Microbiome research is rapidly expanding, which is why SeqBiome uses statistical methods from the front of the field. We provide advice on state-of-the-art experimental design procedures including technical and biological replicates, sample size, sequencing depth, and potential confounders. Our compositionally-robust analyses control for fundamental problems in microbiome data: differences in coverage, false correlation in abundance, and the prevalence of rare features. This gives us the strongest foundation to build on, whether using time series analysis, repeated-measure correlation between microbes, or differential proportionality in multi-omics data.

Microbiome studies are very heterogeneous in terms of environment types (e.g. stool, biopsies, skin, food, marine, soil). Sampling, storage, DNA/RNA extraction and sequencing protocols often differ between and even within academic labs depending on sample type, study and technical staff. SeqBiome has a deep understanding of all these factors, along with a tried-and-tested approach to mitigate known and unknown biases, which is crucial for gaining accurate and robust analysis outcomes. We follow publishable laboratory practice and use extraction methods optimised to sample type, include controls to exclude contaminating microbes, and optimise sequencing coverage to ensure you only pay for what is needed. We can also provide advice on efficient data collection, storage, and transportation for sequencing.

For some questions, the answer is an exact list of the microbes present that can be referenced with past work and carried forward to future studies. Other questions focus on changes in specific microbial strains or metabolic ability, or what biomolecules a community can produce. We draw on all these approaches to reconstruct how microbes behave and interact in the context of your research.

Different methods for surveying microbial communities provide different answers. We advise our clients on the method of sequencing that is most effective for answering their specific questions. The SeqBiome team has experience in working with multiple Illumina, ION and Oxford Nanopore Technology platforms and can work with you to identify the platform that best suits your needs.

SeqBiome employs an extensive array of positive controls (mock communities, replicates across runs to ensure consistent results) and negative controls (e.g., to investigate the presence of kit and other contaminants within samples received).

SeqBiome provides 16S rRNA amplicon, shallow and deep shotgun sequencing of metagenomes and metatranscriptomes. Our bioinformatic analysis services cover a broad range of microbiomes, facilitating in-depth analyses of microbial taxonomy (16S rRNA gene/transcript amplicons), functional potential (metagenomics) and activity (metatranscriptomics).

All good analysis starts with a good question; we help formulate a research hypothesis that can be soundly tested and adequately powered to give reliable results. Whether your interest is “who’s there?” (amplicon), “how are they different?” (comparative genomics), “what can they do?” (metagenomics), or “what are they doing right now?” (metatranscriptomics), we help you frame the right question through the right technology.

SeqBiome has extensive experience of profiling microbiome composition and functions from phylogenetic markers (16S rRNA gene/transcript, ITS) and shotgun meta-genomic/transcriptomic sequencing. Our custom pipeline provides species-level classification for 16S rRNA gene sequences wherever possible, either from OTUs or Amplicon Sequence Variants. We provide compositionally appropriate exploratory data analysis and statistical comparison. We provide strain level resolution and high throughput functional annotation with state-of-the-art bioinformatic approaches.

If you have specific genomes you wish to investigate, our team has considerable experience in comparative genomics, with the ability to identify antibiotic resistance features, virulence factors or other genes of interest with a high degree of accuracy.

We adapt our workflow to meet your research needs. From quality control to in-depth analysis, all of our bioinformatics pipelines are developed for the cloud, allowing us to scale workloads to the client’s needs. We apply state-of-the-art methodologies including contamination checking/tracking, advanced statistical modelling, Machine Learning classification and prediction, or simply process your microbiome dataset quickly and reliably.

Our bioinformaticians have extensive experience analysing NGS data across a number of platforms and applications. We have already helped a wide range of clients overcome their bioinformatics challenges. We provide comprehensive and professional microbiome services to meet the needs of academic, pharmaceutical, and other industrial partners.

Enormous amounts of data are currently being generated but it is not at all clear what it all means; the value lies in the efficiency of interpretation leading to meaningful insights, as well as visually appealing and clearly communicated results. SeqBiome has extensive know-how of peer-reviewed published microbiome research and an interpretational framework.

The most critical part of our work is communicating findings to others, whether in a presentation, report, or publication. SeqBiome’s custom-made presentations are focused on the interests of the client so that both parties are engaged in the research in an interactive process throughout the project. Our experience in high-impact peer-review research means our outputs are tailored for clarity and publication.