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New Findings: What is the central question of the study? Does respiratory support ensure blood gas homeostasis and the relevance of experimental outcomes? What is the main finding and its importance? Spontaneous breathing during surgical intervention under anaesthesia results in impaired gas exchange and loss of diaphragm muscle strength in rats. Subsequent short-term mechanical ventilation restored blood gas homeostasis and diaphragm muscle strength. Blood gas homeostasis interferes substantially with experimental conditions and may alter study results. Monitoring and maintenance of blood gas balance is required to ensure quality and relevance of physiological animal experiments., Abstract: In pre-clinical small animal studies with surgical interventions under general anaesthesia, animals are often left to breathe spontaneously. However, anaesthesia may impair respiratory functions and result in disturbed blood gas homeostasis. In turn, the disturbed blood gas homeostasis can affect physiological functions and thus unintentionally impact the experimental results. We hypothesized that short-term mechanical ventilation restores blood gas balance and physiological functions despite anaesthesia and surgical interventions. Therefore, we investigated variables of blood gas analyses and diaphragm muscle strength in rats anaesthetized with ketamine/medetomidine after tracheotomy and catheterization of the carotid artery under spontaneous breathing and after 20 min of mechanical ventilation following the same surgical intervention. Spontaneous breathing during general anaesthesia and surgical intervention resulted in unphysiological blood oxygen partial pressure (<65 mmHg) and carbon dioxide partial pressure (>55 mmHg). After subsequent short-term mechanical ventilation, blood gas partial pressures were restored to their physiological ranges. Additionally, diaphragm muscle strength of animals breathing spontaneously was lower compared to animals that received subsequent mechanical ventilation (P = 0.0063). We conclude that spontaneous breathing of rats under ketamine/medetomidine anaesthesia is not sufficient to maintain a physiological blood gas balance. Disturbed blood gas balance is related to reduced diaphragm muscle strength. Mechanical ventilation for only 20 min restores blood gas homeostasis and muscle strength. Therefore, monitoring and maintenance of blood gas balance should be conducted to ensure quality and relevance of small animal experiments., (© 2020 The Authors. Experimental Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.)