Abstract

The present invention relates to a method for performing a microbiome-analysis, comprising the steps: a) providing a primary sample derived from a microbiomic sample, the primary sample comprising a first target species at a first concentration and a second target species at a second concentration and different from the first target species, wherein the first target species is indicative of a first element of a microbiome of the microbiomic sample and the second target species is indicative of a second element of the microbiome, and wherein the second concentration is higher than the first concentration; b) providing two or more secondary samples derived from the primary sample, the two or more secondary samples including at least a highest dilution secondary sample, a lowest dilution secondary sample and optionally one or more intermediate dilution secondary samples, wherein the at least two secondary samples have different dilutions, and wherein the lowest dilution secondary sample may be diluted or undiluted primary sample; c) providing a first fluorescent label that is configured to directly or indirectly bind specifically to the first target species to the lowest dilution secondary sample under conditions allowing for labeling the first target species with the first fluorescent label, and providing a second fluorescent label that is configured to directly or indirectly bind specifically to the second target species to the highest dilution secondary sample, but not to the lowest dilution secondary sample, under conditions allowing for labeling the second target species with the second fluorescent label; d) analyzing the first and second target species according to the steps; d1) imaging the secondary samples with fluorescence microscopy and counting the fluorescent first and second labels in the corresponding secondary samples; d2) calculating the ratio of the first target species to the second target species from the results of step d1) and the dilutions of the corresponding secondary samples.

IPC Classes  ?

• C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• C12Q 1/6816 - Hybridisation assays characterised by the detection means
• G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor
• G01N 33/569 - ImmunoassayBiospecific binding assayMaterials therefor for microorganisms, e.g. protozoa, bacteria, viruses
• G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances

Abstract

The relative abundance of bacterial species in a patient ' s microbiome is quantified using DNA nanostructures that fluoresce multiple colors. Immobilizing binders have binding sites with nucleotide sequences complementary to those at a primary site on rRNA subunits of each selected bacterial species. Fluorophore binders have binding sites with nucleotide sequences complementary to those at a secondary site on the rRNA subunits. The fluorophore binders for each bacterial species are attached to nanostructures that fluoresce a particular color for each bacteria. The immobilizing binders are attached to the surface of a microscopy chamber. RNA subunits are extracted from a microbiome sample of the patient and are attached to the corresponding immobilizing binders and fluorophore binders such that the RNA subunits of each bacterial species fluoresce a color unique to the species. DNA nanostructures emitting the same color are counted to determine the relative concentration of the bacterial species in the sample.

IPC Classes  ?

• C12Q 1/6816 - Hybridisation assays characterised by the detection means

Abstract

The relative abundance of bacterial species in a patient’s microbiome is quantified using DNA nanostructures that fluoresce multiple colors. Immobilizing binders have binding sites with nucleotide sequences complementary to those at a primary site on rRNA subunits of each selected bacterial species. Fluorophore binders have binding sites with nucleotide sequences complementary to those at a secondary site on the rRNA subunits. The fluorophore binders for each bacterial species are attached to nanostructures that fluoresce a particular color for each bacteria. The immobilizing binders are attached to the surface of a microscopy chamber. RNA subunits are extracted from a microbiome sample of the patient and are attached to the corresponding immobilizing binders and fluorophore binders such that the RNA subunits of each bacterial species fluoresce a color unique to the species. DNA nanostructures emitting the same color are counted to determine the relative concentration of the bacterial species in the sample.

IPC Classes  ?

• C12Q 1/6816 - Hybridisation assays characterised by the detection means
• C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

Abstract

The present invention relates to a method for performing a microbiome-analysis, comprising the steps: a) providing a primary sample derived from a microbiomic sample, the primary sample comprising a first target species at a first concentration and a second target species at a second concentration and different from the first target species, wherein the first target species is indicative of a first element of a microbiome of the microbiomic sample and the second target species is indicative of a second element of the microbiome, and wherein the second concentration is higher than the first concentration; b) providing two or more secondary samples derived from the primary sample, the two or more secondary samples including at least a highest dilution secondary sample, a lowest dilution secondary sample and optionally one or more intermediate dilution secondary samples, wherein the at least two secondary samples have different dilutions, and wherein the lowest dilution secondary sample may be diluted or undiluted primary sample; c) providing a first fluorescent label that is configured to directly or indirectly bind specifically to the first target species to the lowest dilution secondary sample under conditions allowing for labeling the first target species with the first fluorescent label, and providing a second fluorescent label that is configured to directly or indirectly bind specifically to the second target species to the highest dilution secondary sample, but not to the lowest dilution secondary sample, under conditions allowing for labeling the second target species with the second fluorescent label; d) analyzing the first and second target species according to the steps: dl) imaging the secondary samples with fluorescence microscopy and counting the fluorescent first and second labels in the corresponding secondary samples; d2) calculating the ratio of the first target species to the second target species from the results of step dl) and the dilutions of the corresponding secondary samples.

IPC Classes  ?

• G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor
• C12Q 1/6839 - Triple helix formation or other higher order conformations in hybridisation assays
• C12Q 1/6888 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
• G01N 33/569 - ImmunoassayBiospecific binding assayMaterials therefor for microorganisms, e.g. protozoa, bacteria, viruses
• G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances

Abstract

The present invention relates to a method for performing a microbiome-analysis, comprising the steps: a) providing a primary sample derived from a microbiomic sample, the primary sample comprising a first target species at a first concentration and a second target species at a second concentration and different from the first target species, wherein the first target species is indicative of a first element of a microbiome of the microbiomic sample and the second target species is indicative of a second element of the microbiome, and wherein the second concentration is higher than the first concentration; b) providing two or more secondary samples derived from the primary sample, the two or more secondary samples including at least a highest dilution secondary sample, a lowest dilution secondary sample and optionally one or more intermediate dilution secondary samples, wherein the at least two secondary samples have different dilutions, and wherein the lowest dilution secondary sample may be diluted or undiluted primary sample; c) providing a first fluorescent label that is configured to directly or indirectly bind specifically to the first target species to the lowest dilution secondary sample under conditions allowing for labeling the first target species with the first fluorescent label, and providing a second fluorescent label that is configured to directly or indirectly bind specifically to the second target species to the highest dilution secondary sample, but not to the lowest dilution secondary sample, under conditions allowing for labeling the second target species with the second fluorescent label; d) analyzing the first and second target species according to the steps: dl) imaging the secondary samples with fluorescence microscopy and counting the fluorescent first and second labels in the corresponding secondary samples; d2) calculating the ratio of the first target species to the second target species from the results of step dl) and the dilutions of the corresponding secondary samples.

IPC Classes  ?

• C12Q 1/6839 - Triple helix formation or other higher order conformations in hybridisation assays
• C12Q 1/6888 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
• G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor
• G01N 33/569 - ImmunoassayBiospecific binding assayMaterials therefor for microorganisms, e.g. protozoa, bacteria, viruses
• G01N 33/58 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving labelled substances

Goods & Services

Chemicals, biological and biochemical products used in industry, science, therapy and diagnosis, including for medical diagnostics; reagents for processing, examining and analysis of chemical and biological material; tests for scientific research and laboratory use; diagnostic kits comprising specimen receptors and reagents for testing for selected bacteria; reagents for use in diagnostic tests [other than for medical or veterinary purposes]. Pharmaceutical and medicinal preparations and substances; medical diagnostic test kits; diagnostic agents for medical use; diagnostic kits for medical purposes; test kits for health care. Scientific, optical and measuring apparatus and instruments, especially for and in connection with the separation, analysis, processing and cultivation of biological material; apparatus for research laboratories for measuring, testing and analysing microbiomes; software for diagnostic apparatus; databases. Apparatus and instruments for medical use; medical apparatus for measuring, testing and analysing microbiomes; diagnostic, examination, and monitoring equipment; apparatus for carrying-out diagnostic tests for medical purposes; testing apparatus for medical purposes. Providing of access to databases for scientific and diagnostic purposes. Industrial analysis and testing services; research and development in the field of microbiomes; laboratory services for analytical testing; clinical research. Medical services relating to analysis and diagnostics; conducting and evaluation of microbiome tests for medical purposes.

Goods & Services

Pharmaceutical and medicinal preparations and substances for treating directly or indirectly microbiome-related diseases; medical diagnostic test kits comprised of nucleic acid purification kits, flow cells, buffers, DNA-oligonucleotides, DNA-Nanostructures; diagnostic agents for medical use, namely, DNA-oligonucleotides, DNA-Nanostructures for diagnosing directly or indirectly microbiome-related diseases; diagnostic kits for medical purposes comprised of nucleic acid purification kits, flow cells, buffers, DNA-oligonucleotides, DNA-Nanostructures for diagnosing directly or indirectly microbiome-related diseases; test kits for health care comprised of nucleic acid purification kits, flow cells, buffers, DNA-oligonucleotides, DNA-Nanostructures for diagnosing directly or indirectly microbiome-related diseases Scientific, optical and measuring apparatus and instruments, especially for and in connection with the separation, analysis, processing and cultivation of biological material, namely, microscopes, flow cytometers and lab-automation devices comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler for scientific research use; apparatus for research laboratories for measuring, testing and analysing microbiomes, namely, microscopes and flow cytometers and lab-automation devices comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler for scientific research use; downloadable and/or recorded software for operation of diagnostic apparatus that measures, tests, and analyzes microbiomes; downloadable software and downloadable software in the form of a web interface for analysis, storage, and report generation from raw data, as well as for ordering test kits and pharmaceutical products; downloadable databases and remotely accessible databases for storage of raw data, analyzed data, and apparatus and data quality indicators Apparatus and instruments for medical use, namely, microscopes for diagnostic use and flow cytometers for medical diagnostic use, and lab-automation devices for medical diagnostic use, comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler; medical apparatus for measuring, testing and analysing microbiomes, namely, microscopes for diagnostic use and flow cytometers for medical diagnostic use, and lab-automation devices for medical diagnostic use, comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler; diagnostic, examination, and monitoring equipment, namely, microscopes for diagnostic use and flow cytometers for medical diagnostic use, and lab-automation devices for medical diagnostic use, comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler; apparatus for carrying-out diagnostic tests for medical purposes, namely, microscopes for diagnostic use and flow cytometersfor medical diagnostic use, and lab-automation devices for medical diagnostic use, comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler; testing apparatus for medical purposes, namely, microscopes for diagnostic use and flow cytometers for medical diagnostic use, and lab-automation devices for medical diagnostic use, comprising one or several of incubator, fridge, freezer, centrifuge, thermocycler, pipetting robot, robotic arm, acoustic liquid handler Providing of access to databases for scientific and diagnostic purposes Industrial analysis and testing services in the field of microbiome diagnostics; research and development in the field of microbiomes; laboratory services for analytical testing of gut, skin and vaginal microbiome samples; clinical research in the field of development of microbiome based therapeutics or live bacterial products or targeted antibiotics Medical services relating to analysis and diagnostics; conducting and evaluation of microbiome tests for medical purposes

Goods & Services

Chemicals, biological and biochemical products used in industry, science, therapy and diagnosis, including for medical diagnostics; Reagents for processing, examining and analysis of chemical and biological material; Tests for scientific research and laboratory use; Diagnostic kits comprising specimen receptors and reagents for testing for selected bacteria; Reagents for use in diagnostic tests [other than for medical or veterinary purposes]. Pharmaceutical and medicinal preparations and substances; Medical diagnostic test kits; Diagnostic agents for medical use; Diagnostic kits for medical purposes; Test kits for health care. Scientific, optical and measuring apparatus and instruments, especially for and in connection with the separation, analysis, processing and cultivation of biological material; Apparatus for research laboratories for measuring, testing and analysing microbiomes; Software for diagnostic apparatus; Databases. Apparatus and instruments for medical use; Medical apparatus for measuring, testing and analysing microbiomes; Diagnostic, examination, and monitoring equipment; Apparatus for carrying-out diagnostic tests for medical purposes; Testing apparatus for medical purposes. Providing of access to databases for scientific and diagnostic purposes. Industrial analysis and testing services; Research and development in the field of microbiomes; Laboratory services for analytical testing; Clinical research. Medical services relating to analysis and diagnostics; Conducting and evaluation of microbiome tests for medical purposes.