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Nature versus Nurture in the Differentiation of the Oral Microbiome

Posted by jkaufman1 on 14 Nov 2013 at 22:01 GMT

This paper by Mason and colleagues analyzes data on 48 people in each of 4 self-identified ethnic groups (African American, Caucasian, Chinese, and Latino). These study subjects are apparently volunteers, and the paper only states that they are non-smokers over 18 years old who are free of a list of diagnosed diseases and who have not recently had their teeth cleaned. Based on the text of the published paper, there is no consideration of their age, diet, social class, or even gender. The authors culture bacterial species from the study subjects and process the data through an algorithm that maximizes the prediction of racial group membership based on these measured data.

The prediction is moderately successful, but this could result from any number of unsurprising reasons. For example, if alcohol consumption affects some particular bacterial species, and whites drink more than Asians in central Ohio, then whatever species is diminished by alcohol exposure would help predict that a sample was from a white rather than from an Asian volunteer. And likewise for any of a million possible lifestyle, social class and demographic differences. The authors provide no information about how balanced this sample is with respect to any of these variables. Maybe the 48 Hispanics are younger than the 48 whites on average, or have more tooth decay or eat more refined sugar or any of a million other possibilities. The fact that these countless potentially imbalanced factors get represented in the oral bio-environment hardly seems surprising, and the fact that these behaviors and exposures might be differential by race is an observation that is completely trivial from a sociological perspective.

Astonishingly, however, the authors assert in the published text that these differences do not arise from any of these myriad environmental factors, but from some innate genetic characteristics of the groups. In the Discussion section on page 3 they state that "ethnicity exerts a selection pressure on the oral microbiome, and...this selection pressure is genetic rather than environmental, since the two ethnicities that shared a common food, nutritional and lifestyle heritage (Caucasians and African Americans) demonstrated significant microbial divergence." Here is a remarkable statement, that Caucasians and African Americans experience no differential dietary or lifestyle factors. It is directly contradicted by thousands of published papers in sociology, epidemiology and anthropology that document these differences for reasons of culture, geographic origin, social class and discrimination.

A previous comment on this point has already already been posted by Jonathan Eisen, an evolutionary biologist at UC Davis. The authors responded to this point with the following explanation:

"Subjects were selected based on extensive questionnaire surveys and clinical examinations to ensure homogeneity. These questionnaires evaluated educational level, socio-economic status, diet and nutritional history, systemic health status, oral hygiene habits and dental visits, among other things."

This is an important statement about the research design, but the problem is that it appears nowhere in the peer-reviewed text of the published paper. What exactly do the authors mean when they insist that the study subjects were perfectly balanced on factors such as socio-economic status and nutritional history? These complex social and lifestyle variables are notoriously difficult to define and measure. While the authors describe the laboratory techniques in baroque detail, they do not even mention in the published paper that they measured these factors, let alone how these variables were defined and considered in the analysis. This represents a profound limitation for the reader in assessing the validity of these measures and adjustments, and therefore the adequacy of the claimed "homogeneity". The complete omission of these crucial aspects of the analysis in the paper prevents the reader from investing much confidence in the boldly stated claim that observed differences are "genetic rather than environmental" in origin.

Jay S Kaufman, McGilll University
Duana Fullwiley, Stanford University

No competing interests declared.