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1.
Braz. j. biol ; 82: e240184, 2022. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1278492

RESUMO

Soil quality is usually determined by its physical-chemical characteristics without taking into account the bacterial communities that play a fundamental role in the chemical decomposition of plant nutrients. In this context, the objective of the study was to evaluate bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii cultivation under different gradients of use (first, second and third use) and crop development (pre-sowing, hypocotyl development and post-harvest). The sampling was carried out in the Bombón plateau in the central Andes of Peru, during the rainy and low water seasons, by the systematic method based on a specific pattern assigned in a geometric rectangular shape at a depth of 0 - 20 cm. The characterization of the bacterial communities was carried out through the metagenomic sequencing of the 16S rRNA. 376 families of bacteria were reported, of which it was determined that there was a significant change in bacterial composition and distribution in relation to use pressure. There were no major changes due to the development of Lepidium meyenii. The families most sensitive to use pressure and soil poverty indicators were Verrucomicrobiaceae, Acidobacteraceae and Aakkermansiaceae.


A qualidade do solo é normalmente determinada pelas suas características físico-químicas sem ter em conta as comunidades bacterianas que desempenham um papel fundamental na decomposição química dos nutrientes das plantas. Neste contexto, o objetivo do estudo foi avaliar a diversidade bacteriana em solos de prados andinos elevados perturbados pelo cultivo de Lepidium meyenii sob diferentes gradientes de utilização (primeira, segunda e terceira utilizações) e desenvolvimento das culturas (pré-semeadura, desenvolvimento do hipocótilo e póscolheita). A amostragem foi realizada no planalto de Bombón, nos Andes centrais do Peru, durante as estações das chuvas e das águas baixas, pelo método sistemático baseado num padrão específico atribuído em forma geométrica retangular a uma profundidade de 0 - 20 cm. A caracterização das comunidades bacterianas foi realizada através da sequenciação metagenômica do rRNA 16S. Foram relatadas 376 famílias de bactérias, das quais se verificou uma alteração significativa na composição e distribuição bacteriana em relação à pressão de utilização. Não se registaram grandes alterações devido ao desenvolvimento do Lepidium meyenii. As famílias mais sensíveis à utilização de indicadores de pressão e pobreza do solo foram as Verrucomicrobiaceae, Acidobacteraceae e Aakkermansiaceae.


Assuntos
Lepidium/genética , Peru , Solo , Microbiologia do Solo , Bactérias/genética , RNA Ribossômico 16S/genética , Pradaria , Metagenômica
2.
Acta bioquím. clín. latinoam ; 55(3): 319-345, jul. 2021. graf
Artigo em Espanhol | LILACS, BINACIS | ID: biblio-1374055

RESUMO

Resumen Existen epidemias silenciosas asociadas al estrés y a los malos hábitos de alimentación, tan importantes como las epidemias tradicionales asociadas a la pobreza, a problemas geográficos y climáticos. Numerosos estudios se suman al importante papel de un patrón estable de la microbiota intestinal que favorece el estado saludable en los seres humanos y por lo tanto, su posible implicación en la incidencia y prevalencia de enfermedades que pueden convertirse en epidémicas. En esta revisión se analiza el estado actual de la relación entre los factores demográficos, geográficos, ambientales, patrones de consumo de alimentos con la microbiota intestinal y la aparición de epidemias de origen microbiano, metabólico e inmunológico. Se apoya la iniciativa promovida internacionalmente para la creación de plataformas metagenómicas que contribuyan al estudio del patrón de la microbiota intestinal, el seguimiento epidemiológico y la prevención de las enfermedades epidémicas asociadas con su alteración, así como el diseño de métodos rápidos y económicos para la complementación de estos estudios.


Abstract Silent epidemics associated with stress and unhealthy eating habits are as important as traditional epidemics related to poverty, geographical and climate problems. Many studies incorporate the important role of a stable pattern of gut microbiota that favours the human health status and therefore, its possible implication in incidence and prevalence of diseases that can become epidemics. In this review, the current state-of-art is analysed in terms of relationship between demographic, geographic, environmental factors, and habits with the gut microbiota pattern and the onset of epidemics of microbial, metabolic and immunological origin. The internationally promoted initiative for the creation of metagenomic platforms contributing to studies of the gut microbiota pattern for the epidemiological monitoring and prevention of epidemic diseases associated with its alteration is fostered, as well as the design of rapid and economic methods to complement these studies.


Resumo Existem epidemias silenciosas associadas ao estresse, maus hábitos alimentares, tão importantes quanto as epidemias tradicionais associadas à pobreza, problemas geográficos e climáticos. Numerosos estudos contribuem para o importante papel de um padrão estável de microbiota intestinal que favorece o estado saudável em seres humanos e, portanto, sua possível comprometimento na incidência e prevalência de doenças que podem se tornar epidêmicas. Esta revisão analisa o estado atual da relação entre fatores demográficos, geográficos, ambientais, padrões de consumo de alimentos com a microbiota intestinal e o aparecimento de epidemias de origem microbiana, metabólica e imunológica. É fornecido apoio à iniciativa promovida internacionalmente para a criação de plataformas metagenômicas que contribuam para o estudo do padrão da microbiota intestinal, monitoramento epidemiológico e prevenção de doenças epidêmicas associadas à sua alteração, bem como o desenho de métodos rápidos e baratos para a complementação desses estudos.


Assuntos
Humanos , Trato Gastrointestinal/microbiologia , Microbioma Gastrointestinal/fisiologia , Bactérias , Vírus , Gravidez/fisiologia , Água/administração & dosagem , Imunomodulação , Metagenômica
3.
Electron. j. biotechnol ; 50: 29-36, Mar. 2021. tab, graf
Artigo em Inglês | LILACS | ID: biblio-1292313

RESUMO

BACKGROUND: Lignocellulose is considered a renewable organic material, but the industrial production of biofuel from lignocellulose is challenging because of the lack of highly active hydrolytic enzymes. The guts of herbivores contain many symbiotic microorganisms that have evolved to hydrolyze plant lignocellulose. Chinese bamboo rats mainly consume high-fiber foods, indicating that some members of the intestinal tract microbiota digest lignocellulose, providing these rats with the energy required for growth. RESULTS: Here, we used metagenomics to analyze the diversity and functions of the gut microbiota in Chinese bamboo rats. We identified abundant populations of lignocellulose-degrading bacteria, whose main functions involved carbohydrate, amino acid, and nucleic acid metabolism. We also found 587 carbohydrate-active enzyme genes belonging to different families, including 7 carbohydrate esterase families and 21 glycoside hydrolase families. The glycoside hydrolase 3, glycoside hydrolase 1, glycoside hydrolase 43, carbohydrate esterase 4, carbohydrate esterase 1, and carbohydrate esterase 3 families demonstrated outstanding performance. CONCLUSIONS: The microbes and enzymes identified in our study expand the existing arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. This study also describes a powerful approach for targeting gut microbes and enzymes in numerous industries.


Assuntos
Animais , Ratos , Ceco/enzimologia , Enzimas/metabolismo , Lignina/metabolismo , Ceco/microbiologia , Celulose/metabolismo , Bacteroidetes , Biocombustíveis , Metagenômica , Firmicutes , Microbioma Gastrointestinal
4.
Int. j. morphol ; 39(1): 57-63, feb. 2021. ilus, tab, graf
Artigo em Inglês | LILACS | ID: biblio-1385312

RESUMO

SUMMARY: The insectivorous bat Myotis chiloensis is endemic of South America. Even though potentially pathogenic bacterial species of Mycoplasma have been reported from this species, there are no further studies regarding the bacterial communities they harbor. This may provide important insights for the better understanding of its ecology, diet and implications in cross-species pathogens transmission. Here we report a first survey on bacterial communities of M. chiloensis based on metagenomic analysis of fecal samples. We found that taxonomic profile is dominated by Proteobacteria (23.7 to 57.7 %) and Firmicutes (11.8 to 61.6 %), which main families are represented by Burkholderiaceae- Enterobacteriaceae and Veillonellaceae-Bacillaceae, respectively. Phyla Bacteroidetes, Actinobacteria, Cyanobacteria, Planctomycetes and Acidobacteria were also present with abundance above 1 % of the total reads. Variations among individuals could be observed at genus level and no significant differences were found between sex groups regarding taxonomic profiles and diversity. Potentially pathogenic species were also detected in all the samples, including Staphylococcus aureus and Clostridium perfringens. Our results highlight the significance M. chiloensis as a reservoir of pathogenic bacteria and its microbiota as an interesting ecological model due to its wide distribution. Further metagenomic studies are necessary for a better understanding of M. chiloensis diet and its host-symbiont relationships.


RESUMEN: El murciélago insectívoro Myotis chiloensis es endémico de América del Sur. A pesar de que en esta especie se han reportado bacterias potencialmente patógenas tipo Mycoplasma, no existen estudios sobre sus comunidades bacterianas, lo cual podría proporcionar información importante para una mejor comprensión de su ecología, dieta e implicaciones en la transmisión de patógenos. En el presente trabajo se realiza una descripción de las comunidades bacterianas del murciélago M. chiloensis basada en análisis metagenómico de muestras fecales. El perfil taxonómico encontradofue dominado por Proteobacterias (23,7-57,7 %) y Firmicutes (11,8-61,6 %), cuyas principales familias fueron representadas por Burkholderiaceae-Enterobacteriaceae y Veillonellaceae-Bacillaceae, respectivamente. También se encontraron los filos Bacteroidetes, Actinobacteria, Cyanobacteria, Planctomycetes y Acidobacteria con una abundancia superior al 1 %. Se observaron variaciones entre los individuos a nivel de género, sin diferencias significativas de los perfiles taxonómicos y diversidad según sexo. Se detectaron especies potencialmente patógenas en todas las muestras, entre ellos Staphylococcus aureus y Clostridium perfringens. Nuestros resultados destacan la importancia de M. chiloensis como un reservorio de bacterias patógenas y el estudio de su microbiota como un modelo ecológico debido a su amplia distribución. Más estudios metagenómicos son necesarios para comprender la dieta de M. chiloensis y sus relaciones huésped-simbionte.


Assuntos
Animais , Quirópteros , Fezes/microbiologia , Esterco/microbiologia , Chile , Metagenômica , Microbiota
5.
Braz. j. infect. dis ; 25(2): 101548, 2021.
Artigo em Inglês | LILACS | ID: biblio-1278574

RESUMO

ABSTRACT This report shows the contribution of next-generation metagenomic sequencing (mNGS) as an alternative to challenging diagnostic infection in immunosuppressed individuals. Herein, we report three acute leukemia patients who developed severe invasive infections due to different etiologies: fungi, viruses, and protozoa. mNGS improved the diagnosis of the infections and provided the opportunity for adequate therapy. The mNGS is a hypothesis-free diagnostic platform, increasing potential in challenging diseases in hematological patients due to the extended diagnostic panel and the expedite access to the result.


Assuntos
Humanos , Leucemia , Doenças Transmissíveis , Metagenômica , Sequenciamento de Nucleotídeos em Larga Escala , Fungos
6.
Arch. argent. pediatr ; 118(3): e265-e270, jun. 2020. ilus
Artigo em Inglês, Espanhol | BINACIS, LILACS | ID: biblio-1116917

RESUMO

La metagenómica en el estudio de los ecosistemas bacterianos intestinales ha permitido definir un perfil genético funcional estándar en el recién nacido, de forma que un ecosistema bacteriano será tanto más "normal" cuanto más se parezca su perfil genético funcional a un estándar. El desarrollo de determinado enterotipo funcional en los primeros días de vida tras el parto es fundamental para que tenga lugar el cebado del sistema inmunológico con determinados antígenos bacterianos. Independientemente de si las primeras bacterias intestinales se adquieren antes o justo después del parto, la microbiota del recién nacido va a ser el resultado de una situación de simbiosis con la flora microbiana de su entorno, en especial, con la flora bacteriana de su madre. El tipo de parto, la administración de antibióticos perinatales, el entorno y la exposición nutricional, en especial, la lactancia materna, han demostrado relacionarse de forma importante con el microbioma intestinal predominante


The use of metagenomics in the study of gut bacterial ecosystems has helped to define a standard, functional genetic profile in newborn infants, so that a bacterial ecosystem will be deemed more "normal" the more similar its functional genetic profile is to a standard. The development of a specific functional enterotype in the first days of life after birth is critical for the priming of the immune system with certain bacterial antigens.Regardless of whether the first gut bacteria are acquired before or just after birth, the newborn microbiota will result from the symbiosis with the environmental microbial flora, especially with the bacterial flora of the mother. The type of delivery, the administration of perinatal antibiotics, the environment, and nutritional exposure, especially breastfeeding, have demonstrated an important relationship with the prevalent gut microbiome


Assuntos
Humanos , Masculino , Feminino , Recém-Nascido , Microbiota , Bactérias , Aleitamento Materno , Parto , Metagenômica , Microbioma Gastrointestinal , Saúde do Lactente
7.
Electron. j. biotechnol ; 45: 30-37, May 15, 2020. ilus, graf
Artigo em Espanhol | LILACS | ID: biblio-1177412

RESUMO

BACKGROUND: Traditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS. RESULTS: The glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported. CONCLUSION: Results indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.


Assuntos
Microbiologia do Solo , Bactérias/classificação , Sequenciamento de Nucleotídeos em Larga Escala , Microbiota/genética , Bactérias/isolamento & purificação , Clima Frio , Biologia Computacional , Camada de Gelo , Metagenômica , Genoma Microbiano , Índia
8.
Rev. Hosp. Ital. B. Aires (2004) ; 40(1): 17-24, mar. 2020. ilus
Artigo em Espanhol | LILACS | ID: biblio-1100762

RESUMO

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)


Assuntos
Humanos , Pesquisa Translacional Biomédica/organização & administração , Microbioma Gastrointestinal/genética , Transplante Homólogo , Vietnã , Aztreonam/uso terapêutico , RNA Ribossômico 16S/análise , Neoplasias Colorretais/genética , Neoplasias Colorretais/microbiologia , Neoplasias Colorretais/epidemiologia , Classificação/métodos , Transplante de Células-Tronco Hematopoéticas , Metagenômica , Pesquisa Translacional Biomédica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/tendências , Hepatopatia Gordurosa não Alcoólica/genética , Hepatopatia Gordurosa não Alcoólica/microbiologia , Hepatopatia Gordurosa não Alcoólica/patologia , Hepatopatia Gordurosa não Alcoólica/epidemiologia , Microbioma Gastrointestinal/fisiologia , Índia , América Latina , Sangue Oculto
9.
Electron. j. biotechnol ; 41: 72-80, sept. 2019. ilus, tab, graf
Artigo em Inglês | LILACS | ID: biblio-1087172

RESUMO

Background: Microbial community analysis of electronic waste (e-waste)-polluted environments is of interest to understand the effect of toxic e-waste pollutants on the soil microbial community and to evaluate novel microorganisms resisting the toxic environment. The present study aims to investigate the bacterial community structure in soils contaminated with e-waste from various sites of Loni and Mandoli (National Capital Region (NCR), India) where e-waste dumping and recycling activities are being carried out for many years. Results: Interferences to soil metagenomic DNA extraction and PCR amplification were observed because of the presence of inhibiting components derived from circuit boards. Whole-metagenome sequencing on the Illumina MiSeq platform showed that the most abundant phyla were Proteobacteria and Firmicutes. Deltaproteobacteria and Betaproteobacteria were the most common classes under Proteobacteria. Denaturing gradient gel electrophoresis (DGGE) analysis of the bacterial 16S rRNA gene showed that e-waste contamination altered the soil bacterial composition and diversity. There was a decrease in the number of predominant bacterial groups like Proteobacteria and Firmicutes but emergence of Actinobacteria in the contaminated soil samples. Conclusions: This is the first report describing the bacterial community structure of composite soil samples of ewaste-contaminated sites of Loni and Mandoli, Delhi NCR, India. The findings indicate that novel bacteria with potential bioremediating properties may be present in the e-waste-contaminated sites and hence need to be evaluated further.


Assuntos
Microbiologia do Solo , Bactérias/isolamento & purificação , Bactérias/genética , Resíduo Eletrônico/análise , Poluentes do Solo , Reação em Cadeia da Polimerase , Metais Pesados , Proteobactérias/isolamento & purificação , Metagenômica , Eletroforese em Gel de Gradiente Desnaturante , Microbiota , Firmicutes/isolamento & purificação , Índia
10.
Braz. j. microbiol ; 49(4): 723-730, Oct.-Dec. 2018. graf
Artigo em Inglês | LILACS | ID: biblio-974310

RESUMO

ABSTRACT The soil represents the main source of novel biocatalysts and biomolecules of industrial relevance. We searched for hydrolases in silico in four shotgun metagenomes (4,079,223 sequences) obtained in a 13-year field trial carried out in southern Brazil, under the no-tillage (NT), or conventional tillage (CT) managements, with crop succession (CS, soybean/wheat), or crop rotation (CR, soybean/maize/wheat/lupine/oat). We identified 42,631 hydrolases belonging to five classes by comparing with the KEGG database, and 44,928 sequences by comparing with the NCBI-NR database. The abundance followed the order: lipases > laccases > cellulases > proteases > amylases > pectinases. Statistically significant differences were attributed to the tillage system, with the NT showing about five times more hydrolases than the CT system. The outstanding differences can be attributed to the management of crop residues, left on the soil surface in the NT, and mechanically broken and incorporated into the soil in the CT. Differences between the CS and the CR were slighter, 10% higher for the CS, but not statistically different. Most of the sequences belonged to fungi (Verticillium, and Colletotrichum for lipases and laccases, and Aspergillus for proteases), and to the archaea Sulfolobus acidocaldarius for amylases. Our results indicate that agricultural soils under conservative managements may represent a hotspot for bioprospection of hydrolases.


Assuntos
Solo/química , Proteínas Fúngicas/genética , Archaea/enzimologia , Proteínas Arqueais/genética , Fungos/enzimologia , Hidrolases/genética , Microbiologia do Solo , Soja/crescimento & desenvolvimento , Triticum/crescimento & desenvolvimento , Brasil , Archaea/isolamento & purificação , Archaea/classificação , Archaea/genética , Zea mays/crescimento & desenvolvimento , Agricultura , Metagenoma , Metagenômica , Fungos/isolamento & purificação , Fungos/classificação , Fungos/genética
11.
NOVA publ. cient ; 16(29): 91-100, ene.-jun. 2018. graf
Artigo em Espanhol | LILACS, COLNAL | ID: biblio-976281

RESUMO

Resumen Objetivo. La finalidad de esta revisión es abarcar la temática relacionada con los genes de resistencia a antibióticos, sus orígenes, reservorios y movimientos en los diferentes hábitats mediante la metagenómica funcional que permite aislar, identificar y analizar estos genes, así como el impacto que tienen en salud pública. Durante los últimos años se ha visto un gran avance en la microbiología, una de las grandes limitaciones a las que se venían enfrentado los microbiólogos era no poder acceder a la totalidad de los microorganismos que habitan el planeta. Gracias al desarrollo de diferentes disciplinas como la metagenómica se ha logrado tener el acceso a estos microorganismos. Metodología. La importancia de la metagenómica en la resistencia microbiana radica en que, actualmente, solo el 1 % de los microorganismos que habitan el suelo pueden ser estudiados por técnicas convencionales de microbiología, quedando alrededor del 99 % de estos sin estudiar. Al mitigar este gran inconveniente, la metagenómica permite el estudio de la microbiota del suelo en su totalidad generando nuevo conocimiento e información relevante en diferentes campos científicos. Resultados. Mediante la metagenómica funcional se ha podido determinar que el suelo puede ser un posible reservorio de determinantes de resistencia microbiana, debido a que la microbiota que allí habita contiene en su material genético genes de resistencia a antibióticos que confieren resistencia a un amplio espectro de antibióticos utilizados en terapia humana de forma indiscriminada y además tienen todos los mecanismos de resistencia conocidos, algunos de estos genes son generados por presión selectiva ante diferentes agentes presentes en su medio y otros son genes constitutivos que cumplen con funciones significativas en su hábitat. El gran impacto que tienen estos hallazgos está dado en que pueden representar un posible riesgo en salud pública si se adquieren por los patógenos humanos.


Abstract Objective. The purpose of this review is to cover the issues related to antibiotic resistance genes, their origins, reservoirs and movements in different habitats through functional metagenomics that allows to isolate, identify and analyze these genes, as well as the impact they have on health public. During the last years a great advance in the microbiology has been seen, one of the great limitations to which the microbiologists had been facing was not being able to have access to the totality of the microorganisms that inhabit the planet. Thanks to the development of different disciplines such as metagenomics, access to these microorganisms has been achieved. Method. The importance of metagenomics in microbial resistance lies in the fact that currently only 1 % of the microorganisms that inhabit the soil can be studied by conventional microbiology techniques, leaving about 99 % of these without studying, the metagenomics by mitigating this great disadvantage allows the study of the soil microbiota in its entirety generating new knowledge and relevant information in different scientific fields. Results. Through functional metagenomics it has been possible to determine that the soil can be a possible reservoir of determinants of microbial resistance, because the microbiota that live there contain in their genetic material antibiotic resistance genes that confer resistance to a broad spectrum of antibiotics used in human therapy indiscriminately and also have all known mechanisms of resistance, some of these genes are generated by selective pressure against different agents present in their environment and others are constitutive genes that fulfill significant functions in their habitat. The great impact of these findings is that they can represent a possible public health risk if they were acquired by human pathogens.


Assuntos
Humanos , Resistência Microbiana a Medicamentos , Metagenômica , Genes , Antibacterianos
12.
Braz. j. microbiol ; 49(2): 248-257, Apr.-June 2018. tab, graf
Artigo em Inglês | LILACS | ID: biblio-889237

RESUMO

Abstract In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.


Assuntos
Bactérias/isolamento & purificação , Bactérias/classificação , Microbiologia Ambiental , Biota , Antibiose , Paquistão , Filogenia , Bactérias/crescimento & desenvolvimento , Bactérias/genética , DNA Bacteriano/genética , DNA Bacteriano/química , DNA Ribossômico/genética , DNA Ribossômico/química , RNA Ribossômico 16S/genética , Análise por Conglomerados , Análise de Sequência de DNA , Euryarchaeota/isolamento & purificação , Euryarchaeota/classificação , Euryarchaeota/crescimento & desenvolvimento , Euryarchaeota/genética , DNA Arqueal/genética , DNA Arqueal/química , Metagenômica
13.
Electron. j. biotechnol ; 33: 1-10, May. 2018. graf, tab, ilus
Artigo em Inglês | LILACS | ID: biblio-1022816

RESUMO

Background: Marine ecosystems contain benthic microalgae and bacterial species that are capable of secreting extracellular polymeric substances (EPS), suggesting that settlement of these microorganisms can occur on submerged surfaces, a key part of the first stage of biofouling. Currently, anti-fouling treatments that help control this phenomenon involve the use of biocides or antifouling paints that contain heavy metals, which over a long period of exposure can spread to the environment. The bacterium Alteromonas sp. Ni1-LEM has an inhibitory effect on the adhesion of Nitzschia ovalis, an abundant diatom found on submerged surfaces. Results: We evaluated the effect of the bioactive compound secreted by this bacterium on the EPS of biofilms and associated epiphytic bacteria. Three methods of EPS extraction were evaluated to determine the most appropriate and efficient methodology based on the presence of soluble EPS and the total protein and carbohydrate concentrations. Microalgae were cultured with the bacterial compound to evaluate its effect on EPS secretion and variations in its protein and carbohydrate concentrations. An effect of the bacterial supernatant on EPS was observed by assessing biofilm formation and changes in the concentration of proteins and carbohydrates present in the biofilm. Conclusions: These results indicate that a possible mechanism for regulating biofouling could be through alteration of biofilm EPS and alteration of the epiphytic bacterial community associated with the microalga.


Assuntos
Diatomáceas , Biofilmes , Microalgas , Matriz Extracelular de Substâncias Poliméricas , Ambiente Marinho , Incrustação Biológica , Metagenômica , Microbiota
14.
Electron. j. biotechnol ; 33: 17-28, May. 2018. ilus, tab
Artigo em Inglês | LILACS | ID: biblio-1025039

RESUMO

Genetic manipulation of bacteria is a procedure necessary to obtain new strains that express peculiar and defined genetic determinants or to introduce genetic variants responsible for phenotypic modifications. This procedure can be applied to explore the biotechnological potential associated with environmental bacteria and to utilize the functional properties of specific genes when inserted into an appropriate host. In the past years, marine bacteria have received increasing attention because they represent a fascinating reservoir of genetic and functional diversity that can be utilized to fuel the bioeconomy sector. However, there is an urgent need for an in-depth investigation and improvement of the genetic manipulation tools applicable to marine strains because of the paucity of knowledge regarding this. This review aims to describe the genetic manipulation methods hitherto used in marine bacteria, thus highlighting the limiting factors of the different techniques available today to increase manipulation efficiency. In particular, we focus on methods of natural and artificial transformations (especially electroporation) and conjugation because they have been successfully applied to several marine strains. Finally, we emphasize that, to avoid failure, future work should be carried out to establish tailored methodologies for marine bacteria.


Assuntos
Água do Mar/microbiologia , Bactérias/genética , Engenharia Genética , Transformação Bacteriana , Genoma , Eletroporação , Conjugação Genética , Metagenômica , Análise de Célula Única , Vetores Genéticos
16.
Rio de Janeiro; s.n; 2018. 59 p. ilus.
Tese em Português | LILACS | ID: biblio-1026261

RESUMO

As espécies de simulídeos são vetores de filárias, como as do gênero Onchocerca e Mansonella, que são os agentes etiológicos da oncocercose e mansonellose, respectivamente. Essas duas filárias ocorrem na região Amazônica brasileira e são transmitidas pelas seguintes espécies de vetores: Simulium incrustatum, S. limbatum, S. oyapockense, S. exiguum, S. guianense, e S. roraimense. As espécies de Simulium tem sido designada com base em caracteres morfológicos, os quais, em alguns casos, não são bem discriminativos. Recentemente, o gene mitocondrial Citocromo c-oxidase 1 (CO1) e a região nuclear Internal Transcribed Spacer (ITS) tem sido utilizados para descriminar espécies e definir populações dentro deste gênero. Entretanto, existe um grande gap acerca da informação genética de Simulium, o qual é considerado a linha de base para estudos ecológicos e populacionais. Considerando este cenário, nosso objetivo foi aplicar a metagenômica para recuperar genomas mitocondriais de amostras brasileiras S. incrustatum e S. oyapockense do foco de oncocercose e também a informação genética a respeito de seus microbiomas. O DNA total de dez simulídeos, morfologicamente identificados como S. incrustatum (3) e S. oyapockense (7) foram sequenciados randomicamente na plataforma Illumina HiSeq 2500. Nós recuperamos dez genomas mitocondriais com cobertura média de 15,591 bp e conteúdo médio de GC de 22,94 %, apresentando o mesmo conteúdo gênico e em sintenia. Baseado nestes mitogenomas, no gene mitocondrial CO1, e também na região nuclear (ITS), realizamos análises filogenéticas que mostraram a presença de três espécies conhecidas dentre as amostras: S. incrustatum, S. oyapockense e S. guianense, e também um grupo de amostras pertencentes à Simulium spp. Nós também recuperamos um genoma mitocondrial de Onchocerca volvulus da amostra aqui identificada como S. guianense.


Análises taxonômicas do microbioma dos simulídeos revelaram Proteobacteria e Ascomycota como os filos mais abundantes. A análise funcional revelou que a família de enzimas das Transcriptases Reversas são as mais abundantes. Portanto, nós contribuímos com informação genética original preenchendo parte do viés a respeito das espécies de Simulium associadas ao foco brasileiro de oncocercose. (AU)


Assuntos
Animais , Oncocercose , Simuliidae , Onchocerca volvulus , Genoma Mitocondrial , Metagenômica
17.
Braz. j. microbiol ; 49(supl.1): 1-8, 2018. graf
Artigo em Inglês | LILACS | ID: biblio-974334

RESUMO

Abstract In this study, the development and assessment of a modified, efficient, and cost-efficient protocol for mDNA (metagenomic DNA) extraction from contaminated water samples was attempted. The efficiency of the developed protocol was investigated in comparison to a well-established commercial kit (Epicentre, Metagenomic DNA Isolation Kit for Water). The comparison was in terms of degree of shearing, yield, purity, duration, suitability for polymerase chain reaction and next-generation sequencing in addition to the quality of next-generation sequencing data. The DNA yield obtained from the developed protocol was 2.6 folds higher than that of the commercial kit. No significant difference in the alpha (Observed species, Chao1, Simpson and PD whole tree) and beta diversity was found between the DNA samples extracted by the commercial kit and the developed protocol. The number of high-quality sequences of the samples extracted by the developed method was 20% higher than those obtained by the samples processed by the kit. The developed economic protocol successfully yielded high-quality pure mDNA compatible with complex molecular applications. Thus we propose the developed protocol as a gold standard for future metagenomic studies investigating a large number of samples.


Assuntos
Bactérias/isolamento & purificação , DNA Bacteriano/isolamento & purificação , Métodos Analíticos de Preparação de Amostras/métodos , Metagenômica/economia , Metagenômica/métodos , Água Doce/microbiologia , Filogenia , Bactérias/classificação , Bactérias/genética , DNA Bacteriano/genética , Análise de Sequência de DNA , Métodos Analíticos de Preparação de Amostras/economia , Água Doce/química
18.
Braz. j. microbiol ; 48(4): 801-808, Oct.-Dec. 2017. tab, graf
Artigo em Inglês | LILACS | ID: biblio-889172

RESUMO

ABSTRACT The various types of lignocellulosic biomass found in plants comprise the most abundant renewable bioresources on Earth. In this study, the ruminal microbial ecosystem of black goats was explored because of their strong ability to digest lignocellulosic forage. A metagenomic fosmid library containing 115,200 clones was prepared from the black-goat rumen and screened for a novel cellulolytic enzyme. The KG35 gene, containing a novel glycosyl hydrolase family 5 cellulase domain, was isolated and functionally characterized. The novel glycosyl hydrolase family 5 cellulase gene is composed of a 963-bp open reading frame encoding a protein of 320 amino acid residues (35.1 kDa). The deduced amino acid sequence showed the highest sequence identity (58%) for sequences from the glycosyl hydrolase family 5 cellulases. The novel glycosyl hydrolase family 5 cellulase gene was overexpressed in Escherichia coli. Substrate specificity analysis revealed that this recombinant glycosyl hydrolase family 5 cellulase functions as an endo-β-1,4-glucanase. The recombinant KG35 endo-β-1,4-glucanase showed optimal activity within the range of 30-50 °C at a pH of 6-7. The thermostability was retained and the pH was stable in the range of 30-50 °C at a pH of 5-7.


Assuntos
Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Bactérias/enzimologia , Celulase/química , Celulase/genética , Rúmen/microbiologia , Proteínas de Bactérias/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Celulase/metabolismo , Clonagem Molecular , Estabilidade Enzimática , Microbioma Gastrointestinal , Cabras , Concentração de Íons de Hidrogênio , Metagenoma , Metagenômica
19.
Electron. j. biotechnol ; 29: 13-21, sept. 2017. ilus, tab, graf
Artigo em Inglês | LILACS | ID: biblio-1017057

RESUMO

Background: The past years have witnessed a growing number of researches in biofilm forming communities due to their environmental and maritime industrial implications. To gain a better understanding of the early bacterial biofilm community, microfiber nets were used as artificial substrates and incubated for a period of 24 h in Mauritian coastal waters. Next-generation sequencing technologies were employed as a tool for identification of early bacterial communities. Different genes associated with quorum sensing and cell motility were further investigated. Results: Proteobacteria were identified as the predominant bacterial microorganisms in the biofilm within the 24 h incubation, of which members affiliated to Gammaproteobacteria, Alphaproteobacteria and Betaproteobacteria were among the most abundant classes. The biofilm community patterns were also driven by phyla such as Firmicutes, Bacteroidetes, Chloroflexi, Actinobacteria and Verrucomicrobia. The functional analysis based on KEGG classification indicated high activities in carbohydrate, lipid and amino acids metabolism. Different genes encoding for luxI, lasI, agrC, flhA, cheA and cheB showed the involvement of microbial members in quorum sensing and cell motility. Conclusion: This study provides both an insight on the early bacterial biofilm forming community and the genes involved in quorum sensing and bacterial cell motility.


Assuntos
Água do Mar/microbiologia , Bactérias/crescimento & desenvolvimento , Bactérias/genética , Fenômenos Fisiológicos Bacterianos , Bactérias/isolamento & purificação , Bactérias/classificação , Aderência Bacteriana , Movimento Celular , Biofilmes , Biodiversidade , Percepção de Quorum , Incrustação Biológica , Metagenômica , Sequenciamento de Nucleotídeos em Larga Escala , Maurício
20.
GED gastroenterol. endosc. dig ; 36(3): 89-98, Jul.-Set. 2017. ilus, tab
Artigo em Português | LILACS | ID: biblio-876987

RESUMO

Introdução: a constipação é uma doença crônica que afeta a população mundial, podendo ser consequência do desequilíbrio da microbiota intestinal, conhecida como disbiose. Nesse contexto, os probióticos vêm sendo utilizados com o objetivo de promover o seu equilíbrio, a fim de mantê-la saudável (eubiose). Objetivo: avaliar, em um estudo duplo-cego, randomizado, placebo-controlado, se o uso de uma associação de cepas probióticas contendo lactobacillus e bifidobacterium por 28 dias pode modular a microbiota intestinal em pacientes constipados. Método: a atividade da associação de cepas probióticas foi comparada com placebo (maltodextrina) após a suplementação por 28 dias. Os pacientes foram avaliados por meio da análise de metagenômica e da melhora dos sintomas relacionados à constipação. Os dados do perfil da população de microrganismos presentes no intestino dos pacientes foram correlacionados com os resultados da avaliação dos sintomas abdominais e da percepção de bem-estar geral. O aumento do número de evacuações e a melhora do trânsito intestinal foram avaliados durante o estudo. Resultados: as proporções do gênero Bifidobacterium no grupo teste e controle foram 0.45% vs 0.24% no final do estudo, respectivamente (p<0,05). Adicionalmente, a diferença entre os grupos que receberam associação de cepas probióticas contendo lactobacillus e bifidobacterium e placebo permaneceu também significativamente alta com relação às espécies de Lactobacillus (1,21% vs 0,12%) após 28 dias de tratamento (p<0,05). Além disso, os participantes que receberam o probiótico apresentaram uma tendência de melhora sintomática baseada na comparação da sua microbiota e as respostas oriundas da avaliação dos sintomas abdominais e bem-estar geral. Nenhum evento adverso grave foi relatado. Conclusão: a formulação probiótica modulou a microbiota intestinal de forma diferente do placebo nos participantes do estudo. O consumo dos probióticos aumentou significativamente as bactérias benéficas e reduziu as potencialmente maléficas, contribuindo para o equilíbrio da microbiota intestinal.


Introduction: constipation is a chronic disease that affects the world population, being a consequence of the imbalance of the intestinal microbiota, known as dysbiosis. In light of this context, the probiotics have been used to trigger microbiota intestinal balance, in order to keep it healthy (eubiose) Aim: to evaluate in a double-blind, randomized, placebo-controlled study whether the use of association of probiotic strains containing lactobacillus and bifidobacterium for 28 days can modulate the intestinal microbiota of the constipated participants. Methods: the activity of association of probiotic strains was compared to placebo (maltodextrin) after 28 days of consumption. The patients were evaluated by using metagenomics analyses and improved constipation symptoms. The dates of microorganisms population profile into patients gut were correlated with results of abdominal symptoms evaluation and well-being perception. The increase in the number of evacuations and the intestinal transit were evaluated during the study. Results: the proportions of the genus Bifidobacterium in the test groups and the control group were 0.45% vs 0.24% at the end of the study, respectively (p<0.05). Additionally, the difference between the groups that received association of probiotic strains containing lactobacillus and bifidobacterium and the placebo remained higher for species of the genus Lactobacillus (1.21% vs 0.12%) after 28 days of use (p<0.05). Furthermore, the participants who received the probiotic had a tendency to improve symptomatic based on comparisons of their microbiota and the responses provided patients' abdominal symptoms and well-being. There were no reports of serious adverse events during the study. Conclusion: the probiotic formulation modulated the intestinal microbiota differently from the placebo in constipated participants included in this study. The use of this probiotic significantly increased beneficial bacteria and decreased potentially harmful microbes, which contributed to the maintenance of a healthy intestinal microbiota.


Assuntos
Humanos , Masculino , Feminino , Adolescente , Adulto , Pessoa de Meia-Idade , Bifidobacterium , Constipação Intestinal , Probióticos , Probióticos/farmacologia , Microbioma Gastrointestinal , Microbioma Gastrointestinal/efeitos dos fármacos , Lactobacillus , Método Duplo-Cego , Metagenômica
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