title: Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences.
abstract: BACKGROUND
  The majority of chicken microbiota studies have used the ceca as a sampling site due to the specific role of ceca in chicken productivity, health and wellbeing. However, sampling from ceca and other gastrointestinal tract sections requires the bird to be sacrificed. In contrast, fecal sampling does not require sacrifice and thus allows the same bird to be sampled repeatedly over time. This is a more meaningful and preferred way of sampling as the same animals can be monitored and tracked for temporal studies. The commonly used practice of selecting a subset of birds at each time-point for sacrifice and sampling introduces added variability due to the known animal to animal variation in microbiota.
  
  
  RESULTS
  Cecal samples and fecal samples via cloacal swab were collected from 163 birds across 3 replicate trials. DNA was extracted and 16S rRNA gene sequences amplified and pyrosequenced to determine and compare the phylogenetic profile of the microbiota within each sample. The fecal and cecal samples were investigated to determine to what extent the microbiota found in fecal samples represented the microbiota of the ceca. It was found that 88.55% of all operational taxonomic units (OTUs), containing 99.25% of all sequences, were shared between the two sample types, with OTUs unique for each sample type found to be very rare. There was a positive correlation between cecal and fecal abundance in the shared sequences, however the two communities differed significantly in community structure, represented as either alpha or beta diversity. The microbial populations present within the paired ceca of individual birds were also compared and shown to be similar.
  
  
  CONCLUSIONS
  Fecal sample analysis captures a large percentage of the microbial diversity present in the ceca. However, the qualitative similarities in OTU presence are not a good representation of the proportions of OTUs within the microbiota from each sampling site. The fecal microbiota is qualitatively similar to cecal microbiota but quantitatively different. Fecal samples can be effectively used to detect some shifts and responses of cecal microbiota.
authors.affiliation: Central Queensland University, School of Medical and Applied Sciences, Bruce Highway, Rockhampton, QLD, 4702, Australia. d.stanley@cqu.edu.au.|Australian Animal Health Laboratory, CSIRO Animal, Food and Health Sciences, Geelong, VIC, 3220, Australia. d.stanley@cqu.edu.au.|RMIT University, Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia. d.stanley@cqu.edu.au.
authors.forename: Dragana
authors.initials: D
authors.lastname: Stanley
authors.affiliation: RMIT University, Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia. mark.geier@unisa.edu.au.|South Australian Research and Development Institute, Pig and Poultry Production Institute, Roseworthy, South Australia, 5371, Australia. mark.geier@unisa.edu.au.|The University of Adelaide, School of Animal and Veterinary Sciences Roseworthy, Roseworthy, South Australia, 5371, Australia. mark.geier@unisa.edu.au.|University of South Australia, Research Office, Adelaide, South Australia, 5001, Australia. mark.geier@unisa.edu.au.
authors.forename: Mark S
authors.initials: MS
authors.lastname: Geier
authors.affiliation: Australian Animal Health Laboratory, CSIRO Animal, Food and Health Sciences, Geelong, VIC, 3220, Australia. honglei.chen@csiro.au.
authors.forename: Honglei
authors.initials: H
authors.lastname: Chen
authors.affiliation: RMIT University, Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia. Bob.Hughes@sa.gov.au.|South Australian Research and Development Institute, Pig and Poultry Production Institute, Roseworthy, South Australia, 5371, Australia. Bob.Hughes@sa.gov.au.|The University of Adelaide, School of Animal and Veterinary Sciences Roseworthy, Roseworthy, South Australia, 5371, Australia. Bob.Hughes@sa.gov.au.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hughes
authors.affiliation: Australian Animal Health Laboratory, CSIRO Animal, Food and Health Sciences, Geelong, VIC, 3220, Australia. rob.moore@rmit.edu.au.|RMIT University, Poultry Cooperative Research Centre, University of New England Armidale, New South Wales, 2315, Australia. rob.moore@rmit.edu.au.|RMIT University, Biotechnology and Ecological Biology, School of Applied Sciences, Bundoora, VIC, 3083, Australia. rob.moore@rmit.edu.au.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Moore
mesh_terms: D000818:Animals; D002432:Cecum / Q000382:microbiology*; D002645:Chickens; D016000:Cluster Analysis; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D000069196:Gastrointestinal Microbiome; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S