorganisms. Crit. Rev. Food Sci. Nutr. 2014, 54, 938–956. [Google Scholar] [CrossRef] [PubMed]
- Wilkins, T.; Sequoia, J. Probiotics for gastrointestinal conditions: A Summary of the Evidence. Am. Fam. Phys. 2017, 96, 170–178. [Google Scholar]
- Maldonado Galdeano, C.; Cazorla, S.I.; Lemme Dumit, J.M.; Vélez, E.; Perdigón, G. Beneficial effects of probiotic consumption on the immune system. Ann. Nutr. Metab. 2019, 74, 115–124. [Google Scholar] [CrossRef]
- Zacarías, M.F.; Binetti, A.; Laco, M.; Reinheimer, J.; Vinderola, G. Preliminary technological and probiotic characterization of bifido-bacteria isolated from breast milk for use in dairy products. Int. Dairy J. 2011, 21, 548–555. [Google Scholar] [CrossRef]
- Pavli, F.G.; Argyri, A.A.; Papadopoulou, O.S.; Nychas, G.-J.E.; Chorianopoulos, N.G.; Tassou, C.C. Probiotic potential of lactic acid bacteria from traditional fermented dairy and meat products: Assessment by in vitro tests and molecular characterization. J. Probiotics Health. 2016, 4, 157. [Google Scholar] [CrossRef]
- Argyri, A.A.; Zoumpopoulou, G.; Karatzas, K.-A.G.; Tsakalidou, E.; Nychas, G.-J.E.; Panagou, E.Z.; Tassou, C.C. Selection of potential probiotic lactic acid bacteria from fermented olives by in vitro tests. Food Microbiol. 2013, 33, 282–291. [Google Scholar] [CrossRef] [PubMed]
- Duar, R.M.; Lin, X.B.; Zheng, J.; Martino, M.E.; Grenier, T.; Pérez-Muñoz, M.E.; Leulier, F.; Gänzle, M.; Walter, J. Lifestyles in transition: Evolution and natural history of the genus Lactobacillus. FEMS Microbiol. Rev. 2017, 41, S27–S48. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Wang, T.; Goyal, A.; Dubinkina, V.; Maslov, S. Evidence for a multi-level trophic organization of the human gut microbiome. PLoS Comput. Biol. 2019, 15, e1007524. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Day, M.D.; Beck, D.; Foster, J.A. Microbial Communities as Experimental Units. Bioscience. 2011, 61, 398–406. [Google Scholar] [CrossRef] [Green Version]
- Lugtenberg, B.; Rozen, D.E.; Kamilova, F. Wars between microbes on roots and fruits [version 1; referees: 3 approved]. F1000Research 2017, 6, 343. [Google Scholar] [CrossRef] [Green Version]
- Mokoena, M.P. Lactic acid bacteria and their bacteriocins: Classification, biosynthesis and applications against uropathogens: A mini-review. Molecules 2017, 22, 1255. [Google Scholar] [CrossRef]
- Deveau, A.; Bonito, G.; Uehling, J.; Paoletti, M.; Becker, M.; Bindschedler, S.; Hacquard, S.; Hervé, V.; Labbé, J.; Lastovetsky, O.A.; et al. Bacterial-fungal interactions: Ecology, mechanisms and challenges. FEMS Microbiol. Rev. 2018, 42, 335–352. [Google Scholar] [CrossRef] [Green Version]
- Terpou, A.; Papadaki, A.; Lappa, I.K.; Kachrimanidou, V.; Bosnea, L.A.; Kopsahelis, N. Probiotics in food systems: Significance and emerging strategies towards improved viability and delivery of enhanced beneficial value. Nutrients 2019, 11, 1591. [Google Scholar] [CrossRef] [Green Version]
- Pénicaud, C.; Monclus, V.; Perret, B.; Passot, S.; Fonseca, F. Life cycle assessment of the production of stabilized lactic acid bacteria for the environmentally-friendly preservation of living cells. J. Clean. Prod. 2018, 184, 847–858. [Google Scholar] [CrossRef]
- Dourou, D.; Grounta, A.; Argyri, A.A.; Froutis, G.; Tsakanikas, P.; Nychas, G.E.; Doulgeraki, A.I.; Chorianopoulos, N.G.; Tassou, C.C. Rapid microbial quality assessment of chicken liver inoculated or not with Salmonella Using FTIR spectroscopy and machine learning. Front. Microbiol. 2021, 11, 623788. [Google Scholar] [CrossRef] [PubMed]
- King, K.C.; Stevens, E.; Drew, G.C. Microbiome: Evolution in a world of interaction. Curr. Biol. 2020, 30, R265–R267. [Google Scholar] [CrossRef]
- Zeevi, D.; Korem, T.; Godneva, A.; Bar, N.; Kurilshikov, A.; Lotan-Pompan, M.; Weinberger, A.; Fu, J.; Wijmenga, C.; Zhernakova, A.; et al. Structural variation in the gut microbiome associates with host health. Nature 2019, 568, 43–48. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Barroso-Batista, J.; Pedro, M.F.; Sales-Dias, J.; Pinto, C.J.G.; Thompson, J.A.; Pereira, H.; Demengeot, J.; Gordo, I.; Xavier, K.B. Specific eco-evolutionary contexts in the mouse gut reveal Escherichia coli metabolic versatility. Curr. Biol. 2020, 30, 1049–1062.e7. [Google Scholar] [CrossRef]
- Barreto, H.C.; Frazão, N.; Sousa, A.; Konrad, A.; Gordo, I. Mutation accumulation and horizontal gene transfer in Escherichia coli colonizing the gut of old mice. Commun. Integr. Biol. 2020, 13, 89–96. [Google Scholar] [CrossRef]
- Lekhman, R.; Goodrich, J.K.; Huang, K.; Sun, Q.; Bukowski, R.; Bell, J.T.; Spector, T.D.; Keinan, A.; Ley, R.E.; Gevers, D.; et al. Host genetic variation impacts microbiome composition across human body sites. Genome Biol. 2015, 16, 191–203. [Google Scholar] [CrossRef] [Green Version]
- Cullen, C.M.; Aneja, K.K.; Beyhan, S.; Cho, C.E.; Woloszynek, S.; Convertino, M.; McCoy, S.J.; Zhang, Y.; Anderson, M.Z.; Alvarez-Ponce, D.; et al. Emerging priorities for microbiome research. Front. Microbiol. 2020, 11, 136. [Google Scholar] [CrossRef] [Green Version]
- Macklaim, J.M.; Gloor, G.B.; Anukam, K.C.; Cribby, S.; Reid, G. At the crossroads of vaginal health and disease, the genome sequence of Lactobacillus iners AB-1. Proc. Natl. Acad. Sci. USA 2011, 108, 4688–4695. [Google Scholar] [CrossRef] [Green Version]
- Petrova, M.I.; Reid, G.; Vaneechoutte, M.; Lebeer, S. Lactobacillus iners: Friend or Foe? Trends Microbiol. 2017, 25, 182–191. [Google Scholar] [CrossRef] [PubMed]
- Suez, J.; Zmora, N.; Zilberman-Schapira, G.; Mor, U.; Dori-Bachash, M.; Bashiardes, S.; Zur, M.; Regev-Lehavi, D.; Ben-Zeev Brik, R.; Federici, S.; et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell 2018, 174, 1406–1423.e16. [Google Scholar] [CrossRef] [Green Version]
- Bo, T.B.; Wen, J.; Zhao, Y.C.; Tian, S.J.; Zhang, X.Y.; Wang, D.H. Bifidobacterium pseudolongum reduces triglycerides by modulating gut microbiota in mice fed high-fat food. J. Steroid Biochem. Mol. Biol. 2020, 198, 105602. [Google Scholar] [CrossRef]
- Zmora, N.; Zilberman-Schapira, G.; Suez, J.; Mor, U.; Dori-Bachash, M.; Bashiardes, S.; Kotler, E.; Zur, M.; Regev-Lehavi, D.; Brik, R.B.; et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 2018, 174, 1388–1405.e21. [Google Scholar] [CrossRef] [Green Version]
- Kiousi, D.E.; Rathosi, M.; Tsifintaris, M.; Chondrou, P.; Galanis, A. Pro-biomics: Omics technologies to unravel the role of probiotics in health and disease. Adv. Nutr. 2021, 12, 1802–1820. [Google Scholar] [CrossRef] [PubMed]
- Hemarajata, P.; Versalovic, J. Effects of probiotics on gut microbiota: Mechanisms of intestinal immunomodulation and neuromodulation. Therap. Adv. Gastroenterol. 2013, 6, 39–51. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Metchnikoff, E. The Prolongation of Life. In Optimistic Studies; Mitchell, P.C., Ed.; G. P. Putnam’s Sons: New York, NY, USA, 1910; p. 96. [Google Scholar]
- Dimidi, E.; Christodoulides, S.; Fragkos, K.C.; Scott, S.M.; Whelan, K. The effect of probiotics on functional constipation in adults: A systematic review and meta-analysis of randomized controlled trials. Am. J. Clin. Nutr. 2014, 100, 1075–1084. [Google Scholar] [CrossRef] [Green Version]
- Markowiakm, P.; Śliżewska, K. Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients 2017, 9, 1021. [Google Scholar] [CrossRef] [PubMed]
- Ou, Y.; Chen, S.; Ren, F.; Zhang, M.; Ge, S.; Guo, H.; Zhang, H.; Zhao, L. Lactobacillus casei strain shirota alleviates constipation in adults by increasing the pipecolinic acid level in the gut. Front. Microbiol. 2019, 10, 324. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sakai, T.; Kubota, H.; Gawad, A.; Gheyle, L.; Ramael, S.; Oishi, K. Effect of fermented milk containing Lactobacillus casei strain Shirota on constipation-related symptoms and haemorrhoids in women during puerperium. Benef. Microbes 2015, 6, 253–262. [Google Scholar] [CrossRef] [Green Version]
- Aoyagi, Y.; Amamoto, R.; Park, S.; Honda, Y.; Shimamoto, K.; Kushiro, A.; Tsuji, H.; Matsumoto, H.; Shimizu, K.; Miyazaki, K.; et al. Independent and interactive effects of habitually ingesting fermented milk products containing Lactobacillus casei strain shirota and of engaging in moderate habitual daily physical activity on the intestinal health of older people. Front. Microbiol. 2019, 10, 1477. [Google Scholar] [CrossRef] [Green Version]
- Zhang, X.; Chen, S.; Zhang, M.; Ren, F.; Ren, Y.; Li, Y.; Liu, N.; Zhang, Y.; Zhang, Q.; Wang, R. Effects of fermented milk containing Lacticaseibacillus paracasei strain shirota on constipation in patients with depression: A randomized, double-blind, placebo-controlled trial. Nutrients 2021, 13, 2238. [Google Scholar] [CrossRef]
- Pourrajab, B.; Naderi, N.; Janani, L.; Mofid, V.; Hajahmadi, M.; Dehnad, A.; Shidfar, F. Comparison of probiotic yogurt and ordinary yogurt consumption on serum Pentraxin3, NT-proBNP, oxLDL, and ApoB100 in patients with chronic heart failure: A randomized, triple-blind, controlled trial. Food Funct. 2020, 11, 10000–10010. [Google Scholar] [CrossRef]
- Tonucci, L.B.; Olbrich Dos Santos, K.M.; Licursi de Oliveira, L.; Rocha Ribeiro, S.M.; Duarte Martino, H.S. Clinical application of probiotics in type 2 diabetes mellitus: A randomized, double-blind, placebo-controlled study. Clin. Nutr. 2017, 36, 85–92. [Google Scholar] [CrossRef]
- Mohammadi-Sartang, M.; Bellissimo, N.; Totosy de Zepetnek, J.O.; Brett, N.R.; Mazloomi, S.M.; Fararouie, M.; Bedeltavana, A.; Famouri, M.; Mazloom, Z. The effect of daily fortified yogurt consumption on weight loss in adults with metabolic syndrome: A 10-week randomized controlled trial. Nutr. Metab. Cardiovasc. Dis. 2018, 28, 565–574. [Google Scholar] [CrossRef]
- Cryan, J.F.; O’Riordan, K.J.; Cowan, C.S.M.; Sandhu, K.V.; Bastiaanssen, T.F.S.; Boehme, M.; Codagnone, M.G.; Cussotto, S.; Fulling, C.; Golubeva, A.V.; et al. The microbiota-gut-brain axis. Physiol. Rev. 2019, 99, 1877–2013. [Google Scholar] [CrossRef]
- Hwang, Y.H.; Park, S.; Paik, J.W.; Chae, S.W.; Kim, D.H.; Jeong, D.G.; Ha, E.; Kim, M.; Hong, G.; Park, S.H. Efficacy and safety of Lactobacillus Plantarum C29-Fermented Soybean (DW2009) in individuals with mild cognitive impairment: A 12-week, multi-center, randomized, double-blind, placebo-controlled clinical trial. Nutrients 2019, 11, 305. [Google Scholar] [CrossRef] [Green Version]
- Takada, M.; Nishida, K.; Kataoka-Kato, A.; Gondo, Y.; Ishikawa, H.; Suda, K.; Kawai, M.; Hoshi, R.; Watanabe, O.; Igarashi, T.; et al. Probiotic Lactobacillus casei strain Shirota relieves stress-associated symptoms by modulating the gut-brain interaction in human and animal models. Neurogastroenterol. Motil. 2016, 28, 1027–1036. [Google Scholar] [CrossRef] [Green Version]
- Yong, S.J.; Tong, T.; Chew, J.; Lim, W.L. Antidepressive mechanisms of probiotics and their therapeutic potential. Front. Neurosci. 2020, 13, 1361. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Yu, L.; Han, X.; Cen, S.; Duan, H.; Feng, S.; Xue, Y.; Tian, F.; Zhao, J.; Zhang, H.; Zhai, Q.; et al. Beneficial effect of GABA-rich fermented milk on insomnia involving regulation of gut microbiota. Microbiol. Res. 2020, 233, 126409. [Google Scholar] [CrossRef] [PubMed]
- Suez, J.; Zmora, N.; Segal, E.; Elinav, E. The pros, cons, and many unknowns of probiotics. Nat. Med. 2019, 25, 716–729. [Google Scholar] [CrossRef] [PubMed]
- Park, J.C.; Im, S.H. Of men in mice: The development and application of a humanized gnotobiotic mouse model for microbiome therapeutics. Exp. Mol. Med. 2020, 52, 1383–1396. [Google Scholar] [CrossRef]
- Tegopoulos, K.; Stergiou, O.S.; Kiousi, D.E.; Tsifintaris, M.; Koletsou, E.; Papageorgiou, A.C.; Argyri, A.A.; Chorianopoulos, N.; Galanis, A.; Kolovos, P. Genomic and phylogenetic analysis of Lactiplantibacillus plantarum L125, and evaluation of its anti-proliferative and cytotoxic activity in cancer cells. Biomedicines 2021, 9, 1718. [Google Scholar] [CrossRef]
- Stergiou, O.S.; Tegopoulos, K.; Kiousi, D.E.; Tsifintaris, M.; Papageorgiou, A.C.; Tassou, C.C.; Chorianopoulos, N.; Kolovos, P.; Galanis, A. Whole-genome sequencing, phylogenetic and genomic analysis of Lactiplantibacillus pentosus L33, a potential probiotic strain isolated from fermented sausages. Front. Microbiol. 2021, 12, 746659. [Google Scholar] [CrossRef] [PubMed]
- Ye, T.; Zhou, T.; Xu, X.; Zhang, W.; Fan, X.; Mishra, S.; Zhang, L.; Zhou, X.; Chen, S. Whole-genome sequencing analysis of quorum quenching bacterial strain Acinetobacter lactucae QL-1 identifies the FadY enzyme for degradation of the diffusible signal factor. Int. J. Mol. Sci. 2020, 2, 6729. [Google Scholar] [CrossRef] [PubMed]
- Burton, K.J.; Pimentel, G.; Zangger, N.; Vionnet, N.; Drai, J.; McTernan, P.G.; Pralong, F.P.; Delorenzi, M.; Vergères, G. Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men. PLoS ONE 2018, 13, e0192947. [Google Scholar] [CrossRef] [PubMed]
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Kiousi, D.E.; Chorianopoulos, N.; Tassou, C.C.; Galanis, A. The Clash of Microbiomes: From the Food Matrix to the Host Gut. Microorganisms 2022, 10, 116. https://doi.org/10.3390/microorganisms10010116
Kiousi DE, Chorianopoulos N, Tassou CC, Galanis A. The Clash of Microbiomes: From the Food Matrix to the Host Gut. Microorganisms. 2022; 10(1):116. https://doi.org/10.3390/microorganisms10010116
Chicago/Turabian StyleKiousi, Despoina Eugenia, Nikos Chorianopoulos, Chrysoula C. Tassou, and Alex Galanis. 2022. "The Clash of Microbiomes: From the Food Matrix to the Host Gut" Microorganisms 10, no. 1: 116. https://doi.org/10.3390/microorganisms10010116
APA StyleKiousi, D. E., Chorianopoulos, N., Tassou, C. C., & Galanis, A. (2022). The Clash of Microbiomes: From the Food Matrix to the Host Gut. Microorganisms, 10(1), 116. https://doi.org/10.3390/microorganisms10010116