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An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome

BACKGROUND: Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species,...

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Autores principales: Edlund, Anna, Yang, Youngik, Hall, Adam P, Guo, Lihong, Lux, Renate, He, Xuesong, Nelson, Karen E, Nealson, Kenneth H, Yooseph, Shibu, Shi, Wenyuan, McLean, Jeffrey S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971625/
https://www.ncbi.nlm.nih.gov/pubmed/24451062
http://dx.doi.org/10.1186/2049-2618-1-25
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author Edlund, Anna
Yang, Youngik
Hall, Adam P
Guo, Lihong
Lux, Renate
He, Xuesong
Nelson, Karen E
Nealson, Kenneth H
Yooseph, Shibu
Shi, Wenyuan
McLean, Jeffrey S
author_facet Edlund, Anna
Yang, Youngik
Hall, Adam P
Guo, Lihong
Lux, Renate
He, Xuesong
Nelson, Karen E
Nealson, Kenneth H
Yooseph, Shibu
Shi, Wenyuan
McLean, Jeffrey S
author_sort Edlund, Anna
collection PubMed
description BACKGROUND: Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level. RESULTS: Comparative metagenomic analyses confirmed a high similarity of metabolic potential in biofilms to recently available oral metagenomes from healthy subjects as part of the Human Microbiome Project. A time-series metagenomic analysis of the taxonomic community composition in biofilms revealed that the proportions of major species at 3 hours of growth are maintained during 48 hours of biofilm development. By employing deep pyrosequencing of the 16S rRNA gene to investigate this biofilm model with regards to bacterial taxonomic diversity, we show a high reproducibility of the taxonomic carriage and proportions between: 1) individual biofilm samples; 2) biofilm batches grown at different dates; 3) DNA extraction techniques and 4) research laboratories. CONCLUSIONS: Our study demonstrates that we now have the capability to grow stable oral microbial in vitro biofilms containing more than one hundred operational taxonomic units (OTU) which represent 60-80% of the original inoculum OTU richness. Previously uncultivated Human Oral Taxa (HOT) were identified in the biofilms and contributed to approximately one-third of the totally captured 16S rRNA gene diversity. To our knowledge, this represents the highest oral bacterial diversity reported for an in vitro model system so far. This robust model will help investigate currently uncultivated species and the known virulence properties for many oral pathogens not solely restricted to pure culture systems, but within multi-species biofilms.
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spelling pubmed-39716252014-04-02 An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome Edlund, Anna Yang, Youngik Hall, Adam P Guo, Lihong Lux, Renate He, Xuesong Nelson, Karen E Nealson, Kenneth H Yooseph, Shibu Shi, Wenyuan McLean, Jeffrey S Microbiome Methodology BACKGROUND: Our knowledge of microbial diversity in the human oral cavity has vastly expanded during the last two decades of research. However, much of what is known about the behavior of oral species to date derives from pure culture approaches and the studies combining several cultivated species, which likely does not fully reflect their function in complex microbial communities. It has been shown in studies with a limited number of cultivated species that early oral biofilm development occurs in a successional manner and that continuous low pH can lead to an enrichment of aciduric species. Observations that in vitro grown plaque biofilm microcosms can maintain similar pH profiles in response to carbohydrate addition as plaque in vivo suggests a complex microbial community can be established in the laboratory. In light of this, our primary goal was to develop a robust in vitro biofilm-model system from a pooled saliva inoculum in order to study the stability, reproducibility, and development of the oral microbiome, and its dynamic response to environmental changes from the community to the molecular level. RESULTS: Comparative metagenomic analyses confirmed a high similarity of metabolic potential in biofilms to recently available oral metagenomes from healthy subjects as part of the Human Microbiome Project. A time-series metagenomic analysis of the taxonomic community composition in biofilms revealed that the proportions of major species at 3 hours of growth are maintained during 48 hours of biofilm development. By employing deep pyrosequencing of the 16S rRNA gene to investigate this biofilm model with regards to bacterial taxonomic diversity, we show a high reproducibility of the taxonomic carriage and proportions between: 1) individual biofilm samples; 2) biofilm batches grown at different dates; 3) DNA extraction techniques and 4) research laboratories. CONCLUSIONS: Our study demonstrates that we now have the capability to grow stable oral microbial in vitro biofilms containing more than one hundred operational taxonomic units (OTU) which represent 60-80% of the original inoculum OTU richness. Previously uncultivated Human Oral Taxa (HOT) were identified in the biofilms and contributed to approximately one-third of the totally captured 16S rRNA gene diversity. To our knowledge, this represents the highest oral bacterial diversity reported for an in vitro model system so far. This robust model will help investigate currently uncultivated species and the known virulence properties for many oral pathogens not solely restricted to pure culture systems, but within multi-species biofilms. BioMed Central 2013-10-02 /pmc/articles/PMC3971625/ /pubmed/24451062 http://dx.doi.org/10.1186/2049-2618-1-25 Text en Copyright © 2013 Edlund et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology
Edlund, Anna
Yang, Youngik
Hall, Adam P
Guo, Lihong
Lux, Renate
He, Xuesong
Nelson, Karen E
Nealson, Kenneth H
Yooseph, Shibu
Shi, Wenyuan
McLean, Jeffrey S
An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
title An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
title_full An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
title_fullStr An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
title_full_unstemmed An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
title_short An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
title_sort in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome
topic Methodology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971625/
https://www.ncbi.nlm.nih.gov/pubmed/24451062
http://dx.doi.org/10.1186/2049-2618-1-25
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