Unlock detailed insights into microbial communities with our comprehensive 16S/18S/ITS amplicon sequencing solutions. Designed for complex environmental, agricultural, and host-associated ecosystems, our one-stop microbiome profiling delivers high resolution and actionable data to accelerate your research.
Deliverables Include:
Includes a comprehensive set of key analyses and visuals, ready for paper submission.
Detect microbes down to 0.01% abundance with Illumina and PacBio platforms.
From sample prep to bioinformatics, all steps handled seamlessly.
Microbial communities drive nutrient cycling, suppress diseases, and maintain ecosystem balance. Analyzing their diversity enables researchers to:
Ideal for analyzing microbial community composition.
Technology Features:
Typical Applications:
Environmental microbiome surveys | Gut microbiome screening | Fungal community structure analysis
Provides simultaneous species identification and functional gene profiling.
Technology Features:
Typical Applications: Antibiotic resistance gene studies | Microbial metabolic pathway analysis | Discovery of novel microbial genomes
Note: This page primarily covers 16S/18S/ITS amplicon sequencing for microbial community profiling. For combined species and functional gene insights, explore our metagenomic sequencing services.
We provide targeted and full-length amplicon sequencing solutions designed to meet diverse microbiome research needs:
High-throughput analysis of bacterial diversity focusing on V3–V4 or other key variable regions.
Accurate profiling of archaeal communities from extreme or specialized habitats.
Identification of actinomycete subgroups critical for soil health, antibiotic production, and bioremediation.
High-resolution profiling of fungal communities by targeting ITS1 or ITS2 regions.
Comprehensive detection of eukaryotes, including protists, fungi, and microfauna.
Long-read PacBio sequencing for enhanced taxonomic resolution and detailed phylogenetic insights.
High-precision microbial fingerprinting ideal for complex or low-biomass samples.
Tailored sequencing solutions for diverse microbiome research
Research Application | Recommended Services |
---|---|
Environmental Microbiome Profiling | - Bacterial 16S rRNA Sequencing - Archaeal 16S rRNA Sequencing - Fungal ITS Sequencing - Eukaryotic 18S rRNA Sequencing |
Host-Associated Microbiome Studies | - Full-Length 16S/18S/ITS Sequencing - 2bRAD-M Analysis |
Low-Abundance or Complex Communities | - 2bRAD-M Analysis - Full-Length 16S Sequencing |
Functional and Spatial Analysis | - 2bRAD-M Analysis |
Industrial or Fermentation Microbiome | - Actinomycetes Diversity Analysis - Combined 16S and ITS Amplicon Sequencing |
Not sure which approach fits your study? [Contact our experts] for personalized guidance.
Personalized 1-on-1 experimental design tailored to your research goals
DNA integrity assessment
Concentration normalization to ensure optimal sequencing input
Dual-platform sequencing using Illumina and PacBio
Quality benchmarks: Illumina Q30 ≥ 90%, PacBio CCS accuracy ≥ 99%
Comprehensive package including raw sequencing data and detailed analysis report
Short-read, high-throughput sequencing for diverse amplicon targets
Long-read, high-fidelity sequencing enabling full-length amplicon analysis
Validation and spatial detection methods to complement sequencing data
Our advanced bioinformatics pipeline delivers deep insights into microbial communities, supporting detailed taxonomic, functional, and ecological profiling. With stringent quality control and cutting-edge algorithms, we provide accurate, publication-ready results tailored to your research objectives.
Core Bioinformatics Analyses
Analysis Type | Key Methods | Research Focus |
---|---|---|
Species Annotation | DADA2 (ASV) / UPARSE (OTU) | Identification of bacteria, fungi, and archaea |
Alpha Diversity | Shannon/Chao1 indices, rarefaction curves | Species richness and evenness within samples |
Beta Diversity | PCoA / NMDS + PERMANOVA | Differences in microbial community structure between groups |
Differential Abundance | LEfSe / ANCOM | Detecting significantly different taxa across groups |
Functional Prediction | PICRUSt2 / FAPROTAX | Inferring potential metabolic functions of microbes |
Network Analysis | SparCC / MENA | Exploring co-occurrence and exclusion relationships among microbes |
Advanced Bioinformatics Options
Service | Sample Type | Recommended Quantity | Minimum Quantity | Concentration |
---|---|---|---|---|
16S/18S/ITS Sequencing | Genomic DNA | ≥100 ng | 10 ng | ≥1 ng/μl |
Full-Length 16S/18S/ITS Amplicon Sequencing | Genomic DNA | ≥ 500ng | 10 ng/µL | |
Tissue | 1-3g | 1 g | ||
Thallus | 5 g | 3 g | ||
Interstitial Fluid | 3-5 mL | 1 mL | ||
Environmental Samples | 3-5g | 1 g | ||
Water filter membrane | 3 | 1 |
Note: If you wish to obtain more accurate and detailed information regarding sample requirements, please feel free to contact us directly.
Partial results of our microbial diversity analysis – 16S/18S/ITS sequencing service are shown below:
Microbial Distribution Bar Chart
Classification Heatmap
LEfSe Analysis LDA Bar Chart
LEfSe Analysis Cladogram
Venn Diagram
Beta Diversity Index Heatmap
Microbiota of the Digestive Gland of Red Abalone (Haliotis rufescens) Is Affected by Withering Syndrome
Journal: Microorganisms
Impact factor: 4.26
Published: 2020
Backgrounds
The study centers on Withering Syndrome (WS), an infectious disease that heavily impacts abalone aquaculture. This disease is caused by the intracellular bacterium Candidatus Xenohaliotis californiensis, which infects the digestive glands, disrupting their function and causing progressive wilting in abalones. While the direct effects of WS are understood, its impact on the microbiota of the digestive glands in abalones is not well-studied. The main goal of this research is to determine if there are differences in the digestive gland-associated microbiota between healthy red abalones and those affected by WS.
Materials & Methods
Sample preparation:
Method:
Results
The study found notable differences in microbiota composition between healthy and WS-affected abalones. Healthy abalones exhibited a diverse and balanced bacterial community, whereas WS-affected abalones had a microbiota dominated by specific bacteria associated with the disease. One of the most significant findings was that a certain bacterium was dominant in healthy abalones, while the primary pathogen of WS was more prevalent in the affected group. Interestingly, the pathogen was also present in some healthy specimens, indicating that the balance between different bacterial populations might be crucial in determining the disease status.
Figure 1. (A) Relative abundance of microbiota at the phylum level in the digestive glands of healthy (H1-H5) and withering syndrome-affected red abalone (WS1-WS5). (B) Comparison of relative abundance at the phylum level between healthy (red boxes) and affected (blue boxes) abalone. (C) Comparison at the genus level.
Figure 2. Differences in digestive gland microbiota of healthy red abalones (H) compared with red abalones with withering syndrome disease (WS).
Conclusions
The findings suggest that WS significantly disrupts the microbiota composition in the digestive glands of red abalones. Specific bacterial communities are associated with either health or disease, highlighting the potential ecological role of microbiota in WS pathogenesis. Further research is needed to deepen our understanding of the dynamics of digestive gland microbiota and its influence on the progression of Withering Syndrome in abalones.
Explore representative publications by our clients, showcasing the real-world applications of 16S/18S/ITS sequencing in fields like agriculture, environment, aquaculture, and food safety.
Elucidating the effects of organic vs. conventional cropping practice and rhizobia inoculation on rhizosphere microbial diversity and yield of peanut
Paudel, Dev, et al. | Environmental Microbiome | 2023 | https://doi.org/10.1186/s40793-023-00517-6
Multi-species biofilms of environmental microbiota isolated from fruit packing facilities promoted tolerance of Listeria monocytogenes to benzalkonium chloride
Rolon, M. Laura, et al. Biofilm 2024 https://doi.org/10.1016/j.bioflm.2024.100177
Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils
Ganuza, M., et al. Journal of Applied Microbiology 2019 https://doi.org/10.1111/jam.14147
The effects of atrazine on the microbiome of the eastern oyster: Crassostrea virginica
Britt, Adrian, et al. Scientific reports 2020 https://doi.org/10.1038/s41598-020-67851-4
Exploring actinobacteria associated with rhizosphere and endosphere of the native alpine medicinal plant Leontopodium nivale subspecies alpinum
Oberhofer, Martina, et al. Frontiers in Microbiology 2019 https://doi.org/10.3389/fmicb.2019.02531
Please submit a detailed description of your project. We will provide you with a customized project plan to meet your research requests. You can also send emails directly to info@cd-genomics.com for inquiries.
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