Symbiotic bacteria in animals. Oct 3 2006 Nancy Moran Professor, Ecology and Evolutionary Biology. Reading: The gut flora as a forgotten organ by A. O’Hara and F Shanahan EMBO Reports. 2006. What is symbiosis? .
Reading: The gut flora as a forgotten organ by A. O’Hara and F Shanahan
EMBO Reports. 2006
Diverse microbes in termite gut
Routes of transmission
can increase in frequency
can increase in frequency
Why might vertical transmission be associated with mutualistic effects on hosts?
with the host to form a “super-organism”
--mutually obligate relationship
--very unlike pathogens
Eukaryotic genomes are littered with hundreds of genes from mitochondria and plastids--now apparent from plant and animal genome sequences.
e.g. Arabidopsis genome has >1000 genes from cyanobacteria
Many invertebrates have specialized intracellular associations with bacteria that make nutrients
Examples: marine bivalves, leeches, many insects
Metazoa: ancestral loss of many genes underlying biosynthesis of compounds essential for metabolism, including many amino acids and many cofactors.
Little or no gene uptake
Tree of Life, N. Pace
early embryos with
Buchnera from mother
->Strict vertical transmission since ancient infection of ancestral host
Essential nutrients for animals
Aphid stylet sheaths
in phloem sieve tubes
Schizaphis graminum on barley
trp plasmid in Buchnera (Schizaphis graminum)
= genomic adaptation to make more nutrients for hosts
Lai, Baumann & Baumann PNAS 1994
The Buchnera gene set (570 genes) is a subset of that of E. coli (~4500 genes)
Shigenobu et al 2000 Nature
tyrA tyrA hisC
Chorisimate ---> ---> ---> TYR
proB proA proC
Glutamate ---> ---> ---> PRO
serA serC serB
3-Phosphoglycerate --->---> ---> SER
Serine---> ---> CYS
2-oxoglutarate ---> GLU
Glutamate ---> GLN
Oxaloacetate ---> ASP
Aspartate ---> ASN
Pyruvate ---> ALA
Essential amino acid biosynthetic pathways
argA argB argC argD argE carAB argF argG argH
Glutamate---> ---> ---> ---> ---> Ornithine ---> ---> ---> ---> ARG
ilvHI ilvC ilvD ilvE
Pyruvate ---> ---> ---> ---> VAL
ilvA ilvHI ilvC ilvD ilvE
Threonine ---> a-Ketobutyrate ---> ---> ---> --->ILE
ilvHI ilvC ilvD leuA leuCD leuB ilvE
Pyruvate ---> ---> ---> ---> ---> ---> --->LEU
aroH aroB aroD aroE aroK aroA aroC
PEP+Erythrose ---> ---> ---> ---> ---> ---> ---> Chorismate
pheA pheA hisC
Chorismate ---> ---> ---> PHE
trpEG trpD trpC trpC trpAB
Chorismate ---> ---> ---> ---> ---> TRP
thrA asd thrA thrB thrC
Aspartate ---> ---> ---> Homoserine ---> ---> THR
metB metC metE
Homoserine ---> ---> ---> MET
thrA asd dapA dapB dapD dapC dapE dapF lysA
Aspartate ---> ---> ---> ---> ---> ---> ---> ---> ---> LYS
hisG hisI hisA hisHF hisB hisC hisB hisD
PRPP + ATP ---> ---> ---> ---> ---> ---> ---> ---> HIS
GENE / product present in Buchnera
GENE / product absent in Buchnera
(based on Shigenobu et al 2000)
But other symbionts appear not to have not left a legacy of many genes transferred to host genomes, at least not in animals so far sequenced (e.g., Drosophila)
Eukaryotic genomes contain
many genes from organelles, apparent from eukaryotic genome sequences.
Why this difference?
Not much like pathogens-host has taken over mechanisms of invading host cells and has coevolved to maintain the association
Much more like pathogens--have to invade naïve hosts, overcome immune responses, but typically benefit hosts
Experiments comparing pea aphids with the same genotype but differing in presence of secondary symbionts:
lines established by microinjection and inherited in all descendants
confers protection against parasitoid wasps
Kill developing parasite larva within aphid body
Increases aphid survival & reproduction
Oliver, et al. PNAS 2003 & 2005
Polyketides produced by symbionts of beetles and sponges
Biosynthesis is encoded in a 75kb
acquired chromosome fragment
Used as anti-tumor drugs
J Piel 2002 PNAS 99: 14002
Case of humans
In a person, bacterial cells outnumber somatic and germ cells by >10 fold
Human intestinal microbiota: 500-1,000 different species,
aggregate biomass of ~ 1.5 kg per person
Number of genes in the human ‘microbiome’ may exceed
number of human genes by 100-fold
Xu & Gordon, PNAS, 2003
Summarized in A. O’Hara and F. Shanahan, “The gut flora as a forgotten organ”
Bacteroides thetaiotaomicron in Mouse
JI Gordon lab (Washington University)
Normally infection of the gut occurs at birth
Gnotobiotic = germ-free from birth
Infection of gnotobiotic mice with single strain of B. thetaiotaomicron(LV Hooper et al 2001 Science)
Infection had major effects on expression of >100 mouse genes including genes modulating fundamental intestinal functions, some of these are affected similarly in zebra fish
Major effects on development of intestine, vascularization
induction of capillary networks in intestine, etc.
Absorption and processing of carbohydrates & lipids: germ-free mice require ~30% more calories
IMMUNITY AND DEFENSE
Neutralization of dietary toxins
Mucosal barrier protects against infectious microbes
Bacterial surface molecules affect immune system functioning
is dependent on presence of bacteria
Germ-free conventional B. thetaiotamicron only
Bacteroides thetaiotaomicron genome
Gene content of the bacterium reflects its nutritional role esp in carbohydrate metabolism
172 glycosylhydrolases for breaking down carbohydratess into easily absorbed sugars, many of these are secreted from bacterial cells)
Clear capacity for continued gene turnover and acquisition of new DNA and genes (phage, etc. ).
Symbionts, particularly consortia of commensal bacteria, can be a
means of acquiring novel metabolic functions in eukaryotes
Much of Bt genome is devoted to making binding proteins plus surface-localized glycohydrolases that liberate simple sugars from the carbohydrates.
Sugars available to be used by:
host, Bt, other bacteria
B. thetaiotamicron upregulates a large set of its genes upon colonization of the mouse intestine
64 enzymes for digesting polysaccharides in dietary fiber
Xylan, pectin, arabinose degrading enzymes.
Many of these are secreted by the bacteria.
Expression (transcription) is affected by mouse diet.
Shows adaptation to the gut-bound lifestyle.
Host mucous provides an endogenous source of glycans used by Bt when dietary supply is low.
Bt embed in the mucosal layer (next slide)
Scanning electron microscope images showing distribution of B. thetaiotaomicron within its intestinal habitat.
(A) Low-power view of the distal small intestine of B. thetaiotaomicron– monoassociated gnotobiotic mice, showing a villus (arrow) viewed from above. (B to D) Progressively higher power views showing B. thetaiotaomicron associated with luminal contents (food particles, shed mucus) [arrows in (B) and (C)] and embedded in the mucus layer overlying the epithelium [boxed region in (C), larger image in (D)]. Scale bars, 50 µm (A), 5 µm [(B) and (C)], 0.5 µm (D).
Sonnenberg et al 2005 Science 307:1955
use hydrogen gas (generated by carb digestion) to make
methane, thereby increasing
efficiency of energy conversion
Manipulation of microbial gut
community could lower propensity for obesity?
Determines efficiency of caloric uptake
"Changes in microbial ecology prompted by Western diets, and/or differences in microbial ecology between individuals living in these societies, may function as an 'environmental' factor that affects predisposition toward energy storage and obesity.”
Backhad et al. Proc Natl Acad Sci USA 2004; 101: 15718-15723