The authors portray the belly button as a unique bacterial community. However, they also suggest that microbial diversity on the belly button skin could play some role in allergies. How would the microbial diversity, and the congruent skin immune function, of such a small patch of skin relate the a body-wide allergy?
The study found three phylotypes of Archaea, a domain of life typically found in extreme environments and not previously found on human skin. As two of these three phylotypes were found on an individual who reported not having showered for several years, what condition do you think is provided by this lack of hygiene that makes a habitable environment for this rare domain?
The article "A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable." talks a lot about how the belly button bacterial phylotypes were very diverse. Are phylotypes found in different locations of the body on various individuals also usually diverse. In other words, are the phylotypes found on an individual on any part of their body unique to that person?
Do you think that the number of samples collected in the Belly Button Diversity study fairly represents the biodiversity of these populations, especially considering every sample came from a volunteer?
Why do you think Klebsiella was found in the 1975 belly button study, but was completely absent from this study's results?
By rarefying the data, the researchers state that they lost a number of bacterial phylotypes under consideration. Do you think the researchers needed to sacrifice any of their data analysis in order to make the number of reads consistent per belly button? In other words, by decreasing the number of bacterial phylotypes under consideration as a result of rarefying the data, could researchers miss something important?
From the article, "A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable", it states that there was not even one organism that was recognized throughout all samples. Results also showed that the "...most successful phylotypes are from only a few linages". Why are the bacterial organisms so diverse among humans, yet there are still a few lineages throughout the study that are the most common even though each of our lifestyles are unique?
In the Hulcr 2012 article, they claim that they are looking at two separate populations even though both "populations" came from people within the same city (Raleigh, NC). Do you think these two data sets really represent two separate populations or do you think they would have found different results if they had used samples from more diverse populations (ex: different countries, climates, hygiene culture, etc.)? Do you think this concern is validated by the fact that they found unique archaebacteria in the individual who reported not bathing or showering?
In the primary article, the authors conclude that the average number of species per belly button was about 67 with the highest number being 107 and the lowest being 29. They also note that this could be attributed to differences in health and well-being. Do you think this could have some relation to the prior study about HGC and LGC with higher and lower numbers of species corresponding to varying levels of health?
In the article from Hulcr et al., the authors used only two subsamples whose contents only added up to 60 individuals. Do you think this negatively impacts their conclusions? These individuals were also concentrated around Raleigh, NC. Do you think, had the researchers used samples from across the country, they would have arrived at similar results? Why or why not?
The article by Hulcr et al described subset of frequent phylotypes to be "predictably present and predictably abundant." Since they do not have specific species identified for these similar phylotypes, do you think that the differences between these phylotypes are due to many different species or a result of horizonal gene transfer between a few species?
The primary lit article states that no phylotypes were present on all individuals sampled. Can you suggest some reasons as to why people seem to have such a difference in the diversity of their belly button microbiota, especially given that these samples were taken from people who (I assume) seem to live in the same general area?
The paper states that the bacterial communities in the belly button are “at least as diverse as communities from other skin studies,” and that there are 6 phylotypes that are present on more than 80% of humans. Is this phylotype specific localization present on other areas of the epidermis—for example in between the fingers, under the arms, or between toes—to the same statistical predictability as the phylotypes found in the belly button?
In the Bellybutton article, they only analyzed samples from 60 subjects in North Carolina. Do you think that similar patterns of diversity would be found if they looked at 60 subjects in a different environment? How about 60 random subjects from across the country/world? Basically, how generalizable are these results?
In the paper “Phylogenomics and the reconstruction of the tree of life”, the authors state “the limitations of current phylogenetic reconstruction methods mean that part of the tree of life might prove difficult” and data quality and inference methods are important for phylogenetic analyses. Then specifically what the limitations are and how to determine whether quality of the data is good enough or not.
What factors influence belly button biodiversity? Do a person’s genes play a role? What about their washing habits and other environmental factors? Do people in close contact with one anther (friends and families) have similar microbes in their belly button? Are the microbes found in a person’s belly button fairly consistent over time or do they change?
"...we found that while belly button bacterial phylotypes were diverse, aspects of this diversity were predictable."
Do you think rarefying the data affects the credibility of the above conclusion reached? They used Roche/454 sequencing which usually utilizes de novo assembly, what limitations caused them to still have to rarefy the reads?