How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches

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

(2020) Ching Jian et al.   PLoS One

Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling

(2019) Brian W. Ji et al.   NATURE METHODS

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Stool Consistency: Looking Beyond the Bristol Stool Form Scale

(2019) Lisa Vork et al.   Journal of Neurogastroenterology and Motility

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

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

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Absolute quantitation of microbiota abundance in environmental samples

(2018) Andrzej Tkacz et al.   Microbiome

Response: Commentary: Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis

(2018) Gregory R. Young et al.   Frontiers in Cellular and Infection Microbiology

Absolute bacterial cell enumeration using flow cytometry

(2017) F. Ou et al.   JOURNAL OF APPLIED MICROBIOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Viability-PCR Shows That NAAT Detects a High Proportion of DNA from Non-Viable Chlamydia trachomatis

(2016) Kevin J. H. Janssen et al.   PLoS One

Gut microbiota composition associated with stool consistency

(2015) E F Tigchelaar et al.   GUT

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

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

Absolute quantification by droplet digital PCR versus analog real-time PCR

(2013) Christopher M Hindson et al.   NATURE METHODS

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

(2012) J Gregory Caporaso et al.   ISME Journal

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

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

Accuracy, Precision, and Method Detection Limits of Quantitative PCR for Airborne Bacteria and Fungi

(2010) D. Hospodsky et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology

(2008) Cindy J. Smith et al.   FEMS MICROBIOLOGY ECOLOGY