These microscopic communities, which live inside all of us, play a crucial role in extracting energy from our diets, stimulating hunger and improving our metabolism.
"My work is about looking at the bacteria living inside our gut and find out to what extent and how they signal when we feel full and what we actually want to eat," said Associate Prof Rinki Murphy, who is leading the new study.
She said this might be seen as a radical concept, as we think we're in charge of our bodies and decide what we eat.
"But if there are bugs living in our intestines, they may actually influence that - and it's hard to tell because when people radically change their diet, their bacteria changes, but to what extent they can maintain that change in diet may actually be determined to some extent by bacteria already there."
Gaining a clear picture of how bacteria adapted to their new environments after surgery - as well as the dramatically different diet that followed procedures - had been particularly challenging for scientists.
But Murphy and her colleagues expected to gain these insights by comparing the results of blood, faecal samples and food records the study's 114 patients had kept themselves before and after surgery.
Being able to pinpoint the genetic functions of different bacterial communities, and expose beneficial ones, could reveal novel probiotics, or open the door to new gut microbiota transplant strategies for obese patients with type 2 diabetes that could complement, or even replace, surgery.
"One of the tantalising concepts is that from this study, we could inform the next generation of probiotics that people might use to supplement their diet and displace some of the obesogenic factors that we have today," Murphy said.
The ultimate hope was to remove the need for weight-loss surgery, although Murphy said there were still many hurdles keeping that from becoming reality.
The new study is supported by a $96,000 grant from the Auckland Medical Research Foundation, and by additional funding from the Maurice Wilkins Centre.
• People interested in taking part in another study, investigating probiotic and intermittent fasting to prevent type 2 diabetes, can email profast.bcu@gmail.com. This study hopes to recruit participants with pre-diabetes and obesity who will be able to visit Auckland City hospital for initial screening and two visits for scans, fecal and blood samples at baseline and after 12 weeks of the dietary study.