An in vitrobiofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-10-02

AUTHORS

Anna Edlund, Youngik Yang, Adam P Hall, Lihong Guo, Renate Lux, Xuesong He, Karen E Nelson, Kenneth H Nealson, Shibu Yooseph, Wenyuan Shi, Jeffrey S McLean

ABSTRACT

BackgroundOur 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.ResultsComparative 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.ConclusionsOur 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. More... »

PAGES

25

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/2049-2618-1-25

DOI

http://dx.doi.org/10.1186/2049-2618-1-25

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24451062


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25 Microbiome Project
26 OTU richness
27 Research Laboratory
28 aciduric species
29 addition
30 analysis
31 approach
32 bacterial diversity
33 bacterial taxonomic diversity
34 batch
35 behavior
36 biofilm development
37 biofilm model
38 biofilm model system
39 biofilm samples
40 biofilms
41 capability
42 carbohydrate addition
43 carriage
44 cavity
45 changes
46 community
47 community composition
48 complex microbial communities
49 composition
50 continuous low
51 culture approach
52 culture system
53 date
54 decades
55 decades of research
56 deep pyrosequencing
57 derives
58 development
59 different dates
60 diversity
61 dynamic response
62 enrichment
63 environmental changes
64 extraction techniques
65 function
66 gene diversity
67 genes
68 goal
69 growth
70 healthy subjects
71 high reproducibility
72 high similarity
73 hours
74 hours of growth
75 human oral cavity
76 human oral microbiome
77 human oral taxa
78 inoculum
79 knowledge
80 laboratory
81 levels
82 light
83 limited number
84 low
85 major species
86 manner
87 metabolic diversity
88 metabolic potential
89 metagenomes
90 metagenomic analysis
91 microbial communities
92 microbial diversity
93 microbiome
94 microcosms
95 model
96 model system
97 molecular level
98 multi-species biofilms
99 number
100 observations
101 one-third
102 operational taxonomic units
103 oral bacterial diversity
104 oral biofilm development
105 oral cavity
106 oral metagenome
107 oral microbiome
108 oral pathogens
109 oral species
110 oral taxa
111 order
112 pH profile
113 part
114 pathogens
115 plaques
116 potential
117 primary goal
118 profile
119 project
120 properties
121 proportion
122 pure culture approach
123 pure culture systems
124 pyrosequencing
125 rRNA gene
126 rRNA gene diversity
127 regard
128 reproducibility
129 research
130 response
131 richness
132 robust
133 robust model
134 saliva inoculum
135 samples
136 similar pH profiles
137 similarity
138 species
139 stability
140 study
141 subjects
142 system
143 taxa
144 taxonomic community composition
145 taxonomic diversity
146 taxonomic units
147 technique
148 time-series metagenomic analysis
149 uncultivated species
150 units
151 virulence properties
152 vivo
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