Ingest The Microbe Directory

[realmarcin]

A curated resource of information about 80,000 microbes. This includes viruses which we can deprioritize for now.

The source data tables from The Microbe Directory can be build using 'make' in this repository:
Data:
https://github.com/dcdanko/MD2

Paper:
https://dqo52087pnd5x.cloudfront.net/manuscripts/13832/792ee5f5-ccd8-43b5-8531-9dc29c1fa117_12772_-_christopher_mason.pdf?doi=10.12688/gatesopenres.12772.1&numberOfBrowsableCollections=3&numberOfBrowsableInstitutionalCollections=0&numberOfBrowsableGateways=8

Table 1: Inventory parameters and descriptions

Parameter
Definition and notes
Optimal pH
The optimal pH at which this species grows. If the species was not widely studied, the American Type Culture Collection (ATCC) was used to determine the optimal pH for storage. If two far ranges of pH were determined, the average was taken.
Optimal temperature
The optimal temperature at which this species grows. If the species was not widely studied, the ATCC was used to determine the optimal temperature for storage. If two far ranges of temperatures were determined, the average was taken.
COGEM pathogenicity rating
COGEM released a comprehensive database of pathogenicity assessment of around 2575 bacterial species in 201110. The database ranks the pathogenicity of species on a scale of 1 to 4 - 1 being not belonging to a recognized group of disease-invoking agents in humans or animals and having an extended history of safe usage and 4 being a species that can cause a very serious human disease, for which no prophylaxis is known.
Antimicrobial susceptibility
Are there any known antibiotics that this species is sensitive to? No = 0, Yes = 1
Spore-formation
Is the species spore-forming? No = 0, Yes = 1
Biofilm-formation
Is the species biofilm-forming? No = 0, Yes = 1
Extremophile
Extremophiles are organisms that live in extreme environments, as opposed to organisms that live in moderate (mesophilic) environments. This category includes acidophiles, thermophiles, osmophiles, halophiles, oligotrophs, and others. Mesophiles = 0, Extremophile = 1
Gram-stain
Negative = 0, Positive = 1, Indeterminate = 2
Found in human microbiome
Microbes that live anywhere in the human body and are not pathogenic to humans (i.e. capable of causing human disease) No=0, Yes=1
Plant pathogen
Does the species causes disease in plants? No = 0, Yes = 1
Animal pathogen
Does the species causes disease in animals? No = 0, Yes =1

From GitHub: Details for available fields, across domains of life

Virus

Genetic material: Virus have either RNA or DNA as their genetic material
Strand: The nucleic acid may be single (ss) or double stranded (ds).
Capsid symmetry: The way in which the capsid units are arranged.
Helical
Icosahedral
Complex
Envelop: The outer layer of a virus that protects the nucleic acid. Virus without envelop are called naked.
Is it a pathogen? If yes, which is its host.
Human
Animal
Plant
Bacteria
Fungi

Bacteria and Archaea Only

Gram stain: Used to distinguish and classify bacterial species into two large groups: Gram-positive and Gram-negative.
Antimicrobial resistance (AMR): Antimicrobial resistance occurs naturally over time, usually through genetic changes. However, the misuse and overuse of antimicrobials is accelerating this process.
Type of metabolisms: the nutrition mode of microbes according to the sources of energy and carbon needed for living, growth and reproduction. All sorts of combinations may exist in nature.
Primary source of energy:
Phototrophs: Light is absorbed in photo receptors and transformed into chemical energy
Chemotrophs: Bond energy is released from a chemical compound.
Primary sources of reducing equivalents:
Organotrophs: Organic compounds are used as electron donor.
Lithotrophs: Inorganic compounds are used as electron donor.
Primary sources of carbon
Heterotrophs: Organic compounds are metabolized to get carbon for growth and development.
Autotrophs: Carbon dioxide (CO2) is used as source of carbon.

Bacteria, Archaea and Eukarya

Biofilm forming: Biofilms are multicellular communities held together by a self-produced extracellular matrix. Biofilms impact humans in many ways as they can form in natural, medical, and industrial settings.
Spore forming: Also referred to as endospores, are the dormant form of vegetative microbes and are highly resistant to physical and chemical influences.
Microbiome: Host or environment where microbes are usually found.
Host: Microbes might be commensal or pathogenic to their host. Commensal microbes are found to be crucial to the survival of their hosts.
Sponges
Corals
Fungi
Plant
Animal
Human: Body sites of Human Microbiome Project
Soil: Microbes are essential for soils. They are main drivers of nutrient cycles in soils, decompose organic matter, promote plant growth and control pests and diseases.
Tundra
Grassland
Croplands
Forest
Tropical
Temperate
Boreal
Extreme: Microbes that live in habitats considered hard to survive in due to its extreme conditions such as temperature, accessibility to different energy sources or under high pressure.
Desert
Polar
Deep ocean
Space
Water: Water can support the growth of many types of microorganisms. Microbes are main drivers of biogeochemical processes and nutrient cycling.
Ocean
Fresh
Mangrove
Sediments
Is it a pathogen? if Yes, which is its host:
Fungi
Plant
Animal
Human: Body sites of Human Microbiome Project
Extremophile: a microbe that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. Microbes that can only live under optimal conditions are called Mesophiles.
If extremophile, which type.
Acidophile: Microbes that live in acidic systems with pH -0.06 to 4.0.
Alkaliphile: Microbes capable of survival in alkaline environments with pH 8.5–11
Halophile: Microbes that thrive in high salt concentrations.
Metallotolerant: Microbes that survive in environments with a high concentration of dissolved heavy metals in solution
Barophile: Also called piezophile, are microbes which thrive at high pressures such as deep seas.
Psychrophile: Also called cryophiles, are microbes capable of growth in low temperatures, ranging from −20°C to 10°C.
Radioresistant: Microbes capable of withstand high levels of ionizing radiation.
Thermophile: Microbes that live at high temperatures between 41°C and 122°C.
Xerophile: Microbes that grow and reproduce in conditions with a low availability of water.
Hypolith: Organisms that live underneath rocks in cold deserts.
Oligotroph: Microbes capable of growth in nutritionally limited environments.