An anaerobic organism or anaerobe is any organism that does not require molecular oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenated environment. Anaerobes may be unicellular (e.g. protozoans, bacteria) or multicellular. Most fungi are obligate aerobes, requiring oxygen to survive. However, some species, such as the Chytridiomycota that reside in the rumen of cattle, are obligate anaerobes; for these species, anaerobic respiration is used because oxygen will disrupt their metabolism or kill them. Deep waters of the ocean are a common anoxic environment. 
In his letter of 14 June 1680 to The Royal Society, Antonie van Leeuwenhoek described an experiment he carried out by filling two identical glass tubes about halfway with crushed pepper powder, to which some clean rain water was added. Van Leeuwenhoek sealed one of the glass tubes using a flame and left the other glass tube open. Several days later, he discovered in the open glass tube 'a great many very little animalcules, of divers sort having its own particular motion.' Not expecting to see any life in the sealed glass tube, Van Leeuwenhoek saw to his surprise 'a kind of living animalcules that were round and bigger than the biggest sort that I have said were in the other water.' The conditions in the sealed tube had become quite anaerobic due to consumption of oxygen by aerobic microorganisms.
In 1913 Martinus Beijerinck repeated Van Leeuwenhoek's experiment and identified Clostridium butyricum as a prominent anaerobic bacterium in the sealed pepper infusion tube liquid. Beijerinck commented:
'We thus come to the remarkable conclusion that, beyond doubt, Van Leeuwenhoek in his experiment with the fully closed tube had cultivated and seen genuine anaerobic bacteria, which would happen again only after 200 years, namely about 1862 by Pasteur. That Leeuwenhoek, one hundred years before the discovery of oxygen and the composition of air, was not aware of the meaning of his observations is understandable. But the fact that in the closed tube he observed an increased gas pressure caused by fermentative bacteria and in addition saw the bacteria, prove in any case that he not only was a good observer, but also was able to design an experiment from which a conclusion could be drawn.' 
For practical purposes, there are three categories of anaerobe:
- Obligate anaerobes, which are harmed by the presence of oxygen. Two examples of obligate anaerobes are Clostridium botulinum and the bacteria which live near hydrothermal vents on the deep-sea ocean floor.
- Aerotolerant organisms, which cannot use oxygen for growth, but tolerate its presence.
- Facultative anaerobes, which can grow without oxygen but use oxygen if it is present.
However, this classification has been questioned after recent research showed that human "obligate anaerobes" (such as Finegoldia magna or the methanogenic archaea Methanobrevibacter smithii) can be grown in aerobic atmosphere if the culture medium is supplemented with antioxidants such as ascorbic acid, glutathione and uric acid.
Some obligate anaerobes use fermentation, while others use anaerobic respiration. Aerotolerant organisms are strictly fermentative. In the presence of oxygen, facultative anaerobes use aerobic respiration; without oxygen, some of them ferment; some use anaerobic respiration.
There are many anaerobic fermentative reactions.
Fermentative anaerobic organisms mostly use the lactic acid fermentation pathway:
The energy released in this reaction (without ADP and phosphate) is approximately 150 kJ per mol, which is conserved in generating two ATP from ADP per glucose. This is only 5% of the energy per sugar molecule that the typical aerobic reaction generates taking advantage of the high energy of O2.
Plants and fungi (e.g., yeasts) in general use alcohol (ethanol) fermentation when oxygen becomes limiting:
- C6H12O6 (glucose) + 2 ADP + 2 phosphate → 2 C2H5OH + 2 CO2↑ + 2 ATP + 2 H2O
The energy released is about 180 kJ per mol, which is conserved in generating two ATP from ADP per glucose.
Anaerobic bacteria and archaea use these and many other fermentative pathways, e.g., propionic acid fermentation, butyric acid fermentation, solvent fermentation, mixed acid fermentation, butanediol fermentation, Stickland fermentation, acetogenesis, or methanogenesis.
Since normal microbial culturing occurs in atmospheric air, which is an aerobic environment, the culturing of anaerobes poses a problem. Therefore, a number of techniques are employed by microbiologists when culturing anaerobic organisms, for example, handling the bacteria in a glovebox filled with nitrogen or the use of other specially sealed containers, or techniques such as injection of the bacteria into a dicot plant, which is an environment with limited oxygen. The GasPak System is an isolated container that achieves an anaerobic environment by the reaction of water with sodium borohydride and sodium bicarbonate tablets to produce hydrogen gas and carbon dioxide. Hydrogen then reacts with oxygen gas on a palladium catalyst to produce more water, thereby removing oxygen gas. The issue with the GasPak method is that an adverse reaction can take place where the bacteria may die, which is why a thioglycollate medium should be used. The thioglycollate supplies a medium mimicking that of a dicot, thus providing not only an anaerobic environment but all the nutrients needed for the bacteria to thrive.
Recently, a French team evidenced a link between redox and gut anaerobes  based on clinical studies of severe acute malnutrition. These findings led to the development of aerobic culture of "anaerobes" by the addition of antioxidants in the culture medium.
Few multicellular life forms are anaerobic, since only O2 with its weak double bond can provide enough energy for complex metabolism. Exceptions include three species of Loricifera (< 1 mm in size) and the 10-cell Henneguya zschokkei.
In 2010 three species of anaerobic loricifera were discovered in the hypersaline anoxic L'Atalante basin at the bottom of the Mediterranean Sea. They lack mitochondria which contain the oxidative phosphorylation pathway, which in all other animals combines oxygen with glucose to produce metabolic energy, and thus they consume no oxygen. Instead these loricifera derive their energy from hydrogen using hydrogenosomes.
- Upcroft P, Upcroft JA (January 2001). "Drug Targets and Mechanisms of Resistance in". Clin. Microbiol. Rev. 14 (1): 150–164. doi:10.1128/CMR.14.1.150-164.2001. PMC 88967. PMID 11148007.
- Levinson, W. (2010). Review of Medical Microbiology and Immunology (11th ed.). McGraw-Hill. pp. 91–93. ISBN 978-0-07-174268-9.
- Danovaro R; Dell'anno A; Pusceddu A; Gambi C; et al. (April 2010). "The first metazoa living in permanently anoxic conditions". BMC Biology. 8 (1): 30. doi:10.1186/1741-7007-8-30. PMC 2907586. PMID 20370908.
- Gest, Howard. (2004) The discovery of microorganisms by Robert Hooke and Antoni van Leeuwenhoek, Fellows of the Royal Society, in: 'The Royal Society May 2004 Volume: 58 Issue: 2: pp. 12.
- Prescott LM, Harley JP, Klein DA (1996). Microbiology (3rd ed.). Wm. C. Brown Publishers. pp. 130–131. ISBN 978-0-697-29390-9.
- Brooks GF, Carroll KC, Butel JS, Morse SA (2007). Jawetz, Melnick & Adelberg's Medical Microbiology (24th ed.). McGraw Hill. pp. 307–312. ISBN 978-0-07-128735-7.
- Hogg, S. (2005). Essential Microbiology (1st ed.). Wiley. pp. 99–100. ISBN 978-0-471-49754-7.
- La Scola, B.; Khelaifia, S.; Lagier, J.-C.; Raoult, D. (2014). "Aerobic culture of anaerobic bacteria using antioxidants: a preliminary report". European Journal of Clinical Microbiology & Infectious Diseases. 33 (10): 1781–1783. doi:10.1007/s10096-014-2137-4. ISSN 0934-9723. PMID 24820294. S2CID 16682688.
- Dione, N.; Khelaifia, S.; La Scola, B.; Lagier, J.C.; Raoult, D. (2016). "A quasi-universal medium to break the aerobic/anaerobic bacterial culture dichotomy in clinical microbiology". Clinical Microbiology and Infection. 22 (1): 53–58. doi:10.1016/j.cmi.2015.10.032. PMID 26577141.
- Khelaifia, S.; Lagier, J.-C.; Nkamga, V. D.; Guilhot, E.; Drancourt, M.; Raoult, D. (2016). "Aerobic culture of methanogenic archaea without an external source of hydrogen". European Journal of Clinical Microbiology & Infectious Diseases. 35 (6): 985–991. doi:10.1007/s10096-016-2627-7. ISSN 0934-9723. PMID 27010812. S2CID 17258102.
- Traore, S.I.; Khelaifia, S.; Armstrong, N.; Lagier, J.C.; Raoult, D. (2019). "Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates". Clinical Microbiology and Infection. 25 (12): 1561.e1–1561.e5. doi:10.1016/j.cmi.2019.04.008. PMID 30986553.
- Pommerville, Jeffrey (2010). Alcamo's Fundamentals of Microbiology. Jones and Bartlett Publishers. p. 177. ISBN 9781449655822.
- Slonim, Anthony; Pollack, Murray (2006). Pediatric Critical Care Medicine. Lippincott Williams & Wilkins. p. 130. ISBN 9780781794695.
- Schmidt-Rohr, K. (2020). "Oxygen Is the High-Energy Molecule Powering Complex Multicellular Life: Fundamental Corrections to Traditional Bioenergetics ACS Omega 5: 2221-2233. http://dx.doi.org/10.1021/acsomega.9b03352
- "GasPak System" Archived 2009-09-28 at the Wayback Machine. Accessed May 3, 2008.
- Million, Matthieu; Raoult, Didier (December 2018). "Linking gut redox to human microbiome". Human Microbiome Journal. 10: 27–32. doi:10.1016/j.humic.2018.07.002.
- Million, Matthieu; Tidjani Alou, Maryam; Khelaifia, Saber; Bachar, Dipankar; Lagier, Jean-Christophe; Dione, Niokhor; Brah, Souleymane; Hugon, Perrine; Lombard, Vincent; Armougom, Fabrice; Fromonot, Julien (May 2016). "Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition". Scientific Reports. 6 (1): 26051. Bibcode:2016NatSR...626051M. doi:10.1038/srep26051. ISSN 2045-2322. PMC 4869025. PMID 27183876.
- Guilhot, Elodie; Khelaifia, Saber; La Scola, Bernard; Raoult, Didier; Dubourg, Grégory (March 2018). "Methods for culturing anaerobes from human specimen". Future Microbiology. 13 (3): 369–381. doi:10.2217/fmb-2017-0170. ISSN 1746-0913. PMID 29446650.
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