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

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.

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

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.

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

Necrotic enteritis and coccidiosis are the most economically detrimental enteric diseases of broiler chickens. This study aimed to investigate the association of DNA load of Clostridium perfringens, netB, and five Eimeria species (E. brunetti, E. maxima, E. necatrix, E. acervulina and E. tenella) in poultry house dust and pooled excreta with flock productive performance. The dust and pooled excreta from the floor were collected weekly at days 7, 14, 21, 28 and 35 of chicken age from 16 flocks of eight farms from two Australian integrator companies. The farms were ranked as high or low performers by each integrator according to the production performance of studied flocks. Eimeria tenella and necatrix were not detected in any farm while E. brunetti was detected in a low-performance farm and netB was detected in a high-performance farm. C. perfringens, E. acervulina and E. maxima DNA were detected on all farms with no significant differences in DNA load between high and low-performance farms or companies. The lack of association of pathogen DNA load and farm performance is possibly due to overall low to moderate pathogen DNA load detected in this study. Further studies on a larger number of farms are needed to determine whether these population level measurements of key pathogens based on PCR detection of nucleic acids are correlated with performance variables.

Erratum to "Sero-prevalence of Toxoplasma gondii in sheep in different geographical regions of Nepal" [5C (June 2018) 7-9].

[This corrects the article DOI: 10.1016/j.vas.2018.01.001.].

Methods to prevent PCR amplification of DNA from non-viable virus were not successful for infectious laryngotracheitis virus.

Molecular-based testing of poultry dust has been used as a fast, sensitive and specific way to monitor viruses in chicken flocks but it provides no information on viral viability. Differentiation of viable and nonviable virus would expand the usefulness of PCR-based detection. This study tested three treatments (1. DNAse, 2. propidium monoazide [PMA], 3. immunomagnetic separation [IMS]) applied to dust or virus stock prior to nucleic acid extraction for their ability to exclude nonviable virus from PCR amplification. Infectious laryngotracheitis virus (ILTV) was used as a model. These treatments assume loss of viral viability due to damage to the capsid or to denaturation of epitope proteins. DNAse and PMA assess the integrity of the capsid to penetration by enzyme or intercalating dye, while IMS assesses the integrity of epitope proteins. Treatments were evaluated for their ability to reduce PCR signal, measured as ILTV log10 genomic copies (ILTV GC), of heat and chemically inactivated ILTV in poultry dust and virus stock. Compared to untreated dust samples, there was an overall reduction of 1.7 ILTV GC after IMS treatment (p<0.01), and a reduction of 2.0 ILTV GC after PMA treatment (p<0.0001). DNAse treatment did not reduce ILTV GC in dust (p = 0.68). Compared to untreated virus stocks, there was an overall reduction of 0.5 ILTV GC after DNAse treatment (p = 0.04), a reduction of 1.8 ILTV GC after IMS treatment (p<0.001) and a reduction of 1.4 ILTV GC after PMA treatment (p<0.0001). None of the treatments completely suppressed the detection of inactivated ILTV GC. In conclusion, treatments that use capsid integrity or protein epitope denaturation as markers to assess ILTV infectivity are unsuitable to accurately estimate proportions of viable virus in poultry dust and virus stocks.

Standardized ileal digestibility and digestible indispensable amino acid score of porcine and bovine hydrolyzates in pigs.

BACKGROUND: The use of protein hydrolyzates in food and feed ingredients is a growing area of interest. The present study was conducted aiming to determine the standardized ileal digestibility (SID) and to evaluate protein quality of porcine and bovine hydrolyzates. The SID values were determined in pigs and these values were used to calculate digestible indispensable amino acid score (DIAAS) values. RESULTS: The SID of crude protein of hydrolyzates of porcine plasma, bovine muscle, bovine collagen, porcine heart and porcine muscle was 0.81, 0.84, 0.79, 0.79 and 0.91, respectively. Based on the DIAAS, hydrolyzates of porcine plasma and porcine heart (DIAAS = 87 and 76) are considered as good quality protein sources for younger children. For older children, adolescents and adults, the hydrolyzates of bovine muscle and porcine heart (DIAAS = 81 and 87) are considered as good quality protein sources and the hydrolyzate of porcine plasma (DIAAS = 102) is considered as a high quality protein source. CONCLUSION: DIAAS values indicate that the porcine and bovine hydrolyzates tested in the present study have low and medium to high protein values and also that the protein products can be included in human nutrition. © 2017 Society of Chemical Industry.

Sero-prevalence of Toxoplasma gondii in sheep in different geographical regions of Nepal.

The present study was conducted to investigate the prevalence of Toxoplasma gondii in sheep in Nepal. Blood samples were collected from 235 sheep from three districts of three different eco-zones namely, mountainous Jumla (88), hilly Pokhara (62) and plain/terai Chitwan (85). The samples were tested by using commercial ELISA kit. The overall prevalence of T. gondii infection in sheep was 36.17% (CI: 30.29-42.49%). The region wise prevalence showed highest in Chitwan (57.65%; CI: 47.04-67.60%), followed by Pokhara (32.94%; CI: 23.88-43.48%) and Jumla (9.41%; CI: 4.85-17.49%). Prevalence of T. gondii in Jumla was significantly lower than Pokhara and Chitwan (p < 0.05) but no significant difference in seroprevalence was encountered between Pokhara and Chitwan (p > 0.05). Similarly, no significant difference (p > 0.05) in prevalence of T. gondii was found in sex and age groups (p > 0.05). The result showed that T. gondii parasite is widely spread in the studied geographical regions of Nepal.