Whether or not either of you has their own business, or whether that business is either successful or struggling has no bearing on whether or not you should file jointly or separately. If the business is structured or has made an election to be taxed as a partnership, an S-Corporation, or a C-Corporation, then there is a separate business return that is filed, and through that a document is produced (Schedule K-1) that will allow your wife to claim the income earned on the personal tax return, which may be either joint or separate.
If your wife's business is a sole-member "disregarded" LLC, she will report her income and expenses on Schedule C, which is also a part of the personal tax return (which, if filed jointly, reconciles your income as well). She could have a separate state filing requirement for the LLC, but that does not affect the federal return either. And if she is a true sole-proprietorship, and not an LLC, then she also files Schedule C, and the personal return may be filed either jointly or separately.
There are many advantages to filing jointly over separately, but some have compelling reasons why they choose to file separately. However, when one spouse has his/her own business is not a reason in itself to file separately. For more information on this subject, see the following Help Article: Is it better for a married couple to file jointly or separately?
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