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Table 1 High-level categories (indicated by stars) and characters implemented in MicroPIE

From: Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources

Categories*/characters Example source sentences
G + C Content*
%G + C DNA G + C content is 33.1–34.4 mol%.
Cell Morphology*
Cell Shape Cells are slender, cylindrical, sometimes crooked rods that are 0.35–0.5 μm wide and 2.5 μm long and occur singly or in pairs, or in longer chains.
Cell Diameter Cells are 0.3–0.5 μm in diameter.
Cell Length In glucose broth, the bacilli are longer, up to 4 μm long, and often occur in pairs.
Cell Width In addition, cells have an outer diameter of 1.5–3.0 μm and width of 0.5–0.9 μm.
Cell Relationship & Aggregations A few strains grow in chains of 3 to 6 elements in glucose broth.
Gram Stain Type The cells are Gram-negative, long, slender rods or sometimes filaments, motile by gliding.
External features Cells are frequently occurring in chains and producing appendages in older cultures.
Internal features No spores are observed.
Motility Cells are non-motile, extremely pleomorphic
Pigment Compounds Pigmented red due to carotenoids.
Growth Condition*
NaCl Minimum Growth requires at least 1.7 M NaCl, optimally 3.0–4.3 M NaCl.
NaCl Optimum
NaCl Maximum
pH Minimum Growth occurs at temperatures in the range 38–68 °C (optimum, 60 °C) and at pH 1.8–4.0 (optimum, pH 3.0).
pH Optimum
pH Maximum
Temperature Minimum
Temperature Optimum
Temperature Maximum
Salinity Requirement for Growth Requires sea salts for growth.
Aerophilicity Strictly anaerobic. Obligately anaerobic.
Magnesium Requirement for Growth Mg2+ and Ca2+ enhance growth.
Vitamins and Cofactors Used For Growth Vitamin K1 and haemin are required for growth.
Antibiotic Physiology*
Antibiotic Sensitivity Sensitive to (μg per disc) tetracycline (30), rifampicin (25) and vancomycin (30), but resistant to ampicillin (25), erythromycin (15), streptomycin (10) and gentamicin (10).
Antibiotic Resistant The type strain is resistant to erythromycin.
Colony Morphology*
Colony Shape On MA, colonies are convex, translucent, shiny and smooth.
Colony Margin Colonies are golden-yellow, circular and convex, with an entire edge on MA.
Colony Texture On MA, colonies are convex, translucent, shiny and smooth.
Colony Color Colonies are golden-yellow, circular and convex, with an entire edge and a butyrous consistency on MA.
Metabolic End Products and Secondary Metabolites*
Fermentation Products Acid is produced from glucose and fructose.
Other Metabolic Products Acetoin is produced.
Microbe-Host Interaction*
Pathogenic Pathogenic for humans, causing wound infections.
Disease Caused Pathogenic for honeybees in natural and experimental oral infections.
Pathogen Target Organ Nodosus is infected hooves of sheep and goats.
Haemolytic/Haemadsorption Properties No hemolysis occurs on rabbit blood agar.
Metabolic Substrate*
Organic Compounds Used Or Hydrolyzed Utilize carbohydrates for growth.
Organic Compounds Not Used Or Not Hydrolyzed Arabinose, mannose, N-acetylglucosamine, maltose are used as sole carbon and energy source but not mannitol, gluconate, caprate, adipate, citrate and malate.
Inorganic Substances Used Does not require yeast extract for growth, and can use inorganic nitrogen sources such as sodium nitrate and ammonium chloride.
Inorganic Substances Not Used Does not require yeast extract for growth, and can use inorganic nitrogen sources such as sodium nitrate and ammonium chloride.
Fermentation Substrates Used Ferments proteinaceous compounds.
Fermentation Substrates Not Used And no acid is produced from glycerol, erythritol, L-arabinose, D-ribose, or potassium 5-ketogluconate.
  1. Example source sentences for each character within each category are provided. Bolded text in the source sentences indicates the values that MicroPIE should extract