ISEEM:Paper DiversityMethods Computational methods for microbial diversity review

Paper by Eisen et al for PLoS Computational Biology

= Outline =

Summary and introduction
Organized in part around the metagenomic diversity workflow [[Media:Slide2.jpg| See Here]]

A key point is to compare and contrast tools for analyzing rRNA with those for analyzing metagenomic data.

rRNA PCR
See [[Media:Margulies_etal_Nature_2005.pdf]], [[Media:Mardis_et_al._Cell_2008.pdf]] See "Review and re-analysis of domain-specific 16S primers."
 * Background
 * PCR amplification with conserved primers
 * Sequencing
 * Standard
 * 454
 * Indirect characterization
 * ARISA
 * T-RFLP
 * Array
 * Desantis et al 2007 on array vs. clones
 * Informatics issues
 * Primer design
 * Chimera checking
 * Assembly of sequences from paired ends
 * rRNA databases
 * Greengenes
 * Silva

PCR of other genes

 * Done sometimes to cover broad diversity
 * RecA/RadA best example
 * Frequently done to focus on narrower groups or functional classes
 * Amanox
 * Nitrogen fixation

Metagenomic Sequencing

 * Background
 * Identifying rRNA genes
 * Identifying other genes
 * Which genes should be used?
 * Assembly
 * Metagenomic databases
 * CAMERA
 * RAST
 * IMG/M

Sequence quality issues

 * Chimera checking
 * Bellerephon

Alignment

 * rRNA
 * STAP
 * NAST
 * Sean Eddy's infernal
 * Protein families

Dividing into OTUs

 * rRNA focused methods
 * DOTUR
 * FastGroup II to dereplicate

Phylogenetic trees

 * Building trees
 * Phylogenetic classification
 * Alignment independent method
 * PhyloPythia - doesn't use tree, SVM at each node
 * Phylogenetic structure
 * Phylogenetic based OTUs

Web servers that do multiple things

 * Fast Group II
 * NAST Server
 * EZ TAXON

Richness estimators

 * Reviews
 * Hughes et al. AEM Review
 * Lozupone and Knight FEMS Review
 * Parametric
 * Non parametric

Issues with different sequencing methods

 * 454 Sequencing
 * See recent paper by R. Knight on methods

General approaches and Introduction

 * Multiple ways to compare communities and to think about the comparisons
 * Good discussion of this on p559 in Lozupone and Knight review
 * I (Eisen) view things a little differently
 * Would be useful to at least briefly link the microbial diversity/phylodiversity literature to the non-microbial ecology literature on this subject
 * Note parallel development of methods and tools to answer many of the same questions with different datasets. Emphasize need to unify.
 * First key issue is whether to analyze communities one by one with some metric and then to compare the scores or to develop scores explicitly from comparing communities
 * i.e. alpha vs. beta diversity
 * Within community metric could be
 * Richness
 * Diversity
 * Lozupone and Knight outline a few other issues including
 * Qualitative vs. quantitative
 * Qualitative do not take into account species counts, just presence/absence
 * Species based or tree based

OTU and phylotype focused

 * Presence/absence of OTUs
 * Presence/absence of phylotypes (at all levels)
 * SONS

Coverage and Statistical Significance

 * See f-Libshuff
 * See Original libshuff

Phylogenetic structure of communities

 * See Tree Climber
 * See AP Martin paper on phylogenetic based comparison where FST and P test introduced
 * See AP Martin paper #1
 * Unifrac
 * Online version paper here
 * Original paper here
 * Weighted Unifrac

Metagenomic distances

 * Rohwer Marine Viromes
 * Edwards Rohwer et al Statistics paper
 * Also see Rusch paper

Statistical issues

 * Sampling
 * Statistical concepts (e.g. experimental unit (species, community, environment, day, etc))
 * Assessing reliability and repeatability of results

= Case Studies and Science =

Reviews on methods

 * See New Review by Schloss
 * See new Schloss paper
 * http://www.nature.com/ismej/journal/v2/n7/abs/ismej200844a.html;jsessionid=12A1751090E8D55918D9AC086B76837F
 * http://www.ncbi.nlm.nih.gov/pubmed/18435746?ordinalpos=18&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

Metagenomics informatics

 * Reviews
 * Chen and Pachter. PLoS Comp. Biol 2005
 * Schloss and Handelsman Statistical toolbox
 * Binning
 * Phylopythia by McHardy et al.

General diversity things

 * See Curtis et al. review
 * See Global patterns in microbial diversity paper
 * See Beta diversity paper by Knight
 * See Hughes rarefaction paper

Biogeography

 * See Taxa Area Paper
 * Also see Other island paper
 * See Freir paper
 * See Green et al on microbial euks

= Tables =

Data Types

 * rRNA sequence
 * Pros
 * Cons
 * rRNA tRFLP
 * Pros
 * Cons
 * metagenomics
 * Pros
 * Cons

Diversity Methods

 * alpha diversity
 * Phylogenetic diversity (PD)
 * Pros
 * Cons
 * Applications
 * References
 * beta diversity