ライフサイエンスコーパス: taxonomic

1 limus-treated mouse model, with reduction in taxonomic abundance of butyrate-producing bacteria and d

2 and expands the known geographic extent and taxonomic affiliation of this metabolic pathway in the o

3 ribed and analyzed in order to interpret its taxonomic affinities and its potential significance on o

4 Although gene identities and taxonomic affinities in the developing ash-soils are to

5 Its taxonomic affinity is uncertain as it has a picornavirus

6 hrough sequence comparison, we clear up this taxonomic ambiguity in the invertebrate RNA virosphere.

7 Historical, geographic, and taxonomic analogies can help reduce this uncertainty by

8 Genomic and taxonomic analyses show that both sponges harbor a disti

9 In contrast, taxonomic analysis did not identify notable variability

10 Finer taxonomic analysis revealed that the most reproducible s

11 In response, taxonomic and Antarctic experts undertook a horizon scan

12 historic community structure, and increased taxonomic and climatic differentiation of the species in

13 ity and substrate architecture modulated the taxonomic and functional composition of gypsum endolithi

14 d important roles in promoting the bacterial taxonomic and functional compositional patterns in both

15 few studies have focused on how fire affects taxonomic and functional diversities of soil microbial c

16 Specifically, we understand little about how taxonomic and functional diversity contributes to the sy

17 Taxonomic and functional diversity increased in wetter f

18 loss of soil carbon and a major reduction in taxonomic and functional diversity of soil invertebrates

19 fragmented substrate architecture had higher taxonomic and functional diversity, despite having less

20 n exposure there would be a decrease in both taxonomic and functional diversity.

21 Here, we characterized the taxonomic and functional gene diversity (16S rRNA gene a

22 ntly we have a poor understanding of how the taxonomic and functional microbiome composition and the

23 tablishes globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a

24 terns, we investigate whether the microbiota taxonomic and functional profiles are characteristic of

25 Microbial taxonomic and functional profiles were analyzed along wi

26 We used several taxonomic and functional variables to describe community

27 The software pipeline SHOGUN profiles known taxonomic and gene abundances of short-read shotgun meta

28 pyogenes will effectively serve as valuable taxonomic and genomic references for infectious disease

29 ypothesis being well supported in restricted taxonomic and geographical contexts.

30 and Main Results: Airway metagenomes exhibit taxonomic and metabolic diversity and distinct antimicro

31 hwater ecosystem data, including traditional taxonomic and newer types of data (e.g., eDNA, remote se

32 The taxonomic and nomenclature problems related to insuffici

33 mily signatures from InterPro, combined with taxonomic and other constraints, to select sets of revie

34 we leverage a large botanical dataset to map taxonomic and phylogenetic beta diversity, as mean turno

35 Specifically, we combine taxonomic and phylogenetic data for >7,500 seed plant sp

36 pulations with low dietary diversity in both taxonomic and phylogenetic dimensions may be most vulner

37 pportunity hypotheses using metrics for both taxonomic and phylogenetic diversity and turnover.

38 generate predictive models of regional plant taxonomic and phylogenetic diversity in response to a wi

39 Drier forests showed functional, taxonomic and phylogenetic homogenization.

40 The genus Saimiri is a decades-long taxonomic and phylogenetic puzzle to which cytogenetics

41 of the United States to examine patterns of taxonomic and phylogenetic relatedness between native an

42 ion on geographic range, habitat preference, taxonomic and phylogenetic relationships, and IUCN Red L

43 y of microbial communities in situ with high taxonomic and spatial resolution poses a major challenge

44 omplexity of ocean life across comprehensive taxonomic and spatial scales.

45 s a large set of host species to explore the taxonomic and trait drivers of host-parasite interaction

46 bitat to landscape scales in controlling the taxonomic and trait-based community structure of benthic

47 ps include important spatial, environmental, taxonomic, and functional gaps, and an almost complete a

48 ng from raw sequence reads to functional and taxonomic annotations using state-of-the-art tools to as

49 l animals, so paves the way for much broader taxonomic application.

50 is pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcr

51 des additional information about the sex and taxonomic assignment of other specimens from Dmanisi.

52 required for functional characterization and taxonomic assignment of the human gut microbiota.

53 nd quality control to find the most probable taxonomic assignment.

54 rational Taxonomic Unit (OTU) clustering and taxonomic assignment.

55 stream results, improving the specificity of taxonomic assignments and of k-mer-based clustering.

56 me genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows

57 c method to detect potentially misclassified taxonomic assignments in the NR database.

58 ble species hypotheses, integration with the taxonomic backbone of the Global Biodiversity Informatio

59 names compared to current more comprehensive taxonomic backbones, can have profound impacts on estima

60 ped regions of the Northern Hemisphere and a taxonomic bias towards the most charismatic animals and

61 r unpaired forward ITS1 sequences, and these taxonomic biases need reconsideration for future studies

62 iring ITS1 rDNA Illumina sequences generated taxonomic biases related to sequence length.

63 Second, we expand the taxonomic breadth of tool use to include another group o

64 ess of the training set across all potential taxonomic categories, but also resulting from a nearest-

65 diet) and others tracked with weight loss (7 taxonomic changes in both diets).

66 some of these changes were diet specific (14 taxonomic changes specific to the healthy low-carbohydra

67 fic to the healthy low-carbohydrate diet, 12 taxonomic changes specific to the healthy low-fat diet)

68 gen fingerprints, all indicative of the same taxonomic clade, which includes aurochs and bison (Bos s

69 ncing of 79 bacterial strains from all major taxonomic clades of the conspicuous bacterial phylum Pla

70 al alignment which is widely relied upon for taxonomic classification of metagenomic sequences.

71 ilization of machine learning algorithms for taxonomic classification of plankton species in field st

72 support for an unlimited number of parallel taxonomic classification systems.

73 s origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and

74 Similarly, for taxonomic classification, miBF enables higher sensitivit

75 nal aspects of the microbiome that go beyond taxonomic classification, such as profiling genetic dete

76 s, which are in agreement with their current taxonomic classification.

77 ized pipelines with use of a high-resolution taxonomic classifier.

78 e classifier or in conjunction with existing taxonomic classifiers for more robust classification of

79 m of these faunas by classifying their major taxonomic components into discrete ecomorphological cate

80 l communities are extraordinarily complex in taxonomic composition and comprise interdependent biolog

81 here were no differences in overall parasite taxonomic composition between infected and uninfected in

82 l environmental gradients drove variation in taxonomic composition due to preferences for specific en

83 We described the microbial taxonomic composition of 91 fecal samples from 15 female

84 edictable changes in the local diversity and taxonomic composition of potential reservoir hosts, owin

85 Although the taxonomic composition of the human microbiome varies tre

86 Similarities in taxonomic composition support the microbiota of fungus-g

87 We compared taxonomic composition within term and preterm infant gro

88 ere, we assessed the effects of light on the taxonomic composition, cell integrity and growth respons

89 unities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and eco

90 es, although certainly different in terms of taxonomic composition, may be functionally similar with

91 based on alpha-diversity, beta-diversity and taxonomic composition.

92 We observed altered taxonomic compositions of gut microbiota communities upo

93 models trained using properties, normalized taxonomic count data, and another commonly used dimensio

94 from herbarium material, facilitating broad taxonomic coverage of the family.

95 additional subfamily, thus greatly improving taxonomic coverage.

96 We provide taxonomic descriptions for 22 novel species and 16 gener

97 ght to characterize the relationship between taxonomic dietary diversity (TDD) and phylogenetic dieta

98 ese coral and sponge microbiomes despite the taxonomic differences between the two microbiomes, as we

99 Substantial taxonomic differences in rates of mortality were observe

100 ndicate that, despite their geographical and taxonomic differences, median delta(13)C(diet) values fr

101 timescales and conclude that, despite their taxonomic differences, their populations respond similar

102 The marked taxonomic disparity in bleaching severity, coupled with

103 -like proteins (NLP) have an extremely broad taxonomic distribution; they occur in bacteria, fungi, a

104 of ichthyosauriforms likely fueled the rapid taxonomic diversification of the group after EPME.

105 cusing for the first time on the recovery of taxonomic diversity (TD), phylogenetic diversity (PD) an

106 We also identify that patterns of taxonomic diversity can be incongruent with those of phy

107 cological differentiation is correlated with taxonomic diversity in many clades, and ecological diver

108 This high taxonomic diversity is also reflected in non-hominin spe

109 While the taxonomic diversity of their microbiomes has been well-e

110 y history that involves considerably broader taxonomic diversity, most of it hidden in the fossil rec

111 nomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with

112 terogeneity were the strongest predictors of taxonomic diversity.

113 However, the taxonomic domain of applicability for these predictions

114 alyses, walnut breeding programs, high-level taxonomic evaluations, and genomic studies in Juglandace

115 subjective and usually requires substantial taxonomic expertise.

116 ted whether differences were attributable to taxonomic family, morphology or habitat association.

117 related with wing size, wing colouration and taxonomic family.

118 sights regarding PCB biomagnification across taxonomic, food webs, regional, and global scales can be

119 ified DNA bases functionally distinguish the taxonomic forms of life-5-methylcytosine separates proka

120 concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only a

121 predatory sportfish introduction on multiple taxonomic, functional and phylogenetic dimensions of pre

122 oDIV in the United States) in terms of their taxonomic, functional and phylogenetic diversity and fun

123 onditions, which may induce strong shifts in taxonomic, functional and phylogenetic diversity of fore

124 We generated taxonomic, functional pathway, and resistance gene profi

125 We generated taxonomic, functional pathway, and resistance gene profi

126 tial relationships are mirrored in losses of taxonomic, functional, and phylogenetic diversity over t

127 Our results show that taxonomic generalists can be phylogenetic specialists, a

128 We show that, of taxonomic-geographic systems in the Living Planet Index,

129 inst using the diversity distribution of one taxonomic group as an indication of patterns of richness

130 is-causing RNA virus, unrelated to any other taxonomic group of RNA viruses.

131 cal distribution of specific properties of a taxonomic group or habitat.

132 surveys to compare methods for a conspicuous taxonomic group.

133 The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ra

134 ers of those diversity patterns differ among taxonomic groups (phyla/classes) within bacterial or fun

135 ersity effects differ across trophic levels, taxonomic groups and ecosystem functions and that decrea

136 rsial hypothesis has been tested across many taxonomic groups and environmental contexts, and success

137 ersity and function, although with different taxonomic groups and functions at each site.

138 umption behind this method is that different taxonomic groups are biased toward using different metab

139 ons during wastewater treatment and identify taxonomic groups associated with those biotransformation

140 ent differences in the abundances of certain taxonomic groups between the total and active communitie

141 ies may appropriately vary between different taxonomic groups but should be consistent when possible,

142 onal connectivity of 747 commercially fished taxonomic groups by building a global network of fish la

143 Data on eight taxonomic groups from 35 studies around the world suppor

144 ies over the last century, across a range of taxonomic groups from phytoplankton to fish and marine m

145 ies of alien species numbers for seven major taxonomic groups in eight continents, accounting for var

146 ent by 894 terrestrial alien animals from 11 taxonomic groups including vertebrates and invertebrates

147 ch is suitable for use among a wide range of taxonomic groups inhabiting terrestrial, marine and fres

148 ure of bioluminescent organisms from diverse taxonomic groups is important for determining the biosyn

149 different resilience strategies in these two taxonomic groups open new avenues to improve our underst

150 pecific global contexts (e.g. for individual taxonomic groups or biomes).

151 rder to protect amphibians and reptiles, two taxonomic groups sensitive to environmental changes due

152 ied the temperature sensitivity of these two taxonomic groups to the uptake of algal-derived DOC in t

153 e consistent among biogeoregions, realms and taxonomic groups, and (ii) changes in biodiversity corre

154 Given the variability of the gray zone among taxonomic groups, at least from our current abilities to

155 rsity differ among biogeoregions, realms and taxonomic groups, demonstrating that biodiversity change

156 Among individual taxonomic groups, especially strong increases were proje

157 p sequence cut-off, we show that across most taxonomic groups, ramp sequences are approximately 20-40

158 (RAR) for the same GO term across different taxonomic groups, where those with a relatively low RAR

159 ince disturbance but vary considerably among taxonomic groups.

160 s, although the relationship may vary across taxonomic groups.

161 globally distributed time series across six taxonomic groups.

162 ties as well as the functional redundancy of taxonomic groups.

163 asured mainly through the responses of a few taxonomic groups.

164 To assess the comparability between taxonomic identification methods for phytoplankton, mult

165 d with PLS-DA statistical analysis may allow taxonomic identification of species and, possibly, popul

166 Instead, we find strong support for taxonomic identity (particularly at the family level) as

167 utrient use, whereas developmental stage and taxonomic identity impact morphological traits -especial

168 We used DNA barcoding to determine the taxonomic identity of 449 seafood samples from markets a

169 Our findings demonstrate that taxonomic identity, not trophic status or body size, is

170 nd magnitude of the change was controlled by taxonomic identity.

171 Our study has a range of conservation and taxonomic implications for this species.

172 ies, and is enriched with molecular details, taxonomic information, and bibliographic information.

173 iversal reaction database (MetaCyc) based on taxonomic information.

174 ks enabling computational assignment of host taxonomic information.

175 Facivermis has prompted a history of diverse taxonomic interpretations, including among annelids [1,

176 tead of characterizing biting behaviour on a taxonomic level, we illustrate the importance of assessi

177 Most microorganisms from all taxonomic levels are uncultured.

178 icrobiome signatures showed marked shifts in taxonomic levels in patients with bacterial etiology ver

179 hologous groups (OGs) distributed across 379 taxonomic levels were computed together with their assoc

180 tacularly diverse plant trait, varies across taxonomic levels, geography and in response to environme

181 test, targeting >=300 bacteria on different taxonomic levels.

182 e., order, 20%) and fine (i.e., strain, 58%) taxonomic levels.

183 sing on the evolution of modularity on lower taxonomic levels.

184 These differences among taxonomic/life-history groups possibly reflect that vert

185 trogen-fixing nodule symbiosis occurs in two taxonomic lineages: legumes (Fabaceae) and the genus Par

186 es that must be resolved if such a system of taxonomic list governance and a unified list of accepted

187 e identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is si

188 , -0.11 [95% CI, -.15 to -.077]), functional taxonomic (mean, -0.050 [95% CI, -.084 to -.017]), and r

189 ha-diversity, interindividual gut microbiome taxonomic (mean, -0.11 [95% CI, -.15 to -.077]), functio

190 While taxonomic measures like species richness have been imple

191 thentication of botanical ingredients and/or taxonomic mis-positioning.

192 Variations in taxonomic opinions-whether species are treated by system

193 No taxonomic or functional differences were detected betwee

194 is did not reveal significant differences in taxonomic or functional pathway alpha-diversity between

195 Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent

196 mic regions remain difficult to align across taxonomic orders due to their lack of sequence conservat

197 r and separately for marsupials and the four taxonomic orders with most species in the dataset (Carni

198 ir eggs (n = 1814) from 26 bird species in 6 taxonomic orders, we conducted a meta-analysis to evalua

199 ernal blood THg concentration differed among taxonomic orders, with waterfowl (Anseriformes) transfer

200 ymbiosis occurs in 10 plant lineages in four taxonomic orders: Fabales, Fagales, Cucurbitales, and Ro

201 We evaluated the effects of the taxonomic, phylogenetic, and functional attributes of do

202 isolates raised concerns about their initial taxonomic placement.

203 he origins of nervous systems, as both their taxonomic position and their evolutionary age imply that

204 However, current taxonomic practice continues to rely on cumbersome journ

205 Taxonomic predictions for tick-borne bacteria were excep

206 analyses while simultaneously improving the taxonomic process of species delimitation.

207 ungus-growing insects presents a distinctive taxonomic profile, dominated by Gammaproteobacteria at c

208 g 2,355 metagenomes, yielding functional and taxonomic profiles for 2.9 million spacers by aligning t

209 on alignments, assembly, extensive pruning, taxonomic profiling and reference sequence databases.

210 eather, we can never know the anatomical and taxonomic provenance with 100% certainty.

211 This new release covers an extended taxonomic range of 14 species, including for the first t

212 sh) suggesting there is scope to broaden the taxonomic range of attempted eradication in Europe.

213 growth functions have been applied to a wide taxonomic range of organisms, yet some of these models h

214 trophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon

215 es 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals.

216 ehavior, and exercise-status promotes higher taxonomic rank-level alterations (e.g. family to phyla-l

217 nce between these two taxa, as well as their taxonomic ranking are contentious.

218 nfecting versus non-infecting viruses at all taxonomic ranks of both eukaryote and prokaryote hosts w

219 fied several major lineages, roughly, at the taxonomic ranks of class, order and family.

220 agenomic fragments as short as 100 nt at all taxonomic ranks, and at lower ranks when the fragment si

221 ses: read-binning for targeted assembly, and taxonomic read assignment.

222 in both alpha and beta diversity as well as taxonomic redistribution under both CD and HFD condition

223 ed by society whilst continuing to encourage taxonomic research that leads to new species discoveries

224 ies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), igno

225 read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (

226 d microbiota dynamics with high temporal and taxonomic resolution during antibiotic treatment in a co

227 Our results support the need of improved taxonomic resolution for better characterization of bact

228 y - changes across spatiotemporal scales and taxonomic resolution for both plants and AM fungi.

229 Taxonomic resolution is a major challenge in palynology,

230 able for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes an

231 The high level of taxonomic resolution offered by DNA sequencing (i.e., sp

232 p) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish specie

233 rapid evolutionary rates and consequent high taxonomic resolution, mitochondrial sequences represent

234 cy of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power nee

235 hat fossil data can provide the temporal and taxonomic resolutions necessary to test (paleo)biologica

236 lists in the digital era: reliance on online taxonomic resources alone would have inflated species co

237 negligible (nonsignificant) impacts on local taxonomic richness (i.e. alpha diversity) and trophic st

238 wth media, and found significant increase in taxonomic richness and larger representation of rare and

239 Various taxonomic richness hotspots across the US represent foca

240 nship between ecological differentiation and taxonomic richness was weak early in the evolution of an

241 ion(7,8), but far shorter than the return of taxonomic richness(6).

242 me genera and tend to be affected by initial taxonomic richness.

243 tested on a large sample size and at a broad taxonomic scale in mammals.

244 s for quantitative FLS variation at multiple taxonomic scales using case studies from temperate fores

245 are rather common in bacteria, span various taxonomic scales, and are present in multiple human path

246 te most studies have been conducted at small taxonomic scales.

247 nfer dispersal and diversification rates and taxonomic selectivity of immigrants.

248 Few taxonomic shifts were detected in the tomato leaf surfac

249 in population change, we uncover a distinct taxonomic signal.

250 Our findings suggest that gut taxonomic signatures can predict health status, and high

251 transfusion-associated pathogens that share taxonomic similarity to contaminants commonly found in m

252 ing transfusion-associated pathogens sharing taxonomic similarity to contaminants commonly found in m

253 may be more tractable than those relying on taxonomic specificity.

254 Uncertainty about the taxonomic status and the specificity of a species common

255 The results showed that the taxonomic structure and potential functions of the bacte

256 We found that the taxonomic structure of the gut microbiome was significan

257 consistently to environmental variation than taxonomic structure, regardless of location.

258 no mold homes, as well as distinct community taxonomic structures between moldy and no mold homes (AN

259 teroplasmy at the genome-wide level in other taxonomic systems.

260 n new lines of paleontological research with taxonomic, taphonomic, physiological and ecological impl

261 hould be accepted when there are alternative taxonomic treatments (and, by extension, which scientifi

262 ests across grain sizes, spatial extents and taxonomic treatments.

263 nges in community composition (i.e. temporal taxonomic turnover) in most biogeoregions of Northern an

264 macroecological approaches proliferate, the taxonomic uncertainties in species occurrence data are e

265 ads assembly, chimera filtering, Operational Taxonomic Unit (OTU) clustering and taxonomic assignment

266 e bacteriome of approximately 16 operational taxonomic units (i.e., present across all life stages).

267 logenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700

268 ats analysis identified specific operational taxonomic units (OTUs) falling within the Streptococcus,

269 Of the 396 total operational taxonomic units (OTUs) identified across the samples, 81

270 at may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studi

271 We quantified richness as Operational Taxonomic Units (OTUs) in those samples using three mole

272 Wood-degrading operational taxonomic units (OTUs) such as Mycena, and mycorrhizal a

273 environments (13%), and dominant operational taxonomic units (OTUs) were classified as the Methanobac

274 A total of 1,480 individual operational taxonomic units (OTUs) were identified.

275 nnual campaigns, a total of 4421 operational taxonomic units (OTUs) were obtained, indicating a high

276 detected 1287 Streptomyces rpoB operational taxonomic units (OTUs) with 159 +/- 92 (average +/- SD)

277 iven in part by the diversity of operational taxonomic units (OTUs) within these genera.

278 unity composition, we identified operational taxonomic units (OTUs), Families and Phyla with high her

279 me to more than 11,000 microbial Operational Taxonomic Units (OTUs), many of which exhibit clear annu

280 e the SRT and net growth rate of operational taxonomic units (OTUs).

281 n the contribution of individual operational taxonomic units (OTUs); and tests for individual OTUs, w

282 ed and mapped to the zero-radius operational taxonomic units (zOTUs).

283 Eleven distinctive operational taxonomic units composed a microbe signature specific to

284 ross populations with the lowest operational taxonomic units diversity found where coyotes occurred a

285 g LC-MSMS and defining stool sub-Operational Taxonomic Units from16S ribosomal RNA gene sequencing da

286 Operational taxonomic units in the families Peptococcaceae, Clostrid

287 eritability estimates (+/-SE) of Operational Taxonomic Units ranged from 0.025 (+/-0.0002) to 0.139 (

288 ured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abund

289 56 novel candidate species-level operational taxonomic units spanning 135 phyla.

290 enrichment identified 63.3% more operational taxonomic units than direct sequencing.

291 Most operational taxonomic units that differed between patients on a GFD

292 The most represented operational taxonomic units were assigned to the phylum Gammaproteob

293 biome (which numbers over 40,000 operational taxonomic units(10)), the effect of the microbiome on th

294 dous diversity of animals (8,586 operational taxonomic units), including many small taxa that would b

295 species, which still constitute the smallest taxonomic units.

296 data sets or grouping them into operational taxonomic units.

297 nces to GenBank without significant external taxonomic validation.

298 We identify major axes of taxonomic variance in the gut and a putative diversity m

299 h tick-borne pathogen proteins, evolutionary taxonomic verification for related pathogens, and no ide

300 Despite intensive taxonomic work on the local fauna, the potential forces