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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: Lactobacillus, [[Bifidobacterium]], Methanogens, Sulfate reducing bacteria, [[Bacteroides]], [[Enterococcus]], [[Escherichia coli]], and [[Clostridium]]. In addition, we will discuss a eukaryotic organism, Candida, 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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| [[Lactobacillus|Lactobacilli]] that is commercially distributed is [[Lactobacillus|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|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|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|Lactobacillus Acidophilus]] and other strains of [[Lactobacillus|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 [[Lactobacillus|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. Methanobrevibacter 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 H<sub>2</sub>, but not in water (as would be the case in an aerobic environment). This poses a problem as accumulation of H<sub>2</sub> 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 H<sub>2</sub> 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 H<sub>2</sub> 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 H<sub>2</sub> 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 H<sub>2</sub> 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 H<sub>2</sub> 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.
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| ===Bacteroides===
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| Bacteroides are anaerobic organisms that are characterized by the gram-negative cellular envelope. These bacteria exist symbiotically with the large intestine because the Bacterioides support the core metabolic activities (i.e. amino acid biosynthesis, carbon-oxygen lyases, membrane transport, and etc.) while feeding off dietary fibers passing through the colon. The common species of Bacteroides include B. vulgatus, B. distasoni, B. thetaiotaomicron, and B. fragilis.2
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| These organisms primarily feed off of plant polysaccharides and the host’s mucous glycans.2 Fibrous polymers that pass through the large intestine can be only be broken down by Bacteroides. Once these sugars are in the large intestine, the Bacteriodes metabolize them into their respective monomers so that they can enter central metabolism for energy synthesis.4 A unique trait of B. Thetaiotaomicron is that it can use various polysaccharides to survive. The physiological explanation for this is that B. Thetaiotaomicron possesses 226 glycoside hydrolases and 15 polysaccharide lyases. Note that B. Thetaiotaomicron does not reside in human intestine; thus, we cannot digest such polysaccharides.
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| Bacteroides are also saccharolytic, meaning that they can obtain energy, carbon sources, dietary carbohydrate molecules from the host.3 The products of fermentation reactions include acetate and propionate, which are short chains of fatty acids can then be absorbed via the large intestine.3 B. distasonis are more specific for carbohydrate processing with the enzymes CAZy glycoside hydrolase family 13 and family 73.2 These enzymes aid in breaking down food molecules and supplying vitamins for metabolic purposes.3 It also has more polysaccharide deacetylases, which allow it to deacetylate the O-acetylated sugars of the host’s epithelial glycans to utilize them.
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| ===Enterococcus===
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| Common Species: E. avium, E. durans, E. faecalis, E. faecium, E. solitarius
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| [[Enterococcus|Enterococci]] are gram-positive cocci that are found in many different places – normally found in the feces of people and many animals. Two major species – [[Enterococcus faecalis|E. faecalis]] and E. faecium – can cause urinary tract infections and wound infections in human and animals most commonly. [[Enterococcus faecalis|E. faecalis]] contributes about 90-95% of all species and E. faecium contributes about 5-10%. They can be also the cause of other diseases – bacteraemia (blood stream), endocarditis (heart vales), and meningitis (brain) – which occurs mostly in severely sick people with weak immune system1. Many of these [[Enterococcus]] infections have been commonly found in clinical environment. Healthy people with strong immune system will not be affected by [[Enterococcus|Enterococci]] but they many become potential carriers.
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| [[Enterococcus|Enterococci]] infections can be treated with various types of antibiotics, but unfortunately some of the [[Enterococcus|Enterococci]] have become resistant to many types of antibiotics. They are resistant to β-lactam-based antibiotics (penicillin and cephalosporin) as well as many aminoglycosides2. In recent time, some of the [[Enterococcus|Enterococci]] are found to be resistant to Vancomycin, and they are called VRE (Vancomycin-Resistant [[Enterococcus]]). VRE are especially dangerous because they can easily transmit the resistant genes from another (transformation or conjugation), so if there is small portion of [[Enterococcus|Enterococci]] that are resistant to antibiotics, then the whole community will become resistant and no other antibiotics are effective3.
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| [[Enterococcus|Enterococci]] are commensal bacteria inhabiting in the intestines of both humans and animals.
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| [[Enterococcus|Enterococci]] are capable of living in extremely hardy conditions that most of other bacteria won’t survive. They are likely to inhabit in the bowels of animlas or humans, and they are also found in soil, vegetation, and surface water (mainly due to contamination by animal feces). [[Enterococcus|Enterococci]] are capable of growing at a range of temperatures from 10-45 °C and can grow in any environmental concentrations – hypotonic or hypertonic – and over broad range of pH – acidic or alkaline. Even though they are anaerobes, they can live in both low and high oxygen environments. In fact, [[Enterococcus|Enterococci]] can survive at 60 °C for half an hour. They are also capable of living under high salt concentration (6.5% NaCl) and in high bile salts (40%). Some of them are naturally antibiotic resistant4.
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| [[Enterococcus|Enterococci]] are anaerobes. They ferment carbohydrates to produce lactic acids (lactic acid bacteria). [[Enterococcus|Enterococci]] living in large intestine will use undigested sugars from small intestine and indigestible fibers for their fermentation process. Especially for [[Enterococcus faecalis|E. faecalis]], it contains a large number of sugar uptake systems (PTS: phophoenolypyruvate phosphotransferase system) which recognize sugars outside and transport them with phosphorlyation. This process will use energy (ATP) more efficiently as it is compared to sugar transport by other non-PTS system5. [[Enterococcus faecalis|E. faecalis]] can metabolize following types of sugars: D-glucose, D-fructose, lactose, maltose, etc. It also has cation homeostasis mechanism that contributes to its resistance to change in pH, salt concentration, etc. They under go fermentation process usually because they lack ability to process Kreb’s cycle and following electron transport chain reaction<sup>6</sup>.
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| ===Escherichia Coli===
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| Common Species: Escherichia albertii; E. blattae; [[Escherichia Coli|E. coli]]; E. fergusonii; E. hermannii; E. senegalensis; E. senegalensis; E. vulneris; E. sp.
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| [[Escherichia coli]], also known as [[Escherichia Coli|E. coli]], is an anaerobic gram-negative bacterium that can be found in large intestine of warm-blooded animals and humans. Even though it is a predominant and consistent organism, it contributes to only small portion of the content of total bacteria in GI tract. It is often used as an indicator to test the fecal contamination in nature such as water since [[Escherichia Coli|E. coli]] is able to survive outside the body for a brief time period.[1][2] Because of its simple nutritional requirement and ability to grow rapidly, [[Escherichia Coli|E. coli]] is also useful in studying the organisms’ essential processes of life.[3]
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| [[Escherichia Coli|E. coli]] are both pathogenic and nonpathogenic. Some are nonpathogenic, but it might cause infection if the bacterium is introduced to other tissues in a debilitated host; however, the bacteria from contaminated water or undercooked meat may cause infection in a healthy person as well.[5] Some virulent [[Escherichia Coli|E. coli]] can even lead to urinary tract infections, neonatal meningitis, diarrheal disease, and gastroenteritis.[6] They damage the host in several steps: colonizing the intestinal mucosal surface, evading the defenses by the host, and lastly multiplying themselves in numbers.[5] Since the bacterial infections are usually treated with antibiotics, the antibiotic-resistance became problematic. [[Escherichia Coli|E. coli]] often stay with diverse species of bacteria in a form of biofilm and this causes the transfer of antibiotic-resistant plasmids of [[Escherichia Coli|E. coli]] to other bacteria such as [[Staphylococcus aureus]].[7]
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| Despite the fact that [[Escherichia Coli|E. coli]] is a unicellular organism, it has an amazing ability in interacting with the environment. It can respond to such signals including pH, osmolarity, temperature, and chemicals. With its chemotaxis proteins in cytoplasmic membrane, [[Escherichia Coli|E. coli]] can detect attractants and repellants without any stimuli. With around six flagella, it can swim towards the attractant with counterclockwise flagellar rotation, but bacteria tumbles with clockwise rotation when it senses the repellant.[4] It can also adjust the size of the porins on the outer membrane in order to regulate the temperature and osmolarity by importing or exporting the larger substances such as nutrients. [[Escherichia Coli|E. coli]] can detect the chemicals in the surrounding environment with its complex metabolism mechanism.[4]
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| [[Escherichia Coli|E. coli]] is able to survive with or without oxygen. Unlike aerobic organisms which use oxygen as the final electron acceptor, [[Escherichia Coli|E. coli]] use nitrate or other molecules. The major determinants of organization of bacterium are the type of terminal electron acceptor and the presence of glucose (Barrett). [[Escherichia Coli|E. coli]] demonstrates only six distinct functional states no matter what carbon source or electron acceptor has been used.[6] Unless the carbon sources are available, they do not wastefully make the enzymes for degradation. If the metabolites are available in the environment as nutrients, they also don’t make the enzymes for synthesis.[1]
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| ===Clostridium===
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| Common Species: Clostridium dfficile, Clostridium tetani, Clostridium perfringens, Clostridium acetobutylicum
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| [[Clostridium]], is a gram-positive bacteria belonging to the family of [[Clostridiaceae]]. It is capable of forming endospores during extreme environmental conditions. These organisms are capable of surviving in many environments, but are predominantly found in soil and feces; be that as it may, [[Clostridium]] prefer to live in the human body as such an environment provides optimum growth for the organism. [1]
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| Most of the species in [[Clostridium]] are pathogenic. [[Clostridium deficile]] for instance, may cause inflammation in the colon of the gastrointestinal tract. Ironically, treatment with relevant antibiotics does not kill this organism, but speed its the growth. The only factor that limits its growth is the presence of other bacteria in the colon (i.e. other competitors). [1]
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| [[Clostridium]] is able to survive without oxygen. Unlike aerobic organisms which use oxygen as the final electron acceptor, [[Clostridium]] use nitrate or other molecules. These organisms are usually pathogens that live freely in our gastrointestinal tract. A trademark characteristic of this organism is that it is the major cause of Pseudomembranous Coliits, an inflammatory disease of the colon characterized by exudative plaques on congested mucosa. [1]
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| Studies have shown that commercial broiler chickens that were vaccinated with [[Clostridium perfiringens]] type A Toxoid controlled the growth of necrotic enteritis over a 65 week period. Sera and egg yolk that were injected with the vaccine had higher antibody for [[Clostridium perfiringens|C. perfringers]] compared to controls.
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| ===What other organisms are present (e.g. plants, fungi, etc.)===
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| Species of Candida, such as C. Albicans, C. Glarata, are one of the few fungal organisms that live in the large intestines. Candida is a condition characterized by yeast/fungal overgrowth that can result in symptoms such as incapacitating fatigue, problems with concentration, extreme tightness in shoulders and neck, and etc. They live in its host by adhering to the mucosal lining, which prevents them from dislodgement by secretion of the mucosal lining. Candida are similar to brewers yeast in that they have dimorphic stages (meaning, they are able to grow in two different morphological forms), allowing them to be a yeast cell or in a hyphae form. Depending on the environment (i.e. pH, temperature, or compound availability changes), the organisim can switch between the two forms. If the pH of the environment is about 4.5, the organism will be budding in the yeast form. If the pH is raised to 6.7, the Candida would switch gene expression and begin growing in the hyphae mode. By possessing the ability to switch gene expressions, it ensures the organisms pathogenicity.
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| Because Candida reside in mucosal communities, they live next to the host tissue and interact with the gut immune system. An important fact to note is that many intestinal organisms have immunomodulatory properties, which allow them to affect the activities of the intestinal epithelial cells (B and T lymphocytes) as well as other accessory cells from the mucosal immune system.
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| Despite Candida’s extraordinary ability to evade cell death, its growth can be maintained with the presence of bifidobacterias and similar probiotics. The probiotic bacteria interact with Candida by preventing the organism to propagate uncontrollably. This in turn will reduce inflammatory responses of the intestinal tracts and relieve some of the common symptoms. When Candida proliferate exponentially, this is an implication that there is a deprived presence of bifidobacterias and other probiotics.
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| Candia, like most large intestine residents, are anaerobes due to the oxygen lacking environment. Therefore, their primary metabolism is that of anaerobic metabolism. An interesting fact to note is that Candida are similar to yeast, in that they utilize fermentation.
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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,Alexander Pang] students of [mailto:ralarsen@ucsd.edu Rachel Larsen]
| | <!--Do not edit or remove this line.-->[[Category:Pages edited by students of Rachel Larsen]] |
