Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples

被引:60
作者
Shanks, Orin C.
Santo Domingo, Jorge W.
Lamendella, Regina
Kelty, Catherine A.
Graham, James E.
机构
[1] US EPA, Off Res & Dev, Natl Risk Management Res Lab, Cincinnati, OH 45268 USA
[2] Univ Louisville, Dept Microbiol & Immunol, Louisville, KY 40202 USA
[3] Univ Louisville, Dept Biol, Louisville, KY 40202 USA
关键词
D O I
10.1128/AEM.00023-06
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of Bacteroidales-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select Bacteroidales-like bovine GFE sequences exhibited extremely high specificity (> 99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities.
引用
收藏
页码:4054 / 4060
页数:7
相关论文
共 39 条
[1]   Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons [J].
Acinas, SG ;
Marcelino, LA ;
Klepac-Ceraj, V ;
Polz, MF .
JOURNAL OF BACTERIOLOGY, 2004, 186 (09) :2629-2635
[2]   AN ASSESSMENT OF BACTEROIDES-FRAGILIS GROUP ORGANISMS AS INDICATORS OF HUMAN FECAL POLLUTION [J].
ALLSOP, K ;
STICKLER, DJ .
JOURNAL OF APPLIED BACTERIOLOGY, 1985, 58 (01) :95-99
[3]  
ALTHSCHUL SF, 1997, NUCLEIC ACIDS RES, V25, P3389
[4]  
[Anonymous], 2002, EPA841R02001
[5]   Improved prediction of signal peptides: SignalP 3.0 [J].
Bendtsen, JD ;
Nielsen, H ;
von Heijne, G ;
Brunak, S .
JOURNAL OF MOLECULAR BIOLOGY, 2004, 340 (04) :783-795
[6]  
Benenson AS., 1995, Control of communicable diseases manual. Control of communicable diseases manual, V16th
[7]   Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes [J].
Bernhard, AE ;
Field, KG .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2000, 66 (04) :1587-1594
[8]   A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA [J].
Bernhard, AE ;
Field, KG .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2000, 66 (10) :4571-4574
[9]  
COVERT TC, 1999, SALMONELLA
[10]  
Daly K, 2001, FEMS MICROBIOL ECOL, V38, P141, DOI 10.1111/j.1574-6941.2001.tb00892.x