Metagenomic Approach to Characterizing Disease Epidemiology in a Disease-Endemic Environment in Northern Thailand

Takhampunya, Ratree; Korkusol, Achareeya; Pongpichit, Chalermpol; Yodin, Komsan; Rungrojn, Artharee; Chanarat, Nitima; Promsathaporn, Sommai; Monkanna, Taweesak; Thaloengsok, Sasikanya; Tippayachai, Bousaraporn; Kumfao, Naruemon; Richards, Allen L.; Davidson, Silas A.

The classification of OTUs from each sample were made against Greengenes reference databases, with SILVA reference databases as a secondary database, and the similarity confidence threshold for each taxonomic level was set at 0.97 in CLC microbial genomic module. There were 19 recorded phyla found among all sample types and the ten most abundant phyla were seen in all sample types (Proteobacteria, Firmicutes, Actinobacteria, Spirochaetes, Tenericutes, Bacteroidetes, [Thermi], Planctomycetes, Fusobacteria, Cyanobacteria) ( Figure 3A) . The most prevalent phylum in all sample types was Proteobacteria and it was most abundant in ectoparasites from rodents (88.0%), domesticated mammals (83.0%), and UFI patients (70.0%) (Figure 3A) . In rodent populations, the phyla Proteobacteria, Tenericutes, and Firmicutes were most abundant (38.0, 31.0, and 27.0%, respectively). In chiggers, the highest abundance was of Actinobacteria (43.0%), followed by Firmicutes (32.0%), and Proteobacteria (9.0%). Other interesting phyla include Spirochaetes found in UFI patients (5%), chiggers (5%), and rodents (1%); and two phyla, Thermi and Plantomycetes, that were found most commonly in UFI patients and chigger samples, respectively.