Effects of different substrates/growth media on microbial community of saliva-derived biofilm
Abstract
The aims of this study were to investigate the effects of substrates (glass versus hydroxyapatite [HA]) and growth media (SHI medium versus a modified artificial saliva medium with cysteine) on the microbial community of saliva-derived biofilm in vitro. 16S rRNA gene sequencing technology was used to analyze the microbial community of saliva-derived biofilm cultured for 72 h anaerobically. The metagenomes of biofilms were predicted from the clusters of orthologous groups. No significant difference was found between the saliva-derived biofilms grown on HA and glass in ACE, Chao, Shannon and Simpson indices. The abundances of only a few bacteria on HA were significantly different from those on glass with a low relative abundance (<0.5%). Compared with the biofilms developed in a modified artificial saliva medium with cysteine, biofilms in SHI medium were significantly higher (P < 0.05) in diversity. Linear discriminant analysis coupled with effect size measurement showed that some obligate anaerobic genera (Lactobacillus, Veillonella, Porphyromonas and Leptotrichia) were more abundant in SHI medium biofilms. The biofilms grown in different media were also significantly different in predicted gene categories. In conclusion, the growth media, not the substrates, have significant effects on the microbial community of saliva-derived biofilm in vitro.
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In vitro biofilm culture systems using human saliva or defined media have served as a useful surrogate for oral biofilm research and have shed light on mechanisms involved in microbial adherence, species interactions, antibiofilm treatments, and organization of the microbial community.
“In vitro biofilm culture systems using human saliva or defined media have served as a useful surrogate for oral biofilm research and have shed light on the mechanisms involved in microbial adherence, species interactions, antibiofilm treatments, and organization of the microbial community.55, 56, 57, 58, 59”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [58]
Cites
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works
Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C. R., Yu, W.-H., Lakshmanan, A., & Wade, W. G. (2010) · Journal of Bacteriology · doi:10.1128/jb.00542-10 · Cited by 3,352 · see citing works
The global burden of oral diseases and risks to oral health.
(2005) · Europe PMC (PubMed Central) · Cited by 2,619 · see citing works
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
Cole, J. R. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki038 · Cited by 1,462 · see citing works
Are dental diseases examples of ecological catastrophes?
Marsh, P. D. (2003) · Microbiology · doi:10.1099/mic.0.26082-0 · Cited by 1,256 · see citing works
Nonparametric estimation of Shannon’s index of diversity when there are unseen species in sample
Chao, A., & Shen, T. (2003) · Environmental and Ecological Statistics · doi:10.1023/a:1026096204727 · Cited by 806 · see citing works
Oral Microbiome Metabolism: From “Who Are They?” to “What Are They Doing?”
Takahashi, N. (2015) · Journal of Dental Research · doi:10.1177/0022034515606045 · Cited by 488 · cited 1× · see citing works
“The widely accepted ecological hypothesis of cariogenicity considers dental caries as a result of microecological dysbiosis in dental biofilm (Marsh 2003; Takahashi 2015; Teng et al. 2015; Johansson et al. 2016).”
BackgroundValidation of an in vitro Biofilm Model of Supragingival Plaque
Guggenheim, B., Giertsen, E., Schüpbach, P., & Shapiro, S. (2001) · Journal of Dental Research · doi:10.1177/00220345010800011201 · Cited by 358 · see citing works
Chao, A., Lee, S.-M., & Jeng, S. L. (1992) · Biometrics · doi:10.2307/2532750 · Cited by 314 · see citing works
Loudon, A. H., Woodhams, D. C., Parfrey, L. W., Archer, H. M., Knight, R. D., McKenzie, V. J., & Harris, R. N. (2013) · The ISME Journal · doi:10.1038/ismej.2013.200 · Cited by 306 · see citing works
Chapter 4 In Vitro Biofilm Models
McBain, A. J. (2009) · Advances in applied microbiology · doi:10.1016/s0065-2164(09)69004-3 · Cited by 273 · see citing works
Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota
Teng, F., Yang, F., Huang, S. W., Bo, C., Xu, Z. Z., Amir, A., Knight, R. D., Ling, J., & Xu, J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.08.005 · Cited by 250 · see citing works
Thompson, A. L., Monteagudo-Mera, A., Cadenas, M. B., Lampl, M., & Azcárate-Peril, M. A. (2015) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2015.00003 · Cited by 230 · see citing works
The Microbiome in Populations with a Low and High Prevalence of Caries
Johansson, I., Witkowska, E., Kaveh, B., Holgerson, P. L., & Tanner, A. C. R. (2015) · Journal of Dental Research · doi:10.1177/0022034515609554 · Cited by 227 · see citing works
Sekiguchi, H., Tomioka, N., Nakahara, T., & Uchiyama, H. (2001) · Biotechnology Letters · doi:10.1023/a:1010517117046 · Cited by 207 · see citing works
Meat, dairy and plant proteins alter bacterial composition of rat gut bacteria
Zhu, Y., Lin, X., Zhao, F., Shi, X., He, L., Li, Y., Zhu, W., Xu, X., Li, C., & Zhou, G. (2015) · Scientific Reports · doi:10.1038/srep15220 · Cited by 186 · see citing works
Ling, Z., Jin, C., Xie, T., Cheng, Y., Li, L., & Wu, N. (2016) · Scientific Reports · doi:10.1038/srep30673 · Cited by 185 · see citing works
Exterkate, R. A. M., Crielaard, W., & ten Cate, J. M. (2010) · Caries Research · doi:10.1159/000316541 · Cited by 183 · see citing works
Anti-biofilm dentin primer with quaternary ammonium and silver nanoparticles
Cheng, L., Zhang, K., Melo, M. A. S., Weir, M. D., Zhou, X., & Xu, H. H. K. (2012) · Journal of Dental Research · doi:10.1177/0022034512444128 · Cited by 183 · see citing works
Self-citationEditorial: Prevention of dental caries through the use of fluoride – the WHO approach
Petersen, P. E., & Ogawa, H. (2016) · Community Dental Health · doi:10.1922/cdh_petersen03 · Cited by 181 · see citing works
Edlund, A., Yang, Y., Hall, A. P., Guo, L., Lux, R., He, X., Nelson, K. E., Nealson, K. H., Yooseph, S., Shi, W., et al. (2013) · Microbiome · doi:10.1186/2049-2618-1-25 · Cited by 147 · see citing works
Li, F., Weir, M. D., Fouad, A. F., & Xu, H. H. K. (2014) · Dental Materials · doi:10.1016/j.dental.2013.11.004 · Cited by 146 · see citing works
Tian, Y., He, X., Torralba, M., Yooseph, S., Nelson, K. E., Lux, R., McLean, J. S., Yu, G., & Shi, W. (2010) · Molecular Oral Microbiology · doi:10.1111/j.2041-1014.2010.00585.x · Cited by 133 · see citing works
Mulligan, A. M., Wilson, M., & Knowles, J. C. (2003) · Biomaterials · doi:10.1016/s0142-9612(02)00577-x · Cited by 124 · see citing works
Synthesis of new antibacterial quaternary ammonium monomer for incorporation into CaP nanocomposite
Zhou, C., Weir, M. D., Zhang, K., Deng, D., Cheng, L., & Xu, H. H. K. (2013) · Dental Materials · doi:10.1016/j.dental.2013.05.005 · Cited by 124 · see citing works
Self-citationValappil, S. P., Pickup, D. M., Carroll, D. L., Hope, C. K., Pratten, J. R., Newport, R. J., Smith, M. E., Wilson, M., & Knowles, J. C. (2007) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00605-07 · Cited by 116 · see citing works
Effect of Galla Chinensis on Growth and Metabolism of Microcosm Biofilms
Cheng, L., Exterkate, R. A. M., Zhou, X., Li, J., & ten Cate, J. M. (2011) · Caries Research · doi:10.1159/000324084 · Cited by 76 · see citing works
Self-citationFactors Associated with Alkali Production from Arginine in Dental Biofilms
Huang, X. L., Exterkate, R. A. M., & ten Cate, J. M. (2012) · Journal of Dental Research · doi:10.1177/0022034512461652 · Cited by 66 · see citing works
Xiao, J., Zuo, Y., Liu, Y., Li, J., Hao, Y., & Zhou, X. (2007) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2007.02.009 · Cited by 66 · see citing works
Self-citationAnticaries effect of compounds extracted from Galla Chinensis in a multispecies biofilm model
Xie, Q., Li, J., & Zhou, X. (2008) · Oral Microbiology and Immunology · doi:10.1111/j.1399-302x.2008.00450.x · Cited by 44 · see citing works
Self-citationValappil, S., Coombes, M., Wright, L., Owens, G., Lynch, R. J., Hope, C., & Higham, S. (2012) · Acta Biomaterialia · doi:10.1016/j.actbio.2012.01.017 · Cited by 43 · see citing works
Individual microflora beget unique oral microcosms
Ledder, R. G., Gilbert, P., Pluen, A., Sreenivasan, P. K., Vizio, W. D., & McBain, A. J. (2006) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2006.02847.x · Cited by 41 · see citing works
Effect of pH on Galla chinensis extract's stability and anti-caries properties in vitro
Huang, X., Cheng, L., Exterkate, R. A. M., Liu, M., Zhou, X., Li, J., & ten Cate, J. M. (2012) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2012.04.007 · Cited by 32 · see citing works
Self-citationLedder, R. G., Sreenivasan, P. K., DeVizio, W., & McBain, A. J. (2010) · Journal of Medical Microbiology · doi:10.1099/jmm.0.024372-0 · Cited by 28 · see citing works
Wang, A., Li, M., Li, C., Kou, G., Zuo, X., & Li, Y. (2016) · Scientific Reports · doi:10.1038/srep21952 · Cited by 28 · see citing works
Self-citationRettedal, E. A., Clay, S. A., & Brözel, V. S. (2010) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2010.02097.x · Cited by 25 · see citing works
Yin, X., Gu, X., Yin, T., Wen, H., Gao, X., & Zheng, X. (2015) · Microbial Pathogenesis · doi:10.1016/j.micpath.2015.11.027 · Cited by 19 · see citing works
[Comparative analysis of soil microbial communities by pyrosequencing and DGGE].
Xia, W., & Jia, Z. (2014) · PubMed · Cited by 13 · see citing works
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Jeong, Y., Kim, H., Han, S.-J., & Choi, J. (2021) · Scientific Reports · doi:10.1038/s41598-021-85375-3 · Cited by 61 · see citing works
Kreth, J., Merritt, J. L., Pfeifer, C. S., KHAJOTIA, S. S., & Ferracane, J. L. (2020) · Journal of Dental Research · doi:10.1177/0022034520927690 · Cited by 60 · see citing works
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Li, B., Yang, G., Wu, Y., Chen, J., Xu, H. H. K., Yang, M., Li, M., Ren, B., Feng, M., Weir, M. D., et al. (2017) · Molecules · doi:10.3390/molecules22112013 · Cited by 28 · see citing works
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Li, X., Shang, L., Brandt, B. W., Buijs, M. J., Roffel, S., van Loveren, C., Wim Crielaard, A., Gibbs, S., & Deng, D. (2021) · npj Biofilms and Microbiomes · doi:10.1038/s41522-021-00246-z · Cited by 24 · see citing works
Zhou, W., Peng, X., Zhou, X., Bonavente, A., Weir, M. D., Melo, M. A. S., Imazato, S., Oates, T. W., Cheng, L., & Xu, H. H. K. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21176369 · Cited by 24 · see citing works
Self-citationWu, H., Zeng, B., Li, B., Ren, B., Zhao, J., Li, M., Peng, X., Feng, M., Li, J., Wei, H., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-25636-w · Cited by 23 · see citing works
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Yang, R., Li, J., WEI-XIE, L., & Shao, L. (2020) · Polish Journal of Microbiology · doi:10.33073/pjm-2020-013 · Cited by 17 · see citing works
Huang, Y., Li, H., Zhu, C. G., Zhou, X., Wang, H., Han, Q., Ren, B., & Cheng, L. (2021) · Journal of Dentistry · doi:10.1016/j.jdent.2021.103767 · Cited by 16 · see citing works
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Self-citation
- Authors
- Li, B., Zhou, X., Zhou, X., Wu, P., Li, M., Feng, M., Peng, X., Ren, B., & Cheng, L.
- Affiliations
- Sichuan University (CN)
- Shanghai Majorbio Bio-pharm Technology Co., Ltd, 200120 Shanghai, China
- Corresponding author
- Ren, Biao
- Cheng, Lei
- Venue
- FEMS Microbiology Letters
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-07
- Volume
- 364
- Issue
- 13
- ISSN
- 0378-1097 (ISSN-L)
- 1574-6968
- OpenAlex
- W2729413289
- Cited by
- 30
- References
- 39
- Citations by year
- 2026: 2 · 2025: 2 · 2024: 3 · 2023: 3 · 2022: 4 · 2021: 8 · 2020: 3 · 2019: 2 · 2018: 2 · 2017: 1
- FWCI
- 3.02
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- FEMS Microbiology Letters (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Key Research and Development (2016YFC1102700)
- National Natural Science Foundation of China (81372889, 81600858, 81372890, 81430011)
- State Key Laboratory of Oral Diseases (2040305193002, SKLOD201526)
- Youth Grant of the Science and Technology Department of Sichuan Province (2017JQ0028)
- Scientific Research Starting Foundation for Young Teachers of Sichuan University (2015SCU11015)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
- Health Sciences › Dentistry › Orthodontics › Dental materials and restorations
- Keywords
- microbial communities, culture media, glass substrates, cysteine, oral microbiota, obligate anaerobes, Lactobacillus, Veillonella, Porphyromonas, Leptotrichia
- MeSH terms
- Bacteria, Culture Media, Cysteine, Dental Plaque, Glass, Humans, RNA, Ribosomal, 16S, Saliva, Saliva, Artificial, Linear Models, Durapatite, Biofilms, Microbial Consortia
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