ライフサイエンスコーパス: metagenomics

1 s derived from environmental sampling (i.e., metagenomics).

2 ncing reads is one of the important goals in metagenomics.

3 ysis tools, will enable accurate comparative metagenomics.

4 overwhelming unknown sequences in the viral metagenomics.

5 emains from eighteenth-century Hungary using metagenomics.

6 s in paleogenomics, comparative genomics and metagenomics.

7 ew branch of microbiology called comparative metagenomics.

8 iority for the useful medical application of metagenomics.

9 of modern sequence-based techniques, such as metagenomics.

10 (rRNA) amplicons, a cornerstone technique in metagenomics.

11 H130 protein family discovered by functional metagenomics.

12 data for a variety of other studies such as metagenomics.

13 ommunity ecology directly from time-resolved metagenomics.

14 ncing and followed up a subset using shotgun metagenomics.

15 Next-generation sequencing has changed metagenomics.

16 nalysed the resulting data using comparative metagenomics.

17 ester, and effluent of a domestic WWTP using metagenomics.

18 raphs to improving functional annotation for metagenomics.

19 ng analysis also addresses the challenges in metagenomics.

20 surface microbiome was assessed with shotgun metagenomics.

21 sequencing data is a challenging problem in metagenomics.

22 al gut virome in 44 recipients of HSCT using metagenomics.

23 en using culture-independent high-throughput metagenomics.

24 In metagenomics, 16S and 18S rRNA gene have been widely use

25 Using metagenomics, a partial genome of the predominant DTFO,

26 We sought to validate a Scalable Metagenomics Alignment Research Tool (SMART), a novel se

27 solutions for amplifying sufficient DNA for metagenomics analyses include linear amplification for d

28 Extensive sampling and metagenomics analyses of plankton communities across all

29 of DNA methylation information into shotgun metagenomics analyses will complement existing methods t

30 pplications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism

31 Metagenomics analysis did not detect any adventitious vi

32 The current trend in metagenomics analysis is toward reducing computational c

33 A metagenomics analysis of purified viral particles in unt

34 n a cohort of 103 healthy human subjects, by metagenomics analysis of the shotgun sequencing data gen

35 nalysis, we have developed SmashCell (Simple Metagenomics Analysis SHell-for sequences from single Ce

36 Metagenomics and 16S rRNA gene amplicon sequencing revea

37 Metagenomics and a panmicrobial microarray were used to

38 Combining a metagenomics and case-control format can provide candida

39 al pig diarrhea case and identified by using metagenomics and complete genome sequencing.

40 Shotgun metagenomics and computational analysis are used to comp

41 e and is, therefore, applicable to data from metagenomics and de novo experiments as well as to re-se

42 ropollutant-associated degradation genes via metagenomics and direct measurements of a suite of micro

43 analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays.

44 In this context, metagenomics and functional omics will likely play a cen

45 lations, which provides benchmarks for viral metagenomics and genome-based viral species definitions.

46 After reducing metagenomics and metabolomics data dimensionality, multi

47 s in pediatric NAFLD patients using targeted metagenomics and metabolomics.

48 ments using (15) N methylamine combined with metagenomics and metaproteomics facilitated identificati

49 c acid-stable isotope probing (DNA-SIP) with metagenomics and metaproteomics to characterize an uncul

50 Biomass was sampled from both reactors for metagenomics and metaproteomics, yielding a set of genom

51 s to acetate, CO2 , H2 and formate, combined metagenomics and metatranscriptomics show that unculture

52 Metagenomics and metatranscriptomics together with bioin

53 duce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational

54 tween pairs of coexisting gut microbes using metagenomics and microarray-based metatranscriptomics da

55 Based on metagenomics and microbiological analyses, it was found

56 in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data.

57 Using metagenomics and precision microbiota reconstitution, we

58 A metagenomics and real-time PCR detection approach in car

59 f the gut microbiome from 'large' animals by metagenomics and related 'metaomic' approaches can provi

60 Metagenomics and single-cell genomics can reveal unknown

61 Metagenomics and single-cell genomics have enabled genom

62 incorporates microbial community profiling, metagenomics and single-cell genomics.

63 ts into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal as

64 echnologies (such as genomics, metabolomics, metagenomics and transcriptomics) are enabling detailed

65 ve been used to study viral diversity, viral metagenomics and virus-host interactions in natural ecos

66 their genetic potential (or gene pool) using metagenomics, and describe their ongoing functions using

67 Here we apply single-cell genomics, metagenomics, and metatranscriptomics to study bacterial

68 metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled

69 currently available virus genomes come from metagenomics, and some of these represent extremely abun

70 put sequenced sample is an important task in metagenomics applications.

71 ducted a mesocosm experiment combined with a metagenomics approach (GeoChip 5.0) to elucidate the eff

72 dy of CBM_E1, which was discovered through a metagenomics approach and is the founding member of a no

73 wabs using an RNA sequencing (RNA-seq)-based metagenomics approach and Taxonomer, an ultrarapid, inte

74 lenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructi

75 ntify viruses associated with BRD, we used a metagenomics approach to enrich and sequence viral nucle

76 Here, we use a metagenomics approach to identify filterable and nucleas

77 WGA kits were tested for their utility in a metagenomics approach to identify the pathogens in sonic

78 We used a shotgun metagenomics approach to investigate the taxonomic and f

79 A viral metagenomics approach was taken to assemble segments of

80 Using an unbiased metagenomics approach, we characterized the viruses in r

81 Metagenomics approaches can effectively detect broad pro

82 Filtering using metagenomics approaches generated a draft H. dujardini g

83 Environmental metagenomics approaches that employ next-generation sequ

84 (viromes) in ballast and harbor waters using metagenomics approaches.

85 polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of

86 These results suggest the potential of metagenomics as a culture-independent approach for the i

87 in a dramatic improvement in the quality of metagenomics assemblies.

88 In contrast to earlier metagenomics-based assumptions, isolates were S-layer-de

89 Here we report the single-cell- and metagenomics-based discovery of such producers.

90 host interactions and outlines a functional metagenomics-based pipeline for the systematic identific

91 per, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative

92 By taking advantage of metagenomics, bioinformatics and conventional Sanger seq

93 ntages that single-cell genomics offers over metagenomics, both now and in the near future.

94 Metagenomics brings with it a number of challenges, incl

95 format for directed evolution and functional metagenomics but is currently limited to fluorescence re

96 Using 16S metagenomics by PhyloChip DNA hybridization and deep 454

97 n contrast, next-generation sequencing-based metagenomics can be used for unbiased detection of any e

98 potential for virus discovery through viral metagenomics can help advance a wide array of discipline

99 Metagenomics can serve as a supplementary non-invasive s

100 Metagenomics can yield insights into gene content variat

101 is the first scalable, efficient, and rapid metagenomics classification algorithm capable of matchin

102 datasets used to evaluate Kraken, a similar metagenomics classification tool, were used to measure a

103 e exciting prospects for data sharing in the metagenomics community.

104 Archaea-targeted PCR sequencing and metagenomics confirmed M. oralis along with 14 bacteria,

105 Normalized viral read counts for untargeted metagenomics correlated with viral burden determined by

106 er, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visua

107 nomer, an ultrarapid, interactive, web-based metagenomics data analysis tool, with an FDA-cleared res

108 sical and biological approach, combined with metagenomics data and biotechnological advances, will en

109 These markers were used to screen metagenomics data for "true" cellulases.

110 rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devic

111 ere, Roux and colleagues present time series metagenomics data revealing new virophage genera and the

112 enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers

113 cation programs when used to analyze various metagenomics data sets.

114 y genomics, transcriptomics, epigenomics and metagenomics data stored either locally or retrieved fro

115 describe an approach that combines existing metagenomics data with reverse genetics to engineer reag

116 in bioinformatics including applications to metagenomics data, transctriptomics and alternative spli

117 ommon issues associated with high-throughput metagenomics data.

118 microbial community based on high-throughput metagenomics data.

119 Many of the amplicon-based metagenomics datasets generated over the last several ye

120 elp scientists analyze and compare annotated metagenomics datasets.

121 Metagenomics delineated greater deglucuronidation capabi

122 Time-resolved metagenomics demonstrated that an aerobic cellulolytic c

123 We describe here the metagenomics-derived virome in the feces of 24 healthy a

124 Untargeted metagenomics detected 86% of known respiratory virus inf

125 In addition, untargeted metagenomics detected an additional 12 viruses that were

126 we discuss the advances in the area of viral metagenomics during the last decade and their relevance

127 equences should be avoided in other areas of metagenomics (e.g. biodiversity analyses), conservative

128 red functional components were identified by metagenomics, enabling validation of robust in vivo RNA-

129 A current metagenomics focus is to interpret and transform collect

130 rt highlights the utility and limitations of metagenomics for assessing public health risks regarding

131 pediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvert

132 We discuss the potential of metagenomics for characterization of the normal viral po

133 This study shows the utility of functional metagenomics for identifying potential mechanisms used b

134 Only then can the potential of metagenomics for predictive ecological modeling, well-po

135 ommunities, and highlighted the potential of metagenomics for source tracking purposes.

136 asets such as those produced with the use of metagenomics for surveillance.

137 c Local Alignment Search Tool) alignment and metagenomics fragment recruitment.

138 In this paper we introduce a metagenomics gene caller (MGC) which is an improvement o

139 In this work, we developed a metagenomics gene prediction system Glimmer-MG that achi

140 Metagenomics generates and tests hypotheses about dynami

141 In unselected samples, untargeted metagenomics had excellent agreement with the RVP (93%).

142 Overall, untargeted metagenomics had high agreement with a sensitive RVP, de

143 Metagenomics has a great potential to discover previousl

144 Here, I propose that viral metagenomics has advanced to largely take over study of

145 Shotgun metagenomics has been applied to the studies of the func

146 The modern age of metagenomics has delivered unprecedented volumes of data

147 The introduction of viral metagenomics has demonstrated that dominant viruses in e

148 While metagenomics has emerged as a technology of choice for a

149 In particular, metagenomics has enabled scientists to begin to characte

150 In addition, viral metagenomics has expanded current knowledge of virus-hos

151 The field of viral metagenomics has expanded our understanding of viral div

152 Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence dat

153 Metagenomics has made accessible an enormous reserve of

154 Metagenomics has opened up a vast pool of genes for puta

155 Metagenomics has provided access to genomes of as yet un

156 Targeted metagenomics has provided the complete chloroplast genom

157 Viral metagenomics has recently yielded numerous previously un

158 The emergence of metagenomics has resulted in the generation of vast data

159 Thus, activity-centered metagenomics has revealed diverse enzymes and novel fami

160 Metagenomics has revealed hundreds of species in almost

161 Gut microbiome metagenomics has revealed many protein families and doma

162 With further technical developments, viral metagenomics has the potential to be deployed as a power

163 Metagenomics has transformed our understanding of the mi

164 roduct discovery from environmental genomes (metagenomics) has largely been limited to the screening

165 Metagenomics helps to overcome this limitation, but it i

166 Metagenomics holds enormous promise for discovering nove

167 Functional metagenomics identified beta-lactam-resistance genes in

168 NGS methods using (i) unselected HCV RNA (metagenomics), (ii) preenrichment of HCV RNA by probe ca

169 man parvoviruses were recently discovered by metagenomics in Africa, bufavirus (BuV) in 2012 and tusa

170 , providing a powerful complement to shotgun metagenomics in microbial community studies.

171 aim of this review is to discuss the role of metagenomics in the investigation of the oral resistome,

172 and establishes the value of genome-resolved metagenomics in tracking phase variation.

173 16S chimeras, supporting a role for shotgun metagenomics in validating novel organisms discovered in

174 re we show, by a conjunction of quantitative metagenomics, in silico genome reconstruction and metabo

175 Fundamental questions in metagenomics include the identities, composition and dyn

176 Integration of metagenomics into clinical medicine is a challenge, and

177 Metagenomics is a cultivation-independent approach that

178 EBI metagenomics is a freely available hub for the analysis

179 Metagenomics is a genomics research discipline devoted t

180 Metagenomics is a relatively recently established but ra

181 Viral metagenomics is a useful tool for genetically characteri

182 Viral metagenomics is an effective method for identifying nove

183 Metagenomics is beginning to demonstrate the role of the

184 arly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abu

185 t their experimental discovery by functional metagenomics is difficult, because the odds are stacked

186 d on a handful of known species, and shotgun metagenomics is limited in the ability to detect strain

187 Metagenomics is most commonly used to analyze microbial

188 nologies producing massive short reads data, metagenomics is rapidly growing, especially in the field

189 A major challenge in the field of shotgun metagenomics is the accurate identification of organisms

190 One of the main challenges in metagenomics is the identification of microorganisms in

191 Viral metagenomics is the study of viruses in environmental sa

192 A major goal of metagenomics is to identify and study the entire collect

193 Shotgun metagenomics is widely used to investigate these communi

194 Environmental shotgun sequencing (or metagenomics) is widely used to survey the communities o

195 amplification method can be used to prepare metagenomics libraries for sequencing with next-generati

196 statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the geno

197 Metagenomics/metabolomics indicate microbial composition

198 Meta-omics approaches such as metagenomics, metatranscriptomics and metaproteogenomics

199 ue from periodontitis patients using a viral metagenomics method.

200 Shotgun metagenomics methods enable characterization of microbia

201 al pipelines have been combined into shotgun metagenomics methods that have transformed microbiology.

202 Despite recent advancements in metagenomics, much of their biodiversity remains unchara

203 iomes at different body sites and functional metagenomics must be considered part of systems biology.

204 The combination of DNA-SIP and metagenomics not only permits the detection of rare low-

205 Metagenomics of patient stool samples at diagnosis revea

206 e Darby Island, The Bahamas using predictive metagenomics of the 16S rRNA gene coupled with direct wh

207 combined 249 newly sequenced samples of the Metagenomics of the Human Intestinal Tract (MetaHit) pro

208 a mass ratio approach and conducted shotgun metagenomics on purified viral samples collected from a

209 Metagenomics, or sequencing of the genetic material from

210 Viral metagenomics, or shotgun sequencing of purified viral pa

211 DNA was extracted and shotgun metagenomics performed.

212 These findings set up a 'functional metagenomics' platform for the identification of genes r

213 Numerous metagenomics projects have produced tremendous amounts o

214 ome datasets, illustrating the importance of metagenomics projects in expanding the diversity of cas

215 Data from metagenomics projects remain largely untapped for the an

216 Metagenomics projects use high-throughput sequencing to

217 analyze abundances of individual genomes in metagenomics projects.

218 Advances in metagenomics, proteomics, metabolomics, and systems biol

219 Bioengineering and metagenomics provide access to libraries of glycoside hy

220 f the current software tools for comparative metagenomics provide ecologists with the ability to inve

221 Metagenomics provide unprecedented insights into the gen

222 Metagenomics provides a powerful new tool set for invest

223 Functional metagenomics provides a systematic means of surveying co

224 Comparative metagenomics remains challenging due to the size and com

225 JCVI Metagenomics Reports (METAREP) is a Web 2.0 application

226 Metagenomics research has accelerated the studies of mic

227 ation sequencing technology have facilitated metagenomics research that attempts to determine directl

228 We therefore adapted practices from metagenomics research to rapidly catalog the bacterial c

229 of MetaQuery are a step toward democratizing metagenomics research, which should allow many researche

230 ead counts that may be useful in comparative metagenomics research.

231 e bioinformatic approaches currently used by metagenomics researchers to analyze their data, the issu

232 to these challenges, we have developed a new metagenomics resource that allows users to easily submit

233 This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomic

234 (RDP), the Silva/LTP project and several new metagenomics resources.

235 Viral metagenomics revealed previously undocumented viruses in

236 Time-course metagenomics revealed that community adaptation occurred

237 Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abun

238 Quantitative metagenomics reveals 75,245 genes that differ in abundan

239 This hampers the interpretation of metagenomics sequencing datasets, which are increasingly

240 Metagenomics sequencing provides deep insights into micr

241 RT), a novel searching heuristic for shotgun metagenomics sequencing results.

242 e applied to conjunctival and gut microbiome metagenomics sequencing results.

243 16S rRNA metagenomics sequencing revealed that CB1 blockade drama

244 d a combination of 16S rRNA gene sequencing, metagenomics sequencing, and mass spectrometry-based met

245 In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand sk

246 RNA-Seq context is highly applicable in the metagenomics setting.

247 Metagenomics showed that bacteria composition was positi

248 Here we use single-cell genomics, metagenomics, single-cell amplicon sequencing, and fluor

249 Using metagenomics, single-cell genomics, and metatranscriptom

250 plications such as targeted gene sequencing, metagenomics, small genome sequencing and clinical molec

251 It focuses on recent results from metagenomics studies and discusses the contribution of b

252 uencing technologies, an increased number of metagenomics studies have suggested the dysbiosis in mic

253 Two previous quantitative gut metagenomics studies of T2D patients that were unstratif

254 Metagenomics studies produce huge volumes of data, inclu

255 Despite a wealth of metagenomics studies, methods to leverage these datasets

256 l diversity represent challenging issues for metagenomics studies.

257 eference genomes is an essential analysis in metagenomics studies.

258 e and ankylosing spondylitis, a quantitative metagenomics study based on deep shotgun sequencing was

259 lts from 16S rRNA gene amplicon analysis and metagenomics suggested that disturbances in the system w

260 - and assembly-free strategy for comparative metagenomics that combines shared k-mer and social netwo

261 a de novo assembly approach for comparative metagenomics that directly assembles only the differenti

262 uences, as those coming from next-generation metagenomics, that contain relatively little information

263 The application of metagenomics, the culture-independent capture and subseq

264 Metagenomics, the direct sequencing of DNA from the envi

265 Metagenomics, the sequencing of DNA collected from an en

266 Metagenomics, the sequencing of DNA extracted directly f

267 Given recent advances in metagenomics, the tools are now at hand to accomplish th

268 g technology has enabled characterization of metagenomics through massively parallel genomic DNA sequ

269 Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes

270 apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and r

271 gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatm

272 lation bottleneck on the AGM virome, we used metagenomics to compare the viral nucleic acids in the p

273 ics, toxicology, metabonomics, genomics, and metagenomics to elucidate and validate the mechanism of

274 hnique has now been used in conjunction with metagenomics to establish links between microbial identi

275 ply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated protein

276 Here we use time series metagenomics to identify and study the dynamics of 25 un

277 In this study, we used genome-based metagenomics to investigate the overall community struct

278 lus with a bacteriophage, and used PCR-based metagenomics to monitor phage-derived spacers daily for

279 We utilized shotgun metagenomics to provide a first description of the resis

280 Here, we used metagenomics to reconstruct genomes of strains that colo

281 Here, we use genome-centric metagenomics to recover 17 draft genomes of anammox and

282 niques with gnotobiotic animal husbandry and metagenomics to show that the human fecal microbiota con

283 two years, we have seen a paradigm shift in metagenomics to the application of cross-sectional and l

284 The recent application of metagenomics to the discovery of bioactive small molecul

285 piring communities with isotope labeling and metagenomics to unravel how specific environmental condi

286 ion of high-throughput technologies, such as metagenomics, to identify novel genes and gene transfer

287 We review some of the metagenomics tools and strategies to determine which orp

288 Although practical uses and application of metagenomics, transcriptomics, and proteomics data and a

289 Viral metagenomics using deep sequencing was also done to iden

290 viruses in human populations, shotgun viral metagenomics was applied to 10 sewage sludge samples fro

291 We present a case where metagenomics was used to identify Mycoplasma salivarium

292 about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distributi

293 Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems

294 Archaea-specific quantitative (q) PCR and metagenomics were used to detect specific archaeal seque

295 technology has greatly promoted the field of metagenomics where previously unattainable information a

296 interesting natural products using targeted metagenomics, where environmental samples are prescreene

297 They are not suitable for alignment data in metagenomics, which are often interspecies alignments.

298 ection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prok

299 ssociated viral diversity using viral-tagged metagenomics, which links viruses to specific host cells

300 Metagenomics, which utilizes culture-independent methods

301 specimens and 1/27 controls (P < .003), and metagenomics yielded archaea, mostly methanogens, in 28/