ライフサイエンスコーパス: phage

1 icrobial components, such as bacteriophages (phages).

2 icient for PLE replication in the absence of phage.

3 relies on the target organism resisting the phage.

4 le to acquire the cholera toxin-carrying CTX phage.

5 nter bacterial defenses to co-exist for each phage.

6 more of the observed community dynamics than phages.

7 fication of an expansive group of crAss-like phages.

8 bees, and tested the host range of isolated phages.

9 an immune effector against rapidly evolving phages.

10 wing methanotroph was infected by three pmoC-phages.

11 al CRISPR-Cas systems to eliminate competing phages.

12 charide that defends against a wide array of phages.

13 herent library bias towards sense-containing phages.

14 cquired spacer is easily overcome by escaper phages.

15 lly conserved in all previously solved dsDNA phages.

16 g-focused efforts to understand gut-resident phages.

17 pen ways for genomic manipulation of Thermus phages.

18 ntly improves the genomic editing rate of T4 phages.

19 o understand the bacterial co-evolution with phages.

20 nsmission and strain diversity of crAss-like phages.

21 at confer resistance to one or more of these phages.

22 ety of temperate and virulent superinfecting phages.

23 illustrated for both temperate and virulent phages.

24 the propagation of plasmids and infection by phages.

25 20) of the Myoviridae family and a temperate phage 80alpha of the Siphoviridae family.

26 In addition, pmoC-phage abundance patterns correlate with those of the coe

27 s, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual b

28 To facilitate phage administration while minimizing disruption to host

29 Our data suggest that phage adsorption occurs but that phage genome translocat

30 tion and function, cellular invasiveness and phage adsorption, while galactosylated LTA plays no role

31 Nebulized phages (aerophages) were delivered to the lungs of rats

32 heterologous hosts, these newly isolated ZZ phages also targeted OmpC as an alternative receptor whe

33 ng key differences between this thermophilic phage and its mesophilic counterparts.

34 ons with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play

35 ide the compartment enables targeting of the phage and protection of host cells.

36 fits of phage-encoded acr genes for both the phage and the host under these circumstances.

37 However, the infectious associations between phages and bacteria in the human intestine, which is ess

38 Specific viral taxa, such as Staphylococcus phages and Herpesviridae, were associated with increased

39 e screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activi

40 We explored how interactions between Acr phages and initially sensitive bacteria evolve, both in

41 Pseudomonas phages and plasmids have taken advantage of this regulat

42 robiome-modifying strategies, and engineered phages and probiotics.

43 rs corresponding to both temperate and lytic phages and representing novel genera with a large repert

44 n by the highly dynamic interactions between phages and their hosts, and prophages can confer a varie

45 Vibriophage VP882 is one such phage, and activation of its quorum-sensing pathway lead

46 ability to identify previously unidentified phages, and employ this method to detect unknown phages,

47 Coexistence of bacteriophages, or phages, and their host bacteria plays an important role

48 ted the feasibility of isolating recombinant phage-antibodies against gluten from a non-immunized lib

49 sue specificity, we have previously selected phage antibody display libraries on live mesothelioma ce

50 oli, yet relatively few previously described phages appear to exclusively infect this genus.

51 CrAss-like phages are a recently described expansive group of virus

52 Though phages are abundant in the gut, very few phages have bee

53 conserved biological strategy, and that the phages are distributed across a broad bacterial host ran

54 CrAss-like phages are double-stranded DNA viruses that are prevalen

55 Although phages are not motile themselves, they can infect motile

56 f proliferation and motility of bacteria and phages are the key to formation of the observed lysis pa

57 Bacteriophages (phages) are critical players in the dynamics and functio

58 Here it is shown that filamentous fd phage, as a biomolecular biocompatible nanofiber, can be

59 our approach when examining uncharacterized phages, as well as usefulness of the method for explorin

60 ved the deaminase component of ABE7.10 using phage-assisted non-continuous and continuous evolution (

61 m Lake Rotsee (Switzerland) showed that some phage-associated pmoC genes were highly expressed in sit

62 Future work is needed to determine whether phage-associated PmoC has similar functions to additiona

63 The phage-associated PmoC sequences show high similarity to

64 om the same fecal samples, the host bacteria-phage associations are illustrated for both temperate an

65 Using a novel, phage-based blood assay, we report the first concordant

66 The four TSPs, TSP1-4, attach to the phage baseplate forming a branched structure.

67 used to identify bacterial genes involved in phage binding.

68 leiotropic result, consideration for applied phage biology, and the importance of ecology in evolutio

69 e been limited by certain characteristics of phage biology, with structural fragility under the high

70 on protein fold produces rigid tubes in some phages but flexible tubes in others.

71 ain unclear, in particular, whether and when phages can drive evolutionary trade-offs with antibiotic

72 ainst attack by genetically distinct phages; phages can neutralize these defense systems by coding fo

73 Our results indicate that host responses to phages can occur via diverse cellular mechanisms.

74 Bacteria-infecting viruses, called phages, can encode quorum-sensing components that enable

75 at pathogenic bacteria may be lysogenized by phages carrying genes encoding resistance against second

76 pansion correlated with acquisition of a new phage, carrying gene encoding a putative cell-surface pr

77 epitopes were identified by quantitating the phage clones before and after affinity selection and ali

78 Yet, little is known about the phage community associated with the bee gut, despite its

79 We find that the phage community is prevalent in honey bees across space

80 gut virome consists of a complex and diverse phage community that likely plays an important role in r

81 Although bacteriophages (phages) continue to lack drug approval in Western medici

82 ty of natural defense systems, and discusses phage counter-defense mechanisms.

83 response of bacteria to the threat posed by phages depends on their local environment.

84 For any given bacteriophage genome or phage-derived sequences in metagenomic data sets, we are

85 ntial untapped resource for the discovery of phage-derived therapeutic proteins.

86 s encoded by mRNA, followed by two rounds of phage display and binder identification by ELISA.

87 A synthetic phage display library based on the variable domain of ne

88 Here, we utilize a NoV GI.1 Jun-Fos-assisted phage display library constructed from randomly fragment

89 for many fields including immunodiagnostics, phage display library generation, and "humanness" assess

90 human single-chain variable fragment (scFv) phage display library was screened for binding, internal

91 that are superior to candidates derived from phage display panning experiments.

92 were generated against DT from two different phage display panning strategies using a human immune li

93 Here, we used phage display phenotypic screening to isolate antibodies

94 A phage display screen against EphA2, a receptor tyrosine

95 We therefore developed a platform for rapid phage display screening of deep recombinant libraries co

96 Phage display selection followed by chemical optimizatio

97 in Escherichia coli and used as antigens in phage display selections using a synthetic human single-

98 A (HlgA) and LukS genes into a custom-built phage display system, termed pComb-Opti8.

99 Phage display technology enabled the selection of affini

100 in fragment variable (scFv) was generated by phage display, using the extracellular domain of recombi

101 olation of antibodies from rats using immune phage display.

102 d by immunoblot and by epitope mapping using phage display.

103 eatly expands the chemical space amenable to phage display.

104 ere, we performed proteome-wide programmable phage-display (PhIP-Seq) on sera from a cohort of people

105 In contrast, phage diversity metrics remained stable and were similar

106 recombination is the largest contributor to phage diversity, allowing a variety of host recognition

107 Both recognize and cleave phage DNA at specific sites while protecting their own g

108 The RecBCD complex plays key roles in phage DNA degradation, CRISPR array acquisition (adaptat

109 restriction enzymes are unable to access the phage DNA throughout the infection, but engineering the

110 n spacers were acquired from both strands of phage DNA, indicating that no mechanism ensuring acquisi

111 ility to both methylate and exclude incoming phage DNA.

112 e as an experimental model to study bacteria-phage dynamics in natural microbial communities.

113 ional samples from South Sudan found similar phage effects on RDTs; antibiotics were not assayed.

114 The genomes of all crAss-like phages encode a large virion-packaged protein(2,4) that

115 Listeria monocytogenes temperate phages encode up to three anti-Cas9 proteins, with acrII

116 d highlight the strong selective benefits of phage-encoded acr genes for both the phage and the host

117 epts translation to redirect biosynthesis to phage-encoded functions.

118 When lytic phages encountered motile host bacteria in our experimen

119 Classical T4 phage engineering and several newly proposed methods are

120 ustrial settings is the lack of an efficient phage-engineering platform.

121 ia (bacteriophages; hereafter referred to as phages) enter either a lytic or a lysogenic cycle.

122 of which are highly divergent from the known phage families.

123 a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds

124 y with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacteria

125 % for multiple genes that functionalizes the phages for further applications.

126 rovides insight into selection of the proper phages for use in phage therapy.

127 e Ocr, a DNA mimic protein that protects the phage from the defensive action of type I restriction-mo

128 e dynamics should lead to divergence between phages from similar, geographically isolated ecosystems.

129 ISPR-Cas immune systems cannot eliminate the phages from the bacterial population.

130 Here, we report the genomes of 27 phages from the United States and Bangladesh that infect

131 tified for the majority (five of six) of the phages; furthermore, genes encoding the phage receptor(s

132 Three analyses confirm that the phage G host is a Lysinibacillus, and not Bacillus megat

133 pectrometry analyses, genome sequence of the phage G host, and host range of phage G.

134 uence of the phage G host, and host range of phage G.

135 Discovering phage genes that exclude superinfecting phages not only

136 s constitute a large fraction of the average phage genome and are among the most divergent and diffic

137 35 kb, which is-to our knowledge-the largest phage genome to be described to date.

138 uggest that phage adsorption occurs but that phage genome translocation to the host's cytoplasm is de

139 their cognate regulatory proteins within the phage genome.

140 onstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool

141 In the present study, we reconstructed large phage genomes from freshwater lakes known to contain bac

142 rom diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (k

143 able to store, update, explore, and analyze phage genomics data.

144 nomic studies vastly expanded the crAss-like phage group and demonstrated its global spread and ancie

145 In response to this immunity, many phages have anti-CRISPR (Acr) proteins that inhibit CRIS

146 ugh phages are abundant in the gut, very few phages have been isolated from this ecosystem.

147 In turn, phages have developed equally diverse mechanisms to over

148 It is well accepted that T4 and other phages have evolved counterdefense mechanisms to protect

149 tudied defense mechanisms of bacteria, while phages have evolved covalent modifications as a counterd

150 Phages have evolved multiple mechanisms to target their

151 The CRISPR-Cas systems of phages have the capacity to silence host transcription f

152 Moreover, the phage host range was readily extended within three diffe

153 We employed Raman tweezers to analyze the phage-host interaction of Staphylococcus aureus strain F

154 ) consider the range and nature of temperate phage-host interactions, and (iii) draw on studies of cu

155 PLEs parasitize the lytic phage ICP1, excising from the bacterial chromosome, repl

156 se in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome ed

157 on to the classic exclusion conferred by the phage immunity repressor, the phenotype observed in B3-l

158 erological profiling using a high-throughput phage immunoprecipitation sequencing assay covering the

159 robial community coexistence of bacteria and phages implies their co-propagation in space.

160 nduced mutations in the cII gene from lambda phage in transgenic mouse embryonic fibroblasts during t

161 nd show that it facilitates oral delivery of phage in vivo.

162 ple method for isolating novel environmental phages in a predictable way, i.e. isolating phages that

163 eliably detected the presence of replicating phages in bacterial cells within 5 min after infection.

164 romics) to disentangle the potential role of phages in driving the resilience and functionality of th

165 on hindering the widespread use of synthetic phages in medical and industrial settings is the lack of

166 We constructed lysogens of the seven B3-like phages in strain Ps33 of P. aeruginosa, a novel clinical

167 ersus narrow use of cellular receptors among phages in the biosphere.

168 microscopy, have uncovered a novel role for phages in the human body - the ability to modulate the p

169 at 96 hours, 2) enumeration of bacteria and phages in the lungs and spleen, and 3) lung tissue histo

170 biome, but little is known about the role of phages in this ecosystem.

171 Phages, in turn, have evolved diverse "anti-CRISPR" prot

172 Phage-inducible chromosomal island-like elements (PLEs)

173 We studied Type III spacer acquisition in phage-infected Thermus thermophilus, a bacterium that la

174 identify bacterial host factors important in phage infection and resistance have yet to be fully real

175 We discovered that ssRNA phage infection triggers the release of F-pili from host

176 tions in bacteria that allow them to subvert phage infection, but with a cost to their fitness.

177 In T4 phage infection, lysis occurs when the holin protein (T)

178 Upon phage infection, the host nucleoid condensed and became

179 d the role of the Type I R-M systems against phage infection.

180 provide sequence-specific protection against phage infection.

181 Here, we found that when phage infections occur on solid media, a high proportion

182 sefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-

183 stand how CPSs have an impact on Bacteroides-phage interactions, we isolated 71 Bacteroides thetaiota

184 The phage is genetically engineered to display many copies o

185 The application of bacteriophages (phages) is proposed as a highly specific therapy for int

186 veloped a systematic procedure for medicinal phage isolation, liter-scale cultivation, concentration

187 lococcus aureus strain FS159 with a virulent phage JK2 (=812K1/420) of the Myoviridae family and a te

188 We show that phage K1F is phagocytosed and degraded by constitutive-

189 oth in the presence and absence of competing phages lacking Acrs.

190 election method involving replication of the phage lambda cI repressor gene.

191 e, we investigate how organization underpins phage lambda development and decision-making by characte

192 (VHH) from naive and synthetic humanized VHH phage libraries that specifically bind the S1 SARS-CoV-2

193 o acids (ncAAs) were first incorporated into phage libraries through amber suppression nearly two dec

194 phage allows facile chemical modification of phage libraries, which greatly expands the chemical spac

195 lly, we screened a naive human semisynthetic phage library against RBD, leading to the identification

196 s end, we utilized a sequential panning of a phage library on cultured rat EpiSCs and then subtracted

197 ffinity selection and deep sequencing of the phage library provide sufficient resolution to map multi

198 ctures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles

199 ary for antibiotic protection, we found that phage liquid crystalline droplets form phase-separated o

200 enon but also for the temporal regulation of phage lysis in general.

201 al approaches predict that genes involved in phage lytic function are preferentially lost, resulting

202 In addition, some phages may repurpose bacterial CRISPR-Cas systems to eli

203 Here, we (i) review phage-mediated rewiring of host metabolism, with a focus

204 Although the F-specific ssRNA phage MS2 has long had paradigm status, little is known

205 process, we fluorescently labeled the ssRNA phage MS2 to track F-pilus dynamics during infection.

206 role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overpro

207 ring phage genes that exclude superinfecting phages not only assigns novel functions to orphan genes

208 The binding of E. coli to the M13 phage on the cytosensor surface increased the charge tra

209 ISPR genes have primarily been discovered in phage or prophage genomes.

210 lysis of crAssphage failed to detect related phages, or functionally annotate most of the genes, subs

211 we have developed a new approach to classify phage ORFs into ten major classes of structural proteins

212 Sequencing data of the phage panning experiment are deposited at NIH's Sequence

213 n the replication, packaging, and release of phage particles have been preferentially lost in incompl

214 efend against attack by genetically distinct phages; phages can neutralize these defense systems by c

215 s and slips; (ii) evidence suggests that the phage phi29 motor contacts DNA bases during translocatio

216 Here we show that jumbo phage PhiKZ segregates its DNA from immunity nucleases o

217 ers measurements to compare translocation of phage, plasmid, and synthetic A-philic, GC rich sequence

218 oduction of high-quality and clinically safe phage preparations, we developed a systematic procedure

219 ch reduced endotoxins by up to 10(6)-fold in phage preparations.

220 built a database of 538,213 manually curated phage protein sequences that we split into eleven subset

221 ection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of pr

222 the phages; furthermore, genes encoding the phage receptor(s) were the top hit(s) in the analyses of

223 we are able to confirm previously described phage receptors as well as uncover a number of previousl

224 eful method for high-throughput discovery of phage receptors.

225 lude that the large gene inventories of huge phages reflect a conserved biological strategy, and that

226 ing bacterial methanotrophs, supporting host-phage relationships.

227 tionary interactions between antibiotics and phages remain unclear, in particular, whether and when p

228 e, causing cell death prior to completion of phage replication.

229 minireview, we explore the mechanisms behind phage resistance in bacterial pathogens and the physiolo

230 of this study and future efforts to map the phage resistance landscape will lead to new insights int

231 However, contrary to the hypothesis, some phage resistance mutations pleiotropically confer increa

232 the physiological consequences of acquiring phage resistance phenotypes.

233 In support of the trade-off hypothesis, phage resistance via tolC mutations occurs with a corres

234 nd the importance of ecology in evolution of phage resistance.

235 Although the emergence of phage-resistant bacteria is likely inevitable, there is

236 t similar to antibiotics, the development of phage-resistant bacteria will halt clinical phage therap

237 menon with conserved defensive function of a phage satellite in a disease context, highlighting the i

238 Further, we show that an MGE, the defensive phage satellite PLE, collapses lysis inhibition.

239 As phage Seahorse genome encodes 48 open reading frames wit

240 ring tetracycline treatment, suggesting that phage Seahorse hijacked host biosynthesis pathways throu

241 Phage Seahorse was able to infect the host in a broad ra

242 is a growing body of literature showing that phage selective pressure promotes mutations in bacteria

243 FU/mL, the lowest reported to-date using EIS-phage sensors, and exhibited a high selectivity towards

244 erfect matching of spacers to the integrated phage sequences (prophages).

245 ng tool for alignment-free identification of phage sequences.

246 med CBASS (cyclic oligonucleotide-based anti-phage signaling system).

247 es, and employ this method to detect unknown phages, some of which are highly divergent from the know

248 We also identify both phage-specific mechanisms, such as the unexpected role o

249 rm the rigid inner tubes of contractile tail phages, such as T4, and its C-terminal domain adopt an I

250 active linker to form cyclic peptides on the phage surface while simultaneously introducing an electr

251 tance, CRISPR/Cas systems and virulence with phage susceptibility in Acinetobacter baumannii and inve

252 Whole-genome sequences of seven phage susceptible A. baumannii isolates revealed that si

253 c resistance genes were carried by all seven phage susceptible A. baumannii.

254 baumannii and investigated draft genomes of phage susceptible multidrug resistant A. baumannii strai

255 Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriopha

256 We found that the phage T4 genome modified by cytosine hydroxymethylation

257 modulated by substrate DNA sequence: (i) the phage T4 motor exhibits large translocation rate fluctua

258 nal bypassing of a 50-nt non-coding gap in a phage T4 topoisomerase subunit gene (gp60) requires seve

259 A ribosome profiling analysis of phage T4-infected Escherichia coli yielded protected mRN

260 y characterized viruses of Escherichia coli (phages T6, T2, T4, and T7).

261 Phages tend to be predators finely tuned to attack speci

262 y evolved from conserved nuclease domains in phage terminases.

263 er for Pseudomonas, Klebsiella, and Serratia phages tested.

264 y on cultured rat EpiSCs and then subtracted phage that nonspecifically bound blood immune cells.

265 variable, allowing rapid evolution of mutant phages that escape CRISPR pressure.

266 own about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance.

267 phages in a predictable way, i.e. isolating phages that target a particular receptor(s) of a bacteri

268 t dependencies of two novel Escherichia coli phages, the T1-like siphophage LL5 and the V5-like myoph

269 To understand the functions encoded by phages, their contributions to their environments, and t

270 hich can ultimately be used to design better phage therapeutic treatments and tools for precision mic

271 essential information for the development of phage therapies, have yet to be fully elucidated.

272 and to help gauge their utility as potential phage therapy agents, we have developed a new approach t

273 would be sufficient for most expanded-access phage therapy cases and potentially for clinical phase I

274 Phage therapy is an old idea, long practiced in eastern

275 restoration, nanomaterial-based therapy and phage therapy may help to develop treatments to target s

276 ortant step for the continued development of phage therapy targeting antibiotic-resistant bacterial i

277 This study illustrates the potential of phage therapy targeting infections such as bacterial neo

278 phage-resistant bacteria will halt clinical phage therapy.

279 secondary infections, such as those used in phage therapy.

280 d for developing other technologies, such as phage therapy.

281 to selection of the proper phages for use in phage therapy.

282 bility to confer significant improvements in phage thermal stability.

283 Using the ability of T7 phage to replicate in nitrogen-starved bacteria as a bio

284 By using phages to both kill bacterial cells and 'steer' survivor

285 ssembly of double-stranded DNA viruses, from phages to herpesviruses, is strongly conserved.

286 ver, we show that even partial motifs enable phages to persist cytoplasmically without leading to col

287 tility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.

288 hat harnesses the ability of bacteriophages (phages) to impose strong selection on their bacterial ho

289 Cells with spacers targeting a subset of phage transcripts survived the infection, indicating tha

290 holera, Vibrio cholerae, infected by ICP1, a phage ubiquitous in clinical samples.

291 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 an

292 Characterization of this phage validated the predicted podovirus-like virion stru

293 in the pan-genome interchange to create new phage variants.

294 rsity of the catalytic apparatus employed by phage vB_EcoM_CBA120 TSPs.

295 stems employ RNA-guided nucleases to destroy phage (viral) DNA.

296 Chimeric phages were engineered to attach specifically to several

297 at, when challenged with wild-type temperate phages (which can become lysogenic), type I CRISPR-Cas i

298 ghts into the coevolution of hosts and their phage, which can ultimately be used to design better pha

299 Here, we show that phages with near-identical core genomes in distant, disc

300 There is growing evidence that phages with unusually large genomes are common across va