The gut microbiome is a dynamic and complex microbial ecosystem that plays a pivotal role in human and animal health. Comprising trillions of bacteria, archaea, fungi, and viruses, the gut microbiota significantly influences metabolic, immunological, and neurological processes. As research continues to uncover the profound implications of microbial composition and function, precise, high-throughput sequencing has become indispensable for decoding the gut microbiome.
Creative Biolabs offers comprehensive gut microbiome sequencing and analysis services to support researchers in exploring microbial diversity, gene functions, and host-microbe interactions. Leveraging cutting-edge sequencing platforms and bioinformatics, we empower clients to unlock new findings in microbiome-associated research domains including nutrition, immunology, metabolic health, infectious disease, and next-generation probiotics development.
Importance of Gut Microbiome Sequencing in Research
Growing Research Demand for Microbial Insights
The demand for gut microbiome sequencing has surged due to its relevance across diverse scientific sectors. In microbiome-driven drug development, precision nutrition, and live biotherapeutic product design, a deep understanding of microbial taxa and their expressed functions is essential. Moreover, as microbiome-wide association studies (MWAS) and functional metagenomics gain traction, conventional culture-based approaches have proven inadequate for dissecting the intricate web of microbial interactions.
Technical Superiority of High-Resolution Sequencing
Next-generation sequencing (NGS) offers unparalleled sensitivity and resolution for microbiome profiling. Unlike traditional techniques, NGS allows researchers to bypass the need for culturing, capturing both abundant and rare microbial species, including unculturable taxa. Shotgun metagenomics and microbial transcriptomics extend beyond taxonomic classification by enabling functional gene analysis, metabolic pathway reconstruction, and transcriptomic profiling. Creative Biolabs integrates these powerful methodologies into a one-stop service solution tailored to microbiome research.
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Advanced Technologies Empowering Our Gut Microbiome Analysis
At Creative Biolabs, we deliver high-resolution gut microbiome data using four principal platforms: 16S rRNA gene sequencing, shotgun metagenomic sequencing, microbial metatranscriptomics, and microbiome-wide association studies. Our integrated workflows are executed in a GLP-compliant, research-use-only setting, using high-throughput sequencing instruments and robust computational infrastructure.
Our 16S rRNA gene sequencing service targets conserved and hypervariable regions of the bacterial 16S ribosomal RNA gene to determine community composition. This approach is ideal for cost-effective profiling of bacterial taxa across various phylogenetic levels, particularly for early-stage exploratory studies. Our bioinformatics pipeline includes OTU/ASV clustering, alpha and beta diversity metrics, taxonomy assignment, and comparative analyses.
Shotgun metagenomic sequencing enables comprehensive interrogation of all genomic DNA present in a gut sample. Unlike amplicon-based methods, this technique captures bacteria, archaea, viruses, and fungi without primer bias. Our shotgun platform supports:
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Species and strain-level resolution
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Functional gene and metabolic pathway annotation (e.g., KEGG, eggNOG)
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Resistance gene prediction
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Microbial genome assembly and binning
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Quantification of gene abundance across samples
This service is particularly suitable for studies exploring microbial gene functionality, antimicrobial resistance, and metabolic potential in the gut microbiome.
Metatranscriptomic sequencing focuses on the collective mRNA transcripts within a microbial community, revealing genes actively expressed under given conditions. Our microbial metatranscriptomics platform includes rRNA depletion, cDNA library preparation, Illumina-based sequencing, and downstream transcript quantification. It facilitates:
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Real-time insights into microbial metabolism and stress responses
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Identification of regulatory RNAs
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Host–microbe interaction studies (via dual RNA-seq)
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Response profiling to dietary interventions, drugs, or environmental stressors
Microbiome-Wide Association Studies (MWAS)
MWAS investigates statistical correlations between microbial features and host phenotypes. Our MWAS capabilities include:
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Multivariate association testing between taxa and disease traits
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Integration of metagenomic and clinical metadata
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Statistical correction for confounders (e.g., age, diet, medication)
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Visualization tools (e.g., volcano plots, heatmaps, network analysis)
Our MWAS platform supports both hypothesis-driven and discovery-based approaches to identify candidate microbial biomarkers or functional signatures relevant to health outcomes.
Workflow for Gut Microbiome Sequencing Projects
Creative Biolabs provides a seamless end-to-end workflow, ensuring accuracy, reproducibility, and customization at each step:
What You Receive from Our Microbiome Analysis Service
Upon project completion, Creative Biolabs provides clients with a comprehensive data package that includes:
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High-quality raw sequencing data (FASTQ format)
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Processed data files: taxonomic tables, gene abundance matrices
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Visual reports: PCA plots, heatmaps, rarefaction curves
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Functional pathway annotations (KEGG, MetaCyc)
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Differential abundance and correlation analyses
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MWAS statistical reports (if applicable)
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Optional raw code and computational pipeline documentation
Applications of Gut Microbiome Sequencing
Our gut microbiome sequencing and analysis services are applicable to a wide array of research fields. Some of the key application areas include:
Functional Probiotic Development
Accurate taxonomic and functional profiling of probiotic candidates helps researchers evaluate their colonization efficiency, safety, and metabolic contributions. Shotgun sequencing and metatranscriptomics aid in identifying active pathways such as SCFA production or bile salt hydrolase activity.
Preclinical Microbiota Studies
Our platform supports rodent and in vitro gut model microbiome studies to investigate diet-induced microbial changes, drug-microbiome interactions, and host immune modulation. Metagenomic profiling allows for high-resolution longitudinal tracking.
Infectious Disease and Inflammation Research
Microbiome dysbiosis is implicated in various inflammatory and infectious diseases. Through MWAS and RNA-seq, our services enable the identification of microbial shifts and active inflammatory gene expression signatures in gut-associated disorders.
Personalized Nutrition and Metabolic Health
Understanding how the gut microbiome metabolizes dietary components can inform personalized nutrition strategies. Our functional sequencing platforms reveal microbiota-derived enzymes responsible for fiber fermentation, vitamin synthesis, and bile acid metabolism.
Immune Modulation Mechanism Studies
Transcriptomic insights help characterize microbial signals that influence host innate and adaptive immune responses. Creative Biolabs supports dual RNA-seq studies to examine microbial–host crosstalk at the gene expression level.
Related Services for Microbiome Research
To support microbiome studies comprehensively, Creative Biolabs also offers:
Creative Biolabs is committed to delivering precision sequencing solutions tailored to your microbiome research needs. Whether you aim to explore microbial diversity, discover functional gene expression, or correlate microbiota with host phenotypes, our expert team is ready to assist. Contact us today to start your project.
Microbiome Sequencing Resources
Explains how 16S rRNA's conserved and variable regions enable accurate, culture free bacterial identification with high sensitivity and specificity—ideal for foundational microbial profiling.
Compares targeted 16S profiling and shotgun metagenomics, highlighting trade offs between cost, taxonomic resolution, functional insights, and bioinformatics complexity.
Demonstrates metagenomics' ability to assess biodiversity, temporal shifts, and ecosystem health in environmental and gut microbiome studies.
Covers shotgun metagenomics principles, workflows, and its utility for uncovering genes, metabolic pathways, and strain-level microbial community insights.
FAQs
What is 16S rRNA sequencing for gut microbiome?
16S rRNA sequencing targets conserved and variable regions of the bacterial 16S ribosomal gene to identify and classify gut microbiota, providing a cost-effective method for taxonomic profiling without the need for bacterial cultivation.
How does shotgun metagenomic sequencing differ from 16S rRNA sequencing?
Shotgun metagenomics sequences all microbial DNA in a sample, including bacteria, fungi, viruses, and archaea, offering strain-level resolution and functional insights, while 16S focuses only on bacterial taxonomy using ribosomal gene fragments.
What types of samples are suitable for gut microbiome sequencing?
We accept stool, intestinal contents, biopsy tissues, or in vitro model samples. Proper preservation and timely freezing are essential to maintain microbial integrity for high-quality sequencing and downstream bioinformatics analysis.
Other Resources
References
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Bars-Cortina, David, et al. "Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota." BMC genomics 25.1 (2024): 730. https://doi.org/10.1186/s12864-024-10621-7
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Davenport ER, Cusanovich DA, et al. "Genome-Wide Association Studies of the Human Gut Microbiota." PLoS ONE 10.11 (2015): e0140301. https://doi.org/10.1371/journal.pone.0140301
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Awany D, Allali I, et al "Host and Microbiome Genome-Wide Association Studies: Current State and Challenges." Front. Genet 9(2019):637. https://doi.org/10.3389/fgene.2018.00637
