Mark J. Manary

Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

Not Just Wasting Malnutrition is well known in Malawi, including a severe form—kwashiorkor—in which children do not simply waste away, they also suffer edema, liver damage, skin ulceration, and anorexia. Smith et al. (p. 548; see the Perspective by Relman) investigated the microbiota of pairs of twins in Malawian villages and found notable differences in the composition of the gut microbiota in children with kwashiorkor. In these children, a bacterial species related to Desulfovibrio, which has been associated with bowel disease and inflammation, was noticeable. When the fecal flora from either the healthy or the sick twin was transplanted into groups of germ-free mice, the mice that received the kwashiorkor sample started to lose weight, like their human counterpart. Genomic analyses of gut microbiota explain responses to dietary therapy for severe malnutrition. [Also see Perspective by Relman] Kwashiorkor, an enigmatic form of severe acute malnutrition, is the consequence of inadequate nutrient intake plus additional environmental insults. To investigate the role of the gut microbiome, we studied 317 Malawian twin pairs during the first 3 years of life. During this time, half of the twin pairs remained well nourished, whereas 43% became discordant, and 7% manifested concordance for acute malnutrition. Both children in twin pairs discordant for kwashiorkor were treated with a peanut-based, ready-to-use therapeutic food (RUTF). Time-series metagenomic studies revealed that RUTF produced a transient maturation of metabolic functions in kwashiorkor gut microbiomes that regressed when administration of RUTF was stopped. Previously frozen fecal communities from several discordant pairs were each transplanted into gnotobiotic mice. The combination of Malawian diet and kwashiorkor microbiome produced marked weight loss in recipient mice, accompanied by perturbations in amino acid, carbohydrate, and intermediary metabolism that were only transiently ameliorated with RUTF. These findings implicate the gut microbiome as a causal factor in kwashiorkor.

Antibiotics as part of the management of severe acute malnutrition.

BACKGROUND Severe acute malnutrition contributes to 1 million deaths among children annually. Adding routine antibiotic agents to nutritional therapy may increase recovery rates and decrease mortality among children with severe acute malnutrition treated in the community. METHODS In this randomized, double-blind, placebo-controlled trial, we randomly assigned Malawian children, 6 to 59 months of age, with severe acute malnutrition to receive amoxicillin, cefdinir, or placebo for 7 days in addition to ready-to-use therapeutic food for the outpatient treatment of uncomplicated severe acute malnutrition. The primary outcomes were the rate of nutritional recovery and the mortality rate. RESULTS A total of 2767 children with severe acute malnutrition were enrolled. In the amoxicillin, cefdinir, and placebo groups, 88.7%, 90.9%, and 85.1% of the children recovered, respectively (relative risk of treatment failure with placebo vs. amoxicillin, 1.32; 95% confidence interval [CI], 1.04 to 1.68; relative risk with placebo vs. cefdinir, 1.64; 95% CI, 1.27 to 2.11). The mortality rates for the three groups were 4.8%, 4.1%, and 7.4%, respectively (relative risk of death with placebo vs. amoxicillin, 1.55; 95% CI, 1.07 to 2.24; relative risk with placebo vs. cefdinir, 1.80; 95% CI, 1.22 to 2.64). Among children who recovered, the rate of weight gain was increased among those who received antibiotics. No interaction between type of severe acute malnutrition and intervention group was observed for either the rate of nutritional recovery or the mortality rate. CONCLUSIONS The addition of antibiotics to therapeutic regimens for uncomplicated severe acute malnutrition was associated with a significant improvement in recovery and mortality rates. (Funded by the Hickey Family Foundation and others; ClinicalTrials.gov number, NCT01000298.).

Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children

Microbiota and infant development Malnutrition in children is a persistent challenge that is not always remedied by improvements in nutrition. This is because a characteristic community of gut microbes seems to mediate some of the pathology. Human gut microbes can be transplanted effectively into germ-free mice to recapitulate their associated phenotypes. Using this model, Blanton et al. found that the microbiota of healthy children relieved the harmful effects on growth caused by the microbiota of malnourished children. In infant mammals, chronic undernutrition results in growth hormone resistance and stunting. In mice, Schwarzer et al. showed that strains of Lactobacillus plantarum in the gut microbiota sustained growth hormone activity via signaling pathways in the liver, thus overcoming growth hormone resistance. Together these studies reveal that specific beneficial microbes could potentially be exploited to resolve undernutrition syndromes. Science, this issue p. 10.1126/science.aad3311, p. 854 Microbes from healthy children protect mice from the detrimental effects of the microbiota of malnourished infants. INTRODUCTION As we come to appreciate how our microbial communities (microbiota) assemble following birth, there is an opportunity to determine how this facet of our developmental biology relates to the healthy or impaired growth of infants and children. Childhood undernutrition is a devastating global health problem whose long-term sequelae, including stunting, neurodevelopmental abnormalities, and immune dysfunction, remain largely refractory to current therapeutic interventions. RATIONALE To test the hypothesis that perturbations in the normal development of the gut microbiota are causally related to undernutrition, we first applied random forests (RF), a machine learning method, to bacterial 16S ribosomal RNA data sets generated from fecal samples that were collected serially from healthy Malawian infants and children during their first 3 postnatal years. Age-discriminatory bacterial taxa were identified with distinctive time-dependent changes in their relative abundances; they were used to construct a sparse RF-derived model describing a program of normal postnatal gut microbiota development that is shared across biologically unrelated individuals. A metric based on this model (microbiota-for-age Z-score) was used to define the state of development (maturation) of fecal microbiota from infants and children with varying degrees of undernutrition. Fecal samples obtained from 6- and 18-month-old children with healthy growth patterns or with varying degrees of undernutrition were transplanted into young germ-free mice that were fed a representative Malawian diet. The recipient animals’ rate of lean body mass gain was characterized by serial quantitative magnetic resonance, their metabolic phenotypes were determined by targeted mass spectrometry, and their femoral bone morphologic features were delineated by microcomputed tomography. RESULTS Undernourished children in the Malawian birth cohort that we studied have immature gut microbiota. Unlike microbiota from healthy children, immature microbiota transmit impaired growth, altered bone morphology, and metabolic abnormalities in the muscle, liver, and brain to recipient gnotobiotic mice. The representation of several age-discriminatory taxa in the transplanted microbiota harbored by recipient animals correlated with their growth rates. Microbiota from 6-month-old infants produced greater effects on growth than did microbiota from 18-month-old children, although in each age bin, the growth effects produced by a healthy donor’s community were greater than those produced by an undernourished donor’s community. Cohousing coprophagic mice shortly after they received microbiota from healthy or severely stunted and underweight 6-month-old infants resulted in the invasion of age- and growth-discriminatory taxa from the former into the latter microbiota in the recipient animals, with associated prevention of growth impairments. Introducing cultured members from this group of invasive species ameliorated growth and metabolic abnormalities in recipients of microbiota from undernourished donors. CONCLUSION These preclinical findings provide evidence that gut microbiota immaturity is causally related to childhood undernutrition. The age- and growth-discriminatory taxa that we identified should help direct studies of the effects of host and environmental factors on gut microbial community development, and they represent therapeutic targets for repairing or preventing gut microbiota immaturity. Preclinical evidence that gut microbiota immaturity is causally related to childhood undernutrition. (A) A model of normal gut microbial community development in Malawian infants and children, based on the relative abundances of 25 bacterial taxa that provide a microbial signature defining the “age,” or state of maturation, of an individual’s (fecal) microbiota. (Hierarchical clusterings of operational taxonomic units are indicated on the left.) (B) Fecal samples from healthy (H) or stunted and underweight (Un) infants and children were transplanted into separate groups of young germ-free mice that were fed a Malawian diet. The immature microbiota of Un donors transmitted impaired growth phenotypes to the mice

Home based therapy for severe malnutrition with ready-to-use food

Background: The standard treatment of severe malnutrition in Malawi often utilises prolonged inpatient care, and after discharge results in high rates of relapse. Aims: To test the hypothesis that the recovery rate, defined as catch-up growth such that weight-for-height z score >0 (WHZ, based on initial height) for ready-to-use food (RTUF) is greater than two other home based dietary regimens in the treatment of malnutrition. Methods: HIV negative children >1 year old discharged from the nutrition unit in Blantyre, Malawi were systematically allocated to one of three dietary regimens: RTUF, RTUF supplement, or blended maize/soy flour. RTUF and maize/soy flour provided 730 kJ/kg/day, while the RTUF supplement provided a fixed amount of energy, 2100 kJ/day. Children were followed fortnightly. Children completed the study when they reached WHZ >0, relapsed, or died. Outcomes were compared using a time-event model. Results: A total of 282 children were enrolled. Children receiving RTUF were more likely to reach WHZ >0 than those receiving RTUF supplement or maize/soy flour (95% v 78%, RR 1.2, 95% CI 1.1 to 1.3). The average weight gain was 5.2 g/kg/day in the RTUF group compared to 3.1 g/kg/day for the maize/soy and RTUF supplement groups. Six months later, 96% of all children that reached WHZ >0 were not wasted. Conclusions: Home based therapy of malnutrition with RTUF was successful; further operational work is needed to implement this promising therapy.

Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing

The family Polyomaviridae is comprised of circular double-stranded DNA viruses, several of which are associated with diseases, including cancer, in immunocompromised patients. Here we describe a novel polyomavirus recovered from the fecal microbiota of a child in Malawi, provisionally named STL polyomavirus (STLPyV). We detected STLPyV in clinical stool specimens from USA and The Gambia at up to 1% frequency. Complete genome comparisons of two STLPyV strains demonstrated 5.2% nucleotide divergence. Alternative splicing of the STLPyV early region yielded a unique form of T antigen, which we named 229T, in addition to the expected large and small T antigens. STLPyV has a mosaic genome and shares an ancestral recombinant origin with MWPyV. The discovery of STLPyV highlights a novel alternative splicing strategy and advances our understanding of the complex evolutionary history of polyomaviruses.

Home-based treatment of malnourished malawian children with locally produced or imported ready-to-use food

Objectives: To determine the efficacy of home-based therapy with ready-to-use food (RTUF) in producing catch-up growth in malnourished children and to compare locally produced RTUF with imported RTUF for this purpose. Methods: After a brief inpatient stabilization, 260 children with severe malnutrition were enrolled and systematically allocated to receive home therapy with either imported, commercially produced RTUF or locally produced RTUF. Each child received 730 kJ/kg/day and was followed up fortnightly. Children completed the study when they reached a weight-for-height Z score > −0.5 (WHZ), relapsed, died, or failed to achieve WHZ > −0.5 after 16 weeks. Analyses were stratified by human immunodeficiency virus (HIV) status. Results: 78% of all children reached WHZ > −0.5, 95% of those with HIV-negative status and 59% of those with HIV-positive status. Eighty percent of those receiving locally produced RTUF and 75% of those receiving imported RTUF reached WHZ > −0.5. The difference between recovery rates was 5% (95% confidence interval [CI], −5–15%). The rate of weight gain was 0.4 g/kg/day (95% CI, −0.6, 1.4) greater among children receiving locally produced RTUF. The prevalence of diarrhea reported by mothers was 3.7% for locally produced RTUF and 4.3% for imported RTUF. After completion of home therapy and resumption of habitual diet for 6 months, 91% of all children maintained a normal WHZ. Conclusions: Home-based therapy with RTUF was successful in affecting complete catch-up growth. In this study, locally produced and imported RTUF were similar in efficacy in treating of severe childhood malnutrition.

Complementary feeding with fortified spread and incidence of severe stunting in 6- to 18-month-old rural Malawians.

OBJECTIVE To compare growth and incidence of malnutrition in infants receiving long-term dietary supplementation with ready-to-use fortified spread (FS) or micronutrient-fortified maize-soy flour (likuni phala [LP]). DESIGN Randomized, controlled, single-blind trial. SETTING Rural Malawi. PARTICIPANTS A total of 182 six-month-old infants. INTERVENTION Participants were randomized to receive 1 year of daily supplementation with 71 g of LP (282 kcal), 50 g of FS (FS50) (256 kcal), or 25 g of FS (FS25) (130 [corrected] kcal). OUTCOME MEASURES Weight and length gains and the incidences of severe stunting, underweight, and wasting. RESULTS Mean weight and length gains in the LP, FS50, and FS25 groups were 2.37, 2.47, and 2.37 kg (P = .66) and 12.7, 13.5, and 13.2 cm (P = .23), respectively. In the same groups, the cumulative 12-month incidence of severe stunting was 13.3%, 0.0%, and 3.5% (P = .01), of severe underweight was 15.0%, 22.5%, and 16.9% (P = .71), and of severe wasting was 1.8%, 1.9%, and 1.8% (P > .99). Compared with LP-supplemented infants, those given FS50 gained a mean of 100 g more weight and 0.8 cm more length. There was a significant interaction between baseline length and intervention (P = .04); in children with below-median length at enrollment, those given FS50 gained a mean of 1.9 cm more than individuals receiving LP. CONCLUSION One-year-long complementary feeding with FS does not have a significantly larger effect than LP on mean weight gain in all infants, but it is likely to boost linear growth in the most disadvantaged individuals and, hence, decrease the incidence of severe stunting.

Home-based therapy with ready-to-use therapeutic food is of benefit to malnourished HIV-infected Malawian children.

Aim: To determine if home‐based nutritional therapy will benefit a significant fraction of malnourished, HIV‐infected Malawian children, and to determine if ready‐to‐use therapeutic food (RUTF) is more effective in home‐based nutritional therapy than traditional foods. Methods: 93 HIV‐positive children >1 y old discharged from the nutrition unit in Blantyre, Malawi were systematically allocated to one of three dietary regimens: RUTF, RUTF supplement or blended maize/soy flour. RUTF and maize/soy flour provided 730 kJ·kg−1·d−1, while the RUTF supplement provided a fixed amount of energy, 2100 kJ/d. These children did not receive antiretroviral chemotherapy. Children were followed fortnightly. Children completed the study when they reached 100% weight‐for‐height, relapsed or died. Outcomes were compared using regression modeling to account for differences in the severity of malnutrition between the dietary groups. Results: 52/93 (56%) of all children reached 100% weight‐for‐height. Regression modeling found that the children receiving RUTF gained weight more rapidly and were more likely to reach 100% weight‐for‐height than the other two dietary groups (p<0.05).

Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy

Gut bacterial strains targeted by IgA in undernourished Malawian children produce severe enteropathy in gnotobiotic mice and correlate with health status. BugFACS Inc. In a new study, Kau et al. show that bacterial targets of gut immunoglobulin A (IgA) responses have diagnostic and therapeutic implications for childhood undernutrition. Purifying IgA-targeted microbes from fecal samples collected during the first 2 years of life from Malawian children using a method called BugFACS, these authors demonstrate that IgA responses to several types of bacteria, including Enterobacteriaceae, correlate with undernutrition. Transplanting IgA-bound bacteria from undernourished children to germ-free mice led to disruption of the gut lining (epithelium), weight loss, and sepsis in animals consuming a nutrient-deficient Malawian diet. This was prevented by a nutrient-sufficient diet or two IgA-targeted bacterial species from a healthy donor’s microbiota. Dissecting a collection of cultured IgA-targeted bacterial strains from an undernourished donor revealed that Enterobacteriaceae interacted with other community members to produce pathology. These findings have implications for the diagnosis and treatment of childhood undernutrition. To gain insights into the interrelationships among childhood undernutrition, the gut microbiota, and gut mucosal immune/barrier function, we purified bacterial strains targeted by immunoglobulin A (IgA) from the fecal microbiota of two cohorts of Malawian infants and children. IgA responses to several bacterial taxa, including Enterobacteriaceae, correlated with anthropometric measurements of nutritional status in longitudinal studies. The relationship between IgA responses and growth was further explained by enteropathogen burden. Gnotobiotic mouse recipients of an IgA+ bacterial consortium purified from the gut microbiota of undernourished children exhibited a diet-dependent enteropathy characterized by rapid disruption of the small intestinal and colonic epithelial barrier, weight loss, and sepsis that could be prevented by administering two IgA-targeted bacterial species from a healthy microbiota. Dissection of a culture collection of 11 IgA-targeted strains from an undernourished donor, sufficient to transmit these phenotypes, disclosed that Enterobacteriaceae interacted with other consortium members to produce enteropathy. These findings indicate that bacterial targets of IgA responses have etiologic, diagnostic, and therapeutic implications for childhood undernutrition.

Local Production and Provision of Ready-To-Use Therapeutic Food (Rutf) Spread for the Treatment of Severe Childhood Malnutrition

Background Ready-to-use therapeutic food (RUTF) spread has been shown to be very effective in the rehabilitation of severely malnourished children and facilitates home-based therapy of these children. Objective To describe how RUTF spread can be manufactured on a variety of production scales. Principles of production RUTF spread is an edible lipid-based paste that is energy dense, resists bacterial contamination, and requires no cooking. The primary production principles include grinding all ingredients to a particle size < 200 microns, producing the food without the introduction of water, and embedding the protein and carbohydrate components of the food into the lipid matrix. The most widely used RUTF spread is a mixture of milk powder, sugar, vegetable oil, peanut butter, vitamins, and minerals. Scale of production RUTF spread can be produced in quantities sufficient to treat several hundred children using a planetary mixer in a clinic. Production of larger quantities of RUTF spread can be achieved in partnership with local food companies. Production sufficient to meet the needs of several thousand children can be achieved with a dedicated production facility using technology appropriate for use in the developing world. Care must be taken to avoid aflatoxin contamination, and quality control testing of the product is essential. Conclusions RUTF spread can be safely and easily produced in small or large quantities in most settings worldwide. The local availability of the necessary ingredients limits its use in some settings, and further investigation of alternative ingredients is needed to overcome this limitation.