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 gutDistribution 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

BacteroidesEubacteriumClostridiumRuminococcusBifidobacteriumStreptococcusLactobacillusE. coli

non -E. coli coliformes

Colon

Eckburg et al., 2005 Science

>13 500 sequences 16S rRNA

Metabolism- supplies enzymatic activities not encoded by host- modifies bioavailability and bioactivity- can induce/reduce obesity & T2DProtection- 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 yrsStable?

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” maternallyGut microbes are “inherited” maternally

Species diversity profiling of fecal adult microbiota

Zoetendahl et al. 1998Seksik et al. 2003Vanhoutte et al. 2004

The faecal microbiota is specific of individuals

14 healthy adults

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 carbohydrate reduced(Walker, 2011); high fiber diets (De Filippo 2011); high-fat, high-sugar "Western" diet (Turnbaugh 2010); 2011); high-fat, high-sugar "Western" diet (Turnbaugh 2010); calorie-restricted diets (Santacruz 2009); vegetarianism (Liszt K, calorie-restricted diets (Santacruz 2009); vegetarianism (Liszt K, 2009); alcohol consumption (Mutlu, 2009); high fat (Mozes, 2009); alcohol consumption (Mutlu, 2009); high fat (Mozes, 2008)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 457:480-485.

The microbiota diversity is reduced in obese subjects.

A healthy microflora balances immunological A healthy microflora balances immunological responsesresponses

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 intestinewww.livingfoodsusa.com/library/probiotic.html

Probiotics: Live microorganisms when administered in adequate amounts confer a beneficial health effect on the hostPrebiotics: 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 Agent Disease

E. Coli Urinary infections, septicemia

Pseudomonas aeruginosa Pneumonia, septicemia

M. Tuberculosis Pulmonary, miliary TB

C. Difficile Diarrhea, pseudomembranous colitis

Candida Thrush, systemic candidiasis

Cryptococcus neoformans Meningoencephalitis

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