Spoiled fish: Difference between revisions

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==Introduction==
==Background==
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.
===Spoilage===


==Description of Niche==
Spoilage is the degradation of food such that the food becomes unfit for human consumption. Food can be spoiled by a number of means, including physical and chemical means. However, the most prevalent cause of food spoilage is microbial growth and residence in the food, which results in numerous undesirable metabolites being produced in the food that cause unwanted flavors and odors. Approximately 25% of the world’s food produced post harvest or post slaughter is lost to microbial degradation of food alone.


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 main culprits are microbial organisms known as spoilage specific organisms (SSOs). The concept of SSOs arises from the fact that not all bacteria cause food spoilage; indeed, the degree of food spoilage is not proportional to the amount of microbes present on the food. SSOs are solely responsible for spoilage of the food and the typical characteristics associated with that spoilage. They are typically present in very low numbers and comprise a low percentage of the microflora present on the food.  


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.  
Identification of SSOs is done by comparisons of the physical and chemical features of the collective spoiled products with the individual products left behind by each organism in the spoilage microflora. In particular, the qualitative ability of each organism to produce off-odors (spoilage potential) and the quantitative ability of each organism to produce spoilage metabolites (spoilage activity) are examined. This simple phenotypic identification scheme, along with a 16S rDNA gene sequencing to confirm results, allows scientists to discover which organism or organisms in the spoilage microflora are directly responsible for the spoilage.  


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.  
Each unique environment has its own unique SSOs, because each different environment selects for particular organisms to thrive. The spoilage domain for an SSO is identified based upon the conditions (pH, temperature, water activity, and atmosphere) under which that SSO can grow and produce the metabolites that cause spoilage.


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?==
===Spoiled Food vs. Harmful Food===
 
It is important to note that spoilage bacteria normally outgrow pathogenic bacteria during storage.  Thus some foods may spoil before they become toxic.  Spoilage bacteria and pathogenic species in spoiled food have different effects. Pathogens are responsible for the symptoms that result from eating spoiled food; SSOs may or may not have a direct harmful effect to the consumers.
 
===Spoilage in Fish===
 
Fish spoilage manifests itself physically in numerous ways. In terms of smell, spoiled fish will generally have a fishy, sour, or ammonia-like stench. Appearance-wise, spoiled fish may appear to be dry or mushy in certain areas, and the gills may have slime. Spoiled fish will also have flesh that is soft, or does not spring back when pressed upon. Typically, spoiled fish will also have a green or yellowish discoloration; however, this arises not from spoilage metabolites, but rather the oxidation during frozen storage of the oxygen transporters in fish blood (myoglobin to metamyoglobin).
 
Compared to other foods, fish is unique as a substrate for microbial growth. This uniqueness stems from several important factors: the poikilotherm nature of fish, a high post mortem pH in the flesh (typically greater than 6.0), the presence of non-protein-nitrogen (NPN) in large quantities, and the presence of trimethylamine oxide (TMAO).
 
The poikilotherm nature of fish selects for bacteria that can thrive in a wide range of temperatures. For example, the microflora of temperate water fish is dominated by psychrotrophic Gram-negative, rod-shaped bacteria such as those found in the genera Pseudomonos and Moraxella, with only varying proportions of Gram-positive organisms such as Bacillus.
 
The high post mortem pH of fish flesh is caused by the fact that fish flesh is low in carbohydrates (less than 0.5%) in the muscle tissue and that only small amounts of lactic acid are produced after death. This allows pH sensitive organisms such as Shewanella putrefaciens to grow in seafood but not in other meats.
 
The NPN fraction of the fish flesh consists of low-molecular-weight water-soluble nitrogen contains compounds, particularly free amino acids and nucleotides, that allow it to serve as a readily available bacterial growth substrate. Decomposition of these compounds is responsible for many of the off-odors and off-flavors typically found in spoilage. For example, the breakdown of cysteine and methionine by certain microbes, both sulfur-containing amino acids, forms hydrogen sulfides and methylmercaptane respectively which causes undesirable odors to emanate from spoiled fish.
 
The presence of TMAO in fish is well-established, and it is known to cause a high redox potential in the fish flesh, although the significance of this is not clear. The spoilage of fish is influenced most by the presence of TMAO in conditions where oxygen is not present. Some anaerobic bacteria are able to utilize TMAO as the terminal electron acceptor in an anaerobic respiration process with trimethylamine (TMA) as the primary product; TMA contributes to the characteristic ammonia-like and fishy off-flavours in spoiled fish.
 


===Which microbes are present?===
===Which microbes are present?===
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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.
 
Gram and Dalgaard, 2002 L. Gram and P. Dalgaard, Fish spoilage bacteria-problems and solutions, Current Opinion in Biotechnology 13 (2002), pp. 262–266. Article
 
Gram and Huss, 1996 L. Gram and H.H. Huss, Microbiological spoilage of fish and fish products, International Journal of Food Microbiology 33 (1) (1996), pp. 121–137. Article]




Edited by Tal Do, Phillip Lai, Duy Nguyen, and Tania Yaser, students of [mailto:ralarsen@ucsd.edu Rachel Larsen]
Edited by Tal Do, Phillip Lai, Duy Nguyen, and Tania Yaser, students of [mailto:ralarsen@ucsd.edu Rachel Larsen]

Revision as of 00:50, 29 August 2008

Background

Spoilage

Spoilage is the degradation of food such that the food becomes unfit for human consumption. Food can be spoiled by a number of means, including physical and chemical means. However, the most prevalent cause of food spoilage is microbial growth and residence in the food, which results in numerous undesirable metabolites being produced in the food that cause unwanted flavors and odors. Approximately 25% of the world’s food produced post harvest or post slaughter is lost to microbial degradation of food alone.

The main culprits are microbial organisms known as spoilage specific organisms (SSOs). The concept of SSOs arises from the fact that not all bacteria cause food spoilage; indeed, the degree of food spoilage is not proportional to the amount of microbes present on the food. SSOs are solely responsible for spoilage of the food and the typical characteristics associated with that spoilage. They are typically present in very low numbers and comprise a low percentage of the microflora present on the food.

Identification of SSOs is done by comparisons of the physical and chemical features of the collective spoiled products with the individual products left behind by each organism in the spoilage microflora. In particular, the qualitative ability of each organism to produce off-odors (spoilage potential) and the quantitative ability of each organism to produce spoilage metabolites (spoilage activity) are examined. This simple phenotypic identification scheme, along with a 16S rDNA gene sequencing to confirm results, allows scientists to discover which organism or organisms in the spoilage microflora are directly responsible for the spoilage.

Each unique environment has its own unique SSOs, because each different environment selects for particular organisms to thrive. The spoilage domain for an SSO is identified based upon the conditions (pH, temperature, water activity, and atmosphere) under which that SSO can grow and produce the metabolites that cause spoilage.


Spoiled Food vs. Harmful Food

It is important to note that spoilage bacteria normally outgrow pathogenic bacteria during storage. Thus some foods may spoil before they become toxic. Spoilage bacteria and pathogenic species in spoiled food have different effects. Pathogens are responsible for the symptoms that result from eating spoiled food; SSOs may or may not have a direct harmful effect to the consumers.

Spoilage in Fish

Fish spoilage manifests itself physically in numerous ways. In terms of smell, spoiled fish will generally have a fishy, sour, or ammonia-like stench. Appearance-wise, spoiled fish may appear to be dry or mushy in certain areas, and the gills may have slime. Spoiled fish will also have flesh that is soft, or does not spring back when pressed upon. Typically, spoiled fish will also have a green or yellowish discoloration; however, this arises not from spoilage metabolites, but rather the oxidation during frozen storage of the oxygen transporters in fish blood (myoglobin to metamyoglobin).

Compared to other foods, fish is unique as a substrate for microbial growth. This uniqueness stems from several important factors: the poikilotherm nature of fish, a high post mortem pH in the flesh (typically greater than 6.0), the presence of non-protein-nitrogen (NPN) in large quantities, and the presence of trimethylamine oxide (TMAO).

The poikilotherm nature of fish selects for bacteria that can thrive in a wide range of temperatures. For example, the microflora of temperate water fish is dominated by psychrotrophic Gram-negative, rod-shaped bacteria such as those found in the genera Pseudomonos and Moraxella, with only varying proportions of Gram-positive organisms such as Bacillus.

The high post mortem pH of fish flesh is caused by the fact that fish flesh is low in carbohydrates (less than 0.5%) in the muscle tissue and that only small amounts of lactic acid are produced after death. This allows pH sensitive organisms such as Shewanella putrefaciens to grow in seafood but not in other meats.

The NPN fraction of the fish flesh consists of low-molecular-weight water-soluble nitrogen contains compounds, particularly free amino acids and nucleotides, that allow it to serve as a readily available bacterial growth substrate. Decomposition of these compounds is responsible for many of the off-odors and off-flavors typically found in spoilage. For example, the breakdown of cysteine and methionine by certain microbes, both sulfur-containing amino acids, forms hydrogen sulfides and methylmercaptane respectively which causes undesirable odors to emanate from spoiled fish.

The presence of TMAO in fish is well-established, and it is known to cause a high redox potential in the fish flesh, although the significance of this is not clear. The spoilage of fish is influenced most by the presence of TMAO in conditions where oxygen is not present. Some anaerobic bacteria are able to utilize TMAO as the terminal electron acceptor in an anaerobic respiration process with trimethylamine (TMA) as the primary product; TMA contributes to the characteristic ammonia-like and fishy off-flavours in spoiled fish.


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] [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.

Gram and Dalgaard, 2002 L. Gram and P. Dalgaard, Fish spoilage bacteria-problems and solutions, Current Opinion in Biotechnology 13 (2002), pp. 262–266. Article

Gram and Huss, 1996 L. Gram and H.H. Huss, Microbiological spoilage of fish and fish products, International Journal of Food Microbiology 33 (1) (1996), pp. 121–137. Article]


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