Microbial ecophysiological trait and phenotype ontology
A UCUM code that identifies a unit of measure.
does not use for anaerobic catabolization
does not use for anaerobic growth in the dark
does not use for anaerobic growth with light
Relates a microbe to a temperature observation.
Relates a microbe to an optimum temperature observation.
Relates a microbe to a growth temperature observation.
Relates a microbe to a growth temperature range observation.
Relates a microbe to a temperature tolerance breadth (delta) observation.
Physiology and metabolism.enzymes.[].activity
Relates a microbe to an optimum pH observation.
Relates a microbe to a growth pH observation.
Relates a microbe to a growth pH range observation.
Relates a microbe to a pH tolerance breadth (delta) observation.
Relates a microbe to a NaCl observation.
Relates a microbe to an optimum NaCl observation.
Relates a microbe to a growth NaCl observation.
Relates a microbe to a growth NaCl range observation.
Relates a microbe to a NaCl tolerance breadth (delta) observation.
Relates a microbe to an oxygen observation.
Relates a microbe to an optimum oxygen observation.
Relates a microbe to a growth oxygen observation.
Relates a microbe to a growth oxygen range observation.
Relates a microbe to a oxygen tolerance breadth (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.
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.
A reported temperature value (°C) for this observation.
The minimum temperature (°C) associated with this observation.
The maximum temperature (°C) associated with this observation.
Free-text comments associated with this observation.
True if this observation indicates no growth at the reported temperature (negative result).
Relates any instance to a numerical value
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.
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
A characteristic of an entity that depends on the entity's existence, size, color, and physiological traits.
A temperature phenotype with numerical limits that represents the conditions at which an organism exhibits the most efficient growth and reproduction.
A pH phenotype with numerical limits that represents the conditions at which an organism exhibits the most efficient growth and reproduction.
A salinity phenotype with numerical limits that supports the most efficient growth and reproduction of an organism.
A material entity that is too small to be viewed by the unaided eye, typically requiring microscopy for observation.
METPO is primarily concerned with unicellular, prokaryotic life forms, i.e. bacteria and archea, including the cases of giant bacteria like Thiomargarita
A material entity that is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A phenotype characterized by specific pH values or ranges that define growth or activity 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.
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.
A phenotype that is relating to an organism's oxygen requirements or tolerance for growth.
Physiology and metabolism.oxygen tolerance.oxygen tolerance
An oxygen preference in which growth occurs in the presence of molecular oxygen (O₂), typically using O₂ as the terminal electron acceptor.
An oxygen preference in which growth occurs in the absence of molecular oxygen (O₂).
An oxygen preference that requires molecular oxygen (O₂) at concentrations lower than atmospheric.
An oxygen preference in which growth can occur with or without molecular oxygen (O₂).
An oxygen preference that requires molecular oxygen (O₂) for growth.
An oxygen preference in which molecular oxygen (O₂) inhibits or prevents growth.
An oxygen preference in which growth can occur without oxygen but is capable of aerobic growth.
An oxygen preference that does not use O₂ for growth but tolerates its presence.
An oxygen preference that tolerates low levels of molecular oxygen (O₂) without requiring it.
An obligately anaerobic where a microorganism does not grow in the presence of oxygen gas (O2).
An oxygen preference that describes a microorganism that can grow with or without molecular oxygen.
A phenotype that describes characteristic growth with respect to environmental temperature.
Physiology and metabolism.culture temp.temperature
A temperature preference in which growth is favored at low temperatures, typically near or below ~15 °C.
A temperature preference in which growth is favored at intermediate temperatures, typically ~20–45 °C.
A temperature preference in which growth is favored at elevated temperatures, typically ≥45 °C.
A temperature preference in which growth is favored at very high temperatures, typically ≥80 °C.
A temperature preference in which growth can occur at low temperatures without an obligate low-temperature preference.
A temperature preference in which growth can occur at elevated temperatures without an obligate high-temperature preference.
A halophily preference in which an organism requires high concentrations of salt for growth and survival.
A halophily preference in which an organism requires both high salt concentrations and alkaline pH for optimal growth.
A halophily preference in which an organism can tolerate high salt concentrations but does not require them for growth.
A halophily preference where growth and proliferation requires high levels of sodium chloride, usually above or about 0.2 M.
A halophily preference in which an organism does not require or prefer elevated salt concentrations for growth.
A halophily preference in which an organism requires low to moderate salt concentrations (0.3 to 0.8 M NaCl) for optimal growth.
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.
A halophily preference in which an organism can tolerate a wide range of salinity conditions.
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%.
A phenotype that is relating to an organism's salt concentration requirements or tolerance for growth.
Physiology and metabolism.halophily.halophily level
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.
A phenotype that is describing how an organism obtains carbon and energy for growth and metabolism.
Physiology and metabolism.nutrition type.type
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).
A trophic type in which an organism derives energy from the oxidation of carbon monoxide.
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.
A trophic type in which an organism obtains energy from oxidation of inorganic compounds and carbon from carbon dioxide.
A trophic type in which an organism obtains both energy and carbon from organic compounds.
A trophic type in which an organism obtains energy from oxidation of inorganic compounds (lithotrophy) and carbon from carbon dioxide.
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.
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.
A trophic type in which an organism obtains both energy and carbon from organic compounds through oxidation.
A trophic type in which an organism obtains energy from chemical oxidation of either inorganic or organic compounds.
A nutrient adaptation in which an organism thrives in environments with high nutrient concentrations, typically exhibiting rapid growth rates and utilizing diverse carbon sources.
A trophic type in which an organism obtains carbon from organic compounds rather than from carbon dioxide.
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.
A trophic type in which an organism obtains energy from inorganic electron donors and carbon from carbon dioxide.
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.
A trophic type in which an organism uses inorganic compounds as electron donors for energy generation.
A trophic type in which an organism uses methane as the primary carbon and energy source through oxidation of methane to carbon dioxide.
A trophic type in which an organism obtains energy and carbon from reduced one-carbon compounds.
A trophic type in which an organism can use both organic and inorganic carbon sources for growth.
A nutrient adaptation characterized by the ability to thrive in environments with very low nutrient concentrations, typically possessing efficient nutrient uptake and utilization systems.
A trophic type in which an organism obtains energy from the oxidation of organic compounds.
A trophic type characterized by the use of light as the energy source and carbon dioxide as the primary carbon source for biosynthesis.
A trophic type in which an organism uses light as the energy source and organic compounds as the primary carbon source for biosynthesis.
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.
A trophic type in which an organism obtains energy from light and carbon from organic compounds.
A trophic type characterized by the use of light as the primary energy source for metabolic processes, regardless of carbon source.
A trophic type in which an organism obtains energy through chemical oxidation of organic compounds that also serve as the carbon source for biosynthesis.
A trophic type characterized by the use of organic compounds as both electron donors and primary carbon sources for energy generation and biosynthesis.
A trophic type in which an organism obtains energy from light and carbon from carbon dioxide using inorganic electron donors.
A phenotype that describes the characteristic three-dimensional morphological form of a microbial cell, determined by cell wall structure, cytoskeletal elements, and environmental factors.
A cell shape characterized by an elongated, rod cylindrical morphology with relatively parallel sides and rounded ends.
A cell shape in which an organism has a spherical or nearly spherical morphology, with roughly equal dimensions in all directions.
A cell shape in which spherical cells remain attached in pairs following cell division, forming characteristic doublets.
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.
A cell shape in which an organism has an oval morphology, rounded at both ends with one end often slightly broader than the other.
A cell shape characterized by an ellipsoidal morphology with rounded ends, resembling an elongated sphere.
A cell shape characterized by variable and irregular morphology, where individual cells within a population exhibit multiple distinct shapes.
A cell shape in which an organism forms circular or toroidal structures.
A cell shape in which an organism has an elongated, cylindrical morphology with relatively straight sides and rounded or flat ends.
A cell shape in which an organism has multiple radiating projections from a central body.
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.
A cell shape in which an organism is flat and circular.
A cell shape that is wide in the middle and tapers at both ends.
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.
A phenotype where microorganisms are grouped based on their ability to retain crystal violet dye in the Gram staining procedure.
A gram stain in which an organism retains crystal violet dye and appears purple under microscopy due to a thick peptidoglycan cell wall.
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.
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.
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.
A motility in which an organism has the ability to move independently using metabolic energy.
A motility in which an organism lacks the ability to move independently under its own power.
A motile in which an organism possesses flagella for locomotion.
A motility where the flagellum filament of an organism is located in the periplasm and does not extend past the cell envelope.
A motile in which an organism moves smoothly along solid surfaces without flagella or pili.
A temperature preference characterized by the ability to grow at low temperatures (typically below 20Â°C) while maintaining optimal growth at moderate temperatures.
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.
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.
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.
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.
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.
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.
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.
A metabolism in which acetate is produced as the sole reduced end product from reduction of CO2 via the acetyl-CoA pathway.
A phenotype that is relating to an organism's ability to form dormant, stress-resistant endospores.
Physiology and metabolism.spore formation.spore formation
A sporulation in which an organism has the ability to produce endospores.
A sporulation in which an organism lacks the ability to produce endospores.
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.
An observation that identifies the temperature at which a microorganism exhibits maximum growth rate or metabolic activity.
A quality that categorizes biological agents according to their hazard level and required containment measures.
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.
A biosafety level that pose moderate risk and are associated with human diseases present in the community.
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.
A biosafety level that pose extreme risk of life-threatening disease through aerosol transmission with no available treatment.
A biosafety level that is proposed as a classification beyond BSL-4 for hypothetical biological agents requiring enhanced containment.
A metabolism in which electrons are transferred over centimeter-scale distances through multicellular filaments.
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.
A metabolism in which the metabolism of one species is thermodynamically dependent on the removal of its products by another species.
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.
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.
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.
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.
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.
A phenotype characterized by the color of pigments produced by a microorganism.
A phenotype where a microbe is a pathogen of of some host organism.
A pathogen that infects organisms in the kingdom Metazoa.
A pathogen that infects organisms in the kingdom Viridiplantae.
A pathogen that infects organisms of the species Homo sapiens.
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.