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Microbial Candidates in Next-generation Probiotics Development

Brugère, Jean-François, PhD*; Ben Hania, Wajdi, PhD*,†; Arnal, Marie-Edith, PhD*; Ribière, Céline, PhD; Ballet, Nathalie, PhD§; Vandeckerkove, Pascal, PhD§; Ollivier, Bernard, PhD; O’Toole, Paul W., PhD

Journal of Clinical Gastroenterology: November/December 2018 - Volume 52 - Issue - p S71–S73
doi: 10.1097/MCG.0000000000001043

Pharmabiotics and probiotics in current use or under development belong to 2 of 3 domains of life, Eukarya (eg, yeasts) and Bacteria (eg, lactobacilli). Archaea constitute a third domain of life, and are currently not used as probiotics, despite several interesting features. This includes the absence of known pathogens in humans, animals, or plants and the existence of some archaea closely associated to humans in various microbiomes. We promote the concept that some specific archaea that naturally thrive in the human gut are potential next-generation probiotics that can be rationally selected on the basis of their metabolic phenotype not being encountered in other human gut microbes, neither Bacteria nor Eukarya. The example of the possible bioremediation of the proatherogenic compound trimethylamine into methane by archaeal microbes is described.

*UMR 454 MEDIS, INRA-UCA, Université Clermont-Auvergne, Clermont-Ferrand

Aix Marseille Université, CNRS, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO), Marseille

§Lesaffre International, Lesaffre Group, Marcq-en-Barœul, France

School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland

P.W.O.T.’s laboratory is supported by Science Foundation Ireland through a Centre award to the APC Microbiome Institute (SFI/12/RC/2273). Work in J.-F.B. and P.W.O.T.’s laboratories was funded in part by a nonrestrictive award from Lesaffre International for research development on some aspects of Methanomassiliicoccales biology. The remaining authors declare that they have nothing to disclose.

Address correspondence to: Jean-François Brugère, PhD, UMR 454 MEDIS, INRA-UCA, Université Clermont-Auvergne, 5e CBRV, 28 Place Henri Dunant, F-63000, Clermont-Ferrand, France (e-mail:

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