Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens
In the short life of broiler chickens, their intestinal microbiota undergoes many changes. To study underlying biological mechanisms and factors that influence the intestinal microbiota development, longitudinal data from flocks and individual birds is needed. However, post-mortem collection of samp...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2019-10-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/7/10/431 |
| _version_ | 1818519449307709440 |
|---|---|
| author | Jannigje G. Kers Egil A.J. Fischer J. Arjan Stegeman Hauke Smidt Francisca C. Velkers |
| author_facet | Jannigje G. Kers Egil A.J. Fischer J. Arjan Stegeman Hauke Smidt Francisca C. Velkers |
| author_sort | Jannigje G. Kers |
| collection | DOAJ |
| description | In the short life of broiler chickens, their intestinal microbiota undergoes many changes. To study underlying biological mechanisms and factors that influence the intestinal microbiota development, longitudinal data from flocks and individual birds is needed. However, post-mortem collection of samples hampers longitudinal data collection. In this study, invasively collected cecal and ileal content, cloacal swabs collected from the same bird, and boot sock samples and cecal droppings from the litter of the broilers’ poultry house, were collected on days 0, 2, 7, 14 and 35 post-hatch. The different sample types were evaluated on their applicability and reliability to characterize the broiler intestinal microbiota. The microbiota of 247 samples was assessed by 16S ribosomal RNA gene amplicon sequencing. Analyses of α and β measures showed a similar development of microbiota composition of cecal droppings compared to cecal content. Furthermore, the composition of cecal content samples was comparable to that of the boot socks until day 14 post-hatch. This study shows that the value of non-invasive sample types varies at different ages and depends on the goal of the microbiota characterization. Specifically, cecal droppings and boot socks may be useful alternatives for cecal samples to determine intestinal microbiota composition longitudinally. |
| first_indexed | 2024-12-11T01:24:22Z |
| format | Article |
| id | doaj.art-001b5fda93ec454d97f1d3eed8339726 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-12-11T01:24:22Z |
| publishDate | 2019-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-001b5fda93ec454d97f1d3eed83397262022-12-22T01:25:35ZengMDPI AGMicroorganisms2076-26072019-10-0171043110.3390/microorganisms7100431microorganisms7100431Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler ChickensJannigje G. Kers0Egil A.J. Fischer1J. Arjan Stegeman2Hauke Smidt3Francisca C. Velkers4Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The NetherlandsFaculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The NetherlandsFaculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The NetherlandsLaboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The NetherlandsFaculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The NetherlandsIn the short life of broiler chickens, their intestinal microbiota undergoes many changes. To study underlying biological mechanisms and factors that influence the intestinal microbiota development, longitudinal data from flocks and individual birds is needed. However, post-mortem collection of samples hampers longitudinal data collection. In this study, invasively collected cecal and ileal content, cloacal swabs collected from the same bird, and boot sock samples and cecal droppings from the litter of the broilers’ poultry house, were collected on days 0, 2, 7, 14 and 35 post-hatch. The different sample types were evaluated on their applicability and reliability to characterize the broiler intestinal microbiota. The microbiota of 247 samples was assessed by 16S ribosomal RNA gene amplicon sequencing. Analyses of α and β measures showed a similar development of microbiota composition of cecal droppings compared to cecal content. Furthermore, the composition of cecal content samples was comparable to that of the boot socks until day 14 post-hatch. This study shows that the value of non-invasive sample types varies at different ages and depends on the goal of the microbiota characterization. Specifically, cecal droppings and boot socks may be useful alternatives for cecal samples to determine intestinal microbiota composition longitudinally.https://www.mdpi.com/2076-2607/7/10/431microbiome16s rrnamethodsgutavianpoultry |
| spellingShingle | Jannigje G. Kers Egil A.J. Fischer J. Arjan Stegeman Hauke Smidt Francisca C. Velkers Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens Microorganisms microbiome 16s rrna methods gut avian poultry |
| title | Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens |
| title_full | Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens |
| title_fullStr | Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens |
| title_full_unstemmed | Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens |
| title_short | Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens |
| title_sort | comparison of different invasive and non invasive methods to characterize intestinal microbiota throughout a production cycle of broiler chickens |
| topic | microbiome 16s rrna methods gut avian poultry |
| url | https://www.mdpi.com/2076-2607/7/10/431 |
| work_keys_str_mv | AT jannigjegkers comparisonofdifferentinvasiveandnoninvasivemethodstocharacterizeintestinalmicrobiotathroughoutaproductioncycleofbroilerchickens AT egilajfischer comparisonofdifferentinvasiveandnoninvasivemethodstocharacterizeintestinalmicrobiotathroughoutaproductioncycleofbroilerchickens AT jarjanstegeman comparisonofdifferentinvasiveandnoninvasivemethodstocharacterizeintestinalmicrobiotathroughoutaproductioncycleofbroilerchickens AT haukesmidt comparisonofdifferentinvasiveandnoninvasivemethodstocharacterizeintestinalmicrobiotathroughoutaproductioncycleofbroilerchickens AT franciscacvelkers comparisonofdifferentinvasiveandnoninvasivemethodstocharacterizeintestinalmicrobiotathroughoutaproductioncycleofbroilerchickens |