Apparatus for microorganism isolation, characterization, identification and methods of use thereof

Abstract

The present disclosure relates generally to an apparatus and methods for microorganism isolation, characterization and identification based on oxygen, pressure, culture media gradients and metabolites. In each embodiment, the apparatus of the disclosure is particularly useful for the purpose of novel isolation of never before cultured species of microorganisms and their by-products.

What is claimed is: 
     
         1 . An apparatus for isolating and culturing microorganisms comprising:
 a body having the shape of an elongated cylinder comprising:
 an upper end comprising an opening configured to receiving a sample; 
 a closed lower end opposite the upper end attached to a base allowing the apparatus to remain in an upright position; 
 at least one sidewall between the upper end and lower end, wherein the at least one sidewall forms an interior cavity; and 
 at least one lateral port openings attached to the at least one sidewall of the cylinder between the upper end and lower end, wherein the lateral port opening has an aperture allowing access to the interior of the apparatus. 
   
     
     
         2 . The apparatus of  claim 1 , wherein the body comprises a plurality of lateral port openings. 
     
     
         3 . The apparatus of  claim 1 , wherein the body is comprised of a transparent or semi-transparent material. 
     
     
         4 . The apparatus of  claim 1 , wherein the body includes a plurality of line markings and a plurality of measurement indicia corresponding to the plurality of line markings. 
     
     
         5 . The apparatus of  claim 1 , wherein the lateral port openings comprise a removably attached cap to close said aperture. 
     
     
         6 . The apparatus of  claim 5 , wherein the lateral port openings comprise one or more of a filter, gasket, or septum. 
     
     
         7 . The apparatus of  claim 1 , wherein the lateral port openings are spaced vertically about 2 inches apart. 
     
     
         8 . The apparatus of  claim 1 , wherein interior may hold sample volumes of about 5 ml, about 10 ml, about 15 ml, about 20 ml, about 25 ml, about 30 ml, about 35 ml, about 40 ml, about 45 ml, about 50 ml, about 55 ml, about 60 ml, about 65 ml, about 70 ml, about 75 ml, about 80 ml, about 85 ml, about 90 ml, about 95 ml, about 100 ml, about 150 ml, about 200 ml, about 250 ml, about 300 ml, about 350 ml, about 400 ml, about 450 ml, about 500 ml, about 600 ml, about 700 ml, about 800 ml, about 900 ml, about 1000 ml, or greater. 
     
     
         9 . The apparatus of  claim 1 , wherein the body is constructed of glass or plastic. 
     
     
         10 . A method for isolating and culturing a microorganism, which comprises:
 i. collecting a sample from an environmental source;   ii. diluting the sample in an appropriate medium;   iii. incubating the sample within an apparatus for an appropriate time, the apparatus comprising:
 a body having the shape of an elongated cylinder comprising: 
 an upper end comprising an opening configured to receiving a sample; 
 a closed lower end opposite the upper end attached to a base allowing the apparatus to remain in an upright position; 
 at least one sidewall between the upper end and lower end, wherein the at least one sidewall forms an interior of the cylinder; and 
 a plurality of lateral port openings attached to the at least one sidewall of the cylinder between the upper end and lower end, wherein the lateral port opening has an aperture allowing access to the interior of the apparatus; and; 
   iv. isolating a microorganism(s) from the apparatus using the one or more of the lateral port openings.   
     
     
         11 . The method of  claim 10 , wherein step (iv) is repeated one or more times throughout the incubation period. 
     
     
         12 . The method of  claim 10 , wherein the isolated microorganism is transferred into both aerobic and anaerobic tubes for further subculture and analysis. 
     
     
         13 . The method of  claim 10 , wherein the environmental source from which the samples are collected is any terrestrial, aquatic or marine source, soil, biofilm, sediment, waste water, sludge residue, or crude oil. 
     
     
         14 . The method of  claim 10 , wherein the medium is one or more of sterile water, sterile saline, sterile water containing suitable ingredients for compatibility with the environmental source, glucose enriched MOPS (3-(N-Morpholino) Propane-Sulfonic Acid) broth, enriched Nutrient broth or Tryptic Soy broth. 
     
     
         15 . The method of  claim 14 , wherein the medium further comprises additional vitamins, minerals, amino acids, polypeptides, nucleic acids, or small molecules. 
     
     
         16 . The method of  claim 10 , wherein the sample is incubated within the apparatus for at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 7 days, at least 8 days, at least 9 days, at least 10 days, at least 11 days, at least 12 days, at least 13 days, at least 14 days, at least 15 days, at least 16 days, at least 17 days, at least 18 days, at least 19 days, at least 20 days, at least 21 days, at least 22 days, at least 23 days, at least 24 days, at least 25 days, at least 26 days, at least 27 days, at least 28 days, at least 29 days, at least 30 days, at least 31 days, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months or longer. 
     
     
         17 . The method according to  claim 10 , wherein said appropriate medium of is a medium compatible with the environment from which said sample has been collected. 
     
     
         18 . The method according to  claim 10 , wherein said isolating occurs by inserting a sterile instrument into the specific lateral port opening, wherein said sterile instrument is a syringe. 
     
     
         19 . The method of  claim 10 , wherein the isolated microorganisms is formulated in to a soluble tablet.