Systems Biology of Host–Food–Microbe Interactions in the Mammalian Gut

• Published in: Systems Biology and Livestock Science pp. 109 - 135
• Main Authors: Martins dos Santos, Vitor A. P, Müller, Michael, de Vos, Willem M, Wells, Jerry, te Pas, Marinus F. W, Hooiveld, Guido, van Baarlen, Peter, Smits, Mari A, Keijer, Jaap
• Format: Book Chapter
• Language: English
• Published: United States John Wiley & Sons, Incorporated 2011; Wiley‐Blackwell; John Wiley and Sons
• Subjects: Agricultural science; Animal husbandry; BIOLOGY, LIFE SCIENCES; Chair Nutrition Metabolism and Genomics; CVI Infectiebiologie; CVI Infection Biology; Fysiologie van Mens en Dier; HNE Nutrition, Metabolism and Genomics; HNE Voeding, Metabolisme en Genomics; Host Microbe Interactomics; host–microbe–food interactions; Human and Animal Physiology; Infectiebiologie; Infection Biology; Intestinal tract; Laboratorium voor Microbiologie; Leerstoelgroep Fysiologie van mens en dier; Leerstoelgroep Host Microbe Interactomics; Livestock Research; metagenomic modeling; Microbiological Laboratory; Microbiologie; Microbiology; microbiota; Nutrition, Metabolism and Genomics; Systeem en Synthetische Biologie; Systems and Synthetic Biology; Voeding, Metabolisme en Genomica; Wageningen Livestock Research; WIAS
• ISBN: 0813811740; 9780813811741
• DOI: 10.1002/9780470963012.ch5

Complex and subject‐specific microbial communities colonize since birth the intestinal tract of animals. Microbiota interacts intimately with its host and, through a variety of ways, is essential to maintain body homeostasis. The human adult microbiota has recently been characterized by deep metagenomic sequencing and several hundreds of intestinal genomes have been characterized at the sequence level. Moreover, the transcriptional response of the host and selected microbes has been identified both in animal model systems and in humans. Similarly, the transcriptional response of the mammalian host to different diets has been determined in humans, food‐ producing animals, germ‐free, and gene knockout animals. By providing abundant sets of information, these developments have enabled the application of a range of modeling approaches to explore the mechanisms and processes underlying diet–host–microbiota. Conversely, the models developed assist the rational design of experimental strategies. Thus, an integrated, modular modeling framework that cross‐links top‐down and bottom‐up approaches for the various levels of biological organization is paramount for the understanding of intestinal function.