Taylor TD

References (12)

Title : Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation - Prakash_2011_Cell.Host.Microbe_10_273
Author(s) : Prakash T , Oshima K , Morita H , Fukuda S , Imaoka A , Kumar N , Sharma VK , Kim SW , Takahashi M , Saitou N , Taylor TD , Ohno H , Umesaki Y , Hattori M
Ref : Cell Host Microbe , 10 :273 , 2011
Abstract : Segmented filamentous bacteria (SFB) are noncultivable commensals inhabiting the gut of various vertebrate species and have been shown to induce Th17 cells in mice. We present the complete genome sequences of both rat and mouse SFB isolated from SFB-monocolonized hosts. The rat and mouse SFB genomes each harbor a single circular chromosome of 1.52 and 1.59 Mb encoding 1346 and 1420 protein-coding genes, respectively. The overall nucleotide identity between the two genomes is 86%, and the substitution rate was estimated to be similar to that of the free-living E. coli. SFB genomes encode typical genes for anaerobic fermentation and spore and flagella formation, but lack most of the amino acid biosynthesis enzymes, reminiscent of pathogenic Clostridia, exhibiting large dependency on the host. However, SFB lack most of the clostridial virulence-related genes. Comparative analysis with clostridial genomes suggested possible mechanisms for host responses and specific adaptations in the intestine.
ESTHER : Prakash_2011_Cell.Host.Microbe_10_273
PubMedSearch : Prakash_2011_Cell.Host.Microbe_10_273
PubMedID: 21925114
Gene_locus related to this paper: 9clot-g2ifk0

Title : Complete genome sequences of Arcobacter butzleri ED-1 and Arcobacter sp. strain L, both isolated from a microbial fuel cell - Toh_2011_J.Bacteriol_193_6411
Author(s) : Toh H , Sharma VK , Oshima K , Kondo S , Hattori M , Ward FB , Free A , Taylor TD
Ref : Journal of Bacteriology , 193 :6411 , 2011
Abstract : Arcobacter butzleri strain ED-1 is an exoelectrogenic epsilonproteobacterium isolated from the anode biofilm of a microbial fuel cell. Arcobacter sp. strain L dominates the liquid phase of the same fuel cell. Here we report the finished and annotated genome sequences of these organisms.
ESTHER : Toh_2011_J.Bacteriol_193_6411
PubMedSearch : Toh_2011_J.Bacteriol_193_6411
PubMedID: 22038970
Gene_locus related to this paper: 9prot-e6l4v2 , 9prot-g2hv40 , 9prot-a0a0g9kwp1 , 9prot-g2hwt3

Title : Bifidobacteria can protect from enteropathogenic infection through production of acetate - Fukuda_2011_Nature_469_543
Author(s) : Fukuda S , Toh H , Hase K , Oshima K , Nakanishi Y , Yoshimura K , Tobe T , Clarke JM , Topping DL , Suzuki T , Taylor TD , Itoh K , Kikuchi J , Morita H , Hattori M , Ohno H
Ref : Nature , 469 :543 , 2011
Abstract : The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology. Among the most distinctive benefits of bifidobacteria are modulation of host defence responses and protection against infectious diseases. Nevertheless, the molecular mechanisms underlying these effects have barely been elucidated. To investigate these mechanisms, we used mice associated with certain bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We found that this effect can be attributed, at least in part, to increased production of acetate and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal defence mediated by epithelial cells and thereby protects the host against lethal infection.
ESTHER : Fukuda_2011_Nature_469_543
PubMedSearch : Fukuda_2011_Nature_469_543
PubMedID: 21270894
Gene_locus related to this paper: bifli-c2gxu7 , biflo-BL0073 , biflo-BL0336 , biflo-BL0581 , biflo-BL0582 , biflo-BL0682 , biflo-BL0787 , biflo-BL0807 , biflo-BL1109 , biflo-BL1514 , biflo-PAP , biflo-PTRB , bifln-c2gtr2

Title : Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient - Avasthi_2011_J.Bacteriol_193_3385
Author(s) : Avasthi TS , Devi SH , Taylor TD , Kumar N , Baddam R , Kondo S , Suzuki Y , Lamouliatte H , Megraud F , Ahmed N
Ref : Journal of Bacteriology , 193 :3385 , 2011
Abstract : The diverse clinical outcomes of colonization by Helicobacter pylori reflect the need to understand the genomic rearrangements enabling the bacterium to adapt to host niches and exhibit varied colonization/virulence potential. We describe the genome sequences of the two serial isolates, H. pylori 2017 and 2018 (the chronological subclones of H. pylori 908), cultured in 2003 from the antrum and corpus, respectively, of an African patient who suffered from recrudescent duodenal ulcer disease. When compared with the genome of the parent strain, 908 (isolated from the antrum of the same patient in 1994), the genome sequences revealed genomic alterations relevant to virulence optimization or host-specific adaptation.
ESTHER : Avasthi_2011_J.Bacteriol_193_3385
PubMedSearch : Avasthi_2011_J.Bacteriol_193_3385
PubMedID: 21515762

Title : Genome of Helicobacter pylori strain 908 - Devi_2010_J.Bacteriol_192_6488
Author(s) : Devi SH , Taylor TD , Avasthi TS , Kondo S , Suzuki Y , Megraud F , Ahmed N
Ref : Journal of Bacteriology , 192 :6488 , 2010
Abstract : Helicobacter pylori is a genetically diverse and coevolved pathogen inhabiting human gastric niches and leading to a spectrum of gastric diseases in susceptible populations. We describe the genome sequence of H. pylori 908, which was originally isolated from an African patient living in France who suffered with recrudescent duodenal ulcer disease. The strain was found to be phylogenetically related to H. pylori J99, and its comparative analysis revealed several specific genome features and novel insertion-deletion and substitution events. The genome sequence revealed several strain-specific deletions and/or gain of genes exclusively present in HP908 compared with different sequenced genomes already available in the public domain. Comparative and functional genomics of HP908 and its subclones will be important in understanding genomic plasticity and the capacity to colonize and persist in a changing host environment.
ESTHER : Devi_2010_J.Bacteriol_192_6488
PubMedSearch : Devi_2010_J.Bacteriol_192_6488
PubMedID: 20952566

Title : Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2 - Toh_2010_J.Bacteriol_192_1165
Author(s) : Toh H , Oshima K , Toyoda A , Ogura Y , Ooka T , Sasamoto H , Park SH , Iyoda S , Kurokawa K , Morita H , Itoh K , Taylor TD , Hayashi T , Hattori M
Ref : Journal of Bacteriology , 192 :1165 , 2010
Abstract : Escherichia coli SE15 (O150:H5) is a human commensal bacterium recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B2, which includes the majority of extraintestinal pathogenic E. coli. Here, we report the finished and annotated genome sequence of this organism.
ESTHER : Toh_2010_J.Bacteriol_192_1165
PubMedSearch : Toh_2010_J.Bacteriol_192_1165
PubMedID: 20008064
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C0410 , ecoli-C2429 , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-ypfh , ecoli-ypt1 , ecoli-yqia , ecoli-YfhR , ecos5-d2nhh3 , yerpe-YBTT , ecolx-f4suw9

Title : Complete genome sequence of the probiotic Lactobacillus rhamnosus ATCC 53103 - Morita_2009_J.Bacteriol_191_7630
Author(s) : Morita H , Toh H , Oshima K , Murakami M , Taylor TD , Igimi S , Hattori M
Ref : Journal of Bacteriology , 191 :7630 , 2009
Abstract : Lactobacillus rhamnosus is a facultatively heterofermentative lactic acid bacterium and is frequently isolated from human gastrointestinal mucosa of healthy individuals. L. rhamnosus ATCC 53103, isolated from a healthy human intestinal flora, is one of the most widely used and well-documented probiotics. Here, we report the finished and annotated genome sequence of this organism.
ESTHER : Morita_2009_J.Bacteriol_191_7630
PubMedSearch : Morita_2009_J.Bacteriol_191_7630
PubMedID: 19820099
Gene_locus related to this paper: lacrg-c7tei3 , lacrh-B2CZF3 , lacrh-b5qmk1 , lacrh-pepr , lacrh-pepx , lacrl-pip

Title : Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult - Oshima_2008_DNA.Res_15_375
Author(s) : Oshima K , Toh H , Ogura Y , Sasamoto H , Morita H , Park SH , Ooka T , Iyoda S , Taylor TD , Hayashi T , Itoh K , Hattori M
Ref : DNA Research , 15 :375 , 2008
Abstract : We sequenced and analyzed the genome of a commensal Escherichia coli (E. coli) strain SE11 (O152:H28) recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B1. SE11 harbored a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes. None of the SE11 genes had sequence similarity to known genes encoding phage- and plasmid-borne virulence factors found in pathogenic E. coli strains. The comparative genome analysis with the laboratory strain K-12 MG1655 identified 62 poorly conserved genes between these two non-pathogenic strains and 1186 genes absent in MG1655. These genes in SE11 were mostly encoded in large insertion regions on the chromosome or in the plasmids, and were notably abundant in genes of fimbriae and autotransporters, which are cell surface appendages that largely contribute to the adherence ability of bacteria to host cells and bacterial conjugation. These data suggest that SE11 may have evolved to acquire and accumulate the functions advantageous for stable colonization of intestinal cells, and that the adhesion-associated functions are important for the commensality of E. coli in human gut habitat.
ESTHER : Oshima_2008_DNA.Res_15_375
PubMedSearch : Oshima_2008_DNA.Res_15_375
PubMedID: 18931093
Gene_locus related to this paper: ecoli-Aes , ecoli-rutD , ecoli-bioh , ecoli-C4836 , ecoli-dlhh , ecoli-entf , ecoli-fes , ecoli-mhpc , ecoli-pldb , ecoli-ptrb , ecoli-yafa , ecoli-yaim , ecoli-ybff , ecoli-ycfp , ecoli-ycjy , ecoli-yeiG , ecoli-YFBB , ecoli-yghX , ecoli-yhet , ecoli-yiel , ecoli-yjfp , ecoli-YNBC , ecoli-ypfh , ecoli-yqia , ecoli-Z1930 , ecoli-Z2445 , ecoli-YfhR

Title : Human chromosome 11 DNA sequence and analysis including novel gene identification - Taylor_2006_Nature_440_497
Author(s) : Taylor TD , Noguchi H , Totoki Y , Toyoda A , Kuroki Y , Dewar K , Lloyd C , Itoh T , Takeda T , Kim DW , She X , Barlow KF , Bloom T , Bruford E , Chang JL , Cuomo CA , Eichler E , Fitzgerald MG , Jaffe DB , LaButti K , Nicol R , Park HS , Seaman C , Sougnez C , Yang X , Zimmer AR , Zody MC , Birren BW , Nusbaum C , Fujiyama A , Hattori M , Rogers J , Lander ES , Sakaki Y
Ref : Nature , 440 :497 , 2006
Abstract : Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.
ESTHER : Taylor_2006_Nature_440_497
PubMedSearch : Taylor_2006_Nature_440_497
PubMedID: 16554811
Gene_locus related to this paper: human-PRCP

Title : DNA sequence and analysis of human chromosome 18 - Nusbaum_2005_Nature_437_551
Author(s) : Nusbaum C , Zody MC , Borowsky ML , Kamal M , Kodira CD , Taylor TD , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Abouelleil A , Allen NR , Anderson S , Bloom T , Bugalter B , Butler J , Cook A , Decaprio D , Engels R , Garber M , Gnirke A , Hafez N , Hall JL , Norman CH , Itoh T , Jaffe DB , Kuroki Y , Lehoczky J , Lui A , Macdonald P , Mauceli E , Mikkelsen TS , Naylor JW , Nicol R , Nguyen C , Noguchi H , O'Leary SB , O'Neill K , Piqani B , Smith CL , Talamas JA , Topham K , Totoki Y , Toyoda A , Wain HM , Young SK , Zeng Q , Zimmer AR , Fujiyama A , Hattori M , Birren BW , Sakaki Y , Lander ES
Ref : Nature , 437 :551 , 2005
Abstract : Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.
ESTHER : Nusbaum_2005_Nature_437_551
PubMedSearch : Nusbaum_2005_Nature_437_551
PubMedID: 16177791
Gene_locus related to this paper: human-LIPG

Title : DNA sequence and comparative analysis of chimpanzee chromosome 22 - Watanabe_2004_Nature_429_382
Author(s) : Watanabe H , Fujiyama A , Hattori M , Taylor TD , Toyoda A , Kuroki Y , Noguchi H , BenKahla A , Lehrach H , Sudbrak R , Kube M , Taenzer S , Galgoczy P , Platzer M , Scharfe M , Nordsiek G , Blocker H , Hellmann I , Khaitovich P , Paabo S , Reinhardt R , Zheng HJ , Zhang XL , Zhu GF , Wang BF , Fu G , Ren SX , Zhao GP , Chen Z , Lee YS , Cheong JE , Choi SH , Wu KM , Liu TT , Hsiao KJ , Tsai SF , Kim CG , S OO , Kitano T , Kohara Y , Saitou N , Park HS , Wang SY , Yaspo ML , Sakaki Y
Ref : Nature , 429 :382 , 2004
Abstract : Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.
ESTHER : Watanabe_2004_Nature_429_382
PubMedSearch : Watanabe_2004_Nature_429_382
PubMedID: 15164055
Gene_locus related to this paper: pantr-a0a2j8lmv7

Title : The DNA sequence of human chromosome 21 - Hattori_2000_Nature_405_311
Author(s) : Hattori M , Fujiyama A , Taylor TD , Watanabe H , Yada T , Park HS , Toyoda A , Ishii K , Totoki Y , Choi DK , Groner Y , Soeda E , Ohki M , Takagi T , Sakaki Y , Taudien S , Blechschmidt K , Polley A , Menzel U , Delabar J , Kumpf K , Lehmann R , Patterson D , Reichwald K , Rump A , Schillhabel M , Schudy A , Zimmermann W , Rosenthal A , Kudoh J , Schibuya K , Kawasaki K , Asakawa S , Shintani A , Sasaki T , Nagamine K , Mitsuyama S , Antonarakis SE , Minoshima S , Shimizu N , Nordsiek G , Hornischer K , Brant P , Scharfe M , Schon O , Desario A , Reichelt J , Kauer G , Blocker H , Ramser J , Beck A , Klages S , Hennig S , Riesselmann L , Dagand E , Haaf T , Wehrmeyer S , Borzym K , Gardiner K , Nizetic D , Francis F , Lehrach H , Reinhardt R , Yaspo ML
Ref : Nature , 405 :311 , 2000
Abstract : Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
ESTHER : Hattori_2000_Nature_405_311
PubMedSearch : Hattori_2000_Nature_405_311
PubMedID: 10830953
Gene_locus related to this paper: human-LIPI