title: Protein- and zinc-deficient diets modulate the murine microbiome and metabolic phenotype.
abstract: Environmental enteropathy, which is linked to undernutrition and chronic infections, affects the physical and mental growth of children in developing areas worldwide. Key to understanding how these factors combine to shape developmental outcomes is to first understand the effects of nutritional deficiencies on the mammalian system including the effect on the gut microbiota.
  
  
  
  We dissected the nutritional components of environmental enteropathy by analyzing the specific metabolic and gut-microbiota changes that occur in weaned-mouse models of zinc or protein deficiency compared with well-nourished controls.
  
  
  
  With the use of a1H nuclear magnetic resonance spectroscopy-based metabolic profiling approach with matching 16S microbiota analyses, the metabolic consequences and specific effects on the fecal microbiota of protein and zinc deficiency were probed independently in a murine model.
  
  
  
  We showed considerable shifts within the intestinal microbiota 14-24 d postweaning in mice that were maintained on a normal diet (including increases in Proteobacteria and striking decreases in Bacterioidetes). Although the zinc-deficient microbiota were comparable to the age-matched, well-nourished profile, the protein-restricted microbiota remained closer in composition to the weaned enterotype with retention of Bacteroidetes. Striking increases in Verrucomicrobia (predominantly Akkermansia muciniphila) were observed in both well-nourished and protein-deficient mice 14 d postweaning. We showed that protein malnutrition impaired growth and had major metabolic consequences (much more than with zinc deficiency) that included altered energy, polyamine, and purine and pyrimidine metabolism. Consistent with major changes in the gut microbiota, reductions in microbial proteolysis and increases in microbial dietary choline processing were observed.
  
  
  
  These findings are consistent with metabolic alterations that we previously observed in malnourished children. The results show that we can model the metabolic consequences of malnutrition in the mouse to help dissect relevant pathways involved in the effects of undernutrition and their contribution to environmental enteric dysfunction.
authors.affiliation: Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom.
authors.forename: Jordi
authors.identifier: 0000-0002-6485-4529
authors.initials: J
authors.lastname: Mayneris-Perxachs
authors.affiliation: University of Virginia Center for Global Health and.
authors.forename: David T
authors.initials: DT
authors.lastname: Bolick
authors.affiliation: School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom.
authors.forename: Joy
authors.initials: J
authors.lastname: Leng
authors.affiliation: Department of Biomedical Engineering, University of Virginia, Charlottesville, VA; and.
authors.forename: Greg L
authors.initials: GL
authors.lastname: Medlock
authors.affiliation: University of Virginia Center for Global Health and.
authors.forename: Glynis L
authors.initials: GL
authors.lastname: Kolling
authors.affiliation: Department of Biomedical Engineering, University of Virginia, Charlottesville, VA; and.
authors.forename: Jason A
authors.initials: JA
authors.lastname: Papin
authors.affiliation: Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom; j.swann@imperial.ac.uk.
authors.forename: Jonathan R
authors.identifier: 0000-0002-6485-4529
authors.initials: JR
authors.lastname: Swann
authors.affiliation: University of Virginia Center for Global Health and.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Guerrant
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004032:Diet; D004044:Dietary Proteins / Q000008:administration & dosage*; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology; D000071068:Lipocalin-2 / Q000235:genetics / Q000378:metabolism; D008297:Male; D044342:Malnutrition / Q000378:metabolism / Q000382:microbiology*; D055432:Metabolomics; D051379:Mice; D008810:Mice, Inbred C57BL; D009195:Peroxidase / Q000235:genetics / Q000378:metabolism; D011488:Protein Deficiency / Q000378:metabolism / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014886:Weaning; D015032:Zinc / Q000008:administration & dosage / Q000172:deficiency*
chemical_list: D004269:DNA, Bacterial; D004044:Dietary Proteins; D000071068:Lipocalin-2; D012336:RNA, Ribosomal, 16S; D009195:Peroxidase; D015032:Zinc
keywords: malnutrition; metabolome metabolic phenotype; metabolome metabonomics; microbiome microbiota; protein deficiency; undernutrition; zinc deficiency