METPO Development Team Microbial ecophysiological trait and phenotype ontology 2024-01-01 2025-09-29 METPO 2025-12-12 definition term editor definition source description license title A UCUM code that identifies a unit of measure. UCUM code organism interacts with chemical assimilation assimilates assimilation builds acid from builds acid from builds acid from builds base from builds base from builds base from builds gas from builds gas from builds gas from carbon source uses as carbon source carbon source degradation degrades degradation electron acceptor uses as electron acceptor electron acceptor electron donor uses as electron donor electron donor energy source uses as energy source energy source fermentation ferments fermentation growth uses for growth growth hydrolysis hydrolyzes hydrolysis nitrogen source uses as nitrogen source nitrogen source other uses in other way other oxidation oxidizes oxidation reduction reduces reduction required for growth requires for growth required for growth respiration uses for respiration respiration sulfur source uses as sulfur source sulfur source aerobic catabolization does not use for aerobic catabolization aerobic catabolization aerobic growth does not use for aerobic growth aerobic growth anaerobic catabolization does not use for anaerobic catabolization anaerobic catabolization anaerobic growth does not use for anaerobic growth anaerobic growth anaerobic growth in the dark does not use for anaerobic growth in the dark anaerobic growth in the dark anaerobic growth with light does not use for anaerobic growth with light anaerobic growth with light assimilation does not assimilate assimilation builds acid from does not build acid from builds acid from builds base from does not build base from builds base from builds gas from does not build gas from builds gas from carbon source does not use as carbon source carbon source aerobic catabolization uses for aerobic catabolization aerobic catabolization degradation does not degrade degradation electron acceptor does not use as electron acceptor electron acceptor electron donor does not use as electron donor electron donor energy source does not use as energy source energy source fermentation does not ferment fermentation growth does not use for growth growth hydrolysis does not hydrolyze hydrolysis nitrogen source does not use as nitrogen source nitrogen source other does not use in other way other oxidation does not oxidize oxidation aerobic growth uses for aerobic growth aerobic growth reduction does not reduce reduction required for growth is not required for growth required for growth respiration does not use for respiration respiration sulfur source does not use as sulfur source sulfur source anaerobic catabolization uses for anaerobic catabolization anaerobic catabolization anaerobic growth uses for anaerobic growth anaerobic growth anaerobic growth in the dark uses for anaerobic growth in the dark anaerobic growth in the dark anaerobic growth with light uses for anaerobic growth with light anaerobic growth with light Relates a microbe to a temperature observation. has temperature observation Relates a microbe to an optimum temperature observation. has optimum temperature observation Relates a microbe to a growth temperature observation. has growth temperature observation Relates a microbe to a growth temperature range observation. has range temperature observation Relates a microbe to a temperature tolerance breadth (delta) observation. has temperature delta observation has quality has phenotype capable of dismutates disproportionates dismutates produces produces produces transports imports exports accumulates sequesters compartmentalizes dismutates does not disproportionate dismutates produces does not produce produces does not transport does not import does not export does not accumulate does not sequester does not compartmentalize Relates a microbe to a pH observation. has pH observation Physiology and metabolism.enzymes.[].activity enzyme activity analyzed Physiology and metabolism.enzymes.[].activity Physiology and metabolism.enzymes.[].activity shows activity of Physiology and metabolism.enzymes.[].activity Physiology and metabolism.enzymes.[].activity does not show activity of Physiology and metabolism.enzymes.[].activity Relates a microbe to an optimum pH observation. has optimum pH observation Relates a microbe to a growth pH observation. has growth pH observation Relates a microbe to a growth pH range observation. has range pH observation Relates a microbe to a pH tolerance breadth (delta) observation. has pH delta observation Relates a microbe to a NaCl observation. has NaCl observation Relates a microbe to an optimum NaCl observation. has optimum NaCl observation Relates a microbe to a growth NaCl observation. has growth NaCl observation Relates a microbe to a growth NaCl range observation. has range NaCl observation Relates a microbe to a NaCl tolerance breadth (delta) observation. has NaCl delta observation has observation Relates a microbe to an oxygen observation. has oxygen observation Relates a microbe to an optimum oxygen observation. has optimum oxygen observation Relates a microbe to a growth oxygen observation. has growth oxygen observation Relates a microbe to a growth oxygen range observation. has range oxygen observation Relates a microbe to a oxygen tolerance breadth (delta) observation. has oxygen delta observation A relation between a microbe and a growth medium indicating that the microbe has been demonstrated to grow in that medium under some set of conditions. This relation represents a generalization from experimental observations reported in the literature or databases; it does not imply that the microbe will grow in the medium under all conditions. grows in A relation between a microbe and a growth medium indicating that the microbe has been demonstrated to fail to grow in that medium under some set of conditions. This relation represents a generalization from experimental observations reported in the literature or databases; it does not imply that the microbe cannot grow in the medium under any conditions. does not grow in A reported temperature value (°C) for this observation. has observed spot value The minimum temperature (°C) associated with this observation. has minimum observed value The maximum temperature (°C) associated with this observation. has maximum observed value Free-text comments associated with this observation. has value comments True if this observation indicates no growth at the reported temperature (negative result). is negative data observation data property Relates any instance to a numerical value has value A quality that differentiates specific instances of a species from other instances of the same species. Anthea Guo Luke Wang phenotype A quality that differentiates specific instances of a species from other instances of the same species. A biological process that maintain life in an organism. Anthea Guo metabolism A biological process that maintain life in an organism. A quality that is describing the percentage of guanine and cytosine nucleotides in genomic DNA, calculated as the ratio of GC base pairs to total base pairs. Luke Wang GC content A quality that is describing the percentage of guanine and cytosine nucleotides in genomic DNA, calculated as the ratio of GC base pairs to total base pairs. An object or portion of a substance or mixture of substances that consists of matter Anthea Guo material entity An object or portion of a substance or mixture of substances that consists of matter A characteristic of an entity that depends on the entity's existence, size, color, and physiological traits. quality pH delta temperature delta A temperature phenotype with numerical limits that represents the conditions at which an organism exhibits the most efficient growth and reproduction. Anthea Guo temperature optimum A temperature phenotype with numerical limits that represents the conditions at which an organism exhibits the most efficient growth and reproduction. temperature range A pH phenotype with numerical limits that represents the conditions at which an organism exhibits the most efficient growth and reproduction. pH optimum Luke Wang pH range A salinity phenotype with numerical limits that supports the most efficient growth and reproduction of an organism. Luke Wang NaCl optimum A salinity phenotype with numerical limits that supports the most efficient growth and reproduction of an organism. Anthea Guo NaCl range NaCl delta 42.65 GC_42.65_57.0 GC low 42.65 GC_42.65_57.0 42.65 57 GC_>66.3 GC mid1 57 42.65 GC_>66.3 57 66.3 GC_57.0_66.3 GC mid2 66.3 57 GC_57.0_66.3 66.3 GC_<=42.65 GC high 66.3 GC_<=42.65 10 Cel Psychrophile TO_<=10 temperature optimum very low 10 TO_<=10 10 22 Cel Psychrophile Psychrotolerant TO_10_to_22 temperature optimum low 22 10 TO_10_to_22 22 27 Cel Mesophilie TO_22_to_27 temperature optimum mid1 27 22 TO_22_to_27 27 30 Cel Mesophilie TO_27_to_30 temperature optimum mid2 30 27 TO_27_to_30 30 34 Cel Mesophilie TO_30_to_34 temperature optimum mid3 34 30 TO_30_to_34 34 40 Cel Mesophilie TO_34_to_40 temperature optimum mid4 40 34 TO_34_to_40 40 Cel Thermophile TO_>40 temperature optimum high 40 TO_>40 10 Cel Psychrophile TR_<=10 temperature range very low 10 TR_<=10 10 22 Cel Psychrophile Psychrotolerant TR_10_to_22 temperature range low 22 10 TR_10_to_22 22 27 Cel Mesophilie TR_22_to_27 temperature range mid1 27 22 TR_22_to_27 27 30 Cel Mesophilie TR_27_to_30 temperature range mid2 30 27 TR_27_to_30 30 34 Cel Mesophilie TR_30_to_34 temperature range mid3 34 30 TR_30_to_34 34 40 Cel Mesophilie TR_34_to_40 temperature range mid4 40 34 TR_34_to_40 40 Cel Thermophile TR_>40 temperature range high 40 TR_>40 0 6 Acid Tolerant Acidophile Extreme Acidophile Facultative acidophile Obligative acidophile pHO_0_to_6 pH optimum low 6 0 pHO_0_to_6 6 7 Alkali Tolerant Neutrophile pHO_6_to_7 pH optimum mid1 7 6 pHO_6_to_7 7 8 Alkali Tolerant Alkaliphile Neutrophile pHO_7_to_8 pH optimum mid2 8 7 pHO_7_to_8 8 14 Alkali Tolerant Alkaliphile Extreme Alkaliphile pHO_8_to_14 pH optimum high 14 8 pHO_8_to_14 0 4 Acid Tolerant Acidophile Extreme Acidophile Facultative acidophile Obligative acidophile pHR_0_to_4 pH range very low 4 0 pHR_0_to_4 4 6 Acid Tolerant Acidophile Facultative acidophile Obligative acidophile pHR_4_to_6 pH range low 6 4 pHR_4_to_6 6 7 Alkali Tolerant Facultative acidophile Neutrophile pHR_6_to_7 pH range mid1 7 6 pHR_6_to_7 7 8 Alkali Tolerant Alkaliphile Facultative acidophile Neutrophile pHR_7_to_8 pH range mid2 8 7 pHR_7_to_8 8 10 Alkali Tolerant Alkaliphile Extreme Alkaliphile Facultative acidophile pHR_8_to_10 pH range mid3 10 8 pHR_8_to_10 10 14 Alkali Tolerant Alkaliphile Extreme Alkaliphile 10_to_14 pH range high 14 10 10_to_14 1 % Halotolerant Non-halophile NaO_<=1 NaCl optimum low 1 NaO_<=1 1 3 % Halotolerant Slight halophile NaO_1_to_3 NaCl optimum mid1 3 1 NaO_1_to_3 3 8 % Halotolerant Moderate halophile NaO_3_to_8 NaCl optimum mid2 8 3 NaO_3_to_8 8 % Extreme halophile NaO_>8 NaCl optimum high 8 NaO_>8 1 % Halotolerant Non-halophile NaR_<=1 NaCl range low 1 NaR_<=1 1 3 % Halotolerant Slight halophile NaR_1_to_3 NaCl range mid1 3 1 NaR_1_to_3 3 8 % Halotolerant Moderate halophile NaR_3_to_8 NaCl range mid2 8 3 NaR_3_to_8 8 % Extreme halophile NaR_>8 NaCl range high 8 NaR_>8 1 pHd_<=1 pH delta very low 1 pHd_<=1 1 2 pHd_1_2 pH delta low 2 1 pHd_1_2 2 3 pHd_2_3 pH delta mid1 3 2 pHd_2_3 3 4 pHd_3_4 pH delta mid2 4 3 pHd_3_4 4 5 pHd_4_5 pH delta mid3 5 4 pHd_4_5 5 9 pHd_5_9 pH delta high 9 5 pHd_5_9 1 % Nad_<=1 NaCl delta low 1 Nad_<=1 1 3 % Nad_1_3 NaCl delta mid1 3 1 Nad_1_3 3 8 % Nad_3_8 NaCl delta mid2 8 3 Nad_3_8 8 % Nad_>8 NaCl delta high 8 Nad_>8 1 5 Cel Td_1_5 temperature delta very low 5 1 Td_1_5 5 10 Cel Td_5_10 temperature delta low 10 5 Td_5_10 10 20 Cel Td_10_20 temperature delta mid1 20 10 Td_10_20 20 30 Cel Td_20_30 temperature delta mid2 30 20 Td_20_30 30 Cel Td_>30 temperature delta high 30 Td_>30 A material entity that is too small to be viewed by the unaided eye, typically requiring microscopy for observation. Luke Wang METPO is primarily concerned with unicellular, prokaryotic life forms, i.e. bacteria and archea, including the cases of giant bacteria like Thiomargarita microbe A material entity that is too small to be viewed by the unaided eye, typically requiring microscopy for observation. A material entity that is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity A material entity that is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. enzyme A phenotype characterized by specific pH values or ranges that define growth or activity limits. pH phenotype with numerical limits A phenotype characterized by specific salt concentration values or ranges that define growth or activity limits. salinity phenotype with numerical limits A phenotype characterized by specific temperature values or ranges that define growth or activity limits. temperature phenotype with numerical limits A phenotype characterized by the difference between maximum and minimum values of a growth parameter. delta phenotype with numerical limits A phenotype characterized by the span of values within which an organism can maintain growth. growth range phenotype with numerical limits A phenotype characterized by the value at which an organism exhibits maximum growth rate or activity. optimum phenotype with numerical limits A phenotype that is relating to an organism's oxygen requirements or tolerance for growth. Physiology and metabolism.oxygen tolerance.oxygen tolerance metabolism oxygen preference A phenotype that is relating to an organism's oxygen requirements or tolerance for growth. Physiology and metabolism.oxygen tolerance.oxygen tolerance metabolism An oxygen preference in which growth occurs in the presence of molecular oxygen (O₂), typically using O₂ as the terminal electron acceptor. Ox_aerobic aerobe aerobic aerobic An oxygen preference in which growth occurs in the presence of molecular oxygen (O₂), typically using O₂ as the terminal electron acceptor. Ox_aerobic aerobe aerobic An oxygen preference in which growth occurs in the absence of molecular oxygen (O₂). Ox_anaerobic anaerobe anaerobic anaerobic An oxygen preference in which growth occurs in the absence of molecular oxygen (O₂). Ox_anaerobic anaerobe anaerobic An oxygen preference that requires molecular oxygen (O₂) at concentrations lower than atmospheric. Ox_microerophile microaerophile microaerophilic microaerophilic An oxygen preference that requires molecular oxygen (O₂) at concentrations lower than atmospheric. Ox_microerophile microaerophile microaerophilic An oxygen preference in which growth can occur with or without molecular oxygen (O₂). facultative facultative anaerobe facultatively anaerobic An oxygen preference in which growth can occur with or without molecular oxygen (O₂). facultative facultative anaerobe An oxygen preference that requires molecular oxygen (O₂) for growth. obligate aerobe obligate aerobic obligately aerobic An oxygen preference that requires molecular oxygen (O₂) for growth. obligate aerobe obligate aerobic An oxygen preference in which molecular oxygen (O₂) inhibits or prevents growth. obligate anaerobe obligate anaerobic obligately anaerobic An oxygen preference in which molecular oxygen (O₂) inhibits or prevents growth. obligate anaerobe obligate anaerobic An oxygen preference in which growth can occur without oxygen but is capable of aerobic growth. facultative facultative aerobe facultatively aerobic An oxygen preference in which growth can occur without oxygen but is capable of aerobic growth. facultative facultative aerobe An oxygen preference that does not use O₂ for growth but tolerates its presence. aerotolerant aerotolerant An oxygen preference that does not use O₂ for growth but tolerates its presence. aerotolerant An oxygen preference that tolerates low levels of molecular oxygen (O₂) without requiring it. microaerotolerant microaerotolerant An oxygen preference that tolerates low levels of molecular oxygen (O₂) without requiring it. microaerotolerant An obligately anaerobic where a microorganism does not grow in the presence of oxygen gas (O2). strictly anaerobic strictly anaerobic An obligately anaerobic where a microorganism does not grow in the presence of oxygen gas (O2). strictly anaerobic An oxygen preference that describes a microorganism that can grow with or without molecular oxygen. Ox_facultative_aerobe_anaerobe facultative oxygen preference An oxygen preference that describes a microorganism that can grow with or without molecular oxygen. Ox_facultative_aerobe_anaerobe A phenotype that describes characteristic growth with respect to environmental temperature. Physiology and metabolism.culture temp.temperature range_tmp temperature preference A phenotype that describes characteristic growth with respect to environmental temperature. Physiology and metabolism.culture temp.temperature range_tmp A temperature preference in which growth is favored at low temperatures, typically near or below ~15 °C. psychrophilic psychrophilic A temperature preference in which growth is favored at low temperatures, typically near or below ~15 °C. psychrophilic psychrophilic A temperature preference in which growth is favored at intermediate temperatures, typically ~20–45 °C. mesophilic mesophilic A temperature preference in which growth is favored at intermediate temperatures, typically ~20–45 °C. mesophilic mesophilic A temperature preference in which growth is favored at elevated temperatures, typically ≥45 °C. thermophilic thermophilic A temperature preference in which growth is favored at elevated temperatures, typically ≥45 °C. thermophilic thermophilic A temperature preference in which growth is favored at very high temperatures, typically ≥80 °C. extreme thermophilic hyperthermophilic hyperthermophilic A temperature preference in which growth is favored at very high temperatures, typically ≥80 °C. extreme thermophilic hyperthermophilic A temperature preference in which growth can occur at low temperatures without an obligate low-temperature preference. psychrotolerant psychrotolerant A temperature preference in which growth can occur at low temperatures without an obligate low-temperature preference. psychrotolerant A temperature preference in which growth can occur at elevated temperatures without an obligate high-temperature preference. thermotolerant thermotolerant A temperature preference in which growth can occur at elevated temperatures without an obligate high-temperature preference. thermotolerant A halophily preference in which an organism requires high concentrations of salt for growth and survival. halophilic halophilic A halophily preference in which an organism requires high concentrations of salt for growth and survival. halophilic halophilic A halophily preference in which an organism requires both high salt concentrations and alkaline pH for optimal growth. haloalkaliphilic haloalkaliphilic A halophily preference in which an organism requires both high salt concentrations and alkaline pH for optimal growth. haloalkaliphilic A halophily preference in which an organism can tolerate high salt concentrations but does not require them for growth. halotolerant halotolerant A halophily preference in which an organism can tolerate high salt concentrations but does not require them for growth. halotolerant halotolerant A halophily preference where growth and proliferation requires high levels of sodium chloride, usually above or about 0.2 M. Anthea Guo moderate-halophilic moderately halophilic moderately halophilic A halophily preference where growth and proliferation requires high levels of sodium chloride, usually above or about 0.2 M. moderate-halophilic moderately halophilic A halophily preference in which an organism does not require or prefer elevated salt concentrations for growth. non-halophilic non halophilic non-halophilic non-halophilic A halophily preference in which an organism requires low to moderate salt concentrations (0.3 to 0.8 M NaCl) for optimal growth. slightly halophilic slightly halophilic A halophily preference in which an organism requires low to moderate salt concentrations (0.3 to 0.8 M NaCl) for optimal growth. slightly halophilic A halophily preference in which an organism can only tolerate a narrow range of salinity concentrations and cannot survive significant changes in environmental salt levels. Jed Dongjin Kim-Ozaeta Luke Wang stenohaline stenohaline A halophily preference in which an organism can only tolerate a narrow range of salinity concentrations and cannot survive significant changes in environmental salt levels. stenohaline A halophily preference in which an organism can tolerate a wide range of salinity conditions. euryhaline euryhaline euryhaline A halophily preference in which an organism requires very high salt concentrations (typically 15-30% NaCl or higher) for optimal growth and cannot grow at salt concentrations below approximately 12%. Jed Dongjin Kim-Ozaeta extreme-halophilic extremely halophilic extremely halophilic A halophily preference in which an organism requires very high salt concentrations (typically 15-30% NaCl or higher) for optimal growth and cannot grow at salt concentrations below approximately 12%. extreme-halophilic extremely halophilic A phenotype that is relating to an organism's salt concentration requirements or tolerance for growth. Physiology and metabolism.halophily.halophily level range_salinity halophily preference A phenotype that is relating to an organism's salt concentration requirements or tolerance for growth. Physiology and metabolism.halophily.halophily level range_salinity A execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. biological process A phenotype that is describing how an organism obtains carbon and energy for growth and metabolism. Luke Wang Physiology and metabolism.nutrition type.type nutritional type pathways trophic type Physiology and metabolism.nutrition type.type pathways A trophic type in which an organism produces organic compounds from inorganic carbon sources (primarily carbon dioxide or bicarbonate) using energy from light (photoautotrophy) or from the oxidation of inorganic compounds (chemoautotrophy). Jed Dongjin Kim-Ozaeta TT_autotroph autotroph autotrophy autotrophic A trophic type in which an organism produces organic compounds from inorganic carbon sources (primarily carbon dioxide or bicarbonate) using energy from light (photoautotrophy) or from the oxidation of inorganic compounds (chemoautotrophy). TT_autotroph autotroph autotrophy A trophic type in which an organism derives energy from the oxidation of carbon monoxide. carboxydotrophic A trophic type in which an organism uses chemical oxidation of inorganic compounds as the energy source and carbon dioxide as the primary carbon source for biosynthesis. Luke Wang chemoautolithotroph chemoautolithotrophic A trophic type in which an organism uses chemical oxidation of inorganic compounds as the energy source and carbon dioxide as the primary carbon source for biosynthesis. chemoautolithotroph A trophic type in which an organism obtains energy from oxidation of inorganic compounds and carbon from carbon dioxide. chemoautotroph chemoautotrophic A trophic type in which an organism obtains energy from oxidation of inorganic compounds and carbon from carbon dioxide. chemoautotroph A trophic type in which an organism obtains both energy and carbon from organic compounds. aerobic_chemo_heterotrophy chemoheterotroph chemoheterotrophic A trophic type in which an organism obtains both energy and carbon from organic compounds. aerobic_chemo_heterotrophy chemoheterotroph A trophic type in which an organism obtains energy from oxidation of inorganic compounds (lithotrophy) and carbon from carbon dioxide. chemolithoautotroph chemolithoautotrophic A trophic type in which an organism obtains energy from oxidation of inorganic compounds (lithotrophy) and carbon from carbon dioxide. chemolithoautotroph A trophic type characterized by the use of inorganic chemical compounds as electron donors for energy generation while utilizing organic compounds as the primary carbon source. Anthea Guo chemolithoheterotroph chemolithoheterotrophic A trophic type characterized by the use of inorganic chemical compounds as electron donors for energy generation while utilizing organic compounds as the primary carbon source. chemolithoheterotroph A trophic type characterized by the use of inorganic chemical compounds as electron donors and carbon dioxide as the primary carbon source for energy generation and biosynthesis. Anthea Guo chemolithotroph chemolithotrophic A trophic type characterized by the use of inorganic chemical compounds as electron donors and carbon dioxide as the primary carbon source for energy generation and biosynthesis. chemolithotroph A trophic type in which an organism obtains both energy and carbon from organic compounds through oxidation. chemoorganoheterotroph chemoorganoheterotrophic A trophic type in which an organism obtains both energy and carbon from organic compounds through oxidation. chemoorganoheterotroph A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds. TT_chemotroph chemotroph chemotrophic A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds. TT_chemotroph chemotroph A nutrient adaptation in which an organism thrives in environments with high nutrient concentrations, typically exhibiting rapid growth rates and utilizing diverse carbon sources. Jed Dongjin Kim-Ozaeta copiotroph copiotrophic copiotroph A trophic type in which an organism obtains carbon from organic compounds rather than from carbon dioxide. TT_heterotroph aerobic_heterotrophy heterotroph heterotrophic heterotrophic A trophic type in which an organism obtains carbon from organic compounds rather than from carbon dioxide. TT_heterotroph aerobic_heterotrophy heterotroph heterotrophic A trophic type in which an organism uses molecular hydrogen as an electron donor for energy generation and carbon dioxide as the primary carbon source. Jed Dongjin Kim-Ozaeta Luke Wang hydrogenotrophic A trophic type in which an organism obtains energy from inorganic electron donors and carbon from carbon dioxide. lithoautotroph lithoautotrophic A trophic type in which an organism obtains energy from inorganic electron donors and carbon from carbon dioxide. lithoautotroph A trophic type in which an organism obtains energy from the oxidation of inorganic compounds while using organic compounds as the primary carbon source for biosynthesis. Jed Dongjin Kim-Ozaeta lithoheterotroph lithoheterotrophic A trophic type in which an organism obtains energy from the oxidation of inorganic compounds while using organic compounds as the primary carbon source for biosynthesis. lithoheterotroph A trophic type in which an organism uses inorganic compounds as electron donors for energy generation. Luke Wang TT_lithotroph lithotroph lithotrophic A trophic type in which an organism uses inorganic compounds as electron donors for energy generation. TT_lithotroph lithotroph A trophic type in which an organism uses methane as the primary carbon and energy source through oxidation of methane to carbon dioxide. Luke Wang methanotroph methanotrophic methanotroph A trophic type in which an organism obtains energy and carbon from reduced one-carbon compounds. TT_methylotroph methylotroph methylotrophy methylotrophic TT_methylotroph methylotroph methylotrophy A trophic type in which an organism can use both organic and inorganic carbon sources for growth. mixotroph mixotrophic A trophic type in which an organism can use both organic and inorganic carbon sources for growth. mixotroph A nutrient adaptation characterized by the ability to thrive in environments with very low nutrient concentrations, typically possessing efficient nutrient uptake and utilization systems. Anthea Guo Jed Dongjin Kim-Ozaeta TT_oligotroph oligotroph oligotrophic A nutrient adaptation characterized by the ability to thrive in environments with very low nutrient concentrations, typically possessing efficient nutrient uptake and utilization systems. TT_oligotroph oligotroph A trophic type in which an organism obtains energy from the oxidation of organic compounds. TT_organotroph organotroph organotrophic A trophic type in which an organism obtains energy from the oxidation of organic compounds. TT_organotroph organotroph A trophic type characterized by the use of light as the energy source and carbon dioxide as the primary carbon source for biosynthesis. Anthea Guo anoxygenic_photoautotrophy anoxygenic_photoautotrophy_hydrogen_oxidation anoxygenic_photoautotrophy_iron_oxidation anoxygenic_photoautotrophy_sulfur_oxidation photoautotroph photoautotrophy photoautotrophic A trophic type characterized by the use of light as the energy source and carbon dioxide as the primary carbon source for biosynthesis. anoxygenic_photoautotrophy anoxygenic_photoautotrophy_hydrogen_oxidation anoxygenic_photoautotrophy_iron_oxidation anoxygenic_photoautotrophy_sulfur_oxidation photoautotroph photoautotrophy A trophic type in which an organism uses light as the energy source and organic compounds as the primary carbon source for biosynthesis. Luke Wang photoheterotroph photoheterotrophy photoheterotrophic A trophic type in which an organism uses light as the energy source and organic compounds as the primary carbon source for biosynthesis. photoheterotroph photoheterotrophy A trophic type in which an organism uses light as the energy source and inorganic compounds as electron donors, typically with carbon dioxide as the primary carbon source. Jed Dongjin Kim-Ozaeta Luke Wang photolithotroph photolithotrophic A trophic type in which an organism uses light as the energy source and inorganic compounds as electron donors, typically with carbon dioxide as the primary carbon source. photolithotroph A trophic type in which an organism obtains energy from light and carbon from organic compounds. photoorganoheterotroph photoorganoheterotrophic A trophic type in which an organism obtains energy from light and carbon from organic compounds. photoorganoheterotroph A trophic type characterized by the use of light as the primary energy source for metabolic processes, regardless of carbon source. Anthea Guo TT_phototroph aerobic_anoxygenic_phototrophy phototroph phototrophic A trophic type characterized by the use of light as the primary energy source for metabolic processes, regardless of carbon source. TT_phototroph aerobic_anoxygenic_phototrophy phototroph A trophic type in which an organism obtains energy through chemical oxidation of organic compounds that also serve as the carbon source for biosynthesis. Jed Dongjin Kim-Ozaeta chemoorganotroph chemoorganotrophic A trophic type in which an organism obtains energy through chemical oxidation of organic compounds that also serve as the carbon source for biosynthesis. chemoorganotroph A trophic type characterized by the use of organic compounds as both electron donors and primary carbon sources for energy generation and biosynthesis. Anthea Guo organoheterotroph organoheterotrophic A trophic type characterized by the use of organic compounds as both electron donors and primary carbon sources for energy generation and biosynthesis. organoheterotroph A trophic type in which an organism obtains energy from light and carbon from carbon dioxide using inorganic electron donors. photolithoautotroph photolithoautotrophic A trophic type in which an organism obtains energy from light and carbon from carbon dioxide using inorganic electron donors. photolithoautotroph A phenotype that describes the characteristic three-dimensional morphological form of a microbial cell, determined by cell wall structure, cytoskeletal elements, and environmental factors. Jed Dongjin Kim-Ozaeta Luke Wang Morphology.cell morphology.cell shape cell_shape cell shape A phenotype that describes the characteristic three-dimensional morphological form of a microbial cell, determined by cell wall structure, cytoskeletal elements, and environmental factors. Morphology.cell morphology.cell shape cell_shape A cell shape characterized by an elongated, rod cylindrical morphology with relatively parallel sides and rounded ends. Anthea Guo bacillus bacillus shaped A cell shape characterized by an elongated, rod cylindrical morphology with relatively parallel sides and rounded ends. bacillus A cell shape in which an organism has a spherical or nearly spherical morphology, with roughly equal dimensions in all directions. Jed Dongjin Kim-Ozaeta coccus coccus-shaped coccus shaped A cell shape in which an organism has a spherical or nearly spherical morphology, with roughly equal dimensions in all directions. coccus coccus-shaped Luke Wang crescent-shaped crescent shaped crescent-shaped Anthea Guo S_curved_spiral curved-shaped curved shaped S_curved_spiral curved-shaped A cell shape in which spherical cells remain attached in pairs following cell division, forming characteristic doublets. Luke Wang diplococcus-shaped diplococcus shaped A cell shape in which spherical cells remain attached in pairs following cell division, forming characteristic doublets. diplococcus-shaped S_star_dumbbell_pleomorphic dumbbell-shaped dumbbell shaped S_star_dumbbell_pleomorphic dumbbell-shaped A cell shape in which an organism has an oval or ellipse morphology, elongated along one axis with rounded ends, intermediate between spherical and rod-shaped. Jed Dongjin Kim-Ozaeta Luke Wang ellipsoidal ellipsoidal A cell shape in which an organism has an oval or ellipse morphology, elongated along one axis with rounded ends, intermediate between spherical and rod-shaped. ellipsoidal Luke Wang S_filament filament filament-shaped filament shaped S_filament filament filament-shaped flask flask-shaped flask shaped flask flask-shaped Anthea Guo Jed Dongjin Kim-Ozaeta helical-shaped helical shaped helical-shaped A cell shape in which an organism has an oval morphology, rounded at both ends with one end often slightly broader than the other. Luke Wang S_ovoid ovoid-shaped ovoid shaped A cell shape in which an organism has an oval morphology, rounded at both ends with one end often slightly broader than the other. S_ovoid ovoid-shaped A cell shape characterized by an ellipsoidal morphology with rounded ends, resembling an elongated sphere. Anthea Guo oval-shaped oval shaped A cell shape characterized by an ellipsoidal morphology with rounded ends, resembling an elongated sphere. oval-shaped A cell shape characterized by variable and irregular morphology, where individual cells within a population exhibit multiple distinct shapes. Anthea Guo Jed Dongjin Kim-Ozaeta S_star_dumbbell_pleomorphic pleomorphic pleomorphic-shaped pleomorphic shaped A cell shape characterized by variable and irregular morphology, where individual cells within a population exhibit multiple distinct shapes. S_star_dumbbell_pleomorphic pleomorphic pleomorphic-shaped A cell shape in which an organism forms circular or toroidal structures. ring ring-shaped ring shaped A cell shape in which an organism forms circular or toroidal structures. ring ring-shaped A cell shape in which an organism has an elongated, cylindrical morphology with relatively straight sides and rounded or flat ends. Luke Wang S_rod rod-shaped rod shaped A cell shape in which an organism has an elongated, cylindrical morphology with relatively straight sides and rounded or flat ends. S_rod rod-shaped Anthea Guo spore-shaped spore shaped spore-shaped Anthea Guo S_sphere sphere-shaped sphere shaped S_sphere sphere-shaped Luke Wang S_curved_spiral spiral spiral-shaped spiral shaped S_curved_spiral spiral spiral-shaped A cell shape in which an organism has multiple radiating projections from a central body. S_star_dumbbell_pleomorphic star star-shaped star shaped A cell shape in which an organism has multiple radiating projections from a central body. S_star_dumbbell_pleomorphic star star-shaped A cell shape in which an organism has a curved rod or comma morphology, characterized by a short curved cylindrical form with a single arc. Jed Dongjin Kim-Ozaeta vibrio vibrio-shaped vibrio shaped A cell shape in which an organism has a curved rod or comma morphology, characterized by a short curved cylindrical form with a single arc. vibrio vibrio-shaped branced branched shaped branced coccobacillus coccobacillus shaped coccobacillus A cell shape in which an organism is flat and circular. disc disc shaped disc A cell shape that is wide in the middle and tapers at both ends. fusiform fusiform shaped A cell shape that is wide in the middle and tapers at both ends. fusiform irregular irregular shaped irregular Anthea Guo spindle spindle shaped spindle A cell shape in which an organism has an elongated, tightly coiled helical morphology with periplasmic flagella (endoflagella) located between the cell wall and outer membrane. Jed Dongjin Kim-Ozaeta spirochete spirochete shaped A cell shape in which an organism has an elongated, tightly coiled helical morphology with periplasmic flagella (endoflagella) located between the cell wall and outer membrane. spirochete square square shaped square tailed tailed shaped tailed triangular triangular shaped triangular A phenotype where microorganisms are grouped based on their ability to retain crystal violet dye in the Gram staining procedure. Jed Dongjin Kim-Ozaeta Luke Wang Morphology.cell morphology.gram stain gram_stain gram stain A phenotype where microorganisms are grouped based on their ability to retain crystal violet dye in the Gram staining procedure. Morphology.cell morphology.gram stain gram_stain A gram stain in which an organism retains crystal violet dye and appears purple under microscopy due to a thick peptidoglycan cell wall. G_positive positive gram positive A gram stain in which an organism retains crystal violet dye and appears purple under microscopy due to a thick peptidoglycan cell wall. G_positive positive positive A gram stain in which bacteria do not retain crystal violet dye and appear pink or red after staining, indicating a thin peptidoglycan layer and presence of an outer membrane. Luke Wang G_negative negative gram negative G_negative negative negative A gram stain in which bacteria from the same culture show both gram-positive and gram-negative staining characteristics, often due to age of culture or cell wall degradation. Luke Wang variable gram variable A gram stain in which bacteria from the same culture show both gram-positive and gram-negative staining characteristics, often due to age of culture or cell wall degradation. variable A phenotype in which an organism has the capability to move independently through its environment, typically by means of flagella, pili, gliding mechanisms, or other locomotory structures. Jed Dongjin Kim-Ozaeta Morphology.cell morphology.motility motility motility A phenotype in which an organism has the capability to move independently through its environment, typically by means of flagella, pili, gliding mechanisms, or other locomotory structures. Morphology.cell morphology.motility motility A motility in which an organism has the ability to move independently using metabolic energy. motile yes motile A motility in which an organism has the ability to move independently using metabolic energy. motile yes yes A motility in which an organism lacks the ability to move independently under its own power. no non-motile non motile A motility in which an organism lacks the ability to move independently under its own power. no no non-motile A motile in which an organism possesses flagella for locomotion. flagella flagellated A motile in which an organism possesses flagella for locomotion. flagella A motility where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope. Luke Wang axial filament axially filamented A motility where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope. axial filament A motile in which an organism moves smoothly along solid surfaces without flagella or pili. gliding gliding A motile in which an organism moves smoothly along solid surfaces without flagella or pili. gliding A temperature preference characterized by the ability to grow at low temperatures (typically below 20°C) while maintaining optimal growth at moderate temperatures. Anthea Guo facultative psychrophile facultative psychrophilic facultative psychrophilic A temperature preference characterized by the ability to grow at low temperatures (typically below 20°C) while maintaining optimal growth at moderate temperatures. facultative psychrophilic A temperature preference that grows optimally at temperatures above 90°C. extreme hyperthermophile extremely hyperthermophilic extreme hyperthermophilic A temperature preference that grows optimally at temperatures above 90°C. A trophic type that involves an organism's physiological and metabolic adaptations to specific nutrient availability. Luke Wang nutrient adaptation A trophic type that involves an organism's physiological and metabolic adaptations to specific nutrient availability. A metabolism that is characterized by the method of performing cellular respiration, distinguished primarily by the specific terminal electron acceptor utilized for producing cellular energy. Anthea Guo pathways respiration A metabolism that is characterized by the method of performing cellular respiration, distinguished primarily by the specific terminal electron acceptor utilized for producing cellular energy. pathways A respiration in which molecular oxygen serves as the terminal electron acceptor in the electron transport chain, generating ATP through oxidative phosphorylation with water as the final product. Jed Dongjin Kim-Ozaeta Oxic respiration Oxygen respiration Aerobic respiration A respiration in which molecular oxygen serves as the terminal electron acceptor in the electron transport chain, generating ATP through oxidative phosphorylation with water as the final product. A respiration in which an organism uses electron acceptors other than oxygen for energy production. Anoxic respiration Dissimilatory respiration (non-O₂) Anaerobic respiration A respiration in which an organism uses electron acceptors other than oxygen for energy production. A metabolism that generates ATP through the transfer of electrons from electron donors to electron acceptors via redox reactions, coupled to the pumping of protons across a membrane to create an electrochemical gradient. Anthea Guo Oxidative phosphorylation A metabolism that generates ATP through the transfer of electrons from electron donors to electron acceptors via redox reactions, coupled to the pumping of protons across a membrane to create an electrochemical gradient. A metabolism in which ATP is formed directly by transfer of a phosphoryl group from a substrate to ADP. Substrate-level phosphorylation A metabolism in which electrons are transferred from an electron donor to an electron acceptor. Jed Dongjin Kim-Ozaeta Electron transfer A metabolism in which electrons are transferred from an electron donor to an electron acceptor. A metabolism in which a single substrate simultaneously undergoes both oxidation and reduction reactions, with part of the substrate serving as the electron donor and another part serving as the electron acceptor. Jed Dongjin Kim-Ozaeta Disproportionation A metabolism in which methane is produced as the primary end product through the reduction of carbon-containing compounds, formate, methanol, or acetate, exclusively performed by methanogenic archaea under strictly anaerobic conditions. Jed Dongjin Kim-Ozaeta Luke Wang Biological methanation Biomethanation Carbonate respiration methanogenesis Methanogenesis A metabolism in which methane is produced as the primary end product through the reduction of carbon-containing compounds, formate, methanol, or acetate, exclusively performed by methanogenic archaea under strictly anaerobic conditions. methanogenesis A metabolism that produces acetate as the primary end product through the reduction of carbon dioxide or other carbon compounds using the Wood-Ljungdahl pathway, typically performed by acetogenic bacteria under anaerobic conditions. Anthea Guo Jed Dongjin Kim-Ozaeta Acetate fermentation acetogenesis Acetogenesis acetogenesis A metabolism in which acetate is produced as the sole reduced end product from reduction of CO2 via the acetyl-CoA pathway. Reductive acetyl-CoA pathway Wood-Ljungdahl pathway Homoacetogenesis A phenotype that is relating to an organism's ability to form dormant, stress-resistant endospores. General.keywords Physiology and metabolism.spore formation.spore formation sporulation sporulation A phenotype that is relating to an organism's ability to form dormant, stress-resistant endospores. General.keywords Physiology and metabolism.spore formation.spore formation sporulation A sporulation in which an organism has the ability to produce endospores. spore yes spore forming A sporulation in which an organism has the ability to produce endospores. spore yes yes A sporulation in which an organism lacks the ability to produce endospores. no no_spore non-spore forming A sporulation in which an organism lacks the ability to produce endospores. no no no_spore A phenotype that inheres in a cell by virtue of its longer dimension when viewed on a plane. cell length A phenotype that inheres in a cell by virtue of its longer dimension when viewed on a plane. A phenotype that inheres in a cell by virtue of its shorter dimension when viewed on a plane. cell width A phenotype that inheres in a cell by virtue of its shorter dimension when viewed on a plane. 1.3 um L_<=1.3 cell length very small 1.3 L_<=1.3 1.3 2 um L_1.3_2 cell length small 2 1.3 L_1.3_2 2 3 um L_2_3 cell length medium 3 2 L_2_3 3 um L_>3 cell length large 3 L_>3 0.5 um W_<=0.5 cell width very small 0.5 W_<=0.5 0.5 0.65 um W_0.5_0.65 cell width small 0.65 0.5 W_0.5_0.65 0.65 0.9 um W_0.65_0.9 cell width medium 0.9 0.65 W_0.65_0.9 0.9 um W_>0.9 cell width large 0.9 W_>0.9 observation An observation that identifies the temperature at which a microorganism exhibits maximum growth rate or metabolic activity. Luke Wang optimum temperature observation An observation that identifies the temperature at which a microorganism exhibits maximum growth rate or metabolic activity. growth temperature observation temperature range observation temperature delta observation growth NaCl observation NaCl delta observation NaCl range observation optimum NaCl observation growth pH observation optimum pH observation pH delta observation pH range observation optimum oxygen observation growth oxygen observation oxygen range observation oxygen delta observation oxygen observation temperature observation NaCl observation pH observation A quality that categorizes biological agents according to their hazard level and required containment measures. Safety information.risk assessment.biosafety level biosafety level Safety information.risk assessment.biosafety level A biosafety level that pose minimal potential hazard to laboratory workers and the environment, requiring only standard microbiological practices. Anthea Guo 1 biosafety level 1 1 A biosafety level that pose moderate risk and are associated with human diseases present in the community. 2 biosafety level 2 2 A biosafety level that can cause serious or potentially lethal disease through inhalation or other routes, requiring specialized containment facilities with controlled access, directional airflow, and strict safety protocols. Jed Dongjin Kim-Ozaeta 3 3** biosafety level 3 3 3** A biosafety level that pose extreme risk of life-threatening disease through aerosol transmission with no available treatment. 4 biosafety level 4 4 A biosafety level that is proposed as a classification beyond BSL-4 for hypothetical biological agents requiring enhanced containment. 5 biosafety level 5 5 A metabolism in which electrons are transferred over centimeter-scale distances through multicellular filaments. Cable bacteria metabolism A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors. Luke Wang fermentation Fermentation A respiration that generates energy through the oxidation of organic compounds without using an external electron acceptor, using organic molecules as both electron donors and final electron acceptors. fermentation A metabolism in which the metabolism of one species is thermodynamically dependent on the removal of its products by another species. Jed Dongjin Kim-Ozaeta Syntrophy A phenotype that describes how the rate and extent of population growth are affected by environmental pH. pH growth preference A phenotype that describes how the rate and extent of population growth are affected by environmental pH. A pH growth preference characterized by optimal growth at near-neutral pH values, typically between pH 6.5 and 7.5. Anthea Guo neutralophile neutralophilic neutrophile neutrophilic A pH growth preference characterized by optimal growth at near-neutral pH values, typically between pH 6.5 and 7.5. A pH growth preference in which an organism grows optimally at pH values above 9. alkaliphile alkaliphilic alkalophile alkalophilic alkaphilic A pH growth preference in which an organism grows optimally at pH values above 9. A pH growth preference in which an organism grows optimally at pH values below 5. acidophil acidophile acidophilic A pH growth preference in which an organism grows optimally at pH values below 5. A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH. Luke Wang obligate alkaliphile obligate alkaphilic obligately alkaliphilic obligately alkaphilic A pH growth preference in which an organism requires alkaline conditions (typically pH above 8.5) for growth and cannot grow at neutral or acidic pH. A pH growth preference in which an organism can grow at alkaline pH but does not require it. facultative alkaliphile facultative alkaphilic facultatively alkaliphilic facultatively alkaphilic A pH growth preference in which an organism can grow at alkaline pH but does not require it. A pH growth preference characterized by the requirement for acidic environments (pH below 5.5) for growth, with inability to grow at neutral or alkaline pH values. Anthea Guo Jed Dongjin Kim-Ozaeta obligate acidophile obligately acidophilic obligately acidophilic A pH growth preference characterized by the requirement for acidic environments (pH below 5.5) for growth, with inability to grow at neutral or alkaline pH values. A pH growth preference characterized by optimal growth in acidic environments (pH below 5.5) with the capacity to also grow at near-neutral pH values. Anthea Guo Jed Dongjin Kim-Ozaeta facultative acidophile facultatively acidophilic facultatively acidophilic A pH growth preference characterized by optimal growth in acidic environments (pH below 5.5) with the capacity to also grow at near-neutral pH values. A pH growth preference characterized by the ability to tolerate acidic environments (typically pH below 5.5) while maintaining optimal growth near neutral pH. Anthea Guo Jed Dongjin Kim-Ozaeta aciduric acidotolerant A pH growth preference characterized by the ability to tolerate acidic environments (typically pH below 5.5) while maintaining optimal growth near neutral pH. A pH growth preference in which an organism can tolerate alkaline pH but grows optimally at neutral pH. alkalitolerant alkalotolerant A pH growth preference in which an organism can tolerate alkaline pH but grows optimally at neutral pH. A phenotype characterized by the color of pigments produced by a microorganism. pigmentation A phenotype characterized by the color of pigments produced by a microorganism. Pigment_black black pigmented Pigment_black Pigment_brown brown pigmented Pigment_brown Pigment_cream cream pigmented Pigment_cream Pigment_green green pigmented Pigment_green Pigment_orange orange pigmented Pigment_orange Pigment_pink pink pigmented Pigment_pink Pigment_red red pigmented Pigment_red Pigment_white white pigmented Pigment_white Pigment_yellow yellow pigmented Pigment_yellow Pigment_carotenoid carotenoid pigmentation Pigment_carotenoid A phenotype where a microbe is a pathogen of of some host organism. General.keywords Safety information.risk assessment pathogenic to host A phenotype where a microbe is a pathogen of of some host organism. General.keywords Safety information.risk assessment A pathogen that infects organisms in the kingdom Metazoa. animal pathogen animal pathogen animal pathogen A pathogen that infects organisms in the kingdom Viridiplantae. plant pathogen plant pathogen plant pathogen A pathogen that infects organisms of the species Homo sapiens. human pathogen human pathogen A pathogen that infects organisms of the species Homo sapiens. human pathogen A processed material that provides the nutrients and environmental conditions necessary for the cultivation of microorganisms in vitro. Growth media may be liquid (broth) or solid (agar-based) and are formulated to support the growth of specific types of organisms. This class is equivalent to OBI:0000079 'culture medium'. It is included in METPO to serve as the range for growth-related object properties. growth medium A processed material that provides the nutrients and environmental conditions necessary for the cultivation of microorganisms in vitro. Growth media may be liquid (broth) or solid (agar-based) and are formulated to support the growth of specific types of organisms.