Supplementary figures

2 ​ Supplementary Figure 1 | The calculated (A) 흈 max, (B)rabs,max and (C) Rmax of dipeptides of all ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ species in the dataset were plotted against the number of amino acids in the proteome. These three metrics are the same as defined in Fig. 1b. The dash line indicate the cutoff for the selection of proteomes based on size.

Supplementary Figure 2 | The performance of the linear model based on the frequency of ​ 12 2 seven amino acids I, V, Y, W, R, E, L ​. The R ​ score of the original model is -2.10. If we train the ​ 2​ ​ same linear model again with our dataset, an R ​ score of 0.48 is achieved. ​ ​

Supplementary Figure 3 | The performance of the linear model based on amino acid counts ​ 10 2 from Nakashima et al. ​ The R ​ score of the original model is -0.49. If we train the same linear ​ ​ ​ ​ 2 model again with our dataset, an R ​ score of 0.67 is achieved. ​ ​

Supplementary Figure 4 | Comparison of enzyme Topt distribution between predicted values and ​ ​ ​ ​ experimental values of three microorganisms with rich experimental Topt data in BRENDA. The three ​ ​ ​ histograms in the first row show the distribution of experimental values. The three histograms in the second row show the distribution of predicted values. Each column represent the data from one organism. The dash lines indicate optimal growth temperatures.

Supplementary Tables

Supplementary Table 1 | Experimental OGT from literatures for 54 selected organisms

Organism Domain Growth temperature (°C) Source

Oscillochloris trichoides Bacteria 28 35

Gilvimarinus agarilyticus Bacteria 27.5 36

Francisella persica Bacteria 34 DSMZ (http://www.dsmz.de) ​ ​

Parageobacillus Bacteria 55 37 caldoxylosilyticus

Chryseobacterium tenax Bacteria 20 38

Candidatus midichloria Bacteria NA

Trichodesmium erythraeum Bacteria 24 39

Thermofilum adornatus Archaea 92 40

Candidatus desulfofervidus Bacteria 60 41

Rhodoluna lacicola Bacteria 20 DSMZ (http://www.dsmz.de) ​ ​

Tilletia walkeri eukarya 21 42

Thermofilum uzonense Archaea 85 DSMZ (http://www.dsmz.de) ​ ​

Tepidimonas fonticaldi Bacteria 55 43

Thermococcus Archaea 85 44 eurythermalis

Thermococcus onnurineus Archaea 80 45

Thermococcus nautili Archaea 87.5 46

Vulcanisaeta thermophila Archaea 85 47

Microcystis panniformis Bacteria 25 48

Thermus amyloliquefaciens Bacteria 65 DSMZ (http://www.dsmz.de) ​ ​

Halapricum salinum Archaea 37 49

Thermococcus piezophilus Archaea 75 50

Pyrococcus yayanosii Archaea 95 51

Agrococcus pavilionensis Bacteria 6 52

Candidatus evansia Bacteria NA

Desulfurococcus Archaea 90 DSMZ (http://www.dsmz.de) ​ ​ amylolyticus

Kosmotoga pacifica Bacteria 70 DSMZ (http://www.dsmz.de) ​ ​

Aquifex aeolicus Bacteria 95 53

Fervidobacterium Bacteria 80 54 thailandensis

Metallosphaera Archaea 70 55 yellowstonensis

Acidibacillus ferrooxidans Bacteria 30 56

Vulcanisaeta moutnovskia Archaea 79 57

Rickettsia aeschlimannii Bacteria 32 58

Candidatus Archaea NA methanoperedens

Mannheimia Bacteria 37 59 massilioguelmaensis

Candidatus desulforudis Bacteria 60 60

Halothermothrix orenii Bacteria 60 61

Thermofilum Archaea 90 62 carboxyditrophus

Alicyclobacillus mali Bacteria NA

Sulfolobus islandicus Archaea 77.5 63

Luteipulveratus halotolerans Bacteria 24 64

Thermincola potens Bacteria NA

Acetomicrobium Bacteria 55 DSMZ (http://www.dsmz.de) ​ ​ hydrogeniformans

Kwoniella dejecticola eukarya 27.5 65

Candidatus portiera Bacteria NA

Streptococcus halotolerans Bacteria 37 DSMZ (http://www.dsmz.de) ​ ​

Thermogladius cellulolyticus Archaea 84 66

Stanieria cyanosphaera Bacteria NA

Thermanaerothrix daxensis Bacteria 60 DSMZ (http://www.dsmz.de) ​ ​

Acidianus hospitalis Archaea 80 67

Rhodopirellula sallentina Bacteria 28 DSMZ (http://www.dsmz.de) ​ ​

Batrachochytrium eukarya 25 68 dendrobatidis

Peptostreptococcaceae Bacteria NA bacterium

Candidatus kryptobacter Bacteria NA

Thermus parvatiensis Bacteria 75 DSMZ (http://www.dsmz.de) ​ ​

Supplementary Table 2 | Regression models

Regression Module Hyperparameter range model

Linear model sklearn.linear_model.LinearRegression None

Elastic net sklearn.linear_model.ElasticNetCV Default

Bayes ridge sklearn.linear_model.BayesianRidge None

Support vector sklearn.svm.SVR 'C': regressor numpy.logspace(-5, 10, num=16, base=2.0), 'Epsilon': [0, 0.01, 0.1, 0.5, 1.0, 2.0, 4.0]

Decision tree sklearn.tree.DecisionTreeRegressor 'Min_samples_leaf': numpy.linspace(0.01, 0.5, 10)

Random forest sklearn.ensemble.RandomForestRegre 'Max_features': ssor numpy.arange(0.1, 1.1, 0.1)

References

35. Ivanovsky, R. N. et al. Evidence for the presence of the reductive pentose phosphate cycle

in a filamentous anoxygenic photosynthetic bacterium, Oscillochloris trichoides strain DG-6.

Microbiology 145 ( Pt 7), 1743–1748 (1999).

36. Kim, B.-C. et al. Gilvimarinus agarilyticus sp. nov., a new agar-degrading bacterium isolated

from the seashore of Jeju Island. Antonie Van Leeuwenhoek 100, 67–73 (2011).

37. Ibrahim, M. A. C. & Ahmad, W. A. W. Growth optimization of a thermophilic strain

geobacillus caldoxylosilyticus utm6 isolated from selayang hot spring. eProceedings

Chemistry 2, 119–123 (2017).

38. Söhngen, C. et al. BacDive--The Bacterial Diversity Metadatabase in 2016. Nucleic Acids

Res. 44, D581–5 (2016).

39. Gardner, J. J. & Boyle, N. R. The use of genome-scale metabolic network reconstruction to

predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic

cyanobacterium, Trichodesmium erythraeum. BMC Syst. Biol. 11, 4 (2017).

40. Dominova, I. N. et al. Complete Genomic Sequence of ‘Thermofilum adornatus’ Strain

1910bT, a Hyperthermophilic Anaerobic Organotrophic Crenarchaeon. Genome Announc.

1, (2013).

41. Krukenberg, V. et al. Candidatus Desulfofervidus auxilii, a hydrogenotrophic

sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane.

Environ. Microbiol. 18, 3073–3091 (2016).

42. Frederick, R. D. et al. Identification and Differentiation of Tilletia indica and T. walkeri Using

the Polymerase Chain Reaction. Phytopathology 90, 951–960 (2000).

43. Chen, W.-M. et al. Tepidimonas fonticaldi sp. nov., a slightly thermophilic

betaproteobacterium isolated from a hot spring. Int. J. Syst. Evol. Microbiol. 63, 1810–1816

(2013).

44. Zhao, W., Zeng, X. & Xiao, X. Thermococcus eurythermalis sp. nov., a conditional

piezophilic, hyperthermophilic archaeon with a wide temperature range for growth, isolated

from an oil-immersed chimney in the Guaymas Basin. Int. J. Syst. Evol. Microbiol. 65,

30–35 (2015).

45. Lee, H. S. et al. The complete genome sequence of Thermococcus onnurineus NA1

reveals a mixed heterotrophic and carboxydotrophic metabolism. J. Bacteriol. 190,

7491–7499 (2008).

46. Gorlas, A. et al. Thermococcus nautili sp. nov., a hyperthermophilic archaeon isolated from

a hydrothermal deep-sea vent. Int. J. Syst. Evol. Microbiol. 64, 1802–1810 (2014).

47. Yim, K. J. et al. Vulcanisaeta thermophila sp. nov., a hyperthermophilic and acidophilic

crenarchaeon isolated from solfataric soil. Int. J. Syst. Evol. Microbiol. 65, 201–205 (2015).

48. Zhang, J.-Y. et al. Complete genome sequence and genomic characterization of

Microcystis panniformis FACHB 1757 by third-generation sequencing. Stand. Genomic Sci.

11, 11 (2016).

49. Song, H. S. et al. Halapricum salinum gen. nov., sp. nov., an extremely halophilic archaeon

isolated from non-purified solar salt. Antonie Van Leeuwenhoek 105, 979–986 (2014).

50. Dalmasso, C. et al. Thermococcus piezophilus sp. nov., a novel hyperthermophilic and

piezophilic archaeon with a broad pressure range for growth, isolated from a deepest

hydrothermal vent at the Mid-Cayman Rise. Syst. Appl. Microbiol. 39, 440–444 (2016).

51. Birrien, J.-L. et al. Pyrococcus yayanosii sp. nov., an obligate piezophilic hyperthermophilic

archaeon isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 61,

2827–2831 (2011).

52. White, R. A., 3rd, Grassa, C. J. & Suttle, C. A. First draft genome sequence from a member

of the genus agrococcus, isolated from modern microbialites. Genome Announc. 1, (2013).

53. Deckert, G. et al. The complete genome of the hyperthermophilic bacterium Aquifex

aeolicus. Nature 392, 353–358 (1998).

54. Kanoksilapatham, W. et al. Fervidobacterium thailandense sp. nov., an extremely

thermophilic bacterium isolated from a hot spring. Int. J. Syst. Evol. Microbiol. 66,

5023–5027 (2016).

55. Kozubal, M. A., Dlakic, M., Macur, R. E. & Inskeep, W. P. Terminal oxidase diversity and

function in ‘Metallosphaera yellowstonensis’: gene expression and protein modeling

suggest mechanisms of Fe(II) oxidation in the sulfolobales. Appl. Environ. Microbiol. 77,

1844–1853 (2011).

56. Ramírez, P., Toledo, H., Guiliani, N. & Jerez, C. A. An exported rhodanese-like protein is

induced during growth of Acidithiobacillus ferrooxidans in metal sulfides and different sulfur

compounds. Appl. Environ. Microbiol. 68, 1837–1845 (2002).

57. Gumerov, V. M. et al. Complete genome sequence of ‘Vulcanisaeta moutnovskia’ strain

768-28, a novel member of the hyperthermophilic crenarchaeal genus Vulcanisaeta. J.

Bacteriol. 193, 2355–2356 (2011).

58. Beati, L., Meskini, M., Thiers, B. & Raoult, D. Rickettsia aeschlimannii sp. nov., a new

spotted fever group rickettsia associated with Hyalomma marginatum ticks. Int. J. Syst.

Bacteriol. 47, 548–554 (1997).

59. Hadjadj, L. et al. Genome sequence and description of Mannheimia massilioguelmaensis

sp. nov. New Microbes New Infect 8, 131–136 (2015).

60. Chivian, D. et al. Environmental genomics reveals a single-species ecosystem deep within

Earth. Science 322, 275–278 (2008).

61. Cayol, J. L. et al. Isolation and characterization of Halothermothrix orenii gen. nov., sp.

nov., a halophilic, thermophilic, fermentative, strictly anaerobic bacterium. Int. J. Syst.

Bacteriol. 44, 534–540 (1994).

62. Sokolova, T. G. et al. Diversity and ecophysiological features of thermophilic

carboxydotrophic anaerobes. FEMS Microbiol. Ecol. 68, 131–141 (2009).

63. Jensen, S. M. et al. The Effects of Temperature and Growth Phase on the Lipidomes of

Sulfolobus islandicus and Sulfolobus tokodaii. Life 5, 1539–1566 (2015).

64. Juboi, H. et al. Luteipulveratus halotolerans sp. nov., an actinobacterium

(Dermacoccaceae) from forest soil. Int. J. Syst. Evol. Microbiol. 65, 4113–4120 (2015).

65. Thanh, V. N., Hai, D. A. & Lachance, M.-A. Cryptococcus bestiolae and Cryptococcus

dejecticola, two new yeast species isolated from frass of the litchi fruit borer Conopomorpha

sinensis Bradley. FEMS Yeast Res. 6, 298–304 (2006).

66. Mardanov, A. V. et al. Complete genome sequence of the hyperthermophilic cellulolytic

crenarchaeon ‘Thermogladius cellulolyticus’ 1633. J. Bacteriol. 194, 4446–4447 (2012).

67. You, X.-Y. et al. Genomic analysis of Acidianus hospitalis W1 a host for studying

crenarchaeal virus and plasmid life cycles. Extremophiles 15, 487–497 (2011).

68. Symonds, E. P., Trott, D. J., Bird, P. S. & Mills, P. Growth characteristics and enzyme

activity in Batrachochytrium dendrobatidis isolates. Mycopathologia 166, 143–147 (2008).