A microbiome-directed therapeutic food for children recovering from severe acute malnutrition [Code repository]
Creators: name: Hartman, Steven
Publisher: name: Zenodo
Year: 2024

description: # Code relevant to Hartman, Hibberd, Mostafa, et al.

***Preamble***: We present the code used to analyze the anthropometric, environmental, proteomic and metagenomic datasets collected from the post-SAM MAM trial. With the included code, proteomic datasets, metagenomic reads on the Sequence Read Archive, and reasonable knowledge of high-performance computing, the software included can be adapted to replicate our sequencing-based DNA and aptamer-based proteomic analyses. Most individual statistical analyses can be run in <1 hr on typical desktop/laptop hardware. Steps related to MAG assembly, MAG analyses plasma protein analyses, etc. can be expected to take ~1-24 hours, approximately, depending on parallelization ability and available processors.

We performed the MAG assembly process as described before in (Hibberd, Webber et al., 2023), with the long-read shotgun sequencing steps, taxonomic assignments from Kraken2 or gene annotations from prodigal omitted. Please refer to the [MAG assembly workflow](https://gitlab.com/hibberdm/hibberd_webber_et_al_mdcf_poc_mags/-/tree/main/mag_assembly_workflow?ref_type=heads) for the R, python and bash code templates for MAG generation, quantification, classification, and gene annotations. See methods of (Hartman, Hibberd et al., 2023) for the versions of each tool used.

## The code is archived and maintained at Git Lab: [https://gitlab.com/sjhartman/post-sam-mam-code-repository](https://gitlab.com/sjhartman/post-sam-mam-code-repository)

## The included code (in folders) is listed as follows:

1. **anthropometry**- [x] WLZ, LAZ, HAZ and MUAC response to MDCF-2 and RUSF treatment over time- [x] Flood unaffected vs affected children mixed effects model- [x] WLZ associations with site, gender and treatment arm at enrollment, baseline, end of treatment- [x] Prediction of time to graduate from SAM by enrollment anthropometric features- [x] Anthropometric comparisons of baseline between post-SAM MAM and primary-MAM study

2. **plasma\_proteome**- [x] SOMAmer filtering and QC- [x] WLZ associated somamers in the SAM phase- [x] WLZ associated somamers in the MAM phase- [x] Treatment association of somamers (and GSEA)- [x] CMA of WLZ associated proteins- [x] ORA of GO:BP in CMA WLZ-associated proteins- [x] CMA of treatment associations of WLZ associated proteins- [x] Enrichment analysis of treatment group associations of +/- WLZ associated proteins

3. **enteropathogens**- [x] Relation to the severity of SAM at enrollment- [x] Enteropathogen prevalence by site- [x] Changes in enteropathogen abundance during acute rehabilitation- [x] Changes in enteropathogen abundance by treatment arm during the MAM-phase

4. **metagenomics**- [x] MAG pipeline (discussed in methods to reference Hibberd Webber et al)- [x] MAG abundance associations to site, gender and treatment arm at enrollment, baseline, wk 4, 8, 12 and 1-month follow-up- [x] PCA- [x] WLZ association SAM-phase- [x] WLZ association MAM-phase- [x] MAG abundances associated with treatment- [x] Metabolic pathway correlations with the MAG relation to WLZ in the MAM-phase

## Software versions and installation:* Software versions for R and various HTCF-relevant software packages are stated in the Methods of Hartman, Hibberd, Mostafa et al.