Microorganisms are important for animal and plant life, their presence in the surroundings is essential for survival of all life forms. This importance can be proved by the large number of prokaryotes in human body, mainly bacteria, it was found that there are ten time more bacteria than human cells. Normal flora describe the microbes that colonize human body, during birth and after, and remain for life. Microbes of normal flora are found in many body sites, such as moist skin, gastrointestinal tract, mouth, respiratory tract, urinary tract, and vagina, but other important human organs, such as lungs, brain, and heart are free from microbial flora. Number of microorganisms living in skin is small compared to other sites, because skin medium is dry, and contain dead cells, with slight low pH. The human respiratory tract, mainly nose, is colonized by Staphylococcus aureus , which is main cause of surgical wound infection. The mouth contains biofilms of Streptococcus mutans, which are present as plaque on teeth surface. Similar to the skin, and unlike small intestine, not many microbes live in the stomach, because of the gastric acid, Helicobacter pylori is an example of stomach bacteria.
Human microbial flora are important to the human, staphylococci and propionibacteria, release fatty acids to prevent growth of skin fungi, bacteria in respiratory tract can cause infections when epithelium of respiratory tract get damage. Vaginal flora, mainly lactobacillus protect host, as women with low lactobacillus levels taking antibiotics to treat infection develop other infections.
Human flora also benefit the host, they colonize body sites, making it difficult for external microbes to colonize and infect, they also help in vitamin production, and cause small antibody release , which help in immunity.
Oral microflora produce substances as fatty acid, peroxides to protect from external microbes, and also cause disease such as gingivitis, and dental plaque. Normal flora spread from site to another can cause deadly infections, as from wound. Bacteroides of the gastrointestinal tract produced substances that are carcinogens, and can cause cancer for colon.
Human Microbiome Project (HMP)
Researchers found, usually that everybody carries huge number of pathogens, and microorganisms as possible to cause diseases. While most of these microorganisms coexist with the host body (healthy individuals) and remnant of the human microbiome without any diseas and living with each other in the human body, which are play important vital role in human health. Researchers sampled of healthy volunteers in USA had included total samples was from 15 body sites in men, while in women was 18 body sites, from each volunteer was collected three samples at different body sites.

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Collect the samples from a total of 18 body sites, in 5 major body areas, in males were sampled from the skin, mouth (oral cavity), nose, two sites behind each ear and each area inner elbow, lower part of gastrointestinal tract(stool), and tinal tract regions. On the other hand, in females additionally sampled from three vaginal sites, as following: nine sites in the oral cavity with saliva, four sites on the skin, three sites in the vagina, a pooled sample of the anterior nares (airway), and one sample of stool.
In late 2007 with funding from the National Institutes of Health (NIH) roadmap for biomedical research community, represent important issues that affect human health in general, launched the Human Microbiome Project (HMP), which focuses on describing the different types of microbial which are associated with human health and disease. Human Microbiome Project is to study the microbes which are living in and on the human body and included catalogue the genetic identity and characterize of many organisms such as bacteria, viruses and live in intimate contact with human body. The Human Microbiome Project is became able to uncover microbes and the National Institutes of Health launched the results of the five-year project.
Also, has been developed metagenomic protocols through generation a population-scale framework to produce metagenomic data and large group of quality-controlled resources, during standardized methods. Have been isolated around 800 reference strains from human body sequences. Although, these data are biggest resource to develop of current and future studies and represent a diversity of the human microbiome.
Since launch HMP in late 2007, HMP has received $153 million from Common Fund of National Institutes of Health (NIH) and $20 million an additional.
The main goals of this project are: This project is to prove if there is a shared core microbiome between different groups of people and in and on the different sites of the human body, also to studying different medical conditions and explain whether there are a correlations between changes in microbiome and disease. To take benefit of recent technologies by studying samples from different sites of the human body to characterize the human microbiome, to provide new technological approaches from a standardized data resources, and HMP is working to manipulation of the human microbiome to improve human health. In addition, Human Microbiome Project provided contribution important to develop new fields in the technological and bioinformatic tools, through five year effort.
The first stage of this initiative was included the sequencing of many hundreds of microbial reference genomes which isolated from human body sites. This information acquired from the reference genomes can help to functional annotation and classification of 16S rRNA from microbiome samples. In human body microbial partners carry out a several of metabolic reactions which are important for human health, still are not encoded in the human genome. Although, the large number of microbial kinds existent in the body did not isolated, because, the inability in the lab to reproduce suitable growth conditions for microbial. Therefore there are huge number of microbial are still undetectable. It is important the study of microbial communities directly from their natural habitats by benefit of advances in sequencing technology.
The HMP is working to characterize the human microbiome communities by using different complementary analyses included: 16S ribosomal RNA (rRNA), metagenomic sequencing and whole-genome shotgun (WGS), which focused on examination of the intestine microbiome through the use of WGS data. The metagenome is includes the collective genomes of the human microbial flora. Generating a huge amounts of data from the sequencing and analyzes of reference genomes about the complexity of the human microbiome which are isolate from different sites of the human body and providing more information about human health and disease. 16S and wgs sequencing occurred in a four stages are: containing of a mock data pilot stage, a clinical pilot stage, in July 2010 stage 1 completed and clinical stage 2 currently in progress.
Has been funded Fifteen demonstration projects to explain the nature of relationship between the microbiome, health and disease. It is known that the human microbiome is consists of the genes and genomes of the microbiota which resident throughout human body. The Human Microbiome Project resources, includes the following: 600 microbial reference genomes, 700 metagenomes, 60 million predicted genes, and 70 million 16S sequences from healthy adult microbiomes.
The human microbiome including of microbial genes, genomes, and gene products of the microbiota which interact with the human body host to prime immunity and in same time to maintain host health. Also, the microbiome is contribute to maintenance and development of the immune system.
The HMP is surveying the microbiomes pass the bodies of a group of healthy adults to produce data groups of microbiomes, to developing of reference strains by a classification of microbial genome sequences, and evaluating the properties of microbiomes which associated with specific skin diseases, gastrointestinal tract, and urogenital. Recently, has been developed three programs in technology are: the ethical, legal implications, and computational tools to support this field (microbiome research). In addition, there are four projects listed under the HMP program, depending on the four data sets produced, including: data sets produced in individual demonstration project activities; targeted 16S ribosomal RNA gene sequences; reference strain microbial genome sequences; and whole-genome shotgun metagenomic sequences.
Whereas, the second major resource of the HMP is include five major areas of the human body (healthy adults) are: skin, mouth, nose, gastrointestinal tract, and vagina. In spite of, in the early years at birth, the generating of the microbiome, occurs through interact between the diet, maturing immune system and microbial communities. (Koenig et al., 2011) (Dominguez-Bello et al., 2010) .
Difficult to understand what is happening through interactions between the microbiome function, early microbiome events and changes during the stages of life, such as using antibiotics possible to be predisposing factor to allergies later in life (Bisgaard et al., 2011). Also, because microbiome disorders might occur in childhood can lead to many diseases such as asthma, and type 1 diabetes. Each site of the body contains a unique microbiome important to maintain for the host health, for example the gastrointestinal microbiome which directly interacts with the immune system of the host (Round and Mazmanian, 2009).
In addition to many functions as energy supply for host cells and digestion of food. The microbiome acquired be through anew each generation but it is not inherited.
Currently, a lot of international efforts focused on enhance the understanding of the complexity of the human microbiome and determining the multiple pathological mechanisms for explore in human health and disease.
The International Human Microbiome Consortium (IMHC) is open to support most research programs of human microbiome, the aim of the IMHC is the collection of information and understanding how the human microbiome is working to maintenance of human health and occurrence of diseases, for the purpose of illustrate that the relationship between the human microbiome, human health and disease. Also, other goals are in- depth study in the complexity of the microbiome in health and disease in general, make a full analysis of the human microbiome about human health and/or disease, creating the novel diagnostic tools of the disease and development of new methods to prevent and treat diseases and therapeutic interventions.
In addition, that future researches aims to detect and to look for the important role of metagenomic analyses to defining DNA sequences and help to detected human infections because of the complexity of the human microbiome.