Camila Marcolla | ALES Graduate Seminar

A graduate exam seminar is a presentation of the student’s final research project for their degree.
This is an ALES PhD Final Exam Seminar by Camila Marcolla. This seminar is open to the general public to attend, either in-person or online:

https://ualberta-ca.zoom.us/j/94322494724?pwd=M2ZteUN5OGc4ZmtXTTN5NTdIdERodz09
Meeting ID: 943 2249 4724 | Passcode: 549777

Thesis Topic: Identifying “missing microbes” in commercial broiler production and characterizing the effects of early-life microbial inoculations on broiler microbiota development and physiological responses

PhD with Dr. Benjamin Willing.

Seminar Abstract:

Modern poultry production aims to optimize efficiency and animal health to meet global demand for affordable and safe food products. Intensive farming practices prioritize strict biosecurity procedures to minimize the risk of introducing pathogens to flocks. However, these practices may inadvertently limit exposure to beneficial commensal bacteria that naturally coexist with chickens. Commensal bacteria play a vital role in various aspects of host physiology, including promoting gastrointestinal and immune development, nutrient metabolism, and disease resistance. By hindering the colonization of a healthy and mature microbiota in the chicken’s gastrointestinal tract, the chicken’s ability to resist pathogen colonization may be reduced, along with impaired development of gut-associated lymphoid tissue and decreased nutrient utilization from diets. As a result, broilers raised without a proper commensal microbiota may be more susceptible to diseases, exhibit abnormal immune responses, and have limited growth potential.

Recent advancements in sequencing technologies and bioinformatics have enhanced our understanding of the gut microbiota and its response to interventions. However, our knowledge of the broiler cecal microbiota remains limited to taxonomical descriptions and correlational findings, which alone cannot uncover specific bacterial functions or the mechanisms underlying observed effects on host physiology. Furthermore, most studies have primarily focused on broilers in intensive systems and experimental facilities, potentially failing to represent the microbiota of a “normal” chicken. In natural conditions, chicks hatch in nests and are readily colonized by a mature microbiota from hens, whereas modern broilers are artificially hatched and promptly colonized by bacteria from the hatchery environment. 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’ 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.

Our first study involved characterizing the cecal microbiota of 35-day-old broilers from intensive production systems (IPS) and from extensive production systems (EPS) in 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, several bacterial taxa ubiquitous in EPS microbiota, such as Olsenella, Alistipes, Bacteroides, Barnesiella, Parabacteroides, Megamonas, and Parasutterella were infrequent or absent in IPS microbiota. During this study, we generated a collection of 410 bacterial isolates, representing 87 species (including 5 novel species), and performed genomic characterization of selected isolates.

In our second study, we 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 abundances of Alistipes, Bacteroides, Barnesiella, Mediterranea, Megamonas, Parabacteroides, Phascolarctobacterium, and Subdoligranulum compared to control birds not exposed to microbial preparations. 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.

Finally, we 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. We observed substantial changes in cecal microbiota composition with the introduction of the DC, but moderate effects on host physiology and Salmonella resistance. 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 findings in previous studies.

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 and were successful colonizers in birds exposed to complex or defined communities, suggesting these are host-adapted microbes that have had their dispersal negatively affected by current production practices. The collection of bacterial isolates generated in this study is a valuable resource for future research, and the information generated in this study is pivotal in guiding the development of microbial manipulation strategies using host-adapted bacteria.