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Transcript of Diet, intestinal microbial communities and host health intestinal microbial communities and host...
Diet, intestinal microbial communities and host health
Alan WalkerRowett Institute of Nutrition and Health,
University of Aberdeen
8/9/15
• Human large intestine hosts an enormous number of microbes (“microbiota”)
– 100,000,000,000,000 (1014) bacterial cells
– Greater than the number of human cells
• Thousands of different species colonise
– Most are strict anaerobes
– Each host have a unique and largely stable microbiota
• The cumulative “microbiome” of these cells contains 400x more unique genes than the human genome
– est. 8 million vs ~20-25,000
• Plays a number of key roles in maintaining host health
– Enhances resistance against infection
– Immune system development/maintenance
– Beneficial compound production
– Breakdown dietary fibre
The human intestinal microbiota
Lawley & Walker (2013) Immunology 138, 1-11
Principal substrates available for utilisation by intestinal microbes
Adapted from Cummings & Macfarlane (1991)
Resistant starch
Non-starch polysaccharides
Unabsorbed sugars
Oligosaccharides
Dietary protein
Enzymes / secretions / mucus
5040302010
Amount (gram per day)
Of dietary & intestinal origin: range
Digestibilities for plant cell wall polysaccharides – 7 subjects (Slavin et al J. Nut 1981)
Pure cellulose (Solka Flok) minimal Cellulose (in normal diets) 69.7% (+/-10.7)Hemicellulose 71.7% (+/- 5.4)
[Harry Flint]
• Metabolise dietary components that escape digestion by human enzymes – Endows host with degradative capabilities they have not
needed to evolve themselves
• Vitamin production– K, riboflavin (B2), biotin (B7), folic acid (B9), cobalamin (B12)
• Release of phytochemicals– Phenolic compounds etc
• Primary end products are short chain fatty acids– Acetate (C2), propionate (C3) and butyrate (C4)
• SCFAs are symbiotic compounds– Gut epithelial cells grow on products of bacterial
metabolism
– Derive up to 70% of energy needs from bacterially-produced butyrate
– Increases energy yield from diet (5 to 10% of caloric intake per day)
oligo-, mono-saccharides
complex polysaccharides
Short chain fatty acids
Polysaccharidedegraders
saccharolytic bacteria
Anaerobicfermentation
Fibre utilisation by gut microbes
oxaloacetate
fumarate
succinate
propionyl-CoA
fucose, rhamnose
propane-1,2-diol
propionyl-CoA
DHAP + L-lactaldehydePEP
CO2
lactate
lactoyl-CoA
propionyl-CoA
pyruvate
propionate
hexoses & pentoses
acetyl-CoA
acetoacetyl-CoA
butyryl-CoAacetate
acetyl-CoA
butyrate
acetate
butyryl-P
H2 + CO2
formate
Roseburia inulinivoransRuminococcus obeumSalmonella enterica
methane
Bacteroidetessome Negativicutes
Coprococcus catusMegasphaera elsdenii
Ruminococcusbromii
Eubacterium rectaleEubacterium halliiRoseburia spp.Anaerostipes spp.Coprococcus catusFaecalibacterium prausnitzii
Coprococcus eutactusCoprococcus comes
ethanol
Blautiahydrogenotrophica
Eubacterium halliiAnaerostipes spp.
methanogenicarchaea
hydrogensulphide
sulfate
Desulfovibrio spp.
Major fermentation pathways
Adapted from Louis et al., Nat Rev Microbiol (2014)
• Inhibition of histone deacetylase (butyrate, propionate)
• Altered mucosal gene expression, cell differentiation
• Protection against colorectal cancer, colitis (butyrate)
• Energy source for the colonic epithelium (butyrate)
• Anti-inflammatory effects (including stimulation of Tregs)
• Suppression of colitogenic pathogens (acetate)
• Stimulation of host receptors (FFAR2, FFAR3, GPR109)
• Influence on gut hormones (e.g. GLP-1, PYY) and satiety
• Influences upon gut transit, gut barrier function
• Peripheral energy supply, lipogenesis (acetate)
• Promote intestinal gluconeogenesis (butyrate, propionate)
Impact of gut bacterial short chain fatty acids on the host
Lactate accumulation shown to be due mainly to reduced lactate utilization by other bacteria at pH 5.2 (13C lactate)
0
5
1 0
1 5
2 0
2 5
3 0
C o n tro ls Q u ie s c e n t
c o lit is
M ild c o lit is M o d e ra te
c o lit is
S e v e re
c o lit is
Co
nc
en
tra
tio
n (
mM
)
Lactate accumulation in stool in colitis (Vernia et al 1988)
[Harry Flint]
Belenguer, A. et al (2007) A.E.M. 73, 6526-6533.
• Many diseases are caused by microbes that normally live asymptomatically on the host– e.g. Staphylococcus aureus
(MRSA), Strep throat, gingivitis, acne, meningitis, pneumonia, C. difficile diarrhoea, thrush, UTIs, gastric cancer (Helicobacter pylori).
• A general imbalance (“dysbiosis”) in microbiota composition has been implicated in many disorders– e.g. Inflammatory bowel
diseases, bowel cancer, irritable bowel syndrome, diabetes, liver disease, allergies, atherosclerosis
Round & Mazmanian (2009) Nat. Rev. Immun. 9;313
Host-associated microbes in disease
Anti-oxidant Molecules
Heterocyclic Amines
N-Nitrosamines
Polyamines
Bile Acids
Indoles Anti-Inflammatory Molecules
N
NNH
2NH2
OH
OH
O
OH
H
H
H H
N
NN
NH2
OOH
OH
NN
O
OH
O
OHO
OH
Phytoestrogens
O
OH
Short Chain Fatty Acids
Damaging Protective
OH
O
O
OHOH
H
OH
Impact of microbially derived metabolites on the host
[Sylvia Duncan]
The “Western” diet, microbiota and host health
Koeth R.A. et al. (2013) Nat. Med. 19;576-585
Tang W.H. et al. (2013) NEJM 368; 1575-1584
Walker & Lawley (2013) Pharmacol. Res. 69:75-86.
Altering the intestinal microbiota
Antimicrobials/Pharmabiotics Probiotics Diet Faecal transplants
• The aim of all of these approaches is to shift the composition of the microbiota to a more beneficial state– Is targeted manipulation possible via alterations in host diet?
Short- v long-term impacts of diet on the intestinal microbiota
• Changes in long-term dietary patterns illicit extensive changes in microbiota composition
• Short term dietary regimes can result in reproducible but limited microbiota response
Disappearing human microbiota?• Have host behavioural changes in the urbanisation era introduced changes in
microbiota composition?
Hunter (2012) EMBO reports.13, 498–500
Round & Mazmanian (2009) Nat. Rev. Immun. 9;313
Link between diet, oral microbiota and healthHunter-gatherer Neolithic agriculturist Medieval agriculturist
• Calcified plaque – one of the only preserved records of bacteria
• Densely colonised by oral microbiota
Adler C.J. et al., (2013) Nature Genetics 45, 450-455
Dobney et al., 1994
Image: Dr Jo Buckburry (re-plotted from Moore and Corbett 1978)http://www.leeds.ac.uk/yawya/bioarchaeology/Dental%20disease.html
• Increased caries rate in skeletal records is linked to increased consumption of carbohydrates
• Unknown whether or not these changes were accompanied by shifts in microbiota composition
Oral microbiota changes through history
• Non-pathogenic Ruminococcaceae associated with hunter-gatherers
• Decay-associated Veillonellaceae increase post-farming
Relatively stable diversity estimates
Decrease in bacterial diversity since the industrial revolution(P = < 0.001)
Adler C.J. et al., (2013) Nature Genetics 45, 450-455
[Alan Cooper – University of Adelaide]
Changes in predominant oral pathogens as a result of diet and culture
• These pathogens do not appear to be prominent in hunter-gatherers
• Streptococcus mutans became dominant relatively recently
• Shifts correlate with human behavioural changes (e.g. diet)
• We may need to reconsider what we think of as a normal “healthy” intestinal microbiota
De
Fili
pp
oe
t a
l. P
NA
S(2
01
0)
Age(months)Diarrhoeal cases Healthy controls
PrevotellaEscherichia/Shigella
Pop, M. et al., Genome Biology (2014), 15:R76
Regional variations in gut microbiota composition
[Cooper, P. et al., (2013) PLOS ONE 8,e76573]
Many novel bacteria
Children in :KenyaMaliThe GambiaBangladesh
Links between host diet and microbiota structure
Wu et al. (2011) Science 334;105-8
• Microbiota structures are associated with long term dietary consumption patterns
O’Keefe et al., Nat. Commun. (2014), 6:6342
• O’Keefe et al performed 2-week food exchanges
• African Americans were fed a high-fibre, low-fat African-style diet and rural Africans a high-fat, low-fibre western-style diet
• Resulted in measurable changes in health biomarkers– butyrogenesis, secondary bile acid
synthesis in the African Americans
Links between host diet and microbiota activity
Duncan SH, et al., (2007) A.E.M. 73:1073-8
Impact of low carbohydrate weight loss diets
** P < 0.001
Short chain fatty acids - in faeces
****
**
0
10
20
30
40
50
60
70
80
90
Acetate Propionate Butyrate Iso butyrate Iso Valerate
Faec
al c
once
ntra
tion
(m
M)
1
High
Moderate
Low
Fae
cal S
CFA
le
vels
(m
M)
% Eubacterial (Eub338) count in faeces
***
****
***
*
*
0
5
10
15
20
25
30
35
40
Bac303
Fprau645
Rfla729 +
Rbro
730
Bif164
Erec482
Prop853
Rrec584
Erec -
Rrec
log 1
0 tota
l
Bacterial group (probe)
% E
ub33
8 or
Eub
338
/g
High
Moderate
Low
Mic
rob
iota
co
mp
osi
tio
n
• Low CHO diet leads to reduction in butyrate-producing bacteria
• Reduced faecal butyrate levels
High CHO – 400 g/dModerate CHO – 170 g/dLow CHO – 23 g/d
2
4
6
8
10
12
Ferulic acid 3OMe4OHPPA 34OHPPA 3OHPPA
Maintenance DietLow Carb. Diet 20+/-1 daysLow Carb. Diet 27+/-1 days
P < 0.05 P < 0.001
P < 0.05
Co
nce
ntr
atio
n (
ug
cm-3
)
Ferulic acid derivatives 8 volunteers
Russell WR et al., AJCN (2011) 93, 1062-72
Major fibre derived phenolics in faecal samples
• Low carbohydrate, high protein intake resulted in reduced concentrations of potentially cancer–protective plant phenolic derivatives
14 obese male volunteers with metabolic syndrome (mean age 54 years, mean BMI 39.4 kg/m2)
M NSP RS HPMC
1 wk 3 wks 3 wks 3 wks
Collection of faeces
M NSPRS HPMC
Mean dietary intake [g/d]:
M 427 230 5 28 103 126
NSP 427 138 2 42 102 136
RS 434 275 26 13 109 127
HPMC 201 110 3 22 144 63
CHO: carbohydrate
Diet CHO Starch RS NSP Protein Fat
Weight maintenance
Weight loss
Resistant starch vs non-starch polysaccharide diet
M: Weight maintenance, mixed diet (55% energy from carbohydrates)
NSP : High non-starch polysaccharides (added bran), low RS
RS: High resistant starch (Type III), reduced NSP
HPMC: Reduced calorie intake. Increased % protein, moderate carbohydrate
Walker AW. et al (2011) ISME J 5, 220-230
Volunteer No.
1-P
ears
on
co
rrel
atio
n
Resistant starch vs non-starch polysaccharide diet
Stimulated by NSP Stimulated by RS
• Samples cluster by donor, not by diet
• Sub-group of bacteria are highly responsive to both the NSP and RS-enriched diets– More Ruminococcaceae species
increase with RS
– More Lachnospiraceae species increase with NSP
Salonen, A. et al (2014) ISME J 8, 2218-30.
5040
Resistant starch v non-starch polysaccharide diet
11 12 17 18 19 23 240
20
40
60
80
100
14 15 16 20 22 25 26
volunteer
% r
esid
ual
fae
cal s
tarc
h
RS diet
NSP diet
Residual faecal starch in volunteers100
80
60
40
20
00 10 20 30
Time [h]
% o
f re
sid
ual
sta
rch
V25 faecal sample+ B. adolescentis+ E. rectale+ B. thetaiotaomicron
Volunteer 25 in vitro faecal starch utilisation
+ + R. bromiikeystone species
for starch utilisation
Ruminococcus spp. - qPCR
M NSP
WL
RS
0
10
20
30
40
50
0 10 20 30 40 50 60 70
M NSP RS WL
% o
f u
niv
ersa
l 16
S rR
NA
gen
e co
pie
s
11121718192324
Volunteer
0
10
20
30
40
50
60
70
80
0 10 20 30 40 50 60 70
M RS NSP WL14
1516
20
22
25
26
Volunteer
Time [days] Time [days]
Walker et al. ISME J (2011); Ze et al. ISME J (2012)
Keystone species within the microbiota
Links between diet, microbiota and health
Walker AW & Duncan SH. MNFR (In Prep.)
Conclusions• Long-term dietary patterns have significant impacts on both intestinal
microbiota composition and activity– Fibre consumption appears to be a major driver
• Microbiota composition and activity are strongly correlated with markers of host health/disease– Mechanistic studies now starting to emerge that link diet/microbiota/health
• Specific bacterial groups/species respond strongly to dietary change, but there is inter-individual variation in the groups that respond
• Many gut bacteria appear to be nutritionally specialised; these species are likely to show the greatest responses to dietary manipulation– ‘Keystone’ species may determine the ability to ferment insoluble substrates
• Implications for therapeutic dietary intervention:– The response may depend on the underlying microbiota composition of a
given individual– Need continued and improved characterisation of the microbiota in order to
predict responses to dietary manipulation
Contact : [email protected]
Protection against
colorectal cancer and
colitis
Exposure to metabolites and bacteria that promote
disease
supply of short chain fatty acidsphytochemicals in colon
colonic pH
Fermentable carbohydrates:
Interplay between dietand microbiota
phenols, amines, indoles, N-nitroso compounds,
H2S, amines, bile acids,faecapentaenes, heme
Nutrient supply to mucosa
Barrier against infection
Release of phytochemicals
[Sylvia Duncan]
Interplay between diet and microbiota on gut health
Pathogen Genomics Group
Julian ParkhillPaul Scott
Bacterial Pathogenesis Group
Trevor LawleyMark Stares
Core Sequencing Teams
Carol ChurcherDavid Harris
Richard Rance
All other members of the Sanger Institute’s sequencing teams
Acknowledgements
U. Maryland
Colin StineMihai Pop
Funding Sources:
St. George’s, University of London
Phil Cooper
University of Adelaide
Alan CooperChristina AdlerLaura WeyrichJohn Kaidonis
Wolfgang HaakCorey BradshawGrant Townsend
University of Warsaw
Arkadiusz Sołtysiak
Johannes Gutenberg University of Mainz
Kurt Alt
Rowett Institute of Nutrition and Health/University of Aberdeen
Microbiology Group
Harry FlintSylvia Duncan
Gillian DonachiePetra Louis
Jennifer InceLucy Webster
Xiaolei ZeAurore BergeratFreda McIntosh
Karen ScottJenny Martin
David Brown (Analytical Chem)
Wendy Russell (Mol Nutr)
Alex Johnstone (OMH)
Gerald Lobley (OMH)
Sylvia Stephen (HNU)
Grietje Holtrop (BioSS)
University of Aberdeen
Keith Dobney
University of Modena and Reggio Emilia
Maddalena RossiAndrea Quartieri