Genetic Analysis as

Matforsk; Norwegian Food Research Institute

Knut Rudi

Heidi Cecilie Vebø

Monika Sekelja

Morten Isaksen

Heidi Vebo

Heidi VebØ

Described herein is a set of oligonucleotide probes. Also included are methods of using the oligonucleotide probes in 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. Kits comprising the oligonucleotide probe set described herein are also provided.

Oligonucleotide probe set and methods of microbiota profiling

The invention provides a method for identifying a neonatal subject at risk for NEC, said method comprising (a) profiling the microbiota in a sample from the GI tract of said subject prior to a conclusive diagnosis of NEC and/or prior to full onset of NEC, (b1) comparing said profile to a standard microbiota profile obtained from corresponding samples from neonatal subjects with NEC or subjects which later developed NEC and determining the degree of correlation between said profile and the standard profile(s), and/or (b2) comparing said profile to a standard microbiota profile obtained from corresponding samples from neonatal subjects which did not develop NEC and determining the degree of correlation between said profile and the standard profile, and (c) identifying the subject as being at risk of NEC if significant correlation is observed in (b1) and/or significant correlation is not seen in (b2). An oligonucleotide probe set for use in the method of the invention, and kits containing the same, are also provided.

Method for identifying neonates at risk for necrotizing enterocolitis

Disclosed herein is a method of amplifying a target nucleotide sequence in 16S rRNA or in 16S rDNA that includes (a) contacting a sample that includes a 16S rDNA and/or the reverse transcription product of a 16S rRNA with an oligonucleotide primer having the nucleotide sequence of TCC TAC GGG AGG CAG CAG (SEQ ID NO 1) and an oligonucleotide primer comprising the nucleotide sequence of CGG TTA CCT TGT TAC GAC TT (SEQ ID NO 2); and (b) performing a primer-dependent nucleic acid amplification reaction to amplify the target nucleotide sequence in the 16S rRNA or the 16S rDNA. Also included are methods of measuring the prokaryotic content of a sample and/or determining the taxonomic classification of a prokaryotic organism in a sample by detecting and/or analyzing the amplification product.

Methods of amplifying a target sequence of a 16S rRNA or 16S rDNA in a prokaryotic species

A method of distinguishing between living and dead cells in a sample, the method includes: (a) contacting the sample with a viability probe which modifies the nucleic acid of dead cells within the sample; and (b) detecting nucleic acid from the cells in the sample, wherein detection involves binding of one or more oligonucleotide probes to a target sequence within the nucleic acid. A method of detecting cells in a sample, the method includes: (a) contacting the sample with a viability probe which labels the nucleic acid of dead cells within the sample; (b) separating the nucleic acid from the cells into labelled and non-labelled fraction; and (c) detecting the nucleic acid in one or both of the fractions.

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Vestby, Norway

Knut Rudi