Modeling the Dynamic Digestive System

Microbiome

Anne M. Estes, PhDInstitute for Genome Science, University of Maryland, School of Medicine

Blogger: www.mostlymicrobes.com

Baltimore, MD

• What is a microbiome?• Where do these microbes live?• Which microbes live where?• What is the function of the microbiome?• How stable is the microbiome?

Human microbiome

What is a microbiome?• The microbial communities of an environment.

• Bacteria • Viruses • Fungi• Archaea • Single-celled

eukaryotes

• Humans and other animals

• Plants• Soil

• Beneficial, Commensal, or Pathogenic

Human Microbiome

Human?

• Biomes – specific conditions (temperature, moisture) and characteristic organisms

You are a planet with different ecosystems!

• 3-10 times more microbial cells than human cells• Unique for every person

– Environmentally acquired each generation– “microbial signature”

• Microbes influence our– genetic diversity – normal physiology– health state

Another organ

• 3 - 10 times more bacterial cells ~10% of dry weight ~ 4.5 lbs• 2-5 elephants worth of weight in a lifetime• Important for digestion, defense, immunity,

mood, …???

Plate Count Anomaly• More cells observed than cultured• Only 1% are culturable• Molecular methods

– 16S rRNA

16S rRNA taxonomy • 1,542 bp gene • Encodes small ribosomal subunit• Essential for translation • Highly conserved • Several variable regions • Taxonomically informative• Compare to reference database

Human Microbiome Project 2007-2015• Is there a “core” human microbiome?• Are changes in the human

microbiome correlated with health changes/disease?

• What happens when the microbiome is disrupted daily? Periodically?

• Studies of 242 healthy individuals– 15 male and 18 female body sites

• Human genome – 23,000 protein coding genes

• Microbiome – 3.3 – 8 million genes (Qin 2010 10.1038/nature08821;MHPC 2012, doi:10.1038/nature11234)

– 350 times more microbial genes than human– Bacteria can exchange genes to gain functions

• Metabolome • sum metabolic capabilities

• Holobiont– Can acquire novel traits

Another genome and metabolome

Human Microbiome

• What is a microbiome?• Where do these microbes live?• Do different sites host different microbes?• What is the function of the microbiome?• How stable is the microbiome?

Where do these microbes live?• Different environments for different bacteria• Abiotic factors:

– oxygen - moisture – pH - nutrients

• Biotic factors:– host immunology – microbial interactions

Dunn Lab NCSU

The human as an ecosystem• Ecological principles• Selection• Niche filling• Succession• Disturbance events

– Cyclic (diurnal, seasonal)– Catastrophic

Human Microbiome

• What is a microbiome?• Where do these microbes live?• Do different sites host different microbes?• What is the function of the microbiome?• How stable is the microbiome?

Do different sites host different microbes?• Taxa differ between some sites

Huttenhower et al. 2012; doi:10.1038/nature11234

• Different environments results in different taxa– Variation of moisture, pH, nutrients,

presence of other microbes

Do different sites host different microbes?

• Different environments Different taxa– Variation of moisture, pH, nutrients, presence of other

microbes

Digestive system microbiome• Best studied• Extremely diverse• Extremely dense

– 107 to 108 cells per ml• Some culturable members• Experimental work with gnotobiotic mice• Digestion: food and drugs• Microbiome varies with diet, lifestyle, and host

environment• Site of dysbiosis

The human as an ecosystem• Ecological principles• Selection• Niche filling• Succession• Disturbance events

– Cyclic (diurnal, seasonal)– Catastrophic

Human Microbiome

• What is a microbiome?• Where do these microbes live?• Do different sites host different microbes?• What is the function of the microbiome?• How stable is the microbiome?

What is the function of the microbiome

• Trains the immune system • Fills niches to keep out pathogens• Digests food• Synthesizes vitamins• Detoxifies poisons/ metabolizes drugs• Polyphenols degraded to antioxidants• ???

Bacterial Products Mediating Inflamation• Butyrate

– Energy for cells from starch• Acetate

– Binds to G-protein coupled receptor on immune cells to reduce inflammation

– Protects against pathogenic E. coli

• Propionic acid– Acts on T cells to activate

adaptive immune response• Polyphenols

– Metabolized into urolithin, ellagic acid, equol, etc…

Human Microbiome

• What is a microbiome?• Where do these microbes live?• Do different sites host different microbes?• What is the function of the microbiome?• How stable is the microbiome?

The human as an ecosystem• Ecological principles• Selection• Niche filling• Succession• Disturbance events

– Cyclic (diurnal, seasonal)– Catastrophic

Stability?: Transition to solid food

• With table foods, Bacteroidetes increased• More similar to adult microbiome• Adult microbiome influenced by diet

Koenig et al 2011 PNAS doi:10.1073/pnas.1000081107

Peas and formula introduced

Relative Stability over Time in Gut

• 37 healthy adults– Sampled 2-13 times, 296 weeks apart– 195 + 48 strains found – 60% of strains remaining during 5 years– Bacteroidetes and Actinobacteria most stable– Strains were maintained within family units, but not

unrelated people– Early gut colonizers most stable

Faith,2013;10.1126/science.1237439

The human as an Ecosystem• Ecological principles• Niche filling• Succession• Disturbance events

– Cyclic (diurnal, seasonal)– Catastrophic

Disturbance: Diet shift• Drastic short-term diet shifts changes microbiome

community structure.• Meat and cheese

– Increase in bile-tolerant microbes that can trigger inflammatory bowel disease

– Allstipes, Biophila, Bacteroides• Vegetarian

– Increase in plant polysaccharide degraders– Firmicutes:

• Roseburia, Eubacterium rectale, Ruminococcus bromii– Prevotella

• Bacteria acquired from food were transientDavid et al. 2013;doi:10.1038/nature12820

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• Shift in bacterial taxa • Open habitat• Resistant taxa increase• Opportunistic pathogens in low

abundance in healthy humans

Disturbance: Digestive system distress• Chronic digestive system disorders

– Inflammatory bowel disease – Crohn’s disease– Ulcerative colitis– Clostridium difficile infections

• Microbiome profile different from healthy people

• Chronic diarrhea• Often begins after antibiotic use for an unrelated

issue (pneumonia, surgery, etc..)

Song Y, et al. 2013;10.1371/journal.pone.0081330

Disturbance: C. difficile case study• Symptoms

– 61 year old woman– Chronic diarrhea every 15 minutes for 8 months – Antibiotics for back surgery– Confined to wheelchair– Repeated cycles of antibiotics, symptom remission,

then resurgence– Clostridium difficile found in stool

• Culture and 16S rRNA – Presence of cytotoxins A and B

Khoruts et al. 2010; 10.1097/MCG.0b013e3181c87e02

Disturbance: C. difficile case study• C. difficile associated

diarrhea – 20% of cases recur post-

antibiotics– Spores in intestine regrow– Produces endotoxins A & B– C. difficile dominant

microbiome member

Modeling the microbiome• Examine your “digestive system microbiome”

Meat Feeding Plant Feeding

Environmental bacteria

Dairy Feeding

• What do you feed on?• What kind of diversity do you have?

Bacteria Typical of:

• You get a nasty cut that gets infected and take a broad spectrum antibiotic. Remove

• Examine your microbiome. – How does the diversity compare to previous diversity?– How full is your gut habitat? Is there room for

colonizers?

Modeling the microbiome: Disturbance

• This disturbance event opens habitat for opportunistic pathogens from the environment.

Add a random handful of beans

• Examine your microbiome for lentils.– C. difficile without toxins– C. difficile with toxins

• Do you get C. difficile associated diarrhea?

Modeling the microbiome: Dysbiosis?

C. difficile treatment

1. Metronidazole 2. Oral vancomycin

alone 3. Oral vancomycin

alone with i.v. metronidazole

Rebuild microbime: Fecal Microbiome Transplant

• First record: 4th century, China – Treatment for food poisoning or severe diarrhea

• In U.S. in 1958 Eisenman et al. used for colitis patients

• Goal: reestablish microbiome using the healthy microbiome from another individual

• No set protocols

• Different methods– duodenal infusion– colonoscopy– enema– oral capsules

• Stool donor– Often relative or spouse– Screened stool and blood for:

• known pathogens• chronic conditions (metabolic syndrome, autoimmune disorders,

digestive problems)

MacConnachie et al. 2009; 10.1093/qjmed/hcp118

Rebuild microbime: Fecal Microbiome Transplant

• Doctor suggests Fecal Microbiota Transplantation (FMT)/ Fecal bacteriotherapy

• Results– 2 days - first solid stool in 8 months– 1 month - negative for C. difficile

Disturbance: C. difficile case study

Borody, T. J. & Khoruts, A. 2011; 10.1038/nrgastro.2011.244

Randomized study• 1st randomized controlled trial

for C. difficile• Fecal transplant more

successful than antibiotic• Patient microbiome diversity

similar to donors• The composition of the diversity

not reported

Van Nood et al 2013; 10.1056/NEJMoa1205037

Regulation of FMT• Also successful for ulcerative colitis,

Crohn’s disease, and inflammatory bowel disease

• FDA Regulation of FMT• 2013 feces a “biologic drug”

• “Investigational New Drug” permit• 6 months later “enforcement discretion”• 2014 seeking public comment

• “Stool banks” – MIT – OpenBiome

• Do you get C. difficile associated diarrhea? • How do you recover from your C. diff infection?

• Antibiotics fail and your doctor recommends a fecal transplant. – Who is your source?– Why?

Modeling the microbiome: Dysbiosis?

Lozupone, et al. 2012;10.1038/nature11550

Human Microbiome• You are a bacterial ecosystem• More bacterial cells and genes than human• Microbes are essential for human health• The microbiome is dynamic • Microbiome community influenced by:

– Diet– Antibiotic use