Evaluation of the bacterial microbiome of two flea species using different DNA-isolation techniques provides insights into flea host ecology

• Published in: FEMS microbiology ecology Vol. 91; no. 12; p. 1
• Main Authors: Lawrence, Andrea L., Hii, Sze-Fui, Chong, Rowena, Webb, Cameron E., Traub, Rebecca, Brown, Graeme, Šlapeta, Jan
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.12.2015
• Subjects: Animals; Australia; Bacteria; Bacteroidetes - genetics; Bacteroidetes - isolation & purification; Base Sequence; Cats; Comparative analysis; Cyclooxygenase 1 - genetics; Deoxyribonucleic acid; DNA; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Echidna - microbiology; Ecology; Exoskeleton; Exoskeletons; Fleas; Gene sequencing; Genetic aspects; High-Throughput Nucleotide Sequencing; Host-bacteria relationships; Host-Pathogen Interactions; Microbiology; Microbiomes; Microbiota (Symbiotic organisms); Microbiota - genetics; Nucleic acids; Pests; Physiological aspects; Rickettsia; Rickettsia - genetics; Rickettsia - isolation & purification; RNA, Ribosomal, 16S - genetics; rRNA 16S; Separation; Sequence Analysis, DNA; Siphonaptera; Siphonaptera - microbiology; Species; Species diversity; Sterilization; Vectors; Wolbachia - genetics; Wolbachia - isolation & purification; Australia; cat flea; vector; microbiome; Siphonaptera; Rickettsia; Wolbachia
• ISSN: 1574-6941; 0168-6496; 1574-6941
• DOI: 10.1093/femsec/fiv134

Fleas (Siphonaptera) are ubiquitous blood-sucking pests of animals worldwide and are vectors of zoonotic bacteria such as Rickettsia and Bartonella. We performed Ion Torrent PGM amplicon sequencing for the bacterial 16S rRNA gene to compare the microbiome of the ubiquitous cat flea (Ctenocephalides f. felis) and the host-specific echidna stickfast flea (Echidnophaga a. ambulans) and evaluated potential bias produced during common genomic DNA-isolation methods. We demonstrated significant differences in the bacterial community diversity between the two flea species but not between protocols combining surface sterilisation with whole flea homogenisation or exoskeleton retention. Both flea species were dominated by obligate intracellular endosymbiont Wolbachia, and the echidna stickfast fleas possessed the endosymbiont Cardinium. Cat fleas that were not surface sterilised showed presence of Candidatus ‘Rickettsia senegalensis’ DNA, the first report of its presence in Australia. In the case of Rickettsia, we show that sequencing depth of 50 000 was required for comparable sensitivity with Rickettsia qPCR. Low-abundance bacterial genera are suggested to reflect host ecology. The deep-sequencing approach demonstrates feasibility of pathogen detection with simultaneous quantitative analysis and evaluation of the inter-relationship of microbes within vectors. This study demonstrates changes to the microbial composition of fleas following surface cleaning using a bleach wash and highlights parallels between the flea microbiome and flea host ecology.