The present invention is directed to an isolated synthetic tripeptide of formula H-D-Phe-N-Methyl-L-Val-L-Ala-OMe (SEQ ID NO:1), or a derivative thereof, and to the corresponding lipotripeptides, which are specific to Mycobacterium avium subsp. paratuberculosis (Map)S-type strain, as well as derivatives and conjugates thereof. The invention also concerns the use of these antigens in different methods and tests for detecting Map infection, especially by detecting humoral response and cell mediated response of infected animals. The invention is also directed to a genetic signature of Map and a mass spectrometry and NMR spectroscopy signature of Map presence or infection.

The present invention is directed to an isolated synthetic tripeptide of formula H-D-Phe-N-Methyl-L-Val-L-Ala-OMe (SEQ ID NO:1), or a derivative thereof, and to the corresponding lipotripeptides, which are specific to Mycobacterium avium subsp. paratuberculosis (Map)S-type strain, as well as derivatives and conjugates thereof. The invention also concerns the use of these antigens in different methods and tests for detecting Map infection, especially by detecting humoral response and cell mediated response of infected animals. The invention is also directed to a genetic signature of Map and a mass spectrometry and NMR spectroscopy signature of Map presence or infection.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Provided are methods of producing a nucleic acid complex. In certain aspects, the methods include combining a sample including ribosomal RNA (rRNA) and a probe complement oligonucleotide with an oligonucleotide probe. The oligonucleotide probe includes a 3′ region complementary to a 3′ region of a rRNA, and a 5′ region complementary to the probe complement oligonucleotide. The combining is under conditions in which the 3′ region of the oligonucleotide probe hybridizes to the 3′ region of the rRNA and the 5′ region of the oligonucleotide probe hybridizes to the probe complement oligonucleotide, thereby producing a nucleic acid complex. In certain aspects, the methods find use in producing rRNA libraries that find use, e.g., in rRNA sequencing applications. Oligonucleotide probes, libraries thereof, compositions, and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.

Provided are methods of producing a nucleic acid complex. In certain aspects, the methods include combining a sample including ribosomal RNA (rRNA) and a probe complement oligonucleotide with an oligonucleotide probe. The oligonucleotide probe includes a 3′ region complementary to a 3′ region of a rRNA, and a 5′ region complementary to the probe complement oligonucleotide. The combining is under conditions in which the 3′ region of the oligonucleotide probe hybridizes to the 3′ region of the rRNA and the 5′ region of the oligonucleotide probe hybridizes to the probe complement oligonucleotide, thereby producing a nucleic acid complex. In certain aspects, the methods find use in producing rRNA libraries that find use, e.g., in rRNA sequencing applications. Oligonucleotide probes, libraries thereof, compositions, and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.

Provided are devices, systems, and methods for the identification, quantification, and profiling of microscopic organisms. The methods for the identification, quantification, and profiling of microscopic organisms include, for example, the selective enrichment of microscopic organisms from a heterogeneous sample; subsequent loading of the microscopic organisms into microfluidic channels or reaction chambers; direct amplification of nucleic acids from single, isolated microscopic organisms; and examination of amplification products using digital High Resolution Melting (HRM) analysis.

The present invention relates to a method for identifying a microorganism in a biological sample by polymerase chain reaction (PCR), comprising the steps of a) providing a biological sample suspected of comprising microbes, and optionally isolating nucleic acid sequences from said biological sample; b) PCR amplifying at least one microbial rRNA internal transcribed spacer (ITS) region comprised in said optionally isolated nucleic acid sequences using a set of broad-taxonomic range amplification primers to thereby generate PCR amplicons from nucleic acid sequences of microbial origin; c) recording a high resolution melting curve for the PCR amplicons, and recording the length of the PCR amplicons; d) comparing the high resolution melting curve with a database comprising high resolution melting curves of reference amplicons of known microbial species or strains, to thereby obtain a first identity indicator; e) comparing the length of each PCR amplicon having a distinct length with a database comprising PCR amplicon lengths of reference amplicons of known microbial species or strains, to thereby obtain a second identity indicator; and f) identifying the microorganism present in said sample to the species or strain level if the first and second identity indicator match.

The present invention relates to a method for identifying a microorganism in a biological sample by polymerase chain reaction (PCR), comprising the steps of a) providing a biological sample suspected of comprising microbes, and optionally isolating nucleic acid sequences from said biological sample; b) PCR amplifying at least one microbial rRNA internal transcribed spacer (ITS) region comprised in said optionally isolated nucleic acid sequences using a set of broad-taxonomic range amplification primers to thereby generate PCR amplicons from nucleic acid sequences of microbial origin; c) recording a high resolution melting curve for the PCR amplicons, and recording the length of the PCR amplicons; d) comparing the high resolution melting curve with a database comprising high resolution melting curves of reference amplicons of known microbial species or strains, to thereby obtain a first identity indicator; e) comparing the length of each PCR amplicon having a distinct length with a database comprising PCR amplicon lengths of reference amplicons of known microbial species or strains, to thereby obtain a second identity indicator; and f) identifying the microorganism present in said sample to the species or strain level if the first and second identity indicator match.

Methods of identifying test compounds or mixtures of test compounds from microbiota that bind to a fusion protein, such as a G-protein coupled receptor, are described. Also described are methods for high throughput screening of microbiota metabolites that are capable of activating G-protein coupled receptors.

Methods of identifying test compounds or mixtures of test compounds from microbiota that bind to a fusion protein, such as a G-protein coupled receptor, are described. Also described are methods for high throughput screening of microbiota metabolites that are capable of activating G-protein coupled receptors.