ArticleNature protocols2020
Bacterial mock communities as standards for reproducible cytometric microbiome analysis.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed, 38 citations in OpenAlex.
- A Step-by-Step Guide to Successful Multiparametric Microbiota Flow Cytometry.Current protocols · 2026Article
- Phenotypic heterogeneity optimizes trade-offs during adaptive deployment of the type VI secretion system.PLoS biology · 2026Article
- A Cell-Penetrating Peptide-Derived Fluorescent Probe for Selective Isolation of Bacterial Spores.Microbial biotechnology · 2026Article
- Synechocystis sp. PCC 6803 shows high cell cycle dynamics reflected by an extraordinary genome copy number variation.Microbial cell factories · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- A double-staining automated flow cytometry method for real-time monitoring of bacteria in continuous bioreactors.NPJ systems biology and applications · 2026Article
- Transcriptomic profiling of individual bacteria by MATQ-seq.Nature protocols · 2025Review
- Long-term TCDD oral exposure changes gut microbial glycosylation patterns in female but not male C57BL/6 mice.Archives of toxicology · 2025Article
- Systematic evaluation of metatranscriptomic differential gene expressionbioRxiv : the preprint server for biology · 2025Article
- Integrating taxonomic and phenotypic information through FISH-enhanced flow cytometry for microbial community dynamics analysis.Microbiology spectrum · 2025Article
- Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.Microbiology and molecular biology reviews : MMBR · 2025Review
- Article
- Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.Microorganisms · 2023Article
- Opportunities in optical and electrical single-cell technologies to study microbial ecosystems.Frontiers in microbiology · 2023Review
- Stabilizing microbial communities by looped mass transfer.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification.ISME communications · 2022Article
- Current Production Capability of Drug-Resistant Pathogen Enables Its Rapid Label-Free Detection Applicable to Wastewater-Based Epidemiology.Microorganisms · 2022Article
- Automated flow cytometry as a tool to obtain a fine-grain picture of marine prokaryote community structure along an entire oceanographic cruise.Frontiers in microbiology · 2022Article
- Automatic, fast, hierarchical, and non-overlapping gating of flow cytometric data with flowEMMi v2.Computational and structural biotechnology journal · 2022Article
- Predicting the Presence and Abundance of Bacterial Taxa in Environmental Communities through Flow Cytometric Fingerprinting.mSystems · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Flow cytometry has recently established itself as a tool to track short-term dynamics in microbial community assembly and link those dynamics with ecological parameters. However, instrumental configurations of commercial cytometers and variability introduced through differential handling of the cells and instruments frequently cause data set variability at the single-cell level. This is especially pronounced with microorganisms, which are in the lower range of optical resolution. Although alignment beads are valuable to generally minimize instrumental noise and align overall machine settings, an artificial microbial cytometric mock community (mCMC) is mandatory for validating lab workflows and enabling comparison of data between experiments, thus representing a necessary reference standard for the reproducible cytometric characterization of microbial communities, especially in long-term studies. In this study, the mock community consisted of two Gram-positive and two Gram-negative bacterial strains, which can be assembled with respective subsets of cells, including spores, in any selected ratio or concentration. The preparation of the four strains takes a maximum of 5 d, and the stains are storable with either PFA/ethanol fixation at -20 °C or drying at 4 °C for at least 6 months. Starting from this stock, an mCMC can be assembled within 1 h. Fluorescence staining methods are presented and representatively applied with two high-resolution cell sorters and three benchtop flow cytometers. Benchmarked data sets allow the use of bioinformatic evaluation procedures to decode community behavior or convey qualified cell sorting decisions for subsequent high-resolution sequencing or proteomic routines.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.