The letter b wasn't always in doubt. In Middle English, it was most often spelled douten or duten and also had meanings of "to dread" or "fear", and in Old French it was doter. It isn't until we trace the word back to Latin that we see the b reappear in dubitare, a word with a very similar meaning as today. The reason both the spelling and definition are closer to Latin is that, as Latin grew more influential in English following the Renaissance, scholars tried to push many words back to their roots, and this was one of the victims. The verb dubitare comes from the noun dubius (which, yes, is the direct etymon of dubious). This has a particularly interesting origin: it's composed of the words duo, meaning "two", and habere, meaning "to hold". If you put those together, you're holding two ideas or beliefs, and that's how it's connected to doubt. Duo, through Proto-Italic, is from the Proto-Indo-European reconstruction dwoh, meaning "two". Habere, also through Proto-Italic, hails from PIE gehb, "to grab".
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The Etymology Nerd