The Microbiome and Epigenetics:

Meredith A.J. Hullar, PhD

Division of Public Health Sciences

Fred Hutchinson Cancer Research Center, Seattle WA

We Are Not Alone

Epigenetics and The Microbiome Outline

• In bacteria

DNA methylation

• Between the host and microbiome

DNA methylation

ncRNAs - miRNAs

Microbial metabolites of diet

• Obesity and the microbiome

Epigenetics within the Microbiome DNA methylation

• Humans

N5 methyl cytosine

CpG sequence

• All three types of

methylation

N6 methyl adenine

N5 and N4 methyl cytosine

• DNA methyltransferase

(MTases)

S-adenosyl-L-methionine

(AdoMet)

Epigenetics within the Microbiome DNA methylation

Protect against phage

Restriction Modification System

MTase-methyl transferase

REase-

cuts DNA at internal

phosphodiester bond

Recognition sequence is

unmethylated-4-6 bp

palindrome

Epigenetics within the Microbiome Restriction/Modification

• Recognizes foreign DNA

• Phage escapes and infects

cell progeny has the same

methylation pattern

• Diversification of R/M

systems

Korlach and Turner, 2012, Curr Op inStruct Biol.

Epigenetics within the Microbiome Restriction/Modification

Broadly distributed

2000 RM systems

~43K RM enzymes

3600 isolates (http://REBASE.neb.com/ REBASE/REBASE.html)

Epigenetics within the Microbiome DNA mismatch repair

• New functions

• DNA mismatch repair (dam)

E. coli DNA adenine methylase (dam)

Methylated mark-

Epigenetics within the Microbiome Methylome

Methylation changes gene expression

RM systems

Phage infectivity

Genomic Stability

DNA replication

Stress Response

SOS

Growth and Metabolism

Culturability

Virulence

Host association

Chen et al 2013, TIM

Epigenetics within the Microbiome Methylome

• H. Pylori 26695 and J99-R3

• Differences in R-M systems

and methylation (Krebes, J et al, 2014,

NAR)

• Two strains of B. dorei (Leonard et al, Front. Microb., 2014)

• H. pylori-reduces natural

transformations

• Functional adaptation to

different environments???

Epigenetics between the Host/Microbiome

Upon exposure to infection or microbiome:

Host response

DNA Methylation

ncRNA- microRNA

Microbial metabolites of diet

Epigenetics between the Host/Microbiome DNA methylation: Gut Homeostasis

TLR4-innate immunity

DNA methylation of TLR4

in IECs in-vitro and in-vivo (Takahashi K et al., 2009, J. Immunol.)

> methylation <expression

GF vs Conv mice TLR4 gene methylation in colon (Takahashi K et al., 2011)

TLR2 (Kellermayer, R. et al., 2011, JBC)

Epigenetics between the Host/Microbiome microRNA: Infection

Pathogens affect microRNA profile

(Maudet et al., 2014, FEBS Lett.)

Epigenetics between the Host/Microbiome microRNA :Infection

• Microbiome altered response of

host to infection

• Infect GF or conventionalized

mice (Archambaud et al., 2013, Mbio.)

• 6 miRNAs

• Interplay between host and

microbiome

Epigenetics between the Host/Microbiome Gut Microbial Metabolism

• Unique anaerobic environment

• Colonic fermentation

• Influence host epigenetics Butyrate

Propionate

Long chain 3 w polyunsat. fa

Isothiocyanates

Epigallocatchin-3-gallate (EGCG)

Ellagitannins->Urolithans

Ursodeoxycholate

(Hullar and Fu, 2015, Canc. J.)

Epigenetics between the Host/Microbiome Butyrate

Acetyl CoA 5-35% (100%)

Glutarate 1-3% (100%)

Lysine 5-10% (80%)

Succinate 1-3% (60%)

Vital, M. et al., 2013, Microbiome

BLOOD

Gram-negative

bacteria

SKELETAL

MUSCLE ↑ SCFA

Microbial

Community

LIVER

Fatty acid

oxidation

Adipogenesis

SCFA

Lipogenesis Satiety PYY

GUT LUMEN

Epigenetics between the Host/Microbiome

Fatty acid metabolism

(Fiaf-lipoprotein lipase

inib)

Satiety signal

Gpr43

Histone deacetylation

(hdac3, hadac5)

Fatty acid storage (Ppar

gamma)

Epigenetics between the Host/Microbiome SCFA influences gene expression

Lukovac et al 2014, Mbio.

Summary of Microbiome and Epigenetics

• Burgeoning area of the role of methylation in control

of gene expression within the microbiome and

between host/microbiome

• Microbial metabolism of diet and epigenetics is an

under-explored area at the interface of

microbiome/host

• Prospective studies

Relationship of Diet to Obesity

Energy

imbalance Diet Fuel

availability

>Lipids

>Adipocytes

>Macrophage

>Inflammation

Gut bacteria

Gut Bacteria Influence Metabolism of Diet Obesity-associated Bacterial Genes Are Enriched in

Carbohydrate

Metabolism and Fatty Acid Biosynthesis

Depleted Bacterial chemotaxis

Bacterial motility proteins

Benzoate degradation via CoA ligation

Butanoate metabolism

Citrate cycle (TCA cycle)

Glycosaminoglycan degradation

Other enzymes

Oxidative phosphorylation

Pyruvate/Oxoglutarate oxidoreductases

Starch and sucrose metabolism

Tryptophan metabolism

Enriched Fatty acid biosynthesis

Nicotinate and nicotinamide metabolism

Other ion-coupled transporters

Other transporters

Pentose and glucuronate interconversions

Phosphotransferase system (PTS)

Protein folding and associated processing

Signal transduction mechanisms

Transcription factors

(Turnbaugh, J. et al., 2008, Nature,457:480)

Characterizing the Gut Microbiome:

Bacteroides

Pyramidobacter

Axis 2

Prevotella

P<0.01

P<0.001

Axis 1 (37%)

(30%) Is the microbiome

associated with obesity?

•Cross-sectional study

• Women 40-45 yrs

• No antibiotic use

• Fecal sample

n=107/205

• Adiposity by DEXA

•16S rRNA genes

(Hullar and Lampe, unpubl)

Obesity, Fat Distribution, and Disease Risk

• Health risks due to obesity vary on the type and location of

adipose tissue (Cummings and Schwartz, 2003, Ann. Rev. Med; Cleary and Grossman, 2009,

Endocrinology)

• Ethnic/racial differences in BMI-cancer association linked to

differences in the distribution of adiposity (Conroy, SM. et al. 2011, Breast

Cancer Res Treat ; Lim, U. et al., 2012,Int. J. Cancer)

• Predictors of adiposity

Exposome

Genetic variation

Metabolomics

Microbiome P01 CA168530-01 (LeMarchand)

Supported by: US National Cancer Institute

National Institute of Health

Avon Pilot Project Fund

Kellogg Corporate Citizens Fund

FHCRC

FHCRC

Johanna Lampe, PhD

Fei Li, PhD

Tim Randolph, PhD

Wade Copeland,MS

Keith Curtis, MS

Orsalem Kashai, MS

Wendy Thomas

Elizabeth Traylor

Crystal Bartow

University of Washington

Huei-Hun (Elizabeth) Tseng, PhD

Karlyn Beer, PhD

Sam Lancaster, PhD

University of Bristol

Charlotte Atkinson, PhD