Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Logares, Ramiro; Haverkamp, Thomas; Kumar, Surendra; Lanzén, Anders; Nederbragt, Alexander J.; Quince, Christopher; Kauserud, Håvard

doi:10.1016/j.mimet.2012.07.017

Cited by 115 publications

(79 citation statements)

References 75 publications

(80 reference statements)

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“…to have units that can be used in downstream analyses (Logares et al 2012). Based on correlations and anti-correlations of the OTUs, it is possible to build association networks (Box 3), which can be used to generate hypotheses about which organisms may be interacting, both positively or negatively (Faust & Raes 2012).…”

Section: Understanding Oceanic Microbial Eco-systems As Interaction Nmentioning

confidence: 99%

“…This revolution has generated a wealth of new knowledge, and during the last 8 yr, it has gained renewed momentum with the advent of highthroughput sequencing platforms (Logares et al 2012, Goodwin et al 2016) and a variety of other high-performance approaches such as genomics, transcriptomics, me tagenomics, metatranscriptomics, proteomics and single-cell genomics (metanomics for short). High-throughput sequencing has been a key addition to the molecular toolbox of microbial ecologists, allowing a deeper exploration of microbial diversity, dis tributions and metabolic functions.…”

mentioning

confidence: 99%

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Exploring the oceanic microeukaryotic interactome with metaomics approaches

Krabberød¹,

Bjorbækmo²,

Shalchian-Tabrizi³

et al. 2017

Aquat. Microb. Ecol.

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THE MICROBIAL OCEANOur collective awareness of the significance of marine ecosystems has increased steadily during the last 40 yr, progressing in concert with the development of new technologies that have allowed us to dig deeper into the microbial world. A number of key events can be identified from this period, for example the formulation of the microbial-loop concept, the discovery of abundant photoautotrophic (Synechococcus and Prochlorococcus) and heterotrophic (SAR11) pico-sized prokaryotic plankton as well as novel lineages of heterotrophic picoeukaryotes (e.g. MALV and MAST), the recognition of the importance of Archaea in oceanic plankton, the realization that the majority of marine microbes cannot be cultured, the discovery of the rare biosphere and the key role of viruses in oceanic communities (Kirchman 2008 ABSTRACT: Biological communities are systems composed of many interacting parts (species, populations or single cells) that in combination constitute the functional basis of the biosphere. Animal and plant ecologists have advanced substantially our understanding of ecological interactions. In contrast, our knowledge of ecological interaction in microbes is still rudimentary. This represents a major knowledge gap, as microbes are key players in almost all ecosystems, particularly in the oceans. Several studies still pool together widely different marine microbes into broad functional categories (e.g. grazers) and therefore overlook fine-grained species/population-specific interactions. Increasing our understanding of ecological interactions is particularly needed for oceanic microeukaryotes, which include a large diversity of poorly understood symbiotic relationships that range from mutualistic to parasitic. The reason for the current state of affairs is that determining ecological interactions between microbes has proven to be highly challenging. However, recent technological developments in genomics and transcriptomics (metaomics for short), coupled with microfluidics and high-performance computing are making it increasingly feasible to determine ecological interactions at the microscale. Here, we present our views on how this field will advance thanks to the progress in metaomics approaches as well as potential avenues for future research.

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Section: Understanding Oceanic Microbial Eco-systems As Interaction Nmentioning

confidence: 99%

mentioning

confidence: 99%

Exploring the oceanic microeukaryotic interactome with metaomics approaches

Krabberød¹,

Bjorbækmo²,

Shalchian-Tabrizi³

et al. 2017

Aquat. Microb. Ecol.

View full text Add to dashboard Cite

show abstract

“…Another important aspect in the NGS is the processing of the crude data from the sample DNA runs that has to be translated into important information. One would require higher computational resources, more complex bioinformatic analysis and large data storage for processing NGS datasets, which means we not only require high end servers but also LINUX operative system skills [43]. Although, programming and scripting knowledge are desirable to run and install the available metagenomics software for processing the raw data and interpreting the results.…”

Section: Technological Advancements In the New Era Of "Omics"mentioning

confidence: 99%

Decoding Complex Soil Microbial Communities through New Age "Omics"

Nair¹,

Raja²

2017

J Microb Biochem Technol

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“…H igh-throughput amplicon-based sequencing of microbial DNA from different environments is proving to be an exceptional tool for understanding microbial ecology of various natural systems (Logares et al, 2012;Zhou et al, 2015). Amplicon-based sequencing strategies of the 16S rRNA and functional genes, alongside metagenomic analyses of microbial communities, have allowed researchers to pose questions and find answers to "who" is present in a specific environment and "what" they are doing.…”

mentioning

confidence: 99%

A priori Considerations When Conducting High‐Throughput Amplicon‐Based Sequence Analysis

Sengupta

Dick

2016

Agricultural & Env Letters

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Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside "meta-omics" analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to "who" is present in the environment and "what" they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

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Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

Cited by 115 publications

References 75 publications

Exploring the oceanic microeukaryotic interactome with metaomics approaches

Exploring the oceanic microeukaryotic interactome with metaomics approaches

Decoding Complex Soil Microbial Communities through New Age "Omics"

A priori Considerations When Conducting High‐Throughput Amplicon‐Based Sequence Analysis

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