ライフサイエンスコーパス: virome

1 ify up to 90% of reads in viral metagenomes (viromes).

2 erating viral metagenome sequence libraries (viromes).

3 unprecedented opportunity to study the human virome.

4 y understood members of the human-associated virome.

5 the emergence and evolution of the archaeal virome.

6 ss-sectional studies, changes in the enteric virome.

7 ylogenomic analyses, as applied to the plant virome.

8 hould incorporate examination of the enteric virome.

9 to infect humans or to be part of the human virome.

10 longitudinal quasispecies complexity of the virome.

11 otypes' among this fraction of the human gut virome.

12 into the effects of immune modulation on the virome.

13 of ultrafilters, are part of the human blood virome.

14 ed with significant expansion of the enteric virome.

15 and functional potential of the Indian Ocean virome.

16 l of SIV-associated expansion of the enteric virome.

17 , the picorna-like viruses, dominate the RNA virome.

18 and how we vaccinate to limit or control our virome.

19 ittle-recognized part of our metagenome: our virome.

20 s that comprise a major portion of the human virome.

21 ponent remained dissimilar from the maternal virome.

22 July 2022 and July 2023 to investigate their virome.

23 nes, we attempt a reconstruction of the LUCA virome.

24 ences, including IMG/VR and the Global Ocean Virome.

25 entially ancient component of the eukaryotic virome.

26 A viruses are a major component of the earth virome.

27 role of the microbiome in patterning for the virome.

28 he power of metagenomics to define the human virome.

29 is an integral part of the normal human gut virome.

30 , and diet on the shape of the adult gut DNA virome.

31 dentify 7-38% of 'unknown' sequence space in viromes.

32 the first time to our knowledge within ssDNA viromes.

33 art due to the lack of investigation of tick viromes.

34 ing was performed to characterize intestinal viromes.

35 nd phage sequences dominated the anoxic core viromes.

36 to sequences present in other environmental viromes.

37 all viromic reads annotated in the analysed viromes.

38 onments and microbiomes diverge, so do their viromes.

39 d the richer the microbiomes, the richer the viromes.

40 that is, how many virus species in the earth virome?

41 comprising up to 90% of sequences in the gut virome (4) .

42 mammals is defined in part by our coevolved virome, a concept with profound implications for underst

43 Here, we present viRome, a package for R that takes aligned sequence data

44 e contains a complex microbiome, including a virome about which little is known.

45 al an inverse association between eukaryotic virome abundance and poliovirus shedding.

46 This approach to analyzing whole virome across cohorts highlights significant IBD signals

47 derived cyanophages genes in metagenomes and viromes along depth profiles from the Eastern Tropical N

48 However, most virome analyses have been performed on a limited fractio

49 Comprehensive virome analysis of RNA sequence (RNA-seq) data sets from

50 Using whole-virome analysis on a published keystone inflammatory bow

51 overview of the composition of the human gut virome and associate virome structure with diet.

52 Comprehensive untargeted virome and bacterial analyses of pretreatment bone marro

53 We characterized the enteric virome and bacterial microbiome in a cohort of Ugandan p

54 Here, we characterized the gut virome and bacterial microbiome in a longitudinal cohort

55 The virome and bacterial microbiome were more similar betwee

56 s associated with alterations in the enteric virome and bacterial microbiome, which may contribute to

57 dditional microbial symbionts, including the virome and endogenous retroelements.

58 aviromes have revealed the complexity of the virome and facilitated discovery of new viruses, our und

59 We observe IBD-specific changes to the virome and increased numbers of temperate phage sequence

60 sition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these micr

61 From birth to 2 years of age, the eukaryotic virome and the bacterial microbiome expanded, but this w

62 namic but metastable equilibrium between the virome and the host can be dangerous, benign, or even sy

63 proach for studying interactions between the virome and the immune system.

64 Nonbacterial organisms, particularly the virome and the mycobiome, are important regulators of in

65 are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired

66 obiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory

67 spite remarkable interpersonal variations in viromes and their encoded functions, intrapersonal diver

68 fferences in the temporal scales captured by viromes and total DNA.

69 the viral taxonomic composition in simulated viromes and viral metagenomes from different benthic dee

70 n 'virobiota' and its associated genes (the 'virome'), and have fostered the emerging field of host-v

71 nded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data se

72 nomes and virioplankton shotgun metagenomes (viromes), and estimated to occur within >90% of the dsDN

73 ological dark matter extant in the human gut virome, and bring to light a population of potentially g

74 health and disease states of the respiratory virome, and drive a paradigm shift in how the practicing

75 Microbiome, virome, and proteome profiles of donors and patients wer

76 yotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core v

77 In contrast, viromes are unique to individuals regardless of their de

78 tly healthy cotwins in discordant pairs have viromes associated with, although not necessarily mediat

79 e component evolved to resemble the maternal virome, but by age 3, the human-host component remained

80 Our study demonstrates that elements of the virome can protect against enteric pathogens in an immun

81 Metagenomic study of mammalian viromes can help trace paths of viral transmissions with

82 We used Virome Capture Sequencing for Vertbrate Viruses (VirCapS

83 In this study, next-generation virome capture sequencing of primary and metastatic tumo

84 Here we performed comprehensive virome-capture sequencing to examine all known vertebrat

85 JCPyV polyomavirus, a member of the human virome, causes progressive multifocal leukoencephalopath

86 ics may be a more comprehensive approach for virome characterization than either method alone.

87 and four wild populations were processed for virome characterization using both approaches.

88 and preclude a deeper understanding of human virome community dynamics.

89 rvention was associated with a change in the virome community to a new state, in which individuals on

90 ome-discordant twins display more dissimilar viromes compared to microbiome-concordant twins, and the

91 ETSP virome comparison with surface marine viromes (Sargasso

92 cocktail approach to specifically reduce the virome component of the intestinal microbiota.

93 Cervicovaginal virome composition changes over time, particularly in no

94 rthermore, incorporating both bacteriome and virome composition offered greater classification power

95 Among IBD subjects, the changes in virome composition reflected alterations in bacterial co

96 ontraction of and shift in the bacteriophage virome composition.

97 at a systemic level reflect the upper airway virome composition.

98 We observe marked virome compositional dynamics at the onset of the therap

99 ess is known about the viral microbiome (or 'virome'), consisting of bacteriophages and eukaryotic RN

100 ely, our results show that the honey bee gut virome consists of a complex and diverse phage community

101 The virome contains the most abundant and fastest mutating g

102 Here we report a data set of 27,346 marine virome contigs that includes 44 complete genomes.

103 However, whether the enteric virome contributes to this infection and resulting immun

104 ence in cancers and provides highly relevant virome data for future reference.

105 es (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled vir

106 Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or micro

107 We assembled a human virome database (HuVirDB), encompassing 1,831 samples en

108 ication to 32 viromes from the Pacific Ocean Virome dataset identified clusters of samples broadly de

109 ablish an ~12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now includi

110 ons, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, dou

111 imprint generated by these responses to our virome defines the normal immune system.

112 Viromes derived from virus-like particles are unique to

113 the most prevalent viruses within the human virome, detected in >90% of healthy individuals.

114 As a proof of concept, we demonstrate that viromes discovered in plant metagenomes can be a valuabl

115 mine the relationship between microbiome and virome diversity in 21 adult monozygotic twin pairs sele

116 gree to which the microbiome drives the vast virome diversity is unclear.

117 Our data reveal a virome dominated by papillomaviruses, anelloviruses, her

118 retained over the period surveyed, and with viromes dominated by a few temperate phages that exhibit

119 nderstanding of the bacterial microbiome and virome during early development, conditions that might i

120 -generation sequencing to define the enteric virome during SIV infection in nonhuman primates.

121 rogated the bronchoalveolar lavage and blood viromes during the peritransplant period and 6-16 months

122 y bowel diseases or solid-organ transplants, virome dynamics in allogeneic hematopoietic stem cell tr

123 Overall gut virome ecology and concurrent viral infections may impac

124 inhabiting the intestine termed "the enteric virome." Enteric viruses have intimate functional and ge

125 responses caused by viruses within the human virome, especially at a population scale, remains limite

126 abase, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycli

127 relevance of JCPyV infection and the donor's virome for transplant outcomes.

128 he importance of metagenomic analysis of the virome for understanding AIDS pathogenesis.

129 tools (BLAST, MG-RAST, NBC, VMGAP, MetaVir, VIROME) for analysing the viral taxonomic composition in

130 Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-

131 Here we defined the intestinal virome from birth to the development of autoimmunity in

132 ies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute d

133 Here, we investigate viromes from human subjects on a controlled feeding regi

134 In a study of fecal viromes from patients with NAFLD and control individuals

135 Application to 32 viromes from the Pacific Ocean Virome dataset identified

136 on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-p

137 ConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonom

138 le-virus vSAG 37-F6 and several Global Ocean Viromes (GOV) viral populations, are now further confirm

139 y 500 genotypes estimated in individual WWTP viromes, > 82% were shared.

140 panding, only a tiny fraction of the Earth's virome has been sequenced so far.

141 Within twin pairs, viromes have been shown to be similar for infants, but n

142 Co-evolution may lead to virome host-specificity.

143 ibody efficacy was diminished for stationary-virome HVR1 variants.

144 Overall, the RNA virome identified here provides not only significant ins

145 Here, we report the tomato virome identified through sequencing small RNAs of 170 f

146 ead targeted hypervariation in the human gut virome, identify previously undescribed types of genes t

147 The presence of a highly complex virome implies the substantial genomic and pan-genomic c

148 Here we characterize the longitudinal gut virome in 44 recipients of HSCT using metagenomics.

149 sequencing (mNGS) to characterize the human virome in 492 clinical samples (384 sera, 92 pooled nasa

150 c viral infections and the developing infant virome in affecting immune responses to the oral poliovi

151 metagenomic approach, we surveyed the fecal virome in California sea lions of different ages and hea

152 Here, we report the landscape of the tomato virome in China, the leading country in tomato productio

153 sity, and changing nature of the respiratory virome in health and disease.

154 cognized as the major component of the blood virome in healthy humans.

155 eal an under-appreciated role of the enteric virome in HIV-associated gastroenteritis and pathogenesi

156 investigating the biological role of the gut virome in human physiology, and the importance of our vi

157 ed light on the composition of the human gut virome in IBD beyond this identifiable minority.

158 Our results demonstrate a complex urinary virome in kidney transplant patients with multiple virus

159 omprehensive and systematic screening of RNA virome in medically important mites including house dust

160 However, the effects of the virome in modulating enteric infections remain unexplore

161 A comprehensive understanding of the virome in mosquito vectors is crucial for assessing the

162 f the composition and diversity of the human virome in physiologically healthy individuals.

163 essants strongly affect the structure of the virome in plasma.

164 We describe here the metagenomics-derived virome in the feces of 24 healthy and 12 diarrheic pigle

165 Less is known about the virome in these diseases.

166 human virome, the current literature on the virome in transplant recipients, and near-future applica

167 In this report, we describe HVR1 viromes in chronically infected patients that are define

168 ng the role of these populations (the human "virome") in health and disease requires a much deeper un

169 n about the effects of the viral microbiome (virome) in patients with ALD.

170 nvestigated changes in the viral microbiome (virome) in patients with NAFLD.

171 osition of the diverse community of viruses (virome) in the human gut.

172 ersity and composition of viral communities (viromes) in ballast and harbor waters using metagenomics

173 Exploring the human respiratory virome, in particular, can provide insights into oro-res

174 The mammalian virome includes diverse commensal and pathogenic viruses

175 ls (>60 yr), centenarians had a more diverse virome including previously undescribed viral genera, su

176 ) and richness (p = 0.013) of the eukaryotic virome increased with age and were higher than seen in a

177 The analyses of simulated viromes indicate that all the BLAST tools, followed by M

178 cell-free DNA in plasma to investigate drug-virome interactions in a cohort of organ transplant reci

179 Virome interactions with the host cannot be encompassed

180 We conclude that the virome is a candidate for contributing to, or being a bi

181 thereby giving rise to the concept that the virome is a component of the microbiome.

182 We show that the enteric virome is abnormal in CD and UC patients.

183 Our results show that the honey bee gut virome is composed of at least 118 distinct clusters cor

184 The mammalian virome is constituted of viruses that infect host cells,

185 The virome is dominated by rare genes, many of which might b

186 The gene composition of the marine DNA virome is dramatically different from that of known bact

187 The virome is increasingly recognized as a key part of indiv

188 The global virome is largely uncharacterized but is now being unvei

189 it is a known vector for CCHFV, its general virome is largely unexplored.

190 The virome is mucosal and systemic; it can alter the host re

191 The virome is one of the most variable components of the hum

192 Moreover, it is becoming clear that the virome is part of a dynamic network of microorganisms th

193 recent evidence suggests that the human gut virome is remarkably stable compared with that of other

194 The study of the human virome is still in its infancy, especially with regard t

195 ew viruses, our understanding of the enteric virome is still incomplete.

196 The human gut virome is thought to significantly impact the microbiome

197 However, the role of the enteric virome is understudied relative to the fast-paced resear

198 acterial microbiome in human health, but the virome is understudied.

199 irus infection, a component of the mammalian virome, is regulated by the counterpoised actions of mul

200 the viral component of the microbiome, the "virome," is less advanced.

201 yrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed t

202 rimetric microtiter plate (MTP) systems from ViroMed Laboratories, Inc. (PrimeCapture), CPG, Inc. (Qu

203 scribe the extent and nature of the mosquito virome, little is known about how these viruses persist,

204 data support a model in which changes in the virome may contribute to intestinal inflammation and bac

205 bowel disease and speculate that the enteric virome may play a role in other diseases.

206 ntibodies (enrichment z scores) to the human virome measured using VirScan (phage-displayed immunopre

207 e presence of viruses in blood suggests that virome members can traverse mucosal barriers, as indeed

208 vidual and rapid evolution of some long-term virome members.

209 Here we report sequencing of the viromes (metagenomes) of virus-like particles isolated f

210 To understand the soil virome, much work remains.

211 nts of the gut microbiome, including the gut virome, mycobiome, archaeome, and parasitome, is increas

212 hput sequencing was used to characterize the virome of 638 ticks, including Rhipicephalus microplus (

213 pite their huge impact on public health, the virome of mites remains unknown.

214 ffects of azithromycin on the nasopharyngeal virome of Nigerien children who had received multiple ro

215 To assess the virome of North American bats, we collected fecal, oral,

216 To explore the plasma virome of persons who inject drugs and to characterize t

217 ted sample when we initiated a survey of the virome of Siberian permafrost.

218 present preliminary characterization of the virome of three common North American bat species, inclu

219 Here, we compared the plasma virome of West African green monkeys to that in their de

220 The bacterial microbiome, mycobiome, and virome of wildlings affect the immune landscape of multi

221 ing, we characterized and compared the fecal viromes of captive and wild devils.

222 Intestinal viromes of case subjects were less diverse than those of

223 The viromes of CD and UC patients were disease and cohort sp

224 To characterize the viromes of five widely dispersed plant-pathogenic fungi,

225 We compared the plasma viromes of HIV-infected subjects with low versus high CD

226 y, we characterized six novel viruses in the viromes of laboratory fruit flies and wild populations o

227 natural freshwater systems but distant from viromes of marine and human designed/managed freshwater

228 erence between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting subs

229 Great Lakes viromes were closely related to viromes of other cold natural freshwater systems but dis

230 gh-throughput sequencing to characterize the viromes of these tick species and identified the presenc

231 In this study, we examined the viromes of three tick species from the United States.

232 Compared with gut viromes of younger adults (>18 yr) and older individuals

233 wever, the large viral population diversity (virome) of bats has been partially determined for only a

234 s-related pathology; thus, the impact of the virome on health and disease may be even more relevant i

235 Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between sur

236 and observed that changes in the intestinal virome over time differed between cases and controls.

237 dicate that the gut bacterial microbiome and virome play an important role in healthy infant developm

238 The human virome plays important roles in health and immunity.

239 Thus, changes in the intestinal virome preceded autoimmunity in this cohort.

240 Bacterial phylogeny and virome profile analyses of fecal samples from recipients

241 In this study we investigated the urine virome profile of BKV+ and BKV- kidney transplant recipi

242 Metagenomic DNA was purified, and the virome profile was analyzed using metagenomic shotgun se

243 ot correlate with specific viral families or virome profile; however, low antiviral responders had mo

244 ers had more Prokaryotic and less Eukaryotic virome profiles.

245 , they generate compelling evidence that the virome provides protection from gut inflammatory conditi

246 R sequences and compared them with 2 588 172 virome reads in the saliva of four human subjects over 1

247 GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from techni

248 Comparisons of viromes revealed a striking difference between the two m

249 of the viral populations in any global ocean virome sample.

250 The largest source of variance among virome samples was interpersonal variation.

251 ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Che

252 nmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a similar efficiency of sequence annotatio

253 An analysis of 24 coral reef viromes showed a relative increase in the abundance of h

254 Our study describes an intestinal virome signature associated with AH.

255 Species-specific recruitment patterns and virome simulation data suggest that vSAGs are highly mic

256 mber of prokaryote species with those of the virome size, we obtain back-of-the-envelope estimates of

257 ent and offer a potential application of the virome state to predict immunocompetence.

258 The core virome structure included herpesviruses, papillomaviruse

259 sition of the human gut virome and associate virome structure with diet.

260 t the majority of sequence data in a typical virome study remain unidentified, highlighting the exten

261 ies, the signal was dampened relative to the viromes, suggesting differences in local assembly driver

262 le component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism.

263 When analysing the environmental viromes, tBLASTx, MetaVir, VMGAP and VIROME showed a sim

264 reconstruction suggests a remarkably complex virome that already included the main groups of extant v

265 The results reveal a vast RNA virome that includes many previously unknown groups.

266 Land plants host a vast and diverse virome that is dominated by RNA viruses, with major addi

267 The Chinese tomato virome that we developed provides valuable information t

268 chnical considerations in studying the human virome, the current literature on the virome in transpla

269 is initial characterization of the bat guano virome, the first metagenomic analysis of viruses in wil

270 ight into the relationship between the human virome, the state of the immune system, and the effects

271 ired respiratory viruses and the respiratory virome to better understand the dynamics in acute infect

272 e signature (VES) based on a synthetic human virome to capture the history of virus exposure that is

273 enders analysis of human viral communities ("viromes") to be highly complex.

274 we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriom

275 view of our current understanding of how the virome, together with other components of the microbiome

276 the behavior of full viral populations (the "virome") understudied.

277 were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison.

278 D case-control study using a synthetic human virome, VirScan.

279 expansion and diversification of the enteric virome was secondary to changes in bacterial populations

280 robial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a r

281 te the origin and evolution of the human gut virome, we analyzed the viral community of one adult ind

282 In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot s

283 act of this population bottleneck on the AGM virome, we used metagenomics to compare the viral nuclei

284 Specific components of the virome were both directly and inversely associated with

285 t among the Great Lakes, and the Great Lakes viromes were closely related to viromes of other cold na

286 notation-independent comparisons showed that viromes were distinct among the Great Lakes, and the Gre

287 It followed that stationary viromes were dominated by a single HVR1 variant surround

288 versity between the two genera, although the viromes were very similar among the three Culex species

289 e recombination events highlighted a dynamic virome where subpopulations of variants are in competiti

290 irus that is found in about 50% of human gut viromes where it can comprise up to 90% of the virus seq

291 levels 4.2-fold higher than other published viromes, while carbohydrate and amino acids metabolisms

292 hem were sufficient for parallel or accurate virome-wide detection.

293 sed strategies and directions for developing virome-wide integration detection.

294 cally investigate the strategy and method of virome-wide screening of clonal integrations to identify

295 gy to address these challenges by performing virome-wide screening of early-stage clonal viral integr

296 rmation and global architecture of the plant virome will be of broad interest to plant biologists and

297 cterial populations showed covaration of the virome with the larger microbiome.

298 ies against viruses, using a synthetic human virome, with minimal serum and cost.

299 to characterize and compare the complete RNA virome within mites that are relevant to human health an

300 persistence of a small portion of the global virome within the gut of each individual and rapid evolu