Researchers at Oregon State University have found that a few organisms in the gut microbiome play a key role in type 2 diabetes, opening the door to possible probiotic treatments for a serious metabolic disease affecting roughly one in 10 Americans.
“Type 2 diabetes is in fact a global pandemic and the number of diagnoses is expected to keep rising over the next decade,” said study co-leader Andrey Morgun, associate professor of pharmaceutical sciences in the OSU College of Pharmacy.
“The so-called ‘western diet’ – high in saturated fats and refined sugars – is one of the primary factors.
Formerly known as adult-onset diabetes, type 2 diabetes is a chronic condition affecting the way the body metabolizes glucose, a sugar that’s a key source of energy.
For some patients, that means their body resists the effects of insulin – the hormone produced by the pancreas that opens the door for sugar to enter cells. Other patients don’t produce enough insulin to maintain normal glucose levels.
In either case, sugar builds up in the bloodstream and if left untreated the effect is impairment to many major organs, sometimes to disabling or life-threatening degrees. A key risk factor for type 2 diabetes is being overweight, often a result of a western diet in combination with low physical activity.
The human gut microbiome features more than 10 trillion microbial cells from about 1,000 different bacterial species. Dysbiosis, or imbalance, in the microbiome is commonly associated with detrimental effects on a person’s health.
“Some studies suggest dysbiosis is caused by complex changes resulting from interactions of hundreds of different microbes,” said Natalia Shulzhenko, an associate professor of biomedical sciences in OSU’s Carlson College of Veterinary Medicine and the study’s other co-leader.
“However, our study and other studies suggest that individual members of the microbial community, altered by diet, might have a significant impact on the host.”
Shulzhenko and Morgun used a new, data-driven, systems-biology approach called transkingdom network analysis to study host-microbe interactions under a western diet. That allowed them to investigate whether individual members of the microbiota played a part in metabolic changes the diet induces in a host.
“The analysis pointed to specific microbes that potentially would affect the way a person metabolizes glucose and lipids,” Morgun said.
“Even more importantly, it allowed us to make inferences about whether those effects are harmful or beneficial to the host. And we found links between those microbes and obesity.”
The scientists identified four operational taxonomic units, or OTUs, that seemed to affect glucose metabolism; OTUs are a means of categorizing bacteria based on gene sequence similarity.
The identified OTUs corresponded to four bacterial species: Lactobacillus johnsonii, Lactobacillus gasseri, Romboutsia ilealis and Ruminococcus gnavus.
“The first two microbes are considered potential ‘improvers’ to glucose metabolism, the other two potential ‘worseners,'” Shulzhenko said. “The overall indication is that individual types of microbes and/or their interactions, and not community-level dysbiosis, are key players in type 2 diabetes.”
The researchers fed mice the equivalent of a western diet and then supplemented the rodents’ intake with the improver and worsener microbes. The Lactobacilli boosted mitochondrial health in the liver, meaning improvements in how the host metabolizes glucose and lipids, and the mice receiving those Lactobacilli also had a lower fat mass index than those fed only a western diet.
Checking the mouse results against data from an earlier human study, the scientists found correlations between human body mass index and abundance of the four bacteria—more of the improvers meant a better body mass index, more of the worseners was connected to a less healthy BMI.
“We found R. ilealis to be present in more than 80% of obese patients, suggesting the microbe could be a prevalent pathobiont in overweight people,” Shulzhenko said.
A pathobiont is an organism that normally has a symbiotic relationship with its host but can become disease-causing under certain circumstances.
“Altogether, our observations support what we saw in the western diet-fed mice,” she said. “And in looking at all of the metabolites, we found a few that explain a big part of probiotic effects caused by Lactobacilli treatments.”
Lactobacillus is a microbial genus that contains hundreds of different bacterial strains. Its representatives are common among probiotics and frequently found in many types of fermented foods and Lactobacillus-fortified dairy products, such as yogurt.
“Our study reveals potential probiotic strains for treatment of type 2 diabetes and obesity as well as insights into the mechanisms of their action,” Morgun said. “That means an opportunity to develop targeted therapies rather than attempting to restore ‘healthy’ microbiota in general.”
Bacteria involved in type 2 diabetes (T2D)
Out of 42 human observational studies that investigated T2D and the bacterial microbiome, the majority of studies reported associations between specific taxa and disease or its phenotypes (see Supporting Table 1 and “Search strategy and selection criteria” below). However, only a handful reported similar results.
Among the commonly and consistently reported findings, the genera of Bifidobacterium, Bacteroides, Faecalibacterium, Akkermansia and Roseburia were negatively associated with T2D, while the genera of Ruminococcus, Fusobacterium, and Blautia were positively associated with T2D (Fig. 1).
Lactobacillus genus, while frequently detected and reported, shows the most discrepant results among studies. Interestingly, different macro-metrics of microbial communities, such as several indexes of diversity and the Bacteroidetes/Firmicutes ratio that have been previously suggested as markers of metabolic disease did not show consistent associations with T2D (Table 1).
Number of reports examining association between T2D and diversity of microbiota or Bacteroides/Firmicutes ratio.
|Index||# Reports||No association||References (PMID)||Positive||References (PMID)||Negative||References (PMID)|
|Alpha diversity||Shannon||13||9||24013136, 29998997, 29280312, 29922272, 29596446, 27151248, 26756039||2||30397356, 26941724||2||27974055, 27151248|
|Chao1||8||6||24013136, 29998997, 29280312, 29922272, 26756039, 27151248||2||26941724, 29789365||0|
|Beta diversity||8||7||24988476, 28530702, 24997786, 29280312, 29922272, 29596446, 27151248||0||1||27974055|
|Bacteroides/Firmicutes ratio||14||6||24013136, 26756039, 29789365, 29434314, 29657308, 29998997||3||20140211, 29434314, 23032991||4||23657005, 27974055, 26919743, 22293842|
Bacteroides and bifidobacterium represent beneficial genera most frequently reported in studies of T2D.
Bifidobacterium appears to be the most consistently supported by the literature genus containing microbes potentially protective against T2D. Indeed, nearly all papers report a negative association between this genus and T2D , , , , , , , ; while only one paper reported opposite results .
Furthermore, some studies also found a negative association between specific species such as B. adolescentis, B. bifidum, B. pseudocatenulatum, B. longum, B. dentium and disease in patients treated with metformin or after undergoing gastric bypass surgery [6,11].
According to our literature search, Bifidobacterium has not been used alone as probiotics for T2D. However, almost all animal studies that tested several species from this genus (B. bifidum, B. longum, B. infantis, B. animalis, B. pseudocatenulatum, B. breve) showed improvement of glucose tolerance , , , , . Thus, animal studies strengthen the idea that Bifidobacterium naturally habituating the human gut or introduced as probiotics play protective role in T2D.
The second most commonly reported genus was Bacteroides. Eight studies have reported associations between the abundance of this genus and T2D. Among these, five cross-sectional studies [3,, , , ] show negative associations with disease while three other studies [6,11,21] that involved some type of treatment reported positive associations.
This apparent inconsistency can be explained by previously reported antibiotic effect of metformin  and/or potential feedback mechanisms on gut microbiota resulting from improved human physiology. Interestingly, in He et al. [1,23] 21 out of 23 OTUs of Bacteroides detected in their study were negatively associated with T2D.
Accordingly, in investigations that analyzed this genus on the species level, Bacteroides intestinalis, Bacteroides 20–3 and Bacteroides vulgatus were decreased in T2D patients and Bacteroides stercoris were enriched after sleeve gastrectomy (SG) surgery in T2D patients with diabetes remission [5,11,17,24].
We also found only two experimental animal studies testing the ability of Bacteroides to treat diet induced metabolic disease. In these studies, administration of Bacteroides acidifaciens  and Bacteroides uniformis  improved glucose intolerance and insulin resistance in diabetic mice. Together, these studies indicate that Bacteroides plays a beneficial role on glucose metabolism in humans and experimental animals.
While Roseburia, Faecalibacterium, and Akkermansia were not reported as frequently as the two genera above mentioned (Bifidobacterium, Bacteroides) in the 42 studies we reviewed, but those genera were also found to be consistently negatively associated with T2D in human studies.
In five case-control studies Roseburia was found in lower frequencies in T2D group than in healthy controls [3,17,, , ]. Accordingly, investigations that were able to assign Roseburia to a species level also reported a negative association with disease for Roseburia inulinivorans, Roseburia_272, and one unclassified OTU from this genus [11,17,24]. Only one paper reported an opposite result for Roseburia intestinalis .
Two case-control studies reported lower frequencies in the disease group for Faecalibacterium [2,28]. Nevertheless, this genus was also found to be decreased after different types of antidiabetic treatments ranging from metformin and herbal medicine  to bariatric surgery ; only one study reported an opposite effect .
Moreover, studies that were able to analyze this genus at species level usually detected F. prausnitzii. This species was found to be negatively associated with T2D in four out five human case control studies [17,24,, , ]. While it is a popular probiotic for colitis , there were few attempts to use F. prausnitzii as a probiotic for metabolic disease.
Interestingly, in one study the administration of F. prausnitzii resulted in improvement of hepatic function and decreased liver fat inflammation in mice with diet-induced metabolic disease without affecting blood glucose . Finally, it was also shown that another species of this genus, Faecalibacterium cf, was associated with remission of diabetes after bariatric surgery .
Akkermansia muciniphila is a relatively recently discovered member of commensal microbiota . Its beneficial effect on host glucose metabolism was first reported in animal models [38,39]. In agreement with animal studies, the negative association between the abundance of this bacterium and T2D has been reported in human studies [17,38].
In summary, a decrease in at least one of these five phylogenetically distant genera (Bacteroides, Bifidobacterium, Roseburia, Faecalibacterium, and Akkermansia) in patients was found in approximately half of T2D microbiome studies suggesting their potential role beyond serving as a biomarker.
Supporting this notion, the majority of these bacteria have been tested as probiotics for metabolic disease in mice, but more rarely in humans [, , , , ,25,26,, , , , , , ]. The potential mechanisms of interaction between these microbes and mammalian organisms are discussed later in this paper.
Lactobacillus genus presents a complex case of apparently discordant results when considering all association studies, i.e. including those that analyzed changes after treatments (Fig. 1). However, cross-sectional studies of patients versus controls reported positive association between abundances of this genus and T2D in five out of six papers [, , ,29,43].
Furthermore, several associations of this genus tend to be species-specific. For example, while L. acidophilus , L. gasseri , L. salivarius  were increased, L. amylovorus  was decreased in T2D patients suggesting a high diversity in functional impact on host metabolism by bacteria from this genus. Moreover, several species from this genus have been also tested as probiotics.
Experimental studies in mice show mostly beneficial effects in the models of T2D such as L. plantarum , , , , L. reuteri , L. casei , L. curvatus , L. gasseri , L. paracasei , L. rhamnosus , L. sakei . More importantly, twenty-five human clinical trials , , , , , , , , , , , , , , , , , , , , , , , ,  employed twelve different species of Lactobacillus with ten of those studies [, , , , , , , ,64,79] adding other probiotics.
Out of eleven studies [, , , , , , ,72,76,77,79] that showed some protective effect, the majority combined other genera, most frequently Bifidobacterium [, , , , ,64,79], suggesting that Lactobacillus and Bifidobacterium may work in a synergistic manner. Species L. sporogenes [76,77], L. casei Shirota , L. reuteri  used as mono-probiotics have been reported to improve T2D related symptoms in humans.
L. plantarum, bacteria found in fermented food products, is intensively studied in animal systems, with many studies showing that L. plantarum improves glucose metabolism in diet-induced and genetic models of T2D , , ,  mice; only one reported with no significant effect of this treatment .
However, this species had no significant effect on glucose metabolism in four clinical trials , , , . Thus, it seems that Lactobacilli anti-diabetic effect is seen more frequently when they are a part of probiotic cocktail rather than administered individually [58,61,62,64].
Overall, Lactobacillusgenus is highly diverse and contains the highest number of OTUs in the human gut among potentially probiotic bacteria. Its effects on T2D seems to be species-specific or even strain-specific, which might explain why genus level analysis lacks consistency amongst studies using this bacteria (Fig. 1).
Fewer studies (11 out of 42) reported positive associations (increase in disease) of microbiota with T2D and/or hyperglycemia. Specifically, Ruminococcus, Fusobacterium, and Blautia have been reported in a positive association with T2D.
On one hand, consistent findings have been reported in 5 studies on Ruminococcus genus [3,17,28,31,81] and 3 studies on Fusobacterium [2,4,6]. On the other hand, the studies reporting species levels of these bacteria reported conflicting results [6,11,34].
For example, while one study demonstrated that Ruminococcus sp. SR1/5 enriched by metformin treatment , another found Ruminococcus bromii enriched and Ruminococcus torques decreased after bariatric surgery and diabetes remission . It is possible that different types of treatments might be a major reason for the inconsistences between results of these studies.
Blautia genus has been found increased in disease groups in three out of four cross-sectional studies for T2D [17,18,82,83] and reduced after bariatric surgery . Disagreeing with these reports, Blautia spp. were reported to increase after treatment with metformin in another study . Importantly, results by He et al. 2018 , are concordant with the genus level analyses demonstrating positive associations between T2D and several OTUs of all three of these genera. The question still remains whether these bacteria play a causal role in T2D since there are no studies investigating these potentially harmful bacteria in animal models of T2D.
In summary, our review of literature regarding overall diversity and other macro-metrics of microbial communities failed to show a relation to diabetes (Table 1).
However, some taxa have been systematically implicated in T2D. Surprisingly, some taxa are consistently associated with protection from T2D at genus level (e.g. Bacteroides, Bifidobacterium, etc.) or even phylogenetically at higher levels (e.g. Actinobacteria [7,17]) whereas others (e.g. Lactobacilli) show only species- or strain-specific effects.
This phenomenon might be to be associated with a diversity of a given genus habituating the human gut (i.e. the larger a number of strains of a given genus found in human gut, the more strain-specific effects are observed). Importantly, several of these microbes are currently tested as probiotics in mouse and human studies.
Potential mechanisms of microbiota effects on metabolism in the T2D patient
Multiple molecular mechanisms of gut microbiota contribution to metabolic disease and T2D have been recently reviewed elsewhere . Microbiota modulates inflammation, interacts with dietary constituents, affects gut permeability, glucose and lipid metabolism, insulin sensitivity and overall energy homeostasis in the mammalian host (Fig. 2). Herein, we summarize the mechanisms whereby specific taxa highlighted earlier in this review can affect T2D.
Modulation of inflammation
Overall, T2D is associated with elevated levels of pro-inflammatory cytokines, chemokines and inflammatory proteins.
While some gut microbes and microbial products especially lipopolysaccharides (LPS) promote metabolic endotoxemia and low-grade inflammation, others stimulate anti-inflammatory cytokines and chemokines.
For example, induction of IL-10 by species of Roseburia intestinalis, Bacteroides fragilis, Akkermansia muciniphila, Lactobacillus plantarum, L. casei [37,, , , ] may contribute to improvement of glucose metabolism since overexpression of this cytokine in the muscle protects from ageing-related insulin resistance . R. intestinalis can also increase IL-22 production, an anti-inflammatory cytokine [90,91] known to restore insulin sensitivity and alleviate diabetes .
It can also promote T regulatory cell differentiation, induce TGF-β and suppress intestinal inflammation [85,90,91]. Likewise, Bacteroides thetaiotaomicron induces expression of T regulatory cell gene expression .
Inhibition of pro-inflammatory cytokines and chemokines is another route used by beneficial microbes to prevent inflammation. Various species of Lactobacillus (L. plantarum, L. paracasei, L. casei) can decrease IL-1β, Monocyte Chemoattractant Protein-1, Intercellular adhesion molecule-1, IL-8, CD36 and C-reactive protein [93,94]. L. paracasei and B. fragilis inhibit expression of IL-6 [86,95].
Similarly, Lactobacillus, Bacteroides and Akkermansia have been found to suppress TNF-α [96,, , ,95,97,98]. L. paracasei and microbial anti-inflammatory molecule from F. prausnitzii inhibit the activity of NF-kB [95,99]. Similarly, Roseburia and Faecalibacterium are butyrate producing bacteria and butyrate is also known to inhibit the activity of NF-kB [100,101].
Lactobacillus casei and Roseburia intestinalis decrease another pro-inflammatory cytokine IFN-γ [90,91,102] whereas Roseburia intestinalis can inhibit IL-17 production [90,91]. Bacteroides thetaiotaomicron reduces Th1, Th2 and Th17 cytokines in mono-associated mice .
Potentially detrimental microbes in T2D (pathobionts), like Fusobacterium nucleatum and Ruminococcus gnavus can increase several inflammatory cytokines, albeit in other inflammatory diseases [103,104].
Increased intestinal permeability is a characteristic of human T2D. It results in translocation of gut microbial products into the blood and causes metabolic endotoxemia . Two species (Bacteroides vulgatus and B. dorei) from the potentially beneficial for T2D genera have been found to upregulate the expression of tight junction genes in the colon leading to reduction in gut permeability, reduction of LPS production and amelioration of endotoxemia in a mouse model .
Another probiotic bacterium, Akkermansia muciniphila, decreased gut permeability using extracellular vesicles which improve intestinal tight junctions via AMPK activation in epithelium . The outer membrane protein (Amuc_1100) of this bacterium enhances the expression of occludin and tight junction protein-1 (Tjp-1) and improves gut integrity .
Amuc_1100 also inhibits cannabinoid receptor type 1 (CB1) in the gut, which in turn, reduces gut permeability and systemic LPS levels . While a specific bacterial component was not determined for Faecalibacterium prausnitzii, it was shown that the supernatant from the cultured bacterium enhances the expression of tight junction proteins improving intestinal barrier functions in colitis model .
Finally, butyrate, produced by Faecalibacterium, Roseburia, also have potential to reduce gut permeability through serotonin transporters and PPAR-γ pathways .
Gut microbiota may also affect T2D by influencing glucose homeostasis and insulin resistance in major metabolic organs such as liver, muscle and fat, as well as by affecting digestion of sugars and production of gut hormones that control this process. For example, one of the potential probiotics discussed above (Bifidobacterium lactis) can increase glycogen synthesis and decrease expression of hepatic gluconeogenesis-related genes . In the same report, B. lactis improved the translocation of glucose transporter-4 (GLUT4) and insulin-stimulated glucose uptake.
Lactobacillus gasseri BNR17 also increases GLUT-4 expression in the muscle with potential anti-diabetes effect . Akkermansia muciniphila and Lactobacillus plantarum reduce the expression of hepatic flavin monooxygenase 3 (Fmo3) [37,93], a key enzyme of xenobiotic metabolism, whose knockdown has been found to prevent development of hyperglycemia and hyperlipidemia in insulin resistant mice .
Lactobacillus casei can ameliorate insulin resistance by increasing the mRNA level of phosphatidylinositol-3-kinase (PI3K), insulin receptor substrate 2 (IRS2), AMPK, Akt2 and glycogen synthesis in the liver [97,111]. The effect of this particular microbe is not limited to the effects on liver. Indeed, L. casei also reduces hyperglycemia via a bile acid-chloride exchange mechanism involving the up regulation of multiple genes, i.e., ClC1-7, GlyRα1, SLC26A3, SLC26A6, GABAAα1, Bestrophin-3 and CFTR .
It also decreases the insulin-degrading enzyme (IDE) in the caco-2 cells and insulin-like growth factor binding proteins-3 (IGFBP-3) in the white adipose tissue [97,111,113]. L. rhamnosus, another lactobacillus species, increases adiponectin level in the epididymal fat, thus, improving insulin sensitization .
Some species of Lactobacillii and Akkermansia muciniphila possess potent alpha-glucosidase inhibitory activity that prevents the breakdown of complex carbohydrates and reduces postprandial hyperglycemia . Microbiota and their products can modulate gut hormones and enzymes and improve insulin resistance and glucose tolerance.
Butyrate can act as ligand for G-protein coupled receptors (GPCR41 and GPCR43) in the gut and promotes the release of gut hormones GLP-1, PYY and GLP-2 from entero-endocrine l-cells (reviewed in [114,115]). Bifidobacterium and Lactobacillus produce bile salt hydrolases, which convert primary conjugated bile salts into deconjugated bile acids (BA) that are subsequently converted into secondary BA. Secondary BAs activate the membrane bile acid receptor (TGR5) to induce the production of GLP-1 (reviewed in ).
Fatty acid oxidation, synthesis and energy expenditure
Increasing fatty acid oxidation and energy expenditure and reducing synthesis of fatty acids ameliorates obesity and consequently T2D . Akkermansia muciniphila, Bacteroides acidifaciens, Lactobacillus gasseri and short chain fatty acids have been reported to increase fatty acid oxidation in the adipose tissue.
For example, Akkermansia muciniphila has been found to increase the levels of 2-oleoyl glycerol (2-OG), 2-palmitoylglycerol (2-PG), 2-acylglycerol (2-AG) in the adipose tissue which increase the fatty acid oxidation and adipocyte differentiation . Furthermore, Bacteroides acidifaciens also improves fatty acid oxidation in the adipose tissue via TGR5-PPAR-α pathway .
Likewise, butyrate can promote fatty acid oxidation and thermogenesis by inhibiting the histone deacetylation process in the muscle which increases energy expenditure partially by promoting mitochondrial functions in the muscle . In liver and adipose tissue, butyrate and other two SCFAs, propionate and acetate, decrease the expression of PPAR-γ  which in turns increases fatty acid oxidation.
Lactobacillus gasseri has been shown to reduce obesity by increasing the fatty acid oxidation genes and reducing fatty acid synthesis related genes . Serum level of malonidialdehyde, a marker of oxidative damage of lipids, has been found to be reduced by Akkermansia muciniphila and Lactobacillus caseiin diabetic rodents [87,96].
Hence, members of microbiota with beneficial effect on T2D modulate fatty acid metabolism and associated energy expenditure in the host that results in alleviation of obesity and accompanying T2D.
Combined effects of bacteria
Besides the above-mentioned mechanisms, some microbes can also affect the host physiology by increasing other potential beneficial microbiota or by cross-feeding. Several species of Bifodobacterium were shown to have cross feeding interaction with other microbiota like Faecalibacterium and Roseburia [119,120]. Lactobacillus rhamnosus can increase Bifidobacterium abundance in the cecum of rats . L. casei has been found to increase the butyrate producing bacteria [97,111].
reference link : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6948163/
More information: Nolan K. Newman et al. Host response to cholestyramine can be mediated by the gut microbiota, (2020). DOI: 10.1101/2020.12.08.416487