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Empiric probiotics are commonly consumed by healthy individuals as means of life quality improvement and disease prevention. However, evidence of probiotic gut mucosal colonization efficacy remains sparse and controversial. We metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome. A sequential invasive multi-omics measurement at baseline and during consumption of an 11-strain probiotic combination or placebo demonstrated that probiotics remain viable upon gastrointestinal passage. In colonized, but not germ-free mice, probiotics encountered a marked mucosal colonization resistance. In contrast, humans featured person-, region- and strain-specific mucosal colonization patterns, hallmarked by predictive baseline host and microbiome features, but indistinguishable by probiotics presence in stool. Consequently, probiotics induced a transient, individualized impact on mucosal community structure and gut transcriptome. Collectively, empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa, meriting development of new personalized probiotic approaches.
Niv Zmora,Gili Zilberman-Schapira,Jotham Suez,Uria Mor
Zamir Halpern,Eran Segal,Eran Elinav
Niv Zmora,Gili Zilberman-Schapira,Jotham Suez,Uria Mor,Mally Dori-Bachash,Stavros Bashiardes,Eran Kotler,Maya Zur,Dana Regev-Lehavi,Rotem Ben-Zeev Brik,Sara Federici,Yotam Cohen,Raquel Linevsky,Daphna Rothschild,Andreas E Moor,Shani Ben-Moshe,Alon Harmelin,Shalev Itzkovitz,Nitsan Maharshak,Oren Shibolet,Hagit Shapiro,Meirav Pevsner-Fischer,Itai Sharon,Zamir Halpern,Eran Segal,Eran Elinav