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After mating, earthworms produce cocoons externally which will be colonized with bacteria from their parents and the environment. Due to the key role bacterial symbionts play on earthworm fitness, it is important to study bacterial colonization during cocoon formation. Here we describe the cocoon microbiome of the earthworms<jats:italic>Eisenia andrei<\/jats:italic>and<jats:italic>E. fetida<\/jats:italic>, which included 275 and 176 bacterial species, respectively. They were dominated by three vertically-transmitted symbionts,<jats:italic>Microbacteriaceae<\/jats:italic>,<jats:italic>Verminephrobacter<\/jats:italic>and<jats:italic>Ca<\/jats:italic>. Nephrothrix, which accounted for 88% and 66% of the sequences respectively.<jats:italic>Verminephrobacter<\/jats:italic>and<jats:italic>Ca<\/jats:italic>. Nephrothrix showed a high rate of sequence variation, suggesting that they could be biparentally acquired during mating. The other bacterial species inhabiting the cocoons came from the bedding, where they accounted for a small fraction of the diversity (27% and 7% of bacterial species for<jats:italic>E. andrei<\/jats:italic>and<jats:italic>E. fetida<\/jats:italic>bedding). Hence, earthworm cocoon microbiome includes a large fraction of the vertically-transmitted symbionts and a minor fraction, but more diverse, horizontally and non-randomly acquired from the environment. These data suggest that horizontally-transmitted bacteria to cocoons may play an important role in the adaptation of earthworms to new environments or diets.<\/jats:p>","DOI":"10.1038\/s41598-018-25081-9","type":"journal-article","created":{"date-parts":[[2018,4,20]],"date-time":"2018-04-20T14:42:55Z","timestamp":1524235375000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Diversity, structure and sources of bacterial communities in earthworm cocoons"],"prefix":"10.1038","volume":"8","author":[{"given":"Manuel","family":"Aira","sequence":"first","affiliation":[]},{"given":"Marcos","family":"P\u00e9rez-Losada","sequence":"additional","affiliation":[]},{"given":"Jorge","family":"Dom\u00ednguez","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,4,26]]},"reference":[{"key":"25081_CR1","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/nrmicro2262","volume":"8","author":"M Bright","year":"2010","unstructured":"Bright, M. & Bulgheresi, S. 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