DOI: 10.1111/prd.
12373
REVIEW ARTICLE
Microbiomics: Were we all wrong before?
Purnima S. Kumar
Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA
Correspondence
Purnima S. Kumar, College of Dentistry, The Ohio State University, Columbus, OH 43210, USA.
Email: kumar.83@osu.edu
1 | I NTRO D U C TI O N
Microbiomics, the newest kid on the microbiology block, is the sci-
ence of collectively characterizing and quantifying molecules re-
sponsible for the structure, function, and dynamics of a microbial
1
community. Despite having been around for less than three de-
cades, this field has revolutionized our knowledge of host-associated
microbes, and reconceptualized our definition of “human.” We are
learning that the “human” is a holobiont, a superorganism in which
both human and microbial cells are important for survival;2 and that
microbial DNA can be transmitted from parent to child, making the
microbiome our “second genome.”3 As we embark upon a journey of
self-discovery fueled by the excitement of almost daily discoveries
of novel species and previously unsuspected colonization niches, we
are beginning to realize that there are several unknowns; for exam-
ple, the extent to which an individual's microbiome determines their
4
personal identity, and the ownership of microbes present in human
excreta and expectorations.5
As one of the most microbe-rich niches in the human body,6 the
oral cavity is the ideal ecosystem to showcase the enormous capa-
bilities of microbiomics. Indeed, oral microbiologists were not only
the first to embrace this science,7,8 but also to invest in developing
infrastructure for sequence analysis and in creating and maintain-
ing curated sequence repositories.9 Through these efforts, we have
learned much about our oral fellow travelers, and the communities
they reside and function in. Yet, periodontal microbiology is a cen-
tury-old science, and traditional paradigms of disease causation
followed the “single culprit” or the “multiple culprit” model. The
question that this volume of Periodontology 2000 attempts to answer
is, “How much, if any, did microbiomics change our understanding of
the role subgingival bacteria play in maintaining health and causing
local or systemic disease, or in the way we treat periodontitis?”
© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd
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2 | D E LV I N G D E E PE R I NTO TH E O R A L
M I C RO B I O M E U S I N G “ O M I C S ”
It all began with the simple word semantides; that is, molecules
that carry the memory of the evolutionary travails of a cell.10
Deoxyribonucleic acid (DNA), in whose nucleotide arrangement re-
sides not just the mutational history of the organism but also the
reasons for these shifts, is the primary semantide. Messenger RNA is
the secondary semantide, since it is transcribed from DNA. Tertiary
semantides are polypeptides, that are translated from messenger
ribonucleic acid (RNA).10 By exploiting the enormous amount of
information contained in these semantides, microbiomics not only
circumvented the need to cultivate the members of a community in
order to study them, but also enabled studying them in their natural
environment with their natural partners instead of in isolation in a
petri dish. This open-ended ability to observe communities en masse
and in situ enabled the discovery not only of new species, but also
attributed novel metabolic pathways, interactions, and behaviors to
them.
The first three articles of this volume of Periodontology 2000 are
devoted to exploring the impact of five omics approaches on ex-
panding our horizons about the periodontal microbiome: metatax-
onomics (16S ribosomal RNA gene sequencing), metagenomics
(whole genome shotgun sequencing of community DNA), meta-
transcriptomics (sequencing of community RNA), proteomics, and
metabolomics.
The paper by Kumar et al11 traces the development of DNA se-
quencing as a quantitative, open-ended, comprehensive approach to
characterize microbial communities in their native environments, and
it explores how this technology has shifted traditional dogmas about
the role of the oral microbiome in promoting health causing and per-
petuating disease. However, Kumar and her colleagues acknowledge
Periodontology 2000. 2021;85:8–11.
KUMAR
that DNA cannot be used to distinguish between transcriptionally
active members of a community and those that are inactive or dead.
12
In line with this thinking, Duran-Pinedo's article elucidates
what metatranscriptomics has done to transform our understanding
of periodontal disease. One of the most enduring dilemmas in di-
13
agnosing periodontitis is recognizing sites where disease is active.
Duran-Pinedo elegantly demonstrates that gene expression profiles
of the subgingival microbial community could hold the key to the
question of why certain sites with periodontitis progress while oth-
ers stay stable. We learn from her review that metatranscriptomics
has overset our earlier conceptions that virulence is the property
of certain species and instead shown us that it is a community trait.
We should question not only whether there are true “periodontal
pathogens” but also whether periodontitis is a single-pathogen–led
disease.
Just as soon as we get comfortable with the idea that RNA se-
quencing might answer several questions that have beset periodon-
tal diagnostics, we realize that not all genes that are expressed get
translated to proteins, which are the structural and functional units
of a cell. Therefore, we turn to the review written by Bostanci et al14
to gain deeper insights into bacterial effectors of community be-
havior in health and disease. Bostanci, Grant and their colleagues
present a convincing treatise on the information to be gained from
unraveling the functionality and underlying regulatory processes
within various oral microbial communities.
3 |  PE E R I N G FA RTH E R I NTO TH E
M I C RO B I O M E U S I N G “ O M I C S ”
Assigning a taxonomical identity to a microbial species carries enor-
mous implications for identification of clinical isolates, assigning
virulence profiles, assessing pathogenic potential, and safety of han-
15
dling, to name but a few. In the pre-sequencing era, taxonomy was
assigned to an organism based on its phenotypic characteristics.16
With this approach, several organisms were misclassified. One of the
most notorious instances of misclassification is that of an entire do-
17
main of prokaryotes, the Archaea, as bacteria. DNA-based explo-
rations created the biggest impact in unraveling the members of the
18
unraveling the prokaryotes. Diaz's article sheds light on these and
other numerically minor nonbacterial members of the oral microbi-
ome. Her thesis provides a cogent argument that sequencing-based
approaches have truly expanded our understanding of the role of
fungi, archaea, and viruses in health and disease.
4 |  LO O K I N G BAC K AT TH E M I C RO B I O M E
USING “OMICS”
As we continue to investigate the pathogenesis of periodontal dis-
eases in the omics era, Laura Weyrich,19 a paleomicrobiologist, takes
the position that tracing the evolutionary history of oral microbiota
and the factors that shape its origins will likely unlock information to
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mitigate disease today. Humans likely diverged from other bipedal
hominids about 200 000 years ago, 20 providing ample time for the
separation, diversification, and adaptation of our oral microbiota
from other primates. In her exposition, she traces the evolution of
the oral microbiome alongside changes in human lifestyle from a
hunter-gatherer to a farm-centered communal living, followed by in-
dustrialization and the resulting postindustrial lifestyles.
5 | CO NTE X T UA LIZ I N G TH E O R A L
M I C RO B I O M E U S I N G “ O M I C S ”
Microbiomics has the unique capacity to simultaneously provide a
telescopic, big picture view of the dynamics of an entire commu-
nity and a microscopic view of the behavior of a single gene, protein,
or metabolite across large populations. However, it is important to
parse all this information in the context of the host, since microbi-
omes hosted by eukaryotes rely on a harmonious interaction with
their hosts for survival. The interbacterial interactions in the oral
cavity and their impact on the human host are explored in depth
by the group led by Lux. 21 Their work provides deep insights into
certain bacterial interactions that have been evolutionarily con-
served because of their mutualistic benefits, and it examines how
a breakdown in these interbacterial interactions creates dysbiotic
microbiomes.
However, the responsibility for causing disease cannot be as-
cribed to the microbiome alone. The human is the other half of the
host-microbe interaction, and it is only logical that human behaviors
will significantly impact microbial communities. Buduneli's paper22
elucidates the impact of host behaviors such as smoking, diet, and al-
cohol use on the creation of dysbiotic communities. Her work show-
cases the extent to which periodontal diseases are preventable and
serves to emphasize the contributions of behavior modification to
improving human health.
Not only human behaviors, but also systemic diseases and con-
ditions can change the oral microbiome, 23-26 our second genome,
some of which can be vertically transmitted to offspring. 27,28 We are
also discovering that modulating the oral microbiome has beneficial
effects on conditions such as gut dysbiosis and hyperglycemia. 29,30
In their treatise, Teles et al31 explore the links between systemic
conditions and diseases—such as pregnancy, diabetes, and rheuma-
toid arthritis—and the oral microbiome, highlighting the importance
of periodontal infectogenomics as an emerging field of study.
6 | TR A N S L ATI N G TH E M I C RO B I O M E
I NTO C LI N I C A L PR AC TI C E A N D R E S E A RC H
No monograph of periodontal diseases is complete without dis-
cussing that unique form of periodontitis that affects specific teeth
in individuals of circumpubertal age. Nearly a century of research
has underscored the contributions of genetics to this disease.32,33
In their review, Shaddox et al34 provide an in-depth analysis of the
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10       KUMAR
role played by host genetics in shaping the periodontal microbiome.
They argue that single-nucleotide polymorphisms in genes encoding
immuno-inflammatory molecules set the stage for microbial dysbio-
sis, since inflammation drives a progressive decrease in the microbial
diversity, leading to perturbations in the microenvironment.
Everything we do as researchers is centered on improving oral
health and enhancing therapeutic outcomes. The paper by Feres
et al35 investigates whether omics research has significantly im-
pacted periodontal diagnostics and therapeutics. They find that lack
of well-controlled interventional studies and heterogeneity in study
design, sample size, sampling method, treatment provided, and time
of follow-up are major challenges to definitively answering this
question, but also find that emerging evidence from metagenomics,
proteomics, and metatranscriptomics certainly hold the key to im-
plementing personalized periodontal treatments in the future.
We end this monograph on a cautionary note. As omics tech-
nologies and methodologies begin to enter mainstream research,
they begin to face the challenge that most mainstream technologies
do: that of the “hype cycle.” The Gartner graphic of the hype cycle
delineates five phases: technology trigger, peak of inflated expecta-
tions, trough of disillusionment, slope of enlightenment, and plateau
of productivity. Omics is now entering the third phase, and we are
beginning to understand that there are vulnerabilities inherent in
these methodologies. Several reviews have addressed issues related
to heterogeneity in DNA isolation, sequence generation, quality
assurance, quality control, data normalization, and data reduction
methods. All of these variables have created challenges for repro-
ducibility of omics-based methods. However, when omics methods
are used to examine human samples, additional considerations—for
example, study design, defining primary outcome variables, sample
types, positive and negative control groups of subjects, confounding
and covarying variables, sample biomass, sample collection methods
and material, sample processing and storage, biological and technical
variates, adequately powered studies, sufficient metadata, etc—be-
come critically important. Zaura et al36 provide us with a roadmap
for clinical research involving the oral microbiome based on the cur-
rently available evidence. From their work, we learn how to get most
out of this exciting type of research.
Together, this set of 11 papers demonstrates that microbiomics
provides an unprecedented ability to look broadly and deeply into
the communities that live in us and on us. These technologies allow
us to not only “see” more but to see through a different lens, thereby
allowing us to think outside the box of what is known.
7 |  CO N C LU S I O N
By now, the reader will hopefully have noticed the use of exclusively
feminine pronouns in this article. This is intentional. Historically, fe-
male scientists have played strategic roles in advancing our under-
standing of the microbial world. For instance, the mass production
of penicillin is attributed to Mary Hunt, and Elizabeth Bugie collabo-
rated on the discovery of streptomycin.37 Elizabeth Horning, Doris
Jones, Christine Reilly, Dorris Hutchinson, and Vivian Schatz played
key roles in ushering in the golden age of antibiotics.38 Rosalind
Franklin's contribution to the double-helix DNA model cannot be
forgotten.39 As we usher in the omics era, especially as it relates to
oral microbiology research, several women are playing leading roles,
not only as consumers of these technologies but also as innova-
tors and pioneers. The goal of this monograph is to highlight some
of them and their areas of expertise by inviting them to serve as
lead authors. I hope that this increased visibility of female scientists
will serve to inspire the next generation of women in science and
medicine.
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How to cite this article: Kumar PS. Microbiomics: Were we all
wrong before? Periodontol 2000. 2021;85:8–11.
https://doi.org/10.1111/prd.12373