The metabolism of an animal is estimated by determining rates of carbon dioxide production (VCO2) and oxygen consumption (VO2) of individual animals, either in a closed or an open-circuit respirometry system. Two measures are typically obtained: standard (SMR) or basal metabolic rate (BMR) and maximal rate (VO2max). SMR is measured while the animal is at rest (but not asleep) under specific laboratory (temperature, hydration) and subject-specific conditions (e.g., size or allometry[1]), age, reproduction status, post-absorptive to avoid thermic effect of food) [2]. VO2max is typically determined during aerobic exercise at or near physiological limits [3]. In contrast, field metabolic rate (FMR) refers to the metabolic rate of an unrestrained, active animal in nature [4]. Whole animal metabolic rates refer to these measures without correction for body mass. If SMR or BMR values are divided by the body mass value for the animal, then the rate is termed mass-specific. It is this mass-specific value that one typically hears in comparisons among species.
Respirometry depends on a "what goes in must come out" principle [5]. Consider a closed system first. Imagine that we place a mouse into an air-tight container. The air sealed in the container initially contains the same composition and proportions of gases that were present in the room: 20.95% O2, 0.03% CO2, water vapor (the exact amount depends on air temperature, see dew point), 71% (approximately) N2, and a variety of trace gases making up the rest (see Earth's atmosphere). As time passes, the mouse in the chamber produces CO2 and water vapor, but extracts O2 from the air in proportion to its metabolic demands. Therefore, as long as we know the volume of the system, the difference between the concentrations of O2 and CO2 at the start when we sealed the mouse into the chamber (the baseline or reference conditions) compared to the amounts present after the mouse has breathed the air at a later time must be the amounts of CO2/O2 produced/consumed by the mouse. In a closed system, the mouse will eventually become hypoxic.