"We do know that there is a wide variation between individuals in the amount of fructose that can be absorbed from the gut into our bloodstream," Shepherd said.
"Those who are good at absorbing fructose are going to retain more of the calories from sugar in our diet than those who don't absorb fructose well."
While this could explain why some kids were more at risk than others, there wasn't any real data on how fructose uptake varied in school-age children - and how this related to metabolic problems like obesity.
"If our hypothesis is correct, the information will be important in identifying those most at risk from the modern food environment which will allow targeted interventions," he said.
"I think it might allow us to focus more effort on those who are at most risk rather than spreading our limited resources thinly across everyone."
In the study, targeted at schools with high proportions of Maori and Pasifika students, researchers will use a simple breath test that measures hydrogen gas to record fructose absorption rates.
"The only way the hydrogen can be in the breath in a normal person is if it's produced by the bacteria in our gut, so if we don't absorb the fructose given in the test sample, this will get to the lower part of our gut where it will provide fuel for the gut bacteria to produce hydrogen," Shepherd explained.
The research, involving about 2000 students in its first year, would be carried out in partnerships with the schools, with teachers and students undertaking some of the experiments themselves.
The tests would be linked with specially-designed teaching material to reinforce their learning about nutrition and health.
Shepherd said the study was totally unique, and Cambridge University researchers were now interested in replicating it in Europe.
"The idea that schools can be partners in major research projects arose from discussions between Maurice Wilkins Centre scientists and high school biology teachers over several years, and shows the value of outside-the-box thinking that can arise from bringing different parties together," Shepherd said.
"We believe the project will not only lead to a better understanding of how sugar impacts on our kids but will help teachers by providing real world science investigations they can link into the curriculum to improve educational outcomes."
A teacher from one of the participating schools, Epsom Girls Grammar head of biology Rachel Heeney, said the study was exciting because it combined "real research project with classroom teaching".
"I'm sure the students and staff will be very excited to be part of it and that it will help them understand the nature of science and the impact new knowledge can have on society."
The effort comes as Auckland University researchers begin a separate study that will test whether large-scale interventions targeted at sugary drinks in several Auckland school communities will help bring down rates of obesity.
Sugar Study
• A team of researchers will investigate how well Kiwi kids absorb fructose, a poorly-understood sugar that's likely to be a big contributor to obesity and diabetes.
• The findings could prove crucial in identifying those most at risk from the modern food environment which would allow targeted interventions.
• One third of school-aged Kiwi children are overweight or obese, and one in nine children between 2 and 14 are obese, including 30 per cent of Pacific children and 15 per cent of Maori children.
• One in five children living in socio-economically deprived areas are obese, compared with one in 50 children living in the least deprived areas.
Samoan gene link relevant to NZ - researcher
The renowned US scientist who helped reveal a hidden genetic variation in Samoans linked to obesity says the findings could also be relevant to other Polynesian populations - including Maori.
The study, published last month in the journal Nature Genetics, found the variant was associated with a 35 per cent higher chance of being obese.
Of the more than 5000 individual samples, taken from volunteers in Samoa, 7 per cent had two copies of the mutation and another 38 per cent had one copy.
In New Zealand, there were 144,138 Samoans, or 3.6 per cent of the population, at the last Census in 2013.
The Ministry of Health 2014/15 annual health survey says about two-thirds of Pacific adults and almost one-third of Pacific children are obese.
In an interview with the Herald, study lead author Professor Stephen McGarvey of Brown University said he felt the study would be important to New Zealand, given its potential links to Maori and the country's large Pacific Island population.
"I think that New Zealand as a society may be the among the most important high-income nations for trying to determine how to translate these findings, and those to follow, into effective clinical and public health action," he said.
"This includes especially drug discoveries."
McGarvey, who is now investigating the issue further through analysis of Samoan fat cells, is visiting the country for the Queenstown Research Week conference.
