Spoiled fish

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Introduction

According to the three-domain system, which is a biological classification scheme fabricated by Carl Woese, the cellular organisms that constitute life are divided into archaea, bacteria, and eukarya. Woese devised this categorization scheme by comparing the 16S rRNA sequences of living cells. The use of this specific ribosomal RNA was key to his success, as it was proved to be present in all living organisms. Therefore, comparison of this gene sequence was useful in determining the phylogeny of cellular life. This sequence differed between domains depending on the environment that surrounded the organisms as well as their method of metabolism. As a result, the prokaryotes were split into two domains, the archaea and bacteria, while the eukarya remained in a separate class due to their multicellular characteristics.

Despite the common misconception that bacteria are organisms that only cause disease, they play an important role in facilitating our digestion. For example, the large intestine is home to hundreds of bacteria that aid in absorption, excretion, and catalysis of undigested foods. There are also bacteria present in the small intestine that support break down of foods passed down from the stomach as well as nutrient absorption.

We will be focusing on organisms that are known to be harmful in the large intestine. The bacteria that will be discussed include the following: Heliobacter pylori, Sulfate reducing bacteria, Enterococcus, Bifidiobacteria, Escherichia coli, Bacteriodes, and Clostridium. In addition, we will discuss a eukaryotic organism, Entamoeba histolytica, and see how it effects the large intestine.

Description of Niche

The large intestine, commonly known to be the final stage of digestion, is located in the abdominal cavity; specifically, between the small intestine and the anus. The primary functions of the large intestine include the following: absorbing water from the bolus (which is a round mass of organic matter passed down from the small intestine), storing feces in the rectum prior to excretion, and metabolizing undigested polysaccharides to short-chain fatty acids, which are passively absorbed for energy use.

The large intestine is divided into three main parts: the cecum, the colon, and the rectum. The cecum, also known as the first part of the large intestine, is a pouch-shaped member that connects the colon to the ileum (which is the last part of the small intestine). The colon, which serves as a storage tube for solid wastes, is divided into four subcategories: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon. The ascending colon, which is continuous with the cecum, extends upward towards the under surface of the liver. Then, the transverse colon, which is the longest part of the colon, passes downward near the lower end of the spleen. Next, the descending colon runs further down along the lateral border of the left kidney. When it reaches the lower end of the kidney, the colon turns toward the lateral border of the psoas muscle, where it will connect to the sigmoid colon. The sigmoid colon forms a loop of about 40 centimeters and lies within the pelvis region. Last but not least, the rectum. The rectum is the final straight portion of the large intestine that terminates in the anus. As mentioned before, this is where the feces are stored before being expelled out of the body.

Moving on, the pH of the large intestine varies between 5.5 and 7.0, which indicates a fairly neutral environment. This is different from that of the small intestine, which exhibits a pH of 8.5, enabling absorption in mild alkaline environments; thus, water absorption in the large intestine occurs optimally around a neutral pH.

In addition, the temperature inside the large intestine tends to be between 37-40°C. This is crucial to the breakdown of undigestible fibers, as hyperthermic or hypothermic temperatures proved to depress the catalysis of these carbohydrates. Therefore, the physical conditions in the large intestine are reasonably stable in order to ensure proper digestion of food.

Who lives there?

Which microbes are present?

You may refer to organisms by genus or by genus and species, depending upon how detailed the your information might be. If there is already a microbewiki page describing that organism, make a link to it.

Do the microbes that are present interact with each other?

Describe any negative (competition) or positive (symbiosis) behavior

Do the microbes change their environment?

Do they alter pH, attach to surfaces, secrete anything, etc. etc.

Do the microbes carry out any metabolism that affects their environment?

Do they ferment sugars to produce acid, break down large molecules, fix nitrogen, etc. etc.


Current Research

Enter summaries of the most recent research. You may find it more appropriate to include this as a subsection under several of your other sections rather than separately here at the end. You should include at least FOUR topics of research and summarize each in terms of the question being asked, the results so far, and the topics for future study. (more will be expected from larger groups than from smaller groups)


References

[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.


Edited by Tal Do, Phillip Lai, Duy Nguyen, and Tania Yaser, students of Rachel Larsen