Journal article
Veillonella, Firmicutes: Microbes disguised as Gram negatives
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark1
Comparative Microbial Genomics, Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark2
Department of Systems Biology, Technical University of Denmark3
National Food Institute, Technical University of Denmark4
Division of Food Microbiology, National Food Institute, Technical University of Denmark5
Division of Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark6
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.
| Language: | English |
|---|---|
| Publisher: | Michigan State University |
| Year: | 2013 |
| Pages: | 431-448 |
| ISSN: | 19443277 |
| Types: | Journal article |
| DOI: | 10.4056/sigs.2981345 |
| ORCIDs: | Vesth, Tammi Camilla , Andersen, Sandra Christine , Kaas, Rolf Sommer and Lukjancenko, Oksana |
03502, Genetics - General 03509, Genetics - Population genetics 10066, Biochemistry studies - Lipids 10068, Biochemistry studies - Carbohydrates 2-D clustering method mathematical and computer techniques 31000, Physiology and biochemistry of bacteria 31500, Genetics of bacteria and viruses Anaerobic Gram-Negative Cocci Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Veillonellaceae [07001] Veillonella genus pathogen Biochemistry and Molecular Biophysics Eubacteria Bacteria Microorganisms (Bacteria, Eubacteria, Microorganisms) - Endospore-forming Gram-Positives [07810] Clostridium genus pathogen Infection Microorganisms (Bacteria, Eubacteria, Microorganisms) - Bacteria [05000] Firmicutes higher_taxa pathogen Proteobacteria genus pathogen Negativicutes higher_taxa Molecular Genetics Population Genetics Population Studies Veillonella 16S rRNA gene [Veillonellaceae] amino acid composition conserved proteins evolutionary history genome sequencing laboratory techniques, genetic techniques genomic DNA sequencing laboratory techniques, genetic techniques heatmapping method mathematical and computer techniques lipopolysaccharide synthesis signaling metabolic property metabolism analysis laboratory techniques phylogenetic tree analysis mathematical and computer techniques prokaryotic genome proteome analysis laboratory techniques, genetic techniques taxonomic position tetramer frequency
