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Work Package 2

Comparative genome analysis of the Enterococcus genus

The Enterococcus genus is placed in the Enterococcaceae family and comprises species that occurs in the human and animal gastro-intestinal tract as well as insects and nematodes, traditional fermented food and dairy products and in various environments like plant, soil or water1 2 3. Indeed, they are remarkably resilient organisms that are capable of enduring a broad pH or temperature range, as well as hypotonic and hypertonic conditions, characteristics that likely contribute to their presence in nearly every thing the humans come into contact with4. The enterococci have undergone considerable changes in taxonomy in recent years. During the last decade, numerous novel species have been described as a result of improvements in the methods used for their identification combined with a growing interest in their role as opportunistic pathogens. At the time of writing, the genus Enterococcus comprises 41 validly named species5. Of about thirty species described since 1990, most are associated with non- human reservoirs such as animals, plants, water or food1 5. We believe that Enterococcus faecalis and Enterococcus faecium represent the tip of the iceberg, and that study of enterococcal diversity will illuminate the origins and reservoirs of many traits, especially those found on mobile elements.

The central aim of this research is to determine the relatedness and infer the evolutionary patterns related to niche adaptation and speciation of members of the Enterococcus genus. Expanding of previous projects that characterized the genomes of the Enterococcus species faecalis, faecium, gallinarum and casseliflavus6, we sequenced the genomes of 21 additional genomes to span diversity within the genus (Enterococcus mundtii, durans, hirae, faecium, avium, saccharolyticus, malodoratus, cecorum, raffinosus, sulfureus, casseliflavus, columbae, dispar, villorum, asini, gilvus, pallens, haemoperoxidus, moraviensis, phoeniculicola and caccae). From these genome sequences, we will be able to determine the core gene set that defines the Enterococcus genus, genes that define each species providing insights into their native habitats, and insights into the origins of various traits that find their way into human isolates.

Work plan

Divergence and evolution is being examined by building a SNP-based phylogenomic tree based on the Enterococcus core genome. Importantly, gene content will be investigated to determine orthologous genes that are shared by cluster of species isolated from the same ecological niche. Conversely, genes that are specific to species or group of species that share the same niche will be identified. Besides gene content, variation in metabolic pathways present in different species will be characterized and correlated with adaptations of enterococci to various niches. The diversity of mobile genetic elements, including genomic islands, plasmids, bacteriophages and others, will be examined in each of the genomes. In addition, as recently described in E. faecalis7, the occurence of CRISPR elements as well as their distribution across the phylogenetic tree will be examined. Finally, to identify genes that are under selection during niche adaptation of the enterococci, areas of rapid genetic drift will be examined by determining the ratio of the rate of non-synonymous substitutions to the rate of synonymous substitutions.


  1. Gilmore MS, Clewell DB, Courvalin P, Dunny GM, Murray BE, Rice LB. The Enterococci: Pathogenesis, Molecular Biology, and Antibiotic Resistance. ASM Press, Washington, D.C. 2002 

  2. Franz CM, Stiles ME, Schleifer KH, Holzapfel WH. Enterococci in foods, aconundrum for food safety. Int J Food Microbiol. 2003 Dec 1;88(2-3):105-22. Review. 

  3. Giraffa G. Enterococci from foods. FEMS Microbiol Rev. 2002 Jun;26(2):163-71. Review. 

  4. Sherman JM. The Enterococci and Related Streptococci. J Bacteriol. 1938 Feb; 35(2):81-93. 

  5. J.P. Euz├ęby: List of Prokaryotic names with Standing in Nomenclature. Updated in 2012. 

  6. Palmer KL, Godfrey P, Griggs A, Kos VN, Zucker J, Desjardins C, Cerqueira G, Gevers D, Walker S, Wortman J, Feldgarden M, Haas B, Birren B, Gilmore MS. Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. MBio. 2012 Mar 1;3(1):e00318-11. 

  7. Palmer KL, Gilmore MS. Multidrug-resistant enterococci lack CRISPR-cas. MBio. 2010 Oct 12;1(4). pii: e00227-10. 


Please cite all data relating to this initiative (including individual genes and genomes) as:
"Enterococcus Illumina PacBio initiative, Broad Institute ("