Plant colonization assays using natural microbial barcodes

A composition comprising:

• (a) one or more modified cells comprising, in their genome:
• (i) a naturally occurring first nucleotide sequence, second nucleotide sequence, and third nucleotide sequence, and
• (ii) a native barcode polynucleotide cassette comprising the first, second, and third nucleotide sequences oriented 5′ to 3′ as:
• (1) the first nucleotide sequence, wherein the first nucleotide sequence is a forward primer binding site,
• (2) the second nucleotide sequence, wherein the second nucleotide sequence is a barcode, and
• (3) the third nucleotide sequence, wherein the third nucleotide sequence is a reverse primer binding site;
• wherein the first, second, and third nucleotide sequences of (ii) are in a different proximity to one another as compared to the naturally occurring sequences of (i).