Research Topic

The Role of the Gut Microbiome in the Efficiency of Oral and Parenteral Vaccines in Animals

About this Research Topic

The gut microbiome plays an important role in the development, maturation and regulation of the innate and adaptive immune system in humans and animals. Because of the intimate, co-evolved interaction between both systems, it is not surprising that in recent years, studies in humans and rodent models indicate a significant role of the gut microbiome in shaping the immune response to oral and parenteral vaccines. Transitioning this research from correlation to causation and investigation into the mechanisms is ongoing. Given the generally ubiquitous nature of the interaction between gut microbiome and the immune system in vertebrates, the question arises, if the effects of the altered gut microbiome, either detrimental or beneficial effects, on the success of vaccination programs can be observed in livestock production and companion animals as well. So far, only a very small number of studies have addressed this question. Investigations of the responsible mechanisms, cell types and pathways into certain topics like the relevance of the gut virome or the role of the “Gut-Lung-axis” are much desired.

The influence of the microbiome on vaccination efficiency is most prominent early in life, a time where many vaccines are administered. This period defines a “critical window” where both the immune system and the gut microbiome are extremely vulnerable to alterations. Chances for detrimental effects are especially high in modern animal production with their somewhat artificial practices (e.g. poultry hatcheries, early weaning of piglets, etc). In addition, what is it about later dysbiotic periods in livestock and companion animals which coincide with regular vaccination programs (e.g. mass-antibiotic treatment in poultry; anthelmintic applications in companion animals, horses and cattle; inflammatory bowel disease in working dogs or stress in travelling horses)?

Generally, instances and causes of disruptions of microbiome composition and diversity are manifold during the lifetime of an animal. Apart from intestinal disease, the use of antibiotics is the main cause of dysbiosis.

Thus, we welcome submissions focusing on, but not limited to, the following subtopics related to the association between the gut microbiome and vaccine efficiency in livestock (incl. horses, poultry and fish) and companion animals:

● Quantitative and qualitative description of the effect of various classes of antibiotics and other medications like anthelmintics, anesthesia or NSAIDs on the microbiome in terms of resulting change of vaccination efficiency in different animal species and under diverse extrinsic conditions.
● Impact of feed additives and vaccines used as alternatives to in-feed antibiotics and other drugs on the gut microbiome and subsequently the vaccine response.
● Identification of microbiome targets that correlate with vaccine efficiency.
● Definition of an optimal microbiome to improve vaccine efficiency. Does its characteristics depend on animal species, genetic lineage, production category, age, environment, underlying pathogen burden or the type and combination of vaccines applied?

Preferentially, the outcome of microbiome alterations on vaccination efficiency will be assessed using challenge models given the difficulty to define a 'healthy' microbiome and the common imperfection of seroconversion as correlates of protection.


Keywords: microbiome, dysbiosis, vaccine efficiency, antibiotics, alternatives


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

The gut microbiome plays an important role in the development, maturation and regulation of the innate and adaptive immune system in humans and animals. Because of the intimate, co-evolved interaction between both systems, it is not surprising that in recent years, studies in humans and rodent models indicate a significant role of the gut microbiome in shaping the immune response to oral and parenteral vaccines. Transitioning this research from correlation to causation and investigation into the mechanisms is ongoing. Given the generally ubiquitous nature of the interaction between gut microbiome and the immune system in vertebrates, the question arises, if the effects of the altered gut microbiome, either detrimental or beneficial effects, on the success of vaccination programs can be observed in livestock production and companion animals as well. So far, only a very small number of studies have addressed this question. Investigations of the responsible mechanisms, cell types and pathways into certain topics like the relevance of the gut virome or the role of the “Gut-Lung-axis” are much desired.

The influence of the microbiome on vaccination efficiency is most prominent early in life, a time where many vaccines are administered. This period defines a “critical window” where both the immune system and the gut microbiome are extremely vulnerable to alterations. Chances for detrimental effects are especially high in modern animal production with their somewhat artificial practices (e.g. poultry hatcheries, early weaning of piglets, etc). In addition, what is it about later dysbiotic periods in livestock and companion animals which coincide with regular vaccination programs (e.g. mass-antibiotic treatment in poultry; anthelmintic applications in companion animals, horses and cattle; inflammatory bowel disease in working dogs or stress in travelling horses)?

Generally, instances and causes of disruptions of microbiome composition and diversity are manifold during the lifetime of an animal. Apart from intestinal disease, the use of antibiotics is the main cause of dysbiosis.

Thus, we welcome submissions focusing on, but not limited to, the following subtopics related to the association between the gut microbiome and vaccine efficiency in livestock (incl. horses, poultry and fish) and companion animals:

● Quantitative and qualitative description of the effect of various classes of antibiotics and other medications like anthelmintics, anesthesia or NSAIDs on the microbiome in terms of resulting change of vaccination efficiency in different animal species and under diverse extrinsic conditions.
● Impact of feed additives and vaccines used as alternatives to in-feed antibiotics and other drugs on the gut microbiome and subsequently the vaccine response.
● Identification of microbiome targets that correlate with vaccine efficiency.
● Definition of an optimal microbiome to improve vaccine efficiency. Does its characteristics depend on animal species, genetic lineage, production category, age, environment, underlying pathogen burden or the type and combination of vaccines applied?

Preferentially, the outcome of microbiome alterations on vaccination efficiency will be assessed using challenge models given the difficulty to define a 'healthy' microbiome and the common imperfection of seroconversion as correlates of protection.


Keywords: microbiome, dysbiosis, vaccine efficiency, antibiotics, alternatives


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

31 August 2020 Abstract
02 May 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

31 August 2020 Abstract
02 May 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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