Multi-omics signatures in new-onset diabetes predict metabolic response to dietary inulin: findings from an observational study followed by an interventional trial

AIM

The metabolic performance of the gut microbiota contributes to the onset of type 2 diabetes. However, targeted dietary interventions are limited by the highly variable inter-individual response. We hypothesized (1) that the composition of the complex gut microbiome and metabolome (MIME) differ across metabolic spectra (lean-obese-diabetes); (2) that specific MIME patterns could explain the differential responses to dietary inulin; and (3) that the response can be predicted based on baseline MIME signature and clinical characteristics.

METHOD

Forty-nine patients with newly diagnosed pre/diabetes (DM), 66 metabolically healthy overweight/obese (OB), and 32 healthy lean (LH) volunteers were compared in a cross-sectional case-control study integrating clinical variables, dietary intake, gut microbiome, and fecal/serum metabolomes (16 S rRNA sequencing, metabolomics profiling). Subsequently, 27 DM were recruited for a predictive study: 3 months of dietary inulin (10 g/day) intervention.

RESULTS

MIME composition was different between groups. While the DM and LH groups represented opposite poles of the abundance spectrum, OB was closer to DM. Inulin supplementation was associated with an overall improvement in glycemic indices, though the response was very variable, with a shift in microbiome composition toward a more favorable profile and increased serum butyric and propionic acid concentrations. The improved glycemic outcomes of inulin treatment were dependent on better baseline glycemic status and variables related to the gut microbiota, including the abundance of certain bacterial taxa (i.e., Blautia, Eubacterium halii group, Lachnoclostridium, Ruminiclostridium, Dialister, or Phascolarctobacterium), serum concentrations of branched-chain amino acid derivatives and asparagine, and fecal concentrations of indole and several other volatile organic compounds.

CONCLUSION

We demonstrated that obesity is a stronger determinant of different MIME patterns than impaired glucose metabolism. The large inter-individual variability in the metabolic effects of dietary inulin was explained by differences in baseline glycemic status and MIME signatures. These could be further validated to personalize nutritional interventions in patients with newly diagnosed diabetes.

CRISPR/Cas9 genome editing in ergot fungus Claviceps purpurea

Claviceps purpurea is a filamentous fungus well known as a widespread plant pathogen, but it is also an important ergot alkaloid producer exploited by the pharmaceutic industry. In this work, we demonstrated that CRISPR/Cas9 can be a tool for directed mutagenesis in C. purpurea targeting pyr4 and TrpE genes encoding the orotidine 5'-phosphate decarboxylase involved in pyrimidine biosynthesis and the α-subunit of the anthranilate synthase involved in tryptophan biosynthesis, respectively. After protoplast transformation and single spore isolation, homokaryotic mutants showing uridine or tryptophan auxotrophy were selected. In all cases, insertions or insertions combined with deletions were found mostly 3 bp upstream of the PAM sequence. However, transformation efficiencies of CRISPR/Cas9 and CRISPR/Cas9 mediated homology-directed repair only slightly improved in comparison to homologous recombination-mediated knocking-out of the TrpE gene. Moreover, Trp auxotrophs were non-infectious towards rye plants likely due to a decreased production of the plant hormones auxins, which are synthesized by C. purpurea from indole-3-glycerolphosphate in Trp-dependent and Trp-independent biosynthetic pathways, and help the fungus to colonize the plant host. It was demonstrated that the CRISPR/Cas9 vector containing autonomous replicative sequence AMA1 can be fully removed by further culturing of C. purpurea on non-selective media. This method enables introducing multiple mutations in Claviceps and makes feasible metabolic engineering of industrial strains.

Knockout of MITOGEN-ACTIVATED PROTEIN KINASE 3 causes barley root resistance against Fusarium graminearum

The roles of mitogen-activated protein kinases (MAPKs) in plant-fungal pathogenic interactions are poorly understood in crops. Here, microscopic, phenotypic, proteomic, and biochemical analyses revealed that roots of independent transcription activator-like effector nuclease (TALEN)-based knockout lines of barley (Hordeum vulgare L.) MAPK 3 (HvMPK3 KO) were resistant against Fusarium graminearum infection. When co-cultured with roots of the HvMPK3 KO lines, F. graminearum hyphae were excluded to the extracellular space, the growth pattern of extracellular hyphae was considerably deregulated, mycelia development was less efficient, and number of appressoria-like structures and their penetration potential were substantially reduced. Intracellular penetration of hyphae was preceded by the massive production of reactive oxygen species (ROS) in attacked cells of the wild-type (WT), but ROS production was mitigated in the HvMPK3 KO lines. Suppression of ROS production in these lines coincided with elevated abundance of catalase (CAT) and ascorbate peroxidase (APX). Moreover, differential proteomic analysis revealed downregulation of several defense-related proteins in WT, and the upregulation of pathogenesis-related protein 1 (PR-1) and cysteine proteases in HvMPK3 KO lines. Proteins involved in suberin formation, such as peroxidases, lipid transfer proteins (LTPs), and the GDSL esterase/lipase (containing "GDSL" aminosequence motif) were differentially regulated in HvMPK3 KO lines after F. graminearum inoculation. Consistent with proteomic analysis, microscopic observations showed enhanced suberin accumulation in roots of HvMPK3 KO lines, most likely contributing to the arrested infection by F. graminearum. These results suggest that TALEN-based knockout of HvMPK3 leads to barley root resistance against Fusarium root rot.

Giant Meckel's diverticulum

A case of incomplete intestinal obstruction caused by a giant Meckel's diverticulum in a 13-year-old girl is reported. Short resection of the ileum with the diverticulum and end-to-end anastomosis was carried out. The possibilities of diagnosis and treatment as well as the controversial classification of this rare congenital anomaly are discussed.

Interpreting Cytokinin Action as Anterograde Signaling and Beyond

Among the major phytohormones, the cytokinin exhibits unique features for its ability to positively affect the developmental status of plastids. Even early on in its research, cytokinins were known to promote plastid differentiation and to reduce the loss of chlorophyll in detached leaves. Since the discovery of the components of cytokinin perception and primary signaling, the genes involved in photosynthesis and plastid differentiation have been identified as those directly targeted by type-B response regulators. Furthermore, cytokinins are known to modulate versatile cellular processes such as promoting the division and differentiation of cells and, in concert with auxin, initiating the de novo formation of shoot apical meristem (SAM) in tissue cultures. Yet how cytokinins precisely participate in such diverse cellular phenomena, and how the associated cellular processes are coordinated as a whole, remains unclear. A plausible presumption that would account for the coordinated gene expression is the tight and reciprocal communication between the nucleus and plastid. The fact that cytokinins affect plastid developmental status via gene expression in both the nucleus and plastid is interpreted here to suggest that cytokinin functions as an initiator of anterograde (nucleus-to-plastid) signaling. Based on this viewpoint, we first summarize the physiological relevance of cytokinins to the coordination of plastid differentiation with de novo shoot organogenesis in tissue culture systems. Next, the role of endogenous cytokinins in influencing plastid differentiation within the SAM of intact plants is discussed. Finally, a presumed plastid-derived signal in response to cytokinins for coupled nuclear gene expression is proposed.

Overexpression of Trp-related genes in Claviceps purpurea leading to increased ergot alkaloid production

The parasitic fungus Claviceps purpurea has been used for decades by the pharmaceutical industry as a valuable producer of ergot alkaloids. As the biosynthetic pathway of ergot alkaloids involves a common precursor L-tryptophan, targeted genetic modification of the related genes may improve production yield. In this work, the S76L mutated version of the trpE gene encoding anthranilate synthase was constitutively overexpressed in the fungus with the aim of overcoming feedback inhibition of the native enzyme by an excess of tryptophan. In another approach, the dmaW gene encoding dimethylallyltryptophan synthase, which produces a key intermediate for the biosynthesis of ergot alkaloids, was also constitutively overexpressed. Each of the above manipulations led to a significant increase (up to 7-fold) in the production of ergot alkaloids in submerged cultures.

Influence of fluctuating temperature on soil microflora

The effect of different constant and "square-wave" fluctuating temperatures on the soil microflora was studied in laboratory experiments. The growth of soil microorganisms was higher at lower temperatures, indicating the higher degree of substrate immobilization and the better energy economy of the soil bionta. Microbial counts were slightly higher after five days of incubation at fluctuating temperatures than those obtained at a constant mean temperature. It was important whether the fluctuation started at lower or at higher temperatures. At a fluctuating temperature the amount of nitrates decreased compared to the amount at a constant temperature. The development dynamics of soil microorganisms was accelerated by the fluctuation of temperature as judged by nitrogen transformation and simultaneous changes in microbial counts.

[Immunologic parameters in women with threatened premature labor]

The authors examined some immunological indicators in a group of female patients with imminent premature delivery and compared them, using statistical methods, with findings in a control group. The objective was to find a possible predictive value of the investigated parameters for the diagnosis of subclinical intraamnial infection as the possible cause of so-called idiopathic premature delivery. In the immunoglobulin classes they did not find significant differences between the two groups. In the group of patients with an imminent premature delivery they found, however, statistically significantly higher levels of the C3 component of complement, of orosomucoid, alpha-2 and gamma-globulins. They compared the results with data in the literature and assume that some immunological indicators can, after confirmation of the results by other authors, serve as the prediction of subclinical intraamnial infection with imminent prematurity.

[Comparison of the results of conservative and surgical therapy of dislocated supracondylar fractures of the humerus in children]

The authors evaluate retrospectively in a group of 121 children with a dislocated supracondylar fracture in 1984-1993 the results of different therapeutic methods. The highest percentage of excellent and satisfactory results was recorded in children treated by closed reposition with percutaneous pinning with Kirschner wires (88%). In open reposition with Kirschner wires 60% of the results were excellent of satisfactory. The lowest percentage of excellent and satisfactory results was recorded when fixation with a plaster bandage was used (48%). The highest percentage of poor results was observed in surgical reposition with internal fixation (37%). The cause of failure in the majority of patients is according to the authors inadequate reposition of fragments. The authors discuss different types of treatment. They recommend non-surgical reposition with percutaneous pinning, even for less dislocated extension supracondylar fractures of the humerus as well as for fractures complicated by vascular injuries.

[Cysts and pseudocysts of the spleen in children]

A cyst in the upper pole of the spleen was diagnosed in three children. In all the pole of the spleen was resected -in two instances it contained a cyst, in one a pseudocyst. The postoperative course was without complications. All patients had scintigraphic check-up examinations, in all three instances functional lienal tissue was found which did not differ much as to its size from that of a normal spleen. In cysts situated in the splenic pole the authors consider partial resection of the affected portion of the spleen as the optimal surgical method. In cysts of other portions of the spleen it would be better to select a different surgical procedure, e.g. enucleation of the cysts, partial decapsulation of the cyst or percutaneous puncture of the cyst combined, if necessary, with sclerotization.

[The significance of endoscopic retrograde cholangiopancreatography in the diagnosis of pancreatic injuries in children]

The condition of the main pancreatic duct determines very probably in a decisive way the fate of posttraumatic pancreatic pseudocysts and acute pancreatic injuries. Endoscopic retrograde cholangiopancreatography is the only diagnostic method which makes possible to evaluate the condition of this duct. The authors performed ERCP in three children, in two of them an internal drainage of the pseudocyst was carried out on account of verified ductal rupture. In the third girl, after evidence of an intact main pancreatic duct, conservative therapy was successfully applied. In the discussion the authors summarize data from the literature regarding the use of ERCP in the preoperative diagnosis of posttraumatic pancreatic pseudocysts and acute pancreatic injuries. The authors consider ERCP a method which renders the diagnosis of posttraumatic pancreatic pseudocysts and acute pancreatic injuries more accurate.

[A vesico-sigmoid fistula in a 15-year-old girl]

The authors diagnosed in a fifteen-year-old girl. other wise healthy, a double vesicosigmoidal fistula. It developed probably at the age of two after an acute abdominal attack of inflammatory character which was treated conservatively. The fistulae caused repeated inflammations of the urinary pathways. In the late diagnosis participated among others evaluation of miction cystography which was imperfect from the technical aspect. When repeated, this examination contributed to the diagnosis. After surgery the girl recovered.

The microbial contaminants of plant-based meat analogues from the retail market

The aim of the study was to analyse the key microbial contaminants of plant-based meat analogues (PBMA) from retail. A total of 43 samples of PBMAs (12 frozen/31 chilled) in the "ready-to-cook" category, such as hamburgers, meatballs or breaded imitation steaks were purchased in retail stores in the Czech Republic in summer (n = 21) and autumn 2022 (n = 22). The detected indicator bacteria (total viable count, lactic acid bacteria, Enterobacteriaceae, yeasts, moulds) had relatively low values in the analysed PBMA samples and only rarely reached levels of 7 log CFU/g. E. coli, STEC and coagulase-positive staphylococci were not detected by isolation from plates in any of analysed samples. Mannitol positive Bacillus spp. were isolated from almost half of the analysed samples of the PBMA. B. cereus sensu lato was isolated from 3 samples by isolation from plates, and after enrichment in 35 samples (81 %). Clostridium perfringens could not be detected by isolation from plates, nevertheless after multiplication, it was detected in 21 % of samples. Analyses of PBMA samples revealed considerable variability in microbial quality. The presence of spore-forming bacteria with the potential to cause foodborne diseases is alarming. However, to evaluate the risks, further research focused on the possibilities of growth under different conditions of culinary treatment and preservation is needed.