Rational strategy for studying microbiome of the ocular surface of people using hard contact lenses by method of 16S rRNA gene metabarcoding

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S.É. Avetisov

FGBU "Nauchno-issledovatel'skiĭ institut glaznykh bolezneĭ" RAMN, Moskva

N.D. Abramova

Research Institute of Eye Diseases, Moscow, Russia

N.E. Gogoleva

Kazan Institute of Biochemistry and Biophysics — stand-alone branch of Kazan Scientific Center of RAS, Kazan, Russia;
Kazan Federal University (Volga Region), Institute of Fundamental Medicine and Biology, Kazan, Russia

O.A. Gusev

RIKEN-KFU Translational Genomics Unit, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama City, Japan

T.S. Mitichkina

FGBU "NII glaznykh bolezneĭ" RAMN, Moskva

I.A. Novikov

Institute of Cardiology named after A.L. Myasnikov of National Medical Research Center for Cardiology, Moscow, Russia

A.M. Subbot

FGBU "NII glaznykh bolezneĭ" RAMN, Moskva

E.I. Shagimardanova

Kazan Federal University (Volga Region), Institute of Fundamental Medicine and Biology, Kazan, Russia

Rational strategy for studying microbiome of the ocular surface of people using hard contact lenses by method of 16S rRNA gene metabarcoding

Authors:

S.É. Avetisov, N.D. Abramova, N.E. Gogoleva, O.A. Gusev, T.S. Mitichkina, I.A. Novikov, A.M. Subbot, E.I. Shagimardanova

More about the authors

Journal: Russian Annals of Ophthalmology. 2020;136(3): 3‑9

DOI: 10.17116/oftalma20201360313

Views: 1410

Downloaded: 28

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To cite this article:

Avetisov SÉ, Abramova ND, Gogoleva NE, Gusev OA, Mitichkina TS, Novikov IA, Subbot AM, Shagimardanova EI. Rational strategy for studying microbiome of the ocular surface of people using hard contact lenses by method of 16S rRNA gene metabarcoding. Russian Annals of Ophthalmology. 2020;136(3):3‑9. (In Russ., In Engl.)
https://doi.org/10.17116/oftalma20201360313

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Ozkan J, Nielsen S, Diez-Vives C, Coroneo M, Thomas T, Willcox M. Temporal stability and composition of the ocular surface microbiome. Scientific Reports. 2017;7(1):9880. https://doi.org/10.1038/s41598-017-10494-9
Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, et al. Diversity of Bacteria at Healthy Human Conjunctiva. Invest Ophthalmol Visual Sci. 2011;52(8):5408-5413. https://doi.org/10.1167/iovs.10-6939
Huang Y, Yang B, Li W. Defining the normal core microbiome of conjunctival microbial communities. Clin Microbiol Infect. 2016;22(7):643.e7-643.e12. https://doi.org/10.1016/j.cmi.2016.04.008
Willcox M. Characterization of the normal microbiota of the ocular surface. Exper Eye Res. 2013;117:99-105. https://doi.org/10.1016/j.exer.2013.06.003
Meisel JS, Hannigan GD, Tyldsley AS, SanMiguel AJ, Hodkinson BP, Zheng Q, et al. Skin microbiome surveys are strongly influenced by experimental design. J Invest Dermatol. 2016;136(5):947-956. https://doi.org/10.1016/j.jid.2016.01.016
Herlemann DPR, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 2011;5(10):1571-1579. https://doi.org/10.1038/ismej.2011.41
Ozkan J, Coroneo M, Willcox M, Wemheuer B, Thomas T. Identification and visualization of a distinct microbiome in ocular surface conjunctival tissue. Invest Ophthalmol Vis Sci. 2018;59(10):4268-4276. https://doi.org/10.1167/iovs.18-24651
Shin H, Price K, Albert L, Dodick J, Park L, Dominguez-Bello MG. Changes in the eye microbiota associated with contact lens wearing. MBio. 2016;7(2):e00198-16. https://doi.org/10.1128/mbio.00198-16
Blinkova LP, Pakhomov YuD, Stoyanova LG. Properties of nonculturable and dormant forms of microorganisms. Immunopatologiya, allergologiya, infektologiya. 2010;(2):67-76. (In Russ.).
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature. 2013;499(7459):431-437. https://doi.org/10.1038/nature12352
Baranov AA, Mayansky AN, Chebotar IV, Mayansky NA. The new era in medical Microbiology. Vestnik Rossiyskoy akademii nauk. 2015;85(11):1011-1018. (In Russ.). https://doi.org/10.7868/S086958731511002X
Oliver JD. The viable but nonculturable state in bacteria. J Microbiol. 2005; 43(1):93-100.
Lloyd KG, Steen AD, Ladau J, Yin J, Crosby L. Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. mSystems. 2018;3(5):1-12. https://doi.org/10.1128/mSystems.00055-18
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. https://doi.org/10.1038/nmeth.3869
Brooks JP, Edwards DJ, Harwich MD Jr, Rivera MC, Fettweis JM, Serrano MG, et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 2015;15:66. https://doi.org/10.1186/s12866-015-0351-6
Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol. 2005; 71(12):8966-8969. https://doi.org/10.1128/AEM.71.12.8966-8969.2005
Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol. 2018;16(3):143-155. https://doi.org/10.1038/nrmicro.2017.157
Larkin DF, Leeming JP. Quantitative alterations of the commensal eye bacteria in contact lens wear. Eye (Lond). 1991;5(1):70-74. https://doi.org/10.1038/eye.1991.14
Boost MV, Cho P. Microbial flora of tears of orthokeratology patients, and microbial contamination of contact lenses and contact lens accessories. Optom Vis Sci. 2005;82(6):451-458. https://doi.org/10.1097/01.opx.0000168587.72893.ec
Szczotka-Flynn LB, Pearlman E, Ghannoum M. Microbial contamination of contact lenses, lens care solutions, and their accessories: a literature review. Eye Contact Lens. 2010;36(2):116-129. https://doi.org/10.1097/icl.0b013e3181d20cae.
McAdam TG, Burnes BS. A pilot study of the effects of environmental and physiological stress on the conjunctival bacteria of college student contact wearers. BIOS. 2014;85(2):86-94. https://doi.org/10.1893/0005-3155-85.2.86
Gao Z, Tseng CH, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA. 2007;104(8):2927-2932. https://doi.org/10.1073/pnas.0607077104

Keywords:

microbiome

ocular surface

contact lenses

sequencing

Authors:

S.É. Avetisov

FGBU "Nauchno-issledovatel'skiĭ institut glaznykh bolezneĭ" RAMN, Moskva

N.D. Abramova

Research Institute of Eye Diseases, Moscow, Russia

N.E. Gogoleva

Kazan Institute of Biochemistry and Biophysics — stand-alone branch of Kazan Scientific Center of RAS, Kazan, Russia;
Kazan Federal University (Volga Region), Institute of Fundamental Medicine and Biology, Kazan, Russia

O.A. Gusev

RIKEN-KFU Translational Genomics Unit, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama City, Japan

T.S. Mitichkina

FGBU "NII glaznykh bolezneĭ" RAMN, Moskva

I.A. Novikov

Institute of Cardiology named after A.L. Myasnikov of National Medical Research Center for Cardiology, Moscow, Russia

A.M. Subbot

FGBU "NII glaznykh bolezneĭ" RAMN, Moskva

E.I. Shagimardanova

Kazan Federal University (Volga Region), Institute of Fundamental Medicine and Biology, Kazan, Russia

List of references:

Ozkan J, Nielsen S, Diez-Vives C, Coroneo M, Thomas T, Willcox M. Temporal stability and composition of the ocular surface microbiome. 2017;7(1):9880.
Dong Q, Brulc JM, Iovieno A, Bates B, Garoutte A, Miller D, et al. Diversity of Bacteria at Healthy Human Conjunctiva. 2011;52(8):5408-5413.
Huang Y, Yang B, Li W. Defining the normal core microbiome of conjunctival microbial communities. 2016;22(7):643.e7-643.e12.
Willcox M. Characterization of the normal microbiota of the ocular surface. 2013;117:99-105.
Meisel JS, Hannigan GD, Tyldsley AS, SanMiguel AJ, Hodkinson BP, Zheng Q, et al. Skin microbiome surveys are strongly influenced by experimental design. 2016;136(5):947-956.
Herlemann DPR, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. 2011;5(10):1571-1579.
Ozkan J, Coroneo M, Willcox M, Wemheuer B, Thomas T. Identification and visualization of a distinct microbiome in ocular surface conjunctival tissue. 2018;59(10):4268-4276.
Shin H, Price K, Albert L, Dodick J, Park L, Dominguez-Bello MG. Changes in the eye microbiota associated with contact lens wearing. 2016;7(2):e00198-16.
Blinkova LP, Pakhomov YuD, Stoyanova LG. Properties of nonculturable and dormant forms of microorganisms. 2010;(2):67-76. (In Russ.).
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, et al. Insights into the phylogeny and coding potential of microbial dark matter. 2013;499(7459):431-437.
Baranov AA, Mayansky AN, Chebotar IV, Mayansky NA. The new era in medical Microbiology. 2015;85(11):1011-1018. (In Russ.).
Oliver JD. The viable but nonculturable state in bacteria. 2005; 43(1):93-100.
Lloyd KG, Steen AD, Ladau J, Yin J, Crosby L. Phylogenetically novel uncultured microbial cells dominate Earth microbiomes. 2018;3(5):1-12.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. 2016;13(7):581-583.
Brooks JP, Edwards DJ, Harwich MD Jr, Rivera MC, Fettweis JM, Serrano MG, et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. 2015;15:66.
Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. 2005; 71(12):8966-8969.
Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. 2018;16(3):143-155.
Larkin DF, Leeming JP. Quantitative alterations of the commensal eye bacteria in contact lens wear. 1991;5(1):70-74.
Boost MV, Cho P. Microbial flora of tears of orthokeratology patients, and microbial contamination of contact lenses and contact lens accessories. 2005;82(6):451-458.
Szczotka-Flynn LB, Pearlman E, Ghannoum M. Microbial contamination of contact lenses, lens care solutions, and their accessories: a literature review. 2010;36(2):116-129. https://doi.org/10.1097/icl.0b013e3181d20cae.
McAdam TG, Burnes BS. A pilot study of the effects of environmental and physiological stress on the conjunctival bacteria of college student contact wearers. 2014;85(2):86-94.
Gao Z, Tseng CH, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. 2007;104(8):2927-2932.

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