Human Microbiome journal clubMarch 17th 2011

Jennifer StearnsPostdoctoral fellow

Farncombe Family Digestive Health Research InstituteMcMaster University

A second primer talk

• Current work• Favourite talks• Things to consider

Currently…

• A large emphasis on culture-independent studies – especially metagenomics

• A focus on optimizing protocols and ferreting-out both trends and sources of error

• Large-scale sample collection

• Sequencing• 454, Illumina,

IonTorrent• Phylochips• Culturing• Microfluidic• Bioreactor

Many body sites have been targeted

• Obesity• IBD• CF• Diabetes• Age• Diet • Newborns• Pregnancy • Vaccines• Nationality• Probiotics• Longitudinal studies (stable or

variable over time?)• Viriome

Skin

Airways

Oral cavity

VaginaForeskin

Heart plaqueGI tract

Distal colon/stool

Models in mice

• Germ-free• Humanized – fecal

transplant, transgenic, etc…• Can do more complete

longitudinal studies• Long-term effects of

antibiotics• Colonizaiton resistance• Normal variation in the

system• Variables are far easier to

control

Types of data

• 16S rRNA – for community studies• Whole sample shotgun sequence – for metagenomic studies• WGS of host – for correlation of host genetic factors to

differences in the microbiome• Reference genomes – of cultured organisms and single cells• RNA sequencing and PCR – for microbial gene expression

within a sample• Metabolic studies – to measure function of the bacterial

community

Reference genomes

• Sequencing complete genomes for both environmental and human associated strains

• Can be used as a framework for assembly of metagenomic sequences

• Used to study LGTThe Human Microbiome Jumpstart Reference Strains Consortium

Science 2010;328:994-999

What to do with all the data

http://hmjournalclub.wordpress.com/tips-tricks-tools-and-resources

Things to consider

• In terms of 16S rRNA sequencing, there is considerable variability between people• This is not surprising considering the variables involved

(i.e. genetics, lifestyle, diet, health…)• A the functional level the microbiome seems to have

core functions but even here there are few studies that see clear trends or “smoking guns”

Often no obvious trends – why?

• Analysis of the HMP data• 16 body sites on 103 individuals… no core microbiome

at the “species” level yet there is a functional core, but there is enzyme diversity at each functional pathway

• MetaHit – similar results• Still sifting through the data• Still developing tools and standards• No quantitative DNA isolation• Inability to remove environmental DNA

Things to consider

It is estimated that there are millions of microbial species on the planet, relatively few of which have been isolated in culture. Despite the recognized importance of microorganisms, we still know little about the magnitude and variability of microbial biodiversity in natural environments relative to what is known about plants and animals. This is a major knowledge gap, given that microbes are critical components of our planet, responsible for key ecosystems services including the production of agriculturally critical small molecules, the degradation of environmental contaminants, and the regulation of human host phenotypes.

Sharpton et al., 2001 PLOS Comp. Biol. 7(1): e1001061

Things to consider

• With large differences it’s easy to see trends• The question becomes: why use high throughput

sequencing when another method might be just as informative?

• Variation is often subtle, this creates a few situations:• Are the differences due to real biological effects/causes?• How much variation is introduced by your sampling,

sequencing and analysis methods?

Lessons?

• We should have clear questions that we want to answer with our microbiome studies

• Good experimental design to increase chances of getting answers

• Much of the data analysis relies on databases populated with reliable reference material from studies of the organisms and enzymes themselves

Thank you for your interestPlease sign up to present a paper

Visit the blog at hmjournalclub.wordpress.com

Dennis Kunkel