Clostridium scindens secretome suppresses virulence gene expression of Clostridioides difficile in a bile acid-independent manner.

Clostridioides difficile infection (CDI) is a major health concern and one of the leading causes of hospital-acquired diarrhea in many countries. C. difficile infection is challenging to treat as C. difficile is resistant to multiple antibiotics. Alternative solutions are needed as conventional treatment with broad-spectrum antibiotics often leads to recurrent CDI. Recent studies have shown that specific microbiota-based therapeutics such as bile acids (BAs) are promising approaches to treat CDI. Clostridium scindens encodes the bile acid-induced (bai) operon that carries out 7-alpha-dehydroxylation of liver-derived primary BAs to secondary BAs. This biotransformation is thought to increase the antibacterial effects of BAs on C. difficile. Here, we used an automated multistage fermentor to study the antibacterial actions of C. scindens and BAs on C. difficile in the presence/absence of a gut microbial community derived from healthy human donor fecal microbiota. We observed that C. scindens inhibited C. difficile growth when the medium was supplemented with primary BAs. Transcriptomic analysis indicated upregulation of C. scindens bai operon and suppressed expression of C. difficile exotoxins that mediate CDI. We also observed BA-independent antibacterial activity of the secretome from C. scindens cultured overnight in a medium without supplementary primary BAs, which suppressed growth and exotoxin expression in C. difficile mono-culture. Further investigation of the molecular basis of our observation could lead to a more specific treatment for CDI than current approaches. IMPORTANCE There is an urgent need for new approaches to replace the available treatment options against Clostridioides difficile infection (CDI). Our novel work reports a bile acid-independent reduction of C. difficile growth and virulence gene expression by the secretome of Clostridium scindens. This potential treatment combined with other antimicrobial strategies could facilitate the development of alternative therapies in anticipation of CDI and in turn reduce the risk of antimicrobial resistance.

MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.

Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.

Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System.

Longitudinal studies of gut microbiota following specific interventions are vital for understanding how they influence host health. However, robust longitudinal sampling of gut microbiota is a major challenge, which can be addressed using in vitro fermentors hosting complex microbial communities. Here, by employing 16S rRNA gene amplicon sequencing, we investigated the adaptation and succession of human fecal microbial communities in an automated multistage fermentor. We performed two independent experiments using different human donor fecal samples, one configured with two units of three colon compartments each studied for 22 days and another with one unit of two colon compartments studied for 31 days. The fermentor maintained a trend of increasing microbial alpha diversity along colon compartments. Within each experiment, microbial compositions followed compartment-specific trajectories and reached independent stable configurations. While compositions were highly similar between replicate units, they were clearly separated between different experiments, showing that they maintained the individuality of fecal inoculum rather than converging on a fermentor-specific composition. While some fecal amplicon sequence variants (ASVs) were undetected in the fermentor, many ASVs undetected in the fecal samples flourished in vitro. These bloomer ASVs accounted for significant proportions of the population and included prominent health-associated microbes such as Bacteroides fragilis and Akkermansia muciniphila. Turnover in community compositions is likely explained by feed composition and pH, suggesting that these communities can be easily modulated. Our results suggest that in vitro fermentors are promising tools to study complex microbial communities harboring important members of human gut microbiota. IMPORTANCE In vitro fermentors that can host complex gut microbial communities are promising tools to investigate the dynamics of human gut microbiota. In this work, using an automated in vitro gut fermentor consisting of different colon compartments, we investigated the adaptation dynamics of two different human fecal microbial communities over 22 and 31 days. By observing the temporal trends of different community members, we found that many dominant members of the fecal microbiota failed to maintain their dominance in vitro, and some of the low-abundance microbes undetected in the fecal microbiota successfully grew in the in vitro communities. Microbiome compositional changes and blooming could largely be explained by feed composition and pH, suggesting that these communities can be modulated to desired compositions via optimizing culture conditions. Thus, our results open up the possibility of modulating in vitro microbial communities to predefined compositions by optimizing feed composition and culture conditions.

ADAR1-Dependent RNA Editing Promotes MET and iPSC Reprogramming by Alleviating ER Stress.

RNA editing of adenosine to inosine (A to I) is catalyzed by ADAR1 and dramatically alters the cellular transcriptome, although its functional roles in somatic cell reprogramming are largely unexplored. Here, we show that loss of ADAR1-mediated A-to-I editing disrupts mesenchymal-to-epithelial transition (MET) during induced pluripotent stem cell (iPSC) reprogramming and impedes acquisition of induced pluripotency. Using chemical and genetic approaches, we show that absence of ADAR1-dependent RNA editing induces aberrant innate immune responses through the double-stranded RNA (dsRNA) sensor MDA5, unleashing endoplasmic reticulum (ER) stress and hindering epithelial fate acquisition. We found that A-to-I editing impedes MDA5 sensing and sequestration of dsRNAs encoding membrane proteins, which promote ER homeostasis by activating the PERK-dependent unfolded protein response pathway to consequently facilitate MET. This study therefore establishes a critical role for ADAR1 and its A-to-I editing activity during cell fate transitions and delineates a key regulatory layer underlying MET to control efficient reprogramming.

Influence of gelation on the retention of purple cactus pear extract in microencapsulated double emulsions.

A purple cactus pear (Opuntia ficus-indica) extract (CP) was encapsulated in double emulsions (DE) gelled with gelatin (DE-CP-G) and with gelatin and transglutaminase (DE-CP-GT), as well as in a DE with a liquid external aqueous phase (DE-CP), in order to study the retention of betanin as colorant agent. Both gelled DEs showed a predominantly elastic behavior, in contrast with DE-CP. The degradation rate constant of betanin was significantly higher in DE-CP-GT (90.2 x 10-3 days-1) than in DE-CP-G (11.0 x 10-3 days-1) and DE-CP (14.6 x 10-3 days-1) during cold-storage (4 °C). A shift towards yellow color was found in all the systems during cold-storage (4 °C) and after thermal treatment (70°C/30 min), especially in DE-CP-GT, denoting a higher degradation of betanin. Betalamic acid, cyclo-Dopa 5-O-ß-glucoside, 17-decarboxy-betanin and neobetanin were identified by UHPLC-MS/MS as degradation products of betanin.

RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells.

Ten-eleven translocation (TET) proteins play key roles in the regulation of DNA-methylation status by oxidizing 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), which can both serve as a stable epigenetic mark and participate in active demethylation. Unlike the other members of the TET family, TET2 does not contain a DNA-binding domain, and it remains unclear how it is recruited to chromatin. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We found that PSPC1 and TET2 contribute to ERVL and ERVL-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation.

The SIN3A/HDAC Corepressor Complex Functionally Cooperates with NANOG to Promote Pluripotency.

Although SIN3A is required for the survival of early embryos and embryonic stem cells (ESCs), the role of SIN3A in the maintenance and establishment of pluripotency remains unclear. Here, we find that the SIN3A/HDAC corepressor complex maintains ESC pluripotency and promotes the generation of induced pluripotent stem cells (iPSCs). Members of the SIN3A/HDAC corepressor complex are enriched in an extended NANOG interactome and function in transcriptional coactivation in ESCs. We also identified a critical role for SIN3A and HDAC2 in efficient reprogramming of somatic cells. Mechanistically, NANOG and SIN3A co-occupy transcriptionally active pluripotency genes in ESCs and also co-localize extensively at their genome-wide targets in pre-iPSCs. Additionally, both factors are required to directly induce a synergistic transcriptional program wherein pluripotency genes are activated and reprogramming barrier genes are repressed. Our findings indicate a transcriptional regulatory role for a major HDAC-containing complex in promoting pluripotency.

Should Prophylactic Anticoagulation Be Considered with Large Uterine Leiomyoma? A Case Series and Literature Review.

Introduction. Uterine leiomyomas, also called uterine fibroids or myomas, are the most common pelvic tumors in women. They are very rarely the cause of acute complications. However, when complications occur they cause significant morbidity and mortality. Thromboembolic disease has been described as a rare complication of uterine leiomyomas. DVT is a serious illness, sometimes causing death due to acute PE. Cases. We report a case series of 3 patients with thromboembolic disease associated with uterine leiomyoma at Hurley Medical Center, Flint, Michigan, during 2015 and conduct a literature review on the topic. A literature search was conducted using Medline, PubMed, and PMC databases from 1966 to 2015. Conclusion. The uterine leiomyoma is a very rare cause of PE and only few cases have been reported. DVT secondary to uterine leiomyoma should be considered in a female presenting with abdominal mass and pelvic pressure, if there is no clear common cause for her symptoms. Thromboembolic disease secondary to large uterine leiomyoma should be treated with acute stabilization and then hysterectomy. Prophylactic anticoagulation would be beneficial for lowering the risk of VTE in patients with large uterine leiomyoma.

Microencapsulation of pulp and ultrafiltered cactus pear (Opuntia ficus-indica) extracts and betanin stability during storage.

Pulp (CP) and ultrafiltered (UF) cactus pear extracts were encapsulated with Capsul (C) by applying a central composite design (CP-C and UF-C systems) by spray-drying. To evaluate the effect of the extract, microparticles obtained under optimal conditions were characterised and stored at 60 °C. Betacyanin and betaxanthin encapsulation efficiency reached values above 98% for both systems studied. This efficiency was attributed to strong interactions between betalains and the polymer. Betalain degradation in CP-C and UF-C microparticles followed pseudo-first order kinetics. The betacyanin degradation rate constant was significantly higher for CP-C than for UF-C. These results suggested that the mucilage or higher sugar content of CP increased the hygroscopicity of the CP-C microparticles, leading to the degradation of betalain. The hydrolysis pathway was the main mechanism of betanin degradation during microparticle storage. These results demonstrate the potential utility of both CP-C and UF-C microparticles as natural colourants for healthy foods.

Dietary fibre concentrate from Chilean algarrobo (Prosopis chilensis (Mol.) Stuntz) pods: purification and characterization.

Prosopis species are generally fast-growing, drought-resistant, nitrogen-fixing trees or shrubs. Fruits of Prosopis spp are indehiscent pods, where pericarp is formed by the epicarp, light brown in colour, and fibrous nature; the mesocarp known as pulp, which is rich in sugars; and the endocarp. The aim of this work was to obtain a fibre concentrate from the pods of Prosopis chilensis Mol. (Stuntz) and to determine the chemical, physical, and technological properties of the pod flour (PF) and of a fibre concentrate or pod purified flour (PPF). Acetone, ethanol, and water at different conditions of time and temperature were used in the purification process. PF showed 53.7 g/100 g of total sugar content, 4.2 g/100 g of reducing sugar content, 41.8 g/100 g of total dietary fibre, 35.8 g/100 g of insoluble fibre, and 6.0 g/100 g of soluble fibre content. The PPF has a total sugar content of 3.8 g/100 g, reducing sugar content of 2.2 g/100 g, total dietary fibre content of 80.8 g/100 g, insoluble fibre content of 75.1 g/100 g, and soluble fibre content of 5.7 g/100 g. The scanning electron microscopy analysis showed the existence of voids in the structure of PPF flour, which reveals the efficiency of the purification process with a high decrease in the total sugar content.

Cactus pear cladodes powders as a source of dietary fibre: purification and properties.

Cactus pear cladodes of 2-3 years were used to obtain a natural purified dietary fibre and their physical, chemical and technological properties were determined. The effect of particle size and washing temperature on the technological properties was studied. Purification produces a decrease in green colour (a*) and an increase in total dietary fibre but reduces the total phenolic compounds, mainly when cladodes are washed at higher temperatures. Technological properties did not present changes in the water retention capacity (WRC), water adsorption capacity and cationic exchange capacity, but it did in swelling capacity (SC), oil absorption capacity, apparent density and setting density, which were influenced by the particle size of the cactus powders. The purified fibre shows a high WRC between 5.20 and 5.86 g g(- 1) and a high SC (7.02-8.27 mL g(- 1)). Purified fibre with a particle size between 600 and 1200 µm, independent of the washing temperature had better insoluble to soluble dietary fibre ratio, total phenolic content and technological properties.

[Orange juice residues as dietary fiber source for foods]. / Utilización de residuos de la industria de jugos de naranja como fuente de fibra dietética en la elaboración de alimentos.

Food snacks using powdered residues from the orange juice industry as a source of dietary fiber were formulated. Six formulations utilizing powdered orange residues with three different moisture levels (25%, 15% and 10%) were elaborated. There were used two basic blends. The first one was 33.3% of orange dry powder, 33.3% of honey, 16.6% of roasted peanut, 16.6% of raisins; the second one was 28.6% of orange powder, 35.7% of honey, 17.85% of roasted peanut, 17.85% of raisins. Snacks had spherical shape with 2.5 cm diameter and a weight close to 10g. The snack moisture was between 12.6 and 17.4%, and their aw between 0.65 and 0.71. The snack chemical composition, on dry matter basis, was 1.6 and 1.9% of ash; 12.3 and 15.2% of lipids; 6.1 and 7.1% of proteins; and 56.2 to 59.6% of carbohydrates; the caloric contribution (calculated) was between 326.8 and 342.9 kcal/100g. The powdered orange residue had 64% of total dietary fiber, 54% of insoluble dietary fiber and 10% of soluble dietary fiber. In the snack the fiber amount fluctuated between 20 and 26% of total dietary fiber; 18 and 22% of insoluble dietary fiber, and 3.0 and 4.5% of soluble dietary fiber. The snack with the higher content of orange residue presented the higher content of dietary fiber. The snacks were well accepted by a sensory panel, without showing differences among treatments.

Utilización de residuos de la industria de jugos de naranja como fuente de fibra dietética en la elaboración de alimentos / Orange juice residues as dietary fiber source for foods

En este trabajo se plantea la formulación de un alimento tipo"snack" utilizando residuos en polvo provenientes de la industria procesadora de jugo de naranja, como fuente de fibra dietética. Para ello se elaboraron 6 formulaciones, utilizando el polvo con 3 niveles de humedad (25, 15 y 10%) que se incorporó a 2 mezclas, una compuesta por un 33,3% de polvo de naranja, 33,3% de miel, 16,6% de maní tostado y molido y 16,6% de pasas molidas y otra compuesta por un 28,6% de polvo de naranja, 35,7% de miel, 17,85% de maní y 17,85% de pasas. El residuo de naranja presentó un contenidode 64% de fibra dietética total, 54% fibra dietética insoluble y 10% fibra dietética soluble. Los "snack" tuvieron forma esférica con 2,5cm de diámetro y 10g de peso; una humedad que fluctuó entre 12,6 y 17,4%, y una actividad de agua entre 0,65 a 0,71. La composición proximal (base materia seca), fluctuó entre 1,6 y 1,9% de cenizas; 12,3 y 15,2% de lípidos; 6,1 y 7,1% de proteínas y 56,2 a 59,6% de hidratos de carbono con 326,8 a 342,9 Kcal/100g de producto. El aporte de fibra en los "snack" fluctuó entre un 20 a 26% de fibra dietética total, 18 a 22% de fibra dietética insoluble y 3,0 a 4,5% de fibra dietética soluble. El "snack" con mayor contenido de polvo de naranja presentó el mayor contenido de fibra dietética. Los "snack" fueron bien aceptados por el panel de evaluación sensorial sin registrar diferencias significativas entre los distintos tratamientos.

Orange juice residues as dietary fiber source for foods. Food snacks using powdered residues from the orange juice industry as a source of dietary fiber were formulated. Six formulations utilizing powdered orange residues with three different moisture levels (25%, 15% and 10%) were elaborated. There were used two basic blends. The first one was 33.3% of orange dry powder, 33.3% of honey, 16.6% of roasted peanut, 16.6% of raisins; the second one was 28.6% of orange powder, 35.7% of honey, 17.85% of roasted peanut, 17.85% of raisins. Snacks had spherical shape with 2.5 cm diameter and a weight close to 10g. The snack moisture was between 12.6 and 17.4%, and their aw between 0.65 and 0.71. The snack chemical composition, on dry matter basis, was 1.6 and 1.9% of ash; 12.3 and 15.2% of lipids; 6.1 and 7.1% of proteins; and 56.2 to 59.6% of carbohydrates; the caloric contribution (calculated) was between 326.8 and 342.9 kcal/100g. The powdered orange residue had 64% of total dietary fiber, 54% of insoluble dietary fiber and 10% of soluble dietary fiber. In the snack the fiber amount fluctuated between 20 and 26% of total dietary fiber; 18 and 22% of insoluble dietary fiber, and 3.0 and 4.5% of soluble dietary fiber. The snack with the higher content of orange residue presented the higher content of dietary fiber. The snacks were well accepted by a sensory panel, without showing differences among treatments.

[Use of nopal dietary fiber in a powder dessert formulation]. / Uso de fibra dietética de nopal en la formulación de un polvo para flan.

The development of diverse types of foods of low caloric value and with high content in dietary fiber have occupied a preponderant place in the food industry in the last years, due to the growing interest of the consumers for a healthy and nutritious diet. Pre-cooked or quick to prepare foods are attractive for the time they save; if to this you add their nutritious value, the attractiveness is even greater. For this reason, this study analyzes different formulations of a powder to prepare a dessert (flan), with different percentages of incorporation of nopal flour, as a source of dietary fiber (16%, 18%, 20%). Two flavors (melon and banana) were tried. It was observed that the flan flavored with banana and with 16% of nopal flour, reached better sensorial characteristics. Greater percentages of nopal flour negatively affected the sensorial characteristics, mainly flavor, color and texture. The analysis showed that the powder presented 5.7% of moisture, low water activity (0.48) and therefore a low total recount of microorganisms. The content of protein was high (27.2%), the ether extract low (2.0%) similar to the caloric contribution (40 Kcal/portion). The flan showed a 9.8% of total dietary fiber, being greater the contribution of soluble fiber (6.1%) than that of insoluble fiber (3.7%). Due to these characteristics this formulation could be considered as a food that provides benefits for the human health.