Amplicon Sequencing

Targeted 16S, 18S and ITS amplicon sequencing for microbial community profiling, diversity analysis and taxonomic comparison.

Amplicon sequencing uses PCR amplification of marker regions, such as 16S rRNA, 18S rRNA or ITS, to profile microbial communities across complex biological or environmental samples. It provides a targeted and cost-effective approach for comparing community composition, diversity and relative abundance across sample groups.

Novogene Europe supports short-read and full-length amplicon sequencing options, including Illumina-based 16S/18S/ITS profiling and PacBio full-length 16S/18S/ITS sequencing. Short-read amplicon sequencing is well suited for high-throughput community profiling across large sample sets, while full-length amplicon sequencing can support higher taxonomic resolution for selected study designs.

Service Highlights

Marker-gene Community Profiling

Profile microbial communities using targeted 16S, 18S or ITS marker regions to compare composition, diversity and relative abundance across samples.

Short-read and Full-length Options

Support Illumina short-read amplicon sequencing and PacBio full-length 16S/18S/ITS sequencing, depending on study goals and taxonomic resolution needs.

Diversity and Taxonomic Analysis

Bioinformatics workflows support taxonomic annotation, alpha and beta diversity analysis, community comparison and visualisation of microbial composition.

NovoMagic Analysis Support

Selected 16S, ITS and 18S datasets can be explored through NovoMagic, supporting online analysis, visualisation and result interpretation.

Applications

Microbiome Research

Amplicon sequencing helps researchers investigate microbial community composition and diversity across host-associated, environmental and experimental sample types.

Environmental and Ecological Monitoring

Marker-gene profiling can support studies of microbial diversity in soil, water, marine, plant-associated and other ecosystem samples, helping researchers track community shifts across environments.

Host–Microbe Interaction Studies

Quantify microbial abundance, richness, and evenness, and compare community composition across samples or experimental groups.

Agriculture, Food and Industrial Microbiology

Amplicon sequencing supports microbial community analysis in agricultural systems, food-related samples, fermentation studies and other applied microbiology contexts.

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Specifications

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sample Requirements

The quantities listed are provided for reference only. Please download the Sample Requirements for detailed guidance, or contact us to discuss your project-specific requirements.

Service	Sample Type	Minimum Amount	Minimum Volume	Recommended Concentration	Purity
Amplicon Metagenomic Sequencing	Genomic DNA	≥ 200 ng	≥ 20 μL	≥ 5 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination
PacBio Full -Length 16S/18S/ITS	Genomic DNA	≥ 150 ng	≥ 30 μL	≥ 10 ng/μL	OD260/280 = 1.8-2.0. no degradation, no contamination

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Sequencing and Analysis

Recommended data outputs and analysis examples are provided for reference only. For detailed information, please contact us to discuss your project-specific analysis requirements.

Service	Amplicon Metagenomic Sequencing		PacBio Full -Length 16S/18S/ITS
Sequencing Platform	Illumina NovaSeq System		PacBio Revio
Sequencing Strategy	NovaSeq Reagent (500 Cycles)		CCS (Circular Consensus Sequencing) Mode
Data Output	50K/100K/500K raw tags		10K/20K/30K/50K/100k clean reads
Qiime1 or Qiime2	Core Analysis	Data Quality Control OTU/ASV Clustering Taxonomic Annotation Alpha diversity analysis (rarefaction curve, species boxplot) Beta Diversity Analyses (UPGMA, PCA, PCoA, NMDS) Community Differences Analyses (Anosim, MRPP, Adonis, Simper) Statistical Analyses (T-Test, MetaGenomSeq, Wilcoxon test, Kruskal-Wallis Test, LEfSe) Function Prediction (Qiime2 Only) Community Assembly Mechanisms( beta NTI, NST, iCAMP)	Qiime 2 Analysis - DADA2 denoise, OTU/ASV annotation and relative abundance analysis Alpha diversity analysis (rarefaction curve, species boxplot) Beta diversity analysis (heatmap, PCoA, PCA, NMDS) Comparative analysis between groups and within group (Adonis, Anosim, t-test, MetaGenomeSeq, LEfSe) Function prediction
Qiime1 or Qiime2	Advanced Analysis	Environmental association analysis (Spearman, CCA/RDA, VPA analysis) Correlation analysis (Network analysis, Network3D)

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Primers applied to Amplicon Metagenomic Sequencing

Types	Amplified Region	Fragment Length	Primers	Sequences (5’- 3’)
Bacterial 16S	V4	300 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4	300 bp	806R	GGACTACHVGGGTWTCTAAT
	V3-V4	470 bp	341F	CCTAYGGGRBGCASCAG
	V3-V4	470 bp	806R	GGACTACNNGGGTATCTAAT
	V4-V5	450 bp	515F	GTGCCAGCMGCCGCGGTAA
	V4-V5	450 bp	907R	CCGTCAATTCCTTTGAGTTT
	V5-V7 (for endophytic)	435 bp	799F	AACMGGATTAGATACCCKG
	V5-V7 (for endophytic)	435 bp	1193R	ACGTCATCCCCACCTTCC
	16S Full Length (V1-V9)	~1500 bp	F	AGRGTTYGATYMTGGCTCAG
	16S Full Length (V1-V9)	~1500 bp	R	RGYTACCTTGTTACGACTT
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch519F	CAGCCGCCGCGGTAA
Archaea V4 (AKA. Novel Archaea V4)	V4-V5	415 bp	Arch915R	GTGCTCCCCCGCCAATTCCT
Fungal 18S	V4	350 bp	528F	GCGGTAATTCCAGCTCCAA
	V4	350 bp	706R	AATCCRAGAATTTCACCTCT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-A	AACCTGGTTGATCCTGCCAGT
	18S Full length V1-V9	~1800 - 2000 bp	Euk-B	GATCCTTCTGCAGGTTCACCTAC
	ITS1	200-400 bp	ITS5-1737F	GGAAGTAAAAGTCGTAACAAGG
	ITS1	200-400 bp	ITS2-2043R	GCTGCGTTCTTCATCGATGC
	ITS2	380 bp	ITS3-2024F	GCATCGATGAAGAACGCAGC
	ITS2	380 bp	ITS4-2409R	TCCTCCGCTTATTGATATGC
Fungal ITS	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-F	CTTGGTCATTTAGAGGAAGTAA
	ITS1-1F (for endophytic)	200-400 bp	ITS1-1F-R	GCTGCGTTCTTCATCGATGC
	ITS Full length (1-2)	~500 - 800 bp	ITS9munngs	TACACACCGCCCGTCG
	ITS Full length (1-2)	~500 - 800 bp	ITS4ngsUni	CCTSCSCTTANTDATATGC

Resources

Example Analysis Output

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Taxonomic Composition

Summarise microbial community composition across samples using taxonomic abundance profiles.

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Taxa Heatmap

Compare abundance patterns of annotated taxa across samples and experimental groups.

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Beta Diversity PCoA

Visualise differences in microbial community structure across samples or groups.

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LEfSe Biomarker Analysis

Identify taxa that differ between groups and visualise potential microbial biomarkers.

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Environmental Association

Explore associations between microbial community patterns and environmental or experimental factors.

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Differential Taxa Analysis

Highlight significantly changed taxa across comparison groups based on abundance differences.

Webinars

Decoding Microbial Communities: Sequencing Solutions for Microbiome Research

Explore the latest approaches for studying microbial communities using amplicon sequencing, metagenomics, and metatranscriptomics. This webinar will highlight how these technologies can reveal microbial diversity, function, and interactions across human, environmental, and industrial ecosystems.

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Explore Microbiome Insights

Access webinars, brochures and case studies covering sequencing technologies, study planning and data interpretation.

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