The neural control of breathing involves the coordinated activity of diverse populations of medullary neurons distributed along the rostrocaudal aspect of the ventrolateral medulla. Here, we use high‐density electrophysiological recordings (Neuropixels) to record spiking activity simultaneously from hundreds of neurons across the ventral respiratory column (VRC, including the Bötzinger and pre‐Bötzinger complexes) in anesthetized, freely breathing mice. Across sequential recordings, we have recorded from over 13,000 medullary neurons. We couple this with an optogenetic tagging approach to identify ChAT, Dbx1, Vgat, and Vglut2 positive neurons; and reconstruct the three dimensional location of each recorded neuron. We find diverse patterns of respiratory‐related neural activity throughout the medulla that tile the breathing phase such that discrete functional cell classes cannot be quantitatively defined. Moreover, while certain genotypes are biased towards particular anatomical locations or functional activity patterns, cells active during all parts of the respiratory phase are found across the VRC, and across all genotypes. We use dimensionality reduction techniques to show that the neural populations governing breathing follow rotational trajectories on low dimensional neural manifolds. Analyses of these trajectories indicate that the termination of inspiration (“inspiratory‐off switch”) may represent an attractor in the low‐dimensional neural space. Further, during opioid induced respiratory depression (OIRD), the network reconfigures, but the low‐dimensional trajectories of the neural population are preserved. Thus, patterns of neural coactivity remain the same, while breathing is slowed. Finally, we expose animals to hypoxia which reconfigures the respiratory network into gasping. The low‐dimensional neural activity no longer follows rotational trajectories. Instead, gasping is a ballistic, non‐rotational dynamic mode strikingly different than eupnea or OIRD. The transition to gasping is represented in the low dimensional trajectories by a gradual sequestering of the neural activity away from normal eupneic rotations. Together these data suggest that the VRC functions as a distributed and well‐coordinated population. The eupneic cycle begins with the inspiratory off‐switch and is maintained by the reciprocal interactions between inspiratory and expiratory neurons. This reciprocity is lost as the network transitions into gasping, a rhythm governed by fundamentally different mechanisms.
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