Xanthomonas sontii, and not Xanthomonas sacchari, is the dominant, vertically transmitted core rice seed endophyte

Seeds endophytes, particularly the abundant, core and vertically transmitted species, are major areas of focus in the host microbiome studies. Apart from being the first members to colonize, they accompany the plant throughout its development stages and also to the next generation. In a recently published study from china, a Xanthomonas species was reported as the keystone species that is core endophyte and vertically transmitted in rice with probiotic properties. However, the species status was wrongly reported as X. sacchari. Such report is misleading as Xanthomonas sacchari is a well-known and pathogenic species of sugarcane, and the study did not include the two-probiotic non-pathogenic Xanthomonas species from rice seeds, Xanthomonas sontii and Xanthomonas indica, that were discovered and investigated in details by our group, leading to the wrong inference. By including these species, we have correctly established the phylogenetic and taxonomic identity of keystone species as Xanthomonas sontii, a non-pathogen with plant protective functions. The course correction will enable researchers to use the correct reference or lab strain of X. sontii for further fundamental studies and translational research towards future agriculture.