A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements

A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements


Play all audios:


ABSTRACT Measurement of oxygen consumption is a powerful and uniquely informative experimental technique. It can help identify mitochondrial mechanisms of action following pharmacologic and


genetic interventions, and characterize energy metabolism in physiology and disease. The conceptual and practical benefits of respirometry have made it a frontline technique to understand


how mitochondrial function can interface with—and in some cases control—cell physiology. Nonetheless, an appreciation of the complexity and challenges involved with such measurements is


required to avoid common experimental and analytical pitfalls. Here we provide a practical guide to oxygen consumption measurements covering the selection of experimental models and


instrumentation, as well as recommendations for the collection, interpretation and normalization of data. These guidelines are provided with the intention of aiding experimental design and


enhancing the overall reputability, transparency and reliability of oxygen consumption measurements. Access through your institution Buy or subscribe This is a preview of subscription


content, access via your institution ACCESS OPTIONS Access through your institution Access Nature and 54 other Nature Portfolio journals Get Nature+, our best-value online-access


subscription $32.99 / 30 days cancel any time Learn more Subscribe to this journal Receive 12 digital issues and online access to articles $119.00 per year only $9.92 per issue Learn more


Buy this article * Purchase on SpringerLink * Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS:


* Log in * Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS MULTIFACETED MITOCHONDRIA: MOVING MITOCHONDRIAL SCIENCE


BEYOND FUNCTION AND DYSFUNCTION Article 26 April 2023 MITOCHONDRIAL GENETICS, SIGNALLING AND STRESS RESPONSES Article 10 March 2025 MECHANISMS OF MITOCHONDRIAL RESPIRATORY ADAPTATION Article


08 July 2022 REFERENCES * Pagliarini, D. J. & Rutter, J. Hallmarks of a new era in mitochondrial biochemistry. _Genes Dev._ 27, 2615–2627 (2013). Article  CAS  PubMed  PubMed Central 


Google Scholar  * Viale, A. et al. Oncogene ablation-resistant pancreatic cancer cells depend on mitochondrial function. _Nature_ 514, 628–632 (2014). Article  CAS  PubMed  PubMed Central 


Google Scholar  * Huang, S. C. C. et al. Cell-intrinsic lysosomal lipolysis is essential for alternative activation of macrophages. _Nat. Immunol._ https://doi.org/10.1038/ni.2956 (2014).


Article  PubMed  PubMed Central  Google Scholar  * Tannahill, G. M. et al. Succinate is an inflammatory signal that induces IL-1β through HIF-1α. _Nature_ https://doi.org/10.1038/nature11986


(2013). Article  PubMed  PubMed Central  Google Scholar  * Choi, S. W., Gerencser, A. A. & Nicholls, D. G. Bioenergetic analysis of isolated cerebrocortical nerve terminals on a


microgram scale: spare respiratory capacity and stochastic mitochondrial failure. _J. Neurochem._ https://doi.org/10.1111/j.1471-4159.2009.06055.x (2009). Article  PubMed  PubMed Central 


Google Scholar  * Gubser, P. M. et al. Rapid effector function of memory CD8+ T cells requires an immediate-early glycolytic switch. _Nat. Immunol._ 14, 1064–1072 (2013). Article  CAS 


PubMed  Google Scholar  * Chandel, N. S. Evolution of mitochondria as signaling organelles. _Cell Metab._ https://doi.org/10.1016/j.cmet.2015.05.013 (2015). Article  PubMed  Google Scholar 


* Murphy, M. P. & Hartley, R. C. Mitochondria as a therapeutic target for common pathologies. _Nat. Rev. Drug Discov._ https://doi.org/10.1038/nrd.2018.174 (2018). Article  PubMed 


Google Scholar  * Pelletier, M., Billingham, L. K., Ramaswamy, M. & Siegel, R. M. Extracellular flux analysis to monitor glycolytic rates and mitochondrial oxygen consumption. _Methods


Enzymol._ https://doi.org/10.1016/B978-0-12-416618-9.00007-8 (2014). Article  PubMed  Google Scholar  * Mitchell, P. Chemiosmotic coupling in oxidative and photosynthetic phosphorylation.


_Biochim. Biophys. Acta_ 1807, 1507–1538 (2011). Article  CAS  PubMed  Google Scholar  * Nicholls, D. G. & Ferguson, S. J. _Bioenergetics 4_ (Academic Press, 2013). * Divakaruni, A. S.,


Paradyse, A., Ferrick, D. A., Murphy, A. N. & Jastroch, M. Analysis and interpretation of microplate-based oxygen consumption and pH data. in _Methods in Enzymology_


https://doi.org/10.1016/B978-0-12-801415-8.00016-3 (2014). * Doerrier, C. et al. High-resolution fluorespirometry and oxphos protocols for human cells, permeabilized fibers from small


biopsies of muscle, and isolated mitochondria. in _Methods in Molecular Biology_ https://doi.org/10.1007/978-1-4939-7831-1_3 (2018). * Will, Y., Hynes, J., Ogurtsov, V. I. & Papkovsky,


D. B. Analysis of mitochondrial function using phosphorescent oxygen-sensitive probes. _Nat. Protoc._ https://doi.org/10.1038/nprot.2006.351 (2007). Article  Google Scholar  * Perry, C. G.


R., Kane, D. A., Lanza, I. R. & Neufer, P. D. Methods for assessing mitochondrial function in diabetes. _Diabetes_ https://doi.org/10.2337/db12-1219 (2013). * Schmidt, C. A.,


Fisher-Wellman, K. H. & Neufer, P. D. From OCR and ECAR to energy: perspectives on the design and interpretation of bioenergetics studies. _J. Biol. Chem._ 297, 101140 (2021). Article 


CAS  PubMed  PubMed Central  Google Scholar  * Brand, M. D. & Nicholls, D. G. Assessing mitochondrial dysfunction in cells. _Biochem. J._ https://doi.org/10.1042/BJ20110162 (2011).


Article  PubMed  Google Scholar  * Jones, A. E. et al. Forces, fluxes, and fuels: tracking mitochondrial metabolism by integrating measurements of membrane potential, respiration, and


metabolites. _Am. J. Physiol._ 320, C80–C91 (2021). Google Scholar  * Connolly, N. M. C. et al. Guidelines on experimental methods to assess mitochondrial dysfunction in cellular models of


neurodegenerative diseases. _Cell Death Differ._ https://doi.org/10.1038/s41418-017-0020-4 (2018). Article  PubMed  Google Scholar  * Dranka, B. P., Hill, B. G. & Darley-Usmar, V. M.


Mitochondrial reserve capacity in endothelial cells: the impact of nitric oxide and reactive oxygen species. _Free Radic. Biol. Med._ https://doi.org/10.1016/j.freeradbiomed.2010.01.015


(2010). Article  PubMed  PubMed Central  Google Scholar  * Rogers, G. W. et al. High-throughput microplate respiratory measurements using minimal quantities of isolated mitochondria. _PLoS


ONE_ https://doi.org/10.1371/journal.pone.0021746 (2011). Article  PubMed  PubMed Central  Google Scholar  * Divakaruni, A. S., Rogers, G. W. & Murphy, A. N. Measuring mitochondrial


function in permeabilized cells using the Seahorse XF analyzer or a Clark-type oxygen electrode. _Curr. Protoc. Toxicol._ https://doi.org/10.1002/0471140856.tx2502s60 (2014). Article  PubMed


  Google Scholar  * Hynes, J., Swiss, R. L. & Will, Y. High-throughput analysis of mitochondrial oxygen consumption. in _Methods in Molecular Biology_


https://doi.org/10.1007/978-1-4939-7831-1_4 (2018). * Acin-Perez, R., Benincá, C., Shabane, B., Shirihai, O. S. & Stiles, L. Utilization of human samples for assessment of mitochondrial


bioenergetics: gold standards, limitation and future perspectives. _Life_ 11, 949 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  * Hill, B. G. et al. Integration of cellular


bioenergetics with mitochondrial quality control and autophagy. _Biol. Chem._ 393, 1485–1512 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Frezza, C., Cipolat, S. &


Scorrano, L. Organelle isolation: functional mitochondria from mouse liver, muscle and cultured filroblasts. _Nat. Protoc._ 2, 287–295 (2007). Article  CAS  PubMed  Google Scholar  *


Wieckowski, M. R. M. R., Giorgi, C., Lebiedzinska, M., Duszynski, J. & Pinton, P. Isolation of mitochondria-associated membranes and mitochondria from animal tissues and cells. _Nat.


Protoc._ 4, 1582–1590 (2009). Article  CAS  PubMed  Google Scholar  * Kushnareva, Y. E., Wiley, S. E., Ward, M. W., Andreyev, A. Y. & Murphy, A. N. Excitotoxic injury to mitochondria


isolated from cultured neurons. _J. Biol. Chem._ 280, 28894–28902 (2005). Article  CAS  PubMed  Google Scholar  * Yang, K., Doan, M. T., Stiles, L. & Divakaruni, A. S. Measuring


CPT-1-mediated respiration in permeabilized cells and isolated mitochondria. _STAR Protoc._ 2, 100687 (2021). Article  PubMed  PubMed Central  CAS  Google Scholar  * Benador, I. Y. et al.


Mitochondria bound to lipid droplets have unique bioenergetics, composition and dynamics that support lipid droplet expansion. _Cell Metab._ 27, 869–885 (2018). Article  CAS  PubMed  PubMed


Central  Google Scholar  * Divakaruni, A. S. et al. Thiazolidinediones are acute, specific inhibitors of the mitochondrial pyruvate carrier. _Proc. Natl Acad. Sci. USA_


https://doi.org/10.1073/pnas.1303360110 (2013). Article  PubMed  PubMed Central  Google Scholar  * Salabei, J. K., Gibb, A. A. & Hill, B. G. Comprehensive measurement of respiratory


activity in permeabilized cells using extracellular flux analysis. _Nat. Protoc._ https://doi.org/10.1038/nprot.2014.018 (2014). Article  PubMed  PubMed Central  Google Scholar  * Quintana,


A., Kruse, S. E., Kapur, R. P., Sanz, E. & Palmiter, R. D. Complex I deficiency due to loss of Ndufs4 in the brain results in progressive encephalopathy resembling Leigh syndrome. _Proc.


Natl Acad. Sci. USA_ 107, 10996–11001 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  * Rich, P. R. & Maréchal, A. The mitochondrial respiratory chain. _Essays Biochem._


https://doi.org/10.1042/BSE0470001 (2010). Article  PubMed  Google Scholar  * Kiss, G. et al. The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix


substrate-level phosphorylation. _FASEB J._ 27, 2393–2406 (2013). Article  CAS  Google Scholar  * Ryan, D. G. et al. Coupling Krebs cycle metabolites to signalling in immunity and cancer.


_Nat. Metab._ https://doi.org/10.1038/s42255-018-0014-7 (2019). Article  PubMed  PubMed Central  Google Scholar  * Gray, L. R. et al. Hepatic mitochondrial pyruvate carrier 1 is required for


efficient regulation of gluconeogenesis and whole-body glucose homeostasis. _Cell Metab._ 22, 669–681 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  * Taylor, E. B.


Functional properties of the mitochondrial carrier system. _Trends Cell Biol._ https://doi.org/10.1016/j.tcb.2017.04.004 (2017). Article  PubMed  PubMed Central  Google Scholar  * Woodall,


B. P. et al. Parkin does not prevent accelerated cardiac aging in mitochondrial DNA mutator mice. _JCI Insight_ 5, e127713 (2019). Article  Google Scholar  * Norton, M. et al. ROMO1 is an


essential redox-dependent regulator of mitochondrial dynamics. _Sci. Signal._ 7, ra10 (2014). Article  PubMed  CAS  Google Scholar  * Fu, Z. et al. Requirement of mitochondrial transcription


factor A in tissue-resident regulatory T cell maintenance and function. _Cell Rep._ 28, 159–171 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  * Pagliarini, D. J. et al.


Involvement of a mitochondrial phosphatase in the regulation of ATP production and insulin secretion in pancreatic β cells. _Mol. Cell_ 19, 197–207 (2005). Article  CAS  PubMed  Google


Scholar  * Wang, G. et al. Modeling the mitochondrial cardiomyopathy of Barth syndrome with iPSC and heart-on-chip technologies. _Nat. Med._ 20, 616–623 (2014). Article  PubMed Central 


Google Scholar  * Leonardi, R., Zhang, Y. M., Rock, C. O. & Jackowski, S. Coenzyme A: back in action. _Prog. Lipid Res._ https://doi.org/10.1016/j.plipres.2005.04.001 (2005). Article 


PubMed  Google Scholar  * Solmonson, A. & DeBerardinis, R. J. Lipoic acid metabolism and mitochondrial redox regulation. _J. Biol. Chem._ 293, 7522–7530 (2018). Article  PubMed  Google


Scholar  * Stefely, J. A. & Pagliarini, D. J. Biochemistry of mitochondrial coenzyme Q biosynthesis. _Trends Biochem. Sci._ 42, 824–843 (2017). Article  CAS  PubMed  PubMed Central 


Google Scholar  * Daan Westenbrink, B. et al. Mitochondrial reprogramming induced by CaMKIIδ mediates hypertrophy decompensation. _Circ. Res._ 116, e28–e39 (2015). PubMed  PubMed Central 


Google Scholar  * Rotig, A. et al. Aconitase and mitochondrial iron–sulphur protein deficiency in Friedreich ataxia. _Nat. Genet._ 17, 215–217 (1997). Article  CAS  PubMed  Google Scholar  *


Diers, A. R., Broniowska, K. A., Chang, C. F., Hill, R. B. & Hogg, N. _S_-nitrosation of monocarboxylate transporter 1: inhibition of pyruvate-fueled respiration and proliferation of


breast cancer cells. _Free Radic. Biol. Med._ 69, 229–238 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  * CHANCE, B. & WILLIAMS, G. R. Respiratory enzymes in oxidative


phosphorylation. III. The steady state. _J. Biol. Chem._ 217, 409–427 (1955). Article  CAS  PubMed  Google Scholar  * Estabrook, R. W. Mitochondrial respiratory control and the polarographic


measurement of ADP:O ratios. _Methods Enzymol._ 10, 41–47 (1967). Article  CAS  Google Scholar  * Ernster, L. & Schatz, G. Mitochondria: a historical review. _J. Cell Biol_. 91, 227–255


(1981). * Lopaschuk, G. D., Karwi, Q. G., Tian, R., Wende, A. R. & Abel, E. D. Cardiac energy metabolism in heart failure. _Circ. Res._ 128, 1487–1513 (2021). Article  CAS  PubMed 


PubMed Central  Google Scholar  * Sun, H. & Wang, Y. Branched chain amino acid metabolic reprogramming in heart failure. _Biochim. Biophys. Acta_ 1862, 2270–2275 (2016). Article  CAS 


PubMed  Google Scholar  * White, P. J. & Newgard, C. B. Branched-chain amino acids in disease. _Science_ 363, 582–583 (2019). Article  CAS  PubMed  Google Scholar  * Picard, M. et al.


Mitochondrial structure and function are disrupted by standard isolation methods. _PLoS ONE_ 6, e18317 (2011). Article  CAS  PubMed  PubMed Central  Google Scholar  * Arruda, A. P. et al.


Chronic enrichment of hepatic endoplasmic reticulum–mitochondria contact leads to mitochondrial dysfunction in obesity. _Nat. Med._ 20, 1427–1435 (2014). Article  CAS  PubMed  PubMed Central


  Google Scholar  * Nicholls, D. G. Spare respiratory capacity, oxidative stress and excitotoxicity. _Biochem. Soc. Trans._ https://doi.org/10.1042/BST0371385 (2009). Article  PubMed  Google


Scholar  * Adhihetty, P. J. et al. The role of PGC-1α on mitochondrial function and apoptotic susceptibility in muscle. _Am. J. Physiol. Cell Physiol_ 297, C217–C225 (2009). Article  CAS 


PubMed  Google Scholar  * Agier, V. et al. Defective mitochondrial fusion, altered respiratory function, and distorted cristae structure in skin fibroblasts with heterozygous _OPA1_


mutations. _Biochim. Biophys. Acta_ 1822, 1570–1580 (2012). Article  CAS  PubMed  Google Scholar  * Clerc, P. & Polster, B. M. Investigation of mitochondrial dysfunction by sequential


microplate-based respiration measurements from intact and permeabilized neurons. _PLoS ONE_ 7, e34465 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  * Schulz, I.


Permeabilizing cells: some methods and applications for the study of intracellular processes. _Methods Enzymol._ 192, 280–300 (1990). Article  CAS  PubMed  Google Scholar  * Buescher, J. M.


et al. A roadmap for interpreting 13C metabolite labeling patterns from cells. _Curr. Opin. Biotechnol._ https://doi.org/10.1016/j.copbio.2015.02.003 (2015). Article  PubMed  PubMed Central


  Google Scholar  * Jang, C., Chen, L. & Rabinowitz, J. D. Metabolomics and isotope tracing. _Cell_ https://doi.org/10.1016/j.cell.2018.03.055 (2018). Article  PubMed  PubMed Central 


Google Scholar  * Antoniewicz, M. R. A guide to 13C metabolic flux analysis for the cancer biologist. _Exp. Mol. Med._ https://doi.org/10.1038/s12276-018-0060-y (2018). Article  PubMed 


PubMed Central  Google Scholar  * Divakaruni, A. S. & Brand, M. D. The regulation and physiology of mitochondrial proton leak. _Physiology_ https://doi.org/10.1152/physiol.00046.2010


(2011). Article  PubMed  Google Scholar  * Bertholet, A. M. & Kirichok, Y. Mitochondrial H+ leak and thermogenesis. _Annu. Rev. Physiol._ 84, 381–407 (2022). Article  PubMed  CAS  Google


Scholar  * Duchen, M. R. Ca2+-dependent changes in the mitochondrial energetics in single dissociated mouse sensory neurons. _Biochem. J._ 283, 41–50 (1992). Article  PubMed  PubMed Central


  Google Scholar  * De Stefani, D., Rizzuto, R. & Pozzan, T. Enjoy the trip: calcium in mitochondria back and forth. https://doi.org/10.1146/annurev-biochem-060614-034216 (2016). *


Villalobo, A. & Lehninger, A. L. Inhibition of oxidative phosphorylation in ascites tumor mitochondria and cells by intramitochondrial Ca2+. _J. Biol. Chem._ 255, 2457–2464 (1980).


Article  CAS  PubMed  Google Scholar  * Murphy, A. N., Bredesen, D. E., Cortopassi, G., Wang, E. & Fiskum, G. Bcl-2 potentiates the maximal calcium uptake capacity of neural cell


mitochondria. _Proc. Natl Acad. Sci. USA._ 93, 9893–9898 (1996). Article  CAS  PubMed  PubMed Central  Google Scholar  * Veliova, M. et al. Blocking mitochondrial pyruvate import in brown


adipocytes induces energy wasting via lipid cycling. _EMBO Rep._ 21, e49634 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Gross, M. I. et al. Antitumor activity of the


glutaminase inhibitor CB-839 in triple-negative breast cancer. _Mol. Cancer Ther._ 13, 890–901 (2014). Article  CAS  PubMed  Google Scholar  * Leek, R., Grimes, D. R., Harris, A. L. &


McIntyre, A. Methods: using three-dimensional culture (spheroids) as an in vitro model of tumour hypoxia. _Adv. Exp. Med. Biol._ 899, 167–196 (2016). Article  CAS  PubMed  Google Scholar  *


Simian, M. & Bissell, M. J. Organoids: a historical perspective of thinking in three dimensions. _J. Cell Biol._ 216, 31–40 (2017). Article  CAS  PubMed  PubMed Central  Google Scholar 


* De Graaf, I. A. M. et al. Preparation and incubation of precision-cut liver and intestinal slices for application in drug metabolism and toxicity studies. _Nat. Protoc._ 5, 1540–1551


(2010). Article  PubMed  CAS  Google Scholar  * Lau, A. N. & Vander Heiden, M. G. Metabolism in the tumor microenvironment. _Annu. Rev. Cancer Biol._ 4, 17–40 (2020). Article  Google


Scholar  * Kanow, M. A. et al. Biochemical adaptations of the retina and retinal pigment epithelium support a metabolic ecosystem in the vertebrate eye. _Elife_ 6, e28899 (2017). Article 


PubMed  PubMed Central  Google Scholar  * Harada, A. E., Healy, T. M. & Burton, R. S. Variation in thermal tolerance and its relationship to mitochondrial function across populations of


_Tigriopus californicus_. _Front. Physiol._ 10, 213 (2019). Article  PubMed  PubMed Central  Google Scholar  * Luz, A. L., Smith, L. L., Rooney, J. P. & Meyer, J. N. Seahorse XFe24


extracellular flux analyzer-based analysis of cellular respiration in _Caenorhabditis elegans_. _Curr. Protoc. Toxicol._ 66, 25.7.1–25.7.15 (2015). Article  Google Scholar  * Lay, S.,


Sanislav, O., Annesley, S. J. & Fisher, P. R. Mitochondrial stress tests using seahorse respirometry on intact _Dictyostelium discoideum_ cells. _Methods Mol. Biol_ 1407, 41–61 (2016).


Article  CAS  PubMed  Google Scholar  * Muthusamy, T. et al. Serine restriction alters sphingolipid diversity to constrain tumour growth. _Nature_ 586, 790–795 (2020). Article  CAS  PubMed 


PubMed Central  Google Scholar  * Jiang, L. et al. Reductive carboxylation supports redox homeostasis during anchorage-independent growth. _Nature_ 532, 255–258 (2016). Article  CAS  PubMed


  PubMed Central  Google Scholar  * Tschöp, M. H. et al. A guide to analysis of mouse energy metabolism. _Nat. Methods_ 9, 57–63 (2012). Article  CAS  Google Scholar  * Müller, T. D.,


Klingenspor, M. & Tschöp, M. H. Revisiting energy expenditure: how to correct mouse metabolic rate for body mass. _Nat. Metab._ 3, 1134–1136 (2021). Article  PubMed  Google Scholar  *


Tyrrell, D. J. et al. Blood-cell bioenergetics are associated with physical function and inflammation in overweight/obese older adults. _Exp. Gerontol._ 70, 84–91 (2015). Article  CAS 


PubMed  PubMed Central  Google Scholar  * Kenwood, B. M. et al. Identification of a novel mitochondrial uncoupler that does not depolarize the plasma membrane. _Mol. Metab._ 3, 114–123


(2013). Article  PubMed  PubMed Central  CAS  Google Scholar  * Davila, A. et al. Nicotinamide adenine dinucleotide is transported into mammalian mitochondria. _Elife_ 7, e33246 (2018).


Article  PubMed  PubMed Central  Google Scholar  * Luongo, T. S. et al. SLC25A51 is a mammalian mitochondrial NAD+ transporter. _Nature_ 588, 174–179 (2020). Article  CAS  PubMed  PubMed


Central  Google Scholar  * Affourtit, C. & Brand, M. D. Stronger control of ATP/ADP by proton leak in pancreatic beta cells than skeletal muscle mitochondria. _Biochem. J._


https://doi.org/10.1042/BJ20051280 (2006). Article  PubMed  PubMed Central  Google Scholar  * Krasnikov, B. F. et al. Comparative kinetic analysis reveals that inducer-specific ion release


precedes the mitochondrial permeability transition. _Biochim. Biophys. Acta_ 1708, 375–392 (2005). Article  CAS  PubMed  Google Scholar  * Mookerjee, S. A., Goncalves, R. L. S., Gerencser,


A. A., Nicholls, D. G. & Brand, M. D. The contributions of respiration and glycolysis to extracellular acid production. _Biochim. Biophys. Acta_ 1847, 171–181 (2015). Article  CAS 


PubMed  Google Scholar  * Desousa, B. R. et al. Calculating ATP production rates from oxidative phosphorylation and glycolysis during cell activation. Preprint at _bioRxiv_


https://doi.org/10.1101/2022.04.16.488523 (2022). * Mookerjee, S. A., Gerencser, A. A., Nicholls, D. G. & Brand, M. D. Quantifying intracellular rates of glycolytic and oxidative ATP


production and consumption using extracellular flux measurements. _J. Biol. Chem._ https://doi.org/10.1074/jbc.M116.774471 (2017). Article  PubMed  PubMed Central  Google Scholar  *


Divakaruni, A. S., Andreyev, A. Y., Rogers, G. W. & Murphy, A. N. In situ measurements of mitochondrial matrix enzyme activities using plasma and mitochondrial membrane permeabilization


agents. _Anal. Biochem._ 552, 60–65 (2018). Article  CAS  PubMed  Google Scholar  * Divakaruni, A. S. et al. Inhibition of the mitochondrial pyruvate carrier protects from excitotoxic


neuronal death. _J. Cell Biol._ https://doi.org/10.1083/jcb.201612067 (2017). Article  PubMed  PubMed Central  Google Scholar  * Grassian, A. R., Metallo, C. M., Coloff, J. L.,


Stephanopoulos, G. & Brugge, J. S. Erk regulation of pyruvate dehydrogenase flux through PDK4 modulates cell proliferation. _Genes Dev._ 25, 1716–1733 (2011). Article  CAS  PubMed 


PubMed Central  Google Scholar  * Sullivan, W. J. et al. Extracellular matrix remodeling regulates glucose metabolism through TXNIP destabilization. _Cell_ 175, 117–132 (2018). Article  CAS


  PubMed  PubMed Central  Google Scholar  * Sessions, A. O. et al. Preserved cardiac function by vinculin enhances glucose oxidation and extends health- and life-span. _APL Bioeng._ 2,


036101 (2018). Article  PubMed  PubMed Central  CAS  Google Scholar  * Fan, Y. Y. et al. A bioassay to measure energy metabolism in mouse colonic crypts, organoids, and sorted stem cells.


_Am. J. Physiol. Gastrointest. Liver Physiol._ 309, 1–9 (2015). Article  CAS  Google Scholar  * Taddeo, E. P. et al. Individual islet respirometry reveals functional diversity within the


islet population of mice and human donors. _Mol. Metab._ 16, 150–159 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  * Kooragayala, K. et al. Quantification of oxygen


consumption in retina ex vivo demonstrates limited reserve capacity of photoreceptor mitochondria. _Invest. Ophthalmol. Vis. Sci._ 56, 8428–8436 (2015). Article  CAS  PubMed  PubMed Central


  Google Scholar  * Ludikhuize, M. C., Meerlo, M., Burgering, B. M. T. & Rodríguez Colman, M. J. Protocol to profile the bioenergetics of organoids using Seahorse. _STAR Protoc._ 2,


100386 (2021). Article  PubMed  PubMed Central  CAS  Google Scholar  * Gerencser, A. A. et al. Quantitative microplate-based respirometry with correction for oxygen diffusion. _Anal. Chem._


https://doi.org/10.1021/ac900881z (2009). Article  PubMed  PubMed Central  Google Scholar  * Oliver, D. G., Sanders, A. H., Douglas Hogg, R. & Woods Hellman, J. Thermal gradients in


microtitration plates. Effects on enzyme-linked immunoassay. _J. Immunol. Methods_ 42, 195–201 (1981). Article  CAS  PubMed  Google Scholar  * Lundholt, B. K., Scudder, K. M. & Pagliaro,


L. A simple technique for reducing edge effect in cell-based assays. _J. Biomol. Screen._ 8, 566–570 (2003). Article  CAS  PubMed  Google Scholar  * Schoonen, W. G. E. J., Stevenson, J. C.


R., Westerink, W. M. A. & Horbach, G. J. Cytotoxic effects of 109 reference compounds on rat H4IIE and human HepG2 hepatocytes. III: Mechanistic assays on oxygen consumption with


MitoXpress and NAD(P)H production with Alamar Blue. _Toxicol. In Vitro_ 26, 511–525 (2012). Article  CAS  PubMed  Google Scholar  * Little, A. C. et al. High-content fluorescence imaging


with the metabolic flux assay reveals insights into mitochondrial properties and functions. _Commun. Biol._ 3, 271 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  * Wiley, S.


E. et al. Wolfram syndrome protein, Miner1, regulates sulphydryl redox status, the unfolded protein response, and Ca2+ homeostasis. _EMBO Mol. Med._ 5, 904–918 (2013). Article  CAS  PubMed 


PubMed Central  Google Scholar  * Wettmarshausen, J. & Perocchi, F. Isolation of functional mitochondria from cultured cells and mouse tissues. _Methods Mol. Biol._ 1567, 15–32 (2017).


Article  CAS  PubMed  Google Scholar  * Kirkinezos, I. G. et al. Cytochrome c association with the inner mitochondrial membrane is impaired in the CNS of G93A-SOD1 mice. _J. Neurosci._ 25,


164–172 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  * Rolfe, D. F. S. & Brown, G. C. Cellular energy utilization and molecular origin of standard metabolic rate in


mammals. _Physiol. Rev._ 77, 731–758 (1997). Article  CAS  PubMed  Google Scholar  * Chacko, B. K. et al. Methods for defining distinct bioenergetic profiles in platelets, lymphocytes,


monocytes and neutrophils, and the oxidative burst from human blood. _Lab. Invest._ 93, 690–700 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  * van der Windt, G. J. W. et al.


Mitochondrial respiratory capacity is a critical regulator of CD8+ T cell memory development. _Immunity_ 36, 68–78 (2012). PubMed  Google Scholar  * McMurray, J. et al. Dapagliflozin in


patients with heart failure and reduced ejection fraction. _N. Engl. J. Med._ 381, 1995–2008 (2019). Article  CAS  PubMed  Google Scholar  * Molina, J. R. et al. An inhibitor of oxidative


phosphorylation exploits cancer vulnerability. _Nat. Med._ 24, 1036–1046 (2018). Article  CAS  PubMed  Google Scholar  * Rath, S. et al. MitoCarta3.0: an updated mitochondrial proteome now


with sub-organelle localization and pathway annotations. _Nucleic Acids Res._ 49, D1541–D1547 (2021). Article  CAS  PubMed  Google Scholar  * Nowinski, S. M. et al. Mitochondrial fatty acid


synthesis coordinates oxidative metabolism in mammalian mitochondria. _Elife_ 9, e58041 (2020). Article  Google Scholar  * Floyd, B. J. et al. Mitochondrial protein interaction mapping


identifies regulators of respiratory chain function. _Mol. Cell_ 63, 621–632 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  * Brand, M. D. The efficiency and plasticity of


mitochondrial energy transduction. _Biochem. Soc. Trans._ 33, 897–904 (2005). Article  CAS  PubMed  Google Scholar  * Watt, I. N., Montgomery, M. G., Runswick, M. J., Leslie, A. G. W. &


Walker, J. E. Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria. _Proc. Natl Acad. Sci. USA_ 107, 16823–16827 (2010). Article  CAS  PubMed  PubMed Central


  Google Scholar  * Hinkle, P. C. P/O ratios of mitochondrial oxidative phosphorylation. _Biochim. Biophys. Acta_ 1706, 1–11 (2005). Article  CAS  PubMed  Google Scholar  * Müller, T. D. et


al. P62 links β-adrenergic input to mitochondrial function and thermogenesis. _J. Clin. Invest._ 123, 469–478 (2013). Article  PubMed  CAS  Google Scholar  * Kory, N. et al. MCART1/SLC25A51


is required for mitochondrial NAD transport. _Sci. Adv_ 6, 43 (2020). Article  CAS  Google Scholar  * Bricker, D. K. et al. A mitochondrial pyruvate carrier required for pyruvate uptake in


yeast, _Drosophila_ and humans. _Science_ https://doi.org/10.1126/science.1218099 (2012). Article  PubMed  PubMed Central  Google Scholar  * Herzig, S. et al. Identification and functional


expression of the mitochondrial pyruvate carrier. _Science_ https://doi.org/10.1126/science.1218530 (2012). Article  PubMed  Google Scholar  * Sharma, A. et al. Impaired skeletal muscle


mitochondrial pyruvate uptake rewires glucose metabolism to drive whole-body leanness. _Elife_ 8, e45873 (2019). Article  PubMed  PubMed Central  Google Scholar  * Bertholet, A. M. The use


of the patch-clamp technique to study the thermogenic capacity of mitochondria. _J. Vis. Exp_. 171, (2021). * Gerencser, A. A. et al. Quantitative measurement of mitochondrial membrane


potential in cultured cells: calcium-induced de- and hyperpolarization of neuronal mitochondria. _J. Physiol._ https://doi.org/10.1113/jphysiol.2012.228387 (2012). Article  PubMed  PubMed


Central  Google Scholar  Download references ACKNOWLEDGEMENTS A.S.D. is supported by National Institutes of Health grants R35GM138003, P30DK063491 and P50CA092131, as well as the W. M. Keck


Foundation. M.J. is supported by the Novo Nordisk Research Fonden (NNF20OC0059646). We thank members of both of our laboratories for their helpful discussions during the preparation of this


manuscript, as well as L. Stiles (UCLA), B. Desousa (UCSF) and A. Murphy (Cytokinetics) for their critical perspective. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Molecular


and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA Ajit S. Divakaruni * Department of Molecular Biosciences, The


Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, Stockholm, Sweden Martin Jastroch Authors * Ajit S. Divakaruni View author publications You can also search for


this author inPubMed Google Scholar * Martin Jastroch View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS A.S.D. and M.J. both contributed to


the conceptualization, preparation, writing and editing of this manuscript. CORRESPONDING AUTHOR Correspondence to Ajit S. Divakaruni. ETHICS DECLARATIONS COMPETING INTERESTS The authors


declare no current competing interests. A.S.D. has previously served as a paid consultant for Agilent Technologies. PEER REVIEW PEER REVIEW INFORMATION _Nature Metabolism_ thanks Alexander


Galkin, David Nicholls and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Christoph Schmitt, in collaboration with the


_Nature Metabolism_ team. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.


RIGHTS AND PERMISSIONS Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving


of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law. Reprints and permissions ABOUT THIS ARTICLE CITE THIS


ARTICLE Divakaruni, A.S., Jastroch, M. A practical guide for the analysis, standardization and interpretation of oxygen consumption measurements. _Nat Metab_ 4, 978–994 (2022).


https://doi.org/10.1038/s42255-022-00619-4 Download citation * Received: 28 October 2021 * Accepted: 17 June 2022 * Published: 15 August 2022 * Issue Date: August 2022 * DOI:


https://doi.org/10.1038/s42255-022-00619-4 SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not


currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative