Alternative stable states in human intestinal ecosystem Leo Lahti, Jarkko Salojärvi, Anne Salonen, Marten Scheffer, Willem M de Vos ISME15 (Aug 30, 2014) Twitter & Github: @antagomir
Jul 05, 2015
Alternative stable states inhuman intestinal ecosystem
Leo Lahti, Jarkko Salojärvi, Anne Salonen, Marten Scheffer, Willem M de VosISME15 (Aug 30, 2014)
Twitter & Github: @antagomir
Ecosystem restoration with fecal transplants- van Nood et al. NEJM 2013- Fuentes et al. ISME J 2014
Enterotypes of the human gut microbiome- Arumugam et al. 2011
Mouse & Chimpanzee- Wu et al. Science 2011- Moeller et al. Nat. Comm. 2012- Wang et al. PNAS 2014
Clusters vs. gradients methodological issues:- Jeffery et al. Nat Rev. Microbiol. 2012;- Koren et al. PLoS CB 2013
Prevotella bimodality- Jeffery et al. Nat. Rev. Microbiol.
Koren et al. PLoS CB 2013
Atlas of Human Intestinal Microbiota:
>1,000 Western adults
130gen
us-lik
egroups
1,006 Western adult subjects
Human Intestinal Tract(HIT) Chip: High ResolutionPhylogenetic Microarray
RajilicStojanovic et al. Environ Microbiol 2009Rajilic–Stojanovic et al. Gastroenterology 2011
Blue: Low abundanceRed: High abundance
Characteristic 'abundance types'
in 1000 western adults:
~% indicates proportion among prevalent taxa
~50% ~20%
~10%~10%
~10%
Lahti et al. Nat. Comm. 5:4344, 2014
Quantifying bimodality with Potential analysis
CRAN: earlywarnings
Livina et al. 2011; Scheffer et al. 2012
Lahti et al. Nat. Comm. 5:4344, 2014
Stable attractors in theabundance landscape andmicrobiota composition?
78 subjects~3 months
Dialister spp.
Lahti et al. Nat. Comm. 5:4344, 2014
Bim
odalityscore
(%)
N=401
Bi-stable taxa:
Prevotella groups(oralis & melaninogenica)
Dialister spp.
Uncultured Clostridiales I-II
B. fragilis group
Clostridium groups(difficile, colinum, sensu stricto)
Uncultured Mollicutes
Lactobacillus plantarum
+ evidence in methanogenic archaea Intemediate stability (r); N=78
Confirming bistability with temporal analysis
State transitions show larger shifts> alternative attractors divided by a critical tipping point ?
Bistability and the overall ecosystem: varying scales ?
PCA +Correlation (Spearman)
Only Prevotella statesare visible at ecosystemlevel (high ~10%relative abundance;other bi-stable taxa<2% relativeabundance)
Lahti et al. Nat. Comm. 5:4344, 2014
Low (blue) and High (red)abundance Prevotellasubjects highlighted:
Lahti et al. Nat. Comm. 5:4344, 2014
'Tipping elements' of the intestinal microbiota ?
Uncorrelated state switches -> various combinations !
-> Ecosystem states asspecific combinationsof bi-stable taxa?
http://commons.wikimedia.org/wiki/File:RFremotecontroldipswitchcalculator.png
Ageing and bistability: Uncultured Clostridiales I
Lahti et al. Nat. Comm. 5:4344, 2014
Summary
Evidence for alternative stable states in specific taxa:1) Bimodal log-abundance distributions (~10% of prevalent taxa)2) Reduced stability at the intermediate abundance range
Bistable tipping elements cooccur in various combinations
Links to disease ?- UCI/II: negative association to Obesity/IBS- High Dialister spp. & B. fragilis & Low Prevotella: MetS
Causality: drivers or passengers?- Competition & mutualism- Feed-back loops
Bistable tipping elements in human intestinal microbiota(Lahti et al. Nat. Comm. 5:4344, 2014)
Data: 1,006 western adults x 130 genus-like groups + metadataIn Dryad: http://dx.doi.org/10.5061/dryad.pk75d
Code: CRAN: earlywarningsGithub: microbiome.github.com
Slides: SlideShare
Twitter & Github: @antagomir
#ISME15
Thank You!
Anne SalonenJarkko Salojärvi
Willem M de VosMarten Scheffer HITChip team
#ISME15