Fecal Bacteria as Biomarkers for Predicting Food Intake in Healthy Adults

Abstract

Background Diet affects the human gastrointestinal microbiota. Blood and urine samples have been used to determine nutritional biomarkers. However, there is a dearth of knowledge on the utility of fecal biomarkers, including microbes, as biomarkers of food intake. Objectives This study aimed to identify a compact set of fecal microbial biomarkers of food intake with high predictive accuracy. Methods Data were aggregated from 5 controlled feeding studies in metabolically healthy adults (n = 285; 21–75 y; BMI 19–59 kg/m2; 340 data observations) that studied the impact of specific foods (almonds, avocados, broccoli, walnuts, and whole-grain barley and whole-grain oats) on the human gastrointestinal microbiota. Fecal DNA was sequenced using 16S ribosomal RNA gene sequencing. Marginal screening was performed on all species-level taxa to examine the differences between the 6 foods and their respective controls. The top 20 species were selected and pooled together to predict study food consumption using a random forest model and out-of-bag estimation. The number of taxa was further decreased based on variable importance scores to determine the most compact, yet accurate feature set. Results Using the change in relative abundance of the 22 taxa remaining after feature selection, the overall model classification accuracy of all 6 foods was 70%. Collapsing barley and oats into 1 grains category increased the model accuracy to 77% with 23 unique taxa. Overall model accuracy was 85% using 15 unique taxa when classifying almonds (76% accurate), avocados (88% accurate), walnuts (72% accurate), and whole grains (96% accurate). Additional statistical validation was conducted to confirm that the model was predictive of specific food intake and not the studies themselves. Conclusions Food consumption by healthy adults can be predicted using fecal bacteria as biomarkers. The fecal microbiota may provide useful fidelity measures to ascertain nutrition study compliance.

Gut Microbiota for Health: How Can Diet Maintain A Healthy Gut Microbiota?

“…This holistic approach appears to be very useful to identify new biomarkers and to understand the role of food in health and disease, as well as to identify inter-individual variations useful to formulate personalized dietary recommendations [11]. Fecal bacteria were recently studied as biomarkers of food intake for specific whole foods with high predictive accuracy by Shinn et al [12].…”

A starch‐ and sucrose‐reduced dietary intervention in irritable bowel syndrome patients produced a shift in gut microbiota composition along with changes in phylum, genus, and amplicon sequence variant abundances, without affecting the micro‐RNA levels

“… 50 , 51 Lachnospiraceae UCG‐001 and Lachnospira were among 15 genera included in the model, which had an estimated 85% accuracy for determining intake of four foods, that is, avocado, almonds, walnuts and whole‐grain. 52 Blautia , belonging to the Lachnospiraceae family, has previously been found to be increased in those with self‐reported IBS compared with non‐IBS patients from the same geographic area. 53 In contrast, decrease of two Eubacterium genera was found in participants with exclusion/vegetarian diets.…”

“…Accordingly, Lachnospira is strongly associated with vegetable diets, 18,49 and wholegrain‐rich diet and psyllium husk supplementation 50,51 . Lachnospiraceae UCG‐001 and Lachnospira were among 15 genera included in the model, which had an estimated 85% accuracy for determining intake of four foods, that is, avocado, almonds, walnuts and whole‐grain 52 . Blautia , belonging to the Lachnospiraceae family, has previously been found to be increased in those with self‐reported IBS compared with non‐IBS patients from the same geographic area 53 .…”

Fueling Gut Microbes: A Review of the Interaction between Diet, Exercise, and the Gut Microbiota in Athletes

“…Diet affects the gut microbiota composition and fluctuations ( 7 , 10 ) over both short ( 5 ) and long ( 6 ) time frames. In addition to well-studied nutrients like fiber ( 11 ), the effects of specific foods (e.g., nuts, avocados) ( 12 , 13 ) and dietary patterns (e.g., Mediterranean diet pattern) ( 14 ) are also recognized. Recent reviews have detailed how exercise influences the gut microbiota, depending on the type, intensity, and exercise duration ( 2 , 10 , 15–17 ).…”