木质醋酸菌最早于1886年由英国酿酒专家阿德里安·约翰·布朗(英语:Adrian John Brown)发表描述,当时名称为Gluconacetobacter xylinus,后来许多学者将此菌归入醋杆菌属,名为Acetobacter xylinum。2012年,木质醋酸菌被归入新属驹形杆菌属中,并为该属的模式种[2][3]。
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Yamada, Yuzo; Yukphan, Pattaraporn; Lan Vu, Huong Thi; Muramatsu, Yuki; Ochaikul, Duangjai; Tanasupawat, Somboon; Nakagawa, Yasuyoshi. Description of Komagataeibacter gen. nov., with proposals of new combinations (Acetobacteraceae). The Journal of General and Applied Microbiology. 2012, 58 (5): 397–404. doi:10.2323/jgam.58.397.