Microbiome Analysis

State of the Art and Future Trends

Mitch Fernandez, Vanessa Aguiar-Pulido, Juan Riveros, Wenrui Huang, Jonathan Segal, Erliang Zeng, Michael A Campos, Kalai Mathee, Giri Narasimhan

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The Human Microbiome Project (HMP) focuses on the study of microbial communities that inhabit the healthy human body. Human microbiome studies have revealed that diseases and disorders are strongly correlated with changes in microbial community profiles. Molecular approaches to microbiome studies involve extracting microbial DNA from a sample followed by a process of determining the profile of the microbial community present. Exploiting sequence heterogeneity is clearly a more informative approach than using length heterogeneity. More recent methods involve the use of next-generation sequencing. A large number of open-source analytical tools for metagenomics have emerged in recent years. These include MG-RAST, MOTHUR, QIIME, CloVR, VAMPS, and others. Metagenomic studies require an efficient PCR amplification of the DNA. A study has revealed that the gene content of the bacterial community is more constant than the phylogenetic content. Bacterial communities are intricate collections of bacterial species that each provide functions which contribute to the stability of the community.

Original languageEnglish (US)
Title of host publicationComputational Methods for Next Generation Sequencing Data Analysis
Publisherwiley
Pages401-424
Number of pages24
ISBN (Electronic)9781119272182
ISBN (Print)9781118169483
DOIs
StatePublished - Sep 6 2016

Fingerprint

DNA
Amplification
Genes

Keywords

  • Bacterial communities
  • Human Microbiome Project
  • Microbial communities
  • Open-source analytical tools
  • PCR amplification
  • Sequence heterogeneity

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Fernandez, M., Aguiar-Pulido, V., Riveros, J., Huang, W., Segal, J., Zeng, E., ... Narasimhan, G. (2016). Microbiome Analysis: State of the Art and Future Trends. In Computational Methods for Next Generation Sequencing Data Analysis (pp. 401-424). wiley. https://doi.org/10.1002/9781119272182.ch18

Microbiome Analysis : State of the Art and Future Trends. / Fernandez, Mitch; Aguiar-Pulido, Vanessa; Riveros, Juan; Huang, Wenrui; Segal, Jonathan; Zeng, Erliang; Campos, Michael A; Mathee, Kalai; Narasimhan, Giri.

Computational Methods for Next Generation Sequencing Data Analysis. wiley, 2016. p. 401-424.

Research output: Chapter in Book/Report/Conference proceedingChapter

Fernandez, M, Aguiar-Pulido, V, Riveros, J, Huang, W, Segal, J, Zeng, E, Campos, MA, Mathee, K & Narasimhan, G 2016, Microbiome Analysis: State of the Art and Future Trends. in Computational Methods for Next Generation Sequencing Data Analysis. wiley, pp. 401-424. https://doi.org/10.1002/9781119272182.ch18
Fernandez M, Aguiar-Pulido V, Riveros J, Huang W, Segal J, Zeng E et al. Microbiome Analysis: State of the Art and Future Trends. In Computational Methods for Next Generation Sequencing Data Analysis. wiley. 2016. p. 401-424 https://doi.org/10.1002/9781119272182.ch18
Fernandez, Mitch ; Aguiar-Pulido, Vanessa ; Riveros, Juan ; Huang, Wenrui ; Segal, Jonathan ; Zeng, Erliang ; Campos, Michael A ; Mathee, Kalai ; Narasimhan, Giri. / Microbiome Analysis : State of the Art and Future Trends. Computational Methods for Next Generation Sequencing Data Analysis. wiley, 2016. pp. 401-424
@inbook{caec7be678f5462d88aeb328b0f3c916,
title = "Microbiome Analysis: State of the Art and Future Trends",
abstract = "The Human Microbiome Project (HMP) focuses on the study of microbial communities that inhabit the healthy human body. Human microbiome studies have revealed that diseases and disorders are strongly correlated with changes in microbial community profiles. Molecular approaches to microbiome studies involve extracting microbial DNA from a sample followed by a process of determining the profile of the microbial community present. Exploiting sequence heterogeneity is clearly a more informative approach than using length heterogeneity. More recent methods involve the use of next-generation sequencing. A large number of open-source analytical tools for metagenomics have emerged in recent years. These include MG-RAST, MOTHUR, QIIME, CloVR, VAMPS, and others. Metagenomic studies require an efficient PCR amplification of the DNA. A study has revealed that the gene content of the bacterial community is more constant than the phylogenetic content. Bacterial communities are intricate collections of bacterial species that each provide functions which contribute to the stability of the community.",
keywords = "Bacterial communities, Human Microbiome Project, Microbial communities, Open-source analytical tools, PCR amplification, Sequence heterogeneity",
author = "Mitch Fernandez and Vanessa Aguiar-Pulido and Juan Riveros and Wenrui Huang and Jonathan Segal and Erliang Zeng and Campos, {Michael A} and Kalai Mathee and Giri Narasimhan",
year = "2016",
month = "9",
day = "6",
doi = "10.1002/9781119272182.ch18",
language = "English (US)",
isbn = "9781118169483",
pages = "401--424",
booktitle = "Computational Methods for Next Generation Sequencing Data Analysis",
publisher = "wiley",

}

TY - CHAP

T1 - Microbiome Analysis

T2 - State of the Art and Future Trends

AU - Fernandez, Mitch

AU - Aguiar-Pulido, Vanessa

AU - Riveros, Juan

AU - Huang, Wenrui

AU - Segal, Jonathan

AU - Zeng, Erliang

AU - Campos, Michael A

AU - Mathee, Kalai

AU - Narasimhan, Giri

PY - 2016/9/6

Y1 - 2016/9/6

N2 - The Human Microbiome Project (HMP) focuses on the study of microbial communities that inhabit the healthy human body. Human microbiome studies have revealed that diseases and disorders are strongly correlated with changes in microbial community profiles. Molecular approaches to microbiome studies involve extracting microbial DNA from a sample followed by a process of determining the profile of the microbial community present. Exploiting sequence heterogeneity is clearly a more informative approach than using length heterogeneity. More recent methods involve the use of next-generation sequencing. A large number of open-source analytical tools for metagenomics have emerged in recent years. These include MG-RAST, MOTHUR, QIIME, CloVR, VAMPS, and others. Metagenomic studies require an efficient PCR amplification of the DNA. A study has revealed that the gene content of the bacterial community is more constant than the phylogenetic content. Bacterial communities are intricate collections of bacterial species that each provide functions which contribute to the stability of the community.

AB - The Human Microbiome Project (HMP) focuses on the study of microbial communities that inhabit the healthy human body. Human microbiome studies have revealed that diseases and disorders are strongly correlated with changes in microbial community profiles. Molecular approaches to microbiome studies involve extracting microbial DNA from a sample followed by a process of determining the profile of the microbial community present. Exploiting sequence heterogeneity is clearly a more informative approach than using length heterogeneity. More recent methods involve the use of next-generation sequencing. A large number of open-source analytical tools for metagenomics have emerged in recent years. These include MG-RAST, MOTHUR, QIIME, CloVR, VAMPS, and others. Metagenomic studies require an efficient PCR amplification of the DNA. A study has revealed that the gene content of the bacterial community is more constant than the phylogenetic content. Bacterial communities are intricate collections of bacterial species that each provide functions which contribute to the stability of the community.

KW - Bacterial communities

KW - Human Microbiome Project

KW - Microbial communities

KW - Open-source analytical tools

KW - PCR amplification

KW - Sequence heterogeneity

UR - http://www.scopus.com/inward/record.url?scp=85019552394&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019552394&partnerID=8YFLogxK

U2 - 10.1002/9781119272182.ch18

DO - 10.1002/9781119272182.ch18

M3 - Chapter

SN - 9781118169483

SP - 401

EP - 424

BT - Computational Methods for Next Generation Sequencing Data Analysis

PB - wiley

ER -