The types of bacteria that thrive in your gut varies depending on what you eat.
High fiber is more likely to result in a healthy balance of gut bacteria. However, if you already suffer from a damaged gut, a high fiber diet can be difficult, so be sure to increase fiber slowly, and with awareness of how it affects your body.
That being said, if you want probiotics, plain whole milk yogurt is the way to go. (If you can handle dairy.) I avoid the bifido type bacteria; though that is for very specific reasons. Acidopholus, l. casei, Lactobacillus bulgaricus and Streptococcus thermophilus are all fine, the latter two being the traditional yogurt bacteria.
I have mild IBS and had done some exploration prior to asking this question. In my personal experience, the above is definitely true. The wrong probiotic can worsen symptoms or make you feel sick/feverish. But I eventually found one that works for me, I take it daily and it definitely reduces symptoms and makes my gut feel more solid. (I even have data proving this; I ran two three-month data collection periods to test various interventions, quantified symptoms, ran regressions, etc)
They tested only multi-strain probiotics vs "aFMT" (fecal transplant). That is a far cry from saying "probiotics don't work".
In contrast, fecal transplants have been shown to be effective for some diseases.
Also, I can't even say mine are actually working for me, because my doctor also told me to start taking soluble fiber; that could be my magic bullet. It's a process, I'm still going to be experimenting depending on how the next few weeks go.