is the microbiome really an important player in … · is the microbiome really an important player...
TRANSCRIPT
Is the microbiome really an importantplayer in human disease?
Karen Madsen, PhDUniversity of Alberta
Microbiomania – not a new phenomena
Eclectic Medical Journal 1898
Publications 2000-2014
Probiotics
0
500
1000
1500
2000
2500
3000
3500
4000
4500
5000
Microbiome
0
500
1000
1500
2000
2500
3000
3500
4000
4500
5000
New technologies…
Culture based Whole genome sequencing
Internet 2015
All diseases and humanbehaviour are influenced
by gut microbes!
Therefore, fix yourmicrobes and you willcure your disease and
change your life!
GenesX
Jonathan Eisen blog
Attraction to partners and relationship success is determined byfinding a partner with similar microbiomes to oneself….
And that if the microbiome in a kissing partner is a match thisleads to bliss and addiction
if the bacteria don’t align with your microbes, you actuallyfeel disgust and revolt
Which has led to things like this interview onCBC Fresh Air….
Host microbiota and health
Jeremiah J. Faith et al. PNAS 2015;112:633-640
Genetic and Microbial Inheritance
• Microbial inheritance couldinvolve acquisition of one or anumber of effector strains thatindividually or collectivelymodulate risk of developingcomplex diseases
Model of Microbial Inheritance
Probability that the gut of any individual is colonized with aparticular strain
P(transmission) = depends on factors such as its ability to surviveenvironmental insults and competitiveness
P(access) – depends on microbes abundance in the community aswell as hygiene, frequency of contact with and healthy status
P(resistance) – depends on the current composition of thepotential recipients microbiota
Jeremiah J. Faith et al. PNAS 2015;112:633-640
Changing microbial colonization throughout life
PNAS 2011:108(Suppl 1):4578
Succession of microbes in an infant
Fever
Introductionof formulaand food
In 2011, we were divided into 3 enterotypes!
(Based onsequencingabout 300people…..)
Enterotype 1= High Bacteroides
Enterotype 2= High Prevotella
Enterotype 3= High Ruminococcus
Arumugam et al. Nature 473, 173-180. 2011
2014: Revision: Diet is the main determinant ofgut microbial composition
Voreades et al. Front. Microbiol. Sept 22, 2014
Jeremiah J. Faith et al. Science 2013;341:1237439
Stability of Microbiota over Time
• Followed 30 individuals up to 5 years• Analyzed microbiota at a strain level• Found ~30% of strains shared between unrelated individuals
Microbiome science needs a healthy dose ofskepticism….
• Do microbiome studies showcausation or just correlation?
• Are changes in microbial compositionbiologically relevant?
• Could anything else explain theresults?
Hanage WP (2014) Nature 512:247-8
CORRELATION CAUSATION
Nature 178:488. 2012
MJ Claesson et al. Nature 000, 1-7 (2012) doi:10.1038/nature11319
Living in long-term care resulted in a poorer diet,worse health, and altered microbiome
Diet Microbiome Poor Health
??
178 seniors
Community
Residential care
If gut microbial dysbiosis is the causeof the disease, then
Fixing the dysbiosis should cure the disease
IBD patients have dysbiosis
What about replacing gut microbes by fecalmicrobial transplantation (FMT)?
• Instillation of gut microbiota from ahealthy person into a sick person
• FMT delivered by colonoscopy,nasogastric tube, or pills
– Colonoscopy
• 300-500 ml
– NG/NJ tube• 60 ml
– Pills• 20-40/dose
FMT does cure C. difficile colitis - clearinfectious cause of disease
• Trial terminated earlybecause it wasdeemed unethical tocontinue antibiotictreatment
2 RCT using FMT to treat UC
GroupTotal N
(active/placebo)
Dutch48 (23/25)
McMaster75 (38/37)
Patient population Mild-mod UC Mild-mod UC
Active arm (realFMT)
500 cc nasoduodenal infusion(120 g donor stool) at wk 0 and3
50 cc enema (8g donor stool)weekly X6
Control Sham FMT (patient stool) Water
OutcomesPrimary Remission (SCCAI < 2 + and
> 1 point reduction in MayoRemission (Mayo score < 3and Mayo endo score=0) @wk 7
Primary outcome 7/23 (30%) vs 5/25 (20%)p=0.51
9/38 (24%) vs 2/37 (5%)p=0.03
*Both trials were stopped early by DSMB due to futility
Moayyedi et al Gastroenterology 2015 April 7Rossen et al. Gastroenterology 2015 March 30
Results are generally not maintained in IBDpatients
This suggests that the “dysbiosis” in IBDpatients is a consequence, not the cause
Intestinal inflammation enhances thegrowth of certain facultative
anaerobes while decreasing thegrowth of obligate anaerobes
Intestinal Inflammation InducesDysbiosis
R3-N+-O-
(TMAO)
R2-SO(Sulfoxide)
R2-S(Sulfide)
R3-NH(Trimethyl Amine)
O2-
H2O2
HOCl
NO3-
(nitrate)
SO4-2
(Sulfate)
Intestinal Inflammation
ONOO-
MucolyticBacteria NOCHO
MucolyticBacteria
Inflammation Provides a Selective GrowthAdvantage for Disease-Producing Pathobionts
Increased oxidative stress protection pathways● increased cysteine and GSH transport
● increased riboflavin and sulfur metabolism● increased pentose phosphate shunt pathway
Increased sulfate transport and metabolism
Increase in amino acid transport
Increase in auxotrophy
Decrease in short chain fatty acids and metabolism
Decreased in amino acid biosynthesis
from Morgan et. al., 2012; Kostic et. al. 2014
Alterations in Microbial Function in IBD
AnaerobicRespiration
ClostridiaBacteriodia
Enterobacteriaceae
CHO
Products of Inflammation Feed the Expansion ofColitogenic Pathobionts
Modified from Winter et. al. EMBO, 2013
Microbiome science needs a healthy dose ofskepticism….
• Do microbiome studies showcausation or just correlation?
• Are changes in microbialcomposition biologically relevant?
• Could anything else explain theresults?
Hanage WP (2014) Nature 512:247-8
What do changes in composition anddiversity really tell us?
There are many species of bacteria, but only somehave adapted to life within us
• Over 50 known bacterial phyla
• Generally only 6 phyla found in gut• Bacteroidetes*
• Firmicutes*• Actinobacteria• Proteobacteria
• Verrucomicrobria• Fusobacteria
Tree of life
• 10-100 trillion organisms• >1000 different species• Bacteria, fungi, viruses
The Phylum Level
Bacteria are very different genetically from oneanother
Bacteriodes fragilis Escherichia coli
Shared genes = 40%
Caenorhabditis elegans(nematode)
Human
Shared genes = 38%
What do changes in ratios at the phylumlevel really mean?
Carlotta De Filippo et al. PNAS 2010;107:14691-14696
Microbiome science needs a healthy dose ofskepticism….
• Do microbiome studies showcausation or just correlation?
• Are changes in microbial compositionbiologically relevant?
• Could anything else explain theresults?
Hanage WP (2014) Nature 512:247-8
Technical andcontamination issues
are rampant in themicrobiome literature
Dilution of starting material increases contaminationeffects
• Sequencing results from a pure cultured sample• Increasing dilution = increased contamination• 3 different sites = 3 different results
Salter et al. BMC Biology 2014:12:87
Contamination is kit dependent
Salter et al. BMC Biology 2014:12:87
Analysis of nasopharyngeal samples from children inThailand as a function of age (Birth-2 yrs of age)
Samples cluster byage
No, samples clusterby extraction kit
Re-extractedNo clustering
Salter et al. BMC Biology 2014:12:87 Turner et al. Plos One 2012:7:e38271
Challenges with microbiome studies
• Problems with human studies
– Confounded by age, geographic locations, lifestyles,diets, host genetics
– Lack of standardization (sampling, extraction,processing, sequencing, analyzing)
– Batch effects – technical challenges
Human Microbiome
GOINGFORWARD
Specificity
Ecosystem Effects
Olle Nature Biotechnology 31(4):309. 2013
BUGS IN THE NEWS
Review ArticleAssociation between Faecalibacterium prausnitziiReduction and Inflammatory Bowel Disease: A Meta-Analysisand Systematic Review of the LiteratureYuan Cao, Jun Shen, and Zhi Hua RanRenji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institution of Digestive Disease,Shanghai Inflammatory Bowel Disease Research Center, Shanghai 200127, China
Gastroenterol Res Pract. 2014;2014:872725.
Faecalibacterium prausnitzii
LETTER doi:10.1038/nature13828
Precision microbiome reconstitution restores bileacid mediated resistance to Clostridium difficileCharlie G. Buffie1,2, Vanni Bucci3,4, Richard R. Stein3, Peter T. McKenney1,2, Lilan Ling2, Asia Gobourne2, Daniel No2, Hui Liu5,Melissa Kinnebrew1,2, Agnes Viale6, Eric Littmann2, Marcel R. M. van den Brink7,8, Robert R. Jenq7, Ying Taur1,2, Chris Sander3,Justin R. Cross5, Nora C. Toussaint2,3, Joao B. Xavier2,3 & Eric G. Pamer1,2,8
• “Identify a “probiotic” candidate that cancorrect a clinically relevant microbiome
deficiency”
• Clostridium scindens, a bile acid 7α-dehydroxylatingintestinal microbe, increases resistance to infection
Nature 2015 Jan 8;517(7533):205-8
Clostridium sp and C. difficile colitis
Akkermansia muciniphila and obesity
• A. muciniphila is a normal commensal thatdigests mucus
• Obese people (and fat mice) and those withtype 2 diabetes have much lower levels
• Mice on a high fat diet had less A. muciniphilaand when the levels were restored the micelost weight, had reduced insulin resistance,and reduced metabolic disorders
• Could A. muciniphila be used as a “probiotic”to treat diabetes or help people lose weight?
Everard et al. Proc Natl Acad Sci USA 2013;;110;220:9066
BUGS AND THE BRAIN
My bacteria made me do it…
•Microbes in the gut canalter brain function andbehaviour– Norepinephrine
– Vagus nerve stimulation
– Release of activebiomolecules
Concepts and Questions
• How to identify effector strains within a microbiome thatare responsible for shaping human biology?
• Majority of resident strains are acquired during the first 3years of life
• Once acquired, majority of strains are retained in anindividual for decades
• Effect of a strains residency may take decades tomanifest
Study designs for identifying microbes that modulatecomplex disease risk – Case Control Studies
Jeremiah J. Faith et al. PNAS 2015;112:633-640
Study designs for identifying microbes that modulatecomplex disease risk – Familial Disease
Jeremiah J. Faith et al. PNAS 2015;112:633-640
Geographic Disease Cluster
Jeremiah J. Faith et al. PNAS 2015;112:633-640
Conclusions
• The gut microbiota is dominated by only a few bacterialphyla but great strain-diversity
• Difficulty in identifying causative strains for complexdiseases as most strains are also found in healthyindividuals
• Complex diseases are more likely to reflect thecontributions of multiple microbial strains that both mediateand mitigate pathogenesis in the context of a specific hostgenotype
The End
Multiple stable compositional states in the developing gutmicrobiota of the premature infant.
Morowitz M J et al. PNAS 2011;108:1128-1133
Back in 1917
Clark Stanley, the“Rattlesnake King” in
1917