Unexpected microbiota results?
Published on 29.08.2020 by Gut Health Consultancy
Various factors that can influence microbiota analysis need to be kept in mind. For example:
Sampling - What has been sampled (e.g. ileal microbiota influence on colonic or faecal microbiota in chickens)? Exposure to oxygen? Transport and storage conditions?
In-vitro - Optimal DNA extraction protocol? 16S rRNA gene hypervariable region? Primer selection? Specifics of sequencing platform?
In-silico - Databases or algorithms used for sequence curation, clustering and taxonomic assignment? Realistic taxonomic resolution? Appropriate statistical analyses?
DNA extraction, sequencing methods and bioinformatic processing methods have been identified as particularly important, with the latter having the greatest impact in a recent study (Szamosi et al., 2020).
We have been engaged by several clients to retrospectively interpret unexpected microbiota data. This is challenging. Careful review of procedures beforehand can minimise potential problems.
Intestinal inflammation models - being specific!
Published on 22.08.2020 by Gut Health Consultancy
There are numerous models available to study intestinal inflammation, which often use chemicals, pathogens and/or viscous diets as inducers. Whilst histopathological changes with these models may seem similar, such as inflammatory cell infiltrates and mucosal modifications, the specific changes with each model are important. Important factors include dose, duration, frequency of administration, animal genotype, and even the chemical's molecular weight. For example, some studies suggest that dextran sulfate sodium (DSS; a commonly used chemical) induces inflammation only/mainly in the large intestine, while others have found wider effects (e.g. small intestine); that broilers are less susceptible than layers; while some have found relatively low doses preferable (0.75% DSS in drinking water) for desired effects in broilers, others needed higher doses (2.5% DSS in drinking water) to observe pathology (references available). Gut Health Consultancy have been advising clients on the use of inflammation models and appropriate partners for their work. Getting advice early in these projects can help ensure the validity of the data generated and their interpretation.
Published on 29.08.2020 by Gut Health Consultancy
Various factors that can influence microbiota analysis need to be kept in mind. For example:
Sampling - What has been sampled (e.g. ileal microbiota influence on colonic or faecal microbiota in chickens)? Exposure to oxygen? Transport and storage conditions?
In-vitro - Optimal DNA extraction protocol? 16S rRNA gene hypervariable region? Primer selection? Specifics of sequencing platform?
In-silico - Databases or algorithms used for sequence curation, clustering and taxonomic assignment? Realistic taxonomic resolution? Appropriate statistical analyses?
DNA extraction, sequencing methods and bioinformatic processing methods have been identified as particularly important, with the latter having the greatest impact in a recent study (Szamosi et al., 2020).
We have been engaged by several clients to retrospectively interpret unexpected microbiota data. This is challenging. Careful review of procedures beforehand can minimise potential problems.
Intestinal inflammation models - being specific!
Published on 22.08.2020 by Gut Health Consultancy
There are numerous models available to study intestinal inflammation, which often use chemicals, pathogens and/or viscous diets as inducers. Whilst histopathological changes with these models may seem similar, such as inflammatory cell infiltrates and mucosal modifications, the specific changes with each model are important. Important factors include dose, duration, frequency of administration, animal genotype, and even the chemical's molecular weight. For example, some studies suggest that dextran sulfate sodium (DSS; a commonly used chemical) induces inflammation only/mainly in the large intestine, while others have found wider effects (e.g. small intestine); that broilers are less susceptible than layers; while some have found relatively low doses preferable (0.75% DSS in drinking water) for desired effects in broilers, others needed higher doses (2.5% DSS in drinking water) to observe pathology (references available). Gut Health Consultancy have been advising clients on the use of inflammation models and appropriate partners for their work. Getting advice early in these projects can help ensure the validity of the data generated and their interpretation.