The cecal microbiome of commercial broiler chickens varies significantly by season

Abstract

Next-generation DNA sequencing is rapidly becoming a powerful tool for food animal management. One valuable use of this technology is to re-examine long-standing observations of performance differences associated with animal husbandry practices to better understand how these differences may be modulated by the gastrointestinal (GI) microbiome. The influences of environmental parameters such as air temperature and relative humidity on broiler chicken performance have commonly been observed, but how the GI microbiome may respond to seasonal environmental changes remains largely unknown. The purposes of this study were therefore to: (1) characterize the cecal microflora of commercial broilers (N = 87) collected at harvest across all 4 seasons, and (2) identify any significant changes of the GI microbiome and specific taxa according to season and Campylobacter status. Finding taxa with significant positive or negative correlations with Campylobacter could be useful by identifying indicator or antagonistic taxa and could also inform inferences regarding the ecological niche of Campylobacter. Whole GI tracts were removed from commercial broilers representing 87 independent flocks between April 2013 and May 2014 in the U.S. state of Georgia. Intact ceca were separated, cultured for Campylobacter and cecal contents were frozen. The cecal microbiome was characterized using barcoded sequencing of 16S rRNA genes on the Illumina MiSeq platform. The composition of the microbiome measured at processing was generally not affected by Campylobacter status but was most significantly affected by season of grow-out. Significantly fewer bacterial genera were found in winter than spring or summer. Bacterial genera with prior evidence for both positive or negative influences on gut health outcomes were significantly less abundant in the fall. Identifying specific members of the GI microbiota that vary according to season may help develop novel interventions to improve husbandry practices and growth performance.

Microbiota, Gut Health and Chicken Productivity: What Is the Connection?

“…In a recent study in a broiler farm from Argentina, we observed that there is a strong variation of the cecal microbiota according to seasons, with the highest species richness in summer, doubling that of winter [34]. This agrees with findings of other authors that observed a similar pattern of seasonal variation in alpha diversity when analyzing cecal samples from multiple flocks of broiler chickens in the U.S. [35]. On the other hand, many studies reported differences in the gut microbiota profiles of poultry according to geographic location [26,36,37].…”

Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens

“…Understanding how live vaccines affect microbiota, egg production, and susceptibility to nontarget pathogens will be an important step toward improving management practices and maximizing productivity. Other limitations that need to be addressed in future studies include, but are not limited to, a side-by-side comparison of breeds and management systems as well as sampling across different seasons and flock cycles (7,18).…”

“…Within the gut, the cecum has attracted the most attention because of its high microbial densities and health-related functions, such as urea recycling, carbohydrate fermentation, and water regulation (15). Most studies of the chicken gut microbiota have focused on one segment at a time; fewer studies have compared multiple segments from the same set of birds (15)(16)(17)(18). On this basis, we previously undertook a large comprehensive study of 37 different commercial flocks of Cobb 500 broilers within a vertically integrated broiler system and defined the core microbiota in the ileum and cecum using 16S rRNA gene amplicon sequencing (7).…”

Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity

“…It can potentially improve nutrition efficacy as well as resistance to infections or colonization by zoonotic infectious agents [ 5 , 6 ]. However, its composition varies according to a number of parameters including age, nutrition, seasons [ 7 , 8 ] but also the rearing environment and specific process such as litter management regimen that can potentially impact productivity by contributing to poultry gut microbiota composition [ 9 – 11 ]. The impact of the environment on chicken microbiota composition is increased by the fact that the eggs are separated from the laying birds, and then incubated in clean conditions, with the newly hatched chicks being consequently very susceptible to colonization by environmental bacteria.…”