The gut bacteria/obesity connection has been shown by a number of research groups, only one group has been shamed (at least so far) for falsifying data. The retracted study is from 2014, the fecal transplant/obesity research begins long before then. You can't even tell by the retraction whether the real results failed to replicate earlier findings that fecal transplant from an obese animal caused weight gain, because the specific things that are listed as falsified are mostly about various hormone levels rather than weight gain.

One thing this does illustrate is that the idea of an unbiased researcher is just false. You don't have to be taking money from industry to have a horse in the race, there will generally be greater funding/career potential in some outcomes than in others.