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I'm considering AWS S3 instead of NoSQL database for saving user settings as JSON as it has a simple setup and low costs. So my question is there any disadvantages of using S3 instead of a database?

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The fact is that Amazon S3 is effectively a NoSQL database. Here S3 a key-value store, where the key is the filename and the value is the content of the file that we have. Amazon S3 usually costs significantly less for storage. In situations where you just need to store values with the key and then want to retrieve a value using that key then you are good to go with it.

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