1 Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark2 Comparative Microbial Genomics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark3 Department of Systems Biology, Technical University of Denmark4 National Food Institute, Technical University of Denmark5 Division of Food Microbiology, National Food Institute, Technical University of Denmark6 Division of Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark7 Network Engineering of Eukaryotic Cell factories, Department of Biotechnology and Biomedicine, Technical University of Denmark8 unknown
The Firmicutes represent a major component of the intestinal microflora. The intestinal Firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. Although most Firmicutes are Gram positive, members of the class Negativicutes, including the genus Veillonella, stain Gram negative. Veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerobes. In this work, the genomes of 24 Negativicutes, including eight Veillonella spp., are compared to 20 other Firmicutes genomes; a further 101 prokaryotic genomes were included, covering 26 phyla. Thus a total of 145 prokaryotic genomes were analyzed by various methods to investigate the apparent conflict of the Veillonella Gram stain and their taxonomic position within the Firmicutes. Comparison of the genome sequences confirms that the Negativicutes are distantly related to Clostridium spp., based on 16S rRNA, complete genomic DNA sequences, and a consensus tree based on conserved proteins. The genus Veillonella is relatively homogeneous: inter-genus pairwise comparison identifies at least 1,350 shared proteins, although less than half of these are found in any given Clostridium genome. Only 27 proteins are found conserved in all analyzed prokaryote genomes. Veillonella has distinct metabolic properties, and significant similarities to genomes of Proteobacteria are not detected, with the exception of a shared LPS biosynthesis pathway. The clade within the class Negativicutes to which the genus Veillonella belongs exhibits unique properties, most of which are in common with Gram-positives and some with Gram negatives. They are only distantly related to Clostridia, but are even less closely related to Gram-negative species. Though the Negativicutes stain Gram-negative and possess two membranes, the genome and proteome analysis presented here confirm their place within the (mainly) Gram positive phylum of the Firmicutes. Further studies are required to unveil the evolutionary history of the Veillonella and other Negativicutes.
Standards in Genomic Sciences, 2013, Vol 9, Issue 2, p. 431-448
amino acid composition; evolutionary history; metabolic property; prokaryotic genome; taxonomic position; tetramer frequency; Anaerobic Gram-Negative Cocci Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Veillonellaceae  Veillonella genus pathogen; Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Endospore-forming Gram-Positives  Clostridium genus pathogen; Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteria  Firmicutes higher_taxa pathogen Proteobacteria genus pathogen Negativicutes higher_taxa; Veillonella 16S rRNA gene [Veillonellaceae]; conserved proteins; lipopolysaccharide synthesis signaling; 03502, Genetics - General; 03509, Genetics - Population genetics; 10066, Biochemistry studies - Lipids; 10068, Biochemistry studies - Carbohydrates; 31000, Physiology and biochemistry of bacteria; 31500, Genetics of bacteria and viruses; Biochemistry and Molecular Biophysics; Population Studies; 2-D clustering method mathematical and computer techniques; genome sequencing laboratory techniques, genetic techniques; genomic DNA sequencing laboratory techniques, genetic techniques; heatmapping method mathematical and computer techniques; metabolism analysis laboratory techniques; phylogenetic tree analysis mathematical and computer techniques; proteome analysis laboratory techniques, genetic techniques; Infection; Molecular Genetics; Population Genetics