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SummaryReversible genomic DNA-inversions control expression of numerous bacterial molecules in the human gut, but how this relates to disease remains uncertain. By analyzing metagenomic samples from six human Inflammatory Bowel Disease (IBD) cohorts combined with mice experimentation, we identified multiple invertible regions in which a particular orientation was correlated with disease. These include the promoter of the anti-inflammatory polysaccharide-A (PSA) ofBacteroides fragilis, which is mostly oriented ‘OFF’ during inflammation but switches to the ‘ON’ orientation when inflammation is resolved. We further detected increased abundances ofB. fragilisassociated bacteriophages in patients with the PSA ‘OFF’ orientation. Isolation and analysis of aB. fragilisassociated bacteriophage revealed that it induced the PSA ‘OFF’ switch, thereby altering the bacterial induced immune modulation. Altogether, we reveal large-scale dynamic and reversible bacterial phase variations driven both by bacteriophages and the host inflammatory state signifying bacterial functional plasticity and suggesting potential clinical interventions.

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

Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of extreme 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, the factors that shape chronotypes remain poorly understood. Here, we assessed whether chronotypes are associated with different gut microbiome composition. Using metagenomic sequencing, we established a distinct signature associated with chronotype that involves two bacterial genera Alistipes (elevated in “larks”) and Lachnospira (elevated in “owls”). We have identified four metabolic pathways (e.g. gluconegonesis) that were associated with early chronotype. Significance Statement Studies in recent years uncover a significant relationship between the circadian system and the composition of the gut microbiota. However, the extent to which microbiome variability is associated with individual diurnal timing in humans (chronotype) is unknown. In this study we employed metagenomic sequencing and identified for the first time, a distinct microbiome signature that differs between early and late chronotypes. Given that the microbiome has been shown to be directly linked with food consumption and diet, this study may pave the way for diet-driven interventions aimed to ameliorate health problems associated with extreme chronotypes.

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.

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.

Our emerging view of the gut microbiome largely focuses on bacteria, while less is known about other microbial components such as bacteriophages (phages). Though phages are abundant in the gut, very few phages have been isolated from this ecosystem. Here, we report the genomes of 27 phages from the United States and Bangladesh that infect the prevalent human gut bacterium Bacteroides thetaiotaomicron. These phages are mostly distinct from previously sequenced phages with the exception of two, which are crAss-like phages. We compare these isolates to existing human gut metagenomes, revealing similarities to previously inferred phages and additional unexplored phage diversity. Finally, we use host tropisms of these phages to identify alleles of phage structural genes associated with infectivity. This work provides a detailed view of the gut’s “viral dark matter” and a framework for future efforts to further integrate isolation- and sequencing-focused efforts to understand gut-resident phages.

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.