1,979
Views
3
CrossRef citations to date
0
Altmetric
Original Article

Mapping bacterial diversity and metabolic functionality of the human respiratory tract microbiome

, , , , , , & show all
Article: 2051336 | Received 17 Nov 2021, Accepted 07 Mar 2022, Published online: 16 Mar 2022

References

  • Marchesi JR, Ravel J. The vocabulary of microbiome research: a proposal. Microbiome. 2015;3(1):31.
  • Dekaboruah E, Suryavanshi MV, Chettri D, et al. Human microbiome: an academic update on human body site specific surveillance and its possible role. Arch Microbiol. 2020;202(8):2147–16.
  • Eisenstein M. The skin microbiome and its relationship with the human body explained. Nature. 2020;588(7838):S210–S211.
  • Rooks MG, Garrett WS. Gut microbiota, metabolites and host immunity. Nat Rev Immunol. 2016;16(6):341–352.
  • Cheng HY, Ning MX, Chen DK, et al. Interactions between the gut microbiota and the host innate immune response against pathogens. Front Immunol. 2019;10:607.
  • Visconti A, Le Roy CI, Rosa F, et al. Interplay between the human gut microbiome and host metabolism. Nat Commun. 2019;10(1):4505.
  • Wang XQ, Zhang A-H, Miao J-H, et al. Gut microbiota as important modulator of metabolism in health and disease. Rsc Adv. 2018;8(74):42380–42389.
  • Milani C, Ferrario C, Turroni F, et al. The human gut microbiota and its interactive connections to diet. J Hum Nutr Diet. 2016;29(5):539–546.
  • Valdes AM, Walter J, Segal E, et al. Role of the gut microbiota in nutrition and health. BMJ. 2018;361:k2179.
  • Kolodziejczyk AA, Zheng D, Elinav E. Diet-microbiota interactions and personalized nutrition. Nat Rev Microbiol. 2019;17(12):742–753.
  • Moszak M, Szulinska M, Bogdanski P. You are what you eat-the relationship between diet, microbiota, and metabolic disorders-a review. Nutrients. 2020;12(4):1096.
  • Manor O, Dai CL, Kornilov SA, et al. Health and disease markers correlate with gut microbiome composition across thousands of people. Nat Commun. 2020;11(1):5206.
  • Mancabelli L, Milani C, Lugli GA, et al. Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses. Sci Rep. 2017;7(1):9879.
  • Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol. 2011;9(4):244–253.
  • Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol. 2018;16(3):143–155.
  • Ravel J, Gajer P, Abdo Z, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4680–4687.
  • Mancabelli L, Tarracchini C, Milani C, et al. Vaginotypes of the human vaginal microbiome. Environ Microbiol. 2021;23(3):1780–1792.
  • Man WH, de Steenhuijsen Piters WA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15(5):259–270.
  • Wypych TP, Wickramasinghe LC, Marsland BJ. The influence of the microbiome on respiratory health. Nat Immunol. 2019;20(10):1279–1290.
  • Dickson RP, Erb-Downward JR, Martinez FJ, et al. The microbiome and the respiratory tract. Annu Rev Physiol. 2016;78(1):481–504.
  • Chen CH, Liou M-L, Lee C-Y, et al. Diversity of nasal microbiota and its interaction with surface microbiota among residents in healthcare institutes. Sci Rep. 2019;9(1):6175.
  • Lehtinen MJ, Hibberd AA, Männikkö S, et al. Nasal microbiota clusters associate with inflammatory response, viral load, and symptom severity in experimental rhinovirus challenge. Sci Rep. 2018;8(1):11411.
  • Hsiao CJ, Paulson JN, Singh S, et al. Nasal microbiota and infectious complications after elective surgical procedures. JAMA Network Open. 2021;4(4):e218386.
  • Lee SH, Sung JY, Yong D, et al. Characterization of microbiome in bronchoalveolar lavage fluid of patients with lung cancer comparing with benign mass like lesions. Lung Cancer. 2016;102:89–95.
  • Schneeberger PHH, Prescod J, Levy L, et al. Microbiota analysis optimization for human bronchoalveolar lavage fluid. Microbiome. 2019;7(1):141.
  • Pragman AA, Lyu T, Baller JA, et al. The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease. Microbiome. 2018;6(1):7.
  • Gopinath D, Menon RK, Wie CC, et al. Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer. Sci Rep. 2021;11(1):1181.
  • Yu G, Gail MH, Consonni D, et al. Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. Genome Biol. 2016;17(1):163.
  • Tangedal S, Nielsen R, Aanerud M, et al. Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients. PLoS One. 2019;14(9):e0222449.
  • Li N, Qiu R, Yang Z, et al. Sputum microbiota in severe asthma patients: relationship to eosinophilic inflammation. Respir Med. 2017;131:192–198.
  • Druzhinin VG, Matskova LV, Demenkov PS, et al. Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes. Sci Rep. 2020;10(1):9681.
  • Segal LN, Alekseyenko AV, Clemente JC, et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013;1(1):19.
  • Marsh RL, Kaestli M, Chang AB, et al. The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx. Microbiome. 2016;4(1):37.
  • Segal LN, Clemente JC, Tsay J-CJ, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol. 2016;1(5):16031.
  • Beck JM, Young VB, Huffnagle GB. The microbiome of the lung. Transl Res. 2012;160(4):258–266.
  • Barcik W, Boutin RCT, Sokolowska M, et al. The role of lung and gut microbiota in the pathology of asthma. Immunity. 2020;52(2):241–255.
  • Chiu YC, Lee SW, Liu CW, et al. Relationship between gut microbiota and lung function decline in patients with chronic obstructive pulmonary disease: a 1-year follow-up study. Respir Res. 2022;23(1):10.
  • Santacroce L, Charitos IA, Ballini A, et al. The human respiratory system and its microbiome at a glimpse. Biology (Basel). 2020;9. DOI:10.3390/biology9100318.
  • Broderick DTJ, Regtien T, Ainsworth A, et al. Dynamic upper and lower airway microbiotas in paediatric bronchiectasis exacerbations: a pilot study. Front Cell Infect Microbiol. 2021;11:773496.
  • Earl JP, Adappa ND, Krol J, et al. Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. Microbiome. 2018;6(1). DOI:10.1186/s40168-018-0569-2
  • Johnson JS, Spakowicz DJ, Hong B-Y, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10(1):5029.
  • Biswas K, Hoggard M, Jain R, et al. The nasal microbiota in health and disease: variation within and between subjects. Front Microbiol. 2015;9:134.
  • Gong H, Shi Y, Zhou X, et al. Microbiota in the throat and risk factors for laryngeal carcinoma. Appl Environ Microbiol. 2014;80(23):7356–7363.
  • Gong HL, Shi Y, Zhou L, et al. The composition of microbiome in larynx and the throat biodiversity between laryngeal squamous cell carcinoma patients and control population. PLoS One. 2013;8(6):e66476.
  • Gomes S, Cavadas B, Ferreira JC, et al. Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma. Sci Rep. 2019;9(1):12838.
  • Ramirez-Labrada AG, Isla D, Artal A, et al. The influence of lung microbiota on lung carcinogenesis, immunity, and immunotherapy. Trends Cancer. 2020;6(2):86–97.
  • Millares L, Pascual S, Montón C, et al. Relationship between the respiratory microbiome and the severity of airflow limitation, history of exacerbations and circulating eosinophils in COPD patients. BMC Pulm Med. 2019;19(1):112.
  • Huang YJ, Sethi S, Murphy T, et al. Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease. J Clin Microbiol. 2014;52(8):2813–2823.
  • Leiten EO, Nielsen R, Wiker HG, et al. The airway microbiota and exacerbations of COPD. ERJ Open Res. 2020;6(3):00168–2020.
  • Cameron SJS, Lewis KE, Huws SA, et al. Metagenomic sequencing of the chronic obstructive pulmonary disease upper bronchial tract microbiome reveals functional changes associated with disease severity. PLoS One. 2016;11(2):e0149095.
  • Westbrook A, Ramsdell J, Schuelke T, et al. PALADIN: protein alignment for functional profiling whole metagenome shotgun data. Bioinformatics. 2017;33(10):1473–1478.
  • de Almeida OGG, Carolina Paulino da Costa C, Tonani L, et al. The lung microbiome of three young brazilian patients with cystic fibrosis colonized by fungi. Front Cell Infect Microbiol. 2020;10:598938.
  • Bacci G, Mengoni A, Fiscarelli E, et al. A different microbiome gene repertoire in the airways of cystic fibrosis patients with severe lung disease. Int J Mol Sci. 2017;18(8):1654.
  • Feigelman R, Kahlert CR, Baty F, et al. Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome. 2017;5(1):20.
  • Metwally AA, Ascoli C, Turturice B, et al. Pediatric lung transplantation: dynamics of the microbiome and bronchiolitis obliterans in cystic fibrosis. J Heart Lung Transplant. 2020;39(8):824–834.
  • Dai W, Wang H, Zhou Q, et al. An integrated respiratory microbial gene catalogue to better understand the microbial aetiology of Mycoplasma pneumoniae pneumonia. Gigascience. 2019;8(8). DOI:10.1093/gigascience/giz093
  • Bacci G, Taccetti G, Dolce D, et al. Untargeted metagenomic investigation of the airway microbiome of cystic fibrosis patients with moderate-severe lung disease. Microorganisms. 2020;8(7):1003.
  • Nelson MT, Pope CE, Marsh RL, et al. Human and extracellular DNA depletion for metagenomic analysis of complex clinical infection samples yields optimized viable microbiome profiles. Cell Rep. 2019;26(8):2227–2240 e2225.
  • Pust MM, Wiehlmann L, Davenport C, et al. The human respiratory tract microbial community structures in healthy and cystic fibrosis infants. NPJ Biofilms Microbiomes. 2020;6(1):61.
  • Milani C, Casey E, Lugli GA, et al. Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: mETAnnotatorX. Microbiome. 2018;6(1):145.
  • Milani C, Lugli GA, Fontana F, et al. METAnnotatorX2: a comprehensive tool for deep and shallow metagenomic data set analyses. mSystems. 2021;e0058321. DOI:10.1128/mSystems.00583-21.
  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
  • Langmead B, Wilks C, Antonescu V, et al. Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics. 2019;35(3):421–432.
  • Chen Y, Ye W, Zhang Y, et al. High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic Acids Res. 2015;43(16):7762–7768.
  • Caspi R, Billington R, Ferrer L, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2016;44:D471–480.
  • Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics. 2012;28(1):125–126.
  • Ye Y, Choi JH, Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics. 2011;12(1):159.
  • Vazquez-Baeza Y, Pirrung M, Gonzalez A, et al. EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience. 2013;2(16). DOI:10.1186/2047-217X-2-16
  • Mallick H, Rahnavard A, McIver LJ, et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol. 2021;17(11):e1009442.
  • Duvallet C, Gibbons SM, Gurry T, et al. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun. 2017;8(1):1784.
  • Bisanz JE, Upadhyay V, Turnbaugh JA, et al. Meta-analysis reveals reproducible gut microbiome alterations in response to a high-fat diet. Cell Host Microbe. 2019;26(2):265–272 e264.
  • Greathouse KL, White JR, Padgett RN, et al. Gut microbiome meta-analysis reveals dysbiosis is independent of body mass index in predicting risk of obesity-associated CRC. BMJ Open Gastroenterol. 2019;6(1):e000247.
  • Mancabelli L, Tarracchini C, Milani C, et al. Multi-population cohort meta-analysis of human intestinal microbiota in early life reveals the existence of infant community state types (ICSTs). Comput Struct Biotechnol J. 2020;18:2480–2493.
  • Chen HW, Liu P-F, Liu Y-T, et al. Nasal commensal Staphylococcus epidermidis counteracts influenza virus. Sci Rep. 2016;6(1):27870.
  • Liu Q, Liu Q, Meng H, et al. Staphylococcus epidermidis contributes to healthy maturation of the nasal microbiome by stimulating antimicrobial peptide production. Cell Host Microbe. 2020;27(1):68–78 e65.
  • Esposito S, Polinori I, Rigante D. The gut microbiota-host partnership as a potential driver of kawasaki syndrome. Front Pediatr. 2019;7:124.
  • Campos J, Hernando M, Roman F, et al. Analysis of invasive haemophilus influenzae infections after extensive vaccination against H. influenzae Type b. J Clin Microbiol. 2004;42(2):524–529.
  • de Bentzmann S, Plesiat P. The Pseudomonas aeruginosa opportunistic pathogen and human infections. Environ Microbiol. 2011;13(7):1655–1665.
  • O’Gara JP. Into the storm: chasing the opportunistic pathogen Staphylococcus aureus from skin colonisation to life-threatening infections. Environ Microbiol. 2017;19(10):3823–3833.
  • Weinberger B, Heck DE, Laskin DL, et al. Nitric oxide in the lung: therapeutic and cellular mechanisms of action. Pharmacol Therapeut. 1999;84(3):401–411.
  • Sparacino-Watkins CE, Lai YC, Gladwin MT. Nitrate-Nitrite-Nitric Oxide pathway in pulmonary arterial hypertension therapeutics. Circulation. 2012;125(23):2824–2826.
  • England RJ, Homer JJ, Knight LC, et al. Nasal pH measurement: a reliable and repeatable parameter. Clin Otolaryngol Allied Sci. 1999;24(1):67–68.
  • Silver S, Ji G. Newer systems for bacterial resistances to toxic heavy metals. Environ Health Perspect. 1994;102(3):107–113.
  • Ghorani-Azam A, Riahi-Zanjani B, Balali-Mood M. Effects of air pollution on human health and practical measures for prevention in Iran. J Res Med Sci. 2016;21(1):65.
  • Briffa J, Sinagra E, Blundell R. Heavy metal pollution in the environment and their toxicological effects on humans. Heliyon. 2020;6(9):e04691. doi:ARTN.
  • Adler CJ, Dobney K, Weyrich LS, et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet. 2013;45(4):450–455.
  • Kato I, Vasquez A, Moyerbrailean G, et al. Nutritional correlates of human oral microbiome. J Am Coll Nutr. 2017;36(2):88–98.
  • Shea PR, Beres SB, Flores AR, et al. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations. Proc Natl Acad Sci U S A. 2011;108(12):5039–5044.
  • Sommariva M, Le Noci V, Bianchi F, et al. The lung microbiota: role in maintaining pulmonary immune homeostasis and its implications in cancer development and therapy. Cell Mol Life Sci. 2020;77(14):2739–2749.
  • Wu BG, Segal LN, Britton RA. Lung microbiota and its impact on the mucosal immune phenotype. Microbiol Spectr. 2017;5(3). DOI:10.1128/microbiolspec.BAD-0005-2016
  • O’Dwyer DN, Dickson RP, Moore BB. The lung microbiome, immunity, and the pathogenesis of chronic lung disease. J Immunol. 2016;196(12):4839–4847.