Chronic diseases refer to diseases that have a slow onset, slow progression, long course, and usually cannot be completely cured. In the past few years, the role of gut microbiota in related diseases has been extensively studied, such as ulcerative colitis [
1], irritable bowel syndrome [
2], diabetes [
3], Alzheimer's disease [
4], non-alcoholic fatty liver disease [
5], obesity [
6]. In this case, the role of probiotics becomes particularly important. By regulating the balance of gut microbiota, it is possible to maintain the stability of the gut environment, enhance intestinal barrier function, reduce gut inflammation levels, and help regulate energy metabolism and insulin sensitivity [
7,
8,
9]. For example, in obese individuals, the diversity of the gut microbiota is decreased, which is usually accompanied by changes in key species [
6,
10,
11,
12,
13], like
Firmicutes and
Bacteroidetes [
14,
15]. Diabetes mellitus type 2 (T2DM) is characterized by an impaired gut microbiota [
16,
17], and
Akkermansia and
Enterobacter have been found to have a causal role in the onset and progression of T2DM [
18]. Nonalcoholic fatty liver disease (NAFLD) is regarded as a typical metabolic disorder at the intersection of obesity, metabolic syndrome and T2DM [
19], often with a proliferation of
Enterobacteriaceae and
Escherichia coli [
20]. Dysbiosis of the gut microbiota has also been associated with inflammatory bowel disease (IBD), including encompassing three main phenotypes-Crohn disease (CD) and ulcerative colitis (UC) and IBD unclassified (IBDU) [
21]. There are common microbial patterns among IBD patients, manifested at the phylum level as a loss of
Firmicutes [
22,
23,
24], an increase in
Proteobacteria and potential pathogenic bacteria [
25,
26,
27,
28], At the genus level,
Clostridium and
Escherichia coli were significantly increased in IBD, whereas
Phascolarctobacterium,
Faecalibacterium, and
Roseburia intestinalis were significantly decreased [
27,
29,
30,
31,
32]. The gut-brain axis plays an important role in neurological diseases including Alzheimer's disease (AD), anxiety, and depression. The gut microbiota is linked to central nervous system in a variety of ways, including regulation of immune responses, formation of metabolites (e.g., short-chain fatty acid), and synthesis of neurotransmitters (e.g., serotonin and dopamine). Now some studies have shown that some microorganisms can regulate intestinal homeostasis and hinder the progression of neurological diseases [
33,
34,
35,
36,
37,
38,
39,
40,
41]. In fact, diet is the main determinant that drives the growth of gut microbiota and regulates its interaction with the host. The lack of sufficient functional microbiota and accessible carbohydrates (MAC) is the main reason for the disappearance of important species that regulate intestinal homeostasis [
42,
43]. Indigestible oligosaccharides (NODs) are typical MAC that are easily broken down by
Bacteroides and
Lactobacillus containing metabolic enzymes. The use of oligosaccharide fermentation to improve intestinal health is a widespread and current focus [
44,
45]. The beneficial effects and promising prospects of NODs on the host by targeting the gut microbiota and microbial metabolites are now generally accepted [
46,
47,
48,
49,
50], including improvement of bowel movements, suppression of appetite, enhancement of postprandial glycemic response and promotion of mineral absorption. This article describes the structure and sources of NODs, as well as the factors affecting the microbial fermentation of NODs, and then elucidates the important role of oligosaccharides in chronic diseases by regulating the gut microbiota.