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Research Journal of Biotechnology Vol.

8 (3) March (2012)


Res. J. Biotech

Isolation, Characterization and Extraction of


antimicrobial compound from marine actinomycete
Streptomyces hygroscopicus BDUS 49
Parthasarathi S.,1* Sathya S.,2 Bupesh G.,3 Manikandan M.,4 Kim C.J.,5 Manikandan T.1 and Balakrishnan K.1
1. Department of Biotechnology, Bharathidasan University, Tiruchirrappall, Tamil Nadu, 620 024, INDIA
2. Department of Bionanotechnology, Kyungwon University, Gyeonggi-Do 461 701, SOUTH KOREA
3. Department of Animal Science, Bharathidasan University, Tiruchirrappall, Tamil Nadu, 620 024, INDIA
4. SriKrishna Arts and Science college, Kuniamuthur, Coimbatore 641 008, INDIA
5. Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 305 806, SOUTH KOREA
*sarathimeister@gmail.com

Abstract pharmaceutically relevant microorganis ms, actinomycetes


A total of eight actinomycetes colonies were isolated remain major sources of novel, therapeutically relevant
from near sea shore marine environment locations of natural products2. The majority of these compounds
Bigeum Island, South West coast of South Korea. demonstrate one or more bioactivities, many of them
developed into drugs for treatment of wide range of
Among them, 4 isolates were morphologically distinct
diseases in human, veterinary and agriculture sectors3.
on the basis of spore mass colour, reverse side colour,
aerial and substrate mycelia formation and Searching for novel actinomycetes constitutes an essential
production of diffusible pigment. The majority of these component in natural product-based drug discovery.
isolates were assigned to the genus Streptomyces of Analytical methods continue to improve to allow the rapid
which one isolate showing broad spectrum of elucidation of structures and make natural products
antimicrobial was on the basis of their morphological, valuable components of modern drug discovery. The
physiological and biochemical properties. Phylo isolated compounds from marine actinomycetes have a
genetic analysis of a 16S rRNA gene sequence showed broad spectrum of biological activities such as antibiotic,
that strain Streptomyces hygroscopicus BDUS 49 antifungal, toxic, cytotoxic, neurotoxic, antimitotic,
antiviral and antineoplastic activities.4 Recently, new
forms a distinct clade within the Streptomyces 16S
targets have been added to the general screening like AIDS,
rRNA gene tree and is closely related to Streptomyces immunosuppression, anti-inflammation, Alzheimer disease,
hygroscpicus subsp sub species. aging processes and some tropical diseases and resulted in
discovery of several drugs.5 Studies on marine
This strain possessed a broad spectrum of actinomycetes are facing some unexpected problems.
antimicrobial activity against Gram-positive, Gram-
negative bacteria and fungi. The UV spectra of the For many of the marine actinomycetes, the taxonomy of the
active compounds in ethyl acetate showed peaks strain is very poorly defined so that binomial identifications
between 200 to 295 nm. The bioactive region was are frequently uneasy to be carried out. Streptomycetes,
detected on the TLC plate (Rf 0.40). The structure of Gram (+) filamentous bacteria, are widely distributed in a
the bioactive components was further determined variety of natural and man-made environments and
constitute a significant component of the microbial
using FTIR, MS, 13C NMR and 1H NMR. The
population in most soil.6 The results of extensive screening
molecular formula of the given compound was have been the discovery of about 4000 antibiotic substances
identified as 7, demethoxy rapamycin C50H75NO12+NA from bacteria and fungi, many of which have found
(MW 905.12). applications in human medicine, veterinary medicine and
agriculture. Most of them are produced by streptomycetes.7
Keywords: Actinomycetes, Antimicrobial activity, UV/
VIS, FTIR, MS and NMR spectrum. Most streptomycetes and also other actinobacteria produce
a diverse array of antibiotics, including aminoglycosides,
Introduction macrolides, peptides, polyenes, polyether, tetracyclines etc.
Marine organisms represent a promising source for natural In searching for new antibiotics, over 1000 different
products of the future due to the incredible diversity of bacteria (including actinobacteria), fungi and algae have
chemical compounds that were isolated. The oceans cover been investigated. To prevent exponential emergence of
almost 70% of the earths surface and over 90% of volume microorganisms becoming resistant to the clinically
of its crust1. Marine actinomycetes have been traditionally available antibiotics already marketed, the periodic
a rich source for biologically active metabolites. Although replacement of existing antibiotics is necessary.
heavily studied over the past three decades, actinomycetes
continue to prove themselves as reliable sources of novel There are very few reports on antimicrobial activity from
bioactive compounds. Among the well characterized marine microorganisms from unpolluted Bigeum Island,

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Research Journal of Biotechnology Vol. 8 (3) March (2012)
Res. J. Biotech
South West Coast of South Korea. In bio prospecting point aerial and substrate mycelia were determined and recorded
of view, Bigeum Island marine soil samples possess neutral using National Bureau of Standards (NBS) Colour Name
to alkaline with pH ranging from 6.33 to 7.94 and CaCO3 Charts. The spore chain morphology and spore surface
concentration in soil samples ranged from 1,200 to 9,600 ornamentation were examined by scanning electron
ppm. Interestingly, Syed et al8 isolated few novel microscopy (JEOL) of 14-day-old cultures grown on
microorganisms namely, Frigoribacterium mesophilum sp. oatmeal agar (Figure is not shown).
nov., Nocardioides halotolerans sp. nov., Leifsonia
bigeumensis sp. nov. Phycicoccus bigeumensis sp. nov., All physiological tests were carried out at 30C and at pH
Phycicoccus bigeumensis sp. nov., Leifsonia bigeumensis 7.0 unless otherwise specified. The effect of different
sp. nov., Nocardioides islandiensis sp. nov., Nocardioides temperatures and pH conditions on growth and the
tritolerans sp. nov., Nocardioides islandiensis sp. nov., tolerance of strain S. hygroscopicus to salt were determined
Leifsonia bigeumensis sp. nov. and Nocardioides dilutes sp. by using plates made with modified Bennetts agar
isolated from the Bigeum Island sample. Recently, a medium. Production of melanoid pigments was tested on an
yellow-pigmented actinobacterium, designated strain ISP-7 plate.11 Utilization of carbon source (L-arabinose, D-
Leifsonia kribbensis sp. nov., was isolated from a soil xylose, D-glucose, D-fructose, L-maltose, sorbital, sucrose,
sample collected from Bigeum Island.9 glycerol and mannitol) was examined using ISP-9 as a
basal medium. Decomposition of substrates such as nitrate,
Thus, it is crucial that new groups of marine starch, gelatine, Milk coagulation, melanin production,
microorganisms from hitherto unexplored habitats be pectin and xylan was detected in modified Bennetts
considered as sources of novel bioactive secondary medium. Resistance to some antibiotics was detected by
metabolites. Hence the present investigation deals with the disc diffusion method.
screening and characterization of producers of
antimicrobial substances by marine microorganisms from Chemotaxonomic analysis: Amino acid and sugar
the sea waters of Bigeum Island, South West Coast of analyses of whole cell hydrolysates were performed.13,14
South Korea. Further, the identified antagonistic Fatty acid methyl esters were prepared from 50 mg of wet
actinomycetes were characterized based on morphological, cells. Mixtures of fatty acid methyl esters were prepared
biochemical, physiological, molecular and elemental and analyzed with the MIDI system. Menaquinones were
analysis. extracted, purified and identified by HPLC.15

Material and Methods DNA extraction: The actinomycete isolate was grown in
Collection of sample: The marine soil sediment samples 25 ml Bennetts medium at 28C for 7 days. An early
were collected at the depth of 20 cm, 20 meter near the sea grown actinomycete colony was picked up and suspended
side in Bigeum island, South west in Korea / grid 3445' in 5% chelax resin. After that, the sample was heated in
02.23'' N 125 53' 42.32''. Samples were kindly provided by boiling water for 10 min, cooled in an ice bath for 5 min
Korea Research Institute of Bioscience and Biotechnology and centrifuged at 7,500 g for 3 min. The supernatant (300
(KRIBB), Daejeon, South Korea. The collected soil l) was recovered, transferred to a new tube and stored at
sediment samples were placed in sterile polyethylene bags, 4C until use.16
closed tightly and stored in the refrigerator at 4C until use.
For the isolation of actinomycetes, soil sample were first PCR amplification: PCR amplification of 16S rRNA gene
mixed, suspended in sterile distilled water (1 g in 100 ml) was performed by Maxime PCR PreMix kit (i-Star Taq)
homogenized by vortexing and finally treated 510 min by protocol. The specific actinomycete primers, F27 (5-
sonication according to Ouhdouch methodology10. The AGAGTTTGATCCTGGCTCAG-3) and R1492 (5-
treated samples were serially diluted up to 10-6 and spread GGTTACCTTGTTACGACTT-3) were used to amplify
(0.1 ml) over the surface of starch casein agar (SCA) 16S rDNA. The amplification reaction was performed in a
medium (pH 7.2) supplemented with 25 g ml1 final volume of 20 l containing 10pmol/ l of each primer,
cycloheximide to inhibit fungal growth and 10 g /ml 2.5mM each dNTP, 2.5 units Taq DNA polymerase, 16 l
nalidixic acid to inhibit the bacteria capable of swarming, of sterile distilled water, 1.5 mM MgCl2 and 2 l DNA
without affecting the growth of actinomycetes. All of the sample in 1x Taq polymerase buffer. The amplification was
inoculated plates were incubated at 30C for 710 days. performed on a thermal cycler (PTC-100TM programmable
Thermal Controller, MJ Research Inc, USA). The mixture
Morphological and physiological characteristics: was first denatured at 94C for 5 min. Then, 40 cycles of
Cultural characteristics of strain Streptomyces PCR were performed by denaturation at 94C for 15 sec,
hygroscopicus were examined by eyes of 14-day-old annealing at 55C for 30 s and extension at 72C for 90 s.
culture grown on various International Streptomyces At the end of the last cycle, the mixture was incubated at
Project (ISP) media11 and Bennetts agar medium. Micro 72C for 10 min and then cooled to 4C.
morphology and sporulation were observed under light
microscope by inclined cover slip technique12 on starch For each reaction, a negative control lacking DNA template
casein agar after incubating at 30C for 7 days. Colours of was included. PCR products of the expected size were

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Research Journal of Biotechnology Vol. 8 (3) March (2012)
Res. J. Biotech
revealed on 1% agarose gels containing Ethidium bromide molecular formula of the given compound was identified as
(10g/ml). The resultant 16S rRNA gene sequences were 7, demethoxy rapamycin C50H75NO12+NA (MW 905.12).
aligned manually with corresponding almost complete
sequences from Streptomyces strains retrieved from the Results and Discussion
GenBank database as described previously. Phylogenetic South Pacific coast of Philippines, especially from
tree analysis was performed using the MEGA software Mindanao has wide range of salinities and was selected as
version 4.017. an ecosystem for studying the diversity of actinomycetes
and their antimicrobial properties. All the 68 actinomycetes
Screening for antimicrobial activity: Antimicrobial were identified at a generic level based on the colony
activities of isolate were tested preliminarily by cross streak morphology and microscopic morphology. Identification of
method18. Actinomycetes isolates were streaked across strains by both morphological and cultural characteristics
diameter on starch casein agar plates. After incubation at revealed that most (54%) of the isolates belonged to white
28C for 7 days, 24 hrs cultures of Bacillus subtilis, and grey colour series. Out of 68 isolates, 66% of isolates
Staphylococcus aureus, Escherichia coli, Salmonella typhi, were assigned to the genus Streptomyces sps and the
Candida albicans, Aspergillus niger and Saccharomyces remaining were identified as Nocardiopsis sps (18%),
cerevisiae were streaked perpendicular to the central strip Micromonospora sps (11%) and Actinopolyspora sps (5%)
of actinomycetes culture. All plates were again incubated at (Fig. 1).
30C for 24 hrs and zone of inhibition was measured.

Extraction of antimicrobial compounds: The selected


antagonistic actinomycete isolates were inoculated into
starch casein broth and incubated at 28C in a shaker (200-
250 rpm) for seven days. After incubation the broths were
filtered through Whatmann No.1 filter paper and then
through Millipore filter (Millipore Millex-HV Hydrophilic
PVDF 0.45 m). The filtrate was transferred aseptically
into a conical flask and stored at 4C for further assay. To Fig. 1: Percentage frequency of isolated actinomycetes
the culture filtrate, equal volume of various solvents (viz., genera
chloroform, ethyl acetate and methanol) was added
separately and centrifuged at 8000 rpm for 10 min at 4C to The present study revealed that among the isolates
extract the antimicrobial compound19. The compound Streptomyces was the dominant genera. Frequency and
obtained from each solvent was tested for their activity dominance of Streptomyces among actinomycetes in
against the test pathogens (Bacillus subtilis, Staphylococcus various soil types were reported by several workers.20-22
aureus, Escherichia coli, Salmonella typhi, Candida Similarly the present study also determined that out of 68
albicans, Aspergillus niger and Saccharomyces cerevisiae) strains, 23 isolates had antimicrobial activity, of which 12
by well diffusion method. After incubation for 24 and 48 isolates showed antibacterial activity, 9 isolates showed
hours the zone of inhibition was measured. antifungal activity against C. albicans. However, only one
isolates namely Streptomyces hygroscopicus sps BDUS 49
Isolation of antimicrobial metabolites: Antibacterial had broad spectral antimicrobial activity and was selected
compound was recovered from the filtrate by specific for further studies and they represented marine seashore
solvent extraction like ethyl acetate. Ethyl acetate was soil sample (Fig. 2).
added to the filtrate in the ratio 1:1 (v/v) and shaken
vigorously for 1 hour for complete extraction. The ethyl 25
acetate phase that contains an antibiotic was separated from
the aqueous phase. It was evaporated to dryness in a water 20
% of activity

bath at 80-90C and the residue obtained was weighed.


15
Thus obtained compound was used to determine the
antimicrobial activity. Filter paper disks (6mm in diameter) 10
were impregnated with extracted broth, dried and placed
5
onto BSM plates previously seeded with Bacillus subtilis.
The plates were incubated at 37C for 48h and examined 0
for zones of inhibition. Activity against

The absorption spectrum of each active extract was Antimicrobial activity Antibacterial activity
determined in the UV region (200-400nm) by using a Antifungal activity Gram positive
Perkin-Elmer Lambda 15 UV/VIS spectrophotometer. The Gram negative Both antibacterial and antifungal
structure of the bioactive components was further
determined using FTIR, MS, 13C NMR and 1H NMR. The Fig. 2: Antimicrobial activity of actinomycetes isolate

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Research Journal of Biotechnology Vol. 8 (3) March (2012)
Res. J. Biotech
Strain Streptomyces hygroscopicus BDUS 49 showed ext- using 5 different solvent extracts and ethyl acetate extract
ensively branched substrate mycelia and aerial hyphae und- produced maximum inhibitory zone against all the
er light microscopy. The scanning electron micrograph of pathogens tested followed by methanol, ethy acetate and
strain Streptomyces hygroscopicus BDUS 49 revealed that chloroform extracts. Ethyl acetate extract of the strain
aerial mycelia were highly branched with tight spirales and Streptomyces hygroscopicus BDUS 49 showed maximum
rectiflexibile spore chain. Each spore chain consisted of activity against followed by S. aureus (35 mm), B. subtilis
5060 short rod (0.50.60.70.8 m) hairy surface spores. (25 mm), Aspergillus niger (23 mm), Saccharomyces
cerevisiae (28 mm), Escherichia coli (10 mm), S. typhi (9
The cultural characteristics are shown in table 1. Strain S. mm) and C. albicans (8 mm) (Table 4). Similarly, various
hygroscopicus BDUS 49 grew well on most media except solvents were used for the extraction of antibiotics from
on inorganic salt starch agar. Particularly, the colonies actinomycetes by many workers using ethyl acetate and
were convex and some part of the aerial mycelia and spore methanol and chloroform.23-25
chains could be observed around the colony margin. Aerial
mycelia were initially white, becoming pink to purple The UV spectral data for the ethyl acetate extract of
colour depending on the medium used and gradually dark- selected active fermented broth are shown in figure 5.
ened in old culture. Likewise, vegetative mycelium colour Maximum absorbance peaks range between 200-295 nm
was yellowish-pink to brown depending on the medium. and the characteristics of absorption peaks indicate a highly
Melanin and other soluble pigments were not produced. polyene nature. The bioactive regions were detected on the
TLC plate (Rf 0.70). The bioactive compound exhibited a
The physiological properties are shown in table 2. Strain S. maximum UV absorption at 210 and 225 nm in ethyl
hygroscopicus BDUS 49 showed growth in the pH range acetate. The strain Streptomyces hygroscopicus BDUS 49
6.0-8.2, with optimal growth occurring at pH 7.0. The produced either a broad-spectrum anti-microbial compound
temperature range for growth was 2040C with optimal or several compounds with different activities.
growth occurring at 30C. Good growth was shown at
NaCl concentration up to 8% which could be designed as The antimicrobial compounds in the ethyl acetate were
moderate halophilic actinomycete. No melanoid pigments purified and separated by column and thin layer
were produced. It showed positive results for utilization of chromatography. Single separated band was observed in the
many carbon sources such as D-glucose, L-arabinose, D- sample. The Rf value of S. hygroscopicus BDUS 49 was
xylose, fructose, maltose and glycerol. However, carbon 0.40 in thin layer chromatographic-separation. The
sources sucrose and sorbital could not be utilized. It separated S. hygroscopicus compound was brownish colour
showed sensitive to most antibiotics except Bacitracin and and the melting point was 180C-185 C. The compound
Chloramphenical. All the tested carbon sources could be was stable at pH from 7.0 to 8.0 and at temperatures
decomposed by strain S. hygroscopicus BDUS 49 except ranging from 20-40C, S. hygroscopicus BDUS 49
pectin and xylan. compound revealed that the absorption maximum was 200
to 295 nm in ethyl acetate. The UV spectrum of S.
Chemotaxonomic tests showed that whole-cell hydrolysates hygroscopicus BDUS 49 is shown in fig.5. FTIR spectrum
of strain S. hygroscopicus BDUS 49 were rich in LL- of S. hygroscopicus BDUS 49 compound showed two
diaminopimelic acid (LL-DAP) with no characteristic sugar absorption peaks in the region of 3500 and 1730 cm.-1
and indicated a wall chemotype I. The diagnostic polar
lipids were phosphatidylethanolamine, diphosphati The spectrum indicates that the compound had OH and
dylglycerol, phosphatidylinositol and phosphatidylinositol possibly lactone carbonyl group. Another two absorption
mannoside. Predominant menaquinone was MK9 (H8). peaks were shown in the region of 1700 (carbonyl) and
Chemotaxo-nomic and morphological properties of strain between 1610 and 1630 cm-1. This peaks indicates that the
S. hygroscopicus BDUS 49 are in line with its classification compound had carbonyl and alkenes (C=C) group. The
in the genus Streptomyces12. The assignment of this strain absence of carboxylic acid (COOH) and ester (COOR),
to the genus Streptomyces was also supported by 16S alkynes was confirmed by the lack of bands in the region of
rRNA gene sequence data (Fig. 3). An almost full sequence 1670-1674 and 1700-750 cm-1 respectively (Fig. 6). The
of 16S rRNA gene of strain S. hygroscopicus BDUS 49 mass spectrum showed that the molecular ion peak at 912
(1,404 nucleotides) was obtained and submitted to the m/z (Fig. 7). The large number of peaks through out the 1-
GenBank database under an accession number GU195049. 5 was observed in 13C and 1H NMR spectrum of purified
Comparison of the sequence of strain S. hygroscopicus compound from S. hygroscopicus BDUS 49 (Fig. 8 a and b
BDUS 49 with the corresponding sequences of respectively). Based on the spectral datas, the given
representative strains of the genus Streptomyces showed compound was identified as 7-demethoxy rapamycin with
that this organism formed a distinct phyletic line with a molecular weight and formula as 905.12
clade encompassed by Streptomyces hygroscopicus and (C50H75NO12+NA).
Streptomyces lydicus (Fig. 4).
Conclusion
The antimicrobial efficacy of the isolates was tested by In conclusion, the use of new screening approaches to
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identify microorganisms from original ecosystems is Acknowledgement
essential for the discovery of novel natural substances with The authors wish to thank Dr. J. C. Lee and D. J. Park for
valuable biological activities. In our work, the use of their help. The selected isolates were identified by Korea
marine sea shore soil sample from particular Bigeum Island Research Institute of Bioscience and Biotechnology,
biotopes enabled us to isolate a moderately halophilic Daejeon and Seoul National University, Seoul, Republic of
Streptomyces hygroscopicus BDUS 49 strain secreting an Korea.
active molecule that exhibits broad spectrum antimicrobial
activity.

Fig. 3: Amplified fragment of 16S rRNA gene of strain S. hygroscopicus BDUS 49 (1,404 nucleotides);
M: Marker DNA.

Fig. 4: Neighbor-joining tree based on almost complete 16S rRNA gene sequence showing relationships between
streptomycete isolate Streptomyces hygroscopicus BDUS 49 and related members of the genus Streptomyces. The
numbers at the nodes indicate the level of bootstrap support based on a neighbor-joining analysis of 1,000 resampled
datasets; only values above 50% are given. Scale bar indicates 0.1 substitutions per nucleotide position

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Fig. 5: UV - spectrum of S. hygroscopicus BDUS 49

Fig. 6: FTIR - spectrum of S. hygroscopicus BDUS 49

Fig. 7: Mass spectrum of S. hygroscopicus BDUS 49

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13
Fig. 8(a): C NMR - spectrum of S. hygroscopicus BDUS 49

Fig. 8(b): 1H NMR spectrum of S. hygroscopicus BDUS 49

Table 1
Cultural characteristic of Streptomyces hygroscopicus BDUS 49
Medium Growth Aerial mycelium Substrate mycelium
Yeast extractmalt extract agar Good Whitish, Pale grayish Pale yellow, brown
ISP-3 Good White to chalk white Pale yellow
ISP-4 Good No aerial mycelium Yellow to brown
ISP-5 Good Whitish to pale candy Brownish yellow
Bennetts agar Good Whitish Pale to dark grey
Potato dextrose agar Good Sandal white Yellowish brown
Starch casein agar Good Whitish Yellowish brown

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Table 2
Biochemical and Physiological characteristics of Streptomyces hygroscopicus BDUS 4
Characteristics Results
Sporophore morphology Spirally twisted
Spore surface Smooth
Colour of aerial mycelium Dull white
Colour of substrate mycelium Dull yellowish brown
Spore mass White
Gram staining +
Acid fast Non acid fast
Motility Non motile
Decomposition of
Nitrate +
Starch +
Pectin -
Gelatin liquefactions +
Xylan -
Milk coagulation +
Melanin production +
Carbon source utilization (1% w/v)*
D-glucose +
L-arabinose +
Sucrose _
D-xylose +
Fructose +
Maltose +
Glycerol +
Mannitol +
sorbital _
Glycerol
Resistance to antibiotics (g ml1)
Bacitracin (10 i.u) Resistance
chloramphenical(5 i.u.) Resistance
Amikacin(50) Sensitive
Amphicilin (10) Sensitive
Streptomycin (10) Sensitive
Tetracyclin(30) Sensitive
Temperature for Growth (C)
Range 20-40C
Optimum 28C
pH for growth*
Range 6.0-8.2
Optimum 7.0
Effect of NaCl concentration (w/v)
2% +
4% +
6% +
8% +
10% _
*: Growth of the strain was measured as dry weight of the mycelium, +: positive; -: Negative.

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Table 3
Antimicrobial efficacy of Streptomyces hygroscopicus BDUS 49
Zone of inhibition (mm)
Name of the test organism
Ethyl acetate Methanol Chloroform
Bacillus subtilis 25 18 19
Staphylococcus aureus 35 24 27
Escherichia coli 20 14 16
Salmonella typh 9 5 7
Candida albicans 8 4 5
Aspergillus niger 23 16 18
Saccharomyces cerevisiae 28 21 22

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