Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

Abstract

The bacterial component of the human gut microbiota undergoes a definable program of postnatal development. Evidence is accumulating that this program is disrupted in children with severe acute malnutrition (SAM) and that their persistent gut microbiota immaturity, which is not durably repaired with current ready-to-use therapeutic food (RUTF) interventions, is causally related to disease pathogenesis. To further characterize gut microbial community development in healthy versus malnourished infants/children, we performed a time-series metagenomic study of DNA isolated from virus-like particles (VLPs) recovered from fecal samples collected during the first 30 mo of postnatal life from eight pairs of monoand dizygotic Malawian twins concordant for healthy growth and 12 twin pairs discordant for SAM. Both members of discordant pairs were sampled just before, during, and after treatment with a peanut-based RUTF. Using Random Forests and a dataset of 17,676 viral contigs assembled from shotgun sequencing reads of VLP DNAs, we identified viruses that distinguish different stages in the assembly of the gut microbiota in the concordant healthy twin pairs. This developmental program is impaired in both members of SAM discordant pairs and not repaired with RUTF. Phage plus members of the Anelloviridae and Circoviridae families of eukaryotic viruses discriminate discordant from concordant healthy pairs. These results disclose that apparently healthy cotwins in discordant pairs have viromes associated with, although not necessarily mediators, of SAM; as such, they provide a human model for delineating normal versus perturbed postnatal acquisition and retention of the gut microbiota's viral component in populations at risk for malnutrition.assembly of the human gut DNA virome | childhood malnutrition | age/disease-discriminatory phage and eukaryotic viruses | gnotobiotic mice | epidemiology M alnutrition (undernutrition) is a leading cause of child mortality worldwide (1). Severe acute malnutrition (SAM) can manifest itself as progressive wasting (marasmus) or as a more abrupt onset syndrome characterized by generalized edema, hepatic steatosis, skin rashes and ulcerations, and anorexia (kwashiorkor). The configuration of the bacterial component of the gut microbiota of healthy infants evolves to an adult-like configuration during the first 2-3 y of life (2, 3). Normal postnatal maturation of the gut microbial community is perturbed in SAM; children with SAM living in Malawi and in Bangladesh have gut microbiota with bacterial configurations that appear younger (more immature) than the microbiota of chronologically age-matched individuals with healthy growth phenotypes (3, 4). Moreover, this immaturity is only transiently improved with current ready-to-use therapeutic food (RUTF) interventions (3, 4). These children can be viewed as having a persistent developmental abnormality-one that affects a microbial "organ" whose key functions include the biosynthesis of vitamins and the biotransformation of dietary components into p...

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children

“…Additional comparisons were made between individuals (interpersonal variation). The greatest similarity between fecal viromes was within an individual over time, as reported previously (34). The intrapersonal variation for both controls and cases was significantly (adjusted P < 0.0001) lower than the interpersonal variation within these two groups ( Fig.…”

“…There is great variation in the gut virome among individuals (28,34,46,50). We found the greatest similarity in fecal viromes within an individual over time as reported previously (28,34,46,50). Intrapersonal variation for both control subjects as a group and cases as a group was significantly lower than the interpersonal variation within these two groups ( Fig.…”

“…To identify bacteriophage contigs associated with autoimmunity, we first identified age-discriminative contigs to remove them as a confounding factor. Age affects virome composition during the first 3 y of life (34,46). Consistent with this, we observed a significant correlation between age and the relative abundance of specific bacteriophages and Shannon diversity, as well as richness, using both reads-based methods and contig-based methods (Table S1).…”

“…A normalized matrix of the number of reads per kbp of contig sequence per million raw reads per sample (RPKM) of all the viral contigs was used to create a viral contig abundance matrix. This viral contig abundance matrix was used to measure α and β diversity of the virome (34) and to perform Random Forests analysis.…”

“…Although the presence of these sequences does not prove infection with the viruses detected, the children were exposed to a broad range of eukaryotic viruses (12,23). We measured virome β diversity using the Hellinger distance metric on the RPKM matrix (34). Distances were computed between fecal viromes sampled from a given individual over time (intrapersonal variation).…”