Review Article | Published:

Microbiota restoration: natural and supplemented recovery of human microbial communities

Nature Reviews Microbiology volume 9, pages 2738 (2011) | Download Citation


In a healthy host, a balance exists between members of the microbiota, such that potential pathogenic and non-pathogenic organisms can be found in apparent harmony. During infection, this balance can become disturbed, leading to often dramatic changes in the composition of the microbiota. For most bacterial infections, nonspecific antibiotics are used, killing the non-pathogenic members of the microbiota as well as the pathogens and leading to a substantial delay in the restoration of a healthy microbiota. However, in some cases, infections can self-resolve without the intervention of antibiotics. In this Review, we explore the mechanisms underlying microbiota restoration following insult (antibiotic or otherwise) to the skin, oral cavity, and gastrointestinal and urogenital tracts, highlighting recovery by natural processes and after probiotic administration.

Key points

  • Many infections self-resolve, but in most cases the mechanism of this resolution is unknown.

  • There are several theories concerning how homeostasis might be restored in the oral cavity, skin, and intestinal and urogenital tracts, the sites that collectively contain the bulk of the human microbiome.

  • The shifts in microbial abundance and diversity are often linked with host immunity, and together these influence whether we remain healthy or become sick.

  • By correlating changes in the microbiota with a diseased state, it should be possible to develop novel interventions that help restore health.

  • Mechanisms that seem to be involved in the restoration of homeostasis include: bacterial co-aggregation; production of biosurfactants, antimicrobials and signalling molecules that target the host or pathogens; competitive exclusion of pathogens; immunomodulation; and factors that increase tight junction barrier function on the host epithelia.

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The authors acknowledge support from the Natural Sciences and Engineering Research Council of Canada and Danone Canada. Input from J. Macklaim is appreciated. They also thank E. K. Costello and M. G. Dominguez-Bello for input into figure 1.

Author information


  1. Human Microbiology and Probiotics, F2-116, Lawson Health Research Institute, 268 Grosvenor Street, London, Ontario N6A 4V2, Canada.

    • Gregor Reid
  2. Departments of Microbiology & Immunology, and Surgery, The University of Western Ontario.

    • Gregor Reid
  3. Department of BioMedical Engineering, University Medical Center Groningen and University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.

    • Jessica A. Younes
    • , Henny C. Van der Mei
    •  & Henk J. Busscher
  4. Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada.

    • Gregory B. Gloor
  5. Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA.

    • Rob Knight
  6. Howard Hughes Medical Institute, Boulder, Colorado 80309, USA.

    • Rob Knight


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Competing interests

Gregor Reid has received research support from Danone (although he is not assessing any of their products and does not receive any consulting fees from the company) and retains an association with Chr. Hansen (although he no longer has any ownership interest in Lactobacillus rhamnosus str. GR-1, Lactobacillus reuteri str. RC-14 or patents pertaining to urogenital applications).

Corresponding author

Correspondence to Gregor Reid.



The microorganisms that inhabit a region of the body.


Pertaining to sebum, the substance secreted by glands of the skin.


An imbalance in the bacterial population at a naturally occurring site of colonization, often resulting in health problems.


The state of having a healthy population of bacteria naturally occurring in a body site.


A live microorganism that, when administered in adequate amounts, confer a health benefit on the host.


A condition of equilibrium or stability in the internal environment of the body, which is maintained by adjusting physiological processes to counteract external changes.


A dead keratin-filled squamous cell of the stratum corneum.


An epithelial cell that produces keratin in the process of differentiating into the corneocytes of the stratum corneum.


A contagious bacterial skin infection characterized by the eruption of superficial pustules and the formation of thick yellow crusts.


A localized suppurative staphylococcal skin infection originating in a gland or hair follicle and characterized by pain, redness and swelling.

Toxic shock syndrome

A rare, life-threatening complication of bacterial infection that has been most often associated with the use of superabsorbent tampons and occasionally linked with the use of contraceptive sponges. Often resulting from toxins produced by staphylococci, but also from those produced by group A Streptococcus spp.


A microbial community that is enveloped by extracellular polymer matrices produced by the microorganisms and that adheres to a surface.

Bacterial vaginosis

An aberrant condition in the vagina that is characterized by pH >4.5, malodour and depletion of normal microbiota, particularly lactobacilli.


Referring to microscopic organisms that are suspended in a liquid (for instance, media or a buffer).


An external bacterial product that enables adhesion to and colonization of a host.


A biosurfactant produced by Pseudomonas spp.


Producing or promoting the development of dental caries.

Free radical

An atom or molecule that has at least one unpaired electron and is therefore unstable and highly reactive.


Non-contagious inflammation of the skin, characterized chiefly by redness, itching and the outbreak of lesions that may discharge serous fluid.

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