We Are More Than Just Human

What does it mean?

We Are Superorganisms
Functions of Our Gut Microbiota
Bacterial Diversity Increases
During Our Lives
Lifestyle Affects Microbiota
Dysbiosis Causes and Diseases
Antibiotics and Microbiota
Fecal Transplants
An unconventional treatment - FMT

15
Germ Free Mice
Stefka, Feehley et al PNAS 2014, 111; 13145
 Obesity

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
V. Ridaura et al. Science. 2013.
Does the gut microbiota from healthy or CMA infants differ in
its ability to induce an innate, barrier protective response?

Healthy infant
microbiota Non-allergic
Cow’s milk
allergic (CMA) Sensitize with BLG/CT

infant microbiota

Allergic

Collaboration with Jack Gilbert, Argonne Naitonal Labs and Ecology & Evolution
To identify allergy protective bacterial populations scientists
selectively colonized germ free mice with representatives of
the numerically predominant taxa in the murine colon

2 Bacteroides
are enriched among the
transient bacteria
associated with digesta

1 Clostridia
are resident bacteria
associated with the
apical mucosa

A Clostridia containing
microbiota protects against
allergic responses to food

Nava & Stappenbeck 2011; Gut Microbes 2; 99

Anxiety and the Gut
MIcrobiome
 rRNA Gene Structure
 There are several genes that code for rRNA (7 in E.
coli)
 These genes are universally present in all bacteria
 They consist of regions conserved across species
and regions that are variable and can be used for
species identification.
 Design primers in conserved region
16S Sequence and bacterial
species identification
 The 16S rRNA gene sequence has been
determined for a large number of
strains. GenBank, the largest databank
of nucleotide sequences, has over 20
million deposited sequences, of which
over 90,000 are of 16S rRNA gene. This
means that there are many previously
deposited sequences against which to
compare the sequence of an unknown
strain.
How We Study…
Challenges to studying Microbial
Communities
Cultivable
(<20%)

Non-cultivable

Are there non-cultivation-based approaches to

study the enteric microbiome? 29
 16S Application to Uncultivable Bacteria

OTU. Operational Taxonomic Unit. OTUs are cluster of similar sequence variants of the 16S rDNA
marker gene sequence. Each of these cluster is intended to represent a taxonomic unit of a bacteria species or
genus depending on the sequence similarity threshold. Typically, OTU cluster are defined by a 97% identity
threshold of the 16S gene sequence variants at genus level. 98% or 99% identity is suggested for species
separation.
 Limitations to 16S Use
A.
Not amplified by 16S Primers. No
strain identification.

B.
No Information on genes other
than 16S. No info on variation or
abundance of gene pathways in
community.
 rRNA Gene Structure
 There are several genes that code for rRNA (7 in E.
coli) These genes are universally present in all
bacteria
 They have conserved, essential function and variable
regions unique to specific taxa.
Today’s Experiment

your samples

Primers match the conserved region

and amplify the variable region
Species Identification
 We are going to use this gene to identify
bacterial species
 Once we have our sequence we are
going to compare it against sequences
in “GenBank”
 GenBank is a repository of ALL the
sequences obtained in all the labs in the
world and is maintained by NCBI
16S Sequence and bacterial
species identification
 The 16S rRNA gene sequence has been
determined for a large number of
strains. GenBank, the largest databank
of nucleotide sequences, has over 20
million deposited sequences, of which
over 90,000 are of 16S rRNA gene. This
means that there are many previously
deposited sequences against which to
compare the sequence of an unknown
strain.
Species Identification
 We are going to use this gene to identify
bacterial species
 Once we have our sequence we are
going to compare it against sequences
in “GenBank”
 GenBank is a repository of ALL the
sequences obtained in all the labs in the
world and is maintained by NCBI
16S Sequence and bacterial
species identification
 The 16S rRNA gene sequence has been
determined for a large number of
strains. GenBank, the largest databank
of nucleotide sequences, has over 20
million deposited sequences, of which
over 90,000 are of 16S rRNA gene. This
means that there are many previously
deposited sequences against which to
compare the sequence of an unknown
strain.
 Limitations to 16S Use
A.
Not amplified by 16S Primers. No
strain identification.

B.
No Information on genes other
than 16S. No info on variation or
abundance of gene pathways in
community.