Research Topic

Beyond Conventional Models: Expanding Experimental Systems for Animal-Microbiome Interaction Research

About this Research Topic

The relationship of animals and humans with their associated microorganism are defined by specific interactions between members of the microbiota and their hosts. Understanding these interactions requires the complementation of omics-based methods with mechanistic approaches in model organisms. Considering the suitability of a model organism and the adequate parameters of the model remain critical for the experimental design. For example, it has been shown that the microbiome composition of the laboratory mouse can vary with genotype, sex, age, or diet—among other determinants, which may in turn impact on the experimental outcome. Likewise, the host-specificity of some microorganisms may limit or exclude the use of the model organisms as a host for some microbiota transplants.

Meanwhile, less complex experimental models such as insect gut microbiota as well as in vitro models using cell lines or batch culture system are promising alternative approaches to study specific factors affecting microbiome composition and functions. Considering that the spatial and temporal variations significantly affect microbiome diversity, knowledge integration across various experimental models under different physicochemical conditions may help the discovery of underappreciated key players in animal-microbiome interactions.

The aim of this Research Topic is to better describe understudied traits of widely used model organisms and/or to present novel approaches for mechanistic microbiome experiments going beyond the currently used models. Since the Research Topic ‘Experimental models in animal-associated microbiota’, there have been scientific and technological advances, e.g. in omics methods, which have increased the complexity of research. This current Research Topic provides a platform to present recent comprehensive results and/or to highlight new trends in animal-microbiome interaction research. We therefore welcome submissions of Original Research and Review articles focusing on, but not limited to, the following two areas:

1. Enhanced characterization of already existing animal models for microbiome research, e.g. rodents, insects, livestock animals, and fish. The emphasis here, is on aspects of descriptive research that have been neglected thus far, such as understudied taxonomic groups (e.g., Archaea, Protozoa, Fungi, Phages), and in-depth characterizations advancing the knowledge about the basic functions in established model systems (e.g. use of synthetic microbial consortia in gnotobiotic animals or microbiome biogeography of different body sites in conventionally raised animals).

2. Establishment and/or characterization of novel model systems for microbiome research, particularly, given the limitations of already existing models, which can only be overcome by development of novel experimental approaches. This could include the use of novel or less-widely used animal models, such as gnotobiotic insects (e.g. cockroaches). Studies on in vitro alternatives that have potential to effectively complement or substitute the use of vertebrate animal model organisms will also be considered.

Please note that this Research Topic does not consider submissions of manuscripts reporting on the control, prevention and /or treatment of microbial diseases or reports on animal-gut microbiota studies aimed primarily to improve animal health solely for commercial purposes. Do not hesitate to contact the editorial team if you require further clarification regarding scope.


Keywords: animal models, alternative model system, omics


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 relationship of animals and humans with their associated microorganism are defined by specific interactions between members of the microbiota and their hosts. Understanding these interactions requires the complementation of omics-based methods with mechanistic approaches in model organisms. Considering the suitability of a model organism and the adequate parameters of the model remain critical for the experimental design. For example, it has been shown that the microbiome composition of the laboratory mouse can vary with genotype, sex, age, or diet—among other determinants, which may in turn impact on the experimental outcome. Likewise, the host-specificity of some microorganisms may limit or exclude the use of the model organisms as a host for some microbiota transplants.

Meanwhile, less complex experimental models such as insect gut microbiota as well as in vitro models using cell lines or batch culture system are promising alternative approaches to study specific factors affecting microbiome composition and functions. Considering that the spatial and temporal variations significantly affect microbiome diversity, knowledge integration across various experimental models under different physicochemical conditions may help the discovery of underappreciated key players in animal-microbiome interactions.

The aim of this Research Topic is to better describe understudied traits of widely used model organisms and/or to present novel approaches for mechanistic microbiome experiments going beyond the currently used models. Since the Research Topic ‘Experimental models in animal-associated microbiota’, there have been scientific and technological advances, e.g. in omics methods, which have increased the complexity of research. This current Research Topic provides a platform to present recent comprehensive results and/or to highlight new trends in animal-microbiome interaction research. We therefore welcome submissions of Original Research and Review articles focusing on, but not limited to, the following two areas:

1. Enhanced characterization of already existing animal models for microbiome research, e.g. rodents, insects, livestock animals, and fish. The emphasis here, is on aspects of descriptive research that have been neglected thus far, such as understudied taxonomic groups (e.g., Archaea, Protozoa, Fungi, Phages), and in-depth characterizations advancing the knowledge about the basic functions in established model systems (e.g. use of synthetic microbial consortia in gnotobiotic animals or microbiome biogeography of different body sites in conventionally raised animals).

2. Establishment and/or characterization of novel model systems for microbiome research, particularly, given the limitations of already existing models, which can only be overcome by development of novel experimental approaches. This could include the use of novel or less-widely used animal models, such as gnotobiotic insects (e.g. cockroaches). Studies on in vitro alternatives that have potential to effectively complement or substitute the use of vertebrate animal model organisms will also be considered.

Please note that this Research Topic does not consider submissions of manuscripts reporting on the control, prevention and /or treatment of microbial diseases or reports on animal-gut microbiota studies aimed primarily to improve animal health solely for commercial purposes. Do not hesitate to contact the editorial team if you require further clarification regarding scope.


Keywords: animal models, alternative model system, omics


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

13 November 2020 Abstract
26 February 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

13 November 2020 Abstract
26 February 2021 Manuscript

Participating Journals

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

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