Are the byproducts of mammalian digestion simply depleted versions of the food or liquid consumed?

Are the byproducts of mammalian digestion simply depleted versions of the food or liquid consumed?

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When mammals consume food and digest it or drink fluids that are then filtered by their kidneys, are the waste products generated simply depleted versions of what they consumed?

Are there other byproducts of metabolism and filtration contained in that waste that are generated by the body and are not directly a part of the food or liquid that was consumed that are excreted?

The answer really depends on what aspect of the urine and feces one is considering.

On the atomic level, no, urine and feces are composed entirely of atoms taken from our environment. As one would expect, as there is no "Humanium" on the periodic table. In fact, all the atoms in urine and feces were originally created by stars.

On the molecular level, yes. The body produces molecules that we do not ingest, or that we ingest in minute quantities, such as urea and bile.

On the cellular level, yes. The body produces, for instance, red blood cells even if the person eats a vegan diet with no blood intake. The proteins that make up the cells are created by breaking down ingested proteins into their constituent amino acids, which are then used to construct new proteins.

Also at the cellular level are the huge amount of bacterial cells that we support. Estimates of the number of bacterial cells in our body range from ten to 100 times the number of our own cells. The bacterial component in feces is massive - up to 1/3 of feces by weight are bacteria. Urine, being produced from the blood by the kidneys, is relatively sterile.

Chapter 50 - Digestion and Intestinal Absorption of Dietary Carotenoids and Vitamin A☆

Vitamin A is an essential nutrient for vision and life of humans because it is converted to the visual chromophore, 11-cis-retinal, and to the hormone, retinoic acid. Vitamin A in animal-derived foods is found as long-chain acyl esters of retinol and these are digested to free fatty acids and retinol before uptake by the intestinal mucosal cell. The retinol is then (1) reesterified to retinyl esters for incorporation into chylomicrons along with other dietary lipids and absorbed via the lymphatics or (2) effluxed into the portal circulation facilitated by the lipid transporter, ABCA1. Provitamin A carotenoids such as β-carotene (β-C) are found in plant-derived foods. These and other carotenoids that do not have vitamin A activity are transported into the mucosal cell by scavenger receptor class B type I (SR-BI). Provitamin A carotenoids are partly converted to retinol by oxygenase and reductase enzymes and the retinol so produced is available for absorption via the two pathways described. Carotenoids that are not converted to vitamin A are incorporated into chylomicrons for absorption. The efficiency of vitamin A and carotenoid intestinal absorption is determined by the regulation of a number of proteins involved in the process. Polymorphisms in these genes lead to variability in the metabolism and transport of vitamin A and carotenoids among individuals.


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. [4] In this process, enzymes are secreted into the environment surrounding the organism, where they break down an organic material, and some of the products diffuse back to the organism. Animals 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. [5]

Some organisms, including nearly all spiders, simply 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 or a sac-like structure, through a tube, or through several specialized organs aimed at making the absorption of nutrients more efficient.

Secretion systems

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

Channel transport system

In a channel transupport 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 ABC protein, membrane fusion protein (MFP), and outer membrane protein (OMP) [ specify ] . This secretion system transports various molecules, from ions, drugs, to proteins of various sizes (20–900 kDa). The molecules 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. [6]

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 simply be secreted into the extracellular medium. [7]

Conjugation machinery

The 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). [8] The VirB complex of Agrobacterium tumefaciens is the prototypic system. [9]

The nitrogen fixing Rhizobia are an interesting case, wherein conjugative elements naturally engage in inter-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 crown gall or root tumors. The Ti and Ri plasmids are thus endosymbionts 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 vesicles. [10] [11] 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. [12]

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.

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. [13]


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 phagolysosomes. In humans, Entamoeba histolytica can phagocytose red blood cells. [14]

Specialised organs and behaviours

To aid in the digestion of their food, animals evolved organs such as beaks, tongues, radulae, teeth, crops, gizzards, and others.


Birds have bony beaks that are specialised according to the bird's ecological niche. For example, macaws 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. [15] The beak is the only indigestible part of the squid.


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 utilized to roll food particles into a 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 vascular quality of the oral cavity, and allows for the speedy application of medication into the cardiovascular system, bypassing the gastrointestinal tract.


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. Carnivores have canine teeth which are used to kill and tear meat.

A 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. [16]

Certain insects may have a crop or enlarged esophagus.


Herbivores have evolved cecums (or an abomasum in the case of ruminants). Ruminants have a fore-stomach with four chambers. These are the rumen, 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). 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

Regurgitation has been mentioned above under abomasum and crop, referring to crop milk, a secretion from the lining of the crop of pigeons and doves with which the parents feed their young by regurgitation. [17]

Many 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, practise coprophagia behaviours – eating specialised faeces in order to re-digest food, especially in the case of roughage. Capybara, rabbits, hamsters and other related species do not have a complex digestive system as do, for example, ruminants. Instead they extract more nutrition from grass by giving their food a second pass through the gut. Soft faecal pellets 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.

In most vertebrates, digestion is a multistage process in the digestive system, starting from ingestion of raw materials, most often other organisms. Ingestion usually involves some type of mechanical and chemical processing. Digestion is separated into four steps:

    : placing food into the mouth (entry of food in the digestive system),
  1. Mechanical and chemical breakdown: mastication and the mixing of the resulting bolus with water, acids, bile and enzymes in the stomach and intestine to break down complex molecules into simple structures,
  2. Absorption: of nutrients from the digestive system to the circulatory and lymphatic capillaries through osmosis, active transport, and diffusion, and
  3. Egestion (Excretion): Removal of undigested materials from the digestive tract through defecation.

Underlying the process is muscle movement throughout the system through swallowing and peristalsis. Each step in digestion requires energy, and thus imposes an "overhead charge" on the energy made available from absorbed substances. Differences in that overhead cost are important influences on lifestyle, behavior, and even physical structures. Examples may be seen in humans, who differ considerably from other hominids (lack of hair, smaller jaws and musculature, different dentition, length of intestines, cooking, etc.).

The major part of digestion takes place in the small intestine. The large intestine primarily serves as a site for fermentation of indigestible matter by gut bacteria and for resorption of water from digests before excretion.

In mammals, preparation for digestion begins with the cephalic phase in which saliva is produced in the mouth and digestive enzymes are produced in the stomach. Mechanical and chemical digestion begin in the mouth where food is chewed, and mixed with saliva to begin enzymatic processing of starches. The stomach continues to break food down mechanically and chemically through churning and mixing with both acids and enzymes. Absorption occurs in the stomach and gastrointestinal tract, and the process finishes with defecation. [3]


Below are some definitions of fermentation. They range from informal, general usages to more scientific definitions. [4]

  1. Preservation methods for food via microorganisms (general use).
  2. Any large-scale microbial process occurring with or without air (common definition used in industry).
  3. Any process that produces alcoholic beverages or acidic dairy products (general use).
  4. Any energy-releasing metabolic process that takes place only under anaerobic conditions (somewhat scientific).
  5. Any metabolic process that releases energy from a sugar or other organic molecule, does not require oxygen or an electron transport system, and uses an organic molecule as the final electron acceptor (most scientific).

Along with aerobic respiration, fermentation is a method to extract energy from molecules. This method is the only one common to all bacteria and eukaryotes. It is therefore considered the oldest metabolic pathway, suitable for primeval environments – before plantlife on Earth, that is, before oxygen in the atmosphere. [5] : 389

Yeast, a form of fungus, occurs in almost any environment capable of supporting microbes, from the skins of fruits to the guts of insects and mammals to the deep ocean. Yeasts convert (break down) sugar-rich molecules to produce ethanol and carbon dioxide. [6] [7]

Basic mechanisms for fermentation remain present in all cells of higher organisms. Mammalian muscle carries out fermentation during periods of intense exercise where oxygen supply becomes limited, resulting in the creation of lactic acid. [8] : 63 In invertebrates, fermentation also produces succinate and alanine. [9] : 141

Fermentative bacteria play an essential role in the production of methane in habitats ranging from the rumens of cattle to sewage digesters and freshwater sediments. They produce hydrogen, carbon dioxide, formate and acetate and carboxylic acids. Then consortia of microbes convert the carbon dioxide and acetate to methane. Acetogenic bacteria oxidize the acids, obtaining more acetate and either hydrogen or formate. Finally, methanogens (in the domain Archea) convert acetate to methane. [10]

Fermentation reacts NADH with an endogenous, organic electron acceptor. [2] Usually this is pyruvate formed from sugar through glycolysis. The reaction produces NAD + and an organic product, typical examples being ethanol, lactic acid, and hydrogen gas (H2), and often also carbon dioxide. However, more exotic compounds can be produced by fermentation, such as butyric acid and acetone. Fermentation products are considered waste products, since they cannot be metabolized further without the use of oxygen. [12]

Fermentation normally occurs in an anaerobic environment. In the presence of O2, NADH, and pyruvate are used to generate ATP in respiration. This is called oxidative phosphorylation. This generates much more ATP than glycolysis alone. It releases the chemical energy of O2. [12] For this reason, fermentation is rarely used when oxygen is available. However, even in the presence of abundant oxygen, some strains of yeast such as Saccharomyces cerevisiae prefer fermentation to aerobic respiration as long as there is an adequate supply of sugars (a phenomenon known as the Crabtree effect). [13] Some fermentation processes involve obligate anaerobes, which cannot tolerate oxygen. [ citation needed ]

Although yeast carries out the fermentation in the production of ethanol in beers, wines, and other alcoholic drinks, this is not the only possible agent: bacteria carry out the fermentation in the production of xanthan gum. [ citation needed ]

Ethanol Edit

In ethanol fermentation, one glucose molecule is converted into two ethanol molecules and two carbon dioxide molecules. [14] [15] It is used to make bread dough rise: the carbon dioxide forms bubbles, expanding the dough into a foam. [16] [17] The ethanol is the intoxicating agent in alcoholic beverages such as wine, beer and liquor. [18] Fermentation of feedstocks, including sugarcane, corn, and sugar beets, produces ethanol that is added to gasoline. [19] In some species of fish, including goldfish and carp, it provides energy when oxygen is scarce (along with lactic acid fermentation). [20]

The figure illustrates the process. Before fermentation, a glucose molecule breaks down into two pyruvate molecules (Glycolysis). The energy from this exothermic reaction is used to bind inorganic phosphates to ADP, which converts it to ATP, and convert NAD + to NADH. The pyruvates break down into two acetaldehyde molecules and give off two carbon dioxide molecules as waste products. The acetaldehyde is reduced into ethanol using the energy and hydrogen from NADH, and the NADH is oxidized into NAD + so that the cycle may repeat. The reaction is catalyzed by the enzymes pyruvate decarboxylase and alcohol dehydrogenase. [14]

Lactic acid Edit

Homolactic fermentation (producing only lactic acid) is the simplest type of fermentation. Pyruvate from glycolysis [21] undergoes a simple redox reaction, forming lactic acid. [22] [23] Overall, one molecule of glucose (or any six-carbon sugar) is converted to two molecules of lactic acid:

It occurs in the muscles of animals when they need energy faster than the blood can supply oxygen. It also occurs in some kinds of bacteria (such as lactobacilli) and some fungi. It is the type of bacteria that convert lactose into lactic acid in yogurt, giving it its sour taste. These lactic acid bacteria can carry out either homolactic fermentation, where the end-product is mostly lactic acid, or heterolactic fermentation, where some lactate is further metabolized to ethanol and carbon dioxide [22] (via the phosphoketolase pathway), acetate, or other metabolic products, e.g.:

If lactose is fermented (as in yogurts and cheeses), it is first converted into glucose and galactose (both six-carbon sugars with the same atomic formula):

Heterolactic fermentation is in a sense intermediate between lactic acid fermentation and other types, e.g. alcoholic fermentation. Reasons to go further and convert lactic acid into something else include:

  • The acidity of lactic acid impedes biological processes. This can be beneficial to the fermenting organism as it drives out competitors that are unadapted to the acidity. As a result, the food will have a longer shelf life (one reason foods are purposely fermented in the first place) however, beyond a certain point, the acidity starts affecting the organism that produces it.
  • The high concentration of lactic acid (the final product of fermentation) drives the equilibrium backwards (Le Chatelier's principle), decreasing the rate at which fermentation can occur and slowing down growth.
  • Ethanol, into which lactic acid can be easily converted, is volatile and will readily escape, allowing the reaction to proceed easily. CO2 is also produced, but it is only weakly acidic and even more volatile than ethanol.
  • Acetic acid (another conversion product) is acidic and not as volatile as ethanol however, in the presence of limited oxygen, its creation from lactic acid releases additional energy. It is a lighter molecule than lactic acid, forming fewer hydrogen bonds with its surroundings (due to having fewer groups that can form such bonds), thus is more volatile and will also allow the reaction to proceed more quickly.
  • If propionic acid, butyric acid, and longer monocarboxylic acids are produced (see mixed acid fermentation), the amount of acidity produced per glucose consumed will decrease, as with ethanol, allowing faster growth.

Hydrogen gas Edit

Hydrogen gas is produced in many types of fermentation as a way to regenerate NAD + from NADH. Electrons are transferred to ferredoxin, which in turn is oxidized by hydrogenase, producing H2. [14] Hydrogen gas is a substrate for methanogens and sulfate reducers, which keep the concentration of hydrogen low and favor the production of such an energy-rich compound, [24] but hydrogen gas at a fairly high concentration can nevertheless be formed, as in flatus. [ citation needed ]

For example, Clostridium pasteurianum ferments glucose to butyrate, acetate, carbon dioxide, and hydrogen gas: [25] The reaction leading to acetate is:

Alternative protein Edit

Fermentation can be applied to generate alternative protein sources. For instance, plant based protein foods such as tempeh are produced using fermentation. However, fermentation can also be used to culture animal products made from non-living material in vitro. Eggs, honey, cheese and milk are all examples which are made of various proteins. These proteins can be produced using this particular application of fermentation. Substances that are made using fermentation and which resemble milk are called milk substitutes. Substances that resemble cheese are called cheese analogue and substances that resemble eggs are called egg substitutes. [ citation needed ]

Some companies have started providing fermentation services to farmers (Farming as a Service). [26] [27]

Heme is a protein which gives meat its characteristic texture, flavour and aroma. [28] Impossible Foods used fermentation to generate a particular strand of heme derived from soybean roots, called soy leghemoglobin, which was integrated into the Impossible Burger to mimic meat flavor and appearance. [28]

Other Edit

Most industrial fermentation uses batch or fed-batch procedures, although continuous fermentation can be more economical if various challenges, particularly the difficulty of maintaining sterility, can be met. [29]

Batch Edit

In a batch process, all the ingredients are combined and the reactions proceed without any further input. Batch fermentation has been used for millennia to make bread and alcoholic beverages, and it is still a common method, especially when the process is not well understood. [30] : 1 However, it can be expensive because the fermentor must be sterilized using high pressure steam between batches. [29] Strictly speaking, there is often addition of small quantities of chemicals to control the pH or suppress foaming. [30] : 25

Batch fermentation goes through a series of phases. There is a lag phase in which cells adjust to their environment then a phase in which exponential growth occurs. Once many of the nutrients have been consumed, the growth slows and becomes non-exponential, but production of secondary metabolites (including commercially important antibiotics and enzymes) accelerates. This continues through a stationary phase after most of the nutrients have been consumed, and then the cells die. [30] : 25

Fed-batch Edit

Fed-batch fermentation is a variation of batch fermentation where some of the ingredients are added during the fermentation. This allows greater control over the stages of the process. In particular, production of secondary metabolites can be increased by adding a limited quantity of nutrients during the non-exponential growth phase. Fed-batch operations are often sandwiched between batch operations. [30] : 1 [31]

Open Edit

The high cost of sterilizing the fermentor between batches can be avoided using various open fermentation approaches that are able to resist contamination. One is to use a naturally evolved mixed culture. This is particularly favored in wastewater treatment, since mixed populations can adapt to a wide variety of wastes. Thermophilic bacteria can produce lactic acid at temperatures of around 50 °Celsius, sufficient to discourage microbial contamination and ethanol has been produced at a temperature of 70 °C. This is just below its boiling point (78 °C), making it easy to extract. Halophilic bacteria can produce bioplastics in hypersaline conditions. Solid-state fermentation adds a small amount of water to a solid substrate it is widely used in the food industry to produce flavors, enzymes and organic acids. [29]

Continuous Edit

In continuous fermentation, substrates are added and final products removed continuously. [29] There are three varieties: chemostats, which hold nutrient levels constant turbidostats, which keep cell mass constant and plug flow reactors in which the culture medium flows steadily through a tube while the cells are recycled from the outlet to the inlet. [31] If the process works well, there is a steady flow of feed and effluent and the costs of repeatedly setting up a batch are avoided. Also, it can prolong the exponential growth phase and avoid byproducts that inhibit the reactions by continuously removing them. However, it is difficult to maintain a steady state and avoid contamination, and the design tends to be complex. [29] Typically the fermentor must run for over 500 hours to be more economical than batch processors. [31]

The use of fermentation, particularly for beverages, has existed since the Neolithic and has been documented dating from 7000–6600 BCE in Jiahu, China, [32] 5000 BCE in India, Ayurveda mentions many Medicated Wines, 6000 BCE in Georgia, [33] 3150 BCE in ancient Egypt, [34] 3000 BCE in Babylon, [35] 2000 BCE in pre-Hispanic Mexico, [35] and 1500 BC in Sudan. [36] Fermented foods have a religious significance in Judaism and Christianity. The Baltic god Rugutis was worshiped as the agent of fermentation. [37] [38]

In 1837, Charles Cagniard de la Tour, Theodor Schwann and Friedrich Traugott Kützing independently published papers concluding, as a result of microscopic investigations, that yeast is a living organism that reproduces by budding. [39] [40] : 6 Schwann boiled grape juice to kill the yeast and found that no fermentation would occur until new yeast was added. However, a lot of chemists, including Antoine Lavoisier, continued to view fermentation as a simple chemical reaction and rejected the notion that living organisms could be involved. This was seen as a reversion to vitalism and was lampooned in an anonymous publication by Justus von Liebig and Friedrich Wöhler. [5] : 108–109

The turning point came when Louis Pasteur (1822–1895), during the 1850s and 1860s, repeated Schwann's experiments and showed fermentation is initiated by living organisms in a series of investigations. [23] [40] : 6 In 1857, Pasteur showed lactic acid fermentation is caused by living organisms. [41] In 1860, he demonstrated how bacteria cause souring in milk, a process formerly thought to be merely a chemical change. His work in identifying the role of microorganisms in food spoilage led to the process of pasteurization. [42]

In 1877, working to improve the French brewing industry, Pasteur published his famous paper on fermentation, "Etudes sur la Bière", which was translated into English in 1879 as "Studies on fermentation". [43] He defined fermentation (incorrectly) as "Life without air", [44] yet he correctly showed how specific types of microorganisms cause specific types of fermentations and specific end-products. [ citation needed ]

Although showing fermentation resulted from the action of living microorganisms was a breakthrough, it did not explain the basic nature of fermentation nor, prove it is caused by microorganisms which appear to be always present. Many scientists, including Pasteur, had unsuccessfully attempted to extract the fermentation enzyme from yeast. [44]

Success came in 1897 when the German chemist Eduard Buechner ground up yeast, extracted a juice from them, then found to his amazement this "dead" liquid would ferment a sugar solution, forming carbon dioxide and alcohol much like living yeasts. [45]

Buechner's results are considered to mark the birth of biochemistry. The "unorganized ferments" behaved just like the organized ones. From that time on, the term enzyme came to be applied to all ferments. It was then understood fermentation is caused by enzymes produced by microorganisms. [46] In 1907, Buechner won the Nobel Prize in chemistry for his work. [47]

Advances in microbiology and fermentation technology have continued steadily up until the present. For example, in the 1930s, it was discovered microorganisms could be mutated with physical and chemical treatments to be higher-yielding, faster-growing, tolerant of less oxygen, and able to use a more concentrated medium. [48] [49] Strain selection and hybridization developed as well, affecting most modern food fermentations. [ citation needed ]

The word "ferment" is derived from the Latin verb fervere, which means to boil. It is thought to have been first used in the late 14th century in alchemy, but only in a broad sense. It was not used in the modern scientific sense until around 1600. [ citation needed ]

Monday, 26 November 2007

Botany - What's the name of the fibrous strands that hold the seeds in a pumpkin?

If you cut open a pumpkin, the seeds are suspended inside the pumpkin by some fibrous, slimey strands. You can see them in the middle of this sliced-open pumpkin:

I'm writing a post for the Cooking.SE blog, and am trying to find out the proper botanical term. Someone suggested that might be called the endocarp, but I want to make sure and also see if there is a more specific term.

In "Morpho-Physiological Aspects of Productivity and Quality in Squash and Pumpkins (Cucurbita spp.)" §C.1, I see this:

In the central portion of the fruit, a mass of tough fibers, together with vascular strands connected to the seeds, comprise the placental tissue. The endocarp is made up of small, thin-walled cells that form a membranous tissue that adheres to seed, becoming a transparent skin on dried seeds. (emphasis added)

Am I reading correctly that the name for this part of the pumpkin is "placental tissue", and that the endocarp is just a thin layer on the seeds themselves?


W. Cook carried out C/N ratio measurements in the Duke Environmental Isotope Laboratory. Samples were provided by S. Mills and D. Lafferty (snowshoe hare) E. Ehmke (lemurs) L. McGraw, A. Vogel and C. Clement (prairie vole) D. Koeberl, V. Sakach and L. Morgan (dog) C. Drea (meerkat). Statistical advice was provided by K. Choudhury and S. Mukherjee. The manuscript was improved thanks to comments from J. Heffernan, J. Rawls and P. Turnbaugh. This work was funded by an NSF Doctoral Dissertation Improvement grant to A.T.R., J.P.W. and L.A.D. (grant no. DEB-1501495) and grants from the Hartwell Foundation, Alfred P. Sloan Foundation and Searle Scholars Programme to L.A.D. A.T.R. was supported by the NSF Graduate Research Fellowship Programme under grant no. DGE 1106401. F.C.P. was supported by a European Research Council Marie Curie Individual Fellowship (grant no. 658718). D.B. was supported in part by Austrian Science Fund (grant nos. P26127-B20 and P27831-B28) and European Research Council (Starting Grant: FunKeyGut 741623). M.W. was supported by the European Research Council via the Advanced Grant project ‘NITRICARE 294343’. The contents of this paper are the responsibility of the authors and do not necessarily represent the views of the funding institutions.

The Most Spectacular Mutation in Recent Human History

Photograph by Valentyn Volkov/iStockphoto/Thinkstock.

To repurpose a handy metaphor, let’s call two of the first Homo sapiens Adam and Eve. By the time they welcomed their firstborn, that rascal Cain, into the world, 2 million centuries of evolution had established how his infancy would play out. For the first few years of his life, he would take his nourishment from Eve’s breast. Once he reached about 4 or 5 years old, his body would begin to slow its production of lactase, the enzyme that allows mammals to digest the lactose in milk. Thereafter, nursing or drinking another animal’s milk would have given the little hell-raiser stomach cramps and potentially life-threatening diarrhea in the absence of lactase, lactose simply rots in the guts. With Cain weaned, Abel could claim more of his mother’s attention and all of her milk. This kept a lid on sibling rivalry—though it didn’t quell the animus between these particular sibs—while allowing women to bear more young. The pattern was the same for all mammals: At the end of infancy, we became lactose-intolerant for life.

Two hundred thousand years later, around 10,000 B.C., this began to change. A genetic mutation appeared, somewhere near modern-day Turkey, that jammed the lactase-production gene permanently in the “on” position. The original mutant was probably a male who passed the gene on to his children. People carrying the mutation could drink milk their entire lives. Genomic analyses have shown that within a few thousand years, at a rate that evolutionary biologists had thought impossibly rapid, this mutation spread throughout Eurasia, to Great Britain, Scandinavia, the Mediterranean, India and all points in between, stopping only at the Himalayas. Independently, other mutations for lactose tolerance arose in Africa and the Middle East, though not in the Americas, Australia, or the Far East.

In an evolutionary eye-blink, 80 percent of Europeans became milk-drinkers in some populations, the proportion is close to 100 percent. (Though globally, lactose intolerance is the norm around two-thirds of humans cannot drink milk in adulthood.) The speed of this transformation is one of the weirder mysteries in the story of human evolution, more so because it’s not clear why anybody needed the mutation to begin with. Through their cleverness, our lactose-intolerant forebears had already found a way to consume dairy without getting sick, irrespective of genetics.

Mark Thomas, an evolutionary geneticist at University College London, points out that in modern-day Turkey, where the mutation seems to have arisen, the warm climate causes fresh milk to rapidly change its composition. “If you milk a cow in the morning,” he says, “by lunchtime it’s yogurt.”

Yogurt has plenty of benefits to confer, among them large testicles, swagger, and glossy fur—at least if you’re a mouse—but most salient to our ancestors was that the fermentation process that transforms milk into yogurt consumes lactose, which is a sugar. This is why many lactose-intolerant people can eat yogurt without difficulty. As milk ascends what Thomas calls the “fermentation ladder,” which begins with yogurt and culminates with virtually lactose-free hard cheeses, ever more lactose is fermented out. “If you’re at a party and someone says, ‘Oh, I can’t eat that—I’m lactose intolerant,’ ” he says, “you can tell them to shut up and eat the Parmigiano.”

Analysis of potsherds from Eurasia and parts of Africa have shown that humans were fermenting the lactose out of dairy for thousands of years before lactose tolerance was widespread. Here is the heart of the mystery: If we could consume dairy by simply letting it sit around for a few hours or days, it doesn’t appear to make much sense for evolution to have propagated the lactose-tolerance mutation at all, much less as vigorously as it did. Culture had already found a way around our biology. Various ideas are being kicked around to explain why natural selection promoted milk-drinking, but evolutionary biologists are still puzzled.

“I’ve probably worked more on the evolution of lactose tolerance than anyone in the world,” says Thomas. “I can give you a bunch of informed and sensible suggestions about why it’s such an advantage, but we just don’t know. It’s a ridiculously high selection differential, just insane, for the last several thousand years.”

A “high selection differential” is something of a Darwinian euphemism. It means that those who couldn’t drink milk were apt to die before they could reproduce. At best they were having fewer, sicklier children. That kind of life-or-death selection differential seems necessary to explain the speed with which the mutation swept across Eurasia and spread even faster in Africa. The unfit must have been taking their lactose-intolerant genomes to the grave.

Milk, by itself, somehow saved lives. This is odd, because milk is just food, just one source of nutrients and calories among many others. It’s not medicine. But there was a time in human history when our diet and environment conspired to create conditions that mimicked those of a disease epidemic. Milk, in such circumstances, may well have performed the function of a life-saving drug.

There are no written records from the period when humans invented agriculture, but if there were, they would tell a tale of woe. Agriculture, in Jared Diamond’s phrase, was the “perhaps even acne are direct results of the switch to agriculture.

Meanwhile, agriculture’s alter ego, civilization, was forcing people for the first time to live in cities, which were perfect environments for the rapid spread of infectious disease. No one living through these tribulations would have had any idea that things had ever been, or could be, different. Pestilence was the water we swam in for millennia.

It was in these horrendous conditions that the lactose tolerance mutation took hold. Reconstructed migration patterns make it clear that the wave of lactose tolerance that washed over Eurasia was carried by later generations of farmers who were healthier than their milk-abstaining neighbors. Everywhere that agriculture and civilization went, lactose tolerance came along. Agriculture-plus-dairying became the backbone of Western civilization.

But it’s hard to know with any kind of certainty why milk was so beneficial. It may have been the case that milk provided nutrients that weren’t present in the first wave of domesticated crops. An early, probably incorrect, hypothesis sought to link lactose tolerance to vitamin D and calcium deficiencies. The lactose-intolerant MIT geneticist Pardis Sabeti believes that milk boosted women’s fat stores and thus their fertility, contributing directly to Darwinian fitness, though she and others allow that milk’s highest value to subsisting Homo sapiens may have been that it provided fresh drinking water: A stream or pond might look clean yet harbor dangerous pathogens, while the milk coming out of a healthy-looking goat is likely to be healthy, too.

Each of these hypotheses makes rough-and-ready sense, but not even their creators find them totally convincing. “The drinking-water argument works in Africa, but not so much in Europe,” says Thomas. He favors the idea that milk supplemented food supplies. “If your crops failed and you couldn’t drink milk, you were dead,” he says. “But none of the explanations that are out there are sufficient.”

The plot is still fuzzy, but we know a few things: The rise of civilization coincided with a strange twist in our evolutionary history. We became, in the coinage of one paleoanthropologist, “mampires” who feed on the fluids of other animals. Western civilization, which is twinned with agriculture, seems to have required milk to begin functioning. No one can say why. We know much less than we think about why we eat what we do. The puzzle is not merely academic. If we knew more, we might learn something about why our relationship to food can be so strange.

For the time being, the mythical version of the story isn’t so bad. In the Garden, Adam and Eve were gatherers, collecting fruits as they fell from the tree. Cain the farmer and Abel the pastoralist represented two paths into the future: agriculture and civilization versus animal husbandry and nomadism. Cain offered God his cultivated fruits and vegetables, Abel an animal sacrifice that Flavius Josephus tells us was milk. Agriculture, in its earliest form, brought disease, deformation, and death, so God rejected it for the milk from Abel’s flocks. Cain grew enraged and, being your prototypically amoral city-dweller, did his brother in. God cursed Cain with exile, commanding him to wander the earth like the pastoralist brother he’d killed. Cain and agriculture ultimately won the day—humans settled into cities sustained by farms—but only by becoming a little like Abel. And civilization moved forward.


Metabolomics provides a global insight into metabolism by the identification of multiple metabolites involved in biological responses of individuals exposed to different factors such as nutrition. In fish nutrition, metabolomics studies demonstrate the interest of a non-targeted global analysis and could be used for fish authenticity. They not only confirm the impact of plant feedstuffs on muscle fatty acid composition by the overexpression of SFA, MUFA and DUFA but also reveal other mechanisms related to lipid metabolism and transport through choline or glycerol. Moreover, metabolomic studies highlight metabolites such as glucose, lactate and creatine that have been related to impaired energy metabolism similar to the state of energy deficiency in fasted fish. These studies also demonstrate intermediate metabolic disturbances both by TCA cycle intermediates and metabolites such as amino acids that are the entry point to the TCA cycle. However, interpretation of metabolites requires caution because of the numerous metabolic functions in which one metabolite may be involved. The establishment of a specific database dedicated to fish metabolomics would offset this problem.

Specific care should be taken with sample type and sampling methods since they may introduce a bias in the interpretation of the data, especially time-dependent factors such as post-prandial and post-mortem sampling times. Plasma and serum offer the great advantage of being non-invasive, but the complexity of obtaining fish serum should be taken into account.

In the future, it could be interesting to use fluxomic studies to confirm hypotheses generated by metabolomic approaches. Moreover, metabolomics for fish nutrition will probably focus on interactions with host microbiota. Thus, the combination of metagenomics and metabolomics to characterize bacterial populations, metabolites and host metabolites should gain in importance. Attention to feed characterization is another key point to establish a clear link between novel feedstuff and modulated metabolic fish functions. Although several challenges remain, such as the transposition of results from one species to another, metabolomics has begun a promising integration into the research landscape of fish nutrition.


Figure 1. Schematic diagram of the in vitro lipolysis apparatus (left) coupled with in situ small-angle X-ray scattering (middle) for the determination of self-assembled structures (right) that arise during the digestion of milk and milk substitutes. Liquid crystalline structures were drawn with inspiration from Salentinig et al. and Clulow et al.(14,16)