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Ancient genomes from Bronze Age remains reveal deep diversity and recent adaptive episodes for human oral pathobionts

ABSTRACT: Ancient genomes from Bronze Age remains reveal deep diversity and recent adaptive episodes for human oral pathobionts

PROVIDER: PRJEB64128 | ENA |

REPOSITORIES: ENA

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Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.

Project description:Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.

| S-EPMC10966897 | biostudies-literature

Metagenomics analysis of ancient human remains

Project description:Metagenomics analysis of ancient human remains

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Ancient DNA from Portugal (Neolithic and Bronze Age)

Project description:Ancient DNA from Portugal (Neolithic and Bronze Age)

| PRJEB14737 | ENA

Ancient nuclear genomes enable repatriation of Indigenous human remains

Project description:Ancient nuclear genomes enable repatriation of Indigenous human remains

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Western Russian Stone and Bronze Age ancient DNA

Project description:Genetic ancestry changes in Stone to Bronze Age transition in the East European plain

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Cauldrons of Bronze Age nomads

Project description:Protein analysis of Bronze Age Cauldron residues. Found blood from ruminant caprines, and milk proteins from bovids, including yak (Bos mutus).

2024-01-13 | MSV000093861 | MassIVE

Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete

Project description:Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete

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Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts

Project description:Sequestration of gut pathobionts in intraluminal casts, a mechanism to avoid dysregulated T cell activation by pathobionts

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Plastic remains contained soil sample

Project description:Plastic remains contained soil sample Metagenome

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Authenticated DNA from ancient wood remains.

Project description:BackgroundThe reconstruction of biological processes and human activities during the last glacial cycle relies mainly on data from biological remains. Highly abundant tissues, such as wood, are candidates for a genetic analysis of past populations. While well-authenticated DNA has now been recovered from various fossil remains, the final 'proof' is still missing for wood, despite some promising studies.ScopeThe goal of this study was to determine if ancient wood can be analysed routinely in studies of archaeology and palaeogenetics. An experiment was designed which included blind testing, independent replicates, extensive contamination controls and rigorous statistical tests. Ten samples of ancient wood from major European forest tree genera were analysed with plastid DNA markers.ConclusionsAuthentic DNA was retrieved from wood samples up to 1,000 years of age. A new tool for real-time vegetation history and archaeology is ready to use.

| S-EPMC3292245 | biostudies-literature

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