Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum

Title
Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum
Publication Date
2021-08-05
Author(s)
Bindari, Yugal R
Moore, Robert J
Van, Thi Thu Hao
Hilliar, Matthew
( author )
OrcID: https://orcid.org/0000-0001-7292-0007
Email: mhilliar@myune.edu.au
UNE Id une-id:mhillia2
Wu, Shu-Biao
( author )
OrcID: https://orcid.org/0000-0002-1790-6015
Email: swu3@une.edu.au
UNE Id une-id:swu3
Walkden-Brown, Stephen W
( author )
OrcID: https://orcid.org/0000-0002-0638-5533
Email: swalkden@une.edu.au
UNE Id une-id:swalkden
Gerber, Priscilla F
( author )
OrcID: https://orcid.org/0000-0002-8343-8299
Email: pgerber2@une.edu.au
UNE Id une-id:pgerber2
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Public Library of Science
Place of publication
United States of America
DOI
10.1371/journal.pone.0255633
UNE publication id
une:1959.11/42308
Abstract

Traditional sampling methods for the study of poultry gut microbiota preclude longitudinal studies as they require euthanasia of birds for the collection of caecal and ileal contents. Some recent research has investigated alternative sampling methods to overcome this issue. The main goal of this study was to assess to what extent the microbial composition of non-invasive samples (excreta, litter and poultry dust) are representative of invasive samples (caecal and ileal contents). The microbiota of excreta, dust, litter, caecal and ileal contents (n = 110) was assessed using 16S ribosomal RNA gene amplicon sequencing. Of the operational taxonomic units (OTUs) detected in caecal contents, 99.7% were also detected in dust, 98.6% in litter and 100% in excreta. Of the OTUs detected in ileal contents, 99.8% were detected in dust, 99.3% in litter and 95.3% in excreta. Although the majority of the OTUs found in invasive samples were detected in non-invasive samples, the relative abundance of members of the microbial communities of these groups were different, as shown by beta diversity measures. Under the conditions of this study, correlation analysis showed that dust could be used as a proxy for ileal and caecal contents to detect the abundance of the phylum Firmicutes, and excreta as a proxy of caecal contents for the detection of Tenericutes. Similarly, litter could be used as a proxy for caecal contents to detect the abundance of Firmicutes and Tenericutes. However, none of the non-invasive samples could be used to infer the overall abundance of OTUs observed in invasive samples. In conclusion, non-invasive samples could be used to detect the presence and absence of the majority of the OTUs found in invasive samples, but could not accurately reflect the microbial community structure of invasive samples.

Link
Citation
PLoS One, 16(8), p. 1-17
ISSN
1932-6203
Pubmed ID
34351989
Start page
1
End page
17
Rights
Attribution 4.0 International

Files:

NameSizeformatDescriptionLink
openpublished/MicrobialBindariHilliarWuWalkdenBrownGerber2021JournalArticle.pdf 992.142 KB application/pdf Published version View document