Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification

The effective migration of Massilia sp. WF1 by Phanerochaete chrysosporium and its phenanthrene biodegradation in soil

(2017) Haiping Gu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Resolving Species Level Changes in a Representative Soil Bacterial Community Using Microfluidic Quantitative PCR

(2017) Hannah Kleyer et al.   Frontiers in Microbiology

Soil bacterial quantification approaches coupling with relative abundances reflecting the changes of taxa

(2017) Zhaojing Zhang et al.   Scientific Reports

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR

(2016) Joshua R. Stokell et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Role of microbial reducing activity in antimony and arsenic release from an unpolluted wetland soil: a lab scale study using sodium azide as a microbial inhibiting agent

(2016) Asmaa Rouwane et al.   Environmental Chemistry

Efficient biodegradation of phenanthrene by a novel strain Massilia sp. WF1 isolated from a PAH-contaminated soil

(2016) Haizhen Wang et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

Complete genome sequence of Massilia sp. WG5, an efficient phenanthrene-degrading bacterium from soil

(2016) Jun Lou et al.   JOURNAL OF BIOTECHNOLOGY

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing

(2016) Dieter M. Tourlousse et al.   NUCLEIC ACIDS RESEARCH

A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing

(2016) Wenke Smets et al.   SOIL BIOLOGY & BIOCHEMISTRY

Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils

(2016) Yuanfeng Cai et al.   Nature Communications

Next generation sequencing data of a defined microbial mock community

(2016) Esther Singer et al.   Scientific Data

Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons

(2015) Justyna Połka et al.   FOOD MICROBIOLOGY

Mining the microbial dark matter

(2015) Corie Lok   NATURE

Combining flow cytometry and 16S rRNA gene pyrosequencing: A promising approach for drinking water monitoring and characterization

(2014) E.I. Prest et al.   WATER RESEARCH

Intragenomic Heterogeneity of 16S rRNA Genes Causes Overestimation of Prokaryotic Diversity

(2013) Dong-Lei Sun et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations

(2013) Karen C. Dannemiller et al.   ATMOSPHERIC ENVIRONMENT

Survival of Escherichia coli O157:H7 in soils under different land use types

(2013) Haizhen Wang et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Active microorganisms in soil: Critical review of estimation criteria and approaches

(2013) Evgenia Blagodatskaya et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial Composition of Human Appendices from Patients following Appendectomy

(2013) C. M. Guinane et al.   mBio

Real-Time PCR Methodology for Selective Detection of Viable Escherichia coli O157:H7 Cells by Targeting Z3276 as a Genetic Marker

(2012) Baoguang Li et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Natural Product Biosynthetic Gene Diversity in Geographically Distinct Soil Microbiomes

(2012) Boojala Vijay B. Reddy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Life, Death, and In-Between: Meanings and Methods in Microbiology

(2011) Hazel M. Davey   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Responses of microbial community in rhizosphere soils when ryegrass was subjected to stress from PCBs

(2011) Na Ding et al.   JOURNAL OF SOILS AND SEDIMENTS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Phytoremediation for soils contaminated by phenanthrene and pyrene with multiple plant species

(2010) Shiqiang Wei et al.   JOURNAL OF SOILS AND SEDIMENTS

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree

(2009) Laurent Philippot et al.   ENVIRONMENTAL MICROBIOLOGY