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Bioprocess Biosyst Eng (2016) 39:1527–1537

DOI 10.1007/s00449-016-1628-3

ORIGINAL PAPER

A newly isolated and identified vitamin B12 producing strain:


Sinorhizobium meliloti 320
Huina Dong1,2 • Sha Li1 • Huan Fang1,2 • Miaomiao Xia1,2 • Ping Zheng1,2 •

Dawei Zhang1,2 • Jibin Sun1,2

Received: 30 March 2016 / Accepted: 16 May 2016 / Published online: 9 June 2016
Ó Springer-Verlag Berlin Heidelberg 2016

Abstract Vitamin B12 (Cobalamin, VB12) has several Introduction


physiological functions and is widely used in pharmaceu-
tical and food industries. A new unicellular species was Vitamin B12 (Cobalamin, VB12) is one of the largest
extracted from China farmland, and the strain could pro- known non-polymeric natural compounds, as well as one of
duce VB12 which was identified by HPLC and HPLC–MS/ the most studied compounds [1]. It is involved in wide
MS. 16S rDNA analysis reveals this strain belongs to the range of biochemical processes, such as DNA synthesis
species Sinorhizobium meliloti and we named it S. meliloti and regulation, fatty acid synthesis, amino acid metabolism
320. Its whole genome information indicates that this strain as well as energy production [2]. At present, VB12 has been
has a complete VB12 synthetic pathway, which paves the widely used for the treatment of pernicious anemia and
way for further metabolic engineering studies. The optimal peripheral neuritis [3], and it was found that VB12 was the
carbon and nitrogen sources are sucrose and corn steep essential cofactor for methionine synthase and (R)-
liquor (CSL) plus peptone. The optimal combination of methylmalonyl-CoA mutase in animals and humans [4].
sucrose and CSL was obtained by response surface VB12 is composed of a central cobalt atom that is
methodology as they are the most suitable carbon and coordinated by a tetrapyrrole framework termed the corrin
nitrogen sources, respectively. This strain could produce ring and by two axial ligands. In the biologically active
140 ± 4.2 mg L-1 vitamin B12 after incubating for 7 days forms of cobalamin, adenosylcobalamin (coenzyme B12,
in the optimal medium. Ado-Cbl) and methylcobalamin (Me-Cbl), the upper ligand
consists of either 5-deoxyadenosine or a methyl group,
Keywords Vitamin B12  Sinorhizobium meliloti  respectively (Fig. 1), and the lower ligand, usually 5,6-
Cobalamin  Whole genome sequence  Response surface dimethylbenzimidazole (DMBI), is attached to the corrin
methodology ring via the nucleotide loop. The final products occurring in
nature from vitamin B12-biosynthesis are Ado-Cbl and Me-
Cbl, while vitamin B12 is by definition cyanocobalamin
(CN-Cbl), which represents the form mainly manufactured
H. Dong, S. Li are contributed equally to this work.
by industry [5].
The production of VB12 has received great attention due
& Ping Zheng to the increasing global needs. The microbial synthesis of
zheng_p@tib.cas.cn VB12 takes place via two different pathways, an oxygen-
& Dawei Zhang dependent pathway and an oxygen-independent pathway,
zhang_dw@tib.cas.cn each of which involves more than 20 enzymatic steps. The
1 oxygen-dependent pathway exists in Rhodobacter sphaer-
Tianjin Institute of Industrial Biotechnology, Chinese
Academy of Sciences, Tianjin 300308, China oides and Pseudomonas denitrificans, while the oxygen-
2 independent pathway has been discovered in Bacillus
Key Laboratory of Systems Microbial Biotechnology,
Chinese Academy of Sciences, Tianjin 300308, People’s megaterium, Salmonella enterica, and Propionibacterium
Republic of China freudenreichii [6]. Propionibacterium denitrificans and P.

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Thus, it is one of many bacteria capable of synthesizing


cobalamin de novo through an oxygen-dependent pathway
[1]. Sinorhizobium meliloti may be a candidate to replace
P. freudenreichii or P. denitrificans as industrial VB12
producer in the future.
In this study, a newly S. meliloti stain was isolated from
soil and was named S. meliloti 320. The product VB12 was
identified by HPLC and electrospray ionization (ESI) mass
spectrometry HPLC–MS/MS. Then, the strain was identi-
fied by sequence 16S rDNA and the genome. The fer-
mentation medium and culture conditions were optimized
to maximize the production of VB12. The results showed
that this strain can produce 140 mg L-1 VB12, which lay
the foundation for it to be used as an industrial VB12
producer.

Materials and methods

Species sampling and pre-cultures

Sinorhizobium meliloti 320 was isolated from private


farmland, Tianjin, China and the owner of the land gave
Fig. 1 Structure of vitamin B12. R stands for different ligands of permission to conduct the study on this site. In this study, S.
vitamin B12: 5-deoxyadenosine (adenosylcobalamin), CH3 (methyl-
meliloti 320 was identified as one out of 50 isolated bac-
cobalamin), CN (cyanocobalamin), OH (hydroxylcobalamin)
terial strains due to its growth characteristics and its red
color [13]. Sinorhizobium meliloti 320 was purified by
freudenreichii are used exclusively for the industrial pro- serial dilutions and plating on 1.5 % minimal medium agar
duction of VB12 [5]. The highest titers of VB12 by these containing: KH2PO4, 2.5 g L-1; NaCl, 2.5 g L-1; NH4Cl,
two strains have been reported to be 214 and 206 mg L-1, 0.5 g L-1; MgSO4, 0.13 g L-1; Glucose, 1 g L-1 and
respectively [6]. Propionibacterium freudenreichii belongs CaCl2, 5 g L-1. pH values of media were titrated to pH 7.0
to the generally recognized as safe (GRAS) category of with 1 M HCl. Plates were incubated for 1–2 days at
microorganisms [7], but its use for the production of VB12 30 °C. After colony formation single colonies were iso-
for human consumption is complicated. VB12 production lated and cultivated in 250 mL-flasks. Fermentation media
by P. freudenreichii is performed via a two-step process, contained sucrose, 50 g L-1; CSL, 60 g L-1; (NH4)2SO4,
where pseudo-cobalamin is first produced under anaerobic 2 g L-1; CoCl2, 0.006 g L-1; KH2PO4, 2.6 g L-1; betaine
conditions and DMBI-containing coenzyme B12 is then (N,N,N-trimethylammonioacetat), 6 g L-1 and DMBI
produced from the pseudo-cobalamin under (partially) 1 g L-1 at pH 6.8–7.0 (solid KOH, adjusted before auto-
aerobic conditions [8]. On the contrary, P. denitrificans claving). Individual colonies were incubated at 30 °C in
grows and synthesizes the entire structure of coenzyme B12 fermentation flasks at 200 rpm for 4 days.
via a one stage process aerobically [9]. However, P. den-
itrificans grows slowly to a low cell density, has compli- Extraction and analysis of VB12: mass spectrometry
cated and less understood carbon metabolism, and not well and quantification
established for genetic toolbox for strain improvement
[10]. VB12 concentration in fermentation broth was determined
Sinorhizobium meliloti is a Gram-negative a-pro- by high performance liquid chromatography (HPLC) with
teobacterium that exists either as a free-living member of the method reported previously [14]. Broth sample (4 mL),
the rhizosphere or as an intracellular nitrogen-fixing sym- to which 1 mL of NaNO2 8 % (w/v) and 1 mL of glacial
biont of legumes of the genera Medicago, Trigonella, and acetic acid were added, was boiled for 30 min. The mixture
Melilotus [11]. Cobalamin has been isolated from S. was then centrifuged at 10,000 rpm for 1 min and the
meliloti and shown to contain DMBI as the lower ligand supernatants was filtrated through a 0.22-lm membrane
[12]. The S. meliloti genome contains a complete set of ([ = 0.22 lm) filter. Then, 20 lL of NaCN 2 % (w/v)
genes involved in aerobic cobalamin biosynthetic pathway. was added to 1 mL of the supernatants. To separate the

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compounds aliquots (20 lL) were injected and analyzed Searches against protein data bases with the priority order
using an Agilent 1260 HPLC with a 5C18-250A column of non-redundant protein sequences in NCBI(NR) were
(Agilent, 4.6 mm id 9 250 mm, 5 lm) thermostated at carried out by Kyoto Encyclopedia of Genes and Genomes
35 °C. The mobile phase consists of water: acetonitrile (70: database (KEGG, Ver. 1.67x, http://www.genome.jp/kegg/
30 [v/v]) at a flow rate of 0.8 mL/min. Analytes were ) [21]. Furthermore, searches for Clusters of Orthologous
detected at 361 nm. Groups (COG, http://clovr.org/docs/clusters-of-ortholo
VB12 was qualitative by HPLC connected to an elec- gous-groups-cogs/) [22] were conducted with acritical
trospray mass spectrometer (Micromass Esquire 3000 plus; E value B1e-3. Based on the results of the protein database
Bruker Daltonics, Germany) [15]. The electron spray ion- annotation, Blast2GO (https://www.blast2go.com/) [23]
ization–mass spectrum (ESI–MS) was performed in posi- was applied to obtain the functional classification of the
tive mode using 0.01 % (v/v) formic acid in 15 % (v/v) genomic sequences based on gene ontology (GO) terms.
acetonitrile as mobile phase. Separation was performed at The Nr database was used to perform the GO functional
room temperature at 1 mL/min and the injection volume classification for all genomic sequences.
was 50 lL. Nitrogen was used as both desolvation gas at a
flow rate of 350 L/h and cone gas at 50 L/h. The desol- Optimization of fermentation temperature
vation temperature was set at 350 °C. The ionization
source was working at 105 °C. Capillary and cone voltages The optimal fermentation temperature of strain S. meliloti 320
were 4000 and 180 V, respectively [15, 16]. was tested using the following medium: Sucrose, 60 g L-1;
CSL, 20 g L-1; (NH4)2SO4, 2g L-1; CoCl2, 0.006 g L-1;
Identification of the isolates by 16S rDNA KH2PO4, 2.6 g L-1; betaine, 6 g L-1; DMBI, 1 g L-1. Fer-
sequencing mentation was carried out in 250 mL-Erlenmeyer flasks
containing 30 mL of medium at an agitation rate of 200 rpm
Genomic DNA was isolated from the bacterial isolate and for 7 days. After 7 days fermentation at 25, 30, 35, 40 and
was used as template for polymerase chain reaction (PCR). 45 °C, respectively, fermentation broth was used to assay the
Primers used for the amplification of part of 16S rDNA concentration of VB12.
were 16SF (50 -AGAGTTTGATCCTGGCTCAG-30 ) and
16SR (50 -TACGG TTACCTTGTTACGACTT-30 ). PCR Selection of the optimal carbon source and nitrogen
was carried out in a 50 lL reaction volume containing source
50 ng of genomic DNA, 20 pmol of each primer, 1.25 units
of Q5 High-Fidelity DNA polymerase (New England Applied media for the determination of the optimal carbon
Biolabs, USA), 200 lM of each dNTPs and 1X PCR buf- source contained CSL, 20 g L-1; (NH4)2SO4, 2 g L-1;
fer. PCR was carried out for 30 cycles in a MycyclerTM CoCl2, 0.006 g L-1; KH2PO4, 2.6 g L-1; betaine, 6 g L-1;
(Bio-Rad, USA) with the initial denaturation at 98 °C for DMBI 1 and 60 g L-1 of one of five carbon sources
5 min, cyclic denaturation at 98 °C for 30 s, annealing at (glucose, maltose, sucrose, fructose or starch). VB12-con-
55 °C for 30 s and extension at 72 °C for 1 min with a final centrations in 7 days fermentation broth were determined
extension of 10 min at 72 °C. The PCR product was by HPLC as described above.
checked by agarose gel electrophoresis and was further To determine the most suitable organic nitrogen source,
subjected to sequencing. The sequence data was checked the following medium was used: Sucrose, 60 g L-1;
by BLAST analysis [17]. The phylogenetic analysis of the (NH4)2SO4, 2 g L-1; CoCl2, 0.006 g L-1; KH2PO4,
16S rDNA sequence of the isolate obtained in this study 2.6 g L-1; betaine, 6 g L-1 and DMBI, 1 g L-1. Organic
was conducted with MEGA 5 using neighbor joining nitrogen sources and amounts tested were as following: (1)
method with 1000 bootstrap replicates [18]. 2 % yeast powder (YP), 1 % peptone; (2) 2 % yeast extract
(YE), 1 % peptone; (3) 2 % yeast extract powder (YEP),
Genome analysis of S. meliloti 320 strain 1 % peptone; (4) 2 % yeast extract concentrate (YEC), 1 %
peptone; (5) 2 % autolyzed yeast powder (AYP), 1 %
The genomic DNA of strain S. meliloti 320 was extracted peptone; (6) 2 % CSL; (7) 2 % CSL, 1 % peptone.
from purified bacterial isolates using OMEGA Bacterial Experiments were conducted in 250 mL-Erlenmeyer-flasks
DNA kits (Omega bio-tek, Feyou Biotechnology, China). containing 30 mL of each medium at 30 °C at an agitation
Sinorhizobium meliloti 320 was completely sequenced rate of 200 rpm in rotary shakers for 7 days.
using the sequencing platform on NGS-QC-Toolkit, Response surface methodology (RSM)-central compos-
deleting overlapping sequences. The cut-off-level (cut off ite design (CCD) was employed to find out the optimum
Qual Score) was set to 30 [19]. The resulting genomic concentrations of the optimal carbon source and nitrogen
sequences were determined by BLASTX(V2.2.17) [20]. source and to study their interactions [24]. Experimental

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variable was analyzed at five different levels. An experi-


mental design combining four replicates at the central point
and four axial points (a = 2), with a total of 12 experi-
ments, was used (Table 2). The matrix for this design and
the experimental response values (VB12 concentration) are
shown in Table 2.

Results and discussion

Fig. 2 a The microscope image of S. meliloti 320 dyed by 1 % base Strain selection and identification of VB12
fuchsin; b 6 d fermentation broth of S. meliloti 320 and negative
control
50 bacterial strains were isolated from soil samples and
design, model calculation, graph drawing and other data cultivated in minimum media. Among these strains, only
analysis were all performed on Design Expert software the color of S. meliloti 320 fermentation broth was red
(Version 8.0.6, Stat-Ease Inc., Minneapolis, USA). Each (Fig. 2b) and the microscope image of S. meliloti 320

Fig. 3 Identification of VB12


compound by LC–MS. A HPLC
chromatogram: fermentation
samples (a, b), negative control
(c) and positive control (d).
B This figure shows the MS
spectrum (e) of purified VB12
(big peak at 12 min shown in a,
b, and d) in relative abundance
against m/z. The MS spectra
allow detection of CN-VB12 at
1355.55 m/z and of
characteristic pseudomolecular
fragments of 147.0859,
359.0980 and 678.2894 m/z,
respectively

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Fig. 4 Phylogenetic tree of S.


meliloti 320 based on the 16S-
rDNA-sequence. Given
numbers represent confidence
levels of relation showing
Ensifer adhaerens M14 and
Sinorhizobium s. ZJB1101 as
next relatives of S. meliloti 320

Table 1 General information this product, HPLC–ESI–MS/MS was used to analyze the
Features Value
about sequenced S. meliloti 320 fermentation broth.
genome Genome size (bp) 7256751 Electrospray ionization of the cobalamines in a mass
GC-content 63.2 % spectrometer ion source leads to the formation of not only
Plasmid 0 of some molecular adducts, but also a pattern of frag-
Replicons 1 mentation ions (due to a low chemical stability of the
Total genes 6903 cobalamines). Proper selection of a sufficiently abundant
tRNA genes 3 fragment ion helps achieve the required quantification/de-
rRNA genes 5 tection limits. Results of the HPLC–ESI–MS/MS analysis
CDs 6895 from the cell cultures within the MS are shown in Fig. 3B.
Ionization of CN-Cbl using an ESI source leads to the
formation of the ions 678.3 [M?2H]2?, which was consist
with that reported by Szterk [25]. In this study, only CN-
shows it is a rod-shaped strain and the cell diameter is Cbl could be detected as different kinds of vitamin B12
about 1.0–1.2 lm (Fig. 2a). were all translated to CN-Cbl. Lou et al. [16] also reported
The 56 h fermentation broth was used to assay the the formation of multi-charged molecules during B12
amounts of VB12 by HPLC. In compliance with VB12 vitamin ionization. However, some of such adducts were
standards, mass spectroscopic measurements of corre- not found in this study. This is caused by the differences in
sponding HPLC retention peaks revealed spectra covering the electrospray source operation parameters and differ-
VB12-standard spectra (Fig. 3A). This shows that S. meli- ences in the chemical composition of the LC mobile phase.
loti 320 could produce VB12 when grown under aerobic The ionization process might be also affected by the
conditions. To further identification and characterization of composition of the analyzed matrix.

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Fig. 5 The network of porphyrin and chlorophyll metabolism has shown on KEGG which containing VB12 biosynthetic pathway. Enzyme
classes matching with KEGG analyses are highlighted

Phylogenetic classification of S. meliloti 320 variable regions. This gene is therefore suitable for phylo-
genetic and taxonomic classifications at various levels,
The 16s rDNA gene is a universal characteristic in including intrageneric differentiation [26]. A 1476 bp target
prokaryotes and has both conserved and sufficiently fragment was amplified by PCR using 16S rDNA primers.

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Fig. 6 a GO functional
classification of genes; b COG
functional classification of
genes

We conducted sequence similarity analysis of 16S rDNA Genomic features of S. meliloti 320
genes, and compared them with those of reference organ-
isms obtained from GenBank data libraries. The phyloge- Sinorhizobium meliloti 320 hosts one circular chromosome
netic analysis by MEGA5 [27] revealed that the isolated S. of 7,256,751 bp with an average GC-content of 63.2 %,
meliloti 320 belongs to the species of genus Sinorhizobium/ although no further plasmid was present. The genome
Ensifer (Fig. 4). Sinorhizobium sp. ZJB1101 and Ensifer comprises 6903 genes and 6895 putative genomic coding
adhaerens M14 represent the most related organisms with sequences (CDs). The genome includes 3 tRNA genes and
16S rDNA-sequence similarities of 99 %. 5 rRNA genes in total (Table 1).

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Figure 5 sums up the network of porphyrin and chloro-


phyll metabolism found via KEGG analysis, including VB12
synthetic pathway. Figure 5 emphasizes the separation of
aerobic and anaerobic pathway both ending in cobalt-(II)-
yrinate-a,c-diamide as precursor of VB12. This figure high-
lights the enzymes and enzymatic clusters (colored green)
involved in ALA, following and further metabolic processes
connected to VB12 pathway by showing the metabolic steps
with regard to genomic analyses. The direct comparison of
the anaerobic and aerobic pathway shows that the presences
of enzymes in the aerobic pathway proving a complete VB12
synthetic pathway present in S. meliloti 320. Simultaneously,
this metabolic map generally announces the importance of
cobalt and iron cations as central components in various
porphyrin and chlorophyll metabolism steps.
The GO analysis (Fig. 6a) shows significantly enriched
functional groups related to catalytic and binding functions,
organization of cellular processes, establishment of local-
ization, and metabolic processes. The COG-analysis of all
genes (Fig. 6b) reveals that the top five categories describe
features of general function (R), amino acid transport and
metabolism (E), carbohydrate transport and metabolism
(G), inorganic ion transport and metabolism (P) and tran-
scription (K). These activities are required for amino acid,
carbohydrate, and energy supply, which in turn leads to
active cell division and related molecular events to facili-
tate VB12 production.
The understanding of the genome information could
provide the opportunities for further studies addressing the
bacterial metabolism and its biotechnological potential.
Biochemical mapping may uncover interfaces, options of
metabolic regulation, and chances to optimize VB12 pro-
duction. Moreover, mentioned metabolic features are also
based on transcriptional regulation. Bio-fermentative VB12
production, interfering porphyrin and chlorophyll metabo-
lism, extensively includes parameters and possibilities
which we have to deal with when declaring efficient VB12
production as object of interest.
Deeper insights into metabolic preferences and behavior
of S. meliloti 320 will provide promising opportunities of
genetic and metabolic engineering enhancing its industrial
application in VB12 production. Vast genetic diversity, and
thus, a variety of different physiological and metabolic
preferences, gives a reason to expand systematic screening
efforts on S. meliloti strains maybe exposing strains of
great impact on industrial and biotechnological application.
Fig. 7 a Effect of temperature on vitamin B12 production by S.
meliloti 320. b Effects of different carbon sources on vitamin B12
Optimization of fermentation temperature production by S. meliloti 320. 1 Glucose, 2 fructose, 3 maltose, 4
sucrose and 5 starch. c Effect of different nitrogen sources on VB12
To optimize fermentation temperature for VB12 produc- production. 1 2 % YP, 1 % peptone; 2 2 % YE, 1 % peptone; 3 2 %
YEP, 1 % peptone; 4 2 % YEC, 1 % peptone; 5 2 % AYP, 1 %
tion, fermentations were conducted at different temperature
peptone; 6 2 % CSL; 7 2 % CSL, 1 % peptone
including 25, 30, 35, 40 and 45 °C. As shown in Fig. 7a,

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the highest concentration of VB12, 100 ± 2 mg L-1, was increase VB12 production. The experimental data in
obtained at 30 °C. This temperature was then used in Table 2 were correlated as a second-order polynomial
subsequent experiments. model by nonlinear regression. The empirical relationship
between variables and responses was expressed by the
Selection of carbon source and nitrogen source following second-order polynomial equation:
Y ¼ 126:46 þ 9:58A þ 18:08Bþ8:25AB  11:19A2
To select the optimum carbon source, five different carbon
 9:94B2
sources were investigated initially, at pH 7.0, 30 °C and
200 rpm. When using sucrose, 98 ± 2.8 mg L-1 VB12 was where Y is the predicted response of VB12 production (mg
produced, which is the highest one (Fig. 7b). However, L-1), and A and B are the coded values of sucrose and
when employing starch as carbon source, VB12 concen- CSL, respectively.
tration is only 30 mg L-1. Thus, sucrose was then used in The sufficiency of the second-order model was checked
subsequent experiments. by the analysis of variance (ANOVA) presented in Table 3.
Replacing YP, YE, YEP, YEC or AYP in fermentation The F value of 5.37 implies that the model is significant, as
medium with 20.0 g L-1 CSL resulted in VB12 concen- there is only a 3.21 % probability that a large F value could
tration increased from 10 ± 0.8 to 130 ± 3.2 mg L-1 occur due to noise. The model presents a relatively high
(Fig. 7c). CSL is a cheap organic nitrogen source and is determination coefficient (R2 = 0.8172), explaining
available in large scale fermentation. Thus, in subsequent 81.7 % of the variability in the response. The P values
experiments CSL was chosen as suitable nitrogen source were used to identify the effects of each factor on VB12
and its concentration was further to be optimized. production. A P value below 0.05 indicates that the model
terms are significant. In this case, A2 (sucrose 9 sucrose),
Optimization of the concentration of sucrose B (CSL) and B2 (CSL 9 CSL) are significant (Table 4).
and CSL using RSM The interaction between these two factors is not significant.
The location of the optimum was determined to be
The concentrations of sucrose and CSL were optimized to A = -0.901, and B = 1.283, obtained by the differentia-
find the best combination of them for maximum VB12 tion of the quadratic model given by equation above. The
production. 1 % peptone was added to each experiment to corresponding uncoded values were: 69.0 g L-1 sucrose

Table 2 Experimental design


Run A (coded value) B (coded value) A (sucrose, g L-1) B (CSL, g L-1) VB12 (mg L-1)
and results of RSM
1 -1 -1 50 15 67
2 1 -1 70 15 78
3 -1 1 50 25 83
4 1 1 70 25 127
5 -2 0 40 20 75
6 2 0 80 20 105
7 0 -2 60 10 57
8 0 2 60 30 133
9 0 0 60 20 130
10 0 0 60 20 145
11 0 0 60 20 126
12 0 0 60 20 138

Table 3 ANOVA of the


Source Sum of squares Degrees of freedom Mean square F value P value
quadratic model
Model 8893.54 5 1778.71 5.37 0.0321
Residual 1989.12 6 331.52
Lack of fit 1774.37 3 591.46 8.26 0.0582
Pure error 214.75 3 71.58
Cor total 10882.67 11

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Acknowledgments We are grateful for the support from State Key
analysis of vitamin B12 in food products and in multivitamins-
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