title: A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.
abstract: BACKGROUND
  Gut microbiota and the host exist in a mutualistic relationship, with the functional composition of the microbiota strongly affecting the health and well-being of the host. Thus, it is important to develop a synthetic approach to study the host transcriptome and the microbiome simultaneously. Early microbial colonization in infants is critically important for directing neonatal intestinal and immune development, and is especially attractive for studying the development of human-commensal interactions. Here we report the results from a simultaneous study of the gut microbiome and host epithelial transcriptome of three-month-old exclusively breast- and formula-fed infants.
  
  
  RESULTS
  Variation in both host mRNA expression and the microbiome phylogenetic and functional profiles was observed between breast- and formula-fed infants. To examine the interdependent relationship between host epithelial cell gene expression and bacterial metagenomic-based profiles, the host transcriptome and functionally profiled microbiome data were subjected to novel multivariate statistical analyses. Gut microbiota metagenome virulence characteristics concurrently varied with immunity-related gene expression in epithelial cells between the formula-fed and the breast-fed infants.
  
  
  CONCLUSIONS
  Our data provide insight into the integrated responses of the host transcriptome and microbiome to dietary substrates in the early neonatal period. We demonstrate that differences in diet can affect, via gut colonization, host expression of genes associated with the innate immune system. Furthermore, the methodology presented in this study can be adapted to assess other host-commensal and host-pathogen interactions using genomic and transcriptomic data, providing a synthetic genomics-based picture of host-commensal relationships.
authors.affiliation: Training Program in Biostatistics, Bioinformatics, Nutrition and Cancer, Texas A&M University, 155 Ireland Street, College Station, TX 77843, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.forename: Iddo
authors.initials: I
authors.lastname: Friedberg
authors.forename: Ivan V
authors.initials: IV
authors.lastname: Ivanov
authors.forename: Laurie A
authors.initials: LA
authors.lastname: Davidson
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Goldsby
authors.forename: David B
authors.initials: DB
authors.lastname: Dahl
authors.forename: Damir
authors.initials: D
authors.lastname: Herman
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.forename: Sharon M
authors.initials: SM
authors.lastname: Donovan
authors.forename: Robert S
authors.initials: RS
authors.lastname: Chapkin
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D001942:Breast Feeding; D005243:Feces / Q000382:microbiology; D020869:Gene Expression Profiling; D006801:Humans; D007223:Infant; D041943:Infant Formula / Q000008:administration & dosage* / Q000378:metabolism; D007413:Intestinal Mucosa / Q000166:cytology / Q000276:immunology* / Q000382:microbiology*; D054892:Metagenome / Q000276:immunology*; D056186:Metagenomics / Q000379:methods*; D015999:Multivariate Analysis; D010802:Phylogeny; D020560:Proteobacteria / Q000145:classification / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification; D012329:RNA, Bacterial / Q000032:analysis / Q000235:genetics; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics; D017423:Sequence Analysis, RNA; D013559:Symbiosis; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D012336:RNA, Ribosomal, 16S