Genome Report Template Organism name: Bacteroides Fragilis 638R.

Complete Taxonomy : Bacteria; Bacteroidetes/Chlorobi group; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; Bacteroides fragilis. Replicons Number , Size, Topology (linear or circular): 1 Chromosome circular. 5,37 Mb. Total genome size ( excluding plasmids ): 5,373,121 pb GC% of the genome : 43.42 % GC skew representation for Bacteroides fragilis 638R (NC_016776) Window size = 50,000 bases

Number of protein coding genes: 4290. rRNA genes (16S/23S/5S) + total number of rRNA operons : rRNA: 19 (6 OPERONS). Number of tRNA genes: 72. Phage insertions (if any) number of genes, size, location : 5 (Usually size: 10Kb-100Kb) 1. 18 Genes. [209266-227961]: 18695pb. very small, possibly other phage. (posible resto de fago) 2. 48 Genes. [1381959-1432045]: 50086 pb. Hiphotetical phage. 3. 83 Genes. [2071792-2174716]: 102924pb. Prophage. 4. 150 Genes . [2317303-2470970]: 153667pb. 5. 46 Genes. [4296659-4329148]: 32489pb. DNA invertases of the Ssr family are typically encoded
by elements imported to bacteria from a phage.

Genome Map from the genome publication showing GC content, GC skew

Locations of the genes + Description of the map

Ecology and Physiology of the microbe, Explain links to genomic features if possible. discuss pathogenic features of genomes of a pathogen. Overview of metabolism of the microbe Bacteriodes fragilis lives primarily in humans and animals intestinal/colon flora. As long as Bacteriodes fragilis is retains within the intestinal lumen, its contribution to our body is very diverse. And once Bacteroides fragilis leaves the lumen and travels to adjacent areas and organs, it can be detrimental as it contributed to a variety of infections in the upper body, abdomen, skin and many others. Bacteroides fragilis now act as a pathogen and invades its host by producing the enterotoxins. Due to its role as a pathogen, Bacteroides fragilis can be very complex; they will be able to survive and adapt in most environments like its neighbor, E.coli. Bacteroides fragilis (strain 638R) is an obligate anaerobe, Gram-negative bacterium, which represents a large part of the colonic bacteria flora. It is usually a commensal organism, forming a large component of the normal human gut microbiota. However, it is also an opportunistic pathogen that can severely limit the success of gastro-intestinal surgery, and is frequently associated with extraintestinal infections such as abscesses and soft tissue infections, as well as diarrheal diseases in animals and humans. Presence of flagella: No Human pathogen: Yes Interaction: Animal commensal in Mammalia; Animal pathogen in Mammalia Number of membranes: 2 Number of inteins:0 Zwitterionic capsular polysaccharides from pathogenic bacteria have peculiar immunological properties. They are capable of eliciting T-cell proliferation and modulating the course of abscess formation. We have identified, purified, and characterized an abscess-modulating polysaccharide, PS A2, from the clinical strain Bacteroides fragilis 638R. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic

shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli. Its lifestyles is very diverse; it can utilized simple sugars and involved in many complex pathways necessarily for generation of energy, such as biosynthesis of carbohydrates, lipids, fatty acids and much more. Its also involved in the generation of metabolites and energy through Glycolysis, Pentose Phosphate Pathway, TCA, and much more. Bacteroides fragilis can only utilized simple sugars because most sugars are absorbed into the small intestine, not much gets pass through the upper gastrointestinal tract for Bacteroides fragilis to use. This therefore, limits the complexity of the organism. Bacteroides fragilis are also involved in many important metabolic activities in the human flora of the colon. Bacteroides fragilis also produce by-products, including acetic acid, iso-valeric acid and succinic acid; that are then used to generate energy through different pathways. For example, succinic acid is used as the intermediate for the TCA cycle . Carbohydrate fermentation is another mechanism in which Bacteriodes fragilis utilizes some by-products made and other fatty acids as a source for the production of energy. The Bacteroides species also help degrade and deaminated proteins to ammonia, CO2, fatty acids and others that the body utilizes. The Bacteroides species then use the ammonia as nitrogen source but how the Bacteroides species uses nitrogen is still unclear Include all references for the work, preferably research manuscripts http://patricbrc.vbi.vt.edu/portal/portal/patric/GenomeBrowser?cType=genome&cId=167533&loc=0..10 000&tracks=DNA,CDS(PATRIC),gene(PATRIC),RNA(PATRIC) http://insilico.ehu.es/describe/map.php?016776 http://microbewiki.kenyon.edu/index.php/Bacteroides_fragilis http://patricbrc.vbi.vt.edu/portal/portal/patric/CompPathwayTable?cType=genome&cId=167533&algorit hm=PATRIC#key=765&pS=150&aP=1&aT=0&cwP=false&cwEc=false&cF=&pId=&pName=ALL&ecN=ALL&a lg=PATRIC&pClass=ALL&psort=pathway_id&pdir=ASC&esort=&edir=&fsort=&fdir=