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In this study, we report the microbiota of twenty-nine axenic yeast cultures recovered from different habitats based on their 16S rRNA gene-amplicon metagenomes. Yeasts were identified based on D1\/D2 or ITS gene sequences. Bacterial diversity was widespread, varied and rich among all yeasts except for four strains. Taxa belonging to the phylum <jats:italic>Firmicutes<\/jats:italic>, <jats:italic>Proteobacteria<\/jats:italic>, <jats:italic>Actinobacteria<\/jats:italic> and <jats:italic>Bacteroidetes<\/jats:italic> and the genera; <jats:italic>Streptococcus<\/jats:italic>, <jats:italic>Propionibacterium<\/jats:italic> were common to all the yeasts. <jats:italic>Candida tropicalis<\/jats:italic> was used as a model organism to confirm bacteria through fluorescence in situ hybridization (FISH), isolating and re-introducing the isolated bacteria into the yeast. FISH analysis confirmed the endobacteria of <jats:italic>C. tropicalis<\/jats:italic> and we have successfully isolated four bacteria only after lysis and disruption of yeast cells. These bacteria were identified as species of <jats:italic>Pseudomonas<\/jats:italic>, <jats:italic>Chryseobacterium<\/jats:italic>, <jats:italic>Lysinibacillus<\/jats:italic> and <jats:italic>Propionibacterium<\/jats:italic>. Guestimates indicate 95% of bacterial species of <jats:italic>C. tropicalis<\/jats:italic> are yet-to-be-cultivated. We have successfully reintroduced mCherry tagged <jats:italic>Pseudomonas<\/jats:italic> into <jats:italic>C. tropicalis<\/jats:italic>. Also, auto-fluorescent <jats:italic>Prochlorococcus<\/jats:italic> and <jats:italic>Rhodopseudomonas<\/jats:italic> could be introduced into <jats:italic>C<\/jats:italic>. <jats:italic>tropicalis<\/jats:italic> while mCherry tagged <jats:italic>E. coli<\/jats:italic> or <jats:italic>Salmonella<\/jats:italic> could not be introduced. FISH analysis confirmed the presence of both native and infected bacterial cells present in <jats:italic>C. tropicalis<\/jats:italic>. Our findings unveil the insights into the ghost microbiota associated with yeast, which otherwise are considered to be axenic cultures. Their inherent occurrence, together with co-cultivation experiments under laboratory conditions suggests that yeasts are a thriving hub for bacterial communities.\n<\/jats:p>","DOI":"10.1038\/s41598-021-88658-x","type":"journal-article","created":{"date-parts":[[2021,4,30]],"date-time":"2021-04-30T10:04:45Z","timestamp":1619777085000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Uncovering the hidden bacterial ghost communities of yeast and experimental evidences demonstrates yeast as thriving hub for bacteria"],"prefix":"10.1038","volume":"11","author":[{"given":"B.","family":"Indu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tallapragada","family":"Keertana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sahu","family":"Ipsita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uppada","family":"Jagadeeshwari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chintalapati","family":"Sasikala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chintalapati Venkata","family":"Ramana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,4,30]]},"reference":[{"key":"88658_CR1","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1098\/rstb.2009.0188","volume":"365","author":"EC Nowack","year":"2010","unstructured":"Nowack, E. 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