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Year : 2021  |  Volume : 10  |  Issue : 4  |  Page : 209-218

Oral microflora: Varied habitats, niche and their disparity in systemic health

Department of Oral Pathology and Microbiology, Panineeya Mahavidyalaya Institute of Dental Sciences, Hyderabad, Telangana, India

Date of Submission11-Nov-2020
Date of Decision07-May-2021
Date of Acceptance07-May-2021
Date of Web Publication22-Mar-2022

Correspondence Address:
Dr. Ashalata Gannepalli
Flat No. 101, Nagarjuna Residency, APSRTC Colony, Champapet, Hyderabad - 500 079, Telangana
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jdrntruhs.jdrntruhs_188_20

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The discovery of microbes dates back to the 1700s when Dutchman Antony Van Leeuwenhoek observed his own dental plaque and reported 'little living animalcules prettily moving' further named them as microbes “Dierken”, meaning small lively objects. Since then, the understanding of oral microflora has become profound. Oral microflora is the aggregation of microorganism inhabiting the oral cavity which include bacteria, fungi, viruses and protozoa. The term “microbiome” is defined as the collective genome of microorganisms that reside in the oral cavity. The mouth is an exceedingly complex habitat with its variable niches where microbes settle down and colonize. At present, the connection that has taken a limelight is the link between the oral microbial community and their interactions with the host in the maintenance of homeostasis and in the pathogenesis of many diseases. In today's urbanized society, change in lifestyle, diet along with other environmental factors and distinct health habits, there is precise switching in the composition of the oral microbiota with a remarkable increase in the frequency of systemic diseases. Recently there are few advancements made in the field of 16S RNA sequencing and other technologies. Here in this review, we emphasize on the varied habitats and niches that microorganisms colonize along with their disparity in systemic health and the use of currently available methods to determine the oral microflora.

Keywords: Advancements, habitat, niche, oral microflora, systemic health

How to cite this article:
Jain S, Gannepalli A, Baghirath PV, Vinay B H, Krishna A B. Oral microflora: Varied habitats, niche and their disparity in systemic health. J NTR Univ Health Sci 2021;10:209-18

How to cite this URL:
Jain S, Gannepalli A, Baghirath PV, Vinay B H, Krishna A B. Oral microflora: Varied habitats, niche and their disparity in systemic health. J NTR Univ Health Sci [serial online] 2021 [cited 2023 Feb 7];10:209-18. Available from: https://www.jdrntruhs.org/text.asp?2021/10/4/209/339815

  Introduction Top

The oral cavity is considered to be one of the key interfaces between the body and the external environment.[1],[2] It harbours and nurture numerous microorganisms particularly bacteria.[2],[3] The oral microbiome along with its variable habitats and niches are crucial in maintaining oral as well as systemic health and any imbalance in this may result in the deleterious effects to overall general health of an individual.[1],[3],[4] There are three distinct type of oral microflora ranging from indigenous, supplemental to transient microflora.[5] The relationship of a host to its flora, more commonly bacteria can be described in one of the three ways.[5] When both the host and the bacteria benefit from their inter-relationship which is extremely stable, as the survival of both the members is dependent upon it, it is termed as “symbiosis”.[4],[5] When the bacteria and the host are antagonistic to each other resulting in a very unstable relationship the relationship is said to be antagonistic.[5] When the host and its flora exist in a form of stable balance with each other in an intermediate state the term “amphibiosis” is applied.[5] Most of the oral flora exist in an amphibiotic relationship with their host.[5] This review provides an insight into the acquisition of oral microflora, its varied microbial habitats and niches with disparities in systemic health and the use of currently available methods to determine them.

The resident oral microflora develops in an orderly manner through waves of microbial succession from being sterile before birth to a wide range of alterations in the microbial species depending on the age [Figure 1],[1],[3],[4],[5],[6],[7],[8],[9],[10],[11] tooth eruption, hormone levels, diet, oral hygiene, dentures and medications.
Figure 1: Acquisition of normal oral microflora in different phases of life

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  Oral cavity as a microbial habitat Top

The distribution of microflora varies throughout the oral cavity as different types of surfaces create distinct habitats.[2],[8],[12],[13],[14] Four hallmarks that assist in making the oral cavity distinct from other areas of the body are specialized mucosal surfaces, teeth, saliva and gingival crevicular fluid.[2] Mucosal surfaces which include lips, buccal mucosa, tongue, hard palate, soft palate, tonsils and gingiva shows diversity of the flora due to specialized features and the niche specific to each one of them.[4],[8],[15] Lips, buccal mucosa, hard and soft palate show less diverse microflora when compared to teeth, tongue and tonsils[1],[6],[8],[11],[13] [Table 1].[1],[2],[4],[6],[8],[10-14],[16],[17]
Table 1: Varied oral microbiome in distinct oral habitats

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The tongue shows the highest diversity as it is highly papillated surface and teeth allow the accumulation of large masses of microorganisms (predominantly bacteria) because of non-shedding surface.[1],[2],[4],[6] On the tooth surface, several species of Streptococcus, including S. sanguinis, and S. gordonii, Rothia dentocariosa, G. hemolysans, G. adiacens, Actinomyces spp., and Abiotrophia defectiva are often detected.[1],[5],[10] Other microflora like mycetes are detected belonging to the Saccharomycetales, mainly to the Candida genus, identified as C. albicans species.[1],[17] Fungi represents a very low percentage of the total microbiome exclusively detected in the hard palate, supra-gingival plaque and oral rinse specimens.[1],[17] Among the protozoa: Entamoeba gingivalis, Trichomonas tenax can sometimes be detected.[8]

  Diverse ecological niches in the oral cavity Top

The function or role of microorganisms in a habitat is referred as an ecological niche and a number of ecological niches exist in the oral cavity, including supragingival plaque, subgingival plaque and tongue coating.[16] The tongue coating consists of desquamated epithelium from the tongue, saliva and microorganisms with commensal bacteria such as actinomyces and veillonella responsible for H2S production in healthy individuals on the dorsum of the tongue whereas dental plaque biofilm is a complex, functional community of one or more species of microbes, together with their extracellular products and host compounds.[1],[2],[6],[16] Plaque samples are categorized as supragingival, subgingival, or appliance associated.[8] Composition of dental plaque biofilm vary widely between individuals and also between different sites on the same tooth.[1],[5],[8],[18]

Pellicle formation starts within hours after cleaning the tooth where adsorption of host and bacterial molecules to the tooth surface forms an acquired salivary layer composed of salivary glycoproteins, phosphoproteins, lipids, and components of GCF along with remnants of cell walls of dead bacteria and other microbial products.[1],[8] Oral bacteria initially attach to this pellicle, initial interaction between the microbial cell surface and the pellicle-coated tooth involve reversible and irreversible phase which helps to anchor the organism, after which the organisms multiply on the tooth surface[1],[3],[5],[8],[17-19] [Figure 2].[1],[3],[5],[8],[17],[18],[19]
Figure 2: Biofilm formation and maturation

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Co-adhesion and growth of attached bacteria leads to the formation of distinct microcolonies and between 24 and 48 hours, the biofilm becomes thicker with coaggregation of different species creating “corncob” structures.[1],[5] Metabolic interactions and environmental changes lead to microbial succession (1-7 days) with progressive shift from aerobic and facultatively anaerobic species (mainly streptococcus) to facultative and obligate anaerobic organisms, gram-negative cocci and rods, fusobacteria, spirochetes, and actinobacteria (especially actinomyces) after 9 days later establishing a climax community.[1],[5],[8]

The bacteria that colonize this climax community detach and enter the planktonic phase and transport to new colonization sites, thus restarting the whole cycle with a role in systemic health and disease.[8],[18] [Figure 2].[1],[3],[5],[7],[8],[18],[19] The colonization of root surfaces occurs in the same way but development of plaque on these subgingival surface occurs more rapidly due to the uneven surface topography.[8],[18]

  Host defense Top

One of the least understood phenomena is the ability of the resident microflora to persist in the presence of a broad range of specific and innate host-defense factors.[1],[2],[6],[20] Both arms of the immune system i.e., innate immunity and adaptive immunity provides host protection and are major contributors to the integrity and viability of host tissues.[2],[5],[18],[21]

Innate immunity elicits amplified responses to secondary challenges with an increased intensity compared to initial challenges. These enhanced responses to the secondary challenges have been currently termed as “Primed Responses”, “Trained Immunity”, or more recently “Innate Immune Memory”.[13],[21] Recent reports reveal that innate immune-induced tolerance is crucial in constraining hyperinflammatory responses and protecting the host against harmful inflammatory complications.[13] Adaptive immunity and its mechanisms leading to “Immune Equilibrium” have guaranteed the symbiosis between host and microbiota.[13],[21]

The repetitive nature of pathogenic and non-pathogenic stimulation within the oral cavity make it plausible to propose, for the first time, that an active “innate tolerogenic memory” maybe responsible for regulating the immune responses in oral cavity, particularly in relation to the commensal microbiota.[13],[21] Importantly, this innate tolerogenic memory can be a potential immunotherapeutic target to not only predict but also prevent and treat a variety of inflammatory diseases as well as to help to resolve major problems of healthcare system such as antibiotic resistance.[13],[21]

The oral mucosa is composed of epithelial and lamina propria compartments which play a significant role in the oral immune system.[1],[18],[21] The continuous exfoliation of epithelial cells prevents the colonization by oral microbes and mucosal epithelial cells express antimicrobial peptides like b-defensins, hBD-1 and hBD-2, chemokines, cytokines that activate the adaptive immune system and maintaining the balance between health and disease.[1],[5],[18] The components of acquired immunity present in the mucosa are Langerhans cells, intraepithelial lymphocytes, IgA and IgG where they act as barrier to penetrating antigen.[1],[18] The membrane coating granules secreted by the stratum granulosum also has its role in host defense.[2],[5],[18]

Saliva is a homeostatic fluid that buffers the plaque and consist of some nonspecific and specific factors which help providing nutrients to microflora and also aids in defense.[1],[2],[18] The nonspecific factors include mucin, saliva, bicarbonates and antimicrobial factors, including lysozyme, lactoferrin, the sialo peroxidase system, histatins, cystatins and defensins play a key role in controlling bacterial and fungal colonization of the mouth.[1],[2],[8],[9],[10],[18],[20] The properties of saliva are foundation to the healthy maintenance of oral cavity and hence referred to as the 'defender of the oral cavity'.[1],[2]

The specific factors include immunoglobulins and complement components.[2],[18],[20] The predominant immunoglobulin class in saliva is secretory IgA or sIgA.[1] Secretory immunoglobulin A inhibits microbial attachment.[1] IgG and IgM are also present but in lower concentrations.[1] sIgA is considered the first line of defense against pathogens which colonize and invade surfaces bathed by secretion and helps in inhibition of bacterial adherence, inactivation of bacterial enzymes and toxins, synergism with other defense mechanisms, virus neutralization, complement activation, IgA-dependent cell-mediated functions and immune exclusion[1],[9],[10],[20],[21] [Table 2].[1],[2],[5],[6],[9],[10],[18],[20],[21]
Table 2: Non-specific defense factors

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The complement system is involved in the inflammatory response.[5],[22] They bring about phagocytosis of target cells by means of classical and alternative pathway.[22] Products of C3 activation, C3b and inactivated C3b (iC3b) bind to microorganisms and are recognized by complement receptors (CRs) on phagocytes.[1],[5],[10],[22]

Gingival crevice contain serum transudate that contains tissue and serum proteins as well as free amino acid, vitamins and glucose.[1],[23] It is protective, flushing out nonadherent plaque from the sulcus and bringing phagocytic cells, especially IgG and neutrophils into the area.[2],[8],[18],[23] IgG is the predominant immunoglobulin; IgM and IgA are also present, as is complement.[2],[6],[23] Gingival crevicular fluid contains leukocytes, of which 95% are neutrophils, the remainder being lymphocytes and monocytes.[1],[6],[23] A number of enzymes can be detected in GCF, including collagenase and elastase, which are derived both from phagocytic host cells and subgingival bacteria.[2],[5],[11],[18]

  Disparity of the normal oral microflora in systemic health Top

Oral cavity provides an easy access of the microorganisms to other parts of the body and any disturbance in the equilibrium of normal oral microflora may lead to systemic diseases mainly atherosclerosis, coronary artery disease, gut disorders, liver diseases, endocrine diseases, and autoimmune diseases.[9],[11],[18],[24] Apart from them variations in oral microbiota is also observed in pregnancy with a remarkable impact on promoting the colonisation of various microorganisms that may be a risk factor for the health of pregnant women.[11],[24] Oral microbes secrete peptides and proteases which are responsible for altering the host actin cytoskeleton in the gingival epithelium leading to oral microbial entry into the bloodstream system.[11],[24] Upon gaining entry into the coronary vasculature, these migratory bacteria form biofilm structures within atherosclerotic plaques and causes Coronary artery disease.[11],[14],[24],[25]

Gastrointestinal disorders like inflammatory bowel disease show abundance of streptococcus, Prevotella, Haemophilus, Veillonella, and more recently Klebsiella spp.[9],[15],[26] On the other side the abundance of the genus Veillonella was positively correlated with the levels of proinflammatory cytokines, such as IL1β, IL6, IL-8, and IL-12p70 in the saliva of patients with autoimmune hepatitis.[26],[27] The presence of an immune system disorder and genetic factors can also cause an ecological shift in the microbiome by disrupting the mutual or commensal relationships.[26],[27] Increased IL-17 has been shown in systemic lupus erythematous, rheumatoid arthritis, and type II diabetes contributing to oral microbial changes.[9],[14],[15],[24],[25],[28],[29] These variations are more clearly listed in the [Table 3].[9],[11],[13],[14],[15],[21],[24],[25],[26],[27],[28],[29],[30],[31] Thus, observation of oral microbiota is a major indicator for the development, and prognosis of disease.[11],[24] An oral microbiota-based prediction model can provide the basis for non-invasive diagnosis and facilitate the development of a new standards of personalised medicine.[11],[24],[32] All these can benefit human health in the post-metagenomics era.[11],[24]
Table 3: Diversity of the normal oral microflora in systemic health

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  Methods of determining the composition of the resident oral microflora Top

Conventional methods like culture and microscopic evaluation has been replaced by molecular analysis [Figure 3].[4],[19],[33] Conventional polymerase chain reaction (PCR), real-time quantitative PCR, PCR-DGGE, random amplified polymorphic DNA/arbitrarily primed PCR, repetitive element-based PCR, multilocus sequence typing, PCR-RELP and terminal-RELP are the different PCR-based methods available for the identification of microbes.[4],[19]
Figure 3: Methods of determining the composition of the resident oral microflora

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16S rRNA gene sequencing have enabled the recognition in clinical specimens of species that are as yet unculturable in the laboratory.[4],[33] The location of these organisms can be determined in biofilms such as dental plaque by in situ hybridization, usually with a fluorescent label.[4],[33] A molecular approach such as denaturing gradient gel electrophoresis (DGGE) can be used to compare the diversity of oral microbial communities from different sites in health and disease.[4] Likewise, checkerboard DNA-DNA hybridization techniques can be used to simultaneously screen multiple clinical samples for around 40 different preselected microbial species.[5],[12] In recent years, the largest advancement is by the development of culture-independent “omics” techniques like the microbiomics and metagenomics.[4],[9],[21],[24],[31] These include observation of the DNA, RNA, proteins or metabolites of the whole microbial community.[25],[32]

The Human Microbiome Project (HMP) which was launched in 2007, identifies and characterize human microbial flora whereas Integrative Human Microbiome Project (iHMP) which launched in 2014 generates resources to characterize the microbiome and elucidate the roles of microbes in health and disease states.[4],[19],[24]

The Human Oral Microbiome Database (HOMD) was launched in 2010 for maintaining the information of oral-derived cultivable and non-cultivable isolates and provides a repository of oral bacterial genome sequences and an in-depth resource consisting of the descriptions of oral bacterial taxa whereas expanded HOMD (eHOMD) provide the scientific community with comprehensive curated information on the bacterial species present in the human aerodigestive tract (ADT), which includes the upper digestive and upper respiratory tracts, pharynx, nasal passages, sinuses and oesophagus and the oral cavity.[4],[15],[19],[25]

Next-generation sequencing (NGS) introduced for routine diagnostics in 2014 have revolutionized the study of microbial diversity.[4],[9],[19],[33] This has enabled large-scale sequencing projects to be completed in a few days or sometimes hours.[4] The main NGS technologies are 454 pyrosequencing, applied biosystems, illumina, pacific biosciences and oxford nanopore.[4],[19]

  Conclusion Top

It is vital for the healthcare professionals to better understand the importance of oral microflora and support the concept of a balanced oral microbiome in a healthy way. In today's era with the emergence of new genomic, proteomic, metabolomic technologies and bioinformatic tools, understanding the disparities of the oral microbiome in the systemic health has become elementary and hence can help clinicians to recognize and diagnose diseases at an early and reversible stage. Personalized dental medicine that uses the information of individuals gene, proteins and environment in relation to the oral microbiome also have substantial effects in healthcare by describing which treatment and technique will work best for each patient. Exploration and advancements in the field of personalized medicine is a rapidly growing domain and can act as a revolutionized approach in clinical practice.

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Conflicts of interest

There are no conflicts of interest.

  Multiple ChoiceQuestions Top

  1. Who discovered microbes?

    1. Robert Hooke
    2. Antoni Van Leeuwenhoek
    3. Both a and b
    4. None

  2. What is the most common opportunistic microflora found in oral cavity?

    1. Staphylococcus
    2. Candida
    3. Pseudomonas
    4. Klebsiella

  3. What are the factors that affect the acquisition of normal oral microflora?

    1. Age
    2. Tooth eruption
    3. Diet
    4. All the above

  4. Which surface shows highest diversity of microflora?

    1. Tongue
    2. Teeth
    3. Tonsils
    4. Buccal mucosa

  5. The function or role of microorganisms in a habitat is referred to as?

    1. Microbiome
    2. Ecological niche
    3. Microbial habitat
    4. None

  6. Plaque sample can be categorized as?

    1. Supragingival
    2. Subgingival
    3. Appliance associated
    4. All the above

  7. What is the term used for the innate immunity enhanced responses to the second challenges?

    1. Primed responses
    2. Trained immunity
    3. Innate immune memory
    4. All the above

  8. The disturbance in the equilibrium of normal oral microflora may lead to systemic diseases involving which organ?

    1. Heart
    2. Gut
    3. Liver
    4. All the above

  9. In recent years, What are the largest advancement done by development of culture-independent omics technique?

    1. Microbiomics
    2. Metagenomics
    3. Both
    4. None

  10. What all information is stored by Human Oral Microbiome Database?

  1. Oral-derived cultivable and non-cultivable isolates
  2. Repository of oral bacterial genome sequences
  3. In-depth resource consisting of the descriptions of oral bacterial taxa
  4. All the above

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  [Figure 1], [Figure 2], [Figure 3]

  [Table 1], [Table 2], [Table 3]


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