2007), and a lot of work in the coming years can be expected
to support the different hypotheses. Eukaryotic viruses are
also abundant in this habitat (Monier et al. 2008), and
metagenomic approaches thus now include also phages
(Williamson et al. 2008).
8.5.5 Digestive Tract and Microbial
Communities
The questions that arise regarding the digestive tract relate
to pathogens, to competition and gas production, and to the
effect of food on the comparison between populations and
between age groups.
Microbial ecology of the human gut has been studied
extensively especially regarding some diseases, especially
gastric ulcers and Crohn’s disease.
Foods sometimes contain large amounts of
microorganisms, especially fermented or stale foods. In
addition, birth and contact with the mother and the outside
world are important bacterial inocula to colonize the digestive tract. Molecular inventories of bacteria in the stomach
have demonstrated the presence of 128 phylotypes, belonging mainly to Proteobacteria, Firmicutes, Actinobacteria,
Bacteroidetes, and Fusobacteria (Bik et al. 2006). Most of
these bacteria do not persist in inhospitable habitats such as
the stomach with a pH of 3. However, Helicobacter pylori
has the ability, based on the presence of urease to convert
urea present in the stomach to CO 2 and ammonium, which
will then neutralize the acid pH of the stomach. This capability has the consequence that this bacterium is present in
80 % of human stomachs and causing in many of them ulcers
and tumors. Warren and Marshall have also won the Nobel
Prize for Medicine in 2005 for their demonstration of the
role of Helicobacter pylori in this disease (Forbes et al.
1994) and the ensuing possibility of treating ulcers with
antibiotics or with bismuth. In fact, the bacteria is transmitted within the family, probably swallowed by the child from
the mother’s saliva, and the bacteria is then implanted in the
gastric mucosa. This bacterium mutates quickly so that typing it allows to distinguish human population, based on
samples taken from patients with ulcers, which allowed
Wirth and collaborators (2004) to show by analysis of
samples taken from human populations that Ladakh Muslims
and Buddhists had very different Helicobacter pylori
populations. In fact, this pathogen to commensal ratio behaves
as a very sensitive marker of human populations.
The normal human gut has a much larger and more
diverse microbial community, including enterobacteria,
Bifidobacterium, and Bacteroidetes. The composition of
the community varies along the digestive tract; it also
fluctuates throughout human life (Hayashi et al. 2003), in
particular as a function of the diet (Hayashi et al. 2002) and
of course according to the physiological state of the host.
Many pathogens are also known and discussed in Chap. 11.
If the intestinal microbial community is roughly comparable from one individual to another within a human population, methanogens on the contrary are only present in about
half of the individuals, which means that half the human
population produces methane, while the other half
produces CO 2 .
Microorganisms in the gut play several important roles in
the absorption of nutrients, energy metabolism, and defense
against microbial pathogens (Braun and Wei 2007). There
are several inflammatory bowel diseases (IBD), the best
known being Crohn’s disease and ulcerative colitis. The
etiology of Crohn’s disease is unknown. It results in irritation and inflammation of all or part of the gastrointestinal
tract, which leads to digestive difficulties. Several pathogens
have been tentatively associated to it such as Mycobacterium
spp. or Fusobacterium or an imbalance in the composition of
the intestinal community with a decrease in the proportion of
Firmicutes and Bacteroidetes (Frank et al. 2007), but no
consensus could be reached. However, antibiotic treatment
resulting in lower counts in some members of the
communities of the intestine was correlated with a decrease
in symptoms of colitis (Nomura et al. 2005). It is now
recognized that the normal gut community acts as a barrier
against pathogens, preventing them to establish themselves,
to multiply, and cause various diseases.
Other animals have intestinal flora that are very different
from those of man. Ruminants in particular consume large
amounts of cellulose, a polymer that mammals cannot
metabolize in the absence of cellulase. However, some cellulolytic bacteria can grow in the digestive tract, either in the
rumen or in the single mammalian stomach; these bacteria
are only in the cecum and the glucose produced can only be
adsorbed through coprophagia, a practice found in some
animals such as horses, rabbits, mice, rats, and insects. In
the rumen, cellulolytic bacteria are found such as
Fibrobacter succinogenes, Ruminococcus albus, and
Ruminococcus flavefaciens (Mosoni et al. 2007). These two
genera have contrasting physiological characteristics regarding the production of methane. If several foods did not affect
the microbial balance, the addition of live yeast has allowed
to change it in a favorable direction (increase in the proportion of Ruminococci), which had the effect of reducing the
amount of methane produced. The synthesis of amino acids
(Torrallardona et al. 1996), vitamins (Coburn et al. 1989),
and dinitrogen fixation (Bergersen and Hipsley 1970;
Potrikus and Breznak 1977) or the synthesis of a sleepinducing factor (Brown et al. 1988) have all been proposed
as related to intestinal bacteria.
Another aspect that will continue to expand in the coming
years is mycotoxins humans and animals consume in their
normal diet and their effects on health, starting with the
8 Biodiversity and Microbial Ecosystems Functioning
283
to support the different hypotheses. Eukaryotic viruses are
also abundant in this habitat (Monier et al. 2008), and
metagenomic approaches thus now include also phages
(Williamson et al. 2008).
8.5.5 Digestive Tract and Microbial
Communities
The questions that arise regarding the digestive tract relate
to pathogens, to competition and gas production, and to the
effect of food on the comparison between populations and
between age groups.
Microbial ecology of the human gut has been studied
extensively especially regarding some diseases, especially
gastric ulcers and Crohn’s disease.
Foods sometimes contain large amounts of
microorganisms, especially fermented or stale foods. In
addition, birth and contact with the mother and the outside
world are important bacterial inocula to colonize the digestive tract. Molecular inventories of bacteria in the stomach
have demonstrated the presence of 128 phylotypes, belonging mainly to Proteobacteria, Firmicutes, Actinobacteria,
Bacteroidetes, and Fusobacteria (Bik et al. 2006). Most of
these bacteria do not persist in inhospitable habitats such as
the stomach with a pH of 3. However, Helicobacter pylori
has the ability, based on the presence of urease to convert
urea present in the stomach to CO 2 and ammonium, which
will then neutralize the acid pH of the stomach. This capability has the consequence that this bacterium is present in
80 % of human stomachs and causing in many of them ulcers
and tumors. Warren and Marshall have also won the Nobel
Prize for Medicine in 2005 for their demonstration of the
role of Helicobacter pylori in this disease (Forbes et al.
1994) and the ensuing possibility of treating ulcers with
antibiotics or with bismuth. In fact, the bacteria is transmitted within the family, probably swallowed by the child from
the mother’s saliva, and the bacteria is then implanted in the
gastric mucosa. This bacterium mutates quickly so that typing it allows to distinguish human population, based on
samples taken from patients with ulcers, which allowed
Wirth and collaborators (2004) to show by analysis of
samples taken from human populations that Ladakh Muslims
and Buddhists had very different Helicobacter pylori
populations. In fact, this pathogen to commensal ratio behaves
as a very sensitive marker of human populations.
The normal human gut has a much larger and more
diverse microbial community, including enterobacteria,
Bifidobacterium, and Bacteroidetes. The composition of
the community varies along the digestive tract; it also
fluctuates throughout human life (Hayashi et al. 2003), in
particular as a function of the diet (Hayashi et al. 2002) and
of course according to the physiological state of the host.
Many pathogens are also known and discussed in Chap. 11.
If the intestinal microbial community is roughly comparable from one individual to another within a human population, methanogens on the contrary are only present in about
half of the individuals, which means that half the human
population produces methane, while the other half
produces CO 2 .
Microorganisms in the gut play several important roles in
the absorption of nutrients, energy metabolism, and defense
against microbial pathogens (Braun and Wei 2007). There
are several inflammatory bowel diseases (IBD), the best
known being Crohn’s disease and ulcerative colitis. The
etiology of Crohn’s disease is unknown. It results in irritation and inflammation of all or part of the gastrointestinal
tract, which leads to digestive difficulties. Several pathogens
have been tentatively associated to it such as Mycobacterium
spp. or Fusobacterium or an imbalance in the composition of
the intestinal community with a decrease in the proportion of
Firmicutes and Bacteroidetes (Frank et al. 2007), but no
consensus could be reached. However, antibiotic treatment
resulting in lower counts in some members of the
communities of the intestine was correlated with a decrease
in symptoms of colitis (Nomura et al. 2005). It is now
recognized that the normal gut community acts as a barrier
against pathogens, preventing them to establish themselves,
to multiply, and cause various diseases.
Other animals have intestinal flora that are very different
from those of man. Ruminants in particular consume large
amounts of cellulose, a polymer that mammals cannot
metabolize in the absence of cellulase. However, some cellulolytic bacteria can grow in the digestive tract, either in the
rumen or in the single mammalian stomach; these bacteria
are only in the cecum and the glucose produced can only be
adsorbed through coprophagia, a practice found in some
animals such as horses, rabbits, mice, rats, and insects. In
the rumen, cellulolytic bacteria are found such as
Fibrobacter succinogenes, Ruminococcus albus, and
Ruminococcus flavefaciens (Mosoni et al. 2007). These two
genera have contrasting physiological characteristics regarding the production of methane. If several foods did not affect
the microbial balance, the addition of live yeast has allowed
to change it in a favorable direction (increase in the proportion of Ruminococci), which had the effect of reducing the
amount of methane produced. The synthesis of amino acids
(Torrallardona et al. 1996), vitamins (Coburn et al. 1989),
and dinitrogen fixation (Bergersen and Hipsley 1970;
Potrikus and Breznak 1977) or the synthesis of a sleepinducing factor (Brown et al. 1988) have all been proposed
as related to intestinal bacteria.
Another aspect that will continue to expand in the coming
years is mycotoxins humans and animals consume in their
normal diet and their effects on health, starting with the
8 Biodiversity and Microbial Ecosystems Functioning
283