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Vaginal microbiota form a mutually beneficial relationship with their host and have a major impact on health and disease. In recent years our understanding of vaginal bacterial community composition and structure has significantly broadened as a result of investigators using cultivation-independent methods based on the analysis of 16S ribosomal RNA (rRNA) gene sequences. In asymptomatic, otherwise healthy women, several kinds of vaginal microbiota exist, the majority often dominated by species of Lactobacillus, while others are composed of a diverse array of anaerobic microorganisms. Bacterial vaginosis is the most common vaginal condition and is vaguely characterized as the disruption of the equilibrium of the normal vaginal microbiota. A better understanding of normal and healthy vaginal ecosystems that is based on their true function and not simply on their composition would help better define health and further improve disease diagnostics as well as the development of more personalized regimens to promote health and treat diseases.
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MI66CH18-Ravel ARI 8 August 2012 16:26
Vaginal Microbiome:
Rethinking Health and Disease
Bing Ma,1Larry J. Forney,2and Jacques Ravel1
1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore,
Maryland 21201; email:,
2Department of Biological Sciences and the Initiative for Bioinformatics and Evolutionary
Studies, University of Idaho, Moscow, Idaho 83844; email:
Annu. Rev. Microbiol. 2012. 66:371–89
First published online as a Review in Advance on
June 28, 2012
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vaginal microbiota, vaginal ecosystem, bacterial vaginosis
Vaginal microbiota form a mutually beneficial relationship with their host
and have a major impact on health and disease. In recent years our un-
derstanding of vaginal bacterial community composition and structure
has significantly broadened as a result of investigators using cultivation-
independent methods based on the analysis of 16S ribosomal RNA (rRNA)
gene sequences. In asymptomatic, otherwise healthy women, several kinds
of vaginal microbiota exist, the majority often dominated by species of Lac-
tobacillus, while others are composed of a diverse array of anaerobic microor-
ganisms. Bacterial vaginosis is the most common vaginal condition and is
vaguely characterized as the disruption of the equilibrium of the normal
vaginal microbiota. A better understanding of normal and healthy vaginal
ecosystems that is based on their true function and not simply on their
composition would help better define health and further improve disease
diagnostics as well as the development of more personalized regimens to
promote health and treat diseases.
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microbial community
composition and
INTRODUCTION............................................................... 372
Culture-Dependent and Culture-Independent Approaches to Survey
Microbial Community Composition and Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Lactobacillus-DominatedVaginal Microbiota..................................... 374
Lactobacillus Species’ Antimicrobial Substances Production . . . . . . . . . . . . . . . . . . . . . . . . 376
Other Types of Vaginal Microbiota. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377
BACTERIALVAGINOSIS........................................................ 377
TheBacterial VaginosisEnigma................................................. 377
Complex Etiology of Bacterial Vaginosis ......................................... 379
RETHINKINGNORMAL ANDHEALTHY..................................... 379
TemporalDynamics ofVaginal Communities.................................... 380
Toward a System-Level Understanding of the Vaginal Ecosystem . . . . . . . . . . . . . . . . . 381
CONCLUDINGREMARKS ..................................................... 383
The microbiota normally associated with the human body have an important influence on human
development, physiology, immunity, and nutrition (18, 23, 65, 66, 70, 111). The vast majority of
these indigenous microbiota exist in a mutualistic relationship with their human host, although few
are opportunistic pathogens that can cause both chronic infections and life-threatening diseases.
These microbial communities are believed to constitute the first line of defense against infection
by competitively excluding invasive nonindigenous organisms that cause diseases. Despite their
importance, surprisingly little is known about how these communities differ between individuals
in composition and function and, more importantly, how their constituent members interact with
each other and the host to form a dynamic ecosystem that responds to environmental disturbances.
Major efforts are now under way to better understand the true role of these communities in health
and diseases (84).
The human vagina and the bacterial communities that reside therein are an example of this
finely balanced mutualistic association. In this relationship, the host provides benefit to the mi-
crobial communities in the form of the nutrients needed to support bacterial growth. This is of
obvious importance because bacteria are continually shed from the body in vaginal secretions,
and bacterial growth must occur to replenish their numbers. Some of the required nutrients are
derived from sloughed cells, while others are from glandular secretions. The indigenous bacterial
communities, on the other hand, play a protective role in preventing colonization of the host by
potentially pathogenic organisms, including those responsible for symptomatic bacterial vaginosis,
yeast infections, sexually transmitted infections (STIs), and urinary tract infections (42, 47, 96, 98,
113, 118). Lactobacilli have long been thought to be the keystone species of vaginal communities
in reproductive-age women. These microorganisms benefit the host by producing lactic acid as a
fermentation product that lowers the vaginal pH to 3.5–4.5 (12). Although a wide range of other
species are members of vaginal bacterial communities, their ecological roles and influences on
the overall community dynamics and function are largely undetermined. The vaginal ecosystem
is thought to have been shaped by coevolutionary processes between the human host and specific
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BV: bacterial
community members
represented by a set of
related 16S rRNA
gene sequences
microbial partners, although the selective forces (traits) behind this mutualistic association are still
not clear.
The development of culture-independent approaches has greatly facilitated comprehensive
surveys of the composition of vaginal microbial communities. These studies have shown that
several distinct kinds of vaginal communities with markedly different species composition occur
and that the frequency of these types of microbiota varies in different ethnic groups (86, 122–
124). It is hypothesized that differences in species composition may correlate with how vaginal
communities respond to disturbances (52, 104, 115, 123). Conceptually this is important because
vaginal communities continually experience various kinds of chronic and acute disturbances caused
by human behaviors, such as the use of antibiotics, hormonal contraceptives and other methods of
birth control, sexual activity, vaginal lubricants, douching, and so forth, in addition to many other
intrinsic factors such as the innate and adaptive immune systems of hosts (64, 88, 110). Further,
a disturbed state itself may constitute the clinical syndrome known as bacterial vaginosis (BV),
which as a disruption of ecological equilibria is believed to increase the risk of invasion by infectious
agents. Although knowledge accumulated over the past few decades has provided some insights
into the vaginal ecosystem, there remains a need to define and better understand factors that affect
the composition and dynamics of vaginal microbiota, including the role of human genetics and
physiology in both health and diseases. This knowledge will facilitate the development of new
strategies for disease diagnosis and personalized treatments to promote health and improve the
quality of women’s lives. This cannot be accomplished without addressing the fundamental issue
of what constitutes a normal and healthy vaginal microbiota and understanding its function in
health and diseases.
Comprehensive surveys of vaginal microbial communities using culture-independent approaches
have revealed that Lactobacillus species are the dominant vaginal bacterial species in a majority of
women. However, an appreciable proportion of asymptomatic, otherwise healthy individuals have
vaginal microbiota lacking significant numbers of Lactobacillus spp. and harboring a diverse array
of facultative and strictly anaerobic microorganisms.
Culture-Dependent and Culture-Independent Approaches to Survey
Microbial Community Composition and Structure
Most of our knowledge of the composition, metabolic function, and ecology of indigenous micro-
bial communities associated with humans has come from studies that depended on cultivating mi-
crobial populations. Hence, our current understanding of microbe-host interactions is limited and
skewed because the overwhelming majority of microbial species (>99%) resist cultivation in the
laboratory (8). Our limited ability to culture may result from strict, yet unknown, growth require-
ments, such as the optimal combination of nutrients, growth temperatures, and dissolved-oxygen
levels, or potentially the need to cocultivate with key microbial partners (3, 27). Our knowledge of
microbial diversity has expanded enormously through the use of culture-independent approaches
based on the analysis of 16S rRNA gene sequences (50, 107). These strategies circumvent the need
to cultivate organisms by directly extracting genetic materials from environmental or biological
samples. This is followed by amplification of the 16S rRNA genes using primers that anneal to
highly conserved regions of the gene, followed by sequencing and classification of the phylotypes
present. This constitutes an efficient way to comprehensively characterize microbial diversity. The
development of next-generation sequencing technologies, including the use of massively parallel Vaginal Microbiota and Health 373
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Community class:
clusters of community
state types’ profiles
that have similar
temporal patterns of
bacterial community
dynamics (applies to
time series)
Community state
types: clusters of
community states that
have similar phylotype
composition and
relative abundance
Community states:
phylotype composition
and relative abundance
of a single sample or a
sample in a time series
DNA sequencing of short, hypervariable regions of the 16S rRNA gene, now affords us the op-
portunity to obtain detailed surveys of microbial communities, including the identification of taxa
present in low abundance that compose the rare biospheres (27, 102). Other conserved genes such
as cpn60,rpoC,uvrB,andrecA have also been used for these purposes (92, 114).
Culture-independent methods have demonstrated that, when surveyed cross-sectionally, sev-
eral kinds of vaginal communities (community state types) exist in normal and otherwise healthy
women, each with a markedly different bacterial species composition. These communities either
are dominated by one of four common Lactobacillus species (L. crispatus,L. iners,L. gasseri,andL.
jensenii ) or do not contain significant numbers of lactobacilli, but instead have a diverse array of
strict and facultative anaerobes (86).
Lactobacillus-Dominated Vaginal Microbiota
Members of the genus Lactobacillus are commonly identified as the hallmark of a normal or healthy
vagina (25, 42, 69, 98). Since they were first identified by cultivation in vaginal secretion in the
late nineteenth century by Donderlein (24, 90, 106), Lactobacillus spp. have been thought to play
a major role in protecting the vaginal environment from nonindigenous and potentially harmful
microorganisms. This is accomplished through the production of lactic acid, resulting in a low
and protective pH (3.5–4.5) (1, 11, 12, 54, 87, 91). Interestingly, lactic acid is more effective
than acidity alone as a microbicide against HIV or against pathogens such as Neisseria gonorrhoeae
(38, 60). Exposure to gram-negative bacteria, in the presence of lactic acid, is believed to have
stimulatory effects on the host innate immune defense system (120). A recent study using in
vitro colonization of vaginal epithelial cell monolayers with common bacteria such as L. crispatus,
Prevotella bivia,andAtopobium vaginae demonstrated that these key vaginal bacteria appear to
regulate the epithelial innate immunity in a species-specific manner (32).
L. crispatus was previously thought to be one of the most common species of lactobacilli in the
vagina (5). However, the application of the culture-independent method has identified L. iners,
an organism that is difficult to cultivate and does not grow on traditional culture media, as the
most prevalent vaginal bacterial species (30, 122). In these studies, vaginal microbiota of 42%
(17) and 66% (123) of the reproductive-age women sampled were dominated by L. iners. A recent
large-scale cross-sectional study of 396 healthy asymptomatic women revealed that L. iners was
detected in 83.5% of the subjects and dominated 34.1% of the communities analyzed (86), and
that L. crispatus,L. gasseri,andL. jensenii were present in 64.5, 42.9, and 48.2% of the subjects
and dominated in 26.2, 6.3, and 5.3% of the samples, respectively (86). This large study showed
that vaginal bacterial communities that had similar species composition and abundance could be
classified into five groups, which are referred to as community state types (Figure 1). The four
community state types dominated by Lactobacillus spp. represented 73% of the samples, which
supports the prevailing view that Lactobacillus spp. are important members of vaginal microbiota.
The remaining 27% represented communities that lacked significant numbers of Lactobacillus spp.
but instead were composed of a diverse array of facultative or strictly anaerobic bacteria. Interest-
ingly, the distribution of Lactobacillus spp.–dominated community state types varies significantly
among individuals with different ethnic backgrounds (86, 123, 124). White and Asian women are
more likely than Hispanic and Black women to have vaginal communities dominated by lacto-
bacilli (86). When a Lactobacillus species is present, vaginal communities of Hispanic and Black
women are more often dominated by L. iners (86). The study also noted a higher average pH in
Black and Hispanic women, 4.7 and 5.0 respectively, compared to 4.4 and 4.2 for Asian and White
women. This observation supports the hypothesis that host factors may play an important role in
determining vaginal microbial community composition and structure.
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Lactobacillus iners
Lactobacillus crispatus
Lactobacillus gasseri
Lactobacillus jensenii
Lactobacillus vaginalis
state types
Nugent score
abundance (%)
Community groups
II III I IVV 4.0–4.5
Nugent score
Figure 1
Heatmap of percentage abundance of microbial taxa found in the vaginal microbial communities of 394 reproductive-age women.
(a) Complete linkage clustering of samples based on species composition and abundance in communities defining five community state
types (CST I–V). (b) Nugent scores and pH measurements for each of the 394 samples. Adapted from Reference 86. Vaginal Microbiota and Health 375
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00.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
Gardnerella vaginalis HMP9231 (Mbp)
Gardnerella vaginalis
409–05 (Mbp)
0 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6
Gardnerella vaginalis HMP9231 (Mbp)
Less similarity to
more similarity
Gardnerella vaginalis
ATCC 14019 (Mbp)
Figure 2
Whole-genome comparative analysis of Gardnerella vaginalis using BLAST score ratio analysis. A protein match between two genomes
is represented by a point plotted using the genomic coordinate of both matched proteins as xand ycoordinates. The level of protein
sequence similarity is represented by the color of the points (see scale at right). (a) High degree of protein similarity and synteny are
observed between G. vaginalis strains HMP9231 and ATCC 14019. (b) Lack of synteny and low degree of protein similarity are
observed between G. vaginalis strains HMP9231 and 409-05. The vertical blue bar highlights a set of syntenic genes that is unique to
the G. vaginalis HMP9231 genome and is not present in the other two genomes.
These findings highlight potential differences in the protective capabilities of vaginal Lacto-
bacillus species. Statistically significant differences have been observed in the ability of different
Lactobacillus species to lower pH between different community state types. L. crispatus–dominated
communities are able to acidify the vaginal milieu to pH 4.0; communities dominated by other
species achieved pH ranging from 4.4 to 5.0 (86). Although Lactobacillus spp. drive these processes,
other community members can contribute by either producing or utilizing lactic acid. Moreover,
it is anticipated that strains of the same species will also demonstrate genomic differences that
will result in specific physiological and biochemical traits. Previous comparative genomic analyses
have identified a high level of genetic diversity and varied metabolic potential of closely related
bacterial species or strains of the same species. For example, Escherichia coli strains can vary by as
much as 25% in their gene content (79), and strains of the same serovars of Salmonella enterica can
vary by more than 20% (61). Much of the variation occurs in the form of large genomic islands
or lineage-specific regions that may be involved in adaptation to the host microenvironment (10,
82). No comparative genomic studies of vaginal Lactobacillus spp. have been reported. However, in
Figure 2 we show strains of Gardnerella vaginalis, which is commonly found in the vaginal micro-
biota and associated with bacterial vaginosis (73, 116), can differ by 31% in gene content and gene
order (synteny). Advanced knowledge of genetic variation among Lactobacillus species (or strains)
may provide further insight into their functional potential, which may have significant implica-
tions for health and diseases. Because of species-level or strain-level genomic heterogeneity, the
analysis of 16S rRNA gene sequences, though taxonomically informative, is not able to identify
functional differences without considerable speculation, and attempts to infer the function of any
bacterial community knowing only “who is there” should be made with caution.
Lactobacillus Species’ Antimicrobial Substances Production
Vaginal Lactobacillus species produce antimicrobial compounds in addition to lactic acid, including
target-specific bacteriocins (2, 6) and broad-spectrum hydrogen peroxide (28, 43). Bacteriocins
are proteinaceous, bactericidal substances synthesized by bacteria that have a narrow spectrum of
activity (53). Their antimicrobial activity is usually based on permeabilization of the target cell
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membrane (81). In the vagina, bacteriocins could play a major role in fending off the growth of
nonindigenous or pathogenic organisms (26). Many Lactobacillus spp. produce hydrogen peroxide
in vitro under aerobic conditions, which could inhibit colonization of potential pathogenic bacteria
in vivo (43, 48, 112). However, the vagina is virtually an anaerobic environment wherein dissolved
oxygen levels are low. Therefore, it is unlikely that significant amounts of hydrogen peroxide
are produced and accumulate to a toxic level. Further, a recent study showed that physiologi-
cal concentrations of hydrogen peroxide have no detectable effect on 17 BV-associated bacteria
(BVAB) under anaerobic growth conditions and the presence of vaginal fluid can actually block its
antimicrobial activity (80). In addition, it appears that high concentrations of hydrogen peroxide
are even more toxic to vaginal Lactobacillus than to BVAB (80). Interestingly, some Lactobacillus
species, such as L. iners, fail to produce hydrogen peroxide. This feature has been used to differen-
tiate beneficial versus nonbeneficial vaginal Lactobacillus isolates (5), and it has been suggested that
hydrogen peroxide–producing vaginal Lactobacillus spp. are more likely to be protective against
acquisition of BV (43). Given the information summarized above, it is more likely that in vitro
hydrogen peroxide production is not a significant factor in preventing the emergence of disease-
causing organisms; however, it could be a surrogate marker for other yet unknown biochemical
or physiological traits. Overall, this work suggests that lactic acid, not hydrogen peroxide, is more
likely to contribute to the protective role of vaginal microbiota.
Other Types of Vaginal Microbiota
Recent studies have found that 20–30% of asymptomatic, otherwise healthy women harbor vaginal
communities that lack appreciable numbers of Lactobacillus but include a diverse array of faculta-
tive or strictly anaerobic bacteria that are associated with a somewhat higher pH (5.3–5.5) (86,
122–124). This proportion of communities can reach 40% among Black and Hispanic women
(86). These microbiota include members of the genera Atopobium,Corynebacterium,Anaerococ-
cus,Peptoniphilus,Prevotella,Gardnerella,Sneathia,Eggerthella,Mobiluncus,andFinegoldia, among
others (52, 86, 115, 122–124). These findings challenge the common wisdom that the occur-
rence of high numbers of lactobacilli and a vaginal pH of <4.5 are synonymous with “normal” and
“healthy.” Previous studies have hypothesized non-Lactobacillus-dominant vaginal microbiota may
be nonetheless able to maintain functional vaginal ecosystems by preserving lactic acid produc-
tion and possibly other important functions (36, 86, 122). Many underappreciated microorganisms,
such as members from Atopobium,Streptococcus,Staphylococcus,Megasphaera,andLeptotrichia,are
capable of homolactic or heterolactic acid fermentations (89, 122). The highly diversified micro-
bial community may have accommodated functional redundancy, allowing for the function of the
ecosystem to persist in the face of perturbations (117). In the absence of symptomology, these
types of vaginal bacterial communities might be considered normal and healthy, even though the
composition of these communities closely resembles those associated with symptomatic BV.
BV is a highly prevalent vaginal disorder in reproductive-age women, but its diagnostics and
treatment are disappointingly ineffective. BV is often vaguely characterized as the disruption of
the equilibrium of the normal vaginal ecosystem.
The Bacterial Vaginosis Enigma
BV is the most frequently cited cause of vaginal discharge and malodor, and it is the most common
vaginal condition of reproductive-age women, resulting in millions of health care visits annually Vaginal Microbiota and Health 377
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Nugent-score BV:
BV that is diagnosed
based on Nugent
Gram stain test;
symptomology is not
taken into account
in the United States alone (99). In a cross-sectional study of reproductive-age women in 2001,
the National Health and Nutrition Examination Survey found that the prevalence of BV in the
United States was 29.2% (59). BV is an independent risk factor for the acquisition of STIs (19, 69,
83, 118), the acquisition and transmission of HIV (20–22, 69, 103, 105), the development of pelvic
inflammatory disease (76), as well as for reproductive tract and obstetric sequelae (37, 39, 49, 71,
72). Numerous investigations have identified factors that increase a woman’s risk for BV. Men-
strual blood, a new sexual partner, vaginal douching, smoking, and lack of condom use are among
the strongest risk factors for BV (9, 15, 44, 45, 51, 57, 75, 95, 119). In general, these suspected
factors often manifest themselves as relatively minor risks in clinical studies, and many women
without the above risk factors have BV. In most women, the symptoms of BV resolve on their
own without intervention (58). When necessary, the treatment of BV typically includes antibi-
otics such as metronidazole (oral tablets or topical vaginal gel) or clindamycin vaginal cream (121).
However, recurrence of BV after treatment is common: Fifteen to 30% of women have symp-
tomatic BV 30 to 90 days following antibiotic therapy; 70% of patients experience a recurrence
within nine months (13, 62, 101). Strategies for managing recurrent BV are not standardized
(100), and because the etiology of BV remains unknown, the causes of relapse remain unclear
(13, 97).
The confusion about BV stems in part from the subjective diagnostic criteria used. In clinical
settings, BV is commonly diagnosed on the basis of the clinical criteria described by Amsel et al.
(4), wherein three of the following four symptoms must be evident: (a) a homogenous, white,
noninflammatory discharge that smoothly coats the vaginal walls; (b) the presence of clue cells
(squamous epithelial cells covered with adherent bacteria) on microscopic examination; (c) a vagi-
nal fluid pH over 4.5; and (d) a fishy odor of vaginal discharge before or after addition of 10%
KOH (potassium hydroxide). The reliability of the Amsel criteria has been subject to debate, par-
ticularly in reference to pregnancy, given the increased vaginal discharge that is often experienced
by pregnant women, and to the variation of pH depending on how and where samples are taken
(41). However, not all symptoms are observed in every case (56), and because the diagnosis is
subjective, controversy persists about the definition of BV. The sensitivity and specificity of the
Amsel criteria are 70% and 94%, respectively (93), when compared to another diagnostic assay,
the Nugent Gram stain score, which is used in research and laboratories. In these settings, BV
is traditionally diagnosed by scoring a Gram-stained vaginal smear using the criteria defined by
Nugent et al. (77). The Nugent score reflects the relative abundance of large gram-positive rods
(lactobacilli), gram-negative rods and cocci, gram-variable rods and cocci (e.g., G. vaginalis,Pre-
votella,Porphyromonas,andPeptostreptococcus), and curved gram-negative rods (Mobiluncus). This
technique permits assessment of relative numbers of bacterial morphotypes and other cellular
elements, allowing for a rough evaluation of bacterial load, as well as the presence of polymor-
phonuclear leukocytes, candidal spores, fungal hyphae, and sperm. It is based on a linear scale
ranging from 0 to 10. A score of 0–3 is normal, 4–6 is intermediate, and 7–10 is considered BV.
Although the Nugent criteria are commonly used to assess BV, the scoring of specimens can be
subjective. Nonetheless, with a sensitivity of 89% and specificity of 83% (93) compared to Amsel
criteria, the Nugent Gram stain test remains the preferred diagnostic tool (41, 59), and it can be
performed on self-collected vaginal smears (74), thus facilitating longitudinal field-based studies
(14, 94). Interestingly, as much as 50% of all women with BV (as defined by Nugent score) are
asymptomatic (4), which led to the use of the term Nugent-score BV (85). It is unclear whether
these women are truly without symptoms or whether the symptoms were poorly recognized or
underreported. The meaning and implications of asymptomatic BV are not known. Even so, and
because of growing concern for the complications linked to BV, there is a practice of treating
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asymptomatic disease under certain circumstances, such as prior to a hysterectomy procedure or
in women at high risk for preterm birth (121).
Complex Etiology of Bacterial Vaginosis
Despite decades of research, attempts to find a single causative agent for BV have failed. Con-
sequently, Koch’s postulates are not fulfilled, in which the etiologic agent is both necessary and
sufficient to cause disease and should not be found in subjects without disease (29, 35). Indeed,
there is growing evidence that BV is characterized, and perhaps caused, by disruption of the vaginal
ecosystem, which is reflected in alterations to the composition and structure of vaginal microbial
communities, such that the numbers of lactic-acid-producing bacteria are decreased and the di-
versity and numbers of strictly anaerobic bacteria are increased, including species of Gardnerella,
Atopobium,Mobiluncus,andPrevotella, as well as other taxa of the order Clostridiales (34). The vaginal
microbial community composition associated with BV is somewhat similar to the community state
type described above that is found in asymptomatic healthy women that lack a significant number
of Lactobacillus species. Culture-independent methods have identified potentially BV-associated
bacteria (BVAB) that could not be identified by traditional culture-based methods (31, 34). BVAB
are distantly related to known species of the phyla Actinobacteria and Firmicutes. However, the
significance of these findings remains unclear, as it is not known whether these microorganisms
are pathogens that cause BV or whether they simply are opportunistic organisms that take ad-
vantage of the temporarily higher pH environment and thus increase in numerical dominance.
Overall, these molecular studies have shown that the diversity, composition, and relative abun-
dances of microbial species in the vagina vary dramatically in both normal, healthy women and
women presenting with BV. These diverse organisms accumulate to form different communities,
or profiles, which support the hypothesis that BV is not a single entity, but a syndrome linked to
various community types that cause somewhat similar physiological symptoms. This suggests that
a yet unknown common community function may account for BV and the differing responses to
antibiotic therapies.
However, because these studies often rely on a single sample collected from women presenting
to their physician with symptomatic BV, it is not possible to elucidate the causes of BV (microbi-
ological, biochemical, molecular, or behavioral) without access to samples collected prior to the
diagnosis and during the events leading to BV. Prospective longitudinal studies, in which samples
are collected frequently along with detailed behavioral metadata, are necessary to understand the
causes of BV. Such information is expected to suggest methods to identify women who are at risk
of acquiring symptomatic BV, to identify new targets for intervention and prevention strategies,
and to enable development of more accurate diagnostic criteria.
The paradigm that healthy women are always colonized with high numbers of Lactobacillus species
(46, 48) has previously been challenged as discussed above. Although numerous studies have shown
that women with abundant Lactobacillus species do not have BV, the corollary that women whose
vaginal communities have few or no Lactobacillus species have BV is faulty logic. Unfortunately, the
commonly used diagnostic criteria (both Amsel and Nugent), wherein the degree of healthiness
is in part assessed by scoring the abundance of Lactobacillus morphotypes, tends to overdiagnose
BV. This could account at least partly for the reported high incidence (as high as 42%; 56) of
so-called asymptomatic BV in reproductive-age women, as defined by a positive Nugent score
and no reported vaginal symptoms. It could also explain a portion of BV treatment failures and Vaginal Microbiota and Health 379
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MI66CH18-Ravel ARI 8 August 2012 16:26
the capability of an
ecosystem to resist
change in the face of
apparent recurrences of BV (33). To better understand symptomatic BV, its causes, and the
factors predisposing or triggering the condition, it is essential to apply molecular analyses of
vaginal communities to a statistically significant number of women sampled longitudinally and
prospectively in order to define the diversity and dynamics of the vaginal ecosystem in the general
populace. These studies would help us better understand what constitutes normal and healthy
vaginal microbiota and the fluctuations that commonly occur in normal and healthy communities.
As suggested by Marrazzo et al. (67), only by using such approaches will we be able to change and
refine the definition, etiology, and epidemiology of BV.
The fine line that separates a normal and healthy vaginal microbiota from one that is abnormal
and unhealthy is further complicated by potential confusion between health and the predisposition
to diseases such as STIs, and by the lack of a complete understanding of the functional intricacies
of the host and its vaginal microbiota. It is difficult to envision the evolutionary processes that led
to a vaginal microbiota with the sole function of protecting the host from STIs, mainly because only
a small proportion of women have been or are exposed to STI pathogens. Interestingly, humans
are among the very few mammals with a vaginal microbiota often dominated by Lactobacillus spp.,
and with such a low pH. Hence, it appears that other yet unknown functions must have driven the
composition of the human vaginal microbiota. For example, one potential function could relate
to immune stimulation or microbial protection of the newborn in the first days of life. Without
more knowledge of these functions, one might consider separating the concept of health from the
concept of resistance to STIs. That said, it is essential to understand the factors that increase the
risks of acquiring STIs and the community types that might be more susceptible to infection. It is
conceivable that from time to time a dynamic system such as the vaginal microbiota might enter
states (defined by their composition or their function) that would increase the risk of infection.
The frequency and duration of these states might represent better predictors of risk of infection
than the abundance of a single community member or a given microbial community profile.
With knowledge of the factors driving these dynamics and a better understanding of the func-
tion of the vaginal microbiota, novel prevention strategies could be developed to lower the risks.
These strategies might include driving the maintenance of more protective and highly functional
vaginal microbiota, or possibly using more personalized probiotics or prebiotic mixtures. In addi-
tion, these risks are at play only when a woman has the potential to be exposed to the pathogens.
If exposure is not likely (perhaps through the practice of celibacy or monogamy), it might not be
appropriate to define the healthiness of a woman’s vaginal microbiota by factors associated with
their predisposition to infections. Hence, a new thinking would involve dissociating the concept
of normal and healthy vaginal microbiota from that of predisposition to STIs. A healthy vaginal
microbiota could then be defined as a microbial community with a functional output that is ad-
equately beneficial to the host and not solely defined by its composition, and this function could
be provided by several kinds of vaginal communities. In this context, different types of vaginal
microbiota could be considered healthy in the absence of symptoms, with or without lactobacilli,
while having differing degrees of predisposition to infections by sexually transmitted pathogens.
Temporal Dynamics of Vaginal Communities
To date most studies of vaginal microbiology have employed cross-sectional designs in which
samples are obtained from individuals at a single time point or with long intervals between sampling
times (weeks or months). Although these studies have provided important information on the
species composition of vaginal communities, they yield little insight into the normal temporal
dynamics of these bacterial communities within individuals and do not provide an estimate of
community stability. Daily fluctuations in the composition of the vaginal microbiota have been
380 Ma ·Forney ·Ravel
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microbial community
gene content
previously documented by microscopy (16, 44, 55, 95). Even more recently, a longitudinal study
conducted by our group described the temporal dynamics of vaginal community composition
in 32 healthy reproductive-age women sampled twice weekly over a 16-week period (36). The
study showed that some communities changed markedly over a short period, whereas others
were relatively stable, including communities lacking a significant number of Lactobacillus spp.
(Figure 3). In an effort to model the dependence of vaginal bacterial community stability on
the time in the menstrual cycle and other time-varying factors, menses was identified as having
the most negative effect on stability, along with the type of communities and sexual activity to
a lesser extent. On the other hand, time periods of the menstrual cycle corresponding to a high
level of estrogen or estrogen and progesterone were associated with higher stability. This study
highlights the great potential of prospective longitudinal studies to elucidate the cause and etiology
of multifactorial diseases such as BV compared with studies that often rely on a single sample
collected from women presenting with symptomatic BV. Longitudinal study designs, in which
samples are collected frequently along with detailed behavioral metadata, would afford access to
samples collected prior to the diagnosis and during the events leading to BV. The knowledge
gained from such studies is expected to elucidate factors that govern this dynamic ecosystem, to
forecast symptomatic BV susceptibility, and to enable the development of innovative diagnostic,
intervention, and prevention strategies.
Toward a System-Level Understanding of the Vaginal Ecosystem
Although comprehensive molecular community surveys have provided a great deal of information
about the composition of the vaginal microbiota, its role and the intrinsic dynamics that drive
its interaction with its host are still unknown. In order to have translational impact on women’s
health, it is essential to develop an understanding of healthy and disease states that includes
knowledge of the functional characteristics of the vaginal microbiota and the types of vaginal
microbiota that can provide the needed functions. For example, the notion of an enterotype in
the gut microbiome is defined not by the presence of a core set of organisms, but by a core set of
available conserved genes that are involved in critical metabolic pathways (7, 86, 108, 109). This
notion is informative for subject stratification, but it is still limited to an understanding of the
functional potential of a microbial community, and not of its true function and benefit to the host.
State-of-the-art -omics technologies combined with a statistical modeling framework offer
an opportunity to develop a systems-level understanding of the vaginal ecosystem by measuring
biological components of a system to derive functional modules that reflect specific phenotypic
traits. This could be accomplished by using a multilevel approach based on (a) metagenomics
to catalog the relative abundance of all microbial and, to some extent, human genes and their
polymorphisms, and the functional potentials and their degree of redundancy; and (b) metatran-
scriptomics and metaproteomics to assess levels of differential expression of microbial and host
genes in healthy and disease states or in response to various perturbations. This multilevel ap-
proach would also provide insight into the functional interaction between the vaginal microbiota
and the host by using metabolomics to characterize the products of ecosystem-level physiological
processes and metabolic output. Predictive statistical models used in a systems biology framework
could be used to integrate these various datasets and to quantitatively assess critical biological
processes, environmental conditions, or behaviors associated with healthy states, as well as disease
initiation, progression, and symptomatology (40, 63, 68, 78). The goal of these efforts would be to
develop a systems-level understanding of the molecular events that promote health or lead to dis-
ease, and to spur the development of novel diagnostic screens and enable more holistic prevention
and treatment regimens. Vaginal Microbiota and Health 381
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Lactobacillus iners
Lactobacillus jensenii
Lactobacillus gasseri
Lactobacillus crispatus
Lactobacillus iners
Lactobacillus otu5
Lactobacillus jensenii
Lactobacillus gasseri
Lactobacillus otu3
Lactobacillus vaginalis
Lactobacillus otu4
Lactobacillus iners
Lactobacillus gasseri
Lactobacillus otu4
Lactobacillus iners
Time (weeks)
Phylotype relative
abundance (%)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 150
Time (weeks)
Phylotype relative
abundance (%)
Time (weeks)
Phylotype relative
abundance (%)
1 2 3 4 5 6 7 8 9 1011121314150
Time (weeks)
Phylotype relative
abundance (%)
Figure 3
Temporal dynamics of vaginal bacterial communities in women sampled twice weekly over 16 weeks.
Interpolated bar plot of the relative abundance of phylotypes from four subjects (a–d ) with different
community dynamics profiles. Color key for each phylotype is shown at the top of each graph.
382 Ma ·Forney ·Ravel
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The dynamics of vaginal bacterial communities during the menstrual cycle, and the dramatic
changes associated with transitions between the physiological stages of a woman’s life span, from
the first week of life to puberty, reproductive years, and menopause, are a reflection of the interplay
of the mutualistic relationship between the vaginal microbiota and its human host. The ever-
changing yet finely tuned vaginal ecosystem is a result of adaptive coevolutionary processes that
integrate many different aspects such as sexual hormone levels, features of host physiology, and
composition and functional output of the vaginal microbiota. Study of the systems-level temporal
dynamics of the vaginal ecosystem and its functional output will contribute to our understanding
of what truly constitutes normal and healthy. The application of the modern -omics technologies
to the study of the vaginal ecosystem is expected to translate to better diagnostics and improved
personalized treatments.
1. The development of culture-independent community surveys has greatly advanced our
understanding of the composition and structure of vaginal microbiota.
2. Lactobacillus species dominate vaginal microbiota in most normal and healthy women.
However, an appreciable proportion of asymptomatic, otherwise healthy individuals have
vaginal microbiota that lack significant numbers of Lactobacillus spp. and harbor a diverse
array of facultative and strictly anaerobic microorganisms, challenging the conventional
wisdom that the presence of lactobacilli equates to normal and healthy vaginal microbiota.
3. Neither clinical criteria (using either the Amsel or the Nugent scoring systems) nor
community composition and structure can fully explain symptomatic BV, which appears
to be a multifactorial clinical syndrome with complex and still unknown etiologies.
4. The concept of normal and healthy vaginal microbiota is difficult to define without a
complete understanding of its true function(s) and its effect on host physiology. One
might envision separating the concept of normal and healthy from predisposition to
diseases such as STIs.
1. Study of the vaginal ecosystem using prospective and frequent sampling study design
allows the analysis of samples collected before, during, and after a disease event.
2. There is a need to further characterize the true function of the vaginal microbiota in the
context of vaginal health to better understand disease.
3. The role of host genotype in community assembly, composition, and dynamics requires
further examination.
4. A systems-level model of the vaginal ecosystem should be developed in order to charac-
terize the functional interaction between the vaginal microbiota and the host.
5. It is expected that future effort should be made to translate current knowledge to the de-
velopment of personalized preventive or curative regimens (based on vaginal community
types), including probiotics and prebiotics. Vaginal Microbiota and Health 383
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MI66CH18-Ravel ARI 8 August 2012 16:26
The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.
This work was supported by the National Institute of Allergies and Infectious Diseases, National
Institutes of Health (grant numbers U19 AI084044, UO1 AI070921, and UH2 AI083264).
1. Alakomi HL, Skytta E, Saarela M, Mattila-Sandholm T, Latva-Kala K, Helander IM. 2000. Lactic
acid permeabilizes gram-negative bacteria by disrupting the outer membrane. Appl. Environ. Microbiol.
2. Alpay-Karaoglu S, Aydin F, Kilic SS, Kilic AO. 2002. Antimicrobial activity and characteristics of bac-
teriocins produced by vaginal lactobacilli. Turk. J. Med. Sci. 33:7–12
3. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual
microbial cells without cultivation. Microbiol. Rev. 59:143–69
4. Amsel R, Totten PA, Spiegel CA, Chen KC, Eschenbach D, Holmes KK. 1983. Nonspecific vaginitis:
diagnostic criteria and microbial and epidemiologic associations. Am. J. Med. 74:14–22
5. Antonio MA, Hawes SE, Hillier SL. 1999. The identification of vaginal Lactobacillus species and the demo-
graphic and microbiologic characteristics of women colonized by these species. J. Infect. Dis. 180:1950–56
6. Aroutcheva A, Gariti D, Simon M, Shott S, Faro J, et al. 2001. Defense factors of vaginal lactobacilli.
Am. J. Obstet. Gynecol. 185:375–79
7. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, et al. 2011. Enterotypes of the human gut
microbiome. Nature 473:174–80
8. Bakken LR. 1985. Separation and purification of bacteria from soil. Appl. Environ. Microbiol. 49:1482–87
9. Beigi RH, Wiesenfeld HC, Hillier SL, Straw T, Krohn MA. 2005. Factors associated with absence of
H2O2-producing Lactobacillus among women with bacterial vaginosis. J. Infect. Dis. 191:924–29
10. Beres SB, Sylva GL, Barbian KD, Lei B, Hoff JS, et al. 2002. Genome sequence of a serotype M3 strain of
group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc.
Natl. Acad. Sci. USA 99:10078–83
11. Boskey ER, Cone RA, Whaley KJ, Moench TR. 2001. Origins of vaginal acidity: high D/L lactate ratio
is consistent with bacteria being the primary source. Hum. Reprod. 16:1809–13
12. Boskey ER, Telsch KM, Whaley KJ, Moench TR, Cone RA. 1999. Acid production by vaginal flora in
vitro is consistent with the rate and extent of vaginal acidification. Infect. Immun. 67:5170–75
13. Bradshaw CS, Morton AN, Hocking J, Garland SM, Morris MB, et al. 2006. High recurrence rates of
bacterial vaginosis over the course of 12 months after oral metronidazole therapy and factors associated
with recurrence. J. Infect. Dis. 193:1478–86
14. Brotman RM, Ghanem KG, Klebanoff MA, Taha TE, Scharfstein DO, Zenilman JM. 2008. The effect
of vaginal douching cessation on bacterial vaginosis: a pilot study. Am. J. Obstet. Gynecol. 198:628.e1–7
15. Brotman RM, Klebanoff MA, Nansel TR, Andrews WW, Schwebke JR, et al. 2008. A longitudinal study
of vaginal douching and bacterial vaginosis—a marginal structural modeling analysis. Am. J. Epidemiol.
16. Observes rapid
fluctuation over time of
vaginal microbiota using
Nugent scores, and
suggests the importance
of prospective
longitudinal studies
with frequent sampling.
16. Brotman RM, Ravel J, Cone RA, Zenilman JM. 2010. Rapid fluctuation of the vaginal microbiota
measured by Gram stain analysis. Sex. Transm. Infect. 86:297–302
17. Burton JP, Cadieux PA, Reid G. 2003. Improved understanding of the bacterial vaginal microbiota of
women before and after probiotic instillation. Appl. Environ. Microbiol. 69:97–101
18. Cash HL, Whitham CV, Behrendt CL, Hooper LV. 2006. Symbiotic bacteria direct expression of an
intestinal bactericidal lectin. Science 313:1126–30
384 Ma ·Forney ·Ravel
Annu. Rev. Microbiol. 2012.66:371-389. Downloaded from
by University of Maryland - Baltimore Health Sciences on 09/25/12. For personal use only.
MI66CH18-Ravel ARI 8 August 2012 16:26
19. Cherpes TL, Meyn LA, Krohn MA, Lurie JG, Hillier SL. 2003. Association between acquisition of
herpes simplex virus type 2 in women and bacterial vaginosis. Clin. Infect. Dis. 37:319–25
20. Cohen CR, Duerr A, Pruithithada N, Rugpao S, Hillier S, et al. 1995. Bacterial vaginosis and HIV
seroprevalence among female commercial sex workers in Chiang Mai, Thailand. AIDS 9:1093–97
21. Coleman JS, Hitti J, Bukusi EA, Mwachari C, Muliro A, et al. 2007. Infectious correlates of HIV-1
shedding in the female upper and lower genital tracts. AIDS 21:755–59
22. Cu-Uvin S, Hogan JW, Caliendo AM, Harwell J, Mayer KH, Carpenter CC. 2001. Association between
bacterial vaginosis and expression of human immunodeficiency virus type 1 RNA in the female genital
tract. Clin. Infect. Dis. 33:894–96
23. Dethlefsen L, McFall-Ngai M, Relman DA. 2007. An ecological and evolutionary perspective on human-
microbe mutualism and disease. Nature 449:811–18
24. D¨
oderlein A. 1892. Das Scheidensekret und Seine Bedeutung f ¨
ur DasPuerperalfieber. Zbl. Bakteriol.
25. Donders GG, Bosmans E, Dekeersmaecker A, Vereecken A, Van Bulck B, Spitz B. 2000. Pathogenesis
of abnormal vaginal bacterial flora. Am. J. Obstet. Gynecol. 182:872–78
26. Dover SE, Aroutcheva AA, Faro S, Chikindas ML. 2008. Natural antimicrobials and their role in vaginal
health: a short review. Int. J. Probiotics Prebiotics 3:219–30
27. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. 2005. Diversity of the human
intestinal microbial flora. Science 308:1635–38
28. Eschenbach DA, Davick PR, Williams BL, Klebanoff SJ, Young-Smith K, et al. 1989. Prevalence of
hydrogen peroxide-producing Lactobacillus species in normal women and women with bacterial vaginosis.
J. Clin. Microbiol. 27:251–56
29. Evans M, Dyson P. 1993. Pulsed-field gel electrophoresis of Streptomyces lividans DNA. Trends Genet.
30. Falsen E, Pascual C, Sjoden B, Ohlen M, Collins MD. 1999. Phenotypic and phylogenetic characteri-
zation of a novel Lactobacillus species from human sources: description of Lactobacillus iners sp. nov. Int.
J. Syst. Bacteriol. 49(Pt. 1):217–21
31. Ferris MJ, Masztal A, Aldridge KE, Fortenberry JD, Fidel PL Jr, Martin DH. 2004. Association of
Atopobium vaginae, a recently described metronidazole resistant anaerobe, with bacterial vaginosis. BMC
Infect. Dis. 4:5
32. FichorovaRN, Yamamoto HS, Delaney ML, Onderdonk AB, Doncel GF. 2011. Novel vaginal microflora
colonization model providing new insight into microbicide mechanism of action. mBio 2:e00168–11
33. Forney LJ, Foster JA, Ledger W. 2006. The vaginal flora of healthy women is not always dominated by
Lactobacillus species. J. Infect. Dis. 194:1468–69
34. Identifies three
novel uncultivated
phylotypes that appear
to be associated with
34. Fredricks DN, Fiedler TL, Marrazzo JM. 2005. Molecular identification of bacteria associated
with bacterial vaginosis. N.Engl.J.Med.353:1899–911
35. Fredricks DN, Relman DA. 1996. Sequence-based identification of microbial pathogens: a reconsider-
ation of Koch’s postulates. Clin. Microbiol. Rev. 9:18–33
36. A longitudinal study
of 32 women sampled
twice-weekly that
describes the temporal
dynamics of vaginal
36. Gajer P, Brotman RM, Bai G, Sakamoto J, Schutte U, et al. 2012. Temporal dynamics of the
human vaginal microbiota. Sci. Transl. Med. 4:132ra–52
37. Goldenberg RL, Andrews WW, Yuan AC, MacKay HT, St. Louis ME. 1997. Sexually transmitted
diseases and adverse outcomes of pregnancy. Clin. Perinatol. 24:23–41
38. Graver MA, Wade JJ. 2011. The role of acidification in the inhibition of Neisseria gonorrhoeae by vaginal
lactobacilli during anaerobic growth. Ann. Clin. Microbiol. Antimicrob. 10:8
39. Gravett MG, Nelson HP, DeRouen T, Critchlow C, Eschenbach DA, Holmes KK. 1986. Independent
associations of bacterial vaginosis and Chlamydia trachomatis infection with adverse pregnancy outcome.
JAMA 256:1899–903
40. Greenblum S, Turnbaugh PJ, Borenstein E. 2012. Metagenomic systems biology of the human gut
microbiome reveals topological shifts associated with obesity and inflammatory bowel disease. Proc.
Natl. Acad. Sci. USA 109:594–99
41. Guise JM, Mahon SM, Aickin M, Helfand M, Peipert JF, Westhoff C. 2001. Screening for bacterial
vaginosis in pregnancy. Am. J. Prev. Med. 20:62–72 Vaginal Microbiota and Health 385
Annu. Rev. Microbiol. 2012.66:371-389. Downloaded from
by University of Maryland - Baltimore Health Sciences on 09/25/12. For personal use only.
MI66CH18-Ravel ARI 8 August 2012 16:26
42. Gupta K, Stapleton AE, Hooton TM, Roberts PL, Fennell CL, Stamm WE. 1998. Inverse association
of H2O2-producing lactobacilli and vaginal Escherichia coli colonization in women with recurrent urinary
tract infections. J. Infect. Dis. 178:446–50
43. Hawes SE, Hillier SL, Benedetti J, Stevens CE, Koutsky LA, et al. 1996. Hydrogen peroxide-producing
lactobacilli and acquisition of vaginal infections. J. Infect. Dis. 174:1058–63
44. Hay PE, Ugwumadu A, Chowns J. 1997. Sex, thrush and bacterial vaginosis. Int. J. STD AIDS 8:603–8
45. Hellberg D, Nilsson S, Mardh PA. 2000. Bacterial vaginosis and smoking. Int. J. STD AIDS 11:603–6
46. Hillier SL. 2007. Normal genital flora. In Sexually Transmitted Diseases, ed. KK Holmes, PF Sparling,
WE Stamm, P Piot, JN Wasserheit, et al., 18:289–308. New York: McGraw-Hill Medical
47. Hillier SL, Krohn MA, Klebanoff SJ, Eschenbach DA. 1992. The relationship of hydrogen peroxide-
producing lactobacilli to bacterial vaginosis and genital microflora in pregnant women. Obstet. Gynecol.
48. Hillier SL, Krohn MA, Rabe LK, Klebanoff SJ, Eschenbach DA. 1993. The normal vaginal flora, H2O2-
producing lactobacilli, and bacterial vaginosis in pregnant women. Clin. Infect. Dis. 16(Suppl. 4):S273–81
49. Hillier SL, Nugent RP, Eschenbach DA, Krohn MA, Gibbs RS, et al. 1995. Association between bacterial
vaginosis and preterm delivery of a low-birth-weight infant. N. Engl. J. Med. 333:1737–42
50. Hugenholtz P, Goebel BM, Pace NR. 1998. Impact of culture-independent studies on the emerging
phylogenetic view of bacterial diversity. J. Bacteriol. 180:4765–74
51. Hutchinson KB, Kip KE, Ness RB. 2007. Condom use and its association with bacterial vaginosis and
bacterial vaginosis-associated vaginal microflora. Epidemiology 18:702–8
52. Hyman RW, Fukushima M, Diamond L, Kumm J, Giudice LC, Davis RW. 2005. Microbes on the
human vaginal epithelium. Proc. Natl. Acad. Sci. USA 102:7952–57
53. Jack RW, Tagg JR, Ray B. 1995. Bacteriocins of gram-positive bacteria. Microbiol. Rev. 59:171–200
54. Kashket ER. 1987. Bioenergetics of lactic acid bacteria: cytoplasmic pH and osmotolerance. FEMS
Microbiol. 46:233–44
55. Keane FE, Ison CA, Taylor-Robinson D. 1997. A longitudinal study of the vaginal flora over a menstrual
cycle. Int. J. STD AIDS 8:489–94
56. Klebanoff MA, Schwebke JR, Zhang J, Nansel TR, Yu KF, Andrews WW. 2004. Vulvovaginal symptoms
in women with bacterial vaginosis. Obstet. Gynecol. 104:267–72
57. Koumans EH, Markowitz LE, Berman SM, St Louis ME. 1999. A public health approach to adverse
outcomes of pregnancy associated with bacterial vaginosis. Int. J. Gynaecol. Obstet. 67(Suppl. 1):S29–33
58. Koumans EH, Markowitz LE, Hogan V, Group CBW. 2002. Indications for therapy and treatment
recommendations for bacterial vaginosis in nonpregnant and pregnant women: a synthesis of data. Clin.
Infect. Dis. 35:S152–72
59. Koumans EH, Sternberg M, Bruce C, McQuillan G, Kendrick J, et al. 2007. The prevalence of bacterial
vaginosis in the United States, 2001–2004; associations with symptoms, sexual behaviors, and reproduc-
tive health. Sex. Transm. Dis. 34:864–69
60. Lai SK, Hida K, Shukair S, Wang YY, Figueiredo A, et al. 2009. Human immunodeficiency virus type
1 is trapped by acidic but not by neutralized human cervicovaginal mucus. J. Virol. 83:11196–200
61. Lan R, Reeves PR. 2000. Intraspecies variation in bacterial genomes: the need for a species genome
concept. Trends Microbiol. 8:396–401
62. Larsson PG. 1992. Treatment of bacterial vaginosis. Int. J. STD AIDS 3:239–47
63. Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, et al. 2010. Omic data from evolved E.
coli are consistent with computed optimal growth from genome-scale models. Mol. Syst. Biol. 6:390
64. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, et al. 2008. Evolution of mammals and
their gut microbes. Science 320:1647–51
65. Ley RE, Peterson DA, Gordon JI. 2006. Ecological and evolutionary forces shaping microbial diversity
in the human intestine. Cell 124:837–48
66. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. 2006. Microbial ecology: human gut microbes associated
with obesity. Nature 444:1022–23
67. Marrazzo J. 2006. The vaginal flora of healthy women is not always dominated by Lactobacillus species—
reply to Forney et al. J. Infect. Dis. 194:1469–70
386 Ma ·Forney ·Ravel
Annu. Rev. Microbiol. 2012.66:371-389. Downloaded from
by University of Maryland - Baltimore Health Sciences on 09/25/12. For personal use only.
MI66CH18-Ravel ARI 8 August 2012 16:26
68. Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK, et al. 2007. A top-down systems biology
view of microbiome-mammalian metabolic interactions in a mouse model. Mol. Syst. Biol. 3:112
69. MartinHL, Richardson BA, Nyange PM, Lavreys L, Hillier SL, et al. 1999. Vaginal lactobacilli, microbial
flora, and risk of human immunodeficiency virus type 1 and sexually transmitted disease acquisition.
J. Infect. Dis. 180:1863–68
70. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. 2005. An immunomodulatory molecule of symbi-
otic bacteria directs maturation of the host immune system. Cell 122:107–18
71. McDonald HM, O’Loughlin JA, Jolley P, Vigneswaran R, McDonald PJ. 1992. Prenatal microbiological
risk factors associated with preterm birth. Br.J.Obstet.Gynaecol.99:190–96
72. Meis PJ, Goldenberg RL, Mercer B, Moawad A, Das A, et al. 1995. The Preterm Prediction Study:
significance of vaginal infections. Am. J. Obstet. Gynecol. 173:1231–35
73. Menard JP, Fenollar F, Henry M, Bretelle F, Raoult D. 2008. Molecular quantification of Gardnerella
vaginalis and Atopobium vaginae loads to predict bacterial vaginosis. Clin. Infect. Dis. 47:33–43
74. Morgan DJ, Aboud CJ, McCaffrey IM, Bhide SA, Lamont RF, Taylor-Robinson D. 1996. Comparison
of Gram-stained smears prepared from blind vaginal swabs with those obtained at speculum examination
for the assessment of vaginal flora. Br.J.Obstet.Gynaecol.103:1105–8
75. Ness RB, Hillier S, Richter HE, Soper DE, Stamm C, et al. 2003. Can known risk factors explain racial
differences in the occurrence of bacterial vaginosis? J. Natl. Med. Assoc. 95:201–12
76. Ness RB, Kip KE, Hillier SL, Soper DE, Stamm CA, et al. 2005. A cluster analysis of bacterial vaginosis-
associated microflora and pelvic inflammatory disease. Am. J. Epidemiol. 162:585–90
77. Nugent RP, Krohn MA, Hillier SL. 1991. Reliability of diagnosing bacterial vaginosis is improved by a
standardized method of Gram stain interpretation. J. Clin. Microbiol. 29:297–301
78. Oberhardt MA, Palsson BO, Papin JA. 2009. Applications of genome-scale metabolic reconstructions.
Mol. Syst. Biol. 5:320
79. Ochman H, Jones IB. 2000. Evolutionary dynamics of full genome content in Escherichia coli.EMBO J.
80. Provides
experimental evidence
obtained under
anaerobic conditions
suggesting that lactic
acid, not hydrogen
peroxide, likely plays a
protective role by
BV-associated bacteria.
80. O’Hanlon DE, Moench TR, Cone RA. 2011. In vaginal fluid, bacteria associated with bacterial
vaginosis can be suppressed with lactic acid but not hydrogen peroxide. BMC Infect. Dis. 11:200
81. Oscariz JC, Pisabarro AG. 2001. Classification and mode of action of membrane-active bacteriocins
produced by gram-positive bacteria. Int. Microbiol. 4:13–19
82. Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, et al. 2003. Role of mobile DNA in the
evolution of vancomycin-resistant Enterococcus faecalis.Science 299:2071–74
83. Peters SE, Beck-Sague CM, Farshy CE, Gibson I, Kubota KA, et al. 2000. Behaviors associated with Neis-
seria gonorrhoeae and Chlamydia trachomatis: cervical infection among young women attending adolescent
clinics. Clin. Pediatr. 39:173–77
84. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. 2009. The NIH Human Microbiome
Project. Genome Res. 19:2317–23
85. Rauch M, Lynch S. 2012. The potential for probiotic manipulation of the gastrointestinal microbiome.
Curr. Opin. Biotechnol. 23:192–201
86. Classifies vaginal
bacteria composition
profiles into five
community state types,
and establishes
differences in
community state types
frequencies in four
ethnic groups.
86. Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, et al. 2011. Vaginal microbiome of
reproductive-age women. Proc. Natl. Acad. Sci. USA 108(Suppl. 1):4680–87
87. Redondo-Lopez V, Cook RL, Sobel JD. 1990. Emerging role of lactobacilli in the control and mainte-
nance of the vaginal bacterial microflora. Rev. Infect. Dis. 12:856–72
88. Relman DA. 2008. ‘Til death do us part’: coming to terms with symbiotic relationships. Forward. Nat.
Rev. Microbiol. 6:721–24
89. Rodriguez Jovita M, Collins MD, Sjoden B, Falsen E. 1999. Characterization of a novel Atopobium isolate
from the human vagina: description of Atopobium vaginae sp. nov. Int. J. Syst. Bacteriol. 49(Pt. 4):1573–76
90. Rogosa M, Sharpe ME. 1960. Species differentiation of human vaginal lactobacilli. J. Gen. Microbiol.
91. Russell JB, Diez-Gonzalez F. 1998. The effects of fermentation acids on bacterial growth. Adv. Microb.
Physiol. 39:205–34 Vaginal Microbiota and Health 387
Annu. Rev. Microbiol. 2012.66:371-389. Downloaded from
by University of Maryland - Baltimore Health Sciences on 09/25/12. For personal use only.
MI66CH18-Ravel ARI 8 August 2012 16:26
92. Schellenberg J, Links MG, Hill JE, Dumonceaux TJ, Peters GA, et al. 2009. Pyrosequencing of the
chaperonin-60 universal target as a tool for determining microbial community composition. Appl. Env-
iron. Microbiol. 75:2889–98
93. Schwebke JR, Hillier SL, Sobel JD, McGregor JA, Sweet RL. 1996. Validity of the vaginal Gram stain
for the diagnosis of bacterial vaginosis. Obstet. Gynecol. 88:573–76
94. Schwebke JR, Morgan SC, Weiss HL. 1997. The use of sequential self-obtained vaginal smears for
detecting changes in the vaginal flora. Sex. Transm. Dis. 24:236–39
95. Schwebke JR, Richey CM, Weiss HL. 1999. Correlation of behaviors with microbiological changes in
vaginal flora. J. Infect. Dis. 180:1632–36
96. Sewankambo N, Gray RH, Wawer MJ, Paxton L, McNaim D, et al. 1997. HIV-1 infection associated
with abnormal vaginal flora morphology and bacterial vaginosis. Lancet 350:546–50
97. Sobel JD. 1997. Vaginitis. N. Engl. J. Med. 337:1896–903
98. Sobel JD. 1999. Is there a protective role for vaginal flora? Curr. Infect. Dis. Rep. 1:379–83
99. Sobel JD. 2005. What’s new in bacterial vaginosis and trichomoniasis? Infect. Dis. Clin. N. Am. 19:387–
100. Sobel JD, Ferris D, Schwebke J, Nyirjesy P, Wiesenfeld HC, et al. 2006. Suppressive antibacterial therapy
with 0.75% metronidazole vaginal gel to prevent recurrent bacterial vaginosis. Am. J. Obstet. Gynecol.
101. Sobel JD, Schmitt C, Meriwether C. 1993. Long-term follow-up of patients with bacterial vaginosis
treated with oral metronidazole and topical clindamycin. J. Infect. Dis. 167:783–84
102. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, et al. 2006. Microbial diversity in the
deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. USA 103:12115–20
103. Spear GT, St. John E, Zariffard MR. 2007. Bacterial vaginosis and human immunodeficiency virus
infection. AIDS Res. Ther. 4:25
104. Sundquist A, Bigdeli S, Jalili R, Druzin ML, Waller S, et al. 2007. Bacterial flora-typing with targeted,
chip-based pyrosequencing. BMC Microbiol. 7:108
105. Taha TE, Hoover DR, Dallabetta GA, Kumwenda NI, Mtimavalye LA, et al. 1998. Bacterial vaginosis
and disturbances of vaginal flora: association with increased acquisition of HIV. AIDS 12:1699–706
106. Thomas S. 1928. Doderlein’s bacillus: Lactobacillus acidophilus.J. Infect. Dis. 43:219–27
107. Torsvik V, Ovreas L. 2002. Microbial diversity and function in soil: from genes to ecosystems. Curr.
Opin. Microbiol. 5:240–45
108. Turnbaugh PJ, Gordon JI. 2009. The core gut microbiome, energy balance and obesity. J. Physiol.
109. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. 2009. A core gut microbiome
in obese and lean twins. Nature 457:480–84
110. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The Human
Microbiome Project. Nature 449:804–10
111. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. 2006. An obesity-associated
gut microbiome with increased capacity for energy harvest. Nature 444:1027–31
112. Vallor AC, Antonio MA, Hawes SE, Hillier SL. 2001. Factors associated with acquisition of, or persistent
colonization by, vaginal lactobacilli: role of hydrogen peroxide production. J. Infect. Dis. 184:1431–36
113. van De Wijgert JH, Mason PR, Gwanzura L, Mbizvo MT, Chirenje ZM, et al. 2000. Intravaginal
practices, vaginal flora disturbances, and acquisition of sexually transmitted diseases in Zimbabwean
women. J. Infect. Dis. 181:587–94
114. van der Lelie D, Lesaulnier C, McCorkle S, Geets J, Taghavi S, Dunn J. 2006. Use of single-point
genome signature tags as a universal tagging method for microbial genome surveys. Appl. Environ.
Microbiol. 72:2092–101
115. Verhelst R, Verstraelen H, Claeys G, Verschraegen G, Delanghe J, et al. 2004. Cloning of 16S rRNA
genes amplified from normal and disturbed vaginal microflora suggests a strong association between
Atopobium vaginae,Gardnerella vaginalis and bacterial vaginosis. BMC Microbiol. 4:16
116. Verstraelen H, Verhelst R, Claeys G, Temmerman M, Vaneechoutte M. 2004. Culture-independent
analysis of vaginal microflora: the unrecognized association of Atopobium vaginae with bacterial vaginosis.
Am. J. Obstet. Gynecol. 191:1130–32
388 Ma ·Forney ·Ravel
Annu. Rev. Microbiol. 2012.66:371-389. Downloaded from
by University of Maryland - Baltimore Health Sciences on 09/25/12. For personal use only.
MI66CH18-Ravel ARI 8 August 2012 16:26
117. Wardle DA. 2000. Stability of ecosystem properties in response to above-ground functional group
richness and composition. Oikos 89:11–23
118. Wiesenfeld HC, Hillier SL, Krohn MA, Landers DV, Sweet RL. 2003. Bacterial vaginosis is a strong
predictor of Neisseria gonorrhoeae and Chlamydia trachomatis infection. Clin. Infect. Dis. 36:663–68
119. Wilson JD, Lee RA, Balen AH, Rutherford AJ. 2007. Bacterial vaginal flora in relation to changing
oestrogen levels. Int. J. STD AIDS 18:308–11
120. Witkin SS, Alvi S, Bongiovanni AM, Linhares IM, Ledger WJ. 2011. Lactic acid stimulates interleukin-
23 production by peripheral blood mononuclear cells exposed to bacterial lipopolysaccharide. FEMS
Immunol. Med. Microbiol. 61:153–58
121. Workowski KA, Berman SM. 2006. Sexually transmitted diseases treatment guidelines, 2006. MMWR
Recomm. Rep. 55:1–94
122. Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR, Forney LJ. 2004. Characterization of vaginal
microbial communities in adult healthy women using cultivation-independent methods. Microbiology
123. Demonstrates
differences in the
vaginal microbiota
structure in Caucasian
and Black women.
123. Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, et al. 2007. Differences in the compo-
sition of vaginal microbial communities found in healthy Caucasian and black women. ISME J.
124. Shows variation in
composition and
structure of vaginal
bacterial community of
ethnic groups, and
suggests that host
factors might contribute
to shaping the vaginal
124. Zhou X, Hansmann MA, Davis CC, Suzuki H, Brown CJ, et al. 2010. The vaginal bacterial com-
munities of Japanese women resemble those of women in other racial groups. FEMS Immunol.
Med. Microbiol. 58:169–81 Vaginal Microbiota and Health 389
Annu. Rev. Microbiol. 2012.66:371-389. Downloaded from
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Annual Review of
Volume 66, 2012 Contents
A Fortunate Journey on Uneven Grounds
Agnes Ullmann pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp1
Memories of a Senior Scientist: On Passing the Fiftieth Anniversary
of the Beginning of Deciphering the Genetic Code
Peter Lengyel pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp27
Yeast ATP-Binding Cassette Transporters Conferring
Multidrug Resistance
Rajendra Prasad and Andre Goffeau pppppppppppppppppppppppppppppppppppppppppppppppppppppppp39
‘Gestalt,’ Composition and Function of the
Trypanosoma brucei Editosome
H. Ulrich G¨oringer ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp65
Physiology and Diversity of Ammonia-Oxidizing Archaea
David A. Stahl and Jos´e R. de la Torre ppppppppppppppppppppppppppppppppppppppppppppppppppppp83
Bacterial Persistence and Toxin-Antitoxin Loci
Kenn Gerdes and Etienne Maisonneuve ppppppppppppppppppppppppppppppppppppppppppppppppppp103
Activating Transcription in Bacteria
David J. Lee, Stephen D. Minchin, and Stephen J.W. Busby ppppppppppppppppppppppppppp125
Herpesvirus Transport to the Nervous System and Back Again
Gregory Smith pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp153
A Virological View of Innate Immune Recognition
Akiko Iwasaki ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp177
DNA Replication and Genomic Architecture in Very Large Bacteria
Esther R. Angert pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp197
Large T Antigens of Polyomaviruses: Amazing Molecular Machines
Ping An, Maria Teresa S´aenz Robles, and James M. Pipas pppppppppppppppppppppppppppppp213
Peroxisome Assembly and Functional Diversity
in Eukaryotic Microorganisms
Laurent Pieuchot and Gregory Jedd ppppppppppppppppppppppppppppppppppppppppppppppppppppppp237
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Microbial Population and Community Dynamics on Plant Roots and
Their Feedbacks on Plant Communities
James D. Bever, Thomas G. Platt, and Elise R. Morton ppppppppppppppppppppppppppppppppp265
Bacterial Chemotaxis: The Early Years of Molecular Studies
Gerald L. Hazelbauer pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp285
RNA Interference Pathways in Fungi: Mechanisms and Functions
Shwu-Shin Chang, Zhenyu Zhang, and Yi Liu pppppppppppppppppppppppppppppppppppppppppp305
Evolution of Two-Component Signal Transduction Systems
Emily J. Capra and Michael T. Laub ppppppppppppppppppppppppppppppppppppppppppppppppppppp325
The Unique Paradigm of Spirochete Motility and Chemotaxis
Nyles W. Charon, Andrew Cockburn, Chunhao Li, Jun Liu,
Kelly A. Miller, Michael R. Miller, Md. A. Motaleb,
and Charles W. Wolgemuth ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp349
Vaginal Microbiome: Rethinking Health and Disease
Bing Ma, Larry J. Forney, and Jacques Ravel pppppppppppppppppppppppppppppppppppppppppppp371
Derek R. Lovley ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp391
Origin and Diversification of Eukaryotes
Laura A. Katz pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp411
Genomic Insights into Syntrophy: The Paradigm
for Anaerobic Metabolic Cooperation
Jessica R. Sieber, Michael J. McInerney, and Robert P. Gunsalus ppppppppppppppppppppppp429
Structure and Regulation of the Type VI Secretion System
Julie M. Silverman, Yannick R. Brunet, Eric Cascales, and Joseph D. Mougous ppppppp453
Network News: The Replication of Kinetoplast DNA
Robert E. Jensen and Paul T. Englund pppppppppppppppppppppppppppppppppppppppppppppppppppp473
Pseudomonas aeruginosa Twitching Motility: Type IV Pili in Action
Lori L. Burrows ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp493
Postgenomic Approaches to Using Corynebacteria as Biocatalysts
Alain A. Vert`es, Masayuki Inui, and Hideaki Yukawa pppppppppppppppppppppppppppppppppp521
Cumulative Index of Contributing Authors, Volumes 62–66 ppppppppppppppppppppppppppp551
An online log of corrections to Annual Review of Microbiology articles may be found at
Contents vii
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... In this study, we conducted initial functional characterization of urinary lactobacilli from seven species under uniform conditions. Three of those species (eight strains) are from the abundant and frequently identified species in the female urinary tract: L. crispatus, L. gasseri and L. jensenii (Ma et al., 2012;Komesu et al., 2020;Neugent et al., 2022). While lactobacilli inhabiting other ecological niches have been previously studied, urinary lactobacilli have not previously been characterized, despite their potential for direct interactions with uropathogens and potential clinical implications regarding urinary tract infections. ...
Full-text available
The human urinary microbiome is thought to affect the development and progression of urinary tract infections (UTI), particularly recurrent UTIs in aging populations of women. To understand the possible interactions of urinary pathogens with commensal bacteria inhabiting the aging bladder, we conducted an initial functional assessment of a representative set of urinary lactobacilli that dominate this niche in postmenopausal women. We created a repository of urinary bladder bacteria isolated via Enhanced Quantitative Urinary Culture (EQUC) from healthy postmenopausal women, as well as those with a culture-proven recurrent UTI (rUTI) diagnosis. This repository contains lactobacilli strains from eight different species. As many other lactobacilli are known to inhibit human pathogens, we hypothesized that some urinary lactobacilli will have similar abilities to inhibit the growth of typical uropathogens and thus, provide a link between the urinary microbiome and the predisposition to the rUTI. Therefore, we screened the urinary lactobacilli in our repository for their ability to inhibit model uropathogens in vitro. We observed that many urinary isolates strongly inhibit model strains of gram-negative Escherichia coli and Klebsiella pneumoniae but demonstrate less inhibition of gram-positive Enterococcus faecalis. The observed inhibition affected model strains of uropathogens as well as clinical and multidrug-resistant isolates of those species. Our preliminary analysis of inhibition modes suggests a combination of pH-dependent and cell-dependent inhibition. Overall, inhibition strongly varies among species and strains of urinary lactobacilli. While the strength of the inhibition is not predictive of health outcomes in this limited repository, there is a high level of species and strain diversity that warrants future detailed investigations.
... Although the CVM is composed of different microbe communities, it is highly dominated by the genus Lactobacillus (Lactobacillus crispatus, Lactobacillus iners, Lactobacillus gasseri, or Lactobacillus jensenii) [171,172]. In addition to maintaining tissue homeostasis [173] and a local pH lesser than 4.5 [174], lactobacilli adhere to epithelial cells by forming microcolonies and serve as a barrier to protect the genital environment from infectious pathogens [175], counteracting bacterial vaginosis, yeast infections, and sexually transmitted diseases (STDs) [176,177]. The imbalance of the CVM triggers abnormal cell proliferation, chronic inflammation, genome instability, STDs, premature births, and cancers of the vaginal tract [40, [178][179][180]. ...
Full-text available
Advancement in the development of molecular sequencing platforms has identified infectious bacteria or viruses that trigger the dysregulation of a set of genes inducing the epithelial–mesenchymal transition (EMT) event. EMT is essential for embryogenesis, wound repair, and organ development; meanwhile, during carcinogenesis, initiation of the EMT can promote cancer progression and metastasis. Recent studies have reported that interactions between the host and dysbiotic microbiota in different tissues and organs, such as the oral and nasal cavities, esophagus, stomach, gut, skin, and the reproductive tract, may provoke EMT. On the other hand, it is revealed that certain microorganisms display a protective role against cancer growth, indicative of possible therapeutic function. In this review, we summarize recent findings elucidating the underlying mechanisms of pathogenic microorganisms, especially the microbiota, in eliciting crucial regulator genes that induce EMT. Such an approach may help explain cancer progression and pave the way for developing novel preventive and therapeutic strategies.
... The composition of the female genital tract microbiota is influenced by numerous factors, including age, pH in vagina, hormonal secretions, the menstrual cycle, contraceptives, antibiotic use, and sexual activity (Prince et al., 2015;Nasioudis et al., 2017). Lactobacillus, the dominant bacterium in the vagina of women during pregnancy (Dominguez-Bello et al., 2010;Ma et al., 2012), can bind to the surface of vaginal epithelial cells to prevent the attachment of other microorganisms in the vagina. It can not only produce lactic acid by decomposing glycogen in the vagina to maintain a stable pH, but also kill intracellular microorganisms by inducing the autophagy of vaginal epithelial cells (Witkin and Linhares, 2017). ...
Full-text available
The distribution of the microbiome in women with advanced maternal age (AMA) is poorly understood. To gain insight into this, the vaginal and gut microbiota of 62 women were sampled and sequenced using the 16S rRNA technique. These women were divided into three groups, namely, the AMA (age ≥ 35 years, n = 13) group, the non-advanced maternal age (NMA) (age < 35 years, n = 38) group, and the control group (non-pregnant healthy women, age >35 years, n = 11). We found that the alpha diversity of vaginal microbiota in the AMA group significantly increased. However, the beta diversity significantly decreased in the AMA group compared with the control group. There was no significant difference in the diversity of gut microbiota among the three groups. The distributions of microbiota were significantly different among AMA, NMA, and control groups. In vaginal microbiota, the abundance of Lactobacillus was higher in the pregnant groups. Bifidobacterium was significantly enriched in the AMA group. In gut microbiota, Prevotella bivia was significantly enriched in the AMA group. Vaginal and gut microbiota in women with AMA were noticeably different from the NMA and non-pregnant women, and this phenomenon is probably related to the increased risk of complications in women with AMA.
... All of these microorganisms make up the vaginal microbiota and colonise in a dynamic environment [95]. Though each woman exhibits a different vaginal microbiota community, those with Lactobacillus as the dominant member are more often associated with healthy vaginal homeostasis [96]. ...
Full-text available
Vulvovaginal candidiasis (VVC) is a prevalent gynaecological disease characterised by vaginal wall inflammation that is caused by Candida species. VVC impacts almost three-quarters of all women throughout their reproductive years. As the vaginal mucosa is the first point of contact with microbes, vaginal epithelial cells are the first line of defence against opportunistic Candida infection by providing a physical barrier and mounting immunological responses. The mechanisms of defence against this infection are displayed through the rapid shedding of epithelial cells, the presence of pattern recognition receptors, and the release of inflammatory cytokines. The bacterial microbiota within the mucosal layer presents another form of defence mechanism within the vagina through acidic pH regulation, the release of antifungal peptides and physiological control against dysbiosis. The significant role of the microbiota in maintaining vaginal health promotes its application as one of the potential treatment modalities against VVC with the hope of alleviating the burden of VVC, especially the recurrent disease. This review discusses and summarises current progress in understanding the role of vaginal mucosa and host immunity upon infection, together with the function of vaginal microbiota in VVC.
... Regarding the oral route of administration, it is critical to consider the viability of the probiotics strains under high concentrations of gastric acid and bile salts as well as the time lactobacilli can reach and colonize the vagina, which appear to be different person to person [53]. Marcotte et al. [43] illustrated that the efficacy of probiotics was consistent with the short-term efficacy of antibiotics and that the long-term efficacy of probiotics significantly prevented BV recurrence [54,55]. e results of several trials have shown that pre/probiotics combined with metronidazole (12 trials; 994 populations) or clindamycin (3 trials; 350 populations) are more efficient in reducing BV recurrence rate compared to metronidazole or clindamycin alone. ...
Full-text available
Background: Bacterial vaginosis (BV), caused by an imbalance in the vaginal microbiota, can be treated and prevented by probiotics. Pregnant women with BV can experience premature labor and spontaneous abortions. Probiotics and prebiotics promote the proliferation of beneficial microorganisms, alter the composition of the vaginal microbiota, and prevent intravaginal infections in postmenopausal women. In addition to reducing infection symptoms, pre/probiotics can also help prevent vaginal infections. Materials and methods: A systematic review was conducted on studies from 2010 to 2020 to determine the efficacy of pre/probiotics on the treatment of BV in pregnant and nonpregnant women. The databases Medline, Scopus, Embase, and Google Scholar were systematically searched using the following keywords: "bacterial vaginosis," "probiotics," "prebiotics," and "synbiotics." Results: A total of 1,871 articles were found in the initial search, and 24 clinical trials were considered eligible. In studies comparing the effects of pre/probiotics and placebos with or without antibiotic therapy in patients with BV, significant differences in clinical outcomes were observed. Probiotics reduced the levels of IL-1β and IL-6, as well as the overall Nugent score and Amsel's criteria for restitution of a balanced vaginal microbiota. In addition, probiotics can reduce the vaginal colonization of Group B streptococci among pregnant women. In subjects treated with probiotics, BV cure rates were higher than those in subjects treated with antibiotics. There were no additional adverse events. Conclusion: Pre/probiotic regimens, when used for BV treatment, are usually safe and can exhibit long-term and short-term benefits. In order to prove the benefits of pre/probiotics in BV treatment, additional high-quality research is required.
... In addition to microorganisms within the gut, microorganisms in other niches may profoundly influence host physiology [122][123][124][125] . This includes microorganisms on external surfaces and mucosal sites, and also tissue-resident microorganisms 126 . ...
Microorganisms within the gut and other niches may contribute to carcinogenesis, as well as shaping cancer immunosurveillance and response to immunotherapy. Our understanding of the complex relationship between different host-intrinsic microorganisms, as well as the multifaceted mechanisms by which they influence health and disease, has grown tremendously—hastening development of novel therapeutic strategies that target the microbiota to improve treatment outcomes in cancer. Accordingly, the evaluation of a patient’s microbial composition and function and its subsequent targeted modulation represent key elements of future multidisciplinary and precision-medicine approaches. In this Review, we outline the current state of research toward harnessing the microbiome to better prevent and treat cancer. There exists tremendous opportunity to target microorganisms in the gut and other niches to help treat or even prevent cancer. This Review outlines how microbial targeting could become a pillar of personalized cancer care over the next 5 to 10 years.
... Vaginal taxa from the mother have also been found to transiently colonize the child's fecal and airway microbiota [22]. Vaginal microbiota communities are typically dominated by Lactobacillus species [23,24], specifically L. iners, L. crispatus, L. gasseri, or L. jensenii; yet, significant differences are seen between North American women from different ethnic groups (White, Black, Hispanic, and Asian) [25]. When a misbalance in vaginal microbiota occurs, such as a lower abundance of Lactobacillus, bacterial vaginosis is likely to occur-resulting in unwanted perinatal outcomes, including preterm birth (e.g. ...
Full-text available
The intestinal microbiota plays a crucial role in health and changes in its composition are linked with major global human diseases. Fully understanding what shapes the human intestinal microbiota composition and knowing ways of modulating the composition are critical for promotion of life-course health, combating diseases, and reducing global health disparities. We aim to provide a foundation for understanding what shapes the human intestinal microbiota on an individual and global scale, and how interventions could utilize this information to promote life-course health and reduce global health disparities. We briefly review experiences within the first 1,000 days of life and how long-term exposures to environmental elements or geographic specific cultures have lasting impacts on the intestinal microbiota. We also discuss major public health threats linked to the intestinal microbiota, including antimicrobial resistance and disappearing microbial diversity due to globalization. In order to promote global health, we argue that the interplay of the larger ecosystem with intestinal microbiota research should be utilized for future research and urge for global efforts to conserve microbial diversity.
Background: in recent years, many studies were carried out to explore the role of vaginal microbiota in HPV infections and cervical intraepithelial neoplasia (CIN) progression. The aim of this study was to conduct a review of the literature to analyze the interaction between the vaginal microbiota, the CIN, and the immunological response. Methods: we performed a literature search, considering papers published between November 2015 and September 2021. Results: despite significant evidence suggesting a role of vaginal microbiota in the pathogenesis of HPV-related lesions, some studies still struggle to demonstrate this correlation. However, the vaginal microbiota of HPV-positive women shows an increased diversity, combined with a reduced relative abundance of Lactobacillus spp. and a higher pH. In cervical dysplasia progression, a strong association is found with new bacteria, and with the deregulation of pathways and hyperexpression of cytokines leading to chronic inflammation. Conclusions: in HPV progression, there is a strong correlation between potential biomarkers, such as Sneathia and Delftia found in community state types IV and II, and chronic inflammation with cytokine overexpression. Better analysis of these factors could be of use in the prevention of the progression of the disease and, eventually, in new therapeutic strategies.
Full-text available
For vaginal reconstructive surgery, the vaginal defect sometimes cannot be closed with primary intention due to poor tissue quality or loss of the vaginal wall. To cover the defect, plastic surgeons may be consulted with regard to a tissue advancement flap, a very complex procedure, and urologists may not feel familiar with it or comfortable with carrying it out. The rotational labial and inferior pudendal artery based inner thigh flap, devised by Professor Shlomo Raz, is a simple and useful procedure which urologists can perform with a short learning curve. Therefore , this article aims to demonstrate the surgical technique involved in this flap which can be widely used as an adjunct to any vaginal reconstructive procedures.
Approximately 10% of all pregnancies in the United States end in preterm birth, and over 14% of pregnancies end in preterm birth among Black women. Knowledge on the associations between vaginal microbiome and preterm birth is important for understanding the potential cause and assessing risk of preterm birth.
Full-text available
The aim of this study is to test the production of bacteriocin in vaginal Lactobacilli and determining the characterization and antibacterial activity of this bacteriocin. For this reason 100 Lactobacillus strains were isolated and identified from vaginal swab samples of 75 women who attended obstetric and gynecology clinics. It was determined that six of 100 Lactobacillus strains produced bacteriocin. The antibacterial activity of bacteriocins was examined and found to be effective on vaginal L. gasseri, L. acidophilus, Gardnerella vaginalis ATCC 14018 and Pseudomonas aeroginosa ATCC 10145. We also found that bacteriocins were sensitive to proteinase enzymes and alkalinity, but resistant to catalase. Two of them, TL059a and TL080, were resistant to chloroform and 1 h boiling. It was observed that adding 1% NaCl to medians increased bacteriocin production and it was also found that mitomycin C induced Rogosa SL media was more suitable than MRS (Z = -2, p < 0.05).
Full-text available
A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.
Background: In-vitro research has suggested that bacterial vaginosis may increase the survival of HIV-1 in the genital tract. Therefore, we investigated the association of HIV-1 infection with vaginal flora abnormalities, including bacterial vaginosis and depletion of lactobacilli, after adjustment for sexual activity and the presence of other sexually transmitted diseases (STDs). Methods: During the initial survey round of our community-based trial of STD control for HIV-1 prevention in rural Rakai District, southwestern Uganda, we selected 4718 women aged 15-59 years. They provided interview information, blood for HIV-1 and syphilis serology, urine for detection of Chlamydia trachomatis and Neisseria gonorrhoeae, and two self-administered vaginal swabs for culture of Trichomonas vaginalis and gram-stain detection of vaginal flora, classified by standardised, quantitative, morphological scoring. Scores 0-3 were normal vaginal flora (predominant lactobacilli). Higher scores suggested replacement of lactobacilli by gram-negative, anaerobic microorganisms (4-6 intermediate; 7-8 and 9-10 moderate and severe bacterial vaginosis). Findings: HIV-1 frequency was 14.2% among women with normal vaginal flora and 26.7% among those with severe bacterial vaginosis (p < 0.0001). We found an association between bacterial vaginosis and increased HIV-1 infection among younger women, but not among women older than 40 years; the association could not be explained by differences in sexual activity or concurrent infection with other STDs. The frequency of bacterial vaginosis was similar among HIV-1-infected women with symptoms (55.0%) and without symptoms (55.7%). The adjusted odds ratio of HIV-1 infection associated with any vaginal flora abnormality (scores 4-10) was 1.52 (95% CI 1.22-1.90), for moderate bacterial vaginosis (scores 7-8) it was 1.50 (1.18-1.89), and for severe bacterial vaginosis (scores 9-10) it was 2.08 (1.48-2.94). Interpretation: This cross-sectional study cannot show whether disturbed vaginal flora increases susceptibility to HIV-1 infection. Nevertheless, the increased frequency of HIV-1 associated with abnormal flora among younger women, for whom HIV-1 acquisition is likely to be recent, but not among older women, in whom HIV-1 is likely to have been acquired earlier, suggests that loss of lactobacilli or presence of bacterial vaginosis may increase susceptibility to HIV-1 acquisition. If this inference is correct, control of bacterial vaginosis could reduce HIV-1 transmission.
Numerous previous studies of nonspecific vaginitis have yielded contradictory results regarding its cause and clinical manifestations, due to a lack of uniform case definition and laboratory methods. We studied 397 consecutive unselected female university students and applied sets of well defined criteria to distinguish nonspecific vaginitis from other forms of vaginitis and from normal findings. Using such criteria, we diagnosed nonspecific vaginitis in up to 25 percent of our study population; asymptomatic disease was recognized in more than 50 percent of those with nonspecific vaginitis. A clinical diagnosis of nonspecific vaginitis, based on simple office procedures, was correlated with both the presence and the concentration of Gardnerella vaginalis (Hemophilus vaginalis) in vaginal discharge, and with characteristic biochemical findings in vaginal discharge. Nonspecific vaginitis was also correlated with a history of sexual activity, a history of previous trichomoniasis, current use of non-barrier contraceptive methods, and, particularly, use of an intrauterine device. G. vaginalis was isolated from 51.3 percent of the total population using a highly selective medium that detected the organism in lower concentration in vaginal discharge than did previously used media. Practical diagnostic criteria for standard clinical use are proposed. Application of such criteria should assist in clinical management of nonspecific vaginitis and in further study of the microbiologic and biochemical correlates and the pathogenesis of this mild but quite prevalent disease.
Background: Cross-sectional studies suggest an association between bacterial vaginosis (BV) and HIV-1 infection. However, an assessment of a temporal effect was not possible. Objectives: To determine the association of BV and other disturbances of vaginal flora with HIV seroconversion among pregnant and postnatal women in Malawi, Africa. Design: Longitudinal follow-up of pregnant and postpartum women. Methods: Women attending their first antenatal care visit were screened for HIV after counselling and obtaining informed consent. HIV-seronegative women were enrolled and followed during pregnancy and after delivery. These women were again tested for HIV at delivery and at 6-monthly visits postnatally. Clinical examinations and collection of laboratory specimens (for BV and sexually transmitted diseases) were conducted at screening and at the postnatal 6-monthly visits. The diagnosis of BV was based on clinical criteria. Associations of BV and other risk factors with HIV seroconversion, were examined using contingency tables and multiple logistic regression analyses on antenatal data, and Kaplan–Meier proportional hazards analyses on postnatal data. Results: Among 1196 HIV-seronegative women who were followed antenatally for a median of 3.4 months, 27 women seroconverted by time of delivery. Postnatally, 97 seroconversions occurred among 1169 seronegative women who were followed for a median of 2.5 years. Bacterial vaginosis was significantly associated with antenatal HIV seroconversion (adjusted odds ratio = 3.7) and postnatal HIV seroconversion (adjusted rate ratio = 2.3). There was a significant trend of increased risk of HIV seroconversion with increasing severity of vaginal disturbance among both antenatal and postnatal women. The approximate attributable risk of BV alone was 23% for antenatal HIV seroconversions and 14% for postnatal seroconversions. Conclusions: This prospective study suggests that progressively greater disturbances of vaginal flora, increase HIV acquisition during pregnancy and postnatally. The screening and treating of women with BV could restore normal flora and reduce their susceptibility to HIV.
While there has been a rapidly increasing research effort focused on understanding whether and how composition and richness of species and functional groups may determine ecosystem properties, much remains unknown about how these community attributes affect the dynamic properties of ecosystems. We conducted an experiment in 540 mini-ecosystems in glasshouse conditions, using an experimental design previously shown to be appropriate for testing for functional group richness and composition effects in ecosystems. Artificial communities representing 12 different above-ground community structures were assembled. These included treatments consisting of monoculture and two- and four-species mixtures from a pool of four plant species; each plant species represented a different functional group. Additional treatments included two herbivore species, either singly or in mixture, and with or without top predators. These experimental units were then either subjected to an experimentally imposed disturbance (drought) for 40 d or left undisturbed. Community composition and drought both had important effects on plant productivity and biomass, and on several below-ground chemical and biological properties, including those linked to the functioning of the decomposer subsystem. Many of these compositional effects were due to effects both of plant and of herbivore species. Plant functional group richness also exerted positive effects on plant biomass and productivity, but not on any of the below-ground properties. Above-ground composition also had important effects on the response of below-ground properties to drought and thus influenced ecosystem stability (resistance); effects of composition on drought resistance of above-ground plant response variables and soil chemical properties were weaker and less consistent. Despite the positive effects of plant functional group richness on some ecosystem properties, there was no effect of richness on the resistance of any of the ecosystem properties we considered. Although herbivores had detectable effects on the resistance of some ecosystem properties, there were no effects of the mixed herbivore species treatment on resistance relative to the single species herbivore treatments. Increasing above-ground food chain length from zero to three trophic levels did not have any consistent effect on the stability of ecosystem properties. There was no evidence of either above-ground composition or functional group richness affecting the recovery rate of ecosystem properties from drought and hence ecosystem resilience. Our data collectively point to the role of composition (identity of functional group), but not functional group richness, in determining the stability (resistance to disturbance) of ecosystem properties, and indicates that the nature of the above-ground community can be an important determinant of the consistency of delivery of ecosystem services.