Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity

Abstract

The concept of improving animal health through improved gut health has existed in food animal production for decades; however, only recently have we had the tools to identify microbes in the intestine associated with improved performance. Currently, little is known about how the avian microbiome develops or the factors that affect its composition. To begin to address this knowledge gap, the present study assessed the development of the cecal microbiome in chicks from hatch to 28 days of age with and without a live Salmonella vaccine and/or probiotic supplement; both are products intended to promote gut health. The microbiome of growing chicks develops rapidly from days 1–3, and the microbiome is primarily Enterobacteriaceae, but Firmicutes increase in abundance and taxonomic diversity starting around day 7. As the microbiome continues to develop, the influence of the treatments becomes stronger. Predicted metagenomic content suggests that, functionally, treatment may stimulate more differences at day 14, despite the strong taxonomic differences at day 28. These results demonstrate that these live microbial treatments do impact the development of the bacterial taxa found in the growing chicks; however, additional experiments are needed to understand the biochemical and functional consequences of these alterations.

Long-Term Transcriptomic Effects of Prebiotics and Synbiotics Delivered In Ovo in Broiler Chickens

“…Attaining immune functions by GALT in neonate chickens has been associated with the seeding of the GIT with primary microflora, and its evolution to stable climax microflora that assures immune-microbe homeostasis and competitive exclusion of the enteropathogens [56]. The development of the microbial population is strictly age-dependent, which indicates that early stimulation of beneficial microflora is an absolute necessity, as it affects, to a great extent, the entire life-span of an individual [57]. …”

Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession

“…Poultry is the world's primary source of animal protein (FAO, ); the global population of chicken exceeds 40 billion individuals (Oakley, Lillehoj, et al., ). Broiler chicken meat comprises the majority of the poultry meat industry, and ensuring the health and productivity of broilers has become a key aspect of this industry (Ballou et al., ). Recent studies using high throughput sequencing, have shown the role of the gastrointestinal tract (GIT) microbiome in gastrointestinal development, nutrient absorption, and pathogen invasion resistance (Crhanova et al., ; Pan & Yu, ; Park et al., ; Pedroso & Lee, ; Yeoman et al., ).…”

“…Concurrently, initiatives to control antibiotic use in production animals, especially the restriction in use of growth promoters worldwide to prevent the emergence of antibiotic resistance has made the manipulation of intestinal microbiomes in poultry an attractive alternative to support innate immunity and improve health (Kogut & Arsenault, ; Pedroso & Lee, ), as well as productivity (Singh et al., ). Supplementing the diets of developing broilers with probiotics or applying vaccines have long‐term effects on the broilers’ GIT microbiome composition (Ballou et al., ). In particular, feed additives have altered microbial activity in the GIT as well as disease susceptibility (Engberg, Hedemann, Steenfeldt, & Jensen, ; Mitsch et al., ; Owens, Tucker, Collins, & McCracken, ), but the exact mechanisms responsible for these effects remain unclear (Oakley, Lillehoj, et al., ).…”

“…This concept was developed from studies which found that broilers were most vulnerable to Salmonella infantis during the first week after hatching, and that the oral administration of a mixed bacterial culture derived from the GIT of adult chickens resulted in prevention of colonization by S. infantis in young broilers (Nurmi & Rantala, ; Rantala & Nurmi, ). In parallel, research into the potential of probiotic therapies, as live microbial feed supplements, to alter the chicken GIT microbiome overwhelmingly finds that they are most effective when applied during early life (Ballou et al., ; Oakley, Lillehoj, et al., ).…”

“…A weekly sampling of broilers showed large shifts in the cecal and fecal microbiomes each week as well as a gradual increase in community complexity (Oakley & Kogut, ). Another study found the cecal and ileal communities of 3‐day‐old broilers to be distinct from subsequent samples taken at a weekly interval (Lu et al., ); and yet another study showed major shifts in the cecal microbiome between the first and third days after hatching (Ballou et al., ). From the time of hatching, commercial broilers are exposed to a wide range of sources of microorganisms, being those in the environment, litter, water, and feed, may colonize the broiler GIT in the first weeks of life (Pedroso & Lee, ).…”