Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions

An Advanced Protocol for the Quantification of Marine Sediment Viruses via Flow Cytometry

(2021) Mara Elena Heinrichs et al.   Viruses-Basel

In vitro optoacoustic flow cytometry with light scattering referencing

(2021) Markus Seeger et al.   Scientific Reports

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

(2021) Tjorven Hinzke et al.   eLife

Comparison of Two 16S rRNA Primers (V3–V4 and V4–V5) for Studies of Arctic Microbial Communities

(2021) Eduard Fadeev et al.   Frontiers in Microbiology

CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

(2021) Kasia Piwosz et al.   Frontiers in Microbiology

Experimental parameters defining ultra-low biomass bioaerosol analysis

(2021) Irvan Luhung et al.   npj Biofilms and Microbiomes

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees

(2021) Matteo Callegari et al.   npj Biofilms and Microbiomes

Effect of Lactylate and Bacillus subtilis on Growth Performance, Peripheral Blood Cell Profile, and Gut Microbiota of Nursery Pigs

(2021) Xiaofan Wang et al.   Microorganisms

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

(2020) Ching Jian et al.   PLoS One

Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations

(2020) Kasia Piwosz et al.   mSphere

Seasonal Dynamics of the Activated Sludge Microbiome in Sequencing Batch Reactors using 16S rRNA Transcript Amplicon Sequencing

(2020) Juliet Johnston et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Development of a droplet digital PCR method for detection of Streptococcus agalactiae

(2020) Yi-Fan Zeng et al.   BMC MICROBIOLOGY

Cascading effects in freshwater microbial food webs by predatory Cercozoa, Katablepharidacea and ciliates feeding on aplastidic bacterivorous cryptophytes

(2020) Karel Šimek et al.   FEMS MICROBIOLOGY ECOLOGY

Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions

(2020) Ying Xu et al.   INDOOR AIR

A comparison of culture-based, real-time PCR, droplet digital PCR and flow cytometric methods for the detection of Burkholderia cepacia complex in nuclease-free water and antiseptics

(2020) Youngbeom Ahn et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Diversity and biomass dynamics of unicellular marine fungi during a spring phytoplankton bloom

(2020) Taylor Priest et al.   ENVIRONMENTAL MICROBIOLOGY

Effects of phosphogypsum and medical stone on nitrogen transformation, nitrogen functional genes, and bacterial community during aerobic composting

(2020) Liusheng Lei et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Development of Fluorescence In Situ Hybridization as a Rapid, Accurate Method for Detecting Coliforms in Water Samples

(2020) Jong-Tar Kuo et al.   Biosensors-Basel

Evaluation of different molecular and phenotypic methods for identification of environmental Burkholderia cepacia complex

(2019) João Pedro Rueda Furlan et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Rapid and Sensitive Quantification of Anammox Bacteria by Flow Cytometric Analysis Based on Catalyzed Reporter Deposition Fluorescence In Situ Hybridization

(2019) Yijing Zhu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Improving the Accuracy of Flow Cytometric Quantification of Microbial Populations in Sediments: Importance of Cell Staining Procedures

(2019) Longhui Deng et al.   Frontiers in Microbiology

Longitudinal investigation of the swine gut microbiome from birth to market reveals stage and growth performance associated bacteria

(2019) Xiaofan Wang et al.   Microbiome

16S rDNA droplet digital PCR for monitoring bacterial DNAemia in bloodstream infections

(2019) Ingrid Ziegler et al.   PLoS One

Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples

(2018) Guillaume Gobert et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Use of an improved high-throughput absolute abundance quantification method to characterize soil bacterial community and dynamics

(2018) Li Yang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

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

(2018) Jun Lou et al.   PeerJ

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples

(2018) Jeremiah J. Minich et al.   mSystems

Molecular analyses of protists in long-term observation programmes—current status and future perspectives

(2018) Rowena Stern et al.   JOURNAL OF PLANKTON RESEARCH

Viable bacteria persist on antibiotic spacers following two-stage revision for periprosthetic joint infection

(2017) Dongzhu Ma et al.   JOURNAL OF ORTHOPAEDIC RESEARCH

Temperature variation, bacterial diversity and fungal infection dynamics in the amphibian skin

(2017) Ana V. Longo et al.   MOLECULAR ECOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

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

(2017) Zhaojing Zhang et al.   Scientific Reports

Absolute quantification of microbial taxon abundances

(2016) Ruben Props et al.   ISME Journal

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

Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness

(2016) Hui Yang et al.   Scientific Reports

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

(2016) Monika Mortimer et al.   Nanomaterials

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

Spatio-Temporal Variations of High and Low Nucleic Acid Content Bacteria in an Exorheic River

(2016) Jie Liu et al.   PLoS One

Microbial Infections Are Associated with Embryo Mortality in Arctic-Nesting Geese

(2015) Cristina M. Hansen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A simple separation method for downstream biochemical analysis of aquatic microbes

(2015) Cody E. Garrison et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes

(2015) Alexander Mahnert et al.   PLoS One

Comparison of droplet digital PCR and quantitative real-time PCR for examining population dynamics of bacteria in soil

(2014) Tae Gwan Kim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Catchment-scale biogeography of riverine bacterioplankton

(2014) Daniel S Read et al.   ISME Journal

Linking Host Prokaryotic Physiology to Viral Lifestyle Dynamics in a Temperate Freshwater Lake (Lake Pavin, France)

(2014) S. Palesse et al.   MICROBIAL ECOLOGY

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

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

A Comparison between Droplet Digital and Quantitative PCR in the Analysis of Bacterial 16S Load in Lung Tissue Samples from Control and COPD GOLD 2

(2014) Marc A. Sze et al.   PLoS One

Applications of Flow Cytometry to Characterize Bacterial Physiological Responses

(2014) Verónica Ambriz-Aviña et al.   Biomed Research International

Analytical opportunities of quantitative polymerase chain reaction in dairy microbiology

(2013) Mickaël Boyer et al.   INTERNATIONAL DAIRY JOURNAL

Monitoring microbiological changes in drinking water systems using a fast and reproducible flow cytometric method

(2013) E.I. Prest et al.   WATER RESEARCH

Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples

(2012) Robert Brankatschk et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Crohn's Disease Patients Have More IgG-Binding Fecal Bacteria than Controls

(2012) Hermie J. M. Harmsen et al.   Clinical and Vaccine Immunology

A flow cytometer based protocol for quantitative analysis of bloom-forming cyanobacteria (Microcystis) in lake sediments

(2012) Quan Zhou et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

The evolution of size of the uropygial gland: mutualistic feather mites and uropygial secretion reduce bacterial loads of eggshells and hatching failures of European birds

(2012) J. J. Soler et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

CARD-FISH for Environmental Microorganisms: Technical Advancement and Future Applications

(2012) Kengo Kubota   MICROBES AND ENVIRONMENTS

Similar Gene Estimates from Circular and Linear Standards in Quantitative PCR Analyses Using the Prokaryotic 16S rRNA Gene as a Model

(2012) Athenia L. Oldham et al.   PLoS One

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number

(2011) Benjamin J. Hindson et al.   ANALYTICAL CHEMISTRY

Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria ‘that rule the waves’ (LD12)

(2011) Michaela M Salcher et al.   ISME Journal

Prevalence of potentially pathogenic culturable bacteria on eggshells and in cloacae of female Pied Flycatchers in a temperate habitat in central Spain

(2011) Rafael Ruiz-de-Castañeda et al.   JOURNAL OF FIELD ORNITHOLOGY

Reverse transcriptase real-time PCR for detection and quantification of viable Campylobacter jejuni directly from poultry faecal samples

(2011) Xuan Thanh Bui et al.   RESEARCH IN MICROBIOLOGY

Reliable Detection of Dead Microbial Cells by Using Fluorescent Hydrazides

(2009) C. Saint-Ruf et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Establishment of an Analytical System for the Human Fecal Microbiota, Based on Reverse Transcription-Quantitative PCR Targeting of Multicopy rRNA Molecules

(2009) K. Matsuda et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Feather micro-organisms and uropygial antimicrobial defences in a colonial passerine bird

(2009) Anders P. Møller et al.   FUNCTIONAL ECOLOGY

Isolation and characterization of low nucleic acid (LNA)-content bacteria

(2009) Yingying Wang et al.   ISME Journal

A novel quantitative reverse-transcription PCR (qRT-PCR) for the enumeration of total bacteria, using meat micro-flora as a model

(2008) Anthony Dolan et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE