Methods and systems for microbiome characterization, monitoring and treatment

Abstract

The present disclosure provides methods for profiling a microbiome and therapeutic compositions for treatment. Additionally, the methods, systems, compositions and kits provided herein are directed to assessing or predicting health status in a subject. Some of the embodiments include generating a report.

1 - 38 . (canceled) 
     
     
         39 . A method of profiling a microbiome by assaying a biological sample of a subject, the method comprising:
 (a) obtaining said biological sample from said subject, wherein said biological sample comprises a plurality of microbes, wherein said subject suffers or is at risk from suffering from a condition;   (b) subjecting nucleic acid molecules extracted from said plurality of microbes to sequencing to obtain nucleic acid sequence reads that comprise ribosomal RNA operon sequences from said plurality of microbes, wherein at least one of said nucleic acid sequence reads provides a contiguous sequence spanning at least a 16S region of said ribosomal RNA operon, a 23 S region of said ribosomal RNA operon, or an intergenic region between said 16S region and said 23S region of said ribosomal RNA operon;   (c) aligning said nucleic acid sequence reads of said ribosomal RNA operon sequences to one or more reference sequences to identify said plurality of microbes at a strain level;   (d) using a database to identify metabolic pathways that correspond to said plurality of microbes identified at said strain level in (c); and   (e) based on (d), administering a microbial-based composition to said subject, thereby treating the condition.   
     
     
         40 . The method of  claim 39 , wherein at least one of said nucleic acid sequence reads comprises said contiguous sequence spanning at least said 16S region. 
     
     
         41 . The method of  claim 39 , wherein at least one of said nucleic acid sequence reads comprises said contiguous sequence spanning at least said 23 S region. 
     
     
         42 . The method of  claim 39 , wherein at least one of said nucleic acid sequence reads comprises said contiguous sequence spanning said intergenic region between said 16S region and said 23 S region of said ribosomal RNA operon. 
     
     
         43 . The method of  claim 39 , wherein said plurality of microbes in said microbiome profile comprises 800 or fewer microbes. 
     
     
         44 . The method of  claim 39 , further comprising obtaining said nucleic acid molecules from said plurality of microbes in biological samples taken at least at two different points of time. 
     
     
         45 . The method of  claim 39 , wherein a presence or absence of said plurality of microbes and said metabolic pathways is indicative of said subject having said type 2 diabetes. 
     
     
         46 . The method of  claim 39 , further comprising detecting or measuring an amount of said nucleic acid sequence reads of said plurality of microbes. 
     
     
         47 . The method of  claim 46 , wherein said detecting or measuring said amount of said nucleic acid sequence reads of said plurality of microbes comprises detecting levels of markers from said plurality of microbes. 
     
     
         48 . The method of  claim 39 , wherein at least one of said nucleic acid sequence reads provides a contiguous sequence spanning said 16S region and said 23S region of said ribosomal RNA operon. 
     
     
         49 . The method of  claim 39 , wherein each of said nucleic acid sequence reads is longer than 2000 bases. 
     
     
         50 . The method of  claim 39 , wherein said sequencing of (b) is performed using a long read sequencing platform. 
     
     
         51 . The method of  claim 39 , further comprising extracting said nucleic acid molecules from said plurality of microbes in said biological sample. 
     
     
         52 . The method of  claim 39 , wherein the condition is selected from the group consisting of inflammatory bowel disease, preterm labor, obesity, diabetic foot ulcers, bacteremia, acne, infantile colic, type II diabetes,  C. difficile , irritable bowel syndrome, asthma, autism, psoriasis, allergies, cardiovascular disease, cancer depression, cystic fibrosis, multiple sclerosis, urinary tract infection, radiation enteropathy, drug metabolism, chronic fatigue, type I diabetes, halitosis, and tooth decay.