Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944).

BACKGROUND: With increasing concerns about the impact of frequent antibiotic usage on the human microbiome, it is important to characterize the potential for such effects in early antibiotic drug development clinical trials. In a randomised Phase 2a clinical trial study that evaluated the pharmacokinetics of repeated oral doses of gepotidacin, a first-in-chemical-class triazaacenaphthylene antibiotic with a distinct mechanism of action, in adult females with uncomplicated urinary tract infections for gepotidacin (GSK2140944) we evaluated the potential changes in microbiome composition across multiple time points and body-sites ( ClinicalTrials.gov : NCT03568942). RESULTS: Samples of gastrointestinal tract (GIT), pharyngeal cavity and vaginal microbiota were collected with consent from 22 patients at three time points relative to the gepotidacin dosing regimen; Day 1 (pre-dose), Day 5 (end of dosing) and Follow-up (Day 28 ± 3 days). Microbiota composition was determined by DNA sequencing of 16S rRNA gene variable region 4 amplicons. By Day 5, significant changes were observed in the microbiome diversity relative to pre-dose across the tested body-sites. However, by the Follow-up visit, microbiome diversity changes were reverted to compositions comparable to Day 1. The greatest range of microbiome changes by body-site were GIT followed by the pharyngeal cavity then vagina. In Follow-up visit samples we found no statistically significant occurrences of pathogenic taxa. CONCLUSION: Our findings suggest that gepotidacin alteration of the human microbiome after 5 days of dosing is temporary and rebound to pre-dosing states is evident within the first month post-treatment. We recommend that future antibiotic drug trials include similar exploratory investigations into the duration and context of microbiome modification and recovery. TRIAL REGISTRATION: NCT03568942 . Registered 26 June 2018.

Expanding the drug discovery space with predicted metabolite-target interactions.

Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potential metabolite-target interactions using the Inflammatory Bowel Disease (IBD) cohort dataset of the Human Microbiome Project 2 (HMP2). Using a consensus of multiple machine learning methods, we ranked metabolites based on importance to IBD, followed by virtual ligand-based screening to identify possible human targets and adding evidence from compound assay, differential gene expression, pathway enrichment, and genome-wide association studies. We confirmed known metabolite-target pairs such as nicotinic acid-GPR109a or linoleoyl ethanolamide-GPR119 and inferred interactions of interest including oleanolic acid-GABRG2 and alpha-CEHC-THRB. Eleven metabolites were tested for bioactivity in vitro using human primary cell-types. By expanding the universe of possible microbial metabolite-host protein interactions, we provide multiple drug targets for potential immune-therapies.

Complementary NAD+ replacement strategies fail to functionally protect dystrophin-deficient muscle.

BACKGROUND: Duchenne muscular dystrophy (DMD) is a progressive muscle wasting disorder stemming from a loss of functional dystrophin. Current therapeutic options for DMD are limited, as small molecule modalities remain largely unable to decrease the incidence or mitigate the consequences of repetitive mechanical insults to the muscle during eccentric contractions (ECCs). METHODS: Using a metabolomics-based approach, we observed distinct and transient molecular phenotypes in muscles of dystrophin-deficient MDX mice subjected to ECCs. Among the most chronically depleted metabolites was nicotinamide adenine dinucleotide (NAD), an essential metabolic cofactor suggested to protect muscle from structural and metabolic degeneration over time. We tested whether the MDX muscle NAD pool can be expanded for therapeutic benefit using two complementary small molecule strategies: provision of a biosynthetic precursor, nicotinamide riboside, or specific inhibition of the NAD-degrading ADP-ribosyl cyclase, CD38. RESULTS: Administering a novel, potent, and orally available CD38 antagonist to MDX mice successfully reverted a majority of the muscle metabolome toward the wildtype state, with a pronounced impact on intermediates of the pentose phosphate pathway, while supplementing nicotinamide riboside did not significantly affect the molecular phenotype of the muscle. However, neither strategy sustainably increased the bulk tissue NAD pool, lessened muscle damage markers, nor improved maximal hindlimb strength following repeated rounds of eccentric challenge and recovery. CONCLUSIONS: In the absence of dystrophin, eccentric injury contributes to chronic intramuscular NAD depletion with broad pleiotropic effects on the molecular phenotype of the tissue. These molecular consequences can be more effectively overcome by inhibiting the enzymatic activity of CD38 than by supplementing nicotinamide riboside. However, we found no evidence that either small molecule strategy is sufficient to restore muscle contractile function or confer protection from eccentric injury, undermining the modulation of NAD metabolism as a therapeutic approach for DMD.

Universal Shelter-in-Place Versus Advanced Automated Contact Tracing and Targeted Isolation: A Case for 21st-Century Technologies for SARS-CoV-2 and Future Pandemics.

OBJECTIVE: To model and compare effect of digital contact tracing versus shelter-in-place on severe acute respiratory syndrome - coronavirus 2 (SARS-CoV-2) spread. METHODS: Using a classical epidemiologic framework and parameters estimated from literature published between February 1, 2020, and May 25, 2020, we modeled two non-pharmacologic interventions - shelter-in-place and digital contact tracing - to curb spread of SARS-CoV-2. For contact tracing, we assumed an advanced automated contact tracing (AACT) application that sends alerts to individuals advising self-isolation based on individual exposure profile. Model parameters included percentage population ordered to shelter-in-place, adoption rate of AACT, and percentage individuals who appropriately follow recommendations. Under influence of these variables, the number of individuals infected, exposed, and isolated were estimated. RESULTS: Without any intervention, a high rate of infection (>10 million) with early peak is predicted. Shelter-in-place results in rapid decline in infection rate at the expense of impacting a large population segment. The AACT model achieves reduction in infected and exposed individuals similar to shelter-in-place without impacting a large number of individuals. For example, a 50% AACT adoption rate mimics a shelter-in-place order for 40% of the population and results in a greater than 90% decrease in peak number of infections. However, as compared to shelter-in-place, with AACT significantly fewer individuals would be isolated. CONCLUSION: Wide adoption of digital contact tracing can mitigate infection spread similar to universal shelter-in-place, but with considerably fewer individuals isolated.

Microbiome Metabolite Mimics Accelerate Drug Discovery.

A recent study by Dvorák et al. supports metabolite mimicry as a drug development strategy. A potent agonist of the human pregnane X receptor (hPXR) was designed from two ligands that are products of the microbial catabolism of tryptophan. Its validity was demonstrated in cellular assays and a murine colitis model expressing hPXR by a significant reduction in inflammation biomarkers.

Impact of Soil Microbial Amendments on Tomato Rhizosphere Microbiome and Plant Growth in Field Soil.

There is increased interest by the agricultural industry in microbial amendments that leverage natural beneficial interactions between plants and soil microbes to improve crop production. However, translating fundamental knowledge from laboratory experiments into efficient field application often has mixed results, and there is less clarity about the interaction between added microbes and the native microbial community, where microorganisms belonging to the same phylogenic clades often reside. In this study, four commercially available microbial amendments were examined in two greenhouse experiments using field soil to assess their impact on tomato plant growth and the native soil microbial communities. The amendments contained different formulations of plant growth-promoting bacteria (Lactobacilli, Rhizobia, etc.), yeasts, and mycorrhizal fungi. The application of the tested amendments in greenhouse conditions resulted in no significant impact on plant growth. A deeper statistical analysis detected variations in the microbial communities that accounted only for 0.25% of the total species, particularly in native taxa not related to the inoculated species and represented less than 1% of the total variance. This suggests that under commercial field conditions, additional confounding variables may play a role in the efficacy of soil microbial amendments. This study confirms the necessity of more in-depth validation requirements for the formulations of soil microbial amendments before delivery to the agricultural market in order to leverage their benefits for the producers, the consumers, and the environment.

The Microbiome Factor in Drug Discovery and Development.

Here we review recent studies that illustrate three areas where the microbiome directly impacts drug development: (1) microbial effects on drug safety and efficacy, (2) the effects of drugs on causing collateral restructuring of microbiome communities, and (3) the potential side-effects of novel therapies targeting the microbiome. On the basis of the findings of these and other studies, we advocate the systematic incorporation of microbiome analyses in early to late stage clinical trials as a strategy to increase the overall success rate of the drug discovery and development process.

Containment of a genetically modified microorganism by an activated sludge system.

The effectiveness of physical, chemical and biological barriers to the diffusion of genetically modified microorganisms (GMMs) to prevent their release into the environment is currently under scrutiny worldwide because of the associated potential ecological impacts. An industrial discharge of a non-sterilized fermentation broth containing GMM biomass into a conventional municipal wastewater treatment plant would deliver the GMMs into the activated sludge system process (ASSP). The present work aimed to model and evaluate the containment capability of a small ASSP (part of a 20,000 people equivalent municipal plant) in the event of receiving GMM biomass from a medium-small biotechnological plant dedicated to the production of polyhydroxyalkanoates (3000 t/year of biopolymer). An actual GMM (Pseudomonas putida KTOY06) was injected into a bench-scale ASSP (ASSPLab) in a quantity proportional to the relative dimensions of the plants mentioned. The experimental and model results indicated that the ASSP of the target municipal treatment plant would not be capable of holding back such a sudden input of GMM; 6 h after the discharge, 11-15 % of injected GMM cells were released through the clarified stream of the ASSPLab, with the rest being gradually released over time. Since the GMM employed did not exhibit any growth in the ASSPLab, its concentration in the clarified water stream would not represent a substantial risk of release into the environment if appropriate tertiary treatments were integrated. This study confirmed the necessity of a thorough risk assessment of biotechnological processes prior to their implementation.

Optimization of washing conditions with biogenic mobilizing agents for marine fuel-contaminated beach sands.

Washing is a rapid and effective treatment to remediate contaminated sands impacted by oil spills, although synthetic additives used to increase extraction efficiency may cause additional pollution issues due to their intrinsic toxicity and very often low biodegradability. In this study, different biogenic mobilizing agents (soybean lecithins, cyclodextrins, cholic acids, plant-derived cleaners, rhamnolipids and sophorolipids) were tested in the washing of beach sands artificially contaminated with the Intermediate Fuel Oil IFO-180. Among these, a de-oiled soybean lecithin (SL-1), hydroxypropyl-ß-cyclodextrins (HPB-CD) and sophorolipids (SR) achieved hydrocarbon removals close to those attained with the synthetic surfactant Triton™ X-100 (TX) in preliminary washing tests carried out at constant mixing rate, water/sand ratio and IFO-180 contamination level using agents concentrations close to their critical micelle concentration (0.1% and 1% w/v for microbial and non-microbial agents, respectively). The effects of agent concentration, water/sand ratio, mixing rate and IFO-180 contamination on hydrocarbons removal were modelled using face-centred central composite design and ANOVA. Optimal washing parameters for sand contamination levels in the range 0.5-20 g/kg were identified with response surface methodology. While HPB-CD and SR performed equally to TX only at low sand contaminations, SL-1 attained hydrocarbon removal higher or equal to that of TX at any IFO-180 contamination and at lower application rates. SL-1 also outperformed TX when minimizing the water/sand ratio, i.e., the volume of water used. Considering its lower toxicity, higher biodegradability and higher hydrocarbon removal efficiencies, SL-1 is an effective and environmentally sustainable alternative to synthetic surfactants in washing treatments for marine fuel-contaminated sands.

Identification of two organohalide-respiring Dehalococcoidia associated to different dechlorination activities in PCB-impacted marine sediments.

BACKGROUND: Microbial reductive dechlorination of polychlorinated biphenyls (PCBs) plays a major role in detoxifying anoxic contaminated freshwater and marine sediments from PCBs. Known members of the phylum Chloroflexi are typically responsible for this activity in freshwater sediments, whereas less is known about the microorganisms responsible for this activity in marine sediments. PCB-respiring activities were detected in PCB-impacted marine sediments of the Venice Lagoon. The aim of this work was to identify the indigenous organohalide-respiring microorganisms in such environments and assess their dechlorination specificity against spiked Aroclor™ 1254 PCBs under laboratory conditions resembling the in situ biogeochemistry. RESULTS: High PCB dechlorination activities (from 150 ± 7 to 380 ± 44 µmol of chlorine removed kg-1 week-1) were detected in three out of six sediments sampled from different locations of the lagoon. An uncultured non-Dehalococcoides phylotype of the class Dehalococcoidia closely related to Dehalobium chlorocoercia DF-1, namely phylotype VLD-1, was detected and enriched up to 109 16S rRNA gene copies per gram of sediment where dechlorination activities were higher and 25-4/24-4 and 25-2/24-2/4-4 chlorobiphenyls (CB) accumulated as the main tri-/dichlorinated products. Conversely, a different phylotype closely related to the SF1/m-1 clade, namely VLD-2, also enriched highly where lower dechlorination activity and the accumulation of 25-3 CB as main tri-chlorinated product occurred, albeit in the simultaneous presence of VLD-1. Both phylotypes showed growth yields higher or comparable to known organohalide respirers and neither phylotypes enriched in sediment cultures not exhibiting dechlorination. CONCLUSIONS: These findings confirm the presence of different PCB-respiring microorganisms in the indigenous microbial communities of Venice Lagoon sediments and relate two non-Dehalococcoides phylotypes of the class Dehalococcoidia to different PCB dechlorination rates and specificities.

Impact of bio-palladium nanoparticles (bio-Pd NPs) on the activity and structure of a marine microbial community.

Biogenic palladium nanoparticles (bio-Pd NPs) represent a promising catalyst for organohalide remediation in water and sediments. However, the available information regarding their possible impact in case of release into the environment, particularly on the environmental microbiota, is limited. In this study the toxicity of bio-Pd NPs on the model marine bacterium V. fischeri was assessed. The impacts of different concentrations of bio-Pd NPs on the respiratory metabolisms (i.e. organohalide respiration, sulfate reduction and methanogenesis) and the structure of a PCB-dechlorinating microbial community enriched form a marine sediment were also investigated in microcosms mimicking the actual sampling site conditions. Bio-Pd NPs had no toxic effect on V. fischeri. In addition, they had no significant effects on PCB-dehalogenating activity, while showing a partial, dose-dependent inhibitory effect on sulfate reduction as well as on methanogenesis. No toxic effects by bio-Pd NPs could be also observed on the total bacterial community structure, as its biodiversity was increased compared to the not exposed community. In addition, resilience of the microbial community to bio-Pd NPs exposure was observed, being the final community organization (Gini coefficient) of samples exposed to bio-Pd NPs similar to that of the not exposed one. Considering all the factors evaluated, bio-Pd NPs could be deemed as non-toxic to the marine microbiota in the conditions tested. This is the first study in which the impact of bio-Pd NPs is extensively evaluated over a microbial community in relevant environmental conditions, providing important information for the assessment of their environmental safety.