Human Microbiome Project Analysis

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Introduction

The human body has evolved to harbor a variety of microorganisms. There are specific sites that promote the growth or colonization of the microbes which have led to the gradual development of enriched microbial flora. The important sites are skin, nasal epithelium, gastrointestinal tract, and vagina. Bacteria have dominated the human microbial population. Various sequencing experiments focusing on 16s rRNA in combination with the conventional culture techniques have contributed to the identification of microbial diversity. Bacteria constitute the most important type of microbes in terms of dual role, namely, beneficial and harmful aspects. They could contribute to infections and also fight against the infections. Some of the important microbes include Streptococcus, Staphylococcus, and Escherichia coli. US National Institute of Health (NIH) has set up a Human Microbiome Project in the year 2007. The main goal of this project is to identify the diverse microbial communities in the human body and explore their role in a variety of bodily conditions. The human microbiome contains essential pathways required for amino acid metabolism, vitamins, xenobiotics, etc. The microbial flora of the gastrointestinal tract is believed to harbor several colonies of microorganisms that are suitable for carrying out the metabolism of therapeutics and catabolism of plant-derived polysaccharides. Technical advancements like 3D visualization software packages have made the identification of the human microbiome in patients.

Similarly, web-accessible Human Oral Microbiome Database (HOMD) has emerged for the betterment of studies focused on the oral cavity. Human/Animal models have been devised for studying the diversity and functional aspects of the Microbiome. This was accomplished for exploring the role of gastrointestinal flora in the development of type 1 diabetes. Therefore, the existence of the Human microbiome project would guarantee the discovery of emerging microbes and their incorporation into the databases as per the taxonomic rules.

Analysis and Nature of Microorganisms

Microorganisms are cosmopolitan in distribution. They inhabit almost every available substratum where they could adapt easily. Especially, microorganisms invade animals and humans to predominantly begin their diverse modes of life which may be both beneficial and detrimental to the host. The association between microorganisms and humans is tightly linked with the remote past. This connection has evolved with the changing period. Microbes may be bacteria, viruses, fungi, and several other vast genera. In hygienic individuals, tissues like muscle, brain, blood, etc. are devoid of any microbes. In contrast, tissues like mucous membranes and skin that are present on surfaces establish a connection with the outside atmosphere and become susceptible to colonization by several microbes (Gootenberg and Turnbaugh, 2010). The spectrum of organisms commonly found at a given anatomical region or site is named normal flora. This term is also known as indigenous microbiota by research professionals. The present description is concerned with highlighting the Human Microbiome Project. The normal flora of humans includes protists and a few eukaryotic fungi. Bacteria are high in number and become important microbial constituents of the normal microbial flora of Humans. Most of the bacteria inhabit the skin, conjunctiva, nose, pharynx, mouth, gastrointestinal tract, and vagina. For example, corynebacteria and staphylococci are present in the above-mentioned sites. Staphylococcus epidermidis was considered to survive in human-environment sites (Kenneth, 2009).S. aureus is a pathogen responsible for a bacterial disease that gets transmitted from the nasal membranes to the vulnerable host. Most microbes exist as opportunistic pathogens or pathogens. The bacterium Streptococcus mutants contribute to the development of dental caries and plaques of plaques (Kenneth, 2009). In the United States, the dental disease was regarded as the most commonly occurring and expensive opportunistic infection, United States (Kenneth, 2008).

Significance of intestinal flora for a human organism

The bacterium Enterococcus faecalis also known as Streptococcus faecalis is commonly found in the intestinal flora. It was considered as a good sign of fecal pollution, in many European countries whereas in the US, it is E.coli. There is a need to perform a thorough literature search to obtain significant insights into the Human microbes significance and research interests. Earlier, Wilson and Blitchington (1996) described that the microbes residing in Humans constituted a complex microbial ecosystem that may play role in the host defense (Wilson and Blitchington, 1996). Various cultural techniques have been employed to study their composition (Wilson and Blitchington, 1996). This approach could serve as an aid to modern techniques.

A comparison was made between 16S rRNA genes and a culture technique that accompanied amplification (Wilson and Blitchington, 1996). Using the PCR-based analysis, researchers were ready to obtain rDNA colonies and cloned amplicons to analyze the match between rDNA and culturing Bacteria (Wilson and Blitchington, 1996). The clones identified gave sequences nearly 74% of coverage (Wilson and Blitchington, 1996). In another method that emphasized the digestive tract, bacteria inhabiting the colon and mucosa of the terminal ileum were characterized (Wang et al., 2003). Here, using the PCR, the 16S rDNA, genes were amplified, cloned, and then subjected to sequencing (Wang et al., 2003). Nearly, 360 sequences were produced related to operational taxonomic units (OTU) (Wang et al., 2003). Therefore, a comparison of 16S rDNA clone libraries taken from the source of hindgut could indicate that the microbial phylogenetic group is common regardless of the host species (Wang et al., 2003). The study has shed light on the distribution of gastrointestinal bacteria with regard to the composition (Wang et al., 2003).

MrcA gene: study and research

Studies were focused on the mcrA gene through PCFR and clone library to investigate the methanogen group of bacteria in health and disease and diversity in the human gastrointestinal tract (Scanlan, Shanahan, and Marchesi, 2008). It was revealed that the control group, colorectal cancer, had increased numbers of positive methanogen individuals (Scanlan, Shanahan, and Marchesi, 2008). In inflammatory bowel disease groups, Methanogen was found to be low (Scanlan, Shanahan, and Marchesi, 2008). Restriction fragment length polymorphism experiments revealed that mcrA Gene has dominated the entire sequence library (Scanlan, Shanahan, and Marchesi, 2008). Thus, mcrA gene was considered to play a role as an important biomarker for methanogen identification in the gut and could also reflect the function of the intestine (Scanlan, Shanahan, and Marchesi, 2008). Next, for the bacteria to colonize in the gut certain insoluble components like mucin and fiber-rich diets are important (Walker et al., 2008).

Hence, determination of PCR-amplified 16S rRNA sequences from fecal samples revealed an increased proportion of Firmicutes belonging to bacterial sequences that were particle-associated and of liquid phase (Wang et al., 2003). Ruminococcus flavefaciens and R. bromii were mostly linked with the solid particles significantly compared to that observed with the liquid phase (Wang et al., 2003). These two bacteria represent clostridial cluster IV of Ruminococci (Wang et al., 2003). Thus, only certain bacteria tend to colonize insoluble substrates present in the gut. Recovery processing of the bacteria from the insoluble substrates that are considered as primary degraders is a tedious task (Wang et al., 2003). Microbes contribute to the maintenance of hygienic skin. They prevent the invasion of microorganisms that lead to disease and promote the microorganism growth that favors human health.

Analysis of human skin

From the determination of the 16S ribosomal RNA gene sequence, nearly 20 different sites of human skin were reported to have identical bacterial flora (Grice et al., 2009).The unique features of the skin site influence Microbial community stability ad complexity (Grice et al., 2009). This could indicate that topographical surveys targeting the human skin give a framework for investigations to determine the involvement of Microbial flora disease conditions and their interdependencies essential for hygienic skin maintenance(Grice et al., 2009). It was reported that the composition of the human intestine is of 10(13) to 10(14) microorganisms. Here, the microorganisms are grouped and are referred to by the term microbiome which has genes several times as high as that of the human genome (Gill et al., 2006).

The above-presented result was revealed when the sequences of 16S ribosomal DNA were subjected to a polymerase chain reaction and approximately 80 million base pairs of DNA were determined (Gill et al., 2006). By analyzing metabolic functions, the human genomic content was compared with the microbial genomes that were sequenced earlier (Gill et al., 2006). It was found that the human microbiome possesses high amino acid metabolic states, biosynthesis of xenobiotics, isoprenoids, and vitamins (Gill et al., 2006).

Super Organisms as a Complex of Microbial and Human Features

Therefore, the term superorganism implies to humans that their metabolism is a reflection of a spectrum of microbial and human features (Gill et al., 2006). This study has strengthened another report. Scientists have investigated the stomach microbiota of humans and the influence of colonized Helicobacter pylori (Bik et al., 2006). A method combining the library of 16S rDNA clones and sequences produced by a wide variety of bacterial PCR on biopsy samples was followed by researchers (Bik et al., 2006). In this regard, haplotypes were recognized belonging to the diverse community (Bik et al., 2006). Certain bacterial phenotypes like Deinococcus-related organisms remained uncharacterized (Bik et al., 2006). But their relatives were reported from extreme environments (Bik et al., 2006). Gastric bacteria show great variation as their rDNA was different from the sequences found in the human mouth and esophagus. This adaptability rendered the human stomach home to a distinct microbial ecosystem (Bik et al., 2006). Mammals are considered metagenomic as they harobour self-gene complements and all associated microbes (Ley et al., 2008).

A network-based sequencing of the 16S ribosomal RNA gene was done employing humans and mammalian species which inhabit zoological and forest environments (Ley et al., 2008). The findings indicate that the bacterial diversity is supported by phylogeny and the host diet (Ley et al., 2008). The diversity was reported to increase from carnivory to omnivory to herbivory (Ley et al., 2008). Hence, the bacterial communities and their hosts tend to exhibit codiversification with their hosts whereas the gut microbiota of humans chooses present-day modern lifestyle specific to omnivorous primates (Ley et al., 2008). Recent advances have made the study of the human microbiome much more feasible. High-throughput sequencing technology has furnished better insights on microbial flora concerning health and disease (Moore et al., 2010).

Technical Analysis: Benefits and Limitations

Benefits

With the help of completely inexpensive software and 3D visualization technique, investigators were able to make possible the determination of data related to the increased dimensional human microbiome (Moore et al., 2010). This strategy turned out into a novel significant task in the area of biocomputing and also is a prospect (Moore et al., 2010). This could further connect the potential of commercial video game process technologies to enable an interactive 3D heat map for searching microbial species and their relative wealth in various patients (Moore et al., 2010). The benefit of this strategy is that the 3D technology adds information that is not possible through a traditional 2D heat map (Moore et al., 2010). Hence, the utility of visualization strategy employing microbiome data plays important role in exploring the health aspects (Moore et al., 2010). The gastrointestinal tract of Humans favors the growth of multiple colonies of microorganisms which are responsible for the metabolism of orally given therapeutics, catabolism of polysaccharides obtained from plants, production of vitamins and amino acids (Gootenberg and Turnbaugh, 2010). As such, human models are required through which manipulation of environmental microbial, and host parameters can be achieved in spite of the progress made in studying the human microbiome, comparison of the human microbiome with that of other animals (Gootenberg and Turnbaugh, 2010).

Scientists have described an approach that facilitates the direct operation of host genotype, exposures to the environment, microbial community structure, and other factors (Gootenberg and Turnbaugh, 2010). This also permits the study of the colonization of complex microbial communities with that of germ-free animals also involving those from animal donors and humans (Gootenberg and Turnbaugh, 2010). This experimentation has led to evaluate the gut microbiome to obtain insights on essential microbial functions like dietary periods which influence gene abundance, transports of metabolites from donors to recipients, survival of microbial communities in infants and ex-germ-free adult animals, and microbial ecosystem throughout the gastrointestinal tract (Gootenberg and Turnbaugh, 2010). Therefore, studies on human models may enable novel findings relevant to the human microbiomes of humans and animals (Gootenberg and Turnbaugh, 2010). The study of human microbial flora with models thus may provide better opportunities for further research in the area of comparative and functional genomics.

Limitations

In 2007, researchers from different countries collaborated and developed the Human microbiome, funded by the National Institute of Health (NIH). The objective of this project is to find the existence of a type of microbial community in various parts of the human body and to investigate the variation exhibited by communities during hygienic or disease conditions. For this, purpose NIH awarded $8.2 million to four sequencing centers to initiate developing a paradigm and data resources (Giongo et al., 2010). The institutes that were awarded for one year are the J. Craig Venter Institute, Rockville, MD, the Broad Institute of MIT/ Harvard, Cambridge, Massachusetts, Baylor College of Medicine, Houston, and Washington University School of Medicine, St. Louis, which are part of the NHGRI Large-Scale Sequencing Research Network. The initial work aimed to obtain the genome sequence of 200 microbes that were already isolated from the human body (Giongo et al., 2010).

This approach is considered as a part of the 1,000 microbial genomes collection. The investigators will then initiate employing the healthy volunteers who would be donating the blood taken from different body regions (Giongo et al., 2010). The initial stage of the project was collectively operated by NHGRI, NIAID, and the National Institute of Dental and Craniofacial Research (NIDCR). The upcoming speed and inexpensive sequencing technologies have promising implications for ensuring large volumes of data about the microbial communities (Giongo et al., 2010). This would support the development of analytical tools and strategies. Further, the Human Microbiome Project is considered as a part of the NIH Roadmap for Medical Research (Giongo et al., 2010). The Roadmap comprises a sequence of initiatives developed for complex opportunities and lacunae in biomedical research (Giongo et al., 2010). This collaborative effort could able to provide a possible blow to the smooth progress of medical research (Giongo et al., 2010).

Siqueira and Rôças (2010) described that nucleic acid technology if exploited would allow the determination of the bacterial diversity in the oral cavity in hygienic and diseased states (Siqueira and Rôças, 2010). This would strengthen the data from the previous culture studies and further improve the list of oral inhabitants and candidate pathogens related to the important oral diseases (Siqueira and Rôças, 2010). Several bacterial species residing in the oral cavity have been identified (Dewhirst et al., 2010). Recent findings have employed high-throughput technology to provide information that the size of bacterial diversity is enormous (Dewhirst et al., 2010). The human oral cavity possesses habitat sites that facilitate the growth of microbes (Dewhirst et al., 2010). The sites include tonsils, hard and soft palates, cheeks, tongue, teeth, and gingival sulcus, tongue, and cheeks (Dewhirst et al., 2010). Through molecular techniques focusing on 16S rRNA cloning and the characterization of oral microbial flora has become much feasible (Dewhirst et al., 2010). This might have led to the detection of important oral infections caused by these microbes. However, most of the taxa representing the oral cavity were not assigned names and are provided with accession numbers about GenBank, and clone numbers that have no taxonomic foundation (Dewhirst et al., 2010). The main objective of this research was to gather 16S rRNA gene sequences into the Human Oral Microbiome Database (HOMD), which is regarded as into phylogeny-based database, and enable it web-accessible (Dewhirst et al., 2010). The HOMD comprises 619 taxa in 13 phyla, which are as indicated: Tenericutes, and TM7, SR1, Synergistetes, Proteobacteria, Spirochaetes, Proteobacteria, Fusobacteria, Firmicutes, Euryarchaeota, Chloroflexi, Chlamydiae, Bacteroidetes, and Actinobacteria (Dewhirst et al., 2010). The second objective was to determine 36,043 16S rRNA gene clones isolated to analyze the enormity of taxa and detect the novel candidate taxa (Dewhirst et al., 2010).

Results and Findings

The study has determined nearly 1,180 taxa, where the uncultivated contributed to 70 % cultivated 8%, named, 24% (Dewhirst et al., 2010). After, analysis, new nonsingleton taxa are required for incorporation into the database. Hence, the number of taxa necessary for the database is 90%, 95%, or 99% of the clones evaluated, respectively (Dewhirst et al., 2010). This indicated that the HOMD report is the new documentation about the human-associated microbiome as it serves as an indispensable tool for the role of the microbiome in hygienic and disease conditions (Dewhirst et al., 2010).

Next, from murine models scientists have demonstrated that bacterial flora present in the gut play role in the development of type 1 diabetes (T1D). Certain bacteria have been found well associated with the onset of diabetes in this context. The study was undertaken as there was no information on the involvement of human intestinal microbes in the development of autoimmunity that contribute to T1D, where insulin-secreting pancreatic islet cells are involved (Giongo et al., 2010).

Using high-throughput, culture-independent techniques bacteria were detected that were found associated with T1D-associated autoimmunity in young children (Giongo et al., 2010). These subjects were reported to possess a high genetic susceptibility for this disorder (Giongo et al., 2010).

The proportion of bacterial diversity was found to decrease gradually over time in the autoimmune subjects compared to that of age and genotype-matched, nonautoimmune subjects (Giongo et al., 2010). An increase of 25% related to Bacteroides ovatus was observed among cases in contrast to controls (Giongo et al., 2010). Whereas another bacterium firmicutes strain CO19, contributed to a less proportion of the increase in Firmicutes in contrast to cases (Giongo et al., 2010). It was thought that the microbiomes tend to be hygienic and more robust in healthy infants who proceed towards the toddler stage (Giongo et al., 2010). In contrast, the microbiome tends to be less distributed and less stable in children who are susceptible to autoimmunity (Giongo et al., 2010). Therefore, T1D subjects may have a microbiome different from the hygienic children. It indicates that TID could be diagnosed in advance with bacterial indicators (Giongo et al., 2010). Similarly, bacteria that did not show significant association with autoimmune states may serve as needful tools in the alleviation of autoimmunity in children at risk (Giongo et al., 2010). This report has strengthened a previous description. Although the autoimmune disease is well connected with detectable antibody features, from the genetics perspective, humans were considered as superorganisms in which a spectrum of bacterial genomes exist named as metagenome (Proal, Albert, and Marshall, 2009). According to NIH, the vast majority of the human cells are microbial but not human-related (Proal, Albert, and Marshall, 2009). Few microbes produce metabolites that interrupt the gene expression connected to autoimmune disease (Proal, Albert, and Marshall, 2009).

Human Genes In Relation To Microbial Metabolites

Thus, studying the transcription of human genes in association with microbial metabolites is a question for researchers (Proal, Albert, and Marshall, 2009). It is reasonable to assume that antibodies produced in response to autoimmune disease are not confined to human DNA as autoantibodies. Few models have shed light on the accumulation of human microbiota in the life period keeping given several mechanisms (Proal , Albert, and Marshall, 2009). From animal model studies, the innate immune system gets diminished by the blockage of VDR nuclear-receptor-transcription (Proal, Albert, and Marshall, 2009). This would not enable the production of key antimicrobials, thereby facilitating the persistence of microbes (Proal, Albert, and Marshall, 2009).

The genome of such microbes guarantees an influence on disease progression (Proal , Albert, and Marshall, 2009). There were attempts to lessen the VDR- altering microbiota in autoimmune patients which resulted in autoimmune mechanism reversal (Giongo et al., 2010). Therefore, with the continuity of the Human Microbiome Project, there is a need to further determine the human metagenome, for obtaining novel information on the etiopathogenesis of autoimmune diseases (Proal, Albert, and Marshall, 2009).

In view of the above information, human microbial flora is complex in terms of its diversity. The vast array of microbes presented in various sites of the human body offer both positive and detrimental effects. This is accomplished well in hygienic and diseased conditions. Among the microbes, bacteria have dominated with regard to their presence and activities. The gastrointestinal tract of humans can be considered the best harboring site for microorganisms. The application of technologies like 16 s rRNA sequencing and their comparison with the conventional culture techniques has added much information for understanding the diversity concept. With the advent of the Human Microbiome Project in 2007, many investigations have been initiated from different corners of the world. This rendered further awareness on the Human microbial ecosystem such that the researcher could easily pool the samples for sequencing or nucleic acid technologies. Metagenomics has emerged as a pioneer in the field of bacterial genetics. Mechanisms emphasizing the connection between autoimmune diseases and microbes are important to determine the susceptibility to type I diabetes. Various sequencing projects have already begun to investigate the unnamed or unsequenced microbe. There are still certain discrepancies about the addition of novel microbial taxa groups into the existing databases. An evidence-based approach is also suggested for more advanced information on the human microbial flora.

Reference List

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Dewhirst, F.E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C., Yu, W. H., Lakshmanan, A., and Wade, W. G. 2010. The human oral microbiome. J Bacteriol, 192(19), pp. 5002-17.

Gill, S. R., Pop, M., Deboy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M., and Nelson, K. E. 2006. Metagenomic analysis of the human distal gut microbiome. Science, 312 (5778), pp.1355-9.

Giongo, A., Gano, K. A., Crabb, D. B., Mukherjee, N., Novelo, L. L., Casella, G., Drew, J. C., Ilonen,J, Knip, M., Hyöty, H., Veijola, R., Simell, T., Simell, O., Neu, J., Wasserfall, C,H., Schatz,D., Atkinson, M. A., and Triplett, E. W. 2010. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J. Web.

Gootenberg, D. B., and Turnbaugh, P. J. 2010. Humanized animal models of the microbiome. J Anim Sci. Web.

Grice, E. A., Kong, H. H., Conlan, S., Deming, C. B., Davis, J., and Young, A,C. 2009. Topographical and temporal diversity of the human skin microbiome. Science, 324(5931), pp.1190-2.

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