Title:
OLIGONUCLEOTIDE PROBE SET AND METHODS OF MICROBIOTA PROFILING
Document Type and Number:
WIPO Patent Application WO/2012/080754
Kind Code:
A3
Abstract:
The invention provides a set of oligonucleotide probes, said set comprising:(a) an oligonucleotide comprising a nucleotide sequence selected from SEQ ID NO 1, SEQ ID NO 27 or a sequence capable of hybridising to either sequence under conditions of high stringency;(b) an oligonucleotide comprising a nucleotide sequence selected from SEQ ID NO 2, SEQ ID NO 28 or a sequence capable of hybridising to either sequence under conditions of high stringency;(c) an oligonucleotide comprising a nucleotide sequence selected from SEQ ID NO 3, SEQ ID NO 29 or a sequence capable of hybridising to either sequence under conditions of high stringency;(d) an oligonucleotide comprising a nucleotide sequence selected from SEQ ID NO 4, SEQ ID NO 30 or a sequence capable of hybridising to either sequence under conditions of high stringency; and(e) one or more oligonucleotides comprising a nucleotide sequence selected from those recited in Table 1 or a sequence capable of hybridising to any nucleotide sequence recited in Table 1 under conditions of high stringency; and optionally(f) one or more oligonucleotides comprising a nucleotide sequence selected from those recited in Table 2 and Table 3 or a sequence capable of hybridising to any nucleotide sequence recited in Table 2 and Table 3 under conditions of high stringency. Methods of profiling the microbiota of the GI tract of a subject and methods of diagnosing or monitoring a disease or condition in a subject or predicting or assessing the risk of a subject developing a disease or condition in which the oligonucleotide probe set of the invention is used are also provided. Kits comprising the oligonucleotide probe set of the invention are also provided.
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Inventors:
VEBOE HEIDI (NO)
RUDI KNUT (NO)
SEKELJA MONIKA (NO)
RUDI KNUT (NO)
SEKELJA MONIKA (NO)
Application Number:
PCT/GB2011/052509
Publication Date:
June 20, 2013
Filing Date:
December 16, 2011
Export Citation:
Assignee:
GENETIC ANALYSIS AS (NO)
VEBOE HEIDI (NO)
RUDI KNUT (NO)
ROWE DANIEL (GB)
SEKELJA MONIKA (NO)
VEBOE HEIDI (NO)
RUDI KNUT (NO)
ROWE DANIEL (GB)
SEKELJA MONIKA (NO)
International Classes:
C12Q1/68
Domestic Patent References:
| WO2009123736A2 | 2009-10-08 |
Other References:
H. C. VEBO ET AL: "Temporal Development of the Infant Gut Microbiota in Immunoglobulin E-Sensitized and Nonsensitized Children Determined by the GA-Map Infant Array", CLINICAL AND VACCINE IMMUNOLOGY, vol. 18, no. 8, 8 June 2011 (2011-06-08), pages 1326 - 1335, XP055020163, ISSN: 1556-6811, DOI: 10.1128/CVI.00062-11
PALMER CHANA ET AL: "Development of the human infant intestinal microbiota", PLOS BIOLOGY, vol. 5, no. 7, July 2007 (2007-07-01), pages 1556 - 1573, XP002694662, ISSN: 1544-9173
PENDERS JOHN ET AL: "Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study", GUT, vol. 56, no. 5, May 2007 (2007-05-01), pages 661 - 667, XP002694663, ISSN: 0017-5749
PALIY OLEG ET AL: "High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray.", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 75, no. 11, June 2009 (2009-06-01), pages 3572 - 3579, XP055020698, ISSN: 1098-5336
MERETE EGGESBĂ ET AL: "Development of gut microbiota in infants not exposed to medical interventions", APMIS, vol. 119, no. 1, 25 October 2010 (2010-10-25), publication online, pages 17 - 35, XP055058174, ISSN: 0903-4641, DOI: 10.1111/j.1600-0463.2010.02688.x
HONG PEI-YING ET AL: "Comparative Analysis of Fecal Microbiota in Infants with and without Eczema", PLOS ONE, vol. 5, no. 4, E9964, April 2010 (2010-04-01), pages 1 - 10, XP002694665, ISSN: 1932-6203
VAN ZWOL A ET AL: "Intestinal microbiota in allergic and nonallergic 1-year-old very low birth weight infants after neonatal glutamine supplementation", ACTA PAEDIATRICA, INTERNATIONAL JOURNAL OF PAEDIATRICS, vol. 99, no. 12, 29 October 2010 (2010-10-29), BLACKWELL PUBLISHING LTD GBR, pages 1868 - 1874, XP002694666, ISSN: 0803-5253
COX MICHAEL J ET AL: "Lactobacillus casei Abundance Is Associated with Profound Shifts in the Infant Gut Microbiome", PLOS ONE, vol. 5, no. 1, E8745, January 2010 (2010-01-01), pages 1 - 8, XP002694667, ISSN: 1932-6203
KIRJAVAINEN P V ET AL: "Aberrant composition of gut microbiota of allergic infants: A target of bifidobacterial therapy at weaning?", GUT, vol. 51, no. 1, 1 July 2002 (2002-07-01), BRITISH MEDICAL ASSOCIATION, LONDON, UK, pages 51 - 55, XP009096010, ISSN: 0017-5749, DOI: 10.1136/GUT.51.1.51
MIRJANA RAJILIC-STOJANOVIC ET AL: "Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults", ENVIRONMENTAL MICROBIOLOGY, vol. 11, no. 7, 1 July 2009 (2009-07-01), pages 1736 - 1751, XP055050787, ISSN: 1462-2912, DOI: 10.1111/j.1462-2920.2009.01900.x
C. PALMER: "Rapid quantitative profiling of complex microbial populations", NUCLEIC ACIDS RESEARCH, vol. 34, no. 1, E5, 8 January 2006 (2006-01-08), pages 1 - 10, XP055051215, ISSN: 0305-1048, DOI: 10.1093/nar/gnj007
OIEN T ET AL: "Intestinal microbiota and its effect on the immune system - A nested case-cohort study on prevention of atopy among small children in Trondheim: The IMPACT study", CONTEMPORARY CLINICAL TRIALS, vol. 27, no. 4, 1 August 2006 (2006-08-01), ELSEVIER, GB, pages 389 - 395, XP024919920, ISSN: 1551-7144, [retrieved on 20060801], DOI: 10.1016/J.CCT.2006.02.009
PALMER CHANA ET AL: "Development of the human infant intestinal microbiota", PLOS BIOLOGY, vol. 5, no. 7, July 2007 (2007-07-01), pages 1556 - 1573, XP002694662, ISSN: 1544-9173
PENDERS JOHN ET AL: "Gut microbiota composition and development of atopic manifestations in infancy: the KOALA Birth Cohort Study", GUT, vol. 56, no. 5, May 2007 (2007-05-01), pages 661 - 667, XP002694663, ISSN: 0017-5749
PALIY OLEG ET AL: "High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray.", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 75, no. 11, June 2009 (2009-06-01), pages 3572 - 3579, XP055020698, ISSN: 1098-5336
MERETE EGGESBĂ ET AL: "Development of gut microbiota in infants not exposed to medical interventions", APMIS, vol. 119, no. 1, 25 October 2010 (2010-10-25), publication online, pages 17 - 35, XP055058174, ISSN: 0903-4641, DOI: 10.1111/j.1600-0463.2010.02688.x
HONG PEI-YING ET AL: "Comparative Analysis of Fecal Microbiota in Infants with and without Eczema", PLOS ONE, vol. 5, no. 4, E9964, April 2010 (2010-04-01), pages 1 - 10, XP002694665, ISSN: 1932-6203
VAN ZWOL A ET AL: "Intestinal microbiota in allergic and nonallergic 1-year-old very low birth weight infants after neonatal glutamine supplementation", ACTA PAEDIATRICA, INTERNATIONAL JOURNAL OF PAEDIATRICS, vol. 99, no. 12, 29 October 2010 (2010-10-29), BLACKWELL PUBLISHING LTD GBR, pages 1868 - 1874, XP002694666, ISSN: 0803-5253
COX MICHAEL J ET AL: "Lactobacillus casei Abundance Is Associated with Profound Shifts in the Infant Gut Microbiome", PLOS ONE, vol. 5, no. 1, E8745, January 2010 (2010-01-01), pages 1 - 8, XP002694667, ISSN: 1932-6203
KIRJAVAINEN P V ET AL: "Aberrant composition of gut microbiota of allergic infants: A target of bifidobacterial therapy at weaning?", GUT, vol. 51, no. 1, 1 July 2002 (2002-07-01), BRITISH MEDICAL ASSOCIATION, LONDON, UK, pages 51 - 55, XP009096010, ISSN: 0017-5749, DOI: 10.1136/GUT.51.1.51
MIRJANA RAJILIC-STOJANOVIC ET AL: "Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults", ENVIRONMENTAL MICROBIOLOGY, vol. 11, no. 7, 1 July 2009 (2009-07-01), pages 1736 - 1751, XP055050787, ISSN: 1462-2912, DOI: 10.1111/j.1462-2920.2009.01900.x
C. PALMER: "Rapid quantitative profiling of complex microbial populations", NUCLEIC ACIDS RESEARCH, vol. 34, no. 1, E5, 8 January 2006 (2006-01-08), pages 1 - 10, XP055051215, ISSN: 0305-1048, DOI: 10.1093/nar/gnj007
OIEN T ET AL: "Intestinal microbiota and its effect on the immune system - A nested case-cohort study on prevention of atopy among small children in Trondheim: The IMPACT study", CONTEMPORARY CLINICAL TRIALS, vol. 27, no. 4, 1 August 2006 (2006-08-01), ELSEVIER, GB, pages 389 - 395, XP024919920, ISSN: 1551-7144, [retrieved on 20060801], DOI: 10.1016/J.CCT.2006.02.009
Attorney, Agent or Firm:
DEHNS (10 Salisbury Square, London EC4Y 8JD, GB)
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