Molecular detection of Eimeria species and Clostridium perfringens in poultry dust and pooled excreta of commercial broiler chicken flocks differing in productive performance

Bindari, Yugal Raj; Kheravii, Sarbast K.; Morton, Christine L.; Wu, Shu‐Biao; Walkden‐Brown, Stephen W.; Gerber, Priscilla F.

doi:10.1016/j.vetpar.2021.109361

Cited by 6 publications

(7 citation statements)

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“…Molecular based approaches, mainly using PCR, have been effective to subtype and quantifying Eimeria species in excreta and litter in both experimental and commercial flocks ( Morris and Gasser, 2006 ; Morris et al, 2007 ; Morgan et al, 2009 ; Vrba et al, 2010 ; Godwin and Morgan, 2015 ). More recently, DNA of C. perfringens and Eimeria species have been detected in poultry house dust of experimental and commercial flocks ( Ahaduzzaman et al, 2021a ; Bindari et al, 2021a ).…”

Section: Diseases Of the Enteric Tract: Coccidiosis And Necrotic Enteritismentioning

confidence: 99%

“…One of the major issues with the scoring of intestinal lesions in the field is misidentifying autolytic changes or coccidiosis lesions, especially from E. necatrix, as of NE ( Smyth, 2016 ). Monitoring of both Eimeria species and C. perfringens using noninvasive easy to collect population-level samples would perhaps provide useful research or on-farm tools to evaluate the management interventions of both diseases at flock-level ( Ahaduzzaman et al, 2020 ; Bindari et al, 2021a ).…”

Section: Diseases Of the Enteric Tract: Coccidiosis And Necrotic Enteritismentioning

confidence: 99%

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Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Bindari

Gerber

2022

Poultry Science

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Maintenance of “gut health” is considered a priority in commercial chicken farms, although a precise definition of what constitutes gut health and how to evaluate it is still lacking. In research settings, monitoring of gut microbiota has gained great attention as shifts in microbial community composition have been associated with gut health and productive performance. However, microbial signatures associated with productivity remain elusive because of the high variability of the microbiota of individual birds resulting in multiple and sometimes contradictory profiles associated with poor or high performance. The high costs associated with the testing and the need for the terminal sampling of a large number of birds for the collection of gut contents also make this tool of limited use in commercial settings. This review highlights the existing literature on the chicken digestive system and associated microbiota; factors affecting the gut microbiota and emergence of the major chicken enteric diseases coccidiosis and necrotic enteritis; methods to evaluate gut health and their association with performance; main issues in investigating chicken microbial populations; and the relationship of microbial profiles and production outcomes. Emphasis is given to emerging noninvasive and easy-to-collect sampling methods that could be used to monitor gut health and microbiological changes in commercial flocks.

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Section: Diseases Of the Enteric Tract: Coccidiosis And Necrotic Enteritismentioning

confidence: 99%

Section: Diseases Of the Enteric Tract: Coccidiosis And Necrotic Enteritismentioning

confidence: 99%

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Bindari

Gerber

2022

Poultry Science

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“…The study was conducted on 16 flocks from eight commercial meat chicken farms (n = 2 flocks/farm) in a 2 × 2 × 5 factorial arrangement with two Australian integrator companies (A and B), two levels of farm productive performance (high and low), and five sampling times (7, 14, 21, 28 and 35 days of chicken age) as previously described [ 15 ]. Details of the farms are included in Additional file 1 .…”

Section: Methodsmentioning

confidence: 99%

“…To maximise DNA quality and yields from each sample type different extraction kits were used. DNA extraction of dust was performed using the QIAamp® Fast DNA Stool Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions with minor modifications [ 15 ]. Briefly, 0.4 g of 1 mm glass beads were added to 2 ml microtubes containing 1 ml of InhibitEX and 10 mg of dust and homogenised for 5 min at maximum speed using a Qiagen Tissue Lyser II (Qiagen, Hilden, Germany).…”

Section: Methodsmentioning

confidence: 99%

Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks

et al. 2021

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Background A major focus of research on the gut microbiota of poultry has been to define signatures of a healthy gut and identify microbiota components that correlate with feed conversion. However, there is a high variation in individual gut microbiota profiles and their association with performance. Population level samples such as dust and pooled excreta could be useful to investigate bacterial signatures associated with productivity at the flock-level. This study was designed to investigate the bacterial signatures of high and low-performing commercial meat chicken farms in dust and pooled excreta samples. Poultry house dust and fresh pooled excreta were collected at days 7, 14, 21, 28 and 35 of age from 8 farms of two Australian integrator companies and 389 samples assessed by 16S ribosomal RNA gene amplicon sequencing. The farms were ranked as low (n = 4) or high performers (n = 4) based on feed conversion rate corrected by body weight. Results Permutational analysis of variance based on Bray–Curtis dissimilarities using abundance data for bacterial community structure results showed that company explained the highest variation in the bacterial community structure in excreta (R2 = 0.21, p = 0.001) while age explained the highest variation in the bacterial community structure in dust (R2 = 0.13, p = 0.001). Farm performance explained the least variation in the bacterial community structure in both dust (R2 = 0.03, p = 0.001) and excreta (R2 = 0.01, p = 0.001) samples. However, specific bacterial taxa were found to be associated with high and low performance in both dust and excreta. The bacteria taxa associated with high-performing farms in dust or excreta found in this study were Enterococcus and Candidatus Arthromitus whereas bacterial taxa associated with low-performing farms included Nocardia, Lapillococcus, Brachybacterium, Ruania, Dietzia, Brevibacterium, Jeotgalicoccus, Corynebacterium and Aerococcus. Conclusions Dust and excreta could be useful for investigating bacterial signatures associated with high and low performance in commercial poultry farms. Further studies on a larger number of farms are needed to determine if the bacterial signatures found in this study are reproducible.

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“…A recent study by Luiken et al [ 37 ] that investigated antimicrobial resistant bacteria in farmers and livestock, showed that the microbiota of settled poultry house dust are associated with the microbiota of chicken excreta, providing evidence that this approach could be useful for the study of gut microbiota. In addition, previous studies on molecular testing of poultry dust for population-level monitoring of viruses, protozoa, and bacteria in commercial flocks have shown that dust samples collected at any location of the poultry house could be used to detect microorganisms of interest even at relative low levels of infection (approximately 20% of infected birds) [ 38 – 44 ], suggesting that this may be a practical sample type for population-level monitoring of pathogens and perhaps gut microbiota. This study aimed to compare non-invasive samples (dust, excreta, and litter) to invasive (caecal and ileal contents) sampling methods for studying microbiota composition.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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Molecular detection of Eimeria species and Clostridium perfringens in poultry dust and pooled excreta of commercial broiler chicken flocks differing in productive performance

Cited by 6 publications

References 44 publications

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks

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

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