Biology subjects

Cardenas, J. P.

Publications and source records attributed to Cardenas, J. P..

5 recordsLinked to original sources

bioRxiv2025

Genomic analysis of the probiotic candidate Bifidobacterium bifidum strain 900791 in the context of the B. bifidum pangenome

BackgroundBifidobacterium bifidum is a key commensal bacterium in the human gut microbiota with recognized probiotic properties and health benefits. An underinvestigated strain called 900791, isolated from meconium of a Siberian infant and with a validated role in lactose tolerance, requires more understanding of the genomic basis of its potential probiotic functionality. MethodsWe performed whole genome sequencing of strain 900791 using hybrid sequencing (Illumina NextSeq and Nanopore). The genome was functionally annotated and compared against 228 B. bifidum genomes to elucidate probiotic determinants and evolutionary relationships. Antibiotic resistance profiling was conducted using three independent approaches, carbohydrate-active enzymes (CAZymes) were characterized using dbCAN analysis; additionally different markers for desired phenotypes in probiotics (such as adherence to epithelial cells, resistance to low pH, bile salts and oxidative stress, and the ability to produce bacteriocins) were also investigated. ResultsThe complete genome comprises 2.28 Mb with 62.43% G+C content, encoding 1,852 ORFs, 53 tRNAs, and three complete 16S rRNA genes. Phylogenomic analysis revealed 900791 belongs to a distinct clonal subgroup of nine closely related strains sharing almost identical allelic similarity (observed via cgMLST). The pangenome analysis of 229 B. bifidum genomes showed an open structure with 4,679 orthogroups, including 1,212 core families.The strain 900791 harbors extensive CAZymes from families GH2, GH20, GH33, and GH84 associated with mucin and human milk oligosaccharide degradation, plus GH2 and GH42 families for lactose metabolism. Safety assessment revealed only intrinsic resistance to mupirocin and rifampicin, with no acquired resistance markers or virulence factors. The strain possesses multiple stress tolerance systems including acid resistance (FF-ATPase), bile salt resistance (MFS transporters, BSH hydrolase), and oxidative stress response mechanisms. Predicted probiotic features include adhesion proteins (FimA/FimB, FimM), bacteriocin production capabilities, and comprehensive stress response systems. ConclusionB. bifidum 900791 harbors markers for significant probiotic potential with genetic features optimized for gut colonization, host interaction, and antimicrobial competition. This genomic characterization provides a framework for understanding B. bifidum diversity and supports B. bifidum strain 900791-specific probiotic applications, particularly given its demonstrated efficacy in improving lactose tolerance in human subjects.

microbiology↗

bioRxiv2025

Clade-wide proteome analysis shows widespread non-canonical Dcr proteins in fungi.

Dicers (Dcrs) are central proteins involved in the biogenesis of small RNAs (sRNAs) in eukaryotes. Most of the knowledge on Dcr structure, function and evolution comes from studies conducted in animal and plant species. Comparatively, much less is known in fungi, which are a genetically and ecologically diverse group with important roles in ecosystems, agriculture, medicine, and biotechnology. While canonical Dcrs in plants and animals contain a well-defined domain architecture, most fungal Dcrs with experimentally validated functions lack one or more identifiable canonical domains, raising questions about how RNA-binding and precise sRNA processing is retained. Here, we conducted the most extensive survey of fungal Dcr proteins, analyzing 1,593 proteomes across eight phyla. We found a diversity of Dcr domain architectures, with some of them lacking an identifiable PAZ, Helicase, and/or double-stranded RNA binding domains. Phylogenetic analyses showed that different Dcr classes are distributed across distinct clades that often align with fungal taxonomic groups. Despite the lack of canonical domain architectures, we found that fungal Dcrs fold into a characteristic L-shaped structure and show PAZ-like folds, even in proteins without detectable PAZ sequences. Molecular docking and electrostatic analyses further indicate that these divergent Dcrs maintain key RNA-binding surfaces for proper sRNA processing. Our results indicate a remarkable evolutionary plasticity of Dcr in fungi, showing that essential sRNA processing functions can be retained through structural conservation, and highlighting fungi as models to study the modular evolution of the RNAi machinery in eukaryotes. Significance statementDicer (Dcr) proteins are central to RNA interference (RNAi), a gene regulatory mechanism conserved across eukaryotes. However, current models of Dcr structure, function, and evolution are largely based on studies in animals and plants. Here, we present the most comprehensive analysis to date of Dcr proteins in fungi, a diverse eukaryotic group including many societally important pathogens and symbiotes which are reliant on RNAi. Our findings reveal that despite widespread divergence from canonical Dcr architecture, fungal Dcrs conserve critical folds and RNA-binding features, further suggesting that core RNAi functions are maintained. This work establishes fungi as key models for studying the evolution and functional robustness of the RNAi machinery, offering broader insight into the diversity and plasticity of sRNA biogenesis pathways across eukaryotes.

genomics↗

bioRxiv2018

Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis

Microbial community analysis can be biased by multiple technical factors, such as storage conditions, DNA extraction, or amplification conditions. In a high-throughput laboratory that relies on samples obtained from thousands of different subjects, knowledge of the extent of subject-introduced sampling and storage variation on the outcome of the inferred microbiome, as well as the effect of laboratory-introduced variation caused by reagent batches, equipment, or operator on the consistency of these processes within the laboratory is paramount. Here, we analyzed the effect of sampling from different parts of the same stool specimen or on different consecutive days, as well as short-term storage of samples at different temperatures on microbiome profiles obtained by 16S rRNA gene amplification. Each of these factors had relatively little effect on the microbial composition. In addition, replicate amplification of 44 stool samples showed reproducible results. Finally, 363 independent replicate extractions and amplifications of a single human homogenized stool (HS) specimen showed reproducible results (average Lins correlation = 0.95), with little variation introduced by HS batch, operator, extraction equipment, or DNA sequencer. In all cases, variations between replicates were significantly smaller than those between individual samples; subject identity always was the largest determinant. We propose that homogenized stool specimens could be used as quality control to routinely monitor the laboratory process and to validate new methods.

microbiology↗

bioRxiv2017

A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a womans reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive womens health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 32 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 4 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, healthy ranges were determined in a group of 50 self-reported healthy women. The hrHPV portion of the test was evaluated against the Digene High-Risk HPV HC2 DNA test with vaginal samples obtained from 185 women. Results were concordant for 181/185 of the samples (overall agreement of 97.83%, Cohens kappa = 0.93), with sensitivity and specificity values of 94.74% and 98.64%, respectively. Two discrepancies were caused by the Digene assays known cross-reactivity with low-risk HPV types, while two additional samples were found to contain hrHPV not detected by Digene. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.

microbiology↗

bioRxiv2016

16S rRNA Gene Sequencing as a Clinical Diagnostic Aid for Gastrointestinal-related Conditions

Accurate detection of the microorganisms underlying gut dysbiosis in the patient is critical to initiate the appropriate treatment. However, most clinical microbiology techniques used to detect gut bacteria were developed over a century ago and rely on culture-based approaches that are often laborious, unreliable, and subjective. Further, culturing does not scale well for multiple targets and detects only a minority of the microorganisms in the human gastrointestinal tract. Here we present a clinical test for gut microorganisms based on targeted sequencing of the prokaryotic 16S rRNA gene. We tested 46 clinical prokaryotic targets in the human gut, 28 of which can be identified by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. Using microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay accurately quantified all 28 targets and correctly reflected 38/38 verification samples of real and synthetic stool material containing known pathogens. Thus, we have established a new test to interrogate microbiome composition and diversity, which will improve patient diagnosis, treatment and monitoring. More broadly, our test will facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.

microbiology↗