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Characterizing the Stability of the Gut Microbiome

Key findings

  • Many long-term features of the fecal microbiome were well represented in a single stool sample, including taxonomic composition and metagenomic functional profiles
  • Metatranscriptomes demonstrated greater variability over time and appear to be appropriate markers for short-term exposures, not necessarily long-term relationships between exposure and disease
  • It remains to be determined which microbiome features (if any) will have diagnostic or prognostic value

Understanding normal versus pathological variation over time in the healthy adult fecal microbiome is crucial to using these microbial communities in health care. Examples of these uses include the development of personalized therapies and the use of the microbiome as a predictive biomarker or diagnostic tool.

Building on their previous research, Andrew T. Chan, MD, MPH, instructor in the Department of Medicine, chief of Clinical and Translational Epidemiology and physician in the Mass General Cancer Center, and colleagues report in Nature Microbiology that a single measurement of the fecal microbiome seems to provide long-term information about metagenomics (which microbes are present and what genomic potential they have). However, it may be necessary to make repeated measures of the metatranscriptome, which is an indicator of microbial functional activity.

Dr. Chan's team sequenced fecal microbiomes as part of the Men's Lifestyle Validation Study (MLVS), which is nested within the Health Professionals Follow-Up Study (HPFS), a prospective cohort of 51,529 men followed since 1986. The MLVS was established among 700 men ages 52 to 81 (median age 69) who provided a blood sample and completed the 2010 food frequency questionnaire as part of the HPFS.

The 308 men sampled in this analysis were recruited into the MLVS starting in July 2012 and ending in July 2013. They were asked to collect four stool samples—one pair collected 24 to 72 hours apart and a second pair about six months later. Altogether, 378 samples were evaluated from men who collected samples at both time points and had not used antibiotics during the past year.

The Fecal Metagenome Was More Stable than the Metatranscriptome

The researchers began by comparing the within-person stability of the fecal metatranscriptome (functional elements from RNA) with the stability of the taxonomic composition (species from DNA) and the metagenome (functional elements from DNA) over both short (24–72 hour) and intermediate (six-month) intervals. Confirming an earlier pilot study by the team, the metagenomic functional potential (DNA) was more stable than the metatranscriptome (RNA), which in turn was more stable than the taxonomic composition.

The metagenomic, metatranscriptomic and taxonomic features that remained stable within a subject over a 24- to 72-hour period tended to be similarly stable over six months. This suggests that a subset of features exists that can be consistently measured over time.

Between-person Exceeded Within-person Metagenomic Variation

Over time, variation in taxonomic composition and metagenomic functional potential of the microbiome was greater between subjects than within subjects. This was true over both the short and intermediate time intervals. In contrast, for metatranscriptomes, within-subject variation was similar to between-subject variation.

A single measurement of the fecal microbiome can provide long-term information regarding taxonomic composition and functional potential in an individual. Repeated or short-term measures may be necessary to evaluate the dynamic features identified by metatranscriptomics.

Relationship Between Metagenomic and Metatranscriptomic Stability

Approximately 74% of the instability in the fecal metatranscriptome could be explained by instability in the fecal metagenome. Some of the most highly stable, as well as highly abundant and prevalent species, such as Bacteroides uniformis, were responsible for the dominant expression of a large number of stable genes.

By comparison, Streptococcus salivarius—an unstable species that was probably in transit from the oral cavity—dominantly expressed many of the most variable genes.

Stability of Gene Expression

The research group reports similar findings about the regulation of gene expression. Of the genes identified as significantly differentially transcribed, 79% were consistently over- or under-expressed. Many of the stably expressed pathways were those that are essential to cellular function or are involved in glycolysis, synthesis of amino acids or production of short-chain fatty acids.

Much of the metatranscriptomic variation in stool over time might reflect changes in gene family copy number, driven by factors such as the proliferation of microbes, introduction of new species or host-induced shifts in community structures. In contrast, in the face of relative metagenomic stability, substantial deviations from a common genomic profile may be associated with shifts in disease states.

It remains to be determined which microbiome features (if any) will have diagnostic or prognostic value.

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