Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

The relative importance of the bacterial pathway and soil inorganic nitrogen increase across an extreme wood-ash application gradient

(2018) Mette Vestergård et al.   Global Change Biology Bioenergy

Bioaugmentation of rapid sand filters by microbiome priming with a nitrifying consortium will optimize production of drinking water from groundwater

(2018) Christian Nyrop Albers et al.   WATER RESEARCH

Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples

(2018) Carsten Suhr Jacobsen et al.   Scientific Reports

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation

(2017) Shubin He et al.   Scientific Reports

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Establishment of Bacterial Herbicide Degraders in a Rapid Sand Filter for Bioremediation of Phenoxypropionate-Polluted Groundwater

(2015) Louise Feld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles

(2014) Katherine Kennedy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

The impact of bioaugmentation on dechlorination kinetics and on microbial dechlorinating communities in subsurface clay till

(2013) Jacob Bælum et al.   ENVIRONMENTAL POLLUTION

Commercial DNA extraction kits impact observed microbial community composition in permafrost samples

(2013) Tatiana A. Vishnivetskaya et al.   FEMS MICROBIOLOGY ECOLOGY

Characterization of Depth-Related Changes in Bacterial Communities Involved in Mineral Weathering Along a Mineral-Rich Soil Profile

(2013) Qi Wang et al.   GEOMICROBIOLOGY JOURNAL

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

(2013) Michele Simbolo et al.   PLoS One

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Early life treatment with vancomycin propagates Akkermansia muciniphila and reduces diabetes incidence in the NOD mouse

(2012) C. H. F. Hansen et al.   DIABETOLOGIA

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

(2012) Juan M. Gonzalez et al.   PLoS One

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

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

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

Metagenomic comparison of direct and indirect soil DNA extraction approaches

(2011) Tom O. Delmont et al.   JOURNAL OF MICROBIOLOGICAL METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Optimizing the indirect extraction of prokaryotic DNA from soils

(2010) Kurt. E. Williamson et al.   SOIL BIOLOGY & BIOCHEMISTRY