Biology subjects

Rabasco, J.

Publications and source records attributed to Rabasco, J..

4 recordsLinked to original sources

bioRxiv2026

TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization

BackgroundTransduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a samples ultra-purified VLPs are mapped to metagenomic contigs assembled from the same samples whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the methods use unfeasible for datasets with many samples. ResultsWe developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdents classifications of transductomics datasets to classifications made by human classifiers. TrIdents classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes. ConclusionsThe TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.

genomics↗

bioRxiv2026

Temporal stability and niche partitioning of bacterial communities in paired residential sink P-traps

Sink P-traps harbor microbial communities derived from environmental and human sources, yet longitudinal studies examining their stability and assembly dynamics remain limited. Here, we present, to our knowledge, the longest continuous characterization of bacteria collected from residential sink P-traps, with daily sampling over two months (n = 61 days). Samples were collected from paired sinks in a shared bathroom to identify dominant taxa, quantify temporal stability, and determine how occupant usage patterns influence community assembly. Using full-length 16S rRNA gene sequencing, we identified 3,865 unique taxa, with both sinks dominated by common sink-associated genera, including Pseudomonas, Citrobacter, Klebsiella, and Arcobacter. Despite sharing identical plumbing, environmental conditions, and cleaning regimes, the two sinks maintained distinct communities (p < 0.001). Temporal stability analyses revealed notable differences: Sink A (male; hand washing, toothbrushing, shaving) exhibited deterministic dynamics with low variability (CV = 4.9%), significant temporal autocorrelation (p = 0.001), and predictable trajectories, with time explaining 49.9% of community variation. In contrast, Sink B (female; hand washing, toothbrushing, face washing, mouthwash use) displayed stochastic dynamics with high volatility (CV = 26.5%), no significant autocorrelation (p = 0.53), and minimal temporal predictability. Differential abundance analysis revealed that Sink B was enriched in anaerobes, biofilm-forming taxa, oral microbiome associates, and preservative-resistant and lipid-degrading bacteria, while Sink A harbored a more aerobic, skin-associated community. These findings demonstrate that individual usage patterns (particularly exposure to biocidal agents) can alter P-trap community structure and temporal dynamics, with implications for microbial community prediction in residential and healthcare settings. ImportanceSink drains are increasingly recognized as reservoirs for antimicrobial-resistant pathogens, yet we lack fundamental knowledge about what drives bacterial community dynamics in these environments. By sampling paired residential sink P-traps daily for two months, we show that individual-specific behaviors, such as using products with a biocidal effect, can alter community composition from a stable, predictable state to one characterized by stochastic fluctuations. The sink exposed to mouthwash and face wash harbored more anaerobes, biofilm formers, and oral bacteria, suggesting that repeated exposure promotes disturbance-tolerant taxa rather than reducing bacterial colonization. These results provide a baseline ecological framework for understanding P-trap microbiomes and suggest that predictive monitoring of sink-associated pathogens might be feasible in stable environments but more difficult when there is variable antimicrobial exposure -- a finding directly relevant to hospital infection control.

microbiology↗

bioRxiv2022

Molecular and functional characterization of the Drosophila melanogaster conserved smORFome

Short polypeptides encoded by small open reading frames (smORFs) are ubiquitously found in eukaryotic genomes and are important regulators of physiology, development, and mitochondrial processes. Here, we focus on a subset of 298 smORFs that are evolutionarily conserved between Drosophila melanogaster and humans. Many of these smORFs are conserved broadly in the bilaterian lineage, with [~]182 conserved in plants. Within these conserved smORFs, we observed remarkably heterogenous spatial and temporal expression patterns - indicating wide-spread tissue-specific and stage-specific mitochondrial architectures. In addition, an analysis of annotated functional domains revealed a predicted enrichment of smORF polypeptides localizing to mitochondria. We conducted an embryonic ribosome profiling experiment finding support for translation of 137 of these smORFs during embryogenesis. We further embarked on functional characterization using CRISPR knockout/activation, RNAi knockdown, and cDNA overexpression, revealing diverse phenotypes. This study underscores the importance of identifying smORF function in disease and phenotypic diversity.

genomics↗

bioRxiv2020

Two neuronal peptides encoded from a single transcript regulate mitochondrial function in Drosophila

Naturally produced peptides (<100 amino acids) are important regulators of physiology, development, and metabolism. Recent studies have predicted that thousands of peptides may be translated from transcripts containing small open reading frames (smORFs). Here, we describe two peptides in Drosophila encoded by conserved smORFs, Sloth1 and Sloth2. These peptides are translated from the same bicistronic transcript and share sequence similarities, suggesting that they encode paralogs. Yet, Sloth1 and Sloth2 are not functionally redundant, and loss of either peptide causes animal lethality, reduced neuronal function, impaired mitochondrial function, and neurodegeneration. We provide evidence that Sloth1/2 are highly expressed in neurons, imported to mitochondria, and regulate mitochondrial complex III assembly. These results suggest that phenotypic analysis of smORF genes in Drosophila can provide a wealth of information on the biological functions of this poorly characterized class of genes.

genomics↗