558

Asia Pac J Clin Nutr 2006;15 (4):558-562

Original Article

Intestinal colonisation, microbiota and future

probiotics?
Seppo Salminen PhD,1 Yoshimi Benno DVM PhD2 and Willem de Vos PhD3
1

Functional Foods Forum, University of Turku, 20014 Turku, Finland

Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 3510198, Japan
3
Laboratory of Microbiology, Wageningen University, 6700 EV Wageningen, The Netherlands
2

The human intestine is colonized by a large number of microorganisms, collectively termed microbiota, which
support a variety of physiological functions. As the major part of the microbiota has not yet been cultured,
molecular methods are required to determine microbial composition and the impact of specific dietary
components including probiotics. Probiotics are viable microbial food supplements, which have a beneficial
impact on human health. Health-promoting properties have been demonstrated for specific probiotic products.
The most significant demonstrations for probiotic efficacy include prevention and treatment of antibiotic
associated diarrhea, rotavirus diarrhea and allergy prevention. Lactobacillus rhamnosus GG (=ATCC 53103)
and Bifidobacterium lactis Bb12 are the among the best-characterized and most studied probiotic strains with
demonstrated impact on human health. New complex targets for probiotics include irritable bowel syndrome
and Helicobacter pylori infection. For future probiotics the most important target is a demonstrated clinical
benefit supported by knowledge on the mechanistic actions in the microbiota of the target population. Molecular
and genomics-based knowledge of the composition and functions of the microbiota, as well as deviations from
the balanced microbiota, will advance the selection of new and specific probiotics. Potential combinations of
specific probiotics may prove to be the next step to reduce the risk on intestinal diseases and reconstruct specific
microbial deviations.

Key Words: Intestinal microbiota, diversity, genomics, probiotic, clinical studies, Lactobacillus GG

Introduction
The development of intestinal microbiota in the human
gastrointestinal tract depends on the original inoculum at
birth, living environment and the early feeding practises.
Microbial colonization of the human infant begins at birth
and continues during the early feeding and weaning periods, and results in relatively stable microbial communities in adults.1 The mature intestinal microbiota forms a
physical and immunological barrier between the host and
the environment. The barrier function of microbiota
appears to support the intestinal health and protect the host
by a healthy microecology in the gut.1
The early and matured intestinal microbiota are unique
to each human being. From birth on, during breast feeding
and weaning the microbiota diversifies and becomes stable
with complex metabolic functions and it facilitates a barrier
protecting the host against microbial and other invasions
from the environment.1-4 There is a great need to further
characterize the normal and aberrant microbiota in humans.
New molecular methods have been developed for this work
and more details are revealed at present. The importance
of resident bacteria for the host's physiology include metabolic activities, trophic effects on the intestinal epithelium
and protection of the host against the overgrowth of
potential pathogens in the gastro-intestinal tract.2,3 Above
these effects, specific strains of the gut microbiota have

been found to elicit anti-inflammatory responses in the

intestinal epithelial cells thus strengthening the intestinal
homeostasis.
Probiotics are defined as viable microbial food supplements, which, when taken in the right doses, beneficially
influence human health.5,6 These definitions require that
safety and efficacy have to be scientifically demonstrated
for each strain. Probiotics often act upon modifying the
process of intestinal microbiota development or the composition and activity of fully developed microbiota. Probiotics can also act by direct contact with the mucosal cells
facilitating cross talk between the host and microbes.
Current probiotics have several demonstrated beneficial
effects on human health. These include maintenance of
healthy intestinal microbiota development and counteracting deviations observed in gut inflammatory diseases or
preceding them.

Correspondence address: Dr Seppo Salminen, Fucntional Foods

Forum, University of Turku, 20014 Turku, Finland
Tel: +358-400-601394; Fax: +358-2-3336884
Email: [email protected]
Accepted 30th August 2006

S Salminen, Y Benno and W de Vos

Microbiota
development

Selection of specific
probiotic strains or
strain combination

Microbiota
maintenance

Strain assessment

Identification of
aberrancies

In vivo assessment of
combination and its
properties

559

Target identification for

specific probiotic
combinations

Demonstration of
efficacy in clinical
intervention studies
Health benefit
documentation and
claims

Figure 1. Steps for selecting new target-specific probiotics and probiotic combinations.

Aberrant intestinal microbiota can we define and

influence it?
Several deviations in the intestinal microbiota render us
vulnerable to intestinal inflammatory diseases. Various
deviations that predispose us to gastrointestinal problems
have been characterised. As the methods to characterize
the microbiota improve, more targets for intervention will
be described to form a basis for probiotic action. Specific
Bifidobacterium species in the healthy infant gut are most
predominant and metabolically active and also specific
Clostridium spp. are often present.1 Changes in their
quantitative and qualitative composition appear to serve
as useful indicators of deviations from the balanced
microbiota, denoted here as abberrancies. However, other
specific bacterial genera and species remain to be defined
among the developing intestinal microbiota that impact on
both early and later infant health. It has been reported
that specific deviations in intestinal microbiota (such as,
for example, decreased numbers and an atypical composition of bifidobacteria and aberrancies in the Clostridium
content and composition) may predispose infants to
allergic disease.7 In a similar manner, deviations from the
normal microbiota are associated with frequent antibiotic
side-effects and microbiota changes. Aberrant microbiota
during childhood may comprise a factor predisposing to
both inflammatory gut diseases and diarrhoea.7,8 The

differences in faecal bacterial population between irritable

bowel syndrome (IBS), one of the most common gastrointestinal disorders, and control subjects have been reported in several studies. These observations suggest that
Clostridium spp., some Bifidobacterium spp. and the instability of the active predominant faecal bacterial population, may be involved in IBS.8-10 Such deviations again,
may form the target for probiotics in the future. In
conclusion, advanced understanding of the quantitative
and qualitative aspects of microbiota composition is expected to enhance our knowledge basis for gut-associated
diseases and their clinical impact.
Developing future probiotic combinations
It has been suggested that the intestinal microbiota consists of mainly symbiotic microorganisms.11 These dedicate part of their genomes to processes that are beneficial to the host. Identification of such processes along
with aberrancies in intestinal microbiota will help in the
identification and development of new probiotics. The
combination of specific probiotics to target new microbiota aberrancies offers the next challenge to the research
and development, as single strains have not always been
effective for particular target populations. Negative outcomes for probiotic interventions have been reported for
irritable bowel syndrome, Helicobacter pylori eradi-

560

Intestinal colonisation, microbiota and future probiotics?

cation, travellers diarrhoea and Crohns disease patients.

Probiotic combinations may have additive and synergistic
effects, but at times different strains and species may also
counteract each others beneficial effects. These effects
have been described in vitro and also in this issue.12
Thus, new in vitro tests and innovative approaches are required to facilitate the design of probiotic combinations,
as is illustrated here following the outline of Fig. 1.
The properties of probiotic combinations have been
studied in detail with two different mixtures of strains
and reported also in this issue.12 Two of the strains in the
combinations have been assessed as effective in different
types of gastroenteritis.13,14 These have combined the
well-characterized strains Lactobacillus rhamnosus GG
(=ATCC 53103) and Bifidobacterium lactis Bb12, as well
as Bifidobacterium breve BB99. Additional strains in the
combinations assessed include Lactobacillus rhamnosus
LC 705 and Propionibacterium freudenreichii subsp.
shermanii, which have provided health benefits in human
studies on toxin binding and metabolic activity enhancement.15 Several meta-analysis studies attest to the efficacy
of L. rhamnosuss GG in clinical trials and efficacy data is
available on B. lactis either alone or in combination with
other probiotics. These are some times additive in their in
vitro properties and for instance adhesion can be increased in probiotic combinations. The presence of L.
rhamnosus s GG significantly enhances the adhesion of B.
lactis Bb-12 and P. freudenreichii strain.16 The combinations have demonstrated efficacy in the treatment of
irritable bowel syndrome17 (Kajander et al., 2006) and
Helicobacter pylori infection.18 In meta-analysis studies
also Lactobacillus plantarum has been reported to have a
trend in decreasing irritable bowel syndrome symptoms. 19
Although clinical intervention trials provide important
proof of efficacy for different probiotics and combinations in various disease states, advancing molecular and
genomics-based research will provide data on identification of key processes related to microbiota development and maintenance. These include nutrient-microbe
interactions and more detailed chatacterization of the
transfer of microbial communities from parent to the
infant. Incorporating microbial meta- and post-genomics
approaches together with host gene expression data from
the exposed mucosal sites or aberrant microbiota activity
will advance the understanding the roles of probiotics,
microbiota and microbe-microbe and host-microbe interactions. The availability of probiotic genomes will be
important for the prediction of the intestinal functions and
potential to be used as single strains or in strain combinations. It will also provide information about the mechanisms of action of probiotics, facilitating the development or selection of a new generation of specific
probiotic combinations with enhanced and more sitespecific and target disorder-specific properties. Such data
will reveal new rational improvement of probiotic strains
for long-term use. Comparative genomics in combination
with expression analysis will allow the assessment of
interaction between probiotic, symbiotic, pathogenic
microorganisms, providing valuable insight in the features of these different lifestyles. Ultimately, this would
increase our understanding of the functional properties of

probiotics and their safety as well as the evolutionary

relation among them.
Conclusion
The intestinal microbiota in healthy humans is a
metabolic organ which provides a defence system against
harmful environmental exposures. Deviations in composition can be related to multiple disease states within
the intestine but also beyond it. Similarly, components of
the human intestinal microbiota or organisms entering the
intestine may have both harmful and beneficial effects on
human health. This is illustrated with a specific combination of well-established probiotic strains which in this
issue of the journal have been demonstrated to have
additive and synergistic in vitro properties, have safe
history of use and have verified clinical benefits for
humans. The future target is to increase the genomic
information on both probiotic combinations and microbiota activities to improve the understanding of specific
intestinal diseases. Then the goal is to apply the knowledge of intestinal microbiota composition and aberrancies on selecting the right probiotic combinations for
defined target populations to maintain healthy intestinal
microbiota and to improve human health and well-being.

References
1. Guarner F, Malagelada JR. Gut flora in health and disease.
Lancet 2003; 381: 512-519.
2. Benno Y, Mitsuoka T. Development of intestinal microflora in humans and animals. Bifidobateria Microflora
1986; 5: 13-25.
3. Grnlund MM, Arvilommi H, Kero P, Lehtonen OP,
Isolauri E. Importance of intestinal colonisation in the
maduration of humoral immunity in early infancy: a
prospective follow up study of healthy infants aged 0-6
months. Arch Dis Child 2000; 83: 186-192.
4. Kirjavainen PV, Apostolou E, Arvola T, Salminen SJ,
Gibson GR, Isolauri E. Characterizing the composition of
intestinal microflora as a prospective treatment target in
infant allegic diseases. FEMS Immunol Med Microbiol
2001; 32: 1-7.
5. Salminen S, Bouley C, Bouton-Ruault MC, Cummings JH,
Franck A, et al. Functional food science and gastrointestinal physiology and function. Br J Nutr 1998; 80:
S147S171.
6. WHO 2002.Guidelines for the evaluation of probiotics in
food. http://www.who.int/foodsafety/ fs_management/ en/
probiotic_guidelines.pdf.
7. Kalliomaki M, Kirjavainen P, Eerola E, Kero P, Salminen
S, Isolauri E. Distinct patterns of neonatal gut microflora
in infants in whom atopy was and was not developing. J
Allergy Clin Immunol 2001; 107:129-34.
8. Malinen E, Rinttila T, Kajander K, Matto J, Kassinen A,
Krogius L, Saarela M, Korpela R, Palva A. Analysis of the
fecal microbiota of irritable bowel syndrome patients and
healthy controls with real-time PCR. Am J Gastroenterol.
2005;100:373-82.
9. Maukonen J, Satokari R, Matto J, Soderlund H, MattilaSandholm T, Saarela M. Prevalence and temporal stability
of selected clostridial groups in irritable bowel syndrome in
relation to predominant faecal bacteria. J Med Microbiol.
2006;55: 625-33.

S Salminen, Y Benno and W de Vos

10. Matto J, Maunuksela L, Kajander K, Palva A, Korpela R,

Kassinen A, Saarela M. Composition and temporal stability
of gastrointestinal microbiota in irritable bowel syndrome-a longitudinal study in IBS and control subjects. FEMS
Immunol Med Microbiol 2005; 43: 213-22.
11. Bckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon
JI. Host-bacterial mutualism in the human intestine.
Science 2005; 307: 1915-1920.
12. Collado MC, Gueimonde M, Hernandez M, Sanz Y,
Salminen S. Adhesion of selected Bifidobacterium strains
to human intestinal mucus and its role in enteropathogen
exclusion. J Food Prot 2005; 68 (12): 26722678.
13. Szajewska H, Ruszczynski M, Radzikowski A. Probiotics in
the prevention of antibiotic-associated diarrhea in children:
A meta-analysis of randomized controlled trials. J Pediatr.
2006; 149: 367-372.
14. McFarland LV. Meta-analysis of probiotics for the
prevention of antibiotic associated diarrhea and the treatment of Clostridium difficile disease. Am J Gastroenterol.
2006; 101: 812-22.
15. El-Nezami HS, Polychronaki NN, Ma J, Zhu H, Ling W,
Salminen EK, Juvonen RO, Salminen SJ, Poussa T,
Mykkanen HM. Probiotic supplementation reduces a
biomarker for increased risk of liver cancer in young men
from Southern China. Am J Clin Nutr. 2006; 83:1199-203.

561

16. Ouwehand AC, Isolauri E, Kirjavainen PV, Tolkko S,

Salminen SJ. The mucus binding of Bifidobacterium lactis
Bb12 is enhanced in the presence of Lactobacillus GG and
Lact. delbrueckii subsp. bulgaricus. Lett Appl Microbiol
2000;30:10-13.
17. Kajander K, Hatakka K, Poussa T, Farkkila M, Korpela R.
A probiotic mixture alleviates symptoms in irritable bowel
syndrome patients: a controlled 6-month intervention.
Aliment Pharmacol Ther 2005; 22: 387-94.
18. Myllyluoma E, Veijola L, Ahlroos T, Tynkkynen S,
Kankuri E, Vapaatalo H, Rautelin H, Korpela R. Probiotic
supplementation improves tolerance to Helicobacter pylori
eradication therapy - a placebo-controlled, double-blind
randomized pilot study. Aliment Pharmacol Ther 2005;
21: 1263-72.
19. Floch MH. Use of diet and probiotic therapy in the irritable
bowel syndrome: analysis of the literature. J Clin
Gastroenterol 2005; 39 (Suppl): S243-6.

562

Intestinal colonisation, microbiota and future probiotics?

Original Article

Intestinal colonisation, microbiota and future

probiotics?
Seppo Salminen PhD,1 Yoshimi Benno DVM PhD2 and Willem de Vos PhD3
1

Functional Foods Forum, University of Turku, 20014 Turku, Finland

Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 3510198, Japan
3
Laboratory of Microbiology, Wageningen University, 6700 EV Wageningen, The Netherlands
2

Lactobacil
lus
rhamnosus
GG
(=ATCC
53103)
and
Bifidobacterium
lactis
Bb12

:Lactobacillus GG