Biology subjects

Emiola, A.

Publications and source records attributed to Emiola, A..

3 recordsLinked to original sources

bioRxiv2026

IgG sequencing maps systemic antibody binding to oral commensals and pathobionts in health and periodontitis

The oral cavity harbors one of the body's most diverse microbial communities, which continuously seeds the bloodstream and gastrointestinal tract, particularly in periodontitis, a disease in which both barrier permeability and microbial burden increase. Despite this constant systemic exposure, overt bacteremia from oral organisms is rare, suggesting an active surveillance system that contains this reservoir. Here, we apply IgG-sequencing to comprehensively map mucosal and systemic antibody recognition of the oral microbiome across paired oral fluid and serum from healthy individuals and patients with periodontitis. We find that IgG-binding is only weakly predicted by microbial abundance, suggesting taxon-specific and largely conserved IgG-binding of commensals, many of them streptococci which dominate antibody recognition irrespective of disease state. Periodontitis broadens the repertoire of IgG-bound taxa to include particular disease-associated pathobionts while preserving robust targeting of health-associated symbionts. Comparison of salivary and serum antibody profiles further uncovers a subset of commensal streptococci, including species implicated in infective endocarditis, that acquire disproportionate systemic IgG binding in periodontitis. Together, these findings establish a taxon-level atlas of humoral immunosurveillance at a major mucosal-microbial interface and reveal how periodontal disease reshapes systemic antibody recognition of both pathobionts and commensals.

immunology↗

bioRxiv2024

Quantitative mapping of pseudouridines in bacteria RNA

RNA pseudouridylation is one of the most prevalent post-transcriptional modifications, occurring universally across all organisms. Although pseudouridines have been extensively studied in bacterial tRNAs and rRNAs, their presence and role in bacterial mRNA remain poorly characterized. Here, we used a bisulfite-based sequencing approach to provide a comprehensive and quantitative measurement of bacteria pseudouridines. As a proof of concept in E. coli, we identified 1,954 high-confidence sites in 1,331 transcripts, covering almost 30% of the transcriptome. Furthermore, pseudouridine mapping enabled the detection of differentially expressed genes associated with stress response that were unidentified using conventional RNA-seq approach. We also demonstrate that in addition to pseudouridine profiling, our approach can facilitate the discovery of previously unidentified transcripts. As an example, we identified a small RNA transcribed from the antisense strand of tRNA-Tyr which represses expression of distal genes. Finally, we mapped pseudouridines in oral microbiome samples of human subjects, demonstrating the broad applicability of our approach in complex microbiomes. Altogether, our work highlights the advantages of mapping bacterial pseudouridines and provides a tool to study posttranscription regulation in microbial communities.

microbiology↗

bioRxiv2020

An enhanced characterization of the human skin microbiome: a new biodiversity of microbial interactions

The healthy human skin microbiome is shaped by skin site physiology, individual-specific factors, and is largely stable over time despite significant environmental perturbation. Studies identifying these characteristics used shotgun metagenomic sequencing for high resolution reconstruction of the bacteria, fungi, and viruses in the community. However, these conclusions were drawn from a relatively small proportion of the total sequence reads analyzable by mapping to known reference genomes. Reference-free approaches, based on de novo assembly of reads into genome fragments, are also limited in their ability to capture low abundance species, small genomes, and to discriminate between more similar genomes. To account for the large fraction of non-human unmapped reads on the skin--referred to as microbial dark matter--we used a hybrid de novo and reference-based approach to annotate a metagenomic dataset of 698 healthy human skin samples. This approach reduced the overall proportion of uncharacterized reads from 42% to 17%. With our refined characterization, we revisited assumptions about the skin microbiome, and demonstrated higher biodiversity and lower stability, particularly in dry and moist skin sites. To investigate hypotheses underlying stability, we examined growth dynamics and interspecies interactions in these communities. Surprisingly, even though most skin sites were relatively stable, many dominant skin microbes, including Cutibacterium acnes and staphylococci, were actively growing in the skin, with poor or no relationship between growth rate and relative abundance, suggesting that host selection or interspecies competition may be important factors maintaining community homeostasis. To investigate other mechanisms facilitating adaptation to a specific skin site, we identified Staphylococcus epidermidis genes that are likely involved in stress response and provide mechanisms essential for growth in oily sites. Finally, horizontal gene transfer--another mechanism of competition by which strains may swap antagonistic or virulent coding regions--was relatively limited in healthy skin, but suggested exchange of different metabolic and environmental tolerance pathways. Altogether, our findings underscore the value of a combined reference-based and de novo approach to provide significant new insights into microbial composition, physiology, and interspecies interactions to maintain community homeostasis in the healthy human skin microbiome.

microbiology↗