Metagenomics and microscope revealed  T. trichiura  and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.

Related collections

Most cited references 59

Record: found
Abstract: found
Article: found

Is Open Access

Insights from Characterizing Extinct Human Gut Microbiomes

Raul Y. Tito, Dan Knights, Jessica Metcalf … (2012)

In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.

0 comments Cited 84 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern.

Ian Joint, Beatriz Díez, J. R. Goddard … (2002)

Microbial communities inhabiting a multipond solar saltern were analysed and compared using SSU rRNA polymerase chain reaction (PCR)-based fingerprintings carried out in parallel by four laboratories. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied for Bacteria, Archaea and Eukarya, and laboratories applied their own techniques and protocols on the same set of samples. Members of all three domains were retrieved from all salt concentrations. Three fingerprinting techniques were used: denaturing gradient gel electrophoresis (DGGE), ribosomal internal spacer analysis (RISA), and terminal-restriction fragments length polymorphism (T-RFLP). In addition, each laboratory used its own biomass collection method and DNA extraction protocols. Prokaryotes were addressed using DGGE and RISA with different 'domain-specific' primers sets. Eukaryotes were analysed by one laboratory using DGGE and T-RFLP, but targeting the same 18S rDNA site. Fingerprints were compared through cluster analysis and non-metric multidimensional scaling plots. This exercise allowed fast comparison of microbial assemblages and determined to what extent the picture provided by each laboratory was similar to those of others. Formation of two main, salinity-based groups of samples in prokaryotes (4-15% and 22-37% salinity) was consistent for all the laboratories. When other clusters appeared, this was a result of the particular technique and the protocol used in each case, but more affected by the primers set used. Eukaryotic microorganisms changed more from pond to pond; 4-5% and 8-37% salinity were but the two main groups detected. Archaea showed the lowest number of bands whereas Eukarya showed the highest number of operational taxonomic units (OTUs) in the initial ponds. Artefacts appeared in the DGGE from ponds with extremely low microbial richness. On the other hand, different 16S rDNA fragments with the same restriction or internal transcribed spacer (ITS) length were the main limitations for T-RFLP and RISA analyses, respectively, in ponds with the highest OTUs richness. However, although the particular taxonomic composition could vary among protocols, the general structure of the microbial assemblages was maintained.

0 comments Cited 84 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: found

Is Open Access

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Kirsten A. Ziesemer, Allison E. Mann, Krithivasan Sankaranarayanan … (2015)

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

0 comments Cited 74 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Contributors

Manuela Murgia: manuelamurgia@hotmail.com

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2045-2322

Publication date (Electronic): 29 July 2020

Publication date PMC-release: 29 July 2020

Publication date Collection: 2020

Volume: 10

Electronic Location Identifier: 12656

Affiliations

[1 ]ISNI 0000 0001 2097 9138, GRID grid.11450.31, Department of Biomedical Science, , University of Sassari, ; V. le San Pietro 43/B, 07100 Sassari, Italy

[2 ]Superintendence Archaeology of Sardinia, 07100 Sassari, Italy

[3 ]ISNI 0000 0001 2097 9138, GRID grid.11450.31, Department of Nature and Environmental Sciences, , University of Sassari, ; 07100 Sassari, Italy

[4 ]ISNI 0000 0001 2097 9138, GRID grid.11450.31, Department of Veterinary Medicine, , University of Sassari, ; 07100 Sassari, Italy

[5 ]Unaffiliated, Osilo, Italy

[6 ]ISNI 0000 0001 1092 7967, GRID grid.8273.e, Bob Champion Research and Educational Building, , University of East Anglia, Norwich Research Park, ; Norwich, UK

[7 ]ISNI 0000 0000 9347 0159, GRID grid.40368.39, The Quadram Institute, Norwich Research Park, ; Norwich, UK

[8 ]Comunica Coop, 07100 Sassari, Italy

[9 ]ISNI 0000 0004 1936 8200, GRID grid.55602.34, Department of Microbiology and Immunology, , Dalhousie University, ; Halifax, NS Canada

Author information

Gemma L. Kay http://orcid.org/0000-0002-1176-8459

Article

Publisher ID: 69497

DOI: 10.1038/s41598-020-69497-8

PMC ID: 7391740

SO-VID: a7b72c53-b3a9-4cf4-8a31-11b61d1e5adb

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 3 July 2019

Date accepted : 8 July 2020

Custom metadata

ScienceOpen disciplines: Uncategorized

Keywords: parasite genomics,molecular biology

Data availability:

ScienceOpen disciplines: Uncategorized

Keywords: parasite genomics, molecular biology

Comments

Comment on this article

scite_

Cited by 3

See all cited by

Most referenced authors 1,527

See all reference authors

Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace

Read this article at

Abstract

Related collections

iGEM

Most cited references 59

Insights from Characterizing Extinct Human Gut Microbiomes

Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern.

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Author and article information

Contributors

Journal

Affiliations

Author information

Article

History

Categories

Custom metadata

Comments

Comment on this article

Similar content 115

Cited by 3

Most referenced authors 1,527