Team:Paris Bettencourt/Project/Bioinformatics

Figure 1. Log-scale abundance profiles of body-odor related genes at the five different body sites in males and females.


Figure 2. Abundance of body odor related genes (ackA, leuD, apoD, fadA, fadB, fadD, and fadE) in five different body sites: ear, mouth, nose, stool, and vagina. The data was derived from the HUMAnN analysis of the Human Microbiome Project database. The data was collected for fifteen different body sites; for this analysis, however, the fifteen body sites were combined into the five main ones listed above.

Meta-Analysis of Odor-Related Genes

Introduction
The National Institute of Health's (NIH) Human Microbiome Project (HMP) attempted to "characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health." There were several studies that sprouted from the data produced by the HMP, and one such study was done by the Huttenhower lab called HUMAnN: The HMP Unified Metabolic Analysis Network, a pipeline for efficient and accurate determination of the presence or absence and abundance of microbial pathways in a community using metagenomic data.

The abundances for each orthologous gene family (or groups of genes that perform approximately the same biological role) was reported in the units of read hits. This particular analysis used the KEGG Orthology (KO) database. Read hits refer to a read that maps to a gene sequence within a particular KO. These hits are weighted using two ways: 1. If a read hits multiple sequences, its weight is distributed among them in proportion to the strength of each mapping and 2. hits to longer sequences are down-weighted, since longer sequences contribute more reads to a metagenome due to the random sampling process of metagenomic studies.

The goal of this sub-project was to find genes related to odor from the HUMAnN analysis and see how the odor profile of various body sites (ear, nose, mouth, vagina, stool) and genders varies.

Discussion
There is not a large difference in odor profile between males and females at the body sites sampled. As seen in Fig. 1, in general, the abundance of odor related genes was slightly lower for women than for men; however, the general trend remained the same with both genders.

The difference in odor profile between the five body sites was more stark. Fig. 2 shows the abundance of the seven odor related genes found in the HUMAnN analysis at the varying body sites. It is clear from this figure that acetate kinase (ackA), involved in fermentation pathways which can generate lactic acid and glycerol which can lead to the formation of carboxylic acids that contribute to acidic odor, is most abundant in vaginas. Leucine dehydrogenase (leuD), on the other hand, which leads to the formation of isovaleric acid (a compound with a characteristic cheese smell), is found to be most abundant in the ear.

Outer membrane lipoprotein Blc (apoD) is found to be most abundant in stool samples, which is interesting since this particular protein is most expressed in the apocrine glands, which are found in some parts of the external genitalia. It may be that some of the proteins expressed in the apocrine glands were transported into the stool samples. Finally, fatty acid dehydrogenases (the fad genes) were very abundant in the nose (which the exception of fadD which was found in large abundance in almost all the body sites). These genes are involved in fatty acid metabolism, which can generate volatile fatty acids, typically associated with odor.

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