# Presentation: 344031

## 
Operating as a User Facility
Science
GEBA / Bergey  Pilot Project (part 1)

**Operating as a User Facility**
**Science**
**GEBA / Bergey  Pilot Project (part 1)**
**         **

**Update**

## G5

**Wash U****	****	**
**Baylor****	****	**** ****	**
**Broad (MIT)****	****	**** ****	**
**	****	****            **
**	**

**	****	****            **
***JGI******	*****	**

**Focus of the Sequencing Centers**
**After the Human Genome **

**G5**

**Biomed / Bioenergy / Environ****	****+**
**Biomed****	****+****	****	****	**
**Biomed****	****+ **
**Biomed****	****+****	**** ****	**
**DOE Mission**
**USER FACILITY**

**Notes:**
Data release policy

## Primary JGI User Distribution   

**KEY:  ****RED=Academic****; ****Blue=National Laboratory****; Black=Industry****  **

**Notes:**
Find out how many users

## Slide 4

## 2007 JGI User Meeting

## The Future of SequencingOn the brink of dramatic changes

**Notes:**
What is the difference between metagenomics and genomics

## 	                			      ?  bp/run  

**ABI 3730**

**   ****Sanger Capillary Based Seq**
**          ****70,000 bp/run ****	****	**** ****	**

**	****                ****	****	****	****      ****?****  ****bp/run **** **

**   ****60 Million bp/run**

**   ****~600Million bp/run**

**Notes:**
I would like to pose and invite you to respond to the challenge of what sorts of break throughs in understanding can you come up with if sequencing got enormousely cheaper and faster

##   Scientific Directions  Bioenergy, Bioremediation, C cycling	Plant Genomics 	Metagenomics 	Microbes 	           	

**Notes:**
What is the difference between metagenomics and genomics

## Role of Biology

**Tamar wallaby forestomach**
**Poplar biomass degraders**
**Asian Longhorned Beetle gut**
**Elephant Grass decomposers**

**Sun     Cellulose      Sugar     Alcohol**

**Role of Biology**

**Poplar**** **

**Termite**

***Pichia stipitis***

**Fermenters**

**Biomass converting    organisms**

**Feedstocks**

**White Rot Fungus**
***Clostridium thermocellum***
***Saccharophagus degradans ***
***Acidothermus cellulolyticus***

***Thermoanaerobacter ***
***Ethanolicus***
***Pichia stipitis***

**Soybean,  Maize, Switch Grass, Miscanthus, Sorghum, Cotton, Cassava,Brachypodium, Citrus**

**Notes:**
Lignocellulosic materials, such as crop residues and energy crops, have high energy content but the sugars are less readily available than those in starch.  We need improved technologies for converting these feedstocks to usable fuel, and genomics can play an important role.SORGHUM, Fermenters

## FermentationAlcohol

**Glucose**

**Xylose**

**Sugars from Cellulose and Hemicellulose**

## Pichia stipitis

*Pichia stipitis*

**Tom Jeffries U of Wis**

**Xylose**
***>20% of biomass is comprised of this “wood sugar”***

**A well-studied, xylose-fermenting yeast.**** **

**Notes:**
Xylose is 20% on the average of harvested biomass Ligonocellulosic biomass, a complex of cellulose, hemicellulose, and lignin, is derived from such plant-based “feedstocks” as agricultural waste, paper and pulp, wood chips, grasses, or trees such as poplar, recently sequenced by JGI.  
Enzymes are employed to break down complex carbohydrate into sugars, such as glucose and xylose, which can then be fermented to produce ethanol.  
Additional energy is required for the distillation process to achieve a fuel-grade product. 

## Selection for High EtOH Producers

***Pichia stipitis *****CBS 6054**

**Selection for High EtOH Producers**

**Mutagenesis**
**Selection for rapid growth on L-xylose**

**EtOH**
**Production**
**0.46 g etoh/g xylose**

**FPL Shi21 (*****cyc1::URA3*****)**

**EtOH**
**Production**
**0.41 g etoh/g xylose**

**Tom Jeffries **
**U of Wis**

**One Selexa Sequencing Run: Identified 35 Nucleotide**

## JGI metagenomics projects  (>30 Projects)

**2005**

**2006**

- Gutless worm (MPI)  planktonic archaea (MIT)  EBPR sludge (UW/UQ) groundwater (ORNL)

- AMD nanoarchaea (UCB)  Alaskan soil (UW)  termite hindgut (CalTech) TA-degrading bioreactor (NUS)

- Antarctic bacterioplankton (DRI)  hypersaline mats (UCol)  soil archaea (UW) Korarchaeota enrichment (Diversa)

**2007  ****8 new metagenomic projects**

**Notes:**
The reasons that I am talking about these 3 projects represent 3 different metaagenomic challenges
The termite gut represents a compex microbial community that we are not going to assemble but are mostly ointerested in the genes present.
The gutless worm on the other hand is a simple microbial community that we would like to assemble individual genomes of the microbes but have no interest in the animal host genome
While the neanderthal is a fun project that in fact we are not interested in the microbial community but are exclusively interested in the host animals genome

## Problem with Analysis of Metagenomic DataWe don’t have completed genomes for the vast majority of Archaea and Bacteria 

**Notes:**
Add more pictures depicting this process

## Archaea + Bacteria Genome Projects1473

**http://www.genomesonline.org/**

## At least 40 phyla of bacteria

**At least 40 phyla of bacteria**

## Well sampled phyla

**Acidobacteria**

**Bacteroides**

**Fibrobacteres **

**Gemmimonas**

**Verrucomicrobia **

**Planctomycetes**

**Chloroflexi**

**At least 40 phyla of bacteria**
**Genome sequences are mostly from three phyla**

**Well sampled phyla**

## Well sampled phyla

**Acidobacteria**

**Bacteroides**

**Fibrobacteres **

**Gemmimonas**

**Verrucomicrobia **

**Planctomycetes**

**Chloroflexi**

**At least 40 phyla of bacteria**
**Genome sequences are mostly from three phyla**
**Solution: Deep sampling across phyla**

**Well sampled phyla**

**No cultured taxa**

## A Genomic Encyclopedia of Bacteria and Archaea (GEBA)/ Bergey Project

**Goal**
**Create a reference microbial genome set that broadly covers the diversity of bacteria and archaea particularly those with phenotypic information and research community**

**Notes:**
That is why we need a GEBA

## Why Increase Coverage?

**    ****	**** **
**Recommended by: **
**DOE Life Sciences Division of Visitors Report,**
**Amer Acad of Micro Report “Reconciling Microbial Systemics and Genomics”**
**NRC Metagenomic report**

**Annotation**
**Functional Prediction**
**Gene discovery**
**Species phylogeny and classification**

**Notes:**
My top five mechanisms - DOE favors 2-4

## GEBA / Bergey Pilot Project at JGI

**Goal**
**To finish ~100 bacterial and archaeal genomes **
**Selected based on phylogeny, availability of  phenotype information and community interest **
**Appoach**
**Select 200 organisms**
**Order DNA from culture collections (DSMZ  and ATCC)**
**Sequence 100 for which DNA QC is received**

## GEBA Pilot Project : Components

**Project Lead (Jonathan Eisen JGI/UC Davis)**
**Project management (David Bruce JGI/ LANL)**
**Methods for sequencing in changing technology landscape (Paul Richardson JGI)**
**Linking to educational project (Cheryl Kerfeld JGI)**

**Input / Interactions with: Community Advisory Group , ASM, Academy of Microbiology, Etc...**

**Miscanthus, Soybean,  Maize,****	****Switch Grass, Sorghum, Cotton, Cassava, Brachypodium, Citrus etc..., **