ライフサイエンスコーパス: metagenomic

1 sequencing data is a challenging problem in metagenomics.

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

3 en using culture-independent high-throughput metagenomics.

4 surface microbiome was assessed with shotgun metagenomics.

5 By applying metabolomic and metagenomic (16S ribosomal RNA gene and whole-genome sho

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

7 with a single alcohol dehydrogenase (either metagenomic ADH-150, an ADH from Sphingobium yanoikuyae

8 We describe a statistical metagenomic algorithm that simultaneously identifies mic

9 andards, and a guide for selecting tools for metagenomic analyses by comparing ranges of precision, a

10 Both morphometric and metagenomic analyses have raised questions about the pre

11 Metagenomic analyses of hyper-arid and extreme hyper-ari

12 This allowed for genomic and metagenomic analyses of the host-associated microbiome a

13 Metagenomic analyses revealed that neomycin altered the

14 Extensive sampling and metagenomics analyses of plankton communities across all

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

16 Predicted metagenomic analysis emphasized significant dysbiosis-as

17 Shotgun metagenomic analysis identified a variety of Microcystis

18 Metagenomic analysis identified bacterial sequences in b

19 and fluid chemistry, energetic modelling and metagenomic analysis indicate near functional equivalenc

20 Technical variation in metagenomic analysis must be minimized to confidently as

21 riteria important for efficiently conducting metagenomic analysis of ARGs using ARGs-OAP.

22 Furthermore, metagenomic analysis of human stool samples reveals that

23 he impact that WGA kit selection can have on metagenomic analysis of low-biomass samples and the impo

24 Similarly, GeoChip metagenomic analysis revealed a tremendous enrichment of

25 Metagenomic analysis showed differences in gut microbiot

26 The metagenomic analysis showed that Proteobacteria, Actinob

27 Metagenomic analysis showed that the most abundant taxon

28 ae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polym

29 mplicon sequencing was combined with GeoChip metagenomic analysis to monitor the microbial community

30 ssignment is an important first step in many metagenomic analysis workflows, providing the basis for

31 d nitrite-oxidizing bacteria, identified via metagenomic analysis.

32 ion had the largest effect on the outcome of metagenomic analysis.

33 ion and role of GA1-3 in the human gut using metagenomic analysis.

34 ul application of verified methods for viral metagenomic analysis.

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

36 Here, we present a metagenomic and -transcriptomic survey, with subsequent

37 istic approach that integrates phylogenetic, metagenomic and abundance information, we elucidate patt

38 nities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by dis

39 es toluene from phenylacetate; complementary metagenomic and metaproteomic analyses are also presente

40 Using metagenomic and metaproteomic methods, we investigated t

41 Functional annotation of metagenomic and metatranscriptomic data sets relies on s

42 nd reference-independent analysis of coupled metagenomic and metatranscriptomic data.

43 Analyses of metagenomic and metatranscriptomic datasets revealed tha

44 l public metaproteomic datasets with matched metagenomic and metatranscriptomic sequencing data acqui

45 Metagenomic and metatranscriptomic sequencing recover th

46 Metagenomics and 16S rRNA gene amplicon sequencing revea

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

48 Shotgun metagenomics and computational analysis are used to comp

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

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

51 After reducing metagenomics and metabolomics data dimensionality, multi

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

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

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

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

56 Metagenomics and single-cell genomics can reveal unknown

57 Metagenomics and single-cell genomics have enabled genom

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

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

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

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

62 A metagenomic approach and network analysis were used to e

63 abolisms of these organisms, we used a novel metagenomic approach to recover 227 high-quality genomes

64 We employed a genome-resolved metagenomic approach to recover and characterize genomes

65 ross these spatio-temporal scales and used a metagenomic approach to show that these dominant members

66 A metagenomic approach was taken complemented by detection

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

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

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

70 Metagenomic approaches have significantly expanded our k

71 We adopted phenotypic and metagenomic approaches to investigate phosphatase genes

72 Metagenomics approaches can effectively detect broad pro

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

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

75 it to identify viral sequences directly from metagenomic assemblies.

76 metaSPAdes addresses various challenges of metagenomic assembly by capitalizing on computational id

77 antibiotic resistance genes (ARGs) based on metagenomic assembly to investigate ARGs and their co-oc

78 This ARG annotation pipeline based on metagenomic assembly will help to bridge the knowledge g

79 odiverse and that microdiversity hinders the metagenomic assembly, which could explain why their geno

80 ns, thus further amplifying the challenge of metagenomic assembly.

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

82 Metagenomic binning and phylogenetic analysis revealed t

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

84 and powerful tool for identifying potential metagenomic biomarkers.

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

86 i (FM) index, optimized specifically for the metagenomic classification problem.

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

88 Unlike other ultra-fast metagenomic classifiers, full sequence alignment is perf

89 46 species to evaluate the performance of 11 metagenomic classifiers.

90 Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbio

91 e characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng

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

93 In metagenomic contig binning, Hetero-RP automatically weig

94 lap improved when only using host genomes or metagenomic contigs from the same habitat or samples as

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

96 imized methods for constructing high quality metagenomic cosmid libraries in the best Streptomyces ho

97 ic shotgun sequences, which markedly improve metagenomic data analysis and interpretation.

98 cting novel genomes from complex mixtures of metagenomic data can still be challenging and represents

99 Metagenomic data from 14 samples collected over 5 years

100 Analysis of metagenomic data from the Tara Oceans expedition (7) sho

101 Metagenomic data from this individual also contained a n

102 Both cellular and fractionated viral metagenomic data generate a large number of viral contig

103 he reproducibility of the results drawn from metagenomic data is crucial for clinical applications an

104 bacteriophage, crAssphage, was discovered by metagenomic data mining and reported to be abundant in a

105 yzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biol

106 n of ARG hosts and the shared resistome from metagenomic data sets and successfully establishes the r

107 dentified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80 degree

108 ding ARG-associated genes and ARG hosts with metagenomic data sets.

109 tional and experimental methods can leverage metagenomic data to characterize transcriptional respons

110 tudy, we developed a CRISPR finding tool for metagenomic data without relying on generic assembly, wh

111 transcriptomic data of non-model species and metagenomic data, profile homology search is widely adop

112 icient algorithm for the characterization of metagenomic data.

113 e of two ecotypes has been proposed based on metagenomic data.

114 for reference-based, lossless compression of metagenomic data.

115 a group of giant viruses (Klosneuviruses) in metagenomic data.

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

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

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

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

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

121 ombine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein

122 pplied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and a

123 he proposed method is also applied to a real metagenomic dataset and the results provide an interesti

124 the other hand, de novo assembly of a large metagenomic dataset is computationally demanding and the

125 we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected f

126 The recovery of genomes from metagenomic datasets is a critical step to defining the

127 n detected within many bacteria isolates and metagenomic datasets, including human pathogens, and is

128 terol and arborinol synthases in genomic and metagenomic datasets.

129 t in substandard annotation of proteins from metagenomic datasets.

130 Metagenomics delineated greater deglucuronidation capabi

131 Time-resolved metagenomics demonstrated that an aerobic cellulolytic c

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

133 generate data for lichen-forming fungi from metagenomic DNA extracted from intact lichens.

134 However, when using metagenomic DNA from inseparable symbiotic organisms, RA

135 e composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of TB cases during antimycob

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

137 Modern metagenomic environmental DNA studies are almost complet

138 Three metagenomic enzymes exhibited lipase activity, and seven

139 We found metagenomic evidence that cryptoendolithic microorganism

140 data is generated, e.g. from proteomics and metagenomic experiments.

141 sizes were 2-13 percent of the original raw metagenomic file sizes.

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

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

144 Metagenomics has made accessible an enormous reserve of

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

146 Metagenomics has revealed hundreds of species in almost

147 Metagenomics helps to overcome this limitation, but it i

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

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

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

151 pply reverse genetics based on the available metagenomic information yielded identification of small

152 This study represents the first metagenomic interrogation of Antarctic permafrost and po

153 We present the Metagenomic Intra-species Diversity Analysis System (MID

154 Metagenomics is a cultivation-independent approach that

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

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

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

158 ocillopora represented by 15 coral holobiont metagenomic libraries.

159 her lichen symbionts that are represented in metagenomic libraries.

160 An initial screen of a 1.5 million-membered metagenomic library constructed in Streptomyces albus, t

161 21 fosmid clones from a human gut microbiome metagenomic library that, when expressed in Escherichia

162 tly, we generated empirical RADseq data from metagenomic lichen DNA, with RADseq loci mapped back to

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

164 Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and ge

165 Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous

166 and have been severe obstacles in employing metagenomic methods.

167 Shotgun metagenomics methods enable characterization of microbia

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

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

170 core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specif

171 242 age- and gender-matched controls using a metagenomic multivariate analysis pipeline.

172 This report demonstrates that metagenomic next generation sequencing allows for unbias

173 Metagenomic next generation sequencing can identify unus

174 Metagenomic next generation sequencing of his cerebrospi

175 Using metagenomic next generation sequencing, we detected nucl

176 Cache Valley virus genes were identified via metagenomic next generation sequencing.

177 Metagenomic next-generation sequencing (mNGS) is increas

178 Metagenomic next-generation sequencing (mNGS) was conduc

179 We compared the performance of metagenomic next-generation sequencing (mNGS) with confi

180 om 22 patients in 2016 were obtained using a metagenomic next-generation sequencing assay.

181 Metagenomics of patient stool samples at diagnosis revea

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

183 DNA was extracted and shotgun metagenomics performed.

184 Using state-of-the-art metagenomic population binning and catalyzed reporter de

185 n minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-s

186 affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity s

187 analyze abundances of individual genomes in metagenomics projects.

188 mes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their

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

190 Metagenomics provide unprecedented insights into the gen

191 zed to differentiate sequence read data into metagenomic (random) and amplicon (targeted) sequence da

192 s performed, and the reads were processed by metagenomic rapid annotation.

193 We explore connections between metagenomic read assignment and the quantification of tr

194 suite specialized for FASTA and FASTQ format metagenomic read processing and lossless compression.

195 easures the dissimilarity between contigs of metagenomic reads and that relative sequence composition

196 st thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-cur

197 ate symbiont-specific phylogenomic data from metagenomic reads.

198 r annotation of short peptides identified on metagenomic reads.

199 Metagenomic recruitment also reveals the putative virus

200 Using metagenomic recruitment, strain SPOT01 comprises a major

201 Metagenomic resolution and bioinformatic tools considera

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

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

204 utput of existing binning tools for a single metagenomic sample.

205 ilters for the detection of viral contigs in metagenomic samples ( approximately 6 h), and it describ

206 ecting differentially abundant features from metagenomic samples by comparing different biological/me

207 ; and the scalable clustering of hundreds of metagenomic samples by composition.

208 were also highly conserved in Trichodesmium metagenomic samples from natural populations suggesting

209 any existing contig-binning tools for single metagenomic samples to obtain better binning results.

210 Sequenced metagenomic samples usually comprise reads from a large

211 ide greater resolution of species in complex metagenomic samples, and improve the interpretation of r

212 As a trade-off, we require multiple metagenomic samples, usually >/=10 samples, to get highl

213 iral contigs from >6000 ecologically diverse metagenomic samples.

214 l genome sequences identified primarily from metagenomic samples.

215 s more precise and comprehensive analyses of metagenomic samples.

216 nt on the development of improved functional metagenomic screening methods.

217 Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information abo

218 Metagenomic sequence analysis is rapidly becoming the pr

219 microbial community stability, we generated metagenomic sequence data from longitudinal samples coll

220 oteins by sequence homology from genomic and metagenomic sequence databases is straightforward, predi

221 (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated

222 ee distinct groups of viruses assembled from metagenomic sequence datasets highly enriched for MG-II.

223 We also generated a metagenomic sequence library from X-cell xenomas of blue

224 ges of the persisting populations by mapping metagenomic sequence reads onto single-cell genomes.

225 Next-generation metagenomic sequencing (NGMS) has opened new frontiers i

226 Metagenomic sequencing allowed draft genome assembly of

227 Microbial 16S rRNA metagenomic sequencing analyses were then used to identi

228 We used metagenomic sequencing and activity assays to examine th

229 Advances in metagenomic sequencing and bioinformatics have vastly ex

230 ly, their functional characteristics through metagenomic sequencing and other multi-omic technologies

231 ions of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation interv

232 We demonstrate that metagenomic sequencing can provide accurate diagnostic i

233 onstruct full-length 16S gene sequences from metagenomic sequencing data with high accuracy.

234 l conditions, in particular, for time series metagenomic sequencing data.

235 ble researchers to collect a large volume of metagenomic sequencing data.

236 We used metagenomic sequencing for functional community profilin

237 nificantly perturbed the gut microbiome, and metagenomic sequencing found that diazinon exposure alte

238 Next-generation metagenomic sequencing generated a total of 600 million

239 Microbiome analysis using metagenomic sequencing has revealed a vast microbial div

240 technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in P

241 Metagenomic sequencing is increasingly used to decipher

242 llenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient

243 n this issue, Dudek et al. show that shotgun metagenomic sequencing of a less-well-studied environmen

244 Metagenomic sequencing of incubation samples revealed th

245 We assessed if metagenomic sequencing of total DNA extracts obtained di

246 orm a full-scale computational analysis of a metagenomic sequencing project, involving 12 samples and

247 An unbiased screen using metagenomic sequencing related SAMHD1 to increased expre

248 Quantitative polymerase chain reaction and metagenomic sequencing revealed a significantly higher r

249 Metagenomic sequencing revealed bacterial formate oxidat

250 id culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence in

251 We compared metagenomic sequencing with standard aerobic and anaerob

252 halitosis was implied for the first time via metagenomic sequencing.

253 nd no other viruses were detected by PCR and metagenomic sequencing.

254 otic communities via marker gene and shotgun metagenomic sequencing.

255 Metagenomics sequencing provides deep insights into micr

256 16S rRNA metagenomics sequencing revealed that CB1 blockade drama

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

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

259 ombining a 16S rRNA (16S) gene database with metagenomic shotgun sequences promises unbiased identifi

260 6S gene sequences in the near-terabase-scale metagenomic shotgun sequences, which markedly improve me

261 AFS uses metagenomic shotgun sequencing and sequence read countin

262 l quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis.

263 Metagenomic shotgun sequencing is a new tool to identify

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

265 Using metagenomics, single-cell genomics, and metatranscriptom

266 A total of 23,709 genes and 12 metagenomic species were shown to be differentially abun

267 million non-redundant genes representing 719 metagenomic species.

268 We introduce StrainPhlAn, a novel metagenomic strain identification approach, and apply it

269 The resulting approaches to metagenomic strain profiling are generalizable and can b

270 ods for rapid and accurate quantification of metagenomic strains.

271 biodinium-infecting viruses has emerged from metagenomic studies of corals.

272 Metagenomic studies revealed functional differences in g

273 of viral contigs of length at least 1kbps in metagenomic studies with high accuracy.

274 to cross-sectional data from two large-scale metagenomic studies--the Human Microbiome Project and th

275 he identification of the hosts of contigs in metagenomic studies.

276 new method through both simulation and real metagenomic studies.

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

278 Here, we present a genome-resolved metagenomic study of microbial genotypes from the gastro

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

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

281 genome was identified from a whole community metagenomic survey, and comparative analysis against ext

282 functional genes during decomposition with a metagenomic technique (GeoChip).

283 This method builds upon earlier RNA metagenomic techniques and can play an important role in

284 Metagenomics, the sequencing of DNA extracted directly f

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

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

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

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

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

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

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

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

293 As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a c

294 eatly improve the characterization of novel, metagenomic viruses.

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

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

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

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

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

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