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Diversity Analysis of Actinomycetes


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 particular 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. We can help you clarify the taxonomic assignment of a strain and discover new species by using these practical and discriminatory methods.

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 search and development of a novel class of antibiotic drugs. Diversity analysis of actinomycetes also serves to confirm the diagnosis of actinomycosis. Diversity analysis of actinomycetes has been an important tool used in drug discovery and development, clinical diagnosis, agricultural production, petroleum exploration, and industrial manufacturing, etc.

Diversity Analysis of Actinomyces 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

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

  1. Florent Valour, et. al. Actinomycosis: etiology, clinical features, diagnosis, treatment, and management. Infection and Drug Resistance. 2014:7,183–197.
  2. 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.
  3. 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.

Areas of Interest

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