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.

A community resource for paired genomic and metabolomic data mining

Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding identification of natural product biosynthetic origins and metabolite structures.

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.

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.

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.

Incompatibilities of lansoprazole injection with other drugs during simulated y-site coadministration

The physical compatibility of lansoprazole injection with selected other drugs during simulated Y-site coadministration was evaluated by means of visual observation, turbidity measurement, and particle content assessment. Five-milliliter samples of lansoprazole 0.55 mg/mL in 0.9% sodium chloride injection were conbined with 5 mL of 112 other drugs including antineoplastics, analgesics, antiinfectives, and supportive-care drugs undiluted or diluted in 0.9% sodium chloride injection or 5 % dextrose injection for amphotericin B. Visual examinations were performed with the unaided eye in fluorescent light and by means of a Tyndall beam (a high-intesity, monodirectional light beam) to enhance the visualization of small particles and low-level trubidity. The turbidity of each sample was measured as well. Particle sizing and counting were performed on selected samples. Evaluation of the samples was performed initially and at 1 and 4 hours after preparation. Of the drugs tested, 92 were incompatible with lansoprazole 0.55 mg/mL in 0.9% sodium chloride injection during the 4-hour observation period. Gross precipitation or color changes visible in normal diffuse room light with the unaided eye occurred with 45 drugs. Phenomena not visible with the unaided eye, such as microprecipitation and /or increases in measured turbidity, occurred with 47 drugs. Only 20 drugs were found to be compatible for at least 4 hours. The measured turbidity of the lansoprazole control solutions and the compatible test samples, remained essentially unchanged throughout the study. In addition, the compatible samples exhibited no color change or substantial change in particle size and content throughout the observation period. In conbination with lansoprazole, only 20 drugs were considered to be physically compatible. Ninety-two drugs exhibited frank precipitation, microparticulate formation, color changes, or unacceptable increases of measured turbidity within 4 hours and should not be simultaneously coadministered with lansoprazole.

Octreotide therapy of large-volume refractory AIDS-associated diarrhea: a randomized controlled trial

OBJECTIVE

To compare the effect of octreotide (a long-acting somatostatin analog) to that of antidiarrheal therapy plus placebo on large-volume refractory AIDS-associated diarrhea.

DESIGN

A randomized controlled trial.

SETTING

Referral-based clinic and hospital in a tertiary care center.

PATIENTS

Twenty male patients with AIDS and refractory diarrhea, with stool volume > 1000 ml/day who failed to improve after initial supportive management. All patients finished the study.

INTERVENTIONS

Patients were randomly given either octreotide in doses of 100, 200 and 300 micrograms subcutaneously every 8 h, or high doses of loperamide and diphenoxylate orally plus placebo subcutaneously for 10 days.

MAIN OUTCOME MEASURES

Bowel movements and stool volume were registered before and every day after treatment by the patients themselves and the nursing personnel.

RESULTS

Patients from both groups were similar for age, time of AIDS diagnosis, duration of diarrhea and etiology. Baseline mean bowel movements per day (9.4 +/- 2.8 in the octreotide group versus 10 +/- 3.1 in controls) and baseline mean stool volume (2753 +/- 840 versus 2630 +/- 630 ml/day, respectively) were similar in both groups before therapy (P < 0.05). Mean bowel movements per day after 10 days of therapy was 2.1 +/- 1.6 in the octreotide group versus 7 +/- 3 in controls (P < 0.05). Mean stool volume after 10 days of therapy was 485 +/- 480 in the octreotide group versus 1080 +/- 420 ml/day in controls (P < 0.05). Complete response (stool volume < 250 ml/day) was observed in two patients from the octreotide group and none from controls; partial response (decrease > 50% in stool volume) in four and two; and no response (decrease < 50% or no change) in four and eight (P < 0.05), respectively. Side-effects occurred in eight out of 10 octreotide patients and three out of 10 controls (P < 0.05), but none were significant to result in discontinuation of medication.

CONCLUSION

Octreotide proved to be superior to conventional therapy in this short-term treatment of large-volume refractory AIDS-associated diarrhea.

Macronodular lesions associated with Staphylococcus aureus bacteremia. A condition that resembles a 'lymphocutaneous' syndrome

A 54-year-old man, diagnosed as having Wegener's granulomatosis and treated with a regimen of cyclophosphamide and prednisone and hemodialysis, was found to have Staphylococcus aureus in blood, urine, and pus that were removed from the infected area. He had unusual macronodular lesions of the skin that resembled the lymphocutaneous syndrome. These lesions resolved with antibiotic therapy. To our knowledge, this condition has not been described previously.

Interaction between acetohydroxamic acid and 12 antibiotics against 14 gram-negative pathogenic bacteria

Acetohydroxamic acid (AHA) is a potent inhibitor of urease which prevents alkalinization of urine and stone formation in rats in the presence of infection caused by urease-producing bacteria. Because an antibacterial effect of AHA, and synergy between kanamycin and AHA have also been described, we studied the interaction between AHA and 12 antibiotics against 14 gram-negative bacteria. Synergy, sometimes to a striking degree, was found in 17% of interactions; however, antagonism was detected in 5%. Infecting organisms would need to be studied individually before the antibacterial effect of AHA and an antibiotic could be predicted.