Investigating the cecal microbiota of broilers raised in extensive and intensive production systems

Abstract

Intensive broiler production practices are structured to prevent the introduction and spread of pathogens; however, they can potentially minimize the exposure of broilers to beneficial commensal bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the cecal microbiota of 35-day-old broilers from 22 independent commercial farms rearing broilers under intensive (IPS) or extensive production systems (EPS). We aimed to determine which bacteria are normal inhabitants of the broiler ceca and which bacteria might be missing from broilers in IPS. In addition, we generated a collection of 410 bacterial isolates, including 87 different species, to be used as a resource to further explore the effects of selected isolates on bird physiology and to elucidate the role of individual species within the cecal microbial community. Our results indicated significant differences in the microbiota of broilers between systems: the microbiota of broilers from EPS was dominated by Bacteroidetes {55.2% ± 8.9 [mean ± standard deviation (SD)]}, whereas Firmicutes dominated the microbiota of broilers from IPS (61.7% ± 14.4, mean ± SD). Bacterial taxa found to be core in the EPS microbiota, including Olsenella , Alistipes , Bacteroides , Barnesiella , Parabacteroides , Megamonas , and Parasutterella , were shown to be infrequent or absent from the IPS microbiota, and the EPS microbiota presented higher phylogenetic diversity and greater predicted functional potential than that of broilers in IPS. The bacteria shown to be depleted in broilers from IPS should be further investigated for their effects on bird physiology and potential application as next-generation probiotics. IMPORTANCE Production practices in intensive farming systems significantly reduce the introduction and spread of pathogens; however, they may potentially minimize the exposure of animals to beneficial commensal microorganisms. In this study, we identified core bacteria from the cecal microbiota of broilers raised in extensive production systems that are missing or reduced in birds from intensive systems, including Olsenella , Alistipes , Bacteroides , Barnesiella , Parabacteroides , Megamonas , and Parasutterella . Furthermore, the cecal microbiota of broilers from extensive systems showed higher diversity and greater functional potential than that of broilers from intensive systems. In addition, a collection of bacterial isolates containing 87 different species was generated from the current study, and this important resource can be used to further explore the role of selected commensal bacteria on the microbial community and bird physiology.

A comparison of wild boar and domestic pig microbiota does not reveal a loss of microbial species but an increase in alpha diversity and opportunistic genera in domestic pigs

“…Our study found that Firmicutes and Bacteroidetes dominated the gut microbiota of both domestic and wild pigs with different ratios. The higher Bacteroidetes in wild pigs was consistent with previous studies exploring the gut microbiota of healthy wild boars (27), which has also been observed in extensively raised chickens (57) and in humans living in rural areas (58, 59). It has been shown that Bacteroidetes are capable of breaking down various types of complex non-digestible carbohydrates in the host gastrointestinal tract, while Firmicutes are well-suited to the cross-feeding process in the gut (60).…”

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

“…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". Notably, significantly different microbiomes dominated by Firmicutes and Bacteroidetes (currently Bacillotaand Bacteroidota-dominated) have also been described in broiler chickens under extensive production systems (EPS) or intensive production systems (IPS) [35], which showed low and high phylogenetic diversity, respectively. At the same time, the results of cited and present studies are not identical, since the F1(−) pattern did not include the phylum Pseudomonadota (formerly Proteobacteria), the F1(+) pattern included the ACT component, and there were additional differences from the bacterial taxa found to be at the core of the EPS and IPS microbiomes [11].…”