@article{fdi:010073969,
  title = {{P}athogen species identification from metagenomes in ancient remains : the challenge of identifying human pathogenic species of {T}rypanosomatidae via bioinformatic tools},
  author = {{S}ereno, {D}enis and {D}orkeld, {F}. and {A}khoundi, {M}. and {P}errin, {P}.},
  editor = {},
  language = {{ENG}},
  abstract = {{A}ccurate species identification from ancient {DNA} samples is a difficult task that would shed light on the evolutionary history of pathogenic microorganisms. {T}he field of palaeomicrobiology has undoubtedly benefited from the advent of untargeted metagenomic approaches that use next-generation sequencing methodologies. {N}evertheless, assigning ancient {DNA} at the species level is a challenging process. {R}ecently, the gut microbiome analysis of three pre-{C}olumbian {A}ndean mummies ({S}antiago-{R}odriguez et al., 2016) has called into question the identification of {L}eishmania in {S}outh {A}merica. {T}he accurate assignment would be important because it will provide some key elements that are linked to the evolutionary scenario for visceral leishmaniasis agents in {S}outh {A}merica. {H}ere, we recovered the metagenomic data filed in the metagenomics {RAST} server ({MG}-{RAST}) to identify the different members of the {T}rypanosomatidae family that have infected these ancient remains. {F}or this purpose, we used the ultrafast metagenomic sequence classifier, based on an exact alignment of k-mers ({K}raken) and {B}owtie2, an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. {T}he analyses, which have been conducted on the most exhaustive genomic database possible on {T}rypanosomatidae, show that species assignments could be biased by a lack of some genomic sequences of {T}rypanosomatidae species (strains). {N}evertheless, our work raises the issue of possible co-infections by multiple members of the {T}rypanosomatidae family in these three pre-{C}olumbian mummies. {I}n the three mummies, we show the presence of {DNA} that is reminiscent of a probable co-infection with {L}eptomonas seymouri, a parasite of insect's gut, and {L}otmaria.},
  keywords = {{T}rypanosomatidae ; kraken taxonomic assignment tool ; bowtie2 fast short ; reads aligner ; ancient {DNA} ; parasitome ; co-infection},
  booktitle = {},
  journal = {{G}enes},
  volume = {9},
  numero = {8},
  pages = {art. 418 [12 p.]},
  ISSN = {2073-4425},
  year = {2018},
  DOI = {10.3390/genes9080418},
  URL = {https://www.documentation.ird.fr/hor/fdi:010073969},
}