Introduction to Gut Microbiota

The gut microbiota represents a thriving and intricate community of symbiotic microbes inhabiting the animal gastrointestinal tract. Comparable to an organ in its own right, gut microbiota conduct a plethora of physiological functions that encompass metabolism, immunological regulation, and endocrine operations. Beneficial microbes play a cardinal role in normal gut functionality: they aid in moisture absorption, vitamin synthesis, the mitigation of harmful substances, and the prevention of pathogenic invasion. In contrast, an excess of harmful microbes can lead to invasive pathogens, alterations in gut motility, production of detrimental substances, and poor waste excretion.

The gut microbiota and its metabolic products have been identified as significant players in human health and disease; hence, studying the correlations between gut microbiota metabolites and diseases holds considerable potential for disease prevention and management.

CD Genomics proffers leading-edge, integrated research solutions for the study of gut microbiota, employing advanced metabolomics and high-throughput sequencing technologies.

Our Advantages:

Detection of low abundance species of microbial communities
Flexible sequencing strategies and data analysis
Reliable, high-throughput and sensitive platform for gut metabolomics analysis
Years of commercial experience in life sciences
Quick and affordable services

The advancement in modern technology has fostered a shift towards an integrative approach in the study of gut microbiota. More researchers are harnessing the synergy of microbial sequencing and metabolomics analyses to comprehensively research the gut microbiota and its impact on human health.

Why Adopt Gut Microbiota Sequencing

Employing the advanced high-throughput sequencing technology of 16S rRNA, we can probe the diversity of microbes present in intestinal content or fecal samples. This approach not only permits the taxonomy of gut microbiota at the genetic level but also discloses core details such as microbial species richness, abundance, and distribution. Gathering comprehensive data on the microbiome will offer a wellspring of resources for intricate phenotype analysis, thereby expediting the discovery of therapeutic agents.

Our Gut Microbiota Sequencing Service

To explore the assembly of gut microbial communities, CD Genomics is equipped with various sequencing platforms which include Illumina, PacBio SMRT system and Nanopore system.

We have undertaken testing and analysis of a range of gut microbiota specimens, enabling us to assist in identifying the diversity and relative abundance of microbes resident in the gut, along with their phylogenetic relationships. This, thus, provides comprehensive insights into the gut microbiome at the genetic level.

Bioinformatics Analysis

Basic Analysis	Routine Analysis (According to Customer Requirements)	Advanced Data Analysis
Sequence Filtering and Trimming	Heatmap	Phylogenetic Tree
Sequence Length Distribution	VENN	LDA-Effect Size (LEfSe)
OTU Clustering and Species Annotation	Principal Components Analysis (PCA)	Network Analysis
Diversity Index	Microbial Community Structure Analysis	Correlation Analysis
Shannon-Wiener Curve	α Diversity Index Analysis
Rank-Abundance Curve	Matastats Analysis
Rarefraction Curve	Weighted Unifrac test
Multiple Contrast	CCA/RDA Analysis
Heatmap
Principal Components Analysis (PCA)

Workflow

gut-microbiota-research-solution

Sample Requiremen

DNA sample: total DNA ≥ 300 ng, concentration ≥ 10 ng/uL, OD260/280=1.8-2.0
Be ensure that the DNA is intact and non-degradative, avoiding repeated freezing and thawing cycles.
Please use enough dry ice or ice packs during shipment.
We provide a broad range of oral and fecal sample collection kits for microbial recovery and analysis.

Deliverables

Experimental procedure
Experiment parameter
Original data
Results of sequencing analysis

Sequencing Analysis of Gut Microbiota FAQ:

1. What is gut microbiota responsible for?
- The gut microbiota not only plays an integral role in the digestion and absorption of food for bodily energy supply, but also contributes significantly to the regulation of immune function and participation in metabolic responses within the body. Its capabilities even extend to impacting endocrine functions, suggesting a potential role in the modulation of energy balance, glucose metabolism, and inflammatory responses.
2. What are the 3 types of gut microbiota?
- The primary constituents of the gut microbiota include commensal bacteria, conditional pathogens, and pathogens. Commensal bacteria, often deemed beneficial microbes, mainly comprise various Bifidobacterium species, Lactobacillus species, and others. Conditional pathogens or neutral microbes encompass strains such as Escherichia coli and Enterococcus. Pathogens or harmful microbes incorporate species such as Salmonella and Clostridium perfringens.
3. What is the role of 16S rRNA sequencing analysis in the study of gut microbiota?
- 16S rRNA sequencing represents a pivotal methodological approach in gut microbiota research that relies on high-throughput sequencing. This technique elucidates the compositional structure of the microbial community, explores microbial biodiversity, identifies potential pathogens, monitors therapeutic efficacy, and guides in personalized nutritional interventions.
4. What are the methods for gut microbiome sequencing?
- The methodologies predominantly employed for the examination of gut microbiota encompass 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), microarray technologies, metagenomics, and meta-transcriptomics.

Demo:

gut-microbiota-research-solution Integrated 16S rRNA Gene Sequencing and Metabolomics Analysis to Investigate the Important Role of Osthole on Gut Microbiota and Serum Metabolites in Neuropathic Pain Mice. (Ruili Li et al., 2022)

Introduction to Gut Microbiota Metabolomics

Gut microbiota primarily interacts with its host through the intimate exchange of information via their small molecule metabolites. This interaction plays a pivotal role in various physiological aspects such as metabolism, immunity, diseases, as well as the development and regulation of the nervous system. These microbes significantly influence the host's digestive absorption capacity, resistance to infection, and the host's response to therapeutic drugs, thereby dictating health and disease status in the organism.

Microbiome metabolomics, a field that employs metabolomics technologies to analyze the dynamic variations in the metabolites of gut microbes, aims to identify key microbial metabolites associated with pathological variations in the host. By determining biologically relevant biomarkers associated with specific diseases, microbiome metabolomics can provide innovative methodologies for clinical diagnoses, while charting new directions and insights for therapeutic developments.

Our Gut Metabolomics Services

In a bid to decipher the complexities of the gut microbiome, CD Genomics has established an accurate, sensitive and high-throughput analytics platform for gut metabolomics. Different metabolomics methodologies are employed depending on the design and requirements:

Untargeted metabolomics analysis of the gut microbiota metabolites
Targeted metabolomics analysis of the gut microbiota metabolites
Lipidomics analysis of the gut microbiota metabolites
Stable isotope-assisted metabolic flux analysis of the gut microbiota metabolites

The metabolites we are capable of analyzing encompass short-chain fatty acids, bile acids, secondary bile acids, metabolites of choline, phenolic compounds, indoles, polyamines, lipids, vitamins, hormones, lipopolysaccharides, and trimethylamine, among others.

Bioinformatics Analysis

Univariate statistical analysis
Multivariate statistical analysis
Variance analysis
Annotation analysis of differential substances
Metabolic pathway analysis

Gut Microbiota Metabolomics Workflow

gut-microbiota-research-solution

Sample Requirement

Serum, plasma ≥ 200 ul/sample
Urine ≥ 500 ul/sample
Tissue ≥ 200 mg/sample
Cell ≥ 1×10⁷/sample
Cerebrospinal fluid ≥ 200 ul/sample
Stool and intestinal contents ≥ 500 mg/sample
For other sample types, please consult our technicians.
Note: Avoid repeated freezing and thawing.

Deliverables

Experimental procedure
Mass spectrometry parameters
Mass spectrum picture
Original data
Results of metabolomics analysis

Gut Microbiota Metabolomics FAQ

1. What are the metabolites from the gut microbiota?
- The metabolites primarily generated by the intestinal microbiota encompass lipopolysaccharides, peptidoglycans, trimethylamine, trimethylamine N-Oxide, secondary bile acids, in addition to short-chain fatty acids, among others.
2. What problem is metabolomics used to solve?
- Metabolomics predominantly investigates the metabolic pathways of endogenous metabolites in organisms, organs, or tissues, as well as the influence of intrinsic or extrinsic factors and their temporal dynamics. By unveiling comprehensive metabolic alterations resulting from various internal and external influences, metabolomics captures a series of biological events occurring throughout specific pathophysiological processes.
3. What are the methods of metabolomic analysis?
- At the current stage, the most extensively applied methods in metabolomics research encompass Nuclear Magnetic Resonance spectroscopy (NMR) and Mass Spectrometry (MS) used in conjunction with Gas Chromatography (GC), Liquid Chromatography (LC), or Capillary Electrophoresis (CE).

Demo:

The Implications of Integrative Analysis Through Metabolomics and Sequencing

By integrating and interpreting 16S rRNA sequencing data and metabolomics, it is possible to uncover associations between specific microbial constituents and metabolite groups. This can aid in selecting key strains attributable to variations in microbial metabolic status or functional metabolites. Additionally, exploring the interconnection between metabolites, microbes, and disease through combined metabolomic and 16S rRNA sequencing analyses may facilitate the discovery of biomarkers consequential to disease, fostering their further application in clinical diagnostics.

Our Integrative Analysis Services

CD Genomics, harnessing a varied array of analytical tools such as GC-MS, LC-MS, and Nuclear Magnetic Resonance (NMR), provides targeted and non-targeted metabolomic analysis services for a broad range of samples. Along with 16S rRNA sequencing service integrated with customizable bioinformatics, CD Genomics offers a holistic one-stop solution from experiment design, sample testing, to data analysis– catered to meet multiple detection needs.

Bioinformatics Analysis

Diversity Analysis
Functional analysis
Correlation analysis
Metabolic pathway analysis
Annotation analysis of differential substances
Association analysis between microbial species and metabolites
Correlation analysis of differential functional pathways and metabolites
Correlation analysis of metabolic function and metabolites of different strains
Association analysis of microorganisms and metabolites (broad categories)

Gut Microbiota Integrative Analysis Workflow

gut-microbiota-research-solution

Sample Requirement

DNA sample: total DNA ≥ 300 ng, concentration ≥ 10 ng/uL, OD260/280=1.8-2.0
Be ensure that the DNA is intact and non-degradative, avoiding repeated freezing and thawing cycles.
Please use enough dry ice or ice packs during shipment.
We provide a broad range of oral and fecal sample collection kits for microbial recovery and analysis.
Serum, plasma ≥ 200 ul/sample
Urine ≥ 500 ul/sample
Tissue ≥ 200 mg/sample
Cell ≥ 1×10⁷/sample
Cerebrospinal fluid ≥ 200 ul/sample
Stool and intestinal contents ≥ 500 mg/sample
For other sample types, please consult our technicians.
Note: Avoid repeated freezing and thawing.

Analysis of genomics and metabolomics correlations requires that identical types of samples are separately prepared prior to cryopreservation for both microbial sequencing and metabolomics profiling. This preparation involves taking samples of different types during the same time window, a process without which association would be impossible.

Deliverables

Experimental procedure
Experiment parameter
Mass spectrum picture
Original data
Results of metabolomics analysis and microbiome sequencing

Integrative Analysis Through Metabolomics and Sequencing FAQ

1. What are the advantages of integrating metabolomics and genome analysis?
- The integrative analysis of metabolomics and genomics data provides a more comprehensive pool of quantifiable data, thereby facilitating a holistic interpretation of molecular characteristics, varying pathophysiological states, effects of pharmacological interventions, and alterations due to stress perturbations. This approach has the potential to reveal intricate molecular mechanisms underlying various diseases.
2. Where integration studies of metabolomics and genomic data can be applied?
- The integration of metabolomics and genomics data in research widely applies to various aspects of fundamental medicine, clinical diagnostic procedures, and pharmaceutical development.
3. What is multi-omics integrative analysis?
- The integration of multi-omics data refers to the aggregation, comparative scrutiny, and correlation analysis of big data derived from various biomolecular levels, such as genomics, transcriptomics, proteomics, and metabolomics, through normalization procedures and statistical approaches. This strategy allows for the elucidation of interconnections amongst molecular entities across different tiers.

Demo:

gut-microbiota-research-solution

Integrated 16S rRNA Gene Sequencing and Metabolomics Analysis to Investigate the Important Role of Osthole on Gut Microbiota and Serum Metabolites in Neuropathic Pain Mice. (Ruili Li et al., 2022)

Reference

Li R, Wang F, Dang S, et al. Integrated 16S rRNA Gene Sequencing and Metabolomics Analysis to Investigate the Important Role of Osthole on Gut Microbiota and Serum Metabolites in Neuropathic Pain Mice. Frontiers in Physiology, 2022, 13: 813626.