ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR205/006/SRR2052566/SRR2052566.fastq.gzprimaryOK200GenomicsUniversity of Pretoriahttps://www.ebi.ac.uk/ena/browser/view/PRJNA286696endophyte metagenomeThe Fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with Fynbos plants, despite interactions between primary producers and bacteria impact the physiology of both partners and shape ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendrom laureolum). Using T-RFLP analysis and Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability within hosts in the endophytic bacterial communities was observed. We also detected a stem core microbiome across the three plant species, which accounted for 72% of the sequences. Overall, endophytic bacterial communities were relatively limited and enriched in plant growth-promoting bacteria, thus having the potential to influence host health.ENASvc, sequence, primary structure of sequence macromolecule., Bru, Del(8)44H, Col4a-1, RawMetagenomes.falseendophyte metagenomeFynbos plantas Raw sequence reads2023-05-192015-06-23PRJNA286696483425