High-throughput sequencing is a revolutionary technological in- novation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequenci...High-throughput sequencing is a revolutionary technological in- novation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics. Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, multi- faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. In this paper, we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.展开更多
Drug resistance via drug-resistant mutations in the human immunodeficiency virus(HIV)genome is the primary cause of antiviral therapy failure.Consequently,HIV drug resistance genotyping has become a critical approach ...Drug resistance via drug-resistant mutations in the human immunodeficiency virus(HIV)genome is the primary cause of antiviral therapy failure.Consequently,HIV drug resistance genotyping has become a critical approach in HIV prevention and control.Compared to the Sanger sequencing technology,high-throughput sequencing(HTS)technology has superior sensitivity and timeliness,with strong detection capabilities for low-frequency mutations.With the continued advancement of HTS technologies,their prominence in HIV drug resistance detection techniques has increased accordingly.This article will review the latest developments in HTS technology and its applications in HIV drug resistance testing.展开更多
Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles.Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity,...Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles.Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity,revealing a huge,previously underestimated phylogenetic diversity with many new lineages.This technology has now become the most important tool to understand the ecological signifcance of this huge and novel diversity in polar oceans.In particular,high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments.Here,a brief overview of polar microbial eukaryote diversity,as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene,is presented.Using these‘omic’approaches,further attention still needs to be focused on diferences between specifc locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.展开更多
In this study, the enclosure system exhibited perfect nitrogen removal performance with in situ oxygen-enhanced indigenous aerobic denitrifying bacteria in an enclosure experiment. We explored changes in the microbial...In this study, the enclosure system exhibited perfect nitrogen removal performance with in situ oxygen-enhanced indigenous aerobic denitrifying bacteria in an enclosure experiment. We explored changes in the microbial community during the nitrogen removal process using the MiSeq high-throughput sequencing technology. The results revealed a total of 7974 and 33653 operational taxonomic units(OTUs) for water and sediment systems, respectively, with 97% similarity. The OTUs were found to be affiliated with eight main phyla(Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Firmicutes, and Actinobacteria). The diversity of the enhanced system was found to be higher than that of the control system. Principal component analysis(PCA) revealed that significant spatial and temporal differences were exhibited in the microbial community during nitrogen removal in the enclosure experiment. Redundancy analysis(RDA)indicated that physical parameters(temperature, dissolved oxygen, and pH), nitrogen(total nitrogen and nitrate), functional genes(nirK and nirS), and dissolved organic carbon(DOC) were the most important factors affecting bacterial community function and composition. Lastly, the results suggested that the variation in the microbial community could be analyzed through the MiSeq high-throughput sequencing technology,which may provide technical support for future field tests.展开更多
Microbial diversity in the abyssal sediments beneath the seafloor of 30,94,and 151cm near the southern end of the Mariana Trench was analyzed in the Illumina HiSeq 2500 platform.Results show that the microbial populat...Microbial diversity in the abyssal sediments beneath the seafloor of 30,94,and 151cm near the southern end of the Mariana Trench was analyzed in the Illumina HiSeq 2500 platform.Results show that the microbial populations were dominated by bacteria but merely no archaea were identifi ed at the three depths.In the bacterial community,Proteobacteria and Firmicutes dominated the total taxon tags,followed by Bacteroidetes,Actinobacteria,Planctomycetes,Cyanobacteria,and Chloroflexi,which together account for over 99%of the total population.Similar to that in the seawater in the trench,the operational taxonomic units(OTUs)belonging to Gammaproteobacteria from the sediment samples showed high abundance.However,common bacterial OTUs in the water of the trench including Nitrospirae and Marinimicrobia were hardly found in the sediments from the southern Mariana Trench or the hadal region.Therefore,this study documented for the first time the compositions of microbial diversity in the trench sediments,revealed the difference in microbial diversity in water and sediment of the trench and will enrich the knowledge on the microbial diversity in the abyssal areas.展开更多
Effects of a starter culture composed of Lactobacillus sakei,Pediococcus pentosaceus,Staphylococcus xylosus and S.carnosus at the ratios(m/m)of 1:1:1:1 on bacterial profile and biogenic amine accumulation in Chinese S...Effects of a starter culture composed of Lactobacillus sakei,Pediococcus pentosaceus,Staphylococcus xylosus and S.carnosus at the ratios(m/m)of 1:1:1:1 on bacterial profile and biogenic amine accumulation in Chinese Sichuan sausages were demonstrated.In starter culture-inoculated sausages,Lactobacillus spp.,Pediococcus spp.and Staphylococcus spp.were predominant bacterial genus and their relative abundances ranged from 70.14%to 25.98%,57.66%to 14.08%,and 15.71%to 13.40%during fermentation,respectively.Accordingly,Lactobacillus spp.and Weissella spp.were predominant bacterial genus and their relative abundances ranged from 63.14%to 24.70%and 49.40%to 11.96%during spontaneous fermentation,respectively.Furthermore,the abundances of undesirable microorganisms such as Yersinia spp.,Enterobacter spp.,Acietobacter spp.and Psychrobacter spp.were lower than that of the control.The levels of histamine,putrescine,tyramine and cadaverine in Chinese Sichuan sausages with starter cultures inoculation were significantly lower(P<0.05)than that of the control,and were decreased by 83.09%,69.38%,51.87%and 57.20%,respectively,at the end of the ripening.These results revealed that the starter cultures inoculation was a better alternative for microbial quality improvement and biogenic amine reduction of Chinese Sichuan sausages with good sensory attributes.展开更多
文摘High-throughput sequencing is a revolutionary technological in- novation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics. Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, multi- faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. In this paper, we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.
基金supported by the National Science and Technology Major Project(Grant 2018ZX10101002)the National Natural Science Foundation of China(Grants 81871694)the National Major Project of the State Key Laboratory of Infectious Diseases Prevention and Control(Grant 2011SKLID102).
文摘Drug resistance via drug-resistant mutations in the human immunodeficiency virus(HIV)genome is the primary cause of antiviral therapy failure.Consequently,HIV drug resistance genotyping has become a critical approach in HIV prevention and control.Compared to the Sanger sequencing technology,high-throughput sequencing(HTS)technology has superior sensitivity and timeliness,with strong detection capabilities for low-frequency mutations.With the continued advancement of HTS technologies,their prominence in HIV drug resistance detection techniques has increased accordingly.This article will review the latest developments in HTS technology and its applications in HIV drug resistance testing.
基金This work is supported by the Natural Science Foundation of China(no.41676178)the Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao),China(nos.2018SDKJ0104-4,2018SDKJ0406-6)+1 种基金the National Key Research and Development Program of China(no.2017YFA0603200)the Grant from Education Department of Shandong Province(S190007170001).
文摘Marine microbial eukaryotes are important primary producers and play critical roles in key biogeochemical cycles.Recent advances in sequencing technology have focused attention on the extent of microbial biodiversity,revealing a huge,previously underestimated phylogenetic diversity with many new lineages.This technology has now become the most important tool to understand the ecological signifcance of this huge and novel diversity in polar oceans.In particular,high-throughput sequencing technologies have been successfully applied to enumerate and compare marine microbial diversity in polar environments.Here,a brief overview of polar microbial eukaryote diversity,as revealed by in-situ surveys of the high-throughput sequencing on 18S rRNA gene,is presented.Using these‘omic’approaches,further attention still needs to be focused on diferences between specifc locations and/or entire polar oceans and on bipolar comparisons of diversity and distribution.
基金supported by the National Science and Technology Pillar Program(Grant No.2012BAC04B02)the National Natural Science Foundation of China(Grant No.51478378)
文摘In this study, the enclosure system exhibited perfect nitrogen removal performance with in situ oxygen-enhanced indigenous aerobic denitrifying bacteria in an enclosure experiment. We explored changes in the microbial community during the nitrogen removal process using the MiSeq high-throughput sequencing technology. The results revealed a total of 7974 and 33653 operational taxonomic units(OTUs) for water and sediment systems, respectively, with 97% similarity. The OTUs were found to be affiliated with eight main phyla(Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Firmicutes, and Actinobacteria). The diversity of the enhanced system was found to be higher than that of the control system. Principal component analysis(PCA) revealed that significant spatial and temporal differences were exhibited in the microbial community during nitrogen removal in the enclosure experiment. Redundancy analysis(RDA)indicated that physical parameters(temperature, dissolved oxygen, and pH), nitrogen(total nitrogen and nitrate), functional genes(nirK and nirS), and dissolved organic carbon(DOC) were the most important factors affecting bacterial community function and composition. Lastly, the results suggested that the variation in the microbial community could be analyzed through the MiSeq high-throughput sequencing technology,which may provide technical support for future field tests.
基金supported by the National Science Foundation for Young Scientists of China(No.41706165)the National Science Foundation for Post-doctoral Scientists of China(No.2016M602200)+3 种基金supported by the National Program on Global Change and Air-Sea Interaction and the Fourth Polar Observation Program(i.e.Deep Sea Exploration Program,Qingdao National Laboratory for Marine Science & Technology)supported by grants from the "1000 Talents Program" of Chinathe "100 Talents Program" of the Chinese Academy of Sciencesthe "AoShan Talents Program" of Qingdao National Laboratory for Marine Science and Technology(No.2015ASTP)
文摘Microbial diversity in the abyssal sediments beneath the seafloor of 30,94,and 151cm near the southern end of the Mariana Trench was analyzed in the Illumina HiSeq 2500 platform.Results show that the microbial populations were dominated by bacteria but merely no archaea were identifi ed at the three depths.In the bacterial community,Proteobacteria and Firmicutes dominated the total taxon tags,followed by Bacteroidetes,Actinobacteria,Planctomycetes,Cyanobacteria,and Chloroflexi,which together account for over 99%of the total population.Similar to that in the seawater in the trench,the operational taxonomic units(OTUs)belonging to Gammaproteobacteria from the sediment samples showed high abundance.However,common bacterial OTUs in the water of the trench including Nitrospirae and Marinimicrobia were hardly found in the sediments from the southern Mariana Trench or the hadal region.Therefore,this study documented for the first time the compositions of microbial diversity in the trench sediments,revealed the difference in microbial diversity in water and sediment of the trench and will enrich the knowledge on the microbial diversity in the abyssal areas.
基金supported by National Natural Science Foundation of China(31772093)Key innovation projects of Chengdu Science and Technology(2019-YF05-00066-SN)Key Laboratory of Collaborative Control and Remediation of Soil and Water Pollution(GHBK-003)。
文摘Effects of a starter culture composed of Lactobacillus sakei,Pediococcus pentosaceus,Staphylococcus xylosus and S.carnosus at the ratios(m/m)of 1:1:1:1 on bacterial profile and biogenic amine accumulation in Chinese Sichuan sausages were demonstrated.In starter culture-inoculated sausages,Lactobacillus spp.,Pediococcus spp.and Staphylococcus spp.were predominant bacterial genus and their relative abundances ranged from 70.14%to 25.98%,57.66%to 14.08%,and 15.71%to 13.40%during fermentation,respectively.Accordingly,Lactobacillus spp.and Weissella spp.were predominant bacterial genus and their relative abundances ranged from 63.14%to 24.70%and 49.40%to 11.96%during spontaneous fermentation,respectively.Furthermore,the abundances of undesirable microorganisms such as Yersinia spp.,Enterobacter spp.,Acietobacter spp.and Psychrobacter spp.were lower than that of the control.The levels of histamine,putrescine,tyramine and cadaverine in Chinese Sichuan sausages with starter cultures inoculation were significantly lower(P<0.05)than that of the control,and were decreased by 83.09%,69.38%,51.87%and 57.20%,respectively,at the end of the ripening.These results revealed that the starter cultures inoculation was a better alternative for microbial quality improvement and biogenic amine reduction of Chinese Sichuan sausages with good sensory attributes.
