The study, published in the journal Applied and Environmental Microbiology , again raises concerns about the impact of the prolonged use of very low-carbohydrate weight-loss diets on gut health.
Low carb diets have lost popularity amongst the public with critics saying that the approach puts followers at a higher risk of clogged arteries and heart attack in the long-term.
The new study, by scientists at Aberdeen's Rowett Research Institute, reports that prolonged adherence to the low-carb diet may also adversely affect the gut bacterial populations that beneficially produce a substance called butyrate, which has been shown to be important for keeping the gut healthy including helping to prevent colorectal cancer.
"The changes in faecal butyrate in the present study represent the largest reported in a human dietary trial and provide the strongest evidence to date that butyrate production is largely determined by the content of fermentable carbohydrate in the diet," wrote lead author Sylvia Duncan.
"Furthermore, this study has provided clear evidence that the proportions of certain groups of colonic bacteria, as monitored in faecal samples, respond to dietary carbohydrate intake," she added.
The researchers recruited 19 healthy, obese men (average age 36.7, average BMI 35.4 kg per sq. m) and assigned to consume one of three diets with different carbohydrate levels (high, medium and low) for four weeks in a randomised, cross-over design.
The low (four per cent) and medium-carbohydrate (35 per cent) diets also contained a high proportion of protein (30 per cent protein).
After four-weeks on the diets, the men in the low and medium-carbohydrate diets lost similar amounts of weight and body weight.
However, levels of short chain fatty acids in the faeces differed significantly between the diet groups with levels of 114 mM, 74 mM, and 56 mM for the high, moderate, and low-carb diets, respectively.
Decreasing carb levels also reduced butyrate levels in the faeces.
Levels of so-called beneficial bacteria, particularly the bifidobacteria were also detrimentally affected by decreasing carb levels, with this type of bacteria making up 4, 2.1, and 1.9 per cent of the total faecal bacteria for the high, moderate, and low-carb diets, respectively.
Corresponding author for the study, Professor Harry Flint, said: "We can't be sure from this study about the impact of butyrate production on gut health, but there has been quite a lot of work done which shows that butyrate stops cancer cells from growing, and so helps prevent colorectal cancer.
"If low carbohydrate diets are to be consumed for long periods of time, it may be important to ensure that there is enough of the right sort of carbohydrate in the diet which can be used by the bacteria to produce compounds such as butyrate, which are beneficial for human health.
This means making sure you continue to eat plenty of sources of fibre - such as fruit and vegetable."
Source: Applied and Environmental Microbiology Volume 73, Number 4, Pages 1073-1078 "Reduced Dietary Intake of Carbohydrates by Obese Subjects Results in Decreased Concentrations of Butyrate and Butyrate-Producing Bacteria in Feces" Authors: S.H. Duncan, A. Belenguer, G. Holtrop, A.M. Johnstone, H.J. Flint, and G.E. Lobley