Abstract
Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution.This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
Highlights
Host-associated microbiomes are complex ecosystems with diverse sets of interactions between microbes, the host and abiotic features
Applying ecological approaches to ancient human microbiomes from these materials is a clear step to provide a deeper understanding of biology in the past
We have found that by focusing on ecological elements that can be interpreted from single time-point samples, such as ecological network properties, clusters of bacteria, keystone species, functional redundancy and response diversity, we can gain a glimpse of ecological interactions and functional diversity in ancient human microbiomes
Summary
Host-associated microbiomes are complex ecosystems with diverse sets of interactions between microbes, the host and abiotic features. While there is no unified or singular approach, ecological concepts such as community assembly, succession, response to disturbance, restoration, functional redundancy, response diversity, keystone taxa and genes, and co-occurring networks have made inroads in human microbiome research [9,10,11,12,13,14,15,16,17,18,19] Each of these concepts leads to estimating ecological variables, providing a more nuanced view of human microbiomes, including how they are formed, what factors drive change, and which bacteria play important roles in maintaining homeostasis or stable conditions. To best adapt ecological approaches to ancient coprolites and dental calculus, we focused on analysing the structure and properties of microbiome networks, identification of keystone taxa and functional diversity of specific functions of interest Each of these can be evaluated without time-series data. A more in-depth discussion of our methods and the techniques used for network analysis and keystone taxa identification can be found in the electronic supplementary material
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
