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Microbiome 101: Understanding the human gut
Andres Gomez, PhD
Assistant Professor
Department of Animal Science
Department of Food Science and Nutrition
1
2 http://www.nationalgeographic.com/contributors/o/photographer-martin-oeggerli/
3 Photo: Andres Gomez
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Microbiome Research: At the interface of genomics, nutrition and ecology
Ecosystem
Change
Phenotype?
(Physiology) 4
• Microbial Composition/function?
A B
C D
Ecosystem 1
A B
C D
Ecosystem 2
• Meta-OMICS: metagenOMICS,
metabolOMICS, transcriptOMICS
•
• Bioinformatics
• Data mining
The human gut microbiome
5 Singh et al., 2017
Cellulose-Hemicellulose-Lignin-Pectin
Colon lumen
Colonocyte
Blood
Short chain fatty acids
Acetate
Propionate Butyrate CO2-H2
Nutrient processing and immune regulation by
the gut microbiome
Blood
Fibrobacter Prevotella
Butyrivibrio
Bacteroides
Bacteroides
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NFkB Il-1 IL-6 TNF-α
Enterocyte
Blood
• Diet • Disease • Antibiotics
Colon lumen
Nutrient processing and Immune regulation by
the gut microbiome
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Gut Microbiome-Associated(?) Ecosystem(host) “phenotypes”
Obesity Autism
Psychological
stress
Malnutrition
Neurological
disorders
Cancer
Cardio-vascular
disease
Pre-term birth
Diabetes
Metabolic
disorders
Auto-immune
disease Cystic
Fibrosis HIV
Behavior
Health Disease
8
The Microbiome boom
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What factors shape the human gut microbiome?
Host genotype
Environment/Diet
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Host genotype
Factors shaping the human gut microbiome?
Environment/Diet
11 Diet-genes-microbes in evolutionary context?
Non-human primates: Diet-genes-microbes in evolutionary context
Closest extant relatives
Primate ancestor
Diet as a driver of
primate ecology and
evolution Evolutionary
baseline of
host-microbe
interactions ~>65 Mya
Present
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Diet was likely a major factor driving primate diversification
Taken from: Diet and Primate Evolution Katharine Milton, Scientific American. August,1993
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14 Milton, 1999
Diet was likely a major factor driving primate diversification
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Studying gorilla guts to understand human microbiomes
Photo: Andres Gomez
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Gorillas are our closest extant relatives after chimpanzees
A Scally et al. Nature 483, 169-175 (2012)
6 Mya
10 Mya
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Lowland gorilla diets are highly fibrous
San Diego Zoo Photo: Andres Gomez
Nutrient Mean % year
Fat 0.5%
Protein 11.8%
Sugars 7.7%
Fiber (ADF-NDF) 70%
Tannins 10%
Popovich et al., 1997
Masi, 2008, Remis et al, 2001
% Time
(Feeding scans)
Leaves Ripe Fruit Terrestrial herbs
80%
0%
Dry Wet Dry
Western lowland gorillas experience drastic changes in resource availability
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Western lowland gorillas at the Dzanga-Sangha protected areas- Central African Republic
*
Le zonage du complexe
des Aires Protégées Dzanga Sangha
Légende
!( Villages
#* Campemets de Recherche
#* Campements de Gardes
Routes principales
Pistes forestières
Rivière Sangha
Réserve Spéciale de Dzanga Sangha
Zone de Chasse Communautaire
Pré-Parc
Secteurs de Parc National
Frontière internationale
0 10 205 Kilomètres
Projection: UTM 33
Système géodésique: WGS 84
1 : 600 000
!(
!(
!(
!(
#*
#*
#*
#*
#*
#*
#*
#*
Beya
Salo
Bayanga
Dzanga
Mondika
Mongambe
Bai Hokou
Dakan
Salcapa
Kongana
PN Lobéké
PN Nouabale Ndoki
PN Lobéké
16°30'E
16°30'E
16°0'E
16°0'E
3°0
'N
3°0
'N
2°3
0'N
2°3
0'N
Secteur
Dzanga
Secteur
Ndoki
Le zonage du complexe
des Aires Protégées Dzanga Sangha
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Gorilla poop
Field work is not easy…..
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Fecal Sample Collection:
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Nov.-Dec.
2010
Dry(low-fruit)
season
n=34
Jun.-Jul.
2011
Wet(High-fruit)
season
n=85
Leaves Ripe Fruit
80%
0% Dry Wet
% T
ime
(Fe
ed
ing
sca
ns)
Methodological approach
Stool
DNA extraction
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Gas chromatography- Mass spectrometry (GC-MS)
Diet-host-microbe
co-metabolomic pool (function)
Metabolomics
MiSeq/ HighSeq sequencing
Bacterial community profiling
Community
Composition
Potential
function
Dietary changes across
seasons have a significant
effect on the gorilla gut
microbiome composition
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Leaves Ripe Fruit 80%
0% Wet Dry
80%
% Time (Feeding scans)
Bray-Curtis, Permanova, R2=0.40, P<0.001
-0.3 -0.2 -0.1 0.0 0.1 0.2
-0.3
-0.1
0.1
0.2
PCoA.1(13.6%)
PC
oA
.2(5
.5%
)
Gomez et al, 2016
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LF HF
0102030405060
LF HF
05
1015202530
Prevotella(%) Treponema(%)
*** ***
LF HF
010203040
LF HF
0123456
Lachnospiraceae(%) Ruminococcaceae(%)
*** ***
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-0.3 -0.2 -0.1 0.0 0.1 0.2
-0.3
-0.1
0.1
0.2
PCoA.1(13.6%)
PC
oA
.2(5
.5%
)
High Leaves High Fruit Dietary changes across
seasons have a
significant effect on the
gorilla gut microbiome
composition
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Phosphotransferase system PTS ABC transporters
Two component systemOne carbon pool by folate
Lysine biosynthesisGlycine serine and threonine metabolism
Histidine metabolismPhenylalanine tyrosine and tryptophan biosynthesis
Nicotinate and nicotinamide metabolismVitamin B6 metabolism
Biotin metabolism
Log2(FC)
-1.5 -1.0 -0.5 0.0 0.5
KEGG pathway**
Functional potential of the gorilla gut microbiome across seasons (KEGG pathways)
Wilcoxon **q<0.01
High Leaves Amino acid metab. Metab. Cof.-Vitamins
High Fruit Membrane transport Signal transduction
The gorilla gut
metabolome is
also temporally
dynamic
Partial least square discriminant analysis (PLSDA)
P<0.001, R2 = 0.65, Q2= 0.71
Metabolomic profiles High Fruit
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High leaves
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Discriminant
metabolites
Wilcoxon’s test
FDR-q<0.01
The gorilla gut metabolome is also temporally dynamic
High Fruit High Leaves
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The gorilla gut metabolome is also temporally dynamic
High Leaves
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The gorilla gut metabolome is also temporally dynamic
High Fruit
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These patterns match
their feeding behavior
across seasons
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*** ***
**Wilcoxon’s test, P<0.01
***
***
High Leaves High Fruit
Bark
Leaves
Fruit
Herbs
The gorilla gut microbiome is temporally dynamic
(dietary changes across seasons)
High Fruit High Leaves Temporal
- Dietary complexity +
- Dietary quality +
- Energy turnover +
- Dietary complexity + - Dietary quality +
- Energy turnover +
Spatial/Temporal
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Industrialization/ westernization
Can we extrapolate these microbiome changes to
dietary shifts in human evolution?
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Central Africa
Can we
extrapolate these microbiome
changes to dietary shifts in human
evolution?
-3
-2.5
-2
-1.5
-1
-0.5
0
0.5
1
1.5
Anaerolineaceae
Bacteroidales
Bacteroidetes
TM7
Treponema
Anaeroplasma
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Log-
Rel
ativ
e ab
un
dan
ce
Bacteria lost in humans
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Bacteria gained in humans
Log-
Rel
ativ
e ab
un
dan
ce
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Metabolome composition
P<0.001, R2 = 0. 85, Q2= 0.88
Understanding the human gut metabolome
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Metabolites gained in humans
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Metabolites lost in humans
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40 Sonnenburg et al., 2016
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Understanding the human gut microbiome
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Agile Mangabey
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Is there an evolutionary discordance between westerners and their gut microbes?
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The gut human gut microbiome and “westernization”/”Industrialization”
Dia
bet
es
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The BaAka hunter-gatherers
Central Africa
The Bantu,
Central Africa
The gut human gut microbiome and “westernization”/”Industrialization”
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The BaAka hunter-gatherers
The Bantu agriculturalists
Subsistence patterns impact the gut microbiome
****
****
Gomez et al, 2016
Further Industrialization dramatically impacts the gut
microbiome
Gomez et al, 2016
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Industrialization dramatically impacts the gut
microbiome: The usual suspects
a
b
c
a
b
c
a b c
Different letters, P<0.01
Gomez et al, 2016
Different letters, P<0.01
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Industrialization dramatically impacts the gut
microbiome: Functional analysis Different letters, P<0.01
Gomez et al, 2016
The human gut microbiome was (is being) shaped by dietary shift along human evolution We are what we eat
Summary:
Energy
turnover Phenolics
Fiber 50
Primate
microbiomes
show
increased
plasticity
Prospectus:
Microbiome
Host genes
Diet
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Tracing diet-host(gene)-microbe interactions in primates
= Phenotype
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UnclassifiedLachnospiraceae
OlsenellaRuminococcaceae
BacteroidalesBacteroidetes
AnaerolineaceaeFirmicutesPrevotella
ClostridialesPrevotellaceae
CoriobacteriaceaeMogibacteriumButyricicoccus
BlautiaTreponema
SelenomonadalesErysipelotrichaceae
ButyrivibrioBifidobacterium
0 10 20 30 40
Relative Abundance (%)
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Recovering live gut microbes from primates (probiotics?) Prospectus:
Acknowledgements
• Czech Academy of Sciences
Klara Petrzelkova, Jakub Mazarek, Bara Kalousova, Klara Vcklova
• University of Illinois
Brian White, Paul Garber
• University of Colorado
Steve Leigh
• University of Minnesota
Ran Blekhman, Joanne Slavin
• J. Craig Venter Institute
Karen Nelson, Chris Dupont, Josh Espinoza
53 Makumba
BaAka People
Contact: [email protected]
