Microbial Gene Expression Analysis

Transcriptome and metatranscriptome analysis is important to get an understanding of how bacterial strains, eukaryotes and microbial communities are functioning at a specific time in response to its environment. With our differential gene expression (DGE) analysis service you can detect or investigate active microbial functions such as targets of host- bacterial interaction, virulence, metabolic activity and enzymes of interest.

Next-generation RNA sequencing (RNA-Seq) of bacteria, RNA viruses, and other microbes is increasingly applied for getting insight in gene expression activity. Unlike hybridization-based methods such as microarrays, transcriptome analysis using RNA-Seq enables unbiased strand-specific identification and insight in the full profile of expressed genes which gives an understanding in activity of common as well as novel transcripts. The results can lead to the discovery of pathway fluxes and its regulations. Especially comparing transcriptomes using DGE of organisms or microbiomes harvested under different conditions can give leads to mechanisms behind observations.

Validated protocols for pure bacterial cultures and complex microbiome samples

BaseClear offers complete solutions for bacterial and microbiome RNA-seq projects. BaseClear can advise on the study design, including how many replicates to use for sufficient statistical power and which groups to compare to get the most out of your experimental setup. We have developed optimized RNA extraction protocols to obtain high-quality RNA from a variety of samples. From the total RNA we offer rRNA removal from pure cultures, as well as complex microbiome samples, using validated protocols. After rRNA removal we convert RNA to cDNA, which is used to prepare sequencing libraries. Sequence reads are then mapped back to the reference genome, providing qualitative information on features, as well as quantitative transcript data that can be compared across many experimental sets.  Many samples can be processed at once with a streamlined and automated workflows.

BaseClear solutions for bacterial and microbiome gene expression analysis

BaseClear offers complete transcriptome and metatranscriptome analysis services to discover and profile the entire transcriptome of host or microbiome samples. With no probes or primers to design, our RNA-Seq method can deliver unbiased and unparalleled information about gene expression levels. BaseClear
offers strand-specific RNA-seq analysis based on sequencing on the Illumina platforms, as well as full-length transcriptome analysis. The deliverables of our bioinformatics solutions include gene expression tables and differential gene expressions. In addition BaseClear can support you with metabolic pathway analysis, pathway enrichment analysis, discovery of bioactives, enzyme activities and host-microbiome interactions.

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Metatransciptomics in microbiome research

Technological advances in RNA-seq have recently provided us with an ability to gain insight into the genes that are actively expressed in complex microbial communities, enabling the elucidation of the functional changes that dictate the microbiome functions at given contexts, its interactions with the host, and functional alterations that accompany the conversion of a healthy microbiome toward a disease-driving configuration. Metatranscriptomics can also be applied for enzyme discovery and for measuring and  optimizing fermentation processes.

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