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| ==Introduction== | | {{Uncurated}} |
| 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.
| | ==Classification== |
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| 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.
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| We will be focusing on prokaryotic, as well as eukaryotic, organisms that reside in the large intestine. The bacteria that will be discussed include the following: Sulfate reducing bacteria, methanogens, [[Enterococcus]], [[Bifidobacterium]], [[Escherichia coli]], [[Bacteroides]], and [[Clostridium]]. In addition, we will discuss a eukaryotic organism, [[Entamoeba histolytica]], and see how it effects the large intestine.
| | ===Higher order taxa=== |
| | Bacteria; Phylum; Class; Order; Family; Genus: |
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| ==Description of Niche== | | ===Species=== |
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| 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.
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| 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.
| | ==Description and significance== |
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| 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.
| | ==Include as many headings as are relevant to your microbe (including things like cell metabolism, ecology, pathology, application to biotechnology). Or, if your microbe is very new and not well studied, then include a heading or two with more description about its native environment or something related to its lifestyle.== |
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| 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.
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| ==Who lives there?==
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| ===Lactobacillus===
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| [[Lactobacillus]] is a microbe that aids in production of lactic acid through
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| homolactic fermentation, and can be found in the human gastrointestinal tract. This
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| Gram-positive, rod shaped, bacterium is a beneficial bacterium that assists in
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| enzymatic production to help with digestion, maintain pH balance and aid in healthy
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| bacterium replacement in the gastrointestinal tract. The lactic acid produced by
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| carbohydrate fermentation from lactobacillus, aids in maintaining the correct
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| homeostatic pH to ensure no phage is able to survive at the low pH. Studies also
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| show that it can synthesize necessary vitamins and help lower cholesterol levels
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| (Ray). Lactobacillus also has been observed to degrade carcinogens, reduce or
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| prevent carcinogenesis through antimutagenic activities. One of many strains of
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| [[Lactobacilli]] that is commercially distributed is [[Lactobacillus Acidophilus]],
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| which is categorized as a probiotic. Probiotics are bacterium that can be taken as
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| a supplement to help increase the beneficial bacteria that are normally present in
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| their environment. In the case of [[Lactobacillus Acidophilus]], it has
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| fermentative capabilities, but lacks the ability to synthesize most cofactors and
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| vitamins; which are expected normal capacities of microbes living in such a
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| nutrient-rich niche such as the human gastrointestinal cavity (Altermann). The
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| adherence of [[Lactobacillus Acidophilus]] to the cells lining the colon prevents
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| binding of enteropathogenic and enterotoxigenic pathogens, promoting healthy
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| metabolic activities. [[Lactobacillus Acidophilus]] and other strains of Lactobilli
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| are widely used for treatment in diarrheal diseases, however the mixed results do
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| not allow an exact conclusion on its treatment accuracy (Macfarlene).
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| ===Bifidiobacterium===
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| [[Image:Bifidobacteria.jpg|frame|Figure 1. Gram-Stained Preparation of [[Bifidobacterium]]
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| Adolescentis]]
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| [[Bifidobacterium]] is also considered a probiotic bacterium that inhabits the
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| anaerobic environment of the human gastrointestinal tract. The amount of this
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| bacterium present decreases with age; thus, higher amounts are found in infants, and
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| lower amounts in adults, which may lead to the needs of a probiotic supplement.
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| [[Bifidobacterium]] is also a rod club-shaped (as pictured), Gram-positive cell,
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| which has a symbiotic relationship with the host (gastrointestinal tract),
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| benefiting both bacteria and host. This symbiotic relationship is seen by its
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| adhesive ability to the microflora, the metabolism of undigested dietary
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| carbohydrates and prevents pathogen colonization. This type of beneficial bacteria,
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| similarly to the [[Lactobacilli]], prevents binding of pathogens such as
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| [[Escherichia Coli]], and [[Salmonella Typhimurium]], decreasing susceptibility to
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| possible illnesses such as E. Coli poisoning in humans. The microflora normally
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| lining the gut serves as a protective barrier against pathogens, however this can be
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| compromised due to antibiotic treatments, stress, poor diet or other physiological
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| distress. The [[Bifidobacteria]] can serve as resistance mechanism against the
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| colonization of pathogens in the large intestine (Macfarlene). It has been observed
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| that their competitive nature, against other gastrointestinal bacteria, is due to
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| its ability to scavenge for a large variety of nutrients to use for energy (Schell).
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| Studies also show that [[Bifidobacterium]] has also has potential to prevent cancer
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| by reactivity with certain carcinogens and promotes immune stimulation (O'Sullivan).
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| ===Methanogens and Sulfur reducing bacteria===
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| In addition, methanogenic bacteria (e.g. Methanobabrevibacter smithii) also benefit the gastrointestinal tract in that they reduce carbon dioxide and hydrogen gas to produce methane gas and water. This reduction reaction is an imperative characteristic of the large intestine as it aids in the fermentation of organic matter to obtain energy. For example, prior to entering the large intestine, the small intestine cannot digest or absorb dietary fibers for energy production; thus, these carbohydrates prove to be useless up to this point. However, once the indigestible sugars are in the large intestine, they will be fermented by gut organisms to break down the complex polymers (e.g. resistant starches, non-starch polysaccharides, oligosaccharides and etc.) into its monomeric constituents. These monomers are then oxidized to short chain fatty acids (SCFA), lactate, succinate, ethanol, hydrogen gas and carbon dioxide. The resulting SCFA can then enter central metabolic pathways where it can be converted into energy in the host organism.
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| An important fact to note here is that hydrogen gas and carbon dioxide are products of the fermentation reaction. Since the large intestine is an anaerobic environment, the reducing energy is stored in the form of ethanol, lactate, succinate, or H2, but not in water (as would be the case in an aerobic environment). This poses a problem as accumulation of H2 inhibits oxidation of pyridine nucleotides, which leads to a redundant amount of substrate level phosphorylation. Therefore, in order to avoid this unnecessary energy expenditure, a balance between fermentation and H2 removal is imperative; and this where methanogens come in to save the day.
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| Methanogens live symbiotically with the large intestine. The bacteria grow by reducing carbon dioxide and H2 to produce methane gas and water; hence, the fermentation products now function as nutrients for these organisms and not inhibitory poisons to the environment. The large intestine benefits from the reducing activity of the methanogens because methane is an effective pathway for H2 disposal, which relieves the inhibition of nucleotide oxidation. As a result, superfluous use of energy is avoided.
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| An alternative to methanogenesis is the sulfate reducing pathway. The main substrates for sulfate reducing bacteria are also fermentation products; however, the product of this reduction pathway is a highly toxic hydrogen sulfide which can damage the colonic epithelium. The main organisms that perform this reaction include Desulfovibrio, Desulfobacter, Desulfomonas, Desulfobulbus, and Desulfotomaculum.
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| Fermentation experiments in a lab revealed organisms competing for gaseous nutrients, as sulfate reducing bacteria overpowered methanogens when present in the same environment. However, recent experiments have shown methanogens displacing other H2 consuming bacteria in fecal slurries. In such experiments, the expression of sulfate reducing bacteria was probably limited or nonexistent because it is unlikely for methanogens to competitively overrule them. The reason for this is due to sulfur reducing bacteria having a higher affinity for H2 relative to that of methanogens. Therefore, determination of the more predominant organism depends on the sulfate concentration of the environment. The higher the sulfate concentration, the more reduction performed by sulfate reducing bacteria, and vice versa.
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| ===What other organisms are present (e.g. plants, fungi, etc.)===
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| ==Current Research== | | ==Current Research== |
| | | Include information about how this microbe (or related microbes) are being studied and for what purpose |
| Enter summaries of the most recent research.
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| 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.
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| 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).
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| [[Image:ProbioticTable.jpg|frame|Table 1. Alternative strains of bacteria and yeasts that are currently used as probiotics]]
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| ==References== | | ==References== |
| [Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 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.] | | [Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 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.] |
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| | Edited by (Insert your name here), student of Rachel Larsen at the University of Southern Maine |
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| Edited by [Benjamin Dae Lee, Hilary Otorowski, Julia Son, Rebecca Son] students of [mailto:ralarsen@ucsd.edu Rachel Larsen]
| | <!--Do not edit or remove this line.-->[[Category:Pages edited by students of Rachel Larsen]] |
