Editing Digestion (section)

==Digestive system==

Digestive systems take many forms. There is a fundamental distinction between internal and external digestion. External digestion developed earlier in evolutionary history, and most [[fungi]] still rely on it.<ref>Dusenbery, David B. (1996). "Life at Small Scale", pp. 113–115. Scientific American Library, New York. {{ISBN|0-7167-5060-0}}.</ref> In this process, [[enzyme]]s are [[Secretion|secreted]] into the environment surrounding the organism, where they break down an organic material, and some of the products [[Molecular diffusion|diffuse]] back to the organism. [[Animal]]s have a tube ([[gastrointestinal tract]]) in which internal digestion occurs, which is more efficient because more of the broken down products can be captured, and the internal chemical environment can be more efficiently controlled.<ref>Dusenbery, David B. (2009). ''Living at Micro Scale'', p. 280. Harvard University Press, Cambridge, MA {{ISBN|978-0-674-03116-6}}.</ref>

Some organisms, including nearly all [[spiders]], secrete biotoxins and digestive chemicals (e.g., enzymes) into the extracellular environment prior to ingestion of the consequent "soup". In others, once potential nutrients or food is inside the [[organism]], digestion can be conducted to a [[Vesicle (biology)|vesicle]] or a sac-like structure, through a tube, or through several specialized organs aimed at making the absorption of nutrients more efficient.

[[Image:Conjugation.svg|right|thumb|250px|Schematic drawing of bacterial conjugation. '''1-''' Donor cell produces [[pilus]]. '''2-''' Pilus attaches to recipient cell, bringing the two cells together. '''3-''' The mobile plasmid is nicked and a single strand of DNA is transferred to the recipient cell. '''4-''' Both cells recircularize their plasmids, synthesize second strands, and reproduce pili; both cells are now viable donors.]]

===Secretion systems===
{{Main|Secretion#Secretion in Gram negative bacteria}}

[[Bacteria]] use several systems to obtain nutrients from other organisms in the environments.

====Channel transport system====

In a channel transport system, several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria. It is a simple system, which consists of only three protein subunits: the [[ATP-binding cassette family|ABC protein]], [[membrane fusion protein]] (MFP), and [[outer membrane protein]].{{Specify|date=May 2011}} This secretion system transports various chemical species, from ions, drugs, to proteins of various sizes (20–900 kDa). The chemical species secreted vary in size from the small ''Escherichia coli'' peptide colicin V, (10 kDa) to the ''Pseudomonas fluorescens'' cell adhesion protein LapA of 900 kDa.<ref name= Wooldridge>{{cite book |editor= Wooldridge K | year=2009 |title=Bacterial Secreted Proteins: Secretory Mechanisms and Role in Pathogenesis | publisher=Caister Academic Press | isbn= 978-1-904455-42-4}}</ref>

====Molecular syringe====

A [[type III secretion system]] means that a molecular syringe is used through which a bacterium (e.g. certain types of ''Salmonella'', ''Shigella'', ''Yersinia'') can inject nutrients into protist cells. One such mechanism was first discovered in ''Y. pestis'' and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than be secreted into the extracellular medium.<ref name=Salyers>Salyers, A.A. & Whitt, D.D. (2002). ''Bacterial Pathogenesis: A Molecular Approach'', 2nd ed., Washington, DC: ASM Press. {{ISBN|1-55581-171-X}}</ref>

====Conjugation machinery====
The [[Bacterial conjugation|conjugation]] machinery of some bacteria (and archaeal flagella) is capable of transporting both DNA and proteins. It was discovered in ''Agrobacterium tumefaciens'', which uses this system to introduce the Ti plasmid and proteins into the host, which develops the crown gall (tumor).<ref name=Cascales>{{cite journal |vauthors=Cascales E, Christie PJ |title=The versatile Type IV secretion systems |journal=Nature Reviews Microbiology |volume=1 |issue=2 |pages=137–149 |year=2003 |doi=10.1038/nrmicro753 |pmid=15035043|pmc=3873781 }}</ref> The VirB complex of ''Agrobacterium tumefaciens'' is the prototypic system.<ref name=Christie>{{cite journal |author1=Christie PJ |author2=Atmakuri K |author3=Jabubowski S |author4=Krishnamoorthy V |author5=Cascales E. |title=Biogenesis, architecture, and function of bacterial Type IV secretion systems |journal=Annu Rev Microbiol |volume=59 |pages=451–485 |year=2005 |issue=1 |doi=10.1146/annurev.micro.58.030603.123630 |pmid=16153176|pmc=3872966 }}</ref>

In the [[Diazotroph|nitrogen-fixing]] ''[[Rhizobia]]'', conjugative elements naturally engage in inter-[[Kingdom (biology)|kingdom]] conjugation. Such elements as the ''[[Agrobacterium]]'' Ti or Ri plasmids contain elements that can transfer to plant cells. Transferred genes enter the plant cell nucleus and effectively transform the plant cells into factories for the production of [[opines]], which the bacteria use as carbon and energy sources. Infected plant cells form [[Agrobacterium tumefaciens|crown gall]] or [[Agrobacterium rhizogenes|root tumors]]. The Ti and Ri plasmids are thus [[endosymbiont]]s of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant.

The Ti and Ri plasmids are themselves conjugative. Ti and Ri transfer between bacteria uses an independent system (the ''tra'', or transfer, operon) from that for inter-kingdom transfer (the ''vir'', or [[virulence]], operon). Such transfer creates virulent strains from previously avirulent ''Agrobacteria''.

====Release of outer membrane vesicles====
In addition to the use of the multiprotein complexes listed above, [[gram-negative bacteria]] possess another method for release of material: the formation of [[outer membrane vesicle]]s.<ref name=Chatterjee>{{Cite journal
 | pmid = 4168882|doi=10.1099/00221287-49-1-1
| year = 1967
| last1 = Chatterjee
| first1 = S.N.
| title = Electron microscopic observations on the excretion of cell-wall material by ''Vibrio cholerae''
| journal = Journal of General Microbiology
| volume = 49
| issue = 1
| pages = 1–11
| last2 = Das
| first2 = J
| doi-access = free
}}</ref><ref>{{Cite journal
 | pmid = 16291643
| year = 2005
| last1 = Kuehn
| first1 = M.J.
| title = Bacterial outer membrane vesicles and the host-pathogen interaction
| journal = Genes & Development
| volume = 19
| issue = 22
| pages = 2645–2655
| last2 = Kesty
| first2 = N.C.
| doi = 10.1101/gad.1299905
| doi-access = free
}}</ref>  Portions of the outer membrane pinch off, forming spherical structures made of a lipid bilayer enclosing periplasmic materials.  Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells.  While release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective.<ref name=McBrrom>{{Cite journal
| last1 = McBroom | first1 = A.J.
| last2 = Kuehn | first2 = M.J.
| doi = 10.1111/j.1365-2958.2006.05522.x
| title = Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response
| journal = Molecular Microbiology
| volume = 63
| issue = 2
| pages = 545–558
| year = 2007
| pmid = 17163978
| pmc =1868505
}}</ref>

[[Image:Venus Flytrap showing trigger hairs.jpg|thumb|right|125px|Venus Flytrap (''Dionaea muscipula'') leaf]]

===Gastrovascular cavity===
The [[gastrovascular cavity]] functions as a stomach in both digestion and the distribution of nutrients to all parts of the body.  Extracellular digestion takes place within this central cavity, which is lined with the gastrodermis, the internal layer of [[epithelium]]. This cavity has only one opening to the outside that functions as both a [[mouth]] and an [[anus]]: waste and undigested matter is excreted through the mouth/anus, which can be described as an incomplete [[gut (anatomy)|gut]].

In a plant such as the [[Venus flytrap]] that can make its own food through photosynthesis, it does not eat and digest its prey for the traditional objectives of harvesting energy and carbon, but mines prey primarily for essential nutrients (nitrogen and phosphorus in particular) that are in short supply in its boggy, acidic habitat.<ref name=Leege>{{cite web | url = http://www.sciam.com/article.cfm?id=how-does-the-venus-flytra | work = Scientific American | author = Leege, Lissa | title = How does the Venus flytrap digest flies? | access-date= 2008-08-20 }}</ref>

[[Image:Trophozoites of Entamoeba histolytica with ingested erythrocytes.JPG|thumb|125px|left|[[Trophozoites]] of ''Entamoeba histolytica'' with ingested erythrocytes]]

===Phagosome===
A [[phagosome]] is a [[vacuole]] formed around a particle absorbed by [[phagocytosis]].  The vacuole is formed by the fusion of the [[cell membrane]] around the particle. A phagosome is a [[cellular compartment]] in which [[pathogenic]] microorganisms can be killed and digested. Phagosomes fuse with [[lysosomes]] in their maturation process, forming [[phagolysosome]]s. In humans, ''[[Entamoeba histolytica]]'' can phagocytose [[red blood cell]]s.<ref name=Boettner>{{Cite journal | doi = 10.1371/journal.ppat.0040008| pmid = 18208324| pmc = 2211552| title = Entamoeba histolytica Phagocytosis of Human Erythrocytes Involves PATMK, a Member of the Transmembrane Kinase Family| journal = PLOS Pathogens| volume = 4| issue = 1| pages = e8| year = 2008| last1 = Boettner | first1 = D.R. | last2 = Huston | first2 = C.D. | last3 = Linford | first3 = A.S. | last4 = Buss | first4 = S.N. | last5 = Houpt | first5 = E. | last6 = Sherman | first6 = N.E. | last7 = Petri | first7 = W.A. | doi-access = free}}</ref>

===Specialised organs and behaviours===
To aid in the digestion of their food, animals evolved organs such as beaks, [[tongue]]s, [[radula]]e, teeth, crops, gizzards, and others.

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| image1    = Ara hybrid - Catalina Macaw.jpg
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| caption1  = A [[Bird Hybrids|Catalina Macaw]]'s seed-shearing beak
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| caption2  = Squid beak with ruler for size comparison
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====Beaks====
[[Bird]]s have bony [[beak]]s that are specialised according to the bird's [[ecological niche]]. For example, [[macaw]]s primarily eat seeds, nuts, and fruit, using their beaks to open even the toughest seed. First they scratch a thin line with the sharp point of the beak, then they shear the seed open with the sides of the beak.

The mouth of the [[squid]] is equipped with a sharp horny beak mainly made of cross-linked [[proteins]]. It is used to kill and tear prey into manageable pieces. The beak is very robust, but does not contain any minerals, unlike the teeth and jaws of many other organisms, including marine species.<ref name=Miserez>{{cite journal |last=Miserez|first=A|author2=Li, Y |author3=Waite, H |author4= Zok, F  |year=2007|title=Jumbo squid beaks: Inspiration for design of robust organic composites |journal=[[Acta Biomaterialia]] |volume=3 |issue= 1|pages=139–149 |doi=10.1016/j.actbio.2006.09.004 |pmid=17113369 }}</ref> The beak is the only indigestible part of the squid.

====Tongue====
{{Main|Tongue}}
The '''tongue''' is skeletal muscle on the floor of the [[mouth]] of most vertebrates, that manipulates [[food]] for chewing ([[mastication]]) and [[swallowing]] (deglutition). It is sensitive and kept moist by [[saliva]]. The underside of the tongue is covered with a smooth [[mucous membrane]]. The tongue also has a touch sense for locating and positioning food particles that require further chewing. The tongue is used to roll food particles into a [[Bolus (digestion)|bolus]] before being transported down the [[esophagus]] through [[peristalsis]].

The [[sublingual]] region underneath the front of the tongue is a location where the [[oral mucosa]] is very thin, and underlain by a plexus of veins. This is an ideal location for introducing certain medications to the body. The sublingual route takes advantage of the highly [[Blood vessel|vascular]] quality of the oral cavity, and allows for the speedy application of medication into the cardiovascular system, bypassing the gastrointestinal tract.

====Teeth====
{{Main|Teeth}}
Teeth (singular tooth) are small whitish structures found in the jaws (or mouths) of many vertebrates that are used to tear, scrape, milk and chew food. Teeth are not made of bone, but rather of tissues of varying density and hardness, such as enamel, dentine and cementum. Human teeth have a blood and nerve supply which enables proprioception. This is the ability of sensation when chewing, for example if we were to bite into something too hard for our teeth, such as a chipped plate mixed in food, our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.

The shapes, sizes and numbers of types of animals' teeth are related to their diets. For example, herbivores have a number of molars which are used to grind plant matter, which is difficult to digest. [[Carnivore]]s have [[canine tooth|canine teeth]] which are used to kill and tear meat.

====Crop====
A [[Crop (anatomy)|crop]], or croup, is a thin-walled expanded portion of the [[alimentary tract]] used for the storage of food prior to digestion. In some birds it is an expanded, muscular pouch near the [[gullet]] or throat. In adult doves and pigeons, the crop can produce [[crop milk]] to feed newly hatched birds.<ref name=Gordon>{{cite web | title=The Alimentary Canal in Birds | url=http://www.earthlife.net/birds/digestion.html | author=Gordon John Larkman Ramel | date=2008-09-29 | access-date=2008-12-16}}</ref>

Certain insects may have a crop or enlarged [[esophagus]].

[[Image:Abomasum-en.svg|150px|thumb|Rough illustration of a ruminant digestive system]]

====Abomasum====
{{Main|Digestive system of ruminants}}

[[Herbivore]]s have evolved [[cecum]]s (or an [[abomasum]] in the case of [[ruminant]]s). Ruminants have a fore-stomach with four chambers. These are the [[rumen]], [[Reticulum (anatomy)|reticulum]], [[omasum]], and abomasum. In the first two chambers, the rumen and the reticulum, the food is mixed with saliva and separates into layers of solid and liquid material.  Solids clump together to form the cud (or [[Bolus (digestion)|bolus]]). The cud is then regurgitated, chewed slowly to completely mix it with saliva and to break down the particle size.

Fibre, especially [[cellulose]] and [[hemi-cellulose]], is primarily broken down into the [[volatile fatty acids]], [[acetic acid]], [[propionic acid]] and [[butyric acid]] in these chambers (the reticulo-rumen) by microbes: ([[bacteria]], [[protozoa]], and fungi). In the omasum, water and many of the inorganic mineral elements are absorbed into the blood stream.

The abomasum is the fourth and final stomach compartment in ruminants. It is a close equivalent of a monogastric stomach (e.g., those in humans or pigs), and digesta is processed here in much the same way. It serves primarily as a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further digestion and absorption in the small intestine.  Digesta is finally moved into the small intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulo-rumen are also digested in the small intestine.

====Specialised behaviours====
[[File:Flesh fly concentrating food.jpg|thumb|A flesh fly "blowing a bubble", possibly to concentrate its food by evaporating water]]
[[Regurgitation (digestion)|Regurgitation]] has been mentioned above under abomasum and crop, referring to crop milk, a secretion from the lining of the crop of [[Columbidae|pigeons and doves]] with which the parents feed their young by regurgitation.<ref name="Levi">{{cite book |last=Levi |first=Wendell |title= The Pigeon|year= 1977|publisher= Levi Publishing Co, Inc|location= Sumter, SC|isbn=978-0-85390-013-9 }}</ref>

Many [[Physical characteristics of sharks|sharks]] have the ability to turn their stomachs inside out and evert it out of their mouths in order to get rid of unwanted contents (perhaps developed as a way to reduce exposure to toxins).

Other animals, such as [[rabbits]] and [[rodents]], produce [[Cecotrope|cecotropes]] to re-digest food, especially in the case of roughage. Capybaras, rabbits, hamsters, and other related species do not have a complex digestive system as ruminants. They instead extract more [[nutrition]] by giving their food a second pass through the [[gut (anatomy)|gut]]. Soft cecotropes of partially digested food are excreted and generally consumed immediately. They also produce normal droppings, which are not eaten.

Young elephants, pandas, koalas, and hippos eat the faeces of their mother, probably to obtain the bacteria required to properly digest vegetation. When they are born, their intestines do not contain these bacteria (they are completely sterile). Without them, they would be unable to get any nutritional value from many plant components.

===In earthworms===
An [[earthworm]]'s digestive system consists of a mouth, [[pharynx]], [[esophagus]], crop, [[gizzard]], and [[intestine]]. The mouth is surrounded by strong lips, which act like a hand to grab pieces of dead grass, leaves, and weeds, with bits of soil to help chew. The lips break the food down into smaller pieces. In the pharynx, the food is lubricated by mucus secretions for easier passage. The esophagus adds calcium carbonate to neutralize the acids formed by food matter decay. Temporary storage occurs in the crop where food and calcium carbonate are mixed. The powerful muscles of the gizzard churn and mix the mass of food and dirt. When the churning is complete, the glands in the walls of the gizzard add enzymes to the thick paste, which helps chemically breakdown the organic matter. By [[peristalsis]], the mixture is sent to the intestine where friendly bacteria continue chemical breakdown. This releases carbohydrates, protein, fat, and various vitamins and minerals for absorption into the body.