Multi-omics Analysis of Gut Microbiota, Metabolites and Aroma Components by Next-Generation Sequencer and GC/MS

Importance of the Topic

The human gut microbiota influences digestion, nutrient metabolism and immune function. Metabolites and aroma compounds produced by microbial activity affect host physiology and may play roles in preventing or treating chronic diseases. Integrating microbial, metabolic and volatilomic data can reveal key interactions but must account for individual variability due to diet, lifestyle and genetics.

Study Objectives and Overview

This work aimed to characterize the gut ecosystem by profiling microbial species, metabolites and aroma compounds in human fecal samples. Monthly samples from a male subject (nine months) and single samples from seven other volunteers (two women, five men) were analyzed. A multi-omics framework combining next-generation sequencing and GC/MS measurements enabled data integration through principal component analysis, volcano plots and metabolic pathway mapping.

Methodology

• Sample collection: fecal specimens collected monthly from Subject A and once from Subjects B–H.
• Microbial profiling: sequencing of the 16S rRNA V1–V2 region on an Illumina MiSeq system, identifying ~250 bacterial species per sample.
• Metabolome analysis: GCMS-TQ8040 NX with Smart Metabolites Database; ~488 primary metabolites quantified using internal standard correction.
• Volatilome analysis: SPME Arrow GC/MS measurement of ~484 aroma compounds at 40 °C using Smart Aroma Database.
• Data analysis: Multi-omics Analysis Package for PCA, volcano plots and metabolic pathway projection.

Used Instrumentation

• Gas chromatograph mass spectrometer GCMS-TQ8040 NX
• Illumina MiSeq next-generation sequencer
• VD-800R freeze dryer and bead-based DNA extraction
• SPME Arrow for aroma compound sampling

Main Results and Discussion

• Gender differences: PCA separated two female outliers, with females showing enrichment in lysine degradation metabolites. Males exhibited relative suppression of pyrimidine metabolism.
• Key discriminant compounds: 2-hydroxyglutaric acid, octanoic acid and 2,5-dimethylpyrazine varied significantly by sex.
• Enterotype stability: Subject A’s microbial enterotype remained consistent over nine months, indicating strong genetic/environmental influences over diet or health fluctuations.
• Bacteria–metabolite correlations: Christensenella abundance correlated positively with taurine biosynthesis and acetoin production, and negatively with certain aroma compounds. Ruminococcus UCG-003 levels affected glycerolipid and para-aminobenzoate pathways and were inversely related to skatole (fecal odor compound).

Practical Applications and Benefits

• Identification of sex-specific metabolic signatures may guide personalized dietary or probiotic interventions.
• Correlating bacterial taxa with health-promoting metabolites (e.g., butyrate producers) supports biomarker discovery for gut health monitoring.
• Longitudinal multi-omics monitoring can inform lifestyle or therapeutic strategies to maintain microbiome balance and prevent disease.

Future Trends and Potential Uses

• Expansion to larger, diverse cohorts to validate and generalize findings.
• Integration of host genomics and transcriptomics with microbiome data for causal inference.
• Development of targeted microbiota-based therapies, precision nutrition products and diagnostic tools.
• Real-time monitoring platforms for personalized gut health management.

Conclusion

A combined next-generation sequencing and GC/MS multi-omics approach successfully characterized the gut microbiota, metabolite and aroma profiles in human fecal samples. The study revealed stable enterotypes, sex-dependent metabolic differences and specific microbe–metabolite associations. These insights lay the groundwork for personalized strategies to monitor and modulate gut health.

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