International Journal of Food Microbiology 153 (2012) 166–170

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International Journal of Food Microbiology

journal homepage: www.elsevier.com/locate/ijfoodmicro

Safety assessment of Lactobacillus plantarum JDM1 based on the complete genome

Zhuo-Yang Zhang a, Chang Liu a, Yong-Zhang Zhu a, Yan-Xia Wei a, Fei Tian a,
Guo-Ping Zhao b, Xiao-Kui Guo a,⁎
a
Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
b
Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China

a r t i c l e i n f o a b s t r a c t

Article history: We performed a comprehensive safety assessment of a probiotic based on the whole genome sequence and
Received 9 June 2011 corresponding phenotypes. This was performed on Lactobacillus plantarum JDM1, a widely used commercial
Received in revised form 3 November 2011 probiotic strain in China. The minimal inhibitory concentrations (MICs) of sixteen antibiotics and the biogen-
Accepted 6 November 2011
ic amine production of JDM1 were tested to supplement a traditional oral toxicity test. In total, fifty-one
Available online 12 November 2011
antibiotic resistance-associated genes, one hundred twenty-six virulence-associated genes, and twenty-
Keywords:
three adverse metabolism-associated genes were found in JDM1. However, there were no toxin or hemolysin
Safety encoding genes, and safety-associated genes were rarely transferable. This approach can be generalized to
Probiotics provide a deep safety investigation of novel probiotic strains and greatly reveal the potential danger determi-
Genome nants and their molecular mechanisms. However, this kind of analysis reveals the theoretical maximum risk
Antibiotic resistance level as not all genes are efficient depending on environmental conditions.
Gene transfer © 2011 Elsevier B.V. All rights reserved.

1. Introduction proved by traditional safety assessment approaches, such as adher-

It is well known that probiotics, as live microorganisms, are valu-
able to human and animal health. When administered in adequate
amounts, they can produce beneficial effects on the host (FAO/
WHO, 2001). Probiotics are generally applied in food fermentation,
industrial lactic acid production and medical care. The main probiotic
organisms utilized are from the genera Lactobacillus and Bifidobacter-
ium, most of which are lactic acid bacteria (LAB) (Donohue, 2006).
Although the use of LAB has a long, safe history and has acquired
the ‘Generally Regarded As Safe’ (GRAS) status, the safety of other
selected strains remains obscure. As probiotics are live organisms,
their safety assessment should be separated from other food additives
and drug compounds. With the exception of traditional oral toxico-
logic tests (Bhardwaj et al., 2010), multidisciplinary approaches are
necessary for the systematical safety evaluation of probiotic strains.
These approaches should address antibiotic resistance (Bernardeau
et al., 2008; Kiwaki and Sato, 2009), adverse metabolic activity,
immune response (Bhardwaj et al., 2009), and gene transfer. Howev-
er, most of the safety assessments of probiotics focus on only one or
some of these areas. A deep and complete evaluation is needed for
each novel probiotic strain and for those probiotic strains that have
been in use over a long period of time.
As a government-approved and widely used Chinese commercial
probiotic strain, the safety of Lactobacillus plantarum JDM1 had been
ence, cytotoxicity and various clinical trials (Commission, 2010). We
sequenced the complete genome of JDM1 to reassure its safety and
for further functional study (Zhang et al., 2009).
2. Materials and methods
2.1. Reference genome
L. plantarum WCFS1 was isolated from human saliva, whose com-
plete genome had been sequenced and was used as the reference
genome (Kleerebezem et al., 2003). All of the sequences for the genes
and proteins of L. plantarum WCFS1 (AL935263) were downloaded
from NCBI FTP (ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
Lactobacillus_plantarum). The genome sequence of L. plantarum JDM1
(CP001617) was previously determined (Zhang et al., 2009).
2.2. Measurement of biogenic amine production
The production of the biogenic amines tyramine, histamine, pu-
trescine, cadaverine, spermine, and tryptamine was screened by a
type of decarboxylase synthetic plate containing amino acid precur-
sors, such that the color of the plates changed if the amine was pre-
sent (Liu et al., 2009a).
2.3. Measurement of antibiotic resistance phenotypes

⁎ Corresponding author. Tel./fax: + 86 21 64453285. The resistance to sixteen antibiotics was analyzed by disc diffusion
E-mail address: microbiology@sjtu.edu.cn (X.-K. Guo). and E-test methods as previously described (Liu et al., 2009b).

0168-1605/$ – see front matter © 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.ijfoodmicro.2011.11.003
 Z.-Y. Zhang et al. / International Journal of Food Microbiology 153 (2012) 166–170 167

According to the results of disc diffusion, the minimum inhibitory
concentration (MIC) of each of the following antimicrobial agents
to JDM1 was measured by E-test (AB Biodisk, Solna, Sweden):
amoxicillin (AC, 0.016–256 mg/L), amikacin (AK, 0.016–256 mg/
L), ampicillin (AM, 0.016–256 mg/L), bacitracin (BA, 0.016–
256 mg/L), cephalothin (CE, 0.016–256 mg/L), ciprofloxacin (CI,
0.002–32 mg/L), chloramphenicol (CL, 0.016–256 mg/L), cefotaxime
(CT, 0.016–256 mg/L), erythromycin (EM, 0.016–256 mg/L), gentamy-
cin (GM, 0.016–256 mg/L), imipenem (IP, 0.002–32 mg/L), rifampicin
(RI, 0.016–256 mg/L), streptomycin (SM, 0.016–256 mg/L), tetracycline
(TC, 0.016–256 mg/L), trimethoprim/sulphamethoxazole (TS, 0.002–
32 mg/L), and vancomycin (VA, 0.016–256 mg/L). MICs were measured
after anaerobic incubation at 37 °C for 24 h with MRS. Each experiment
was performed in triplicate. The breakpoints were calculated as previous-
ly described (Ammor et al., 2007; Liu et al., 2009b; von Wright, 2005).
2.4. Identification of safety-associated genes
3. Results and discussion
3.1. General genome comparison of L. plantarum JDM1 and WCFS1
The complete genome of L. plantarum JDM1 contains a single, cir-
cular chromosome of 3,197,750 bp coding 2948 proteins (Fig. 1).
Compared with WCFS1, an isolated strain from saliva, the genome
of JDM1 was smaller and encoded fewer genes (Table 1). By genomic
comparison, there were 416 unique genes in WCFS1 and 307 unique
genes in JDM1. Most of these genes were prophage associated genes
and hypothetical protein-coding genes. Many exopolysaccharide
biosynthesis protein and phosphotransferase system (PTS) coding
genes were absent. JDM1 grew in rich, nutritional medium long-
term, so that the genome might degenerate gradually.
However, JDM1 had many cell surface protein-coding genes
uniquely, such as JDM1_0663, JDM1_1104, and JDM1_2368. These
genes might be associated with the adhesion ability, which was
important to probiotics.

All annotated genes of JDM1 were compared with an antibiotic re-

sistance genes database (ARDB, http://ardb.cbcb.umd.edu/) (Liu and
Pop, 2009), virulence factors database (VFDB, http://www.mgc.ac.
cn/VFs/main.htm) (Chen et al., 2005), and genes related with adverse
metabolites by BLASTN. The genes with more than 70% coverage
and 30% identity were kept as the results. The sequences of the
adverse metabolite genes, including histidine decarboxylase, beta-
galactosidase/beta-glucuronidase, arylsulphatase, FMN-dependent
NADH-azoreductase, D-lactate dehydrogenase, nitroreductase, tyro-
sine decarboxylase, and aromatic-L-amino-acid decarboxylase were
downloaded from GenBank.
3.2. Antibiotic resistance and associated genes
The MICs of sixteen antimicrobial agents of L. plantarum JDM1
were screened (Table 2). JDM1 was resistant to six antibiotics, GM,
AK, BA, CI, SM, and VA. The MICs of them were larger than the maxi-
mal concentrations, 256 mg/L and 32 mg/L, separately. The MIC of GM
was 48 mg/L. JDM1 was sensitive to the other antimicrobials tested,
with MICs b 2 mg/L. The antimicrobial resistance profile of JDM1 was
consistent with that of L. plantarum (Ammor et al., 2007; Liu et al.,
2009b).

Fig. 1. Genome-atlas view of the L. plantarum JDM1 chromosome. The six circles (outer to inner) show the following. Circles 1 and 2 are color coded according to the COG classi-
fication of the genes present on the forward and reverse strands. Circle 3 (purple) shows the GC percentage of the CDSs on the genome. Circle 4 (light blue and green) represents the
GC skew (step by 500 bp); the origin and terminus are clearly marked by the change in GC skew. Circle 5 shows the tRNA genes (blue) and the rRNA regions (red). Circle 6 shows
the IS elements (dark green) and prophage fragments (orange).
168 Z.-Y. Zhang et al. / International Journal of Food Microbiology 153 (2012) 166–170

Table 1 genes, it has become the consensus that bacteria used as probiotics
General feature comparison between JDM1 and WCFS1. for humans or additives for animal feed should not carry transferable
Feature JDM1 WCFS1 antimicrobial resistance genes (von Wright, 2005). Because most
LABs were intrinsically resistant to many antimicrobial agents, no
Size (bp) 3,197,759 3,308,274
Plasmid 2 3 particular safety concern was associated with this intrinsic type of
G + C content (%) 44.67% 44.50% resistance. However, the intrinsic antibiotic resistance genes on the
Protein-coding genes chromosome should not be flanked by transposable elements, such
With assigned function 2273 2120
as integrase and transposase.
Conserved and hypothetical 684 932
Total 2951 3052
Transfer RNA 62 62
3.3. Virulence factors
Ribosomal RNA
23S 5 5
16S 5 5 One hundred twenty-six genes related to virulence were identi-
5S 6 6 fied in JDM1. Most of these were defensive, or non-classical, virulence
Insertion sequences 11 18 factors, such as thirty-five transporter protein genes, seventeen of
which were genes associated with iron, magnesium, and manganese
uptake. There were nineteen genes associated with carbohydrate syn-
Fifty-one antibiotic resistance genes were identified in the
thesis and modification, seventeen genes involved in protein synthe-
genome using BLAST searches with the ARDB. Most of these genes in-
sis and modification, fifteen transcriptional regulator genes, eight
cluded drug export proteins (25), an undecaprenyl pyrophosphate
genes involved in DNA metabolism, six stress protein genes, three
phosphatase, and genes associated with resistance to VA (13), quater-
antibiotic resistance genes, and two adhesion protein genes. Twelve
nary ammonium (3), TS (3), CL (2), TC (1), SM (1), fusidic acid (1),
genes were duplicates of previously identified antibiotic resistance-
quinolone (1), and penicillin (1) (bracketed numbers reflect the inci-
associated genes.
dence of each drug-associated gene) (Table S.1).
Virulence factors mainly included bacterial toxins, cell surface
Compared with other molecular methods employed to search
proteins that mediate bacterial attachment, cell surface carbohy-
for antibiotic resistance genes, such as PCR and DNA array (Burton
drates and proteins that protect a bacterium, and hydrolytic enzymes
et al., 2006; Hummel et al., 2007), determination of the entire
that may contribute to the pathogenicity of the bacterium (Chen
genome sequence could provide more direct information. However,
et al., 2005). Though many genes correlated with virulence factors
it takes longer and is more expensive.
were found in JDM1, they did not represent as really harmful. No in-
L. plantarum was thought to be intrinsically resistant to vancomy-
vasion or toxin proteins, which are actually offensive virulence fac-
cin due to its peptidoglycan precursors; they are composed of D-
tors, were identified. Some genes, such as the fibrinogen-binding
lactate rather than D-alanine at the C-terminus. The VA resistance
protein and bile salt hydrolase encoding genes, are important to the
genes in JDM1 encode a D-ala-D-ala dipeptidase (VanX), four essen-
characteristics of probiotics and should not be considered offensive
tial dehydrogenases (VanH), a D-alanine:D-lactate ligase (VanD),
virulence factors.
six response regulators (VanR), and one histidine kinase (VanS).
JDM1_0636 (vanX) was an essential precursor of the cell wall and
highly specific for hydrolyzing D-ala-D-ala dipeptides. vanX was rare- 3.4. Putatively adverse metabolites
ly transferable, without any flanking transfer elements.
Generally, the genotype and phenotype did not completely coin- The metabolic activity of bacteria in food matrix or culture media
cide. For example, chloramphenicol O-acetyltransferase (JDM1_ is easily characterized and reflected in traditional taxonomic
1505) is the determinant gene of CL resistance (Murray and Shaw, approaches based on metabolic profiles. However, the metabolic
1997), but JDM1 was sensitive to CL. The penicillin and TC resistance activity in various gastrointestinal tracts within one person's body
genes of JDM1 (JDM1_1841 and JDM1_0084) encode targets of drugs, is relatively hard to characterize. Several enzymes involved in the
but not real antibiotic resistance genes. formation of putatively adverse metabolites or side effects include
With increasing apprehension that food and/or communal bacte- beta-glucosidase (GS), arylsulphatase (AS), beta-glucuronidase
ria may act as potential reservoirs for antimicrobial resistance (GN), nitroreductase (NR), azoreductase (AR), D-lactate dehydroge-
nase (DLD), amino acid decarboxylase (AD), conjugated bile salt
hydrolase (CBSH), and bile salt-7-hydroxylase (BHX) (McBain and
Table 2 Macfarlane, 1997). The hydrolases, GS, and various glycosidases
Antibiotics resistance of JDM1 by E-test.
influence the bioavailability of a variety of toxicants and phase 2 me-
Antibiotics Short E-test tabolites, which are more readily absorbed upon removal of the glu-
Form curonic acid or sugar moeity (John et al., 1999). CBSH possesses bile
UI mg/L MIC mg/L
salt deconjugase activity and may lead to deconjugation in the small
Cefodizime CT 0.016–256 0.047
Amoxicillin AC 0.016–256 0.064 intestine. AR and NR activity may be associated with undesirable tox-
Ampicillin AM 0.016–256 0.064 icological effects, especially with respect to carcinogen activation.
Trimethoprim/ DLD is involved in D-lactate production, and consumption of Lactoba-
Sulphamethoxazole TS 0.002–32 0.19 cillus spp. tablets has also been associated with D-lactic acidosis (Ku
Rifampicin RI 0.016–256 0.25
et al., 2006). Eleven GS genes, four CBSH genes, four NR genes, two
Cephalothin CE 0.016–256 0.5
Imipenem IP 0.002–32 0.6 AR genes, and two DLD genes were identified in JDM1 (Table 3)
Erythromycin EM 0.016–256 0.75 (details in Table S.2). Being both flexible and adaptive, L. plantarum
Chloramphenicol CL 0.016–256 1 has encountered many different environmental niches and thus has
Tetracycline TC 0.016–256 1.5
a relatively large number of metabolic enzymes. There is no evidence
Gentamicin GM 0.016–256 48
Amikacin AK 0.016–256 >256 for any adverse reactions to JDM1. If these genes were not overex-
Bacitracin BA 0.016–256 >256 pressed, it is hard to determine whether they may contribute to
Ciprofloxacin CI 0.002–32 >32 adverse reactions.
Streptomycin SM 0.016–256 >256 Besides these genes, a bile acid 7-alpha-dehydratase (lp_0874),
Vancomycin VA 0.016–256 >256
which could function as a BHX, is found in WCFS1 but is absent in
 Z.-Y. Zhang et al. / International Journal of Food Microbiology 153 (2012) 166–170
Table 3
Putative adverse metabolic genes.
Product name Gene_ID Product name
Beta-glucosidase JDM1_0370 Conjugated bile salt hydrolase
(11) JDM1_0756 (4)
JDM1_1173
JDM1_2229
JDM1_2230 Nitroreductase (4)
JDM1_2411
JDM1_2504
JDM1_2802
JDM1_2814 Azoreductase (2)
JDM1_2815
JDM1_2899 D-Lactate dehydrogenase
(2)
The numbers in bracket stand for the gene copies.
JDM1. This suggests that JDM1 might have a less substantial effect on
the host secondary bile acid biosynthesis than WCFS1.
3.5. Biogenic amine production
Biogenic amines have been implicated in food poisoning incidents,
usually from the consumption of fermented foods. These amines are
mainly produced by microbial decarboxylation of amino acids, partic-
ularly tyrosine, histidine, and tryptophan to tyramine, histamine and
tryptamine respectively.
The ability of JDM1 to produce biogenic amine products had been
tested qualitatively by decarboxylase plates containing six precursor
amino acids. JDM1 could not produce enough tyramine, histamine,
putrescine, cadaverine, spermine or tryptamine to change the color
of the plates. There was only one amino acid decarboxylase present,
a glutamate decarboxylase. Therefore, no toxic biogenic amines
could be produced, which was confirmed by phenotype.
There is only one amino acid decarboxylase in JDM1, glutamate
decarboxylase (JDM1_2723). It evidenced JDM1 can't produce bio-
genic amine based on genome.
3.6. Genome stability of JDM1
Genome stability is affected by many transition elements, such as
plasmids, insertion sequence (IS), and prophages. A comparison with
the reference strain, WCFS1, showed the relative stability of JDM1.
JDM1 contained only two cryptic plasmids that do not encode any es-
sential proteins, and three prophage elements. All three of the pro-
phages are incomplete sequences and have lost their lysogenicity.
The prophage sequences and locations within JDM1 and WCFS1
were highly variable. Eleven repeated sequences, designated ISP2,
were found in the chromosome of JDM1. These sequences were iden-
tified as a class of transposase-encoding regions, representing mobile
genetic elements in WCFS1.
Three genes associated with virulence and antibiotics mentioned
above, JDM1_0448, JDM1_1119 and JDM1_1629, are flanked by IS
elements, indicating a relatively greater possibility for transfer.
JDM1_0448 encodes a lysyl-tRNA synthetase, and the other two
genes both encode transport proteins. The other safety-associated
genes nearby the IS elements or prophage sequences were mostly
transporters or transcription regulators. Therefore, the potential safe-
ty genes, such as those encoding enzymes associated with antibiotic
resistance or adverse metabolites, had fewer chances to transfer to
other organisms.
Mutations, which may cause genetic changes in multiple regions
of the genome, play only a minor role in the development of resis-
tance and virulence. Horizontal transfer enhances evolution in micro-
bial communities by transferring genes across species and genus
borders through conjugative plasmids, transposons, integrons,
169
insertional elements, and lytic and temperate bacteriophages. As ele-
gantly demonstrated in Escherichia coli, reducing the number of IS el-
Gene_ID ements renders bacterial genomes more stable (Posfai et al., 2006).
JDM1 had fewer IS elements by number and category compared
JDM1_0076
JDM1_2822 with WCFS1, suggesting higher genome stability.
JDM1_2068 The transfer of antibiotic resistance genes from probiotics is con-
JDM1_2695 sistently one of the most important safety problems. The phenotype
JDM1_0072
of antibiotic resistance can be easily tested. The positive phenotypes
JDM1_0692
JDM1_2080 attract more attention, but the negative phenotypes should not be ig-
JDM1_2377 nored. According to the genome information, the antibiotic resistance
JDM1_0792 genes or other safety-associated genes flanked by transferable ele-
JDM1_0083 ments should be noticed as a potential risk of a probiotic strain. The
JDM1_0728
suspected known antibiotic resistance genes can be identified by
JDM1_1719
PCR or DNA microarray, but the complete genome information has
enabled us to identify the potential adverse genes and evaluate the
possibility for gene transfer.
3.7. Conclusions
There has been an increased focus on the bio-safety of food and
medicine. Probiotics actively evolve to adapt to nutritionally rich en-
vironments. Traditional achievements for assessing the safety of
probiotics seem to be limited. Additional evidence regarding the func-
tional mechanism and potential side effects of probiotics can be ex-
plored by complete genome sequencing and data mining. Although
all the predictions are made in the basis of annotation, it reveals the
maximum potential risk.
For comparative study, we identified the safety-associated genes
of WCFS1 in the same way. Sixty-six antibiotic resistance genes and
162 virulence factor genes were found, which were a little more
than JDM1 and still without actually offensive virulence factors and
antibiotic resistance determinant. The similar results were found in
ST-III, another L. plantarum isolates from kimchi (Wang et al., 2011).
It confirmed the GRAS status given for L. plantarum. However, wheth-
er other strains are with genomic safety still need further study. With
more and more complete genomes published, this method will be
improved.
A safety-associated gene database specifically for probiotics is
needed. With the development of high-throughput sequencing tech-
nology and the decreased cost, complete genome sequencing would
be an indispensable way to evaluate the safety and control the quality
of probiotic strains.
Acknowledgements
This work was supported by grants from the National Natural Sci-
ence Foundation of China (30770111, 30900051, and 30970125), the
National Key Program for Infectious Diseases of China (2008ZX10004,
and 2009ZX10004), the Program of Shanghai Subject Chief Scientist
(09XD1402700), the Program of Shanghai Research and Develop-
ment (10JC1408200), and the Program of Shanghhai Jiao Tong Uni-
versity (YZ 1017).
Appendix A. Supplementary data
Supplementary data to this article can be found online at doi:10.
1016/j.ijfoodmicro.2011.11.003.
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