United States research published in JAMA Pediatrics last week found children given broad spectrum antibiotics in the first two years of their lives were at greater risk of becoming obese in early childhood.
It was the latest research to demonstrate a link between the two, although the issue remains controversial and unproven.
Prof Gerald Tannock, of the University of Otago's department of microbiology and immunology, said he was analysing faecal samples collected for the prevention of overweight in infancy study led by Otago child health researcher Prof Barry Taylor.
''We're in the process of analysing the composition of the faecal microbiota, and of course they have a lot of fantastic data on these children, which they've been collecting since they were born, and so they will have all that sort of information about whether they have had antibiotics.''
Prof Tannock said much of the relevant research used animal models, and there were fewer studies in humans.
Studies to date produced inconsistent results, and it was still unclear whether the link between gut bacteria and obesity existed.
He believed the Dunedin research would be the first New Zealand research into the link.
''I'm sure there's a hell of a lot of people working on this [around the world] but I think the strength of the study here in Dunedin is there are a very large number of children involved. It's about 500, and they've been followed from birth.''
Prof Tannock hoped to release results from the microbiota analysis early next year. When contacted, Prof Barry Taylor said his advice was that parents and doctors should avoid antibiotic use when possible.
''We're using a lot of antibiotics, often for reasons that are not needed, and so I think we should be cautious.''
The microbe-obesity research was a young area, full of speculation and suggestion, but few solid facts yet, he said.
''It's still part of a very rapidly evolving area where we try to understand what's called the microbiome, and it does look as though the bugs that are inside us do determine to some degree what we absorb, and also perhaps some of our energy metabolism."
It was possible techniques would be developed to populate babies with bacteria to prevent obesity, Prof Taylor said.
Dunedin-based Artemis Natural Healthcare founder Sandra Clair, a medical herbalist, said antibiotics had changed from being the ''miracle drug'' to one that caused serious concern.
Clinical evidence was mounting that implicated antibiotics in disruptions to gut ecology that led to problems like obesity, allergies, and autoimmune diseases.
