Evaluation of a nucleic acid preservation protocol for microbiome studies involving samples from the oral cavity.

Purpose: The accuracy of oral microbiome research depends significantly on specimen sampling protocols, as well as their storage and preservation. Traditional methods, such as freezing, may not only involve logistical hurdles but can also impact the quality of microbial data, leading to difficulties in the comparability between different studies. This study evaluates the effectiveness of the room temperature nucleic acid preservation protocol using DNA/RNA Shield buffer as compared to standard freezing in preserving oral microbial communities over the course of 7 days.

Short- and long-term impact of aseptic bathing strategies on the skin microbiome in ICU patients.

Bathing strategies with antiseptic agents, such as Chlorhexidine and Octenidine, have been widely adopted to mitigate infection risks in intensive care units (ICU). However, concerns exist regarding their long-term effects on skin microbiome structures and potential unintended consequences, including antibiotic cross-resistance. This longitudinal study characterized the compositional changes of the skin microbiome of ICU patients upon these two antiseptic bathing strategies when compared to standard water and soap bathing.

Mediterranean diet component oleic acid decreases systemic impact of periodontal Porphyromonas gingivalis-infection in age: addressing role of stress resistance and microbiome.

Periodontitis (PD) is an age-associated infectious periodontal disease driven by dysbiosis and hyperinflammatory host response, resulting in bone and tissue loss. Often linked to systemic inflammatory comorbidities, modulating host response emerged as promising clinical target. This study investigates whether nutritional intervention mitigates age-associated systemic impact of oral infection with PD key pathogen Porphyromonas gingivalis.

Clostridioides difficile evolution in a tertiary German hospital through a retrospective genomic characterization.

Purpose: Clostridioides difficile is a major cause of healthcare-associated infections, contributing to significant morbidity and mortality. This study aimed to investigate the genomic characteristics, antimicrobial resistance (AMR) profiles, and temporal dynamics of C. difficile strains isolated from hospitalized patients in a German tertiary hospital over nearly two decades (1997-2015).

Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights.

Community-acquired pneumonia (CAP) is a significant health threat for adults. Although conjugate vaccines have reduced pneumococcal CAP incidence in children, Streptococcus pneumoniae-related CAP remains prevalent among older adults. The nasopharynx acts as a reservoir for S.

MftG is crucial for ethanol metabolism of mycobacteria by linking mycofactocin oxidation to respiration.

Mycofactocin is a redox cofactor essential for the alcohol metabolism of mycobacteria. While the biosynthesis of mycofactocin is well established, the gene , which encodes an oxidoreductase of the glucose-methanol-choline superfamily, remained functionally uncharacterized. Here, we show that MftG enzymes are almost exclusively found in genomes containing mycofactocin biosynthetic genes and are present in 75% of organisms harboring these genes.

Skin dysbiosis and loss of microbiome site specificity in critically ill patients.

An increasing amount of evidence has linked critical illness with dysbiotic microbiome signatures in different body sites. The disturbance of the indigenous microbiota structures has been further associated with disease severity and outcome and has been suggested to pose an additional risk for complications in intensive care units (ICUs), including hospital-acquired infections. A better understanding of the microbial dysbiosis in critical illness might thus help to develop strategies for the prevention of such complications.

Role of Lectin-Like Oxidized Low-Density Lipoprotein Receptor-1 in Inflammation and Pathogen-Associated Interactions.

Background: Lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1) is known as a major receptor for oxidized low-density lipoproteins (oxLDL) and plays a significant role in the genesis of atherosclerosis. Recent research has shown its involvement in cancer, ischemic stroke, and diabetes. LOX-1 is a C-type lectin receptor and is involved in the activation of immune cells and inflammatory processes.

Differential Transcriptional Responses of Human Granulocytes to Fungal Infection with and .

Neutrophils are critical phagocytic cells in innate immunity, playing a significant role in defending against invasive fungal pathogens. This study aimed to explore the transcriptional activation of human neutrophils in response to different fungal pathogens, including and , compared to the bacterial pathogen . We identified distinct transcriptional profiles and stress-related pathways in neutrophils during fungal infections, highlighting their functional diversity and adaptability.

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.

Extraction of High-Quality RNA from Internalized by Endothelial Cells.

evades antibiotic therapy and antimicrobial defenses by entering human host cells. Bacterial transcriptomic analysis represents an invaluable tool to unravel the complex interplay between host and pathogen. Therefore, the extraction of high-quality RNA from intracellular lays the foundation to acquire meaningful gene expression data.

induces tolerance in human monocytes accompanied with expression changes of cell surface markers.

Exposure of human monocytes to lipopolysaccharide (LPS) or other pathogen-associated molecular pattern (PAMPs) induces a temporary insensitivity to subsequent LPS challenges, a cellular state called endotoxin tolerance (ET), associated with the pathogenesis of sepsis. In this study, we aimed to characterize the cellular state of human monocytes from healthy donors stimulated with in comparison to TLR2-specific ligands. We analyzed induced gene expression changes after 2 and 24 hours by amplicon sequencing (RNA-AmpliSeq) and compared the pro-inflammatory response after 2 hours with the response in re-stimulation experiments.

Comparative analysis of surface sanitization protocols on the bacterial community structures in the hospital environment.

Objectives: In hospital hygiene, it remains unclear to what extent surface contamination might represent a potential reservoir for nosocomial pathogens. This study investigates the effects of different sanitization strategies on the microbial structures and the ecological balance of the environmental microbiome in the clinical setting.

Methods: Three cleaning regimes (disinfectants, detergents, and probiotics) were applied subsequently in nine independent patient rooms at a neurological ward (Charité, Berlin).

Antibody ligation of CEACAM1, CEACAM3, and CEACAM6, differentially enhance the cytokine release of human neutrophils in responses to Candida albicans.

Invasive candidiasis is a healthcare-associated fungal infection with a high mortality rate. Neutrophils, the first line of defense during fungal infections, express the immunoregulatory Candida albicans receptors CEACAM1, CEACAM3, and CEACAM6. We analyzed the effects of specific antibodies on C.

Inhibition of the NLRP3/IL-1β axis protects against sepsis-induced cardiomyopathy.

Background: Septic cardiomyopathy worsens the prognosis of critically ill patients. Clinical data suggest that interleukin-1β (IL-1β), activated by the NLRP3 inflammasome, compromises cardiac function. Whether or not deleting Nlrp3 would prevent cardiac atrophy and improve diastolic cardiac function in sepsis was unclear.

Context-dependent regulation of immunoglobulin mutagenesis by p53.

p53 plays a major role in genome maintenance. In addition to multiple p53 functions in the control of DNA repair, a regulation of DNA damage bypass via translesion synthesis has been implied in vitro. Somatic hypermutation of immunoglobulin genes for affinity maturation of antibody responses is based on aberrant translesion polymerase action and must be subject to stringent control to prevent genetic alterations and lymphomagenesis.

Bacterial colonization dynamics and antibiotic resistance gene dissemination in the hospital environment after first patient occupancy: a longitudinal metagenetic study.

Background: Humans spend the bulk of their time in indoor environments. This space is shared with an indoor ecosystem of microorganisms, which are in continuous exchange with the human inhabitants. In the particular case of hospitals, the environmental microorganisms may influence patient recovery and outcome.

Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels.

Candida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants of fungal abundance.

Characterization of the pathoimmunology of necrotizing enterocolitis reveals novel therapeutic opportunities.

Necrotizing enterocolitis (NEC) is a severe, currently untreatable intestinal disease that predominantly affects preterm infants and is driven by poorly characterized inflammatory pathways. Here, human and murine NEC intestines exhibit an unexpected predominance of type 3/T17 polarization. In murine NEC, pro-inflammatory type 3 NKp46RORγtTbet innate lymphoid cells (ILC3) are 5-fold increased, whereas ILC1 and protective NKp46RORγt ILC3 are obliterated.

A simple sequence-based filtering method for the removal of contaminants in low-biomass 16S rRNA amplicon sequencing approaches.

Controlling for contaminant sequences in microbiome experiments involving low-biomass samples is a highly challenging task which still lacks of standardized protocols. Here we propose a simple sequence-based filtering method for 16S rRNA gene microbial profiling approaches, and validate its efficiency using mock community dilution series and environmental samples collected in a clinical setting.

Early Bacterial Colonization and Antibiotic Resistance Gene Acquisition in Newborns.

Several studies have recently identified the main factors contributing to the bacterial colonization of newborns and the dynamics of the infant microbiome development. However, most of these studies address large time periods of weeks or months after birth, thereby missing on important aspects of the early microbiome maturation, such as the acquisition of antibiotic resistance determinants during postpartum hospitalization. The pioneer bacterial colonization and the extent of its associated antibiotic resistance gene (ARG) dissemination during this early phase of life are largely unknown.

Unaltered Fungal Burden and Lethality in Human CEACAM1-Transgenic Mice During Dissemination and Systemic Infection.

Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1, CD66a) is a receptor for It is crucial for the immune response of intestinal epithelial cells to this opportunistic pathogen. Moreover, CEACAM1 is of importance for the mucosal colonization by different bacterial pathogens. We therefore studied the influence of the human CEACAM1 receptor in human CEACAM1-transgenic mice on the colonization and infection utilizing a colonization/dissemination and a systemic infection mouse model.

Controlling intestinal colonization of high-risk haematology patients with ESBL-producing Enterobacteriaceae: a randomized, placebo-controlled, multicentre, Phase II trial (CLEAR).

Objectives: We assessed the efficacy and safety of an oral antimicrobial regimen for short- and long-term intestinal eradication of ESBL-producing Escherichia coli and Klebsiella pneumoniae (ESBL-EC/KP) in immunocompromised patients.

Methods: We performed a randomized (2:1), double-blind multicentre Phase II study in four haematology-oncology departments. Patients colonized with ESBL-EC/KP received a 7 day antimicrobial regimen of oral colistin (2 × 106 IU 4×/day), gentamicin (80 mg 4×/day) and fosfomycin (three administrations of 3 g every 72 h), or placebo.

AmpliSeq Screening of Genes Encoding the C-Type Lectin Receptors and Their Signaling Components Reveals a Common Variant in Associated with Pulmonary Tuberculosis in an Indian Population.

Tuberculosis (TB) is a multifactorial disease governed by bacterial, host and environmental factors. On the host side, growing evidence shows the crucial role that genetic variants play in the susceptibility to (Mtb) infection. Such polymorphisms have been described in genes encoding for different cytokines and pattern recognition receptors (PRR), including numerous Toll-like receptors (TLRs).