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Title: Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum
Contributor(s): Bindari, Yugal R (author); Moore, Robert J (author); Van, Thi Thu Hao (author); Hilliar, Matthew  (author)orcid ; Wu, Shu-Biao  (author)orcid ; Walkden-Brown, Stephen W  (author)orcid ; Gerber, Priscilla F  (author)orcid 
Publication Date: 2021-08-05
Open Access: Yes
DOI: 10.1371/journal.pone.0255633
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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.

Publication Type: Journal Article
Source of Publication: PLoS One, 16(8), p. 1-17
Publisher: Public Library of Science
Place of Publication: United States of America
ISSN: 1932-6203
Fields of Research (FoR) 2020: 300304 Animal protection (incl. pests and pathogens)
300903 Veterinary bacteriology
300303 Animal nutrition
Socio-Economic Objective (SEO) 2020: 100411 Poultry
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
Appears in Collections:Journal Article
School of Environmental and Rural Science

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