Core microbiome

Despite the notion of a core microbiome and the stability of the gut microbial ecosystem over time without major changes in dietary habits, each individual person harbors their own characteristic intestinal microbiota (in the sense of a persmialized fingerprint). Indeed, there are large interindividual differences in both intestinal bacterial compositiOTi (proportion of taxa) and diversity (qualitative pattern of... 

C. berteri, 2889 C. officinalis, 2889 C. rubens (Jania rubens), 2890 Corallinaceae, 2889 Corallinales, 2889-2890 Cordia verbenacea, 4119 Core microbiome, 2441 Coriandrum sativum, 2979, 4090 Coriobacteriaceae, 2444 Com oil, 1736... 

Huse SM, Ye Y, Zhou Y, Fodor AA. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One. 2012 7(6) e34242. 

The stomach-associated bacterium Helicobacter pylori exemplifies co-evolution between microorganisms and humans. Patterns of H. sapiens migration from Africa across the globe can be traced from the strain diversity of this bacterial species. Comparing the human gut microbiota and microbiome worldwide is the only way, in principle, to reveal if there is a core set of gut microbial genes and organismal lineages that are shared by most, if not all, humans. 

Understanding the compositional and functional differences in the gut microbiota can lay the foundation to relate these differences to human health. Differences in the microbiota and the microbiome could help to explain the variation in the gut metabolic processes of individuals, including the metabolism of drugs and food. Many of these metabolic pathways are outside the common functional core, so they can underlie host-specific responses. 

Tumbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009 457 480-484. 

Huse SM, Ye Y, Zhou Y, Fodor AA. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS ONE. 2012 7 e34242. Koren O, Knights D, Gonzalez A, et al. A guide to enterotypes across the human body meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol. 2013 9 el002863. 

In summary, our intestinal microbiome encodes numerous core functions of importance for the conversion of dietary phenolics, yet interindividual differences in the makeup of bacterial species that colonize our gut underlie interindividual differences in phenolic metabolism and thereby in possible health effects. In Sect. 5, we will give more details on active bacterial members and central metabolic reactions involved in phenolic conversion prior to focusing on health effects of isoflavones and lignans. 

Tumbaugh, P.J. and Gordon, J.I. 2009. The core gut microbiome, energy balance, and obesity. 

Tolasch T, Solter S, Toth M et al (2003) (/ )-Acetoin-female sex pheromone of the summer chafer Amphimallon solstitiale (L.). J Chem Ecol 29 1045-1050 Tumbaugh PJ, Hamady M, Yatsunenko T et al (2009) A core gut microbiome in obese and lean twins. Nature (Lond) 457 480-484... 

Human Health Performance Directorate, NASA Johnson Space Center, Houston, USA Department of Cell Biology and Physiology, and Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, USA... 

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