Microbiome depiction through user-adapted bioinformatic pipelines and parameters-Reference-Cited by-同舟云学术

Microbiome depiction through user-adapted bioinformatic pipelines and parameters

Published:2023-10-12 Issue:10 Volume:72 Page:
ISSN:0022-2615
Container-title:Journal of Medical Microbiology
language:en
Short-container-title:

Author:

Nayman Eric I.¹²^ORCID,Schwartz Brooke A.¹²,Polanco Fantaysia C.¹,Firek Alexandra K.³,Gumabong Alayna C.²,Hofstee Nolan J.²,Narasimhan Giri⁴¹^ORCID,Cickovski Trevor¹^ORCID,Mathee Kalai⁴²^ORCID

Affiliation:

1. Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, Miami, FL, USA

2. Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA

3. Translational Glycobiology Institute, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA

4. Biomolecular Sciences Institute, Florida International University, Miami, FL, USA

Abstract

Graphical Abstract Determining microbiome composition is a multi-step process. The 16S rRNA gene is amplified from the extracted DNA, sequenced, and then metagenomic data are input into a bioinformatic workflow. This paper describes how choices of bioinformatic pipelines, databases, and parameter values, such as maxEE and QTrim, can impact microbial compositional output.

Publisher

Microbiology Society

Subject

Microbiology (medical),General Medicine,Microbiology

Link

https://www.microbiologyresearch.org/content/journal/jmm/10.1099/jmm.0.001756?crawler=true&mimetype=application/pdf

Reference138 articles.

1. Correction to: Microbiome definition re-visited: old concepts and new challenges

2. Gut microbiota functions: metabolism of nutrients and other food components

3. The Human Microbiome and Its Impacts on Health

4. Dysbiosis and Its Discontents

5. The Human Gut Microbiome and Body Metabolism: Implications for Obesity and Diabetes

Cited by 1 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus;Scientific Reports;2024-02-26