Template:Genus larsen

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 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.

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?

Lactobacillus

Lactobacillus is a microbe that aids in production of lactic acid through homolactic fermentation, and can be found in the human gastrointestinal tract. This Gram-positive, rod shaped, bacterium is a beneficial bacterium that assists in enzymatic production to help with digestion, maintain pH balance and aid in healthy bacterium replacement in the gastrointestinal tract. The lactic acid produced by carbohydrate fermentation from lactobacillus, aids in maintaining the correct homeostatic pH to ensure no phage is able to survive at the low pH. Studies also show that it can synthesize necessary vitamins and help lower cholesterol levels (Ray). Lactobacillus also has been observed to degrade carcinogens, reduce or prevent carcinogenesis through antimutagenic activities. One of many strains of Lactobacilli that is commercially distributed is Lactobacillus Acidophilus, which is categorized as a probiotic. Probiotics are bacterium that can be taken as a supplement to help increase the beneficial bacteria that are normally present in their environment. In the case of Lactobacillus Acidophilus, it has fermentative capabilities, but lacks the ability to synthesize most cofactors and vitamins; which are expected normal capacities of microbes living in such a nutrient-rich niche such as the human gastrointestinal cavity (Altermann). The adherence of Lactobacillus Acidophilus to the cells lining the colon prevents binding of enteropathogenic and enterotoxigenic pathogens, promoting healthy metabolic activities. Lactobacillus Acidophilus and other strains of Lactobilli are widely used for treatment in diarrheal diseases, however the mixed results do not allow an exact conclusion on its treatment accuracy (Macfarlene).

Bifidiobacterium

Figure 1. Gram-Stained Preparation of Bifidobacterium Adolescentis

Bifidobacterium is also considered a probiotic bacterium that inhabits the anaerobic environment of the human gastrointestinal tract. The amount of this bacterium present decreases with age; thus, higher amounts are found in infants, and lower amounts in adults, which may lead to the needs of a probiotic supplement. Bifidobacterium is also a rod club-shaped (as pictured), Gram-positive cell, which has a symbiotic relationship with the host (gastrointestinal tract), benefiting both bacteria and host. This symbiotic relationship is seen by its adhesive ability to the microflora, the metabolism of undigested dietary carbohydrates and prevents pathogen colonization. This type of beneficial bacteria, similarly to the Lactobacilli, prevents binding of pathogens such as Escherichia Coli, and Salmonella Typhimurium, decreasing susceptibility to possible illnesses such as E. Coli poisoning in humans. The microflora normally lining the gut serves as a protective barrier against pathogens, however this can be compromised due to antibiotic treatments, stress, poor diet or other physiological distress. The Bifidobacteria can serve as resistance mechanism against the colonization of pathogens in the large intestine (Macfarlene). It has been observed that their competitive nature, against other gastrointestinal bacteria, is due to its ability to scavenge for a large variety of nutrients to use for energy (Schell). Studies also show that Bifidobacterium has also has potential to prevent cancer by reactivity with certain carcinogens and promotes immune stimulation (O'Sullivan).

Methanogens and Sulfur reducing bacteria

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.

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.

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.

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.

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.

Enterococcus

common species: E. avium, E. durans, E. faecalis, E. faecium, E. solitarius

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 – E. faecalis and E. faecium – can cause urinary tract infections and wound infections in human and animals most commonly. 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 Enterococci but they many become potential carriers.

Enterococci infections can be treated with various types of antibiotics, but unfortunately some of the 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 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 Enterococci that are resistant to antibiotics, then the whole community will become resistant and no other antibiotics are effective3.

Enterococci are commensal bacteria inhabiting in the intestines of both humans and animals. 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). 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, 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.

Enterococci are anaerobes. They ferment carbohydrates to produce lactic acids (lactic acid bacteria). Enterococci living in large intestine will use undigested sugars from small intestine and indigestible fibers for their fermentation process. Especially for 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. 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 reaction⁶.

Escherichia Coli

Common Species: Escherichia albertii; E. blattae; E. coli; E. fergusonii; E. hermannii; E. senegalensis; E. senegalensis; E. vulneris; E. sp. Escherichia coli, also known as 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 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, E. coli is also useful in studying the organisms’ essential processes of life.[3]

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 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. E. coli often stay with diverse species of bacteria in a form of biofilm and this causes the transfer of antibiotic-resistant plasmids of E.coli to other bacteria such as Staphylococcus aureus.[7]

Despite the fact that 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, 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. E. coli can detect the chemicals in the surrounding environment with its complex metabolism mechanism.[4]

E. coli is able to survive with or without oxygen. Unlike aerobic organisms which use oxygen as the final electron acceptor, 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). 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]

Clostridium

Common Species: Clostridium dfficile, Clostridium tetani, Clostridium perfringens, Clostridium acetobutylicum

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 in 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]

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]

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]

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 C. perfringers compared to controls.

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).

Table 1. Alternative strains of bacteria and yeasts that are currently used as probiotics

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 [Benjamin Dae Lee, Hilary Otorowski, Julia Son, Rebecca Son] students of Rachel Larsen