The gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.
Key Findings
Results
Broad microbiome profiles at discharge were not associated with acute malnutrition relapse at 1-month follow-up.
The study used mixed linear effect models to evaluate associations of microbiome features with AM relapse 1-month post-recovery.
Microbiome features evaluated included microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways.
Children were discharged from treatment for uncomplicated SAM in South Sudan under community-based management of acute malnutrition (CMAM).
Overall, no significant associations were found between broad microbiome profiles and AM relapse at the 1-month timepoint.
Results
Higher MUAC at discharge was associated with increased abundance of Sutterella wadsworthensis.
MUAC (mid-upper arm circumference) was used as a proxy measure and a key anthropometric indicator in this study.
Higher MUAC may be a proxy for future health trajectories in children recovering from SAM.
The association was identified through mixed linear effect models examining microbiome features against anthropometric measurements.
Sutterella wadsworthensis was identified as a key microbe meriting further research in the context of SAM recovery.
Results
Higher MUAC at discharge was associated with increased carriage of trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes.
Trimethoprim-resistant dihydrofolate reductase genes represent a specific antimicrobial resistance (AMR) gene feature of the gut microbiome.
This association was identified alongside the Sutterella wadsworthensis finding in the context of MUAC as a proxy for health trajectories.
AMR gene carriage was one of three microbiome feature categories evaluated (alongside microbial composition and predicted functional pathways).
The clinical significance of this AMR gene association in the context of SAM recovery requires further investigation.
Background
The gut microbiome of children recovering from SAM in South Sudan represents a geographically underrepresented population in microbiome research.
The study characterizes gut microbiome features of children from South Sudan, a region traditionally underrepresented in gut microbiome research.
Children were enrolled under the community-based management of acute malnutrition (CMAM) program, the standard of care in South Sudan and many low-resource settings.
SAM was defined by anthropometric measurements including weight-for-height z score and mid-upper arm circumference (MUAC) falling significantly below healthy standards.
The study contributes baseline microbiome characterization data for this understudied population.
Conclusions
The gut microbiome at discharge, in isolation, likely holds low predictive value for relapse to acute malnutrition following CMAM treatment.
The study hypothesized that gut microbiome features at discharge may be associated with AM relapse at 1-month follow-up, but this was not supported by the overall findings.
Relapse to AM following anthropometric recovery is a frequent outcome for children treated for SAM under CMAM.
The findings suggest that a standalone microbiome-based diagnostic tool using discharge samples would have limited utility for identifying relapse risk.
The authors note that key microbes and microbial features identified (including Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase genes) merit further research.
What This Means
This research examined whether the gut bacteria (microbiome) of young children in South Sudan who had been successfully treated for severe acute malnutrition (SAM) could predict whether those children would relapse back into malnutrition within one month. SAM is a life-threatening form of malnutrition defined by very low weight-for-height measurements and small upper arm circumference, and despite treatment, many children relapse. The researchers collected stool samples from children when they were discharged from treatment and analyzed the types of bacteria present, their resistance to antibiotics, and the biological functions those bacteria might perform.
The main finding was that the overall pattern of gut bacteria at discharge was not linked to which children relapsed to malnutrition within a month. However, the researchers did find that children with higher mid-upper arm circumference measurements — a sign of better nutritional status — tended to have more of a specific bacterium called Sutterella wadsworthensis and more genes associated with resistance to the antibiotic trimethoprim in their gut. These specific associations suggest there may be subtle microbiome differences between children on better versus worse recovery trajectories, even if the overall microbiome picture does not clearly predict relapse.
This research suggests that a single gut microbiome snapshot taken at discharge is unlikely to be useful on its own as a tool to predict which children are at high risk of relapsing into malnutrition. However, the specific bacterial and antibiotic resistance gene associations identified point to areas worth investigating further. The study also provides valuable microbiome data from South Sudan, a region rarely included in this type of research, which helps build a broader understanding of how malnutrition and the gut microbiome interact across different global contexts.
Yang K, King S, Marshak A, D'Mello-Guyett L, Grignard L, Knee J, et al.. (2026). Gut microbiome associations with acute malnutrition relapse in South Sudan.. Microbiology spectrum. https://doi.org/10.1128/spectrum.03587-25