Table 3.

Microbiome studies in ALS experimental models.

Study	Key Bacterial changes	Sample size	Methods	Reference
Leaky intestine and impaired microbiome in SOD1 G93A	Reduced butyrate-producing bacteria (Butyrivibrio Fibriosolvens), E. coli, and Fermicus in ALS mice at the age of 2 months	SOD1 G93A mice and age-matched wild-type mice	Western blot analysis, immunofluorescence, ELISA, real-time qPCR, fetal microbiome sequencing	https://pubmed.ncbi.nlm.nih.gov/25847918/
Target Intestinal microbiota to alleviate disease progression in ALS	Butyrate treatment significantly increased Butyrivibrio species, also significantly increased Bacteroide, Odoribacter, Eubacterium, significantly depleted Tannerella	SOD1 G93A and age-matched wild-type mice	Western blot analysis, immunofluorescence, cell transfection and live cell imaging, real-time qPCR	https://pubmed.ncbi.nlm.nih.gov/28129947/
Effects of Intraoperative Vagal Nerve Stimulation (VNS) on the microbiome in SOD1 G93A mice	In all mice, the most abundant bacteria were in the Bacteroidales group and the bacterial families of Rikenellaceae and Lachnospiraceae. VNS did not change the microbiome in the SOD1 G39A mice.	30 SOD1G93A mice and 30 age-matched WT controls	Vagal nerve surgical stimulation, fecal collection, DNA extraction, rRNA sequencing	https://pubmed.ncbi.nlm.nih.gov/30424824/
Microbiome, immune system and epigenome with disease progression in SOD1 G93A mice.	In the ileum, Firmicutes were more abundant than Bacteroidetes in SOD1G93A mice versus WT mice. At 90 days, Firmicutes were less abundant than Bacteroidetes in SOD1 G93A mice versus WT mice. In feces, Firmicutes were more abundant in SOD1G93A mice aged 37 and 60 days compared to WT mice. Bacteroidetes were more abundant in colon from the SOD1G93A 60-day-old mice.	8 30-day-old SOD1G93A mice and WT control littermates for each comparison	Motor function assessed using rotarod, collected fecal and intestinal content samples, isolated bacterial DNA for sequencing, blood, brain, spleen, and spinal cord leukocytes collected, bone marrow collected, flow cytometry	(Figueroa-Romero et al., 2019) https://pubmed.ncbi.nlm.nih.gov/31597644/
C9orf72 suppresses systemic and neural inflammation induced by bacteria	Helicobacter, Pasteurella pneumotropica, Tritrichomonas muris were significantly more common in C9orf72(Harvard) mice than in C9orf72(Broad) mice. Helicobacter were found in both pro-inflammatory environments but were not found in pro-survival environments.	Range between experiments from 10 to 114;C9orf72+/+, C9orf72+/-, C9orf72-/- mice	Motor behavior assessed using rotarod, fecal pellets and intestinal contents collected, immunofluorescence, flow cytometry, PCR	https://pubmed.ncbi.nlm.nih.gov/32483373/
Longitudinal studies of ENS, SOD1G93A aggregation, and microbiome modulation by butyrate or antibiotics	Butyrate or antibiotic treatment resulted in a significantly longer latency to fall in the rotarod test, reduced SOD1G93A aggregation, and enhanced enteric neuromuscular function. Feces from 2-month-old SOD1G93A mice significantly enhanced SOD1G93A aggregation in human colonoids transfected with a SOD1G93A-GFP plasmid. Longitudinal studies of microbiome data showed the altered bacterial community related to autoimmunity (e.g., Clostridium sp. ASF502, Lachnospiraceae bacterium A4), inflammation (e.g., Enterohabdus Muris), and metabolism (e.g., Desulfovibrio fairfieldensis) at 1- and 2-month-old SOD1G93A mice, suggesting the early microbial contribution to the pathological changes.	Presymptomatic and symptomatic	Wild-type and mSOD1 G93A mice with butyrate or antibiotic treatment, from 6-20 mice per comparison Human colonoids transfected with a SOD1G93A-GFP plasmid	(Zhang et al., 2021)
Gut microbiome and metabolites in modulating ALS in mice	Addition of E.coli nadA-/- decreased hanging-wire grip test performance and worsened neurological score in SOD1 mice compared to WT mice. Adding P. distasonis and R. torques exacerbated progression of the disease. A. muciniphila improves motor neuron degeneration and increases lifespan in SOD1 mice. Mice given A. muciniphila accumulate nicotinamide in the central nervous system. Nicotinamide alone had a limited protective role to slow the disease progression. Facility-dependent changes of microbiome were found, suggesting that genetic susceptibility to ALS and a locally prevalent microbial signature drive early dysbiosis.	For mice, varies with experiment. Pooled results = ~10-30 mice	For mice, depleting the microbiome and quantifying motor abilities, DNA sequencing, mono-inoculating 11 strains of bacteria into mice, untargeted metabolomic profiling.	https://pubmed.ncbi.nlm.nih.gov/31330533/