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

A relatively easy means of identifying a certain amount of bacteria and their species (including uncultivable pathogens) for clinical microbiology applications.

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.

Raw sequences data

The paired-end 150bp raw sequence files of 12 samples obtained by Illumina sequencing machine.

R1_gut.fq.gz R2_gut.fq.gz

Integrative Systems Biology Lab ( ISBLab ) aims to integrate interdisciplinary approaches for provide the insights into important biological problems and the industrial value of clinical applications. We also enable the development of new biological resources with broad applications, especially in microRNAs, protein modifications and gene regulation. Recently, high-throughput sequencing and microarray technology become our major focus both in scientific research and clinical applications.

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