Activated Sludge Microbiome Analysis

Since 2014, GWMC launched the Municipal Wastewater Microbiome Initiative and focused on Activated Sludge Microbiome. Activated sludge (AS), a representative biological treatment technology, is widely used to remediate municipal and industrial wastewaters. High-throughput DNA sequencing technology is nowadays considered the most reliable and cost-effective tool for microbial composition and ecological dynamics evaluation. Various technologies including 16S rRNA gene, 454 pyrosequencing, and metagenomic sequencing, have been used to characterize and investigate the activated sludge bacterial diversity and community dynamics.

Activated Sludge Microbiome Analysis

Potential Research Directions of Activated Sludge Microbiota Analysis

• Explore the differences in activated sludge bacterial community and content to disentangle the complexity and diversity
• Explore the important role in enabling and facilitating particular ecosystem functions, such as nutrients removal
• Explore the activated sludge bacterial composition and ecological dynamics to assess WWTP performance and prevent activated sludge disruptions
• Explore the seasonal/regional dynamics of microbial activity variations in activated sludge
• Characterize "active" populations (via protein synthesis potential) and gain a deeper understanding of microbial activity patterns within activated sludge

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 activated sludge microbiota. 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
Gut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome Analysis
Nanopore system PCR-DGGE Real-time qPCR Clone library
Gut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome AnalysisGut Microbiome Analysis

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. De Celis, M., Belda, I., Ortiz-Álvarez, R., Arregui, L., Marquina, D., Serrano, S., & Santos, A. (2020). Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning. Scientific Reports, 10(1).
2. Ye, L., Mei, R., Liu, WT. et al. Machine learning-aided analyses of thousands of draft genomes reveal specific features of activated sludge processes. Microbiome 8, 16 (2020).
3. Puig-Castellví, F., Cardona, L., Jouan-Rimbaud Bouveresse, D., Cordella, C. B. Y., Mazéas, L., Rutledge, D. N., & Chapleur, O. (2020). Assessment of the microbial interplay during anaerobic co-digestion of wastewater sludge using common components analysis. PLOS ONE, 15(5), e0232324.
4. Rehman, Z. U., Fortunato, L., Cheng, T., & Leiknes, T. (2019). Metagenomic analysis of sludge and early-stage biofilm communities of a submerged membrane bioreactor. Science of The Total Environment, 134682.

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