Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples
An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific f...
Saved in:
| Published in | FEMS microbiology letters Vol. 213; no. 2; pp. 175 - 182 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier B.V
06.08.2002
|
| Subjects | |
| Online Access | Get full text |
Cover
Loading…
| Abstract | An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides.
Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were
Bacteroides thetaiotaomicron,
Bacteroides vulgatus,
Bacteroides fragilis,
Bacteroides distasonis,
Clostridium clostridiiforme,
Clostridium leptum,
Fusobacterium prausnitzii,
Peptostreptococcus productus,
Ruminococcus obeum,
Ruminococcus bromii,
Ruminococcus callidus,
Ruminococcus albus,
Bifidobacterium longum,
Bifidobacterium adolescentis,
Bifidobacterium infantis,
Eubacterium biforme,
Eubacterium aerofaciens,
Lactobacillus acidophilus,
Escherichia coli, and
Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples. |
|---|---|
| AbstractList | An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides.
Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were
Bacteroides thetaiotaomicron,
Bacteroides vulgatus,
Bacteroides fragilis,
Bacteroides distasonis,
Clostridium clostridiiforme,
Clostridium leptum,
Fusobacterium prausnitzii,
Peptostreptococcus productus,
Ruminococcus obeum,
Ruminococcus bromii,
Ruminococcus callidus,
Ruminococcus albus,
Bifidobacterium longum,
Bifidobacterium adolescentis,
Bifidobacterium infantis,
Eubacterium biforme,
Eubacterium aerofaciens,
Lactobacillus acidophilus,
Escherichia coli, and
Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples. |
| Author | Wang, Rong-Fu Beggs, Marjorie L Robertson, Latriana H Cerniglia, Carl E |
| Author_xml | – sequence: 1 givenname: Rong-Fu surname: Wang fullname: Wang, Rong-Fu email: rwang@nctr.fda.gov organization: Microbiology Division, National Center for Toxicological Research, US-FDA, Jefferson, AR 72079, USA – sequence: 2 givenname: Marjorie L surname: Beggs fullname: Beggs, Marjorie L organization: University of Arkansas for Medical Sciences, Department of Geriatrics, Core Microarray Facility, Little Rock, AR, USA – sequence: 3 givenname: Latriana H surname: Robertson fullname: Robertson, Latriana H organization: Microbiology Division, National Center for Toxicological Research, US-FDA, Jefferson, AR 72079, USA – sequence: 4 givenname: Carl E surname: Cerniglia fullname: Cerniglia, Carl E organization: Microbiology Division, National Center for Toxicological Research, US-FDA, Jefferson, AR 72079, USA |
| BookMark | eNo9kMtKAzEUhoNUsK0-gpClLkZP5p6VSL1CwYW6DqfJSRuZSWSSFvTpnXpb_fDxnwvfjE188MTYqYALAaK-fIaiaTMBsjmD_ByghTyTB2wqqqbMalm3Ezb9rxyxWYxvAFDmUE_Z5w1Ft_YcveG0w26LyQXPg-Whc-vgt7qjkJyhrHd6CDgM-MF7SptguA0DTxvihhLpv7HNtkfPnU8Uk_PY8RXqRIPDkXFLeiQR-_eO4jE7tNhFOvnNOXu9u31ZPGTLp_vHxfUyI5GXKatXTWUtSWw1iCa31BZYY2tRWC1RYmFRy6ZuKrJgCltUuqRSCNtUYFamksWcXf3spfHIztGgonbkNRk3jH8rE5wSoPYq1bdKtfekIFffKpUsvgCYB212 |
| ContentType | Journal Article |
| Copyright | 2002 Federation of European Microbiological Societies |
| Copyright_xml | – notice: 2002 Federation of European Microbiological Societies |
| DOI | 10.1016/S0378-1097(02)00802-9 |
| DatabaseTitleList | |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1574-6968 |
| EndPage | 182 |
| ExternalDocumentID | S0378109702008029 |
| GroupedDBID | --- --K -~X .3N .GA .Y3 05W 0R~ 10A 1B1 1OC 1TH 1~5 29H 31~ 36B 3V. 4.4 48X 4G. 50Y 50Z 51W 51X 52M 52N 52O 52P 52S 52T 52W 52X 53G 5GY 5HH 5LA 5VS 5WD 66C 7-5 702 7PT 7X7 8-0 8-1 8-3 8-4 8-5 88E 8AO 8C1 8FE 8FH 8FI 8FJ 8UM 8WZ 930 A03 A6W A8Z AABJS AABMN AAEDT AAESY AAHHS AAIMJ AAIYJ AAJQQ AALRI AAMDB AAMVS AAOGV AAONW AAPQZ AAPXW AAQFI AAQXK AAUQX AAVAP AAWDT AAXUO ABCQN ABEFU ABEML ABEUO ABIXL ABJNI ABMAC ABPTD ABQLI ABSAR ABSMQ ABUWG ABXVV ACBWZ ACCFJ ACFRR ACGFO ACGFS ACIUM ACPRK ACSCC ACUFI ACUTJ ACXQS ADBBV ADEIU ADEZT ADGZP ADHKW ADHZD ADIPN ADMUD ADORX ADQLU ADRIX ADRTK ADVEK ADYVW ADZOD AEEZP AEGPL AEJOX AEKSI AELWJ AEMDU AENEX AENZO AEPUE AEQDE AETBJ AEWNT AFBPY AFFZL AFGWE AFIYH AFKRA AFOFC AFRAH AFULF AFXEN AFYAG AFZJQ AGINJ AGSYK AHEFC AI. AIKOY AITUG AIWBW AJAOE AJBDE AJEEA AKWXX ALMA_UNASSIGNED_HOLDINGS ALUQC ANFBD APIBT APWMN ARIXL ASAOO ATDFG AVWKF AXUDD AYOIW AZBYB AZQFJ BAFTC BAYMD BBNVY BCRHZ BDRZF BENPR BEYMZ BFHJK BHONS BHPHI BPHCQ BQDIO BSWAC BVXVI BY8 BYORX CAG CASEJ CCPQU CDBKE COF CS3 CXTWN D-E D-F DAKXR DC6 DCZOG DFGAJ DILTD DPPUQ DR2 DU5 EBS EDH EJD EMB EMOBN ESTFP F00 F01 F04 F5P FDB FEDTE FGOYB FHSFR FLUFQ FOEOM FYUFA FZ0 G-S G.N GAUVT GI5 GJXCC GODZA H.T H.X HAR HCIFZ HF~ HMCUK HOLLA HVGLF HZI HZ~ I-F IAO IEP IHE IHR ISR ITC IX1 J0M J21 K48 KAQDR KBUDW KOP KSI KSN LC2 LC3 LH4 LK8 LP6 LP7 LW6 LW9 M1P M41 M7P MK4 MM. N04 N05 N9A NF~ NLBLG NOMLY NQ- NVLIB O9- OAWHX OBOKY ODMLO OJQWA OJZSN OK1 OVD OWPYF P2P P2X P4D PAFKI PEELM PQQKQ PROAC PSQYO Q.N Q11 Q5Y QB0 R.K R2- RIG ROL ROX ROZ RPZ RUSNO RX1 RXO SEW SIN SSZ SUPJJ SV3 TCN TEORI TLC TOX UB1 UKHRP V8K VH1 W8V W99 WQJ WRC WYUIH XFK XG1 XPP Y6R YAYTL YKOAZ YXANX ZCN ZXP ~02 ~IA ~KM ~WT |
| ID | FETCH-LOGICAL-e124t-6b75ffe9a8c0172fe83a6a8fa1fc9a9a3fac97675ef0d3f35c4e411f750dbd593 |
| ISSN | 0378-1097 |
| IngestDate | Fri Feb 23 02:34:08 EST 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 2 |
| Keywords | Polymerase chain reaction 16S rDNAs amplification Human intestinal bacterium Oligonucleotide-microarray |
| Language | English |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-e124t-6b75ffe9a8c0172fe83a6a8fa1fc9a9a3fac97675ef0d3f35c4e411f750dbd593 |
| PageCount | 8 |
| ParticipantIDs | elsevier_sciencedirect_doi_10_1016_S0378_1097_02_00802_9 |
| PublicationCentury | 2000 |
| PublicationDate | 2002-08-06 |
| PublicationDateYYYYMMDD | 2002-08-06 |
| PublicationDate_xml | – month: 08 year: 2002 text: 2002-08-06 day: 06 |
| PublicationDecade | 2000 |
| PublicationTitle | FEMS microbiology letters |
| PublicationYear | 2002 |
| Publisher | Elsevier B.V |
| Publisher_xml | – name: Elsevier B.V |
| References | Zoetendal, Akkernams, DeVos (BIB15) 1998; 64 Drasar, B.S. and Roberts, A.K. (1990) Control of the large bowel microflora. In: Human Microbial Ecology (Hill, M.J. and Marsh, P.D., Eds.), pp. 95–100. CRC Press, Florida. Schneider, Gall, Le Girard-Pipqu, Piche, Pompei, Nano, Hebuterne, Rampal (BIB7) 2000; 39 Tannock, Munro, Harmsen, Welling, Smart, Gopal (BIB10) 2000; 66 Wang, Cao, Cerniglia (BIB23) 1997; 11 Wang, Cao, Campbell, Hairston, Franklin, Cerniglia (BIB21) 1994; 124 Song, Kato, Liu, Matsumya, Kato, Watanabe (BIB17) 2000; 187 Langendijk, Schut, Jansen, Raangos, Kamphuis, Wilkinson, Welling (BIB16) 1995; 61 McCartney, Wenzhi, Tannock (BIB18) 1996; 62 Witte (BIB9) 2000; 14 Wang, Cao, Cerniglia (BIB22) 1996; 62 Wu, Thompson, Li, Hurt, Tiedje, Zhou (BIB24) 2001; 67 Moore, Moore (BIB1) 1995; 61 Moore, Holdeman (BIB2) 1974; 27 Shoemaker, Vlamakis, Hayes, Salyers (BIB5) 2001; 67 Chizhikov, Rasooly, Chumakov, Levy (BIB25) 2001; 67 Wilson, Blitchington (BIB19) 1996; 62 Tannock (BIB20) 2002; 73 Call, Brockman, Chandler (BIB26) 2001; 67 Cerniglia, Howard, Fu, Franklin (BIB11) 1984; 123 Drasar, B.S. and Duerden, B.I. (1991) Anaerobes in the normal flora of man. In: Anaerobes in Human Disease (Duerden, B.I. and Drasar, B.S., Eds.), pp. 162–179. Wiley-Liss, New York. Falk, Hooper, Midtvedt, Gordon (BIB14) 1998; 62 Chadwick, George, Claxton (BIB12) 1992; 24 Tannock (BIB6) 1999; 76 Cerniglia, Kotarski (BIB8) 1999; 29 Von den Bogaard, Stobberingh (BIB4) 1999; 58 |
| References_xml | – volume: 11 start-page: 259 year: 1997 end-page: 265 ident: BIB23 article-title: PCR detection of publication-title: Mol. Cell. Probes – volume: 67 start-page: 71 year: 2001 end-page: 80 ident: BIB26 article-title: Detection and genotyping publication-title: Int. J. Food Microbiol. – volume: 62 start-page: 1157 year: 1998 end-page: 1170 ident: BIB14 article-title: Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology publication-title: Microbiol. Mol. Biol. Rev. – volume: 64 start-page: 3854 year: 1998 end-page: 3859 ident: BIB15 article-title: Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria publication-title: Appl. Environ. Microbiol. – volume: 67 start-page: 561 year: 2001 end-page: 568 ident: BIB5 article-title: Evidence for extensive resistance gene transfer among publication-title: Appl. Environ. Microbiol. – volume: 76 start-page: 265 year: 1999 end-page: 278 ident: BIB6 article-title: Analysis of the intestinal microflora: A renaissance publication-title: Antonie van Leeuwenhoek – volume: 58 start-page: 589 year: 1999 end-page: 607 ident: BIB4 article-title: Antibiotic usage in animals: Impact on bacterial resistance and public health publication-title: Drugs – reference: Drasar, B.S. and Duerden, B.I. (1991) Anaerobes in the normal flora of man. In: Anaerobes in Human Disease (Duerden, B.I. and Drasar, B.S., Eds.), pp. 162–179. Wiley-Liss, New York. – volume: 73 start-page: 410s year: 2002 end-page: 414s ident: BIB20 article-title: Molecular assessment of intestinal microflora publication-title: Am. J. Clin. Nutr. – reference: Drasar, B.S. and Roberts, A.K. (1990) Control of the large bowel microflora. In: Human Microbial Ecology (Hill, M.J. and Marsh, P.D., Eds.), pp. 95–100. CRC Press, Florida. – volume: 124 start-page: 229 year: 1994 end-page: 237 ident: BIB21 article-title: The use of PCR to monitor the population abundance of six human intestinal bacterial species in an in vitro semicontinuous culture system publication-title: FEMS Microbiol. Lett. – volume: 61 start-page: 3069 year: 1995 end-page: 3075 ident: BIB16 article-title: Quantitative fluorescence in situ hybridization of publication-title: Appl. Environ. Microbiol. – volume: 14 start-page: 321 year: 2000 end-page: 325 ident: BIB9 article-title: Ecological impact of antibiotic use in animals on different complex microflora: Environment publication-title: Int. J. Antimicrob. Agents – volume: 24 start-page: 425 year: 1992 end-page: 492 ident: BIB12 article-title: Role of gastrointestinal mucosa and microflora in the bioactivation of dietary and environmental mutagens or carcinogens publication-title: Drug Metab. Rev. – volume: 66 start-page: 2578 year: 2000 end-page: 2588 ident: BIB10 article-title: Analysis of the fecal microflora of human subjects consuming a probiotic product containing publication-title: Appl. Environ. Microbiol. – volume: 187 start-page: 167 year: 2000 end-page: 173 ident: BIB17 article-title: Rapid identification of 11 human intestinal publication-title: FEMS Microbiol. Lett. – volume: 67 start-page: 5780 year: 2001 end-page: 5790 ident: BIB24 article-title: Development and evaluation of functional gene arrays for detection of selected genes in the environment publication-title: Appl. Environ. Microbiol. – volume: 62 start-page: 4608 year: 1996 end-page: 4613 ident: BIB18 article-title: Molecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans publication-title: Appl. Environ. Microbiol. – volume: 27 start-page: 961 year: 1974 end-page: 979 ident: BIB2 article-title: Human fecal flora: The normal flora of 20 Japanese-Hawaiians publication-title: Appl. Microbiol. – volume: 62 start-page: 1242 year: 1996 end-page: 1247 ident: BIB22 article-title: PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples publication-title: Appl. Environ. Microbiol. – volume: 62 start-page: 2273 year: 1996 end-page: 2278 ident: BIB19 article-title: Human colonic biota studied by ribosomal DNA sequence analysis publication-title: Appl. Environ. Microbiol. – volume: 61 start-page: 3202 year: 1995 end-page: 3207 ident: BIB1 article-title: Intestinal floras of populations that have a high risk of colon cancer publication-title: Appl. Environ. Microbiol. – volume: 123 start-page: 262 year: 1984 end-page: 270 ident: BIB11 article-title: Metabolism of nitropolycyclic aromatic hydrocarbons by human intestinal microflora publication-title: Biochem. Biophys. Res. Commun. – volume: 29 start-page: 238 year: 1999 end-page: 261 ident: BIB8 article-title: Evaluation of veterinary drug residue in food for their potential to affect human intestinal microflora publication-title: Regul. Toxicol. Pharmacol. – volume: 39 start-page: 248 year: 2000 end-page: 255 ident: BIB7 article-title: Total artificial nutrition is associated with major changes in the fecal flora publication-title: Eur. J. Nutr. – volume: 67 start-page: 3258 year: 2001 end-page: 3263 ident: BIB25 article-title: Microarray analysis of microbial virulence factors publication-title: Appl. Environ. Microbiol. |
| SSID | ssj0004206 |
| Score | 2.0700216 |
| Snippet | An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA... |
| SourceID | elsevier |
| SourceType | Publisher |
| StartPage | 175 |
| SubjectTerms | 16S rDNAs amplification Human intestinal bacterium Oligonucleotide-microarray Polymerase chain reaction |
| Title | Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples |
| URI | https://dx.doi.org/10.1016/S0378-1097(02)00802-9 |
| Volume | 213 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Nj9MwELXKIiQuiE8BC8gHDqCVl8RJm_iIylYrRDmwu6K3aJLYVVFJpJAedv_Z_jtmbDeOtCDBXqIqcmLJ8zp-nsybYextVaWphLwSBh2kSGtAP6giI6gKapaUWZ1JEicvv85OL9LPq-lqMrkeZS3t-vK4uvqjruQ2VsV7aFdSyf6HZYeX4g38jfbFK1oYr_9k4082_cLG_0PVbqJ_7XazbhsqVdz2m1qLn5R2B10Hl75l9JBdWOteVwNrtBF9qiCBf3yiqaWr5QwUFTHaCiiBygn_GnPaxcny7MjOsK_otLUaoYGtf_cx6W9tsxaL3RAB0D4uv4TuR4tH9qMhEO3yvb0Y7At1EYAGgo5irrtms_Z5vnPotl5PsY9eSJs7NwshtRuyGifloqNt5BJ3j7X3zFkqqJLP2HVLp2P1GJUjRxy7fix-T49dg6Mb24WLXJwN8yGpp4K0yiqQhQp75JC5aMfS0EjaQeoOuyvxhELNM7JVFiS5MnKfyf2bg3jsQ5juXSTf-6lGXGjEb84fsgf-YMI_OpQ9YhPdPGb3XKvSyyfsymGNI9Z4wBpvDf871rjDGkesccQaH7BGj1ms8YA1vsca3uMWa9xj7Sm7WJycz0-F79shNLLFXszKbGqMVugCKMJgdJ7ADHIDsakUKEgMVIqKCGkT1YlJplWq0zg2SF7rsp6q5Bk7aNpGP2e8ljUeOHBfydGpJBGyBDyAVyAhKxPA3eYFy_fLVnjK6KhggSYuQgYjrrjPtZCFXfFCvbz9o4fsfsDyK3bQdzv9GrlpX76xKPgNVj6Pog |
| linkProvider | ProQuest |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Design+and+evaluation+of+oligonucleotide-microarray+method+for+the+detection+of+human+intestinal+bacteria+in+fecal+samples&rft.jtitle=FEMS+microbiology+letters&rft.au=Wang%2C+Rong-Fu&rft.au=Beggs%2C+Marjorie+L&rft.au=Robertson%2C+Latriana+H&rft.au=Cerniglia%2C+Carl+E&rft.date=2002-08-06&rft.pub=Elsevier+B.V&rft.issn=0378-1097&rft.eissn=1574-6968&rft.volume=213&rft.issue=2&rft.spage=175&rft.epage=182&rft_id=info:doi/10.1016%2FS0378-1097%2802%2900802-9&rft.externalDocID=S0378109702008029 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0378-1097&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0378-1097&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0378-1097&client=summon |