metagenomics

Mini Review
Systems-based approaches to unravel multi-species microbial community functioning
Florence Abram

http://www.sciencedirect.com/science/article/pii/S2001037014000506#

Abstract

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
Salter S. J. et al. (2014), BMC Biology 12: 84.
http://www.biomedcentral.com/content/pdf/s12915-014-0087-z.pdf

Background: The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents.

Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization
Nikolina Udikovic-Kolica,b,1, Fabienne Wichmanna,c,1, Nichole A. Brodericka, and Jo Handelsmana,2

http://www.yale.edu/handelsmanlab/publications/pdf/BloomofResidentAntibi...
PNAS

The increasing prevalence of antibiotic-resistant bacteria is a global
threat to public health. Agricultural use of antibiotics is believed to
contribute to the spread of antibiotic resistance, but the mechanisms
by which many agricultural practices influence resistance

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0106833

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0106707

I am a microbial ecologist in Kirsten Hofmockel’s lab with broad interests in ecosystem processes, microbial communities, plant-microbe symbiotic relationships, and nutrient cycling.
More specifically, my research focuses on the long-term consequences of organic amendments and crop-system diversification on soil microbial community composition, as well as the metabolically active populations involved in carbon and nitrogen transformations.

I am a Ph.D. student in the Interdepartmental Microbiology program. My research focuses on determining the key microbial organisms involved in C cycling, particularly cellulose degradation. I use a combination of field experiments, to determine the impact of plant/soil interactions on microbial cellulose degradation, and lab incubations with fluorescently labeled cellulose nanocrystals to directly determine the key microbes involved in C cycling.

Email - [email protected]

Verastegul et al. 2014 Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities. mBio 5(4): doi:10.1128/mBio.01157-14.

Open Access:
http://mbio.asm.org/content/5/4/e01157-14.full.pdf+html

ABSTRACT

Relating the metatranscriptome and metagenome of the human gut, Franzoa et al. 2014 PNAS

http://www.pnas.org/content/early/2014/05/14/1319284111.full.pdf+html

Abstract

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2013254a.html