Biology subjects

Fall, T.

Publications and source records attributed to Fall, T..

3 recordsLinked to original sources

bioRxiv2026

Sex shapes the human genitourinary microbiome, including many species recognized as uropathogens: urine profiles from a population-level shotgun metagenomics study

Background: The urinary tract was long considered sterile. The discovery of the urinary microbiome has attracted interest in its role in urinary health and disease. Population-level urinary microbiome composition remains poorly defined and previous studies relied on selected populations and low-resolution sequencing. We characterized the microbial composition of voided urine from adults without urinary symptoms in a large Swedish population cohort to establish a population-based reference for microorganisms detected in voided urine using shotgun metagenomics. Methods: We performed shotgun metagenomic sequencing of voided urine samples from 2,062 participants of the population-based Swedish CArdioPulmonary bioImage Study (SCAPIS; 55% women, 50-65 years). Results: Among 3,668 identified species, 90% were classified at the species level. Microbial profiles differed substantially between sexes, with lactobacilli and bifidobacteria enriched in females, while Cutibacterium acnes, Enterococcus and Propionimicrobium lymphophilum were enriched in males. Recognized uropathogens, including Enterococcus faecalis and Escherichia coli, were frequently detected despite participants having no urinary symptoms. Males showed higher alpha diversity (Shannon and inverse Simpson indices), whereas richness did not differ by sex. Age showed only modest associations with alpha diversity, and beta diversity differed by sex but showed minimal age-related variation. Conclusions: This study provides a population-based reference for interpreting microorganisms detected in routine voided urine samples. Biological sex was the principal determinant of microbial composition, supporting routine consideration of sex in future studies of the urogenital microbiota using routine voided urine samples.

microbiology↗

bioRxiv2024

The urinary microbiome in association with diabetes and diabetic kidney disease: A systematic review

BackgroundThe urinary microbiome, or urobiome, is a novel area of research that has been gaining attention recently, as urine was thought to be sterile for years. There is limited information about the composition of the urobiome in health and disease. The urobiome may be affected by several factors and diseases such as diabetes, a disease that often leads to kidney damage. Thus, we need to understand the role of the urobiome to assess and monitor kidney disease related to diabetes over time. MethodsWe conducted a systematic review to summarize knowledge about the urobiome in association with diabetes mellitus and diabetic kidney disease. The search was conducted in several electronic databases until November 2024. ResultsEighteen studies were selected including cross-sectional case-control studies, cross-sectional surveys and one prospective longitudinal study. In total, the urobiome of 1,571 people was sequenced, of which 662 people had diabetes, and of these 36 had confirmed diabetic kidney disease; 609 were healthy individuals, 179 had prediabetes or were at risk of type 2 diabetes mellitus and 121 did not have diabetes but had other comorbidities. Eight studies analysed data from females, one was focused on male data, and the other nine had mixed female-male data. Most of the studies had a small sample size, used voided midstream urine, and used 16S rRNA sequencing. ConclusionThis systematic review summarizes trends seen throughout published data available to have a first baseline knowledge of the urinary microbiome, and its microbiota, in association with diabetes including the decreased richness and -diversity in urinary microbiota in individuals with diabetes compared to healthy controls and the decreased -diversity with the evolution of kidney disease independently of the cause.

microbiology↗

bioRxiv2021

Mendelian randomization suggests a bidirectional, causal relationship between physical inactivity and obesity

Physical inactivity is associated with excess weight gain in observational studies. However, some longitudinal studies indicate reverse causality where weight gain leads to physical inactivity. As observational studies suffer from reverse causality, it is challenging to assess the true causal directions. Here, we assess the bidirectional causality between physical inactivity and obesity by bidirectional Mendelian randomization analysis. We used results from genome-wide association studies for accelerometer-based physical activity and sedentary time in 91,105 individuals and for body mass index (BMI) in 806,834 individuals. We implemented Mendelian randomization using CAUSE method that accounts for pleiotropy and sample overlap using full genome-wide data. We also applied inverse variance-weighted, MR-Egger, weighted median, and weighted mode methods using genome-wide significant variants only. We found evidence of bidirectional causality between sedentary time and BMI: longer sedentary time was causally associated with higher BMI [beta (95%CI) from CAUSE method: 0.11 (0.02, 0.2), P=0.02], and higher BMI was causally associated with longer sedentary time (0.13 (0.08, 0.17), P=6.3.x10-4). Our analyses suggest that higher moderate and vigorous physical activity are causally associated with lower BMI (moderate: -0.18 (-0.3,-0.05), P=0.006; vigorous: -0.16 (-0.24,-0.08), P=3.8x10-4), but indicate that the association between higher BMI and lower levels of physical activity is due to horizontal pleiotropy. The bidirectional, causal relationship between sedentary time and BMI suggests that decreasing sedentary time is beneficial for weight management, but also that targeting obesity may lead to additional health benefits by reducing sedentary time.

genetics↗