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1.
Braz. j. biol ; 82: e240184, 2022. tab, graf
Article in English | MEDLINE, LILACS, VETINDEX | ID: biblio-1278492

ABSTRACT

Abstract 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.


Resumo 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 pós-colheita). 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.


Subject(s)
Lepidium/genetics , Peru , Soil , Soil Microbiology , Bacteria/genetics , RNA, Ribosomal, 16S/genetics , Grassland , Metagenomics
2.
Electron. j. biotechnol ; 50: 29-36, Mar. 2021. tab, graf
Article in English | LILACS | ID: biblio-1292313

ABSTRACT

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.


Subject(s)
Animals , Rats , Cecum/enzymology , Enzymes/metabolism , Lignin/metabolism , Cecum/microbiology , Cellulose/metabolism , Bacteroidetes , Biofuels , Metagenomics , Firmicutes , Gastrointestinal Microbiome
4.
Article in English | WPRIM | ID: wpr-887762

ABSTRACT

OBJECTIVES@#This study aimed to compare and analyze the consistency and difference between metageno-mic next-generation sequencing (mNGS) and conventional bacterial culture in the detection of pathogenic microorganisms in maxillofacial space infection, as well as to provide a new detection method for the early clinical identification of pathogenic bacteria in maxillofacial space infection.@*METHODS@#The clinical data of 16 patients with oral and maxillofacial space infections in the First Affiliated Hospital of Zhengzhou University from March 2020 to June 2020 were collected. mNGS and conventional bacterial culture methods were used to detect pus. We then analyzed and compared the test results of the two methods, including the test cycle, positive detection rate, anaerobic bacteria, facultative anaerobes and aerobic bacteria detection rates, distribution of pathogenic bacteria, relative species abundance, and resistance genes.@*RESULTS@#The average inspection period of mNGS was (18.81±3.73) h, and the average inspection period of bacterial culture was (83.25±11.64) h, the former was shorter than the latter (@*CONCLUSIONS@#Compared with conventional bacterial culture, mNGS has the characteristics of short test time, high sensitivity, and high accuracy. Thus, it is a new detection method for the early identification of pathogenic bacteria in maxillofacial space infection and is beneficial to the early clinical diagnosis and treatment of the disease.


Subject(s)
Bacteria/genetics , High-Throughput Nucleotide Sequencing , Humans , Metagenomics , Sensitivity and Specificity , Technology
5.
Chinese Journal of Biotechnology ; (12): 3276-3292, 2021.
Article in Chinese | WPRIM | ID: wpr-921424

ABSTRACT

Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.


Subject(s)
Carbon , Ecosystem , Metagenomics , Nitrogen , Soil Microbiology , Wetlands
6.
Arch. argent. pediatr ; 118(3): e265-e270, jun. 2020. ilus
Article in English, Spanish | LILACS, BINACIS | ID: biblio-1116917

ABSTRACT

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


Subject(s)
Humans , Male , Female , Infant, Newborn , Microbiota , Bacteria , Breast Feeding , Parturition , Metagenomics , Gastrointestinal Microbiome , Infant Health
7.
Electron. j. biotechnol ; 45: 30-37, May 15, 2020. ilus, graf
Article in Spanish | LILACS | ID: biblio-1177412

ABSTRACT

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.


Subject(s)
Soil Microbiology , Bacteria/classification , High-Throughput Nucleotide Sequencing , Microbiota/genetics , Bacteria/isolation & purification , Cold Climate , Computational Biology , Ice Cover , Metagenomics , Genome, Microbial , India
8.
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
9.
Chinese Journal of Biotechnology ; (12): 2610-2621, 2020.
Article in Chinese | WPRIM | ID: wpr-878515

ABSTRACT

Strain is the fundamental unit in microbial taxonomy. The functional diversity among strains has great influence on host phenotypes. With the development of microbiome research, knowing the composition and functional capacities of complex microbial communities at the strain level has become increasingly valuable in scientific research and clinical applications. This review introduces the principles of bioinformatics algorithms for strain analysis based on metagenomic data, the applications in microbiome research and directions of future development.


Subject(s)
Algorithms , Computational Biology , Metagenome , Metagenomics , Microbiota/genetics
10.
Chinese Journal of Biotechnology ; (12): 2598-2609, 2020.
Article in Chinese | WPRIM | ID: wpr-878514

ABSTRACT

Metagenomic next-generation sequencing (mNGS) could be used for pathogen detection from nearly all types of clinical samples. Especially, the unique diagnostic capability of pathogen mNGS detecting unknown causative agent of infectious diseases makes this method become an importation complement and irreplaceable component for conventional routine laboratory test. However, the complexity of the testing process, the rapid product update, and the insufficiency in quality control and evaluation methods that all make clinical transformation, industry development, and regulation of this technology full of challenge and uncertainty. This review briefly introduces the technical advantages and challenges, and describes the general workflow and quality control steps in details. Finally, it focuses on current considerations regarding quality evaluation methods and standards for pathogen mNGS.


Subject(s)
Communicable Diseases , High-Throughput Nucleotide Sequencing , Humans , Metagenome , Metagenomics , Quality Control
11.
Chinese Journal of Biotechnology ; (12): 2566-2581, 2020.
Article in Chinese | WPRIM | ID: wpr-878512

ABSTRACT

Virome is the collective term for the viral collection or viral metagenomes that are distributed in various environments. Viruses can be found in bodies of water, glaciers, plants, animals, and even some viruses, which are classified as eukaryotes, prokaryotes and subviruses. Viruses play very important role in maintaining environmental homeostasis and ecosystem balance, and are especially closely related to human health. In recent years, with the advancement of sequencing technology and data analysis, we are able to gain more insights into the virome and explore its potential role in the ecological niche by metagenomic sequencing. A large amount of viral data have been obtained from glaciers, oceans, and various plants and animals, and numerous unknown viruses have been discovered. Virome has been studied mainly through metagenomic data mining, as well as virus-like particles separation and enrichment. To date, several different methods for viral isolation and enrichment exist, and numerous bioinformatic analyses of the virome have been performed. However, there is a lack of specific and complete reviews on the enrichment and data analysis methods for the virome. Thus, our review will summarize viral isolation and enrichment methods and data analysis, and present some of the landmark research conducted by the enrichment method, to provide a reference for researchers of interest and further advance the field of virome research.


Subject(s)
Animals , Humans , Metagenome , Metagenomics , Microbiota/genetics , Virome , Viruses/genetics
12.
Chinese Journal of Biotechnology ; (12): 2541-2547, 2020.
Article in Chinese | WPRIM | ID: wpr-878509

ABSTRACT

Metagenomic sequencing provides a powerful tool for microbial research. However, traditional experimental DNA extraction process will inevitably mix with environmental microorganisms which float in the air. It is still unclear whether the mixed environmental microbial DNA will heavily affect the metagenomic results of samples with extremely low microbial content. In this study, we first collected environmental bacteria in the laboratory and quantified the mixed environmental microbial DNA content during DNA extraction based on a qPCR-based quantification assay. We then extracted DNA from pure water in order to determine the mixed microbial taxons during extraction under open environment. At last, we extracted total DNA from a skin sample in a Biosafety cabinet or under open laboratory environment, to assess the impact of the mixed environmental microorganisms on the metagenomic results. Our results showed that DNA extraction under open laboratory environment in Beijing region resulted in 28.9 pg contaminant, which may accout for 30% of total DNA amount from skin samples. Metagenomic analysis revealed that the main incorporated environmental taxons were Cutibacterium acnes and Escherichia coli. Tens of environmental bacteria were foisted in the skin DNA samples, which largely decreased the relative abundance of dominant species and thus deteriorated the result accuracy. Therefore, analyzing microbial composition of samples with extremely low DNA content should better performed under aseptic environment.


Subject(s)
DNA , DNA, Bacterial/genetics , Laboratories , Metagenomics , RNA, Ribosomal, 16S , Sequence Analysis, DNA
13.
Electron. j. biotechnol ; 41: 72-80, sept. 2019. ilus, tab, graf
Article in English | LILACS | ID: biblio-1087172

ABSTRACT

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.


Subject(s)
Soil Microbiology , Bacteria/isolation & purification , Bacteria/genetics , Electronic Waste/analysis , Soil Pollutants , Polymerase Chain Reaction , Metals, Heavy , Proteobacteria/isolation & purification , Metagenomics , Denaturing Gradient Gel Electrophoresis , Microbiota , Firmicutes/isolation & purification , India
14.
Article in English | WPRIM | ID: wpr-764413

ABSTRACT

The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.


Subject(s)
Bacteria , Colon , Dental Caries , Diagnosis , DNA Fingerprinting , Generalization, Psychological , Genes, Microbial , Genome, Microbial , Genomics , Human Body , Metabolism , Metabolomics , Metagenome , Metagenomics , Methods , Microbiota , Mouth
15.
Article in English | WPRIM | ID: wpr-764311

ABSTRACT

BACKGROUND: Gut microbiota is closely associated with development and exacerbation of inflammatory bowel diseases (IBD). The aim of this study was to investigate differences in gut microbiota depending on sex and changes of gut microbiota during IBD developments. METHODS: 16s rRNA metagenomic sequencing was performed for fecal materials from 8-week-old wild type (WT) and interleukin 10 (IL-10) knockout (KO) C57BL/6 mice of both sexes. Diversity indices, relative abundance of microbiota, and linear discriminant analysis effect size were examined to compare microbial communities between groups. Clustering of groups was performed by principal coordinates analysis (PCoA) and unweighted pair group method with arithmetic mean (UPGMA). Functional capabilities of microbiota were estimated using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) based on Kyoto Encyclopedia of Genes and Genomes database. RESULTS: PCoA and UPGMA tree analysis of beta-diversity demonstrated significant differences in gut microbiota between male and female groups of WT mice, but not of IL-10 KO mice. Firmicutes to Bacteroides ratio was higher in male group than that in female group in both WT mice and IL-10 KO mice. Phylum Proteobacteria significantly increased in female IL-10 KO mice than that in female WT mice. At species level, Lactobacillus murinus, Bacteroides acidifaciens, and Helicobacter hepaticus significantly increased in IL-10 KO mice than in WT mice. The relative abundance of beta-glucuronidase (K01195) was higher in female IL-10 KO mice than that in female WT mice by PICRUSt. CONCLUSIONS: Our results suggest that microbiota-host interactions might differ between sexes during development of IBD.


Subject(s)
Animals , Bacteroides , Female , Firmicutes , Gastrointestinal Microbiome , Genome , Glucuronidase , Helicobacter hepaticus , Humans , Inflammatory Bowel Diseases , Interleukin-10 , Lactobacillus , Male , Metagenomics , Methods , Mice , Microbiota , Proteobacteria , Sequence Analysis , Sex Characteristics , Trees
16.
Article in English | WPRIM | ID: wpr-763797

ABSTRACT

Understanding the role of the microbiome in human health and how it can be modulated is becoming increasingly relevant for preventive medicine and for the medical management of chronic diseases. The development of high-throughput sequencing technologies has boosted microbiome research through the study of microbial genomes and allowing a more precise quantification of microbiome abundances and function. Microbiome data analysis is challenging because it involves high-dimensional structured multivariate sparse data and because of its compositional nature. In this review we outline some of the procedures that are most commonly used for microbiome analysis and that are implemented in R packages. We place particular emphasis on the compositional structure of microbiome data. We describe the principles of compositional data analysis and distinguish between standard methods and those that fit into compositional data analysis.


Subject(s)
Biomarkers , Chronic Disease , Genome, Microbial , Humans , Metagenome , Metagenomics , Microbiota , Models, Statistical , Preventive Medicine , Sequence Analysis, DNA , Statistics as Topic
17.
Article in English | WPRIM | ID: wpr-772954

ABSTRACT

Identifying antimicrobial resistant (AMR) bacteria in metagenomics samples is essential for public health and food safety. Next-generation sequencing (NGS) technology has provided a powerful tool in identifying the genetic variation and constructing the correlations between genotype and phenotype in humans and other species. However, for complex bacterial samples, there lacks a powerful bioinformatic tool to identify genetic polymorphisms or copy number variations (CNVs) for given genes. Here we provide a Bayesian framework for genotype estimation for mixtures of multiple bacteria, named as Genetic Polymorphisms Assignments (GPA). Simulation results showed that GPA has reduced the false discovery rate (FDR) and mean absolute error (MAE) in CNV and single nucleotide variant (SNV) identification. This framework was validated by whole-genome sequencing and Pool-seq data from Klebsiella pneumoniae with multiple bacteria mixture models, and showed the high accuracy in the allele fraction detections of CNVs and SNVs in AMR genes between two populations. The quantitative study on the changes of AMR genes fraction between two samples showed a good consistency with the AMR pattern observed in the individual strains. Also, the framework together with the genome annotation and population comparison tools has been integrated into an application, which could provide a complete solution for AMR gene identification and quantification in unculturable clinical samples. The GPA package is available at https://github.com/IID-DTH/GPA-package.


Subject(s)
Bacteria , Genetics , Bayes Theorem , DNA Copy Number Variations , Genome, Bacterial , Genotyping Techniques , High-Throughput Nucleotide Sequencing , Humans , Klebsiella pneumoniae , Genetics , Metagenomics , Methods , Polymorphism, Genetic , Software
18.
Article in English | WPRIM | ID: wpr-772950

ABSTRACT

Despite the documented antibiotic-induced disruption of the gut microbiota, the impact of antibiotic intake on strain-level dynamics, evolution of resistance genes, and factors influencing resistance dissemination potential remains poorly understood. To address this gap we analyzed public metagenomic datasets from 24 antibiotic treated subjects and controls, combined with an in-depth prospective functional study with two subjects investigating the bacterial community dynamics based on cultivation-dependent and independent methods. We observed that short-term antibiotic treatment shifted and diversified the resistome composition, increased the average copy number of antibiotic resistance genes, and altered the dominant strain genotypes in an individual-specific manner. More than 30% of the resistance genes underwent strong differentiation at the single nucleotide level during antibiotic treatment. We found that the increased potential for horizontal gene transfer, due to antibiotic administration, was ∼3-fold stronger in the differentiated resistance genes than the non-differentiated ones. This study highlights how antibiotic treatment has individualized impacts on the resistome and strain level composition, and drives the adaptive evolution of the gut microbiota.


Subject(s)
Adult , Anti-Bacterial Agents , Pharmacology , Bacteria , Genetics , Drug Resistance, Bacterial , Genetics , Female , Gastrointestinal Microbiome , Humans , Metagenomics , Prospective Studies
19.
Braz. j. microbiol ; 49(4): 723-730, Oct.-Dec. 2018. graf
Article in English | LILACS | ID: biblio-974310

ABSTRACT

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.


Subject(s)
Soil/chemistry , Fungal Proteins/genetics , Archaea/enzymology , Archaeal Proteins/genetics , Fungi/enzymology , Hydrolases/genetics , Soil Microbiology , Soybeans/growth & development , Triticum/growth & development , Brazil , Archaea/isolation & purification , Archaea/classification , Archaea/genetics , Zea mays/growth & development , Agriculture , Metagenome , Metagenomics , Fungi/isolation & purification , Fungi/classification , Fungi/genetics
20.
NOVA publ. cient ; 16(29): 91-100, ene.-jun. 2018. graf
Article in Spanish | LILACS, COLNAL | ID: biblio-976281

ABSTRACT

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.


Subject(s)
Humans , Drug Resistance, Microbial , Metagenomics , Genes , Anti-Bacterial Agents
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