Biology subjects

Steglich, M.

Publications and source records attributed to Steglich, M..

9 recordsLinked to original sources

bioRxiv2026

Post-Weaning Gut Microbiota Colonization Reveals Divergent Recovery of Skeletal Muscle and Peripheral Nerves

We previously demonstrated that the absence of a complex gut microbiota (CGM) impairs the postnatal development of peripheral nerves and motor targets in germ-free (GF) mice. In this study, we investigated whether establishing a complex gut microbiota after weaning could reverse these developmental alterations. To address this question, GF mice were colonized with a complex gut microbiota by co-housing with conventionally raised mice. Microbiota composition, peripheral nerve morphology and transcriptional profiles, skeletal muscle proteome, neuromuscular junction architecture and circulating metabolites were comprehensively analyzed and compared with those of GF, gnotobiotic OMM12 and CGM mice. Post-weaning colonization partially restored microbial diversity and resulted in a compositionally distinct microbial community with reduced alpha diversity and enrichment of Duncaniella muris strain B8. Despite successful microbial colonization, peripheral nerve abnormalities persisted, including axon hypermyelination, transcriptional alterations in sciatic nerves, elongated nodes of Ranvier, and dysregulated axon-glia interactions. In contrast, skeletal muscle defects were largely rescued, with restoration of muscle mass, normalization of proteomic profiles, recovery of metabolic and structural pathways, and reduced fragmentation of the postsynaptic neuromuscular junction, although presynaptic abnormalities persisted. These findings demonstrate that microbiota-dependent developmental alterations differ markedly in their reversibility across the neuromuscular system. Specifically, post-weaning colonization with a complex gut microbiota resulted in broad recovery of skeletal muscle but failed to rescue peripheral nerve abnormalities. Our findings provide a framework for future studies investigating how the timing of microbial colonization, microbiota composition, and microbiota-derived signals influence the reversibility of microbiota-dependent neuromuscular alterations.

neuroscience↗

bioRxiv2026

Profiling of DNA-methylation signatures in human ILCs during homeostasis and allergic disease

The transcriptional programs of human ILCs are increasingly defined, but the DNA-methylation landscapes that stabilize their identity and function remain poorly understood. Here, we generated genome-wide DNA methylomes of human NK cells, ILC1, ILC2, and ILC3 from blood and lymphoid tissues. Subset-specific differentially methylated regions distinguished all populations and mapped to canonical regulators, including TBX21, GATA3, and RORC, as well as genes not previously linked to ILC biology, such as ERN1, DDX47, JAML, BTLA, and NRROS. Because ILC2 showed a particularly distinct methylation landscape and contribute to allergic inflammation, we tested whether selected ILC2-specific regions were functionally relevant. ILC2 marker regions were largely stable across tissues and during cytokine-driven expansion. CRISPR/Cas9-mediated deletion of the HPGDS or NRROS DMR revealed that these elements act as cis-regulatory sites controlling HPGDS/NRROS expression and promoting production of the type 2 cytokines IL-4, IL-5 and IL-13. Finally, methylome profiling of ILC2 from healthy, atopic, and asthmatic children identified disease-associated DMRs linked to PTGS2, QKI, and GIMAP4. These findings define stable epigenetic signatures of human ILC identity and uncover regulatory elements connecting ILC2 methylation to allergic disease.

immunology↗

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

Invasive species drive polymicrobial resistance to amoxicillin in oral biofilms through beta-lactamase release

Since bacterial biofilms often cause refractory infections, antimicrobial susceptibility testing (AST) is highly desirable even for oral peri-implant biofilms. However, characterization of polymicrobial drug resistance is challenging due to high diversity and complexity of these biofilms. In this work, we developed laser-assisted AST and detected polymicrobial amoxicillin resistance in peri-implantitis. TEM-1 {beta}-lactamase production enabled an Enterobacter sp. strain SPS_532 to protect its otherwise susceptible biofilm cohabitants. To understand the {beta}-lactamase driven cross-protection in the human microbiome we aggregated genomic (n = 200,000) and patient microbial data (n = 27,000), developed a cross-protection assay, studied a representative strain collection (n = 118) and established a complex biofilm in vitro model (with an average of 133 species from 164 found in dental plaque). Multiple oral allochthonous species, e.g., Enterobacter, Klebsiella, Escherichia, Staphylococcus, and only a single typical oral microorganism, Haemophilus, were able to cross-protect. Diverse bla genes conferred activity, via a high expression of chromosomal gene, e.g., blaAmpC gene or by the presence of plasmidic gene, e.g., blaTEM-1 gene. Invaders not only cross-protected the biofilm from the antibiotic, but also supported expansion of opportunistic pathogens like Fusobacterium species. Cross-protection in complex biofilms depended on the diffusion rate and population size of the invader, which could be bio-controlled with a phage. Deciphering polymicrobial resistance might support the development of diagnostic and therapeutic approaches to combat implant-associated biofilm infections in the human mouth.

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↗

bioRxiv2022

Bursts in biosynthetic gene cluster transcription are accompanied by surges of natural compound production in the myxobacterium Sorangium sp.

We have investigated the time course of genome-wide transcription in the myxobacterium Sorangium sp. So ce836 in relation to its production of natural compounds. Time-resolved RNA sequencing revealed that core biosynthesis genes from 48 biosynthetic gene clusters (BGCs; 92% of all BGCs encoded in the genome) were actively transcribed at specific time points in a batch culture. The majority (80%) of polyketide synthase and non-ribosomal peptide synthetase genes displayed distinct peaks of transcription during exponential bacterial growth. Strikingly, these bursts in BGC transcriptional activity were associated with surges in the production of known natural compounds, indicating that their biosynthesis was critially regulated at the transcriptional level. In contrast, BGC read counts from single time points had limited predictive value about biosynthetic activity, since transcription levels varied >100-fold among BGCs with detected natural products. Taken together, our time-course data provide unique insights into the dynamics of natural compound biosynthesis and its regulation in a wild-type myxobacterium, challenging the commonly cited notion of preferential BGC expression under nutrient-limited conditions. The close association observed between BGC transcription and compound production warrants additional efforts to develop genetic engineering tools for myxobacterial producer strains, to boost compound yields by manipulating transcriptional activity.

genomics↗

bioRxiv2019

The global phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia

Recent studies portend a rising global spread and adaptation of human- or healthcare-associated pathogens. Here, we analysed an international collection of the emerging, multidrug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harboured strains of all degrees of human virulence. Lineage Sm6 comprised the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identified potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals.\n\nOne Sentence SummaryThe S. maltophilia complex comprises genetically diverse, globally distributed lineages with evidence for intra-hospital transmission.

genomics↗

bioRxiv2019

Global genomic population structure of Clostridioides difficile

Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce EnteroBase, a publicly accessible database (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that the identification of highly related genomes is 89% consistent between cgMLST and single-nucleotide polymorphisms. EnteroBase currently contains 13,515 quality-controlled genomes which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. Hierarchical clustering can be used to identify populations of C. difficile at all epidemiological levels, from recent transmission chains through to pandemic and endemic strains, and is largely compatible with prior ribotyping. Hierarchical clustering thus enables comparisons to earlier surveillance data and will facilitate communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.

microbiology↗

bioRxiv2016

Rapid and consistent evolution of colistin resistance in Pseudomonas aeruginosa during morbidostat culture

Colistin is a last resort antibiotic commonly used against multidrug-resistant strains of Pseudomonas aeruginosa. To investigate the potential for in-situ evolution of resistance against colistin and map the molecular targets of colistin resistance, we exposed two P. aeruginosa isolates to colistin using a continuous culture device known as morbidostat. Colistin resistance emerged within two weeks along with highly stereotypic yet strain specific mutation patterns. The majority of mutations hit the prmAB two component signaling system and genes involved in lipopolysaccharide synthesis, including lpxC, pmrE, and migA. In seven out of 18 cultures, we observed mutations in mutS along with a mutator phenotype that seemed to facilitate resistance evolution.

microbiology↗