We used anthropometric data collected from members of a birth cohort study (14) of 100 children living in Mirpur thana in Dhaka, Bangladesh, to define whether they were healthy or undernourished (table S1).<\/p>\n
Those with height-for-age z scores (HAZ) greater than or equal to \u00e2\u02c6\u20192 were classified as “healthy,” whereas those with scores less than or equal to \u00e2\u02c6\u20193 were deemed severely stunted. At 18 months, 30 and 25 children satisfied these criteria for healthy and severely stunted, respectively, whereas at 24 months, 27 and 20 children received these designations; the remaining children were classified as moderately stunted (HAZ between \u00e2\u02c6\u20192 and \u00e2\u02c6\u20193). A PCR-based screen for ETBF targeting all three fragilysin gene subtypes (14) was performed using DNA isolated from fecal samples that had been collected from these children at 18 and 24 months of age.<\/p>\n
The results revealed that ETBF was variably present between individuals and within a given individual over time, with a total of 25 of 24-month-old children having a positive test (table S1). In this small cohort, ETBF carriage was not significantly correlated with indices of linear or ponderal growth .<\/p>\n
We combined anthropometric and PCR data to select fecal samples collected at 24 months from two children: (i) a healthy individual (child ID 7114 in table S1) with a HAZ score of \u00e2\u02c6\u20190.71, a WAZ score of \u00e2\u02c6\u20191.49, and a WHZ score of \u00e2\u02c6\u20191.62 who was ETBF-negative at the two time points tested, and (ii) a severely stunted and moderately underweight individual (child ID 7004) with a HAZ score of \u00e2\u02c6\u20193.02, a WAZ score of \u00e2\u02c6\u20192.51, and a WHZ score of \u00e2\u02c6\u20191.34 who was ETBF-positive at both time points. Of the 35 individuals with a positive ETBF test at either time point, only this stunted\/underweight child was positive at both 18 and 24 months of age.<\/p>\n
Fecal samples obtained from members of this singleton birth cohort were screened for parasites using microscopic methods (5); neither of the two donors tested positive (see Materials and Methods for details). To define the effects of diet and these two childrens’ gut microbiota on host biology, we generated three representative versions (embodiments) of the diets consumed by the population represented by the donors.<\/p>\n
To do so, we determined the relative daily caloric contributions of various selected ingredient types, based on a study by Arsenault and coworkers (16). Selection of specific food items as representative of each ingredient type was based on consumption incidence surveys tabulated by Islam et al. (17), and the results were incorporated into a database consisting of 54 food ingredients. We filtered this database to remove items consumed by<\/p>\n