Biology subjects

Behrens, W.

Publications and source records attributed to Behrens, W..

3 recordsLinked to original sources

bioRxiv2025

High-resolution taxonomic profiling and metatranscriptomics identify microbial, biochemical, host and ecological factors in peri-implant disease

Biofilm-associated diseases like peri-implant mucositis (PIM) and peri-implantitis (PI) are significant clinical challenges affecting millions of dental implant patients globally. Although studies have described the role of microbial, host, or environmental factors in disease development, their complex interplay, particularly during dysbiosis remains poorly understood. This cross-sectional study characterized the microbiome composition and metatranscriptomes of 125 peri-implant biofilms from 48 individuals uncovering molecular signatures linked to peri-implant health (PIH), PIM, and PI. Distinct variations were observed in biofilm amount, composition, activity, phage populations and host response. Biofilms were categorized into four community types (CTs) based on the bacterial transcriptional activity: one linked to PIH, one to PI, and two to PIM. PIH and PIM were primarily characterized by aerotolerant taxa with increased anabolic processes, while PI was dominated by obligate anaerobes with complex biofilm morphology, and heightened catabolic activity and virulence. PIM samples, relative to PIH were characterized by biofilm expansion with minimal functional changes, except for the Neisseria-rich PIM subtype showing higher pyruvate and lipoic acid metabolism. The phagome mirrored the bacterial compositional variations across disease states. Furthermore, human transcriptome responses varied indicating increased keratinization in PIH, enhanced expression of ribosome components in PIM, and inflammatory signaling and hypoxia in PI. Additionally, we identified complex species-enzyme, phage-bacteria, and host-microbe associations within the peri-implant ecosystem. Our integrative multi-omics approach provides a comprehensive view of microbial, biochemical, host, and ecological factors associated with dysbiosis, offering novel insights into peri-implant disease dynamics. ImportancePeri-implant mucositis and peri-implantitis are highly prevalent inflammatory conditions that compromise the long-term survival and success of dental implants, yet their underlying biological mechanisms are largely unresolved. While next-generation sequencing has advanced our understanding of microbial composition across health and peri-implant diseases, it falls short of capturing microbial activity and the broader molecular context of peri-implant dysbiosis. Metatranscriptomics overcomes this limitation by profiling actively transcribed genes within the biofilm, offering direct insights into microbial community functions. In this study, we integrated full-length 16S rRNA gene amplicon sequencing with metatranscriptomic profiling to simultaneously assess microbial taxonomy, functional activity, phage dynamics, and host gene expression in peri-implant biofilms. Importantly, we provide a systems-level view and report previously undescribed associations between different molecular signatures in peri-implant ecosystem.

microbiology↗

bioRxiv2025

Integrative microbiome- and metatranscriptome-based analyses reveal diagnostic biomarkers for peri-implantitis

Peri-implantitis is a severe biofilm-associated infection of the tissues around dental implants that increases the risk of implant failure. The prognosis of peri-implantitis treatment is compromised by the resistance of well-organized and mature bacterial biofilms. Thus, early diagnosis of a pathogenic biofilm would enable treatment at a prognostically favourable stage. However, relatively little is known about how the microbial constitution of the biofilm changes during disease development. The aim of this cross-sectional study was therefore to identify peri-implant taxonomic and functional biomarkers that reliably indicate peri-implantitis using paired data from full length 16S rRNA gene amplicon sequencing (full-16S) and metatranscriptomics (RNAseq). Disease signatures were identified using 24 healthy and 24 peri-implantitis-associated biofilm samples from 32 patients. The taxonomic measurements were validated with 68 additional full-16S samples from another 40 patients. Both full-16S and RNAseq revealed significant differences between healthy and peri-implantitis samples, with respect to both the microbiome and functional profiles. A shift from aerotolerant Gram-positive bacteria to anaerobic Gram-negative bacteria was observed in peri-implantitis. Distinct metabolic pathways were expressed in healthy and peri-implantitis samples. Our results, based on paired taxonomic and functional profiles, provide for the first time important insights into the complex peri-implant biofilm ecology related to amino acid metabolism. Integrating taxonomic and functional information improved the predictive ability (AUC = 0.85) of the machine learning models and revealed diagnostic biomarkers with large effect sizes (Cohens d > 0.8). Primary biomarkers included health-associated Streptococcus, Rothia species and enzymes associated with peri-implantitis (urocanate hydratase, tripeptide aminopeptidase, NADH:ubiquinone reductase, phosphoenolpyruvate carboxykinase and polyribonucleotide nucleotidyltransferase - mostly expressed by Fusobacteriia and Bacteroidia). Thus, biofilm profiling at these two molecular levels reveals highly predictive disease biomarkers and provide the basis for developing early diagnostics and individualized therapy approaches for peri-implant diseases.

microbiology↗

bioRxiv2021

Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile

During a field experiment applying broiler manure for fertilization of agricultural land, we detected viable Clostridioides (formerly, Clostridium) difficile in broiler feces, manure, dust, and fertilized soil. A large diversity of toxigenic C. difficile isolates was recovered, including PCR ribotypes common from human disease. Genomic relatedness of C. difficile isolates from dust and from soil, recovered more than two years after fertilization, traced their origins to the specific chicken farm that had delivered the manure. We present evidence of long-term contamination of agricultural soil with manure-derived C. difficile and demonstrate the potential for airborne dispersal of C. difficile through dust emissions during manure application. Clostridioides genome sequences virtually identical to those from manure had been recovered from chicken meat and from human infections in previous studies, suggesting broiler-associated C. difficile are capable of zoonotic transmission.

microbiology↗