scholarly journals Microbial communities in Antarctic lakes: Entirely new perspectives from metagenomics and metaproteomics

2011 ◽  
Vol 32 (4) ◽  
pp. 157 ◽  
Author(s):  
Sheree Yau ◽  
Ricardo Cavicchioli
Keyword(s):  
Dna Sequencing ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Ecosystem Function ◽  
Exponential Growth ◽  
Genetic Material ◽  
Microbial Evolution ◽  
Antarctic Lakes ◽  
Sequencing Technologies ◽  
Level Of Understanding

Driven by advances in DNA sequencing technologies, an astounding amount of data is being generated from genetic material sourced directly from the environment, and this exponential growth of data is set to continue. By surmounting the challenges of working with such vast datasets, a whole new level of understanding is being gained about microbial diversity, microbial evolution and whole ecosystem function. For precious, pristine and logistically difficult to obtain Antarctic samples, metagenomic and metaproteomic approaches are providing the basis for fundamental new discoveries about how Antarctic systems function.

scholarly journals ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 103 ◽  
Author(s):  
Subina Mehta ◽  
Marie Crane ◽  
Emma Leith ◽  
Bérénice Batut ◽  
Saskia Hiltemann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Human Health ◽  
Genetic Material ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Taxonomic Composition ◽  
Sequencing Technologies ◽  
The Galaxy ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

The Human Microbiome Project (HMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) in human health and disease. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). Conversely, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

scholarly journals Linking microbial communities to ecosystem functions: what we can learn from genotype–phenotype mapping in organisms

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190244 ◽  
Author(s):  
Andrew Morris ◽  
Kyle Meyer ◽  
Brendan Bohannan
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Ecosystem Function ◽  
Tropical Soils ◽  
Ecosystem Functions ◽  
Published Data ◽  
Microbial Biodiversity ◽  
Scale Functions ◽  
Oxidation Rates ◽  
Positive Correlations

Microbial physiological processes are intimately involved in nutrient cycling. However, it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. There are many examples of positive correlations between microbial diversity and ecosystem function, but how microbial communities ‘map' onto ecosystem functions remain unresolved. This uncertainty limits our ability to predict and manage crucial microbially mediated processes such as nutrient losses and greenhouse gas emissions. To overcome this challenge, we propose integrating traditional biodiversity–ecosystem function research with ideas from genotype–phenotype mapping in organisms. We identify two insights from genotype–phenotype mapping that could be useful for microbial biodiversity–ecosystem function studies: the concept of searching ‘agnostically' for markers of ecosystem function and controlling for population stratification to identify microorganisms uniquely associated with ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity–ecosystem function relationships by analysing a subset of published data measuring methane oxidation rates from tropical soils. We assert that combining the approaches of traditional biodiversity–ecosystem function research with ideas from genotype–phenotype mapping will generate novel hypotheses about how complex microbial communities drive ecosystem function and help scientists predict and manage changes to ecosystem functions resulting from human activities. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

scholarly journals ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 103
Author(s):  
Subina Mehta ◽  
Marie Crane ◽  
Emma Leith ◽  
Bérénice Batut ◽  
Saskia Hiltemann ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Genetic Material ◽  
Taxonomic Composition ◽  
Training Material ◽  
Sequencing Technologies ◽  
The Galaxy ◽  
Ngs Data Analysis ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the ‘microbiome’) and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community’s RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome.  In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking.  In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.

scholarly journals Microbial diversity-ecosystem function relationships across environmental gradients

2020 ◽  
Vol 6 ◽  
Author(s):  
Anna Heintz-Buschart ◽  
Carlos Guerra ◽  
Ika Djukic ◽  
Simone Cesarz ◽  
Antonis Chatzinotas ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Ecosystem Function ◽  
Environmental Gradients ◽  
Human Life ◽  
Environmental Drivers ◽  
Ecosystem Functions ◽  
Next Generation ◽  
Generation Sequencing

In light of increasing anthropogenic pressures on ecosystems around the globe, the question how biodiversity change of organisms in the critical zone between Earth’s canopies and bedrock relates to ecosystem functions is an urgent issue, as human life relies on these functions. Particularly, soils play vital roles in nutrient cycling, promotion of plant growth, water purification, litter decomposition, and carbon storage, thereby securing food and water resources and stabilizing the climate. Soil functions are carried to a large part by complex communities of microorganisms, such as bacteria, archaea, fungi and protists. The assessment of microbial diversity and the microbiome's functional potential continues to pose significant challenges. Next generation sequencing offers some of the most promising tools to help shedding light on microbial diversity-function relationships. Studies relating microbial diversity and ecosystem functions are rare, particularly those on how this relationship is influenced by environmental gradients. The proposed project focuses on decomposition as one of the most important microbial soil ecosystem functions. The researchers from the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig combine an unparalleled range of expertise from next generation sequencing- based analysis of microbial communities (“meta-omics”) to soil ecology and biodiversity-ecosystem function research. This consortium will make use of soil samples from large international networks to assess microbial diversity both at the taxonomic and functional level and across the domains of life. By linking microbial diversity to functional measurements of decomposition and environmental gradients, the proposed project aims to achieve a comprehensive scale-independent understanding of environmental drivers and anthropogenic effects on the structural and functional diversity of microbial communities and subsequent consequences for ecosystem functioning.

scholarly journals From Genetics to Genomics of Epilepsy

2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Silvio Garofalo ◽  
Marisa Cornacchione ◽  
Alfonso Di Costanzo
Keyword(s):  
Dna Sequencing ◽  
Dna Microarrays ◽  
Molecular Cytogenetics ◽  
Entire Genome ◽  
Sequencing Technologies ◽  
Genomic Approach ◽  
Molecular Karyotype ◽  
High Throughput Dna Sequencing ◽  
Laboratory Technology ◽  
Near Future

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.

Test genetici e consenso informato

2012 ◽  
pp. 68-95
Author(s):  
Marco Seri ◽  
Claudio Graziano ◽  
Daniela Turchetti ◽  
Juri Monducci
Keyword(s):  
Dna Sequencing ◽  
Human Genetics ◽  
Ethical Issues ◽  
Clinical Care ◽  
Genomic Medicine ◽  
Genome Project ◽  
Ethical Challenges ◽  
Sequencing Technologies ◽  
The Human Genome Project

The pace of discovery in the field of human genetics has increased exponentially in the last 30 years. We have witnessed the completion of the Human Genome Project, the identification of hundreds of disease-causing genes, and the dawn of genomic medicine (clinical care based on genomic information). Reduction of DNA sequencing costs, thanks to the so-called "next generation sequencing" technologies, is driving a shift towards the era of "personal genomes", but scientific as well as ethical challenges ahead are countless. We provide an overview on the classification of genetic tests, on informed consent procedures in the context of genetic counseling, and on specific ethical issues raised by the implementation of new DNA sequencing technologies.

STUDY OF MICROBIAL COMMUNITIES IN MEAT PROCESSING ENTERPRISES

2021 ◽  
Author(s):  
Anastasia Arturovna Semenova ◽  
◽  
Yulia Konstantinovna Yushina ◽  
Maria Alexandrovna Grudistova ◽  
Elena Viktorovna Zaiko ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Biofilm Formation ◽  
Pathogenic Microorganisms ◽  
Meat Processing ◽  
Production Environment

The article discusses the results of a study of the microbial diversity of objects in the production environment of two meat processing enterprises, including antibiotic resistance, isolated strains of pathogenic microorganisms and their ability to biofilm formation.

Phylum-Specific Primer Design and Implication in Quantification of the Microbial Community Structure in GuJingGong Pit Mud

2014 ◽  
Vol 1051 ◽  
pp. 311-316 ◽  
Author(s):  
Xi Mei Luo ◽  
Zhi Lei Gao ◽  
Hui Min Zhang ◽  
An Jun Li ◽  
Hong Kui He ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Community Structure ◽  
Real Time Quantitative Pcr ◽  
Sequencing Technologies ◽  
Specific Pcr ◽  
Pit Mud ◽  
Almost All ◽  
Polymerase Chain Reaction Primers

In recent years, despite the significant improvement of sequencing technologies such as the pyrosequencing, rapid evaluation of microbial community structures remains very difficult because of the abundance and complexity of organisms in almost all natural microbial communities. In this paper, a group of phylum-specific primers were elaborately designed based on a single nucleotide discrimination technology to quantify the main microbial community structure from GuJingGong pit mud samples using the real-time quantitative PCR (qPCR). Specific PCR (polymerase chain reaction) primers targeting a particular group would provide promising sensitivity and more in-depth assessment of microbial communities.

scholarly journals A phylogenetic transform enhances analysis of compositional microbiota data

2016 ◽  
Author(s):  
Justin D Silverman ◽  
Alex Washburne ◽  
Sayan Mukherjee ◽  
Lawrence A David
Keyword(s):  
Microbial Communities ◽  
Relative Abundance ◽  
Dominant Role ◽  
Phylogenetic Information ◽  
Abundance Data ◽  
Sequencing Technologies ◽  
Environmental Selection ◽  
Health And Disease ◽  
High Throughput Dna Sequencing ◽  
Spurious Results

ABSTRACTHigh-throughput DNA sequencing technologies have revolutionized the study of microbial communities (microbiota) and have revealed their importance in both human health and disease. However, due to technical limitations, data from microbiota surveys reflect the relative abundance of bacterial taxa and not their absolute levels. It is well known that applying common statistical methods, such as correlation or hypothesis testing, to relative abundance data can lead to spurious results. Here, we introduce the PhILR transform, a data transform that utilizes microbial phylogenetic information. This transform enables off-the-shelf statistical tools to be applied to microbiota surveys free from artifacts usually associated with analysis of relative abundance data. Using environmental and human-associated microbial community datasets as benchmarks, we find that the PhILR transform significantly improves the performance of distance-based and machine learning-based statistics, boosting the accuracy of widely used algorithms on reference benchmarks by 90%. Because the PhILR transform relies on bacterial phylogenies, statistics applied in the PhILR coordinate system are also framed within an evolutionary perspective. Regression on PhILR transformed human microbiota data identified evolutionarily neighboring bacterial clades that may have differentiated to adapt to distinct body sites. Variance statistics showed that the degree of covariation of bacterial clades across human body sites tended to increase with phylogenetic relatedness between clades. These findings support the hypothesis that environmental selection, not competition between bacteria, plays a dominant role in structuring human-associated microbial communities.

scholarly journals Lack of evidence for microbiota in the placental and fetal tissues of rhesus macaques

2020 ◽  
Author(s):  
Kevin R. Theis ◽  
Roberto Romero ◽  
Andrew D. Winters ◽  
Alan H. Jobe ◽  
Nardhy Gomez-Lopez
Keyword(s):  
Dna Sequencing ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Rhesus Macaques ◽  
Uterine Wall ◽  
Bacterial Burden ◽  
Multiple Modes ◽  
Fetal Tissues ◽  
Microbial Invasion ◽  
Cutibacterium Acnes

ABSTRACTThe prevailing paradigm in obstetrics has been the sterile womb hypothesis. However, some are asserting that the placenta, intra-amniotic environment, and fetus harbor microbial communities. The objective of this study was to determine if the fetal and placental tissues of rhesus macaques harbor viable bacterial communities. Fetal, placental, and uterine wall samples were obtained from cesarean deliveries without labor (∼130/166 days gestation). The presence of viable bacteria in the fetal intestine and placenta was investigated through culture. The bacterial burden and profile of the placenta, umbilical cord, and fetal brain, heart, liver, and colon were determined through quantitative real-time PCR and DNA sequencing. These data were compared with those of the uterine wall, as well as to negative and positive technical controls. Bacterial cultures of fetal and placental tissues yielded only a single colony of Cutibacterium acnes. This bacterium was detected at a low relative abundance (0.02%) in the 16S rRNA gene profile of the villous tree sample from which it was cultured, yet it was also identified in 12/29 background technical controls. The bacterial burden and profile of fetal and placental tissues did not exceed or differ from those of background technical controls. In contrast, the bacterial burden and profiles of positive controls exceeded and differed from those of background controls. Among the macaque samples, distinct microbial signals were limited to the uterine wall. Therefore, using multiple modes of microbiologic inquiry, there was not consistent evidence of viable bacterial communities in the fetal and placental tissues of rhesus macaques.IMPORTANCEMicrobial invasion of the amniotic cavity (i.e. intra-amniotic infection) has been causally linked to pregnancy complications, especially preterm birth. Therefore, if the placenta and the fetus are typically populated by low biomass yet viable microbial communities, current understanding of the role of microbes in reproduction and pregnancy outcomes will need to be fundamentally reconsidered. Could these communities be of benefit by competitively excluding potential pathogens or priming the fetal immune system for the microbial bombardment it will experience upon delivery? If so, what properties (e.g. microbial load, community membership) of these microbial communities preclude versus promote intra-amniotic infection? Given the ramifications of the in utero colonization hypothesis, critical evaluation is required. In this study, using multiple modes of microbiologic inquiry (i.e. culture, qPCR, DNA sequencing) and controlling for potential background DNA contamination, we did not find consistent evidence for microbial communities in the placenta and fetal tissues of rhesus macaques.

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