Abstract
Respiratory bacterial microbiota plays a key role in human health. Lung cancer microbiome is a significant yet an understudied area while bronchiectasis microbiome is often studied. We assessed the bacterial microbiota in the upper and lower respiratory tract of the patients with lung cancer and bronchiectasis against a healthy group and their variations in individuality. 16S rRNA gene based metagenomic sequencing was used to detect entire bacterial community along with conventional aerobic bacterial culturing. In comparison to healthy, increased bacterial diversity was observed in diseased population. Abundance of more than 1% was considered and bacteria were identified in 97% similarity. Only lung cancer patients exhibited bacteria specific to the disease: Corynebacterium tuberculostearicum and Keratinibaculum paraultunense. However, Enterococcus faecalis and Delftia tsuruhatensis were also observed limited to lung cancer and bronchiectasis respectively, in less than 1% but supported with bacterial culturing. In conclusion the disease condition and intra-group variability should be considered in future with larger cohorts to understand individual patient variability highlighting the social habits and gender of the individual.
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Lederberg J, McCray JE (2001) ‘Ome Sweet’ Omics—a genealogical treasury of words | The Scientist Magazine®. In: Sci. https://www.the-scientist.com/commentary/ome-sweet-omics—a-genealogical-treasury-of-words-54889. Accessed 7 March 2019
Young RP, Hopkins RJ, Christmas T et al (2009) COPD prevalence is increased in lung cancer, independent of age, sex and smoking history. Eur Respir J 34:380–386. https://doi.org/10.1183/09031936.00144208
Yu Y-H, Liao C-C, Hsu W-H et al (2011) Increased lung cancer risk among patients with pulmonary tuberculosis: a population cohort study. J Thorac Oncol 6:32–37. https://doi.org/10.1097/JTO.0b013e3181fb4fcc
Wu BG, Cahaney CF, Tsay JJ et al (2015) C99 genomics and cancer: has it borne scientific and clinical fruit? Evaluation of the microbiome associated with lung cancer. In: American Thoracic Society 2015 international conference
Hosgood HD, Sapkota AR, Rothman N et al (2014) The potential role of lung microbiota in lung cancer attributed to household coal burning exposures. Environ Mol Mutagen 55:643–651. https://doi.org/10.1002/em.21878
Geller LT, Barzily-Rokni M, Danino T et al (2017) Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. Science 357:1156–1160. https://doi.org/10.1126/science.aah5043
King P (2009) The pathophysiology of bronchiectasis. Int J Chron Obstruct Pulmon Dis 4:411. https://doi.org/10.2147/COPD.S6133
Liu JC, Modha DE, Gaillard EA (2013) What is the clinical significance of filamentous fungi positive sputum cultures in patients with cystic fibrosis? J Cyst Fibros 12:187–193. https://doi.org/10.1016/j.jcf.2013.02.003
Purcell P, Jary H, Perry A et al (2014) Polymicrobial airway bacterial communities in adult bronchiectasis patients. BMC Microbiol 14:130. https://doi.org/10.1186/1471-2180-14-130
Rogers GB, Zain NMM, Bruce KD et al (2014) A novel microbiota stratification system predicts future exacerbations in bronchiectasis. Ann Am Thorac Soc 11:496–503. https://doi.org/10.1513/AnnalsATS.201310-335OC
Boom R, Sol CJ, Salimans MM et al (1990) Rapid and simple method for purification of nucleic acids. J Clin Microbiol 28:495–503
Tripathi K, Tripathi PC, Nema S et al (2014) Modified Petroff’s method: an excellent simplified decontamination technique in comparison with Petroff’s method. Statperson Publications
Somerville W, Thibert L, Schwartzman K, Behr MA (2005) Extraction of Mycobacterium tuberculosis DNA: a Question of Containment. J Clin Microbiol 43:2996–2997. https://doi.org/10.1128/JCM.43.6.2996-2997.2005
Lane DJ, Pace B, Olsen GJ et al (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82:6955–6959. https://doi.org/10.1073/pnas.82.20.6955
Dereeper A, Guignon V, Blanc G et al (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36:W465–W469. https://doi.org/10.1093/nar/gkn180
Dereeper A, Audic S, Claverie J-M, Blanc G (2010) BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol 10:8. https://doi.org/10.1186/1471-2148-10-8
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334
Chevenet F, Brun C, Bañuls A-L et al (2006) TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7:439. https://doi.org/10.1186/1471-2105-7-439
Letunic I, Bork P (2016) Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242–W245. https://doi.org/10.1093/nar/gkw290
Liu H-X, Tao L-L, Zhang J et al (2018) Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects. Int J Cancer 142:769–778. https://doi.org/10.1002/ijc.31098
Hinic V, Lang C, Weisser M et al (2012) Corynebacterium tuberculostearicum: a potentially misidentified and multiresistant Corynebacterium species isolated from clinical specimens. J Clin Microbiol 50:2561–2567. https://doi.org/10.1128/JCM.00386-12
Berghmans T, Sculier J-P, Klastersky J (2003) A prospective study of infections in lung cancer patients admitted to the hospital. Chest 124:114–120. https://doi.org/10.1378/chest.124.1.114
Boonanantanasarn K, Gill AL, Yap Y et al (2012) Enterococcus faecalis enhances cell proliferation through hydrogen peroxide-mediated epidermal growth factor receptor activation. Infect Immun. https://doi.org/10.1128/IAI.00479-12
Krzymińska S, Mokracka J, Koczura R, Kaznowski A (2009) Cytotoxic activity of Enterobacter cloacae human isolates. FEMS Immunol Med Microbiol 56:248–252. https://doi.org/10.1111/j.1574-695X.2009.00572.x
Merlos A, Rodríguez P, Bárcena-Uribarri I et al (2015) Toxins secreted by bacillus isolated from lung adenocarcinomas favor the penetration of toxic substances. Front Microbiol 6:1301. https://doi.org/10.3389/fmicb.2015.01301
Marsland BJ, Trompette A, Gollwitzer ES (2015) The gut-lung axis in respiratory disease. In: Annals of the American Thoracic Society. American Thoracic Society, pp S150–S156
Metersky ML, Aksamit TR, Barker A et al (2018) The prevalence and significance of staphylococcus aureus in patients with non-cystic fibrosis bronchiectasis. Ann Am Thorac Soc 15:365–370. https://doi.org/10.1513/AnnalsATS.201706-426OC
Hogg JC, van Eeden S (2009) Pulmonary and systemic response to atmospheric pollution. Respirology 14:336–346. https://doi.org/10.1111/j.1440-1843.2009.01497.x
Segal LN, Alekseyenko AV, Clemente JC et al (2013) Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome 1:19. https://doi.org/10.1186/2049-2618-1-19
De Escalante Yangüela B, Gracia Gutiérrez A, Gracia Tello B et al (2017) Bilateral bronchopneumonia due to Rothia mucilaginosa. An Sist Sanit Navar 40:479–483. https://doi.org/10.23938/ASSN.0090
Org E, Mehrabian M, Parks BW et al (2016) Sex differences and hormonal effects on gut microbiota composition in mice. Gut Microbes 7:313–322. https://doi.org/10.1080/19490976.2016.1203502
Falagas ME, Mourtzoukou EG, Vardakas KZ (2007) Sex differences in the incidence and severity of respiratory tract infections. Respir Med 101:1845–1863. https://doi.org/10.1016/J.RMED.2007.04.011
Fan X, Peters BA, Jacobs EJ et al (2018) Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults. Microbiome 6:59. https://doi.org/10.1186/s40168-018-0448-x
Acknowledgements
The authors would like to acknowledge the support given by the members of the Respiratory Unit 2 at Teaching Hospital, Kandy and financial assistance provided by National Institute of Fundamental Studies, Kandy, Sri Lanka.
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AE and DNM designed the study. DM did clinically assess the patients and carried out sampling procedures. AE collected the samples, processed and did the experiments with analysis. DNM and NVC supervised the study. AE wrote the manuscript. All authors reviewed the manuscript.
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Informed consent was obtained from all individual participants included in the study.
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Further data of the research can obtain by contacting the corresponding author. The sequences of the identified organisms were deposited in NCBI GenBank nucleotide database (accession numbers MF498492.1-MF498510.1, MG733159.1-MG733173.1, MG738354.1). 16S rRNA gene sequence trimmed reads are deposited in NCBI Sequence Read Archive (SRA) database under the BioProject ID number PRJNA477678. Further details on the organisms and the metagenomics sequencing is provided in electronic supplementary material.
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Ekanayake, A., Madegedara, D., Chandrasekharan, V. et al. Respiratory Bacterial Microbiota and Individual Bacterial Variability in Lung Cancer and Bronchiectasis Patients. Indian J Microbiol 60, 196–205 (2020). https://doi.org/10.1007/s12088-019-00850-w
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DOI: https://doi.org/10.1007/s12088-019-00850-w