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

The ISME Journalvolume 12pages24032416 (2018) | Download Citation


Endospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endospores in situ and how sporulation varies across individuals and over time. Here we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.

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We thank Fatima Hussain and Mathieu Groussin for extensive discussion and experimental advice. We thank the MIT BioMicro Center for sequencing service. We thank the members of the Losick lab for helpful advice and feedback on assaying sporulation phenotypes. Special thanks to Claire Duvallet for feedback on figure design and editing and manuscript clarity as well as the MIT Biological Engineering Communication Lab. We thank the members of the Alm Lab in general for intellectual support, discussion of data, and design of experiments. We thank Hilary Browne for discussions involving the cultivation and revival of endospore-forming organisms in the gut.We thank the MIT BioMicro Center for sequencing service. We thank the Chisholm lab and the Weiss Lab at MIT for allowing us to use their microscopes and qPCR machines.


The funding was provided by the Broad Institute BN10 Training Grants. S.M.K. was funded by an NSF Graduate Research Fellowship.

Author information


  1. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    • Sean M. Kearney
    • , Sean M. Gibbons
    • , Mathilde Poyet
    • , Thomas Gurry
    •  & Eric J. Alm
  2. The Broad Institute, Cambridge, MA, USA

    • Sean M. Kearney
    • , Sean M. Gibbons
    • , Mathilde Poyet
    • , Thomas Gurry
    • , Kevin Bullock
    • , Clary B. Clish
    •  & Eric J. Alm
  3. The Center for Microbiome Informatics and Therapeutics, Cambridge, MA, USA

    • Sean M. Kearney
    • , Sean M. Gibbons
    • , Mathilde Poyet
    • , Thomas Gurry
    •  & Eric J. Alm
  4. Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA

    • Jessica R. Allegretti
  5. Harvard Medical School, Boston, MA, USA

    • Jessica R. Allegretti


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The authors declare that they have no conflict of interest.

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Correspondence to Eric J. Alm.

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