Microbiome Lecture Slides PDF

Human Microbiome!!!!!  WHY DO WE CARE? HUMAN MICROBIOME  It’s estimated we have over 100 trillion bacteria in, & on us, outnumbering the number of our cells  Bacterial genes account for more than 100x the human genome  The microbiome may weigh as much as 5 lbs!  Gut microbiome:  Hel...

Human Microbiome!!!!!  WHY DO WE CARE? HUMAN MICROBIOME  It’s estimated we have over 100 trillion bacteria in, & on us, outnumbering the number of our cells  Bacterial genes account for more than 100x the human genome  The microbiome may weigh as much as 5 lbs!  Gut microbiome:  Helps digest food  Helps regulate immune system  Protect against disease causing bacteria  Produce vitamins B12, thiamine & riboflavin, & vitamin K (blood coagulation)  Gut-brain axis  ~10 QUINTILLION virus particles on the planet!!! They outnumber bacteria 10-1 in most ecosystems!!!! The Virome  CLASS OBJECTIVES  Define vocab words & use them appropriately  Identify the normal microbiota and where it colonizes  Define opportunistic vs. strict pathogens (DITKI)  List examples of the role of the normal microbiota (“flora”)  Understand what happens during dysbiosis and the consequences of  Compare & contrast probiotic & prebiotic  Define tissue tropism & identify what is required for it  Learn the 6 steps required for the establishment of infectious diseases  Be able to apply some of today’s material to clinical settings Vocab words  THE MICROBIOTA  Core Microbiome- Species that are present at a specific site in 95% or more of individuals  With some transient e.g., Streptococcus pneumoniae- not a large component of normal microbiome, but present during certain infections  Colonization required  Secondary microbiome- small numbers of many species that may not be widely shared by individuals  Taxonomic diversity of a population is great, but the functional properties are highly conserved (functional redundancy) in microbiomes associated with health  “Normal” flora depends on pathogenicity & virulence & host response  Usually a mutualistic relationship  NORMAL MICROBIOTA Common Locations:  Skin: moist areas especially, such as the groin and between the toes  Respiratory tract: nose and oropharynx  Digestive tract: mouth and large intestine  Urinary tract: anterior parts of the urethra  Genital system: vagina Less common locations:  Rest of respiratory & digestive tract  Urinary bladder  Uterus Diagnostically Significant Locations:  Blood  Cerebrospinal Fluid (CSF)  Synovial fluid  Deep tissues  ROLE OF NORMAL FLORA 1. Keeping out invaders (aka “dibs”)  Can inhibit newcomers with bacteriocins 2. Role in human nutrition & metabolism?  Synthesize Vitamin K & B vitamins 3. Good & bad conversion of ingested compounds  Bacteria can make carcinogenic heterocyclic amines (cooked meat) less toxic  Cyclamate (artificial sweetener) is converted to carcinogen cycohexamine by bacterial sulfatases ROLE OF NORMAL MICROBIOTA 4. Immune stimulation  Normal microbiota can stimulate antibodies (like immunoglobulin A aka IgA)  Can provide their own “immunity” (nude mice & bacteroides) 5. Common source of infection  If a normal microbiota ends up in a place they’re not supposed to be  i.e. E.coli from GI tract causing UTI  FREQUENT TYPES OF NORMAL BACTERIAL MICROBIOTA  Effect of antibiotics on gut microbiota. Fecal samples were collected from 4 patients treated with antibiotics:  Patient A, moxifloxacin  Patient B, penicillin + clindamycin  Patient C, cefazolin followed by ampicillin/sulbactam  Patient D, amoxicillin  Fecal samples collected before, during (e.g., 3_D is day 3 of therapy), & after therapy were used to assess total microbiota. Changes are noted both during therapy & after therapy is discontinued.  A, Total microbiota (16S rRNA gene)  B, Metabolically active microbiota (16S rRNA transcripts)  WHAT HAPPENS WHEN THE NORMAL MICROFLORA IS DISRUPTED? Dysbiosis!  Linked to:  Anxiety, depression, schizophrenia (~90% of serotonin made in the digestive tract)  Obesity (twin studies- obese twins have lower bacterial diversity & higher levels of enzymes)  Type 1 diabetes- less diverse gut microbiome  Celiac disease (not every patient with the genetic predisposition develop  Etc. DID YOU KNOW… 1/3 OF YOUR FECES IS BACTERIA?! PROBIOTIC VS. PREBIOTIC  Prebiotic- Food ingredient that supports the growth of one of more members of the microbiota  Come from types of carbs (mostly fiber) that humans can’t digest  Beneficial bacteria in your gut eat this fiber  Probiotic- live organism that, when ingested, is believed to provide benefit to the host  Commonly gram-positive bacteria (e.g., Bifidobacterium, Lactobacillus ) & yeasts (e.g., Saccharomyces )  Found in ingestible capsules & as food supplements (e.g., yogurt, kefir, kombucha) TEST YOUR KNOWLEDGE #1  What is a role of the normal microbiota?  Keeping out invaders  Role in human nutrition & metabolism  Conversion of ingested compounds (good AND bad)  Immune stimulation  Common source of infection TISSUE TROPISM OF INFECTIOUS AGENTS  Tissue Tropism= site preferences  Hepatitis viruses=liver, cholera bacillus=small intestine  HIV=any site, Staphylococcus=any site  Tissue tropism affected by 1. Site of entry  e.g., Gonococcus  Pharyngeal gonorrhea  Opthalmia  Gonococcal arthritis 2. Affinity for host receptors (i.e. ACE2 with SARS-CoV-2 virus spike protein) 3. Temperature of organ (i.e. outside of feet cooler than internal organs = athlete’s feet fungal infection) BACTERIAL COLONIZATION  Must resist host defenses  Must compete successfully with other microbial species  Take advantage of host features like fibronectin on epithelial cells  Fibronectin has high preference for Gram+  In poor health/hospitalization, decrease fibronectin=increase Gram- infection (like Gram- pneumonia) Table 2-1 MMD  ESTABLISHMENT OF INFECTIOUS DISEASES 1. Encounter: The agent meets the host 2. Entry: The agent enters the host 3. Spread: The agent spreads from the site of entry 4. Multiplication: The agent multiplies in the host 5. Damage: The agent, the host response, or both cause tissue damage 6. Outcome: The agent or the host wins out, or they learn to coexist **each of these events requires breach of host defenses  1. ENCOUNTER  Fetus is mostly sterile environment (some pathogens can cross placenta “congenital infections” – HIV, CMV, rubella)  First encounter at parturition Exo (aka birth), prepared with mother’s antibodies via blood Exo & colostrum Exo  Exogenously vs. Endogenously Acquired Diseases Endo  Exo=external Exo environment/others  Endo= agents already in or on body 2. ENTRY  Ingress of microorganisms into body cavities from outside environment  Inhalation- cholera, whooping cough, Covid  Ingestion- cholera, traveler’s diarrhea, food-poisoning  Penetration of microorganisms into deeper tissue after crossing epithelial barrier  Insect bites- malaria, plague, African sleeping sickness, Chagas disease, elephantiasis  Cuts & wounds- staph infections (MRSA), subacute bacterial endocarditis (strep viridans)  Depends on inoculum size & number of invading organisms  Organ transplants & blood transfusions- HIV, HBV, Creutzfeldt-Jacob disease  “Burrowing” of hook worms  3. SPREAD  Lateral propagation- travel to contiguous tissue (e.g. infected papercut on your finger that spreads to your hand)  Dissemination- travel to distant sites (e.g. via blood or CSF)  Things that affect spread:  Anatomical Factors  e.g. bacterial abscess in lung, if it ruptures inwards bronchial tree affected (pneumonia), if it ruptures outward into pleural cavity (pleurisy)  Fluid dynamics e.g. spread in fluids like blood, CSF, synovial fluid, lymph, etc.  4. MULTIPLICATION  # of microorganisms present must >threshold  Incubation period- time needed for infectious agents to overcome host’s early defenses  Environmental factors affect multiplication- i.e. temp, pH, osmotic pressure  Must evade host defenses:  Constitutive defenses  ComplEment  Phagocytosis  Induced defenses  Humoral immunity  Cellular immunity 5. DAMAGE  Type & intensity of damage depends on the tissues & organs affected  Not always caused directly by pathogen, but as a consequence of host immune response i.e. cytokine storm  Direct tissue damage usually caused by toxins (i.e. botulinum), cell death  Endotoxin (remember “LPS” for later) damage depends on amount.  Little=fever, Lot=shock & intravascular coagulation  6. OUTCOME  Depends on what happens at all of the above stages  Think of a bad paper cut:  Was there an endogenous encounter?  Did the pathogen gain entry via the cut?  Did the pathogen spread to contiguous or distant tissue?  Did the pathogen multiply?  Did the pathogen cause damage?  * Did the pathogen subvert normal immune responses at every step?* =Infectious Disease TEST YOUR KNOWLEDGE #2  What are the six things needed for establishing a viral infection? 1. Encounter 2. Entry 3. Spread 4. Multiplication 5. Damage 6. Outcome TEST YOUR KNOWLEDGE #3  A 22-year-old female patient presents to your gynecologist office for her annual physical. She confides in you that she recently had unprotected sex with a person she met on (insert whatever hip dating site exists now). After reminding her of the dangers of unprotected sex, you take some vaginal and blood samples to test for various sexually transmitted infections. Her vaginal culture comes back positive for a large quantity of N. gonorrhoeae, however she isn’t reporting any symptoms like abdominal pain, foul smelling vaginal discharge or fever.  At what stage of the establishment of infectious disease would you suspect your patient is currently in?  ALSO A SCIENTIST Elisabeth Bik, PhD - Utrecht University for undergrad & PhD (Netherlands(  PhD worked on developing vaccines for new class of Vibrio cholerae causing epidemics in Bangladesh & India  Moved to Stanford & studied how the human oral microbiota is distinct from the gut microbiota https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2941673/  Studied dolphin microbiome & its distinction from other mammals & sea dependent  uBiome where she sequenced human microbiomes  Started “Microbiome Digest” a blog on daily microbiome research &  Scientific Integrity: has identified over 400 published papers with figure manipulation  Follow her on TWITTER: @MicrobiomDigest (for fun bio games)