Surviving antibiotic treatment as a gut bacterium: genomic characterization of an Enterobacter cloacae.

Enterobacter cloacae complex is a group of common opportunistic pathogens on intensive care units. On intensive care units sepsis is treated with high doses of antibiotics. This treatment does not only eliminate pathogenic bacteria but parts of the microbiome community as well.

Myoglobin expression improves T-cell metabolism and antitumor effector function.

Background: The tumor microenvironment is frequently hypoxic and characterized by a scarcity of nutritional resources including a shortage of glucose. As effector T cells have high energy demands, tumor metabolism can contribute to T-cell dysfunction and exhaustion.

Methods: In this study, we determined hypoxia in spleen and tumor tissue from tumor-bearing C57BL/6J mice using reverse transcription polymerase chain reaction (RT-PCR), histology and flow cytometry.

A Neural Network for Atrial Fibrillation Detection via PPG.

Atrial fibrillation (AF) is a prevalent cardiac arrhythmia associated with severe complications such as ischemic stroke and heart failure. Early detection is essential for timely intervention; however, traditional diagnostic methods often lack scalability and accessibility. This project explores the use of photoplethysmography (PPG) signals recorded via smartphone applications to develop a predictive neural network model for AF detection.

Rustims: An Open-Source Framework for Rapid Development and Processing of timsTOF Data-Dependent Acquisition Data.

Mass spectrometry is essential for analyzing and quantifying biological samples. The timsTOF platform is a prominent commercial tool for this purpose, particularly in bottom-up acquisition scenarios. The additional ion mobility dimension requires more complex data processing, yet most current software solutions for timsTOF raw data are proprietary or closed-source, limiting integration into custom workflows.

The RMaP challenge of predicting RNA modifications by nanopore sequencing.

The field of epitranscriptomics is undergoing a technology-driven revolution. During past decades, RNA modifications like N6-methyladenosine (mA), pseudouridine (ψ), and 5-methylcytosine (mC) became acknowledged for playing critical roles in cellular processes. Direct RNA sequencing by Oxford Nanopore Technologies (ONT) enabled the detection of modifications in native RNA, by detecting noncanonical RNA nucleosides properties in raw data.

Comparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.

Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies).

Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites.

We present Sci-ModoM, the first next-generation RNome database offering a holistic view of the epitranscriptomic landscape. Sci-ModoM has a simple yet powerful interface, underpinned by FAIR data principles, a standardized nomenclature, and interoperable formats, fostering the use of common standards within the epitranscriptomics community. Sci-ModoM provides quantitative measurements per site and dataset, enabling users to assess confidence levels based on score, coverage, and stoichiometry.

The effects of photoactivated ciprofloxacin and bile acids on biofilms on bile duct catheters.

Objectives: This study examined the potential of a novel photoactivatable ciprofloxacin to act against bacterial infections and microbiomes related to biliary diseases. It also evaluated treatment by combining the impact of bile acids and antibiotics on biofilms. Innovative strategies were evaluated to address the elusive bile duct microbiome resulting in biofilm-related infections linked to biliary catheters.

Gut microbiome in atypical depression.

Background: Recent studies showed that immunometabolic dysregulation is related to unipolar major depressive disorder (MDD) and that it more consistently maps to MDD patients endorsing an atypical symptom profile, characterized by energy-related symptoms including increased appetite, weight gain, and hypersomnia. Despite the documented influence of the microbiome on immune regulation and energy homeostasis, studies have not yet investigated microbiome differences among clinical groups in individuals with MDD.

Methods: Fifteen MDD patients with atypical features according to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5)-5, forty-four MDD patients not fulfilling the DSM-5 criteria for the atypical subtype, and nineteen healthy controls were included in the study.

NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis.

Summary: Oxford Nanopore Technologies' (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the clinical context. Although some tools for the real-time analysis of DNA-sequencing data already exist, there is currently no application available for differential transcriptome data analysis designed for scientists or physicians with limited bioinformatics knowledge.

Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.

Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP).

Characterisation of a Isolate Carrying Phage-Borne Enterotoxin E from a European Badger ().

() colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors.

Microbiome and immuno-metabolic dysregulation in patients with major depressive disorder with atypical clinical presentation.

Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression disorder (MDD), suggesting different manifestations of underlying pathophysiological mechanisms.

beeRapp: an R shiny app for automated high-throughput explorative analysis of multivariate behavioral data.

Summary: Animal behavioral studies typically generate high-dimensional datasets consisting of multiple correlated outcome measures across distinct or related behavioral domains. Here, we introduce the BEhavioral Explorative analysis R shiny APP (beeRapp) that facilitates explorative and inferential analysis of behavioral data in a high-throughput fashion. By employing an intuitive and user-friendly graphical user interface, beeRapp empowers behavioral scientists without programming and data science expertise to perform clustering, dimensionality reduction, correlational and inferential statistics and produce up to thousands of high-quality output plots visualizing results in a standardized and automated way.

An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness.

Antibiotics are commonly used in the Intensive Care Unit (ICU); however, several studies showed that the impact of antibiotics to prevent infection, multi-organ failure, and death in the ICU is less clear than their benefit on course of infection in the absence of organ dysfunction. We characterized here the compositional and metabolic changes of the gut microbiome induced by critical illness and antibiotics in a cohort of 75 individuals in conjunction with 2,180 gut microbiome samples representing 16 different diseases. We revealed an "infection-vulnerable" gut microbiome environment present only in critically ill treated with antibiotics (ICU).

Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.

Background: We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation "short-read" and third-generation "long-read" sequencing methods.

Bacterial gastroenteritis caused by the putative zoonotic pathogen : First reported case in Germany.

Foodborne campylobacteriosis is the most common cause of human bacterial enteritis in Germany. and are the main causative agents for enteric disease, but a number of other species are involved, including rare ones. These rare spp.

Draft Genome Sequence of Persistent Klebsiella grimontii AT013-Mero-001, Isolated from Human Feces.

Here, we report the draft genome sequence of AT013-Mero-001, which was isolated from feces from a sepsis patient treated with meropenem. This isolate is an antibiotic-susceptible but persistent strain.

Antimicrobial Susceptibility and Genomic Analysis of and , Two Rarely Detected Species.

and are two rarely detected species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide.

Newly Isolated Animal Pathogen Is Cytotoxic to Human Epithelial Cells.

is a newly identified animal pathogen of forest animals such as roe deer and wild boars. The species is closely related to the emerging human pathogen and the widely distributed animal pathogen . In this study, strain W25 was characterized with respect to its interaction with human cell lines.

Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential.

Clostridium perfringens causes a plethora of devastating infections, with toxin production being the underlying mechanism of pathogenicity in various hosts. Genomic analyses of 206 public-available C. perfringens strains´ sequence data identified a substantial degree of genomic variability in respect to episome content, chromosome size and mobile elements.

Using affinity propagation clustering for identifying bacterial clades and subclades with whole-genome sequences of Francisella tularensis.

By combining a reference-independent SNP analysis and average nucleotide identity (ANI) with affinity propagation clustering (APC), we developed a significantly improved methodology allowing resolving phylogenetic relationships, based on objective criteria. These bioinformatics tools can be used as a general ruler to determine phylogenetic relationships and clustering of bacteria, exemplary done with Francisella (F.) tularensis.