The present invention provides methods and systems to accurately detect and measure levels of endogenous antibodies, for examples endogenous IgA, to particular antigens in a biological sample from a companion animal, which is useful to diagnose inflammatory conditions, including bowel disease (IBD), gastrointestinal infections, and food sensitivities in companion animals, e.g., dogs or cats, and to distinguish among such gastrointestinal disorders. Such methods and systems identify whether a sample from the patient is associated with an inflammatory condition, infection, and/or food sensitivity condition, by using non-invasive means, thus conveniently providing information useful for guiding treatment decisions.

Provided herein are biomarkers that can be altered in the gut of a mammal having CDI. One or more biomarkers can be used to predict Clostridium difficile infection (CDI) treatment outcome (e.g., response to primary CDI treatment and/or risk of recurrence after primary CDI treatment) in a mammal (e.g., a human) having CDI. Methods for using one or more biomarkers can be used to predict response to primary CDI treatment in a mammal having CDI. Methods for using one or more biomarkers can be used to predict risk of recurrence in a mammal having CDI. Also provided are methods of treating CDI.

The subject matter of the invention relates to a method for in vitro diagnosis of Lyme disease and a method for in vitro differential diagnosis of Lyme arthritis versus rheumatoid arthritis, in which methods, in a sample from a subject, the level of lysophosphatidylethanolamine comprising myristic acid (LysoPE(14:0)) is determined and such determined level of lysophosphatidylethanolamine is compared with the level of lysophosphatidylethanolamine comprising myristic acid in a reference sample; in wherein the level of lysophosphatidylethanolamine comprising myristic acid which is higher than the level in the said reference sample indicates that the subject suffers from Lyme disease. The subject matter of the invention further relates to lysophosphatidylethanolamine comprising myristic for use as a biomarker of Lyme disease, as a biomarker of Lyme arthritis, as a biomarker for differential diagnosis of Lyme arthritis versus rheumatoid arthritis, as a biomarker of neuroborreliosis. The subject matter of the invention also relates to a kit for in vitro diagnosis of Lyme disease and a kit for in vitro differential diagnosis of Lyme arthritis, which kits comprise a means for determining the level of lysophosphatidylethanolamine comprising myristic acid and instructions for carrying out the methods for diagnosis according to the invention.

Generally, this disclosure relates to expression constructs that encode a reporter enzyme-affinity binding tag fusion protein that is produced after the construct is inserted into bacteriophage and the bacteriophage infects bacteria. In some embodiments, the fusion protein is captured and produces a detectable signal. Signal intensity may correlate with the number of bacterial cells in a fluid sample. Methods of detecting bacteria using the expression constructs, and microfluidic devices for detecting bacteria using the expression constructs are also disclosed.

Disclosed herein are methods of detecting microbial infection in mammalian subjects comprising treatment of a sample and detection of galactofuranose (galF)-containing antigenic components utilizing monoclonal antibodies. The methods disclosed provide for pretreatment of biological samples, such as urine samples, to maximize detection of galF antigens and improvement of sensitivity of galF antigen detection assays. The methods include minimizing intelectin-1 binding to galF antigens and improvement of monoclonal antibody binding. The detection methods are useful for identifying the presence of microbial antigens related to bacterial, fungal, and parasitic pathogens, including Streptococcus pneumoniae, Aspergillus species, Fusarium species, Coccidioides species, Cryptococcus species, Histoplasma species, and Leishmania species.

The present invention relates to a method for measuring gut health comprising the steps of: a) collecting or receiving at least one, preferably two faecal samples, preferably three or more faecal samples from a human or animal, and the sample comprises markers; b) using the sample of step a), to generate output databased on a composition and/or function and/or metabolic activity of gut microbiota; c) measuring output data in relation to level and/or stability of one or more marker sand/or relation between different markers to generate a result on gut health.

Methods and compositions for diagnosing and vaccinating against Ehrlichia chaffeensis are provided.

Disclosed are methods, systems, devices, and kits for diagnosing and/or monitoring a bacterial infection in a subject in need thereof. The methods, systems, devices, and kits are useful for identifying causative bacteria, such as Pseudomonas aeruginosa, by, for example, detecting the presence of one or more quorum sensing (QS) molecules associated with the bacteria. For P. aeruginosa these can include C4 homoserine lactone and/or C12 homoserine lactone. The methods, systems, devices, and kits can further include steps or features for obtaining diagnosis results and/or prescribing an antibiotic for the subject if, for example, the presence and/or increased levels of the QS molecule are detected. The methods, systems, devices, and kits can further include steps or features guiding a treatment regimen, such as whether to initiate or continue treatment of a bacterial infection caused by bacteria, such as P. aeruginosa, detected using the disclosed methods, systems, devices, and kits.

The present invention provides devices, test strip and methods for testing breastmilk and providing feedback for improving the quality thereof.

The present invention relates to compositions, methods, and kits for predicting a subject's response to a CAR T cell therapy, by analyzing the intestinal microbiome of the subject. The present disclosure also provides a method of detecting patients at risk for a poor response to CAR T cell therapy by measuring the level of the presently disclosed bacteria or bacterial genes in the microflora or microbiome of a patient receiving or considered for CAR T cell therapy. The present disclosure further provides therapeutic compositions and methods for treating a subject having a cancer, by improving the subject's response to a CAR T cell therapy.