carcinogenic aflatoxin produced by the wheat-colonizing
Aspergillus flavus, the psychotropic ergotamine produced by
the rye ergot pathogen Claviceps purpurea, and the
immunotoxic patulin produced by several apple-colonizing
molds, such as Aspergillus and Penicillium. The list of such
toxins (ochratoxin, citrinin, fumonisins, trichothecenes,
zearalenone, beauvericin, enniatins, butenolide, equisetin,
fusarins) is thus likely to expand in the coming years along
with studies on their effects on human health (Juan-Garcı ´a
et al. 2013).
It is likely that work on nutrition will be increased in the
coming years to identify risk factors for various diseases. We
can already see the work on the link between nutrition,
intestinal metabolites, colorectal cancer, and microbial
communities (O’Keefe et al. 2007) or between microflora
and irritable bowel syndrome (Lee and Pimentel 2006). We
should also see work on other aspects such as the link
between microbial communities and cardiovascular
diseases, immune diseases, and neurological diseases.
8.5.6 Skin and Other Body Parts
The digestive tract is the part of the body with the highest
density of microbial cells, as compared to the skin and
mucous membranes such as the urogenital or the nasal cavity
that also host microbial communities both pathogenic and
nonpathogenic. A study by pyrosequencing targeting the 16S
rRNA gene has permitted to identify on the hands’ skin over
150 phylotypes per individual out of a total of 4,742
phylotypes in the sample with strong variations between
individuals and between the two hands and as explanatory
“factors of diversity, gender, laterality, and time since last
hand washing” (Fierer et al. 2008). In the case of superficial
and deeper skin of the elbow, one study showed the presence
of bacteria belonging to six divisions, with a dominance of
Proteobacteria and a structure similar to that of mouse skin
(Grice et al. 2008). Another study on the skin of the arms
instead showed the presence of Actinobacteria, Firmicutes,
and Proteobacteria as dominant taxa (Gao et al. 2007).
Another area studied in humans for its bad smell is the
armpit where long-chain fatty acids secreted by the skin
are converted into smelly volatile compounds. One study
showed the presence of four major bacterial groups
(staphylococci, aerobic coryneform, micrococci, and
propionibacteria) and yeasts of the genus Malassezia with
a correlation between odor intensity and presence of aerobic
coryneform (Taylor et al. 2003).
The healthy vagina has been studied in comparison with
that of patients infected with HIV or by bacterial vaginosis
by pyrosequencing of 16S rRNA. This study showed a
greater bacterial diversity in patients with bacterial vaginosis, which was not the case of HIV-infected women.
Healthy women had a predominance of Lactobacillus spp.
(96 %) with taxa such as Prevotella, Megasphaera,
Gardnerella, Coriobacterineae, Lachnospira, Sneathia,
Propionibacterineae, Citrobacter, and Anaerococcus present below 1 %. The most surprising is the existence of a
greater diversity in women with vaginitis and HIV (Spear
et al. 2008).
Milk and colostrum have also been studied, showing the
presence of dominant bacteria such as Staphylococcus
epidermidis and Enterococcus faecalis, followed by Streptococcus mitis, Propionibacterium acnes, and Staphylococcus lugdunensis without pathogenic bacteria (Martin et al.
2007; Jimenez et al. 2008). Similar work on cow’s milk was
also conducted.
8.5.7 Depollution
Anaerobic digesters are attractive biotechnological tools to
reduce pollution caused by organic waste. To successfully
carry out such processes, the biological anaerobic ecosystem
must be fully characterized. The microorganisms involved in
this process are generally divided into four trophic groups.
The first three steps (hydrolysis, acidogenesis, and
acetogenesis) are performed by Bacteria, while the last
step (methanogenesis) is performed by Archaea. Acidogenic
and methanogenic groups have nutritional needs, physiological pH optima, and growth requirements that are completely
different. Digesters combine conventional acidogenic bacteria and archaeal methanogens in a single reactor imposing
uniform conditions for both groups. To optimize the process,
it makes sense to separate the two steps in two reactors.
Digesters have been developed where two-phase acidification and methanogenesis take place in two reactors
connected in series. Monitoring of bacterial communities
by SSCP showed that bacterial communities are different
between the two reactors. During the implementation process, the bacterial communities were significantly altered,
and a significant reduction in bacterial diversity was
observed in both reactors (Khelifi et al. 2009). It seems that
both reactors are two different ecosystems with one population being common to both reactors. The challenge is to
maintain control of these communities when these digesters
are used to treat other types of pollutants such as polycyclic
aromatic hydrocarbons (Bernal-Martinez et al. 2007). A
metagenomics approach has demonstrated the presence in
an anaerobic digester of bacteria belonging to an abundant
taxon unknown so far, named WWE3 (Waste Water of Evry
3) (Guermazi et al. 2008).
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P. Normand et al.
Aspergillus flavus, the psychotropic ergotamine produced by
the rye ergot pathogen Claviceps purpurea, and the
immunotoxic patulin produced by several apple-colonizing
molds, such as Aspergillus and Penicillium. The list of such
toxins (ochratoxin, citrinin, fumonisins, trichothecenes,
zearalenone, beauvericin, enniatins, butenolide, equisetin,
fusarins) is thus likely to expand in the coming years along
with studies on their effects on human health (Juan-Garcı ´a
et al. 2013).
It is likely that work on nutrition will be increased in the
coming years to identify risk factors for various diseases. We
can already see the work on the link between nutrition,
intestinal metabolites, colorectal cancer, and microbial
communities (O’Keefe et al. 2007) or between microflora
and irritable bowel syndrome (Lee and Pimentel 2006). We
should also see work on other aspects such as the link
between microbial communities and cardiovascular
diseases, immune diseases, and neurological diseases.
8.5.6 Skin and Other Body Parts
The digestive tract is the part of the body with the highest
density of microbial cells, as compared to the skin and
mucous membranes such as the urogenital or the nasal cavity
that also host microbial communities both pathogenic and
nonpathogenic. A study by pyrosequencing targeting the 16S
rRNA gene has permitted to identify on the hands’ skin over
150 phylotypes per individual out of a total of 4,742
phylotypes in the sample with strong variations between
individuals and between the two hands and as explanatory
“factors of diversity, gender, laterality, and time since last
hand washing” (Fierer et al. 2008). In the case of superficial
and deeper skin of the elbow, one study showed the presence
of bacteria belonging to six divisions, with a dominance of
Proteobacteria and a structure similar to that of mouse skin
(Grice et al. 2008). Another study on the skin of the arms
instead showed the presence of Actinobacteria, Firmicutes,
and Proteobacteria as dominant taxa (Gao et al. 2007).
Another area studied in humans for its bad smell is the
armpit where long-chain fatty acids secreted by the skin
are converted into smelly volatile compounds. One study
showed the presence of four major bacterial groups
(staphylococci, aerobic coryneform, micrococci, and
propionibacteria) and yeasts of the genus Malassezia with
a correlation between odor intensity and presence of aerobic
coryneform (Taylor et al. 2003).
The healthy vagina has been studied in comparison with
that of patients infected with HIV or by bacterial vaginosis
by pyrosequencing of 16S rRNA. This study showed a
greater bacterial diversity in patients with bacterial vaginosis, which was not the case of HIV-infected women.
Healthy women had a predominance of Lactobacillus spp.
(96 %) with taxa such as Prevotella, Megasphaera,
Gardnerella, Coriobacterineae, Lachnospira, Sneathia,
Propionibacterineae, Citrobacter, and Anaerococcus present below 1 %. The most surprising is the existence of a
greater diversity in women with vaginitis and HIV (Spear
et al. 2008).
Milk and colostrum have also been studied, showing the
presence of dominant bacteria such as Staphylococcus
epidermidis and Enterococcus faecalis, followed by Streptococcus mitis, Propionibacterium acnes, and Staphylococcus lugdunensis without pathogenic bacteria (Martin et al.
2007; Jimenez et al. 2008). Similar work on cow’s milk was
also conducted.
8.5.7 Depollution
Anaerobic digesters are attractive biotechnological tools to
reduce pollution caused by organic waste. To successfully
carry out such processes, the biological anaerobic ecosystem
must be fully characterized. The microorganisms involved in
this process are generally divided into four trophic groups.
The first three steps (hydrolysis, acidogenesis, and
acetogenesis) are performed by Bacteria, while the last
step (methanogenesis) is performed by Archaea. Acidogenic
and methanogenic groups have nutritional needs, physiological pH optima, and growth requirements that are completely
different. Digesters combine conventional acidogenic bacteria and archaeal methanogens in a single reactor imposing
uniform conditions for both groups. To optimize the process,
it makes sense to separate the two steps in two reactors.
Digesters have been developed where two-phase acidification and methanogenesis take place in two reactors
connected in series. Monitoring of bacterial communities
by SSCP showed that bacterial communities are different
between the two reactors. During the implementation process, the bacterial communities were significantly altered,
and a significant reduction in bacterial diversity was
observed in both reactors (Khelifi et al. 2009). It seems that
both reactors are two different ecosystems with one population being common to both reactors. The challenge is to
maintain control of these communities when these digesters
are used to treat other types of pollutants such as polycyclic
aromatic hydrocarbons (Bernal-Martinez et al. 2007). A
metagenomics approach has demonstrated the presence in
an anaerobic digester of bacteria belonging to an abundant
taxon unknown so far, named WWE3 (Waste Water of Evry
3) (Guermazi et al. 2008).
284
P. Normand et al.