Microbial ecosystems of traditional fermented meat products: The importance of indigenous starters.

Abstract

This paper reviews the diversity of microbiota, both in the environment and in traditional fermented European sausages. The environments of processing units were colonised at variable levels by resident spoilage and technological microbiota, with sporadic contamination by pathogenic microbiota. Several critical points were identified such as the machines, the tables and the knives - knowledge crucial for the improvement of cleaning and disinfecting practices. Traditionally fermented sausages generally did not present a sanitary risk. The great diversity of lactic acid bacteria and staphylococci was linked to manufacturing practices. Development of indigenous starters is very promising because it enables sausages to be produced with both high sanitary and sensory qualities. Our increasing knowledge of the genomes of technological bacteria will allow a better understanding of their physiology in sausages.

Full text

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Microbial ecosystems of traditional fermented meat products:
The importance of indigenous starters
R. Talon*, S. Leroy, I. Lebert
Institut National de la Recherche Agronomique (INRA), Centre de Clermont-Ferrand Theix, Unite ´ de Recherche Microbiologie,
63122 Saint-Gene `s Champanelle, France
Abstract
This paper reviews the diversity of microbiota, both in the environment and in traditional fermented European sausages. The envi-
ronments of processing units were colonised at variable levels by resident spoilage and technological microbiota, with sporadic contam-
ination by pathogenic microbiota. Several critical points were identified such as the machines, the tables and the knives – knowledge
crucial for the improvement of cleaning and disinfecting practices. Traditionally fermented sausages generally did not present a sanitary
risk. The great diversity of lactic acid bacteria and staphylococci was linked to manufacturing practices. Development of indigenous
starters is very promising because it enables sausages to be produced with both high sanitary and sensory qualities. Our increasing knowl-
edge of the genomes of technological bacteria will allow a better understanding of their physiology in sausages.
Keywords: Microbial ecosystem; Traditional fermented sausage; Indigenous starter; Lactic acid bacteria; Coagulase-negative cocci
1. Introduction
In Europe, naturally fermented sausages have a long tra-
dition originating from Mediterranean countries during
Roman times (Comi et al., 2005). Production then spread
to Germany, Hungary and others countries including the
United States, Argentina and Australia (Demeyer, 2004).
Europe is still currently the major producer and consumer
of dry fermented sausages (Talon, Leroy-Se ´trin, & Fadda,
2004).
There is a wide variety of dry fermented products on the
European market as a consequence of variations in the raw
materials, formulations and manufacturing processes,
which come from the habits and customs of the different
countries and regions. However, Northern products have
a pH below 5, while Mediterranean products have a pH
of 5.3–6.2 and are highly desiccated. In both categories,
industrial development has led to the use of starter cultures
to standardise and control sausage manufacturing. How-
ever, artisanal slightly fermented sausages form a group
of traditional Mediterranean products with a great regional
diversity, both between and within countries. These tradi-
tional sausages can be defined as a meat product made of
a mixture of meat (often pork), pork fat in variable ratio
and salt including eventually sugar, nitrate and/or nitrite
(Fontana, Cocconcelli, & Vignolo, 2005; Lebert et al.,
2007). The fermentation and ripening/drying do not always
constitute two separated steps and they can be carried out
in a natural dryer depending on local climatic conditions
(Corbie `re Morot-Bizot, Leroy, & Talon, 2006; Lebert
et al., 2007). Traditional dry sausages rely on natural con-
tamination by environmental microflora. This contamina-
tion occurs during slaughtering and increases during
manufacturing.
The objective of this paper is to review the diversity of
microbiota both in the environment and in traditional fer-
mented sausages. The diversity of the technological micro-
biota (lactic acid bacteria or LAB, and coagulase-negative

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cocci or CNC) is also highlighted. Finally, the importance
of developing indigenous starters and of increasing knowl-
edge on starters is underlined.
2. Microbiota in the environment of small-scale processing
units
Many authors support the belief that the microorgan-
isms present in traditional sausages are derived from the
raw materials or from the environment of manufacturing
(Mauriello, Casaburi, Blaiotta, & Villani, 2004; Rantsiou,
Urso et al., 2005). This microbiota is usually referred to
as ‘‘house flora’’ (Garcia-Varona, Santos, Jaime, & Rovira,
2000). If the microbiota isolated from traditional sausages
is well described (see paragraph below), the resident micro-
biota in the environment of the processing units is still
poorly known.
We have shown by studying a French small-scale pro-
cessing unit manufacturing sausages that all the process-
ing surfaces and the equipments were colonised by CNC
and yeasts/moulds (Chevallier et al., 2006; Corbie `re
Morot-Bizot et al., 2006). Their level and particularly
for CNC could reach up to 4.7 log cfu/cm2(cfu = colony
forming unit). Sporadic cases of contamination was
recorded for Staphylococcus aureus and Listeria monocyt-
ogenes. By extending our research to 10 traditional
French processing units (PUs) during the European pro-
jectTradisausage (QLK1-CT-2002-02240,
www2.clermont.inra.fr/tradisausage), we have shown that
regardless of the microorganisms, cold rooms and mixing
machines had the lowest levels of contamination with
median levels of 2.2 log cfu/100 cm2, while knives and
tables had the highest ones (from 2.1 to 4.4 log cfu/
100 cm2) (Table 1) (Lebert et al., 2007). CNC and
yeasts/moulds but also Pseudomonas colonised all the sur-
faces and equipments of these processing units (Table 1).
Considering the pathogenic bacteria, Salmonella and S.
aureus were not detected in the environment while L.
monocytogenes was enumerated in the table and the knife
of one processing unit (Lebert et al., 2007). In the Euro-
pean project Tradisausage, the residual microbiota was
also assessed in the environment of 43 traditional process-
ing units of Spain, Portugal, Italy, Greece and Slovakia
(Talon et al., 2007). All the PUs’ environments were col-
http://
onised at variable levels by spoilage and technological
microbiota with some PUs having too high contamina-
tion. Salmonella and L. monocytogenes were detected in
4.8% and 7.6% of the samples and S. aureus was enumer-
ated in 6.1%. Several critical points were identified such as
the machines for S. aureus and the tables and the knives
for L. monocytogenes; their knowledge is crucial for the
improvement of the control systems. The variability of
the residual contamination highlighted the different clean-
ing, disinfecting and manufacturing practices of the small-
scale processing units (Talon et al., 2007). In fact,
unclean, insufficiently or inadequately cleaned pieces of
equipment have often been identified as the source of
pathogens (Reij & Den Aantrekker, 2004). Many studies
investigated the pathogen flora of food processing envi-
ronments and food processing lines such as L. monocytog-
enes in pork and poultry processing plants and products
(Chasseignaux et al., 2002) and Salmonella species in pork
slaughter and cutting plants (Giovannacci et al., 2001).
3. Microbiota of products
Fermentation of traditional dry sausages relies on the
indigenous microbiota. We have shown that this microbi-
ota was enumerated in the batters manufactured in French
traditional processing units at average level of 4.0 log cfu/g
(Fig. 1) (Lebert et al., 2007). It was composed of useful
microorganisms (CNC, LAB, yeasts/moulds) for the fer-
mentation and flavour of sausages, but also spoilage micro-
biota (Pseudomonas, enterobacteria) and enterococci. This
indigenous microbiota could arise from the raw materials
or from the environment of manufacturing (microbiota
described in Table 1) as mentioned by several authors.
However, in this study, we found no evidence of cross-con-
tamination between environment and meat. We assumed
that the contamination of the batter was mainly due to
the microbiota of the raw materials and sometimes of the
casings. We have shown that lean meat and fat used to pre-
pare the batter were sometimes contaminated with high
levels of CNC, yeasts/moulds, coliforms and Pseudomonas
(Chevallier et al., 2006). Comi et al. (2005) also showed
that raw meats had total aerobic counts of between 4.3
and5.8 log cfu/g and casings
6.1 log cfu/g.
of between3.8 and
Table 1
Microbiota of the environments of 10 French processing units manufacturing traditional fermented sausages
TablesKnives Cold room Mincing machinesMixing machinesStuffing machines
Median Min MaxMedian Min Max MedianMinMax Median Min MaxMedian Min Max MedianMin Max
Y/M
LAB
CNC
ENC
ENB
PSE
4.0
4.0
4.4
2.2
3.2
4.3
<0.7
<1.7
<1.7
<0.7
<0.7
<0.7
6.8
7.1
6.9
3.1
6.4
7.1
3.7
3.3
4.0
2.6
2.7
4.2
2.7
1.7
6.7
5.6
5.3
5.0
6.0
7.3
1.1<0.7
<1.7
<1.7
<0.7
<0.7
<0.7
6.7
5.0
4.8
4.7
1.7
3.9
2.6
2.6
3.4
2.2
1.5 4.7
5.5
5.5
3.4
3.1
5.3
1.8<0.7
<1.7
<1.7
<0.7
<0.7
<0.7
5.4
5.8
5.3
4.0
2.1
3.5
2.9
2.2
2.7
1.7
1.7
2.7
<0.7
<1.7
<1.7
<0.7
<0.7
<0.7
6.7
5.4
5.7
3.9
6.1
7.1
<1.7
0.9
0.2
< 0.7
1.5
<1.7
1.7
<0.7
<0.7
<0.7
<1.7
2.3
<0.7
<0.7
1.5
<1.7
<0.7
<0.7
2.7
<0.7
2.2
Data expressed in log cfu/100 cm2. Y/M, yeasts and moulds; LAB, lactic acid bacteria; CNC, coagulase-negative cocci; ENC, enterococci; ENB,
enterobacteria; PSE, Pseudomonas.

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The type of microbiota that develops in traditional sau-
sages is related to the diversity in formulation, and to the
fermentation and ripening practices. These practises could
be very different in terms of temperature, duration and rel-
ative humidity (Lebert, Leroy, & Talon, 2007). In Europe,
fermentation can be carried out at high temperature (18–
24 ?C) between 1 and 2 days (Cocolin, Manzano, Cantoni,
& Comi, 2001; Comi et al., 2005; Mauriello et al., 2004) or
at low temperature (10–12 ?C) during 1 week (Lebert et al.,
2007; Mauriello et al., 2004). Similarly, temperatures of
drying/ripening ranged mainly between 10 and 14 ?C for
French (Lebert et al., 2007), Italian (Cocolin et al., 2001;
Cocolin, Manzano, Aggio, Cantoni, & Comi, 2001; Comi
et al., 2005; Coppola, Mauriello, Aponte, Moschetti, & Vil-
lani, 2000; Rantsiou, Drosinos et al., 2005) and Greek sau-
sages (Papamanoli, Tzanetakis, Litopoulou-Tzanetaki, &
Kotzekidou, 2003). The duration of this step varied from
4 to 12 weeks. The diversity in the relative humidity leads
to variable water content of traditional sausages at the
end of drying ranging from 0.83 to 0.93 in French, Spanish,
Portuguese and Italian sausages (Lebert, Leroy et al.,
2007).
Despite the different practises within the countries, or
the regions, the microbial populations showed similar evo-
lutions as those we have shown for French sausages
(Fig. 1). In traditional sausages, LAB constituted the major
microbiota at the end of the ripening stage (Fig. 1a). Even
if their initial levels varied their final levels were close to the
one of industrial products manufactured with starter cul-
tures. LAB usually increased the very first days of fermen-
tation and they remained constant during ripening at 7–
9 log cfu/g (Cocolin et al., 2001; Comi et al., 2005) or they
can increased during all the process as shown for French
sausages in Fig. 1a and reached similar final value. The ini-
tial population can be low, as observed in Salame Milano
in Italy (Rebecchi, Crivori, Sarra, & Cocconcelli, 1998)
and in a French sausage manufactured at low temperature
(Chevallier et al., 2006) but it was generally comprised
between 3.2 and 5.3 log cfu/g. LAB growth was often cor-
related with the decrease in pH in the first stage of matura-
tion (Cocolin et al., 2001; Cocolin et al., 2001).
CNC constituted the second microbiota at the end of
ripening with a population of 6–8 log cfu/g, population
generally inferior to that of the LAB and closed to the
one reached in industrial sausages (Fig. 1a). Their initial
level varied from 3.1 to 4.4 log cfu/g (Lebert et al., 2007).
CNC sometimes grew during the fermentation period to
106–108cfu/g or they can grow during ripening (Comi
et al., 2005) or during all the process (Fig. 1a).
Spoilage bacteria such as Pseudomonas and enterobacte-
ria had far different initial levels according to the type of
sausages. They ranged from 1.7 to 4.4 log cfu/g for entero-
bacteria and from 1.5 to 5.2 log cfu/g for Pseudomonas
(Lebert et al., 2007). In French sausages, they remained
constant during the fermentation and decreased during
the ripening (Fig. 1b). In Greek sausages, they were pro-
gressively eliminated regardless of their initial population
(Drosinos et al., 2005; Samelis, Metaxopoulos, Vlassi, &
Pappa, 1998). Other authors found that enterobacteria
and Pseudomonas increased during the fermentation (Comi
et al., 2005). Then enterobacteria remained constant until
the end while Pseudomonas remained constant or disap-
peared (Chevallier et al., 2006; Comi et al., 2005).
Yeasts and moulds were usually detected in all sausages
in the batter at levels varying from 2.0 to 4.5 log cfu/g
(Lebert et al., 2007). Some authors observed growth during
the fermentation period with levels not increasing above
5 log cfu/g (Fig. 1c), then a stability or decrease in the pop-
ulation (Comi et al., 2005; Drosinos et al., 2005). Yeasts
and moulds were not detected in Italian dry sausages Sal-
ame Milano at the end of ripening (Rebecchi et al., 1998).
Enteroccocci had an initial level between 2 and
4 log cfu/g (Fig. 1c). Enterococci usually grew during early
fermentation and remained constant at a level of 4–6 log
until the end of the whole process (Fig. 1c) (Comi et al.,
2005; Drosinos et al., 2005; Rebecchi et al., 1998). In few
1.5
2.5
3.5
4.5
5.5
6.5
7.5
8.5
ZMF
log(CFU/g)
1.5
2.5
3.5
4.5
5.5
6.5
7.5
8.5
ZMF
1.5
2.5
3.5
4.5
5.5
6.5
7.5
8.5
ZMF
Fig. 1. Evolution of the microbiota during the processing of 10 traditional French fermented sausages: batter (Z), after fermentation (M) and final product
(F). (a) (—j—) Coagulase-negative cocci; (--r--) lactic acid bacteria. (b) (—j—) Pseudomonas; (--r--) Enterobacteriaceae. (c) (—j—) Enterococcus;
(--r--), yeasts and moulds. Data were calculated from the average of the 10 processing units (log cfu/g). Vertical lines: standard deviation.

Page 4

cases their counts declined. Enterococci are poor acidifiers
and in traditional sausages of high pH they find good con-
ditions for survival and growth (Hugas, Garriga, & Ayme-
rich, 2003). There is still controversy over considering them
as Generally Recognised as Safe (GRAS) microorganisms
(Giraffa, 2002). However, studies point out that meat
enterococci, especially Enterococcus faecium have a much
lower pathogenicity potential than clinical strains and
some strains of E. faecium are already used as starter cul-
ture or probiotic (Hugas et al., 2003; Martı´n, Garriga,
Hugas, & Aymerich, 2005).
Considering the pathogenic bacteria, we have shown in
the European project Tradisausage, that Salmonella was
detected in 5.6% of 54 ripened sausages, S. aureus was enu-
merated in 7.4% of the sausages at a level in excess of the
limit of 2.7 log cfu/g (Commission Regulation (EC) No.
2073/2005, 2005) and L. monocytogenes was numerated
at a level in excess of the limit of 2.0 log cfu/g (Commission
Regulation (EC) No. 2073/2005, 2005) in only one sample.
In Salame Milano, S. aureus was observed at the beginning
of the production process, decreased during ripening until
it was undetectable at the end of the process (Rebecchi
et al., 1998). While, it was still enumerated in sausages pro-
duced in Italian artisanal plants from level ranging from 2
to 4 log cfu/g (Blaiotta et al., 2004). L. monocytogenes was
sometimes present in initial samples, but diminished or was
not detected by the end of fermentation in Greek sausages
(Drosinos et al., 2005; Samelis et al., 1998).
4. Diversity of technological microbiota
Lactic acid bacteria and Staphylococcus or Kocuria
belonging to the CNC group are considered as technolog-
ical microbiota because they are involved in the develop-
ment of hygienic and sensory qualities of the final
product. Lactic acid bacteria are involved mainly through
their acidification. Staphylococcus and Kocuria contribute
to the development of colour and flavour in fermented
meat products mainly by degrading free amino acids and
inhibiting the oxidation of unsaturated free fatty acids
(Talon & Leroy, 2006; Talon et al., 2004).
4.1. Lactic acid bacteria (LAB)
Phenotypical methods have been widely used to identify
LAB, however, methods relying on these methods are
ambiguous and time consuming. Molecular methods such
as species-specific PCR (Aymerich et al., 2006), PCR-dena-
turing gel electrophoresis (Rantsiou, Drosinos et al., 2005)
and real time PCR (Furet, Quenee, & Tailliez, 2004) have
been developed.
By using these molecular methods, it has been shown
that the LAB species the most commonly identified in tra-
ditional fermented sausages were Lactobacillus sakei, Lac-
tobacillus curvatus and Lactobacillus plantarum (Lebert,
Leroy et al., 2007). L. sakei is often the dominant one
and can represent more than 42% of the isolates (Comi
et al., 2005; Coppola et al., 2000; Greco, Mazette, De San-
tis, Corona, & Cosseddu, 2005; Papamanoli et al., 2003;
Urso, Comi, & Cocolin, 2006). Aymerich et al. (2006)
showed that L. sakei was identified in all of the Spanish
sausages and represented 89% in chorizo and 76% in a tra-
ditional Spanish sausage ‘‘fuet’’. In a French sausage, L.
sakei represented 100% of the isolates on the final products
although it was minor in the raw materials (Ammor et al.,
2005). L. curvatus is the second species identified; it is dom-
inant in some Greek or Italian sausages (Comi et al., 2005;
Rantsiou, Drosinos et al., 2005). L. plantarum is the third
one; it dominates the LAB flora in a Greek sausage (Dro-
sinos et al., 2005). Many other LAB are identified but rep-
resent a minor population (L. alimentarius, L. casei, L.
delbrueckii, L. farciminis, L. paraplantarum, L. pentosus
and L. sharpeae).
The diversity at strain level inside the dominant species
is important. The combination of results obtained with
plasmid profiling and randomly amplified polymorphic
DNA (RAPD)-PCR, allowed to distinguish 112 different
strains out of 185 isolates of L. sakei and 23 profiles for
53 isolates of L. curvatus (Aymerich et al., 2006). The
analysis by RAPD-PCR of 100 strains of L. curvatus iso-
lated from Greek, Hungarian and Italian naturally fer-
mented sausagesrevealed
obtained, while 168 strains of L. sakei from the same sam-
ples gave 19 major clusters (Rantsiou, Drosinos et al.,
2005). Urso et al. (2006) have also used RAPD to deter-
mine the diversity and the distribution of 353 strains of L.
sakei and 67 strains of L. curvatus during a natural fer-
mentation of three Italian sausages. Clusters containing
strains isolated from different plants but also clusters
formed by strains isolated from a specific fermentation
were observed.
thatnine profiles were
4.2. Coagulase-negative cocci (CNC)
The identification of staphylococci to the species level by
phenotypical methods has limitations and may have
resulted in misidentifications (Giammarinaro, Leroy, Cha-
cornac, Delmas, & Talon, 2005). To provide increasingly
reliable identifications, several molecular methods have
been developed, including PCR-based methods such as
PCR-DGGE (Cocolin et al., 2001), species-specific PCR
(Aymerich, Martı´n, Garriga, & Hugas, 2003; Morot-Bizot,
Talon, & Leroy-Se ´trin, 2003), multiplex PCR (Corbie `re
Morot-Bizot et al., 2006) and oligonucleotide array target-
ing sodA gene (Giammarinaro et al., 2005). This last
method developed in our laboratory identifies the 36 vali-
dated species and constitutes presently a powerful tool
for the identification of staphylococci (Giammarinaro
et al., 2005).
Staphylococcus xylosus is the most common species in
Greek, Italian and Spanish traditional products at the
end of ripening (Blaiotta et al., 2004; Cocolin et al., 2001;
Garcia-Varona et al., 2000; Iacumin, Comi, Cantoni, &
Cocolin, 2006a; Martı´n et al., 2006; Mauriello et al.,

Page 5

2004; Papamanoli et al., 2003; Rebecchi et al., 1998). It rep-
resents from 17% to 100% of the isolates according to the
type of sausages. Even if it was not the dominant species
in the batter, S. xylosus became rapidly dominant in Sal-
ame Milano (Rebecchi et al., 1998). S. saprophyticus is
the second dominant species identified. It is dominant in
some Greek and Italian sausages (Drosinos et al., 2005;
Mauriello et al., 2004; Papamanoli et al., 2003). In the Ital-
ian products, Staphylococcus equorum and Staphylococcus
succinus were also isolated (Mauriello et al., 2004). In three
French small producers, we have shown that the staphylo-
coccal microflora of the product and the environment was
dominated by S. equorum (49%, 56% and 71% of the iso-
lates), the second species was S. succinus for two producers
(33% and 12%) while it was S. xylosus (19%) and S. sap-
rophyticus (19%) for the third producer (Corbie `re Morot-
Bizot et al., 2006; Leroy, Chevallier, Lebert, Chacornac,
& Talon, 2006). Many other minor species were identified
in the different traditional sausages (S. aureus, S. auricu-
laris, S. carnosus, S. cohnii, S. epidermidis, S. haemolyticus,
S. hominis, S. intermedius, S. lentus, S. pasteuri, S. vitulus
and S. warneri).
The diversity of S. xylosus strains have been character-
ised by different typing methods. The combination of plas-
mid profiling and RAPD-PCR allowed the discrimination
of 169 different profiles out of 194 S. xylosus isolates
(Martı´n et al., 2006). By genotypic clustering based on
comparison of RAPD-PCR profiles (Rossi, Tofalo, Torri-
ani, & Suzzi, 2001) distinguished 22 clusters at 70% of
homology. A total of 249 strains of S. xylosus isolated from
three plants manufacturing sausages were genetically char-
acterised using RAPD, Rep-PCR and Sau-PCR techniques
(Iacumin, Comi, Cantoni, & Cocolin, 2006b). The results
obtained allowed the discrimination of the strains coming
from different plants.
5. Importance of the indigenous starter
The manufacture of traditional sausages is more an art
depending on the skill and experience of the meat manufac-
turer rather than a process fully based on scientific and
technological means. This is because meat fermentation is
a complex biological phenomenon accelerated by the desir-
able action of certain microbes in the presence of a great
variety of competing or synergistically acting species. These
traditional practises lead to a great variability in the quality
of the products. Few sporadic studies conducted on tradi-
tional products have shown that hygienic shortcomings
can lead up to 25% of product loss with high economic
consequences and may undermine consumer confidence
for traditional products.
The development of starters from the natural fermenta-
tive communities of traditional fermented products may
avoid or limit this variability in the production. Moreover,
the development of indigenous starters may diversify the
market that will be able to produce many typical regional
fermented sausages with specific flavours.
The development of indigenous starters improving
hygienic quality and keeping the sensorial one is a real
challenge. This challenge was considered in the European
project Tradisausage. We have developed a starter com-
posed of a mixture of the indigenous bacteria isolated from
a traditional sausages manufactured by a French producer,
it consisted of L. sakei, S. equorum and S. succinus (Lebert,
Leroy, Lebecque, Chacornac, & Talon, 2006; Talon, 2006).
This starter was added to the batter and positive results
were observed. Its addition resulted in sausages with higher
sanitary qualities compared to the control: reduction of the
level of L. monocytogenes (1.1 log cfu/g versus 2.7 for the
control) and enterococci (4.2 log cfu/g versus 6.2 for the
control), reduction of 1.7-fold the level of biogenic amines
(233.8 mg/kg DM versus 404.4 mg/kg DM), reduction of
lipid oxidation (0.61 mg MDA/kg versus 0.71 mg MDA/
kg) and total cholesterol oxides (0.95 mg/kg versus
4.75 mg/kg). Finally this starter did not modify the flavour
of the sausages as evaluated by a panel of jury but
improved slightly the texture. Similar experiences have
been carried out in different countries in the EU project
Tradisausage and have lead to close conclusion.
6. Towards genomics and post-genomics to characterise
starters
Up to recently, classical methods based on biochemical
and physiological traits have been used to select the most
performing strains for technological use. They were mainly
based on acidification and antimicrobial properties for lac-
tic acid bacteria and colour and flavour developments for
staphylococci (Talon & Leroy, 2006). During the last dec-
ade, genetic studies have provided basic knowledge on tar-
geted metabolic activities. Now global approaches with the
sequencing of whole genome of bacteria are developed and
will allow a better understanding of their physiology in
meat ecosystem (Champomier-Verge `s et al., 2007; Talon
& Leroy, 2006).
Most of the genetic information concerned L. sakei 23K,
initially isolated from a fermented dry sausage (Champo-
mier-Verge `s, Chaillou, Cornet, & Zagorec, 2002). Its chro-
mosome map was obtained by the use of 47 genetic loci
(Dudez et al., 2002). In parallel, a proteomic approach
was developed to study the genes involved in adaptation
to its environment (Marceau, Mera, Zagorec, & Champo-
mier-Verge `s, 2001). In 2005, the complete genome sequence
of L. sakei 23K was published (Chaillou et al., 2005). From
the known involvement of L. sakei as sausage starter, the
genome analysis confirmed that the main role of L. sakei
is to ferment sugars into lactic acid, and that it lacks main
aroma production pathways. L. sakei 23K also lacks genes
responsible for biogenic amine production. A battery of
functions was identified which might explain adaptation
or resistance of this species to stressing environmental con-
ditions used during sausage manufacturing (presence of
curing agents, spices, smoke, low temperature) (Chaillou
et al., 2005).

Page 6

The physical and genetic map of S. carnosus TM300 was
established and the size of the chromosome was estimated
to be 2590 kb (Wagner, Doskar, & Go ¨tz, 1998). Eighteen
genetic markers were located within them genes related to
sugar metabolism and to nitrate and nitrite reduction
which are important traits for meat fermentation and col-
our development. Other genes of S. carnosus involved in
technological properties such as the branched-chain amino
acid aminotransferaseproducing
(Madsen et al., 2002), the superoxide dismutase and the
catalase contributing to the control of lipid oxidation (Bar-
rie `re, Bru ¨ckner, & Talon, 2001) have been also identified,
sequenced and characterised. The annotation of the com-
pleted sequence of the chromosome of S. carnosus
TM300 is under way (Rosenstein, Nerz, Resch, & Go ¨tz,
2005). The first comparison of the gene products revealed
that about 20% were specific of this species. Their identifi-
cation will reveal the originality of this species.
We have established the physical and genetic map of S.
xylosus C2a by locating 47 restriction fragments and 33
genetic markers (Dordet-Frisoni, Talon, & Leroy, 2007).
Twenty-three previously identified loci mainly concerned
carbohydrate utilization and carbon catabolite repression
(Bassias & Bru ¨ckner, 1998; Bru ¨ckner, Wagner, & Go ¨tz,
1993; Egeter & Bru ¨ckner, 1996; Fiegler, Bassias, Jankovic,
& Bru ¨ckner, 1999) and antioxidant capacities (Barrie `re
et al., 2001; Barrie `re, Leroy-Se ´trin, & Talon, 2001) and
10 were newly identified (Dordet-Frisoni et al., 2007).
The S. xylosus C2a chromosome contains six rrn operons,
this number varies among strains from 5 to 6 as already
observed in other staphylococcal species. The sequencing
of the complete genome of S. xylosus in collaboration with
the genoscope(http://www.genoscope.cns.fr)
achieved. In parallel we have developed a proteomic
approach to study the physiology of S. xylosus C2a strain
in biofilm to allow a better understanding of its survival in
food processing plants (Planchon, 2006).
flavour compounds
is just
7. Conclusion
This review outlined the diversity in the microbiota of
naturally fermented sausages but also the strong impact
of the process on its growth. Traditional fermented sau-
sages generally did not present a sanitary risk. The great
diversity in the LAB and staphylococci species and also
within the species was certainly linked to the formulation,
fermentation and ripening practices. The most promising
strains for starter cultures are those which are isolated from
the indigenous microbiota of traditional products. These
strains are well adapted to the meat environment and to
the specific manufacturing process and thus are capable
of dominating the microbiota of products. Above all,
development of indigenous starters leads to sausages with
high sanitary quality and typical sensorial quality. The
exploitation of the data of the genomes of species of tech-
nological interest will offer new research opportunities by
revealing some properties that could explain their adapta-
tion to the meat environment. Global approaches based
on proteomics and transcriptomics are in progress and will
allow a better understanding of their interactions with the
ecosystem and the meat substrate.
Acknowledgement
Parts of the data of this review come from EU Program
QLK1-CT2002-02240.
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