Data processing: measuring – calibrating – or testing – Measurement system in a specific environment – Biological or biochemical
Reexamination Certificate
2006-01-12
2009-12-01
Brusca, John S (Department: 1631)
Data processing: measuring, calibrating, or testing
Measurement system in a specific environment
Biological or biochemical
C435S006120
Reexamination Certificate
active
07627437
ABSTRACT:
The present disclosure provides methods for defining one or more microbial communities. In an example, the method can include providing a plurality of microbial profiles, wherein each microbial profile is established from a sample of microorganisms obtained from an individual subject. The method can also include identifying one or more consensus profiles from among the plurality of microbial profiles. These methods can be used to characterize normal and pathological microflora in vaginal samples.
REFERENCES:
patent: 6180100 (2001-01-01), Bruce
patent: 2004/0022775 (2004-02-01), Reid et al.
patent: 2004/0126369 (2004-07-01), Payne
patent: 2005/0026188 (2005-02-01), Van Kessel et al.
Coolen et al. Characterization of the microbial flora of the human vulva by analysis of terminal restriction fragment polymorphism (T-RFLP) of 16s rDNA genes. Abstracts of the General Meeting of the American Society for Microbiology. vol. 101, p. 262 (2001).
Moore et al. Human fecal Flora: The Normal Flora of 20 Japanese-Hawaiians Applied Microbiology vol. 27, pp. 961-979 (1974).
Moore et al. 95 Intestinal Floras of Populations That Have a High Risk of Colon Cancer Applied and Environmental Microbiology vol. 61 pp. 3202-3207 (1995).
Abdo et al., “Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes,”Environ. Microbiol., 8(5):929-938, 2006.
Antonio et al., “The Identification of VaginalLactobacillusSpecies and the Demographic and Microbiologic Characteristics of Women Colonized by These Species,”J. Infect. Dis., 180:1950-1956, 1999.
Bergeron et al., “New DNA-based PCR approaches for rapid real-time detection and prevention of group B streptococcal infections in newborns and pregnant women,”Exp. Rev. Mol. Med., (01)00380-5a.pdf, Nov. 8, 2001.
Burton et al., “Evaluation of the Bacterial Vaginal Flora of 20 Postmenopausal Women by Direct (Nugent Score) and Molecular (Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis) Techniques,”J. Infect. Dis., 186:1770-1780, 2002.
Burton et al., “Improved Understanding of the Bacterial Vaginal Microbiota of Women before and after Probiotic Instillation,”Appl. Enviro. Microbiol., 69(1):97-101, 2003.
Burton et al., “Detection ofAtopobium vaginaein Postmenopausal Women by Cultivation-Independent Methods Warrants Further Investigation,”J. Clin. Microbiol., 42(4):1829-1831, 2004.
Cadieux et aL, “Lactobacillusstrains and vaginal ecology,”JAMA, 287(15):1940-1941, 2002.
Chang et al., “Inhibition of HIV infectivity by a natural human isolate ofLactobacillus jenseniiengineered to express functional two-domain CD4,”PNAS, 100(20):11672-11677, 2003.
Cole et al., “The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy,”Nucl. Acids Res., 31(1):442-443, 2003.
Cook et al., “Clinical, Microbiological, and Biochemical Factors in Recurrent Bacterial Vaginosis,”J. Clin. Microbiol., 30(4):870-877, 1992.
Coolen et al., “Characterization of Microbial Communities Found in the Human Vagina by Analysis of Terminal Restriction Fragment Length Polymorhisms of 16S rRNA Genes,”Appl. Env. Microbiol., 71(12):8729-8737, 2005.
Delaney et al., “Nugent Score Related to Vaginal Culture in Pregnant Women,”The Am. College of Obstet. And Gynecol., 98(1):79-84, 2001.
Engebretson et al., “Fidelity of Select Restriction Endonucleases in Determining Microbial Diversity by Terminal-Restriction Fragment Length Polymorphism,”Appl. Environ. Microbiology, 69(8):4823-4829, 2003.
Eschenbach et al., “Prevalence of Hydrogen Peroxide-ProducingLactobacillusSpecies in Normal Women and Women with Bacterial Vaginosis,”J. Clin. Microbiol., 27(2):251-256, 1989.
Eschenbach et al., “Influence of the Normal Menstrual Cycle on Vaginal Tissue, Discharge, and Microflora ,”Clin. Infect. Dis., 30:901-907, 2000.
Ezaki et al., “Proposal of the generaAnaerococcusgen. nov.,Peptoniphilusgen. nov. AndGallicolagen. nov. For members of the genusPeptostreptococcus,”Int. J. Syst. Evol. Microbiol., 51:1521-1528, 2001.
Falsen et al., “Phenotypic and phylogenetic characterization of a novelLactobacillusspecies from human source: description ofLactobacillus inerssp. nov.,”Int. J. Syst. Bacteriol., 49:217-221, 1999.
Favier et al., “Molecular Monitoring of Succession of Bacterial Communities in Human Neonates,”App. Environ. Microbiol., 68(1):219-226, 2002.
Ferris et al., “Use of Species-Directed 16S rRNA Gene PCR Primers for Detection ofAtopobium vaginaein Patients with Bacterial Vaginosis,”J. Clin. Microbiol., 42(12):5892-5894, 2004.
Forney et al., “Molecular microbial ecology: land of the one-eyed king,”Curr. Opin. Microbiology, 7:210-220, 2004.
Forney et al., “The vaginal flora of healthy women is not always dominated by lactobacillus species,”J. Infec. Dis., 194(10):1468-9, 2006.
Frank et al., “Culture-Independent Molecular Analysis of Microbial Constituents of the Healthy Human Outer Ear,”J. Clin. Microbiol., 41(1):295-303, 2003.
Gupta et al., “Inverse association of H202-producing Lactobacilli and vaginalEscherichia colicolonization in women with recurrent urinary tract infections,”J. Infect. Dis., 178:446-450, 1998.
Gupta et al. “Effects of Contraceptive Method on the Vaginal Microbial Flora: A Prospective Evaluation,”J. Infect. Dis., 181:595-601, 2000.
Hay, P.E., “Bacterial vaginosis and miscarriage,”Curr. Opin. Infect. Dis., 17:41-44, 2004.
Hilton et al., “LactobacillusGG Vaginal Suppositories and Vaginitis,”J. Clin. Microbiol., 33(5):1433, 1995.
Ison et al., “Validation of a simplified grading of Gram stained vaginal smears for use in genitourinary medicine clinics,”Sex. Transm. Infect., 78:413-415, 2002.
Jovita et al., “Characterization of a NovelAtopobiumIsolate from the Human Vagina: Description ofAtopobium vaginaesp. nov.,”Int. J. Syst. Bacteriol., 49:1573-1576, 1999.
Jukes et al., “Evolution of Protein Molecules,”Mammalian Protein Metabolism, Academic Press, Inc., New York and London, 1969.
Kazor et al., “Diversity of Bacterial Populations on the Tongue Dorsa of Patients with Halitosis and Healthy Patients,”J. Clin. Micrbiol., 41(2):558-563, 2003.
Kitts, C.L., “Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics,”Curr. Issues Infest. Microbiol., 2(1):17-25, 2001.
Klebanoff et al., “Viricidal Effect ofLactobacillus acidophiluson Human Immunodeficiency Virus Type 1: Possible Role in Heterosexual Transmission,”J. Exp. Med., 174:289-292, 1991.
Kroes et al., “Bacterial diversity within the human subgingival crevice,”PNAS, 96(25):14547-14552, 1999.
Larsen et al., “Understanding the Bacterial Flora of the Female Genital Tract,”Clin. Infect. Dis., 32:e69-e77, 2001.
Lindner et al., “Quantitative studies of the vaginal flora of healthy women and of obstetric and gynaecological patients,”J. Med. Microbiol., 11:233-241, 1978.
Liu et al., “Characterization of Microbial Diversity by Determining Terminal Restriction Fragment Length Polymorphisms of Genes Encoding 16S rRNA,”Appl. Env. Microbiol., 63(11):4516-4522, 1997.
Martin et al., “Vaginal Lactobacilli, Microbial Flora, and Risk of Human Immunodeficiency Virus Type 1 and Sexually Transmitted Disease Acquisition,”J. Infect. Dis., 180:1863-1868, 1999.
Masfari et al., “Quantitative studies of vaginal bacteria,”Genitourin Med., 62:256-263, 1986.
Massi et al., “Identification method based on PCR combined with automated ribotyping for tracking probioticLactobacillusstrains colonizing the human gut and vagina,ȁ
Abdo Zaid
Brown Celeste
Forney Larry J.
Foster James
Johnson Audra
Brusca John S
Idaho Research Foundation
Klarquist & Sparkman, LLP
LandOfFree
Categorization of microbial communities does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Categorization of microbial communities, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Categorization of microbial communities will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-4057740