Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota

Abundo, Michael Edward C; Ngunjiri, John M.; Taylor, Kara; Ji, Hana; Ghorbani, Amir; Kc, Mahesh; Elaish, Mohamed; Jang, Hyesun; Weber, Bonnie; Johnson, Timothy J.; Lee, Chang-Won

doi:10.1637/aviandiseases-d-19-00200

Cited by 7 publications

(39 citation statements)

References 29 publications

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“…The Ohio State University is accredited by the Association for the Assessment and Accreditation of Laboratory Animal Care International. White leghorn chickens were obtained from our institution’s (Food Animal Health Research Program, Wooster, OH [17]. The chickens were provided with ad libitum access to feed and water and their welfare was monitored twice daily.…”

Section: Methodsmentioning

confidence: 99%

“…All birds were clinically healthy and were all included in the study. Prior to the collection of invasive samples, the birds were humanely euthanized through carbon dioxide exposure as previously described [17].…”

Section: Methodsmentioning

confidence: 99%

“…For example, protocol-associated-between-studies-variation in biodiversity profiles in human gut and environmental microbiota has been widely reported [6–14]. We and others have evaluated the sample collection methods for poultry respiratory and gut microbiota [2, 15–17]. However, protocol-associated-confounding-factors for DNA extraction, sequencing strategies, and bioinformatic analysis in poultry microbiota remain to be studied.…”

Section: Introductionmentioning

confidence: 99%

“…Five different DNA extraction kits have been used in poultry respiratory microbiota studies, including BiOstic FFPE Tissue DNA Isolation Kit, PowerSoil DNA Isolation Kit, QIAmp DNA Mini Kit, Maxwell RSC PureFood Pathogen Kit, and Qiagen DNeasy Blood and Tissue Kit [2, 15–17, 25–28]. These kits typically employ a combination of mechanical, chemical, and enzymatic disruption methods to increase DNA yields.…”

Section: Introductionmentioning

confidence: 99%

“…These kits typically employ a combination of mechanical, chemical, and enzymatic disruption methods to increase DNA yields. In our previous poultry respiratory microbiota studies [2, 15–17], the Qiagen DNeasy Blood and Tissue kit (BT kit), which utilizes chemical and enzymatic lysis, was used. The BT kit uses a broad-spectrum serine protease (proteinase K) that can potentially lyse all types of bacteria, but an optional use of lysozyme can ensure complete lysis of Gram-positive bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

Abundo

Ngunjiri

Taylor

et al. 2020

Preprint

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Characterization of poultry microbiota is becoming increasingly important due to the growing need for microbiome-based interventions to improve poultry health and production performance. However, the lack of standardized protocols for sampling, sample processing, DNA extraction, sequencing, and bioinformatic analysis can hinder data comparison between studies. Here, we investigated how the DNA extraction process affects microbial community compositions and diversity metrics in different chicken respiratory sample types including choanal and tracheal swabs, nasal cavity and tracheal washes, and lower respiratory lavage. We did a side-by-side comparison of the performances of Qiagen DNeasy blood and tissue (BT) and ZymoBIOMICS DNA Miniprep (ZB) kits. In general, samples extracted with the BT kit yielded higher concentrations of total DNA while those extracted with the ZB kit contained higher numbers of bacterial 16S rRNA gene copies per unit volume. Therefore, the samples were normalized to equal amounts of 16S rRNA gene copies prior to sequencing. For each sample type, all predominant taxa detected in samples extracted with one kit were present in replicate samples extracted with the other kit and did not show significant differences at the class level. Furthermore, between-kit differences in alpha and beta diversity metrics were statistically indistinguishable. Therefore, both kits perform similarly with regard to 16S rRNA gene-based poultry microbiome analysis.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

Abundo

Ngunjiri

Taylor

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

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Omics technologies in poultry health and productivity - part 1: current use in poultry research

et al. 2022

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In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.

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Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

Oladokun,

Sharif

2024

anim microbiome

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An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

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Evaluation of Sampling Methods for the Study of Avian Respiratory Microbiota

Cited by 7 publications

References 29 publications

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

Assessment of two DNA extraction kits for profiling poultry respiratory microbiota from multiple sample types

Omics technologies in poultry health and productivity - part 1: current use in poultry research

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

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