Ancient human microbiomes

Warinner, Christina; Speller, Camilla; Collins, Matthew J.; Lewis, Cecil M.

doi:10.1016/j.jhevol.2014.10.016

Cited by 137 publications

(82 citation statements)

References 204 publications

(243 reference statements)

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“…However, these investigations are still in their infancy. At present, knowledge of ancient human oral and gut microbiota is mainly derived from a relatively small number of specimens dating to the past 8000 years, with the majority of samples originating from Europe and the Americas [3]. …”

Section: Ancient Microbiome Researchmentioning

confidence: 99%

“…Over the past decade, it has become increasingly clear that the study of human evolution is not complete without consideration of the human microbiome [1–3]. In addition to our own somatic cells, our bodies are a patchwork landscape that is home to thousands of different microbial species that number in the tens of trillions of cells [4•].…”

Section: Introductionmentioning

confidence: 99%

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Insights into human evolution from ancient and contemporary microbiome studies

Schnorr

Sankaranarayanan

Lewis

et al. 2016

Current Opinion in Genetics & Development

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Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.

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Section: Ancient Microbiome Researchmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Insights into human evolution from ancient and contemporary microbiome studies

Schnorr

Sankaranarayanan

Lewis

et al. 2016

Current Opinion in Genetics & Development

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“…Recently, dental calculus has been identified as an abundant, nearly ubiquitous, and long-term reservoir of ancient host-associated biomolecules, including human DNA (Warinner et al 2015a; Warinner et al 2015b). Dental calculus (tartar) is the product of in vivo calcification of dental plaque on the dentition.…”

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confidence: 99%

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ozga

Nieves-Colón

Honap

et al. 2016

American J Phys Anthropol

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Objectives Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Results Full mitogenomes (7-34x) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains.

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“…The use of microbial fossils represents a powerful and so far little-explored approach to studying microbiome evolution, allowing us to quantify how these complex communities and individual members change through time. Unfortunately, host-associated microbial communities rarely fossilise, with the exception of coprolites and dental calculus 10 . Coprolites, petrified faecal matter which capture components of the gut microbiome, are rare and show poor DNA preservation, because faeces are rapidly colonised by environmental bacteria and decompose quickly after deposition 10 .…”

Section: Introductionmentioning

confidence: 99%

A roadmap to mammalian oral microbiome evolution with dental calculus

Brealey

Leitão

Valk

et al. 2019

Preprint

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Animals and their associated microbiomes share a long evolutionary history, influenced by a complex interplay between extrinsic environmental and intrinsic host factors. However, we know little about microbiome responses to long-lasting environmental and host-centred processes, which require studying microbiome changes through time. Here, we apply a temporal metagenomics approach to dental calculus, the calcified oral microbial biofilm. We establish dental calculus as a valuable tool for the study of host microbiome evolution by characterising the taxonomic and functional composition of the oral microbiome in a variety of wild mammals. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterise antibiotic resistance genes even before the advent of industrial antibiotic production, reconstruct components of the host diet and recover host genetic profiles. Our work demonstrates how dental calculus can be used in the future to study the evolution of oral microbiomes and pathogens, and the impact of anthropogenic changes on wildlife and the environment.

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Ancient human microbiomes

Cited by 137 publications

References 204 publications

Insights into human evolution from ancient and contemporary microbiome studies

Insights into human evolution from ancient and contemporary microbiome studies

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

A roadmap to mammalian oral microbiome evolution with dental calculus

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