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

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 stu...

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Autores principales:	Yugal R Bindari, Robert J Moore, Thi Thu Hao Van, Matthew Hilliar, Shu-Biao Wu, Stephen W Walkden-Brown, Priscilla F Gerber
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/54f0f4b047274a62b274e081d2565b75
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spelling	oai:doaj.org-article:54f0f4b047274a62b274e081d2565b752021-12-02T20:15:11ZMicrobial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.1932-620310.1371/journal.pone.0255633https://doaj.org/article/54f0f4b047274a62b274e081d2565b752021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255633https://doaj.org/toc/1932-6203Traditional 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.Yugal R BindariRobert J MooreThi Thu Hao VanMatthew HilliarShu-Biao WuStephen W Walkden-BrownPriscilla F GerberPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 8, p e0255633 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yugal R Bindari Robert J Moore Thi Thu Hao Van Matthew Hilliar Shu-Biao Wu Stephen W Walkden-Brown Priscilla F Gerber Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
description	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.
format	article
author	Yugal R Bindari Robert J Moore Thi Thu Hao Van Matthew Hilliar Shu-Biao Wu Stephen W Walkden-Brown Priscilla F Gerber
author_facet	Yugal R Bindari Robert J Moore Thi Thu Hao Van Matthew Hilliar Shu-Biao Wu Stephen W Walkden-Brown Priscilla F Gerber
author_sort	Yugal R Bindari
title	Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
title_short	Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
title_full	Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
title_fullStr	Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
title_full_unstemmed	Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
title_sort	microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/54f0f4b047274a62b274e081d2565b75
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Microbial communities of poultry house dust, excreta and litter are partially representative of microbiota of chicken caecum and ileum.

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