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Recent studies have shown how intestinal parasites can modulate gut microbiota. This observation is not surprising since the human intestinal lumen, like any other niche, is a battlefield of microbial competition, and Eukaryotes can affect bacterial populations. Intestinal pathogenic protist has been associated with reshaping the microbial community structure; however, the interactions between the colonic bacterial communities and parasites like Blastocystis spp., Entamoeba coli, and Endolimax nana have been poorly studied. In this work, we studied the distal intestinal bacterial microbiota of 49 children attending 7 public daycare centers in Medellin, Colombia, and compared the bacterial microbiota structure in the presence or absence of the protists Blastocystis spp., E. coli, and E. nana. Parasite colonization was associated with an increase in bacterial richness. Moreover, Blastocystis spp. presented a positive relationship with Prevotella, since this bacterium was selectively enriched in children carrying it. Remarkably, the E. coli colonized children showed a microbial profile that was closer to uninfected controls, although some bacterial taxa displayed to be enriched. This is the case for Akkermansia, which showed to be favored in E. coli colonized individuals, while notably reduced in the Blastocystis spp. parasitized group.

Abundance and diversity of microbial communities in biosolids are variable and poorly studied in the tropics, and it is known that rainfall is one of the events that could affect the phylogenetic and functional microbial structure. In the present study, using NGS technics, we studied the microbial diversity as well as the methanogenesis pathway in one of the largest WWTP in Colombia. Besides, we sampled and analyzed biosolids from rainy season and dry season. Phylogenetic classification showed a predominance of bacteria in both samples and difference in the dominant groups depending on the rainfall season. Whereas Pseudomonas was the dominant bacteria in the dry season, Coprothermobacter was in the rainy season. Archaea abundance was higher in the rainy season (11.5%) doubling dry season proportion. The bioreactor biogas production and total solids content showed similar results between rainy and dry season at the sampling dates. The most abundant Archaea related with methanogenesis was Methanosaeta, which is a methanogenic microorganism that exclusively uses acetate to produce methane. Moreover, annotation of the methanogenic pathway in the metagenome showed abundance in genes encoding Acetyl-CoA synthetases (ACSS), an enzyme that catalyzes acetate activation. Our results suggest that the microbial diversity was stable among the two time points tested, rainy season and dry season; and, although there were changes in the microbial abundance of dominant bacterial species, anaerobic digester performance is not affected.

The heterogeneity of the clinical outcome of Mycobacterium tuberculosis (Mtb) infection may be due in part to different strategies used by circulating strains to cause disease. This heterogeneity is one of the main limitations to eradicate tuberculosis disease. In this study, we have compared the transcriptional response of two closely related Colombian clinical isolates (UT127 and UT205) of the LAM family under two axenic media conditions. These clinical isolates are phenotypically different at the level of cell death, cytokine production, growth kinetics upon in vitro infection of human tissue macrophages, and membrane vesicle secretion upon culture in synthetic medium. Using RNA-seq, we have identified different pathways that account for two different strategies to cope with the stressful condition of a carbon-poor media such as Sauton's. We showed that the clinical isolate UT205 focus mainly in the activation of virulence systems such as the ESX-1, synthesis of diacyl-trehalose, polyacyl-trehalose, and sulfolipids, while UT127 concentrates its efforts mainly in the survival mode by the activation of the DNA replication, cell division, and lipid biosynthesis. This is an example of two Mtb isolates that belong to the same family and lineage, and even though they have a very similar genome, its transcriptional regulation showed important differences. This results in summary highlight the necessity to reach a better understanding of the heterogeneity in the behavior of these circulating Mtb strains which may help us to design better treatments and vaccines and to identify new targets for drugs.

Anaerobic digestion is a microbe-driven process widely applied to treat activated sludge from municipal wastewater treatment plants. It is one of the most efficient solutions for sludge reduction along with biogas production. However, the knowledge of the microbial consortium involved in this process is still unknown in full-scale anaerobic digesters from Latin America. This study aimed to elucidate the dynamics of the microbial community of a full-scale anaerobic digester for a year using 16S rDNA amplicon sequencing with the Illumina Miseq platform. The results showed fluctuations in the frequencies of dominant phyla with a decrease of Proteobacteria and Bacteroidetes after a temporary suspension of anaerobic digester. The core community was affiliated with bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Chloroflexi. The core community was represented by 154 OTUs that accounted for 74% of all the processed reads. The Anaerolineaceae family, within Chloroflexi phylum, was the most frequently observed taxonomic group in all samples analyzed. Despite the microbial fluctuations, the biogas production was stable over the studied year (average 66% methane production), which might indicate a functional redundancy in the microbial consortium.

CARD9 deficiency is an inborn error of immunity that predisposes otherwise healthy humans to mucocutaneous and invasive fungal infections, mostly caused by Candida, but also by dermatophytes, Aspergillus, and other fungi. Phaeohyphomycosis are an emerging group of fungal infections caused by dematiaceous fungi (phaeohyphomycetes) and are being increasingly identified in patients with CARD9 deficiency. The Corynespora genus belongs to phaeohyphomycetes and only one adult patient with CARD9 deficiency has been reported to suffer from invasive disease caused by C. cassiicola. We identified a Colombian child with an early-onset, deep, and destructive mucocutaneous infection due to C. cassiicola and we searched for mutations in CARD9. We reviewed the medical records and immunological findings in the patient. Microbiologic tests and biopsies were performed. Whole-exome sequencing (WES) was made and Sanger sequencing was used to confirm the CARD9 mutations in the patient and her family. Finally, CARD9 protein expression was evaluated in peripheral blood mononuclear cells (PBMC) by western blotting. The patient was affected by a large, indurated, foul-smelling, and verrucous ulcerated lesion on the left side of the face with extensive necrosis and crusting, due to a C. cassiicola infectious disease. WES led to the identification of compound heterozygous mutations in the patient consisting of the previously reported p.Q289* nonsense (c.865C > T, exon 6) mutation, and a novel deletion (c.23_29del; p.Asp8Alafs10*) leading to a frameshift and a premature stop codon in exon 2. CARD9 protein expression was absent in peripheral blood mononuclear cells from the patient. We describe here compound heterozygous loss-of-expression mutations in CARD9 leading to severe deep and destructive mucocutaneous phaeohyphomycosis due to C. cassiicola in a Colombian child.

Background Hot spring bacteria have unique biological adaptations to survive the extreme conditions of these environments; these bacteria produce thermostable enzymes that can be used in biotechnological and industrial applications. However, sequencing these bacteria is complex, since it is not possible to culture them. As an alternative, genome shotgun sequencing of whole microbial communities can be used. The problem is that the classification of sequences within a metagenomic dataset is very challenging particularly when they include unknown microorganisms since they lack genomic reference. We failed to recover a bacterium genome from a hot spring metagenome using the available software tools, so we develop a new tool that allowed us to recover most of this genome. Results We present a proteobacteria draft genome reconstructed from a Colombian’s Andes hot spring metagenome. The genome seems to be from a new lineage within the family Rhodanobacteraceae of the class Gammaproteobacteria, closely related to the genus Dokdonella. We were able to generate this genome thanks to CLAME. CLAME, from Spanish “CLAsificador MEtagenomico”, is a tool to group reads in bins. We show that most reads from each bin belong to a single chromosome. CLAME is very effective recovering most of the reads belonging to the predominant species within a metagenome. Conclusions We developed a tool that can be used to extract genomes (or parts of them) from a complex metagenome. Electronic supplementary material The online version of this article (10.1186/s12864-018-5191-y) contains supplementary material, which is available to authorized users.

To describe bacterial microbiota in the biosolids generated in one of the largest wastewater treatment plants of Colombia.Using NGS technology, 16S rRNA Gene Amplicon libraries were amplified and sequenced. The Roche 454 FLX Titanium platform was used, while the V1-V3 and V6-V9 hypervariable regions were amplified and analyzed independently. Amplicon processing and bacterial classification were performed using the AmpliconNoise pipeline and the RDP Classifier tool.The analysis showed that the most dominant Phyla in the biosolids were Chlo-roflexi, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most dominant genera were Pseudomonas, Dysgonomonas and Proteiniphilum; however, the dominant group according in the V1-V3 variable region was Anaerolineaceae, which does not conform to the species described for this family. Pathogenic bacteria such as Salmonella and E. coli/Shigella were not detected in the studied biosolid sample.In the biosolids samples analyzed, environmental bacteria involved in organic matter stabilization processes during secondary biological treatments and anaerobic digestion were predominant. One of the dominant species in this sludge is a novel species of the Anaerolineaceae group. At the time of the study, it was found that the anaerobic digester system was able to maintain pathogenic bacteria at very low concentrations.Caracterizar la microbiota bacteriana presente en los biosólidos generados en una de las plantas de tratamiento de aguas residuales más grande de Colombia.Se utilizó la plataforma de secuenciamiento 454 de la compañía Roche para secuenciar las regiones variables V1-V3 y V6-V9 del marcador molecular 16S rRNA y caracterizar la microbiota. Adicionalmente, se aplicaron estrategias filogenéticas para la identificación de especies bacterianas de importancia.Nuestros análisis muestran que los Phyla más abundantes son Chloro-flexi, Proteobacteria, Bacteroidetes, Actinobacteria y Firmicutes. Los géneros clasificados más abundantes fueron Pseudomonas, Dysgonomonas y Proteiniphilum. Sin embargo, el grupo dominante según la región variable V1-V3 es una Anaerolineaceae que no se ajusta a las especies descritas para esta familia.En las muestras de biosólido analizadas predominan bacterias ambientales que participan en los procesos de estabilización de la materia orgánica durante los tratamientos biológicos de tipo secundario y la digestión anaerobia. Se detectaron secuencias de especies dentro de la familia Anaerolineaceae, los análisis filogenéticos muestran que probablemente se trata de especies no descritas. En el momento del estudio, se encontró que en el sistema de digestión anaerobia se genera biosolido con una baja carga de bacterias potencialmente patógenas.