Phylogenomics and Evolutionary Studies on Bacteriodetes, Chlorobi and Fibrobacteres Species

The Fibrobacteres, Chlorobi and Bacteroidetes are presently recognized as three of the main divisions (or phyla) within Bacteria. Species belonging to these groups exhibit enormous phenotypic and metabolic diversity. Fibrobacteres are major rumen bacteria, which enable the ruminants to breakdown and digest plant cellulose. The Chlorobi, also known as Green sulfurbacteria, are obligate photolithotrophs which carry out anaerobic photosynthesis withdrawing electrons from hydrogen sulfide. They are mainly found in anoxic aquatic environment where sunlight is able to penetrate. The bacteria belonging to Bacteroidetes division, previously known as the Cytophaga-Flavobacteria-Bacteroides (CFB) group, are widely distributed in different habitats ranging from Antarctic ice to fresh and salt water lakes, to terrestrial soil and hydrothermal Obsidian pool. Many of the CFB group bacteria show close association with human and animal hosts, where they perform useful functions and are also the causative agents of a variety of diseases. Until recently, except for their branching patterns in the 16S rRNA trees, no distinctive biochemical or molecular characteristics were known which could clearly distinguish species belonging to these phyla from other bacteria. The relationships of these phyla to each other and to other main divisions within bacteria were also not understood. However, in the past few years, comparative and phylogenomic analyses of various genomes from these groups of species have led to identification of numerous RGCs (conserved inserts and whole proteins) that are distinctive characteristics of these groups of species and clarify how they are related to each other and to other groups of bacteria. Describe below are a number of RGCs that are either distinctive of Bacteriodetes or Chlorobi species, or are common shared by Bacteriodetes and Chlorobi, or they are uniquely present in various Bacteroidetes,Chlorobi and Fibrobacteres homologs. These signatures provide evidence that these groups of bacteria shared a common ancestor exclusive of all other bacteria and they diverged from this common ancestor in the following order: Fibrobacteres -> Chlorobi -> Bacteriodetes. These inferences are strongly supported by phylogenetic analyses. Signature sequences in many other proteins provide information regarding the branching order of these bacteria relative to other bacterial phyla

. CFB branching order

Click below for more information:

1. Phylogenetic Trees

2. Conserved Indels

3. Signature Proteins

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Selected References:

Eisen,J.A., Nelson,K.E., Paulsen, (2002). The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium. Proc.Natl.Acad.Sci.U.S.A, 99(14), 9509-9514.

Griffiths, E. and Gupta, R.S. (2001) The use of Signature Sequences in Different Proteins to determine the branching order of bacterial divisions: Evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacteria-Bacteriodes Division. Microbiology, 147: 2611-2622. [PDF]

Gupta, R.S. (2004) The phylogeny and signature sequences characteristics of Fibrobacteres, Chlorobi and Bacteroidetes. Crit. Rev. in Microbiology 30: 123-143. [PDF]

Gupta, R. S. and Lorenzini, E. (2007) Phylogeney and Molecular Signatures (Conserved proteins and indels) that are specific for the Bacteriodetes and Chlorobi Species. BMC Evol. Biol. May 8, 7(1), 71[Abstract]

Imhoff, J. F. (2003) : Phylogenetic taxonomy of the family Chlorobiaceae on the basis of 16S rRNA and fmo (Fenna-Matthews-Olson protein) gene sequences. Int J Syst Evol Microbiol 2003, 53: 941-951.

Montgomery,L., Flesher,B., & Stahl,D.A. (1988). Transfer of Bacteroides succinogenes (Hungate) to Fibrobacter Fibrobacter succinogenes comb. nov. and Description of Fibrobacter intestinalis sp .nov. , EPA/600/J-88/357. Int.J.Syst.Bacteriol., 38, 430-435.

Oren, A. (2003) The Genera Rhodothermus, Thermonema, Hymenobacter and Salinibacter: In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, Ed M. e. al. Dworkin. Springer-Verlag: New York.

Overmann, J. (2000) The Family Chlorobiaceae: In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, Ed M. e. al. Dworkin. Springer-Verlag: New York.

Shah,H.N., Gharbia,S.E., & Duerden,B.I. (1998). Bacteroides, Prevotella and Porphyromonas. InA.Balows & B.I.Duerden (Eds.), Topley &Wilson's Microbiology and Microbial Infections vol. 2 Systematic Bacteriology (pp. 1305-1330). London: Arnold.

Smith, C. J., Rocha, E. R. and Paster, B.J. (2003) The medically important Bacteroides spp. in health and disease: In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, M. Dworkin, et al. (ed) Springer-Verlag: New York.

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Citation for this webpage:
Bacterial (Prokaryotic) Phylogeny Webpage (March 2007).