ISCs and their relationship with the intestinal microbiota: a feasible pathway to alleviate intestinal diseases. The intestine harbors multiple microbial communities that coexist and closely interact with ISCs. Microbial communities and ISCs jointly play key roles in modulating intestinal disorders. The intestinal microbiota can affect the mucosa immune system and regulate ISCs. PRRs, especially TLRs and NLRs, regulated by the intestinal microbiota are capable of regulating the ISC niche downstream. Microbial communities involved in this pathway include but are not limited to Fusobacteria, Proteobacteria, Firmicutes, Lachnospiraceae, Coriobacteria, Helicobacter pylori, and Vibrio cholerae. Bacteria, such as Serratia marcescens, Erwinia carotovora carotovora‐15, and Pseudomonas entomophila, participate in intestinal homeostasis maintaince, injury repair and ISC status via these pathways. AhR, aryl hydrocarbon receptor; Bmi1, B cell‐specific Moloney murine leukemia virus integration site 1; cAMP, cyclic adenosine monophosphate; DSS, dextran sulfate sodium; IL‐22, interleukin 22; ISC, intestinal stem cell; Lgr5, leucine‐rich repeat‐containing G protein‐coupled receptor 5; LRP6, lipoprotein receptor‐related protein 6; NLRs, NOD‐like receptors; NOD2, nucleotide‐binding oligomerization domain 2; PKA, protein kinase A; PRR, pattern recognition receptor; Reg3, antimicrobial‐regenerating islet‐derived 3 lectins; ROS, reactive oxygen species; TLRs, Toll‐like receptors; TNF‐α, tumor necrosis factor alpha; Upd, uniparental disomy.