High throughput sequencing methods and analysis for microbiome research

Bella, Julia M. Di; Bao, Yige; Gloor, Gregory B.; Burton, Jeremy P.; Reid, Gregor

doi:10.1016/j.mimet.2013.08.011

Cited by 240 publications

(190 citation statements)

References 194 publications

(162 reference statements)

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“…They are anked by conserved sequences that enable PCR ampli cation of targeted sequences (amplicons) using universal or speci cally designed primers. However, depending on the chosen variable regions and primers, the resulting OTUs clusters and estimations of diversity may not be the same (see for example [21], [22]). Moreover, amplicon sequencing excludes unknown species or highly diverged microbes from the analysis.…”

Section: Choice Of Datamentioning

confidence: 99%

Machine learning for metagenomics: methods and tools

Soueidan¹,

Nikolski²

2017

Metagenomics

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Owing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis. We review here the contribution of machine learning techniques for the eld of metagenomics, by presenting known successful approaches in a uni ed framework. This review focuses on ve important metagenomic problems: OTU-clustering, binning, taxonomic pro ing and assignment, comparative metagenomics and gene prediction. For each of these problems, we identify the most prominent methods, summarize the machine learning approaches used and put them into perspective of similar methods. We conclude our review looking further ahead at the challenge posed by the analysis of interactions within microbial communities and di erent environments, in a eld one could call "integrative metagenomics".

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Section: Choice Of Datamentioning

confidence: 99%

Machine learning for metagenomics: methods and tools

Soueidan¹,

Nikolski²

2017

Metagenomics

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“…previously thought, suggesting the existence of a "gut-brain axis" whereby the gut microbiome modulates the CNS and/or vice versa (11)(12)(13)(14). Still, these differences are only correlative, and to date causative mechanistic relationships between alterations in the microbiome, also known a microbial dysbiosis, and human pathology have yet to be discovered.…”

mentioning

confidence: 99%

Gut microbiome and chronic prostatitis/chronic pelvic pain syndrome

Arora¹,

Eng²,

Shoskes³

2017

Ann. Transl. Med.

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“…With the advent of the faster, higher-throughput, and cheaper NGS technologies, metagenomic shotgun sequencing has become very handy and routinely produces large metagenomic datasets (Simon and Daniel 2009, Hentschel, Piel et al 2012, Di Bella, Bao et al 2013, Ferreira, Siam et al 2014, Sharpton 2014. In the shotgun sequencing approach, already applied earlier to cultured microbes and human genomes, metagenomic DNA is randomly sheared and sequenced in short reads.…”

Section: Shotgun Metagenomicsmentioning

confidence: 99%