ライフサイエンスコーパス: metagenome

1 that matched a partial viral genome from the metagenome.

2 es that is highly prevalent in the human gut metagenome.

3 se of the fragmented nature of the reference metagenome.

4 ly derived natural products using the global metagenome.

5 ow rumen, termite hindgut and chicken caecum metagenome.

6 hallenging tasks such as the assembly of the metagenome.

7 e metabolic network defined by the annotated metagenome.

8 hat diazinon exposure altered the functional metagenome.

9 hotgun reads without considering a reference metagenome.

10 of the largest resources of analysed shotgun metagenomes.

11 hroughput recovery of microbial genomes from metagenomes.

12 ate mercury were notably absent from sea-ice metagenomes.

13 igh-throughput DNA sequencing of genomes and metagenomes.

14 50-75% of the known functional potential of metagenomes.

15 reads that distinguish between two groups of metagenomes.

16 ere predominantly detected in Atlantic Ocean metagenomes.

17 ified natural products directly from complex metagenomes.

18 l metabolites, bacterial taxa, and bacterial metagenomes.

19 ibitors within 185 globally distributed soil metagenomes.

20 ealthy subjects but is more prevalent in IBD metagenomes.

21 , and in a subset of aquatic and terrestrial metagenomes.

22 a method to estimate and project coverage in metagenomes.

23 riptomes, amplified single-cell genomes, and metagenomes.

24 that XyGULs are ubiquitous in surveyed human metagenomes.

25 d for strain/species-level identification in metagenomes.

26 e some of the first deep pelagic ocean viral metagenomes.

27 spread, occurring in 94% of 137 investigated metagenomes.

28 both within a single metagenome and between metagenomes.

29 n existing virus like particle-derived viral metagenomes.

30 analysis of genes from microbial genomes and metagenomes.

31 tect and quantify target genes in short-read metagenomes.

32 ESMAN for De novo Extraction of Strains from Metagenomes.

33 ng pathways, using publically available soil metagenomes.

34 ucleotide polymorphisms (SNPs), from shotgun metagenomes.

35 proximately 2.5% of publicly available viral metagenomes.

36 ellowstone National Park hot spring sediment metagenomes.

37 of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites w

38 Mammals are defined by their metagenome, a combination of host and microbiome genes.

39 c tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences abo

40 Metagenome analyses also revealed recurrent patterns at

41 rapidly while the computational methods for metagenome analysis are still in their infancy.

42 ew program MeganServer that allows access to metagenome analysis files hosted on a server, we provide

43 Whole metagenome analysis has the potential to reveal function

44 ation of 16S rRNA gene profiling and shotgun metagenome analysis of the microbiota associated with wi

45 rescence in situ hybridization, and targeted metagenome analysis were combined with geochemical analy

46 s, Elviz can greatly accelerate the speed of metagenome analysis.

47 ings and the potential for this approach for metagenome analysis.

48 n of genomic variation, both within a single metagenome and between metagenomes.

49 I further address the effect of the metagenome and exposome as key modifiers of immune-syste

50 trait locus (QTL), transcriptome, proteome, metagenome and metabolome data sets--by far the largest

51 alcohol-associated changes to the intestinal metagenome and metabolome, characterized by reduced synt

52 ases impact the interpretation of how marine metagenome and metatranscriptome functional capacity cha

53 Here, we reconstructed the metagenome and metatranscriptome of a population of SAR3

54 Finally, systematic comparison of the gut metagenome and metatranscriptome revealed that a substan

55 selenocysteine tRNAs in terabytes of genome, metagenome and metatranscriptome sequences.

56 Identifying bacterial strains in metagenome and microbiome samples using computational an

57 udy outlines CAZyme profile of buffalo rumen metagenome and provides a scope to study the role of abu

58 ing and debranching enzymes in buffalo rumen metagenome and that of cellulases and hemicellulases in

59 subfamily comparison of genes from multiple metagenomes and comparisons with genes from microbial is

60 We explored these findings in metagenomes and metatranscriptomes and observed similar

61 We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with o

62 Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich h

63 and gradient relationships between genomes, metagenomes and metatranscriptomes.

64 than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quan

65 tool for the visual exploration of assembled metagenomes and their complex metadata.

66 Comparisons among other metagenomes and these Microviridae major-capsid sequence

67 l reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectivel

68 ied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prev

69 ichia coli, was retrieved from chicken feces metagenomes and was determined to carry diverse ARGs (mu

70 cosal homeostasis via their composite genes (metagenome) and metabolic products (metabolome).

71 t microbiome community structure, functional metagenome, and associated metabolic profiles in a sex-s

72 ion of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis o

73 We identify best practices in metagenome annotation and use them to guide the developm

74 them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP).

75 nnotation is carried out by JGI's genome and metagenome annotation pipelines.

76 publicly available genomes, expert review of metagenome annotations (IMG/M ER) and Human Microbiome P

77 publicly available genomes, expert review of metagenome annotations and Human Microbiome Project (HMP

78 Microbial genome and metagenome application specific data marts and user inte

79 Large multi-sample metagenomes are being generated but strain variation res

80 ch microbiome studies are replicable and new metagenomes are easily and rapidly integrated with exist

81 because protein coding genes predicted from metagenomes are incomplete and fragmental.

82 the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independe

83 versus protein metabolism in the functional metagenome, as well as differences in plant- versus meat

84 Our experiments on metagenomes assembled from long reads show that BIGMAC c

85 (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not

86 Nitrosotalea metagenome-assembled genome from an acidic fen, and perf

87 Here we reconstruct 73 metagenome-assembled genomes (MAGs) from two geochemical

88 Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve s

89 Here, metagenome-assembled genomes representing Marinimicrobia

90 global ocean virome data sets than published metagenome-assembled viral genomes or isolates.

91 Omega (overlap-graph metagenome assembler) was developed for assembling and s

92 rk metaSPAdes against other state-of-the-art metagenome assemblers and demonstrate that it results in

93 Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and sca

94 tively evaluating the accuracy of single and metagenome assemblies and for automatically detecting an

95 Metagenome assemblies are far from perfect, partially ex

96 e far from perfect, partially explaining why metagenome assemblies are not used for the analysis of m

97 nterpretation of individual gene surveys and metagenome assemblies in environmental microbiology.

98 ng--to generate previously intractable large metagenome assemblies.

99 ification, and none are designed to evaluate metagenome assemblies.

100 ts the de Bruijn graph structure reported by metagenome assembly algorithms to generate a comprehensi

101 o metatranscriptome assembly using graphs of metagenome assembly as the reference.

102 rized microbial 16S rRNA amplicons and phage metagenomes associated with Montastraea annularis corals

103 ck by untargeted shotgun sequencing of whole metagenomes at affordable cost.

104 Disease activity and stool metagenomes at baseline, and weeks 14, 30, and 54 after

105 tion of CPV sequencing reads to those of the metagenome background ranging from 0.0015-6.7%.

106 abases and a dedicated computing cluster, or metagenome-based approaches that have not been fully eva

107 led metagenome, MGIIa_P, was recovered using metagenome binning methods.

108 a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help

109 e show that homology-based screening of soil metagenomes can be used to specifically target the disco

110 frequencies of word patterns in genomes and metagenomes can potentially be useful for the analysis o

111 oups, each of which were predicted to encode metagenomes capable of producing metabolites characteris

112 nt was associated with an altered microbiota metagenome characterized by elevated levels of lipopolys

113 Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynam

114 expanding database of microbial genomes and metagenomes, combined with direct experiments, resulted

115 ntifying putative cas genes from genomes and metagenomes, combining similarity searches with genomic

116 ent development of alignment-free genome and metagenome comparison based on the frequencies of word p

117 Amordad places the metagenome comparison problem in a geometric context, an

118 Alignment-free genome and metagenome comparisons are increasingly important with t

119 We established a catalog of the mouse gut metagenome comprising approximately 2.6 million nonredun

120 er, there has been no information on the gut metagenome configuration in hunter-gatherer populations,

121 The amplified ambient metagenome contained genomes similar to an RNA-DNA hybri

122 MGIIa_P is the first assembled MGII metagenome containing a catalase gene, which might be in

123 Metagenome content was predicted using PiCRUST.

124 for analysis of 16S rRNA gene diversity and metagenome content.

125 Analyses of metagenome data (MG) and metatranscriptome data (MT) are

126 Metagenome data from a tractable, thermoacidophilic micr

127 viral community from publicly available gut metagenome data sets from human populations with differe

128 h the rapid growth in the number and size of metagenome data sets handled by the system.

129 sion on artificial as well as real human gut metagenome data sets.

130 As sponge metagenome data strongly suggest the presence of associa

131 rofiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmark

132 We then integrate metagenome data, contact-based structure matching, and R

133 s, and assessments of annotation accuracy on metagenome data.

134 GRASPx was also applied to a human saliva metagenome dataset and shows superior performance for bo

135 Genomes and metagenome datasets are processed using IMG's microbial

136 is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Instit

137 ity metrics that are suitable for evaluating metagenome de novo assembly.

138 The metagenome-derived gene and an ortholog from an uncultur

139 and represent abundant and widespread viral metagenome-derived protein clusters (PCs).

140 PICRUSt-predicted metagenomes displayed differential effects of Ag treatme

141 e have screened over one million clones from metagenome DNA libraries derived from sixteen different

142 more than 125 species in more than 1500 gut metagenomes drawn from populations spanning North and So

143 , a high viral diversity was observed in the metagenomes, especially among the Lipothrixviridae, as i

144 garithmic query time for identifying similar metagenomes even as the database size reaches into the m

145 teractions, including 16S rRNA gene surveys, metagenome experiments, and metatranscriptome studies.

146 Across metagenomes, fluctuations of the microbial community str

147 stitute a systematic interrogation of a soil metagenome for gene clusters capable of encoding natural

148 omplete genome of this phylotype from a soil metagenome for which we propose the provisional name 'Ca

149 iofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRU

150 We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants ov

151 We also sequenced metagenomes from a subset of the sites to determine how

152 e genes across 1267 publicly available fecal metagenomes from American, European and Chinese individu

153 c composition in simulated viromes and viral metagenomes from different benthic deep-sea ecosystems.

154 genomes, recently sequenced genomes and real metagenomes from different body sites, suggesting that t

155 and the application of MaxBin 2.0 to several metagenomes from environmental samples demonstrated that

156 ured archaea, bacteria and viruses and (iii) metagenomes from environmental, host associated and engi

157 h confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacif

158 Sediment metagenomes from four high-latitude regions of both Hemi

159 rmination from raw sequencing reads of fecal metagenomes from mice orally infected with this pathogen

160 n Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of o

161 We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding e

162 Here, by sequencing Hodgkinia metagenomes from the remaining six Magicicada and two si

163 ome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition.

164 The mddA gene is present in metagenomes from varied environments, being particularly

165 Metagenome functional prediction supported decreased fat

166 ed lipid pathways, consistent with predicted metagenome functionality.

167 General metagenome functions often correlate with the underlying

168 ) single cell genomes (SCG) and genomes from metagenomes (GFM) from uncultured archaea, bacteria and

169 , metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmen

170 resent a graph-centric approach to improving metagenome-guided peptide and protein identification in

171 of RNA viruses in these Antarctic RNA virus metagenomes had +ssRNA genomes most closely related to v

172 Recent studies of metagenomes have begun to characterize the composition o

173 Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these

174 the natural history of changes in the fecal metagenome in SIV-infected monkeys.

175 nce genomes, (2) define core microbiomes and metagenomes in these model systems, (3) elucidate the ru

176 is of microbial community aggregate genomes (metagenomes) in the context of a comprehensive set of re

177 ing for (de)halogenating enzymes in the soil metagenome including specific and unspecific halogenases

178 Analysis of metagenomes indicated phoA, phoD and phoX, and histidine

179 Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy

180 The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged t

181 The metagenome is a complex community dominated by bacteria

182 ss of stress response genes, and instead the metagenome is enriched in genes involved with dormancy a

183 istance and virulence, detecting them within metagenomes is therefore vital.

184 etrieved viral sequences from six hot spring metagenomes isolated worldwide, revealing a wide distrib

185 composition and functional capacity, linking metagenome-level compositional shifts to strain-level va

186 Analysis of environmental metagenome libraries detected PHV sequences in coastal m

187 (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Proj

188 A nearly completely assembled metagenome, MGIIa_P, was recovered using metagenome binn

189 ysis drawing on all publicly available viral metagenomes observed a mere 257,698 viral genotypes on E

190 iles was explored according to the predicted metagenomes obtained by PICRUSt (phylogenetic investigat

191 Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora

192 ion based on genomic bins assembled from the metagenome of deep-sea subsurface sediments shows that t

193 We sequenced the metagenome of the soil-inhabiting fungus Mortierella elo

194 find within-sample genomic variation in the metagenomes of a kimchi fermentation process, the microb

195 tibiotic Resistance Database (CARD) from the metagenomes of each sample using the Short, Better Repre

196 n and its co-occurring temperate population, metagenomes of each type were prepared from the same sea

197 Predicted metagenomes of particular microbiota members involved in

198 tides, are widely distributed in genomes and metagenomes of the human microbiota.

199 To understand MRE biology, we sequenced metagenomes of three MRE populations, each associated wi

200 yTaxa on in silico generated (mock) and real metagenomes of varied read length (100-2000 bp) revealed

201 The collective genetic potential (metagenome) of the human microbiome is orders of magnitu

202 However, the now-documented influence of the metagenome on experimental results and the reproducibili

203 mplex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencin

204 n a tour-de-force effort, map the human skin metagenomes over time.

205 ydratase gene cluster (pduCDE) in Firmicutes metagenomes predicted from the 16S rRNA gene.

206 rgeted metagenomic sequencing and functional metagenome prediction.

207 a community's functional potential; however, metagenome predictions based on 16S rRNA sequence tags c

208 Metagenome predictions supported the premise that L. pla

209 onal plugin provides features for common 16S metagenome profiling analysis such as chimera filtering,

210 terns can be further extended to problems in metagenome profiling and cell type inference.

211 In addition, predicted functional metagenome profiling suggested an over-representation of

212 acterial DNA, which appears to be sampled by metagenome projects non-specifically.

213 set analysis, which runs in conjunction with Metagenome-RAST (MG-RAST) servers.

214 were first evaluated against mock community metagenomes, recently sequenced genomes and real metagen

215 -CO2 environment by assembly and analysis of metagenomes recovered from geyser water filtrate.

216 thousands of novel CRISPR spacers from each metagenome, reinforcing the notion of high viral diversi

217 The predicted metagenomes related to carbohydrate and energy metabolic

218 PICRUSt analysis revealed that the predicted metagenomes related to the glycan biosynthesis and metab

219 omic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects rese

220 ew species as well as reconstructing complex metagenomes remains major technological challenges.

221 0% of the assembled sequences from human gut metagenomes represent novel species with no sequenced re

222 ls from corresponding gastrointestinal tract metagenomes, respectively.

223 VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all hu

224 Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60-76% a

225 luorescence in situ hybridization images and metagenome results suggest that Methanobacterium spp. ma

226 However, metagenomes revealed mixed acid and Entner-Dourdoroff fe

227 Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for ye

228 equences recovered from over 6,000 assembled metagenomes sampled globally.

229 and Human Microbiome Project (HMP)-specific metagenome samples (IMG/M HMP).

230 We evaluated 11 metagenome samples and demonstrated that microbes inhabi

231 Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition revea

232 and Human Microbiome Project (HMP)-specific metagenome samples.

233 s of interactions between microbial species, metagenome-scale models of community-level metabolism, a

234 teins that belong to large families and that metagenome sequence data more than triple the number of

235 e processed using IMG's microbial genome and metagenome sequence data processing pipelines and are in

236 of isolate microbial genomes, plasmidome and metagenome sequence data.

237 The metagenome sequence of Candidatus Lokiarchaeon has ident

238 While genome and metagenome sequences are being produced at breakneck spe

239 Assembly of metagenome sequences does not output whole genomes, so c

240 Phylogenetic analysis of metagenome sequences indicated the phenotypic shift obse

241 rding to 16S rRNA pyrosequencing and shotgun metagenome sequencing analyses, the most abundant specie

242 to the detection of MDR bacteria by shotgun metagenome sequencing as a novel method that might bette

243 Genome and metagenome sequencing efforts that span the past decade

244 We investigated shotgun metagenome sequencing for the detection of methicillin-r

245 Shotgun metagenome sequencing has become a fast, cheap and high-

246 arge volumes of sequencing data required for metagenome sequencing has led to unacceptably high false

247 By deep metagenome sequencing of faecal DNA from 287 pigs, we id

248 iotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals.

249 Metagenome sequencing revealed integrons in the gut meta

250 quence information derived from accompanying metagenome sequencing to accurately correct errors in SA

251 Over the past decade, the application of metagenome sequencing to elucidate the microbial composi

252 ality genome sequences and single time-point metagenome sequencing to infer microbial population repl

253 ion of 16S rRNA amplicon sequencing, shotgun metagenome sequencing, and liquid chromatography tandem

254 onomic and functional diversity with shotgun metagenome sequencing.

255 erial 16S ribosomal RNA (rRNA) gene or whole metagenome shotgun (WMS) sequencing provides more precis

256 ul and complete pipeline for the analysis of metagenome shotgun sequences.

257 Whole metagenome shotgun sequencing is a powerful approach for

258 The Hadza gut metagenome structure allows us to appreciate the co-adap

259 re both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genom

260 ix times more abundant in publicly available metagenomes than all other known phages together; it com

261 In the functional analysis of metagenomes, the features may refer to the pathways, sub

262 SUPER-FOCUS was tested with over 70 real metagenomes, the results showing that it accurately pred

263 Trichodesmium isolates and two Trichodesmium metagenomes, thereby identifying highly conserved, novel

264 With thousands of publicly available metagenomes, these questions should be easy to answer.

265 e-free analyses captured the uncharacterized metagenome through the development of a multi-kingdom ge

266 rce environments (HREs) and sequenced twelve metagenomes to characterize their metabolic potential.

267 Here, we use triplicate metagenomes to compare common aquatic viral concentratio

268 We then assemble two large soil metagenomes totaling 398 billion bp (equivalent to 88,00

269 Viral metagenomes typically contain many unknown sequences.

270 Genomes extracted from metagenomes using homology and compositional approaches

271 The problem of de-novo assembly for metagenomes using only long reads is gaining attention.

272 e double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morpholo

273 thin viral genomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90

274 lity to identify up to 90% of reads in viral metagenomes (viromes).

275 rom a reactor biomass community for which no metagenome was available.

276 68% of the health-associated metagenome was dedicated to energy utilization through o

277 The induced viral metagenome was higher in identifiable virus sequences an

278 The human gut metagenome was recently discovered to encode vast collec

279 e, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental meta

280 file highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis tec

281 ificant numbers of dsyB homologues in marine metagenomes, we propose that bacteria probably make a si

282 s for a microbial community that had a known metagenome were identified by matching mass and elution

283 ccus (VRE), and MDR Enterobacteriaceae Fecal metagenomes were analyzed from high-risk inpatients and

284 Both of the amplified contemporary metagenomes were enriched in single-stranded DNA (ssDNA)

285 Bacterial metagenomes were predicted from 16S rRNA data by using P

286 To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Lin

287 p. CCM components in the Global Ocean Survey metagenomes were very similar to those in the genomes of

288 . fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the

289 usly, novel genes dominate viral genomes and metagenomes, which has led to the suggestion that viruse

290 nt in the majority of published human faecal metagenomes, which we refer to as crAssphage.

291 ied out metagenomic shotgun sequencing and a metagenome-wide association study (MGWAS) of fecal, dent

292 We performed a metagenome-wide association study and serum metabolomics

293 Here, we perform a metagenome-wide association study on stools from 218 ind

294 Here, the authors perform a metagenome-wide association study on stools from individ

295 side hydrolase (GH) profile of buffalo rumen metagenome with cow rumen, termite hindgut and chicken c

296 Sensitivity evaluation against synthetic metagenomes with different coverage suggested that 50 GS

297 ed to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in

298 s used in amplification impact the resulting metagenomes, with TaKaRa enriching for 'rare' reads rela

299 ort reads can be challenging for genomes and metagenomes without template sequences, making alignment

300 identify microbial strains/species from raw metagenomes, without the effort of complex data pre-proc