Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers.

Silvia Turroni,Manuela Centanni,Clarissa Consolandi,Marco Severgnini,Simone Rampelli,Patrizia Brigidi,Stephanie L Schnorr,Clelia Peano,Matteo Soverini,Marco Candela,Alyssa N Crittenden,Mirella Falconi,Amanda G Henry

doi:10.3389/fmicb.2016.00865

Abstract

By means of a recently developed non-invasive ex vivo minimal model based on the interaction of the human enterocyte-like HT29 cell line and fecal slurries, we explored the enterocyte-associated microbiome of 21 Hadza hunter-gatherers and nine urban living Italians. Though reductionist, this model allows inferring the microbiota structural and functional arrangement as it interacts with enterocytes. Microbial suspensions obtained from Hadza or Italian stools were first evaluated for structural integrity by high resolution-scanning electron microscopy and co-incubated with HT29 cell monolayers. The enterocyte adherent microbiota fraction was then characterized by 16S rRNA gene sequencing and predictive functional profiling using PICRUSt. Compared to Italians, the Hadza enterocyte-associated microbiome was characterized by a greater amount of adhesive microorganisms with pathogenic potential, such as Proteobacteria, Erysipelotrichaceae, Enterococcus, Clostridium and Sarcina. These compositional characteristics were reflected in a functional enrichment in membrane transport, signal transduction, signaling molecules and interaction. Our results depict a new interesting mutualistic configuration of the enterocyte-associated microbiome in Hadza, stressing the importance of microbe-host interaction at the mucosal surface along the course of human evolution.

Highlights

We recently explored the fecal microbial community of Hadza hunter-gatherers from Tanzania (Schnorr et al, 2014; Rampelli et al, 2015), one of the last remaining hunting and gathering communities in the world (Blurton Jones et al, 1992)
1010 total viable bacterial cells in ice-cold Dulbecco’s modified Eagle’s medium (DMEM) were added to HT29 cell monolayers and incubated as in standard bacterial adhesion assays (Candela et al, 2008)
HT29 cell-associated bacterial cells were characterized by 16S rRNA gene sequencing and compared with the respective fecal microbial communities (Schnorr et al, 2014)

Summary

Introduction

We recently explored the fecal microbial community of Hadza hunter-gatherers from Tanzania (Schnorr et al, 2014; Rampelli et al, 2015), one of the last remaining hunting and gathering communities in the world (Blurton Jones et al, 1992) According to these previous findings, the structural and functional configuration of the Hadza gut microbiota is well aligned with the dietary and environmental factors characteristic of their foraging lifestyle, supporting the importance of microbiota as an evolutionary legacy that provides specific adaptive versatility to disparate human subsistence and environmental occupation. From a functional point of view, the Hadza gut microbiota was adapted for broad-spectrum carbohydrate metabolism, and equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis (Rampelli et al, 2015). Microbial components of the adherent microbiome have been shown to control defensin secretion, wound healing (Gallo and Hooper, 2012) and, more importantly, the functioning of the adaptive immune system (Maynard et al, 2012)

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Results

Conclusion