Method and system for microbiome analysis

A method for analyzing a microbiome of a subject, comprising:

• providing a sampling kit to the subject at a remote location, the sampling kit including a sample container having a pre-process reagent component within a compartment of the sample container and configured to receive a sample from a collection site of the subject;
• from the remote location, receiving the sample container with the sample from the collection site of the subject;
• with a laboratory automation workstation of a sample processing system, the laboratory automation workstation comprising an actuation and fluid handling subsystem with a set of actuators and fluid handlings apparatus, generating a mixture within a process container upon combining the sample with process reagents having a first identification sequence;
• with an amplification substrate of a next generation sequencing platform of the sample processing system, generating a microbiome sequence dataset based upon sequencing nucleic acid content of a microorganism portion of the sample;
• at a computing device of the sample processing system in communication with the next generation sequencing platform by a communication link, identifying a set of microorganism features represented in the microorganism portion;
• at the sample processing system, generating an analysis based upon the set of microorganism features;
• and
• associating the analysis with the subject, based upon the first identification sequence.