US 7326551B2
· Maupin-Furlow et al.
· 2008
[cited by applicant]
US 20040028689A1
· Borody
· 2004
[cited by applicant]
JP 2001069990A
· 2001
[cited by examiner]
WO WO2010062369A2
· 2010
[cited by examiner]
WO WO2012142605A1
· 2012
[cited by examiner]
WO WO2013053836A1
· 2013
[cited by applicant]
WO WO2013080561A1
· 2013
[cited by examiner]
WO WO2013171515A1
· 2013
[cited by applicant]
Kitahara et al. Int J Syst Evol Microbiol. 2000;50 Pt 3:971-978.
[cited by examiner]
Wells et al. Clinica Chimica Acta 331.2003:127-134.
[cited by examiner]
Ridlon, JM. Enzymology And Molecular Biology Of Bile Acid 7-alpha- And 7-beta-Dehydroxylation By The Intestinal Bacteria Clostridium scindens And Clostridium hylemonae. VCU Theses and Dissertations, 2008.
[cited by examiner]
Definition of kit. http://oxforddictionaries.com/search?q=kit&view=uk retrieved Aug. 13, 2010.
[cited by examiner]
U.S. Appl. No. 16/523,414 (11,471,495 B2) filed Jul. 26, 2019 (Oct. 18, 2022).
[cited by applicant]
U.S. Appl. No. 15/312,610 (Abandoned) filed Nov. 18, 2016.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Jul. 15, 2022 Issue Fee Payment.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Jul. 11, 2022 Notice of Allowance.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed May 11, 2022 Response to Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Feb. 11, 2022 Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Dec. 10, 2021 Response to Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Jun. 11, 2021 Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Mar. 8, 2021 Response to Final Office Action with Request for Continued Examination (RCE).
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Nov. 6, 2020 Response to Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Sep. 9, 2020 Response to Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Jun. 9, 2020 Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed May 5, 2020 Response to Restriction Requirement.
[cited by applicant]
U.S. Appl. No. 16/523,414, filed Feb. 5, 2020 Restriction Requirement.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Jul. 27, 2019 Abandonment.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed May 7, 2019 Advisory Action.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Apr. 26, 2019 Response after Final Office Action.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Feb. 26, 2019 Final Office Action.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Dec. 12, 2018 Response to Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Jul. 10, 2018 Non-Final Office Action.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Nov. 13, 2017 Response to Restriction Requirement.
[cited by applicant]
U.S. Appl. No. 15/312,610, filed Sep. 13, 2017 Restriction Requirment.
[cited by applicant]
U.S. Appl. No. 16/523,414, dated Jul. 15, 2022 Issue Fee Payment.
[cited by applicant]
Abt et al., “Commensal Bacteria Calibrate the Activation Threshold of Innate Antiviral Immunity,” Immunity, 37(1): 158-170 (2012).
[cited by applicant]
Atarashi et al., “Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota,” Nature, 500:232-236 (2013).
[cited by applicant]
Bakken et al., “Treating Clostridium difficile infection with Fecal Microbiota Transplantation,” Clin Gastroenterol Hepatol., 9(12):1044-1049 (2011).
[cited by applicant]
Barrasa et al., “Bile acids in the colon, from healthy to cytotoxic molecules,” Toxicology In Vitro 27:964-977 (2013).
[cited by applicant]
Bartlett et al., “Antibiotic-Associated Pseudomembranous Colitis Due To Toxin- Producing Clostridia,” N. Engl. J. Med. 298(10):531-534 (1978).
[cited by applicant]
Basler et al., “Tit-for-tat: Type VI secretion system counterattack during bacterial cell-cell interactions,” Cell, 152(4):884-894 (2013).
[cited by applicant]
Basler et al., “Type VI secretion requires a dynamic contractile phage tail-like structure,” Nature, 483(7388): 182-186 (2013).
[cited by applicant]
Bernstein et al., “Bile acids as carcinogens in human gastrointestinal cancers,” Mutation Res 589:47-65 (2005).
[cited by applicant]
Brandl et al., “Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficit,”. Nature 455(7214): 804-807 (2008).
[cited by applicant]
Britton et al., “Role of the Intestinal Microbiota in Resistance to Colonization by Clostridium difficile,” Gastroenterology 146:1547-1553 (2014).
[cited by applicant]
Buffie et al., “Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to
[cited by applicant]
Buffie et al., “Microbiota-mediated colonization resistance against intestinal pathogens,” Nature Reviews Immunology 13(11):790-801 (2013).
[cited by applicant]
Buffie et al., “Precision microbiome reconstitution restores bile acid mediated resistance to
[cited by applicant]
Caporaso et al., “QIIME allows analysis of high-throughput community sequencing data,” Nat Methods. 7(5):335-336 (2010).
[cited by applicant]
Caporaso et al., “Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms,” The ISME Journal 6:1621-1624 (2012).
[cited by applicant]
Carlier et al., “Proposal to unify
[cited by applicant]
Chang et al., “Decreased Diversity of the Fecal Microbiome in Recurrent
[cited by applicant]
Chen et al., “A Mouse Model of
[cited by applicant]
Chen et al., “Overview of
[cited by applicant]
Chung et al., “Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota,” Cell 149(7): 1578-1593 (2012).
[cited by applicant]
Cohen, Statistical Powerr Analysis for the Behavioral Sciences, Second Edition Routledge, Hillsdale, NJ, 1988).
[cited by applicant]
Collins et al., “The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations,” Int J Syst Bacteriol 44(4):812-826 (1994).
[cited by applicant]
Cruz et al. Antimicrob. Agents Chemother. Jan. 2000 vol. 44 No. 1 143-149.
[cited by applicant]
De Aguiar Vallim et al., “Pleiotropic Roles of Bile Acids in Metabolism,” Cell Metab. 17(5):657-669 (2013).
[cited by applicant]
Dethlefsen et al., “Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation,” PNAS 108(Suppl. 1):4554-4561 (2011).
[cited by applicant]
Diehl et al., “Microbiota Restricts Trafficking of Bacteria to Mesenteric Lymph Nodes by CX(3)CRI(hi) Cells,” Nature 494(7435):116-120 (2013).
[cited by applicant]
Duan et al., “Microbial colonization drives expansion of IL-1 receptor 1 expressing, IL-17 producing gamma/delta T cells,” Cell Host Microbe, 7(2): 140-150 (2010).
[cited by applicant]
Edgar et al., “UCHIME improves sensitivity and speed of chimera detection,” Bioinformatics 27(16):2194-2200 (2011).
[cited by applicant]
Farache et al., “Luminal Bacteria Recruit CD103(+) Dendritic Cells into the Intestinal Epithelium to Sample Bacterial Antigens for Presentation,” Immunity, 38(3):581-595 (2013).
[cited by applicant]
Ferreira et al., “The Intestinal Microbiota Plays a Role in Salmonella-Induced Colitis Independent of Pathogen Colonization,” PLoS One 6(5):e20338 (2011).
[cited by applicant]
Giel et al., “Metabolism of Bile Salts in Mice Influences Spore Germination in Clostridium difficile,” PLoS ONE, 5(1):e8740 (2010).
[cited by applicant]
“Gut” definition. Merriam Webster Dictionary. https://www.merriam-webster.com/dictionary/gut retrieved Feb. 20, 2019/.
[cited by applicant]
Hall, “Building Phylogenetic Trees from Molecular Data with MEGA,” Mol. Biol. Evol. 30(5):1229-1235 (2013).
[cited by applicant]
Hamilton et al., “High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria,” Gut Microbes 4(2): 125-135 (2013).
[cited by applicant]
Hand et al., “Acute Gastrointestinal Infection Induces Long-Lived Microbiota-Specific T Cell Responses,” Science, 337(6101): 1553-1556 (2012).
[cited by applicant]
Heeg et al., “
[cited by applicant]
Hill et al., “Commensal bacteria-derived signals regulate basophil hematopoiesis and allergic inflammation,” Nat Med., 18(4):538-546 (2012).
[cited by applicant]
Huse et al., “Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing,” PLoS Genet 4(11):e1000255 (2008).
[cited by applicant]
International Search Report mailed Sep. 8, 2015 in International Application No. PCT/US15/31627.
[cited by applicant]
Ivanov et al., “Induction of intestinal Th17 cells by segmented filamentous bacteria,” Cell, 139(3):485-498 (2009).
[cited by applicant]
Kang et al., “
[cited by applicant]
Kinnebrew et al., “Early
[cited by applicant]
Koeth et al., “Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis,” Nat Med. 19(5):576-585 (2013).
[cited by applicant]
Krishna et al., “Risk Factors, preemptive therapy, and antiperistaltic agents for Clostridium difficile infection in cancer patients,” Transplant Infect Dis., 15:493-501 (2013).
[cited by applicant]
Kyne et al., “Health Care Costs and Mortality Associated with Nosocomial Diarrhea Due to
[cited by applicant]
Langille et al., “Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences,” Nat Biotechnol 31(9):814-821 (2013).
[cited by applicant]
Lathrop et al., “Peripheral education of the immune system by colonic commensal microbiota,” Nature, 478(7368):250-254 (2012).
[cited by applicant]
Lawley et al., “Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing
[cited by applicant]
Liu et al., “Reclassification of
[cited by applicant]
Louie et al., “Tolevamer, a Novel Nonantibiotic Polymer, Compared with Vancomycin in the Treatment of Mild to Moderately Severe
[cited by applicant]
Lozupone et al., “UniFrac: a New Phylogenetic Method for Comparing Microbial Communities,” Appl Environ Microbiol 71(12):8228-8235 (2005).
[cited by applicant]
Macpherson et al., “Induction of Protective IgA by Intestinal Dendritic Cells Carrying Commensal Bacteria,” Science, 303:1662-1665 (2004).
[cited by applicant]
Manges et al., “Comparative Metagenomic Study of Alterations to the Intestinal Microbiota and Risk of Nosocomial
[cited by applicant]
Marcus et al. Gut, 1988, 29, 522-533.
[cited by applicant]
Marsh et al., “Association of Relapse of
[cited by applicant]
Olszak et al., “Microbial Exposure During Early Life has Persistent Effects on Natural Killer T Cell Function,” Science, 336(6080):489-493 (2012).
[cited by applicant]
Ott et al., “Quantification of Intestinal Bacterial Populations by Real-Time PCR with a Universal Primer Set and Minor Groove Binder Probes: a Global Approach to the Enteric Flora,” Journal of Clinical Microbiology, 42(…
[cited by applicant]
Out et al., “Bile acid sequestrants: more than simple resins,” Curr Opin Lipidol 23:43-55 (2012).
[cited by applicant]
Pamer, “Fecal microbiota transplantation: effectiveness, complexities, and lingering concerns,” Mucosal Immunol 7(2):210-214 (2014).
[cited by applicant]
Partial Supplementary European Search Report dated Jan. 4, 2018 in Application No. 15796000.6.
[cited by applicant]
Petrof et al., “Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut,” Microbiome 1:3, pp. 1-12 (2013).
[cited by applicant]
Rakoff-Nahoum et al., “Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis,” Cell, 118:229-241 (2004).
[cited by applicant]
Rasti et al. Journal of Food Agriculture and Environment 11(2):127-131, Apr. 2013.
[cited by applicant]
Rea et al., “Effect of broad- and narrow-spectrum antimicrobials on Clostridium difficile and microbial diversity in a model of the distal colon,” PNAS 108(Suppl. 1):4639-4644 (2011).
[cited by applicant]
Rea et al., “Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against
[cited by applicant]
Reeves et al., “The interplay between microbiome dynamics and pathogen dynamics in a murine model of
[cited by applicant]
Ridlon et al., “Bile salt biotransformations by human intestinal bacteria,” J Lipid Res 47:241-259 (2006).
[cited by applicant]
Ridlon et al., “
[cited by applicant]
Ridlon et al., “Identification and characterization of two bile-acid coenzyme A transferases from
[cited by applicant]
Rupnik et al., “Clostridium difficile infection: new developments in epidemiology and pathogenesis,” Nat Rev Microbiol 7:526-536 (2009).
[cited by applicant]
Schloss et al., “Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities,” Appl Environ Microbiol 75(23):7537-7541 (2009).
[cited by applicant]
Sheneman et al., “Clearcut: a fast implementation of relaxed neighbor joining,” Bioinformatics 22(22):2823-2824 (2006).
[cited by applicant]
Sorg et al., “Bile Salts and Glycine as Cogerminants for
[cited by applicant]
Sorg et al., “Chenodeoxycholate is an Inhibitor of
[cited by applicant]
Stein et al., “Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota,” PLoS Comput Biol 9(12):e1003388 (2013).
[cited by applicant]
Surawicz et al., “Treatment of refractory and recurrent
[cited by applicant]
Taur et al., “Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation,” Clin Infect Dis 55(7):905-914 (2012).
[cited by applicant]
The Human Microbiome Project Consortium: “Structure, Function and Diversity of the Healthy Human Microbiome,” Nature 486(7402):207-214 (2013).
[cited by applicant]
Theriot et al., “Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to
[cited by applicant]
Turnbaugh et al., “A core gut microbiome in obese and lean twins,” Nature 457(7228): 480-484 (2009).
[cited by applicant]
Ubeda et al., “Intestinal Microbiota Containing
[cited by applicant]
Ubeda et al., “Vancomycin-resistant
[cited by applicant]
van Nood et al., “Duodenal Infusion of Donor Feces for Recurrent
[cited by applicant]
Vogt et al. Anaerobe 34 (2015)106-115.
[cited by applicant]
Weingarden et al., “Microbiota transplantation restores normal fecal bile acid composition in recurrent
[cited by applicant]
Wells et al., “Identification and Characterization of a Bile Acid 7β-Dehydroxylation Operon in
[cited by applicant]
Wingender et al., “Intestinal Microbes Affect Phenotypes and Functions of Invariant Natural Killer T Cells in Mice,” Gastroenterology, 143(2):418-428 (2012).
[cited by applicant]
Yutin et al., “A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia,” Environ Microbiol. 15(10):2631-2641 (2013).
[cited by applicant]
Zar et al., “A Comparison of Vancomycin and Metronidazole for the Treatment of
[cited by applicant]
Zhao et al., “RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data,” Bioinformatics 28(1): 125-126 (2012).
[cited by applicant]
Zilberberg et al., “Increase in Adult
[cited by applicant]