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The text below issplit into the

following sections:

Overview

Phylogeny

Environmentalniche

Pathogenicity andVirulence

What are Bacteroides ?

The paragraph below is a brief overview of for something much moredetailed, just scroll down.

Bacteroides

are not ! They are not even that closely related to eachother. Howeverthey can both be found in the same place: Each and every one of us containmany billions of these bugs inside their gut. are specialists in this environmeas they are adapted to grow where there is no oxygen. can grow both with andwithout oxygen and is consequently a generalist and not as good at growing in eithercondition as a true anaerobe ( ) or a true aerobe ( ). In fact

are one of the most numerous of the intestinal bugs and we get to see a greatmany everyday as about 30 % of what comes out of the intestine is bacteria! Most of thetime we get on perfectly well with , in fact they assist in breaking down food

products and supply some vitamins and other nutrients that we cannot make ourselves. Tproblem with is when they get out of the intestine and into our bodies. One the most common results of this is an abscess, which is a big ball of puss comprised mostof bacteria (especially ). If the ball breaks then billions of bacteria wreak havokin the body often resulting in death. Luckily this dosn't happen too often as bacteria aresusceptable to antibiotics. Unfortunately the are very good at finding ways t

become resistant to all of the antibiotics that we use so developing new ways to fight thebugs is a great importance.

Bacteroides E. colithe intestine.

BacteroidesE. coli

B. fragilis Bacillus subtillusBacteroides

Bacteroides

Bacteroides

B. fragilis

Bacteroides

The text below contains more information about than you ever knew existedIt was taken from the introduction of Gena Tr

Bacteroidesibbles' Doctoral thesis entitled: Developme

of a Model of Transposition for the mobilizable transposon TNBacteroides 4555.

Phylogeny

Anaerobes comprise the majority of bacteria in the human colon; the most numericallypredominant of these are members of the genus . Originally described in1898 ( ), for many years the were a vague conglomeration of host-associated, obligately anaerobic, gram-negative, pleomorphic rods that could not beconvincingly assigned to any other genera. Physiological analysis of this genus revealedconsiderable heterogeneity with regard to their biochemical properties, indicating these

bacteria did not represent a true phylogenetic grouping. With the advent of phylogeneticanalysis techniques, several investigators have tried to redefine this group of bacteria usin

physiological characteristics ( ), serotyping ( ), bacteriophage typing ( ), lipidanalysis ( ), oligonucleotide cataloging ( ), and 5S - 16S rRNA sequence comparison( , , , ). Based on this information, the original members have

been partitioned into three genera: ( )( ) and ( ) The are found predominantly in

the colon of mammals, while the and generally are associatwith the oral cavity and the rumen.

Bacteroides115 Bacteroides

39 50 659 73

46 72 113 116 BacteroidesBacteroides 99,

Prevotella 97, Porphyromonas 98 . BacteroidesPrevotella Porphyromonads

The current definition of species is as follows: a) obligately anaerobic, GramBacteroides

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Antibioticresistance

negative, b) saccharolytic, producing acetate and succinate as the major metabolic endproducts, c) contain enzymes of the hexose monophosphate shunt-pentose phosphatepathway, d) have a DNA-base composition in the range 40-48 mol% GC, e) membranescontain sphingolipids, and contain a mixture of long-chain fatty acids, mainly straightchain saturated, anteiso-methyl, and iso-methyl branched acids, f) possess menaquioneswith MK-10 and MK-11 as the major components, and g) contain -diaminopimelicacid in their peptidoglycan ( ). This definition restricts the to ten species:

and with as the type

strain. The , along with and form one major subgroup in the bacterial phylum Cytophaga-Flavobacter-Bacteroides ( ). This phylumdiverged quite early in the evolutionary lineage of bacteria, and thus the ,although gram-negative organisms, are not closely related to the enteric gram-negativessuch as (Fig. 1.1).

meso96 Bacteroides B

fragilis, B. thetaiotaomicron, B. vulgatus, B. ovatus, B. distasonis, B. uniformis, B.stercoris, B. eggerthii, B. merdae, B. caccae, B. fragilis

Bacteroides Prevotella Porphyromonas,27Bacteroides

Escherichia coli

FIG. 1.1. Phylogenetic tree of Eubacteria based on 16s rRNA sequence comparisons. Thevolutionary relationship between prokaryotic phyla are shown. Branch lengths on the trrepresent evolutionary distance. Grey wedges represent divergence within the individual

phyla. Derived from ( ). (Click image for larger version)116

as Commensal OrganismsBacteroides

The inhabit the human colon, which contains the largest, most complexbacterial population of any colonized area of the human body. The colonic contentscontain in excess of 1011 organisms per gram of wet weight, representing over 400species ( ). The are the most numerous members of the normal flora,representing nearly 1011 organisms per gram of feces (dry weight) ( ). Gut organisms ainvolved in numerous metabolic activities in the colon, including fermentation of

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carbohydrates, utilization of nitrogenous substances, and biotransformation of bile acidsand other steroids ( ). In order to maintain their high numbers, the areevidently able to compete with other members of the flora, as well as transient organismsfor utilization of these resources. While the role of the microflora in the physiology of thehuman intestine is not well studied, it is clear that the anaerobic members of this ecosyste

play a fundamental role in the processing of complex molecules into simpler compoundsand through their metabolic activities the human microflora participate in the complex

physiology of the host ( ).

36 Bacteroides

8Most intestinal bacteria are saccharolytic, obtaining carbon and energy by hydrolysis of

host and dietary carbohydrate molecules ( ). Simple sugars are rarely encountered in thcolon as most are absorbed in the small intestine, however it is estimated thatapproximately 2% of simple sugars can pass through the upper gastrointestinal tract whenlarge amounts of starch and complex carbohydrates are also present duringdigestion ( ). species are able to utilize simple sugars when present ( ,

but due to their limited availability, simple sugars are probably not the main source ofenergy for the . Much more prevalent in the colon are polysaccharides, fromdietary sources and host cells. Polysaccharides from plant fibers, such as cellulose, xylanarabinogalactan, and pectin, and vegetable starches such as amylose and amylopectincontain have been shown to have a variety of glucosidase activities, includina b-1,3-glucosidase activity responsible for laminarin degradation ( ), and a variety of aand b-1, 4 and -1, 6 xylosidase and glucosidase activities induced by the presence of

hemicellulose ( ). Originally it was believed that these enzymatic activities wereextracellular, and the short oligosaccharides and monosaccharides produced by hydrolyswere taken up into the cell for fermentation. Analysis of the starchutilization system (sus) ( ), has revealed the polysaccharides to be bound to an outermembrane receptor system ( ), and pulled into the periplasm for degradation intomonosaccharides. The use a similar approach for uptake and degradation ofchondroitin sulfate ( ), indicating this technique may provide a competitive advantage ithe human gut, as polysaccharides sequestered in the periplasm are less likely to be"stolen" by other intestinal organisms or lost by diffusion.

75

92 Bacteroides 44 95

Bacteroides

Bacteroides94

83

B. thetaiotaomicron16

85Bacteroides

10

Interestingly, utilization of chondroitin sulfate by isrepressed in the presence of glucose ( ), while utilization of other sugars in

is tightly regulated in the presence of mannose ( ). This implies

the may have a catabolite repression mechanism to allow for the utilization oselect carbon sources in preference to others. If so, this system is probably not similar tothe catabolite repression systems of enteric bacteria, as the do not possesscyclic AMP ( ). It is likely that most polysaccharide utilization systems arecontrolled by repressor/inducer mechanisms, as and are abto utilize several sugars simultaneously ( ), and several polysaccharide utilization geneshave been shown to be activated in the presence of their substrate ( , , ).

Bacteroides thetaiotaomicron93 B.

thetaiotaomicron 52

Bacteroides

Bacteroides42 Bacteroides

B. ovatus B. thetaiotaomicron52

18 120 81Carbohydrate fermentation by the and other intestinal bacteria results in the

production of a pool of volatile fatty acids, predominately acetate, propionate (fromsuccinate), and butyrate. These short chain fatty acids are reabsorbed through the largeintestine, and utilized by the host as an energy source ( ). It has been estimated thatabsorption of the short chain fatty acids could provide up to 540 kcal/d, a significant

proportion of the host's daily energy requirement ( ).

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56

15The utilization of nitrogen sources by the intestinal is not well understood, amost work in the area of nitrogen uptake has been done with rumen organisms. Howeveseveral parallels may be drawn between intestinal and rumen bacteria, providing a

paradigm of nitrogen utilization in the human gut. There are three major sources ofnitrogen in the mammalian intestine: dietary protein, epithelial cell and mucinglycoproteins, and ammonia ( ). Most dietary protein is degraded and absorbed beforereaching the large intestine, but once in the colon, these peptides and amino acids are notable to be absorbed by the host ( ). Instead, a two step degradation process occurs,during which peptides are proteolysed to amino acids, which are subsequently deaminate

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to form ammonia, CO2, volatile fatty acids, and branched chain fatty acids ( ). Theammonia is utilized by the intestinal bacteria as a nitrogen source ( ).

has been shown to produce three major proteases ( ), with activityagainst a variety of proteins, including casein, trypsin, and chymotrypsin, but not collageelastin, or gelatin ( ). The also encode glutamine synthetase ( ) andglutamate dehydrogenase ( ), which are important for ammonia assimilation but theregulation of these activities is not yet understood.

12238

Bacteroides fragilis 28

29 Bacteroides 1084

The play a key role in the enterohepatic circulation of bile acids. Cholic acidand chenodeoxycholic acid are the two main bile acids synthesized in the human liver,

where they are conjugated to taurine or glycine polar side groups before secretion in bileOnce bile enters the gut, the conjugated bile acids assist in the absorption of dietary fats. the bile acids are not reabsorbed in association with fat in the upper intestine, they aredeconjugated by bacteria to secondary bile acids, primarily deoxycholic and lithocholicacid, although the microflora can generate 15-20 other secondary bile acids from thesesame precursors ( ). Deconjugation allows the bile acids to reenter the enterohepaticcirculation via the portal system, where they are returned to the liver and reconjugated fofurther use ( ). The secondary bile acids deoxycholic and lithocholic acid are produced b7 alpha-dehydrogenation of the primary bile acids ( ); once these secondary bile acids a

produced, a variety of other bacterial reactions can occur, including oxidation-reduction,desulphation, and dehydrogenation ( ), producing a variety of isomers of secondary bilacids. The have been found to play a major role in the biotransformation of

bile acids, and contain many enzymes required for these reactions, including ahydrolase ( ), dehydrogenase ( ), and dehydroxylase ( , ). The direct benefit to thost is obvious, as deconjugation of the primary bile acids allow them to be reabsorbed inthe large intestine instead of lost in the feces. The benefit to the and otherintestinal bacteria is not clear, but may contribute to energy metabolism.

Bacteroides

41

541

24Bacteroides

109 43 21 87

Bacteroides

Aside from their metabolic activities, the and other anaerobes provide anadditional benefit to their host in excluding pathogenic organisms from colonizing theintestine ( ). Colonization resistance mediated by anaerobes is thought to occur by foumechanisms: competition for nutrients, competition for intestinal wall attachment sites,

production of volatile fatty acids, and release of free bile acids ( ). The intestinalmicroflora adhere to the surface of epithelial cells and mucin associated with the intestinawall, with being the most common anaerobic colonizer ( ). By coating the

walls of the intestine, it is believed that the microflora prevent transient bacteria fromobtaining a binding site on the intestinal surface, and the transients are subsequently lostwith the luminal contents during peristalsis. The volatile fatty acids produced as metaboliend products by the are also believed to play a role in colonization resistance

by lowering the pH and oxidation-reduction potential of the intestinal milieu, resulting inunfavorable growth conditions for transient bacteria ( ). The most notable pathogensinhibited under these conditions are ( ) and

( ) Production of free bile acids also plays a role in inhibition of pathogens, asbile salts are toxic to many organisms, including ( )

Bacteroides

114

37

Bacteroides 11

Bacteroides

37Salmonella enteritidis 57, Shigella

flexineri 53 .Clostridium botulinum 40 .

Pathogenicity and Virulence

While the occupy a significant position in the normal flora, they also areopportunistic pathogens, primarily in infections of the peritoneal cavity. is themost notable pathogen; although it makes up only 1-2% of the normal flora, it isthe species isolated from 81% of anaerobic clinical infections ( ).

is not overtly invasive, but is capable of participating in intraabdominal infectionsin the event the mucosal wall of the intestine is disrupted. Incidences duringwhich infections may be initiated include gastrointestinal surgery, perforated

BacteroidesB. fragilis

Bacteroides 118 B.fragilis

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or gangrenous appendicitis, perforated ulcer, diverticulitis, trauma, and inflammatorybowel disease ( ).101The current model for development of abdominal infections is based on the concept ofsynergism, during which cooperation between different species of bacteria aids in theestablishment of persistent infection ( ). Synergism has been most clearly established iinfections involving both and ( ), although other combinations ofaerobes and anaerobes also are synergistic ( ). After disruption of the intestinal wall,members of the normal flora infiltrate the normally sterile peritoneal cavity, and during thearly, acute stage of infection (approximately 20 hours), the aerobes, such as are

the most active members of infection ( ), establishing preliminary tissue destruction andreducing the oxidation-reduction potential of the oxygenated tissue. Once sufficientoxygen has been removed to allow the anaerobic to replicate, these bacteria

begin to predominate during the second, chronic stage of infection ( ).

121E. coli B. fragilis 48

125

E. coli,

70

Bacteroides121

The contribute to development of a synergistic infection in three ways:stimulation of abscess formation, reduced phagocytosis by polymorphonuclear leukocyte(PMN's), and inactivation of antibiotics by b lactamase production ( ). Abscessformation is a major complication of intestinal infections, and results in the formation of afibrous membrane surrounding a mass of cellular debris, dead PMN's, and a mixed

population of bacteria. If not removed, the abscess will expand, possibly causing intestinobstruction, erosion of resident blood vessels, and ultimately fistula formation ( ).Abscesses may also metastasize, resulting in bacteremia and disseminated infection (

Formation of the abscess is a pathological response of the immune system to the presencof the capsular polysaccharide. is the only bacterium that has beenshown to induce abscess formation as the sole infecting organism ( ). Purified capsulecan stimulate formation of a histologically identical abscess, indicating that it is thiscomponent of the bacterium which stimulates the host immune system to deposit fibrin,forming the outer membrane of the abscess. The capsule has been shown tohave an unusual structure, composed of repeating units of two distinct polysaccharides,each of which contains exposed positively and negatively charged side-chains ( ). Mo

bacterial polysaccharides stimulate an antibody-mediated immune response, but thecapsule stimulates a T cell-mediated response ( , , ). Presumably, the

intention of the cell-mediated immune response is to wall off the infection and protect thehost from dissemination, but in fact, formation of an abscess protects the and

neighboring bacteria from exposure to high concentrations of antibiotics and further attacfrom the immune system.

Bacteroides

121

121101

Bacteroides B. fragilis68

Bacteroides

112B.

fragilis 69 100 124

Bacteroides

Another important synergistic virulence factor of is the ability to inhibitphagocytosis. Once the actively begin to replicate, they are able to interferewith attack by the immune system in two ways. First, production of the capsule itself isable to reduce the ability of the PMN's to phagocytose the bacterial cells ( , ).Secondly, the are able to secrete an as yet uncharacterized factor whichdegrades complement proteins, and thus inhibits both chemotaxis of PMN's andopsonization of itself and neighboring bacteria ( , , ).

B. fragilisBacteroides

67 86Bacteroides

19 45 91A final contribution of the to a successful synergistic infection is the

production of b-lactamase. Most strains express constitutive b-lactamaseactivity ( ); the enzyme is extra-cellular, and thus is capable of diffusing within an

abscess or other site of infection. Production of extra-cellular b-lactamases has been showto protect other organisms in the vicinity during a mixed infection ( ).

BacteroidesBacteroides

66

34These bacteria have several other features that contribute to their pathogenicity.The are among the most aerotolerant of anaerobes, able to tolerateatmospheric concentrations of oxygen for up to three days ( ). During initiation of anintraabdominal infection, oxygen tolerance is believed to allow the bacteria to survive inthe oxygenated tissue of the abdominal cavity until and other synergistic organismare able to reduce the redox potential at the site of infection. Additionally, this oxygentolerance may help in surviving free radical production by the immune systemPMNs. have been found to encode two major oxidative stress response gene

Bacteroides111

E. coli

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catalase ( ) and superoxide dismutase ( ), as well as approximately 28 other oxygen-induced proteins ( ).

88 3287

Although a commensal organism, can occasionally cause diarrhea.Strains of isolated from some patients with undiagnosed diarrhea were foundto be enterotoxigenic, and in patients less than three years age they were associated withintestinal cramping, vomiting, and bloody stools ( ). The purified toxin, fragilysin, wasfound to be a metalloprotease capable of hydrolysing gelatin, actin, tropomyosin, andfibrinogen ( ). In a study comparing the frequency of enterotoxigenic and noenterotoxigenic bacteria involved in various infection sites, the enterotoxic strains were

found in higher frequencies in bacteremias ( ). It is possible that fragilysin is involved ireleasing the organism from an abscess or other site of infection and allowing it to enter t

blood stream, thus disseminating infection throughout the body.

BacteroidesBacteroides

62

60 B. fragilis

47

Antibiotic Resistance

is the most common anaerobic organism isolated from clinical infections, anduntreated has a mortality rate of 60% ( ). This mortality rate can be greatly improved,however, with use of appropriate antimicrobial therapy ( ). The are

potentially resistant to a broad range of antibiotics, and resistance to a given antimicrobiacan vary greatly between institutions. Resistance to any antimicrobial agent may occur bthree mechanisms: altered target binding affinity, decreased permeability for the antibiotior the presence of an inactivating enzyme ( ). The are adept at antimicrobievasion, and may use any or all of the above mechanisms to thwart effective clinicaltherapy.

B. fragilis65

84 Bacteroides

80 Bacteroides

Antimicrobial agents may target several areas of bacterial physiology: protein translationnucleic acid synthesis, folic acid metabolism, or cell wall synthesis ( ). Protein synthesiinhibitors bind either the 30s subunit of the ribosome (aminoglycosides, tetracycline), orthe 50s subunit (macrolides, lincosamides, chloramphenicol) ( ). areinherently resistant to aminoglycosides, as uptake of this drug is energy dependent, andrequires an oxygen or nitrate dependent electron transport chain which is lacking in these

anaerobes ( ). The have acquired resistances to the other protein synthesisinhibitors; resistance to clindamycin/erythromycin (macrolide-lincosamide antibiotics), antetracycline will be discussed as pertinent examples.

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31 Bacteroides

9 Bacteroides

Resistance to clindamycin and erythromycin has slowly but steadily increased over the la20 years ( ). In the early 1970's, all clinical isolates tested were susceptible to theseantibiotics ( , ), but late in the decade the first reports of resistance were beginning tosurface ( ). Three closely related genes were identified that conferred both clindamycinand erythromycin resistance in ( , , ). These genes are similar tomacrolide/lincosamide/ streptogramin resistance genes in gram positive organisms,implying that they may confer resistance by the same mechanism, namely methylation ofthe ribosome target site ( ). Clindamycin and erythromycin resistance has been shown t

be transferable between species, either in association with a conjugative

plasmid ( , , ), or a chromosomal element ( ). Resistance determinants in thechromosome are often associated with tetracycline resistance, and in such instances bothare cotransferred in association with a conjugative transposon ( ). Resistance to to theantimicrobials in clinical isolates is variable from one clinical setting toanother; currently resistance rates average 6%, although rates as high as 22% have beenreported ( ).

8049 58

35Bacteroides 33 82 103

80Bacteroides

76 110 117 54

102Bacteroides

107Tetracycline was once the first-line antibiotic for treatment of anaerobic infections.Antibiotic resistance surveys from the 1950's indicated all strains of weresusceptible to tetracycline ( ), and this antibiotic remained a frequent treatment ofanaerobic infections throughout the 1960's. By the early 1970's, however, significant

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numbers of resistant organisms were appearing in clinical infections ( , ), and todaynearly all isolates are resistant, (80-90%) ( ). Tetracycline resistance inthe is attributable almost exclusively to the presence of the Q gene ( ),which encodes a protein that is believed to alter the ribosome target site for theantibiotic ( ). Q genes from several sources have been sequenced,revealing that this gene is only distantly related to other ribosomal protection genes Mand O ( ). The Q gene is chromosomally located, but can be transferred by aconjugation-like mechanism ( , , , ). This transfer has been attributed to the

presence of the Q gene on large, conjugative transposons called Tcr elements.

49 58Bacteroides 80

Bacteroides tet 26

64 Bacteroides tettet

tet 80 tet55 77 78 106

tet

Another class of antimicrobials used to treat anaerobic infections are the , themost common mechanism of resistance to these compounds is productionof species are primarily cephalosporinases, directed against the penicillin-derived cephalosporins originally developed in the 1960's for treatment of gram-negativeorganisms ( ).

Bacteroides

Bacteroides

51At least 90% of all species encode a chromosomal ( ) and

( ) showed them to be members of the Ambler class ABacteroides B. fragilis 90 B.

uniformis 104In addition to the endogenous also possess enzymes with activity againstextended-spectrum cephalosporins (cefoxitin), and carbapenems (imipenem) ( , , )The cefoxitin resistance gene, A ( ), has been shown to be distantly related to the

endogenous A ( ). Cefoxitin was first introduced in the 1970's, and by 1980the non- species showed significant resistance to this antimicrobial, as high as 84%

in ( ) In general, resistance to cefoxitin has remained low in , withrates remaining in the range of 3-6% ( , ), although percentages as high as 11% have

been reported ( ).

Bacteroides13 23 51

cfx 71 B.fragilis cep 90

fragilis

B. ovatus 35 . B. fragilis2 107

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Bacteroides fragilis group and other anaerobes by traditional MIC results and statisticamethods. Journal of Anitmicrobial Chemotherapy. 39:319-324.3.Ambler, R. P. 1980. The structure of B-lactamases. Philosphical Transactions of the

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