ライフサイエンスコーパス: taxonomic

1 in-specific markers instead of species-level taxonomic abundance.

2 A k-mer based method provides greater taxonomic accuracy than other classifiers and a three or

3 erite covered Cambrian organism of uncertain taxonomic affinity, seemingly representing an intermedia

4 At coarse levels of taxonomic aggregation, phytoplankton and zooplankton com

5 when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified b

6 Taxonomic analysis suggests that these freshwater viroph

7 labor-intensive approaches that are prone to taxonomic and enumeration mistakes.

8 P-use efficiency, which were related to both taxonomic and environmental variability.

9 g steps, such as protein grouping as well as taxonomic and functional annotation.

10 ndance information, we elucidate patterns of taxonomic and functional change that characterize the co

11 gun metagenomics approach to investigate the taxonomic and functional changes of the bacterial commun

12 Taxonomic and functional changes to the composition of t

13 and computational framework that integrates taxonomic and functional comparative analyses to accurat

14 anding on how protist predation modifies the taxonomic and functional composition of bacterial commun

15 changes in environmental conditions, and how taxonomic and functional diversity mediate these changes

16 g the effects of anthropogenic inputs on the taxonomic and functional diversity of bacterioplankton c

17 revealed that average fruit size tracks the taxonomic and functional diversity of frugivorous birds

18 er Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metageno

19 mputational analysis are used to compare the taxonomic and functional profiles of microbial communiti

20 of the human microbiome have identified both taxonomic and functional shifts that are associated with

21 Our results demonstrate that plant taxonomic and functional turnover are decoupled, which m

22 hensively within pathosystems, expanding the taxonomic and genetic breadth of the systems studied, ev

23 that are similar to focal data, in terms of taxonomic and genetic sampling, and uses them to inform

24 tion in 163 vervet monkeys from across their taxonomic and geographic ranges.

25 nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defi

26 accordance with metabolic theory of ecology, taxonomic and phylogenetic diversity of soil bacteria, f

27 f barcoded fungal species in light of modern taxonomic and phylogenetic studies.

28 we show that resveratrol ingestion produces taxonomic and predicted functional changes in the gut mi

29 nd empirical advances often failing to cross taxonomic and sensory divides.

30 for testing hypotheses at broad geographic, taxonomic, and temporal scales.

31 Taxonomic annotation of these reads, including phylogeny

32 The integrative taxonomic approach has helped deliver significant advanc

33 en bypass the cost and time-demanding morpho-taxonomic approaches in future biomonitoring.

34 orld, revealed stark differences in terms of taxonomic as well as functional microbial community stru

35 line information to better facilitate proper taxonomic assignment and minimize erroneous identificati

36 ls for benthic monitoring, regardless of the taxonomic assignment of eDNA sequences.

37 put sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operation

38 the contribution of each database hit to the taxonomic assignment of the query sequence is weighted b

39 High-resolution bioinformatics enabled taxonomic assignment to the species and subspecies level

40 Here we compare how three common fungal OTU taxonomic assignment tools (RDP Classifier, UTAX, and SI

41 criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency

42 fossils and validate their morphology-based taxonomic assignments.

43 To assess whether the geographic and taxonomic biases of data could undermine effectiveness o

44 ect to recorder contribution and spatial and taxonomic biases, i.e. when, where and what volunteers r

45 This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the prim

46 Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are o

47 The geographic, temporal and taxonomic breadth of sampling in this study allows for a

48 ing the typical distribution of items within taxonomic categories is an important question with appli

49 The model also predicts the number of taxonomic categories that remain unrepresented in a fini

50 darians were bioluminescent, and 9 of the 13 taxonomic categories were found to be bioluminescent dom

51 m the images), distributed within 13 broader taxonomic categories.

52 ere similar (P = .73) across all genus-level taxonomic categories.

53 multaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community

54 In anticipation of subsequent taxonomic changes being compiled by the Journal of Clini

55 icle summarizes the most recent (since 2012) taxonomic changes in the genus Mycobacterium Only those

56 We first propose six taxonomic changes that raise the generic species total t

57 otations can be retrieved individually or by taxonomic clade.

58 he global distribution of IS families across taxonomic clades in Archaea and Bacteria.

59 tion of alien species richness for an entire taxonomic class.

60 e and geographic location of the samples, or taxonomic classification according to hallmark viral gen

61 k-SLAM's speed allows a full taxonomic classification and gene identification to be t

62 e extraction that permits accurate automated taxonomic classification and quantitative data about org

63 ce scores to evaluate the reliability of our taxonomic classification assignments based on multiple d

64 Furthermore, our method can be applied for taxonomic classification of any phylogenetic marker gene

65 rature, less attention has been given to the taxonomic classification of these sequences, upon which

66 for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequenc

67 Genus-level taxonomic classification was correctly done for only 50.

68 operational taxonomic unit (OTU) generation, taxonomic classification, alpha- and beta-diversity meas

69 an have a dramatic effect on the accuracy of taxonomic classification, and alpha- and beta-diversity

70 Without taxonomic classification, functional and biological info

71 ss-kingdom analysis, the vast differences in taxonomic classification, genome size, and radioresistan

72 terature and common understanding of current taxonomic classification, which we attempt to do here in

73 rly the need to standardize nomenclature and taxonomic classification, while incorporating new allele

74 sults showed strong clustering that reflects taxonomic classification.

75 and variant calling in addition to accurate taxonomic classification.

76 do not convey the hierarchical structure of taxonomic classifications and are limited by the use of

77 Taxonomic classifications are assigned from the species

78 ensus TAXonomy), a Python tool that compares taxonomic classifications of the three programs and merg

79 n parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifier

80 ly tephritid taxonomists, but also the wider taxonomic community.

81 ll in turn pave the way for replicated cross-taxonomic comparisons with the primate lineage, enabling

82 ge assumed a different and fairly persistent taxonomic composition and functional structure.

83 We thus sought to determine the taxonomic composition and potential metabolic function o

84 ecline in microbiota richness and a shift in taxonomic composition driven by a reduction in the relat

85 prehistoric pottery with faunal analyses of taxonomic composition from the earliest farming sites in

86 AP, MetaVir, VIROME) for analysing the viral taxonomic composition in simulated viromes and viral met

87 We profiled the taxonomic composition of 2,179 vaginal swabs collected p

88 In this study, we explored the taxonomic composition of bacterial and fungal communitie

89 rds this end, we characterized the bacterial taxonomic composition of fecal samples from participants

90 interaction both through alterations in the taxonomic composition of gut microbial communities as we

91 , we could not identify major drivers of the taxonomic composition of the N functional groups.

92 e that azithromycin alters the diversity and taxonomic composition of the salivary microbiome; howeve

93 large number of studies to characterize the taxonomic composition of the skin microbiome at various

94 Identifying the taxonomic composition of viruses is crucial for understa

95 The nematode community taxonomic composition was similar in the WM, GM and MDM

96 cesses are responsible for driving arthropod taxonomic composition while environmental filtering is t

97 variation in functional composition but not taxonomic composition.

98 The bacterial taxonomic compositions are distinct from those of other

99 Bacterial taxonomic compositions in the first 26 weeks of life wer

100 Taxonomic compositions, phylogenetic diversity, and comm

101 -level classification of the group, and some taxonomic confusion persists as a result.

102 +/- 3.16% percent error through classifying taxonomic data at the family versus class level.

103 t production was successfully predicted from taxonomic data.

104 or extracting measurement values from spider taxonomic descriptions and are more effective when the d

105 Taxonomic details of diversity are an essential scaffold

106 populations with low genomic diversity, with taxonomic differences in patterns of genomic variation b

107 The taxonomic dissimilarity of the communities was significa

108 nd demographic history, often reflecting the taxonomic distinctness of lineages spanning it.

109 e encodes a putative effector with a limited taxonomic distribution among plant pathogenic fungi.

110 From Recent data, given the taxonomic distribution of a marsupium of four pairs of o

111 study was conducted, including evaluation of taxonomic distribution, phylogenetic inferences and micr

112 n microbes accounts for expansins' irregular taxonomic distribution.

113 hin and between taxa and clear evidence that taxonomic divergence was reticulate rather than followin

114 an interval of conspicuous morphological and taxonomic diversification among ray-fins centred on the

115 While taxonomic diversity (TD) is the most commonly assessed a

116 ated that the cuckoo can predict hotspots of taxonomic diversity and functional diversity of bird com

117 evolution of life through not only reducing taxonomic diversity but also reshaping ecosystems and bi

118 ework in which to understand how patterns of taxonomic diversity in hominins may have developed.

119 le bioinformatic tools for investigating the taxonomic diversity of viruses in benthic ecosystems in

120 ver, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood,

121 traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity.

122 he treatments had little effect on microbial taxonomic diversity, but were found to decrease function

123 plant clade/taxonomic diversity to microbial taxonomic diversity.

124 ve mostly been studied independently and the taxonomic drivers of functional imbalances have not been

125 Our study provides an in-depth taxonomic evaluation of micro-eukaryotic diversity, and

126 We provide cross-taxonomic evidence that changes in the autocorrelation o

127 tinction, which dominated in the Ordovician, taxonomic evolutionary rates were relatively low and the

128 tion in the hands of researchers with little taxonomic experience.

129 ations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight again

130 o-invertebrates, which is time-consuming and taxonomic-expertise demanding.

131 ed matrix level of contamination, genus, and taxonomic family.

132 ght how stable or even increasing metrics of taxonomic, functional, or phylogenetic diversity may occ

133 nce of individuals in addition to metrics of taxonomic, functional, or phylogenetic diversity, thus c

134 as well as antibiotics resistance genes, and taxonomic gene markers for pathogens.

135 Moreover, we contend that the lack of taxonomic granularity and use of vague generic names in

136 ented rates of 14-55 km/decade, depending on taxonomic group and scenario.

137 at many important axes of variation within a taxonomic group may be unique and not generalizable to o

138 Based on morphology and the taxonomic group to which the specimens belong, the autho

139 nomic analysis showed that the most abundant taxonomic group was distantly related to Thermodesulfovi

140 variant viruses may behave similarly in this taxonomic group whereby many waterfowl species are susce

141 tion in neuron distributions in this diverse taxonomic group.

142 se to algal pigment levels, depending on the taxonomic group.

143 in understudied terrestrial systems, guilds, taxonomic groups and top-down controls (e.g. pathogens),

144 mbined with areas of high priority for other taxonomic groups and with social, economic, and politica

145 escent and non-bioluminescent animals within taxonomic groups changes with depth for Ctenophora, Scyp

146 Cluster analyses revealed that most taxonomic groups could be discriminated based on somatod

147 evident variations in abundance for several taxonomic groups in OLP.

148 adapted to the presence or absence of whole taxonomic groups in their local microbial community, but

149 e size and a more balanced representation of taxonomic groups might improve efficiency for simple tra

150 s across 56 wildlife species and three broad taxonomic groups of parasites to identify host-level tra

151 enes is widespread and is found in all major taxonomic groups of Viridiplantae investigated.

152 iversity varies greatly across the different taxonomic groups that comprise the Tree of Life (ToL).

153 best practices and enables the detection of taxonomic groups that often go undetected with existing

154 results underscore the need to sample across taxonomic groups to understand evolutionary patterns of

155 nally, the sequence read number of different taxonomic groups using metabarcoding was positively corr

156 For all taxonomic groups, the increase in numbers of alien speci

157 cross disparate regions, fishing fleets, and taxonomic groups.

158 mine their conservation across data sets and taxonomic groups.

159 ted idiosyncratic geometry across and within taxonomic groups.

160 equency matrices for multiple species in six taxonomic groups.

161 st array of species across most, if not all, taxonomic groups.

162 mely large differences in sensitivity across taxonomic groups.

163 any training datasets specific for different taxonomic groups.

164 he understanding of the genetic potential of taxonomic groups.

165 tus of understanding of the general biology, taxonomic history, diversity, geographical patterns, hos

166 The genus has a complicated taxonomic history; this is especially true for Nocardia

167 nce instead of Euclidean distance for better taxonomic identification during initialization.

168 of the site is unclear owing to unsupported taxonomic identification of these fossils and uncertaint

169 nd/or excavation strategies and questionable taxonomic identifications.

170 d the utility of DNA barcoding to verify the taxonomic identity of fungi found commonly in the food a

171 he range (trailing, leading or centroid) and taxonomic identity of species.

172 However, the taxonomic identity of these early anoxygenic phototrophs

173 ectomycorrhizal fungi, and yeasts) based on taxonomic identity.

174 The method does not require prior taxonomic information and integrates variation in plant

175 lish species limits, and rapidly disseminate taxonomic information prior to completion of formal taxo

176 ssive zero observations; and it incorporates taxonomic information.

177 The fundamental reason for different taxonomic interpretations is that they are based upon di

178 tent traps and were identified with standard taxonomic keys.

179 he strength of competition within and across taxonomic kingdoms.

180 ies, genera or families, at the most precise taxonomic level defined from the images), distributed wi

181 n the relative contribution of function at a taxonomic level.

182 izing the viral sequences into quasi-species taxonomic-level groups ( approximately 10 min).

183 ification of 15 bacterial species at various taxonomic levels achieving 90-100% accuracy, and 9 cance

184 axonomy, and reads are typically assigned to taxonomic levels where they are unambiguous.

185 en the two groups at both family and species taxonomic levels.

186 ing cetacean microbiomes, even at fine-scale taxonomic levels.

187 showed strong similarities across the higher taxonomic levels.

188 omplete lineage sorting obscure well-defined taxonomic lineages.

189 The scope of lipids as taxonomic markers in microbial ecological studies is lim

190 tions over time, but with spatially distinct taxonomic, metabolic potential, and gene transcription p

191 obial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which va

192 Various strategies can ameliorate taxonomic misclassification, including abundance filteri

193 firm hidden cryptic diversity under a single taxonomic name.

194 oteome scale can normalize against potential taxonomic nomenclature anomalies.

195 scribing soil microbial communities at broad taxonomic or phylogenetic levels of resolution.

196 novel activities toward insects from distant taxonomic Orders and establish this technology based on

197 l mammals, including 4,018 species across 26 taxonomic Orders.

198 to find variants and genes along with their taxonomic origins enables novel strains to be characteri

199 across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and (ii) determine t

200 much finer levels of structural detail, but taxonomic placement is uncertain because plumage is rare

201 bed from the west coast of Sweden, but their taxonomic placement remains unstable.

202 tive removal/true positive ranking, chemical taxonomic prediction and differential evolution based gl

203 Methods for assembly, taxonomic profiling and binning are key to interpreting

204 Taxonomic profiling and binning programs were proficient

205 erational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analys

206 xpeditions, we validate its applicability to taxonomic profiling and ecosystem analyses, and discuss

207 t a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (

208 These PNA blockers will facilitate taxonomic profiling of the eukaryotic microbiota of the

209 Overall, the utility of metabarcoding for taxonomic profiling of zooplankton communities was valid

210 l community profiling and 16S sequencing for taxonomic profiling.

211 s did not differ significantly between major taxonomic radiations.

212 ommunities (per sample) differed most at the taxonomic rank approximating to order level.

213 ore that finds an objective cut-off for each taxonomic rank using information for the current classif

214 s the proportion of assigned OTUs at a given taxonomic rank, varied among the classifiers.

215 Our approach to identify taxonomic ranks enables taxonomists to revise and propos

216 Comparable taxonomic ranks within clades can facilitate more consis

217 and binning programs were proficient at high taxonomic ranks, with a notable performance decrease bel

218 Here we use a temporal approach to identify taxonomic ranks.

219 elies heavily on memorizing near-meaningless taxonomic ranks.

220 Our results allowed for the first taxonomic reconstruction of the complex viral metacommun

221 lar relatedness despite their high degree of taxonomic relatedness.

222 There has never been a better time for a taxonomic renaissance.

223 only effectively transferred the beneficial taxonomic repertoire to WT recipients, but also enabled

224 of fecal DNA demonstrated minimal shifts in taxonomic representation over the week due to predatory

225 clusters by keywords and explore their MSAs, taxonomic representation, and annotations.

226 opulations and, in time, will provide higher taxonomic resolution and more precise estimation of abun

227 molecular analysis to augment detection and taxonomic resolution of prey collected from stomach-cont

228 at defining plankton communities at a deeper taxonomic resolution than by functional groups and accou

229 rared microspectroscopy method offers better taxonomic resolution, as well as faster, more economical

230 ity of microbiome signatures at a meaningful taxonomic resolution.

231 al visits, though rarely correlated at lower taxonomic resolution.

232 within the Chlorella clade, suggesting that taxonomic revision is needed for one or both genera.

233 this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from hu

234 ic information prior to completion of formal taxonomic revisions.

235 environments; in contrast, they support high taxonomic richness and contribute significantly to regio

236 The taxonomic richness and Shannon index were comparable bet

237 s as terrestrial and lotic habitats (reduced taxonomic richness) in urban environments; in contrast,

238 greater than fivefold increase in bacterial taxonomic richness.

239 derstand these events, we need comprehensive taxonomic sampling as well as homology inference methods

240 nships using a 1,719-gene dataset with dense taxonomic sampling of non-bilaterian animals that was as

241 Analyses at finer taxonomic scales showed that different lepidopteran clad

242 hape correlates with flight ability on broad taxonomic scales, suggesting that adaptations for flight

243 and community ecology analyses at different taxonomic scales.

244 asets, we find that the major Middle Miocene taxonomic shift in primate diversity is characterized by

245 and typical nosZ transcripts and resulted in taxonomic shifts among the typical nosZ-expressing micro

246 Overall, opposing trends in taxonomic similarity among different subsets of species

247 We examined the extent to which taxonomic similarity, pathogen traits, contact opportuni

248 a function of time, whether exploring novel taxonomic space affords an advantage in terms of novel c

249 are assigned to 5306 consistent and accurate taxonomic species clusters based on previously establish

250 alyses and species descriptions according to taxonomic standards for Recent organisms.

251 regarding its phylogeographic structure and taxonomic status.

252 aining variants, raising questions about its taxonomic status.

253 iversity, as well as the microbial community taxonomic structure following each unit operation in a c

254 Our objective was to determine the taxonomic structure of the bacterial communities present

255 The taxonomic structure was maintained to the level of class

256 To investigate their taxonomic structure, binning assembled contigs into disc

257 taken root and have accelerated traditional taxonomic studies as well as distribution modeling and g

258 Across taxonomic subfamilies, variations in intelligence (G) ar

259 , a computational pipeline, which integrates taxonomic tree search and Dirichlet process clustering t

260 dependencies; (ii) localize lineages on the taxonomic tree that are associated with covariates (e.g.

261 environmental gradients, we find significant taxonomic turnover in both clusters.

262 work centred upon a Burkholderia operational taxonomic unit (OTU) and a reconfiguration to a summer s

263 significant effect on EM fungal operational taxonomic unit (OTU) diversity.

264 Here we evaluate the accuracy of operational taxonomic unit (OTU) generation, taxonomic classificatio

265 ents as measured by the observed operational taxonomic unit (OTU) richness (p=0.0012), Chao estimated

266 ated with decreased abundance of operational taxonomic unit 1341 (OTU1341; Prevotella) among individu

267 ty, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene seq

268 ively associated with a specific operational taxonomic unit from the genus Moraxella in children not

269 -Mann-Whitney test for comparing operational taxonomic unit-specific abundances between two samples (

270 ve abundances of fecal microbial operational taxonomic units (OTUs) and abdominal adiposity measures.

271 egion suggest little exchange of Operational Taxonomic Units (OTUs) between depths with the nematodes

272 it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling a

273 ) of 16S bacteria rRNA to define operational taxonomic units (OTUs) of the microbiome.

274 Several operational taxonomic units (OTUs) related to the Ruminococcaceae fa

275 is identified a higher number of Operational Taxonomic Units (OTUs) unique to FW compared to SW, with

276 Although succession of specific operational taxonomic units (OTUs) was unique to each animal, beta-d

277 on pool; instead, many bacterial operational taxonomic units (OTUs) were overrepresented or underrepr

278 lankton system comprised of 464 operational taxonomic units (OTUs) with at least 97% 18 S identity,

279 Based on operational taxonomic units (OTUs), bacterial diversity and composit

280 associations between DHA and 38 operational taxonomic units (OTUs), the strongest ones being with OT

281 relative abundances of bacterial operational taxonomic units (OTUs).

282 gnment of sequences belonging to operational taxonomic units (OTUs).

283 e identified 526 total bacterial operational taxonomic units (OTUs, 97% similarity), primarily from F

284 We found 12,890 operational taxonomic units (OTUs; 97% sequence identity level) incl

285 dominance of Haemophilus species operational taxonomic units (P = .01).

286 Sequences were clustered into operational taxonomic units and taxonomy assigned via the Human Oral

287 the abundance of 13.6% and 7.3% Operational Taxonomic Units in fecal microbial communities in health

288 tinal permeability and relative abundance of taxonomic units in the gut bacterial community.

289 Operational taxonomic units representing 94.5% of the average ANG ab

290 also non-autoregressive and that Operational Taxonomic Units strongly correlated with dietary variabl

291 libraries, four Pseudomonas sp. operational taxonomic units surprisingly accounted for approximately

292 ven by community changes in rare taxa, those taxonomic units that made up less than 0.31% of reads pe

293 Operational taxonomic units were pyrosequenced targeting 16S ribosom

294 Twenty-eight species-level operational taxonomic units were significantly different between the

295 robiota (overall composition and operational taxonomic units) and demographic variables, diet, consti

296 eaction), and specific microbial operational taxonomic units, as well as with lavage and peripheral b

297 t sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal

298 IBS, consisting of 90 bacterial operational taxonomic units.

299 ical feature selection, and discovery of new taxonomic variants.

300 Inter-continental and inter-taxonomic variation can be largely attributed to the dia