Chicken caecal enterotypes in indigenous Kadaknath and commercial Cobb chicken lines are associated with Campylobacter abundance and influenced by farming practices

Abstract

Identifying farming practices that decrease susceptibility to infectious diseases and optimise food conversion efficiency is valuable for chicken welfare and productivity, the environment, and public health. Enterotypes can be used to define microbial community phenotypes that have differential, potentially significant impacts on gut health. In this study, we delineated enterotypes by analysing the microbiomes of 300 indigenous Kadaknath and 300 commercial Cobb400 broiler chickens raised across 60 farms in western India. Using a compositional data approach, we identified three distinct enterotypes: PA1 (n=290), PA2 (n=142) and PA3 (n=67). PA1 and PA2 clustered more closely with each other than with PA3, however, PA2 had significantly lower alpha diversity than PA1. PA1 had a high Firmicutes: Bacteroides ratio, was dominated by Faecalibacterium and had a higher abundance of Prevotellamassilia than other enterotypes. PA2 was characterised by its low alpha diversity, a high abundance of the common taxa Phascolarctobacterium A and Phocaeicola dorei and a significantly higher Campylobacter abundance than PA1. PA3 had the highest Bacteroidota abundance of the three enterotypes and was defined by high prevalence of lower abundance taxa such as CAG-831 and Mucispirillum schaedleri. Network analysis showed that all enterotypes have different proportions of competing Firmicutes-dominant and Bacteroidota-dominant guilds. Random Forest Modelling using defined farm characteristics was predictive for enterotype. Factors affecting enterotype include whether farms were open, enclosed or caged, the location of farms, whether visitors were allowed inside, the number of people in contact with the chickens, chicken line, the presence of dogs and whether flock thinning took place. This study suggests that enterotypes are influenced by farming practices, hence modification of practices could potentially be used to reduce the burden of zoonotic pathogens such as Campylobacter.

Multi-omics analysis reveals regime shifts in the gastrointestinal ecosystem in chickens following anticoccidial vaccination andEimeria tenellachallenge

“…On average a low alpha diversity index of microbial richness was found in all chickens across all groups (71.64±14.21) compared to a previous study by Hay et al (2023) (493.13±201.60, re-analysed using the same pipeline used in the present study)[27]. This disparity may be due to requirement for broad-spectrum enrofloxacin treatment during this trial (Figure 2E).…”

“…Using 16S rDNA amplicon sequencing from caecal contents and caecal tissue of experimentally vaccinated and challenged chickens (specific pathogen-free sourced), the microbiota richness was lower than in a previous farm study (Hay et al 2023), likely due to the necessary enrofloxacin medication in the early rearing period to control an outbreak of colibacillosis. Indeed, it is well described that antibiotic treatment severly impacts on microbiome composition and richness, but recovering to its normal composition after stopping the treatment.…”

“…(2023) (493.13±201.60, re-analysed using the same pipeline used in the present study) [27]. This disparity may be due to requirement for broad-spectrum enrofloxacin treatment during this trial (Figure 2E).…”

“…A PERMANOVA test confirmed significant differences in microbiota (R 2 =0.33, p=0.001) (Figure 2A) and there were significant correlations with caecal lesion scores (|r|=0. [27]. This disparity may be due to requirement for broad-spectrum enrofloxacin treatment during this trial (Figure 2E).…”

Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis

“…However, considering the "enterotypes" criticism [33], and since we obtained not a discrete, but a variable taxa distribution in the bacterial communities, in the present study, we used the term "pattern" as the most correct designation of the different compositions of cecal microbiomes. Thus, we can state a certain similarity of the F1(+) and F1(−) patterns with the PA1-3 chicken cecal enterotypes, demonstrating significant differences in the Firmicutes/Bacteroidetes (currently Bacillota/Bacteroidota) ratio, as well as differences in the alpha biodiversity, which was identified in a comparative study of 600 chickens belonging to two different breeds/lines from 60 farms with different farming practices [34]. Unfortunately, the chickens analyzed were often colonized by the Campylobacter genus, the most common zoonotic pathogen of foodborne diseases, which distorts microbial networks and does not allow their microbial networks to be considered "normal".…”