Biology subjects

Rounge, T. B.

Publications and source records attributed to Rounge, T. B..

10 recordsLinked to original sources

bioRxiv2026

CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut

Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we examined bacteria, MGEs, and CRISPR-Cas in the gut microbiome. Using fecal shotgun metagenomes from 1034 Norwegians, we constructed an extended microbiome resource comprising 1.7K prokaryotic mOTUs, 19.5K viral vOTUs and 24.2K plasmid PTUs. We also recovered 74.2K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. We did not find evidence that CRISPR-Cas spacers were related to characteristics of the human host, beyond the host-bacteria associations. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome, and their contribution to microbial ecosystem dynamics.

molecular biology↗

bioRxiv2025

Longitudinal analysis of the hand microbiome in response to chlorine-based antiseptic use during a military field exercise

Hand hygiene is essential for infection control, yet the impact of frequent antiseptic use on the skin microbiome, which is crucial for skin barrier function and pathogen exclusion, remains underexplored, especially in field conditions. In high-risk military settings, there is a need for safe, multipurpose antiseptics that avoid the drawbacks of alcohol-based options, including skin irritation, flammability, and unsuitability for wound application. We conducted a longitudinal study during the Norwegian-led military exercise Cold Response 2022 to assess the effects of repeated use of stabilized hypochlorous acid, a non-alcoholic antiseptic, on the hand microbiome of soldiers in a field environment. Participants used either the chlorine-based antiseptic (n = 20) or standard hygiene practices, mainly alcohol-based sanitizers (n = 19), for 10 days. Skin swabs from hands and untreated forearms were collected at baseline, post-intervention, and three weeks after discontinuation, and analyzed using 16S rRNA sequencing. Overall, our data revealed that field exposure accounted for more variation in bacterial composition than antiseptic use. When comparing alpha and beta diversity trajectories between the two antiseptic groups, there was minimal divergence during active field use, but a significant post-treatment increase in alpha diversity associated with the use of chlorine-based antiseptic. In contrast, untreated forearms showed no such group-level differences. These findings suggest that antiseptic-driven microbiome shifts are most apparent during recovery, with non-alcoholic formulations supporting faster recolonization after treatment. Stabilized hypochlorous acid represents a promising alternative to standard alcohol-based antiseptics for military personnel. IMPORTANCEEffective hand hygiene reduces pathogen transmission, but its influence on the skin microbiome has rarely been studied. Our research emphasizes the importance of longitudinal assessments by identifying greater antiseptic-driven differences occurring after cessation of treatment than during repeated use. Service members frequently use antiseptics in challenging environments, highlighting the operational need for a non-alcoholic, multipurpose product that can be safely used on both intact skin and wounds. Our findings suggest that a chlorine-based non-alcoholic antiseptic permits faster recovery of bacterial diversity after perturbation, informing product selection and hygiene policies in defense and other high-risk settings.

microbiology↗

bioRxiv2025

VirMake: a flexible and user-friendly pipeline for viral taxonomic and functional characterisation from shotgun metagenomic sequencing data

BackgroundBacteriophages (phages) are recognized as key regulators of microbial communities, and it is pivotal to understand viral ecology, diversity, and evolution. However, identification and characterization of phages from shotgun metagenome sequencing pose unique bioinformatic challenges owing to the inherent complexity and scale of the data. ResultsHere, we introduce VirMake, a comprehensive, flexible, and scalable pipeline developed for viral taxonomic and functional analysis of shotgun metagenome data. It enables high-throughput end-to-end processing, assembly, and annotation of metagenomic data, including viral sequence identification, taxonomic and functional annotation, and using a modular framework, allows users to integrate viral analysis at different stages of metagenome data analysis. VirMake can be installed on Linux operating systems that support Conda and is freely available at https://github.com/Rounge-lab/VirMake. Here, we showcase VirMake capabilities using three metagenome datasets of varying sizes (up to 2.9 Tbp), generated from various environments (human gut and water) and using different sample preparation protocols (VLP enrichment and bulk DNA extraction). ConclusionsVirMake enabled robust processing of all datasets, showing viral genome richness, taxonomy and integration status to vary according to sampling environments and laboratory protocols.

bioinformatics↗

bioRxiv2024

Skin bacterial community dynamics of hands and forearms before and after military field exercise

The human skin microbiome is crucial for skin health and immunity, especially in the context of extreme conditions faced by military personnel. Soldiers encounter unique stressors and hygienic challenges that can impact the microbial composition of their skin during field exercises and in regular occupational settings. In this study, we aimed to investigate the impact of a military field exercise on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study during the NATO exercise Cold Response 2022, involving Norwegian soldiers (n = 19) engaged in outdoor training operations. Skin swabs were taken from soldiers hands and forearms directly before and after the 10-day winter field exercise, and following a 3-week post-exercise leave. Our results reveal hand and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers microbiomes became more similar during the exercise, followed by divergence in the leave period. Neither skin site returned to original composition at follow-up, indicating that field exercises may have lasting effects on the microbiome. Our findings highlight the impact of outdoor exposure on microbial communities and suggest that resilience and stability differ between skin sites. ImportanceOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the bodys first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome, but can also inform hygiene management and disease prevention in comparable situations.

microbiology↗

bioRxiv2024

GENOMICON-Seq: A comprehensive tool for the simulation of mutations in amplicon and whole exome sequencing

GENOMICON-Seq is a comprehensive genomic sequencing simulation tool that enables the assessment of laboratory and bioinformatics parameters influencing the detection of mutations. The tool generates genomes with mutations, mimicking processes such as low-frequency mutations, APOBEC3 activity in viruses, somatic mutations and single base substitution (SBS) mutational signals. GENOMICON-Seq adds amplicon and whole exome sequencing biases and errors. It outputs sequencing reads compatible with mutation detection tools and a report on mutation origin (generated mutations and PCR errors), nucleotide context, and position. GENOMICON-Seq aids in the evaluation of bioinformatics tools and experimental designs, reducing the need for costly real-world sequencing experiments.

bioinformatics↗

bioRxiv2022

Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

The annotation of microRNAs, an important class of post-transcriptional regulators, depends on the availability of transcriptomics data and expert knowledge. This led to a large gap between novel genomes made available and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in MirMachine, our new tool for the annotation of conserved microRNA complements from genomes only. We successfully applied MirMachine to a wide range of animal species, including those with very large genomes, additional genome duplications and extinct species, where smallRNA sequencing will be hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field facilitating automated genome annotation pipelines and deeper studies on the evolution of genome regulation, even in extinct organisms. HighlightsO_LIAn annotation pipeline using trained covariance models of microRNA families C_LIO_LIEnables massive parallel annotation of microRNA complements of genomes C_LIO_LIMirMachine creates meaningful annotations for very large and extinct genomes C_LIO_LImicroRNA score to assess genome assembly completeness C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/517654v2_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1ee2bf1org.highwire.dtl.DTLVardef@18719c1org.highwire.dtl.DTLVardef@abcfb6org.highwire.dtl.DTLVardef@1d1c368_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

HoCoRT: Host contamination removal tool

BackgroundShotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, to reduce downstream computational load, or for privacy reasons in case of a human host. The tools that we identified as designed specifically to perform host contamination sequence removal were either outdated, not maintained or complicated to use. We have therefore created HoCoRT, a fast and user friendly tool that implements several methods for optimised host sequence removal, and evaluated the speed and accuracy of these methods. ResultsHoCoRT is an open-source command-line tool for host contamination removal. It is designed to be simple to install and use, including a one-step option for genome indexing. HoCoRT uses a range of well-known mapping, classification and alignment methods for the classification of reads. The underlying classification method to be used and its parameters are selectable by the user, enabling adaptation to different circumstances. Based on our investigation of the performance of a range of methods and parameters on artificial human gut and oral microbiomes, recommendations are provided for typical data sets with short and long reads. ConclusionsTo decontaminate a human microbiome with HoCoRT, the best combination of speed and accuracy was found with BioBloom, Bowtie2 in end-to-end mode, or HISAT2 for short reads, while BioBloom performed best for long reads. For the oral microbiome, Bowtie2 was slightly more accurate than the other two, at the expense of speed. HoCoRT using Bowtie2 in end-to-end mode was found to be much faster and slightly more accurate than the dedicated DeconSeq tool. HoCoRT is distributed as a Bioconda package. Source code and documentation are available at https://github.com/ignasrum/hocort for Linux and macOS under the MIT licence.

bioinformatics↗

bioRxiv2020

Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis

Small non-coding RNAs such as microRNAs are master regulators of gene expression. One of the most promising applications of miRNAs is the use as liquid biopsy. Especially early diagnosis is an effective means to increase patients overall survival. E.g. in oncology a tumor is detected at best prior to its clinical manifestation. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analyzed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom later developed cancer. We selected 210 serum samples of patients with lung, colon or breast cancer at three time points prior to diagnosis, after cancer diagnosis and controls. The controls were matched with regard to age of the blood donor and to the time points of blood drawing, which were 27, 32, or 38 years prior to diagnosis. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 had adjusted p-values<10-10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p<0.05). Unsupervised competitive learning by self-organized maps indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. Self-organized maps also highlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51% of all miRNAs were highly specific, either for a time-point or a cancer entity. Our results indicate that tumors may be indicated by serum miRNAs decades prior the clinical manifestation.

cancer biology↗

bioRxiv2018

Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity

Non-coding RNAs (ncRNA) are regulators of cell functions and circulating ncRNAs from the majority of RNA classes, such as miRNA, tRNA, piRNAs, lncRNA, snoRNA, snRNA and miscRNAs, are potential non-invasive biomarkers. Understanding how non-disease traits influence ncRNA expression is essential for assessing their biomarker potential.\n\nWe studied associations of common traits (sex, age, smoking, body mass, physical activity, and technical factors such as sample storage and processing) with serum ncRNAs. We used RNAseq data from 526 donors from the Janus Serum Bank and traits from health examination surveys. We identified associations between all RNA classes and traits. Ageing showed the strongest association with ncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. Serum processing modifications and storage times significantly altered expression levels of a number of ncRNAs. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some isomiRs, mRNA fragments and tRNAs smoking-related expression levels persisted.\n\nOur results show that common traits influence circulating ncRNA expression. Therefore it is clear that ncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific ncRNAs identified in our study, analyses should also be adjusted for body mass, smoking, physical activity and serum processing and storage.

molecular biology↗

bioRxiv2017

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling

Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 {+/-} 0.097 and 13.56 {+/-} 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.

microbiology↗