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Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools

Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequenc...

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Autores principales: Sereno, Denis, Dorkeld, Franck, Akhoundi, Mohammad, Perrin, Pascale
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115896/
https://www.ncbi.nlm.nih.gov/pubmed/30127280
http://dx.doi.org/10.3390/genes9080418
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author Sereno, Denis
Dorkeld, Franck
Akhoundi, Mohammad
Perrin, Pascale
author_facet Sereno, Denis
Dorkeld, Franck
Akhoundi, Mohammad
Perrin, Pascale
author_sort Sereno, Denis
collection PubMed
description Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect’s gut, and Lotmaria.
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spelling pubmed-61158962018-08-31 Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools Sereno, Denis Dorkeld, Franck Akhoundi, Mohammad Perrin, Pascale Genes (Basel) Article Accurate species identification from ancient DNA samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. The field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. Nevertheless, assigning ancient DNA at the species level is a challenging process. Recently, the gut microbiome analysis of three pre-Columbian Andean mummies (Santiago-Rodriguez et al., 2016) has called into question the identification of Leishmania in South America. The accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in South America. Here, we recovered the metagenomic data filed in the metagenomics RAST server (MG-RAST) to identify the different members of the Trypanosomatidae family that have infected these ancient remains. For this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers (Kraken) and Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. The analyses, which have been conducted on the most exhaustive genomic database possible on Trypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of Trypanosomatidae species (strains). Nevertheless, our work raises the issue of possible co-infections by multiple members of the Trypanosomatidae family in these three pre-Columbian mummies. In the three mummies, we show the presence of DNA that is reminiscent of a probable co-infection with Leptomonas seymouri, a parasite of insect’s gut, and Lotmaria. MDPI 2018-08-20 /pmc/articles/PMC6115896/ /pubmed/30127280 http://dx.doi.org/10.3390/genes9080418 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sereno, Denis
Dorkeld, Franck
Akhoundi, Mohammad
Perrin, Pascale
Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
title Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
title_full Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
title_fullStr Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
title_full_unstemmed Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
title_short Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools
title_sort pathogen species identification from metagenomes in ancient remains: the challenge of identifying human pathogenic species of trypanosomatidae via bioinformatic tools
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6115896/
https://www.ncbi.nlm.nih.gov/pubmed/30127280
http://dx.doi.org/10.3390/genes9080418
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