Diversity Analysis of Actinomycetes

Overview

Actinomyces is a genus of the Actinobacteria class of bacteria. Actinomyces has been reported as an agent of actinomycosis-like infections and are associated with specific clinical syndromes. The 16S rRNA gene is a generally accepted molecular marker for bacteria, and is commonly used for bacterial identification and diversity analysis. We have developed validated primers that specifically amplify 16S rRNA gene in actinomycetes (such as bifidobacterium) and the optimized sequence assembly process, to improve the detection rate and accuracy of actinomycetes.

Our Advantages:

Closely work with you to determine the best experimental design and analysis pipeline
The optimized and validated primers that specifically amplify 16S rRNA gene in actinomycetes
An experienced expert team and flexible, comprehensive approaches
Next-generation sequencing (NGS) and long-read sequencing platforms
Cost-efficiency, and fast turnaround time

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Introduction to Diversity Analysis of Actinomycetes

We provide comprehensive diversity analysis of actinomycetes using molecular methods including 16S ribosomal RNA (rRNA) gene sequencing and amplified 16S ribosomal DNA restriction analysis (ARDRA). 16S rRNA sequencing generally involves the selective PCR amplification using appropriate primers that target the16S rRNA gene, followed by next/third generation sequencing. ARDRA is a reliable identification method based on restriction endonuclease (such as AluI, HaeIII, MspI, etc.) digestion of the amplified bacterial 16S rDNA. Our service can help with strain assignment and new species discovery.

Since actinomycetes have been considered as the richest source of secondary metabolites such as antibiotics, diversity analysis of actinomycetes aims to investigate the diversity of antibiotic-producing actinomycetes and accelerate the development of a novel antibiotic drugs. Diversity analysis of actinomycetes can also confirm the diagnosis of actinomycosis. The importance of this analysis has been demonstrated in areas such as drug discovery and development, agricultural production, petroleum exploration, and industrial manufacturing, etc.

Actinomyces diversity analysis workflow

Bioinformatics Analysis

Our bioinformatics analysis includes six parts: raw data processing, taxonomic assignment, diversity and richness analysis, comparative analysis, evolutionary analysis, and custom analysis. We are flexible to your needs.

Pipeline	Analysis Content
Raw data processing	Filtering and trimming of poor-quality sequences
Taxonomic assignment	Operation Taxonomic unit (OTU) clustering
Diversity and richness analysis	Venn diagram, Heatmap, Alpha diversity analysis, Beta diversity analysis, etc.
Comparative analysis	PCoA analysis, PCA analysis, NMDS analysis, LEfSe analysis, etc.
Evolutionary analysis	(Un)weighted UniFrac analysis, phylogenetic trees
Custom analysis	CCA analysis, Network analysis, etc.

Sample Requirement

1. DNA > 300 ng, 1.8 < OD_260/280 < 2.0, OD_260/230 ≥ 1.8, concentration ≥ 30 ng/μL.
2. No obvious degradation or protein/host contamination.
3. Avoid repeated freezing-and-thawing cycles.

Sampling kits: We provide a range of MicroCollect™ oral and fecal sample collection products for microbial recovery and analysis.

Deliverables: Raw sequencing data (FASTQ), trimmed and stitched sequences (FASTA), quality-control dashboard, statistic data, and your designated bioinformatics report.

References

Florent Valour, et. al. Actinomycosis: etiology, clinical features, diagnosis, treatment, and management. Infection and Drug Resistance. 2014:7,183–197.
Peivern Fong, et. al. Identification and diversity of Actinomyces species in a clinical microbiology laboratory in the MALDI-TOF MS era. Clinical microbiology. 2018: 54,151-158.
T. Lynch, et. al. Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene. Journal of Clinical Microbiology. 2016:54(3), 712-718.

* For Research Use Only. Not for use in diagnostic procedures or other clinical purposes.