Question 1
Compare and contrast the concept of metagenome and microbiome.
The microbiome is a term used in describing the entire habitat; it includes microorganisms and their genomes and the surrounding environmental conditions. The microbiome is defined based on the biotic and abiotic factors in a specified environment. On the other hand, metagnome can be defined as a collection of genes and genomes normally from the members of the microbiota. Microbiota is an ecological community that includes symbiotic and pathogenic microorganisms that share our body space.
The analysis of microbiome can be done for a large number of samples and can be divided into two namely taxonomy dependent and phylogeny-dependent. Phylogeny dependent results into accurate view but involves intensive computation. It should, however, be noted that methods used in phylogeny-dependent are normally not high throughput and are normally used in the estimation of richness and diversity (Dreher & Gray, 2009). Different snapshot of the population can be provided by metagenome analysis. Further doing of the taxonomic analysis results in difference in relative ratios. Functional composition of the community may be done through metagenome analysis.
Human cells have the same DNA but have different gene expression a situation referred to as gene regulation. For successful cellular functions, protein gene codes are needed examples of proteins required are the biomarkers (Dreher & Gray, 2009). Research and study of these proteins provide necessary information used in the regulation of proteins and thus can be employed in the assessment of anti-aging properties of most ingredients and other cosmetic products. The genome is made up of the organism’s information normally encoded on the DNA or RNA in most cases of viruses.
As defined above, a microbiome is seen as a collection of all microbes in a habitat, their interactions to each other and the host. The microbiome plays an important role especially to the skin, the skin’s functions are explicit and include among other functions, prevention of water loss regulation of the body temperature, protection of the internal organs from externally caused injuries (Dreher & Gray, 2009). The microbiome gives the skin the protection that it requires through a variety of mechanisms that include transients and pathogens exclusion through competition for the habitat and the nutrients. Many skin conditions that include dandruff, dermatitis, and axillary odor are highly controlled through the skin microbiome. (Sangwan, Xia, & Gilbert, 2016)
On the other hand, a metagenome consist of all genetic elements found I the host and further consist of the genetic elements of the microorganisms (microbiome) living in or on the host (Dreher & Gray, 2009). The use of the metagenomic approach lead to the launch of the human microbiome project (HMP) by the National Institute of Healths. It aimed at defining five human microbiomes, for example, the one for the skin.
References
Sangwan, N., Xia, F., & Gilbert, J. (2016). Recovering complete and draft population genomes from metagenome datasets. Microbiome, 4(1). http://dx.doi.org/10.1186/s40168-016-0154-5
Dreher, M. & Gray, J. (2009). Compare, Contrast, Comprehend: Using Compare-Contrast Text Structures With ELLs in K-3 Classrooms. The Reading Teacher, 63(2), 132-141. http://dx.doi.org/10.1598/rt.63.2.4
Question 2; Barriers of using genomic sequencing as a clinical diagnostic tool
The human microbiome’s importance in health and disease is increasingly being recognized as it entails all the microbes in and out of the body. The microbes that constitute the microbiome have been quantified in an orderly manner because of the advanced high-throughput sequencing. In most cases a single sample results into the production of millions of short sequencing reads. Biological inferences are however difficult to draw based on the unique data characteristics and the new technologies used (Kundu, 2013). The analysis of the resulting big amounts of data and their computations have resulted in great statistical and computational challenges.
Advanced technology has led to the decline in the time and cost of performing complete sequencing. For example in 2007, the cost of performing complete sequencing $350,000 while in 2010 the cost of performing the same had rapidly reduced to less than $1000, making it too affordable for individuals to perform a personal genome sequence (Kundu, 2013).
In the wake up of these advances, several challenges are still experienced regarding decoding and interpretation of the DNA data sequence generated. In clinical medicine, these data are applied in the form of personalized medicine that is still under intense research in basic and applied sciences. For validation of the present genetic tests well-designed clinical trials are still needed this is due to the complex interactions that normally exist between environmental and the genes that are associated with the diseases.
In clinical practice and the developments of the pharmaceutical industries personalized medicine portray early signs of therapeutic potentials. An example is the treatment of colon cancer by the use of panitumumab that has been shown to be very effective in cases where there is no KRAS mutation in cases of tumor development (Kundu, 2013). This enables and prevents the wrong administration of other patients, thus making pharmacogenetic tests realistic strategy and acts to avoid the adverse effects of wrong drug insemination. From the above-discussed examples, it is clear that genetic testing facilities that are tailor-made to particular treatments results into the improved effectiveness and a reduced number of adverse effects. The genetic risk for different diseases may also be predicted through conducting genetic tests thus forming an important surveillance tool.
Genome sequencing advancements are becoming more affordable by day, resulting in increased demand for the genomic data use for clinical practice by patients. The increase in demand may result in a plethora of patient’s expectations thus prompting the integration of genomic data into clinical care. Increased research in this field may result in increased number of discoveries that may prompt complex diagnosis of diseases and thus the corresponding interventions. For example, the availability of different therapeutic approaches in accordance to the genotype of the patients thus resulting into complications to the physicians and other health care personnel on diagnosis and treatment of diseases (Ravel & Wommack, 2015).
In more advanced cases of genomics application in clinical settings, the health care provides readiness and preparedness to use the new genetic tests is to be assessed. Several assessments have been done in the form of interviews to investigate the role of physicians and health care professionals in the administration of personalized medicine (Gohardehi, Fakhar, & Madjidaei, 2012). Most of the studies are normally qualitative in nature, for better inferences to be made the qualitative should be supplemented by quantitative data
References
Kundu, H. (2013). Assessment of TMJ Disorders Using Ultrasonography as a Diagnostic Tool: A Review. JCDR. http://dx.doi.org/10.7860/jcdr/2013/6678.3874
Lo, Y. & Chiu, R. (2009). Next-Generation Sequencing of Plasma/Serum DNA: An Emerging Research and Molecular Diagnostic Tool. Clinical Chemistry, 55(4), 607-608. http://dx.doi.org/10.1373/clinchem.2009.123661
Question 3: The use of genomic science in identifying, preventing and treating of infectious diseases.
Genomics is used in the identification and treatment of tropical diseases. Most tropical diseases affect the poorest of the world’s populations. They are however relatively little known regarding their biology. The study of these diseases has been greatly improved through genomics thus enabling researchers and scientists develop new strategies for treatment and prevention of these diseases.
Through genomics, organisms causing neglected tropical diseases have been studied and fully sequenced, and the others that have not been fully sequenced are currently undergoing sequencing. His has enabled scientists to identify much more on how the diseases develop. Schistosomiasis is one of the known tropical diseases; it occurs as a result of a group of parasitic warms known as schistosomes. The warms are transmitted by snails living in fresh water, the larva form of the parasite results in the infections, and this may occur when one comes into contact wit the water. It is a disease of the poor community’s having non-proper sanitation. The symptoms of this condition range from high temperatures, muscle aches, and chronic ill health. According to the most recent statistics, schistosomiasis affects 240 million persons all over the world and result in 200,000 fatalities per year.
In cases where safe and ethical intervention exist it is seldom necessary to use genomic information for stratification of patients and management of diseases. It is wiser and safer for persons with high risks of infection to receive the intervention regardless of the genotype. For example the association of the CCR5Δ32 to HIV-1 resistance (Ravel & Wommack, 2015). The use of genomic science in the treatment of these conditions have however become very common due to the ineffectiveness of other therapies that were being used previously. For example, the genotype that is associated with hepatitis C was associated with burdensome injections that resulted in side effects. In such cases genotyping reduces the risk of individuals risk to disease infection and is used as a source of effective treatment. An example of the use of genomic science in identification and management of infection is discussed below with Hepatitis B.
Hepatitis B is an infectious disease found in almost all corners of the world. The main causative agent of this disease is the HBV. Mothers infected with HBV have a higher risk of infecting their infants with chronic infections (Ravel & Wommack, 2015). Almost 30% of patients infected with the HBV infection risk morbidity and mortality resulting from complications such as cirrhosis and hepatocellular carcinoma. These condition has always been treated and detected using antiviral therapies however t is important to note that the therapies are always lifelong and complicated resulting into the development of drug resistance and such side effects (Ravel & Wommack, 2015). Genomic science has been used over time to come up with effective vaccines leading to prevention f this condition at 90 to 95% and thus recommended that the use of antiviral therapies.
References
Gohardehi, S., Fakhar, M., & Madjidaei, M. (2012). Avian Schistosomes and Human Cercarial Dermatitis in a Wildlife Refuge in Mazandaran Province, Northern Iran. Zoonoses And Public Health, 60(6), 442-447. http://dx.doi.org/10.1111/zph.12020
Ravel, J. & Wommack, K. (2015). Reviewer acknowledgment 2014. Microbiome, 3(1), 4. http://dx.doi.org/10.1186/s40168-015-0068-7
