SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota.

Background: Clustering of sequences into operational taxonomic units (OTUs) and denoising methods are a mainstream stopgap to taxonomically classifying large numbers of 16S rRNA gene sequences. Environment-specific reference databases generally yield optimal taxonomic assignment.

Results: We developed SpeciateIT, a novel taxonomic classification tool which rapidly and accurately classifies individual amplicon sequences ( https://github.

Use of drugs for hypertension or heart failure and the risk of death in COVID-19: association with loop-diuretics.

Purpose: To study the association between the use of drugs for hypertension or heart failure, particularly diuretics, and risk of death in COVID-19.

Methods: We conducted a cohort study, based on record linked individual-based data from national registers, of all Swedish inhabitants 50 years and older (n = 3,909,321) at the start of the first SARS-CoV-2 wave in Sweden. The association between use of angiotensin-converting enzyme inhibitors (ACEI), angiotensin II receptor blockers (ARB), thiazides, loop diuretics, aldosterone antagonists, beta blocking agents and calcium channel blockers at the index date 6 March 2020, and death in COVID-19 during 7 March to 31 July 2020, was analysed using Cox-proportional hazards regression, adjusted for a wide range of possible confounders.

SpeciateIT and vSpeciateDB: Novel, fast and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota.

Clustering of sequences into operational taxonomic units (OTUs) and denoising methods are a mainstream stopgap to taxonomically classifying large numbers of 16S rRNA gene sequences. We developed speciateIT, a novel taxonomic classification tool which rapidly and accurately classifies individual amplicon sequences (https://github.com/Ravel-Laboratory/speciateIT).

Integrating compositional and functional content to describe vaginal microbiomes in health and disease.

Background: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.

Investigating the impact of condomless vaginal intercourse and lubricant use on the vaginal metabolome: a pre-post observational study.

Objective: The vaginal metabolome is a significant factor in the vaginal microenvironment, and data are emerging on its independent role in urogenital health. Condomless vaginal intercourse and personal lubricant use are common practices that may affect the vaginal metabolome. The aim of the present study is to describe the associations between condomless intercourse and lubricant use on the vaginal metabolome.

and genital health: molecular clues to an enigmatic vaginal species.

Purpose Of Review: Vaginal lactobacilli are recognized as important drivers of genital health including protection against bacterial vaginosis and sexually transmitted infections. is distinct from , and by its high global prevalence in vaginal microbiomes, relatively small genome, production of only L-lactic acid, and inconsistent associations with genital health outcomes. In this review, we summarize our current understanding of the role of in the vaginal microbiome, highlight the importance of strain-level consideration for this species, and explain that while marker gene-based characterization of the composition of the vaginal microbiota does not capture strain-level resolution, whole metagenome sequencing can aid in expanding our understanding of this species in genital health.

Association of Pregnancy and HIV Status With Molecular-Bacterial Vaginosis in Indian Women.

Background: Bacterial vaginosis (BV) is a highly prevalent disorder of the cervicovaginal microbiota. Molecular-BV may put women at increased risk for adverse reproductive and obstetric outcomes. We investigated the association of HIV and pregnancy on the vaginal microbiota and associations with molecular-BV in women of reproductive age from Pune, India.

High-resolution functional description of vaginal microbiomes in health and disease.

Background: A dominated vaginal microbiome provides the first line of defense against numerous adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this limitation, we developed metagenomic community state types (mgCSTs) which uses metagenomic sequences to describe and define vaginal microbiomes based on both composition and function.

A prognostic model for predicting the duration of 20,049 sickness absence spells due to shoulder lesions in a population-based cohort in Sweden.

Main Objective: Sickness absence duration for shoulder lesion patients is difficult to prognosticate, and scientific evidence for the sick-listing practice is lacking. Our objective was to develop a clinically implementable prediction model for the duration of a sickness absence spell due to shoulder lesions.

Methods: All new sickness absence spells due to shoulder lesions (ICD-10-code: M75) issued in the period January 2010-June 2012 that were longer than 14 days were identified through the nationwide sickness absence insurance register.

Dynamics of the Gut Microbiome in -Infected Children during the First Two Years of Life.

continues to be a major contributor to diarrheal illness and dysentery in children younger than 5 years of age in low- and middle-income countries. Strategies for the prevention of shigellosis have focused on enhancing adaptive immunity. The interaction between and intrinsic host factors, such as the microbiome, remains unknown.

Wellbeing and mental health amongst medical students in Canada.

Research: There is abundant data revealing that there is significant rate of rates of Psychiatric morbidity, psychological stress, and burnout in the medical student population. A core study group in the UK collaborated with 12 countries around the world to review medical student wellness. In this context we surveyed 101 medical students at the Cummings medical school, Calgary, Canada during the height of the COVID pandemic regarding their wellbeing and mental health.

Mortality in hospitalized COVID-19 patients was associated with the COVID-19 admission rate during the first year of the pandemic in Sweden.

Introduction: Studies from the first pandemic wave found associations between COVID-19 hospital load and mortality. Here, we aimed to study if mortality of hospitalized COVID-19 patients was associated with the COVID-19 admission rate during a full year of the pandemic in Sweden.

Method: Observational review of all patients admitted to hospital with COVID-19 in Sweden between March 2020 and February 2021 ( = 42,017).

Assessing the Concordance Between Urogenital and Vaginal Microbiota: Can Urine Specimens Be Used as a Proxy for Vaginal Samples?

Background: The vaginal microbiota play a key role in defense against reproductive tract infections; however, many population-based women's health studies do not collect vaginal samples. Molecular examinations of urine samples have revealed common vaginal bacteria. We sought to assess the extent that community state type assignments of archived random-catch and clean-catch urine samples agreed with the paired vaginal samples in both reproductive-age and peri/post-menopausal women.

Predicting the duration of sickness absence due to knee osteoarthritis: a prognostic model developed in a population-based cohort in Sweden.

Background: Predicting the duration of sickness absence (SA) among sickness absent patients is a task many sickness certifying physicians as well as social insurance officers struggle with. Our aim was to develop a prediction model for prognosticating the duration of SA due to knee osteoarthritis.

Methods: A population-based prospective study of SA spells was conducted using comprehensive microdata linked from five Swedish nationwide registers.

Refinement of 16S rRNA gene analysis for low biomass biospecimens.

High-throughput phylogenetic 16S rRNA gene analysis has permitted to thoroughly delve into microbial community complexity and to understand host-microbiota interactions in health and disease. The analysis comprises sample collection and storage, genomic DNA extraction, 16S rRNA gene amplification, high-throughput amplicon sequencing and bioinformatic analysis. Low biomass microbiota samples (e.

Mortality trends among hospitalised COVID-19 patients in Sweden: A nationwide observational cohort study.

Background: It is important to know if mortality among hospitalised COVID-19 patients has changed as the pandemic has progressed. The aim of this study was to describe the dynamics over time of mortality among patients hospitalised for COVID-19 in Sweden, using nationwide data compiled by the Swedish National Board of Health and Welfare.

Methods: Observational cohort study where all patients hospitalised in Sweden between March 1 and September 30, 2020, with SARS-CoV-2 RNA positivity 14 days before to 5 days after admission and a discharge code for COVID-19 were included.

Concordance of Immunohistochemistry-Based and Gene Expression-Based Subtyping in Breast Cancer.

Background: Use of immunohistochemistry-based surrogates of molecular breast cancer subtypes is common in research and clinical practice, but information on their comparative validity and prognostic capacity is scarce.

Methods: Data from 2 PAM50-subtyped Swedish breast cancer cohorts were used: Stockholm tamoxifen trial-3 with 561 patients diagnosed 1976-1990 and Clinseq with 237 patients diagnosed 2005-2012. We evaluated 3 surrogate classifications; the immunohistochemistry-3 surrogate classifier based on estrogen receptor, progesterone receptor, and HER2 and the St.

VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition.

Background: Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epidemiological studies, and statistical modeling. Vaginal communities are typically assigned to CSTs based on the results of hierarchical clustering of the pairwise distances between samples.

Systemic anti-commensal response to fungi analyzed by flow cytometry is related to gut mycobiome ecology.

Background: Interest for the study of gut mycobiota in relation with human health and immune homeostasis has increased in the last years. From this perspective, new tools to study the immune/fungal interface are warranted. Systemic humoral immune responses could reflect the dynamic relationships between gut mycobiota and immunity.

Comparative Metagenome-Assembled Genome Analysis of " Lachnocurva vaginae", Formerly Known as Bacterial Vaginosis-Associated Bacterium-1 (BVAB1).

Bacterial vaginosis-associated bacterium 1 (BVAB1) is an as-yet uncultured bacterial species found in the human vagina that belongs to the family within the order . As its name suggests, this bacterium is often associated with bacterial vaginosis (BV), a common vaginal disorder that has been shown to increase a woman's risk for HIV, , and infections as well as preterm birth. BVAB1 has been further associated with the persistence of BV following metronidazole treatment, increased vaginal inflammation, and adverse obstetrics outcomes.

A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina.

Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. In this study, we assemble a comprehensive human vaginal non-redundant gene catalog (VIRGO) that includes 0.

Wellbeing and mental health amongst medical students in Canada.

Across the world there is significant evidence that medical students have high levels of mental ill-health and psychological distress with subsequent concerning effects on personal and occupational functioning. In Canada, recent studies have demonstrated worrying levels of burnout and depressive symptoms among practising doctors. In common with other countries, Canadian medical students are also subject to a high-pressure environment - with long clinical weeks and significant stressors - and these soon-to-be doctors have been previously shown to already demonstrate high levels of burnout.