Community-based Clinical Trial With Microbiota Directed Complementary Foods (MDCFs) Made of Locally Available Food Ingredients for the Management of Children With Post-severe Acute Malnutrition Moderate Acute Malnutrition (Post-SAM MAM)
Community-based Clinical Trial With Microbiota Directed Complementary Foods (MDCFs) Made of Locally Available Food Ingredients for the Management of Children With Post-severe Acute Malnutrition Moderate Acute Malnutrition (Post-SAM MAM)
Background (brief):

 1. Burden: A total of 52 million children under 5 are suffering from acute malnutrition
 globally, of whom 33 million suffer from moderate acute malnutrition (MAM). In
 Bangladesh, around 2 million children suffer from MAM. In absolute numbers, according to
 Bangladesh Demographic Health Survey 2014, 26%, 25% and 17% of children aged less than
 two years are stunted, underweight and wasted respectively.1

 2. Knowledge gap: We have already demonstrated that children with acute malnutrition have
 immature gut microbiota that is partially corrected with treatment. Children with MAM
 have an increased risk of mortality, infections and impaired physical and cognitive
 development compared to well-nourished children. Although the global caseload of MAM is
 much greater than that of SAM, the condition has not received the same level of
 attention or priority. Through our previous and ongoing research we now know about the
 members of the gut microbiota that can promote growth in children and also about certain
 food ingredients that promote the proliferation of such beneficial microbiota. However,
 this knowledge needs to be applied on a large scale community-based clinical trial.

 3. Relevance: The rationale for this study is to assess whether long-term administration of
 complementary food made of locally available food ingredients that can stimulate the
 proliferation of growth promoting gut microbiota (MDCF-2), as identified in our Pre-POC
 trial, is able to produce predictable changes in the microbiota of Bangladeshi children
 with Post-SAM MAM as well as in their nutritional status. We would now like to do a
 community-based clinical trial of this potential MDCF-2 in the management of children
 with Post-SAM MAM.

 Hypothesis (if any): Complementary foods made of locally available food ingredients that
 stimulate the proliferation of growth promoting gut microbiota (MDCF-2) will improve clinical
 outcomes.

 Objectives: To investigate the efficacy of complementary food made of locally available food
 ingredients that can stimulate the proliferation of growth promoting gut microbiota
 (Microbiota Directed Complementary Food: MDCF-2) in (i) promoting repair of microbiota
 immaturity (ii) promoting proliferation of beneficial bacteria (iii) improving both linear
 and ponderal growth in children with Post-SAM MAM (iv) improving the metabolomic profile of
 children with Post-SAM MAM

 Methods: We will conduct a proof of concept (POC) clinical trial in 12-18 months old children
 with post-SAM MAM (Weight-for-Length Z-score, WLZ <-2 to -3) over the course of approximately
 two years. This study will be undertaken at Mirpur area of Dhaka city and in Kurigram. We
 will produce MDCF-2 at the icddr,b Food Processing Laboratory in sufficient quantities for
 the trial. This formulation is matched for energy density and micronutrient content of ready
 to use supplementary food (RUSF) used for MAM. It itself is not a ready-to-use food but is
 rather a cooked food made of locally available food ingredients (chickpea, green banana,
 peanut, soybean flour) which have been found to enhance growth promoting members of the gut
 microbiota in children. We will test MDCF-2 and the current RUSF standard of care for Post
 SAM MAM to see the effect on growth, proteomics and metabolomics of an intervention for 12
 weeks, with a 4-week post-intervention phase.

 Outcome measures/variables:

 -  Ponderal growth (rate of weight gain as the primary outcome variable), measured at
 different time points by anthropometry

 -  Linear growth, measured at different time points by anthropometry

 -  Proteomic profile, assayed by DNA aptamer based SOMAlogic scan

 -  Morbidity, assessed by daily records

 -  Change in microbiota-for-age Z score

 Hypothesis to be tested:

 Complementary food made of locally available food ingredients that can stimulate the
 proliferation of growth promoting gut microbiota (MDCF-2) will improve nutritional outcomes.

 Specific Objectives To investigate the efficacy of complementary food made of locally
 available food ingredients that can stimulate the proliferation of growth promoting gut
 microbiota (Microbiota Directed Complementary Food: MDCF-2) in

 (i) promoting repair of microbiota immaturity (ii) promoting proliferation of beneficial
 bacteria (iii) improving both linear and ponderal growth in children with Post-SAM MAM (iv)
 improving the metabolomic profile of children with Post-SAM MAM
Background:

 Moderate acute malnutrition (MAM), a major global health problem, is defined as wasting (i.e.
 weight-for-height between <-2 and -3 Z-scores of the WHO Child Growth Standards) and/or
 mid-upper-arm circumference (MUAC) greater or equal to 115 mm and less than 125 mm. According
 to the Global Nutrition Report 2017, 8% or 52 million under-five children were acutely
 malnourished globally in 2016 and stunting or chronic malnutrition affected 23% or 155
 million children. Approximately one in 6 children under 5 years in South Asia suffered from
 MAM in 2013 (i.e. 17%). These children are at increased risk of severe acute malnutrition
 (SAM), and have a three times higher risk of mortality from common communicable diseases than
 the well-nourished peers. Bangladesh has one of the highest childhood malnutrition burdens in
 the world. According to Bangladesh Demographic Health Survey 2014, the prevalence of stunting
 in the country among under-five children is 36%, among them 12% suffer from severe stunting
 (LAZ <-3).1 Around 15% of children are wasted (weight-for-length, WLZ <-2); more than 2
 million children suffer from MAM, while 3% or 450,000 children suffer from the deadly form of
 SAM. Malnutrition costs Bangladesh an estimated US $1 billion a year.

 According to WHO recommendations, infants and children aged 6-59 months with MAM need to
 consume nutrient-dense foods to meet their extra needs for weight and height gain and
 functional recovery. Currently there are no evidence-informed recommendations on the
 composition of supplementary foods used to treat children with MAM. Interventions to address
 undernutrition should therefore include a strong component of MAM management. MAM prevention
 should be taken into consideration in food security and other development strategies as the
 situation becomes critical in populations where food insecurity is rampant. It is important
 therefore to develop interventions that depend upon locally available food ingredients which
 in small quantities are able to harness the beneficial power of the gut microbiota on infant
 and child growth.

 One of the major factors limiting the impact of nutrition interventions is the inability of
 the malnourished children to increase their intake to meet increased metabolic demands. In
 collaborative studies between icddr,b and the Gordon Lab at Washington University in St.
 Louis during the Jumpstart Phase of the Breast Milk, Microbiota and Immunity (BMMI) Project,
 we applied Random Forests, to bacterial 16S rRNA (ribosomal RiboNucleic Acid ) datasets
 generated from monthly fecal samples obtained from a birth-cohort of children living in an
 urban slum of Dhaka, Bangladesh. These children exhibited consistently healthy growth (WLZ
 -0.32+0.98). Bacterial strains were identified whose proportional representation defines a
 healthy gut microbiota as it assembles during the first 2-3 postnatal years. In a randomized
 clinical trial at icddr,b of two therapeutic foods (imported ready-to-use therapeutic food
 [RUTF, Plumpy'Nut] versus locally prepared rice/lentil-based Khichuri and Halwa) in
 Bangladeshi children with severe acute malnutrition (SAM), it was observed that the
 microbiota immaturity is incompletely and only transiently improved, with children remaining
 markedly stunted and underweight throughout the follow-up period. Bangladeshi children with
 MAM also exhibited significant microbiota immaturity, although less severe than children with
 SAM. Microbiota immaturity thus serves as a potential biomarker to identify infants at risk
 for undernutrition and to monitor treatment and prevention strategies. In our previous study
 approved by the ERC (PR-09023), we compared the gut microbiota of healthy children living in
 slum of Mirpur with children hospitalized for the treatment of severe acute malnutrition. The
 microbiota was assessed by 16S Ribosomal RNA sequencing. We found that the gut microbiota of
 children with SAM lags chronologically behind microbiota of healthy children. For example, a
 two year old child with SAM may have the gut microbiota similar to that of a one year old
 healthy child. This is known as immaturity of the gut microbiota. We have developed two
 metrices to represent this gut immaturity - the relative microbiota maturity index and the
 microbiota-for-age Z score; SAM is associated with significant relative microbiota immaturity
 that is only partially ameliorated following nutritional interventions. .

 We recently developed ready-to-use therapeutic foods using locally available food
 ingredients-rice, lentil, and chickpeas that are culturally relevant and acceptable. We found
 through a double-blind RCT (Randomized Controlled Trial ) that the Bangladeshi chickpea-based
 and rice-lentil-based RUTF (Ready To Use Therapeutic Food) we developed were as effective as
 the commercial peanut based-RUTF and well accepted by children with SAM. Through a
 combination of the above mentioned RCT and clinical translational studies conducted over the
 last 7-8 years, we have identified growth promoting age-discriminatory beneficial microbiota
 and locally available food ingredients that support proliferation of these beneficial
 microbiota. Besides, earlier studies done on gnotobiotic animals in Washington University
 Centre for Genome Science has led us to suggest that a combination of food ingredients
 (chickpea, soy flour, peanut and green banana) being informed by studies done in Dhaka will
 be worth studying with respect to the diet's impact on stimulating proliferation of
 growth-discriminatory microbiota as well as cost and sustainability.

 Recently we successfully completed an IRB approved study, 'Pre-Proof of Concept clinical
 trials to optimize lead microbiota-directed complementary food (MDCF) prototypes for their
 ability to repair microbiota immaturity and establish their organoleptic acceptability'
 (PR-16099). The main objective of this pilot study was to demonstrate a Pre-proof of Concept
 that certain complementary foods would have a beneficial effect on young children suffering
 from MAM, by stimulating the proliferation of particular members of gut microbiota that are
 known for their growth promoting effects. In that pilot study we investigated
 Microbiota-for-age Z (MAZ) score as well as the impact of proliferation of good members of
 the gut microbiota on certain body systems. This study was designed to test the effects of
 three locally produced MDCF prototypes (MDCF-1, MDCF-2 and MDCF-3) and a locally produced
 rice-lentil-based RUSF. The results of the Pre POC pilot trial conclusively showed that one
 of the three MDCFs (namely MDCF-2) was associated with increased levels of certain amino
 acids that have a key role in development of long bones, development of the brain and
 increased production of IGF-1 (Insulin like Growth Factor-1) which are critical factors in
 the biology of child growth. Also it is effective in stimulating the growth of growth
 promoting members of the gut microbiota, for example Faecalibacterium prausnitzii. Based on
 the result of this Pre-POC pilot trial we now plan to do a larger clinical trial using the
 most promising MDCF-2 on the management of Post-SAM MAM children with the primary end point
 being linear growth.

 Research Design and Methods We will conduct a clinical trial among 12-18 months old children
 with Post-SAM MAM (WLZ <-2 to -3) over the course of approximately two years. The trial will
 be conducted at Bauniabadh and RADDA MCH-FP clinic in Mirpur area of Dhaka city, and at the
 Special Nutrition Unit (SNU) run by Terre des Hommes (TdH) in Kurigram. The TdH SNU has been
 selected because we want to expedite the enrolment and we have a good track record of working
 there; the last efficacy trial we conducted on our local RUTFs was also done there partly.
 Children will be screened and enrolled through household survey by Field Research Assistants
 (FRAs) following pre-specified inclusion criteria. Fulfilling the enrolment criteria and upon
 receiving the consent for study participation from the parents or legal guardians, the
 children with the respective mother/caregiver will be enrolled and randomly assigned to one
 of the two arms according to computer-generated random numbers. The code of assigned type of
 diet will be kept in closed opaque envelopes for each individual, and will be opened only
 when the caregiver signs the consent form. This trial will not fall under any typical drug
 trial. However, if we are to consider this trial under any phase, then it would fall under
 phase II, because we have already done a pilot trial looking at the impact on
 microbiota-for-age Z score as well as adverse effects.

 First of all, there will be the stabilization phase, which will be for 4-8 days, during that
 time each child will be managed as per WHO (World Health Organization) / icddr,b guidelines
 for the management of SAM. This includes programmed feeding, micronutrient supplementation,
 judicious rehydration, broad spectrum antibiotic treatment and prompt recognition and
 management of complications. Upon recovery from the stabilization phase nutritional
 rehabilitation will continue for approximately 2 weeks during which the icddr,b standard of
 care dietary protocol based upon the local diets Halwa and Khichuri will be served. Upon
 graduation from SAM to MAM (edema-free WLZ <-2), children will be randomly assigned to one of
 the two arms (Rice-lentil based RUSF and MDCF-2).

 The post randomization nutritional rehabilitation component will have 3 phases. The first
 phase will involve onsite feeding of the diet twice daily for 1 month at the nutrition
 centres established in Mirpur and Kurigram. The second phase will entail feeding the children
 once at the nutrition center and once at home. During the third phase the children will be
 fed the diets twice daily at home. The children will be observed for 4 weeks in the
 post-intervention phase. During the entire study period, anthropometric data, food diversity
 data and samples (blood, stool, and urine) will be collected. We will collect weekly
 qualitative dietary intake data of over the last 24 hours by using Food Frequency
 Questionnaires during the dietary intervention for all study participants.

 Randomization After the stabilization and nutritional rehabilitation phases when the children
 will reach to MAM state they will be randomly assigned to one of the two arms (Rice-lentil
 based RUSF and MDCF-2). The code of the assigned type of treatments will be kept in closed
 opaque envelopes until assigned to an enrolled child.

 Arm 1- Rice-lentil based RUSF (rationale: reference standard of care for post-SAM, MAM; based
 on knowledge of its effects on child growth and the gut microbiota) Arm 2- MDCF-2 prototype
 with four complimentary food ingredients without powdered milk (rationale: lead with evidence
 from the recently completed pre-POC clinical trial of promoting growth promoting microbiota
 and positive effects on growth).

 Recruitment, Screening and Consenting Children with SAM will be identified through direct
 observation and screening in icddr,b Dhaka Hospital, RADDA-MCH-FP Clinic in Mirpur, the SNU
 of TdH in Kurigram, as well as through screening in the communities in Mirpur and Sadar,
 Ulipur and Chilmari Upazilas of Kurigram district. Those who require stabilization care will
 be admitted in the facilities mentioned above where the standard of care for the acute phase
 treatment of SAM will be provided. In brief; this stabilization care is based upon programmed
 feeding, micronutrient supplementation, judicious rehydration, broad spectrum antibiotic
 treatment and prompt recognition and management of complications. They will subsequently be
 treated with the standard of care dietary protocol for nutritional rehabilitation. Upon
 graduation into MAM, parents of children who meet the MAM criteria for post-SAM MAM trial
 will be approached about enrolment into the study. A trained Field Research Assistant (FRA)
 will explain the study in detail, answer any questions from the parent(s), and invite the
 parent(s) to enrol the child in the study.

 At the beginning of the study, information will be sought on the demographic characteristics
 and FRAs will record the children's weight using a digital scale with 2 g precision (Seca,
 model 728, Germany), length (using infantometer, Seca, model 416, Germany), and mid-upper-arm
 circumference to the nearest mm (using a non-stretch insertion tape). Anthropometrics will be
 done according to the standard procedures. Study participants will be asked to come to the
 designated nutrition center for nutritional therapy to ensure intake of the MDCF/RUSF. They
 will be provided with a phone number to reach the clinic staff, and a member of the staff may
 visit a family's household for directly observed nutritional therapy with prior arrangement
 if needed. The programmed feeding of the MDCF-2 or RUSF for three months after nutritional
 rehabilitation is illustrated in the figure.

 Preparation of MDCF-2 and RUSF:

 Based on compatible combinations of complementary food ingredients identified in the Pre-POC
 study mentioned above, we will prepare MDCF-2 as well as RUSF at the icddr,b Food Processing
 facility in Mirpur and in Kurigram in sufficient quantities for the clinical study. The two
 diets will be matched in energy density and micronutrient content. The energy density of
 MDCF-2 is targeted at 125 kcal/25 g (per serving), and caloric distribution is targeted to be
 45-50 percent from fat and 8-10 percent from protein. The two servings of MDCF-2 or RUSF will
 provide 250 Kcal and the necessary micronutrients in addition to providing the substrate for
 the beneficial microbiota proliferation. The servings are meant to be a top up to the usual
 diet received by these children at home. Mothers/primary caregivers will be advised to
 maintain their child's current dietary and breastfeeding practices.

 Experiments in development of the MDCF-2 prototypes and assessment of the organoleptic
 properties have been done in the Pre-POC clinical trial.

 Food will be prepared everyday to ensure that no unexpected contamination and nutrient losses
 occur during preparation. Although raw food ingredients will be very carefully procured from
 the local market and stored in reasonable quantities, we will prepare, dispense, and feed the
 children the same day the MDCF-2 and RUSF are prepared.

 After receiving the raw materials (rice/lentil/chickpea) we will take out the foreign
 materials/grains or seeds (if there is any) those can be discarded, and then in an open pan
 the raw materials will be roasted. We will maintain the temperature at 120-130°C for
 roasting. Usually it takes 8-10 minutes for roasting 100g of each raw material. Continuous
 stirring is essential to ensure roasting of single seeds/grains. After completion of roasting
 we will keep it aside for cooling and then we will grind. We will take the powder and strain
 it using a strainer. After straining for 4 to 5 times, we will take the fine powder for
 mixing with the other ingredients (milk powder/oil). We will also grind the sugar and the
 fine powder will be used for mixing. Finally we will add the pre-weighed premix powder. The
 processing of whole green banana is different from the other ingredients. Green banana with
 skin will be placed in a deep pan in boiling water (100°C-110°C) and boiled for about 17-20
 minutes until they are cooked and tender. The skin of the green banana will be peeled off and
 the edible white part would be taken and grated into small pieces. Then they will be taken in
 a pot and allowed to cool. We will smash the small pieces of banana with spoon/hand crusher.
 The weights of all other ingredients will be recorded. Potential recipes will be produced in
 small batches by mixing all ingredients in an electric blender. Preparation of food under
 different steps, that is, roasting, particle size reduction, homogeneous blending, and
 supplying to the nutrition centres will be monitored by icddr,b investigators. Food will be
 prepared everyday to ensure that no unexpected contamination and nutrient losses occur during
 preparation. Although raw food ingredients will be very carefully procured from the local
 market and stored in reasonable quantities, we will prepare, dispense, and feed the children
 the same day the MDCF and RUSF are prepared.

 Feeding sessions:

 The children and mothers/caregivers will be requested to come to the nutrition centers
 established at the sites preferably between 9-11 am and 3-5 pm every day for the first month.
 The mothers will be requested not to give any food and breast milk in the 2 hours preceding
 the observed meal time. The child will be offered 25 grams of MDCF-2 or RUSF per serving as
 decided by randomization. The mothers will be asked to spoon feed the pre-weighed diets to
 their children until s/he refuses to eat, as described below. After a two-minute pause, the
 same diet will be offered a second time until s/he refuses again. After a second two-minute
 pause, the diet will be offered a third time until refused again. After this third refusal,
 the feeding episode will be considered as 'terminated'. The duration of the feeding
 (excluding the intervening 'rest periods') will be recorded by stopwatch, and the total
 duration of the feeding will be noted. This feeding episode will last for maximum 60 minutes.
 Measured volumes of plain water will also be given and the amount of water taken during this
 meal period of 60 minutes will be measured. The feeding episode will take place under the
 direct supervision of trained study personnel. Children will be considered as refusing
 further intake if they move their head away from the food, cry, clamp the mouth or clinch the
 teeth, or become agitated, spit out the food or refuse to swallow. The amount of MDCF-2/RUSF
 actually ingested will be calculated by subtracting the left over from the offered amount, or
 by asking the mother when fed at home. The enrolled children will be monitored daily by Field
 Research Assistants for any possible side effects/adverse events (e.g. rash, urticaria due to
 food allergy or any significant changes in clinical status) for a week. If any side
 effects/adverse events are observed, they will be treated according to standard of care. A
 standardized production procedure will be followed to control the quality of RUSF and MDCF-2.
 Every child will be offered 25gm of the diet twice daily at the feeding center for the first
 4 weeks. In the following month, the child will be offered 25gm of the diet at the feeding
 center and additional 25gm will be provided in a clean container to feed at home. In the
 third month, two separate containers containing 25gm diet will be provided every day to each
 enrolled child at participant's home. Feeding information will be collected from mothers and
 amount consumed will be measured from the left outs. Food will be kept in sterile containers
 and at room temperature in between the feeding session. Quality of the food will be ensured
 by having samples of the prepared foods tested for microbes and moulds every 2 months at
 icddr,b. Samples selected for testing will include food stored for 2 and 6 hours after
 cooking. The samples will also be tested for Aflatoxin every six months at SGS Laboratories,
 Delhi.

 In this study nutritional status will be assessed through anthropometry, comparing with WHO
 growth reference standards. At the beginning of the study, information will be sought on the
 demographic characteristics (families' wealth, standard of housing, family structure and
 parental characteristics etc.), and FRAs will record the children's weight using a digital
 scale with 2g precision (Seca, model 728, Germany), length (using infantometer, Seca, model
 416, Germany), and mid upper-arm circumference to the nearest mm (using a non-stretch
 insertion tape). Anthropometrics will be done according to the standard procedures and all
 measurements will be taken thrice and the average value will be recorded.

 Fecal sample collection In acute phase of stabilization fecal samples will be collected every
 alternative day. During the rehabilitation phase, weekly fecal samples (1-2g) will be
 collected within 30 minutes of production (at home and transported back to the icddr,b) using
 the Nitrogen dry shipper specimen collection SOP (Standard Operating Procedure) used in the
 recent Pre-POC clinical trial (Appendix-A). Specimens will be stored at -80◦C before being
 sent to the Gordon Lab at the end of each study for analysis of microbiota maturity (measured
 before, during and after cessation of treatment with MDCF-2 and RUSF) and PCR-based
 assessment of enteropathogen burden in fecal samples (measured before and after MDCF-2
 treatment). A total of 12 fecal samples will be collected from each child at different time
 points during whole study period. Assuming 62 study participants / arm, a total of 1488 fecal
 specimens will be collected in this study. Along with that 2 gm of fecal sample will be
 collected from the mothers at the beginning of stabilization phase.

 Urine sample collection A total of 7 urine samples (2 ml each) will be collected from each
 child at different time points during the whole study period. Assuming 62 study participants
 / arm, a total of 868 urine samples will be collected in this study. Along with that 5 ml of
 urine samples will be collected from the mothers at the beginning of stabilization phase.

 Blood sample collection A total of 4 blood samples (2 ml each) will be collected at different
 time points during the whole study period. Each will be collected from every child at the
 beginning of stabilization phase, prior to intervention; end of first month of intervention
 and just after the intervention is complete.

 Assuming 62 study participants / arm, a total of 496 plasma samples will be collected in this
 study. Along with that, 5 ml of blood samples will be collected from the mothers at the
 beginning of stabilization phase.

 Maternal nutritional status is associated with child nutritional status, as shown through the
 results of our eight country MAL-ED study. In addition, antenatal and maternal factors were
 early determinants of lower length-for-age, and their contribution remained important
 throughout the first 24 months of life. As such, we will record maternal height and weight.
 In order to understand the biological state of nutrition of the mother, enrolment samples of
 stool, blood and urine will be asked of the mother. These samples will be analyzed for gut
 microbiota, and proteomics, and the results correlated with those of the enrolled children.

 Anthropometry The age of the child will be verified against documentation (birth certificate
 or immunization card, if available) or caregiver's report of the child's birth date. Length
 will be measured by a infantometer sensitive to 0.1 cm. Body weight will be measured by a
 balance sensitive to 2g (SECA 7281321009, Hamburg, Germany). Length-for-age (LAZ),
 weight-for-length (WLZ) and weight-for-Age (WAZ) Z-scores will be calculated following the
 Multicentre Growth Reference Study (MGRS) WHO growth standards. Edema will be examined by
 pressing the upper side of both feet for 3 seconds. Mid-upper arm circumference (MUAC) will
 be measured using TALC MUAC tape (UK). Regular standardization of the measuring equipments
 will be done using standards everyday by trained field research assistant.

 Analyses of plasma and fecal samples Plasma samples collected from this trial will be sent to
 Dr Jeffrey Gordon's lab in the Center for Genome Sciences and Systems Biology at Washington
 University in St. Louis. Advanced mass spectroscopic- and immunoassay-based methods will be
 used to obtain new knowledge about the role of gut microbiota immaturity and the effects of
 attempting acute repair of this immaturity with lead microbiota-directed complementary food
 (MDCF-2) on biomarkers and mediators of healthy growth. Comparisons will be made with the
 control group (i.e., those consuming reference RUSF standard). Targeted Ultra Performance
 Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry
 (GC-MS) will be used to profile analytes of specific interest in plasma and/or fecal samples
 including bile acids and short chain fatty acids (SCFAs); markers of mitochondrial function
 (e.g., β-hydroxybutyrate, acylcarnitines/acylCoAs, TCA cycle intermediates); amino acids in
 serum plus fecal samples [branch chain amino acids, tryptophan and tryptophan metabolites
 related to growth and inflammatory status, including those produced by bacterial tryptophan
 metabolism (e.g. indole acetic acid derivatives)]. In addition, key mediators/biomarkers of
 linear growth (e.g., growth hormone and IGF-1), energy utilization (insulin, leptin), and
 bone biology [IL-6 (interleukin-6), osteoprotegerin, the C-terminal peptide of type I
 collagen (CTX, a marker of osteoclast activity/bone resorption), and the amino-terminal
 propeptide of Type 1 procollagen (P1NP, a marker of osteoblast activity/bone formation)], and
 systemic inflammation (CRP, AGP) will be quantified using established ELISA/Luminex assays.
 Proteins in blood will be identified using the SOMAlogic scan that permits identification of
 more than 1300 different proteins. The proteomic study done on plasma samples from children
 with SAM in our previous Pre-POC trial done in Dhaka has already demonstrated a number of
 significant and clinically relevant associations between certain proteins and clinical
 phenotypes using the SOMAlogic scan.

 Information gathered will be used to select human fecal samples for transplantation into
 germ-free animals; these animals, who will be fed the diets of their human microbiota donors,
 will be used to further characterize the mechanisms that link MDCF-2 prototypes, the gut
 microbiota, and host physiology/metabolism. In addition, these plasma and fecal biomarkers
 will be used to determine that MDCF-2 promotes repair of microbiota immaturity and improves
 biological state in children.

 Sample Size Calculation In the pre-POC trial of different MDCFs, the baseline
 weight-for-length Z score of children who received MDCF2 (Microbiota Directed Complementary
 Food 2) was -2.2 and after one month of supplementation was -1.7. If we consider the WLZ -2
 at baseline and -1.7 at end line, pooled SD (standard deviation) as 0.53 then the sample size
 is 49 in each arm at 80% power and 5% level of significance. With 20% attrition 62 children
 will be required to be enrolled in each arm. Therefore, for this trial, 62 children will
 receive MDCF-2 and 62 children Rice-lentil RUSF.

 Data Analysis:

 The two groups of children with Post SAM-MAM will be compared at baseline and at different
 time points as shown in the illustration on trial design. The clinical outcome variables for
 comparison will include rate of weight gain, anthropometric indices, and morbidity. All
 analytes mentioned in the section 'Analyses of plasma and fecal samples' will be compared
 between MDCF-2 and RUSF groups.

 Ethical Assurance for Protection of Human rights The study has been started after obtaining
 IRB (Institutional Review Board ) approval by the icddr,b Research Review Committee and
 Ethical Review Committee. Before enrolment in the study, informed written consent are being
 taken from the legal guardian of the study participants. Personal identifications taken
 during enrolment and other study procedures are being kept under lock and key.

 Expected risks/adverse events for this protocol are those related to blood sample collection,
 fecal sample collection and feeding of microbiota directed complementary food. None of these
 qualify as a serious adverse event (SAE). Expected Adverse Events (EAEs) related to blood
 draw are as follows:

 -  discomfort

 -  pain

 -  introduction of infection

 -  bleeding

 -  fainting or bruising

 -  Precaution will be taken to avoid introduction of infection by disinfecting the
 site of venipuncture and using sterile equipment

 -  The risk of bleeding and bruising will be minimized by immediate application of
 pressure after venipuncture

 -  The participant (child) will be in the sitting or supine position during blood
 draws to avoid injuries from fainting

 All possible adverse events will be treated appropriately. These will include:

 -  Vomiting

 -  Diarrhoea

 -  Skin rash

 -  Urticaria from food allergy

 -  Abdominal distension

 -  Pain abdomen Assessment of Adverse Events Both serious and non-serious adverse events
 will be assessed for severity; relationship to study participation; actions taken; and
 outcomes. All SAEs must be reported to the ERC (Ethical Review Committee) of icddr,b
 within 24 hours of the site's awareness of the event that will in turn be distributed to
 the sponsor. This will be done by direct telephone communication, fax or e-mail.

 icddr,b IRB recommended guidelines would be followed for grading the adverse events, if any
 that take place.

 Severity:

 1. Mild

 2. Moderate

 3. Severe

 Relationship to Study participation:

 1. Definitely related:Clear cut temporal association, no other possible cause

 2. Possibly related:Less clear cut temporal association, other causes possible

 3. Unrelated: Independent of study, evidence exists that event is definitely related to
 another etiology

 Actions:

 None Remedial therapy (more than one dose of medicine required) Permanently discontinued from
 study participation Hospitalization Other

 Outcomes:

 Resolved Continuing Unknown Collaborative Arrangements This project is a collaborative effort
 between the investigators at the Washington University School of Medicine and the
 International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b). The clinical
 works, field activities will be undertaken in Dhaka and Kurigram, Bangladesh, under the
 direct supervision of the Principal Investigator whereas the laboratory analyses will be
 conducted at the Gordon Lab at Washington University in St. Louis. All research units and the
 collaborating investigators have long histories of international collaborations. All
 investigators have communicated during development of this project and are committed to its
 successful implementation.

 Facilities Available icddr,b has a well-equipped Food Processing Lab that will facilitate
 experiments on the diet recipes. We have ongoing studies in the Baoniabad area in Mirpur. A
 number of project offices are located there. More importantly, we have an excellent rapport
 with the community. The Terre des Hommes that runs the SNU in Kurigram where a part of the
 trial will be conducted. In the past we helped in the development of the SNU and have
 performed studies there. The SNU has a great reputation in the community.

 Center for Genome Sciences, Washington University in St. Louis:

 The stool samples will be aliquoted at icddr,b. Stool samples will be sent to Prof Jeffery
 Gordon's Lab in St Louis for the high throughput 16S ribosomal RNA gene sequencing. The
 presence/abundances of a broad range of enteropathogens in stool samples before and after
 MDCF-2 treatment will be determined using a PCR (Polymerase Chain Reaction)-based assay.
 Stool samples may also be used to culture constituent bacterial strains for use in future
 studies in gnotobiotic mice in the Gordon Lab. It is pertinent to mention here that the
 assays and equipment to carry out those are currently available only in a few labs in the
 world, including the one at St Louis. The Center is home to an interdisciplinary,
 multi-departmental, multi-generational team of investigators from multiple schools that focus
 on comparative genomics, statistical genomics, and systems biology It serves as 'proving
 ground' for developing new strategies for educating students and faculty who wish to work at
 the interface of the biological, physical, computational and engineering sciences.
Inclusion Criteria:

 -  Parent(s) willing to sign consent form; the informed consent document will explicitly
 request permission to use the collected fecal samples for future studies, including
 but not limited to culturing component bacterial strains

 -  Child age 12-18 months

 -  WLZ between <-2 and -3 without bilateral pedal edema at the time of randomization

 -  Parent(s) willing to bring the child to the feeding centre twice daily for 4 weeks for
 nutritional therapy, once daily for next 4 weeks and administer the feeds provided by
 study staff once daily at home for 4 weeks and twice daily for next 4 weeks.

 Exclusion Criteria

 -  Medical conditions: Children with tuberculosis (diagnosis based on WHO 2014 guidelines
 which have been incorporated in the national TB control guidelines of Bangladesh). The
 guidelines depend upon the following five diagnostic principles (three out of five
 should be positive): 1. Specific symptoms of TB, 2. Specific signs, 3. Chest X-ray, 4.
 Mantoux test, and 5. History of contact,[9] or any congenital/acquired disorder
 affecting growth i.e. known case of trisomy-21 or cerebral palsy; children on an
 exclusion diet for the treatment of persistent diarrhea; having known history of soy,
 peanut or milk protein allergy- Severe anemia (<8mg/dl), will be assessed by Hemocue
 (Model no. Hemocue Hb 301)

 -  Failure to obtain informed written consent from parents or caretakers