I seem to only lose weight when I starve myself. I was on a low-carb diet for 5 months last year and didn't drop a pound despite eating less than I ever have before in my life (it did make me feel better though, except for it was hard on my stomach and I had to stop - I have chronic gastritis and the diet irritated it too much). I never cheated once for 5 months and was very strict. I stayed away from high fat meats, I ate tons of veggies etc. Didn't matter.
I've since been diagnosed as having non-ulcer dyspepsia w/chronic gastritis. I've also had IBS for years. My gastroenterologist put me on "Align" for probiotics. It has helped with all my symptoms if you were looking at a probiotic that has scientific studies associated with it (for IBS anyway). There have been studies that link antibiotic use in babies and children with obesity - which ties in with the article you posted. I was constantly on antibiotics as a kid, for ear infections as a baby and constant tonsillitis/strep throat as a child. Also, I was fed soy formula as an infant which can affect some gut enzymes that control metabolism of some medications according to studies, which, I'm hypothesizing, can in turn affect gut flora.
Neither of my parents are overweight. In fact, my mom is very petite and thin. Neither had antibiotics until their teens. I recently lived with my parents for a few months, and I ate what my mom ate, and didn't lose anything, while she did (and she didn't need to). I lost 60 lbs when my husband left me and I had what could be deemed a nervous breakdown. I couldn't eat for months. Afterwards, I totalled the calories I was taking in during the day (I ate the same thing every day, the only few things I could stomach) - I was averaging 300-500 cals/day. Apparently that's the only way I can lose weight. Once I was back up to 1200-1500 cals/day, I gained it all back within a year.
I don't drink any soda either, just water, sometimes carbonated water or tea. I eat plenty of veggies. I do occasionally eat junk, because if it's in the house I'm eating it (4 picky eater kids makes it hard to eat all healthy all the time) but I balance it with healthy foods and I exercise by walking my kids to the bus stop every day and picking them up (About 20 min total of walking). I lived with my mother who binged on potato chips and wine on the weekends (I'm not a drinker) and she never gained because she kept it to the weekends only, which is usually how I do it too. That said - I could probably improve my diet, and I know I have food issues thanks to my mother - she always controlled my food and shamed me because I was always a bigger child...'normal' weight but not small boned or thin at all. I am very muscular though, even now I'm ridiculously strong for a woman. I understand I need to have a healthier relationship with food, but even considering that, I shouldn't be as large as I am.
I don't think it's ALL gut flora for me, but it's a piece in the puzzle. I also believe that 'obesogens' play a role ( http://www.davidsuzuki.org/blogs/panther-lounge/2012/01/is-pollution-making-us-fat/ ). It's possible GMO plays a role - perhaps it affects gut flora as well. Add in HFCS in everything, medications that cause weight gain (hello SSRIs! Glad I'm off YOU.) and overall less movement during the day due to office work, and it's no wonder there's a higher rate of obesity overall. Some of these factor into my problems and I'm trying to control what I can and accept that I'll likely never be 'skinny' no matter what I do due to those factors beyond my control.
Anyway, I've babbled on enough.
I get how much it sucks to be obese and feel like it's beyond your control.