Background Airway and gut dysbiosis have been reported in Chronic Obstructive Pulmonary Disease (COPD); however, their relationship and association with clinical features remain poorly understood. We aimed to characterise the lung and gut microbiome in patients with stable COPD and controls. Methods Prospective, multicentre, longitudinal and controlled study of n = 60 stable patients with COPD and n = 30 controls. In them, we analysed 16S rRNA-seq in oropharyngeal (OP) swabs, sputum, bronchoalveolar lavage fluid (BALF) and stool. Weighted gene co-expression network analysis (WGCNA) was employed in each sample type to identify modules of co-abundant bacteria associated with clinical traits. Findings We found that the microbiome in airway and stool samples was highly dissimilar both in patients and controls, with 0.37% of this diversity associated to COPD. The microbiome taxa associated with COPD in OP swabs and sputum were highly similar, but different from BALF, suggesting that OP swabs can be a surrogate sample of sputum. Finally, using WGCNA, we identified: (a) 5 modules in OP swabs and 3 in sputum associated with FEV1, but some of them were also associated with exacerbations, dyspnoea and inhaled steroid (ICS) use; (b) In BALF 4 modules associated with FEV1 and dyspnoea, and 2 modules with ICS; and, finally, (c) in stool, 1 module related to FEV1, 1 to exacerbations and 3 with ICS. Interpretation The gut and lung microbiomes in patients with COPD are distinct, but both clinically relevant as both present bacterial associations with airflow limitation, exacerbation history, and ICS use. Funding ISC-III PI24/00476. FRPA.2014, ICREA-2024.

OBJECTIVE:To characterize the clinical phenotype and disease burden in patients with concomitant spondyloarthritis (SpA) and hidradenitis suppurativa (HS) versus patients with SpA alone. METHODS:We conducted a multicenter, retrospective and matched case-control study. Cases were adults with SpA and dermatologist‑confirmed HS; controls had SpA without HS. Data from the preceding three years were extracted from electronic medical records. RESULTS:We included 39 cases and 111 controls. Among cases, 64% had axial SpA (axSpA) and 36% peripheral SpA (pSpA). Compared with controls, patients with axSpA+HS had less HLA-B27 positivity (46%vs. 79%, p = 0.002), less radiographic sacroiliitis (60%vs. 86%, p = 0.007), and more frequent arthritis (40%vs. 23%; p = 0.081). Several comorbidities were more prevalent in axSpA+HS: active smoking (68%vs. 35%; p = 0.006), hypertension (44%vs. 17%; p = 0.011), and anxiety-depressive disorders (36%vs. 16%; p = 0.046). Among EMM, IBD was more frequent in axSpA+HS than in controls (20%vs. 3%; p = 0.020). Patients with axSpA+HS presented higher disease activity (ASDAS-CRP: 3.0 vs. 2.1, p = 0.003; CRP: 11.3 vs. 3.3 mg/L, p = 0.001), had received a greater number of different biologic agents (p = 0.028), showed more frequent csDMARD use (52%vs. 28%; p = 0.018), and had more rheumatology visits (median 9.0 vs. 7.0; p = 0.050). CONCLUSIONS:Concomitant SpA and HS appears to be associated with a distinct clinical phenotype and higher disease burden that translates into greater therapeutic complexity and healthcare utilization. These findings support the hypothesis that HS may form part of the broader spectrum of immune-mediated manifestations associated with SpA, although further investigation is required.

BACKGROUND:The relationship between hidradenitis suppurativa (HS) and arthritis is well-established; however, the impact of their combined disease burden and the associated treatment pattern has not been determined yet. This study aimed to assess disease burden and therapeutic approaches in HS patients with and without arthritis and estimate arthritis prevalence and subtypes. METHODS:A multicenter, retrospective, case-control study of 272 adults (69 with HS and arthritis; 203 with HS only), drawn from a hospital-based cohort of 3644 HS patients across 10 Spanish centers. Controls were matched 1:3 by sex, age, and HS duration. Statistical analysis included non-parametric tests, logistic regression, and linear mixed-effects models adjusted for confounders. RESULTS:HS patients with arthritis had higher rates of immune-mediated diseases, including inflammatory bowel disease (odds ratio [OR] 9.44, p < 0.0001) and psoriasis (OR 2.99, p = 0.0038), higher Dermatology Life Quality Index (DLQI) scores (6.30 vs. 4.03, p = 0.031), more dermatology visits (7.00 vs. 5.00, p = 0.0077), and greater biologic therapy use (72.07% vs. 39.90%, p < 0.0001). The prevalence of arthritis among HS patients was 1.70% (95% confidence interval [CI]: 1.00%-2.70%), with spondyloarthritis being the most common subtype (66.6%). CONCLUSIONS:HS patients with arthritis have a greater disease burden and higher biologic therapy utilization, emphasizing the need for interdisciplinary care and optimizing resources.

IntroductionWhen collecting oral and fecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing are not always feasible. It is essential to study the impact of temporary room temperature (RT) storage on microbiome diversity.MethodsWe conducted a pilot study to validate a sampling protocol based on the viability of 16S rRNA gene sequencing in microbiome samples. Fecal and oral samples from five participants were collected and preserved under different conditions: a) 70% ethanol; b) FIT tube for stool; and c) chlorhexidine solution for oral wash. Four aliquots per sample were stored at RT and frozen at days 0, 5, 10, and 15.ResultsAlpha diversity showed a maximum average decrease of 0.3%, 1.6%, and 1.7% after 5 days for oral, stool in ethanol, and stool in FIT samples, respectively. The relative abundances of the main phyla and orders remained stable throughout the 15 days.DiscussionMicrobiome diversity appears remarkably resilient. Fecal and oral samples stored at RT in 70% ethanol, chlorhexidine, and FIT tubes exhibited minimal changes over 15 days. These results support the feasibility of large-scale microbiome studies with delayed sample processing.

Hybridisation is a source of genetic diversity, can drive adaptation to new niches and has been found to be a frequent event in lineages harbouring pathogenic fungi. However, little is known about the genomic implications of hybridisation nor its impact on pathogenicity-related traits. A common limitation for addressing these questions is the narrow representativity of sequenced genomes, mostly corresponding to strains isolated from infected patients. The opportunistic human pathogen Candida metapsilosis is a hybrid that descends from the crossing between unknown parental lineages. Here, we sequenced the genomes of five new C. metapsilosis isolates, one representing the first African isolate for this species, and four environmental isolates from marine niches. Our comparative genomic analyses, including a total of 29 sequenced strains, shed light on the phylogenetic relationships between C. metapsilosis hybrid isolates and show that environmental strains are closely related to clinical ones and belong to different clades, suggesting multiple independent colonisations. Furthermore, we identify a new diverging clade likely emerging from the same hybridisation event that originated two other previously described hybrid clades. Lastly, we evaluate phenotypes relevant during infection such as drug susceptibility, thermotolerance or virulence. We identify low drug susceptibility phenotypes which we suggest might be driven by loss of heterozygosity events in key genes. We discover that thermotolerance is mainly clade-dependent and find a correlation with the faecal origin of some strains which highlights the adaptive potential of the fungus as commensal.

Introduction: Considering the growing recognition of the association between hidradenitis suppurativa (HS) and spondyloarthritis, this study addresses a gap in clinical practice in HS consultation: the absence of a validated arthritis screening tool. Methods: Drawing on interdisciplinary collaboration between dermatology and rheumatology, we assayed a modified version of the PURE-4 tool: patient and dermatologist Psoriatic Arthritis Uncluttered Screening Evaluation-5 (p- and dPURE-5), adapted to reflect clinical features relevant to this population. Results: Of 214 HS patients, 125 (58.4%) were male, with a median age of 42 years (IQR 30-49). Buttock involvement was observed in 64 patients (29.9%) and was more common in males (35.7%) than in females (21.6%) (p = 0.26). Of the 214 patients, 82 (38.3%) answered negatively to all questions, while 118 (55.6%) answered positively to at least one question in the pPURE-5 but were later dismissed by the trained dermatologist after a more detailed interview. Finally, 14 patients (6.5%) were referred to Rheumatology due to a positive dPURE-5. Of these, 2 (14.3%) were diagnosed with inflammatory chronic arthritis, yielding a positive predictive value of 14.3%. Conclusion: To conclude, the PURE-5 questionnaire appeared valuable for guiding anamnesis and facilitating rheumatology referrals. Even so, there is still a need for new and validated screening tools for detecting arthritis in the HS population.

Gut colonization by Extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-E), is increasing among nonhospitalized children, but the impact of ESBL-E carriage on the intestinal microbiota remains unknown. In this study, we compared the fecal bacterial composition in 24 children (3-11 years old) that were carriers of Escherichia producing ESBL (ESBL-Es) to that of an age- and gender-matched group of non-carriers using 16S rRNA gene amplicon sequencing. Alpha diversity of the community was similar in both groups. No significant differences in relative abundance at the phylum, class, and order levels were found. Significant differences at the genus and species level were identified. The genus Blautia and the species Blautia obeum were more abundant in non-carriers, whereas the genus Coprococcus and Coprococcus eutactus species were more abundant in carriers. Generalized linear models, confirmed these differences and identified additional ones at the family (Tannerellaceae is more abundant in carries), genus (Parabacteroides is more abundant in carriers), and species (Bifidobacterium longum and Ruminococcus gauvreauii are more abundant in non-carriers, and Parabacteroides distasonis in carriers) levels. However, statistical significance was lost in all cases after applying multiple testing correction. Altogether, this study uncovers a differential microbiological signature between pediatric ESBL-Es carriers and non-carriers, despite an overall similar diversity and composition of their gut microbiota. Further studies are required to explore if these differences predispose to, or are a consequence of ESBL-Es carriage, and if modulation of the gut microbiota community may help to prevent or eliminate ESBL-Es colonization.

Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Our work addresses the gap between RNA structure and their biology by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5′ untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species. Additionally, we provide the first experimental characterization of lncRNA structures in Candida species. Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana, suggesting a conserved role for these structures. In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.

Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.

BACKGROUND:Gut dysbiosis has been associated with colorectal cancer (CRC), the third most prevalent cancer in the world. This study compares microbiota taxonomic and abundance results obtained by 16S rRNA gene sequencing (16S) and whole shotgun metagenomic sequencing to investigate their reliability for bacteria profiling. The experimental design included 156 human stool samples from healthy controls, advanced (high-risk) colorectal lesion patients (HRL), and CRC cases, with each sample sequenced using both 16S and shotgun methods. We thoroughly compared both sequencing technologies at the species, genus, and family annotation levels, the abundance differences in these taxa, sparsity, alpha and beta diversities, ability to train prediction models, and the similarity of the microbial signature derived from these models. RESULTS:As expected, the results showed that 16S detects only part of the gut microbiota community revealed by shotgun, although some genera were only profiled by 16S. The 16S abundance data was sparser and exhibited lower alpha diversity. In lower taxonomic ranks, shotgun and 16S highly differed, partially due to a disagreement in reference databases. When considering only shared taxa, the abundance was positively correlated between the two strategies. We also found a moderate correlation between the shotgun and 16S alpha-diversity measures, as well as their PCoAs. Regarding the machine learning models, only some of the shotgun models showed some degree of predictive power in an independent test set, but we could not demonstrate a clear superiority of one technology over the other. Microbial signatures from both sequencing techniques revealed taxa previously associated with CRC development, e.g., Parvimonas micra. CONCLUSIONS:Shotgun and 16S sequencing provide two different lenses to examine microbial communities. While we have demonstrated that they can unravel common patterns (including microbial signatures), shotgun often gives a more detailed snapshot than 16S, both in depth and breadth. Instead, 16S will tend to show only part of the picture, giving greater weight to dominant bacteria in a sample. Therefore, we recommend choosing one or another sequencing technique before launching a study. Specifically, shotgun sequencing is preferred for stool microbiome samples and in-depth analyses, while 16S is more suitable for tissue samples and studies with targeted aims.

Hybrids are chimeric organisms carrying genetic material from at least two divergent parental lineages. Hybridization can contribute to the emergence of novel lineages with unique phenotypic traits that may facilitate their adaptation to new environments. In recent years, genomic analyses have revealed the hybrid nature of several opportunistic human pathogenic yeasts. One of them is Pichia inconspicua, , a member of the Pichia cactophila species complex, for which all sequenced strains isolated from Europe are hybrids with so far unknown parentals. It has been recently proposed that P. inconspicua and P. cactophila s.s. should be ranked as the same species due to their genetic similarity. To obtain a better understanding of the evolution of this clade, we sequenced the genomes of the P. cactophila type strain, of its close-relative - relative Pichia pseudocactophila, , and of a putative P. inconspicua clinical isolate from Alaska and compared them with the previously sequenced genomes of Pichia norvegensis, , P. inconspicua and the recently described Pichia galeolata. . Our results show evidence for the existence of distinct lineages with a hybrid origin within this clade and suggest an intricate scenario of recurrent hybridizations in this species complex, some of them giving rise to lineages with the ability to infect humans. Given their different hybridization histories, we propose that P. inconspicua, , P. cactophila, , and the new clinical isolate from Alaska should represent three distinct species and suggest the name Pichia alaskaensis for the new taxon. Our results clarify the evolutionary relationships within the P. and underscore the of non-vertical - vertical evolution.

Hidradenitis suppurativa (HS) is recognized as a systemic immune-mediated disease (IMID), sharing genetic and environmental risk factors with other IMIDs such as inflammatory bowel disease and psoriasis. Over time, correlating clinical findings with genetic, proteomic, and metabolomic results has been challenging due to diverse sampling methods, analysis techniques, and the use of variable clinical phenotype descriptions across studies. This review aims to summarize the results from various omics fields to explore the etiopathology of HS. Genetic studies highlight defects in Notch and γ-secretase signaling and inflammasome function. Syndromic HS involves specific mutations in autoinflammatory syndromes such as pyogenic sterile arthritis, pyoderma gangrenosum, and acne (PAPA) and pyoderma gangrenosum, acne, and HS (PASH). Proteomic analyses reveal key inflammatory pathways indicating activation of both innate and adaptive immunity. Additionally, microbiome studies show an increased presence of anaerobes like Prevotella in HS lesions and a decreased presence of commensals such as Staphylococcus epidermidis. Gut microbiota dysbiosis, particularly involving Ruminococcus gnavus and Clostridium ramosum, is associated with HS. Moreover, metabolomic profiling indicates dysregulated tryptophan catabolism and lipid metabolism, with increased 5-lipoxygenase-derived metabolites and odd-chain fatty acids suggesting bacterial involvement. In summary, despite advances, robust associations between genetics, proteomics, microbiome, and metabolomics in HS are still lacking. Integrating these datasets could identify new clinical phenotypes, genetic predispositions, microbial signatures, and therapeutic targets, enhancing personalized treatment strategies and biomarker discovery for HS classification, prognosis, and treatment response.

Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer deaths worldwide. Early diagnosis of CRC, which saves lives and enables better outcomes, is generally implemented through a two-step population screening approach based on the use of Fecal Immunochemical Test (FIT) followed by colonoscopy if the test is positive. However, the FIT step has a high false positive rate, and there is a need for new predictive biomarkers to better prioritize cases for colonoscopy. Here we used 16S rRNA metabarcoding from FIT positive samples to uncover microbial taxa, taxon co-occurrence and metabolic features significantly associated with different colonoscopy outcomes, underscoring a predictive potential and revealing changes along the path from healthy tissue to carcinoma. Finally, we used machine learning to develop a two-phase classifier which reduces the current false positive rate while maximizing the inclusion of CRC and clinically relevant samples.

Additional file 13. Detected non-reciprocal recombination events in C. orthopsilosis.

Understanding the intricate roles of RNA molecules in virulence and host-pathogen interactions can provide valuable insights into combatting infections and improving human health. Although much progress has been achieved in understanding transcriptional regulation during host-pathogen interactions in diverse species, more is needed to know about the structure of pathogen RNAs. This is particularly true for fungal pathogens, including pathogenic yeasts of the Candida genus, which are the leading cause of hospital-acquired fungal infections. Deciphering the relation between RNA structure and their biology remains a significant gap. Despite advancements in transcriptional regulation studies, especially for fungal pathogens like Candida , the structural aspects of pathogenic RNAs remain understudied. Our work addresses this gap by employing genome-wide structure probing to comprehensively explore the structural landscape of mRNAs and long non-coding RNAs (lncRNAs) in the four major Candida pathogens. Specifically focusing on mRNA, we observe a robust correlation between sequence conservation and structural characteristics in orthologous transcripts, significantly when sequence identity exceeds 50%, highlighting structural feature conservation among closely related species. We investigate the impact of single nucleotide polymorphisms (SNPs) on mRNA secondary structure. SNPs within 5’ untranslated regions (UTRs) tend to occur in less structured positions, suggesting structural constraints influencing transcript regulation. Furthermore, we compare the structural properties of coding regions and UTRs, noting that coding regions are generally more structured than UTRs, consistent with similar trends in other species.Additionally, we provide the first experimental characterization of lncRNA structures in Candida species . Most lncRNAs form independent subdomains, similar to human lncRNAs. Notably, we identify hairpin-like structures in lncRNAs, a feature known to be functionally significant. Comparing hairpin prevalence between lncRNAs and protein-coding genes, we find enrichment in lncRNAs across Candida species, humans, and Arabidopsis thaliana , suggesting a conserved role for these structures.In summary, our study offers valuable insights into the interplay between RNA sequence, structure, and function in Candida pathogens, with implications for gene expression regulation and potential therapeutic strategies against Candida infections.### Competing Interest StatementThe authors have declared no competing interest.

Additional file 16. List of essential genes for the occurrence of meiotic recombination, and their respective orthologs in C. orthopsilosis, C. metapsilosis and Clavispora lusitaniae, determined by EggNOG-mapper v1.0.3 using Diamond algorithm.

Additional file 7. P-values obtained from the hypergeometric test applied to compare the overlap of heterozygous and homozygous regions in each pair of strains or clades.

Long noncoding RNAs (lncRNAs) are emerging players in cancer and they entail potential as prognostic biomarkers or therapeutic targets. Earlier studies have identified somatic mutations in lncRNAs that are associated with tumor relapse after therapy, but the underlying mechanisms behind these associations remain unknown. Given the relevance of secondary structure for the function of some lncRNAs, some of these mutations may have a functional impact through structural disturbance. Here, we examined the potential structural and functional impact of a novel A > G point mutation in NEAT1 that has been recurrently observed in tumors of colorectal cancer patients experiencing relapse after treatment. Here, we used the nextPARS structural probing approach to provide first empirical evidence that this mutation alters NEAT1 structure. We further evaluated the potential effects of this structural alteration using computational tools and found that this mutation likely alters the binding propensities of several NEAT1-interacting miRNAs. Differential expression analysis on these miRNA networks shows upregulation of Vimentin, consistent with previous findings. We propose a hybrid pipeline that can be used to explore the potential functional effects of lncRNA somatic mutations.

The study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing medical concern. Four phylogenetically diverse species account for over 90% of Candida infections, and their specific interactions with various human tissues are still poorly understood. To enable in vivo transcriptomic analysis in these species, we designed and validated pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes. The probe-based enrichment approach outperformed enrichment based on differential lysis of host cells, and showed similar enrichment performance as an existing capture design, yet achieving better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs. In addition, we show that our probe-based enrichment strategy allows robust genotype-based identification of the infecting strain present in the sample.