The 19 genomes used, and their *pldA* EMBL IDs, along with their expected *Helicobacter pylori* biogeographic traits are listed below:

· European traits: HPAG1, Lithuania75, P12, 52, 26695, SJM180, India7 [NCBI NC_008086.1, CP002334.1, NC_011498.1, CP001680.1, NC_000915.1, NC_014560.1, CP002331.1];

· African traits: J99, 2017, 2018, 908 and SouthAfrica7 [NCBI NC_000921.1, CP002571.1, CP002572.1, CP002184.1, CP002336.1, CP002337.1, ];East Asian traits: F16, F30, 35A, PeCan4, Shi470, 83 and Sat464 [NCBI AP011940.1, AP011941.1, CP002096.1, CP002074.1, NC_010698.2, CP002605.1, CP002071.1].

Genes that coded for truncated proteins (*pldA* OFF) were not included in this study.

The 169 AtpA sequences used in the HGT analysis

AtpA [NCBI: EHB93466.1, EEB65020.1, EGK01617.1, EAZ96951.1, EIA10014.1, EHO10730.1, EHQ42656.1, EAS72787.1, AAZ48838.1, ACV28038.1, EGK08739.1, EEG10159.1, EDM84731.1, EGC64000.1, AAZ98752.1, ACN14443.1, EAT15601.1, ADW17434.1, ACD96878.1, EFU68802.1, ADG93995.1, BAK73949.1, EDZ61621.1, EIB16597.1, EAT97454.1, EAU01020.1, ABK81906.1, EEV18591.1, ABS52242.1, ADN90332.1, EET80348.1, EHL90702.1, EFU71262.1, CAJ99396.1, EEO22948.1, CCF80240.1, EFR48376.1, EFR47618.1, CBY83548.1, AAP77024.1, EEQ62944.1, AAD08176.1, EFX42435.1, EEO26643.1, ABB44682.1, ACZ11550.1, ADR33423.1, CAE09651.1, CAL18176.1, EAW26695.1, AEB00215.1, EEY85631.1, EDX91133.1, CAQ80745.1, AEF05917.1, EAR22945.1, EHD23759.1, AAO91433.1, EHL85304.1, ACQ68874.1, YP_001451687.1, AAZ26667.1, CBG90709.1, ABE60630.1, ABU79194.1, ADN00765.1, CBJ48151.1, AEN67142.1, EDS93360.1, EFV38590.1, CAX62120.1, EFC54899.1, AEW75952.1, CAG77409.1, CAP78192.1, CAQ91467.1, GAB51972.1, ACR71021.1, EHQ52780.1, ABP62783.1, EFE21167.1, EGW54096.1, ADN77981.1, AEC17221.1, AEP31454.1, GAB56517.1, AEE25184.1, CBV44330.1, ABC33685.1, ACX97137.1, EHK61102.1, EGP19691.1, EAQ31531.1, AAV83453.1, EHS93248.1, AEK00623.1, EGL54277.1, ADP99760.1, EDM48519.1, ABM20945.1, EGE27602.1, EAW32658.1, EHJ04715.1, ADZ93414.1, AEF56544.1, EBA00697.1, EAQ64801.1, ABR73359.1, EDM65164.1, EEF79996.1, EAS66680.1, EEB44391.1, ABG42796.1, EEX50537.1, EGI73341.1, ABM05406.1, GAA05763.1, AET16617.1, EEI49869.1, EAS45491.1, EEG87182.1, EFE51392.1, EFB70640.1, EFM18673.1, ADU71268.1, EIB97664.1, EAR55051.1, EDU61485.1, GAA64110.1, EAR27048.1, AEX54272.1, GAB59628.1, EAR11223.1, ABM01849.1, CCC32467.1, AEG13513.1, ABE57027.1, CAR35257.1, ABI73872.1, BAE75687.1, ABZ78836.1, ABO25710.1, EFA14838.1, ABV89552.1, ACJ31773.1, ADV56630.1, EIC83933.1, ABV39090.1, EGM67869.1, BAJ04308.1, ACA89149.1, EGV28007.1, EGV18064.1, EGZ46719.1, EAS75526.1, EAS62862.1, AAW87061.1, EEX40605.1, EGF42098.1, EDL54805.1, EGD19228.1, ZP_09853641.1, EEP94770.1, EEQ08006.1, EEQ18999.1, YP_654074.1, EEQ03775.1, EEQ00089.1, EHM50189.1].

The 171 OMPLA sequences used in the HGT analysis

OMPLA: [NCBI EAZ99640.1, ADW17991.1, EHQ52957.1, EGL54504.1, EGK10785.1, EGV19191.1, CAQ79680.1, EEY87557.1, EEB64935.1, EHO08344.1, EGC65261.1, EIA07918.1, EAR22975.1, EGD17737.1, EHK60019.1, AAZ46833.1, AAZ96049.1, EGP20312.1, EHB92999.1, EDM47887.1, ZP_09857083.1, EHJ06187.1, EAS71795.1, EDM84432.1, ABM17560.1, GAB54415.1, AEP29176.1, EGK01773.1, CAL17552.1, EEF79803.1, ACN14146.1, ADR35309.1, EDX88885.1, EHQ44562.1, EET80219.1, ABB43297.1, AEF53991.1, ADP95974.1, AEE23125.1, ADZ90582.1, EAR10180.1, EAQ32639.1, CBV41928.1, EDL54875.1, ABR72196.1, EAQ63108.1, ACV26008.1, EAS65010.1, EGZ42951.1, EGV31023.1, ZP_01234806.1, GAA04467.1, EEG09398.1, EDZ63591.1, EAR56640.1, EGF41493.1, AAV83321.1, AEF05108.1, AEA97203.1, EAU01382.1, ACQ67963.1, CAD32066.1, EAS76085.1, ADG93813.1, ABM05176.1, EAZ96211.1, ABE58799.1, ABS52347.1, AAW86051.1, ABG40599.1, EDM67950.1, EEV17429.1, ADN76662.1, EHD19745.1, ABC27991.1, ADN00421.1, EFB72463.1, BAK72959.1, ABV35292.1, BAJ03481.1, GAB60703.1, ACA85081.1, EAR28662.1, EGI74195.1, EEB46686.1, GAA62323.1, EAT16431.1, EAS40470.1, ACJ30728.1, ACD97136.1, AEN66963.1, EAW30307.1, ABZ78078.1, EFE52140.1, EDU58126.1, EFC53577.1, ABO22543.1, ABV11329.1, ACX96270.1, EAW29496.1, EIC83527.1, ABV85988.1, ABM01096.1, BAE75613.1, CAR35328.1, EEP97888.1, EGM70992.1, CAA54224.1, EFA15011.1, ABU78936.1, AET16551.1, EFU69622.1, ABI73025.1, EGW55053.1, ACZ13275.1, EEQ18686.1, EEP94174.1, ABE54243.1, AEG10235.1, CAQ91143.1, EHL84474.1, CAX57751.1, 1FW2, ABP62630.1, EHM51878.1, GAB53576.1, EHS92439.1, CBG90636.1, EFV38511.1, EAT97941.1, CCC32538.1, CAA54223.1, EIB97812.1, EEG87253.1, CAE01133.1, ADV55550.1, EDS90253.1, EEX50977.1, EEQ03301.1, AAD03498.1, AEX54094.1, ABK82197.1, ACR67376.1, EEQ04956.1, EFM18818.1, EEI47649.1, ADU67494.1, ACV41773.1, CAA71915.1, EFE21458.1, AEC17546.1, CAE09192.1, CAJ99604.1, EEO25025.1, CCF79664.1, EES88872.1, EFR45804.1, CBY82368.1, AAP77450.1, EEQ63232.1, AAD07564.1, EFX41646.1, EEO25572.1] [SwissProt C9PFN8_VIBFU, D4ICJ7_ERWAE, D6DP51_ENTCL, E6LA24_CAMUP, Q0P8Q8_CAMJE, Q83E43_COXBU] [PRF 3020410HLP, 3117429CWR].