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Microbial Diversity in the Biofilms

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Introduction to Biofilm Microorganisms

Microbial Diversity in the Biofilms

Biofilms refer to the bacterial communities that are attached to a surface. They contribute to the health and resilience of ecosystems via their important roles in biogeochemical cycling, their interactions with each other and their provision of chemicals. Although aquatic biofilms are important to the health of marine ecosystems, they also have deleterious outcomes like biocorrosion, biofouling and antibiotic resistance. When it comes to human health, microbes can form biofilms on any surface of the human body and offer resistance to antimicrobial agents, which could cause a number of persistent and chronic bacterial infections. Biofilm infections have sharply come into prominence in the last few decades. Next-generation sequencing (NGS) provides a powerful tool in the studies of biofilm microbiomes. Genomic studies have revealed the complexity and diversity of the biofilms.

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Accelerate Research and Practice in Microbial Diversity in Biofilms

We provide advanced genomics methods to explore the microbial diversity and structure of biofilm samples, and discover previously undetected microbial species and predict their roles in biofilm formation, human health or environments. Our solutions include real-time PCR, 16S/18S/ITS sequencing, metagenomics, metatranscriptomics and powerful bioinformatics analysis. Based on Illumina Hiseq/Miseq, PacBio and Oxford nanopore sequencing platforms, we are dedicated to ensuring an accurate & comprehensive microbial profiling and elaborate bioinformatics analysis pipeline with standardized laboratory methods.

The Main Directions

  • Exploration of microbial diversity and structure of biofilms
  • Functional core analysis and discovery of persistent and distinct functional cores
  • Studies of community succession and microbe-host interactions
  • Diagnosis and treatment of different biofilm infections

What Can We Do?

  1. 1. Identification of biofilm microorganisms and taxonomic profiling
  2. 2. Quantitation of biofilm microorganisms
  3. 3. Functional core analysis and exploration of novel functional potential

Note: our service is for research use only, not for diagnosis.

Detectable Objects

Artificial biofilms, marine microbial biofilms and other biofilms on any surface.

Detectable Microorganisms

Archaea, bacteria, eukaryotes, etc.

Technical Platforms

We are equipped with Illumina Hiseq/Miseq, PacBio Sequel, Oxford MinIONTM, Oxford GridIONTM, PCR-DGGE (PCR-denaturing gradient gel electrophoresis), real-time qPCR, clone library and other platforms.

Sample Requirement

    1. DNA sample: DNA ≥ 300 ng, concentration ≥ 10 ng/ul, OD260/280 = 1.8 – 2.0
    2. Make sure the DNA is intact and non-degraded, avoiding repeated freezing and thawing cycles.
    3. Please prepare enough dry ice or ice packs to ensure low temperature during sample delivery.

Workflow

High throughput sequencing analysis processFigure 1. High throughput sequencing analysis process

PCR-DGGE analysis processFigure 2. PCR-DGGE analysis process

Bioinformatics Analysis

Our bioinformatics analysis pipeline is flexible to your needs.

Basic Analysis Routine Analysis (According to Customer Requirements) Advanced Data Analysis
Read QC Heatmap Phylogenetic Tree
Sequence Length Distribution VENN Functional Core Analysis
OTU Clustering and Taxonomic Profiling Principal Components Analysis (PCA) LDA-Effect Size (LEfSe)
Diversity Index Microbial Community Structure Analysis Network Analysis
Shannon-Wiener Curve α Diversity Index Analysis Correlation Analysis
Rank-Abundance Curve Matastats Analysis
Rarefraction Curve Weighted Unifrac test
Multiple Contrast CCA/RDA
Heatmap
Principal Components Analysis (PCA)

References

  1. Zhang W, Ding W, Li Y X, et al. Marine biofilms constitute a bank of hidden microbial diversity and functional potential. Nature communications, 2019, 10(1): 517.
  2. Sauer K. The genomics and proteomics of biofilm formation. Genome biology, 2003, 4(6): 219.
  3. Bjarnsholt T. The role of bacterial biofilms in chronic infections. Apmis, 2013, 121: 1-58.

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