Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota

Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented "OFF" in IBD patients, which correlated with increased B. fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B. fragilis, induction of colitis caused a decline of PSA in the "ON" orientation that reversed as inflammation resolved. Monocolonization of mice with B. fragilis revealed that bacteriophage infection increased the frequency of PSA in the "OFF" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.

Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel

Lynch syndrome (LS) is a hereditary cancer syndrome caused by autosomal dominant mutations, with high probability of early onset for several cancers, mainly colorectal cancer (CRC). The gut microbiome was shown to be influenced by host genetics and to be altered during cancer development. Therefore, we aimed to determine alterations in gut microbiome compositions of LS patients with and without cancer. We performed fecal microbiome analyses on samples of LS and non-LS members from the Druze ethnoreligious community in Israel, based on both their LS mutation and their cancer history. Our analysis revealed specific bacterial operational taxonomic units (OTUs) overrepresented in LS individuals as well as bacterial OTUs differentiating between the LS individuals with a history of cancer. The identified OTUs align with previous studies either correlating them to pro-inflammatory functions, which can predispose to cancer, or to the cancer itself, and as such, these bacteria can be considered as future therapeutic targets.

Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects

The gut microbiota is now well known to affect the host's immune system. One way of bacterial communication with host cells is via the secretion of vesicles, small membrane structures containing various cargo. Research on vesicles secreted by Gram-positive gut bacteria, their mechanisms of interaction with the host and their immune-modulatory effects are still relatively scarce. Here we characterized the size, protein content, and immune-modulatory effects of extracellular vesicles (EVs) secreted by a newly sequenced Gram-positive human gut symbiont strain - Bifidobacterium longum AO44. We found that B. longum EVs exert anti-inflammatory effects, inducing IL-10 secretion from both splenocytes and dendritic cells (DC)-CD4+ T cells co-cultures. Furthermore, the EVs protein content showed enrichment in ABC transporters, quorum sensing proteins, and extracellular solute-binding proteins, which were previously shown to have a prominent function in the anti-inflammatory effect of other strains of B. longum. This study underlines the importance of bacterial vesicles in facilitating the gut bacterial immune-modulatory effects on the host and sheds light on bacterial vesicles as future therapeutics.

Microbiome Characterization of Infected Diabetic Foot Ulcers in Association With Clinical Outcomes: Traditional Cultures Versus Molecular Sequencing Methods

Background

Infected diabetic foot ulcers (IDFU) are a major complication of diabetes mellitus. These potentially limb-threatening ulcers are challenging to treat due to impaired wound healing characterizing diabetic patients and the complex microbial environment of these ulcers.

Aim

To analyze the microbiome of IDFU in association with clinical outcomes.

Methods

Wound biopsies from IDFU were obtained from hospitalized patients and were analyzed using traditional microbiology cultures, 16S rRNA sequencing and metagenomic sequencing. Patients’ characteristics, culture-based results and sequencing data were analyzed in association with clinical outcomes.

Results

A total of 31 patients were enrolled. Gram-negative bacteria dominated the IDFU samples (79%, 59% and 54% of metagenomics, 16S rRNA and cultures results, respectively, p<0.001). 16S rRNA and metagenomic sequencing detected significantly more anaerobic bacteria, as compared to conventional cultures (59% and 76%, respectively vs. 26% in cultures, p=0.001). Culture-based results showed that Staphylococcus aureus was more prevalent among patients who were treated conservatively (p=0.048). In metagenomic analysis, the Bacteroides genus was more prevalent among patients who underwent amputation (p<0.001). Analysis of metagenomic-based functional data showed that antibiotic resistance genes and genes related to biofilm production and to bacterial virulent factors were more prevalent in IDFU that resulted in amputation (p<0.001).

Conclusion

Sequencing tools uncover the complex biodiversity of IDFU and emphasize the high prevalence of anaerobes and Gram-negative bacteria in these ulcers. Furthermore, sequencing results highlight possible associations among certain genera, species, and bacterial functional genes to clinical outcomes.

"More Guts Than Brains?"-The Role of Gut Microbiota in Idiopathic Intracranial Hypertension

BACKGROUND

Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity. Accordingly, we investigated whether the gut microbiome is modified in IIH patients compared with healthy controls, and provide possible new treatment venues.

METHODS

Shotgun metagenomic sequencing of the gut microbiome of 25 cases of IIH patients (according to the modified Dandy criteria) and 20 healthy controls. Participants were further stratified according to their body mass index. The total DNA from each sample was extracted using the PureLink Microbiome DNA Purification Kit A29789 (Invitrogen, Thermo Fisher Scientific, US). Library preparation was performed using the Nextera DNA Flex Library Prep Kit. Samples were sequenced on the Illumina Novaseq 6000 device. A list of bacterial species that significantly differed between the IIH patients and healthy controls was produced in addition to species diversity. In addition, patients' cohort alone was analyzed, (excluding the healthy controls), and the effect of acetazolamide treatment on their gut microbiota was analyzed.

RESULTS

IIH patients have a lower diversity of bacterial species compared with healthy individuals. These bacteria, that is, Lactobacillus ruminis (L. ruminis) (p<6.95E-08), Atopobium parvulum (p<3.9E-03), Megamonas hypermegale (p<5.61E-03), Ruminococcus gnavus (p<1.29E-02), MEL.A1 (p<3.04E-02), and Streptococcus sp. I-G2 (p<3.04E-02), were previously characterized with beneficial health effects. Moreover, we found that Lactobacillus brevis, a beneficial bacterium as well, is more abundant in acetazolamide treated patients (p<7.07E-06).

CONCLUSIONS

Gut microbiota plays a potential role in IIH etiology and therefore, can provide a promising new treatment approach for this disease.

The Mechanical Cost of Decreasing Conduction Velocity: A Mathematical Model of Pacing-Induced Lower Strain

Purpose

To simulate the effect of decreasing conduction velocity (Cvel) on average segmental myocardial strain using mathematical modeling.

Methods

The simulation was run using MatLab version 7.4 (The MathWorks, Inc. Natick, Massachusetts). A normal strain-time curve pattern was sampled from a normal human echo study using the 2D strain imaging software (GE Healthcare, Milwaukee, Wisconsin). Contraction was simulated from simultaneous segmental activation (Cvel=∞) through normal activation (Cvel=400cm/sec) to pacing Cvel (100 to 10cm/sec). The simulation generated average segmental strain-time waveforms for each velocity and peak strain as a function of Cvel and time to peak strain as a function of Cvel curves.

Results

With decreasing Cvel, average peak segmental strain was found to be decreased and delayed. The following correlation equation represents the correlation betweenpeak strain and Cvel : strain= -20.12+27.65 x e (-0.29 x Cvel). At the highest pacing Cvel (100cm/sec) average peak segmental strain dropped by 10%, at 50cm/sec by 30% and at the lowest pacing Cvel (10cm/sec) peak strain dropped by >90%. Time to peak segmental strain was minimally longer with decreasing Cvel down to 70cm/sec (pacing velocity range). Further decreased velocity dramatically increased time to peak strain of the simulated segment.

Conclusions

The simulation yielded a predictive correlation between slower conduction velocities and decreased and delayed segmental strain.

1018. Bacterial Bioburden Characterization of Infected Diabetic Foot Ulcers in Hospitalized Patients in Association with Clinical Outcomes: Traditional Cultures vs. Molecular Sequencing Methods

Background

Infected diabetic foot ulcers (IDFU) are a major complication of diabetes mellitus. These potentially limb-threatening ulcers are challenging to treat due to the impairment of wound healing in diabetic patients and the complex microbial environment characterizing these ulcers. Our aim was to analyze the microbiome of IDFU in association with clinical outcomes.

Methods

Wound biopsies from IDFU were obtained from hospitalized patients and were analyzed using traditional microbiology cultures, 16S rRNA sequencing and shotgun metagenomic sequencing. Patients’ characteristics, culture-based results and sequencing data were analyzed in association with clinical outcomes.

Study Design

Results

31 patients were enrolled. Significantly more anaerobic and Gram-negative bacteria were detected with sequencing methods compared to conventional cultures (59% and 76% were anaerobes according to 16SrRNA and metagenomic respectively vs. 26% in cultures, p=0.001, and 79%, 59% and 54% were Gram negative bacteria respectively, p< 0.001). Culture-based results showed that Staphylococcus aureus was more prevalent among patients who were conservatively treated (p=0.048). In metagenomic analysis the Bacteroides genus was more prevalent among patients who underwent toe amputation (p< 0.001). Analysis of metagenomic-based functional data showed that antibiotic resistance genes and genes related to biofilm production and to bacterial virulent factors were more prevalent in IDFU that resulted in toe amputation (p< 0.001).

Occurrences and mean relative abundances of the most prevalent bacteria of IDFU

Comparison between [A] traditional cultures, 16S rRNA sequencing and metagenomic sequencing results (genera level - 12 samples) [B] traditional cultures and metagenomic sequencing results (species level – 30 samples) [C] traditional cultures and 16S rRNA sequencing results (genera level - 30 samples) CUL – cultures; 16S - 16S rRNA sequencing; MTG – metagenomic sequencing

Bacteroides genus association with toe amputation

Bacteroides genera was more common among samples of patients who underwent toe amputation compared with samples of patients who were conservatively treated (p < 0.001). Species level analysis showed that Bacteroides fragilis and Bacteroides xylanisolvens predominated IDFU of patients who underwent toe amputation (p=0.04, p=0.002 respectively). No – conservative treatment; Yes – toe amputation.

Functional genes differentiating patients who underwent toe amputation from conservatively treated

Yellow stars – indicate genes that were associated with bacterial virulent factors, biofilm formation and resistant mechanisms – all were more prevalent in patients who underwent toe amputation (with p values<>

Conclusion

Molecular sequencing tools uncover the complex biodiversity of IDFU and emphasize the high prevalence of anaerobes and Gram-negative bacteria in these ulcers. Furthermore, sequencing results highlighted the possible association between certain genera, species, and bacterial functional genes to clinical outcomes

Disclosures

Yossi Paitan, PhD, Ilex Medical Ltd (Employee, Other Financial or Material Support, As of 01.01.2021 I am the Laboratories Manager of Ilex Labs)

Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes

Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of opposite chronotypes. Growing evidence suggests that the late chronotype significantly impacts the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. Despite the vast potential of utilizing chronotype information for precision medicine, those factors that shape chronotypes remain poorly understood. Here, we assessed whether the various chronotypes are associated with different gut microbiome compositions. Using metagenomic sequencing analysis, we established a distinct signature associated with chronotype based on two bacterial genera, Alistipes (elevated in "larks") and Lachnospira (elevated in "owls"). We identified three metabolic pathways associated with the early chronotype, and linked distinct dietary patterns with different chronotypes. Our work demonstrates an association between the gut microbiome and chronotype and may represent the first step towards developing dietary interventions aimed at ameliorating the deleterious health correlates of the late chronotype.

Utilization and complications of catheter ablation for ventricular arrhythmias in patients with mechanical valves

Background

Catheter ablation (CA) for ventricular arrhythmias (VAs) is increasingly utilized in the recent years. Ablation for VAs in patients with mechanical valves (MVs), can be challenging due to the chronic anticoagulation therapy, limitations in accessing the cardiac chambers, the risk for entrapment of mapping or ablation catheters between the leaflets of MVs and more.

Purpose

To investigate the nationwide trends in utilization and complications of CA for VAs in patients with prior MVs.

Methods

We drew data from the US National Inpatient Sample database to identify cases of VA ablations, including premature ventricular contraction (PVC) and ventricular tachycardia (VT) ablations, in patients with MVs between 2003 and 2015. Sociodemographic and clinical data were collected, and incidence of catheter ablation complications, mortality, and length of stay were analyzed. We compared the outcomes to a propensity matched cohort of patients without prior valve surgery.

Results

The study population included a weighted total of 647 CA cases in patients with prior MVs. The annual number of ablations almost doubled, from 34 ablations on average during the “early years” (2003–2008) to 64 annual ablation procedures on average during the “late years” (2009–2015) of the study (p=0.001). Length of stay at the hospital did not differ significantly between patients with MVs and 649 matched patients without prior MVs (5.4±0.4, 4.7±0.3 days respectively, p=0.12). The incidence of complications was higher among patients with and without MVs (12.6% vs. 7.5% respectively, p=0.14), however, not reaching statistical significance. Moreover, the data revealed a trend toward higher mortality among patients with MVs undergoing CA compared to matched control patients without MVs (3.7% vs. 0.7% respectively, p=0.087).

Conclusion

The utilization of catheter ablations for ventricular arrhythmias in patients with mechanical valves increased substantially over the years. The data show a trend towards increased incidence of morality and complications in the study population, requiring further investigation in larger population cohort.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): Padeh Medical Center Research Fund

Oral Capsulized Fecal Microbiota Transplantation for Eradication of Carbapenemase-producing Enterobacteriaceae Colonization With a Metagenomic Perspective

BACKGROUND

Carbapenemase-producing Enterobacteriaceae (CPE) infections lead to considerable morbidity and mortality. We assessed the potential of fecal microbiota transplantation (FMT) to eradicate CPE carriage and aimed to explain failure or success through microbiome analyses.

METHODS

In this prospective cohort study, all consenting eligible CPE carriers received oral capsulized FMT for 2 days. Primary outcome was CPE eradication at 1 month, defined by 3 consecutive negative rectal swabs, the last also negative for carbapenemase gene by polymerase chain reaction. Comprehensive metagenomics analysis of the intestinal microbiome of donors and recipients before and after FMT was performed.

RESULTS

Fifteen CPE carriers received FMT, 13 of whom completed 2 days of treatment. CPE eradication at 1 month was successful in 9/15 and 9/13, respectively. Bacterial communities showed significant changes in both beta and alpha diversity metrics among participants who achieved CPE eradication that were not observed among failures. Post-FMT samples' beta-diversity clustered according to the treatment outcome, both in taxonomy and in function. We observed a significant decrease in beta diversity in participants who received post-FMT antibiotics. Enterobacteriaceae abundance decreased in post-FMT samples of the responders but increased among failures. Functionally, a clear demarcation between responders (who were similar to the donors) and failures was shown, driven by antimicrobial resistance genes.

CONCLUSIONS

Our study provides the biological explanation for the effect of FMT against CPE carriage. Decolonization of CPE by FMT is likely mediated by compositional and functional shifts in the microbiome. Thus, FMT might be an efficient strategy for sustained CPE eradication.

CLINICAL TRIALS REGISTRATION

NCT03167398.

Validation of an artificial intelligence-based tool for automated evaluation of RV size and function from ultrasound examinations

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): Study sponsored by DiA Imaging Analysis

Background

 The assessment of the right ventricular (RV) function is an essential part of every transthoracic echocardiographic examination. It plays an important role in the diagnosis and management of many diseases and conditions. In covid-19 patients, there is evidence showing that enlarged RV and abnormal Free Wall Strain (FWS) correlate with high mortality. Assessment of the RV in the Point of Care settings can assist the differential diagnosis and provide important clinical information in early stages, close to the onset of symptoms, however, it is done qualitatively by visual estimation and thus subjective and requires high level of expertise. The presented study aims to validate the use of a novel artificial intelligence tool (LVivo RV by DiA imaging analysis) that uses deep learning and image processing algorithms to automatically evaluate RV size and function from apical 4 chamber (4CH) focused or modified ultrasound clips.

Methods

 A retrospective study of 100 patients who underwent routine echocardiographic examination was conducted in three medical centers in US and Israel. The apical 4CH focused or modified clips were interpreted by experts to evaluate RV size and function. The End Diastolic Area (EDA) measured manually by two sonographers and the FWS measured by semi-automated Velocity Vector Imaging software (VVI by Siemens) were compared to the same parameters obtained automatically by the LVivo RV, using linear regression and Bland Altman analysis.

Results

 100 cases were included, 39% females and 61% males. Mean age was 64.7 [19-92]. Mean BMI was 28.1 [6.8-17.6]. 74% had pulmonary hypertension and 19% had lung disease. 36% were considered abnormal by their fractional area change values and 64% were considered normal. Three cases were non-interpretable by the physicians thus excluded from the analysis. The LVivo RV was able to process 99% of the cases. Excellent correlation was obtained for EDA between the sonographers" average of manual measurements and the automated EDA by LVivo RV with r = 0.92 (p &lt; 0.0001, 95%CI 0.88-0.94). The bias and limits of agreement for EDA were 0.87 ± 5.76cm^2. For FWS, 4 cases were manually excluded due to insufficient image quality. The Bland Altman analysis for FWS showed small bias and limits of agreement of 0.7 ± 12.2%. A very good correlation of r= 0.78, (95% CI 0.69-0.85) was found, indicating good compatibility between the methods. The specificity and sensitivity for FWS were 80% and 77% respectively, using an optimal cutoff value of -16%, and the overall agreement was 79%.

Conclusions

 The performance of LVivo RV demonstrated a very good agreement with manual and semi-automated quantitative methods for RV assessment. LVivo RV provides fast, accurate, objective and reproducible results and has the potential to be used at the Point of Care settings as a powerful tool for RV size and function evaluation.

Abstract Figure.

Analysis of a phase-variable restriction modification system of the human gut symbiont Bacteroides fragilis

The genomes of gut Bacteroidales contain numerous invertible regions, many of which contain promoters that dictate phase-variable synthesis of surface molecules such as polysaccharides, fimbriae, and outer surface proteins. Here, we characterize a different type of phase-variable system of Bacteroides fragilis, a Type I restriction modification system (R-M). We show that reversible DNA inversions within this R-M locus leads to the generation of eight specificity proteins with distinct recognition sites. In vitro grown bacteria have a different proportion of specificity gene combinations at the expression locus than bacteria isolated from the mammalian gut. By creating mutants, each able to produce only one specificity protein from this region, we identified the R-M recognition sites of four of these S-proteins using SMRT sequencing. Transcriptome analysis revealed that the locked specificity mutants, whether grown in vitro or isolated from the mammalian gut, have distinct transcriptional profiles, likely creating different phenotypes, one of which was confirmed. Genomic analyses of diverse strains of Bacteroidetes from both host-associated and environmental sources reveal the ubiquity of phase-variable R-M systems in this phylum.

Phage-Bacteria Associations: Analyze. Match. Develop Therapies

Although bacteriophages are highly abundant in the gut microbiome, little is known about their potential effects on gut bacteria. In this issue of Cell Host & Microbe, Hryckowian et al. (2020) and Fujimoto et al. (2020) combined metagenomic analysis and experiments to study phage-bacteria associations in order to develop future research tools and therapies.

Disseminated fat necrosis with asymptomatic pancreatitis: a case report and review of the literature

A 62-year-old man with multiple nontender skin nodules is presented. Some of these nodules discharged a purulent looking fluid. At presentation, the patient did not have any other complaints. No infectious, neoplastic, or immunologic origin could be found for the nodular rash. Biochemical profile, imaging, and skin biopsy confirmed the diagnosis of disseminated fat necrosis (DFN) accompanying asymptomatic pancreatitis. The process involved the mesenteric, subcutaneous, and intramedullary fat. The skin lesions were surgically treated. Mesenteric and intramedullary fat necrosis were watched closely. A year later, the patient was readmitted with a diagnosis of pancreatitis. Subcutaneous and intramedullary necrosis were completely resolved at this time, and only mesenteric fat necrosis prevailed. The clinical syndrome of DFN, its etiology, pathophysiology, treatment, and prognosis are discussed.

Computerized analysis of myocardial echocardiographic enhancement during coronary revascularization by high-speed rotational atherectomy

A previous report demonstrated transient myocardial echocardiographic contrast (MEC) enhancement following high-speed rotational atherectomy (HSRA). This phenomenon was found to be correlated to the speed and duration of rotation and related to creation of cavitations. To determine other correlations and the significance of MEC, continuous echocardiographic recording was performed in 10 patients undergoing HSRA. Images were digitized and videointensity-time curves generated. Curve parameters were calculated and correlated with procedural variables, plaque mass, and side effects. Twenty-nine ablation passes in 10 patients were analyzed. Videointensity peaked 9-44 sec from initiation of ablation and decayed to a higher baseline level after each consecutive ablation. Increase in peak contrast intensity (PCI) from baseline and the percentage of the left ventricle undergoing enhancement were highest (33 +/- 31 gray level/pixel and 32% +/- 8%, mean +/- SD, respectively) after the second rotation and were not influenced by the duration of rotation. PCI, side effects, and transient left ventricular wall motion abnormalities were positively correlated with plaque mass, defined by the product of lesion length, diameter, and percent stenosis. HSRA resulted in significant myocardial echocardiographic contrast. PCI is related to ablation sequence and plaque mass. Plaque debris embolization is probably responsible for myocardial echocardiographic contrast and transient wall motion abnormalities. Cathet. Cardiovasc. Intervent. 49:39-44, 2000.

Combining transmural left ventricular mechanics and energetics to predict oxygen demand

This study relates to our earlier study which predicts the transmural distribution as well as the global left ventricular (LV) function and oxygen demand, based on the LV structure, geometry and sarcomere function. Here, we test the predicted global oxygen demand against experimental data in anesthetized, open chest dogs under changing working conditions. The experimental oxygen demand was calculated from the arterio-venous difference in oxygen content times the measured coronary flow. LV load was manipulated by a combination of a pressurized chamber connected to the femoral artery, phenylephrine infusion and an adjustable arteriovenous shunt. The heart was paced in two present heart rates. The study demonstrates that the global predictions, based on the local distributed oxygen demand model, are comparable to those obtained by other methods of global metabolic predictions. However, unlike other global methods, the distributed model gives spatial information and predicts an endo/epi ratio of oxygen demand ranging between 1.05 to 1.14, depending on the loading conditions, which is comparable to available experimental data. For the experimental conditions studied here (stroke volume, heart rate, aortic pressure), the theoretical analysis shows that only the end diastolic volume is significantly correlated to the endo/epi ratio of the transmural oxygen demand.