Tel: 1-631-338-8059    Fax: 1-631-614-7828    Email: info@cd-genomics.com Inquiry
x
quote Request a Quote

Precise Microbial Diversity Analysis — Fast, Sensitive 16S/18S/ITS Sequencing Services

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:

  • Raw sequencing data
  • Quality-filtered sequences
  • Detailed data quality control report
  • Bioinformatics analysis report
  • Alpha and beta diversity statistics
  • Phylogenetic and functional predictions
  • Graphical visualizations
Request Quote View Services

Our Advantages

Publication-ready reports

Includes a comprehensive set of key analyses and visuals, ready for paper submission.

Ultra-sensitive detection

Detect microbes down to 0.01% abundance with Illumina and PacBio platforms.

One-stop workflow

From sample prep to bioinformatics, all steps handled seamlessly.

Service OverviewApplicationsWorkflowBioinformaticsSample RequirementDemoCasePublicationFAQs

Why Microbial Diversity Analysis Matters

Microbial communities drive nutrient cycling, suppress diseases, and maintain ecosystem balance. Analyzing their diversity enables researchers to:

How to Choose Your Microbial Diversity Sequencing Approach

Option 1: 16S/18S/ITS Amplicon Sequencing

Ideal for analyzing microbial community composition.

Technology Features:

  • Illumina short-read sequencing targeting V3–V4 regions — cost-effective and high-throughput
  • PacBio HiFi CCS long-read sequencing for full-length amplicons — delivers high-accuracy, strain-level resolution

Typical Applications:

Environmental microbiome surveys | Gut microbiome screening | Fungal community structure analysis

Option 2: Metagenomic Sequencing

Provides simultaneous species identification and functional gene profiling.

Technology Features:

  • Illumina short-read sequencing — high throughput for functional gene annotation
  • Long-read sequencing — enables microbial genome reconstruction

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.

Our 16S/18S/ITS Sequencing Services at a Glance

We provide targeted and full-length amplicon sequencing solutions designed to meet diverse microbiome research needs:

Bacterial 16S rRNA Sequencing

High-throughput analysis of bacterial diversity focusing on V3–V4 or other key variable regions.

Get Service Info

Archaeal 16S rRNA Sequencing

Accurate profiling of archaeal communities from extreme or specialized habitats.

Get Service Info

Actinomycetes Diversity Analysis

Identification of actinomycete subgroups critical for soil health, antibiotic production, and bioremediation.

Get Service Info

Fungal ITS Sequencing

High-resolution profiling of fungal communities by targeting ITS1 or ITS2 regions.

Get Service Info

Eukaryotic 18S rRNA Sequencing

Comprehensive detection of eukaryotes, including protists, fungi, and microfauna.

Get Service Info

Full-Length 16S/18S/ITS Sequencing

Long-read PacBio sequencing for enhanced taxonomic resolution and detailed phylogenetic insights.

Get Service Info

2bRAD-M Microbiome Analysis

High-precision microbial fingerprinting ideal for complex or low-biomass samples.

Get Service Info

Research Applications & Recommended Sequencing Services

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.

End-to-End Workflow: Tailored Solutions from Sample to Insight

Step 1: Project Consultation

Personalized 1-on-1 experimental design tailored to your research goals

Step 2: Sample Quality Control

DNA integrity assessment

Concentration normalization to ensure optimal sequencing input

Step 3: Sequencing & Data Analysis

Dual-platform sequencing using Illumina and PacBio

Quality benchmarks: Illumina Q30 ≥ 90%, PacBio CCS accuracy ≥ 99%

Step 4: Report Delivery

Comprehensive package including raw sequencing data and detailed analysis report

Request Quote

Technology Platforms We Use

Illumina NovaSeq / MiSeq / PE250

Short-read, high-throughput sequencing for diverse amplicon targets

PacBio SMRT (HiFi CCS)

Long-read, high-fidelity sequencing enabling full-length amplicon analysis

qPCR / Sanger

Validation and spatial detection methods to complement sequencing data

Comprehensive Bioinformatics Analysis

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

The Workflow of Antibiotic Resistance Genes (ARGs) Analysis Solution.

Sample Requirement

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.

Demo

Partial results of our microbial diversity analysis – 16S/18S/ITS sequencing service are shown below:

Distribution histogram illustrating the presence of resistance genes.

Microbial Distribution Bar Chart

Circos diagram depicting the distribution of resistance genes.

Classification Heatmap

Two-dimensional PCoA plot representing the variation of resistance genes.

LEfSe Analysis LDA Bar Chart

Adonis/PERMANOVA analysis comparing resistance gene groups.

LEfSe Analysis Cladogram

LEfSe analysis highlighting the differences among resistance gene groups.

Venn Diagram

Boxplot showing the differential expression of resistance genes.

Beta Diversity Index Heatmap

Customer Case

Customer Case

Microbiota of the Digestive Gland of Red Abalone (Haliotis rufescens) Is Affected by Withering Syndrome
Journal: Microorganisms
Impact factor: 4.26
Published: 2020

Find out more

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:

  • Red abalone
  • Converted land samples
  • DNA extraction

Method:

Data Analysis:

  • Statistical analysis
  • Beta diversity measures
  • Community composition testing
  • Differential abundance analysis

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.

Fig 1. Composition of ARGs and regulatory genes across 26 soil metagenomes. (Qian et al., 2021)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.

Fig 2. Diversity and abundance of ARGs in soils from three distinct ecosystems. (Qian et al., 2021)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.

Published Research Supported by Our 16S/18S/ITS Sequencing Services

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

FAQ

microbioseq
SUITE 111, 17 Ramsey Road, Shirley, NY 11967, USA
Tel: 1-631-338-8059
Fax: 1-631-614-7828
Email: info@cd-genomics.com

Follow us on:

Copyright © 2025 CD Genomics. All rights reserved. Terms of Use | Privacy Notice

We use cookies to understand how you use our site and to improve the overall user experience. This includes personalizing content and advertising. Read our Privacy Policy

Accept Cookies
x