title: The interplay between Campylobacter and Helicobacter species and other gastrointestinal microbiota of commercial broiler chickens.
abstract: BACKGROUND
  Poultry represent an important source of foodborne enteropathogens, in particular thermophilic Campylobacter species. Many of these organisms colonize the intestinal tract of broiler chickens as harmless commensals, and therefore, often remain undetected prior to slaughter. The exact reasons for the lack of clinical disease are unknown, but analysis of the gastrointestinal microbiota of broiler chickens may improve our understanding of the microbial interactions with the host.
  
  
  METHODS
  In this study, the fecal microbiota of 31 market-age (56-day old) broiler chickens, from two different farms, was analyzed using high throughput sequencing. The samples were then screened for two emerging human pathogens, Campylobacter concisus and Helicobacter pullorum, using species-specific PCR.
  
  
  RESULTS
  The gastrointestinal microbiota of chickens was classified into four potential enterotypes, similar to that of humans, where three enterotypes have been identified. The results indicated that variations between farms may have contributed to differences in the microbiota, though each of the four enterotypes were found in both farms suggesting that these groupings did not occur by chance. In addition to the identification of Campylobacter jejuni subspecies doylei and the emerging species, C. concisus, C. upsaliensis and H. pullorum, several differences in the prevalence of human pathogens within these enterotypes were observed. Further analysis revealed microbial taxa with the potential to increase the likelihood of colonization by a number of these pathogens, including C. jejuni.
  
  
  CONCLUSIONS
  Depletion of these taxa and the addition of taxa that compete with these pathogens, may form the basis of competitive exclusion strategies to eliminate them from the gastrointestinal tract of chickens.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Nadeem O
authors.initials: NO
authors.lastname: Kaakoush
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Sodhi
authors.affiliation: Birling Avian Laboratories, Bringelly, NSW 2556, Australia.
authors.forename: Jeremy W
authors.initials: JW
authors.lastname: Chenu
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia ; Faculty of Science, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Julian M
authors.initials: JM
authors.lastname: Cox
authors.affiliation: Gastrointestinal and Liver Unit, The Prince of Wales Hospital, Randwick, NSW 2031, Australia ; Prince of Wales Clinical School, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Riordan
authors.affiliation: School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Hazel M
authors.initials: HM
authors.lastname: Mitchell
keywords: Broiler chicken; Campylobacter; Campylobacter concisus; Gallibacterium; Gastrointestinal tract; Helicobacter; Microbiota; Pathogen