{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T08:39:57Z","timestamp":1772267997003,"version":"3.50.1"},"reference-count":112,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2020,10,20]],"date-time":"2020-10-20T00:00:00Z","timestamp":1603152000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000936","name":"Gordon and Betty Moore Foundation","doi-asserted-by":"crossref","award":["GBMF5603"],"award-info":[{"award-number":["GBMF5603"]}],"id":[{"id":"10.13039\/100000936","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    Koalas (\n                    <jats:italic>Phascolarctos cinereus<\/jats:italic>\n                    ) are highly specialized herbivorous marsupials that feed almost exclusively on\n                    <jats:italic>Eucalyptus<\/jats:italic>\n                    leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that\n                    <jats:italic>Lonepinella koalarum<\/jats:italic>\n                    , a bacterium in the Pasteurellaceae family, can break down some of these toxic chemical compounds. Furthermore, in a previous study, we identified\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    as the most predictive taxon of koala survival during antibiotic treatment. Therefore, we believe that this bacterium may be important for koala health. Here, we isolated a strain of\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    from a healthy koala female and sequenced its genome using a combination of short-read and long-read sequencing. We placed the genome assembly into a phylogenetic tree based on 120 genome markers using the Genome Taxonomy Database (GTDB), which currently does not include any\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    assemblies. Our genome assembly fell in the middle of a group of\n                    <jats:italic>Haemophilus<\/jats:italic>\n                    ,\n                    <jats:italic>Pasteurella<\/jats:italic>\n                    and\n                    <jats:italic>Basfia<\/jats:italic>\n                    species. According to average nucleotide identity and a 16S rRNA gene tree, the closest relative of our isolate is\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    strain Y17189. Then, we annotated the gene sequences and compared them to 55 closely related, publicly available genomes. Several genes that are known to be involved in carbohydrate metabolism could exclusively be found in\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    relative to the other taxa in the pangenome, including glycoside hydrolase families GH2, GH31, GH32, GH43 and GH77. Among the predicted genes of\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    were 79 candidates putatively involved in the degradation of plant secondary metabolites. Additionally, several genes coding for amino acid variants were found that had been shown to confer antibiotic resistance in other bacterial species against pulvomycin, beta-lactam antibiotics and the antibiotic efflux pump KpnH. In summary, this genetic characterization allows us to build hypotheses to explore the potentially beneficial role that\n                    <jats:italic>L. koalarum<\/jats:italic>\n                    might play in the koala intestinal microbiome. Characterizing and understanding beneficial symbionts at the whole genome level is important for the development of anti- and probiotic treatments for koalas, a highly threatened species due to habitat loss, wildfires, and high prevalence of\n                    <jats:italic>Chlamydia<\/jats:italic>\n                    infections.\n                  <\/jats:p>","DOI":"10.7717\/peerj.10177","type":"journal-article","created":{"date-parts":[[2020,10,20]],"date-time":"2020-10-20T05:46:44Z","timestamp":1603172804000},"page":"e10177","source":"Crossref","is-referenced-by-count":8,"title":["Isolation and sequence-based characterization of a koala symbiont:\n                    <i>Lonepinella koalarum<\/i>"],"prefix":"10.7717","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6532-3407","authenticated-orcid":true,"given":"Katherine E.","family":"Dahlhausen","sequence":"first","affiliation":[{"name":"Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8746-2632","authenticated-orcid":true,"given":"Guillaume","family":"Jospin","sequence":"additional","affiliation":[{"name":"Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A.","family":"Coil","sequence":"additional","affiliation":[{"name":"Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0159-2197","authenticated-orcid":true,"given":"Jonathan A.","family":"Eisen","sequence":"additional","affiliation":[{"name":"Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA"},{"name":"Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA"},{"name":"Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0756-8339","authenticated-orcid":true,"given":"Laetitia G.E.","family":"Wilkins","sequence":"additional","affiliation":[{"name":"Genome and Biomedical Sciences Facility, University of California, Davis, Davis, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2020,10,20]]},"reference":[{"issue":"5","key":"10.7717\/peerj.10177\/ref-1","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1002\/open.201700113","article-title":"Tannins and their complex interaction with different organic nitrogen compounds and enzymes: old paradigms versus recent 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