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This study evaluated the effects of different storage conditions on microbial DNA preservation in\n                    <jats:italic>Coffea arabica<\/jats:italic>\n                    fruit samples. Coffee cherries were harvested directly from plants, placed in plastic tubes, and stored at 4\u00a0\u00b0C before being subjected to four treatments: lyophilization, cryopreservation at \u2212\u200980\u00a0\u00b0C, and refrigeration at 4\u00a0\u00b0C. Samples were stored for 3 and 13 days. Microbial communities were characterized by next-generation sequencing. Lyophilization retained more than 80% of the ASVs shared between days 3 and 13 of storage, whereas refrigeration at 4\u00a0\u00b0C retained less than 50%. These findings demonstrate that preservation method significantly affects the integrity of bacterial and fungal microbiomes in\n                    <jats:italic>C. arabica<\/jats:italic>\n                    beans. The absence of a time-zero control, chemical preservative comparisons, and the study\u2019s limited scope (single variety, location, and short storage period) warrant cautious interpretation of the findings. Although lyophilization was the best-performing physical preservation strategy evaluated here, broader validation across coffee cultivars, environments, and storage durations is still required before it can be considered a standard preservation protocol for preserving microbial materials derived from coffee samples.\n                  <\/jats:p>","DOI":"10.1007\/s00203-026-05046-7","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T08:32:25Z","timestamp":1783931545000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparison of physical preservation strategies for accurate characterization of the coffee fruit microbiome"],"prefix":"10.1007","volume":"208","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1067-9320","authenticated-orcid":false,"given":"Etztli Itzel Morales","family":"Reyes","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6704-6505","authenticated-orcid":false,"given":"Tom\u00e1s Gomes Reis","family":"Veloso","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9826-7982","authenticated-orcid":false,"given":"Jos\u00e9 Maria Rodrigues","family":"da Luz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4721-7368","authenticated-orcid":false,"given":"Monalisa Araujo","family":"Aziz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8110-1051","authenticated-orcid":false,"given":"Mart\u00edn Alejandro Bola\u00f1os","family":"Gonz\u00e1lez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4678-7876","authenticated-orcid":false,"given":"Marliane de Cassia Soares","family":"da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"issue":"7","key":"5046_CR1","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) DADA2: High-resolution sample inference from Illumina amplicon data. 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