Alex eMira

Egija eZaura

PubMed

Zaura, E.

Mira, A.

International Migration, Integration and Social Cohesion online publications

UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl)UvA-DARE (Digital Academic Repository)EditorialThe oral microbiome in an ecological perspectiveZaura, E.; Mira, A.DOI10.3389/fcimb.2015.00039Publication date2015Document VersionFinal published versionPublished inFrontiers in Cellular and Infection MicrobiologyLicenseCC BYLink to publicationCitation for published version (APA):Zaura, E., & Mira, A. (2015). Editorial: The oral microbiome in an ecological perspective.Frontiers in Cellular and Infection Microbiology, 5, [39].https://doi.org/10.3389/fcimb.2015.00039General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s)and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an opencontent license (like Creative Commons).Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, pleaselet the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the materialinaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letterto: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. Youwill be contacted as soon as possible.Download date:11 Mar 2023EDITORIALpublished: 29 April 2015doi: 10.3389/fcimb.2015.00039Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 1 April 2015 | Volume 5 | Article 39Edited and reviewed by:Yousef Abu Kwaik,University of Louisville School ofMedicine, USA*Correspondence:Egija Zaura,e.zaura@acta.nlReceived: 10 April 2015Accepted: 16 April 2015Published: 29 April 2015Citation:Zaura E and Mira A (2015) Editorial:The oral microbiome in an ecologicalperspective.Front. Cell. Infect. Microbiol. 5:39.doi: 10.3389/fcimb.2015.00039Editorial: The oral microbiome in anecological perspectiveEgija Zaura 1* and Alex Mira 21Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and FreeUniversity Amsterdam, Amsterdam, Netherlands, 2Department of Genomics and Health, FISABIO Foundation, Center forAdvanced Research in Public Health, Valencia, SpainKeywords: metatranscriptomics, horizontal gene transfer, fungal–bacterial interactions, quorum sensing, immunesystem, dental plaque, biofilm, oral ecologyPure cultures have been the basis for microbiology research over a century. However, althoughworking with clonal lineages in the laboratory has allowed fundamental advances in microbialphysiology and genetics, microorganisms are never alone. Even extreme environments likehypersaline waters or acidic ponds are not formed by single species. The human body is noexception, and the oral cavity contains hundreds of bacterial species, that together with fungal andviral inhabitants form highly complex communities where they interact with each other and withthe host. These interactions include physical coaggregation, chemical signaling, transfer of geneticinformation, stimulation of the immune system, metabolic complementation, growth synergismand antagonism or pH buffering among others, and they are so intricate that the final contributingoutput of the whole community is much larger than the addition of the individual species formingit. This is why the use of holistic, metagenomic approaches to study oral microbial ecology becomesfundamental to understand the ecosystem in health and disease.The advent of high throughput sequencing techniques has allowed gathering a wealth of dataon the bacterial content of the oral cavity. However, most of this work has initially been focusedon descriptive studies in which the general taxonomy composition of microbial communitieswas depicted. We must now enter a second phase in which more functional approaches areperformed, including bona fide metagenomic and metatranscriptomic approaches in whichthe total gene repertoire and actively expressed genes in the community are identified underdifferent circumstances, without the biases imposed by PCR or cloning procedures. Experimentalapproaches are also required to validate the correlations that may have been suggested bytaxonomic studies and to describe the molecular basis for inter-species interactions. Finally, wecannot forget the physical environment where oral microbes thrive and where the immune systemprobably plays a crucial role in selecting for a given community. We believe that understanding thebasis for these ecological interactions will provide formidable insights to diagnose oral diseases andto prevent its development, and hope that this special issue may contribute to that purpose.In this topic two functional studies have been included, in which RNAseq strategy has allowedresearchers to describe the mRNA populations of dental plaque in twins, in an attempt to normalizefor genetic host factors (Peterson et al., 2014); and to focus on the gene expression patterns ofdifferent Veillonella species within caries lesions (Do et al., 2015). One of the consequences of theclose physical interaction in oral biofilms is the possibility for horizontal genetic transfer (reviewedby Roberts and Kreth, 2014), with important consequences in relation to antibiotic resistance.As Bachtiar and colleagues show, inter-species interactions are not limited to closely relatedorganisms but can actually cross kingdom borders, and the authors describe a surprising case ofquorum sensing signals produced by a gram-negative bacterium that inhibits biofilm formationin Candida (Bachtiar et al., 2014). In fact, the ecology of fungal–bacterial interactions may beinstrumental for development of oral biofilms. Microbiome studies have been severely biasedtoward the prokaryotic component, assuming that fungal species only play a role as opportunisticZaura and Mira The oral microbiomepathogens. This view is changing fast, and the potential relevanceof bacterial–fungal interactions to oral health is now beingevaluated as shown by the review by Diaz et al. (2014).The new technical possibilities in unraveling the complexityof the oral ecosystem are brought forward by McLean, whereadvancements toward a systems level understanding of thehuman oral microbiome are presented (McLean, 2014). Anapplied aspect of ecological interactions is shown by studyingthe effect of an oxygenating agent on oral microorganismsin vivo, where twice daily exposure to this agent in the formof a mouthwash prevented plaque growth and induced shift inmicrobial composition (Fernandez y Mostajo et al., 2014).The role of indigenous microbiome in maintaining oral healthhas been addressed by Kumar and Mason, where the interactionof the microbiome and the host receives the attention (Kumarand Mason, 2015). Continuing along the same lines on theinteraction of microbes with the immune system, Zaura andcollaborators propose an interesting hypothesis about how anormal oral microbiome is acquired (Zaura et al., 2014). Theirview is that fetal tolerance toward the mother’s microbiota duringpregnancy is amajor factor selecting for the acquisition of the oralmicrobiome.There is no doubt that the next generation sequencing (NGS)technologies have revolutionized the field of microbiology.However, the price to pay for the high throughput output is lowtaxonomical accuracy and sequencing bias. Schulze-Schweifingand colleagues compare the different approaches for microbiomecharacterization: culture, traditional cloning and sequencing aswell as high throughput sequencing (Schulze-Schweifing et al.,2014), while Lazarevic and colleagues demonstrate the difficultiesin work with low DNA yield samples (Lazarevic et al., 2014).The overall purpose of the studies on ecological interactionsof oral microbial communities is to be able to apply thatknowledge to understand and prevent oral diseases. In thisdirection, Rosier and colleagues present a comprehensive andhelpful review on the historical hypotheses that have attemptedto explain the development of oral diseases (Rosier et al.,2014). With this topic we have summarized the current insightsand identified the goals for future research in oral microbialecology. We believe the field will benefit enormously fromthese ecological approaches, which certainly show that oralmicrobial communities cannot be understood by the isolatedstudy of their individual microorganisms and that they aremuch more complex than the addition of its microbial and hostcomponents.FundingThis work was funded by grant BIO2012-40007 from SpanishMINECO to AM.ReferencesBachtiar, E. W., Bachtiar, B. M., Jarosz, L. M., Amir, L. R., Sunarto, H., Ganin,H., et al. (2014). AI-2 of Aggregatibacter actinomycetemcomitans inhibitsCandida albicans biofilm formation. Front. Cell. Infect. Microbiol. 4:94. doi:10.3389/fcimb.2014.00094Diaz, P. I., Strausbaugh, L. D., andDongari-Bagtzoglou, A. (2014). Fungal-bacterialinteractions and their relevance to oral health: linking the clinic and the bench.Front. Cell. Infect. Microbiol. 4:101. doi: 10.3389/fcimb.2014.00101Do, T., Sheehy, E. C., Mulli, T., Hughes, F., and Beighton, D. (2015).Transcriptomic analysis of three Veillonella spp. present in carious dentine andin the saliva of caries-free individuals. Front. Cell. Infect. Microbiol. 5:25. doi:10.3389/fcimb.2015.00025Fernandez y Mostajo, M., van der Reijden, W. A., Buijs, M. J., Beertsen, W., Vander Weijden, F., Crielaard, W., et al. (2014). Effect of an oxygenating agent onoral bacteria in vitro and on dental plaque composition in healthy young adults.Front. Microbiol. 4:95. doi: 10.3389/fcimb.2014.00095Kumar, P. S., and Mason, M. R. (2015). Mouthguards: does the indigenousmicrobiome play a role inmaintaining oral health? Front. Cell. Infect. Microbiol.5:35. doi: 10.3389/fcimb.2015.00035Lazarevic, V., Gaïa, N., Emonet, S., Girard, M., Renzi, G., Despres, L., et al.(2014). Challenges in the culture-independent analysis of oral and respiratorysamples from intubated patients. Front. Cell. Infect. Microbiol. 4:65. doi:10.3389/fcimb.2014.00065McLean, J. S. (2014). Advancements toward a systems level understandingof the human oral microbiome. Front. Cell. Infect. Microbiol. 4:98. doi:10.3389/fcimb.2014.00098Peterson, S. N., Meissner, T., Su, A. I., Snesrud, E., Ong, A. E., Schork, N. J., et al.(2014). Functional expression of dental plaque microbiota. Front. Cell. Infect.Microbiol. 4:108. doi: 10.3389/fcimb.2014.00108Roberts, A. P., and Kreth, J. (2014). The impact of horizontal gene transfer on theadaptive ability of the human oral microbiome. Front. Cell. Infect. Microbiol.4:124. doi: 10.3389/fcimb.2014.00124Rosier, B. T., De Jager, M., Zaura, E., and Krom, B. P. (2014). Historical andcontemporary hypotheses on the development of oral diseases: are we thereyet? Front. Cell. Infect. Microbiol. 4:92. doi: 10.3389/fcimb.2014.00092Schulze-Schweifing, K., Banerjee, A., and Wade, W. G. (2014). Comparisonof bacterial culture and 16S rRNA community profiling by clonal analysisand pyrosequencing for the characterization of the dentine caries-associatedmicrobiome. Front. Cell. Infect.Microbiol. 4:164. doi: 10.3389/fcimb.2014.00164Zaura, E., Nicu, E. A., Krom, B. P., and Keijser, B. J. (2014). Acquiring andmaintaining a normal oral microbiome: current perspective. Front. Cell. Infect.Microbiol. 4:85. doi: 10.3389/fcimb.2014.00085Conflict of Interest Statement: The authors declare that the research wasconducted in the absence of any commercial or financial relationships that couldbe construed as a potential conflict of interest.Copyright © 2015 Zaura and Mira. This is an open-access article distributedunder the terms of the Creative Commons Attribution License (CC BY). The use,distribution or reproduction in other forums is permitted, provided the originalauthor(s) or licensor are credited and that the original publication in this journalis cited, in accordance with accepted academic practice. No use, distribution orreproduction is permitted which does not comply with these terms.Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 2 April 2015 | Volume 5 | Article 39

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Editorial:The oral microbiome in an ecological perspective

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Editorial: The oral microbiome in an ecological perspective

Egija Zaura

Alex Mira

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EDITORIAL
published: 29 April 2015
doi: 10.3389/fcimb.2015.00039
Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 1 April 2015 | Volume 5 | Article 39
Edited and reviewed by:
Yousef Abu Kwaik,
University of Louisville School of
Medicine, USA
*Correspondence:
Egija Zaura,
e.zaura@acta.nl
Received: 10 April 2015
Accepted: 16 April 2015
Published: 29 April 2015
Citation:
Zaura E and Mira A (2015) Editorial:
The oral microbiome in an ecological
perspective.
Front. Cell. Infect. Microbiol. 5:39.
doi: 10.3389/fcimb.2015.00039
Editorial: The oral microbiome in an
ecological perspective
Egija Zaura 1* and Alex Mira 2
1Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Free
University Amsterdam, Amsterdam, Netherlands, 2Department of Genomics and Health, FISABIO Foundation, Center for
Advanced Research in Public Health, Valencia, Spain
Keywords: metatranscriptomics, horizontal gene transfer, fungal–bacterial interactions, quorum sensing, immune
system, dental plaque, biofilm, oral ecology
Pure cultures have been the basis for microbiology research over a century. However, although
working with clonal lineages in the laboratory has allowed fundamental advances in microbial
physiology and genetics, microorganisms are never alone. Even extreme environments like
hypersaline waters or acidic ponds are not formed by single species. The human body is no
exception, and the oral cavity contains hundreds of bacterial species, that together with fungal and
viral inhabitants form highly complex communities where they interact with each other and with
the host. These interactions include physical coaggregation, chemical signaling, transfer of genetic
information, stimulation of the immune system, metabolic complementation, growth synergism
and antagonism or pH buffering among others, and they are so intricate that the final contributing
output of the whole community is much larger than the addition of the individual species forming
it. This is why the use of holistic, metagenomic approaches to study oral microbial ecology becomes
fundamental to understand the ecosystem in health and disease.
The advent of high throughput sequencing techniques has allowed gathering a wealth of data
on the bacterial content of the oral cavity. However, most of this work has initially been focused
on descriptive studies in which the general taxonomy composition of microbial communities
was depicted. We must now enter a second phase in which more functional approaches are
performed, including bona fide metagenomic and metatranscriptomic approaches in which
the total gene repertoire and actively expressed genes in the community are identified under
different circumstances, without the biases imposed by PCR or cloning procedures. Experimental
approaches are also required to validate the correlations that may have been suggested by
taxonomic studies and to describe the molecular basis for inter-species interactions. Finally, we
cannot forget the physical environment where oral microbes thrive and where the immune system
probably plays a crucial role in selecting for a given community. We believe that understanding the
basis for these ecological interactions will provide formidable insights to diagnose oral diseases and
to prevent its development, and hope that this special issue may contribute to that purpose.
In this topic two functional studies have been included, in which RNAseq strategy has allowed
researchers to describe the mRNA populations of dental plaque in twins, in an attempt to normalize
for genetic host factors (Peterson et al., 2014); and to focus on the gene expression patterns of
different Veillonella species within caries lesions (Do et al., 2015). One of the consequences of the
close physical interaction in oral biofilms is the possibility for horizontal genetic transfer (reviewed
by Roberts and Kreth, 2014), with important consequences in relation to antibiotic resistance.
As Bachtiar and colleagues show, inter-species interactions are not limited to closely related
organisms but can actually cross kingdom borders, and the authors describe a surprising case of
quorum sensing signals produced by a gram-negative bacterium that inhibits biofilm formation
in Candida (Bachtiar et al., 2014). In fact, the ecology of fungal–bacterial interactions may be
instrumental for development of oral biofilms. Microbiome studies have been severely biased
toward the prokaryotic component, assuming that fungal species only play a role as opportunistic
Zaura and Mira The oral microbiome
pathogens. This view is changing fast, and the potential relevance
of bacterial–fungal interactions to oral health is now being
evaluated as shown by the review by Diaz et al. (2014).
The new technical possibilities in unraveling the complexity
of the oral ecosystem are brought forward by McLean, where
advancements toward a systems level understanding of the
human oral microbiome are presented (McLean, 2014). An
applied aspect of ecological interactions is shown by studying
the effect of an oxygenating agent on oral microorganisms
in vivo, where twice daily exposure to this agent in the form
of a mouthwash prevented plaque growth and induced shift in
microbial composition (Fernandez y Mostajo et al., 2014).
The role of indigenous microbiome in maintaining oral health
has been addressed by Kumar and Mason, where the interaction
of the microbiome and the host receives the attention (Kumar
and Mason, 2015). Continuing along the same lines on the
interaction of microbes with the immune system, Zaura and
collaborators propose an interesting hypothesis about how a
normal oral microbiome is acquired (Zaura et al., 2014). Their
view is that fetal tolerance toward the mother’s microbiota during
pregnancy is amajor factor selecting for the acquisition of the oral
microbiome.
There is no doubt that the next generation sequencing (NGS)
technologies have revolutionized the field of microbiology.
However, the price to pay for the high throughput output is low
taxonomical accuracy and sequencing bias. Schulze-Schweifing
and colleagues compare the different approaches for microbiome
characterization: culture, traditional cloning and sequencing as
well as high throughput sequencing (Schulze-Schweifing et al.,
2014), while Lazarevic and colleagues demonstrate the difficulties
in work with low DNA yield samples (Lazarevic et al., 2014).
The overall purpose of the studies on ecological interactions
of oral microbial communities is to be able to apply that
knowledge to understand and prevent oral diseases. In this
direction, Rosier and colleagues present a comprehensive and
helpful review on the historical hypotheses that have attempted
to explain the development of oral diseases (Rosier et al.,
2014). With this topic we have summarized the current insights
and identified the goals for future research in oral microbial
ecology. We believe the field will benefit enormously from
these ecological approaches, which certainly show that oral
microbial communities cannot be understood by the isolated
study of their individual microorganisms and that they are
much more complex than the addition of its microbial and host
components.
Funding
This work was funded by grant BIO2012-40007 from Spanish
MINECO to AM.
References
Bachtiar, E. W., Bachtiar, B. M., Jarosz, L. M., Amir, L. R., Sunarto, H., Ganin,
H., et al. (2014). AI-2 of Aggregatibacter actinomycetemcomitans inhibits
Candida albicans biofilm formation. Front. Cell. Infect. Microbiol. 4:94. doi:
10.3389/fcimb.2014.00094
Diaz, P. I., Strausbaugh, L. D., andDongari-Bagtzoglou, A. (2014). Fungal-bacterial
interactions and their relevance to oral health: linking the clinic and the bench.
Front. Cell. Infect. Microbiol. 4:101. doi: 10.3389/fcimb.2014.00101
Do, T., Sheehy, E. C., Mulli, T., Hughes, F., and Beighton, D. (2015).
Transcriptomic analysis of three Veillonella spp. present in carious dentine and
in the saliva of caries-free individuals. Front. Cell. Infect. Microbiol. 5:25. doi:
10.3389/fcimb.2015.00025
Fernandez y Mostajo, M., van der Reijden, W. A., Buijs, M. J., Beertsen, W., Van
der Weijden, F., Crielaard, W., et al. (2014). Effect of an oxygenating agent on
oral bacteria in vitro and on dental plaque composition in healthy young adults.
Front. Microbiol. 4:95. doi: 10.3389/fcimb.2014.00095
Kumar, P. S., and Mason, M. R. (2015). Mouthguards: does the indigenous
microbiome play a role inmaintaining oral health? Front. Cell. Infect. Microbiol.
5:35. doi: 10.3389/fcimb.2015.00035
Lazarevic, V., Gaïa, N., Emonet, S., Girard, M., Renzi, G., Despres, L., et al.
(2014). Challenges in the culture-independent analysis of oral and respiratory
samples from intubated patients. Front. Cell. Infect. Microbiol. 4:65. doi:
10.3389/fcimb.2014.00065
McLean, J. S. (2014). Advancements toward a systems level understanding
of the human oral microbiome. Front. Cell. Infect. Microbiol. 4:98. doi:
10.3389/fcimb.2014.00098
Peterson, S. N., Meissner, T., Su, A. I., Snesrud, E., Ong, A. E., Schork, N. J., et al.
(2014). Functional expression of dental plaque microbiota. Front. Cell. Infect.
Microbiol. 4:108. doi: 10.3389/fcimb.2014.00108
Roberts, A. P., and Kreth, J. (2014). The impact of horizontal gene transfer on the
adaptive ability of the human oral microbiome. Front. Cell. Infect. Microbiol.
4:124. doi: 10.3389/fcimb.2014.00124
Rosier, B. T., De Jager, M., Zaura, E., and Krom, B. P. (2014). Historical and
contemporary hypotheses on the development of oral diseases: are we there
yet? Front. Cell. Infect. Microbiol. 4:92. doi: 10.3389/fcimb.2014.00092
Schulze-Schweifing, K., Banerjee, A., and Wade, W. G. (2014). Comparison
of bacterial culture and 16S rRNA community profiling by clonal analysis
and pyrosequencing for the characterization of the dentine caries-associated
microbiome. Front. Cell. Infect.Microbiol. 4:164. doi: 10.3389/fcimb.2014.00164
Zaura, E., Nicu, E. A., Krom, B. P., and Keijser, B. J. (2014). Acquiring and
maintaining a normal oral microbiome: current perspective. Front. Cell. Infect.
Microbiol. 4:85. doi: 10.3389/fcimb.2014.00085
Conflict of Interest Statement: The authors declare that the research was
conducted in the absence of any commercial or financial relationships that could
be construed as a potential conflict of interest.
Copyright © 2015 Zaura and Mira. This is an open-access article distributed
under the terms of the Creative Commons Attribution License (CC BY). The use,
distribution or reproduction in other forums is permitted, provided the original
author(s) or licensor are credited and that the original publication in this journal
is cited, in accordance with accepted academic practice. No use, distribution or
reproduction is permitted which does not comply with these terms.
Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 2 April 2015 | Volume 5 | Article 39


UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl)UvA-DARE (Digital Academic Repository)EditorialThe oral microbiome in an ecological perspectiveZaura, E.; Mira, A.DOI10.3389/fcimb.2015.00039Publication date2015Document VersionFinal published versionPublished inFrontiers in Cellular and Infection MicrobiologyLicenseCC BYLink to publicationCitation for published version (APA):Zaura, E., & Mira, A. (2015). Editorial: The oral microbiome in an ecological perspective.Frontiers in Cellular and Infection Microbiology, 5, [39].https://doi.org/10.3389/fcimb.2015.00039General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s)and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an opencontent license (like Creative Commons).Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, pleaselet the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the materialinaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letterto: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. Youwill be contacted as soon as possible.Download date:26 Jul 2022EDITORIALpublished: 29 April 2015doi: 10.3389/fcimb.2015.00039Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 1 April 2015 | Volume 5 | Article 39Edited and reviewed by:Yousef Abu Kwaik,University of Louisville School ofMedicine, USA*Correspondence:Egija Zaura,e.zaura@acta.nlReceived: 10 April 2015Accepted: 16 April 2015Published: 29 April 2015Citation:Zaura E and Mira A (2015) Editorial:The oral microbiome in an ecologicalperspective.Front. Cell. Infect. Microbiol. 5:39.doi: 10.3389/fcimb.2015.00039Editorial: The oral microbiome in anecological perspectiveEgija Zaura 1* and Alex Mira 21Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and FreeUniversity Amsterdam, Amsterdam, Netherlands, 2Department of Genomics and Health, FISABIO Foundation, Center forAdvanced Research in Public Health, Valencia, SpainKeywords: metatranscriptomics, horizontal gene transfer, fungal–bacterial interactions, quorum sensing, immunesystem, dental plaque, biofilm, oral ecologyPure cultures have been the basis for microbiology research over a century. However, althoughworking with clonal lineages in the laboratory has allowed fundamental advances in microbialphysiology and genetics, microorganisms are never alone. Even extreme environments likehypersaline waters or acidic ponds are not formed by single species. The human body is noexception, and the oral cavity contains hundreds of bacterial species, that together with fungal andviral inhabitants form highly complex communities where they interact with each other and withthe host. These interactions include physical coaggregation, chemical signaling, transfer of geneticinformation, stimulation of the immune system, metabolic complementation, growth synergismand antagonism or pH buffering among others, and they are so intricate that the final contributingoutput of the whole community is much larger than the addition of the individual species formingit. This is why the use of holistic, metagenomic approaches to study oral microbial ecology becomesfundamental to understand the ecosystem in health and disease.The advent of high throughput sequencing techniques has allowed gathering a wealth of dataon the bacterial content of the oral cavity. However, most of this work has initially been focusedon descriptive studies in which the general taxonomy composition of microbial communitieswas depicted. We must now enter a second phase in which more functional approaches areperformed, including bona fide metagenomic and metatranscriptomic approaches in whichthe total gene repertoire and actively expressed genes in the community are identified underdifferent circumstances, without the biases imposed by PCR or cloning procedures. Experimentalapproaches are also required to validate the correlations that may have been suggested bytaxonomic studies and to describe the molecular basis for inter-species interactions. Finally, wecannot forget the physical environment where oral microbes thrive and where the immune systemprobably plays a crucial role in selecting for a given community. We believe that understanding thebasis for these ecological interactions will provide formidable insights to diagnose oral diseases andto prevent its development, and hope that this special issue may contribute to that purpose.In this topic two functional studies have been included, in which RNAseq strategy has allowedresearchers to describe the mRNA populations of dental plaque in twins, in an attempt to normalizefor genetic host factors (Peterson et al., 2014); and to focus on the gene expression patterns ofdifferent Veillonella species within caries lesions (Do et al., 2015). One of the consequences of theclose physical interaction in oral biofilms is the possibility for horizontal genetic transfer (reviewedby Roberts and Kreth, 2014), with important consequences in relation to antibiotic resistance.As Bachtiar and colleagues show, inter-species interactions are not limited to closely relatedorganisms but can actually cross kingdom borders, and the authors describe a surprising case ofquorum sensing signals produced by a gram-negative bacterium that inhibits biofilm formationin Candida (Bachtiar et al., 2014). In fact, the ecology of fungal–bacterial interactions may beinstrumental for development of oral biofilms. Microbiome studies have been severely biasedtoward the prokaryotic component, assuming that fungal species only play a role as opportunisticZaura and Mira The oral microbiomepathogens. This view is changing fast, and the potential relevanceof bacterial–fungal interactions to oral health is now beingevaluated as shown by the review by Diaz et al. (2014).The new technical possibilities in unraveling the complexityof the oral ecosystem are brought forward by McLean, whereadvancements toward a systems level understanding of thehuman oral microbiome are presented (McLean, 2014). Anapplied aspect of ecological interactions is shown by studyingthe effect of an oxygenating agent on oral microorganismsin vivo, where twice daily exposure to this agent in the formof a mouthwash prevented plaque growth and induced shift inmicrobial composition (Fernandez y Mostajo et al., 2014).The role of indigenous microbiome in maintaining oral healthhas been addressed by Kumar and Mason, where the interactionof the microbiome and the host receives the attention (Kumarand Mason, 2015). Continuing along the same lines on theinteraction of microbes with the immune system, Zaura andcollaborators propose an interesting hypothesis about how anormal oral microbiome is acquired (Zaura et al., 2014). Theirview is that fetal tolerance toward the mother’s microbiota duringpregnancy is amajor factor selecting for the acquisition of the oralmicrobiome.There is no doubt that the next generation sequencing (NGS)technologies have revolutionized the field of microbiology.However, the price to pay for the high throughput output is lowtaxonomical accuracy and sequencing bias. Schulze-Schweifingand colleagues compare the different approaches for microbiomecharacterization: culture, traditional cloning and sequencing aswell as high throughput sequencing (Schulze-Schweifing et al.,2014), while Lazarevic and colleagues demonstrate the difficultiesin work with low DNA yield samples (Lazarevic et al., 2014).The overall purpose of the studies on ecological interactionsof oral microbial communities is to be able to apply thatknowledge to understand and prevent oral diseases. In thisdirection, Rosier and colleagues present a comprehensive andhelpful review on the historical hypotheses that have attemptedto explain the development of oral diseases (Rosier et al.,2014). With this topic we have summarized the current insightsand identified the goals for future research in oral microbialecology. We believe the field will benefit enormously fromthese ecological approaches, which certainly show that oralmicrobial communities cannot be understood by the isolatedstudy of their individual microorganisms and that they aremuch more complex than the addition of its microbial and hostcomponents.FundingThis work was funded by grant BIO2012-40007 from SpanishMINECO to AM.ReferencesBachtiar, E. W., Bachtiar, B. M., Jarosz, L. M., Amir, L. R., Sunarto, H., Ganin,H., et al. (2014). AI-2 of Aggregatibacter actinomycetemcomitans inhibitsCandida albicans biofilm formation. Front. Cell. Infect. Microbiol. 4:94. doi:10.3389/fcimb.2014.00094Diaz, P. I., Strausbaugh, L. D., andDongari-Bagtzoglou, A. (2014). Fungal-bacterialinteractions and their relevance to oral health: linking the clinic and the bench.Front. Cell. Infect. Microbiol. 4:101. doi: 10.3389/fcimb.2014.00101Do, T., Sheehy, E. C., Mulli, T., Hughes, F., and Beighton, D. (2015).Transcriptomic analysis of three Veillonella spp. present in carious dentine andin the saliva of caries-free individuals. Front. Cell. Infect. Microbiol. 5:25. doi:10.3389/fcimb.2015.00025Fernandez y Mostajo, M., van der Reijden, W. A., Buijs, M. J., Beertsen, W., Vander Weijden, F., Crielaard, W., et al. (2014). Effect of an oxygenating agent onoral bacteria in vitro and on dental plaque composition in healthy young adults.Front. Microbiol. 4:95. doi: 10.3389/fcimb.2014.00095Kumar, P. S., and Mason, M. R. (2015). Mouthguards: does the indigenousmicrobiome play a role inmaintaining oral health? Front. Cell. Infect. Microbiol.5:35. doi: 10.3389/fcimb.2015.00035Lazarevic, V., Gaïa, N., Emonet, S., Girard, M., Renzi, G., Despres, L., et al.(2014). Challenges in the culture-independent analysis of oral and respiratorysamples from intubated patients. Front. Cell. Infect. Microbiol. 4:65. doi:10.3389/fcimb.2014.00065McLean, J. S. (2014). Advancements toward a systems level understandingof the human oral microbiome. Front. Cell. Infect. Microbiol. 4:98. doi:10.3389/fcimb.2014.00098Peterson, S. N., Meissner, T., Su, A. I., Snesrud, E., Ong, A. E., Schork, N. J., et al.(2014). Functional expression of dental plaque microbiota. Front. Cell. Infect.Microbiol. 4:108. doi: 10.3389/fcimb.2014.00108Roberts, A. P., and Kreth, J. (2014). The impact of horizontal gene transfer on theadaptive ability of the human oral microbiome. Front. Cell. Infect. Microbiol.4:124. doi: 10.3389/fcimb.2014.00124Rosier, B. T., De Jager, M., Zaura, E., and Krom, B. P. (2014). Historical andcontemporary hypotheses on the development of oral diseases: are we thereyet? Front. Cell. Infect. Microbiol. 4:92. doi: 10.3389/fcimb.2014.00092Schulze-Schweifing, K., Banerjee, A., and Wade, W. G. (2014). Comparisonof bacterial culture and 16S rRNA community profiling by clonal analysisand pyrosequencing for the characterization of the dentine caries-associatedmicrobiome. Front. Cell. Infect.Microbiol. 4:164. doi: 10.3389/fcimb.2014.00164Zaura, E., Nicu, E. A., Krom, B. P., and Keijser, B. J. (2014). Acquiring andmaintaining a normal oral microbiome: current perspective. Front. Cell. Infect.Microbiol. 4:85. doi: 10.3389/fcimb.2014.00085Conflict of Interest Statement: The authors declare that the research wasconducted in the absence of any commercial or financial relationships that couldbe construed as a potential conflict of interest.Copyright © 2015 Zaura and Mira. This is an open-access article distributedunder the terms of the Creative Commons Attribution License (CC BY). The use,distribution or reproduction in other forums is permitted, provided the originalauthor(s) or licensor are credited and that the original publication in this journalis cited, in accordance with accepted academic practice. No use, distribution orreproduction is permitted which does not comply with these terms.Frontiers in Cellular and Infection Microbiology | www.frontiersin.org 2 April 2015 | Volume 5 | Article 39

http://dx.doi.org/10.3389/fcimb.2015.00039

Editorial on The oral microbiome in an ecological perspective: More than just a sum of microbes

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