{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,22]],"date-time":"2024-08-22T07:39:48Z","timestamp":1724312388781},"reference-count":38,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T00:00:00Z","timestamp":1700697600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chung-Ang University Research Grants in 2023"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:sec>\n<jats:title>Background<\/jats:title>\n<jats:p>We compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) <jats:italic>via<\/jats:italic> NGS analysis.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Methods<\/jats:title>\n<jats:p>We prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>Among the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups.<\/jats:p>\n<\/jats:sec>\n<jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>Here, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC <jats:italic>via<\/jats:italic> NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data.<\/jats:p>\n<\/jats:sec>","DOI":"10.7717\/peerj.16366","type":"journal-article","created":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T08:06:13Z","timestamp":1700726773000},"page":"e16366","source":"Crossref","is-referenced-by-count":1,"title":["Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) <i>via<\/i> endotracheal tube: has NAC caused any change?"],"prefix":"10.7717","volume":"11","author":[{"given":"Hee Yeon","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Surgery, Busan Paik Hospital, Inje University, Busan, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tae Hyun","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Surgery, Busan Paik Hospital, Inje University, Busan, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeong Hwan","family":"Shin","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine and Paik Institute for Clinical Research, Inje University, Busan, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwangrae","family":"Cho","sequence":"additional","affiliation":[{"name":"Department of Anesthesiology and Pain Medicine, Busan Paik Hospital, Inje University, Busan, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heon-Kyun","family":"Ha","sequence":"additional","affiliation":[{"name":"Department of Surgery, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Chung-Ang University, Gyeonggi-do, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anbok","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Surgery, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Chung-Ang University, Gyeonggi-do, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Young Jin","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Medical Center, Seoul, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"4443","published-online":{"date-parts":[[2023,11,23]]},"reference":[{"issue":"1","key":"10.7717\/peerj.16366\/ref-1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1140\/epjc\/s2003-01257-6","article-title":"Measurement and QCD analysis of neutral and charged current cross sections at HERA","volume":"30","author":"Adloff","year":"2003","journal-title":"The European Physical Journal C"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-2","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1164\/ajrccm.161.1.9903059","article-title":"Pulmonary toxicity of induction chemotherapy prior to standard or high-dose chemotherapy with autologous hematopoietic support","volume":"161","author":"Bhalla","year":"2000","journal-title":"American Journal of Respiratory and Critical Care Medicine"},{"key":"10.7717\/peerj.16366\/ref-3","doi-asserted-by":"publisher","first-page":"aad3311","DOI":"10.1126\/science.aad3311","article-title":"Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children","volume":"351","author":"Blanton","year":"2016","journal-title":"Science"},{"issue":"7","key":"10.7717\/peerj.16366\/ref-4","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nature Methods"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-5","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"10.7717\/peerj.16366\/ref-6","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nature Methods"},{"key":"10.7717\/peerj.16366\/ref-7","doi-asserted-by":"publisher","first-page":"e1847","DOI":"10.1002\/cnr2.1847","article-title":"Gut microbiome influences incidence and outcomes of breast cancer by regulating levels and activity of steroid hormones in women","volume":"13","author":"Chapadgaonkar","year":"2023","journal-title":"Cancer Reports"},{"issue":"3","key":"10.7717\/peerj.16366\/ref-8","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1007\/s10549-019-05407-5","article-title":"The microbiome and breast cancer: a review","volume":"178","author":"Chen","year":"2019","journal-title":"Breast Cancer Research and Treatment"},{"issue":"11","key":"10.7717\/peerj.16366\/ref-9","doi-asserted-by":"publisher","first-page":"e0259596","DOI":"10.1371\/journal.pone.0259596","article-title":"Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes","volume":"16","author":"Cho","year":"2021","journal-title":"PLOS ONE"},{"issue":"5960","key":"10.7717\/peerj.16366\/ref-10","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1126\/science.1177486","article-title":"Bacterial community variation in human body habitats across space and time","volume":"326","author":"Costello","year":"2009","journal-title":"Science"},{"issue":"6","key":"10.7717\/peerj.16366\/ref-11","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1513\/AnnalsATS.201501-029OC","article-title":"Spatial variation in the healthy human lung microbiome and the adapted Island model of lung biogeography","volume":"12","author":"Dickson","year":"2015","journal-title":"Annals of the American Thoracic Society"},{"issue":"5","key":"10.7717\/peerj.16366\/ref-12","doi-asserted-by":"publisher","first-page":"e97214","DOI":"10.1371\/journal.pone.0097214","article-title":"Changes in the lung microbiome following lung transplantation include the emergence of two distinct Pseudomonas species with distinct clinical associations","volume":"9","author":"Dickson","year":"2014","journal-title":"PLOS ONE"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-13","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1146\/annurev-physiol-021115-105238","article-title":"The microbiome and the respiratory tract","volume":"78","author":"Dickson","year":"2016","journal-title":"Annual Review of Physiology"},{"key":"10.7717\/peerj.16366\/ref-14","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1658\/1100-9233(2003)014[0927:Vaporf]2.0.Co;2","article-title":"VEGAN, a package of R functions for community ecology","volume":"14","author":"Dixon","year":"2003","journal-title":"Journal of Vegetation Science"},{"issue":"4","key":"10.7717\/peerj.16366\/ref-15","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.ejcts.2004.07.015","article-title":"Preoperative chemotherapy increases cytokine production after lung cancer surgery","volume":"26","author":"Endo","year":"2004","journal-title":"European Journal of Cardio-Thoracic Surgery"},{"issue":"4","key":"10.7717\/peerj.16366\/ref-16","doi-asserted-by":"publisher","first-page":"1602086","DOI":"10.1183\/13993003.02086-2016","article-title":"The microbiome in respiratory medicine: current challenges and future perspectives","volume":"49","author":"Faner","year":"2017","journal-title":"European Respiratory Journal"},{"issue":"22","key":"10.7717\/peerj.16366\/ref-17","doi-asserted-by":"publisher","first-page":"4287","DOI":"10.1007\/s00018-015-2004-1","article-title":"From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems","volume":"72","author":"Garza","year":"2015","journal-title":"Cellular and Molecular Life Sciences"},{"issue":"2","key":"10.7717\/peerj.16366\/ref-18","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/mi.2016.108","article-title":"The respiratory tract microbiome and lung inflammation: a two-way street","volume":"10","author":"Huffnagle","year":"2017","journal-title":"Mucosal Immunology"},{"issue":"6161","key":"10.7717\/peerj.16366\/ref-19","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1126\/science.1240527","article-title":"Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment","volume":"342","author":"Iida","year":"2013","journal-title":"Science"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-20","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/s12915-019-0703-z","article-title":"The microbiome of the upper respiratory tract in health and disease","volume":"17","author":"Kumpitsch","year":"2019","journal-title":"BMC Biology"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-21","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1186\/s12885-021-08917-y","article-title":"Characteristics in gut microbiome is associated with chemotherapy-induced pneumonia in pediatric acute lymphoblastic leukemia","volume":"21","author":"Liu","year":"2021","journal-title":"BMC Cancer"},{"issue":"3","key":"10.7717\/peerj.16366\/ref-22","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1007\/s00253-015-7177-x","article-title":"The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy","volume":"100","author":"Magalhaes","year":"2016","journal-title":"Applied Microbiology and Biotechnology"},{"issue":"4","key":"10.7717\/peerj.16366\/ref-23","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1111\/resp.12732","article-title":"COPD and the microbiome","volume":"21","author":"Mammen","year":"2016","journal-title":"Respirology"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-24","doi-asserted-by":"publisher","first-page":"3","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.Journal"},{"key":"10.7717\/peerj.16366\/ref-25","doi-asserted-by":"publisher","first-page":"318","DOI":"10.3389\/fonc.2018.00318","article-title":"Study of microbiomes in aseptically collected samples of human breast tissue using needle biopsy and the potential role of in situ tissue microbiomes for promoting malignancy","volume":"8","author":"Meng","year":"2018","journal-title":"Frontiers in Oncology"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-26","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1016\/j.amjsurg.2020.09.042","article-title":"Neoadjuvant chemotherapy for pancreatic cancer and changes in the biliary microbiome","volume":"222","author":"Nadeem","year":"2021","journal-title":"American Journal of Surgery"},{"key":"10.7717\/peerj.16366\/ref-27","doi-asserted-by":"publisher","first-page":"7","DOI":"10.3390\/cancers14010007","article-title":"Evaluation of changes to the oral microbiome based on 16S rRNA sequencing among children treated for cancer","volume":"14","author":"Proc","year":"2022","journal-title":"Cancers"},{"issue":"2","key":"10.7717\/peerj.16366\/ref-28","doi-asserted-by":"publisher","first-page":"119","DOI":"10.4048\/jbc.2017.20.2.119","article-title":"Recent advances in the neoadjuvant treatment of breast cancer","volume":"20","author":"Rubovszky","year":"2017","journal-title":"Journal of Breast Cancer"},{"issue":"6","key":"10.7717\/peerj.16366\/ref-29","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biology"},{"issue":"23","key":"10.7717\/peerj.16366\/ref-30","doi-asserted-by":"publisher","first-page":"1806","DOI":"10.1093\/jnci\/93.23.1806","article-title":"Risk of pneumonitis in breast cancer patients treated with radiation therapy and combination chemotherapy with paclitaxel","volume":"93","author":"Taghian","year":"2001","journal-title":"JNCI: Journal of the National Cancer Institute"},{"issue":"10","key":"10.7717\/peerj.16366\/ref-31","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1164\/rccm.201210-1937OC","article-title":"Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation","volume":"187","author":"Tunney","year":"2013","journal-title":"American Journal of Respiratory and Critical Care Medicine"},{"key":"10.7717\/peerj.16366\/ref-32","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1016\/j.cell.2016.04.007","article-title":"Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans","volume":"165","author":"Vatanen","year":"2016","journal-title":"Cell"},{"issue":"2","key":"10.7717\/peerj.16366\/ref-33","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.ccm.2016.12.005","article-title":"Bacterial pneumonia in patients with cancer: novel risk factors and management","volume":"38","author":"Wong","year":"2017","journal-title":"Clinics in Chest Medicine"},{"key":"10.7717\/peerj.16366\/ref-34","article-title":"Breast cancer 2020 (updated 26 March 2021; cited 2022 14 Jan 2022)","author":"World Health Organization (WHO)","year":"2020"},{"key":"10.7717\/peerj.16366\/ref-35","doi-asserted-by":"publisher","first-page":"433","DOI":"10.2147\/BCTT.S305486","article-title":"Effect of chemotherapy on the gut microbiome of breast cancer patients during the first year of treatment","volume":"14","author":"Wu","year":"2022","journal-title":"Breast Cancer-Targets and Therapy"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-36","doi-asserted-by":"publisher","first-page":"e83744","DOI":"10.1371\/journal.pone.0083744","article-title":"Microbial dysbiosis is associated with human breast cancer","volume":"9","author":"Xuan","year":"2014","journal-title":"PLOS One"},{"issue":"19","key":"10.7717\/peerj.16366\/ref-37","doi-asserted-by":"publisher","first-page":"10872","DOI":"10.3390\/ijms221910872","article-title":"The lung microbiome during health and disease","volume":"22","author":"Yagi","year":"2021","journal-title":"International Journal of Molecular Sciences"},{"issue":"1","key":"10.7717\/peerj.16366\/ref-38","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1186\/s13059-016-1021-1","article-title":"Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features","volume":"17","author":"Yu","year":"2016","journal-title":"Genome Biology"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/16366.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/16366.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/16366.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/16366.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,23]],"date-time":"2023-11-23T08:06:22Z","timestamp":1700726782000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/16366"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,23]]},"references-count":38,"alternative-id":["10.7717\/peerj.16366"],"URL":"https:\/\/doi.org\/10.7717\/peerj.16366","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,23]]},"article-number":"e16366"}}