Preprint Article Version 1 This version is not peer-reviewed

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

Version 1 : Received: 6 July 2018 / Approved: 6 July 2018 / Online: 6 July 2018 (16:58:45 CEST)

A peer-reviewed article of this Preprint also exists.

Sereno, D.; Dorkeld, F.; Akhoundi, M.; Perrin, P. Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools. Genes 2018, 9, 418. Sereno, D.; Dorkeld, F.; Akhoundi, M.; Perrin, P. Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools. Genes 2018, 9, 418.

Journal reference: Genes 2018, 9, 418
DOI: 10.3390/genes9080418

Abstract

Proper species identification from ancient DNA samples is a difficult task that sheds 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 [1](Santiago-Rodriguez et al. 2016) has called into question the identification of Leishmania in South America. Here, the metagenomic data filed in MG-RAST (Metagenomics RAST server) were used for a further attempt to identify members of the Trypanosomatidae family infecting these ancient remains. For this purpose, we used two metagenomic analysis tools. In the first step, data were analysed using the ultrafast metagenomic sequence classifier, based on exact alignment of k-mers (Kraken). In the second step, we used Bowtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. We then compared the output results. These approaches highlight some interesting findings on potential infections by human pathogenic trypanosomatids in these three pre-Columbian mummies.

Subject Areas

Trypanosomatidae; Kraken taxonomic assignment tool; Bowtie2 fast short reads aligner; Ancient DNA; Parasitome; Co-infection

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