ABSTRACT
Gut microbiome sequencing studies have great potential to translate microbial analysis outcomes into human health research. Sequencing strategies of 16S amplicon and whole-metagenome shotgun (WMS) are two main methods in microbiome research with respective advantages. However, how sample heterogeneity, sequencers and library preparation protocols affect the sequencing reproducibility of gut microbiome needs further investigation. This study aims to provide a reference for the selection of sequencing technologies by comparing differences in microbial composition from different sampling sites. The results of three widely adopted sequencers showed that the technical repetition correlation (r= 0. 94) was high in WMS method, while the biological repetition correlation (r = 0. 69) was low. Bray-Curtis distance identified that dissimilarity from biological replicates was larger than that of technical replicates (P<0. 001). In addition, dissimilarity and specific taxonomic profiles were observed between 16S and WMS datasets. Our results imply that homogenization is a necessary step before sample DNA extraction. The sequencers contributed less to taxonomic variation than the library preparation protocols. We developed an empirical Bayes approach that " borrowed information" in calculations and analyzed batch effect parameters using standardized data and prior distributions of (non-) parameters, which may improve population comparability between 16S and WMS and provide a basis for further application to fusion analysis of published 16S and microbial datasets.
ABSTRACT
<p><b>OBJECTIVE</b>To explore the short-term impact of ambient PM(10) on daily non-accidental death, cardiovascular and respiratory death of residents in Beijing.</p><p><b>METHODS</b>Mortality data of residents in Beijing during 2006 to 2009 were obtained from public health surveillance and information service center of Chinese Center for Disease Control and Prevention, contemporaneous data of average daily air concentration of PM(10), SO(2), NO(2) were obtained from Beijing Environment Protection Bureau (year 2005 - 2006) and public website of Beijing environmental protection (year 2007 - 2009), respectively, contemporaneous meteorological data were obtained from china meteorological data sharing service system. Generalized addictive model (GAM) of time serial analysis was applied. In additional to the control of confounding factors such as long-term trend, day of the week effect, meteorological factors, lag effect and the effects of other atmospheric pollutants were also analyzed.</p><p><b>RESULTS</b>During year 2006 to 2009, the number of average daily non-accidental death, respiratory disease caused death, cardiovascular and cerebrovascular diseases caused death among Beijing residents were 140.1, 15.0, 65.8, respectively;contemporaneous medians of average daily air concentration of PM(10), SO(2), NO(2) were 123.0, 26.0, 58.0 µg/m(3), respectively;contemporaneous average atmosphere pressure, temperature and relative humidity were 10.1 kPa, 13.5°C and 51.9%, respectively. An exposure-response relationship between exposure to ambient PM(10) and increased daily death number was found as every 10 µg/m(3) increase in daily average concentration of PM(10), there was a 0.1267% (95%CI: 0.0824% - 0.1710%) increase in daily non-accidental death of residents, 0.1365% (95%CI: 0.0010% - 0.2720%) increase in respiratory death and 0.1239% (95%CI: 0.0589% - 0.1889%) increase in cardiovascular death. Ambient PM(10) had greatest influence on daily non-accidental and cardiovascular death of the same day, while its greatest influence on respiratory death occurred 5 days later.</p><p><b>CONCLUSION</b>The ambient PM(10) pollution increased daily non-accidental, respiratory disease caused, cardiovascular and cerebrovascular diseases caused deaths among residents in Beijing, and lag effect existed as for the effect of ambient PM(10) pollution on respiratory disease caused death.</p>