The Normal Microbiota

Natural Human Flora What organisms are part of normal flora Where do they colonize - microbial ecosystems How are they able to cause disease? - exposure - virulence factors

NATURE REVIEWS | MICROBIOLOGY VOLUME 9 | APRIL 2011 | 279 MICROBIAL COMMUNITY COMPOSITION IN A HEALTHY HUMANS

Colon Distribution of bacterial species along the gut Stomach Streptococcus Small bowel (ileum) Lactobacillus Streptococcus E. coli Clostridium Bacteroides Eubacterium Vellonella Bacteroides Eubacterium Clostridium Ruminoccus Bifidobacteriu m Streptococcus Lactobacillus E. coli Bacteroides Eubacterium Clostridium Ruminococcus Bifidobacterium Streptococcus Lactobacillus E.coli non-E.colicoliformes Colon Eckburg et al., 2005 Science > sequences 16S rRNA

Metabolism -supplies enzymatic activities not encoded by host -modifies bioavailability and bioactivity -can induce/reduce obesity & T2D Protection - develops local and systemic immunity - regulates tolerance, allergies & homeostasis A healthy microflora regulates diverse biological roles Behavior - alters host behavior through its effects on the central nervous system

Adult microbiota: acquired by 2 yrs Stable? In utero = sterile “germ free” Birth: colonization begins Environment & host influence species dominance Maternal vaginal, colonic & skin microflora Vaginal vs C-section Antibiotics Initial feedings Developing immune system Stability could impart resilience to disturbance to ensure continued gut function, but in a disease context, this could be detrimental if the gut community is pathogenic. Gut microbes are “inherited” maternally

Microbiota is variable between individuals but each individual microbiota is stable Once colonized your microflora is stable throughout life. Denaturing/thermal gradient gel electrophoresis separates DNA by differing thermal stability; patterns reflect bacterial diversity

Factors can change the microbiota composition: dysbiosis Stress: (O'Mahony, 2009) Stress: (O'Mahony, 2009) Exercise: (Matsumoto, 2008) Exercise: (Matsumoto, 2008) Inflammation: Inflammation: (Lupp, 2007) Old Age: (Biagi, 2010) Old Age: (Biagi, 2010) Diet: Diet: carbohydrate reduced(Walker, 2011); high fiber diets (De Filippo 2011); high-fat, high-sugar "Western" diet (Turnbaugh 2010); calorie-restricted diets (Santacruz 2009); vegetarianism (Liszt K, 2009); alcohol consumption (Mutlu, 2009); high fat (Mozes, 2008) carbohydrate reduced(Walker, 2011); high fiber diets (De Filippo 2011); high-fat, high-sugar "Western" diet (Turnbaugh 2010); calorie-restricted diets (Santacruz 2009); vegetarianism (Liszt K, 2009); alcohol consumption (Mutlu, 2009); high fat (Mozes, 2008)

Diseases associated with gut microbial dysbiosis  Inflammatory Bowel Disease  Type I and II Diabetes  Irritable Bowel Syndrome  Celiac’s Disease  Autism? Does dysbiosis cause disease?

Obesity-Associated Gut Microbiota Induces Adiposity Mice + lean microflora = resistant to the fattening effects of high fat diets, despite eating the same amount of food. Microflora from an obese mouse Microflora from a lean mouse (Turnbaugh et al, 2006 Nature).

Reduced Microbiota Diversity with Obesity Turnbaugh et al. 2009, Nature 457: The microbiota diversity is reduced in obese subjects.

A healthy microflora balances immunological responses

Probiotics  Can probiotics treat or prevent disease?  Assumed to be a safe benign treatment  All yogurts have at least two probiotics Lactobacillus bulgaricus Streptococcus thermophilus Bifidobacteria isolated from the intestine ary/probiotic.html Probiotics: Live microorganisms when administered in adequate amounts confer a beneficial health effect on the host Prebiotics: compounds that promote the growth of probiotics

– Some microbes that are non-pathogenic in normal host can produce severe life-threatening disease in immunodeficient – may be normal flora components (endogenous) Ex. Fungal pathogens; Infection with organisms of known pathogenicity – Reactivation Ex. TB in AIDS patients – Exogenous Pathogens which normally cause mild conditions can cause life- threatening illness in immunodeficient Opportunist infections

Causes of Immunodeficiency Disease or trauma – Ex. HIV; neoplasia; burns; compromised clearance (ex. cystic fibrosis, obstructed urine flow) Therapy – Ex. steroids, chemotherapeutic cytotoxic agents, radiotherapy, splenectomy; prosthetic devices; catheters Age – Neonates (immature immune system) – Elderly (decrease in immunity, malnutrition

Some Common Causes of Infection in Immunocompromised Patients Infectious AgentDisease E. ColiUrinary infections, septicemia Pseudomonas aeruginosaPneumonia, septicemia M. TuberculosisPulmonary, miliary TB C. DifficileDiarrhea, pseudomembranous colitis CandidaThrush, systemic candidiasis Cryptococcus neoformansMeningoencephalitis

Clostridium difficile Present in less than 5% of people in their normal flora at very low numbers Can be “acquired” through community or hospital Antibiotic use (particularly broad spectrum) causes disruption of normal flora → overgrowth of C. difficile → C. difficile produces exotoxins → – Diarrhea – Characteristic fibrinous pseudomembrane covers colonic mucosa (hence the name “pseudomembranous colitis”) Treatment: metronidazole or oral vancomycin (resistance has emerged) Oral fecal bacterial therapy has been successful

C. difficile is acquired the hospital: patients are exposed through contact with the hospital environment or health care workers. After antibiotic- treatment they can develop infection but only if the strain is toxigenic and they fail to produce IgG responses.

Bioterrorism = intentional or threatened use of viruses, bacteria, fungi, or toxins from living organisms to produce death or disease in humans, animals, and plants – Agent chosen for mass casualties Biocrime: agent chosen as a means for a localized attack Characteristics that favour use of particular agent: – Invisible, odourless, tasteless – Difficult to detect – Take hours or days before awareness that they have been used

Examples of Intentional Uses of Biological Agents for Criminal or Terror Intent 1984 in Dalles, Oregon – Salmonella typhimurium in 10 restaurant salad bars 1996 in Texas – Intentional release of Shigella dysentariae in a hospital lab break room 2001 in seven eastern U.S. states – Use of weaponized Bacillus anthracis spores delivered through U.S. postal systems – 22 infected persons – Five deaths

Agents Considered a High Priority Threat Yersinia pestis Francisella tularensis Small pox Bacillus anthracis Botulinum toxin Exotic viruses (ex. Ebola, Marburg) Genetically modified organisms