Shotgun Metagenome Sequencing

In metagenomics, genomes from environmental samples are analyzed without the prior isolation and cultivation of individual species, and, therefore, it is a powerful technique for studying microbial communities in their natural habitat, with a broad range of applications.

The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. Shotgun metagenomics also provides a means to study unculturable microorganisms that are otherwise difficult or impossible to analyze.

Unlike capillary sequencing or PCR-based approaches, next-generation sequencing (NGS) allows researchers to sequence thousands of organisms in parallel. With the ability to combine many samples in a single sequencing run and obtain high sequence coverage per sample, NGS-based metagenomic sequencing can detect very low abundance members of the microbial community that may be missed or are too expensive to identify using other methods.

At Nucleome our customers can rely on our expertise in NGS to help them explore the rich genetic repertoire of microbial communities, while also benefiting from our bioinformatics expertise to help identify the species, genes, and pathways represented in their samples. Nucleome provides metagenomic sequencing service with Illumina NovaSeq platform and assembly-first strategy, and our bioinformatics analyses provide gene predictions, function annotations, and taxonomic annotations.

We also offer Metagenome profiling and Metagenome assembled genome sequencing under HiFi metagenomics services on the PacBio platform. Please visit the PacBio service page for more information.

16S rRNA Sequencing

The 16S ribosomal RNA (16 rRNA) sequencing is a common amplicon sequencing method used to identify and compare bacteria present within a given sample. The 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

16s Amplicon sequencing is frequently used to identify and differentiate microbial species. Short (< 500 bp) hypervariable regions of conserved genes or intergenic regions are amplified by PCR, analyzed using NGS technology, and the resulting sequences are compared against microbial databases. We can provide this service on Illumina MiSeq/NovaSeq PE 250bp read length and on PacBio Sequel II.

Nucleome is the only company in India that offers Full-length 16s amplicon sequencing on PacBio Sequel II. Full-length 16s amplicon sequencing can reveal the true diversity of complex microbiomes with highly accurate, species- and strain-level resolution using PacBio high quality and accurate HiFi reads.

For bacteria and archaea, the 16S rRNA gene is the most common target for amplicon sequencing. For fungi, three target genes are generally sequenced: the 18S rRNA gene and two internal transcribed spacers (ITS) located between rRNA genes. These regions are usually sufficiently divergent to separate even highly related species, and can sometimes differentiate subspecies.

Our standard bioinformatics analyses include alpha-diversity analysis, OTU analysis, species annotation, beta-diversity analysis, and multi-variate statistical analysis. Applications range from identifying a single species in pure culture to characterizing the microbiota of animals or plants to comparing species diversity and population structure in various environmental sources or geographic regions. Our specialists can advise you on the appropriate analyses for your project.

Metatranscriptome Sequencing

Microbial transcriptome and metatranscriptome information is important for predicting resistance to specific antibiotics, understanding host-pathogen immune interactions, quantifying gene expression changes, and tracking disease progression. Next-generation RNA-Seq (RNA sequencing) of bacteria, viruses, and other microbes has become a standard method for analyzing transcriptome and metatranscriptome information.

Cellular RNA is extracted and converted to cDNA, which is used to prepare sequencing libraries. Sequence reads are then mapped back to the reference genome, providing qualitative information on features such as exon junctions and splicing sites, as well as quantitative transcript data that can be compared across many experimental sets.
Unlike hybridization-based methods such as microarrays, RNA-Seq enables unbiased strand-specific identification of common and novel transcripts. A wide dynamic range enables confident identification of both high and low expressors in a single bacterial, viral, or other microbial RNA-Seq experiment. Multiple samples can be processed at once with a streamlined workflow suitable for automation.

Microbial Genome Sequencing

De Novo Microbial Genome Sequencing

De novo whole-genome sequencing involves assembling a genome without the use of a genomic reference and is often used to sequence novel microbial genomes. Illumina sequencers provide high coverage but shorter read lengths of unparalleled raw read accuracy. We also use PacBio RS II or Sequel for its higher read length and read depth for high-quality draft and complete microbial genome assemblies.

Microbial Whole-Genome Resequencing

Nucleome provides microbial whole-genome resequencing services to sequence the entire genome of a bacteria, virus, or other microbe, and comparing the sequence to that of a known reference for detecting low frequency mutations, finding key deletions and insertions, and discovering other genetic changes among microbial strains.

Plant Viral RNA and DNA Sequencing at Nucleome

Nucleome Informatics is committed to advancing plant genomics through cutting-edge sequencing technologies tailored for the detection and analysis of viral RNA and DNA. Our services are designed to meet the needs of researchers in agriculture, biotechnology, and virology, providing comprehensive solutions for understanding plant viruses.

Overview of Services

Our plant viral RNA and DNA sequencing services utilize Next-Generation Sequencing (NGS) technologies, including Illumina and PacBio platforms. These advanced methodologies enable us to detect a wide array of plant viruses, facilitating studies on viral diversity, host-pathogen interactions, and the development of disease-resistant crops.

Key Features

Comprehensive Virus Detection: Our sequencing protocols are optimized for identifying both known and novel plant viruses. By employing ribosomal RNA depletion techniques, we enhance the yield of viral sequences, which is crucial for accurate detection and characterization. We can do Viral genome sequencing on short read and long read technology both.

Bioinformatics Expertise: We provide robust bioinformatics support to analyze sequencing data. Our pipelines are designed to efficiently remove host sequences and classify viral genomes, ensuring high-quality results that contribute to your research objectives.

Customizable Solutions: Understanding that each project has unique requirements, we offer customizable sequencing strategies. Whether you need total RNA sequencing or focused studies on specific viral genomes, our experienced team will tailor the approach to fit your needs.

Human Pathogen Testing up to BSL-II Level at Nucleome

At Nucleome Informatics, we offer specialized testing services for human pathogens up to Biosafety Level 2 (BSL-II). Our advanced facilities and expertise enable us to handle and analyze infectious agents that pose moderate risks to human health, ensuring compliance with international safety standards.

Key Features of Our BSL-II Testing Services

• Comprehensive Pathogen Detection: Leveraging state-of-the-art sequencing platforms like Illumina NovaSeq 6000 and PacBio Sequel II, we provide accurate identification of bacterial and viral pathogens.
• Safety-First Approach: Our BSL-II laboratories are equipped with stringent safety protocols, including controlled access, personal protective equipment (PPE), and decontamination procedures.
• Customized Solutions: We tailor our testing workflows to meet the specific needs of clinical diagnostics, research, and vaccine development.
• Advanced Bioinformatics: Our bioinformatics pipelines ensure precise data analysis for pathogen identification, genetic characterization, and comparative studies.

Applications

• Clinical Diagnostics: Detection of pathogens causing diseases such as hepatitis, influenza, and bacterial infections.
• Research and Development: Studying pathogen behavior, host-pathogen interactions, and resistance mechanisms.
• Vaccine Studies: Supporting the development of vaccines by analyzing pathogen genomes.

For Non-Plant Viral RNA sequencing, please discuss with the sequencing team before sending the samples. DNA/RNA samples from Pathogenic viruses  may require extra permissions in clearance. Write to our technical team before sending the samples.

Applications

Our plant viral RNA and DNA sequencing services are applicable in various research areas:

Crop Health Monitoring: Identify and monitor viral infections in crops to improve management practices.

Genetic Research: Explore the genetic basis of virus resistance in plants, contributing to breeding programs aimed at enhancing crop resilience.

Virology Studies: Investigate the mechanisms of viral infection and replication in host plants.

Why Choose Nucleome?

Nucleome stands out as a leader in genomics services in India, with over  years of experience in NGS technologies. Our commitment to quality, precision, and customer satisfaction ensures that your research is supported by reliable data and expert analysis. Partner with us to unlock the potential of your plant viral studies and drive innovation in agricultural genomics.