Molecular framework underlying floral bilateral symmetry and nectar spur development in Tropaeolum, an atypical member of the Brassicales

PREMISE

Floral spurs are key innovations associated with elaborate pollination mechanisms that have evolved independently several times across angiosperms. Spur formation can shift the floral symmetry from radial to bilateral, as it is the case in Tropaeolum, the only member of the Brassicales with floral nectar spurs. The genetic mechanisms underlying both spur and bilateral symmetry in the family have not yet been investigated.

METHODS

We studied flower development and morphoanatomy of Tropaeolum longifolium. We also generated a reference transcriptome and isolated all candidate genes involved in adaxial-abaxial differential growth during spur formation. Finally, we evaluated the evolution of the targeted genes across Brassicales and examined their expression in dissected floral parts.

RESULTS

Five sepals initiate spirally, followed by five petals alternate to the sepals, five antesepalous stamens, three antepetalous stamens, and three carpels. Intercalary growth at the common base of sepals and petals forms a floral tube. The spur is an outgrowth from the adaxial region of the tube, lined up with the medial sepal. We identified Tropaeolum specific duplications in the TCP3/4L and STM gene lineages, which are critical for spur formation in other taxa. In addition, we found that TM6 (MADS-box), RL2 (RAD-like7), and KN2/6L2 and OSH6L (KNOX1 genes), have been lost in core Brassicales but retained in Tropaeolum.

CONCLUSIONS

Three genes are pivotal during the extreme adaxial-abaxial asymmetry of the floral tube, namely, TlTCP4L2 restricted to the adaxial side where the spur is formed, and TlTCP12 and TlSTM1 to the abaxial side, lacking a spur.

Gene expression underlying floral epidermal specialization in Aristolochia fimbriata (Aristolochiaceae)

BACKGROUND AND AIMS

The epidermis constitutes the outermost tissue of the plant body. Although it plays major structural, physiological and ecological roles in embryophytes, the molecular mechanisms controlling epidermal cell fate, differentiation and trichome development have been scarcely studied across angiosperms, and remain almost unexplored in floral organs.

METHODS

In this study, we assess the spatio-temporal expression patterns of GL2, GL3, TTG1, TRY, MYB5, MYB6, HDG2, MYB106-like, WIN1 and RAV1-like homologues in the magnoliid Aristolochia fimbriata (Aristolochiaceae) by using comparative RNA-sequencing and in situ hybridization assays.

KEY RESULTS

Genes involved in Aristolochia fimbriata trichome development vary depending on the organ where they are formed. Stem, leaf and pedicel trichomes recruit most of the transcription factors (TFs) described above. Conversely, floral trichomes only use a small subset of genes including AfimGL2, AfimRAV1-like, AfimWIN1, AfimMYB106-like and AfimHDG2. The remaining TFs, AfimTTG1, AfimGL3, AfimTRY, AfimMYB5 and AfimMYB6, are restricted to the abaxial (outer) and the adaxial (inner) pavement epidermal cells.

CONCLUSIONS

We re-evaluate the core genetic network shaping trichome fate in flowers of an early-divergent angiosperm lineage and show a morphologically diverse output with a simpler genetic mechanism in place when compared to the models Arabidopsis thaliana and Cucumis sativus. In turn, our results strongly suggest that the canonical trichome gene expression appears to be more conserved in vegetative than in floral tissues across angiosperms.

The apicoplast of Haemoproteus columbae: A comparative study of this organelle genome in Haemosporida

Apicomplexa is a phylum of parasitic protozoa; among them are the order Haemosporida, vector-borne parasites that include those that cause malaria (genus Plasmodium). Most Apicomplexa species have a non-photosynthetic plastid or apicoplast. Given its unique metabolic pathways, this organelle is considered a target for malaria therapeutics. Regardless of its importance, there is a paucity of complete apicoplast genome data hindering comparative studies. Here, the Haemoproteus (Haemoproteus) columbae apicoplast genome (lineage HAECOL1) was obtained using next-generation sequencing. This genome was included in a comparative analysis with other plastids. This 29.8 kb circular genome shares the same structure found in Plasmodium parasites. It is A + T rich (87.7%), comparable but at the higher end of A + T content observed in Plasmodium species (85.5-87.2%). As expected, considering its high A + T content, the synonymous codon usage (RSCU) and the effective number of codons (ENc) showed a moderate codon bias. Several apicoplast genes have a phylogenetic signal. However, unlike mitochondrial genes, single-gene phylogenies have low support in haemosporidian clades that diverged recently. The H. columbae apicoplast genome suggests that the apicoplast function may be conserved across Haemosporida. This parasite could be a model to study this organelle in a non-mammalian system.

Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales

Flavonoids, carotenoids, betalains, and chlorophylls are the plant pigments responsible for floral color. Anthocyanins, a class of flavonoids, are largely responsible for the red, purple, pink, and blue colors. R2R3-MYB genes belonging to subgroup 6 (SG6) are the upstream regulatory factors of the anthocyanin biosynthetic pathway. The canonical members of these genes in Arabidopsis include AtMYB75, AtMYB90, AtMYB113, and AtMYB114. The Aristolochiaceae is an angiosperm lineage with diverse floral groundplans and perianth colors. Saruma henryi exhibits a biseriate perianth with green sepals and yellow petals. All other genera have sepals only, with colors ranging from green (in Lactoris) to a plethora of yellow to red and purple mixtures. Here, we isolated and reconstructed the SG6 R2R3-MYB gene lineage evolution in angiosperms with sampling emphasis in Aristolochiaceae. We found numerous species-specific duplications of this gene lineage in core eudicots and local duplications in Aristolochiaceae for Saruma and Asarum. Expression of SG6 R2R3-MYB genes examined in different developmental stages and plant organs of four Aristolochiaceae species, largely overlaps with red and purple pigments, suggesting a role in anthocyanin and flavonoid synthesis and accumulation. A directed RNA-seq analysis corroborated our RT-PCR analyses, by showing that these structural enzymes activate during perianth development in Aristolochia fimbriata and that the regulatory genes are expressed in correlation with color phenotype. Finally, the reconstruction of the flavonoid and anthocyanin metabolic pathways using predicted peptides from transcriptomic data show that all pivotal enzymes are present in the analyzed species. We conclude that the regulatory genes as well as the biosynthetic pathway are largely conserved across angiosperms. In addition, the Aristolochiaceae emerges as a remarkable group to study the genetic regulatory network for floral color, as their members exhibit an outstanding floral diversity with elaborate color patterns and the genetic complement for SG6 R2R3-MYB genes is simpler than in core eudicot model species.

Comparative genomic analysis of the principal Cryptosporidium species that infect humans

Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.

Antibiotic Production and Antibiotic Resistance: The Two Sides of AbrB1/B2, a Two-Component System of Streptomyces coelicolor

Antibiotic resistance currently presents one of the biggest threats to humans. The development and implementation of strategies against the spread of superbugs is a priority for public health. In addition to raising social awareness, approaches such as the discovery of new antibiotic molecules and the elucidation of resistance mechanisms are common measures. Accordingly, the two-component system (TCS) of Streptomyces coelicolor AbrB1/B2, offer amenable ways to study both antibiotic production and resistance. Global transcriptomic comparisons between the wild-type strain S. coelicolor M145 and the mutant ΔabrB, using RNA-Seq, showed that the AbrB1/B2 TCS is implicated in the regulation of different biological processes associated with stress responses, primary and secondary metabolism, and development and differentiation. The ΔabrB mutant showed the up-regulation of antibiotic biosynthetic gene clusters and the down-regulation of the vancomycin resistance gene cluster, according to the phenotypic observations of increased antibiotic production of actinorhodin and undecylprodigiosin, and greater susceptibility to vancomycin. The role of AbrB1/B2 in vancomycin resistance has also been shown by an in silico analysis, which strongly indicates that AbrB1/B2 is a homolog of VraR/S from Staphylococcus aureus and LiaR/S from Enterococcus faecium/Enterococcus faecalis, both of which are implied in vancomycin resistance in these pathogenic organisms that present a serious threat to public health. The results obtained are interesting from a biotechnological perspective since, on one hand, this TCS is a negative regulator of antibiotic production and its high degree of conservation throughout Streptomyces spp. makes it a valuable tool for improving antibiotic production and the discovery of cryptic metabolites with antibiotic action. On the other hand, AbrB1/B2 contributes to vancomycin resistance and is a homolog of VraR/S and LiaR/S, important regulators in clinically relevant antibiotic-resistant bacteria. Therefore, the study of AbrB1/B2 could provide new insight into the mechanism of this type of resistance.

New Conjugated Compound T5 Epidioxy-Sterol-ANB Inhibits the Growth of Mycobacterium tuberculosis Affecting the Cholesterol and Folate Pathways

The upsurge and persistence of drug resistant strains of Mycobacterium tuberculosis (Mtb) is an important limitant to the battery of drugs available for the elimination of tuberculosis (TB). To avoid future scarcity of antibiotics against Mtb, it is important to discover new effective anti-mycobacterial agents. In this study, we present data from a series of experiments to determine in vitro and in vivo anti-mycobacterial activity of a library of epidioxy-sterol analogs. We test 15 compounds for their ability to reduce the viability of Mtb. We found that one compound called T5 epidioxy-sterol-ANB display significant potency against Mtb in vitro specifically inside macrophages but without effectivity in axenic cultures. A viability assay confirms that this T5 compound is less toxic for macrophages in vitro as compared to the current Mtb drug Rifampicin at higher concentrations. We use a transcriptomic analysis of Mtb inside macrophages after T5 epidioxy-sterol-ANB treatment, and we found a significant down-regulation of enzymes involved in the cholesterol and folic acid pathways. In vivo, significant differences were found in the lungs and spleen CFUs of Mtb infected mice treated with the T5 epidioxy-sterol-ANB as compared with the untreated control group, which provides additional evidence of the effectivity of the T5 compound. Altogether these results confirm the potential of this T5 epidioxy-sterol-ANB compound against Mtb.

Evolution of Class II TCP genes in perianth bearing Piperales and their contribution to the bilateral calyx in Aristolochia

Controlled spatiotemporal cell division and expansion are responsible for floral bilateral symmetry. Genetic studies have pointed to class II TCP genes as major regulators of cell division and floral patterning in model core eudicots. Here we study their evolution in perianth-bearing Piperales and their expression in Aristolochia, a rare occurrence of bilateral perianth outside eudicots and monocots. The evolution of class II TCP genes reveals single-copy CYCLOIDEA-like genes and three paralogs of CINCINNATA (CIN) in early diverging angiosperms. All class II TCP genes have independently duplicated in Aristolochia subgenus Siphisia. Also CIN2 genes duplicated before the diversification of Saruma and Asarum. Sequence analysis shows that CIN1 and CIN3 share motifs with Cyclin proteins and CIN2 genes have lost the miRNA319a binding site. Expression analyses of all paralogs of class II TCP genes in Aristolochia fimbriata point to a role of CYC and CIN genes in maintaining differential perianth expansion during mid- and late flower developmental stages by promoting cell division in the distal and ventral portion of the limb. It is likely that class II TCP genes also contribute to cell division in the leaf, the gynoecium and the ovules in A. fimbriata.

Contrasting microbiota profiles observed in children carrying either Blastocystis spp. or the commensal amoebas Entamoeba coli or Endolimax nana

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.

DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework

Background

A prime objective in metagenomics is to classify DNA sequence fragments into taxonomic units. It usually requires several stages: read’s quality control, de novo assembly, contig annotation, gene prediction, etc. These stages need very efficient programs because of the number of reads from the projects. Furthermore, the complexity of metagenomes requires efficient and automatic tools that orchestrate the different stages.

Method

DATMA is a pipeline for fast metagenomic analysis that orchestrates the following: sequencing quality control, 16S rRNA-identification, reads binning, de novo assembly and evaluation, gene prediction, and taxonomic annotation. Its distributed computing model can use multiple computing resources to reduce the analysis time.

Results

We used a controlled experiment to show DATMA functionality. Two pre-annotated metagenomes to compare its accuracy and speed against other metagenomic frameworks. Then, with DATMA we recovered a draft genome of a novel Anaerolineaceae from a biosolid metagenome.

Conclusions

DATMA is a bioinformatics tool that automatically analyzes complex metagenomes. It is faster than similar tools and, in some cases, it can extract genomes that the other tools do not. DATMA is freely available at https://github.com/andvides/DATMA.

De novo assembly and characterization of the liver transcriptome of Mugil incilis (lisa) using next generation sequencing

Mugil incilis (lisa) is an important commercial fish species in many countries, living along the coasts of the western Atlantic Ocean. It has been used as a model organism for environmental monitoring and ecotoxicological investigations. Nevertheless, available genomic and transcriptomic information for this organism is extremely deficient. The aim of this study was to characterize M. incilis hepatic transcriptome using Illumina paired-end sequencing. A total of 32,082,124 RNA-Seq read pairs were generated utilizing the HiSeq platform and subsequently cleaned and assembled into 93,912 contigs (N50 = 2,019 bp). The analysis of species distribution revealed that M. incilis contigs had the highest number of hits to Stegastes partitus (13.4%). Using a sequence similarity search against the public databases GO and KEGG, a total of 7,301 and 16,967 contigs were annotated, respectively. KEGG database showed genes related to environmental information, metabolism and organismal system pathways were highly annotated. Complete or partial coding DNA sequences for several candidate genes associated with stress responses/detoxification of xenobiotics, as well as housekeeping genes, were employed to design primers that were successfully tested and validated by RT-qPCR. This study presents the first transcriptome resources for Mugil incilis and provides basic information for the development of genomic tools, such as the identification of RNA markers, useful to analyze environmental impacts on this fish Caribbean species.

Annual microbial community dynamics in a full-scale anaerobic sludge digester from a wastewater treatment plant in Colombia

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.

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia

Rhipicephalus microplus is recognized as a tick species highly prevalent in cattle, with a wide pantropical distribution that seems to continue spreading geographically. However, its role as a biological vector has been scarcely studied in the livestock context. In this study, a 16S rRNA next-generation sequencing analysis was used to determine bacterial diversity in salivary glands and gut of R. microplus from two contrasting livestock agroecosystems in Antioquia, Colombia. Both the culture-independent approach (CI) and the culture-dependent (CD) approach were complementarily adopted in this study. A total of 341 unique OTUs were assigned, the richness showed to be higher in the Northern than in the Middle Magdalena region, and a high diversity was found at the phylum and genus levels in the samples obtained. With the CI approach, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most common phylum of bacteria regardless of the organ, or geographic origin of the specimens analyzed. While the relative abundance of bacteria at a phylum level with the CD approach varied between analyzed samples, the data obtained suggest that a high diversity of species of bacteria occurs in R. microplus from both livestock agroecosystems. Bacterial genera such as Anaplasma, Coxiella, and Ehrlichia, recognized for their implications in tick-borne diseases, were also detected, together with endosymbionts such as Lysinibacillus, previously reported as a potential tool for biological control. This information is useful to deepen the knowledge about microbial diversity regarding the relations between endosymbionts and pathogens and could facilitate the future development of epidemiological surveillance in livestock systems.

Common occurrence of Cryptosporidium hominis in children attending day-care centers in Medellin, Colombia

Cryptosporidium spp. are apicomplexan protozoa associated with chronic diarrhea in AIDS and other immunocompromised patients, and one of the commonest causes of childhood diarrhea and malnutrition, particularly in low-income settings. In Colombia, there are few molecular epidemiological studies on Cryptosporidium spp.; thereby, the transmission dynamics of this parasite in the country is poorly known. This study evaluated the diversity of Cryptosporidium at species, subtype family, and subtype level in children attending various day-care centers in Medellin, Colombia. Two hundred and ninety stool samples from children < 5 years of age were collected from April to November of 2015. All samples were processed by PCR and sequence analysis of the ssu RNA gene and the gp60 gene. An infection rate of 2.4% was observed, with only two Cryptosporidium species identified: C. hominis (6/7) and C. meleagridis (1/7). Cryptosporidium hominis isolates belonged to the subtypes IbA10G2, IaA13R6 and IaA13R7; IIIbA26G1R1 C. meleagridis subtype was also detected. There is a C. hominis predominance in the children evaluated, suggesting an important role of the anthroponotic transmission cycle in the day-care centers analyzed. Further investigation is required to determine infection sources and susceptible hosts in order to define appropriate management of cryptosporidiosis.

Metatranscriptomic virome assessment of Rhipicephalus microplus from Colombia

Ticks (Ixodida) are hematophagous ectoparasites that harbor and transmit diverse species of viruses, some of which cause serious diseases with worldwide veterinary and human health consequences. Rhipicephalus microplus is an important cattle tick in Colombia, where it causes significant economic losses. Despite the importance of this tick, its viral profile is unknown. RNA sequencing was used in this study as a surveillance method for virus detection in R. microplus. Most of the viral origin contigs were assigned to two putative viruses: one chuvirus (Wuhan tick virus 2) and one phlebovirus-like (Lihan tick virus). In addition, viral contigs corresponding to two jingmenviruses previously reported in R. microplus from China and Brazil were detected, as well as a novel putative tymovirus, named here as Antioquia tymovirus-like 1 (ATV-like 1). The presence of some of these viruses across numerous regions in the world could have several explanations, including i) a long-term association between those viruses and R. microplus and ii) a consequence of livestock historical trade. Our results shed new light on the virus diversity of this tick species and provide a basis for further studies on the evolutionary history and pathogenic potential of these interesting viruses.

Differential determinants of virulence in two Mycobacterium tuberculosis Colombian clinical isolates of the LAM09 family

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.

Evolution and Expression of Reproductive Transition Regulatory Genes FT/TFL1 With Emphasis in Selected Neotropical Orchids

Flowering is a rigorously timed and morphologically complex shift in plant development. This change depends on endogenous as well as environmental factors. FLOWERING LOCUS T (FT) integrates several cues from different pathways acting as a flowering promoter. Contrary to the role of FT, its paralog TERMINAL FLOWER 1 (TFL1) delays floral transition. Although FT/TFL1 homologs have been studied in model eudicots and monocots, scarce studies are available in non-model monocots like the Orchidaceae. Orchids are very diverse and their floral complexity is translated into a unique aesthetic display, which appeals the ornamental plant market. Nonetheless, orchid trade faces huge limitations due to their long vegetative phase and intractable indoor flowering seasons. Little is known about the genetic basis that control reproductive transition in orchids and, consequently, manipulating their flowering time remains a challenge. In order to contribute to the understanding of the genetic bases that control flowering in orchids we present here the first broad-scale analysis of FT/TFL1-like genes in monocots with an expanded sampling in Orchidaceae. We also compare expression patterns in three selected species and propose hypotheses on the putative role of these genes in their reproductive transition. Our findings show that FT-like genes are by far more diversified than TFL1-like genes in monocots with six subclades in the former and only one in the latter. Within MonFT1, the comparative protein sequences of MonFT1A and MonFT1B suggest that they could have recruited functional roles in delaying flowering, a role typically assigned to TFL1-like proteins. On the other hand, MonFT2 proteins have retained their canonical motifs and roles in promoting flowering transition. This is also shown by their increased expression levels from the shoot apical meristem (SAM) and leaves to inflorescence meristems (IM) and floral buds (FBs). Finally, TFL1-like genes are retained as single copy and often times are lost. Their loss could be linked to the parallel recruitment of MonFT1A and MonFT1B homologs in delaying flowering and maintaining indeterminacy of the inflorescence meristem. These hypotheses lay the foundation for future functional validation in emerging model orchid species and comparative analyses in orchids with high horticultural potential in the market.

Mitochondrial genomics of human pathogenic parasite Leishmania (Viannia) panamensis

Background

The human parasite Leishmania (V.) panamensis is one of the pathogenic species responsible for cutaneous leishmaniasis in Central and South America. Despite its importance in molecular parasitology, its mitochondrial genome, divided into minicircles and maxicircles, haven’t been described so far.

Methods

Using NGS-based sequencing (454 and ILLUMINA), and combining de novo genome assembly and mapping strategies, we report the maxicircle kDNA annotated genome of L. (V.) panamensis, the first reference of this molecule for the subgenus Viannia. A comparative genomics approach is performed against other Leishmania and Trypanosoma species.

Results

The results show synteny of mitochondrial genes of L. (V.) panamensis with other kinetoplastids. It was also possible to identify nucleotide variants within the coding regions of the maxicircle, shared among some of them and others specific to each strain. Furthermore, we compared the minicircles kDNA sequences of two strains and the results show that the conserved and divergent regions of the minicircles exhibit strain-specific associations.

Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae

This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 10⁹ CFU mL^-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.

Metagenomic assessment of the microbial community and methanogenic pathways in biosolids from a municipal wastewater treatment plant in Medellín, Colombia

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.

Intestinal parasitic infection alters bacterial gut microbiota in children

The study of the burden that parasites can exert upon the bacterial gut microbiota was restricted by the available technologies and their costs. Currently, next-generation sequencing coupled with traditional methodologies allows the study of eukaryotic parasites (protozoa and helminths) and its effects on the human bacterial gut microbiota diversity. This diversity can be altered by a variety of factors such as age, diet, genetics and parasitic infections among others. The disturbances of the gut microbiota have been associated with a variety of illnesses. Children population in developing countries, are especially susceptible to parasitic infections because of the lack of proper sanitation and undernutrition, allowing both, the thriving of intestinal parasites and profound alteration of the gut microbiota. In this work, we have sampled the stool of 23 children from four different children's care-centers in Medellin, Colombia, and we have identified the eukaryotic parasites by traditional and molecular methodologies coupled with microbial profiling using 16S rDNA sequencing. This mixed methodology approach has allowed us to establish an interesting relationship between Giardia intestinalis and helminth infection, having both effects upon the bacterial gut microbiota enterotypes, causing a switch from a type I to a type II enterotype upon infection.

Molecular Identification and Antifungal Susceptibility of Clinical Isolates of Sporothrix schenckii Complex in Medellin, Colombia

BACKGROUND

Sporotrichosis is a subcutaneous mycosis that affects humans and other animals. Infection prevails in tropical and subtropical countries. Until a few years ago, it was considered that two varieties of Sporothrix schenckii caused this mycosis, but by applying molecular taxonomic markers, it has been demonstrated that there are several cryptic species within S. schenckii complex which varies in susceptibility, virulence, and geographic distribution.

OBJECTIVE

This study aimed to identify the clinical isolates of Sporothrix spp. from patients with sporotrichosis in Medellin, Colombia, using two markers and to evaluate the in vitro susceptibility to itraconazole.

METHODS

Thirty-four clinical isolates of Sporothrix spp. from Colombia, three from Mexico, and one from Guatemala were identified through sequencing of the noncoding region ITS-1 + 5.8SDNAr + ITS-2 and of the fragment containing exons 3 and 4 of the β-tubulin gene. Clinical isolate sequences were compared with GenBank reference sequences using the BLASTN tool, and then, phylogenetic analysis was performed. Besides, the in vitro susceptibility to itraconazole was evaluated by determining the minimum inhibitory concentrations according to the CLSI M38-A2 method.

RESULTS

Clinical isolates were identified by morphology as Sporothrix spp. Using the molecular markers, ITS and β-tubulin, isolates were identified as S. schenckii sensu stricto (25) and Sporothrix globosa (13). Susceptibility to itraconazole was variable among clinical isolates.

CONCLUSION

This is the first scientific publication that identifies species that cause sporotrichosis in Colombia, along with the antifungal susceptibility to itraconazole.