Recent studies have identified a larger role of gut microbiota in gut-immune homeostasis and in intestinal pathology. The human intestinal microbiota is dominated by five phyla: Bacillota (aka Firmicutes), Bacteroidota, Actinomycetota (aka Actinobacteria), Pseudomonadota (aka Proteobacteri), and Verrucomicrobiota [
122]. In contrast, the intestinal microbiota of mice is dominated by four phyla: Bacillota, Bacteroidota, Deferribacterota, and Pseudomonadota [
123], where the phylum Deferribacterota is in high abundance and the phyla Actinomycetota and Verrucomicrobiota are in low abundance compared to humans. In human adults, more than 80% of the species belong to just two phyla: Gram-negative Bacteriodota and Gram-positive Bacillota (aka Firmicutes). In mouse colonic mucosa samples, 19 phyla were identified [
124]. The high-abundant (≥1%) phyla included Bacillota, Bacteroidota, Deferribacterota, and Pseudomonadota [
124] (
Figure 7). The low-abundant (<1%) phyla included the following: Actinomycetota (aka Actinobacteria), Parcubacteria (aka OD1), Saccharibacteria (aka TM7), Omnitrophota (aka OP3), Acidobacteriota, Armatimonadota, Chlamydiae, Chlorobiota, Cyanobacteria, Fibrobacterota, Mycoplasmatota (aka Tenericutes), Lentisphaerota, Planctomycetota, Spirochaetes, and Verrucomicrobiota) [
124] (
Figure 7). Although CST failed to alter bacterial populations in the four high-abundant phyla, it altered colonic mucosa-associated bacterial community composition at lower taxonomic levels. Thus, CST showed a positive association with Orders including Bacteroidales, Clostridiales, and YS2; Families including Chitinophagaceae, Clostridiaceae, Coriobacteriaceae, Pseudomonadaceae, Rikenellaceae, and Ruminococcaceae; and Genera
Bifidobacterium and
Stenotrophomonas [
124]. Fecal samples identified 10 phyla including the high-abundant (≥1%) Bacillota, Bacteroidota, Pseudomonadota, and Deferribacterota and low-abundant (<1%) Actinomycetota, Cyanobacteria, Fibrobacterota, Saccharibacteria, Mycoplasmotota and Verrucomicrobiota [
124]. The relative abundance of Bacteroidota was observed to increase significantly after CST treatment. In contrast, CST was learned to cause a marked decrease in Bacillota population. Like mucosal samples, fecal samples disclosed positive associations with the Class Alpharoteobacteria; Orders including Bacteroidales, RF32, and YS2; and genera
Prevotella,
Bacteroides,
Ovatus,
Parabacteroidesdistarosis,
Parabacteroides, and
Dorea (
Figure 7).
Bacteroides and
Parabacteroides species, representing ~25% of the colonic microbiota, transform simple and complex sugars into volatile short-chain fatty acids (SCFAs) such as acetate, butyrate, and propionate [
125,
126,
127], which are absorbed in colon as a nutrient [
128,
129,
130]. Besides colonic nutrients, SCFAs are well established for their roles in accelerating gut transit time via release of serotonin [
131,
132,
133,
134]. SCFAs also release glucagon-like peptide 1 (GLP1) from the enteroendocrine L-cells [
135,
136,
137,
138] and improve insulin sensitivity [
139,
140,
141].
Bacteroides thetaiotaomicron produces significant amounts of glycosylhydrolases, which prevent obesity [
142]. Other
Bacteroides species are also reported to prevent obesity and increase insulin sensitivity [
143,
144,
145,
146]. Furthermore,
Bacteroides fragilis produces zwitterionic polysaccharide, which activates CD4
+ T cells to produce interleukin 10 (IL-10). IL-10 plays crucial roles in preventing abscess formation and other unchecked inflammatory responses [
142,
147,
148]. Negative association of CST was reported for the Class Clostrida, Families Bacteroidaceae and Ruminococcaceae, and Genera
Adlercreutzia and
Allobaculum [
124]. Interestingly, the functional correlation between different CST mutants across species and their respective microbiota remains elusive. It is important to decipher the effect of different CST mutant on microbial diversity between species.