Meets Thursdays, 2:30-3:30 PM, Lillie 103, unless otherwise stated.

MBL Micro-Eco Discussion Group, Fall 2009


September 24, Show and tell (new grants)

Joe Vallino and Julie Huber

Jessica Mark Welch and colleagues


October 8 & 15, David Mark Welch

Tour of errors associated with (but not necessarily caused by) pyrosequencing, and how 454 informatics gurus are investigating and dealing with those errors.


Victor Kunin, Anna Engelbrektson, Howard Ochman and Philip Hugenholtz.  (2009) Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environmental Microbiology (in press).


Supplementary papers:

Quince C, Lanzen A, Curtis TP, et al. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. NATURE METHODS Volume: 6 Issue: 9 Pages: 639-U27

Reeder J, Knight R (2009) The 'rare biosphere': a reality check. NATURE METHODS Volume: 6 Issue: 9 Pages: 636-637


Oct. 22, Zoe Cardon

Lauber CL, Hamady M, Knight R, et al. (2009) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. APPLIED AND ENVIRONMENTAL MICROBIOLOGY Volume: 75 Issue: 15 Pages: 5111-5120

Also mentioned:

Vogel TM, Simonet P, Jansson JK, et al. (2009) TerraGenome: a consortium for the sequencing of a soil metagenome. NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 4 Pages: 252-252

And in response to this terragenome announcement, a little disagreement about where resources should be directed when trying to understand soil function and diversity...
Singh BK, Campbell CD, Sorenson SJ, et al. (2009) Soil genomics. NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 10

Baveye PC (2009) To sequence or not to sequence the whole-soil metagenome? NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 10

And Vogel et al's response to these responses...
Vogel TM, Hirsch PR, Simonet P, et al. (2009) Advantages of the metagenomic approach for soil exploration: reply from Vogel et al. NATURE REVIEWS MICROBIOLOGY Volume: 7 Issue: 10


Oct. 29 More show and tell (more new grants)

Jeremy Rich, Anne Giblin, and Joe Vallino

Anton Post


Nov. 5 Emelia DeForce

Report on a soil metagenomics/MG-RAST workshop she attended a few weeks ago, and discussion of the Vogel et al. metagenome paper (and responses) briefly mentioned Oct. 22.


Nov. 12 Laura Williams

Laura brought this paper up at the end of our discussion Nov. 5, as an example of functional characterization of microbes using culture-independent sampling. 

Sommer MOA, Dantas G, and Church GM (2009) Functional characterization of the antibiotic resistance reservoir in the human microflora.  Science 325: 1128.

Nov. 19 Gretta Serres

A "reverse ecology" paper:

Elhanan Borenstein, Martin Kupiec, Marcus W. Feldman, and Eytan Ruppin (2008)Large-scale reconstruction and phylogenetic analysis of metabolic environments. PNAS 105:14482–14487




Dec. 3 Phil Neal

Dagmar Woebken, Bernhard M. Fuchs, Marcel M. M. Kuypers, and Rudolf Amann (2007) Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System.  APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73: 4648–4657


Dec. 10 Linda Amaral Zettler and Sheri Simmons

Gregory J Dick, Anders F Andersson, Brett J Baker, Sheri L Simmons, Brian C Thomas, A Pepper Yelton and Jillian F Banfield (2009)  Community-wide analysis of microbial genome sequence signatures. Genome Biology 10(8),R85