Normal Human Flora Lecture-08 PDF

Lecture-8 Normal Human Flora What is normal human microflora? – Interaction with microflora How to determine the composition of microflora? Role of normal microflora in human health Dr. Manish Kumar  Is your body mostly microbes? Actually,...

Lecture-8 Normal Human Flora What is normal human microflora? – Interaction with microflora How to determine the composition of microflora? Role of normal microflora in human health Dr. Manish Kumar  Is your body mostly microbes? Actually, we have no idea How one eccentric scientist’s estimate became the most famous “fact” about the microbiome? http://www.bostonglobe.com/ideas/2014/09/13/your-body-mostly-microbes- actually-have-idea/qlcoKot4wfUXecjeVaFKFN/story.html?event=event25  Terms Pathogen Non-pathogen (saprophyte) Opportunistic pathogen Virulence Infection – Clinical infection (disease) – Subclinical infection (carrier state, latent infection) predation, parasitism, commensalism, mutualism (symbiosis), competition, neutralism  Normal Flora protective function against pathogens recycle host material produce vitamins and other growth factors aid in digestion potential reservoir of infection contaminate in clinical samples stimulate development of immune system (lamina propria in GI tract) gnotobiotic animal: germ free animals or the microflora is known  Control of Normal Flora Environmental considerations in different regions (skin, GI tract, urinary tract, etc) Diet, gender, environmental exposure Non specific host defense mechanisms Host immune system Competition and interactions with other organisms  Culture Based Flora Region Characteristics Flora Skin and hair dry to moist, salts S. aureus, S. and fatty acids epidermidis, present, aerobic Micrococcus, P. with anaerobic acnes, microenvironments diptheroids, yeasts Conjunctivae moist, lysozyme S. epidermidis, present, mechanical diptheroids action of eyelids Nasophary dry to moist, hairs for filtering, S. aureus, S. ngeal mucus traps organisms epidermidis, region swallowed Streptococcus sp Mouth moist, aerobic to anaerobic, large variety of mechanical chewing, saliva, organisms e.g. mucus Streptococcus sp, Bacteroides, Veillonella, Porphyromonas, etc. Stomach stomach pH 2, organisms live in Lactobacillus, and small mucus, intestine buffered by Streptococcus, intestine bicarbonate, presence of bile Enterococcus, salts and digestive enzymes, yeasts, Veillonella, mucus and epithelial turnover, Enterobacteriaceae anaerobic Colon Anaerobic, similar similar to small to small intestine, intestine with more higher populations diversity and number of organisms Genitourinary tract voiding of urine, large variety of GAG layer, epithelial organisms at distal turnover, native flora end including in distal regions, Lactobacillus sp, sIgA, mucosa upper regions sterile Circulatory system flow, constant sterile except for exposure to immune brief periods of system transient bacteremia Nervous system histiocytes, tissue Sterile barrier against pathogen entry  Development of Flora Prior to birth, organism is sterile Microbial succession begins at birth Type of birth (C-section, vaginal), nursing, diet, home environment, physiology/genetics of individual all play a role Major changes in diet (solid food) Culture-based work – GI flora is stable Sequence-based work (different answer) Human Microbiome NIH Human Microbiome Project Launched in 2008, a five-year project, total budget of $115 million. To test how changes in the human microbiome are associated with human health or disease.  Microbial Forensics? Can bacteria be used to identify individuals? Fierer et al., Forensic identification using skin bacterial communities. PNAS 107: 6477-81, 2010 (Rob Knight lab, University of Colorado) Sequence-based information to see if computer users could be identified on basis of skin flora left on computer keys Match between bacterial communities on individual keyboards and the fingers of the owners of the keyboards. Fierer N et al. PNAS 2010;107:6477-6481 What type of microbes are present? PCR amplification using primers that binds to 16S rRNA Sequence and look for data base Limitation : some species are missed, not quantitative What are the clonal relationship among different isolates of same species restriction enzyme digestion profiling Limitation : do not provide taxonomic identification of community members What are the physiological potential of members of microbial population ? -Metagenomic analysis Isolate DNA, shear/ digest in to small fragments Clone and sequence Use data base comparisons Limitation : Major sequencing capacity is required Many are genes of unknown function Difficult to associate a particular gene with a particular microbe Strategies Used for Sequencing (Metagenomics)  Analysis of Metagenomic Data PLoS Computational Biology 6: e1000667, 2010  Normal Flora and Disease Reservoir of opportunistic infections (cause disease under special circumstances) Risk factors: 1. Alteration in numbers of normal flora 2. Translocation of normal flora 3. Weakened host defences due to trauma, stress or disease 4. Circumvention of host defences e.g. catheterization Disease Suspected microbe Gastric ulcers H. Pylori Gastric cancer (some cases) H. Pylori Peridontal disease Porphymonas gingivalis and other agents Atherosclerosis Chlamydophilia pneumoniae Low birth weight and preterm Bacterial vaginosis and babies microbiota shifts Cerebral palsy Placental infection Rheumatoid arthritis Intestinal anaerobic bacteria, B. burgdorferi (Lyme disease) Crohn’s disease Mycobacterium avium paratuberculosis, or shift of intestinal bacterial population How normal flora influence human health : C. difficile associated diarrhea Infected Antibiotics such as Clindamycin wipes out the normal flora and C. difficile takes over. Can be treated with Normal Metronidazole and Vancomycin 20% relapse rate. Restoration of normal flora by fecal implant.  How normal flora influence human health : A gut microbe that stops food allergies Clostridia keeps peanut allergy away Commensal bacteria protect against food allergen sensitization Andrew T. Stefka et al (2014) PNAS vol. 111 no. 36 pg.13145–13150  How normal flora influence human health : Oxalobacter and kidney stones Urinary oxalate in relation to O. formigenes in patients with recurrent CaOx kidney stones and control subjects* *Based on the average values of repeat 24-h urine collections in a subset of 139 case patients and 138 control subjects. Kaufman DW, Kelly JP, Curhan GC, et al. Oxalobacter formigenes May Reduce the Risk of Calcium Oxalate Kidney Stones. Journal of the American Society of Nephrology : JASN. 2008;19(6):1197-1203.  What about our gut feeling? Check these links for basics about normal flora https://www.youtube.com/watch?v=5DTrENdWvvM https://www.youtube.com/watch?v=EEZSuwkx7Ik