Nature: pay attention to DNA pollution in bacteriomics research

DNA pollution is very common in laboratory instruments, which has no problem in many molecular biology experiments However, in the analysis of Bacteriology, this kind of harm needs to be paid more attention Because this kind of pollution can cause serious misleading on key data The important relationship between in vivo microorganisms and health and diseases has been widely recognized, and genetic methods have gradually become an important technology for microbiome analysis However, the novice researchers in this field are easy to fail because of the lack of understanding of the seriousness of the pollution of experimental instruments That's what Alan walker, a microbiologist at the University of Aberdeen, thinks As long as we look at the relevant literature, the harm of DNA pollution has been recognized by scholars decades ago At present, with the enthusiasm of microbiology research, many new people do not necessarily understand these historical documents Walker et al Recently carried out the first systematic study on this issue, and found that two conventional techniques for microbiomics, 16S rRNA and whole genome shotgun macrogenomics, could lead to complete failure or false research results due to DNA pollution The team used two techniques, as well as a ready-made DNA extraction kit, to analyze the culture of pure Salmonella bacteria and different diluted samples, which obviously contained a single type of bacteria In order to avoid operation deviation, the experiment was carried out in three laboratories of different research institutions The results of all experiments show that with the increase of sample dilution, the influence of DNA pollution increases gradually, which quickly leads to the concealment of Salmonella signal On November 12, this research paper was published on BMC biology If the research is described in a more straightforward language, if the bacterial abundance is not high, the existing technology can not distinguish the bacteria in the sample from the contaminated DNA, or the conventional microbiological technology can not avoid the data damage caused by DNA pollution It is believed that part of the pollution is caused by DNA extraction kits, and the reagents in such kits are contaminated, but researchers always assume that these kits do not have this problem Walker told reporters that if the test sample is a sample containing a large number of microorganisms, such as feces, the problem is not serious, because the signal in the sample is relatively strong, far more than the pollution signal, but if the sample is a biological sample with a very low concentration of bacteria, such as cerebrospinal fluid, blood and lung tissue, the harm is very obvious In Walker's lab, they routinely use balanced controls to test for possible levels of contamination Walker said that they have repeatedly found so-called positive results reported in other studies in simple control experiments He said that he did not want to directly deny these studies, and they hoped that this information would attract enough attention of relevant scholars Coincidentally, in PLoS One last month, the analysis data published by Richard lusk group of the University of Michigan also showed that the diluted samples also had pollution hazards Lusk believes that both studies have shown the seriousness of the problem, so it is necessary to use a very strict control experiment to eliminate this interference, which is particularly important to improve the rigor of the study Strategic molecular, a German biomedical technology company, which provides such kits, said that it was clear in the instructions that the product was suitable for fecal samples, but not for diluted samples This PSP fecal DNA extraction kit is neither sterile nor DNA free, so there is a certain degree of DNA pollution is inevitable With current analytical techniques, any DNA contamination can be detected Hilden Qiagen, another German company, also stressed that the kit was not DNA free and could not be used for diluted biological samples But they think that this kind of research is very valuable to improve the strictness of research design and to pay attention to the importance of control experiments in sequence analysis Both companies are considering developing kits that do not contain DNA pollution Although there are no technical barriers, the price may increase a lot Some scholars also think that the kit is only an important aspect of the problem In fact, there may be deviations in many processes such as sample collection, common DNA extraction, sequence determination, etc Original search: Daniel Cressey Microbiome science threaded by contract Nature, 12 November 2014; doi: 10.1038/nature.2014.16327