Merge pull request #62 from cherman2/microbiome-edits

minor formating fixes

13-microbiome.Rmd

@@ -14,6 +14,7 @@ This chapter is incomplete! If you wish to contribute, please [go to this form](
 ```{r, fig.alt = "Learning Objectives", out.width = "100%", echo = FALSE}
 ottrpal::include_slide("https://docs.google.com/presentation/d/1YwxXy2rnUgbx_7B7ENH9wpDX-j6JpJz6lGVzOkjo0qY/edit#slide=id.g2668d07d0b9_0_0")
 ```
+
 ## A Brief Introduction to Microbiomes
 
 
@@ -35,7 +36,9 @@ Microbes almost never live alone in the real world (i.e., outside of a laborator
 
 Microbiome science is everywhere. There are tens of articles published daily in the scientific literature, and many popular science articles and books present these findings to the world of non-scientists. Understanding the promises and limitations of the methods of microbiome science can help avoid misconceptions about microbiome research, and it’s important for practitioners of microbiome science to understand and convey the promise and limitations of our field. Misconceptions abound, frequently arising from the same sources as high-quality popular science microbiome reporting.
 
-    For example, on 5 Feb 2015 an article appeared in the New York Times noting (almost offhand) that Yersinia pestis, the organism responsible for Bubonic plague, had been found in multiple locations throughout the New York City subway system as part of its normal built environment microbiome. This was rapidly followed up on 6 Feb 2015 with an article noting that there was probably not Bubonic plague on the subway system after all, but rather that the approaches used by the research team are limited in their taxonomic resolution, and that likely a harmless close relative of Y. pestis was observed: “What the researchers probably found, [a spokesman for the university where the study originated] said, was bacteria from an unknown species or from organisms that happened to share some gene sequences with the plague bacterium…”.
+```
+For example, on 5 Feb 2015 an article appeared in the New York Times noting (almost offhand) that Yersinia pestis, the organism responsible for Bubonic plague, had been found in multiple locations throughout the New York City subway system as part of its normal built environment microbiome. This was rapidly followed up on 6 Feb 2015 with an article noting that there was probably not Bubonic plague on the subway system after all, but rather that the approaches used by the research team are limited in their taxonomic resolution, and that likely a harmless close relative of Y. pestis was observed: “What the researchers probably found, [a spokesman for the university where the study originated] said, was bacteria from an unknown species or from organisms that happened to share some gene sequences with the plague bacterium…”.
+```
 
  As microbiome services and products are increasingly marketed directly to the public, consumers of microbiome research findings, products, and services need to know how to critically evaluate these offerings and their associated claims. As practitioners in the field, we can help by ensuring that the methods we apply are appropriate and reliable, and that we make our work accessible.