The Human MicrobiomeChristine Rodriguez, Ph.D.
Harvard Outreach 2012
Summer 2012 Workshop in Biology andMultimedia for High School Teachers
Microbes are all over ushttp://www.outreach.mcb.harvard.edu/Microbiome/download/Microbiome.pptx 11/4/16, 8=29 AM
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Thousands of different species on the skin aloneSome thrive on dry patches of the elbow, othersthrive in moist environment of armpit
There are millions of microbes persquare inch on your body
It is estimated that there are more microbes inyour intestine than there are human cells in yourbody!
What is the Human Microbiome?
Microbe: tiny living organism, such as bacterium,
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Summer 2012 Workshop in Biology andMultimedia for High School Teachers
fungus, protozoan, or virus
Microbiome: collectively all the microbes in thehuman body; a community of microbes
Biofilm: a community of microbes that livetogether on a surface
Microbes in the Human Microbiome include speciesfrom each major domain
“Extremophile”Archaebacteria
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Bacteria
Fungi
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What features distinguish themicrobial domains?
Generalizedbacteria andarchaebacteriacell
Bacteria• Have no nucleus or membrane bound organelles• Often sphere (cocci) or rod (bacillus) shape, but others as well
Archeabacteria• Have no nucleus or membrane bound organelles• Can look similar to bacteria or drastically different shapes,
such as flat and square• Have some metabolic similarities to eukaryotes
Eukaryotes• Have a true nucleus and membrane bound organelles
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Generalizedeukaryotic cell
• Wide variety of shapes. For this presentation, we will focus on fungi• Fungi are unique since they have a cell wall and form spores during
reproduction
Microbes are normally found in andon the human body
The following sites are “hotspots” for microbial life
Summer 2012 Workshop in Biology and
Let’sexplore
these fiveregions
Some microbes are native,normally found in the body
Some microbes areintroduced, suddenlyarriving at a new residence inthe body
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Multimedia for High School Teachershttp://nihroadmap.nih.gov/hmp/
Summer 2012 Workshop in Biology andMultimedia for High School Teachers
What’s Happeningin the Nose?
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There is a delicate balance of microbes that are maintained to keep that environment healthy.Weakened immune systems can throw off that balance and allow the wrong microbes togrow out of control.
Inflammationfrom viralinfection andallergic reactions
Inhaled medicinesand oral antibiotics
Cilia and mucouslining trap inhaledmicrobes
The nose is aprimary defenderagainst inhaledpathogens
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The interior lining of the nose contains mucous secreting glands. A wide variety ofmicrobes are normally found there. Here’s a few:
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Staphylococcus epidermidis bacteria forms a biofilm thatcoats the mucosal lining
Staphylococcus aureus bacteria is fine when kept undercontrol by a protease found in S. epidermidis, but if left togrow out of control, S. aureus can become pathogenic andcause infection
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Nose
Aspergillus fungal spores are often inhaled
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through the nose. If the immune systemfails to clear these, mold can grow in thelungs
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Corneybacterium accolens bacteria is rarely a pathogen,but if it enters the bloodstream due to a torn bloodvessel, it can cause serious infections
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What’s Happening inthe Oral Cavity?
A wide varietyof microbesregularly enterthe oral cavity saliva, pH,
Brushing and flossing teethclears some built up biofilm
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temperature, immunesystem prevent manyspecies from surviving
Oral antibioticsinhibit growth
Symbiosis of the oral microbes that are able to survive these conditions form an elaboratescaffold that lives on the tooth enamel and at the interface with the gums. It forms a barrierfor incoming bacteria.
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Oral CavityThe oral cavity has a wide variety of microbes normally found there. Here’s a few:
Streptococcus mitisbacteria typically forms a
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Fusobacterium sp.bacteria is a largerbacteria that helpsform a scaffold formany other bacteriain the oral biofilm
biofilm on the hardenamel surfaces of theteeth. If gums getinflamed, it can enter thebloodstream and causeinfection
Oral Cavity
Prevotella sp. bacteria have natural antibiotic resistancegenes. They can attach to epithelial cells or other bacteriaand cause larger infections in inflamed areas.
Candida albicans fungus can cause oral infection known asthrush
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What’s Happeningon the Skin?
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There are several skinenvironments: oily, dry,moist. Some microbesprefer one over another.
The skin has naturaldefenses includingslightly acidic sweat andantimicrobial peptides.
Microbes hide in crevicesto recolonize skin afterwashing with soap
Antibiotic washes andoral antibiotics disturbnormal balance ofmicrobes on the skin
There is a normal balance of microbes on the skin that protect introduced microbes fromharming us. Damaged skin gives opportunities for microbes to invade the bloodstream andcause serious illness.
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Skin
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• Propionibacterium acnes bacteria colonizes healthy pores, but if poresbecome clogged, it grows out of control
• Staphylococcus epidermidis bacteria normally colonizes on the skin. But whenP. acnes clogs pores, S. epidermidis also grows out of control in the infectedpores
• Staphylococcus aureus bacteria can also infect clogged pores like Staphepidermidis. Even worse, many antibiotic resistant strains of Staph aureusmake it difficult to treat the infection.
Skin
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Trichophyton and Microsporum fungi feast on keratin in the skinand cause ringworm fungal infections
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What’s Happeningin the Gut?
Major barriers for microbes entering the gut:• low pH• Saliva and Bile• Immune system
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• Finding a place to attach to intestinal wall• Surviving a widely varied diet
For those microbes that manage to colonize the gut:• gut flora perform regular tasks of digestion, vitamin production, many others• Gene transfer between the myriad of species in the gut can generate new
combinations of drug resistant “superbugs”
GutBacteroides thetaiotaomicronbacteria ferments simplecarbohydrates in the gut,releasing hydrogen and CO2.
+ carbohydrates
CO2 and H2
Methanobrevibacter smithiiCH4 Methane
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archeabacteria consumes hydrogengas from Bacteroides andproduces methane, which is lostfrom gut as “gas”
Gas
Gut
Ruminococcus sp. bacteria can be found in significantlyhigh numbers in the gut flora. They break down cellulosein the gut, helping with digestion.
Helicobacter pylori bacteria has a helical shape and colonizes thestomach and upper G.I. tract. It is known to be a major cause ofstomach ulcers, although many with H. pylori do not get ulcers.
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What’s Happening in theUrogenital Tract?
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Urinary system almoststerile due to urea andother chemicals
Urine often flushesout microbes that findtheir way in
Introducing a catheter intothe urethra can introducemicrobes directly into thebladder, where a biofilm cangrow and cause bladderinfection
The vagina has a low pH due to Lactobacillus secreting lactic acid and hydrogen peroxide.Let’s explore the microbiome of this region further.
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Urogenital
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Lactobacillus and vaginal epithelialcell
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Lactobacillusnormally maintainlow pH while otherspecies are kept insmall numbers inthe vagina If Lactobacillus
decreases fromantibiotics…
Candida albicanscan take over andcause a yeastinfection
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G. vaginalis and vaginal epithelialcell
Gardnerella vaginaliscan grow too muchand cause bacterialvaginosis.
Urogenital
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The urinary tract is normally sterile due to urine flushing out the tract.
But, Escherichia coli from GI tract can infect urinary tract due to poor hygieneand contamination from nearby GI tract opening.
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Urine sample infected with E.coli
Urine sample infected with E.coli
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Interplay Between Medicine and Microbes
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Antibiotics
Kills infectious bacteria but also disruptsnatural flora. Can result in yeastinfections, digestive problems, etc.
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Chemotherapy drugs
Gut flora has been shown to modify somedrugs during metabolism. This causesmany side effects, including upsetstomach.
Use of Antimicrobial ProductsHow many do we really need?
But do we need someWill this allow “superbugs”that can barely survive these
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Products kill germsto reduce infection
natural exposure togerms to keep ournormal flora around?
treatments to grow andbecome more prevalent…causing problems for thefuture?
Is My Gut Microbiome theSame as Yours?
The number and amountof the many differentmicrobes can varygreatly from person toperson.
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Summer 2012 Workshop in Biology andMultimedia for High School Teachers
Relative amounts of species
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The Microbiome of one personcan be different than others inspecies and relative amounts
Research in the Human MicrobiomeProject is starting to identify the relativeamount of each microbe present atdifferent locations in the body.
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So many new questions to answerabout the Human Microbiome…
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How does the gut floramodify drugs, andhow can we minimizeside effects?
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Why does my gut flora lookdifferent than yours? Howdoes that affect obesity,food allergies, and ability tofight disease?
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Are we making germs moreresistant to anitmicrobials?What happens when thegerms are resistant to all ofthe drugs in our arsenal?
What do you want toknow?
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