4.4 Article

A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes

Related references

Note: Only part of the references are listed.
Article Environmental Sciences

Quantitative 16S rRNA Gene Amplicon Sequencing for Comprehensive Pathogenic Bacterial Tracking in a Municipal Wastewater Treatment Plant

Rasindu Galagoda et al.

Summary: Quantitative sequencing (qSeq) with spike-in internal standards was used to comprehensively quantify bacterial pathogens in a municipal wastewater treatment plant (WWTP). A novel bacterial pathogen database based on biosafety levels (BSLs) was constructed for rapid pathogen identification. The concentrations of total pathogens decreased gradually from 6.8 +/- 4.9 x 10(7) copies/mL in the influent to 1.6 +/- 1.4 x 10(5) copies/mL in the effluent.

ACS ES&T WATER (2023)

Article Engineering, Environmental

Distinct comammox Nitrospira catalyze ammonia oxidation in a full-scale groundwater treatment bioreactor under copper limited conditions

Kazuyoshi Koike et al.

Summary: Microbial ammonia oxidation is an important step in water treatment processes, and the discovery of complete ammonia-oxidizing bacteria has added a novel member to this group. In this study, a full-scale bioreactor was used to treat ammonium in groundwater, and Nitrospira was found to be the predominant ammonia-oxidizing prokaryote. Copper addition was found to affect the population structure of ammonia-oxidizing bacteria.

WATER RESEARCH (2022)

Article Biotechnology & Applied Microbiology

The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa (United States)

Jingjie Hao et al.

Summary: This study investigated the differences in microbial community abundance, composition, and diversity in soils from corn and soybean fields in Iowa using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities with increasing soil depth, with Proteobacteria dominating deep agricultural soils. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. Understanding how soil depth influences microbial communities is crucial for guiding sampling approaches in agricultural soils and enhancing soil sustainability for food security.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2021)

Article Microbiology

A comprehensive evaluation of single-end sequencing data analyses for environmental microbiome research

Meganathan P. Ramakodi

Summary: This study demonstrates the potential benefits of using single-end (SE) sequencing data in microbiome research when dealing with high numbers of low-quality reverse reads in Illumina MiSeq PE datasets. Care should be taken when interpreting microbiome structure as some taxa observed in the PE datasets may be absent in the SE datasets.

ARCHIVES OF MICROBIOLOGY (2021)

Article Microbiology

Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data

Shilei Wang et al.

Summary: The study introduced a gradient internal standard absolute quantification method to address the issue of amplicon sequencing's inability to determine microbiota absolute abundance. Demonstrated through experiments, the method proved reliable and accurate, with potential for rapid application in various ecosystem studies.

MSYSTEMS (2021)

Article Biotechnology & Applied Microbiology

Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal

Norihisa Matsuura et al.

Summary: This study evaluated the effect of sulfate concentration on enhanced biological phosphorus removal (EBPR). Results showed that high sulfate concentration can improve phosphorus removal efficiency and promote the growth of polyphosphate-accumulating and sulfur-reducing bacteria, which play key roles in the process under high sulfate conditions.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2021)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Agricultural Engineering

A bioelectrochemical-system-based trickling filter reactor for wastewater treatment

Qiaochu Liang et al.

BIORESOURCE TECHNOLOGY (2020)

Article Ecology

Soil microbial responses to drought and exotic plants shift carbon metabolism

Sherlynette Perez Castro et al.

ISME JOURNAL (2019)

Article Biotechnology & Applied Microbiology

Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

Morgan E. Teachey et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2019)

Article Multidisciplinary Sciences

Archaea dominate oxic subseafloor communities over multimillion-year time scales

Aurele Vuillemin et al.

SCIENCE ADVANCES (2019)

Article Microbiology

Absolute quantitation of microbiota abundance in environmental samples

Andrzej Tkacz et al.

MICROBIOME (2018)

Article Biotechnology & Applied Microbiology

Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing

Oemer K. Coskun et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2018)

Article Ecology

Absolute quantification of microbial taxon abundances

Ruben Props et al.

ISME JOURNAL (2017)

Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

Article Biotechnology & Applied Microbiology

Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR

Arnaud Dechesne et al.

MICROBIAL BIOTECHNOLOGY (2016)

Review Multidisciplinary Sciences

Microbiomes in light of traits: A phylogenetic perspective

Jennifer B. H. Martiny et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

Steven F. Stoddard et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

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

Christian Quast et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemistry & Molecular Biology

Sequence-specific error profile of Illumina sequencers

Kensuke Nakamura et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biotechnology & Applied Microbiology

Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example

D. Bru et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biotechnology & Applied Microbiology

Real-time PCR assay for the simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge

Joke Geets et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2007)

Article Biochemistry & Molecular Biology

Improved PCR method for amplification of GC-Rich DNA sequences

F Hubé et al.

MOLECULAR BIOTECHNOLOGY (2005)

Article Engineering, Environmental

Real-time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant

G Harms et al.

ENVIRONMENTAL SCIENCE & TECHNOLOGY (2003)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biotechnology & Applied Microbiology

Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils

DG Bourne et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2001)

Article Biotechnology & Applied Microbiology

Molecular characterization of methanotrophic isolates from freshwater lake sediment

AJ Auman et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2000)