“Missing microbes” in commercial broiler production and the effects of early-life microbial inoculations on broiler microbiota development
Creators: Schultz Marcolla, Camila
Publisher: name: University of Alberta Library
Year: 2023

<p>Modern poultry production relies on strict biosecurity procedures to minimize the risk of introducing pathogens to flocks, and may inadvertently limit exposure to beneficial commensal bacteria that naturally coexist with chickens. Commensal bacteria promote gastrointestinal and immune development, nutrient metabolism, and disease resistance. Consequently, broilers raised without a proper commensal microbiota may be more susceptible to diseases, exhibit abnormal immune responses, and have limited growth potential. Although recent advancements in sequencing technologies and bioinformatics have enhanced our understanding of broiler gut microbiota, most research is still limited to taxonomical descriptions and correlational findings, which alone cannot uncover specific bacterial functions or the mechanisms underlying observed effects on host physiology. In addition, studies have primarily focused on broilers in intensive systems and experimental facilities, potentially failing to represent the microbiota of a &quot;normal&quot; chicken, that would naturally hatch in a nest and be readily colonized by a mature microbiota from hens. Given that the gut microbiota contributes significantly to host health and that coevolution shapes host-microbe relationships to be beneficial, it is reasonable to expect that a mature hen’s microbiota would more accurately represent a normal, healthy, and stable microbiota, than that of an intensively raised broilers. Therefore, we hypothesize that intensive farming practices limit broilers&#39; exposure to coevolved bacteria that would typically be present in the chicken gut under more natural circumstances. Additionally, we hypothesize that early-life exposure to chicken commensal bacteria can modulate broiler immune responses and disease resistance, and that coevolved native bacteria possess the ability to efficiently colonize the chicken gut after a single exposure.<br>
The first study characterized the cecal microbiota of 35-day-old broilers from intensive production systems (IPS) and from extensive production systems (EPS) on commercial farms in Alberta. We aimed to identify the core microbiota of broiler ceca and determine which bacteria were absent in IPS broilers. We found that the microbiota of broilers in EPS had higher phylogenetic diversity and greater predicted functional potential compared to IPS. Additionally, bacterial taxa ubiquitous in EPS microbiota, such as Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella were infrequent or absent in the microbiota of IPS broilers. Additionally, we collected and identified 410 bacterial isolates, representing 87 unique species, that can be used as a resource in future studies.<br>
The second study evaluated the impact of different microbial preparations, inoculation strategies, and inoculum sources on the gut microbiota and physiological responses of broilers. We found that chicks exposed to cecal contents or microbial cultures were readily colonized by Bacteroidetes and showed higher abundance of Alistipes, Bacteroides, Barnesiella, Mediterranea, Megamonas, Parabacteroides, Phascolarctobacterium and Subdoligranulum compared to control birds without microbial exposure. We also found that gavage, spray, and cohousing methods were effective to promote colonization, and that all microbial preparations promoted a reduction in the relative abundance of Escherichia-Shigella in exposed birds.<br>
The third study evaluated the effect of early-life introduction of M. hypermegale alone or in combination with a defined community (DC) of bacteria on broiler gut microbiota development and ability to resist Salmonella infection. Substantial changes in cecal microbiota composition were observed with the introduction of the DC, but effects on host physiology and Salmonella resistance were moderate. We identified A. finegoldii, B. gallinaceum, B. viscericola, P. vulgatus, L. crispatus, and L. agilis as good colonizers of the chicken gut. Moreover, the introduced bacteria caused a reduction in the relative abundance of Escherichia-Shigella, which was consistent with previous findings.<br>
In summary, broilers in IPS exhibited lower abundance of core microbes and putative functions in their cecal microbiota compared to broilers in EPS. We identify bacterial lineages that were reduced in IPS but were successful colonizer in birds exposed to complex or defined communities, suggesting these are host-adapted microbes that have had their dispersal among broilers negatively affected by current production practices. Despite the significant effects of microbial preparations on the microbiota community of inoculated birds, the effects on measured host responses were moderate. The collection of bacterial isolates generated in this study is a valuable resource for future research.</p>