title: Early life microbial colonization of the gut and intestinal development differ between genetically divergent broiler lines.
abstract: BACKGROUND
  Host genetic makeup plays a role in early gut microbial colonization and immune programming. Interactions between gut microbiota and host cells of the mucosal layer are of paramount importance for a proper development of host defence mechanisms. For different livestock species, it has already been shown that particular genotypes have increased susceptibilities towards disease causing pathogens. The objective of this study was to investigate the impact of genotypic variation on both early microbial colonization of the gut and functional development of intestinal tissue. From two genetically diverse chicken lines intestinal content samples were taken for microbiota analyses and intestinal tissue samples were extracted for gene expression analyses, both at three subsequent time-points (days 0, 4, and 16).
  
  
  RESULTS
  The microbiota composition was significantly different between lines on each time point. In contrast, no significant differences were observed regarding changes in the microbiota diversity between the two lines throughout this study. We also observed trends in the microbiota data at genus level when comparing lines X and Y. We observed that approximately 2000 genes showed different temporal gene expression patterns when comparing line X to line Y. Immunological related differences seem to be only present at day 0, because at day 4 and 16 similar gene expression is observed for these two lines. However, for genes involved in cell cycle related processes the data show higher expression over the whole course of time in line Y in comparison to line X.
  
  
  CONCLUSIONS
  These data suggest the genetic background influences colonization of gut microbiota after hatch in combination with the functional development of intestinal mucosal tissue, including the programming of the immune system. The results indicate that genetically different chicken lines have different coping mechanisms in early life to cope with the outside world.
authors.affiliation: Wageningen Livestock Research, Wageningen, The Netherlands. dirkjan.schokker@wur.nl.
authors.forename: Dirkjan
authors.initials: D
authors.lastname: Schokker
authors.affiliation: Cobb Europe BV, Boxmeer, The Netherlands. Gosse.Veninga@cobb-europe.com.
authors.forename: Gosse
authors.initials: G
authors.lastname: Veninga
authors.affiliation: Central Veterinary Institute, Lelystad, The Netherlands. stephanie.vastenhouw@wur.nl.
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Vastenhouw
authors.affiliation: Central Veterinary Institute, Lelystad, The Netherlands. alex.bossers@wur.nl.
authors.forename: Alex
authors.initials: A
authors.lastname: Bossers
authors.affiliation: Central Veterinary Institute, Lelystad, The Netherlands. freddy.debree@wur.nl.
authors.forename: Freddy M
authors.initials: FM
authors.lastname: de Bree
authors.affiliation: Wageningen Livestock Research, Wageningen, The Netherlands. lucia.kaal@wur.nl.
authors.forename: Lucia M T E
authors.initials: LM
authors.lastname: Kaal-Lansbergen
authors.affiliation: Central Veterinary Institute, Lelystad, The Netherlands. annemarie.rebel@wur.nl.
authors.forename: Johanna M J
authors.initials: JM
authors.lastname: Rebel
authors.affiliation: Wageningen Livestock Research, Wageningen, The Netherlands. mari.smits@wur.nl.
authors.forename: Mari A
authors.initials: MA
authors.lastname: Smits
mesh_terms: D000818:Animals; D002645:Chickens / Q000145:classification / Q000235:genetics* / Q000382:microbiology; D004269:DNA, Bacterial / Q000032:analysis*; D041981:Gastrointestinal Tract / Q000382:microbiology; D015964:Gene Expression Regulation, Bacterial; D014644:Genetic Variation; D007422:Intestines / Q000382:microbiology*; D064307:Microbiota; D008969:Molecular Sequence Data; D013045:Species Specificity
chemical_list: D004269:DNA, Bacterial