Scholten Johannes C M, Culley David E, Nie Lei, Munn Kyle J, Chow Lely, Brockman Fred J, Zhang Weiwen
Microbiology Department, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Biochem Biophys Res Commun. 2007 Jun 29;358(2):571-7. doi: 10.1016/j.bbrc.2007.04.160. Epub 2007 May 4.
The application of DNA microarray technology to investigate multiple-species microbial communities presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri, and Methanospirillum hungatei, and their application to analyze global gene expression in a four-species microbial community in response to oxidative stress. In order to minimize the possibility of cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. This study showed that S. fumaroxidans and M. hungatei responded to the oxidative stress with up-regulation of several genes known to be involved in reactive oxygen species (ROS) detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. However, D. vulgaris seemed to be less sensitive to the oxidative stress as a member of a four-species community, since no gene involved in ROS detoxification was up-regulated. Our work demonstrated the successful application of microarrays to a multiple-species microbial community, and our preliminary results indicated that this approach could provide novel insights on the metabolism within microbial communities.
应用DNA微阵列技术研究多物种微生物群落面临巨大挑战。在本研究中，我们报告了针对两种互营细菌（普通脱硫弧菌和富马酸氧化互营杆菌）、两种古生甲烷菌（巴氏甲烷八叠球菌和亨氏甲烷螺菌）设计的四种全基因组寡核苷酸微阵列及其质量评估，并将其应用于分析一个四物种微生物群落中全局基因表达对氧化应激的响应。为了将交叉杂交的可能性降至最低，我们进行了全基因组比较，以确保所有探针在每个基因组中都是独特的，从而使微阵列能够提供物种水平的分辨率。通过多个生物学和分析重复实验测量的良好重现性验证了微阵列的质量。本研究表明，富马酸氧化互营杆菌和亨氏甲烷螺菌对氧化应激的反应是上调了几个已知参与活性氧（ROS）解毒的基因，如富马酸氧化互营杆菌中的过氧化氢酶和红素氧还蛋白，以及亨氏甲烷螺菌中的硫氧还蛋白和热休克蛋白Hsp20。然而，作为四物种群落的一员，普通脱硫弧菌似乎对氧化应激不太敏感，因为没有参与ROS解毒的基因被上调。我们的工作证明了微阵列在多物种微生物群落中的成功应用，我们的初步结果表明，这种方法可以为微生物群落内的代谢提供新的见解。
