Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt

Simone Rampelli,Silvia Turroni,Cecil M Lewis,Stefano Benazzi,Courtney A Hofman,Annalisa Astolfi,Patrizia Brigidi,Elena Biagi,Cristo Hernandez,Bertila Galván,Marco Candela,Ainara Sistiaga,Christina Warinner,Carolina Mallol,Stephanie L Schnorr

doi:10.1038/s42003-021-01689-y

Abstract

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

Highlights

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota
Ancient DNA analysis based on shotgun metagenomic sequencing is emerging as an attractive and reliable opportunity to directly investigate the microbial ecology of our ancestors[12,13,14,15]
We attempted to identify ancient human gut microbiome components by shotgun metagenomic analysis of ancient DNA (aDNA) extracted from archeological sedimentary samples (ES1 to ES7) from the stratigraphic unit (SU) X of the Middle Paleolithic open-air site, El Salt (Alicante, Spain)[25] (Fig. 1)

Summary

Introduction

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. We attempted to identify ancient human gut microbiome components by shotgun metagenomic analysis of aDNA extracted from archeological sedimentary samples (ES1 to ES7) from the stratigraphic unit (SU) X (subunit Xb-H44) of the Middle Paleolithic open-air site, El Salt (Alicante, Spain)[25] (Fig. 1).

Results

Conclusion