The Microbial Rosetta Stone Database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents

Abstract

Background: Thousands of different microorganisms affect the health, safety, and economic stability of populations. Many different medical and governmental organizations have created lists of the pathogenic microorganisms relevant to their missions; however, the nomenclature for biological agents on these lists and pathogens described in the literature is inexact. This ambiguity can be a significant block to effective communication among the diverse communities that must deal with epidemics or bioterrorist attacks.

Results: We have developed a database known as the Microbial Rosetta Stone. The database relates microorganism names, taxonomic classifications, diseases, specific detection and treatment protocols, and relevant literature. The database structure facilitates linkage to public genomic databases. This paper focuses on the information in the database for pathogens that impact global public health, emerging infectious organisms, and bioterrorist threat agents.

Conclusion: The Microbial Rosetta Stone is available at http://www.microbialrosettastone.com/. The database provides public access to up-to-date taxonomic classifications of organisms that cause human diseases, improves the consistency of nomenclature in disease reporting, and provides useful links between different public genomic and public health databases.

Figure 1

Symbol key. These symbols are used in the Figures 2 through 7 to link pathogen names to their originating Additional Files.

Figure 2

Bacterial pathogens. Bacterial phylogeny is based on work by Hugenholtz et al. [69]. Bacterial phyla are shown on the leaves, with the Firmicutes and the Proteobacteria subdivided to the class level (taxa are shown in italics). Their phylogeny is further broken down to the order level with the use of smaller branches. These two phyla account for roughly three quarters of the described infectious bacterial species (with the noticeable exception of deltaproteobacteria pathogens). Proteobacteria contain both important plant and animal pathogens. Proteobacterial plant pathogens are not clustered, but are observed in alpha, beta, and gamma subdivisions. Some plant and animal pathogen species share the same genus classification (e.g. Ralstonia and Pseudomonas), and for at least one species, Burkholderia cepacia, different subspecies are plant and human pathogens. Of the 20 bacterial phyla currently recognized in the NCBI taxonomy, thirteen are not present in Figure 2 due to the absence of noteworthy pathogens. Some of these missing phyla are relatively important, like the Cyanobacteria, but most of the remaining phyla are restricted to a handful of species and/or environmental niches. Also of interest is the relative weight of the infectious agents within their respective phylum: While virtually all Spirochaetes and Chlamydiae constitute potential infectious agents due to their parasitic lifestyle, the phylum Actinobacteria has few pathogens relative to the overall diversity of the phylum. It should be cautioned that our current view of bacterial diversity is biased towards cultivatable organisms, which represent a small fraction of bacterial diversity [69]. Therefore, this compilation represents the well-recognized infectious bacterial agents, but should in no way be considered exhaustive or complete.

Figure 3

Eukaryotic pathogens. Eukaryotic pathogen life forms are clearly dominated by the fungi and protists. Within the Fungi, the phylum Ascomycota has many human, animal, and plant pathogens and is a major source of toxins. Protist species are responsible for globally important diseases such as the malaria-causing Plasmodium species and the Leishmania and Trypanosoma species that cause significant mortality in the developing world. The eukaryotic phylogeny tree is based on ribosomal and housekeeping gene sequence analysis [70], but different taxonomy levels are simultaneously represented as the topology has not yet been reliably determined.

Figure 4

DNA viruses. The relationships for large genome DNA viruses on this chart was derived from the work of Iyer, Aravind & Koonin, who showed the common ancestry of four large DNA virus families [72]. Noteworthy in this figure are the number of viruses that may be readily bioengineered.

Figure 5

Single-stranded negative strand RNA viruses. The common origin of RNA viruses and their tentative relationships as indicated on this chart are based on an extensive analysis of their RNA-dependent RNA- or DNA-polymerases (C.M. manuscript in preparation). The branching of double-stranded RNA viruses is unresolved in light of their apparent polyphyly [73]. Virtually all known branches of ssRNA(-) viruses harbor pathogens and thus are represented in this panel. Only the rhabdoviridae family harbors both animal and plant pathogens. Particularly noteworthy are the deadly Ebola and Influenza viruses, the latter has claimed tens of millions of human lives in the past century.

Figure 6

Single-stranded positive strand RNA viruses. The Togaviridae and Flaviviridae, and to a lesser extent the Coronaviridae and Picornaviridae, families are the most prominent human pathogens. Important plant viruses affect major cereal grains causing severe crop damages worldwide and affecting the nutrition of entire populations.

Figure 7

Retroid viruses and double-stranded RNA viruses. The most prominent include the two HIV viruses and the Hepatitis B virus, and the main family of double-stranded RNA viruses, the Orbiviridae. The latter family is an example of a virus family that includes both animal and plant pathogens. The plant pathogens primarily infect rice cultures.