Microbiomes Diseases by Taxonom

Question: 1: Name 2 barriers that prevent bacteria from entering and subsequently colonising the gut. 2: In what instance can S.Aureus become pathogenic 3: What bacterial species can typically form a biofilm on enamel? 4: Give one example each of a gut, skin and urogenital microbe 5: How does 16S RNA satisfy the criteria as a marker and name one database commonly used for analysing 16s sequence data. 6: Define an operational taxonomic unit (OTU) and what does the binning process allow. What type of analysis is used to determine which OTUs represent significant changes in population? 7: How does a Whole Metagenomics shotgun (WMS) analysis differ from a Metatranscriptomics analysis. 8: Give one example of a catalogue of reference pathways and describe the pathway inference process. 9: What is a gnotobiotic process and give an example of one bacterial phylum that is perturbed during obesity 10: Give an example of disease treated with a fecal microbiota transplantation. Answer: Microbiome Several barriers prevent bacteria from entering and subsequently colonizing the gut. Firstly, highly concentrated hydrochloric acid is secreted in the gastric cavity not only to activate digestive enzymes but also kills pathogens that are likely to colonize the gastrointestinal tract and cause infection. The high acidic condition in the stomach makes it impossible for most of the bacteria not to thrive hence it serves as a protective measure against infections. Secondly, the gut is composed of several microflorae from just after the birth of an individual. These commensal microorganisms contribute to the development of a mucosal immune system that responds and protects the gut from bacterial colonization. Disruption of this microflora may result in pseudomembranous colitis, inflammatory bowel disease and neonatal necrotizing enterocolitis (Baker, Nicklin Griffiths, 2011). Staphylococcus Aureus is naturally found in the skin, nose mucous membrane and the respiratory tract but causes no infection under normal circumstances. However, it may cause infection when there is reduced integrity of the skin and mucous membranes that allow it to gain access to the systemic circulation. It usually causes pneumonia in immunosuppressed patients such as those suffering from HIV/AIDS and therefore immunosuppression is another factor that is implicated in infection causation by Aureus (Baker, Nicklin Griffiths, 2011). Biofilm on the enamel is formed from a series of phases that result in the colonization and formation of highly adhesive The bacterial species that are mostly involved in this biofilm formation include Streptococcus mutans, Streptococcus mitis, Streptococcus oralis and Actenomyces viscosus among other gram positive and negative bacteria (Baker, Nicklin Griffiths, 2011). Different body parts are composed of microbes which cause no infection under normal health conditions of an individual. They are generally beneficial as they protect one from infection by other more harmful pathogens (Bauman, 2014). The bacteria found in the gut are Actinomyces viscosus, Bacteroides gingivalis, Clostridium defficile and Citrobacter freundii Those found on the skin are Staphylococcus epidermidis, Staphylococcus haemolyticus, Streptococcus viridans and Epidermophyton floccosum. In the urogenital, there exists Staphylococcus aureus, Streptococcus viridans, Candida albicans, and Streptococcus anginosus. The gene 16S of rRNA is preferred as a marker for the identification of bacteria because DNA analysis is more reliable than the classification of bacteria based on their phenotypic nature. Secondly, the 16S rRNA gene is present in almost all bacteria, and it is distinct from its homologous gene 18S in eukaryotic rRNA, and therefore it becomes very crucial in distinguishing a bacteria from eukaryotic DNA in the same sample. It is also 1.5 kb and therefore significantly shorter than several unique prokaryotic genes, hence can be sequenced faster and in a comparatively cheaper manner. The commonly used databases for analyzing and sequencing 16S data are EzTaxon-e and Ribosomal Database Project (Pevsner, 2015) Operational taxonomic unit (OTU) is a cluster of organisms that are being studied that share significantly diverse characteristics and DNA gene sequence of above 97%.The Binning process allows grouping of these cluster of organisms and assigning them to OUT by use of algorithms based on composition, alignment similarity or both. The phylogenic analysis is used to determine which OUTs represent significant changes in a population by noting the dissimilarities (Pevsner, 2015). Metagenomic shotgun (WMS) analysis differs from a Metatranscriptomics analysis in that WMS reveals functional and metabolic processes that are possible and present in a microbial community while Metatranscriptomics analysis is able to reveal which of these metabolic processes are active, their regulation and expression (Pevsner, 2015). An example of a catalog of reference pathways are metabolic and catalogue gene pathways. The gene pathway inference process involves chemical recognition of the chromosomal origin of replication, replicative supercoiling of replication origin, unwinding of the replication origin, replicative DNA helicase loading through the ring-breaking mechanism, replicative DNA helicase loading through ring making mechanism and DNA unwinding ahead of replication fork (Pevsner, 2015). The gnotobiotic process is the controlling and accounting for of all microorganism present within an organism. During obesity, there is typically reduced motility throughout the gastrointestinal tract. Thus the microbiota may be perturbed since they have significantly increased the time for multiplication and therefore cause intestinal bacteria overgrowth that can lead to several conditions that include irritable bowel syndrome. One of the bacterial phyla that are disturbed is Proteobacteria In which Campylobacter coli belong, a normal flora (microbiota) normally present throughout the gut (Bauman, 2014). Fecal microbiota transplantation is the process of collecting, treating and transferring of fecal matter mixed with fluid from a tested individual to another person with diminished beneficial normal flora for replacement. A common disease treated through this procedure is pseudo membranous colitis that is caused by clostridium difficile infection (Bauman, 2014). References Bauman, R. W. (2014),Microbiology with diseases by taxonomy, Harlow Pearson Baker, S., Nicklin, J., Griffiths, C. (2011),Microbiology, New York: Garland Science. Pevsner, J. (2015),Bioinformatics and functional genomics, Chichester : Wiley-Blackwel.