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We should note here that in our target article we referred to ‘Clostridium difficile’, the spore-forming pathogen in intestines that can cause illness and death. However, in 2016, the genus this organism belongs to was renamed, and we should have said Clostridiodes difficile (Lawson et al. 2016). C. difficile throughout our response now refers accordingly, although it is commonly known as C. diff. Nomenclature may soon become even more complicated because C. difficile appears to be speciating (N. Kumar et al. 2019).
However, FMT risk calculations are likely to increase in practical importance after recent warnings of fatalities following FMTs in immunocompromised hosts (FDA 2019).
Here, we dispute Attah et al.’s (2020) characterization of our position as dichotomous: either individual microbes are causal, or emergent properties are causal. We do not think emergent causation is at work in microbiome-host relationships.
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Lynch, K.E., Parke, E.C. & O’Malley, M.A. Microbiome causality: further reflections (a response to our commentators). Biol Philos 35, 29 (2020). https://doi.org/10.1007/s10539-020-9742-7