細菌常因環境中溫度、酸鹼度、養分與離子濃度的變化，而遭逢到生存的壓力，為了在逆境中繼續生存、繁衍，細菌會藉由水平基因轉移 (Horizontal gene transfer、HGT) 的方式，由其他細菌處獲得新的蛋白質，以對抗生存環境的變化。由分子演化的觀點來看，愈重要、愈不可取代的蛋白質，在演化的過程中愈不會改變；站在結構生物學與網路生物學的角度，參與愈多交互作用的蛋白質，其結構和序列也會愈穩定。本研究以細菌的最小基因組為基礎，從430株細菌中篩選出40個各細菌均具有的蛋白質序列，進行系統性的分析，並且提出兩種可能的機制，探討在環境的變動之下，天擇 (Natural selection) 如何作用於細菌的蛋白質序列。
以16S rRNA將細菌分類之結果，與40個蛋白質將細菌分類之結果，在門的層次上分析比較後發現，40個細菌間共通的蛋白質中，有7個分別是SecY、LepA、MG_419、PrfA、DnaK、Obg、GyrA等，其分析結果與16S rRNA的較為相近，而根據其他文獻的研究，猜測是這些蛋白質因參與較多的分子間交互作用，使其序列與結構在不同的細菌中也能保持相似性；而AspS、DnaB、DnaJ、Deoxyribonuclease、Fus、GltX、GyrB、IleS、InfB、LueS、Map、MetS、 MG_024、MG_046、MG_222、MG_262、MG_311、MG_329、NusA、ParC、ParE、PheS、Pth、RpL16、 RpL20、Rps9、RpsC、SerS、TdhF、ThrS、TrpS、ValS等，其分析之結果與16S rRNA的較為不相近，而這些蛋白質大多都與細菌在使用能量方面有關係，猜測是細菌以生存而最佳化其能量利用為由，在彼此之間頻繁地交換這些蛋白質的基因，因此使這些蛋白質序列能在細菌間保持相似性。
原核生物的統一生命樹 (Universal Tree of Life)，展現了物種之間的演化關係。隨著分子生物技術的進步，以及基因體時代的來臨，原核生物的演化分類法也與時俱進，然而，即使目前已可在基因體的層次上進行分析，對於水平基因轉移所扮演的腳色輕重，仍有很大爭議。如果水平基因轉移確實是個很重要的因素，則舊有僅考慮垂直演化的分類法 (如 16S rRNA)，可能就不是非常完備的分類方式。

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