Abstract
Growing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genus Bartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.
Highlights
Since the proposal of DNA barcoding by Hebert et al (2003) as a new methodology for identification of biological species, it has been utilized on a wide variety of taxa for the purposes of identifying museum specimens, evaluation of population and community diversity, discovery of cryptic species, and other forensic applications
There are four primary problems with this approach: (1) increasing sequence diversity in a gene diminishes the ability to design conserved primers that can be utilized across a broad taxonomic diversity of bacteria; (2) homologous recombination is widespread (Vos and Didelot, 2008) and can obscure phylogenetic inference (Fraser et al 2007) and estimates of species diversity if only one marker is used; (3) bacterial genomes are very flexible in gene content, even for closely related species (Konstantinidis et al 2006), so a locus may not exist in all species surveyed; and (4) multiple species may be present in the sample, but may not be detectable due to variation in abundance or primer amplification bias
Issues related to isolation of cultures, homologous recombination, coinfections, sensitivity and phylogenetic resolution of molecular markers, variation in detection across different tissues, and variation in marker usage across studies are certainly not restricted to studies of Bartonella
Summary
Since the proposal of DNA barcoding by Hebert et al (2003) as a new methodology for identification of biological species, it has been utilized on a wide variety of taxa for the purposes of identifying museum specimens, evaluation of population and community diversity, discovery of cryptic species, and other forensic applications. Bacterial DNA analysis has been readily accepted for measuring the assembly, diversity and distribution of entire microbial communities in different environments (DeLong and Pace, 2001), application of universal barcoding approaches to bacteria may face challenges unique to prokaryotes. Many microbial species are challenging to culture by traditional methods (Schloss and Handelsman, 2004), which will curtail a microbiologist’s ability to characterize these species beyond molecular approaches. We argue that our ability to measure bacterial diversity at a massive scale has increased in recent decades, the identification of bacterial species is complex and may not be amenable to one universal approach
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
