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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Temporal variability in quantitative human gut microbiome profiles and implications for clinical research
Doris Vandeputte1,2, Lindsey De Commer1, Raul Y Tito1,2
1KU Leuven - University of Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Herestraat 49, B-3000, Leuven, Belgium.
Nature Communications
|November 19, 2021
Summary
Daily gut microbiome analysis revealed significant temporal variation, with most genera showing greater day-to-day shifts within individuals than between them. Stool moisture and diet were key drivers of this gut microbiota variability.
Area of Science:
- Microbiology
- Human Microbiome Research
- Metagenomics
Background:
- Understanding gut microbiota variation is crucial for clinical research.
- Temporal variability and its comparison to cross-sectional variation are under-explored.
- Reference knowledge of healthy gut microbial dynamics is needed.
Purpose of the Study:
- To investigate the temporal variability of the human gut microbiota.
- To compare within-subject and between-subject variation.
- To identify drivers of gut microbiota temporal fluctuations.
Main Methods:
- Daily quantitative microbiome profiling of 713 fecal samples from 20 women over six weeks.
- Collection of anthropometric, blood, dietary, and stool characteristic data.
- Analysis of temporal and cross-sectional variation in microbial abundance and diversity.
Main Results:
- Most major gut microbial genera exhibited substantial day-to-day absolute abundance variation, often exceeding between-subject variation.
- Up to 100-fold shifts in microbial abundance were observed over the study period.
- Stool moisture and diet were identified as significant covariates of temporal microbiota changes, while menstrual cycle did not show significant effects.
Conclusions:
- Gut microbiota composition exhibits significant temporal instability within individuals.
- Repeated measurement designs and analysis of community-wide microbiome descriptors may enhance diagnostic and target discovery power.
- The dysbiotic Bact2 enterotype displayed increased variability.
