Table 1.

Studies investigating the microbiomes of mouse models of ALS

Study	Animal model	Numbers and phenotypes	Intervention/Hypothesis generating	Sample	Methodology	Outcomes
Wu, S., et al. 2015 [21]	SOD1G93A	3 mutant, 3 WT in each analysis.	Hypothesis generating	Faecal	16S microbe identification method on extracted DNA	Structural changes in intestines of ALS model mice: Abnormal tight junction structure; reduced levels of ZO-1 and E-cadherin proteins. Increased gut permeability. Increased number of abnormal Paneth cells. Decreased level of defensin 5 alpha (antimicrobial peptide). Changes in ALS mouse model microbiota. Reduction in butyrate-producing bacteria: Escherichia coli, Butyrivibrio fibrisolvens and Fermicus.
Zhang, Y.G., et al. 2017 [22]	SOD1G93A	~ 9 per group in each analysis NB: in most cases groups are SOD1G93A vs SOD1G93A plus butyrate, with WT controls included in some analyses.	Interventional	Faecal	16S microbe identification method on extracted DNA. Intervention: 2 groups, one with 2% sodium butyrate added to water stock, the other without.	Butyrate treatment: Delayed disease onset and increased lifespan. Restored levels of butyrate-producing bacteria in gut. Reduced intestinal permeability and corrected structural changes in the ALS model.
Haney, M.M., et al. 2018 [24]	SOD1G93A (mild form with low expression of transgene)	30 mutant, 30 WT. All 5 month-old animals, which is 1 month prior to disease onset in this model.	Hypothesis generating	Faecal	16S microbe identification method on extracted DNA. Ventral neck surgery enabling stimulation of vagus nerve for 1 h. Control treatment groups: surgery plus 1 h sham treatment and no surgical intervention. Faecal pellets collected prior to surgery (day 0) and 8 days later.	Found no difference between the gut microbiomes of the mutant and WT animals at any time point. Found no difference between the gut microbiomes of any treatment group. Therefore conclude that short vagus nerve stimulation has no long-term impact on composition of gut microbiota.
Blacher, E., et al. 2019 [17]	SOD1G93A	n numbers vary from 5 to 62 depending on analysis.	Both	Faecal	16S microbe identification method and shotgun metagenomic sequencing on extracted DNA. Intervention: treatment with Akkermansia muciniphila.	Identified changes in the gut microbiota of ALS model mice prior to onset of motor dysfunction. Correlate 11 bacteria with disease severity. Evidence that Akkermansia muciniphila has a protective effect on the host whereas Ruminococcus torques and Parabacteroides distasonis are associated with increased disease severity. Akkermansia muciniphila therapy improves disease outcomes. Observed differences in microbiota in different facilities.
Figueroa-Romero, C., et al. 2019 [23]	SOD1G93A	~  8 per group for each separate comparison	Hypothesis generating	Faecal	Longitudinal study with the following aspects assessed in parallel: gut microbiome, immunophenotyping, motor function testing and histology of tissue samples. 16S microbe identification method on extracted DNA	Identified changes in the gut microbiota of ALS model mice prior to onset of motor dysfunction, muscle atrophy and activation/expansion of immune cells. Found evidence that microbiome changes and immune responses are related. Noted that SOD1G93A mutant mice have different life expectancies at different facilities.
Burberry et al. 2020 [18]	C9ORF72-null mutant mice (+/+, +/−, −/−)	Range between experiments from 10 to 114 of a given mutant genotype, but mostly between 10 and 25.	Both	Faecal	The following aspects were analysed: Gut microbiome, immunophenotyping, inflammatory markers, motor function. 16S microbe identification method on extracted DNA. Faecal transfer intervention post antibiotic treatment.	Evidence that gut microbiota plays role in pathology of C9ORF72 genetic subtype of ALS: Inflammation/immunological phenotypes significantly reduced when certain bacterial groups are absent or at low abundance. Noted that the heterozygote and double negative C9ORF72-null mutant mice have different life expectancies at different facilities.