Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls

Gheorghe, Cassandra E.; Ritz, Nathaniel L.; Martin, JA; Wardill, Hannah R.; Cryan, John F.; Clarke, Gerard

doi:10.1080/19490976.2021.1941711

Cited by 86 publications

(56 citation statements)

References 487 publications

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“…recommended that fecal samples should be kept at 4°C or on ice after collection and during transportation to better maintain the viability of microbiota for FMT. 30 Burz et al . provided a comprehensive guideline in handling and storing stools for FMT through a systemic evaluation using 16S rRNA sequencing, metabolomic fingerprinting and flow cytometry, which also suggested that fresh samples should refrigerated at 4℃ if the transformation to transplant process exceeded 24 hours.…”

Section: Discussionmentioning

confidence: 99%

Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics

Zhang

Mayne

et al. 2022

Gut Microbes

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Biobanking of live microbiota is becoming indispensable for mechanistic and clinical investigations of drug–microbiome interactions and fecal microbiota transplantation. However, there is a lack of methods to rapidly and systematically evaluate whether the biobanked microbiota maintains their cultivability and functional activity. In this study, we use a rapid ex vivo microbiome assay and metaproteomics to evaluate the cultivability and the functional responses of biobanked microbiota to treatment with a prebiotic (fructo-oligosaccharide, FOS). Our results indicate that the microbiota cultivability and their functional responses to FOS treatment were well maintained by freezing in a deoxygenated glycerol buffer at −80°C for 12 months. We also demonstrate that the fecal microbiota is functionally stable for 48 hours on ice in a deoxygenated glycerol buffer, allowing off-site fecal sample collection and shipping to laboratory for live microbiota biobanking. This study provides a method for rapid evaluation of the cultivability of biobanked live microbiota. Our results show minimal detrimental influences of long-term freezing in deoxygenated glycerol buffer on the cultivability of fecal microbiota.

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Section: Discussionmentioning

confidence: 99%

Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics

Zhang

Mayne

et al. 2022

Gut Microbes

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“…While these guidelines provide the much-needed structure for preclinical FMT protocols, it is critical to emphasize that we do not aim to recommend what methods should be used, as different experimental endpoints and research questions will clearly need a different methodological design (as previously discussed by Gheorghe et al 12 ). However, by consistently reporting the following set of guidelines, future studies will be more reproducible and thus be more likely to generate clinically relevant outcomes.…”

Section: The Graft Recommendations and Future Stepsmentioning

confidence: 99%

“…While the sample size for the donor FMT group was not extracted in our analysis due to low levels of reporting, it is also important to acknowledge that this should also be clearly reported alongside information on whether FMT contents are pooled across multiple donor samples. Donor sample size is particularly pertinent in the use of human donors, as recently outlined by Gheorghe et al with the use of a single donor considered N = 1 12 .…”

Section: Study Characteristicsmentioning

confidence: 99%

“…While our systematic review intentionally restricted our search to studies with mice, we argue that, given the similarity in FMT procedures across species, the GRAFT recommendations can also be used to guide FMT use in other species, and may offer guidance in human-animal transplantation if followed in combination with the recommendations presented by Walter et al (2020). 13 While these guidelines provide the much-needed structure for preclinical FMT protocols, it is critical to emphasize that we do not aim to recommend what methods should be used, as different experimental endpoints and research questions will clearly need a different methodological design (as previously discussed by Gheorghe et al 12 ). However, by consistently reporting the following set of guidelines, future studies will be more reproducible and thus be more likely to generate clinically relevant outcomes.…”

Section: The Graft Recommendations and Future Stepsmentioning

confidence: 99%

“…However, there are vast differences in the antibiotic treatment specifications used in animal models, including FMT. These include type, dose and duration, which can introduce significant variability in ablative capacity, with persisting pathogens confounding results (for a comprehensive review of this topic, please see Gheorghe et al 12 ).…”

Section: Introductionmentioning

confidence: 99%

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Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols

et al. 2021

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Fecal microbiota transplant (FMT) is a powerful tool used to connect changes in gut microbial composition with a variety of disease states and pathologies. While FMT enables potential causal relationships to be identified, the experimental details reported in preclinical FMT protocols are highly inconsistent and/or incomplete. This limitation reflects a current lack of authoritative guidance on reporting standards that would facilitate replication efforts and ultimately reproducible science. We therefore systematically reviewed all FMT protocols used in mouse models with the goal of formulating recommendations on the reporting of preclinical FMT protocols. Search strategies were applied across three databases (PubMed, EMBASE, and Ovid Medline) until June 30, 2020. Data related to donor attributes, stool collection, processing/storage, recipient preparation, administration, and quality control were extracted. A total of 1753 papers were identified, with 241 identified for data extraction and analysis. Of the papers included, 92.5% reported a positive outcome with FMT intervention. However, the vast majority of studies failed to address core methodological aspects including the use of anaerobic conditions (91.7% of papers lacked information), storage (49.4%), homogenization (33.6%), concentration (31.5%), volume (19.9%) and administration route (5.3%). To address these reporting limitations, we developed the Guidelines for Reporting Animal Fecal Transplant (GRAFT) that guide reporting standards for preclinical FMT. The GRAFT recommendations will enable robust reporting of preclinical FMT design, and facilitate high-quality peer review, improving the rigor and translation of knowledge gained through preclinical FMT studies.

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Inflammation, Lifestyle Factors, and the Microbiome‐Gut‐Brain Axis: Relevance to Depression and Antidepressant Action

Donoso

Cryan

Olavarría-Ramírez

et al. 2022

Clin Pharma and Therapeutics

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Depression is considered a major public health concern, where existing pharmacological treatments are not equally effective across all patients. The pathogenesis of depression involves the interaction of complex biological components, such as the immune system and the microbiota-gut-brain axis. Adjunctive lifestyle-oriented approaches for depression, including physical exercise and special diets are promising therapeutic options when combined with traditional antidepressants. However, the mechanisms of action of these strategies are incompletely understood. Accumulating evidence suggests that physical exercise and specific dietary regimens can modulate both the immune system and gut microbiota composition. Here, we review the current information about the strategies to alleviate depression and their crosstalk with both inflammatory mechanisms and the gut microbiome. We further discuss the role of the microbiota-gut-brain axis as a possible mediator for the adjunctive therapies for depression through inflammatory mechanisms. Finally, we review existing and future adjunctive strategies to manipulate the gut microbiota with potential use for depression, including physical exercise, dietary interventions, prebiotics/probiotics, and fecal microbiota transplantation.

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Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls

Cited by 86 publications

References 487 publications

Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics

Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics

Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols

Inflammation, Lifestyle Factors, and the Microbiome‐Gut‐Brain Axis: Relevance to Depression and Antidepressant Action

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