Oral Microbiome Analysis

The human oral cavity contains a plethora of bacteria which include bacteria, fungi, viruses and protozoa. In addition to being the initiation point of digestion, the oral microbiome plays an intimate and essential role in the microbial community and human health. Interaction of variable oral microorganisms contributes to human body protection against invasion of undesirable stimulation outside. However, imbalance of microbial flora is also closely related to the different systemic diseases include cardiovascular disease, diabetes, obesity, and cancer. Consequently, oral microbiota might be a new target to make effect on human health improvement.

The emergence of new genomic technologies including next-generation sequencing and bioinformatics has uncovered the complexity of its bacterial component and dramatically expanded our knowledge of the composition and function of the oral microbiome in health and disease. Understanding the oral microbiome in health and disease will give further directions to explore the functional and metabolic alterations associated with the diseased states and to identify molecular signatures for drug development and targeted therapies which will ultimately help in rendering personalized and precision medicine.

Oral-Microbiome-Analysis

Respiratory tract Microbiota Analysis

Like human oral cavity, the upper respiratory tract is also a complex organ system which colonized by a variety of different microbial species. Understanding the respiratory microbiome in health and disease will give further directions to explore the medical diagnostics and as a target for therapy. Modern molecular techniques have contributed to revealing the complexity of the respiratory tract microbiome.  

Technical Platforms

With our next-generation sequencing (NGS) technology, PacBio SMRT sequencing, and Nanopore sequencing platforms, we have the tool to identify, quantify and analysis the oral microbiome. With this high-throughput technology we can perform complete metagenomics studies capable of surveying the genomes of entire communities, including those of unculturable organisms.

Illumina Hiseq Illumina Miseq Ion PGM PacBio SMRT system
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Nanopore system PCR-DGGE Real-time qPCR Clone library
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What Can Creative Biogene Do?

Creative Biogene offers extensive microbiome analysis portfolio includes not only consultancy, study design, sampling solutions and sequencing, but also downstream bioinformatic and biostatistical analyses. 

Project Workflow

High-throughput sequencing analysis process

Fig.1 High-throughput sequencing analysis process

High-throughput sequencing analysis process

Fig.2 PCR-DGGE analysis process

Service Specifications

Sample requirements and preparation

• Sample: Genomic DNA
• Quality requirements: ≥ 300 ng, ≥ 10 ng/μL, OD260/280=1.8-2.0, non-degradative
• Shipment: Dry ice or ice packs
• Repeated freeze-thaw cycles should be avoided

Detectable Microorganisms

• Bacteria
• Fungi
• Viruses

Basic analysis

• Sequence Filtering and Trimming
• Sequence Length Distribution
• OTU Clustering and Species Annotation
• Diversity Index
• Shannon-Wiener Curve
• Rank-Abundance Curve
• Rarefraction Curve
• Multiple Contrast
• Heatmap
• Principal Components Analysis (PCA)

Routine analysis

• Heatmap
• VENN
• Principal Components Analysis (PCA)
• Microbial Community Structure Analysis
• α Diversity Index Analysis
• Matastats Analysis
• Weighted Unifrac test
• CCA/RDA Analysis

Advanced data analysis

• Phylogenetic Tree
• LDA-Effect Size (LEfSe)
• Network Analysis
• Correlation Analysis

References
1. Willis, J.R.; Gabaldón, T. The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems. Microorganisms 2020, 8, 308.
2. Deo PN, Deshmukh R. Oral microbiome: Unveiling the fundamentals. J Oral Maxillofac Pathol. 2019 Jan-Apr;23(1):122-128.

For research use only.

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