metagenomics biocuration 2013
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Understanding the Gut Superorgan using Metagenomics
Iddo FriedbergMiami UniversityOxford, Ohio
Page: iddo-friedberg.net
Blog: bytesizebio.net
Twitter: @iddux
The Gut Ecosystem
~500-1,000 ribotypes (97% ID)
47 GB protein coding
Firmicutes
Bacteroidetes
Crohn's
Obesity
Celiac
The Gut Superorgan
Maloy & Powrie Nature (2011)
What can we learn and how?
Babies are a Good Model for Humans
Gut Microbiome Changes over Time
0
6
85
92
96
100
118
371
413
441
432
454
Firmicutes
Firmicutes dominate
ActinobacteriaFever at day 92?
Bacteroidetes:Eat plant matter
Bacteroidetes
Actinobacter
Proteobacter
Euryachaeota
Verrumicrobia
Viruses
Fungi
BenefitsImproved immune healthFewer infectionsReduced SIDSLess obesityBeneficial to mothers too
Not always possibleEconomicSocialMedical
Breastfeeding vs. Bottle Feeding
Microbial community(metagenome)
Gut epithelial cells(transcriptome)
Effect of Diet on Superorgan
Microbial community(metagenome)
Gut epithelial cells(transcriptome)
454 sequencing
Who? (Phylogenetic analysis)
What? (functional analysis)
Clean & RT poly-A
Codelink chip
What? (functional analysis)
Correlations
Goals: understand effects of breast feeding and formula feeding on gut microbiota
Understand effect on gut epithelium
Method: find correlations between bacterial gene presence and host gene expression
Diet
Microbiome
Epithelialtranscriptome
Who is there (phyla)?
Schwartz, Friedberg et al. in revision
Firmicutes
Actinobacteria
Proteobacteria
Bacteoidetes
Verrumicrobia
16S vs. GreenGenes
Firmicutes
Actinobacteria
Proteobacteria
Bacteoidetes
Verrumicrobia
PhymmBL
Who is there?
Variance in breastfed infants is larger than in formula-fed
Firmicutes dominate in FF, Bacteroidetes & Actinobacteria in BF
What are they doing?
What are they doing?
What are they doing?
More virulence-related genes in microbiome of breast-fed babies
Major contribution: secretion systems, and miscellaneous
Type IIISecretionSystem
Meanwhile, in the gut epithelium...
(BF+FF)/2
(BF+FF)/2
Gut / Microbiome gene correlations
Goal: establish a significant covariance between epithelium expression and microbiome frequency
Many genes: multivariate assessment
Canonical Correlation Analysis (CCA) determines if a global relationship between 2 types of data-sets exists
CCA for Gut Superorgan
CCA
Bacterial DNA
Epithelial mRNA
Function Annotation
Expression levels
Gut mRNA expression vs.
Microbiome Function
Highly Expressed Host Genes in Correlation with Virulence
GeneRole
REL*General transcription factor Proto-oncogene that may play a role in differentiation and lymphopoiesis. Component of NF-kB heterodimer RELA/p65-c-Rel
ALOX5*Leukotriene synthesis. Leukotrienes are mediators of some inflammatory and allergic conditions
NDST1Participates in biosynthesis of heparan sulfate that can ultimately serve as L-selectin ligands, thereby playing a role in inflammatory response
AOC3participates in lymphocyte recirculation.
VAV2**Vascular endothelial cell migration
DUOX2 lactoperoxidase-mediated antimicrobial defense atthe surface of mucosa
Enrichment Score: 3.799
Term
GO:0002768~immune response-regulating cell surface receptor signaling pathway
GO:0002764~immune response-regulating signal transduction
GO:0046649~lymphocyte activation
Enrichment Score: 2.365
Term
GO:0046635~positive regulation of alpha-beta T cell activation
GO:0046634~regulation of alpha-beta T cell activation
GO:0050870~positive regulation of T cell activation
GO:0050863~regulation of T cell activation
GO Enrichment Analysis of Differential Epithelial Transcripts
Conclusions
Host:11 Immunity related genes correlated with microbiome virulence genes
Up-regulated in breast-fed infants
Microbiome:scavenging mechanisms, resistance to antibiotics and toxic compounds, Type III, Type IV, ESAT secretion systems, Type VI secretion systems all more frequent in breastfed infants.
Future Work:RNASeq analysis for host
Metaproteomics?
People & Funding
StaffRajeswari Swaminatham (Programmer)
Graduate studentsDavid Ream (Operon evolution)
Andrew Oberlin (Mycoplasma Genome Database)
Ashwani Kumar
CollaboratorsMitchell Balish (MU) (Mycoplasma)
Predrag Radivojac (IU) (CAFA )
Robb Chapkin (TAMU) (Baby gut)
Sharon Donovan (UIUC) (Baby gut)
Scott Schwarz (TAMU) (Baby gut)
Jennifer Goldsby (TAMU) (Baby gut)
Alexandra Schnoes (UCSF) (CAFA) (poster 82)
Steven Brenner (UC Berkeley) (CAGI)
Miami University Supercomputing team
FundingNIH
NSF
Interwebs:Page: iddo-friedberg.net
Blog: bytesizebio.net
Twitter: @iddux
Postdocs and students:
END SLIDE
Results: microbiome
Correlations
Host Metabolomics
Microbiome Metabolomics
Superorgan metabolomics
David Artis Nature Reviews Immunology 8, 411-420 (June 2008)
Gut and Immunity
The Trouble with Triples
Problem: too many genes few samples
Reduce number of variables by grouping genes in triples
Triples that come up
Virulence and immunity