The role of the microbiome in animal models' applicability to human research, and reproducibility
Are experiments in mice and rats applicable to humans and reproducible?
A large portion of mouse studies are not applicable to humans, or reproducible. It turns out that gut microbiome differences play a major role. Dogs have more similiar microbiomes to humans and may be better models in some cases.
Mice:
Preclinical research: Make mouse studies work (2014) https://www.nature.com/articles/507423a
Even after animal studies suggest that a treatment will be safe and effective, more than 80% of potential therapeutics fail when tested in people
Of mice and men (2005) https://pmc.ncbi.nlm.nih.gov/articles/PMC1369270/#t1
Mice and humans are good examples of this metabolic homogeneity—they have the same organs and systemic physiology, and they also show great similarities in disease pathogenesis. However, mouse metabolism is seven times greater, among other important differences.
Mouse Models of Inflammation Are Basically Worthless (2013) https://www.science.org/content/blog-post/mouse-models-inflammation-are-basically-worthless-now-we-know
Gut microbiome differences are a major factor:
Reivew, 2018: The role of the gut microbiota on animal model reproducibility https://onlinelibrary.wiley.com/doi/full/10.1002/ame2.12022
Mouse microbes may make scientific studies harder to replicate. The zoo of bacteria and viruses within each lab animal may be confounding experiments (2016) https://www.science.org/content/article/mouse-microbes-may-make-scientific-studies-harder-replicate
Vendor effects on murine gut microbiota influence experimental abdominal sepsis (2017) https://www.sciencedirect.com/science/article/abs/pii/S0022480416305583
Gut bacteria from wild mice boost health in lab mice (2017) https://phys.org/news/2017-10-gut-bacteria-wild-mice-boost.html Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance. "The immunological benefits from the wild mice's gut bacteria may, in part, explain a persistent problem in disease research: Why disease experiments in lab mice, such as vaccine studies, turn out very differently in humans or other animals."
Faecal microbiota transplant into germ-free mice replicated donor susceptibility, revealing that variability was due to changes in the gut microbiota composition. (2019): https://www.nature.com/articles/s41564-019-0407-8 Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection.
"Biomedical research relies on the use of animal models, and the animals used in those models receive medical care, including antibiotics for brief periods of time to treat conditions such as dermatitis, fight wounds, and suspected bacterial pathogens of unknown etiology. These data highlight the need to consider the impact on GM of brief and seemingly routine use of antibiotics in the clinical care of research animals" (2020) https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-020-00839-0 Acute and long-term effects of antibiotics commonly used in laboratory animal medicine on the fecal microbiota.
"Only 2.65% of bacterial species are shared between mouse and human" (2021) https://www.biorxiv.org/content/10.1101/2021.02.11.430759v1.full Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics.
Supplier-origin mouse microbiomes significantly influence locomotor and anxiety-related behavior, body morphology, and metabolism (2021) https://www.nature.com/articles/s42003-021-02249-0
Effects of water decontamination methods and bedding material on the gut microbiota (2018) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0198305
H2Oh No! The importance of reporting your water source in your in vivo microbiome studies (2018) https://www.tandfonline.com/doi/full/10.1080/19490976.2018.1539599
Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility (2018): https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.01598/full "Overall, our findings raise the possibility that previously reported microbiome-disease associations from murine studies conducted in a single facility may be heavily influenced by facility-specific effects."
Microbiota may contribute to unexplained variation either within or between experiments in a number of different, often difficult-to-predict, ways (2017) https://www.science.org/doi/10.1126/scisignal.aam9011
Replacing laboratory mice's gut microbiomes with the microbial communities of their wild counterparts alters the lab animals' immune systems and boosts their resistance to colorectal cancer development and influenza (2017) https://aacrjournals.org/cancerdiscovery/article/8/1/6/112824/Wild-Microbiome-Stems-Tumorigenesis-in-Lab Wild Microbiome Stems Tumorigenesis in Lab Mice.
Human microbiota-transplanted C57BL/6 mice and offspring display reduced establishment of key bacteria and reduced immune stimulation compared to mouse microbiota-transplantation (May 2020) https://www.nature.com/articles/s41598-020-64703-z
Impact of the gut microbiota on chemical risk assessment (2018): https://www.sciencedirect.com/science/article/pii/S2468202018300172 "Gut microbiota is an important factor to include in the interpretation of toxicological endpoints obtained by animal experimentation."
Behavioral response to fiber feeding is cohort-dependent and associated with gut microbiota composition in mice (2018) https://www.sciencedirect.com/science/article/abs/pii/S0166432818310684 - Two cohorts of C57Bl/6?J mice had distinct gut microbial communities after a fiber intervention. Differences in behavior were associated with differences in the microbiota. Microbiota variability may partly explain the reproducibility crisis in psychology.
"While fecal microbiota is partially normalized by extended co-housing, mucosal communities associated with the proximal colon and terminal ileum remain stable and distinct" https://www.cell.com/cell-reports/fulltext/S2211-1247(19)30488-7. Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models (2019).
Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity (2022) https://gut.bmj.com/content/72/5/896
Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility (2023) https://www.sciencedirect.com/science/article/pii/S0300908423000160
Batch effect exerts a bigger influence on the rat urinary metabolome and gut microbiota than uraemia: a cautionary tale (2019) https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0738-y "These results challenge the assumption that experimental animals obtained from the same supplier are metabolically comparable, and provide metabolomic evidence that batch-to-batch variations in the microbiome of experimental animals are significant confounders in an experimental study"
New Mouse Model Predicts Two Clinical Trial Failures in Humans. The lab animals had more natural microbiomes seeded by wild mice, unlike conventional models that are kept in sterile conditions. Laboratory mice born to wild mice have natural microbiota and model human immune responses (2019) https://www.the-scientist.com/new-mouse-model-predicts-two-clinical-trial-failures-in-humans--66223
Dogs:
Reivew, 2022: "The physiologies of the domestic dog and human are more similar than those of the human and mouse. Thus, the dog has the potential to be a useful animal model" https://www.mdpi.com/2076-2607/10/5/949 Domestic Environment and Gut Microbiota: Lessons from Pet Dogs.
"These findings suggest that dogs could be a better model for nutrition studies than pigs or mice and we could potentially use data from dogs to study the impact of diet on gut microbiota in humans" (2018): https://phys.org/news/2018-04-dogs-similar-humans-thought.html Similarity of the dog and human gut microbiomes in gene content and response to diet.
Pigs:
Microbial consortia that are responsible for degradation of these glycans differ substantially from the microbial consortia that degrade the same glycans in humans. https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0662-1 Metagenomic reconstructions of gut microbial metabolism in weanling pigs (Mar 2019).
Multiple:
Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces (2018) https://www.frontiersin.org/articles/10.3389/fmicb.2018.02897/full Based on β-diversity, the gut microbiota in humans seems to be closer to NHPs than to mice and rats; however, among rodents, mice microbiota appears to be closer to humans than rats. Also, fecal levels of lactate are higher in mice and rats vs. NHPs and humans, while acetate is highest in human feces.
FMT:
"In a systematic review, we found that 95% of published studies (36/38) on HMA rodents reported a transfer of pathological phenotypes to recipient animals. We posit that this exceedingly high rate of inter-species transferable pathologies is implausible. We advocate for a more rigorous and critical approach for inferring causality to avoid false concepts and prevent unrealistic expectations that may undermine the credibility of microbiome science and delay its translation" (Jan 2020) https://www.cell.com/cell/fulltext/S0092-8674(19)31387-X Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents.
"241 papers were analyzed. 92.5% reported a positive outcome with FMT intervention" https://www.tandfonline.com/doi/full/10.1080/19490976.2021.1979878 Guidelines for reporting on animal fecal transplantation (GRAFT) studies: recommendations from a systematic review of murine transplantation protocols (2021).