Microbial Communities found within the human body

Microbial Communities found within the human body


The study by Costello et al., (2009) explored the distribution of bacterial communities in the gut, oral cavity, internal auditory canal, nostrils, hair, and skin in healthy individuals. This study aimed at establishing the spread of different bacterial species in different and their adaptation to different body environments and places. The study intended to identify the different communities of bacteria in the human body, mainly in 27 body sites. Seven to nine adults participated in the study. The study was extensive because it surveyed the human-associated microorganisms of different phylum using modern sequencing techniques to identify bacterial communities in the human body. The molecular technique used in this study was the multiplexed barcoded pyrosequencing. Samples were analyzed using the bacterial 16S ribosomal RNA (rRNA) gene to identify the microorganisms. The DNA of bacteria was amplified by polymerase chain reaction (PCR). The phylogeny-based metric UniFRac used to compare the different communities and groups in order to identify different bacterial phylum. The UniFRac method was used to determine the phylogenic distance of different bacteria.  The relatively shorter distance of UniFrac is an indication that those microorganisms may be similar, consisting of families with a common evolutionary background. The difference in the communities’ composition was primarily determined by body habitat. Within the habitats, individuals showed minimal temporal variability, while interpersonal variability was high. The skin communities were diverse and harbored different communities than the gut and mouth.

The authors collected bacteria of 22 phyla. However, most of the bacteria (92.3%) belonged to the phyla Actinobacteria (36.6%), Firmiticus (34.3%), Proteobacteria (11.9%) and Bacteroides (9.5). Interestingly, the suborder Propionibacterineae was abundant (60-80%) in hair, forehead, external nose and external ears hence referred to as the “head group”. The suborder Propionibacterineae belongs to the phyla Actinobacteria and orden Actinomicetales (LPSN). However, in the “group arm” (forearms, palms, index fingers), Propionibacterineae were less abundant (20-40%). The trunk and legs were dominated by Staphylococcus and Corynebacterium. The bacteria Lactobacillus spp. were abundant in the women’s system urogenital. Lactobacilli are microorganisms of the normal flora that are common in the system urogenitae of women. These bacteria have probiotic properties such as the production of acid, bacteriocines, hydrogen peroxide, and biosurfactants that protect the host (Reid, 2001). On the other hand, Actinobacteriaropionibacterineae, Corynebacterineae, Micrococcineae, and Firmicutes (Staphylococcus spp.) were abundant in the skin, hair, and within the nostrils. In the oral cavity, the most abundant bacteria were Streptococcus (18.7%), Pasteurella (15.9%), Veillonella (13.9), Prevotella (13.6%s), and Neisseria (9.9%). Within the external auditory canal it was found that the microorganisms Carnobacteriaceae (30.8%), the genus Staphylococcus (24.1%), Propionibacterineae (20%), and Bifidobacteriales (19.2%) enjoyed the majority of the dominance share. The results of this study revealed that normal microbiota was found in healthy individuals. In addition, it is interesting to note that the microbiome varied among the participants.

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 Bacterial diversity in the external auditory canal, hair, oral cavity, gut, skin, and nostril in healthy individuals

                   Glossary scientific terminology

Microbiota or microbiome: is the group of microorganisms that live in the human body.

16S rRNA: is the 16S ribosomal RNA and is used in gene sequencing to study the phylogeny and taxonomy of bacteria.

Unifrac: is a method of calculating the distance between microbial communities using the phylogenic information.

Actinabacteria: is a group of Gram-positive bacteria.

Firmiticus: are Gram-positive bacteria that include the Enterococcaceae, Lactobacillaceae families, Lactococcus species, and numerous species that belong to the Clostridia class (Gallo and Hooper 2012).

Proteobacteria: This represents a set of bacteria that mainly include several pathogens such as Escherichia, Salmonella, Helicobacter, Vibrio (Mims et al., 2004).

Bacteroides: this group of bacteria includes Gram-negative, obligate anaerobic, and non-endospore forming bacilli (Gallo and Hooper 2012).

Staphylococcus: is a Gram-positive bacteria that forms clusters as a bunch of grapes. The Staphylococcus aurous is a pathogen that causes infections. Some strains are resistant to antibiotics as S. aureus Methicillin-resistant (MRSA) (Mims et al., 2004).

Corynebacterium: is Gram-positive rod-shaped bacteria that serve as human pathogen.

Lactobacillus: is a Gram-positive, facultative anaerobic rod-shaped microorganism. This bacterium is common in the intestine, vagina, and mouth.

Propionibacterium spp.: is a rod-shaped Gram-positive anaerobic bacteria. These bacteria grow slowly and do not form spores.

Polymerase Chain Reaction (PCR): is the technology that serves to amplify the DNA sequences.

Pyrosequencing: is a technique responsible for the DNA sequencing based on the synthesis sequencing principle.


These study findings are very critical and interesting in regard to understanding these tiny organisms. In addition, these findings because determined the biogeography of microbial communities in healthy individuals in order to have a baseline to detect the differences associated to diseases. The baselines of the healthy individuals in different times were important to establish the normal microbial communities that can have a role in skin protection. The skin is a powerful barrier that prevents the entrance of pathogens inside the human body. This research will explore the possibility of identifying the microorganisms that can be involved in the protection of the skin. Some of these bacteria can produce antimicrobial compounds that can help protect the skin and destroy any microorganism pathogen. Also, it is important to know the microbial communities in a healthy individual to determine the bacteria that are more beneficial to health. Actually, there is an increased interest on the human microbiome to better understand its benefits to human health, and how commensal bacteria can become pathogens. Also, it has been found that the microbiome has therapeutic properties that help fight disease (Mims, 2004; Wallace and Redinbo 2013). There is interest to find the microorganisms that are associated with disease such as opportunistic bacteria that can become pathogen when the immune defense of host is low, or when the normal flora of microorganisms decreases. Actually, there is a lack of integrated “whole-body” view of the bacterial communities in healthy people under different time and situations. This study can be applied in the prevention and treatment of diseases caused by bacteria. For example, the study suggested that microorganisms that are found in HIV infected persons may not be as simple as previously perceived. Furthermore, this study opens the possibility to engineering microbial bacteria to provide treatment to fragile parts of the body that are more vulnerable to pathogenic attacks. One of the major weaknesses of this study was the small sample size. It will be interesting to perform this study using a large sample sized. Also, it would be important to analyze more physical body parts to cover the fingers, body, feet, knees, etc. Furthermore, it is necessary to use other techniques to identify not only the bacteria family but also the mutants or pathogenic bacteria in different parts of the body. This research originates emerging themes to study human-associated microbial communities in gut, skin, and oral cavity, and relative stability within individuals. Also, this study leaves room for the possibility of determining a group of beneficial microorganisms for therapeutic purposes. The different microbiome communities found in the human body can be applied in personalized medicine with the primary aim of increasing the quality of medical services and treatment.


Costello, E.K., Lauber, C.L., Hamady, M. Noah Fierer, N. Gordon, J.I., Knight, R. (2009) Bacterial Community Variation in Human Body Habitats Across Space and Time. Science. 326 pp. 1694-1697. [online] Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602444/ [Accessed on March 12, 2014].

Gallo, R.L. and Hooper, L.V. (2012) The microbiota of the intestine and skin. Nature Reviews Immunology. 12 pp. 503-516. [online] Available from: http://www.nature.com/nri/journal/v12/n7/box/nri3228_BX2.html [Accessed on March 12, 2014].

LPSN. List of prokaryotic names with standing in nomenclature. [online] Available from:  http://www.bacterio.net/propionibacterineae.html [Accessed on March 12, 2014].

Mims, C.D., Hazel, M., Goering, R.V. Mims, C.A. (2004) Medical Microbiology 3rd. Edition. Edinburgh: Mosby.

Reid, G. (2001) Probiotic agents to protect the urogenital tract against infection1,2,3. The American Journal of Clinical Nutrition. 73(2) pp. 437s-443s. [online] Available from: http://ajcn.nutrition.org/content/73/2/437s.full [Accessed on March 12, 2014].

Wallace, B.D., Redinbo, M.R. (2013) The human microbiome is a source of therapeutic drug targets. Curr Opin Chem Biol. 17(3) pp. 379-384. [online] Available from: http://www.ncbi.nlm.nih.gov/pubmed/23680493 [Accessed on March 12, 2014].







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