Rita Colwell: Genomic Sequencing as a Usef

Berkeley Regents' Lectureship, 2011 - Ruchira S. Datta

being introduced by Prof. Steven Lindow in the Microbial Biology Seminar Series - Ruchira S. Datta

she got the National Medal of Science from George W. Bush - Ruchira S. Datta

she has 48 honorary degrees - Ruchira S. Datta

has organized int'l network to address issues in water & health - Ruchira S. Datta

Distinguished Professor at U. Maryland, author of 17 books & 700 scientific publications - Ruchira S. Datta

produced film Invisible Seas - Ruchira S. Datta

she speaks on: biocomplexity - Ruchira S. Datta

take information from molecular level to environmental and ecological level. understand genomics from environment & ecosystem - Ruchira S. Datta

'discovery foments in the "hyphenated" zones of convergence' - Ruchira S. Datta

shows dust plume crossing the Mediterranean Sea from Sahara desert. large numbers of microorganisms: bacteria & fungi are transmitted in this dust - Ruchira S. Datta

look at what people have put in culture collections: have focused on soil, plant-associated bacteria, water-associated bacteria, sewage. US is primarily water & soil - Ruchira S. Datta

Japanese is primarily soil, they've been focused on antibiotic collection - Ruchira S. Datta

"I'm not sure how to interpret the German collection, it's mostly sewage." - Ruchira S. Datta

we have been focused on size, morphology & simple phenetic characteristics. but now that we study bacteria, the notion of size being critical has changed. some bacteri are bigger than red blood cells, others are 1/2 or 1 micron - size of virus. - Ruchira S. Datta

Pelagibacter has very small genome size. Some bacteria have smaller genomes than largest virus genome size. 1-11 Megabases. - Ruchira S. Datta

Claire Fraser-Ligett et al have been studying comparative genomics at levels of genus, species, and strains - Ruchira S. Datta

early study from Fred Blattner's group showed that E. coli strains only had ~40% of genes in common - Ruchira S. Datta

in some cases, 25% of genes were unique to a single strain. so it's not possible to describe a species by a single genome - Ruchira S. Datta

the more strains you sequence, the fewer genes lie in the "core" genome - Ruchira S. Datta

thus, the pan-genome: includes non-essential genes, laterally transferring genes among strains. have open pan-genome. the more diverse the lifestyles, the more laterally transferred genes - Ruchira S. Datta

Adam Philippi produced thesis 10 months ago at U.Md w/ Steven Salzberg, on pan-genome of Listeria monocytogenes - 3 lineages - Ruchira S. Datta

could the characteristics of the species be defined by the conserved genes coupled with the accessory genes - Ruchira S. Datta

exponential decay in number of genes specific to the given species as increase number of strains sequenced - Ruchira S. Datta

demonstrated three lineages in combined tree LI, LII, and LIII. Defined by genes not present in the other lineages -- 86 missing from LIII - Ruchira S. Datta

"Let me discuss my favorite bacterium, Vibrio cholerae, and the genus Vibrio" - Ruchira S. Datta

V. cholerae causes cholera. We're seeing the earthquake in Japan, but also the earthquake in Haiti that was followed by cholera outbreak, w/ question of whether it was introduced by peacekeepers. - Ruchira S. Datta

she was with team (Venter, Fraser, etc.) that sequenced the first V. cholerae. They found it has two chromosomes, as do most of Vibrio - Ruchira S. Datta

they had strains that were isolated in 1910 from Saudi Arabia, recent isolates from Bangladesh a few years ago, and many others. - Ruchira S. Datta

sequenced many Vibrios - Ruchira S. Datta

comparative genomics with V. cholerae and other Vibrios. they built a tree that separated pandemic V. cholerae from other V. cholerae - Ruchira S. Datta

within V. cholerae, sufficient variation that no two strains are identical - Ruchira S. Datta

have been able to track serotypes and various pathogenic strains: have tracked the known pathogenicity islands as well as strain-specific genomic islands - Ruchira S. Datta

were able to chronologically & geographically track the genomic changes in this species that has caused epidemics throughout the world - Ruchira S. Datta

had cholera epidemics in US until 1910 introduction of clean, chlorinated water - Ruchira S. Datta

until then, New York, Washington DC, and Montreal were centers of cholera - Ruchira S. Datta

Washington DC was a "miasmic swamp. It still is..." - Ruchira S. Datta

miasma, or bad air was thought to be the cause of disease - Ruchira S. Datta

V. cholerae serotype 01 was first epidemic strain. Another epidemic strain 0139 emerged in India in 1991. - Ruchira S. Datta

Found that the oligosaccharide antigen which had been used to track the 01 strain was actually coded for by a laterally transferred gene - Ruchira S. Datta

there are genomic shifts and drifts - Ruchira S. Datta

on the biosulfate/biosalts(sp?) medium used to isolate cholera, usually V. cholerae is bright yellow. But isolated strains from Chesapeake Bay, one of which was green on this medium, though o/w phenotypically similar. - Ruchira S. Datta

sequencing found that they were <95% similar to V. cholerae, so they were two new species V. parilis and V. metecus - Ruchira S. Datta

they found the genomic islands unique to this species, and also in other non-cholerae Vibrio speices - Ruchira S. Datta

so, they wondered how so-called "human" pathogenicity islands are distributed in the environment - Ruchira S. Datta

V. cholerae BX 330286 was isolated from a river in Australia in 1986, 9 years after there had been an epidemic of cholera had occurred in Australia, and 25 years after the 7th pandemic of cholera that started in Indonesia - Ruchira S. Datta

they sequenced it and found it fell within the 7th pandemic clade. thus the river served as a reservoir of this pathogenicity island. - Ruchira S. Datta

there was some divergence, and the changes that occurred, e.g., maltose metabolism, affected the secretion of the cholera toxin. so the so -called genes associated with pathogenicity have a function in the natural environment - Ruchira S. Datta

the pathogenic strains do live outside in the natural environment and form a part of the ecosystem - Ruchira S. Datta

in 1970, Colwell showed by very tedious procedure, density-gradient hybridization, that a strain from the environment was identical to one isolated from a patient. this created a great uproar, because the dogma was that V. cholerae only existed in the human body. - Ruchira S. Datta

another strain Vibrio mimicus resulted in a taxonomic controversy: was it a variant of V. cholerae, or a different species? - Ruchira S. Datta

they sequenced the strains, and showed the core genes were present in V. cholerae. But species-specific genes were present in the small chromosome. It is actually a chromosome and not a large plasmid: if the chromosome is eliminated, V. mimicus does not replicate. - Ruchira S. Datta

there are several virulence determinants in V. mimicus, incl CTX prophage and Vibrio Pathogenicity Island. - Ruchira S. Datta

the phylogenomics showed clearly that this is a different species from V. cholerae - Ruchira S. Datta

it also has internal variations. but its genomic relation to the 6th pandemic of V. cholerae is very interesting. the 5th, 6th, and 7th pandemics are rearrangements of V. cholerae itself. - Ruchira S. Datta

what we call virulence genes are important for the fitness of V. cholerae in its native aquatic environment - Ruchira S. Datta

as director of NSF, Colwell got to do fun things, incl. a dive in Alvin. saw what looked like copepods, asked to take a sample. - Ruchira S. Datta

their work in Chesapeake bay showed V. cholerae is associated with copepods - Ruchira S. Datta

they were with a scientist looking at methanogenic anaerobic bacteria - Ruchira S. Datta

a student had previously shown that V. cholerae could grow absolutely anaerobically. So, they streaked the 4 isolates from the hydrothermal vent anaerobically on TCBS. Did find bright yellow bacteria. - Ruchira S. Datta

Neighbor-joining on 16S put them between V. harveyi, V. alinolyticus, V. parahaemolyticus, V. diabolicus. - Ruchira S. Datta

the French had patented V. diabolicus, so couldn't get a strain, but used their published data - Ruchira S. Datta

however, these four Vibrio strains are all pathogenic in human - Ruchira S. Datta

work of Nir Hasan, about to publish the total sequence of this Vibrio sp. EX25 from the deep sea - Ruchira S. Datta

approximately 3K genes in common w/ V. agrolyticus and V. parahaemolyticus - Ruchira S. Datta

EX25 is a new species, per their sequence analysis. it is most closely related to alginolyticus. - Ruchira S. Datta

They call it Vibrio antiquarius: a Vibrio of the aquatic environment derived from the antiquity of the deep sea - Ruchira S. Datta

they found a variety of genes that have been associated with pathogenicity traits: Type III secretion system, Type VI secretion system, adherence, and pathogenicity islands - Ruchira S. Datta

V. antiquarius genome encodes many genes that can be interpreted as contributing to its being native to the deep sea, e.g., conferring barotolerance (high pressures) - Ruchira S. Datta

suspect that many so-called pathogenicity genes actually contribute to commensal relationships with zooplankton and copepods - Ruchira S. Datta

this would explain common evolution of Vibrio species that have ended up as pathogens of human and fish - Ruchira S. Datta

large number of tandem repeates suggest the genome is capable of evolving quickly to adapt to rapidly changing environments of deep sea - Ruchira S. Datta

Bradd Haley went on Fulbright and studied with Eva Benediktsdottir. They are studying sites off of Iceland - Ruchira S. Datta

Cholera is a reported disease in Iceland, and has never been reported there. - Ruchira S. Datta

whats your take on the m130 gene being found in an entire village in SOuth India ?? Proving that earlier inhabitants were 70,000 yrs ago from Africa ? - Peter Dawson

Brad and Eva isolated V. cholerae from these sites w/ water temperatures above 17 degrees C - Ruchira S. Datta

various virulence factors are present, incl. cholera toxin and even a new toxin - Ruchira S. Datta

why isn't there any cholera in Iceland. they collect rainwater, filter it through basaltic rock, and then convert it to steam. they don't eat shellfish. they don't interact with or consume the foods that are vehicles of cholera transmission - Ruchira S. Datta

the so-called virulence factors have a role in the environment. e.g., blue mussels have a high concentration of sialic acid, and Vibrio Pathogenicity Island - 2 has genes involved in sialic acid utilization - Ruchira S. Datta

the lens that we have used has been anthropocentric. instead, look at those genes as an ecologist or environmental scientist. those genes have function in the natural environment - Ruchira S. Datta

the earthquake in Haiti occurred in January 2009. it was followed by a hurricane in fall. this was followed by a massive epidemic of cholera. - Ruchira S. Datta

the peacekeepers had already come in, in January. however, because there had been a cholera epidemic in Nepal, and some of the peacekeepers were from Nepal. so there were riots in Haiti, and some Haitians lost their lives - Ruchira S. Datta

the CDC used Pulsed Field Gel Electropheresis to show the cholera strain in Haiti was similar to South Asian strains. Pac Bio very quickly sequenced a strain isolated from a Haitian patient and found it similar - Ruchira S. Datta

Colwell et al, with Jim Yorke, a mathematician of U Md - winner of Japan Prize for chaos theory -- have been working on new mathematical method for identifying bacterium from just 17-19 bp - Ruchira S. Datta

worked with Boyd Livingston, mathematician from NSA, and a statistical physicist, and a couple of bioinformaticists, and a couple of software engineers - Ruchira S. Datta

they have developed an algorithm that just needs 50-100bp straight off Illumina, w/ no need for PCR or hybridization - Ruchira S. Datta

they showed that in fact, when you sweep out the laterally transferred genes, the isolated strains from Haiti form a separate clade from the South Asian strains - Ruchira S. Datta

they now have grant from NIH to do 70 strains from patients all over Haiti, as well as some water samples - Ruchira S. Datta

will receive tomorrow or Friday, the full sequence of 16 of these from Claire Fraser-Ligett & Jack Ravel at sequencing center in Baltimore - Ruchira S. Datta

they will investigate relationship between Haitian isolates and the CIRS101 South Asian strain, which Colwell et al had previously sequenced and published in PNAS - Ruchira S. Datta

the genotype in their hands shows a newly identified genotype in Haiti. they have 45 days from getting the sequences to putting them into Genbank. "stay tuned!" - Ruchira S. Datta

even the 43 loci of the Haitian strains are different from each other. these are not the same strain, and they can say right now that the Haitian strain is more likely environmentally originated - Ruchira S. Datta

^^^^ FriendFeed as note-taking tool, I like it! - Stephen Mack

team w/ Dr. Balakrish Nayar (sp?) in Calcutta. isolated clinical samples from 50 patients who came in with V. cholerae. Also took controls w/ no symptoms of cholera. He has had his team do 26 tests, for salmonella, shigella, cryptospiridium, rotavirus, etc. - Ruchira S. Datta

cholera victim in Kolkata is nearly dying from cholera. he finds that the victim carries anywhere from 2 to 7 other pathogens. - Ruchira S. Datta

they have confirmed this with metagenomics on the controls: Campylobacter, Klebsiella, Shigella, Helicobacter pylori, etc., at low levels, not detectable by culture - Ruchira S. Datta

with their methods, can identify at strain level - Ruchira S. Datta

took pondwater from Bangladesh, seeded it with a strain of cholera, but found other naturally occurring strains, in the water that was being drunk during the epidemic - Ruchira S. Datta

see the next day's talk http://ff.im/zu2hW - Ruchira S. Datta

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