Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported(1,2). In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis(3,4). Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa(3,4). These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication

Microbiota signatures in type-2 diabetic patients with chronic kidney disease - A Pilot Study

The human microbiota is paramount for normal host physiology. Altered host-microbiome interactions are part of the pathogenesis of numerous common ailments. Currently, much emphasis is placed on the involvement of the microbiome in the pathogenesis of type-2 diabetes mellitus (T2DM), impaired glucose tolerance, and other metabolic disorders (i.e. obesity). Several studies found highly significant correlations of specific intestinal bacteria with T2DM. A better understanding of the role of the microbiome in diabetes and its complications might provide new insights in the development of new therapeutic principles. Our pilot study investigates the microbiota patterns in Romanian type-2 diabetic patients with diabetic kidney disease. Fecal samples were collected from type 2-diabetic patients and healthy controls and further used for bacterial DNA isolation. Using 16 rDNA qRT-PCR, we analyzed phyla abundance (Bacteroidetes, Firmicutes) as well as the relative abundance of specific bacterial groups (Lactobacillus sp., Enterobacteriaceae, Ruminococus sp., Prevotella sp., Faecalibacterium sp., Clostridium coccoides, Clostridium leptum). Our study also investigates the diabetic fungal microbiome for the first time. Furthermore, we report significant correlations between the treatment regimen and microbiota composition in diabetic nephropathy

Role of Microbiome in Impacting Treatment of Obesity and Type 2 Diabetes

Metabolic Syndrome is a constellation of metabolic abnormalities associated with insulin resistance and obesity, including hyperglycemia and hypertension. Metabolic syndrome often progresses to type 2 diabetes, hypertension, cardiovascular disease, and liver disease. Metabolic syndrome is increasingly appreciated to be an inflammatory disease in that is associated with increased expression of pro-inflammatory genes and markers, remodeling of adipose tissue, and markedly increased incidence in the last 50 years. Additionally, both diseases alter the microbiota, specifically with alteration in gut microbiota composition. Metabolic syndrome requires a microbiota in that disease is not observed in germ- free mice, and some aspects of the disease can be transferred by fecal transplant. There is a probable correlation between metabolic disorder and gut microbiota. It’s also been shown that the efficacy of systemic medications can be affected by the gut microbiota and that some medications can alter the microbiota. Metformin is believed to be one of those medications. Accordingly, the results of the present study could be employed to develop novel methods for treating metabolic syndrome using medications such as metformin. Furthermore, this study can set the stage for further research towards the application of fecal transplantation as a treatment strategy for individuals with conditions like metabolic syndrome. The overall goal of my studies was to investigate this hypothesis. First, I comprehensively examined the existing gut microbiota literature to discern the range of treatment of type 2 diabetes mellitus that have been associated with, or attributed to, changes in microbiota composition. Chapter 1 outlines findings from this effort. Next, I performed experiments to investigate the extent to which metformin attenuates metabolic syndrome and inflammation by alternation of intestinal microbiota. My results support the notion that metformin induces changes in gut microbiota composition. However, such changes were not necessary for metformin to alleviate parameters of metabolic syndrome indicating that metformin can, at least in part act independently of gut microbiota. Rather Metformin reduced indices of inflammation in both conventional germ-free conditions. These results support a role for metformin’s anti-inflammatory effects rather than its direct action on microbiota for its beneficial metabolic impacts

Drug-microbiota interactions and treatment response: Relevance to rheumatoid arthritis

Knowledge about associations between changes in the structure and/or function of intestinal microbes (the microbiota) and the pathogenesis of various diseases is expanding. However, interactions between the intestinal microbiota and different pharmaceuticals and the impact of these on responses to treatment are less well studied. Several mechanisms are known by which drug-microbiota interactions can influence drug bioavailability, efficacy, and/or toxicity. This includes direct activation or inactivation of drugs by microbial enzymes which can enhance or reduce drug effectiveness. The extensive metabolic capabilities of the intestinal microbiota make it a hotspot for drug modification. However, drugs can also influence the microbiota profoundly and change the outcome of interactions with the host. Additionally, individual microbiota signatures are unique, leading to substantial variation in host responses to particular drugs. In this review, we describe several known and emerging examples of how drug-microbiota interactions influence the responses of patients to treatment for various diseases, including inflammatory bowel disease, type 2 diabetes and cancer. Focussing on rheumatoid arthritis (RA), a chronic inflammatory disease of the joints which has been linked with microbial dysbiosis, we propose mechanisms by which the intestinal microbiota may affect responses to treatment with methotrexate which are highly variable. Furthering our knowledge of this subject will eventually lead to the adoption of new treatment strategies incorporating microbiota signatures to predict or improve treatment outcomes

Fecal Enterobacteriales enrichment is associated with increased in vivo intestinal permeability in humans

Type 2 diabetes (T2D) has been linked with increased intestinal permeability, but the clinical significance of this phenomenon remains unknown. The objective of this study was to investigate the potential link between glucose control, intestinal permeability, diet and intestinal microbiota in patients with T2D. Thirty‐two males with well‐controlled T2D and 30 age‐matched male controls without diabetes were enrolled in a case–control study. Metabolic parameters, inflammatory markers, endotoxemia, and intestinal microbiota in individuals subdivided into high (HP) and normal (LP) colonic permeability groups, were the main outcomes. In T2D, the HP group had significantly higher fasting glucose (P = 0.034) and plasma nonesterified fatty acid levels (P = 0.049) compared with the LP group. Increased colonic permeability was also linked with altered abundances of selected microbial taxa. The microbiota of both T2D and control HP groups was enriched with Enterobacteriales. In conclusion, high intestinal permeability was associated with poorer fasting glucose control in T2D patients and changes in some microbial taxa in both T2D patients and nondiabetic controls. Therefore, enrichment in the gram‐negative order Enterobacteriales may characterize impaired colonic permeability prior to/independently from a disruption in glucose tolerance

New insights along the gut-liver axis in cardiometabolic disease

In this thesis we targeted the human gut microbiome for the development of therapeutic strategies in metabolic disorders. In chapter 3 we performed a randomized placebo-controlled cross-over study in individuals with the metabolic syndrome in which we showed that a single duodenal infusion of A. soehngenii improved peripheral glycemic control. In chapter 4 we studied the effect of a 2 weeks oral A. soehngenii treatment in individuals with T2D treated with metformin on their glycemic control.The second part of the thesis focused on MASLD, currently the most common cause of chronic liver dysfunction worldwide. In chapter 5 we reviewed the gut microbial and gut microbial-derived metabolite signatures associated with the development and disease progression of MASLD. To dissect causality of intestinal microbiota in MASLD, in chapter 6 we performed a single-center, double-blind, randomized controlled proof-of-principle pilot study comparing the effect of three 8-weekly lean vegan donor FMT versus autologous FMT on the severity of MASLD, using liver biopsies in individuals with hepatic steatosis on ultrasound. Moreover, we aimed to identify and validate noninvasive diagnostic methods in disease progression in MASLD. Hence, in chapter 7 we examined the diagnostic performance of multiparametric MRI for the assessment of disease severity along the MASLD disease spectrum with comparison to histological scores

Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus

Biogeographic variations in the gut microbiota are pivotal to understanding the global pattern of host–microbiota interactions in prevalent lifestyle-related diseases. Pakistani adults, having an exceptionally high prevalence of type 2 diabetes mellitus (T2D), are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by bacterial 16S ribosomal RNA gene and fungal internal transcribed spacer (ITS) region amplicon sequencing and eubacterial qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide-binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis of the bacterial microbiota. Overall, urbanized Pakistanis’ gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations, e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for a more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.Peer reviewe