-
1
-
-
84866895877
-
Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria
-
Ventura, M., Turroni, F., Motherway, M. O., MacSharry, J. and van Sinderen, D. Host-microbe interactions that facilitate gut colonization by commensal bifidobacteria. Trends in microbiology 20, 467-476, doi: 10.1016/j.tim.2012.07.002 (2012).
-
(2012)
Trends in Microbiology
, vol.20
, pp. 467-476
-
-
Ventura, M.1
Turroni, F.2
Motherway, M.O.3
MacSharry, J.4
Van Sinderen, D.5
-
2
-
-
84945904142
-
-
Springer, New York
-
Bergey, D. H., Goodfellow, M., Whitman, W. B. and Parte, A. C. 1 online resource (2 v.) (Springer, New York, 2012).
-
(2012)
1 Online Resource (2 V.)
-
-
Bergey, D.H.1
Goodfellow, M.2
Whitman, W.B.3
Parte, A.C.4
-
3
-
-
84861011960
-
Diversity of bifidobacteria within the infant gut microbiota
-
Turroni, F. et al. Diversity of Bifidobacteria within the Infant Gut Microbiota. PLoS One 7, e36957, doi: 10.1371/journal. pone.0036957 (2012).
-
(2012)
PLoS One
, vol.7
, pp. e36957
-
-
Turroni, F.1
-
4
-
-
84880286399
-
Assessing the fecal microbiota: An optimized ion torrent 16S rRNA gene-based analysis protocol
-
Milani, C. et al. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One 8, e68739, doi: 10.1371/journal.pone.0068739 (2013).
-
(2013)
PLoS One
, vol.8
, pp. e68739
-
-
Milani, C.1
-
5
-
-
62149124800
-
Exploring the diversity of the bifidobacterial population in the human intestinal tract
-
Turroni, F. et al. Exploring the diversity of the bifidobacterial population in the human intestinal tract. Applied and environmental microbiology 75, 1534-1545, doi: 10.1128/AEM.02216-08 (2009).
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 1534-1545
-
-
Turroni, F.1
-
6
-
-
84879411201
-
The abundance and variety of carbohydrate-active enzymes in the human gut microbiota
-
El Kaoutari, A., Armougom, F., Gordon, J. I., Raoult, D. and Henrissat, B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 11, 497-504, doi: 10.1038/nrmicro3050 (2013).
-
(2013)
Nat Rev Microbiol
, vol.11
, pp. 497-504
-
-
El Kaoutari, A.1
Armougom, F.2
Gordon, J.I.3
Raoult, D.4
Henrissat, B.5
-
7
-
-
84859925158
-
How glycan metabolism shapes the human gut microbiota
-
Koropatkin, N. M., Cameron, E. A. and Martens, E. C. How glycan metabolism shapes the human gut microbiota. Nature reviews. Microbiology 10, 323-335, doi: 10.1038/nrmicro2746 (2012).
-
(2012)
Nature Reviews. Microbiology
, vol.10
, pp. 323-335
-
-
Koropatkin, N.M.1
Cameron, E.A.2
Martens, E.C.3
-
8
-
-
57649184474
-
Genome-scale analyses of health-promoting bacteria: Probiogenomics
-
Ventura, M. et al. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nature reviews. Microbiology 7, 61-71, doi: 10.1038/nrmicro2047 (2009).
-
(2009)
Nature Reviews. Microbiology
, vol.7
, pp. 61-71
-
-
Ventura, M.1
-
9
-
-
84907266451
-
Genomic encyclopedia of type strains of the genus Bifidobacterium
-
Milani, C. et al. Genomic encyclopedia of type strains of the genus Bifidobacterium. Applied and environmental microbiology 80, 6290-6302, doi: 10.1128/AEM.02308-14 (2014).
-
(2014)
Applied and Environmental Microbiology
, vol.80
, pp. 6290-6302
-
-
Milani, C.1
-
10
-
-
84907267761
-
Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics
-
Lugli, G. A. et al. Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics. Applied and environmental microbiology 80, 6383-6394, doi: 10.1128/AEM.02004-14 (2014).
-
(2014)
Applied and Environmental Microbiology
, vol.80
, pp. 6383-6394
-
-
Lugli, G.A.1
-
11
-
-
84891757311
-
EggNOG v4.0: Nested orthology inference across 3686 organisms
-
Powell, S. et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids research 42, D231-239, doi: 10.1093/nar/gkt1253 (2014).
-
(2014)
Nucleic Acids Research
, vol.42
, pp. D231-D239
-
-
Powell, S.1
-
12
-
-
34247592087
-
Genomics as a means to understand bacterial phylogeny and ecological adaptation: The case of bifidobacteria
-
Ventura, M., Canchaya, C., Fitzgerald, G. F., Gupta, R. S. and van Sinderen, D. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie Van Leeuwenhoek 91, 351-372, doi: 10.1007/s10482-006- 9122-6 (2007).
-
(2007)
Antonie van Leeuwenhoek
, vol.91
, pp. 351-372
-
-
Ventura, M.1
Canchaya, C.2
Fitzgerald, G.F.3
Gupta, R.S.4
Van Sinderen, D.5
-
13
-
-
84891763855
-
The carbohydrate-active enzymes database (CAZy) in 2013
-
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M. and Henrissat, B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic acids research 42, D490-495, doi: 10.1093/nar/gkt1178 (2014).
-
(2014)
Nucleic Acids Research
, vol.42
, pp. D490-D495
-
-
Lombard, V.1
Golaconda Ramulu, H.2
Drula, E.3
Coutinho, P.M.4
Henrissat, B.5
-
14
-
-
80054971682
-
Carbohydrate metabolism in Bifidobacteria
-
Pokusaeva, K., Fitzgerald, G. F. and van Sinderen, D. Carbohydrate metabolism in Bifidobacteria. Genes and nutrition 6, 285-306, doi: 10.1007/s12263-010-0206-6 (2011).
-
(2011)
Genes and Nutrition
, vol.6
, pp. 285-306
-
-
Pokusaeva, K.1
Fitzgerald, G.F.2
Van Sinderen, D.3
-
16
-
-
84883755642
-
The effects of dietary fibre addition on the quality of common cereal products
-
Foschia, M., D. P., Sensidoni, A. and Brennan, C. S. The effects of dietary fibre addition on the quality of common cereal products. Journal of Cereal Science 58, 216-227 (2013).
-
(2013)
Journal of Cereal Science
, vol.58
, pp. 216-227
-
-
Foschia, M.D.P.1
Sensidoni, A.2
Brennan, C.S.3
-
17
-
-
84925175059
-
Saccharide breakdown and fermentation by the honey bee gut microbiome
-
Lee, F. J., Rusch, D. B., Stewart, F. J., Mattila, H. R. and Newton, I. L. Saccharide breakdown and fermentation by the honey bee gut microbiome. Environmental microbiology 17, 796-815, doi: 10.1111/1462-2920.12526 (2015).
-
(2015)
Environmental Microbiology
, vol.17
, pp. 796-815
-
-
Lee, F.J.1
Rusch, D.B.2
Stewart, F.J.3
Mattila, H.R.4
Newton, I.L.5
-
18
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359, doi: 10.1126/science.1124234 (2006).
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
-
19
-
-
84862276328
-
Function and diversity of the healthy human microbiome
-
Human Microbiome Project, C. Structure
-
Human Microbiome Project, C. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214, doi: 10.1038/nature11234 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
20
-
-
78650609691
-
Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging
-
Turroni, F. et al. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc Natl Acad Sci USA 107, 19514-19519, doi: 10.1073/pnas.1011100107 (2010).
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 19514-19519
-
-
Turroni, F.1
-
21
-
-
79952552818
-
An exo-alpha-sialidase from bifidobacteria involved in the degradation of sialyloligosaccharides in human milk and intestinal glycoconjugates
-
Kiyohara, M. et al. An exo-alpha-sialidase from bifidobacteria involved in the degradation of sialyloligosaccharides in human milk and intestinal glycoconjugates. Glycobiology 21, 437-447, doi: 10.1093/glycob/cwq175 (2011).
-
(2011)
Glycobiology
, vol.21
, pp. 437-447
-
-
Kiyohara, M.1
-
22
-
-
75849133666
-
Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology
-
Karp, P. D. et al. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in bioinformatics 11, 40-79, doi: 10.1093/bib/bbp043 (2010).
-
(2010)
Briefings in Bioinformatics
, vol.11
, pp. 40-79
-
-
Karp, P.D.1
-
23
-
-
80054980829
-
Glycogen with short average chain length enhances bacterial durability
-
Wang, L. and Wise, M. J. Glycogen with short average chain length enhances bacterial durability. Die Naturwissenschaften 98, 719-729, doi: 10.1007/s00114-011-0832-x (2011).
-
(2011)
Die Naturwissenschaften
, vol.98
, pp. 719-729
-
-
Wang, L.1
Wise, M.J.2
-
24
-
-
84922248771
-
Insights into glycogen metabolism in Lactobacillus acidophilus: Impact on carbohydrate metabolism, stress tolerance and gut retention
-
Goh, Y. J. and Klaenhammer, T. R. Insights into glycogen metabolism in Lactobacillus acidophilus: impact on carbohydrate metabolism, stress tolerance and gut retention. Microbial cell factories 13, 94, doi: 10.1186/s12934-014-0094-3 (2014).
-
(2014)
Microbial Cell Factories
, vol.13
, pp. 94
-
-
Goh, Y.J.1
Klaenhammer, T.R.2
-
25
-
-
46249088487
-
Glycogen and maltose utilization by Escherichia coli O157:H7 in the mouse intestine
-
Jones, S. A. et al. Glycogen and maltose utilization by Escherichia coli O157:H7 in the mouse intestine. Infection and immunity 76, 2531-2540, doi: 10.1128/IAI.00096-08 (2008).
-
(2008)
Infection and Immunity
, vol.76
, pp. 2531-2540
-
-
Jones, S.A.1
-
26
-
-
0036716927
-
Glycogen metabolism loss: A common marker of parasitic behaviour in bacteria?
-
Henrissat, B., Deleury, E. and Coutinho, P. M. Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria? Trends in genetics: TIG 18, 437-440 (2002).
-
(2002)
Trends in Genetics: TIG
, vol.18
, pp. 437-440
-
-
Henrissat, B.1
Deleury, E.2
Coutinho, P.M.3
-
27
-
-
84909606775
-
Phylogenomics resolves the timing and pattern of insect evolution
-
Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763-767, doi: 10.1126/ science.1257570 (2014).
-
(2014)
Science
, vol.346
, pp. 763-767
-
-
Misof, B.1
-
28
-
-
77956724014
-
The biochemistry of sugars and polysaccharides in insects
-
Wyatt, G. R. The Biochemistry of Sugars and Polysaccharides in Insects. Advances in Insect Physiology 4, 287-360 (1967).
-
(1967)
Advances in Insect Physiology
, vol.4
, pp. 287-360
-
-
Wyatt, G.R.1
-
29
-
-
84926468863
-
Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium
-
Egan, M. et al. Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium. BMC microbiology 14, 282, doi: 10.1186/s12866-014-0282-7 (2014).
-
(2014)
BMC Microbiology
, vol.14
, pp. 282
-
-
Egan, M.1
-
30
-
-
33845508443
-
Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host
-
Sonnenburg, J. L., Chen, C. T. and Gordon, J. I. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol 4, e413, doi: 10.1371/journal.pbio.0040413 (2006).
-
(2006)
PLoS Biol
, vol.4
, pp. e413
-
-
Sonnenburg, J.L.1
Chen, C.T.2
Gordon, J.I.3
-
31
-
-
84874953256
-
Human milk and related oligosaccharides as prebiotics
-
Barile, D. and Rastall, R. A. Human milk and related oligosaccharides as prebiotics. Current opinion in biotechnology 24, 214-219, doi: 10.1016/j.copbio.2013.01.008 (2013).
-
(2013)
Current Opinion in Biotechnology
, vol.24
, pp. 214-219
-
-
Barile, D.1
Rastall, R.A.2
-
32
-
-
84866789452
-
Bifidobacterial enzymes involved in the metabolism of human milk oligosaccharides
-
Kitaoka, M. Bifidobacterial enzymes involved in the metabolism of human milk oligosaccharides. Advances in nutrition 3, 422S-429S, doi: 10.3945/an.111.001420 (2012).
-
(2012)
Advances in Nutrition
, vol.3
, pp. 422S-429S
-
-
Kitaoka, M.1
-
33
-
-
57749113201
-
The genome sequence of Bifidobacterium longum subsp. Infantis reveals adaptations for milk utilization within the infant microbiome
-
Sela, D. A. et al. The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America 105, 18964-18969, doi: 10.1073/pnas.0809584105 (2008).
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 18964-18969
-
-
Sela, D.A.1
-
34
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature methods 9, 811-814, doi: 10.1038/nmeth.2066 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
-
35
-
-
80052661466
-
Method for milk oligosaccharide profiling by 2-aminobenzamide labeling and hydrophilic interaction chromatography
-
Marino, K. et al. Method for milk oligosaccharide profiling by 2-aminobenzamide labeling and hydrophilic interaction chromatography. Glycobiology 21, 1317-1330, doi: 10.1093/glycob/cwr067 (2011).
-
(2011)
Glycobiology
, vol.21
, pp. 1317-1330
-
-
Marino, K.1
-
36
-
-
0017184389
-
A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
-
Bradford, M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical biochemistry 72, 248-254 (1976).
-
(1976)
Analytical Biochemistry
, vol.72
, pp. 248-254
-
-
Bradford, M.M.1
-
37
-
-
58149203228
-
SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny
-
Wilson, D. et al. SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic acids research 37, D380-386, doi: 10.1093/nar/gkn762 (2009).
-
(2009)
Nucleic Acids Research
, vol.37
, pp. D380-D386
-
-
Wilson, D.1
-
38
-
-
0001760677
-
Molecular cloning: A laboratory manual
-
NY: Cold Spring Harbor Laboratory
-
Sambrook, J., E. F. F. and Maniatis, T. Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 545 (1989).
-
(1989)
Cold Spring Harbor
, vol.545
-
-
Sambrook, J.E.F.F.1
Maniatis, T.2
-
39
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li, H. and Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760, doi: 10.1093/bioinformatics/btp324 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
40
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. and Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome biology 15, 550, doi: 10.1186/s13059-014-0550-8 (2014).
-
(2014)
Genome Biology
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
41
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
U357-U354
-
Langmead, B. and Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-U354, doi: Doi 10.1038/ Nmeth.1923 (2012).
-
(2012)
Nature Methods
, vol.9
-
-
Langmead, B.1
Salzberg, S.L.2
-
42
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079, doi: 10.1093/bioinformatics/ btp352 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
43
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan, A. R. and Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842, doi: 10.1093/bioinformatics/btq033 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
|