Abstract
Although poultry microbiome discoveries are increasing due to the potential impact on poultry performance, studies examining the poultry respiratory microbiome are challenging because of the low microbial biomass and uniqueness of the avian respiratory tract, making it difficult to sample enough material for microbial analysis. Invasive sampling techniques requiring euthanasia are currently used to increase microbial mass for the analysis, thus making it impossible to sample individual birds longitudinally. In this study, we compared invasive (nasal wash, upper tracheal wash, lower tracheal wash, and lower respiratory lavage) and noninvasive (tracheal and choanal swabs) respiratory sampling techniques in two independent experiments by using 4-wk-old chickens. We first established the experimental baseline of respiratory microbiota by using invasive techniques to enable reasonable comparisons between sampling methods and between experiments. Although noninvasive sampling (live-bird swabs) resulted in lower 16S ribosomal RNA gene copy numbers compared with invasive sampling, live swabs were able to detect the dominant microbes captured by invasive techniques. Nevertheless, swabs from euthanatized birds were more reflective of the...Continue Reading
References
Jan 16, 2007·Applied and Environmental Microbiology·Catherine A LozuponeRob Knight
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Sep 29, 2011·PloS One·Michael D DumasK Eric Wommack
Mar 10, 2012·The ISME Journal·J Gregory CaporasoRob Knight
Nov 30, 2012·Nucleic Acids Research·Christian QuastFrank Oliver Glöckner
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Nov 22, 2013·Gut Microbes·Deng Pan, Zhongtang Yu
Apr 8, 2014·American Journal of Respiratory and Critical Care Medicine·Katrine L WhitesonPaul B Rainey
Sep 30, 2014·FEMS Microbiology Letters·Brian B OakleyNelson A Cox
Nov 13, 2014·BMC Biology·Susannah J SalterAlan W Walker
Feb 11, 2015·Poultry Science·Muhammad Zubair ShabbirEric Thomas Harvill
Mar 31, 2015·Journal of Microbiological Methods·Vanessa L HaleKatherine R Amato
Nov 4, 2015·Annual Review of Physiology·Robert P DicksonGary B Huffnagle
Jan 15, 2016·BMC Genomics·Rosalinda D'AmoreNeil Hall
Feb 18, 2016·Korean journal of anesthesiology·Francis Sahngun Nahm
May 24, 2016·Nature Methods·Benjamin J CallahanSusan P Holmes
Oct 5, 2016·PloS One·Elahe KiaMichael W Taylor
Oct 27, 2016·PeerJ·Torbjørn RognesFrédéric Mahé
Nov 7, 2016·BMC Genomics·Erik Scott Wright, Kalin Horen Vetsigian
Jan 18, 2017·Molecular and Cellular Pediatrics·Sébastien Boutin, Alexander H Dalpke
Oct 27, 2017·PloS One·Brian BushnellEsther Singer
Nov 23, 2017·PloS One·Laura GlendinningLonneke Vervelde
Apr 8, 2018·Applied and Environmental Microbiology·Timothy J JohnsonChang-Won Lee
May 19, 2018·Microbiome·Nicholas A BokulichJ Gregory Caporaso
Mar 3, 2019·Applied and Environmental Microbiology·John M NgunjiriChang-Won Lee
Jun 6, 2019·MSystems·Lisa KarstensShannon McWeeney