Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing

Chih Min Chiu, Feng Mao Lin, Tzu Hao Chang, Wei Chih Huang, Chao Liang, Ting Yang, Wei Yun Wu, Tzu Ling Yang, Shun Long Weng, Hsien Da Huang

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Background: The human body plays host to a vast array of bacteria, found in oral cavities, skin, gastrointestinal tract and the vagina. Some bacteria are harmful while others are beneficial to the host. Despite the availability of many methods to identify bacteria, most of them are only applicable to specific and cultivable bacteria and are also tedious. Based on high throughput sequencing technology, this work derives 16S rRNA sequences of bacteria and analyzes probiotics and pathogens species.Results: We constructed a database that recorded the species of probiotics and pathogens from literature, along with a modified Smith-Waterman algorithm for assigning the taxonomy of the sequenced 16S rRNA sequences. We also constructed a bacteria disease risk model for seven diseases based on 98 samples. Applicability of the proposed platform is demonstrated by collecting the microbiome in human gut of 13 samples.Conclusions: The proposed platform provides a relatively easy means of identifying a certain amount of bacteria and their species (including uncultivable pathogens) for clinical microbiology applications. That is, detecting how probiotics and pathogens inhabit humans and how affect their health can significantly contribute to develop a diagnosis and treatment method.

Original languageEnglish
Article number1
JournalJournal of Clinical Bioinformatics
Volume4
Issue number1
DOIs
Publication statusPublished - Jan 13 2014

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Probiotics
Bacteria
Microbiota
Vagina
Microbiology
Human Body
Sequence Analysis
Mouth
Gastrointestinal Tract
Databases
Technology
Skin
Health

ASJC Scopus subject areas

  • Health Informatics

Cite this

Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. / Chiu, Chih Min; Lin, Feng Mao; Chang, Tzu Hao; Huang, Wei Chih; Liang, Chao; Yang, Ting; Wu, Wei Yun; Yang, Tzu Ling; Weng, Shun Long; Huang, Hsien Da.

In: Journal of Clinical Bioinformatics, Vol. 4, No. 1, 1, 13.01.2014.

Research output: Contribution to journalArticle

Chiu, Chih Min ; Lin, Feng Mao ; Chang, Tzu Hao ; Huang, Wei Chih ; Liang, Chao ; Yang, Ting ; Wu, Wei Yun ; Yang, Tzu Ling ; Weng, Shun Long ; Huang, Hsien Da. / Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing. In: Journal of Clinical Bioinformatics. 2014 ; Vol. 4, No. 1.
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AU - Yang, Ting

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