Table 4.

Microbiome studies in patients with ALS.

Study	Key Bacterial changes	Sample size	Methods	Reference
Microbial diversity in ALS	Bacteroidetes, bacteroidia, bacteroidales, and dorea were significantly higher in ALS patients. A significant decrease of Oscillibacter, Anaerostipes, and Lachnospiraceae in ALS patients compared to controls.	Six ALS patients and five healthy people without ALS	Extracted genomic DNA and high-throughput sequencing.	https://pubmed.ncbi.nlm.nih.gov/27703453/
The alteration of gut microbiome and metabolism in ALS patients	Increases in Bacteriodetes, Kineothrix, Parabacteroides, Odoribacter, Sporobacter, Eisenbergiella, Mannheimia, Anaerotruncus, unclassified Porphyromonadaceae in ALS patients. Significant reduction in Firmicutes and Megamonas in ALS patients compared to control patients.	20 patients with probable or definite ALS and 20 healthy controls	16s rRNA sequencing; Shotgun sequencing (consisting of 10 ALS patients and 10 controls; Metabolomics analysis.	https://pubmed.ncbi.nlm.nih.gov/32747678/
The fecal microbiome of ALS patients	Different proportions of Ruminococcaceae	25 ALS patients (2 familial, 23 sporadic) and 32 controls	Fecal samples collected, extraction of nucleic acids, qRT-PCR, 16S rRNA sequencing analysis	https://pubmed.ncbi.nlm.nih.gov/29065369/
Gut inflammation and dysbiosis	A low Firmicutes/Bacteroidetes ratio and low Ruminococcus spp. in ALS patients 1,3, and 5, low Clostridium spp. and Roseburia spp. in patient 1, high Bacteroides-Prevotella, Odoribacter spp. Barnesiella spp., and Bacteroides vulgatus in patient 5, and high Bacteroides vulgatus in patient 3	5 ALS patients and 96 healthy individuals	Collected stool samples, commensal bacteria PCR, bacterial and mycological cultures, mass spectrometry, enzyme immunoassay	https://pubmed.ncbi.nlm.nih.gov/28947596/
A prospective longitudinal study on the microbiota composition in ALS	longitudinal study addressing the microbiota composition in ALS patients and the role of a probiotic supplementation on the gut microbiota and disease progression. Lower Clostridium and higher E. coli and Enterobacteriaceae were detected in ALS patients. Members of the Cyanobacteria phylum were significantly higher in ALS patients. The control group showed a higher relative abundance of Veillonellaceae, Promicromonosporaceae, and Peptostreptococcaceae.	50 ALS patients and 50 matched controls	DNA extraction from fecal samples, quantitative PCR, PCR-DGGE	(Di Gioia et al., 2020) https://pubmed.ncbi.nlm.nih.gov/32546239/
Assessment of bidirectional relationships between 98 genera of the human gut microbiota and ALS	OTU10032 unclassified Enterobacteriaceae was associated with a higher risk of ALS. Unclassified Acidaminococcaceae was associated with a higher risk of ALS. Gamma-glutamylphenylalanine showed a significantly increased risk of ALS. Two metabolites, 1-arachidonoyl-GPI and 3-methyl-2-oxobutyrate, were associated with a higher risk of ALS. A genetically predicted increase in the levels of 4-acetamidobutanoate may lower the risk of ALS. Genetically predicted ALS was associated with an increase in the relative abundance of OTU4607_Sutterella and Lactobacillales_order.	98 genera of gut microbiota, GWAS of ALS involving 20,806 patients and 59,804 controls of European ancestry	Genome wide association study, Mendelian randomization analysis, identification of independently significant SNPs	https://pubmed.ncbi.nlm.nih.gov/34979977/
The human gut microbiota in people with ALS	There was a significantly lower abundance of both Roseburia intestinalis and Eubacterium rectale in patients in their first year of diagnosis compared to healthy controls. These results were similar to patients who were not taking Riluzole at the time of sample collection, and patients not using a gastrostomy tube. The relative abundance of the family Lachnospiraceae was lower in ALS patients compared to healthy controls, but the results were not statistically significant. The total relative abundance of the eight dominant butyrate producers was significantly lower in ALS patients compared to controls. A higher abundance of butyrate-producing bacteria was associated with a significantly lower risk of ALS.	66 patients with ALS, 61 healthy controls, 12 neurodegenerative controls	Clinical information was collected, stool sample self-collected, DNA and RNA extraction, metagenomic shotgun sequencing and profiling, ribosomal sequencing and profiling	https://pubmed.ncbi.nlm.nih.gov/33135936/
The Gut Microbiota-Immunity Axis in ALS: A role in deciphering disease heterogeneity	ALS patients displayed lower amounts of cytokines IL-15, IL-8, MCP-1 and VEGF-A compared to healthy controls ALS patients with a classical phenotype showed a lower microbial diversity compared to others	19 ALS patients and 9 healthy family caregivers matched for sex and closely aligned age	Fecal samples collected, tested 30 cytokines using Luminex MAGPIX detection system, qualitative and quantitative evaluation of SCFAs, genomic DNA extraction and sequencing	https://pubmed.ncbi.nlm.nih.gov/34209688/
Progression and Survival of patients with motor neuron disease relative to their fecal microbiota	There were no significant differences in the distribution of bacteria, Proteobacteria, and F/B between ALS patients and controls. ALS patients with greater richness and evenness of their fecal microbiome had worse survival from the onset of their symptoms than ALS patients who had a decreased richness and evenness.	64 patients with ALS and 74 controls (spouses, friends, or family members of ALS patients)	Measurements of whole-body composition and resting energy expenditure, fecal sample collection, DNA extraction, and 16s rRNA amplicon sequencing	https://pubmed.ncbi.nlm.nih.gov/32643435/
Bacterial and archaeal communities, butyrate concentration analyses in ALS patients	The richness and evenness of bacterial and archaeal communities of healthy controls was “healthier” than those found in ALS patients. The average relative abundance of phylum Firmicutes in ALS patients was 4.7% higher than the relative abundance in controls. The relative abundance of Negativicutes and Bacili on the class levels were decreased in ALS patients compared to controls. The relative abundance of phylum Euryarchaeota, class Methanobacteria and genus Methanobrevibacter was significantly increased in ALS patients. There was no significant difference in fecal butyrate concentration between patients with ALS and healthy controls.	8 patients with ALS and 8 healthy individuals	Fecal samples collected, PCR amplification, enzyme linked immunosorbent assay (ELISA), fecal metabolites, endotoxin, short-chain fatty acids, NO2-N/NO3-N, and γ-aminobutyric acid, were evaluated by spectrophotometry	https://pubmed.ncbi.nlm.nih.gov/31306225/
Potential roles of gut microbiome and metabolite nicotinamide in modulating ALS	Confirm the dysbiosis and aberrant metabolism of nicotinamide in the ALS patients. Significant alterations in key molecules of the tryptophan–nicotinamide metabolic pathway in sera of patients with ALS—among them indoleacetate, kynurenine, serotonin and circulating nicotinamide.	37 human ALS patients and 29 age-matched controls	For human patients, collected their stool samples and sequenced their gut microbiome metagenomes, targeted serum metabolomics	https://pubmed.ncbi.nlm.nih.gov/31330533/
Gut microbiome differences between ALS patients and spouse controls	ALS patients lacked ASVs of the Prevotella genus compared to their spouses, particularly P. timonensis. There was no difference in stool and plasma inflammatory biomarkers between ALS patients and their spouses. ALS patients had a difference in beta diversity from their spouses. Butanoate metabolic pathway enzymes were missing in patients with ALS.	10 individuals with ALS and their spouses and 10 healthy couples	Rectal and blood sample collection, DNA extractions and 16s rRNA gene sequencing, measurement of inflammatory markers, enzyme linked immunosorbent assay (ELISA) bioinformatics	https://pubmed.ncbi.nlm.nih.gov/33818222/
Potential Role of Gut Microbiota in ALS Pathogenesis and Possible Novel Therapeutic Strategies	There was a lower DNA concentration in ALS patients compared to the healthy controls. There was a low abundance of Clostridium and yeast and a high abundance of E. coli and Enterobacteria in ALS patients compared to controls. There was a clear cluster division between the bacterial profiles of ALS patients compared to the healthy controls. There was no association between yeast profiles and the presence or absence of ALS.	50 ALS patients and 50 healthy controls, matched for sex, age, and origin	Fecal sample collection, total genomic DNA extraction, PCR-denaturing gradient gel electrophoresis analysis, quantitative pCR, double-blind treatment of ALS patients	https://pubmed.ncbi.nlm.nih.gov/29782468/