A Review of Methods to Determine Viability, Vitality, and Metabolic Rates in Microbiology

Next-generation physiology approaches to study microbiome function at single cell level

(2020) Roland Hatzenpichler et al.   NATURE REVIEWS MICROBIOLOGY

Determining the viability of Schistosoma mansoni cercariae using fluorescence assays: An application for water treatment

(2020) Laura Braun et al.   PLoS Neglected Tropical Diseases

An automated Raman-based platform for the sorting of live cells by functional properties

(2019) Kang Soo Lee et al.   Nature Microbiology

The Chemical Transformation of the Cellular Toxin INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) as an Indicator of Prior Respiratory Activity in Aquatic Bacteria

(2019) Josué Villegas-Mendoza et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

(2019) Cornelia List et al.   ENVIRONMENTAL MICROBIOLOGY

Mass spectrometry-based non-targeted metabolic profiling for disease detection: Recent developments

(2019) Xiaoling Zang et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Increasing Temperature and Microplastic Fibers Jointly Influence Soil Aggregation by Saprobic Fungi

(2019) Yun Liang et al.   Frontiers in Microbiology

Measuring mitochondrial respiration in adherent cells infected with Trypanosoma cruzi Chagas, 1909 using Seahorse extracellular flux analyser

(2019) Laura Maria Gonzalez-Ortiz et al.   FOLIA PARASITOLOGICA

A Minimally Invasive Microsensor Specially Designed for Simultaneous Dissolved Oxygen and pH Biofilm Profiling

(2019) Xavier Guimerà et al.   SENSORS

Identification of alkaline pH optimum of human glucokinase because of ATP-mediated bias correction in outcomes of enzyme assays

(2019) Daniela Šimčíková et al.   Scientific Reports

Current methodology of MTT assay in bacteria – A review

(2018) Ewa Grela et al.   ACTA HISTOCHEMICA

Tetrazolium salts and formazan products in Cell Biology: Viability assessment, fluorescence imaging, and labeling perspectives

(2018) Juan C. Stockert et al.   ACTA HISTOCHEMICA

Long-term metabolic persistence of gram-positive bacteria on health care-relevant plastic

(2018) Loree C. Heller et al.   AMERICAN JOURNAL OF INFECTION CONTROL

Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean

(2018) Xiaoyan Jing et al.   ENVIRONMENTAL MICROBIOLOGY

Automated rapid blood culture sensor system based on diode laser wavelength-modulation spectroscopy for microbial growth analysis

(2018) Jie Shao et al.   SENSORS AND ACTUATORS B-CHEMICAL

Laser spectroscopy for breath analysis: towards clinical implementation

(2018) Ben Henderson et al.   APPLIED PHYSICS B-LASERS AND OPTICS

The bulk fluorescein diacetate assay (FDA) as a technique for evaluating biotic impacts of crude oil to coastal sediments

(2018) Edem Mahu et al.   Environmental Earth Sciences

Capturing the genetic makeup of the active microbiome in situ

(2017) Esther Singer et al.   ISME Journal

Chemical tools for detecting Fe ions

(2017) Tasuku Hirayama et al.   JOURNAL OF CLINICAL BIOCHEMISTRY AND NUTRITION

Quantification of anaerobic thermophilic endospores in marine sediment by microcalorimetry, and its use in bioprospecting for gas and oil

(2017) Søren Dollerup Nielsen et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Respiration: comparison of the Winkler technique, O2 electrodes, O2 optodes and the respiratory electron transport system assay

(2017) Daniel R. Bondyale-Juez et al.   MARINE BIOLOGY

Spectrophotometric assays for measuring redox biomarkers in blood and tissues: the NADPH network

(2017) Aristidis S. Veskoukis et al.   REDOX REPORT

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies

(2017) Viktória Feigl et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Tunable diode laser absorption spectroscopy as method of choice for non-invasive and automated detection of microbial growth in media fills

(2017) David Brueckner et al.   TALANTA

Using Click-Chemistry for Visualizing in Situ Changes of Translational Activity in Planktonic Marine Bacteria

(2017) Ainara Leizeaga et al.   Frontiers in Microbiology

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

(2017) Joanne B. Emerson et al.   Microbiome

Metabolic activity of mature biofilms of Mycobacterium tuberculosis and other non-tuberculous mycobacteria

(2017) Anna Solokhina et al.   Scientific Reports

Single cell stable isotope probing in microbiology using Raman microspectroscopy

(2016) Yun Wang et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bioenergetic profiling of Trypanosoma cruzi life stages using Seahorse extracellular flux technology

(2016) Sheena Shah-Simpson et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Automated determination of nitrate plus nitrite in aqueous samples with flow injection analysis using vanadium (III) chloride as reductant

(2016) Shu Wang et al.   TALANTA

Behavior and stability of adenosine triphosphate (ATP) during chlorine disinfection

(2016) Alina Nescerecka et al.   WATER RESEARCH

Comparison of Tunable Diode Laser Absorption Spectroscopy and Isothermal Micro-calorimetry for Non-invasive Detection of Microbial Growth in Media Fills

(2016) David Brueckner et al.   Scientific Reports

Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies

(2016) Matias Fuentealba et al.   PLoS One

Microbial activity in surface sediments of Chacopata-Bocaripo lagoon axis, Sucre State, Venezuela

(2015) Mary Isabel Segnini de B et al.   MARINE POLLUTION BULLETIN

Calorespirometry of terrestrial organisms and ecosystems

(2015) Lars Wadsö et al.   METHODS

Microcalorimetric assays for measuring cell growth and metabolic activity: Methodology and applications

(2015) O. Braissant et al.   METHODS

INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) Is Toxic to Prokaryote Cells Precluding Its Use with Whole Cells as a Proxy for In Vivo Respiration

(2015) Josué Villegas-Mendoza et al.   MICROBIAL ECOLOGY

Transmutation of Personal Glucose Meters into Portable and Highly Sensitive Microbial Pathogen Detection Platform

(2015) Zhenzhen Wang et al.   Small

Non-specific interaction of carbon nanotubes with the resazurin assay reagent: Impact on in vitro assessment of nanoparticle cytotoxicity

(2015) Dalibor Breznan et al.   TOXICOLOGY IN VITRO

Early non-destructive biofouling detection and spatial distribution: Application of oxygen sensing optodes

(2015) N.M. Farhat et al.   WATER RESEARCH

Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats

(2015) Hon Lun Wong et al.   Scientific Reports

NADPH-generating systems in bacteria and archaea

(2015) Sebastiaan K. Spaans et al.   Frontiers in Microbiology

The Application of the Biolog EcoPlate Approach in Ecotoxicological Evaluation of Dairy Sewage Sludge

(2014) Agata Gryta et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Isolation and characterization of oxalotrophic bacteria from tropical soils

(2014) Daniel Bravo et al.   ARCHIVES OF MICROBIOLOGY

In situvisualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry

(2014) Roland Hatzenpichler et al.   ENVIRONMENTAL MICROBIOLOGY

Characterization of bacterial diversity associated with microbial mats, gypsum evaporites and carbonate microbialites in thalassic wetlands: Tebenquiche and La Brava, Salar de Atacama, Chile

(2014) M. E. Farías et al.   EXTREMOPHILES

Analysis of Metabolism in Dormant Spores of Bacillus Species by31P Nuclear Magnetic Resonance Analysis of Low-Molecular-Weight Compounds

(2014) Sonali Ghosh et al.   JOURNAL OF BACTERIOLOGY

Diabetic glucose meter for the determination of glucose in microbial cultures

(2014) Raphael Flavigny   JOURNAL OF MICROBIOLOGICAL METHODS

A fast and direct spectrophotometric method for the sequential determination of nitrate and nitrite at low concentrations in small volumes

(2014) Emilio García-Robledo et al.   MARINE CHEMISTRY

Diel fluctuations in solute distributions and biogeochemical cycling in a hypersaline microbial mat from Shark Bay, WA

(2014) Anais Pages et al.   MARINE CHEMISTRY

On the Dynamics of the Adenylate Energy System: Homeorhesis vs Homeostasis

(2014) Ildefonso M. De la Fuente et al.   PLoS One

Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging

(2014) Hideyuki Yaginuma et al.   Scientific Reports

Viability Assays for Cells in Culture

(2014) Jessica M. Posimo et al.   Jove-Journal of Visualized Experiments

Raman Activated Cell Ejection for Isolation of Single Cells

(2013) Yun Wang et al.   ANALYTICAL CHEMISTRY

Oxygen Consumption Rates of Bacteria under Nutrient-Limited Conditions

(2013) T. E. Riedel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Release of extracellular ATP by bacteria during growth

(2013) Roberto Mempin et al.   BMC MICROBIOLOGY

Toxic effects of resazurin on cell cultures

(2013) Richard Thomas Pace et al.   CYTOTECHNOLOGY

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology

(2013) Martin von Bergen et al.   ISME Journal

NMR-based metabolomics in human disease diagnosis: applications, limitations, and recommendations

(2013) Abdul-Hamid M. Emwas et al.   Metabolomics

Functional Assays and Metagenomic Analyses Reveals Differences between the Microbial Communities Inhabiting the Soil Horizons of a Norway Spruce Plantation

(2013) Stéphane Uroz et al.   PLoS One

The use of resazurin as a novel antimicrobial agent against Francisella tularensis

(2013) Deanna M. Schmitt et al.   Frontiers in Cellular and Infection Microbiology

Stable Isotope Probing and Raman Spectroscopy for Monitoring Carbon Flow in a Food Chain and Revealing Metabolic Pathway

(2012) Mengqiu Li et al.   ANALYTICAL CHEMISTRY

Comparison of different live/dead stainings for detection and quantification of adherent microorganisms in the initial oral biofilm

(2012) P. N. Tawakoli et al.   Clinical Oral Investigations

Inside the alkalinity engine: the role of electron donors in the organomineralization potential of sulfate-reducing bacteria

(2012) K. L. Gallagher et al.   Geobiology

Differential utilization of carbon substrates by aggregate-associated and water-associated heterotrophic bacterial communities

(2012) M. M. Lyons et al.   HYDROBIOLOGIA

Understanding tetrazolium reduction and the importance of substrates in measuring respiratory electron transport activity

(2012) F. Maldonado et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Measuring aerobic respiration in stream ecosystems using the resazurin-resorufin system

(2012) Ricardo González-Pinzón et al.   JOURNAL OF GEOPHYSICAL RESEARCH

Reevaluation of colorimetric iron determination methods commonly used in geomicrobiology

(2012) Juliane Braunschweig et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Recent advances in electrochemical glucose biosensors: a review

(2012) Chao Chen et al.   RSC Advances

Multiparameter Viability Assay for Stress Profiling Applied to the Food Pathogen Listeria monocytogenes F2365

(2011) Andreas Nocker et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Examination and Refinement of the Determination of Aqueous Hydrogen Sulfide by the Methylene Blue Method

(2011) Brandi Kiel Reese et al.   AQUATIC GEOCHEMISTRY

The copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) “click” reaction and its applications. An overview

(2011) Liyuan Liang et al.   COORDINATION CHEMISTRY REVIEWS

Electrochemical Analysis of Some Toxic Metals by Ion–Selective Electrodes

(2011) Vinod K. Gupta et al.   CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY

Use of an isothermal microcalorimetry assay to characterize microbial oxalotrophic activity

(2011) Daniel Bravo et al.   FEMS MICROBIOLOGY ECOLOGY

Evaluation of a low-cost calorimetric approach for rapid detection of tuberculosis and other mycobacteria in culture

(2011) D. Rodríguez et al.   JOURNAL OF APPLIED MICROBIOLOGY

An Experimentally Validated Genome-Scale Metabolic Reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

(2011) Y.-C. Liao et al.   JOURNAL OF BACTERIOLOGY

In vivo electron transport system activity: a method to estimate respiration in natural marine microbial planktonic communities

(2011) Sandra Martínez-García et al.   LIMNOLOGY AND OCEANOGRAPHY-METHODS

Time resolved protein-based stable isotope probing (Protein-SIP) analysis allows quantification of induced proteins in substrate shift experiments

(2011) Martin Taubert et al.   PROTEOMICS

Limitation of the MTT and XTT assays for measuring cell viability due to superoxide formation induced by nano-scale TiO2

(2011) Shuguang Wang et al.   TOXICOLOGY IN VITRO

A simple optode based method for imaging O2 distribution and dynamics in tap water biofilms

(2011) M. Staal et al.   WATER RESEARCH

Bromodeoxyuridine (BrdU) Labeling and Subsequent Fluorescence Activated Cell Sorting for Culture-independent Identification of Dissolved Organic Carbon-degrading Bacterioplankton

(2011) Steven Robbins et al.   Jove-Journal of Visualized Experiments

Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry

(2010) Hilal Taymaz-Nikerel et al.   BIOTECHNOLOGY AND BIOENGINEERING

Use of ionic chromatography in determining the contamination of apple juice by lactic acid

(2010) M. Wojtczak et al.   Food Additives and Contaminants Part A-Chemistry Analysis Control Exposure & Risk Assessment

The effect of hydrogen peroxide on the growth of thermophilic lactic starter and acid gelation of UHT milk

(2010) Tiina Kriščiunaite et al.   INTERNATIONAL DAIRY JOURNAL

Biothermodynamics of live cells: a tool for biotechnology and biochemical engineering

(2010) Urs von Stockar   JOURNAL OF NON-EQUILIBRIUM THERMODYNAMICS

Calorimetric approach to metabolic carbon conversion efficiency in soils

(2010) N. Barros et al.   JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY

Protein-based stable isotope probing

(2010) Nico Jehmlich et al.   Nature Protocols

Quantitative Microplate-Based Respirometry with Correction for Oxygen Diffusion

(2009) Akos A. Gerencser et al.   ANALYTICAL CHEMISTRY

Rapid depletion of dissolved oxygen in 96-well microtiter plateStaphylococcus epidermidisbiofilm assays promotes biofilm development and is influenced by inoculum cell concentration

(2009) John J. Cotter et al.   BIOTECHNOLOGY AND BIOENGINEERING

Acid Production by Oral Strains of Candida albicans and Lactobacilli

(2009) T. Klinke et al.   CARIES RESEARCH

Contrasting ability to take up leucine and thymidine among freshwater bacterial groups: implications for bacterial production measurements

(2009) María Teresa Pérez et al.   ENVIRONMENTAL MICROBIOLOGY

Oxygen detection in biological systems

(2009) Gernot Renger et al.   PHOTOSYNTHESIS RESEARCH

What heat is telling us about microbial conversions in nature and technology: from chip- to megacalorimetry

(2009) Thomas Maskow et al.   Microbial Biotechnology

Fluorescein diacetate hydrolysis, respiration and microbial biomass in freshly amended soils

(2008) M. A. Sánchez-Monedero et al.   BIOLOGY AND FERTILITY OF SOILS

Glucose sensors: a review of current and emerging technology

(2008) N. S. Oliver et al.   DIABETIC MEDICINE

Characteristics and turnover of exopolymeric substances in a hypersaline microbial mat

(2008) Olivier Braissant et al.   FEMS MICROBIOLOGY ECOLOGY

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY

Rapid and sensitive anthrone–sulfuric acid assay in microplate format to quantify carbohydrate in biopharmaceutical products: Method development and validation

(2007) Alberto Leyva et al.   BIOLOGICALS