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1.
Rev. Hosp. Ital. B. Aires (2004) ; 40(1): 17-24, mar. 2020. ilus
Article in Spanish | LILACS | ID: biblio-1100762

ABSTRACT

Se estima que aproximadamente 100 trillones de microorganismos (incluidos bacterias, virus y hongos) residen en el intestino humano adulto y que el total del material genético del microbioma es 100 veces superior al del genoma humano. Esta comunidad, conocida como microbioma se adquiere al momento del nacimiento a través de la flora comensal de la piel, vagina y heces de la madre y se mantiene relativamente estable a partir de los dos años desempeñando un papel crítico tanto en el estado de salud como en la enfermedad. El desarrollo de nuevas tecnologías, como los secuenciadores de próxima generación (NGS), permiten actualmente realizar un estudio mucho más preciso de ella que en décadas pasadas cuando se limitaba a su cultivo. Si bien esto ha llevado a un crecimiento exponencial en las publicaciones, los datos sobre las poblaciones Latinoamérica son casi inexistentes. La investigación traslacional en microbioma (InTraMic) es una de las líneas que se desarrollan en el Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). Esta se inició en 2018 con la línea de cáncer colorrectal (CCR) en una colaboración con el Colorectal Cancer Research Group del Leeds Institute of Medical Research en el proyecto Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents. A fines de 2019 se cumplió el objetivo de comprobar la factibilidad de la recolección, envío y análisis de muestras de MBF en 5 continentes, incluyendo muestras provenientes de la Argentina, Chile, India y Vietnam. Luego de haber participado de capacitaciones en Inglaterra, se ha cumplido con el objetivo de la etapa piloto, logrando efectivizar la recolección, envío y análisis metagenómico a partir de la secuenciación de la región V4 del ARNr 16S. En 2019, la línea de enfermedad de hígado graso no alcohólico se sumó a la InTraMic iniciando una caracterización piloto en el marco de una colaboración con el laboratorio Novartis. Los resultados de ese estudio, así como el de cáncer colorrectal, están siendo enviados a publicación. En 2020, con la incorporación de la línea de trasplante alogénico de células progenitoras hematopoyéticas, fue presentado un proyecto para un subsidio del CONICET que ha superado la primera etapa de evaluación. En el presente artículo se brinda una actualización sobre la caracterización taxonómica de microbioma y se describen las líneas de investigación en curso. (AU)


It is estimated that approximately 100 trillion microorganisms (including bacteria, viruses, and fungi) reside in the adult human intestine, and that the total genetic material of the microbiome is 100 times greater than that of the human genome. This community, known as the microbiome, is acquired at birth through the commensal flora of the mother's skin, vagina, and feces and remains relatively stable after two years, playing a critical role in both the state of health and in disease. The development of new technologies, such as next-generation sequencers (NGS), currently allow for a much more precise study of it than in past decades when it was limited to cultivation. Although this has led to exponential growth in publications, data on Latin American populations is almost non-existent. Translational research in microbiome (InTraMic) is one of the lines developed at the Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB). This started in 2018 with the Colorectal Cancer Line (CRC) in a collaboration with the Colorectal Cancer Research Group of the Leeds Institute of Medical Research in the project "Large bowel microbiome disease network: Creation of a proof of principle exemplar in colorectal cancer across three continents". At the end of 2019, the objective of verifying the feasibility of collecting, sending and analyzing MBF samples on 5 continents, including samples from Argentina, Chile, India and Vietnam, was met. After having participated in training in England, the objective of the pilot stage has been met, achieving the collection, delivery and metagenomic analysis from the sequencing of the V4 region of the 16S rRNA. In 2019, the non-alcoholic fatty liver disease line joined InTraMic, initiating a pilot characterization in the framework of a collaboration with the Novartis laboratory. The results of that study, as well as that of colorectal cancer, are being published. In 2020, with the incorporation of the allogeneic hematopoietic stem cell transplantation line, a project was presented for a grant from the CONICET that has passed the first stage of evaluation. This article provides an update on the taxonomic characterization of the microbiome and describes the lines of ongoing research. (AU)


Subject(s)
Humans , Translational Medical Research/organization & administration , Gastrointestinal Microbiome/genetics , Transplantation, Homologous , Vietnam , Aztreonam/therapeutic use , RNA, Ribosomal, 16S/analysis , Colorectal Neoplasms/genetics , Colorectal Neoplasms/microbiology , Colorectal Neoplasms/epidemiology , Classification/methods , Hematopoietic Stem Cell Transplantation , Metagenomics , Translational Medical Research/methods , High-Throughput Nucleotide Sequencing/trends , Non-alcoholic Fatty Liver Disease/genetics , Non-alcoholic Fatty Liver Disease/microbiology , Non-alcoholic Fatty Liver Disease/pathology , Non-alcoholic Fatty Liver Disease/epidemiology , Gastrointestinal Microbiome/physiology , India , Latin America , Occult Blood
2.
Rev. argent. microbiol ; 51(2): 110-118, jun. 2019. ilus, tab
Article in English | LILACS | ID: biblio-1013359

ABSTRACT

Although Cr(VI)-reducing and/or tolerant microorganisms have been investigated, there is no detailed information on the composition of the microbial community of the biocathode microbial fuel cell for Cr(VI) reduction. In this investigation, the bacterial diversity of a biocathode was analyzed using 454 pyrosequencing of the 16S rRNA gene. It was found that most bacteria belonged to phylum Proteobacteria (78.8%), Firmicutes (7.9%), Actinobacteria (6.6%) and Bacteroidetes (5.5%), commonly present in environments contaminated with Cr(VI). The dominance of the genus Pseudomonas (34.87%), followed by the genera Stenotrophomonas (5.8%), Shinella (4%), Papillibacter (3.96%), Brevundimonas (3.91%), Pseu-dochrobactrum (3.54%), Ochrobactrum (3.49%), Hydrogenophaga (2.88%), Rhodococcus (2.88%), Fluviicola (2.35%), and Alcaligenes (2.3%), was found. It is emphasized that some genera have not previously been associated with Cr(VI) reduction. This biocathode from waters contaminated with tannery effluents was able to remove Cr(VI) (97.83%) in the cathodic chamber. Additionally, through use of anaerobic sludge in the anodic chamber, the removal of 76.6% of organic matter (glucose) from synthetic waste water was achieved. In this study, an efficient biocathode for the reduction of Cr(VI) with future use in bioremediation, was characterized.


Aunque se ha investigado sobre los microorganismos reductores y/o tolerantes de Cr(VI), no hay información detallada sobre la composición de la comunidad microbiana del cátodo de una Celda de Combustible Microbiana para la reducción de Cr(VI). En esta investigación se analizó la diversidad bacteriana de un biocátodo usando pirosecuenciación 454 del gen 16S rRNA. Se encontró que la mayoría de las bacterias pertenecieron a los filos Proteobac-teria (78,8%), Firmicutes (7,9%), Actinobacteria (6,6%) y Bacteroidetes (5,5%), comúnmente presentes en ambientes contaminados con Cr(VI). Se encontró como género dominante a Pseudomonas (34,87%), seguido por los géneros Stenotrophomonas (5,8%), Shinella (4%), Papil-libacter (3,96%), Brevundimonas (3,91%), Pseudochrobactrum (3,54%), Ochrobactrum (3,49%), Hydrogenophaga (2,88%), Rhodococcus (2,88%), Fluviicola (2,35%) y Alcaligenes (2,3%). Se destaca que algunos géneros no han sido previamente asociados con la reducción de Cr(VI). Este biocátodo procedente de aguas contaminadas con efluentes de curtiembres fue capaz de remover Cr(VI) (97,83%) en la cámara catódica. Adicionalmente, a través del uso de lodo anaeróbico en la cámara anódica, se logró la remoción del 76,6% de materia orgánica (glucosa) a partir de agua residual sintética. En este estudio se caracterizó un eficiente biocátodo para la reducción de Cr(VI) con futuro uso en biorremediación.


Subject(s)
RNA, Ribosomal, 16S/analysis , Actinobacteria/isolation & purification , Waste Water/microbiology , Bacteria/growth & development , Biodegradation, Environmental , Environmental Monitoring , Reducing Agents/analysis
3.
Rev. biol. trop ; 67(1): 321-336, Jan.-Mar. 2019. tab, graf
Article in English | LILACS | ID: biblio-1041913

ABSTRACT

Abstract Phytoplasmas (class Mollicutes) are causal agents of plant diseases with an economic impact on crops or threatening local biodiversity. A survey was conducted from 2012 to 2016 on infected Catharanthus roseus plants that exhibited symptoms reminiscent of phytoplasma infection throughout Costa Rica. A total of 73 plants were collected exhibiting symptoms such as virescence, phyllody, axillary proliferation, little leaf, leaf malformation, chlorosis, or yellowing. All samples were tested by nested PCR using phytoplasma universal and specific primer pairs. Phytoplasma infection was detected in 52 (71.2 %) of the plants collected. Phytoplasmas of six subgroups belonging to 16Sr groups I, III, IX, XIII and XV were identified based on sequencing and in silico RFLP analyses. 'Candidatus Phytoplasma asteris' (16SrI) was the predominant group among the positive samples (n = 30) showing variety of symptoms and wide distribution from sea level to ca. 1 400 m.a.s.l. in six of the seven Costa Rican provinces. Group 16SrIII was the second most abundant (14 samples); and the remaining three groups were seldom found in C. roseus (8 samples). Moreover, group 16SrXIII phytoplasma was detected for the first time in the country. To the best of our knowledge, this is the first report of natural infection of C. roseus with phytoplasma subgroups 16SrI-B, 16SrI-P, 16SrIII-F, 16SrIX-F, 16SrXIII-A, and 16SrXV-B in Costa Rica and Central America.


Resumen Los fitoplasmas (clase Mollicutes) son agentes causales de enfermedades de plantas que provocan pérdidas económicas o amenazan la biodiversidad local. Una recolecta de plantas de Catharanthus roseus que mostraban síntomas de posible infección con fitoplasmas se realizó en diferentes lugares de Costa Rica desde 2012 a 2016. Un total de 73 plantas fueron recolectadas con síntomas tales como viriscencia, filodia, brotación axilar múltiple, reducción foliar, deformación foliar, clorosis, y amarillamiento. Todas las muestras fueron evaluadas mediante PCR anidado usando los pares de imprimadores universales y específicos para fitoplasmas. Infección por fitoplasmas se detectó en 52 (71.2 %) de las muestras. Fitoplasmas de seis subgrupos dentro de los grupos 16Sr I, III, IX, XIII y XV fueron identificados basados en secuenciación del ADN y análisis de polimorfismos de restricción (RFLP) in silico. El grupo predominante encontrado en las muestras positivas (n = 30) fue el 16SrI ('CandidatusPhytoplasma asteris'), éste mostró variedad de síntomas y amplia distribución desde el nivel del mar hasta casi los 1 400 m.s.n.m. en seis de las siete provincias de Costa Rica. El grupo 16SrIII fue el segundo más abundante (14 muestras); y los restantes tres grupos se encontraron en pocas muestras de C. roseus (8 muestras). Además, fitoplasmas del grupo 16SrXIII se detectaron por primera vez en el país. De acuerdo a nuestro conocimiento, este es el primer informe de infección natural de C. roseus con fitoplasmas de los subgrupos 16SrI-B, 16SrI-P, 16SrIII-F, 16SrIX-F, 16SrXIII-A y 16SrXV-B en Costa Rica y Centroamérica.


Subject(s)
RNA, Ribosomal, 16S/analysis , Polymerase Chain Reaction/instrumentation , Vinca , Biodiversity , Infections/diagnosis
4.
Rev. argent. microbiol ; 51(1): 22-25, mar. 2019. ilus, tab
Article in Spanish | LILACS | ID: biblio-1041815

ABSTRACT

Las micobacterias de crecimiento rápido son una rara causa de endocarditis bacteriana. Durante las últimas décadas han aumentado las infecciones debido a este tipo de micobacterias, en especial las postraumáticas y las posquirúrgicas. Estas infecciones pueden ser localizadas o diseminadas, y también pueden producir brotes nosocomiales debido a la contaminación del equipamiento médico. Por lo general, las tinciones para bacterias ácido-alcohol resistentes no se emplean de rutina en el procesamiento de hemocultivos positivos. Sin embargo, el microbiólogo debe estar atento al ver un bacilo gram positivo, ya que podría tratarse de una micobacteria de crecimiento rápido. Describimos un caso de endocarditis por de Mycobacterium mageritense en una paciente con parche pericárdico autógeno y un catéter para medir la presión en la aurícula izquierda. La bacteria fue identificada por espectrometría de masas (MALDI-TOF MS), score 2,3, y luego confirmada por secuenciación y análisis del gen ARNr 16s con las bases de datos del NCBI y EzTaxon, con una concordancia del 99,8 y el 100%, respectivamente.


Rapidly growing non-tuberculosis mycobacteria are a rare cause of bacterial endocarditis. During the last decades, there has been an increase in infections due to rapidly growing mycobacteria, mainly after trauma and post-surgical procedures, both localized and disseminated, as well as nosocomial outbreaks due to contamination of medical equipment. Routine acid-fast staining for blood culture bottles is not always performed; however, the microbiologist should be aware of potential RGM infections especially when gram positive bacilli are observed. We describe a case of endocarditis caused by Mycobacterium mageritense in a patient with an autologous pericardial patch and a pressure catheter in the left auricle. The bacterial species was identified as Mycobacterium mageritense by mass spectrometry (MALDI-TOF MS), score 2.3, and confirmed by 16S rRNA analysis with 99.8 and 100% agreement, respectively.


Subject(s)
Humans , Female , Adult , Endocarditis, Bacterial/microbiology , Catheter-Related Infections/diagnosis , Mycobacterium/isolation & purification , Mass Spectrometry/methods , RNA, Ribosomal, 16S/analysis , Catheter-Related Infections/therapy , Blood Culture/methods
5.
Braz. j. biol ; 79(1): 29-37, Jan.-Mar 2019. tab, graf
Article in English | LILACS | ID: biblio-984009

ABSTRACT

Abstract Three phosphate solubilizing bacteria were isolated and identified by 16S rRNA sequencing as Pseudomonas putida, Pseudomonas sp and Pseudomonas fulva . The strains were subjected to plant biochemical testing and all the PGPR attributes were checked in the presence of pesticides (chlorpyrifos and pyriproxyfen). The phosphate solubilizing index of strain Ros2 was highest in NBRIP medium i.e 2.23 mm. All the strains showed acidic pH (ranges from 2.5-5) on both medium i.e PVK and NBRIP. Strain Ros2 was highly positive for ammonia production as well as siderophore production while strain Rad2 was positive for HCN production. The results obtained by the strains Rad1, Rad2 and Ros2 for auxin production were 33.1, 30.67 and 15.38 µg ml-1, respectively. Strain Rad1 showed 16% increase in percentage germination in comparison to control in the presence of pesticide stress. Most promising results for chlorophyll content estimation were obtained in the presence of carotenoids upto 6 mgg-1 without stress by both strains Rad1 and Rad2. Study suggests that especially strain Ros2 can enhance plant growth parameters in the pesticide stress.


Resumo Três bactérias solubilizantes de fosfato foram isoladas e identificadas por seqüenciamento de rRNA 16S como Pseudomonas putida, Pseudomonas sp e Pseudomonas fulva. As estirpes foram submetidas a testes bioquímicos de plantas e todos os atributos PGPR foram verificados na presença de pesticidas (clorpirifos e piriproxifeno). O índice de solubilização de fosfato da estirpe Ros2 foi mais elevado no meio NBRIP, isto é, 2,23 mm. Todas as estirpes apresentaram um pH ácido (varia de 2,5-5) em ambos os meios, isto é PVK e NBRIP. A estirpe Ros2 foi altamente positiva para a produção de amoníaco, bem como a produção de sideróforos enquanto a estirpe Rad2 foi positiva para a produção de HCN. Os resultados obtidos pelas estirpes Rad1, Rad2 e Ros2 para a produção de auxina foram 33,1, 30,67 e 15,38 μg ml-1 , respectivamente. A deformação Rad1 mostrou aumento de 16% na germinação percentual em comparação com o controlo na presença de stress de pesticida. Os resultados mais promissores para a estimativa do teor de clorofila foram obtidos na presença de carotenóides até 6 mgg-1 sem estresse por ambas as cepas Rad1 e Rad2. Estudo sugere que especialmente a estirpe Ros2 pode melhorar parâmetros de crescimento de plantas no estresse de pesticidas.


Subject(s)
Phosphates/metabolism , Pseudomonas/physiology , Pyridines/administration & dosage , Triticum/growth & development , Chlorpyrifos/administration & dosage , Insecticides/administration & dosage , Pakistan , Pseudomonas/drug effects , Triticum/metabolism , Triticum/microbiology , RNA, Bacterial/analysis , RNA, Ribosomal, 16S/analysis , Pseudomonas putida/drug effects , Pseudomonas putida/physiology , Sequence Analysis, RNA
6.
J. appl. oral sci ; 27: e20180635, 2019. tab, graf
Article in English | LILACS, BBO | ID: biblio-1012524

ABSTRACT

Abstract Acetaldehyde, associated with consumption of alcoholic beverages, is known to be a carcinogen and to be related to the tongue dorsum. Objective The aim of this study was to investigate the relationship between acetaldehyde concentration in mouth air and bacterial characteristics on the tongue dorsum. Methodology Thirty-nine healthy volunteers participated in the study. Acetaldehyde concentrations in mouth air were evaluated by a high-sensitivity semiconductor gas sensor. A 16S rRNA gene sequencing technique was used to compare microbiomes between two groups, focusing on the six samples with the highest acetaldehyde concentrations (HG) and the six samples with lowest acetaldehyde concentrations (LG). Results Acetaldehyde concentration increased in correlation with the increase in bacterial count (p=0.048). The number of species observed in the oral microbiome of the HG was higher than that in the oral microbiome of the LG (p=0.011). The relative abundances of Gemella sanguinis, Veillonella parvula and Neisseria flavescens in the oral microbiome of the HG were higher than those in the oral microbiome of the LG (p<0.05). Conclusion Acetaldehyde concentration in mouth air was associated with bacterial count, diversity of microbiome, and relative abundance of G. sanguinis, V. parvula, and N. flavescens.


Subject(s)
Humans , Male , Female , Adult , Young Adult , Tongue/microbiology , Microbiota , Acetaldehyde/analysis , Mouth/surgery , Reference Values , Bacteria/isolation & purification , Bacteria/genetics , Tongue/metabolism , Candida/isolation & purification , Alcohol Drinking/metabolism , RNA, Ribosomal, 16S/analysis , RNA, Ribosomal, 16S/metabolism , Smoking/metabolism , Cross-Sectional Studies , Surveys and Questionnaires , Statistics, Nonparametric , Bacterial Load , Japan , Acetaldehyde/metabolism , Mouth/metabolism
7.
Gastroenterol. latinoam ; 30(2): 58-63, 2019. tab
Article in English | LILACS | ID: biblio-1103903

ABSTRACT

ANTECEDENTES: La colangitis biliar primaria (CBP) es una enfermedad hepática inflamatoria crónica colestásica de causa desconocida. Varios patógenos virales y bacterianos han sido propuestos como factores que podrían gatillar una respuesta inmune por mimetismo molecular, o directamente estar relacionados en la persistencia del daño biliar. Existen reportes controversiales respecto al rol de en la patogenia de CBP. OBJETIVOS: Investigar marcadores de infección de séricos y en hígado de pacientes con CBP. PACIENTES Y MÉTODOS: Veinte pacientes diagnosticados con CBP y 20 pacientes control con otras enfermedades hepáticas crónicas no colestásicas fueron estudiados. Se determinaron anticuerpos séricos anti- (IgG). Se realizó detección inmunohistoquímica de antígenos de en hígado. Se extrajo DNA de hígado para amplificación de la secuencia específica de rRNA 16S de por PCR. Fueron usados controles de amplificación de DNA bacteriano y humano. Los pacientes firmaron consentimiento informado. Se realizó un metaanálisis de la diferencia de riesgo de CBP en pacientes infectados por y en un grupo control. RESULTADOS: Los anticuerpos séricos fueron positivos en 30% de los pacientes con CBP y 50% de los controles (p = NS). Antígenos de no fueron detectados en tejido hepático de pacientes con CBP ni de controles. No se amplificó ADN bacteriano en ninguna de las muestras. El metaanálisis de la diferencia de riesgo mostró gran heterogeneidad de los estudios, por lo que no se realizó una estimación de diferencia de riesgo agrupada. DISCUSIÓN: No encontramos asociación entre infección por y CBP. En la evidencia actual, un estudio presenta resultados a favor de la asociación entre y CBP y tres estudios resultados en contra.,


Primary biliary cholangitis (PBC) is a chronic cholestatic inflammatory liver disease of unknown cause. Several viral and bacterial pathogens have been proposed as factors that could either trigger an immune response by molecular mimicry or directly be involved in the persistence of biliary damage. There are conflicting reports respecting the role of in the pathogenesis of PBC. To investigate markers of infection in serum and liver tissue from patients with PBC. Twenty patients with diagnosis of PBC and 20 control patients with other non-cholestatic chronic liver diseases were studied. Serum anti- antibodies (IgG) were determined. Liver tissue was available for immunohistochemistry detection of antigens. DNA was extracted from liver tissue and a specific sequence of 16S rRNA gene was amplified by CPR. Adequate controls of bacterial and human DNA amplification were used. Informed consent was obtained from patients. A meta-analysis of risk difference of PBC in Chlamydophila pneumoniae infected patients and in the control groupwas performed. Serum antibodies were positive in 30% of patients with PBC and 50% of controls (p = NS). antigens were not detected in liver tissue neither of patients with PBC nor controls. Bacterial DNA did not amplify in any of the samples, despite good amplification of internal and external controls. Risk difference meta-analysis showed high heterogeneity between studies. Therefore, we did not estimate a pooled risk difference. Our results do not support the association between infection and PBC. In the current literature only one study shows an association between and PBC, but other three studies do not support it.


Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Aged , Chlamydia Infections/diagnosis , Chlamydophila Infections/complications , Liver Cirrhosis, Biliary/diagnosis , Liver Cirrhosis, Biliary/microbiology , DNA, Bacterial , Immunoglobulin G , Immunohistochemistry , RNA, Ribosomal, 16S/analysis , Case-Control Studies , Polymerase Chain Reaction , Chlamydophila pneumoniae/genetics , Liver/microbiology , Liver Cirrhosis, Biliary/etiology
8.
Clinics ; 74: e1198, 2019. tab, graf
Article in English | LILACS | ID: biblio-1039552

ABSTRACT

OBJECTIVES: The gut microbiota is associated with obesity and weight loss after bariatric surgery and has been related to its changing pattern. Exactly how the bacterial population affects weight loss and the results of surgery remain controversial. This study aimed to evaluate the intestinal microbiota of superobese patients before and after gastric bypass surgery (RYGB). METHOD: DNA fragments for the microbiota obtained from stool samples collected from nine superobese patients before and after bariatric surgery were sequenced using Ion Torrent. RESULTS: We observed that with a mean follow-up of 15 months, patients achieved 55.9% excess weight loss (EWL). A significant population reduction in the Proteobacteria phylum (11 to 2%, p=0.0025) was observed after surgery, while no difference was seen in Firmicutes and Bacteroidetes. Further analyses performed with two specific individuals with divergent clinical outcomes showed a change in the pattern between them, with a significant increase in Firmicutes and a decrease in Bacteroidetes in the patient with less weight loss (%EWL 50.79 vs. 61.85). CONCLUSIONS: RYGB affects the microbiota of superobese patients, with a significant reduction in Proteobacteria in patients with different weight loss, showing that different bacteria may contribute to the process.


Subject(s)
Humans , Male , Adolescent , Adult , Middle Aged , Young Adult , Obesity, Morbid/surgery , Obesity, Morbid/microbiology , Weight Loss , Bariatric Surgery , Gastrointestinal Microbiome , RNA, Ribosomal, 16S/analysis , Follow-Up Studies , Longitudinal Studies , Feces/microbiology
9.
J. pediatr. (Rio J.) ; 94(3): 258-267, May-June 2018. tab, graf
Article in English | LILACS | ID: biblio-954614

ABSTRACT

Abstract Objective Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors. Methods Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices. DNA was extracted from fecal samples of each child and subjected to Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis. Results The results revealed a pattern of similarity between the time points for those who were on exclusive breastfeeding or predominant breastfeeding. Although there were changes in intensity and fluctuation of some bands, the Denaturing Gradient Gel Electrophoresis patterns in the one-year microbial analysis were stable for breastfeeding children. There was uninterrupted ecological succession despite the influence of external factors, such as complementary feeding and antibiotic administration, suggesting microbiota resilience. This was not observed for those children who had mixed feeding and introduction of solid food before the 5th month of life. Conclusion These results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding, reinforcing the importance of exclusive breastfeeding until the 6th month of life.


Resumo Objetivo Como nosso grupo já havia descrito a composição da microbiota intestinal de neonatos brasileiros em baixo nível socioeconômico, o objetivo deste estudo foi analisar alterações estruturais da comunidade microbiana desse grupo de neonatos no início de sua vida devido a fatores externos. Métodos Amostras fecais foram coletadas mensalmente de 11 neonatos durante o primeiro ano de vida. Os neonatos foram acompanhados com relação a informações clínicas e nutricionais e caracterizados de acordo com práticas de amamentação. O DNA foi extraído das amostras fecais de cada criança e submetido a análise através da técnica de Reação em Cadeia da Polimerase - Eletroforese em Gel de Gradiente Desnaturante. Resultados Os resultados revelaram um padrão de similaridade entre seus próprios pontos temporais em indivíduos em aleitamento materno exclusivo ou predominante. Apesar de variações na intensidade e flutuação de algumas bandas, o padrão Eletroforese em Gel de Gradiente Desnaturante na análise microbiana de um ano foi estável em crianças em aleitamento materno. Houve sucessão ecológica ininterrupta apesar da influência de fatores externos, como alimentação complementar e administração de antibióticos, sugeriu resiliência da microbiota. Isso não foi observado nas crianças com alimentação heterogênea e introdução de alimentos sólidos antes do quinto mês de vida. Conclusão Nossos resultados sugerem um padrão de microbiota intestinal resiliente a forças externas, devido a efeitos probióticos e prebióticos do aleitamento materno exclusivo, reforçam a importância do aleitamento materno exclusivo até o sexto mês de vida.


Subject(s)
Humans , Male , Female , Infant, Newborn , Infant , Bacteria/immunology , Breast Feeding , Feces/microbiology , Intestines/microbiology , Anti-Bacterial Agents/administration & dosage , Bacteria/drug effects , Bacteria/genetics , RNA, Bacterial/analysis , RNA, Ribosomal, 16S/analysis , Polymerase Chain Reaction , Electrophoresis, Agar Gel
10.
Arq. bras. med. vet. zootec. (Online) ; 69(3): 559-569, jun. 2017. ilus, tab
Article in English | LILACS, VETINDEX | ID: biblio-846888

ABSTRACT

Bovine digital dermatitis (BDD) is an infectious and contagious disease characterized by ulcerative and proliferative lesions affecting the skin on the bulbs of the heel or the interdigital cleft in dairy cattle, often associated with lameness. Evidences on the etiology of BDD indicate that it is multifactorial, involving environmental factors and multiple bacterial colonization. We isolated and identified microorganisms from BDD biopsy samples obtained from five Holstein Friesian and two Jersey cows by cultivation and molecular identification of bacterial isolates using 16S rRNA gene sequence analysis. We identified six bacterial species: Spirochetes as Treponema pedis and Leptospira broomi/L. fainei, L. licerasiae/L. wolffii; Corynebacterium appendicis, Cupriavidus gilardii and Enterococcus casseliflavus/E. gallinarum. It was quite surprising to have isolated and identified Leptospira species in three out of seven cultures, from different individual cows and two different farms. The species identified belong to the intermediate pathogenic clade, which is a group found to cause human and animal disease. Our findings indicate the need to further investigate the association of Leptospira of intermediate pathogenicity with BDD lesions and whether its presence would have any veterinary and medical significance both in Leptospirosis and with the pathogenesis of BDD lesions, especially in tropical countries.(AU)


Dermatite digital bovina (DDB) é uma doença infecciosa, contagiosa, caracterizada por lesões ulcerativas e proliferativas da região dos talões e/ou do espaço interdigital, frequentemente associada com claudicação. Evidências indicam que a etiologia da DDB é multifatorial, envolvendo fatores ambientais e colonização polimicrobiana. Relata-se aqui o isolamento e a identificação bacteriana em amostras de biópsias em lesões de DDB, obtidas de cinco vacas da raça Holandesa e duas da raça Jersey, por meio de cultivo e identificação molecular de isolados, com base na análise de sequências de genes 16S rRNA. São identificadas seis espécies bacterianas: as espiroquetas Treponema pedis e Leptospira broomi/L. fainei, L. licerasiae/L. wolffii; Corynebacterium appendicis, Cupriavidus gilardii e Enterococcus casseliflavus/E. gallinarum. O isolamento e a identificação de espécies de Leptospira surpreenderam, destacando-se sua presença em três dos sete cultivos obtidos em diferentes vacas, de duas fazendas distintas. As espécies identificadas pertencem ao grupo tipificado como de patogenicidade intermediária, causador de doenças em animais e no homem. Os resultados apresentados indicam a necessidade de maiores investigações sobre a associação entre Leptospira de patogenicidade intermediária e a patogênese das lesões DDB, investigando-se sua presença e significado nas medicinas veterinária e humana, especialmente em países tropicais.(AU)


Subject(s)
Animals , Cattle , Digital Dermatitis/microbiology , Leptospira/isolation & purification , RNA, Ribosomal, 16S/analysis , Treponema/isolation & purification , Polymerase Chain Reaction/veterinary
12.
Rev. argent. microbiol ; 47(4): 328-330, dic. 2015.
Article in Spanish | LILACS | ID: biblio-1141103

ABSTRACT

Anaerobiospirillum thomasii ha sido descrito como causante de diarrea en humanos, pero no se han informado bacteriemias asociadas a este organismo. En esta comunicación describimos el primer aislamiento de A. thomasii como causa de bacteriemia fatal en una paciente alcohólica


Anaerobiospirillum thomasii has been reported as a causative agent of diarrhea in humans; however no bacteremia associated with this pathogen has been described so far. We present here the first case of fatal A. thomasii bacteremia in an alcoholic patient


Subject(s)
Humans , Female , Middle Aged , Bacteremia/complications , Anaerobiospirillum/pathogenicity , RNA, Ribosomal, 16S/analysis , Bacteremia/microbiology , Fatal Outcome , Anaerobiospirillum/metabolism
13.
Article in English | WPRIM | ID: wpr-34573

ABSTRACT

BACKGROUND: By conventional methods, the identification of anaerobic bacteria is more time consuming and requires more expertise than the identification of aerobic bacteria. Although the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are relatively less studied, they have been reported to be a promising method for the identification of anaerobes. We evaluated the performance of the VITEK MS in vitro diagnostic (IVD; 1.1 database; bioMerieux, France) in the identification of anaerobes. METHODS: We used 274 anaerobic bacteria isolated from various clinical specimens. The results for the identification of the bacteria by VITEK MS were compared to those obtained by phenotypic methods and 16S rRNA gene sequencing. RESULTS: Among the 249 isolates included in the IVD database, the VITEK MS correctly identified 209 (83.9%) isolates to the species level and an additional 18 (7.2%) at the genus level. In particular, the VITEK MS correctly identified clinically relevant and frequently isolated anaerobic bacteria to the species level. The remaining 22 isolates (8.8%) were either not identified or misidentified. The VITEK MS could not identify the 25 isolates absent from the IVD database to the species level. CONCLUSIONS: The VITEK MS showed reliable identifications for clinically relevant anaerobic bacteria.


Subject(s)
Bacteria, Anaerobic/genetics , Bacterial Typing Techniques/instrumentation , Body Fluids/microbiology , Databases, Genetic , Humans , RNA, Ribosomal, 16S/analysis , Sequence Analysis, DNA , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
15.
Rev. argent. microbiol ; 46(2): 119-121, jun. 2014.
Article in English | LILACS | ID: biblio-1016516

ABSTRACT

Diferentes especies del género Mycoplasma pueden afectar al ganado bovino y causar varias enfermedades. La técnica de PCR, secuenciación y posterior análisis de la región ITS 16S-23S ARNr ha mostrado que existe una importante variabilidad interespecies entre Mollicutes. Se realizó la amplificación (región ITS 16S-23S ARNr) de 16 aislamientos sospechosos de corresponder a alguna especie de Mycoplasma, que habían sido obtenidos de muestras de leche provenientes de rodeos lecheros. Catorce de esos aislamientos fueron PCR positivos. Para confirmar la identidad de Mycoplasma bovis, dichos aislamientos fueron evaluados por otra PCR especie-específica. Siete aislamientos dieron un resultado positivo. Los productos de la PCR de la ITS 16S-23S ARNr de un aislamiento identificado como M. bovis y de otros dos aislamientos identificados como no-M. bovis fueron seleccionados al azar, secuenciados y analizados. Las tres secuencias (A, B y C) mostraron 100 % de similitud con cepas de M. bovis, Mycoplasma canadense y Mycoplasma californicum, respectivamente


Different species of Mycoplasma can affect bovine cattle, causing several diseases. PCR sequencing and further analysis of the 16S-23S rRNA ITS region have shown a significant interspecies variability among Mollicutes. Sixteen suspected isolates of Mycoplasma spp. obtained from milk samples from dairy herds were amplified (16S-23S rRNA ITS region). Fourteen out of those 16 suspected Mycoplasma spp. isolates were PCR-positive. To confirm the identity of Mycoplasma bovis, these 14 isolates were tested by another species-specific PCR. Seven of the isolates rendered a positive result. The products of 16S-23S rRNA ITS PCR from one isolate that was identified as M. bovis and from two other isolates, identified as non- M. bovis were randomly selected, sequenced and analyzed. The three sequences (A, B and C) showed 100% similarity with M. bovis, Mycoplasma canadense and Mycoplasma californicum respectively


Subject(s)
Animals , Cattle , Argentina/epidemiology , Cattle Diseases/diagnosis , Mycoplasma Infections/diagnosis , RNA, Ribosomal, 16S/analysis , RNA, Ribosomal, 23S/analysis , Bacterial Typing Techniques/methods , Tenericutes/isolation & purification , Mycoplasma bovis/isolation & purification
16.
Biol. Res ; 47: 1-6, 2014. graf, tab
Article in English | LILACS | ID: biblio-950763

ABSTRACT

BACKGROUND: Marine invertebrate-associated microbial communities are interesting examples of complex symbiotic systems and are a potential source of biotechnological products. RESULTS: In this work, pyrosequencing-based assessment from bacterial community structures of sediments, two sponges, and one zoanthid collected in the Mexican Caribbean was performed. The results suggest that the bacterial diversity at the species level is higher in the sediments than in the animal samples. Analysis of bacterial communities' structure showed that about two thirds of the bacterial diversity in all the samples belongs to the phyla Acidobacteria and Proteobacteria. The genus Acidobacteriumappears to dominate the bacterial community in all the samples, reaching almost 80% in the sponge Hyrtios. CONCLUSIONS: Our evidence suggests that the sympatric location of these benthonic species may lead to common bacterial structure features among their bacterial communities. The results may serve as a first insight to formulate hypotheses that lead to more extensive studies of sessile marine organisms' microbiomes from the Mexican Caribbean.


Subject(s)
Animals , Porifera/microbiology , Anthozoa/microbiology , Acidobacteria/physiology , Sympatry , Microbiota/physiology , Phylogeny , Porifera/classification , Symbiosis/physiology , RNA, Ribosomal, 16S/analysis , Caribbean Region , Geologic Sediments/microbiology , Proteobacteria/classification , Proteobacteria/physiology , Anthozoa/classification , Biodiversity , Mexico
18.
Article in English | WPRIM | ID: wpr-178236

ABSTRACT

BACKGROUND: The aim of this study was to evaluate a newly developed PCR-based reverse blot hybridization assay (PCR-REBA), REBA Sepsis-ID (M&D, Wonju, Korea), to rapidly detect the presence of bacteremia and antimicrobial resistance gene in blood culture samples. METHODS: One thousand four hundred consecutive blood culture samples from patients with a delta neutrophil index greater than 2.7% were selected from March to July in 2013. Three hundred positive and 1,100 negative for bacterial growth in blood culture bottles samples were tested by conventional and real-time PCR-REBA, respectively. RESULTS: The overall agreement between the conventional identification test and the REBA Sepsis-ID test was 95.3% (286/300). Agreement for gram-positive bacteria, gram-negative bacteria, fungi, and polymicrobials was 94.5% (190/201), 97.3% (71/73), 100% (14/14), and 91.7% (11/12), respectively. The detection rate of the mecA gene from methicillin-resistant Staphylococcus isolates was 97.8% (90/92). The vanA gene was detected in one blood culture sample from which vancomycin-resistant Enterococcus was isolated. When the cycle threshold for real-time PCR was defined as 30.0, 2.4% (26/1,100) of negative blood culture samples tested positive by real-time PCR. CONCLUSIONS: The REBA Sepsis-ID test is capable of simultaneously and quickly detecting both causative agents and antimicrobial resistance genes, such as mecA and van, in blood culture positive samples.


Subject(s)
Bacteremia/microbiology , Bacterial Proteins/genetics , Bacteriological Techniques/methods , Carbon-Oxygen Ligases/genetics , Drug Resistance, Bacterial/genetics , Enterococcus/genetics , Humans , Methicillin-Resistant Staphylococcus aureus/genetics , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/analysis , Reagent Kits, Diagnostic , Real-Time Polymerase Chain Reaction
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