No, this is, actually, correct: the main reason it smells worse in the morning is that the mouth is not well ventilated during the night. Brushing your teeth has little effect on the bacteria: the way brushing works is that fluoride in the toothpaste is included into the tooth enamel making it more difficult for the bacteria to destroy the enamel by secretion of acid. Otherwise, it has almost no effect. You remove some residues etc. but there is plenty of protein in the saliva and the tissues to feed the bugs. Some bad odor comes from the stomach (the amines, for example) and this is what might make it better or worse on different days. Halitosis is specifically volatile S-compounds from the mouth; bad breath is a more general problem. Most people do not clean their tongue from bacterial films, while most of the anaerobic bacteria are at back of the tongue. Said that, food does have effect on the microbial activity. For example, aerobic bacteria turn carbohydrates into lactic acid, and it suppresses the anaerobic activity. The problem, of course, is that this acid destroys the teeth, so it is not good, long-term. The current wisdom is that halitosis depends first and foremost on the kind of the bacteria in the mouth; everything else is secondary. Admittedly, I have not read anything about it for a decade, but such was the learned opinion a while ago.
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