Abstract: Methods, compositions, and systems are provided for detecting one or more a bacterial vaginosis issues by characterizing the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for the bacterial vaginosis issue. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model and/or therapy model for bacterial vaginosis.

Abstract: Embodiments of a method and/or system (e.g., for improved single molecule sequencing, etc.) can include preparing a set of unique molecular identifier (UMI)-based molecules associated with a set of target nucleic acid sequences; facilitating generation of (e.g., generating, etc.) a set of tagged nucleic acid molecules based on the set of UMI-based molecules and a set of nucleic acid molecules corresponding to (e.g., including, etc.) the set of target nucleic acid sequences; and/or facilitating (e.g., performing, etc.) single molecule sequencing with the set of tagged nucleic acid molecules.

Abstract: Therapeutic compositions and an associated method for improving a Toll-like receptor (TLR)-related condition, including determining a set of peptide sequences associated with a microorganism-related modulator of a TLR, determining a first set of binding parameters for the set of peptide sequences in relation to the TLR, selecting a target subset of peptide sequences from the set of peptide sequences based on the first set of binding parameters, reengineering the target subset of peptide sequences based on mutating amino acid residues of the target subset of peptide sequences, determining a second set of binding parameters for the reengineered target subset of peptide sequences in relation to the TLR, and identifying a first peptide for use in a therapeutic composition for improving the TLR-related condition, based on the second set of binding parameters for the reengineered target subset of peptide sequences.

Abstract: Disclosed are a method for DNA extraction in a sample for next generation sequencing (NGS) and a method of constructing a NGS library using the extracted DNA. The method for DNA extraction includes: preparing a mixture by mixing a biological sample with a buffer; applying microwaves to the mixture; and recovering DNA. The method of constructing a NGS library includes: extracting DNA according to the method for DNA extraction; amplifying a target DNA using primers; and purifying the amplified product and subjecting the purified product to library pooling.

Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.

Abstract: Methods, compositions, and systems are provided for detecting one or more effects of antibiotic usage for an infectious disease or other health condition on the microbiome of an individual, monitoring such effects, and/or determining, displaying, or promoting a therapy for such an effect. Methods, compositions, and systems are also provided for generating and comparing microbiome composition and/or functional diversity datasets. Methods, compositions, and systems are also provided for generating a characterization model for antibiotic usage.

Abstract: Embodiments of the system and/or method can include and/or apply a magnetic device for facilitating a magnetic field for isolating the nucleic acid material from a sample, the magnetic device including a support component; and a set of magnetic pins attached to the support component and movable with at least three degrees of freedom when attached to the support component, where the set of magnetic pins provide adaptability to shapes of sample compartments of a sample container.

Abstract: Embodiments of a method and/or system, such as for characterizing at least one microorganism-related condition, can include: determining a set of associations (e.g., positive associations such as positive correlations, negative associations such as negative correlations, non-associations such as no correlation or minimal correlation, etc.) between a set of microorganism taxa and at least one microorganism-related condition; determining a set of reference features (e.g., reference abundance ranges, etc.) for the set of microorganism taxa; and determining one or more significance index metrics based on the set of associations and the set of reference features.

Abstract: Embodiments of a method and system for improved microbiome sequencing can include: generating guide RNA complexes for a set of targets corresponding to a set of taxa associated with the microorganism-related condition; processing the biological sample with the gRNA complexes to generate microorganism nucleic acid fragments comprising a set of end regions associated with the set of targets; ligating the set of end regions with a set of adapters sharing an adapter sequence; and amplifying the set of targets based on the ligated set of end regions and a set of primers sharing a primer sequence associated with the adapter sequence.

Abstract: The present disclosure related to a method of detecting a molecule using an antibody-DNA conjugate, and pharmaceutical compositions comprising new polypeptides and use thereof.

Abstract: Embodiments of a method and/or system can include administering, to a patient with one or more conditions associated with at least one of TMA, TMAO, and/or derivatives thereof, a therapeutically effective amount of a compound for affecting inhibiting one or more CutC enzymes and/or CntA enzymes associated with microorganisms from at least one taxon from a set of microorganism taxa.

Abstract: The present disclosure relates to pharmaceutical compounds and compositions and methods for treating an allergy and Crohn's disease. Methods for treating an allergy can include (a) predicting potential epitopes based proteomes of microbiome and that of an allergen, (b) filtering the potential epitopes obtained in step a) to result in a list of epitopes; and (c) reengineering the list of epitopes obtained in step b) to result in the new epitope. Methods for treating Crohn's disease can include (a), identifying one or more binding regions of an HLA class II protein and/or hemagglutinin to I2 superantigen; (b) determining a first peptide sequence corresponding to the one or more binding regions, and (c) producing a peptide inhibitor having a second peptide sequence that is a mutation of the first peptide sequence, wherein the second peptide sequence has a stronger binding affinity to the I2 superantigen than the first peptide sequence.

Abstract: A method for treating a microorganism-related condition in a patient may include detecting microorganisms in a set of samples collected from a population and comparing a relative abundance of and co-occurrence between different microbial taxa in the set of samples. The method further includes associating a change in the relative abundance of or the co-occurrence between the microbial taxa with samples from people, among the population, with the microorganism-related condition and samples from people, among the population, without the microorganism-related condition to determine a target taxa. A blend of bacteriophages is then identified, the blend being configured to remove the target taxa from a community of microorganisms A therapeutic composition comprising the blend is then administered to the patient with the microorganism-related condition.

Abstract: A method for characterizing compatibility of a drug for a user includes collecting a set of samples from a set of individuals comprising a set of first individuals who respond to a therapy for a microbiome-related condition and a set of second individuals who do not respond to the therapy for the microbiome-related condition and determining one or more datasets based on the set of samples. A set of microbiome features is extracted from the one or more microbiome datasets, the microbiome features facilitating differentiation between individuals who respond and individuals who do not respond to the therapy. A companion diagnostics model is determined based on the set of microbiome features. The compatibility of the drug for the user is then determined using the companion diagnostics model.

Abstract: The present application relates to new HtrA inhibitors and use thereof. Additionally, the present application also relates to new peptides for inhibiting CagA and use thereof.

Abstract: Embodiments of a method and/or system for characterizing one or more female reproductive system-related conditions can include determining a microorganism dataset associated with a set of subjects; and/or performing a characterization process associated with the one or more female reproductive system-related conditions, based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing a female reproductive system-related characterization process for the one or more female reproductive system-related conditions, and/or determining one or more therapies.

Abstract: Disclosed is a method of providing biological data. The method includes the following steps performed by a data processing device: selecting a biological data set from a biological data pool; encrypting biological data included in the biological data set to produce encrypted biological data; transferring the encrypted biological data to a user; receiving a result of analysis on the encrypted biological data from the user; and transferring information on the encrypted biological data included in the result of the analysis to the user. The data processing device encrypts the biological data with a key determined according to a combination of biological data constituting the biological data set.

Abstract: Disclosed are a method for DNA extraction in a sample for next generation sequencing (NGS) and a method of constructing a NGS library using the extracted DNA. The method for DNA extraction includes: preparing a mixture by mixing a biological sample with a buffer; applying microwaves to the mixture; and recovering DNA. The method of constructing a NGS library includes: extracting DNA according to the method for DNA extraction; amplifying a target DNA using primers; and purifying the amplified product and subjecting the purified product to library pooling.

Abstract: A system and method for sample droplet processing, the system including a substrate, an electrode array network coupled to the substrate and configured to provide a pattern of controlled electric fields for manipulation of the set of sample droplets; a first layer in communication with the electrode array network, the first layer separating the electrode array network from fluid of the set of sample droplets; and a second layer opposing the first layer and displaced from the first layer to define a region wherein droplets of the set of sample droplets can reside. In some variations, the system can additionally include an electronics subsystem coupled to at least one of the substrate and the electrode array network, and a control module in communication with the electronics subsystem, wherein the control module generates and manipulates the pattern of controlled electric fields.

Abstract: A method for at least one of characterizing, diagnosing, and treating an endocrine system condition in at least a subject, the method comprising: receiving an aggregate set of biological samples from a population of subjects; generating at least one of a microbiome composition dataset and a microbiome functional diversity dataset for the population of subjects; generating a characterization of the endocrine system condition based upon features extracted from at least one of the microbiome composition dataset and the microbiome functional diversity dataset; based upon the characterization, generating a therapy model configured to correct the endocrine system condition; and at an output device associated with the subject, promoting a therapy to the subject based upon the characterization and the therapy model.