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  Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities

Sabin, S., Yeh, H.-Y., Pluskowski, A., Clamer, C., Mitchell, P. D., & Bos, K. I. (2020). Estimating molecular preservation of the intestinal microbiome via metagenomic analyses of latrine sediments from two medieval cities. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 375(1812): 20190576. doi:10.1098/rstb.2019.0576.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0007-4598-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0007-4599-F
Genre: Journal Article

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https://doi.org/10.6084/m9.figshare.c.5092177 (Supplementary material)
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 Creators:
Sabin, Susanna1, Author              
Yeh, Hui-Yuan, Author
Pluskowski, Aleks, Author
Clamer, Christa, Author
Mitchell, Piers D., Author
Bos, Kirsten I.2, 3, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2CoDisEASe, Max Planck Institute for the Science of Human History, Max Planck Society, ou_3033585              
3tide, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2591691              

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Free keywords: metagenomics, parasitology, archaeology, aDNA, microbiome
 Abstract: Ancient latrine sediments, which contain the concentrated collective biological waste of past whole human communities, have the potential to be excellent proxies for human gastrointestinal health on the population level. A rich body of literature explores their use to detect the presence of gut-associated eukaryotic parasites through microscopy, immunoassays and genetics. Despite this interest, a lack of studies have explored the whole genetic content of ancient latrine sediments through consideration not only of gut-associated parasites, but also of core community gut microbiome signals that remain from the group that used the latrine. Here, we present a metagenomic analysis of bulk sediment from medieval latrines in Riga (Latvia) and Jerusalem. Our analyses reveal survival of microbial DNA representative of intestinal flora as well as numerous parasites. These data are compared against parasite taxon identifications obtained via microscopy and ELISA techniques. Together, these findings provide a first glimpse into the rich prokaryotic and eukaryotic intestinal flora of pre-industrial agricultural populations, which may give a better context for interpreting the health of modern microbiomes.

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Language(s): eng - English
 Dates: 2020-10-052020-11
 Publication Status: Published in print
 Pages: 15
 Publishing info: -
 Table of Contents: 1. Introduction
(a) Latrine sediment samples

2. Results
(a) Library inhibition
(b) α-Diversity
(c) Estimated source contributions to bacterial and archaeal diversity
(d) Eukaryotic pathogens
(i) Jerusalem
(ii) Riga

3. Discussion
(a) Gut microbiome preservation and prospects for regional comparisons
(b) Eukaryotic parasites: the promise and limitations of ancient metagenomics
(c) Template volume did not impact metagenomic α-diversity

4. Conclusion

5. Material and methods
(a) Sampling and DNA extraction
(b) Library preparation
(i) Initial screening and inhibition test
(ii) Indexing, amplification and sequencing
(c) Computational methods
(i) Pre-processing and mapping to HG19
(ii) Metagenomic profiling and pathogen detection
(iii) Community diversity
(iv) Mapping to Ascaris lumbricoides and Dibothriocephalus latus
 Rev. Type: Peer
 Identifiers: DOI: 10.1098/rstb.2019.0576
Other: shh2725
 Degree: -

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Project name : CoDisEASe
Grant ID : 805268
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

Source 1

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Title: Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences
  Other : Philosophical Transactions B
  Abbreviation : Phil. Trans. R. Soc. B
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: London : Royal Society
Pages: - Volume / Issue: 375 (1812) Sequence Number: 20190576 Start / End Page: - Identifier: ISSN: 0962-8436
CoNE: https://pure.mpg.de/cone/journals/resource/963017382021_1