Microbiota is widely present in all sorts of environments, including inner and surface of plants and animals. Microbiota is composed of bacteria, archaea, fungi, and viruses. Studies have found that microbiota is essential for ecological balance and the host's immune, hormonal, and metabolic homeostasis. Microbial transcriptomics is a subject that studies gene transcription and gene expression activity by profiling RNA transcripts in complex microbial communities. RNA/transcriptome sequencing is a key method for studying the activities of the microbiota, and has great potential for applications in industry as well as medical and health fields. For example, bacterial expression profiling has identified significant changes in the expression of metabolic pathways related to the pathogenesis of human microbiome disease. Microbial transcriptomics is also important for predicting resistance to specific antibiotics, exploring host-pathogen immune interactions, and tracking disease progression.

Accelerate Research and Practice in Microbiota

Based on multiple RNA sequencing platforms, CD Genomics provides comprehensive microbiota transcriptome research solutions. We can provide prokaryotic RNA sequencing, eukaryotic RNA sequencing, viral RNA sequencing, and meta-transcriptome sequencing. Illumina next-generation sequencing and long-read sequencing practiced on PacBio or Nanopore platforms can accurately and efficiently analyze the expression of microbial genes, interpret the functions and activities of microorganisms, and better understand how microorganisms interact with the environment and their host. In addition, our team of scientists and bioinformaticians can implement every step from experimental design to data analysis, helping you to realize a variety of valuable applications through microbial RNA sequencing.

Our advantages
Abundance of sample handling experience
Enrichment and extraction of low-abundance microorganisms
Multiple sequencing platforms to choose from
High accuracy of sequencing results
Comprehensive bioinformatics analysis and customized analysis

The issues that can be addressed with our RNA sequencing services
Microbiota and host health
Microbiota interaction study
Microbial drug resistance research
Biomedical applications
Food and industrial applications
Environmental science research and applications

Note: Our services are for research use only, not for disease diagnosis and treatment.

What can we do?

Sequencing targets: bacteria, archaea, fungi, and viruses
Data delivery: transcriptome assembly, transcriptome/unigene length statistics, transcriptome function annotation, differential expression analysis, CDS predictive parsing, SNP/InDel analysis

Service Workflow

Sequencing Platforms

Illumina NextSeq/HiSeq/NovaSeq	PacBio RS IL / Sequel	Nanopore
Microbial gene discovery Microbial gene expression Splice variation	Microbial gene expression Microbial transcript structures Microbial gene discovery Splicing / alternative splicing Transcription initiation RNA cleavage / adenylation	Microbial gene expression Microbial transcript structures Microbial gene discovery Splicing / alternative splicing Transcription initiation RNA cleavage / adenylation RNA modification

Bioinformatics Analysis Contents

BIOINFORMATICS PIPELINES	DETAILS
Read QC	Determination of per base sequence quality, removal of reads with lower quality, removal of adapter/linker, trimming of the read sequence, etc.
Alignment & Assembly	Read mapping, FPKM estimation, novel transcript assembly, variant calling, etc.
Differential Expression	Perform differential expression of reference and novel transcripts/genes with Cuffdiff 2 algorithm and DESeq2.
Advanced Analysis	Metabolic pathway integration analysis, gene co-expression network analysis, mRNA-sRNA co-expression network analysis, etc.
Differential Expression	Perform differential expression of reference and novel transcripts/genes with Cuffdiff 2 algorithm and DESeq2.
Enrichment analysis	KEGG pathway: Gene-enriched signaling pathway, linking genomic information with higher order functional information. GO analysis: Gene product annotations in the areas of molecular function, biological process and cellular component eggNOG/COG: Annotation of orthologous groups of genes, prediction of evolutionary genealogy of genes
Multi-sample comparative analysis	Clustering: Discover classifications within complex data sets PCoA: Differences in functional distribution between different samples, explore the functional composition of multiple samples
Correlation analysis	Study the relationships between microbes and environmental factors

Comprehensive Solutions to Accelerate Your Microbiota Research

CD Genomics has a professional technical team and bioinformatics analysis team, as well as more than ten years of project experience in the sequencing field. We have optimized to a mature technical route, providing accurate and reliable data and high-quality results that meet your requirements. We are committed to providing efficient, cost-effective, and satisfying sequencing services to help your microbial transcriptomics research.