# Presentation: 573295

## Creating theGenomic Encyclopedia for Bacteria and Archaea

- Veronika Vonstein, Sveta Gerdes, Folker Meyer, Kevin White,
- Tim Lilburn, Barney Whitman, et. al.

***Creating the******Genomic Encyclopedia for Bacteria and Archaea***

*Rick Stevens **	**	**	**	** Eddy Rubin*
*Argonne National Laboratory**	**	**Joint Genome Institute*
*The University of Chicago**	**	**	**Berkeley Lab*

## The Basic Idea of the Project

- To build an enterprise that can take advantage of the expected exponential improvements of sequencing capabilities to sequence “all known” cultured and described prokaryotes
- Ride the expected “Moore’s law” of sequencing capability
- To develop a distributed high-throughput “industrial” approach to the cultivation, characterization, sequencing, annotation and analysis of prokaryotic genomes
- Build a team from groups that have expertise and track records
- To build and curate a database of genome sequences, metabolic reconstructions, and standardized phenotype assays associated with each target organism
- Streamline the release of data, provide a foundation for derivative projects

## Concept of the Bergey’s/GEBA Sequencing Project

*A Fixed cost* annual investment
- Each year more can be sequenced as sequencing costs decrease and as cultivation efficiencies improve based on experience
- Leverage the expected improvement of sequencing costs
- Address the overall scope within 5 to 6 years
- Increase amount of near complete sequences per year
- Optimize the choice of organisms to maximize diversity at each stage
- Exploit the Bergey’s Trust and International Committee on Systematics for Prokaryotes for Taxonomic coverage (e.g. Garrity and Whitman)
- Involve the microbiology community for prioritization
*Industrialize* the pipeline
- Biological Resource Centers to produce and characterize type material
- DOE JGI, NIAID/DMID Centers, NSF/USDA Centers for Sequencing
- Laboratories for bioinformatics (Argonne, JGI, TIGR, ORNL, etc.)
- Universities and Laboratories for modeling and analysis

## The Question is not if, but When and How ?

- Why should we want to accelerate this transition?
- Why not just let it happen as a matter of course?
- What is in the current sequencing pipeline?
- Completed Genomes		Ongoing/In the Pipeline
- Archaeal 	  29				 56
- Bacterial	397				991
- Eukaryal	  44				631
- The existing process of bottoms up selection of organisms for sequencing is leaving many important groups underrepresented, closure will take a long time
- There are groups are well represented in the literature, but not in the sequencing databases
- Under representation  is  also an issue in environmental sequencing data

## Tapping into prokaryotic biodiversity - Industrial Biotechnology

**Hans E. Schoemaker, et al. 2003. Science 299:1694-97**

- • Rapidly growing field
- 	 • by 2010 biocatalysis will be used in production of 60% of fine chemicals (McKinsey analysis)
- 	 • In US coordinated by USDA Biobased Products and Bioenergy Coordination Council (BBCC)
- • Applications:
-   pharmaceuticals
-   food ingredients (sweeteners, vitamins)
-   feed additives and other agrochemicals
-   organic solvents
-   polymer raw materials
-   biofuels
- • Advantages over chemical methods:
-     • exquisite substrate specificity
-     • excellent chemo-, regio-  and stereoselectivity
-     • environmentally friendly “green chemistry”   based on biorenewables
- • Needed:
-    • novel enzymes and pathways
-    • “Periodic table” of biochemical transformations

**Straathof et al. 2002. Curr Opinion Biothech 13:548-56**

- ~150 compounds are currently produced on industrial scale using biocatalysts.  Examples:

## Analysis of 1000s of new bacterial genomes will likely yield completely novel pathways and enzymes for industrial applications     

**Still to be discovered:** enzymes involved in the biosynthesis or catabolism of approximately 40 naturally occurring chemical functional groups are still not known

- L.P. Wackett. 2004. Current Opinion in Biotechnology, 15:280–284

- Examples of recently discovered biocatalytic transformations of novel organic functional groups:

- • Current approaches to discovery of new enzymes:
- Screening environmental    samples by enrichment cultures (BUT: only <<1% prokaryotes are currently culturable)
- Metagenome approach: cloning & expression of DNA samples in a surrogate host, then screening for desired function (BUT: only known functions can be screened for, new biochemistry cannot be discovered)
-   Sequence-based discovery      (growing explosively, generating knowledge base for basic sciences and biotechnological applications)

## Building the Case

- There is a disparity between the literature and the existing genomes
- We can’t fully exploit the community’s historical knowledge and investments without closing this gap
- There is a disparity between the rank/abundance curves from 16s studies and from environmental sequencing projects and the existing genomes
- We can’t fully understand the new datasets without closing this gap (I.e. lack of complete sequence coverage of known culturables is holding back future work)
- There is likely to be new biochemical pathways and novel enzymes in the set of culturable but unsequenced organisms, sequencing non-cultured organisms to expand diversity
- These represent the low hanging fruit for discovery since the investment has already be made in determining culture conditions
- A comprehensive database produced under controlled conditions that includes phenotype data and genotype data will accelerate research in understanding the genotype-phenotype relationship
- Genome-Scale reconstruction and modeling will be dramatically accelerated by comprehensive databases that include phenotype data

## Estimated Sequencing Rates

***Estimated Sequencing Rates***

- Selection
- of Targets

- Produce
- DNA

- Sequencing
- Assembly

- Rapid
- Annotation
- (24 Hours)

- Metabolic
- Reconstruction

- Model
- Generation

- Phenotype
- Prediction

- Database
- Repository

## Technical Feasibility FAQ

- How many genomes would the project propose to sequence?
- About 5000 over 5-7 years
- Who would produce the biomass needed for DNA extraction?
- Type culture centers until enrichment and environmental methods mature
- Will the biomass/DNA be available for distribution?
- Yes, both the DNA and the libraries could be stored for distribution
- What throughput is needed for DNA production?
- In the beginning of the project ~300 taxa per year to 2000 per yr at the end
- What combinations of sequencing technologies need to be employed?
- Sanger and Pyrosequencing initially, others as they come online
- What throughput is needed for annotation?
- 24 hour turnaround from assembled sequence to initial availability this has already been achieved at Argonne, TIGR and elsewhere
- Is is possible to have a standard set of phenotype assays given the broad spectrum of organisms and conditions?
- We are considering Biolog as a model, but it is too limited
- How would the genomes be selected and prioritized?
- At each cycle we choose genomes (e.g. via 16s) to minimize the diversity gaps
- Community input would be solicited to insure the project is tracking the communities interests
- Is it necessary to “close” the genomes?
- We think no.  Libraries would be archived for groups that might be interested in closing.

## The Project Would Provide a Comprehensive Set of Genome Sequences for: 

- Biofuels, and bioproduction of alternative feedstocks
- Understanding and managing the microbial carbon cycle
- Soil and subsurface microbial ecology
- Bioremediation and bioconversion of waste streams
- Evolution and microbial ecological dynamics
- Context for environmental sequencing and metagenomics
- Basis for developing predictive models of phenotypes
- Source of components for synthetic biology
- Improving our understanding of cultivability
- Dramatically improving the reliability and quality of genome annotations

## How Many Known Cultured Organisms?

- Latest version of the Prokaryotic Taxonomic Outline will contain **7951** named species of *Bacteria* and *Archaea*.
- Of these, 178 are non-cultivable or not represented by viable type material.
- An additional 1222 are synonyms.
- Of the 6543 type strains for which viable material is reportedly deposited, we have assembled a minimal set of **6389** strains that are available from 16 major public culture collections or biological resource centers in the US, Europe, and Asia.
- The remaining 154 are in minor or non-public collections.
- This information is derived from Release 6.1 of the Taxonomic Outline of the Prokaryotes which will be published in 2007 and is current through May 2006.

## What Has Been Sequenced or is In Play

- Of the 6400 strains available from public sources
- About 380 are human, animal or plant pathogens
- Order 1/3-1/2 of the known pathogens have been sequenced
- 360 complete prokaryotic genomes published
- 56 archaeal and 940 bacterial genomes in progress
- From 897 prokaryotic genomes in progress in GOLD
- ~400 are pathogens (many duplicate taxa)
- ~221 are supported by DOE (156 biotech, 51 environment)
- Approximately ~5000 prokaroytes not yet in play
- We estimate about 4800 non-pathogen taxa

## Strain Distribution in Collections

**US Collections / BRCs****	****	****	****	****Strains**
- American Type Culture Collection (ATCC)		 4027
- USDA ARS Collection (NRRL)			   223
**European Collections**
- 	Deutsche Sammlung vor Microoransmen (DSMZ)	1302
- 	Culture Collection University Gottenberg (CCUG)	  183
- 	Pasteur Institute (CIP)			  170
- 	Laboratory for Micrbiology, Gent (LMG)		  101
- 	National Collection of Industrial and
- 		Marine Bacteria			    25
- 	French Collection of Phytopathogens (CFPB)	    15
- 	National Collection of Type Cultures (NCTC)	    12
- 	National Collection of Phytopathogenic
- 		Bacteria				    11
**Asia**
- 	Japan Collection of Microorganisms (JCM)		  185
- 	Institute of Fermentation, Osaka (IFO)		    34
- 	Korean Collection of Type Cultures (KCTC)	    28
- 	Institute of Applied Microbiology, Tokyo (IAM)    	    26
- 	National Institute of Technology
- 		And Evaluation (NBRC)		    24
- 	All-Russian Collection of Microorganisms (VKM)	    13

## Distribution of Genome Sizes in the Pipeline

- Average Sequence ~ 4Mbp

## Getting Value from the Genomes

- Genomes would be assembled by the groups doing the sequencing
- Assembled contigs would be sent to the initial high-throughput annotation server for draft annotations and immediately published on-line
- The accumulated (additional) genomes will be used to improve annotations (gene calls, functional coupling)
- Genomes will be integrated into databases to support comparative analysis and evolutionary analysis
- Annotated genomes can be used to semi-automatically construct genome-scale models which could be used to make metabolic phenotype predictions

## Background

- online at
- _[http://www.sequencingbergeys.org](http://www.sequencingbergeys.org/)_
- login required (just ask us)
- guest read-only access after the meeting?
- make maximum information available
- Bergey hierarchy, NCBI taxonomy, 16s RNA, strain collections, GOLD, SEED,

## List of organisms for sequencing

**- based on 16s clusters**

## Cluster Page

**select strain for cluster**

## “Bergey” Browser

## Species Page