Malte Rühlemann
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View article: Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis
Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis Open
The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed …
View article: First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study
First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study Open
The prospective Kiel Inflammatory Bowel Disease (IBD) Family Cohort Study (KINDRED cohort) was initiated in 2013 to systematically and extensively collect data and biosamples from index IBD patients and their relatives, a population at hig…
View article: Genome-scale metabolic models predict diet-and lifestyle-driven shifts of ecological interactions in the gut microbiome
Genome-scale metabolic models predict diet-and lifestyle-driven shifts of ecological interactions in the gut microbiome Open
1. Abstract Microbiomes and their host environments form complex, interconnected ecosystems. The microbial species within a microbiome, on the one hand, compete for resources, while on the other hand, they exchange vital metabolites to sup…
View article: The Fecal Mycobiome in Chronic Pancreatitis Is Characterized by an Increase in Candida species and Nakaseomyces
The Fecal Mycobiome in Chronic Pancreatitis Is Characterized by an Increase in Candida species and Nakaseomyces Open
INTRODUCTION: The exocrine pancreas is an important determinant of the intestinal microbiome composition and stability. Although chronic pancreatitis (CP) is known to severely affect the bacterial community, its impact on the intestinal my…
View article: Lower cardiorespiratory fitness is associated with an altered gut microbiome. The Study of Health in Pomerania (SHIP)
Lower cardiorespiratory fitness is associated with an altered gut microbiome. The Study of Health in Pomerania (SHIP) Open
View article: The C-type lectin receptor MINCLE interferes with eosinophil function and protective intestinal immunity in Strongyloides ratti-infected mice
The C-type lectin receptor MINCLE interferes with eosinophil function and protective intestinal immunity in Strongyloides ratti-infected mice Open
Strongyloides ratti is a helminth parasite that displays tissue-migrating and intestinal life stages. Myeloid C-type lectin receptors (CLRs) are pattern recognition receptors that recognize pathogen-derived ligands and initiate immune resp…
View article: Dietary Diversity, Rather Than Quality, Parallels a Reduction in Metabolic Syndrome and a Favorable Gut Microbiome: The Dietary Diversity Score
Dietary Diversity, Rather Than Quality, Parallels a Reduction in Metabolic Syndrome and a Favorable Gut Microbiome: The Dietary Diversity Score Open
Dietary diversity, as determined by the novel DDS, reduces MetS risk, whereas dietary quality was less important in that regard. Greater dietary diversity was paralleled by greater microbiota diversity and a healthier gut microbiome. Futur…
View article: Fecal glycoprotein 2 is a marker of gut microbiota dysbiosis and systemic inflammation
Fecal glycoprotein 2 is a marker of gut microbiota dysbiosis and systemic inflammation Open
Background Antimicrobial autoantigenic glycoprotein 2 (GP2) is an important component of the innate immune system which originates from the exocrine pancreas as well as from the small intestines. The relationship of GP2 with the intestinal…
View article: Changes in Periodontal Parameters and Microbiome Composition of Periodontal Pocket in Patients with Chronic Inflammatory Diseases Receiving Targeted Anti-Cytokine Therapy
Changes in Periodontal Parameters and Microbiome Composition of Periodontal Pocket in Patients with Chronic Inflammatory Diseases Receiving Targeted Anti-Cytokine Therapy Open
Periodontitis is associated with systemic chronic inflammatory diseases. There is limited evidence on the influence of anti-cytokine therapies on the periodontal condition and microbiome in the tooth pocket of such patients, so the aim of …
View article: The composition of the stent microbiome is associated with morbidity and adverse events during endoscopic drainage therapy of pancreatic necroses and pseudocysts
The composition of the stent microbiome is associated with morbidity and adverse events during endoscopic drainage therapy of pancreatic necroses and pseudocysts Open
Background Development of pancreatic necroses or pseudocysts are typical complications of pancreatitis and may require endoscopic drainage therapy using metal or plastic stents. Microbial infection of these lesions poses a major challenge.…
View article: Changes of Periodontal Parameters and Microbiome Composition of Tooth Pocket in Patients with Chronic Inflammatory Diseases Receiving Targeted Anti-Cytokine Therapy
Changes of Periodontal Parameters and Microbiome Composition of Tooth Pocket in Patients with Chronic Inflammatory Diseases Receiving Targeted Anti-Cytokine Therapy Open
Background: Periodontitis is associated with systemic chronic inflammatory diseases. There is limited evidence on the influence of anti-cytokine therapies on the periodontal condition and microbiome in the tooth pocket of such patients, so…
View article: On the limits of 16S rRNA gene-based metagenome prediction and functional profiling
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling Open
Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective techn…
View article: The archaeome in metaorganism research, with a focus on marine models and their bacteria–archaea interactions
The archaeome in metaorganism research, with a focus on marine models and their bacteria–archaea interactions Open
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often rem…
View article: Functional host-specific adaptation of the intestinal microbiome in hominids
Functional host-specific adaptation of the intestinal microbiome in hominids Open
View article: Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease
Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease Open
Inflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of…
View article: On the limits of 16S rRNA gene-based metagenome prediction and functional profiling
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling Open
Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective techn…
View article: Impaired Abcb1a function and red meat in a translational colitis mouse model induces inflammation and alters microbiota composition
Impaired Abcb1a function and red meat in a translational colitis mouse model induces inflammation and alters microbiota composition Open
Inflammatory Bowel Disease (IBD) affects approximately 0.3% of the global population, with incidence rates rising dramatically worldwide. Emerging evidence points to an interplay between exposome factors such as diet and gut microbiota, ho…
View article: Author Correction: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer
Author Correction: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer Open
View article: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer
Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer Open
The role of the human gut microbiome in colorectal cancer (CRC) is unclear as most studies on the topic are unable to discern correlation from causation. We apply two-sample Mendelian randomization (MR) to estimate the causal relationship …
View article: Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer
Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer Open
View article: MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids Open
This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <…
View article: MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids
MAG Collection - Rühlemann et al.: Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids Open
This tar-Archives hold the complete collection of n=7,506 metagenome-assembled genomes presented in the preprint "Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids" by Rühlemann <…
View article: Functional host-specific adaptation of the intestinal microbiome in hominids
Functional host-specific adaptation of the intestinal microbiome in hominids Open
Summary Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To…
View article: Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice
Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice Open
The breadth of phenotypes influenced by the gut microbiome in multicellular hosts has attracted the keen and renewed interest of evolutionary biologists. Comparative studies suggest that coevolutionary processes may occur as hosts and thei…
View article: Network-based quantitative trait linkage analysis of microbiome composition in inflammatory bowel disease families
Network-based quantitative trait linkage analysis of microbiome composition in inflammatory bowel disease families Open
Introduction: Inflammatory bowel disease (IBD) is characterized by a dysbiosis of the gut microbiome that results from the interaction of the constituting taxa with one another, and with the host. At the same time, host genetic variation i…
View article: Activated regulatory T-cells promote duodenal bacterial translocation into necrotic areas in severe acute pancreatitis
Activated regulatory T-cells promote duodenal bacterial translocation into necrotic areas in severe acute pancreatitis Open
Objective In acute pancreatitis (AP), bacterial translocation and subsequent infection of pancreatic necrosis are the main risk factors for severe disease and late death. Understanding how immunological host defence mechanisms fail to prot…
View article: Host genetic factors related to innate immunity, environmental sensing and cellular functions are associated with human skin microbiota
Host genetic factors related to innate immunity, environmental sensing and cellular functions are associated with human skin microbiota Open
Despite the increasing knowledge about factors shaping the human microbiome, the host genetic factors that modulate the skin-microbiome interactions are still largely understudied. This contrasts with recent efforts to characterize host ge…
View article: <tt>MAGScoT</tt>: a fast, lightweight and accurate bin-refinement tool
MAGScoT: a fast, lightweight and accurate bin-refinement tool Open
Motivation Recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic data is an important task for the comprehensive analysis of microbial communities from variable sources. Single binning tools differ in their ability to le…
View article: Exploring the causal role of the human gut microbiome in colorectal cancer: Application of Mendelian randomization
Exploring the causal role of the human gut microbiome in colorectal cancer: Application of Mendelian randomization Open
Aim The role of the human gut microbiome in colorectal cancer (CRC) is unclear as most studies on the topic are unable to discern correlation from causation. We apply two-sample Mendelian randomization (MR) to estimate the causal relations…
View article: MAGScoT bin refinement benchmarking data and output
MAGScoT bin refinement benchmarking data and output Open
This repository holds the data to benchmark the new metagenomic bin-refinement tool MAGScoT (in review; preprint: https://www.biorxiv.org/content/10.1101/2022.05.17.492251v1; github: https://github.com/ikmb/MAGScoT) in comparison to the go…