ライフサイエンスコーパス: metagenome

1 all microbial genomes in a sample (i.e. the metagenome).

2 omic sequence variation is present in a real metagenome.

3 he cde biosynthetic gene cluster from a soil metagenome.

4 fDNA, and to profile the bacterial and viral metagenome.

5 stimate the containment of a genome within a metagenome.

6 es of extracellular DNA in the environmental metagenome.

7 f a novel polyomavirus species from a public metagenome.

8 ynthase gene clusters from an Antarctic soil metagenome.

9 xert selective pressures upon the microbiome metagenome.

10 of assembling viral genomes from short-read metagenomes.

11 ibution of any protein domain in short-reads metagenomes.

12 estimating the resemblance of two genomes or metagenomes.

13 tion and cannot handle highly complex single metagenomes.

14 epresentative marine phytoplankton and ocean metagenomes.

15 isleading due to the unknown genomes in real metagenomes.

16 utationally predicted from assembled shotgun metagenomes.

17 g-read sequencing, and screening of existing metagenomes.

18 rstand large-scale structures in genomes and metagenomes.

19 us-like sequences from microbial genomes and metagenomes.

20 15 distinct Lak phage genomes recovered from metagenomes.

21 nd 63.80% of genera were shared between both metagenomes.

22 onal cohorts, considering in total 969 fecal metagenomes.

23 deconvoluting individual genomes from single metagenomes.

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

25 densoviral genomes were recovered from viral metagenomes.

26 it to >800 soil and plant-associated shotgun-metagenomes.

27 88 oral cavities worldwide with paired stool metagenomes.

28 community and previously published human gut metagenomes.

29 to a better understanding of how to harness metagenomes.

30 er 1300 E. rectale high-quality genomes from metagenomes.

31 in earlier, more preliminary comparisons of metagenomes across biomes.

32 ffectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably

33 mmunity ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic wat

34 We studied soil bacterial metagenomes along a precipitation gradient on the easter

35 ng, by 24 months and 36 months, the ash-soil metagenomes already showed a similar diversity of functi

36 These comprehensive metagenome analyses reveal not only host bacteria-phage

37 Metagenome analysis coupled with publicly available micr

38 sed host transcriptome pathway and microbial metagenome analysis in airway brushes and compared machi

39 Metagenome analysis indicates the presence of a single s

40 Using whole metagenome analysis of skin microbiomes of patients with

41 In addition, predicted metagenome analysis revealed no significant difference i

42 , and computational efficiency) of different metagenome analysis tools for extracting the CDS content

43 In the metagenome and amplicon sequencing of hgcAB diversity, t

44 aligning the spacer content to each sample's metagenome and corresponding gene families.

45 or every NCBI RefSeq genome within every SRA metagenome and demonstrate the identification of a novel

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

47 predict the systemic effects of the altered metagenome and metabolite profiles.

48 terize the structure and function of vaginal metagenome and metatranscriptome datasets.

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

50 GS and ACN metagenomic traits on unassembled metagenomes and allow researchers to improve their metag

51 10 times more protein sequences from complex metagenomes and can assemble huge datasets.

52 with the ethical standard of data sharing of metagenomes and DNA sequence data more broadly.

53 ircumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shot

54 searching a small sample size of all public metagenomes and genomes, many new encapsulin systems wer

55 of 307 healthy men, we profiled serial stool metagenomes and metatranscriptomes and assessed diet usi

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

57 annans and whose genes are abundant in rumen metagenomes and metatranscriptomes.

58 Marine metagenomes and microbial genomes show that Verrucomicro

59 se results illustrate the power of combining metagenomes and pangenomes to investigate the ecology an

60 isolate genomes and Human Microbiome Project metagenomes and provide these data through a public web

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

62 ance of 18 host-derived cyanophages genes in metagenomes and viromes along depth profiles from the Ea

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

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

65 metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species w

66 f VIRGO, we analyze 1,507 additional vaginal metagenomes, and identify a high degree of intraspecies

67 s studies of thousands of microbial species, metagenomes, and infectious disease pathogens.

68 ncluding Staphylococcus aureus isolates, gut metagenomes, and meta-analyses demonstrate the ability o

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

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

71 ousands of community profiles for which only metagenomes are currently available.

72 Shotgun metagenomes are often assembled prior to annotation of g

73 key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nan

74 cs to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic

75 .6 T of Illumina data to construct 469 draft metagenome-assembled bacterial genomes, including 460 no

76 s were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate

77 about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncult

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

79 We obtained a 99.8%-complete metagenome-assembled genome for this strain, allowing us

80 Metagenome-assembled genome sequences (MAGs) representin

81 Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the dat

82 rative genomic analysis of 12 Thermoplasmata metagenome-assembled genomes (MAGs) basal to the Methano

83 and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effecti

84 eductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potenti

85 olism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existin

86 Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental D

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

88 embly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge i

89 We assembled five potentially novel metagenome-assembled genomes (MAGs) of core bacteria in

90 Metagenome-assembled genomes (MAGs) of these Petromonas

91 Our set of metagenome-assembled genomes (MAGs) represents >400 yet-

92 Metagenome-assembled genomes (MAGs) revealed that phenan

93 We assembled 4,941 rumen microbial metagenome-assembled genomes (MAGs) using approximately

94 enabled the rapid assembly of near-complete metagenome-assembled genomes (MAGs), and there is a need

95 embly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 ba

96 ough an analysis of metabolic pathways in 64 metagenome-assembled genomes (MAGs), we show that MAG tr

97 vered as single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs).

98 shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs).

99 can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local ass

100 We recovered 82 metagenome-assembled genomes affiliated with 21 differen

101 We recovered 49 metagenome-assembled genomes and assessed the microbial

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

103 We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR-Ca

104 e bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut micro

105 g data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat el

106 xperimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from

107 Here we generate 501 metagenome-assembled genomes of Nucleo-Cytoplasmic Large

108 Furthermore, these metagenome-assembled genomes often exclude repeated geno

109 This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel c

110 lysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-sp

111 t microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative

112 From metagenome-assembled genomes we identified over 90 putat

113 The two metagenome-assembled genomes were compared with other re

114 -including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better

115 licable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN

116 Based on 1,364 de novo metagenome-assembled genomes, we uncover four distinct f

117 d CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR a

118 s arising from cultivated viral isolates and metagenome-assembled viruses.

119 We recover metagenome-assembled-genomes for a core microbiome of <

120 DEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance prote

121 of the largest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers a

122 ltiassembly; rather, having a fast, scalable metagenome assembler enables a user to more easily perfo

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

124 We selected four advanced metagenome assemblers, MEGAHIT, MetaSPAdes, IDBA-UD and

125 y emerged from dmdA sequences recovered from metagenome assemblies and single-cell sequencing, includ

126 organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environ

127 ivivax streblomastigis, as well as a complex metagenome assembly of at least 8 other Bacteroidetes ba

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

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

130 This study presents the largest metagenome-based association study on plasma metabolism

131 Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly a

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

133 feature, new statistical tools, and supports metagenome binning.

134 Metagenome bins, representing the predominating microbes

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

136 ew viral sequences have been identified from metagenomes, but the quality and completeness of these s

137 ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of mi

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

139 Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all

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

141 Studying how metagenome composition and diversity varies along enviro

142 of the sequences were obtained from cellular metagenomes confirming that they represent an important

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

144 Single-cell genomes and metagenomes continue to increase the known diversity of

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

146 After binning the metagenome data, we assembled and annotated the Endogona

147 idly increasing amount of publicly available metagenome data.

148 ols to assemble, annotate, quantify, and bin metagenome data.

149 arly challenging when large whole-genome and metagenome databases are involved.

150 eated from multi-sources of whole-genome and metagenome databases through complementary hidden Markov

151 ence bacterial genome sequences to interpret metagenome datasets and guide functional analyses.

152 ember EnvSia156 was isolated from hot spring metagenomes, defines an unusual structural fold and acti

153 Examination of metagenomes demonstrates that viruses with high genetic

154 Here we analyzed two metagenomes derived from virus-like particles, analyzed

155 Functional analysis of the recombinant metagenome-derived enzyme showed high specificity toward

156 ry relationships between traits of the fecal metagenome, disease markers, and risk exposures.

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

158 stomes.Measurements and Main Results: Airway metagenomes exhibit taxonomic and metabolic diversity an

159 of 29 species significantly enriched in CRC metagenomes (false discovery rate (FDR) < 1 x 10(-5)).

160 nd resolve eukaryotic draft genomes from SCG metagenomes, finding significant variation in outcomes.

161 , by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductas

162 tion screening and retrospective analysis of metagenomes for novel genome discovery.

163 mics, we explore new applications of oceanic metagenomes for protein structure and function predictio

164 (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 count

165 a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stati

166 We used 247 microbial metagenomes from 18 biomes to determine which set of gen

167 ntegrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected dai

168 dy, integrative analysis on 4347 human stool metagenomes from 34 published studies across healthy and

169 adapted microorganisms, here we investigated metagenomes from a 45 degrees C gradient of temperate-to

170 Analysis of 50 metagenomes from a variety of YNP springs reveals that g

171 axonomy tool can be automated and applied to metagenomes from any environment for virus classificatio

172 clustering performance on transcriptomes and metagenomes from both short and long read sequencing tec

173 We obtained stool metagenomes from CD patients in remission and assessed g

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

175 ive genomics study on 1,773 human-associated metagenomes from four different body sites.

176 microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bow

177 of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered envi

178 of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host ra

179 Here, we reveal that metagenomes from no fewer than 20% of the papers found i

180 ck-specific microbial community by comparing metagenomes from samples collected in a Greenlandic fjor

181 en a model trained on paired metabolomes and metagenomes from the environment of interest.

182 erized siderophore-like BGCs in genomes from metagenomes from the infant and adult gut microbiome.

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

184 Here, we assemble metagenomes from tongue and dental plaque samples from m

185 his study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases

186 we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gu

187 draft prokaryotic genomes from 3,810 faecal metagenomes, from geographically and phenotypically dive

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

189 bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and ev

190 Analysis of ancient metagenomes highlighted patterns of P. copri presence co

191 comparative analysis of isolate genomes and metagenomes in IMG.

192 on-redundant protein database and all of the metagenomes in the sequence read archive, and found that

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

194 hesis and UV protection were enriched in the metagenomes, indicating the significance of these functi

195 d to our understanding of microbial species, metagenomes, infectious diseases and more.

196 he initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenie

197 SAAVs partitioned metagenomes into two main groups matching large-scale oc

198 ce of antimicrobial resistance genes in milk metagenome, investigate their genetic position and their

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

200 The annotation of short-reads metagenomes is an essential process to understand the fu

201 g five clades and utilize ~100 environmental metagenomes largely sourced from the TARA Oceans project

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

203 om a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes.

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

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

206 Centrifuge analysis of metagenomes obtained from samples of VAP, infected DFUs,

207 Korarchaeota, which were retrieved from the metagenome of a circumneutral, suboxic hot spring that c

208 rotein-coding sequences (CDS) present in the metagenome of the community.

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

210 promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals.

211 Shotgun metagenomes of DNA extracted from human fecal samples se

212 lete Wolbachia genomes from individual ovary metagenomes of four wild Culex pipiens mosquitoes captur

213 bility of a viral community by analysing the metagenomes of near-surface 0.02-0.2 mum samples from th

214 both tools, we analyzed the 139 prokaryotic metagenomes of TARA Oceans and revealed the ecological s

215 biota alterations in the quantitative faecal metagenomes of the cross-sectional MetaCardis Body Mass

216 rent assembly programs used either simulated metagenomes or real metagenomes with unknown genome comp

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

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

219 orrelation between the metatranscriptome and metagenome predictions for both hosts.

220 Metagenome predictions supported the premise that L. pla

221 entify discrete protein domains in sequenced metagenomes processed with MG-RAST.

222 d to identify divergent immune and microbial metagenome profiles of stressed gestating mice that may

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

224 The explosive growth in taxonomic metagenome profiling methods over the past years has cre

225 Using data from one of the largest human metagenome projects to date, the American Gut Project (A

226 Collectively, this metagenome provides high-quality references and begins t

227 microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic

228 taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surfa

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

230 Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs

231 Functional analysis of CRC metagenomes revealed enriched protein and mucin cataboli

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

233 Screening of publicly available metagenomes revealed that Sulfurimonas spp. with only th

234 compare these isolates to existing human gut metagenomes, revealing similarities to previously inferr

235 f 479 genomes reconstructed from the biofilm metagenomes reveals novel biosynthetic gene clusters and

236 ith other available chemosynthetic community metagenomes reveals similarly high diversity and functio

237 asets suggest that the contribution from the metagenome sequence data is significant with P-values le

238 ed to three factors: the deeper MSA from the metagenome sequence data, improved feature design in Dee

239 sed on the improved MSA constructed from the metagenome sequence data, we developed MapPred, a new de

240 Metagenome sequence datasets can contain terabytes of re

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

242 Phylogenetic analysis of metagenome sequences indicated the phenotypic shift obse

243 Metagenome sequences were obtained using shotgun metagen

244 y (H, n = 7) milk samples through deep whole metagenome sequencing (WMS).

245 nerable, and LL/resilient rats using shotgun metagenome sequencing and observed increased expression

246 We analyzed whole-metagenome sequencing data from 163 longitudinally colle

247 We analyzed whole-metagenome sequencing data from 163 longitudinally colle

248 ata measured for each species separately and metagenome sequencing data revealing adaptive mutations

249 les can be assigned, are found in genome and metagenome sequencing data.

250 The resulting metagenome sequencing datasets were analyzed with both g

251 We applied MetaMarker on whole-metagenome sequencing of colorectal cancer (CRC) stool s

252 Advances in metagenome sequencing of the human microbiome have provi

253 by exploring the rich sequence data from the metagenome sequencing projects.

254 Although whole metagenome sequencing promises enough raw data to study

255 iscovering metagenomic biomarkers from whole-metagenome sequencing samples.

256 occaceae and Veillonellaceae species undergo metagenome sequencing, and four representative species a

257 Using high-throughput amplicon and metagenome sequencing, combined with X-ray computed tomo

258 We term this approach leaderboard metagenome sequencing.

259 genome sequences were obtained using shotgun metagenome sequencing.

260 of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream appl

261 y, and improves read error correction in the metagenome setting.

262 tential has been under-explored. Using whole-metagenome shotgun sequencing data in 1,004 twins, we fi

263 By analyzing 16S rRNA and whole metagenome shotgun sequencing data in tandem with cultur

264 mics data, including both 16S rRNA and whole-metagenome shotgun sequencing data, enhanced our abiliti

265 Whole metagenome shotgun sequencing is a powerful approach for

266 manually curated datasets from 16S and whole metagenome shotgun sequencing.

267 Pooled analysis of raw metagenomes showed that the choline trimethylamine-lyase

268 Using metagenomes simulated from a database of experimentally

269 and HMMER searches of additional genomes and metagenomes spanning a range of environments returned 26

270 ted to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe.

271 sed binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconst

272 production of secondary bile acids from CRC metagenomes, suggesting a metabolic link between cancer-

273 film and virulence pathways in the microbial metagenome that are linked to clinical healing outcomes.

274 ten DNA fragments from human oral and fecal metagenomes that inhibit Streptococcus pyogenes Cas9 (Sp

275 reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiom

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

277 r long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,0

278 profiles were then used to scan genomes and metagenomes to identify a large number of formerly unkno

279 We used public metagenomes to investigate one adaptive mutation common

280 We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45

281 newly sequenced datasets and the Tara Oceans metagenomes to study the diversity of biofilm-forming ma

282 genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial resident

283 Genomes extracted from metagenomes using homology and compositional approaches

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

285 less GCs, previously recovered from the oral metagenome, was verified by cloning them upstream of a g

286 ng a uniquely broad global dataset of 13 483 metagenomes, we analysed the microbiome structure and fu

287 Using publicly available metagenomes, we evaluated library size selection, paired

288 ss-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the

289 ible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants

290 Using genuine and mock SCG metagenomes, we show that our approach corrects for vari

291 of 483.38 million reads generated from both metagenomes were analyzed through PathoScope (PS) and MG

292 The surface snow metagenomes were characterized by the occurrence of gene

293 Paired patient-inhaler metagenomes were compared (n = 31) to assess for the pre

294 Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RA

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

296 However, the high complexity of soil metagenomes, which can contain thousands of bacterial sp

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

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

299 ms used either simulated metagenomes or real metagenomes with unknown genome compositions.

300 n the body-wide human microbiome using 2,355 metagenomes, yielding functional and taxonomic profiles