Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea.

This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within the Chloroflexota phylum. Employing a multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration of adaptive features, the research unveils novel insights into the family's taxonomy and evolutionary dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, a novel mesophilic lineage, tentatively named Mesolinea, emerges within Anaerolineaceae, showcasing a distinctive genomic profile and apparent adaptation to a mesophilic lifestyle. The comprehensive genomic analyses shed light on the family's complex evolutionary patterns, including the conservation of key operons in thermophiles, providing a foundation for understanding the diverse ecological roles and adaptive strategies of Anaerolineaceae members.

Monitoring potentially pathogenic protists in sewage sludge using Metataxonomics.

Intestinal parasites continue to pose a significant threat to human health worldwide, particularly among children. Contaminated water and soil serve as major transmission vehicles for these parasites and intestinal protists are among the most prevalent parasites in both developed and developing nations. Traditionally, parasites have been studied using human or animal fecal samples, while studying them in environmental samples has been challenging due to technical limitations. However, advancements in Next-Generation Sequencing (NGS) and bioinformatic approaches now enable the detection of parasite DNA in environmental samples. In this study, we applied a metataxonomic and phylogenetic strategy to detect and classify DNA of protists present in sewage sludge from two major cities in Colombia: Medellin and Cali. We successfully detected several human pathogenic parasites including Giardia intestinalis, Entamoeba histolytica, and Blastocystis sp., among other protists, in all sludge samples examined. We also investigated the entry and exit of parasite DNA from the San Fernando wastewater treatment plant (WWTP). We observed a higher number of parasite DNA sequences in the plant's influent wastewater, but we also detected the discharge of DNA from pathogenic parasites in both effluent waters and biosolids.

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.

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.

Descripción de la microbiota bacteriana residente en el biosólido generado en la planta de tratamiento de aguas residuales San Fernando. Itagüí, Colombia / Description of bacterial microbiota in biosolids generated in the San Fernando wastewater treatment plant. Itagüí, Colombia

RESUMEN Objetivo Caracterizar la microbiota bacteriana presente en los biosólidos generados en una de las plantas de tratamiento de aguas residuales más grande de Colombia. Materiales y Métodos 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. Resultados 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. Conclusiones 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.(AU)

ABSTRACT Objective To describe bacterial microbiota in the biosolids generated in one of the largest wastewater treatment plants of Colombia. Materials and Methods 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. Results 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. Conclusions 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.(AU)

[Description of bacterial microbiota in biosolids generated in the San Fernando wastewater treatment plant. Itagüí, Colombia]. / Descripción de la microbiota bacteriana residente en el biosólido generado en la planta de tratamiento de aguas residuales San Fernando. Itagüí, Colombia.

OBJECTIVE: To describe bacterial microbiota in the biosolids generated in one of the largest wastewater treatment plants of Colombia. MATERIALS AND METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.

OBJETIVO: Caracterizar la microbiota bacteriana presente en los biosólidos generados en una de las plantas de tratamiento de aguas residuales más grande de Colombia. MATERIALES Y MÉTODOS: 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. RESULTADOS: 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. CONCLUSIONES: 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.

Caracterización de biosólidos generados en la planta de tratamiento de agua residual San Fernando, Itagüí (Antioquia, Colombia) / The characterization of biosolids produced by the San Fernando wastewater treatment plant in Itagui, Antioquia, Colombia

RESUMEN Objetivo Realizar la caracterización físico-química, microbiológica y parasitológica en biosólidos generados en la planta de tratamiento de agua residual San Fernando, Itagüí (Antioquia, Colombia). Métodos Se analizaron 12 muestras de biosólido tomadas cada mes, de enero a diciembre de 2010 a las cuales se les realizó un análisis físico-químico y microbiológico de acuerdo a lo establecido en la Norma Técnica Colombiana 5167. Para la determinación y viabilidad de huevos de helmintos se siguió el protocolo descrito en la Norma Oficial Mexicana 004 con modificaciones. Resultados En las doce muestras analizadas, se encontró una concentración de huevos de Ascarislumbricoides en un rango entre 4 a 22 huevos viables/2g ST. Salmonella estuvo presente en todas las muestras y las Enterobacterias estuvieron en una concentración mínima de 3000 UFC/g. La concentración de los metales pesados estuvo dentro de los valores recomendados por la norma. Los macro y micronutrientes cumplieron con los parámetros establecidos para los materiales orgánicos usados como abonos. No hubo asociación entre la precipitación y el contenido de patógenos en los biosólidos. Conclusión Los biosólidos generados en la planta San Fernando tienen un gran potencial para ser usados como abono orgánico, no obstante, deben ser sometidos a procesos de sanitización con el propósito de cumplir con los parámetros indicados en la Norma NTC 5167.

ABSTRACT Objective This study was aimed at evaluating pertinent physicochemical and microbiological (bacteria and parasites) parameters regarding the biosolids produced by the San Fernando wastewater treatment plant (WWTP) in Itagui, Antioquia, Colombia. Methods Twelve samples were collected and evaluated every month from January to December during 2010. The chemical, physical and microbiological tests followed the protocol described in Colombian technical guideline 5167. The protocol described in Mexican official Norm 004 (with some modifications) was used for identifying helminth ova and assessing their viability. Results All samples proved positive for Ascarislumbricoides, viable ova count ranging from 4 to 22 eggs/2gTS. Both Salmonella and Enterobacteriawere detected in all samples evaluated, the latter having 3,000 colony forming unit (CFU)/g minimum concentration. Biosolid sample values met the heavy metal concentration requirement established by national guidelines. There was no statistical association between rainfall and the pathogen's presence in the biosolids. Conclusion Our results suggested that the biosolids being produced by the San Fernando wastewater treatment plant (WWTP) could be used as organic fertilizer; however they should be treated/sanitized to meet the stipulations in Colombian technical guideline 5167.

Frecuencia de parásitos intestinales y evaluación de métodos para su diagnóstico en una comunidad marginal de Medellín, Colombia / Frequency of intestinal parasites and evaluation of methods for their diagnosis in a marginal community of Medellin, Colombia

Introducción: las parasitosis intestinales siguen siendo un problema de salud pública, que ha sido poco estudiado en Medellín, Colombia. Objetivo: determinar la frecuencia de parasitismo intestinal en habitantes de una comunidad marginal de Medellín y evaluar la validez, el desempeño, la eficiencia y la confiabilidad del examen directo en su diagnóstico. Materiales y métodos: estudio transversal y de evaluación de pruebas diagnósticas con fuente de información primaria. Se calcularon las proporciones con su intervalo de confianza y se hicieron pruebas de estadística no paramétrica y análisis de sensibilidad, especificidad, valores predictivos, razón de verosimilitud negativa y kappa. Resultados: la frecuencia global de parásitos, según el examen por concentración, fue 74,4%; la evaluación se hizo para parasitismo general y para las categorías protozoos, helmintos, comensales y patógenos; se hallaron sensibilidad superior al 68%, especificidad y valor predictivo positivo del 100%, valor predictivo negativo mayor de 74%, razón de verosimilitud negativa menor de 0,32, kappa superior a 0,77 y eficiencia superior al 90%. Conclusión: el problema del parasitismo intestinal amerita una pronta intervención por parte de las autoridades sanitarias dado que su frecuencia sigue siendo tan elevada como hace tres décadas y las pruebas disponibles para estudiarlo, incluyendo el examen directo de la materia fecal, tienen alto valor diagnóstico.

Background: Intestinal parasitism is still a public health problem. It has not been thoroughly studied in Medellin, Colombia. Objective: To determine the prevalence of intestinal parasites in residents of a marginal community in Medellin and to evaluate the validity, efficiency and reliability of direct examination in its diagnosis. Methods:Cross-sectional study and evaluation of diagnostic tests. Data were collected from a primary information source. Proportions with their confidence intervals were calculated; non-parametric statistical tests and analysis of sensitivity, specificity, predictive values, negative likelihood ratio and kappa were done. Results: Prevalence of parasites, according to the results of the concentration test, was 74.4%. Evaluation was done for intestinal parasites in general and for the following categories: protozoa, helminthes, commensals and pathogens. Sensitivity war over 68%, specificity and positive predictive value were 100%, negative predictive value was over 74%, negative likelihood ratio was less than 0.32, kappa was greater than 0.77 and efficiency was over 90%. Conclusion: Prevalence of intestinal parasitism is as high as it was three decades ago; its solution needs prompt and effective intervention of health authorities. The tests available for its study, including direct examination of stools, are of high diagnostic value.

[The characterization of biosolids produced by the San Fernando wastewater treatment plant in Itagui, Antioquia, Colombia]. / Caracterización de biosólidos generados en la planta de tratamiento de agua residual San Fernando, Itagüí (Antioquia, Colombia).

ABSTRACT Objective This study was aimed at evaluating pertinent physicochemical and microbiological (bacteria and parasites) parameters regarding the biosolids produced by the San Fernando wastewater treatment plant (WWTP) in Itagui, Antioquia, Colombia. Methods Twelve samples were collected and evaluated every month from January to December during 2010. The chemical, physical and microbiological tests followed the protocol described in Colombian technical guideline 5167. The protocol described in Mexican official Norm 004 (with some modifications) was used for identifying helminth ova and assessing their viability. Results All samples proved positive for Ascarislumbricoides, viable ova count ranging from 4 to 22 eggs/2gTS. Both Salmonella and Enterobacteriawere detected in all samples evaluated, the latter having 3,000 colony forming unit (CFU)/g minimum concentration. Biosolid sample values met the heavy metal concentration requirement established by national guidelines. There was no statistical association between rainfall and the pathogen's presence in the biosolids. Conclusion Our results suggested that the biosolids being produced by the San Fernando wastewater treatment plant (WWTP) could be used as organic fertilizer; however they should be treated/sanitized to meet the stipulations in Colombian technical guideline 5167.