Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus

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’.

Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle

“…Datasets were chosen because they represent a wide diversity of lifestyles, have a minimum of 20 samples per population, and were sequenced to an average read depth of 10 million reads per sample. We used 20 samples as a threshold based on previous research 42 showing that at least 20 samples per population are required for the types of ecological analyses pursued in this study. Similarly, 10 million reads was chosen as a threshold to allow for sufficient read depth to attain coverage of as many genes as possible from each metagenome.…”

Insights into health and disease from ancient biomolecules

“…In the past 10 years, new fields have emerged to characterize ancient microbiomes, proteomes and metabolomes that contribute to the understanding of changes in human health and human microbe interactions over time. In this issue, Jacobson et al [27] apply macroecological approaches to global ancient metagenomes, including novel data from ancient Mayan and Sardinian samples. Microbiomes are ecologies, which can easily be lost when the field is driven by successful and simple associations between taxa and hosttraits.…”

“…Microbiomes are ecologies, which can easily be lost when the field is driven by successful and simple associations between taxa and hosttraits. Jacobson et al [27] put the biome back in microbiome to expose ecological vulnerabilities within these ancient ecologies, particularly when compared to contemporary populations, and to identify temporal and spatial dynamics of putative keystone taxa. Their study also outlines the challenges of ecological approaches, the need for larger sample sizes and sensitivities to database bias.…”

Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens

“…[139] Oral microbiome, including pathogens [95][96][97]100,[140][141][142][143] Paleofeces -Tropism for gastro-intestinal tract…”