Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota.

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PubMed ID: 29899513

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Kearney SM, Gibbons SM, Poyet M, Gurry T, Bullock K, Allegretti JR, Clish CB, Alm EJ

ISME J. Oct 2018. doi: 10.1038/s41396-018-0192-z

COMMENT: This paper implements a resistant cell fraction enrichment protocol from human fecal samples and 16S rDNA sequencing to investigate the presence of bacteria with resistant states in the mammalian gut environment and whether these resistant states contribute to prevalence and transmission to new host.


Here we investigate which organisms are present as endospores or as other resistant cell types in the human gastrointestinal tract. We modified previously described methods to enrich fecal samples for endospores and obtain paired bulk community and resistant fraction 16S rDNA sequence data for 24 healthy individuals and one individual across 24 days.


We consistently enriched for putatively endospore-forming taxa in all samples, as well as other taxa, predominantly from the Actinobacteria phylum, that show high levels of lysis resistance.

All of the resistant OTUs (rOTUs) are either Firmicutes or Actinobacteria. In fact, when grouping OTUs at the genus level, the top two most enriched genera (Bifidobacterium, Collinsella) are both Actinobacteria.

We compared resistant OTUs (rOTUs) and non-resistant OTUs (nOTUs) to identify ecological characteristics differing between these groups….rOTUs are more shared than nOTUs among individuals.

Using a database of rOTUs identified in this study, we find consistent signals for these organisms in their responses to a variety of successional states across multiple independent datasets.

Overall, we show a tight association between the ecological role of these resistant organisms and their distribution within and across human hosts.


Gut bacteria in the resistant fraction were more shared across individuals and showed more correlated dynamics compared to non-resistant organisms.

Resistant taxa show greater turnover following large-scale disturbance events, as in the case of C. difficile and Salmonella infection, which suggests that many of these organisms are sensitive to environmental fluctuations and respond to stress by entering into a dormant, seed-like state.

The growth of many resistant organisms was associated with dietary fatty acids.


Diana López-Farfán