1. Jenq RR, van den Brink MR. Allogeneic haematopoietic stem cell transplantation: individualized stem cell and immune therapy of cancer. Nat Rev Cancer. 2010; 10(3):213–21. Epub 2010/02/20. https://doi. org/10.1038/nrc2804 PMID: 20168320.
2. Copelan EA, Chojecki A, Lazarus HM, Avalos BR. Allogeneic hematopoietic cell transplantation; the current renaissance. Blood Rev. 2019; 34:34–44. Epub 2018/11/24. https://doi.org/10.1016/j.blre.2018. 11.001 PMID: 30467067.
3. Copelan EA. Hematopoietic stem-cell transplantation. N Engl J Med. 2006; 354(17):1813–26. Epub 2006/04/28. https://doi.org/10.1056/NEJMra052638 PMID: 16641398.
4. Becattini S, Taur Y, Pamer EG. Antibiotic-Induced Changes in the Intestinal Microbiota and Disease. Trends Mol Med. 2016; 22(6):458–78. Epub 2016/05/15. https://doi.org/10.1016/j.molmed.2016.04.003 PMID: 27178527; PubMed Central PMCID: PMC4885777.
5. Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis. 2012; 55(7):905–14. Epub 2012/06/22. https://doi.org/10.1093/cid/cis580 PMID: 22718773; PubMed Central PMCID: PMC3657523.
6. Shono Y, Docampo MD, Peled JU, Perobelli SM, Velardi E, Tsai JJ, et al. Increased GVHD-related mor- tality with broad-spectrum antibiotic use after allogeneic hematopoietic stem cell transplantation in human patients and mice. Sci Transl Med. 2016; 8(339):339ra71. Epub 2016/05/20. https://doi.org/10. 1126/scitranslmed.aaf2311 PMID: 27194729; PubMed Central PMCID: PMC4991773.
7. Golob JL, Pergam SA, Srinivasan S, Fiedler TL, Liu C, Garcia K, et al. Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplanta- tion. Clin Infect Dis. 2017; 65(12):1984–91. Epub 2017/10/12. https://doi.org/10.1093/cid/cix699 PMID: 29020185; PubMed Central PMCID: PMC5850019.
8. Peled JU, Devlin SM, Staffas A, Lumish M, Khanin R, Littmann ER, et al. Intestinal Microbiota and Relapse After Hematopoietic-Cell Transplantation. J Clin Oncol. 2017; 35(15):1650–9. Epub 2017/03/16. https://doi.org/10.1200/JCO.2016.70.3348 PMID: 28296584; PubMed Central PMCID: PMC5455763.
9. Taur Y, Jenq RR, Perales MA, Littmann ER, Morjaria S, Ling L, et al. The effects of intestinal tract bacte- rial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood. 2014; 124 (7):1174–82. Epub 2014/06/19. https://doi.org/10.1182/blood-2014-02-554725 PMID: 24939656; PubMed Central PMCID: PMC4133489.
10. Dahlen G. Bacterial infections of the oral mucosa. Periodontol 2000. 2009; 49:13–38. Epub 2009/01/21. https://doi.org/10.1111/j.1600-0757.2008.00295.x PMID: 19152524.
11. Muro M, Soga Y, Higuchi T, Kataoka K, Ekuni D, Maeda Y, et al. Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiol- ogy of oral mucositis. Folia Microbiol (Praha). 2018; 63(5):587–97. Epub 2018/03/14. https://doi.org/10. 1007/s12223-018-0596-1 PMID: 29532421.
12. Ames NJ, Barb JJ, Ranucci A, Kim H, Mudra SE, Cashion AK, et al. The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study. Ann Hematol. 2019; 98(6):1351–65. Epub 2019/03/29. https://doi.org/10.1007/s00277-019-03599-w PMID: 30919073.
13. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome biology. 2012; 13(6):R42. Epub 2012/06/16. https://doi.org/10.1186/gb-2012-13-6-r42 PMID: 22698087; PubMed Central PMCID: PMC3446314.
14. Mager DL, Ximenez-Fyvie LA, Haffajee AD, Socransky SS. Distribution of selected bacterial species on intraoral surfaces. J Clin Periodontol. 2003; 30(7):644–54. Epub 2003/07/02. 376 [pii]. https://doi.org/ 10.1034/j.1600-051x.2003.00376.x PMID: 12834503.
15. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, et al. Biogeography of the ecosystems of the healthy human body. Genome biology. 2013; 14(1):R1. Epub 2013/01/16. https://doi.org/10.1186/gb-2013-14-1-r1 PMID: 23316946; PubMed Central PMCID: PMC4054670.
16. Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic informa- tion. Database (Oxford). 2010:baq013. Epub 2010/07/14. https://doi.org/10.1093/database/baq013 baq013 [pii]. PMID: 20624719; PubMed Central PMCID: PMC2911848.
17. Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK. Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system. PeerJ. 2016; 4:e1869. https://doi.org/10. 7717/peerj.1869 PMID: 27069806; PubMed Central PMCID: PMC4824876.
18. Wagner J, Coupland P, Browne HP, Lawley TD, Francis SC, Parkhill J. Evaluation of PacBio sequenc- ing for full-length bacterial 16S rRNA gene classification. BMC Microbiol. 2016; 16(1):274. https://doi. org/10.1186/s12866-016-0891-4 PMID: 27842515; PubMed Central PMCID: PMC5109829.
19. Stelzmueller I, Biebl M, Wiesmayr S, Eller M, Hoeller E, Fille M, et al. Ralstonia pickettii-innocent bystander or a potential threat? Clin Microbiol Infect. 2006; 12(2):99–101. Epub 2006/01/31. https://doi. org/10.1111/j.1469-0691.2005.01309.x PMID: 16441445.
20. Czekaj T, Ciszewski M, Szewczyk EM. Staphylococcus haemolyticus—an emerging threat in the twi- light of the antibiotics age. Microbiology. 2015; 161(11):2061–8. Epub 2015/09/14. https://doi.org/10. 1099/mic.0.000178 PMID: 26363644.
21. Kristich CJ, Rice LB, Arias CA. Enterococcal Infection-Treatment and Antibiotic Resistance. In: Gilmore MS, Clewell DB, Ike Y, Shankar N, editors. Enterococci: From Commensals to Leading Causes of Drug Resistant Infection. Boston2014.
22. Brooke JS. Stenotrophomonas maltophilia: an emerging global opportunistic pathogen. Clinical microbi- ology reviews. 2012; 25(1):2–41. Epub 2012/01/11. https://doi.org/10.1128/CMR.00019-11 PMID: 22232370; PubMed Central PMCID: PMC3255966.
23. Dortet L, Legrand P, Soussy CJ, Cattoir V. Bacterial identification, clinical significance, and antimicrobial susceptibilities of Acinetobacter ursingii and Acinetobacter schindleri, two frequently misidentified opportunistic pathogens. J Clin Microbiol. 2006; 44(12):4471–8. Epub 2006/10/20. https://doi.org/10. 1128/JCM.01535-06 PMID: 17050816; PubMed Central PMCID: PMC1698419.
24. Takeuchi F, Watanabe S, Baba T, Yuzawa H, Ito T, Morimoto Y, et al. Whole-genome sequencing of staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species. J Bacteriol. 2005; 187(21):7292–308. Epub 2005/10/21. https://doi.org/10.1128/JB.187.21.7292-7308.2005 PMID: 16237012; PubMed Central PMCID: PMC1272970.
25. Peduzzi P, Concato J, Feinstein AR, Holford TR. Importance of events per independent variable in pro- portional hazards regression analysis. II. Accuracy and precision of regression estimates. Journal of clinical epidemiology. 1995; 48(12):1503–10. Epub 1995/12/01. https://doi.org/10.1016/0895-4356(95) 00048-8 PMID: 8543964.
26. Asakawa M, Takeshita T, Furuta M, Kageyama S, Takeuchi K, Hata J, et al. Tongue Microbiota and Oral Health Status in Community-Dwelling Elderly Adults. mSphere. 2018; 3(4). https://doi.org/10.1128/ mSphere.00332-18 PMID: 30111628; PubMed Central PMCID: PMC6094060.
27. Takeshita T, Nakano Y, Yamashita Y. Improved accuracy in terminal restriction fragment length poly- morphism phylogenetic analysis using a novel internal size standard definition. Oral Microbiol Immunol. 2007; 22(6):419–28. Epub 2007/10/24. OMI384 [pii] https://doi.org/10.1111/j.1399-302X.2007.00384.x PMID: 17949346.
28. Takeshita T, Kageyama S, Furuta M, Tsuboi H, Takeuchi K, Shibata Y, et al. Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study. Scientific reports. 2016; 6:22164. https://doi. org/10.1038/srep22164 PMID: 26907866; PubMed Central PMCID: PMC4764907.
29. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nature methods. 2013; 10(10):996–8. Epub 2013/08/21. https://doi.org/10.1038/nmeth.2604 PMID: 23955772.
30. Lozupone C, Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 2005; 71(12):8228–35. Epub 2005/12/08. 71/12/8228 [pii] https://doi.org/10.1128/ AEM.71.12.8228-8235.2005 PMID: 16332807; PubMed Central PMCID: PMC1317376.
31. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nature methods. 2016; 13(7):581–3. https://doi.org/10. 1038/nmeth.3869 PMID: 27214047; PubMed Central PMCID: PMC4927377.
32. Mori Y, Yoshimoto G, Nishida R, Sugio T, Miyawaki K, Shima T, et al. Gastrointestinal Graft-versus- Host Disease Is a Risk Factor for Postengraftment Bloodstream Infection in Allogeneic Hematopoietic Stem Cell Transplant Recipients. Biol Blood Marrow Transplant. 2018; 24(11):2302–9. Epub 2018/06/18. https://doi.org/10.1016/j.bbmt.2018.06.002 PMID: 29909153.