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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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The Korean Journal of Microbiology
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Journal DOI :
The Microbiological Society of Korea
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Volume & Issues
Volume 49, Issue 4 - Dec 2013
Volume 49, Issue 3 - Sep 2013
Volume 49, Issue 2 - Jun 2013
Volume 49, Issue 1 - Mar 2013
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Mutational Analysis Elucidates the Role of Conserved 237 Arginine in 23S rRNA Methylation, Which is in the Concave Cleft Region of ErmSF
Jin, Hyung Jong ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 105~111
DOI : 10.7845/kjm.2013.3038
The Erm family of adenine-
methyltransferases (MTases) is responsible for the development of resistance to macrolide-lincosamide-streptogramin B antibiotics through the methylation of 23S ribosomal RNA. Recently, it has been proposed that well conserved amino acids in ErnC' located in concave cleft between N-terminal 'catalytic' domain and C-terminal 'RNA-binding' domain interacts with substrate RNA. We carried out the site-directed mutagenesis and studied the function of the ErmSF R237 mutant in vitro and in vivo. R237 amino acid residue is located in the concave cleft between two domains. Furthermore this residue is very highly conserved in almost all the Erm family. Purified mutant protein exhibited only 51% enzyme activity compared to wild-type. Escherichia coli with R237A mutant protein compared to the wild-type protein expressing E. coli did not show any difference in its MIC (minimal inhibitory concentration) suggesting that even with lowered enzyme activity, mutant protein was able to efficiently methylate 23S rRNA to confer the resistance on E. coli expressing this protein. But this observation strongly suggests that R237 of ErmSF probably interacts with substrate RNA affecting enzyme activity significantly.
Development of PCR Diagnosis System for Plant Quarantine Seed-borne Wheat Streak Mosaic Virus
Lee, Siwon ; Kang, Eun-Ha ; Chu, Yeon-Mee ; Shin, Yong-Gil ; Ahn, Tae-Young ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 112~117
DOI : 10.7845/kjm.2013.3013
Wheat streak mosaic virus (WSMV), a member of the genus Tritimovirus in Potyviridae, severely impacts wheat and corn seed worldwide, but has yet to be detected in Korea, and hence, every effort should be made to prevent its introduction. To prevent WSMV from entering the country, it is necessary to prepare a specific, sensitive, simple, and fast detection method for routine application to plant quarantine procedures. For this reason, a two-step diagnosis system consisting of RT-PCR and nested PCR is being used for WSMV detection. In addition, a novel positive control was developed for use with the system. WSMV has been detected in seed sweet corn from Japan and seed wheat from USA by a two-step diagnosis system, the details of which are described in this study. After sequence analysis, similarities of 80.6 and 100.0% with other isolates were determined by BLAST. They showed the same topology, which was classified as 4 genotypes by various phylogenetic trees, using a poly protein encoding sequence amplification. In this analysis, WSMV-JSweet-corn2868 (JX845574) is classified as clade B, while WSMV-Uwheat1944-1 (KC754959) and WSMV-Uwheat1944-2 (KC754960) belong to clade D.
Antibiotic Resistance Among Salmonella spp. Isolated from Feces of Patients with Acute Diarrhea in Gwangju Area, Korea, during 2000-2009
Kim, Tae Sun ; Kim, Min Ji ; Kim, Sun Hee ; Seo, Jin-Jong ; Kee, Hye Young ; Chung, Jae Keun ; Kim, Eun Sun ; Moon, Yong Woon ; Ha, Dong Ryong ; Kim, Min Kyeong ; Lim, Suk Kyung ; Nam, Hyang-Mi ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 118~125
DOI : 10.7845/kjm.2013.3032
Antibiotic susceptibility was examined for 596 Salmonella isolates from patients with acute gastroenteritis during 2000-2009 in Gwangju area in South Korea. Of 16 antibiotics tested, ampicillin resistance (43%) was the most commonly observed resistance among the 596 Salmonella sp. isolates, followed by tetracycline (35.9%), nalidixic acid (31.5%), and chloramphenicol (26.2%). Antibiotic resistance varied among serotypes: The highest resistance of S. Enteritidis and S. Typhimurium was to ampicillin (51.1%) and tetracycline (77.9%), respectively. A total of 89 resistance patterns were observed, and 26% (155/596) of Salmonella isolates were susceptible to all antibiotics tested in this study. About 21% (127/596) and 15% (87/596) of the isolates were resistant to one and two antibiotics, respectively. The rest of Salmonella isolates (227/596, 38%) were resistant to three or more antibiotic agents. The highest multi-drug resistance (MDR) was observed in serotype S. Paratyphi B (76.5%), followed by S. Typhimurium (58.2%), and S. Enteritidis (40.2%). The most common resistance pattern of MDR isolates was ampicillin-chloramphenicol-nalidixic acid-ticarcillin (36/227, 15.8%), most of which (35/36, 97.2%) were S. Enteritidis.
Distribution of Multidrug Efflux Pump Genes in Enterococci spp. Isolated from Bovine Milk Samples and Their Antibiotic Resistance Patterns
Kang, SoWon ; Lee, SangJin ; Choi, SungSook ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 126~130
DOI : 10.7845/kjm.2013.3025
The major aim of this study was to investigate the distribution of genes that encode multidrug efflux pumps in Enterococci spp. isolates from bovine milk samples and antibiotic resistance patterns of these strains. Of the 245 isolates, 44.1% showed ampicillin resistance, 79.2% showed erythromycin resistance, 76.3% showed tetracycline resistance and 36.3% showed chloramphenicol resistance. In case of vancomycin and ciprofloxacin, all of the isolates were susceptible to these antibiotics. Of the 245 enterococcal isolates, 82.1% have MFS type eme(A) gene, 72.7% have ABC type efr(A) gene, 77.1% have ABC type efr(B) gene, and 71.8% have ABC type lsa gene. In case of Enterococcus faecalis, the original strain for these genes, 92.5% have eme(A), 87.4% have efr(A), 88.4% have efr(B), and 88.4% have lsa. Interestingly, in case of different species of Enterococci, eme(A) was also detected in four strains of E. faecium, seven strains of E. avium, four strains of E. durans and two strains of E. raffinosus. efr(A) was also detected in two strains of E. faecium and two strains of E. durans and efr(B) was also detected in four strains of E. faecium, five strains of E. avium and four strains of E. durans. This means the possibility of co-transfer of resistance genes between Enterococci species in natural environment. These results are the first report describing the presence of same multidrug efflux pumps in different species of Enterococci in Korea.
Screening of Rhizobium, Hairy Vetch Root Nodule Bacteria, with Promotion of Nodulation and Nitrogen Fixation
Jang, Jong-Ok ; Kwon, Mi-Kyung ; Park, Dong-Jin ; Sung, Chang Keun ; Kim, Chang-Jin ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 131~136
DOI : 10.7845/kjm.2013.3024
This study was conducted to select rhizobia from hairy vetch (Vicia villosa Roth) with nodulation and excellent nitrogen-fixing ability. Hairy vetch root was collected from 7 of cultivation region of all over the country, rhizobia were isolated from the root nodules. Isolates were re-inoculated into a hairy vetch separately and studied nodulation and nitrogen-fixing ability. As a result, total of 52 Rhizobium isolates were isolated from the hairy vetch root nodules, among these, 16 isolates were Rhizobium which show good growth at more than 0.5% NaCl concentration. These 16 isolates were re-inoculated separately, 8 weeks after, good root nodule formation was observed from Rhizobium sp. RH1, RH3, RH81, RH82, RH84, and RH93 strain treated samples. Six isolates were positive for nitrogen fixing ability, the highest acetylene reduction activity was shown by Rhizobium sp. RH84. Results suggest that the Rhizobium sp. RH84 could be used as the possibility of its application as a green manure crop of hairy vetches in nonuniform salt distribution reclaimed land.
Changes of Nitrifying Bacteria Depending on the Presence and Absence of Organic Pollutant in Nak-Dong River
Jin, Seon-Yeong ; Lee, Young-Ok ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 137~145
DOI : 10.7845/kjm.2013.3029
This study was performed at 2 sites of Nak-Dong River to investigate the changes of nitrifiers depending on the presence and absence of organic pollutants (due to the effluents of domestic wastewater treatment plant, WWTP). Conventional chemical parameters such as T-N,
-N were measured and the quantitative nitrifiers at the 2 sites were analyzed comparatively by fluorescent in situ hybridization (FISH) with NSO190 and NIT3, after checking the presence of gene amoA of ammonia oxidizing bacteria (AOB) and 16S rDNA signature sequence for Nitrobacter sp. that belongs to nitrite oxidizing bacteria (NOB). Also
-Proteobacteria were detected using FISH to get a glimpse of the general bacterial community structure of the sites. Based on the distribution structure of the
-Proteobacteria and the measurement of nitrogen in different phases, it could be said that the site 2 was more polluted with organics than site 1. Corresponding to the above conclusion, the average numbers of AOB and NOB detected by NSO160 and NIT3, respectively, at site 2 [AOB,
(cells/ml)] was more than those at site 1 [AOB,
(cells/ml)] and also their ratios to total counts were higher at site 2 (AOB, 27%; NOB, 34%) than those at site 1 (AOB, 18%; NOB, 23%). Thus, it could be concluded that the nitrification at site 2 was more active due to continuous loading of organics from the effluents of domestic WWTP, compared to site 1 located closed to raw drinking water supply and subsequently less polluted with organics.
Antibiotic Susceptibility of Vibrio spp. Isolated from West Sea
Kang, Chang-Ho ; Oh, Soo Ji ; So, Jae-Seong ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 146~149
DOI : 10.7845/kjm.2013.3028
Bacteria of genus Vibrio are Gram-negative, curved, halophilic, nonspore-forming bacteria, autochthonous inhabitans of the marine and estuarine environments. Some of the Vibrio species such as V. parahaemolyticus, V. vulnificus, and V. cholerae are associated with human disease. Each year many people have been suffering from food-borne disease caused by the ingestion of seafood. In this study, we have monitored antibiotic resistance of this microorganism in 6 coastal areas of West Sea by sampling shellfish monthly. Vibrio spp. were detected from 23.3% of 120 samples analyzed using TCBS agar plates as well as API 20E kit. Among 16 antibiotics tested, resistance to vancomycin and ampicillin was observed in 82.1% of the isolates, and Vibrio spp. resistant to rifampin (71.4%) and cephalothin (53.6%) were also high. Most of the isolates were sensitive to chloramphenicol (92.9%), sulfamethoxazole/trimethoprim (92.9%), and tetracycline (96.4%). About 71.4% of the isolates showed multiple drug resistance toward 3 antibiotics including vancomycin and ampicillin.
Use of Pyrosequencing for Characterizing Microbial Community at Phylum Level in Yeongsan River Watershed during Early Summer
Chung, Jin ; Park, Sang Jung ; Unno, Tatsuya ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 150~155
DOI : 10.7845/kjm.2013.3031
We have conducted pyrosequencing for freshwater microbial community analyses. Fourteen sites along the Yeongsan river were selected for this study, and samples were collected monthly from May to July, 2012. Total 987,380 reads were obtained from 42 samples and used for taxonomic classification and OTU distribution analysis. Our results showed that high geographical and temporal variation in the phylum level bacterial composition, suggesting that microbial community is a very sensitive parameter affected by the surrounding environments including tributaries and land use nearby. In addition, we conducted an OTU-based Microbial Source Tracking to identify sources of fecal pollution in the same region. From this study Firmicutes was found to be the most influential taxa in this region. Here, we report that the use of pyrosequencing based microbial community analysis may give an additional information on freshwater quality monitoring, in addition to the currently used water quality parameters, such as BOD and pH.
Diversity and Antimicrobial Activity of Actinomycetes from Fecal Sample of Rhinoceros Beetle Larvae
Lee, Hye-Won ; Ahn, Jae-Hyung ; Kim, Minwook ; Weon, Hang-Yeon ; Song, Jaekyeong ; Lee, Sung-Jae ; Kim, Byung-Yong ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 156~164
DOI : 10.7845/kjm.2013.3041
Actinomycetes produce diverse secondary metabolites which have the primary importance in medicine, agriculture and food production, and key to this is their ability to interact with other organisms in natural habitats. In this study, we have investigated the taxonomical and functional diversity of actinomycetes in fecal sample of rhinoceros beetle larvae (Allomyrina dichotoma L.) by using culture-dependent and -independent approaches. For the culture-independent approach, the community DNA was extracted from the sample and 16S rRNA genes of actinomycetes were amplified using actinomycetes-specific PCR primers. Thirty-seven clones were classified into 15 genera and 24 species of actinomycetes. For the culture-dependent approach, 53 strains were isolated from larval feces, of which 27 isolates were selected based on morphological characteristics. The isolates were classified into 4 genera and 14 species, and 24 isolates (89%) were identified as the genus Streptomyces. Many of the representative isolates had antimicrobial activities against plant pathogenic fungi and Gram-positive bacteria. In addition, most of the isolates (78%) showed biochemical properties to hydrolyze cellulose and casein. The results demonstrated that diverse and valuable actinomycetes could be isolated from insect fecal samples, indicating that insect guts can be rich sources for novel bioactive compounds.
Detection of Antifungal Endolichenic Fungi and Antifungal Compound
Cheon, Da-Mi ; Jang, Da Som ; Kim, Hye Young ; Choi, Kap Seong ; Choi, Sang Ki ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 165~171
DOI : 10.7845/kjm.2013.3023
To isolate a novel antifungal compound, we obtained 571 kinds of endolichenic fungi from Lichen Bioresources Center and examined their antifungal abilities. Four fungi Stereocaulon sp. (1429), Stereocaulon sp. (1430), Cryptosporiopsis sp. (0156), and Graphis sp. (1245) showed high antifungal activity against Candida albicans when they grew in both liquid and solid media. We extracted the culture supernatants of these fungi with chloroform and then ethyl acetate. The chloroform fraction exhibited the highest anti-fungal activities when those fractions were examined for the growth inhibition of Candida albicans with disc diffusion method. To see information for the inhibitor present in chloroform fraction we employed GC-MS for the fractions of Stereocaulon sp. (1429). We found that hexamethylcyclotrisiloxane, decanoic acid, hexadecanonic acid-methyl ester, 14-octadecenoic acid-methyl ester, and octadecenoic acid-methyl ester were present more in chloroform fraction than in ethylacetate fraction. This indicates that those compounds could be possible antifungal candidates since antifungal activity of chloroform extract was two times higher than that of ethyl acetate extract.
Dietary Administration of Probiotics, Bacillus sp. IS-2, Enhance the Innate Immune Response and Disease Resistance of Paralichthys olivaceus against Streptococcus iniae
Jang, Ik-Soo ; Kim, Dong-Hwi ; Heo, Moon-Soo ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 172~178
DOI : 10.7845/kjm.2013.3033
The strains were added to the feed in the concentration of
CFU/kg and 2% of fishes were given the feed twice a day (8 AM and 5 PM) for 12 weeks. In result of the nonspecific immune response study to examine Respiratory burst activity, Lysozyme activity and Phagocytosis activity every two weeks until the end of the study, all test samples showed greater activities than control samples and improved immune activity with Bacillus sp. IS-2. The mortality test performed by artificial infection using Streptococcus iniae, a pathogenic bacterium, after the completion of this study also showed over 55% greater survival rate in all test samples. In result of performing PCR using the universal primer to verify that the probiotic stays in the intestines of the fishes, all test samples showed PCR product of 1,465 bp. Based on the above findings, it was concluded that Bacillus sp. IS-2 in the feed improved farmed flatfish's immune system and resistance against diseases as the probiotics. Also, the physiological indicators discovered by this study would be useful for identifying the mechanisms of probiotics.
Isolation and Structure Determination of Metabolites from Cultures of Aspergillus protuberus
Baek, So Yoon ; Shim, Sang Hee ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 179~183
DOI : 10.7845/kjm.2013.3026
Marine-derived microbes have yielded a variety of metabolites so far. In the course of the project to find metabolites from marine microbes, an isolate of Aspergillus protuberus (SF 5767) was selected for chemical investigation. A large scale culture of this strain in PDA media was extracted with an organic solvent and the extract was fractionated by silica gel column chromatography. Repeated reverse phase HPLC of the fractions led to the isolation of three metabolites. Their chemical structures were elucidated as deoxybrevianamide E (1), brevianamide V (2), and ergosterol peroxide (3) on the basis of spectroscopic data including MS, NMR, and UV. To the best of our knowledge, chemical investigation of A. protuberus was conducted for the first time in this study.
A Unique Prokaryotic Assemblage of Wall Biofilm of a Volcanic Cave (Daesubee) in Jeju
Moon, Jong-Geun ; Jung, Man-Young ; Kim, Jong-Geol ; Park, Soo-Je ; Kim, Dae-Shin ; Kim, Jong-Shik ; Rhee, Sung-Keun ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 184~190
DOI : 10.7845/kjm.2013.3027
Cave environment provides special ecosystems for evolution of lives distant from surface environments. We investigated bacterial and archaeal communities of wall biofilm obtained from of a volcanic cave (Daesubee) in Jeju, Republic of Korea. Bacterial and archaeal 16S rRNA genes were PCR-amplified and sequenced using pyrosequencing technologies. Unique prokaryotic communities with low diversities were observed. The main bacterial sequences (ca. 83% of total reads) were affiliated with Pseudonocardia mongoliensis of phylum Actinobacteria and clustered with clones obtained from various caves. Reflection of light on the wall surface of cave might be caused by formation of beads of water caused by hydrophobic filaments of actinobacterial colonies. Main archaeal sequences (ca. 65.7% of total reads) were related with those of I.1a-Associated group of phylum Thaumarchaeota. The sequences were related with that of Candidatus Nitrosotalea devanaterra which was known to oxidize ammonia under acidic condition (ca. pH 5.0). Nutrients leached through volcanic soils contribute formation of unique microbial communities of wall biofilm of cave Daesubee.
Ultraviolet (UV)-B Irradiation Increased Vitamin D
Contents in the Fruit Bodies of Pleurotus eryngii var. ferulae
Rho, Jae-Young ; Park, Sang-Don ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 191~194
DOI : 10.7845/kjm.2013.3034
The fresh fruit bodies of Pleurotus eryngii var. ferulae was irradiated with ultraviolet (UV)-B (280-320 nm) in order to increase vitamin
contents, which was assayed using HPLC (Waters 1525, USA). The vitamin
after 3 min UV-B irradiation (
after 5 min UV-B irradiation (
), respectively, which showed the significant increase considering the vitamin
) before UV-B irradiation. This increasing effect was confirmed also for other edible mushrooms; Pleurotus eryngii, from
(3 min) and
(5 min); Lentinus edodes, from
(3 min) and
(5 min); Pleurotus ostreatus, from
(3 min) and
(5 min). Although the original content of vitamin
was the highest in P. ostreatus, the extent of increase by UV irradiation was remarkably high in P. eryngii var. ferulae.
Isolation of Bacillus atrophaeus MPL-01 from A Wild Boar and Characterization of Its Antifungal Activity
Yun, Sung-Jo ; Rho, Jae-Young ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 195~199
DOI : 10.7845/kjm.2013.3035
A bacterial strain MPL-01 was isolated from the large intestine of a wild boar. The strain was shown to have morphological, physiological and biochemical characteristics, fatty acids composition typical of Bacillus. The 16S rRNA gene sequence showed that the isolate formed distinct phyletic line that was most closely related to this of Bacillus atrophaeus (99.99%). It was proposed that the strain is classified as B. atrophaeus MPL-01. The strain MPL-01 exhibited the strongest antifungal activity against Colletotrichum acutatum, the pathogen of anthracnose of chili peppers. The ethyl acetate extract of culture filtrate possessed not only the antifungal activity but also the bio-surfactant activity. Therefore, the strain MPL-01 could be a useful bacterium in the development of bio-control process against the pathogenic fungi.
Construction of Amylolytic Industrial Strains of Saccharomyces cerevisiae for Improved Ethanol Production from Raw Starch
Im, Young-Kum ; Park, Jin-Yeong ; Lee, Ja-Yeon ; Choi, Seung-Hyun ; Chin, Jong-Eon ; Ko, Hyun-Mi ; Kim, Il-Chul ; Bai, Suk ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 200~204
DOI : 10.7845/kjm.2013.3037
To contruct amylolytic industrial strains of Saccharomyces cerevisiae which produce ethanol efficiently from raw starch, the Bacillus amyloliquefaciens
-amylase genes (Amy) or Aspergillus awamori glucoamylase genes (GA1) was separately introduced into the ribosomal DNA loci in the chromosomes of the raw starch fermenting-parental strain (ATCC 9763/
), using double 18S rDNA-integration system. Ethanol production after 3 days of fermentation by the strain that produced ethanol most efficiently from raw starch (ATCC 9763/
/YIpAG2rD) among the transformant strains was 1.5-times higher than that by the parental strain. This new strain generated 9.2% (v/v) ethanol (72 g/L) from 20% (w/v) raw corn starch and consumed 75% of the raw starch content during the same period.
Construction, Expression, and Purification of N-Terminal Variants of Lumazine Protein from Photobacterium leiognathi
Kang, Kyoung-Suk ; Kim, So-Young ; Choi, Ji-Sun ; Kim, Young-Doo ; Pokoo, Robert ; Nam, Ki-Seok ; Lee, Chan Yong ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 205~210
DOI : 10.7845/kjm.2013.3022
Lumazine protein is a fluorescent protein isolated from the bioluminescent bacteria of Photobacterium species. To generate minimal size of lumazine protein with possessing fluorescent characteristic, the gene coding for the wild type N-terminal domain of lumazine protein (N-LumP 118) containing amino acids up to 118 from Photobacterium leiognathi was produced. In addition, the genes coding for the variant proteins of N-LumP 118, replaced with one tryptophan amino acid (N-LumP 118 V41W, S48W, T50W, D64W, and A66W), were also constructed by Polymerase Chain Reaction and Site Directed Mutagenesis. These proteins were expressed in Escherichia coli by transformation with recombinant plasmids and purified by 6X-His tagging system. Spectroscopic studies have show that the purified proteins are capable of binding to the fluorescent ligand 6,7-dimethyl-8-ribityllumazine, resulted in showing of fluorescent characteristic with the minimal size of protein. From these studies, the mutant proteins containing single tryptophan amino acid residue, possessing its own intrinsic flouophore character at the different position, will be able to the use as a probe for further studies to deduce their three dimensional structure and the binding modes.
Screening of Peptide Sequences with Affinity to Bisphenol A by Biopanning
Yoo, Ik-Keun ; Choe, Woo-Seok ;
The Korean Journal of Microbiology, volume 49, issue 2, 2013, Pages 211~214
DOI : 10.7845/kjm.2013.3039
Bisphenol A (BPA) is a highly hazardous component to human since it is regarded as one of endocrine disruptors. For the analysis and/or removal of BPA, the searching for the specific ligand with a selective affinity to target BPA is required. In order to find the peptide moiety that specifically binds to BPA, the ultrasound-assisted biopanning was carried out with a phage-displayed peptide library expressing constrained heptamer. After six rounds of positive screening against BPA particles followed by the negative screening against the surface of eppendorf tube, the peptide sequence (CysLysSerLeuGluAsnSerTyrCys) with affinity to BPA was screened based on the order of frequency from the screened phage clones. To further verify the specificity of screened peptide sequence, the cross-binding affinity of the phage peptide toward BPA analogues such as Bisphenol S (BPS) and Bisphenol F (BPF) was also assessed, where the selected phage peptide showed a higher affinity to BPA over BPS and BPF.