mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms

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Chagas disease (CD) is a zoonotic parasitic disease caused by Trypanosoma cruzi, mainly transmitted to mammals through feces and urine of triatomines known as kissing bugs (Hemiptera: Reduviidae). Triatoma dimidiata is the main vector of CD in the Yucatan Peninsula (YP). To better understand ecological interactions shaping transmission cycles of T. cruzi in a sylvatic ecotope of the YP, a metabarcoding approach was used to simultaneously identify vector blood meals, gut microbiome composition, genetic diversity, as well as T. cruzi genetic diversity from a sample of 33 T. dimidiata individuals collected in 2019 by the owner of an isolated rural dwelling on a conserved sylvatic site of the Balam Kú State Reserve (Campeche, Mexico). Infection prevalence with T. cruzi was 27.3% (9/33). We identified thirteen blood-meal sources (the most prevalent being Homo sapiens, Sus scrofa, Mus musculus), six bacterial Orders (Bacillales, Oceanospirillales and Micrococcales being the most abundant), two T. cruzi DTUs (TcI and TcIV), as well as two T. dimidiata genetic subgroups (ITS-2 Haplogroups 2 and 3).