CorpoGen (Colombia)

Microbiome composition through the redundancy of oxalate-degrading bacteria, critically influence oxalate metabolism, explaining variable outcomes of Oxalobacter formigenes therapy and offers insights for improving probiotic selection and clinical trial strategies.

Decades of research have made clear that host-associated microbiomes touch all facets of health. However, effective therapies that target the microbiome have been elusive given its inherent complexity. Here, we experimentally examined diet-microbe-host interactions through a complex systems framework, centered on dietary oxalate. Using multiple, independent molecular, animal, and in vitro experimental models, we found that microbiome composition influenced multiple oxalate-microbe-host interfaces. Importantly, administration of the oxalate-degrading specialist, Oxalobacter formigenes, was only effective against a poor oxalate-degrading microbiota background and gives critical new insights into why clinical intervention trials with this species exhibit variable outcomes. Data suggest that, while heterogeneity in the microbiome impacts multiple diet-host-microbe interfaces, metabolic redundancy among diverse microorganisms in specific diet-microbe axes is a critical variable that may impact the efficacy of bacteriotherapies, which can help guide patient and probiotic selection criteria in probiotic clinical trials.

The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.

Bacterial regional demonstration after global dissemination is an essential pathway for selecting distinct finesses. However, the evolution of the resistome during the transition to endemicity remains unaddressed. Using the most comprehensive whole-genome sequencing dataset of Salmonella enterica serovar Gallinarum (S. Gallinarum) collected from 15 countries, including 45 newly recovered samples from two related local regions, we established the relationship among avian-specific pathogen genetic profiles and localization patterns. Initially, we revealed the international transmission and evolutionary history of S. Gallinarum to recent endemicity through phylogenetic analysis conducted using a spatiotemporal Bayesian framework. Our findings indicate that the independent acquisition of the resistome via the mobilome, primarily through plasmids, transposons, and prophages, shapes a unique antimicrobial resistance profile among different lineages. Notably, the mobilome-resistome combination among distinct lineages exhibits a geographical-specific manner, further supporting a localized endemic mobilome-driven process. Collectively, this study elucidates resistome adaptation in the endemic transition of an avian-specific pathogen, likely driven by the localized farming style, and provides valuable insights for targeted interventions.

Piangua, Anadara tuberculosa, is an economically important mollusk for the human population living on the Colombian Pacific Coast. In the last years, the demand and exploitation of this mollusk have increased, putting it at risk to the point of being endangered. This research aimed to identify the genetic diversity and population structure of piangua in two localities on the Pacific Coast of Colombia. We assembled a chromosome-level genome using PacBio-Hifi and Arima sequencing. We obtained 274 scaffolds with an N50 of 45.42 Mbp, a total size of 953 Mbp, and a completeness of 91% based on BUSCO scores. The transposable elements accounted for 30.29% of the genome, and 24,317 genes were annotated. Genome-guided variant calling for 89 samples using DArT sequencing data delivered 4,825 bi-allelic SNPs, which supported genetic diversity and population structure analyses. Data showed that the piangua populations in the two localities were under expansion events more than 100k years ago. However, results also showed a reduction in genetic diversity, as evidenced by the loss of heterozygosity, which may be caused by high levels of inbreeding, probably due to a recent overexploitation. Furthermore, although we evidenced gene flow between the two localities, there is also a subtle geographical population structure between the two localities and among mangroves in one of the localities. This is the first study in Colombia that provides relevant genetic information on piangua to lay the foundations for conservation strategies.

Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. difficile, in particular in C. difficile infection (CDI) cases, remains poorly characterised. To investigate the gut microbiome composition in CDI patients, we analysed 534 metagenomes from 10 publicly available CDI study populations. We then tracked C. difficile on a global scale, screening 42,900 metagenomes from 253 public studies. Among the CDI cohorts, we detected C. difficile in only 30% of the stool samples from CDI patients. However, we found that multiple other toxigenic species capable of inducing CDI-like symptomatology were prevalent. In addition, the majority of the investigated studies did not adhere to the recommended guidelines for a correct CDI diagnosis.In the global survey, we found that C. difficile prevalence, abundance and biotic context were age-dependent. C. difficile is a rare taxon associated with reduced diversity in healthy adults, but common and associated with increased diversity in infants. We identified a group of species co-occurring with C. difficile exclusively in healthy infants, enriched in obligate anaerobes and in species typical of the healthy adult gut microbiome. C. difficile in healthy infants was therefore associated with multiple indicators of healthy gut microbiome maturation.Our analysis raises concerns about potential CDI overdiagnosis and suggests that C. difficile is an important commensal in infants and that its asymptomatic carriage in adults depends on microbial context.

ResumenIntroducción. La colonización por microorganismos patógenos de los dispositivos médicos usados en las unidades de cuidados intensivos es un factor de riesgo para el aumento de infecciones asociadas con la atención en salud y, por lo tanto, al de la morbilidad y la mortalidad de los pacientes intubados. En Colombia, no se ha descrito la colonización por hongos de los tubos endotraqueales, con lo cual se podrían considerar nuevas opciones terapéuticas para el beneficio de los pacientes.Objetivo. Describir los hongos que colonizan los tubos endotraqueales de los pacientes en unidades de cuidados intensivos, junto con su perfil de sensibilidad a los antifúngicos.Materiales y métodos. Se realizó un estudio observacional, descriptivo, en dos centros hospitalarios durante 12 meses. Se recolectaron tubos endotraqueales de pacientes de las unidades de cuidados intensivos. Estos fueron procesados para cultivar e identificar hongos, y para establecer su perfil de sensibilidad a los antifúngicos.Resultados. Se analizaron 121 tubos endotraqueales obtenidos de 113 pacientes. De estos, el 41,32 % se encontró colonizado por los hongos Candida albicans (64,61 %), C. no-albicans (30,77 %), Cryptococcus spp. (3,08 %) o mohos (1,54 %). Todos los hongos evaluados presentaron una gran sensibilidad a los antifúngicos, con un promedio del 91 %. Conclusión. Se encontró colonización fúngica en los tubos endotraqueales de pacientes con asistencia respiratoria mecánica. El perfil de sensibilidad en estos pacientes fue favorable. Se requiere un estudio clínico para correlacionar los microorganismos colonizadores y su capacidad de generar infección.