Abstract: Methods and compositions are provided herein for treating autism spectrum disorder in a subject, using one or more metabolites such as glutamate, malate, ursodeoxycholate, 5-dodecenoate, N-acetyl-L-glutamate, citrate, glycodeoxycholate, and carboxyethyl aminobutyric acid (CEGABA) and/or using one or more bacterial species such as bacterial species from the Streptococcaceae, Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Butyricicoccaceae, and/or Pasteurellaceae families; from the Streptococcus, Blautia, Haemophilus, Faecalibacterium, Bacteroides, Roseburia, Fusicatenibacter, Lachnospira, and/or Agathobaculum genera, or Blautia wexlerae, Bacteroides vulgatus, Bacteroides ovatus, Roseburia inulinivorans, Roseburia intestinalis, Fusicatenibacter saccharivorans, and/or Agathobaculum butyriciproducens.

Abstract: Compositions, systems and methods for generating and using internal standard spike-in mixes including a combination of template spikes. Compositions, systems and methods described herein are directed to using the internal standard spike-in mixes to evaluate a set of workflow pipelines to perform differential abundance analyses on a sample containing variations of a target nucleic acid sequence of interest. Compositions, systems and methods described herein are directed to using the internal spike-in mixes to validate results obtained from differential abundance analyses performed on a sample containing variations of a target nucleic acid sequence of interest, where the variations may be of highly variable levels of relative abundance.

Abstract: The disclosure provides therapeutic peptides and pharmaceutical compositions comprising the peptides, which have utility in treating various human diseases. In particular aspects, the disclosed therapeutic peptides are useful as immunotherapeutics for modulating regulatory and effector molecules of the mammalian immune system to mitigate disease.

Abstract: The disclosure relates to live biotherapeutic products, probiotics, pharmaceutical compositions comprising said probiotics, and methods of using them to treat a gastrointestinal disease or disorder. In some aspects, the disclosure provides such compositions comprising strains of the bacterium Anaerostipes hadrus and their uses in treating intestinal diseases or disorders.

Abstract: Compositions, systems and methods for generating and using internal standard spike-in mixes including a combination of template spikes. Compositions, systems and methods described herein are directed to using the internal standard spike-in mixes to evaluate a set of workflow pipelines to perform differential abundance analyses on a sample containing variations of a target nucleic acid sequence of interest. Compositions, systems and methods described herein are directed to using the internal spike-in mixes to validate results obtained from differential abundance analyses performed on a sample containing variations of a target nucleic acid sequence of interest, where the variations may be of highly variable levels of relative abundance.

Abstract: The present invention discloses methods and systems for designing and using organism-specific and/or operational taxon unit (OTU)-specific probes. The methods and systems allow for detecting, identifying and quantitating a plurality of biomolecules or microorganisms in a sample based on the hybridization or binding of target molecules in the sample with the probes. Some embodiments provide methods of selecting an oligonucleotide probe specific for a node on a clustering tree. Other embodiments provide methods of selecting organism-specific or OTU-specific oligonucleotide probes for use in accurately detecting a plurality of organisms in a sample with high confidence. Some embodiments provide methods and systems to detect the presence of a rare OTU in a sample.

Abstract: The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.

Abstract: Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).

Abstract: The present embodiments relate to an array system for detecting and identifying biomolecules and organisms. More specifically, the present embodiments relate to an array system comprising a microarray configured to simultaneously detect a plurality of organisms in a sample at a high confidence level.

Abstract: The present invention discloses methods and systems for designing and using organism-specific and/or operational taxon unit (OTU)-specific probes. The methods and systems allow for detecting, identifying and quantitating a plurality of biomolecules or microrganisms in a sample based on the hybridization or binding of target molecules in the sample with the probes. Some embodiments provide methods of selecting an oligonucleotide probe specific for a node on a clustering tree. Other embodiments provide methods of selecting organism-specific or OTU-specific oligonucleotide probes for use in accurately detecting a plurality of organisms in a sample with high confidence. Some embodiments provide methods and systems to detect the presence of a rare OTU in a sample.

Abstract: Herein is described methods for a high-sensitivity means to measure the incorporation of stable isotope labeled substrates into RNA following stable isotope probing experiments (SIP). RNA is hybridized to a set of probes such as phylogenetic microarrays and isotope incorporation is quantified such as by secondary ion mass spectrometer imaging (NanoSIMS).