The Lactobacillus genus comprises of over 200 physiologically diverse gram-positive, non-spore forming lactic acid bacteria. Despite its positive association with T2DM, Lactobacillus species such as Lactobacillus paracasei (63), Lactobacillus fermentum (64) Lactobacillus acidophilus and Lactobacillus rhamnosus (65, 66) have demonstrated anti-inflammatory properties or benefits on host metabolism as a combination probiotic with Bifidobacterium lactic (65, 66).

The positive association of Lactobacillus with T2DM may therefore be driven by Metformin. Metformin, a first-line antihyperglycemic agent for treatment of T2DM, may alter bacterial abundances depending on the taxon’s resistance or sensitivity to the drug. In 2015, using 784 human gut metagnomes, Forslund et al. confirmed this positive association between metformin and Lactobacillus (55).

Among the eleven studies that reported an increase in Lactobacillus abundance (15–17, 21, 33, 49–54), only three studies (21, 50, 52) accounted for metformin use. Among these, one study found higher Lactobacillus levels regardless of metformin use (50), one found higher levels only in participants on unspecified oral antihyperglycemic agents (21), while the last study found no difference when accounting for metformin (52). More studies on treatment naïve T2DM or controlled for Metformin use are warranted.

The Escherichia-Shigella genus, part of the family Enterobacteriaceae, includes multiple opportunistic pathogens (67). These gram-negative bacteria produce proinflammatory components such as lipopolysaccharide (LPS) and peptidoglycans, leading to intestinal and systemic inflammation (12). This systemic inflammation and consequent insulin resistance are key drivers for T2DM.

Unsurprisingly, Escherichia-Shigella abundance correlates with variables related to diabetes and obesity, including insulin resistance, diminished beta cell function (56), fasting glucose (41), HBA1c and BMI (47). This genus has been implicated in T2DM complications such as peripheral neuropathy (68), autonomic neuropathy (69), retinopathy (70), diabetic nephropathy (71) and chronic diabetic foot infections (72). Escherichia-Shigella has also been associated with an increasing abundance from healthy controls, pre-diabetes to T2DM (56). An increase in Escherichia-Shigella has also been associated with metformin use (13, 73). The outlier study that reported decreased Escherichia-Shigella abundance may be due to dietary or environmental differences (36).

Subdoligranulum are anaerobic, spore-free gram-negative bacteria (12). This genera remains relatively underexplored and has only two known species - Subdoligranulum variabile and Subdoligranulum didolesgii. Four studies (12, 30, 32, 38) found Subdoligranulum more common in T2DM ( Table 4 ) while two studies reported a negative association between T2DM and Subdoligranulum variabile (46, 74). These discrepancies may be related to species-specific properties.

Subdoligranulum has been linked to both promotion (75) and reduction of chronic inflammation (74). Subdoligranulum didolesgii has been associated with rheumatoid arthritis by triggering synovitis, while Subdoligranulum variabile has anti-inflammatory properties through short chain fatty acid (SCFA) production. Decreased levels of Subdoligranulum variabile in T2DM individuals may be suggestive of an overall state of inflammation (46).

Subdoligranulum’s positive association with T2DM may be influenced by metformin use (55). Of four studies reporting increased Subdoligranulum, two did not report metformin use (12, 32), one excluded metformin users (30), and one found an increase regardless of metformin use (38).

Enterococcus are gram-positive facultative anaerobic cocci found in intestinal microbiota and on the skin. Some species are opportunistic pathogens causing severe infections such as bacterial endocarditis and spontaneous bacterial peritonitis, while others (Enterococcus durans) produce anti-inflammatory SCFAs (76).

Enterococcus may contribute to the development of T2DM through two mechanisms. Firstly, Enterococcus faecalis secretes matrix metalloprotease gelatinase causing chronic intestinal inflammation and impaired gut barrier integrity (77), leading to systemic inflammation. Secondly, Enterococcus has been linked to impaired glucose homeostasis. Associations include higher HBA1c (16, 27), fasting (27) and post prandial (16) glucose levels, and impaired beta cell function (27). Mechanistically this may relate to overgrowth of enterococcus leading to proportional decreases in beneficial anti-inflammatory bacteria (50).

Fusobacterium are anaerobic gram-negative rod bacteria. Similar to Enterococcus, this genus is part of the regular colorectal microbiota. Fusobacterium, in particular Fusobacterium nucleatum, has been associated with increased production of inflammatory cytokines such as IL-6, IL-8, TNF-α and COX-2 (78). This may contribute to the chronic inflammatory state seen in T2DM. Fusobacterium has also been associated with diabetic nephropathy (79) and its species found increased among individuals with T2DM (23, 44).

Akkermansia is gram-negative bacterium belonging to the Verrucomicrobia phylum. Akkermansia mucinphilia, a symbiont microbe colonizing the human intestinal mucosal barrier, is a promising next generation probiotic. It plays a critical role in the maintenance of intestinal barrier, production of anti-inflammatory cytokines and SCFA benefiting host metabolism. In diabetic rat models, administration of live attenuated Akkermansia reduced oxidative stress, lipotoxicity, LPS and inflammation (80). In individuals with T2DM, combined probiotics containing Akkermansia muciniphila reduced HBA1c and postprandial glucose control (81).

Reduced levels of Akkermansia mucinphilia are associated with T2DM. Akkermansia is inversely correlated with HBA1c and fasting glucose and positively with anti-oxidants (41).

Bifidobacterium is a dominant non-spore-forming, gram-positive taxa that help maintain balances between the various intestinal floras (82). Key Bifidobacterium species include Bifidobacteroim bifidum, Bifidobacterium adolescentis and Bifidobacterium longum. These species have been used as probiotics in humans (65, 66, 83) and administered in animal studies (84, 85) leading to reduced cytokine production and improved metabolic parameters such as glucose and HBA1c (66, 84).

Apart from SCFA production, in vivo and in vitro studies show that Bifidobacterium administration markedly decreased intestinal permeability by increasing tight junction expression and reducing inflammatory cytokines such as IL-6 and TNF-α (86). This reduces metabolic endotoxaemia, systemic inflammation and may explain its overall negative association with T2DM ( Table 5 ). An increase in Bifidobacterium has been attributed to antihyperglycemic agents (16) or a U shaped association with T2DM (26, 59).

Bacteroides is a gram-negative obligate anaerobic taxa constituting approximately 25% of the intestinal gut microbiota. As commensals, these taxa generally maintain a beneficial relationship with the human gut. Overall, Bacteroides species including Bacteroides fragilis, Bacteroides thetaiotamicron, Bacteroides vulgutas or Bacteroides dorei have been associated with a protective effect against T2DM through anti-inflammatory properties (87) and an improved gut barrier integrity from mucus (88) and SCFA production (89). Bacteroides species also have a structurally different LPS that is less pro-inflammatory than classical enterobacterial LPS (90). Discrepancies in Bacteroides abundance ( Table 5 ) may be due to the bacteriostatic and bactericidal effect of metformin (55) or potential pathogenic Bacteroides species that can contribute to chronic inflammation (39).

Roseburia is a gram-positive, SCFA-producing member of the Firmicutes phylum that inhabits the human colon. Roseburia has been identified as a pathognomonic bacteria in T2DM (91) with significant lower levels in participants. Reduced species include Roseburia hominis (23, 46), Roseburia intestinalis and Roseburia inulinivorans (32, 53, 55). Roseburia improves glucose homeostasis and intestinal permeability through SCFA production and anti-inflammatory properties (92). Gut microbiota transplantations from lean donors to recipients with metabolic syndrome led to increased fecal Roseburia and butyrate levels, correlating with improved insulin sensitivity (93).

Faecalibacterium are human gut colonizers and well-known SCFA producers. Faecalibacterium and Faecalibacterium prausnitzii were consistently reduced in T2DM ( Table 5 ), with the later being highly discriminant (91). In mice, Faecalibacterium prausnitzii administration was associated with improved glucose levels and HBA1c, making it a promising orally administered probiotic (94). Faecalibacterium is negatively associated with HBA1c (39).

Prevotella has been linked to both pathogenic effects including systemic inflammation and insulin resistance (95) and beneficial effects like SCFA production (96) and reduced gut permeability via increased production of tight junction proteins (97). Prevotella is negatively correlated with HBA1c (16, 41, 98), but positively with blood glucose (10, 41). The discrepancies within the Prevotella genus may be due to diet (24) and genetic diversity within its species (99).

The intestinal lining composed of epithelial cells assisted by tight junctions (TJ), acts as a physical barrier against microorganisms and antigens. TJ controls intestinal permeability (104). In T2DM, reduction in beneficial microbes Bacteroides, Bifidobacterium, Faecalibacterium, Roseburia and Akkermansia, leads to decreased gene expression and therefore reduced localization, production, and distribution of TJ proteins. This results in increased gut permeability.

Mouse studies show that pre-treatment with Bifidobacterium (86), Bacteroides vulgatus, Bacteroides dorei (105) or Prevotella histicola (97), upregulates TJ genes leading to reduced intestinal permeability and inflammation. Bacteroides fragilis (106–108), Bacteroides facies (109), Bifidobacterium bifidum (110), Bifidobacterium adolescentis (111) and Bifidobacterium longum (112) have also been found to increase TJ proteins.

Faecalibacterium prausnitzii and Roseburia intestinalis reduce gut permeability by production of butyrate and upregulation of TJ proteins (89, 109). Butyrate is essential for colonic epithelial cells, offering anti-inflammatory properties and protecting against pathogens (30). In db/db mice, Faecalibacterium prausnitzii also produces microbial anti-inflammatory molecule, increasing TJ expression and restoring the damaged intestinal barrier (113).

Akkermansia muciniphila decreases gut permeability by promoting TJ protein expression via its outer membrane protein Amuc_1100. Additionally, it improves intestinal TJ via AMPK activation in the epithelium (114) and modulation of the endocannabinoid system (115).

Less understood are the bacteria Rumincoccaeceae and Blautia which may be associated with increased gut permeability (116). Further studies are needed to confirm these findings and understand their mechanisms.

There is growing evidence that the endocannabinoid system regulates intestinal inflammation and mucosal barrier permeability, thus influencing T2DM pathophysiology.

The endocannabinoid system, historically associated with cognitive and emotional processes, also regulates intestinal inflammation. The two main endocannabinoids are anadamide (AEA) and 2 arachidonylglycerol (2-AG). They act primarily through cannabinoid receptors CB1R and CB2R. CB1R is expressed in gastrointestinal epithelial cells and myenteric and submucosal plexuses while CB2R may be found on enteric neurons (117).

Overactivation of CB1R via AEA and 2-AG leads to increased gut permeability (117). In T2DM mice models, CB1R antagonists were shown to decrease gut permeability by reducing inflammation and alterations in TJ proteins (118). Akkermansia muciniphila antagonises CB1R through its outer membrane protein Amuc_1100, reducing gut permeability, LPS levels and systemic inflammation (115). Bacteroides fragilis also affects epithelial barrier permeability through the endocannabinoid system (119).

Oxidative stress, inflammation, and insulin secretion contribute to T2DM and its complications. Although unrelated to gut permeability, CB2R activation decreases inflammation and oxidative stress and promotes pancreatic insulin secretion via calcium signal regulation (120). This suggests potential benefits of CB2R agonists in T2DM management.

SCFAs are produced by gut microbiota from non-digestible carbohydrates. They provide energy to colonocytes, reduce inflammation and regulate satiety (121). The most common SCFAs are acetate, propionate and butyrate, and are predominantly produced by anaerobic Bacteroidetes and Firmicutes phyla.

SCFAs have multiple beneficial effects such as maintaining gut permeability, modulating host metabolism and anti-inflammatory effects. Reduced levels of SCFA-producing bacteria including Bacteroides, Bifidobacterium, Faecalibacterium, Prevotella and Akkermansia. are associated with T2DM. This is reflected by the reduced acetate (38), propinionate (38, 98), butyrate (38, 98) and other SCFA (38, 51) concentrations in T2DM fecal samples. Functional analysis of gut microbiota showed reduced SCFA-producing pathways in T2DM compared to controls (61).

Individuals with T2DM related complications had lower SCFA fecal concentrations than those without complications (38). Increased dysbiosis severity and reduced production of SCFA may contribute to the development and progression of T2DM complications.

Bile acids, known for their role in digestion of dietary fats, have recently gained attention due to their possible influence on metabolic processes, particularly in the context of T2DM. Primary bile acids (PBAs), cholic acid (CA) and chenodeoxycholic acid (CDCA) are synthesized from cholesterol in hepatocytes and released into the duodenum. They are then uncoupled by bile saline hydrolysase before being converted into more hydrophobic secondary bile acids (SBAs) through bile acid deconjugation and the rate limiting 7α-dehydroxylase enzyme. Bacteroides and Enterococcus are involved in the initial deconjugation, while Bifidobacterium, Lactobacillus and Enterococcus utilize bile saline hydrolase. Meanwhile, selected bacteria from the Lachnospiraceae and Ruminococcaceae family perform the subsequent 7α-dehydroxylase conversion of CA and CDCA to generate the SBAs deoxycholic acid (DCA) and lithocholic acid (LCA) respectively (130). The abundance of these bacteria are described in Table 8.

Interestingly, the profiles of bile acids in patients with T2DM vary across different studies. Some studies indicate higher levels of total bile acids, PBA and SBA, among individuals with T2DM (131, 132). In contrast, other studies have found no significant differences in total serum bile acid levels between T2DM patients and controls (133). Nonetheless, the majority of these studies do suggest a relationship between increased insulin resistance and higher total bile acids (132, 133), highlighting the therapeutic potential of targeting bile acids in T2DM. Alterations in bile acids have been associated with complications of T2DM including cardiovascular disease (134) and diabetic kidney disease (135).

T2DM is associated with chronic low-grade systemic inflammation caused by metabolic endotoxaemia and cytokine stimulation by microbes leading to oxidative stress, macrophage activity and insulin resistance. Insulin resistance occurs due to activation of the inflammatory cascade, subsequent activation of serine kinases, insulin receptor substrate serine phosphorylation and consequent insulin signaling inhibition causing cellular insulin resistance (159).

Pathogenic bacteria including Enterococcus and Escherichia-Shigella may outcompete beneficial bacteria, such as Faecalibacterium, Roseburia and Bifidobacterium, perpetuating negative effects on gut health and inflammation.