Microbial metagenomics: beyond the genome

JA Gilbert, CL Dupont - Annual review of marine science, 2011 - annualreviews.org
Metagenomics literally means “beyond the genome.” Marine microbial metagenomic
databases presently comprise∼ 400 billion base pairs of DNA, only∼ 3% of that found in 1 …

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

N Lombard, E Prestat, JD van Elsas… - FEMS microbiology …, 2011 - academic.oup.com
Metagenomics approaches represent an important way to acquire information on the
microbial communities present in complex environments like soil. However, to what extent …

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

P Rausch, A Rehman, S Künzel… - Proceedings of the …, 2011 - National Acad Sciences
The FUT2 (Secretor) gene is responsible for the presence of ABO histo-blood group
antigens on the gastrointestinal mucosa and in bodily secretions. Individuals lacking a …

Current and future resources for functional metagenomics

KN Lam, J Cheng, K Engel, JD Neufeld… - Frontiers in …, 2015 - frontiersin.org
Functional metagenomics is a powerful experimental approach for studying gene function,
starting from the extracted DNA of mixed microbial populations. A functional approach relies …

Two decades of describing the unseen majority of aquatic microbial diversity

L Zinger, A Gobet, T Pommier - Molecular ecology, 2012 - Wiley Online Library
Aquatic environments harbour large and diverse microbial populations that ensure their
functioning and sustainability. In the current context of global change, characterizing …

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

L Tasse, J Bercovici, S Pizzut-Serin, P Robe… - Genome …, 2010 - genome.cshlp.org
The human gut microbiome is a complex ecosystem composed mainly of uncultured
bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material …

Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

JL Morgan, AE Darling, JA Eisen - PloS one, 2010 - journals.plos.org
Background Microbial life dominates the earth, but many species are difficult or even
impossible to study under laboratory conditions. Sequencing DNA directly from the …

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

Y Shi, GW Tyson, JM Eppley, EF DeLong - The ISME journal, 2011 - academic.oup.com
As part of an ongoing survey of microbial community gene expression in the ocean, we
sequenced and compared∼ 38 Mbp of community transcriptomes and∼ 157 Mbp of …

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics

BL Hurwitz, L Deng, BT Poulos… - Environmental …, 2013 - Wiley Online Library
Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer,
yet their study is limited by complex methodologies with little validation. Here, we use …

Comparative Genomics Reveals Adaptation by Alteromonas sp. SN2 to Marine Tidal-Flat Conditions: Cold Tolerance and Aromatic Hydrocarbon Metabolism

RK Math, HM Jin, JM Kim, Y Hahn, W Park… - PLoS …, 2012 - journals.plos.org
Alteromonas species are globally distributed copiotrophic bacteria in marine habitats.
Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen …