Genomic and metabolomic foundations of human-microbial symbiosis in the gut

ABSTRACT Acute malnutrition (wasting) affects >45M children under the age of 5; two-thirds suffer from moderate acute malnutrition (MAM) while the remainder have severe acute malnutrition (SAM). Besides accounting for 21% of life-years lost among children younger than 5 years, undernutrition leads to long term growth impairments, immune and metabolic dysfunction, and altered CNS development. Current treatments have limited effectiveness. We found that MAM and SAM are associated with impaired gut microbial community development (microbiota immaturity). We then screened Bangladeshi complementary foods in gnotobiotic animals for their capacity to improve the fitness and expressed beneficial functions of key growth-promoting bacterial taxa underrepresented in the microbiota of children with malnutrition. This yielded a `microbiota- directed complementary food' formulation (MDCF-2) that in a randomized controlled clinical trial (RCT), repaired the microbiota of 12-18-month-old Bangladeshi children with MAM and accelerated weight gain/ameliorated stunting compared to an existing ready-to-use supplementary food (RUSF) that was 15% more calorically dense. The efficacy of MDCF-2 was confirmed in a second RCT. We identified metabolic pathways in metagenome-assembled genomes (MAGs) belonging to specific strains of Prevotella copri that are differentially expressed in response to MDCF-2 and positively associated with growth (weight-for-length Z score; WLZ); this differential expression was associated with the metabolism of specific glycan structures in MDCF-2 and with the magnitude of clinical response to treatment. Tests of MDCF-2 derivatives in which single ingredients were replaced by `glyco-equivalent' food staples, conducted in gnotobiotic mice harboring MAM- donor microbiota, followed by a pilot translational study in Bangladeshi children with MAM, further highlighted glycan structures targeting P. copri. We will use 2 specific aims to build on these findings. Aim1-Perform a pan-genome analysis to define features of P. copri MAGs positively associated with WLZ in our RCTs that are highly conserved in P. copri strains we culture from Bangladeshi children, and strains obtained from other countries. Combine in vitro growth assays, microbial RNA-Seq and mass spectrometry to test the effects of lead glycan structures obtainable at scale singly and in combination, on cultured P. copri strains with carbohydrate utilization machinery exemplifying the different strains documented in the pan-genome analysis. Results will identify strains/glycan combinations that approximate the MAG expression profiles observed in our RCTs and gnotobiotic models and refine selection of prebiotic candidates. Aim2-Use a gnotobiotic mouse model of intergenerational microbiota transmission to perform mechanistic studies (microbial RNA-Seq/host bulk and snRNA-Seq/microbial community and host targeted MS-based metabolomics) of the effects of prebiotic single or combination glycan leads from Aim1 on targeted P. copri strains and on host growth and expression of metabolic/signaling pathways in intestinal cell lineages distributed along the length of the gut.