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Evolution of Symbiotic Bacteria in the
Distal Human Intestine
Xu et. al, PLoS Biology 2007, 5 (7), 1574-1586
Anoop Mayampurath
Human Microbiome
Turnbaugh et al. “The Human Microbiome Project” Nature 2007, 449
804-810
Backhed et al. “Host-Bacterial Mutualism in the Human Intestine,
Science 2005, 307 (5717), 1915-1920
Gut microbiota nutrient sources
- Plant polysaccharides
- Undigested plant proteins
- Host glycans
~90% belong to Bacteroidetes and
Firmicutes
Eckburg et al. “Diversity of the Human Intestinal Microbial Flora”,
Science 2005 308(5728) 1635-1638.
Questions
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How has evolution shaped by the
effect of intestinal environment?
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“Top-Down” selection
“Bottom-up” selection
Nature of adaptation in species
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general (gut vs non-gut)
specialized (within a species)
Approach
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Sequenced B. vulgatus and B. distasonis
Compare genomes to other sequenced
(gut/non-gut) Bacteroidetes.
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Orthologs that are shared between gut and
non-gut
Orthologs unique to gut
Detect “niche” specialization
Analyze functions of these special genes
along with their origin (role of LGT)
- 1416 orthologs among
all gut species
GO Terms comparison
5w – all 5 gut
7w – 5 gut plus 2 non gut
(shared)
5wU – 5 gut plus 2 non
gut (unique to gut)
Enrichment
P < 0.05 : pink
P < 0.001 : red
Depletion
P < 0.05 : light blue
P < 0.001 : dark blue
Inference
- All bacteroidetes had a share core metablome
- Bacteroidetes specific to the gut have enriched genes for polysaccharide
metabolism, environment sensing and membrane transport
GO Term comparison (individual
comparison)
Inference
- Each species
has a “niched”
specialization
What are these niches?
(B. thetaioataomicron)
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Forages polysaccharides
“Opportunistically” deploys SusC and SusD
membrane proteins along with hydrolases
and lysases.
Most glycoside hydrolases for plant glycans
Only sequenced species that contain lyases
for animal glycans
Most enzymes for host glycan harvesting
What are these niches?
(B. distasonis)
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Lacks many glycosyldases
Smaller proteome
Only one candidate alpha-fucodiase
Two abundant hydrolases
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Family 13 (alpha-amylase proteins)
Family 73 (host glycan harvesting)
Has the capacity to harvest host glycans in
spite of glycan sialic acid termination
More protein degradation than B.
thetaiotaomicron
What are these niches?
(B. vulgatus)
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Intermediate between B.distasonis
and B. thetaiotamicron
Enzymes targeting pectin
Only species containing a gene
encoding xylanase
Role of LGT
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Phylogentic approach
 Genes transferred into one lineage and genes
lost in lineage except one.
Genes satisfying one of the following conditions
 No homologs were found in NCBI nR database
 Only homologs were found in that species
 Only homologs were found in non-gut
 More closely related to non-gut than gut
Tamamens and Moya, “Estimating the extent of horizontal gene transfer in metagenomic sequences” BMC Genomics 2008, 9 :136.
Role of LGT
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“lateral” genes differ from the rest of
the genome in terms of GC content
and codon bias.
~5% of genes in each genome as
being present on account of LGT.
Distribution of LGT genes
Light-Blue: Whole Genome
Red: DNA Methylation
Green: CPS loci
Yellow: Glycosyltranferases
Light-Blue: B. distasonis
Red: B. vulgatus
Yellow: B. thetaiotaomicron
Green: B. fragills NCTC
9343
Purple : B. fragilis YHC 46
Orange: P. Gingivalis
CPS Loci
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Regulatory cassette
Structural cassette that code for
glycotransferases and carbohydrate
transporters.
CPS Loci are extremely polymorphic
CPS Diversity through
recombination
CPS Diversity through phage
SusC and SusD paralogs
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SusC are membrane proteins which
along with glycan binding, also aid in
transport.
SusD are secreted proteins which bind
to glycans using a lipid tail
SusC/SusD phylogeny
SusC/SusD diversification through
gene duplication
1- Conserved hypothetical
lipidated protein
2 – SusD paralog
3 – SusC paralog
4 – NHL repeat-containing
protein
5 – Glutaminase A
1- Sulfatase
2- SusD
3- SusC
4 – Anti sigma factor
5- ECF sigma factor
Discussion
“The B.
thetaiotaomicron genome
contains 261 glycoside
hydrolases and
polysaccharide lyases
currently annotated in the
Carbohydrate-Active
Enzymes (CAZy)
Database (24).
Remarkably, this
organism's genome also
contains 208 homologs
of susC and susD,
suggesting that the
molecular strategy for
starch utilization has been
expanded to target other
nutrients”
Martens et al. “Complex
Glycan Catabolism by the
Human Gut Microbiota: The
Bacteroidetes Sus-like
Paradigm” J Biol Chem 2009,
284(37) 24673-24677
How do they survive?
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Both “top down” and “bottom up” are
present.
LGT plays a role. When and How are
still left to open question
Importance of glycosyltransferases.
Persistence from one generation to
next?
Personalized microbial communities
Other work
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Mahowald et al. “Characterizing a model human gut microbiota composed of
members of its two dominant bacterial phyla”, PANS 2009, 106(14)
“B. thetaiotaomicron adapts to E. rectale by up-regulating expression of a variety of
polysaccharide utilization loci encoding numerous glycoside hydrolases, and by signaling
the host to produce mucosal glycans that it, but not E. rectale, can access. E.
rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading
enzymes, increasing expression of selected amino acid and sugar transporters, and
facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from
acetate, which in turn is used by the gut epithelium. ”
Brigham et al. “Sialic Acid (N-Acetyl Neuraminic Acid) Utilization by Bacteroides
fragilis Requires a Novel N-Acetyl Mannosamine Epimerase”, J. Bacteriology 2009,
191(11)
- Characterization of nanLET operon in Bacteroides fragilis
Coyne et al. “Role of glycan synthesis in colonization of the mammalian gut by the
bacterial symbiont Bacteroides fragilis” , PANS 2008, 105(13), 13099-13104
- Construct mutants defective in certain enzymes that result in inability to synthesize
polysacchrides
-