{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T04:26:48Z","timestamp":1772252808278,"version":"3.50.1"},"reference-count":28,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T00:00:00Z","timestamp":1534723200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>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\u2019s gut, and Lotmaria.<\/jats:p>","DOI":"10.3390\/genes9080418","type":"journal-article","created":{"date-parts":[[2018,8,20]],"date-time":"2018-08-20T11:23:06Z","timestamp":1534764186000},"page":"418","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Pathogen Species Identification from Metagenomes in Ancient Remains: The Challenge of Identifying Human Pathogenic Species of Trypanosomatidae via Bioinformatic Tools"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0034-9291","authenticated-orcid":false,"given":"Denis","family":"Sereno","sequence":"first","affiliation":[{"name":"IRD, Montpellier University, InterTryp, 34394 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Franck","family":"Dorkeld","sequence":"additional","affiliation":[{"name":"INRA-UMR 1062 CBGP (INRA, IRD, CIRAD), Montpellier SupAgro, Montferrier-sur-Lez, 34988 Languedoc Roussillon, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad","family":"Akhoundi","sequence":"additional","affiliation":[{"name":"Parasitology-Mycology Department, Avicenne Hospital, AP-HP, 93000 Bobigny, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pascale","family":"Perrin","sequence":"additional","affiliation":[{"name":"Montpellier University, IRD, CNRS, MIVEGEC, 34394 Montpellier, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2018,8,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Santiago-Rodriguez, T.M., Fornaciari, G., Luciani, S., Dowd, S.E., Toranzos, G.A., Marota, I., and Cano, R.J. (2016). Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies. FEMS Microbiol. Ecol., 92.","DOI":"10.1093\/femsec\/fiw182"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Sereno, D., Akhoundi, M., Dorkeld, F., Oury, B., Momen, H., and Perrin, P. (2017). What pre-Columbian mummies could teach us about South American leishmaniases?. Pathog. Dis., 75.","DOI":"10.1093\/femspd\/ftx019"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1159\/000334087","article-title":"Paleopathology in South American mummies: A review and new findings","volume":"79","author":"Gerszten","year":"2012","journal-title":"Pathobiology"},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Costa, M.A., Matheson, C., Lachetta, L., Llagostera, A., and Appenzeller, O. (2009). Ancient leishmaniasis in a highland desert of Northern Chile. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0006983"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., Turner, P., Parkhill, J., Loman, N.J., and Walker, A.W. (2014). Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol., 12.","DOI":"10.1186\/s12915-014-0087-z"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1146\/annurev-genom-091416-035526","article-title":"A robust framework for microbial archaeology","volume":"18","author":"Warinner","year":"2017","journal-title":"Annu. Rev. Genom. Hum. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Eisenhofer, R., Cooper, A., and Weyrich, L.S. (2017). Reply to Santiago-Rodriguez et al.: Proper authentication of ancient DNA is essential. FEMS Microbiol. Ecol., 93.","DOI":"10.1093\/femsec\/fix042"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Eisenhofer, R., and Weyrich, L.S. (2018). Proper authentication of ancient DNA is still essential. Genes.","DOI":"10.3390\/genes9030122"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Toranzos, G.A., Santiago-Rodriguez, T.M., Cano, R.J., and Fornaciari, G. (2017). Proper authentication of ancient DNA is essential, yes; but so are undogmatic approaches. FEMS Microbiol. Ecol., 93.","DOI":"10.1093\/femsec\/fix043"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Wood, D.E., and Salzberg, S.L. (2014). Kraken: Ultrafast metagenomic sequence classification using exact alignment. Genome Biol., 15.","DOI":"10.1186\/gb-2014-15-3-r46"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkp851","article-title":"TriTrypDB: A functional genomic resource for the Trypanosomatidae","volume":"38","author":"Aslett","year":"2010","journal-title":"Nucl. Acids Res."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Ondov, B.D., Bergman, N.H., and Phillippy, A.M. (2011). Interactive metagenomic visualization in a Web browser. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-385"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map (SAM) format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_15","unstructured":"World Health Organization (2018, April 15). Fact Sheet on Chagas Disease. Available online: http:\/\/www.who.int\/chagas\/resources\/en\/."},{"key":"ref_16","unstructured":"World Health Organization (2018, April 15). Fact Sheet on Leishmaniasis. Available online: http:\/\/www.who.int\/leishmaniasis\/resources\/en\/."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Breni\u00e8re, S.F., Waleckx, E., and Barnab\u00e9, C. (2016). Over six thousand Trypanosoma cruzi strains classified into discrete typing units (DTUs): Attempt at an inventory. PLoS Negl. Trop. Dis., 10.","DOI":"10.1371\/journal.pntd.0004792"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2034","DOI":"10.1073\/pnas.0307312101","article-title":"A 9000-year record of chagas\u2019 disease","volume":"101","author":"Aufderheide","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1590\/0074-02760140401","article-title":"Evolution of Trypanosoma cruzi: Clarifying hybridisations, mitochondrial introgressions and phylogenetic relationships between major lineages","volume":"110","author":"Tomasini","year":"2015","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mam.2016.11.012","article-title":"Leishmania infections: Molecular targets and diagnosis","volume":"57","author":"Akhoundi","year":"2017","journal-title":"Mol. Asp. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"732","DOI":"10.4269\/ajtmh.1986.35.732","article-title":"Isolation of Leishmania mexicana amazonensis from the bone marrow in a case of American visceral leishmaniasis","volume":"35","author":"Barral","year":"1986","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"536","DOI":"10.4269\/ajtmh.1991.44.536","article-title":"Leishmaniasis in Bahia, Brazil: Evidence that Leishmania amazonensis produces a wide spectrum of clinical diseases","volume":"44","author":"Barral","year":"1991","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Kraeva, N., Butenko, A., Hlavacova, J., Kostygov, A., Myskova, J., Grybchuk, D., Lestinova, T., Votypka, J., Volf, P., and Opperdoes, F. (2015). Leptomonas seymouri: Adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co-infection with Leishmania donovani. PLoS Pathog., 11.","DOI":"10.1371\/journal.ppat.1005127"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1128\/JCM.00966-12","article-title":"Coinfection of Leptomonas seymouri and Leishmania donovani in Indian leishmaniasis","volume":"50","author":"Ghosh","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1002\/ece3.2796","article-title":"Host sharing by the honey bee parasites Lotmaria passim and Nosema ceranae","volume":"7","author":"Tritschler","year":"2017","journal-title":"Ecol. Evol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1089\/vbz.2015.1771","article-title":"Trypanosoma cruzi and Leishmania infantum chagasi infection in wild mammals from Maranh\u00e3o state, Brazil","volume":"15","author":"Costa","year":"2015","journal-title":"Vector Borne Zoonotic Dis."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Mart\u00ednez, D.Y., Verdonck, K., Kaye, P.M., Adaui, V., Polman, K., Llanos-Cuentas, A., Dujardin, J.C., and Boelaert, M. (2018). Tegumentary leishmaniasis and coinfections other than HIV. PLoS Negl. Trop. Dis., 12.","DOI":"10.1371\/journal.pntd.0006125"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1111\/j.1550-7408.2000.tb00008.x","article-title":"Leishmania, Trypanosoma and monoxenous Trypanosomatids as emerging opportunistic agents","volume":"47","author":"Dedet","year":"2000","journal-title":"J. Eukaryot. Microbiol."}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/9\/8\/418\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T15:19:46Z","timestamp":1760195986000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/9\/8\/418"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,8,20]]},"references-count":28,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2018,8]]}},"alternative-id":["genes9080418"],"URL":"https:\/\/doi.org\/10.3390\/genes9080418","relation":{"has-preprint":[{"id-type":"doi","id":"10.20944\/preprints201807.0124.v1","asserted-by":"object"}]},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,20]]}}}