JOURNAL OF BACTERIOLOGY, Jan. 1991, p. 697-703 Vol. 173, No.

2
0021-9193/91/020697-07$02.00/0
Copyright © 1991, American Society for Microbiology

16S Ribosomal DNA Amplification for Phylogenetic Study

WILLIAM G. WEISBURG,* SUSAN M. BARNS, DALE A. PELLETIER, AND DAVID J. LANE
GENE-TRAK Systems, 31 New York Avenue, Framingham, Massachusetts 01701
Received 16 April 1990/Accepted 7 November 1990

A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on
aphylogenetically and taxonomically wide range of bacteria is described along with methods for their use and
examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from
many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for
purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An
obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S
rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera
Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material
found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the
phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the
need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is
possible can be derived from a readily obtainable lyophilized bacterial culture.

The comparison of rRNA sequences is a powerful tool for 5% of this resuspended DNA was put into the PCR amplifi-
deducing phylogenetic and evolutionary relationships among cation.
bacteria, archaebacteria, and eucaryotic organisms. These PCR amplification and purification of product. Approxi-
sequences have been derived previously by methods includ- mately 1 to 3 ,ug of genomic DNA was amplified in a 100-pu
ing oligonucleotide cataloging (6), sequencing of clones, reaction by using the Geneamp kit (U.S. Biochemicals,
direct sequencing of RNA by using reverse transcriptase Cleveland, Ohio; presently, these kits are only available
(11), and sequencing of material amplified by polymerase from Perkin-Elmer Cetus, Norwalk, Conn.). When the ly-
chain reaction (PCR) (3, 5, 15). The present study expands ophilized ampoule DNA was amplified, 1 plI was routinely
on the use of DNA amplification technology for the study of used. Conditions consisted of 25 to 35 cycles of 95°C (2 min),
rRNA sequences within the eubacteria. Several primers are 42°C (30 s), and 72°C (4 min), plus one additional cycle with
described, and novel methods for their use are presented. a final 20-min chain elongation. The temperature and salt
Sogin and coworkers (15) described a primer pair for the conditions were not optimized for low inputs of template
enzymatic amplification of eucaryotic small-subunit rRNA DNA. Between 25 and 35 cycles, the number of cycles did
gene (rDNA) sequences. Boettger (3) and Edwards and not seem to appreciably affect yield of product. All amplifi-
coworkers (5) examined the sequence of Mycobacterium cations were performed in a Perkin-Elmer temperature con-
bovis 16S rRNA PCR products without cloning. They also troller, although a cursory examination of other instruments
examined a limited set of organisms with their PCR primers: indicated that they may all perform adequately under these

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four gamma purple bacteria and two gram-positive species reaction conditions (data not shown). The amplification
with high G+C content were experimentally amplified. products were purified on Centricon 100 columns (Amicon),
The present study describes primers for the amplification by following the specifications of the manufacturer, followed
of most eubacterial 16S rRNAs, details preparation of sam- by ethanol precipitation.
ples, and presents our current sequencing procedures. Cloning. Cloning of PCR products was done by using
standard methods (13). Amplified products were partially
MATERIALS AND METHODS purified with spin columns (see above), cleaved at the
appropriate restriction endonuclease sites within the linkers
Nucleic acid preparation. Genomic DNAs were prepared (see Table 1 and Fig. 1) and ligated into correspondingly
by using standard methods (13, 14). Preparation of DNA restricted pGEM-3 or pGEM-4 vectors (Promega Corp.,
from lyophilized ampoules consisted of suspending the ly- Madison, Wis.). We were able to successfully clone rDNAs
ophilized cells in 0.2 ml of 10 mM Tris hydrochloride (pH that had been either agarose gel purified or not gel purified.
8.3)-2.5 mM MgCl2-50 mM KCl. This was added to approx- Plasmid preparation was performed by using the alkaline
imately 0.1 ml of 0.1-mm-diameter acid-washed glass beads, lysis method (2, 13) followed by phenol extraction. For
10 ,u of 20% sodium dodecyl sulfate, and approximately 200 cloning of PCR products into plasmid vectors, approxi-
RI of phenol, saturated with the above buffer. This sample mately 20 ,g of plasmid DNA restriction endonuclease cut
was shaken in a 500-,u microcentrifuge tube, seated within a with a combination of SalI and BamHI (rarely found inter-
2-ml tube, in a Mini-Bead Beater (Biospec Products) for 2 nally within 16S) was dephosphorylated with calf intestinal
min. After phase separation (10 min at approximately 15,000 alkaline phosphatase, gel purified, and stored frozen. This
x g), the aqueous phase was ethanol precipitated. The pellet vector preparation should be enough for 20 or more cloning
was suspended in 20 to 50 RI of TE buffer (10 mM Tris experiments. Anaplasma marginale rDNA was cloned into
hydrochloride [pH 8.0], 1 mM EDTA), and between 2 and the SalI-BamHI site in this manner.
Sequencing methods. The sequencing method of plasmid-
cloned material used the T7 polymerase (Sequenase; U. S.
*
Corresponding author. Biochemicals) kit, and standard procedures were followed
697
698 WEISBURG ET AL. J. BACTERIOL.

TABLE 1. Summary of primers for the PCR amplification of eubacterial 16S rDNAa
Primer Sequence (5' to 3') Designed for:
fDl ccgaattcgtcgacaacAGAGTTTGATCCTGGCTCAG Most eubacteria
fD2 ccgaattcgtcgacaacAGAGTTTGATCATGGCTCAG Enterics and relatives
fD3 ccgaattcgtcgacaacAGAGTTTGATCCTGGCTTAG Borrelia spirochetes
fD4 ccgaattcgtcgacaacAGAATTTGATCTTGGTTCAG Chlamydiae
rDl cccgggatccaagcttAAGGAGGTGATCCAGCC Many eubacteria
rPl cccgggatccaagcttACGGTTACCTTGTTACGACTT Enterics (and most eubacteria)
rP2 cccgggatccaagcttACGGCTACCTTGTTACGACTT Most eubacteria
rP3 cccgggatccaagcttACGGATACCTTGTTACGACTT Fusobacteria (and most eubacteria)
a Primer abbreviations: f, forward; r, reverse; D, distal; P, proximal. All primer sequences are presented in 5' to 3' orientation. Linker sequences containing restriction
sites for cloning are designated in lowercase letters. The "f ' series of linkers all contain EcoRI and SalI sites, and the "r" series all contain HindIJl, BamHI, and XmaI
recognition sequences. Reverse primers produce sequences complimentary to the rRNA. Primers rPl, rP2, and rP3 are identical except for the 17th base from the 3'
end. Under most amplification conditions, they should be functionally equivalent. Primer rP2 has the sequence corresponding to the greatest diversity of bacteria.

CONS=90% AGAGUUUGAUC UGGCUCAG GAACGCUGGCGG - GC U A ACAUGCAAGUCG CG

E. coli AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCA--GGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGC
An. marg i agaguuugauccuggcucagAACGAACGCUGGCGGCA-AGCUUAACACAUGCAAGUCGAACGGACCGUAUACGCAGCUUGC
f Dl 5' ccaattcgtcgacaacAGAG¶TTGATCCTGGCTCAG-3' (extend)>
fD2 5 'ccqaattcgtcgacaacAGAGTITGATCATGGCTCAG-3' (extend) ---->
fD3 5'ccqaattcgtcgacaacAGAGTl'GATCCTGGCTrAG-3' (extend) ---->
fD4 5' ccqaattcgtcgacaacAGAA TTGATC'ITGGTTCAG-3' (extend) ---->
CONS=90% G GGC ACGGGUG GUAA U A U CC GG A A C GAAA UAAUACC AU
E. coli UUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCG
An. zuargi UGCGUGUAUGGUUAGUGGCAGACGGGUGAGUAAUGCAUAGGAAUCUACCUAGUAGUAUGGGAUAGCCACUAGAAAUGGUGtGUAAUACUGUAUAAUCCUG
CONS=90% AAAG GA AU AG U GUUGG GGUAA GGC ACCAAG C A GA U
E. coli CAAGACCAAAGAGCGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCU
An. marqi C-GGGGGAAAGA--------UUUA -----UCGCUAUUAGAUGAGCCUAUGUCAGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCGGUGAUCUGU
CONS=90% A C G CUGAGAGG GA C G CACA UGG ACUGAGACACGG CCA ACUCCUACGGGAGGCAGCAGU GGAAU UU CAAUGG G AA CU
E. col i AGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCU
An .margi AGCUGGUCUGAGAGGAUGAUCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGWGCAAGCCU
CONS=90% GA AGC A GCCGCGUG GA GA G U GG GUAAA CU U GA G UGAC UA
E. coli GAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUA
An.margi GAUCCAGCUAUGCCGCGUGAGUGAGGAAGGCCUUAGGGUUGUAMAACUCUUUCAGUAGGGAAGAU- ------------------------MUGACGGUA
CONS=90% A AAGC CGGCUAACU GUGCCAGCAGCCGCGGUMUAC AGG GC AGCGUU CGGA U A UGGGCGUAAAG G G AGG G
E. coli CCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGMUUACUGGGCGUAAAGCGCACGCAGGCG
An.margi CCUACAGAAGAAGUCCCGGCAAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGGGCAAGCGUUGUUCGGAMUAUUGGGCGUAAAGGGCAUGUAGGCG
CONS=90% G AGU G GU AAA GCU AAC A AC CU GA AG GG GAAUU GUGUA
E. coli GUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAWUUCCAGGUGUA
An.margi GUUUGGUAAGUUAAAGGUGAAAUACCAGGGCUUAACCCUGGGGCUGCUUUUAAUACUGCAGGACUAGAGUCCGGAAGAGGAUAGCGGAAUUCCUAGUGUA
CONS=90% G GGUGAMU CGUAGA AU A GAA ACC U GCGAAGGC CUGG A UGAC CU A G CGAMGCGUGGGGAGC MCAGA
E. coli GCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGMGACUGACGCUCAGGUGCGAMGCGUGGGGAGCAMCAGGA
An.margi GAGGUGAAAUUCGUAGAUAUUAGGAGGAACACCAGUGGCGAAGGCGGCUGUCUGGUCCGGUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGA

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CONS=90 WUAGAUACCCUGGUAGUCCACGC UAAACGAUG U GU G G AG AACGC UAA CCGCCUGGG
E. coli UUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGG
An.marqi UUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGAGUGCUGAAUGUWGGGC-UUUU--GCCUWGUGWGUAgcUAACGCGWAAGCACUCCGCWGGG
CONS=90% AGUACG CGCAAG U AAACUCAAA GAAUUGACGGGG CCCGCACAAGCGG GGAG AUGUGGUUUAAUUCGA G ACGCG GAACCUUACC
E. coli GAGUACGGCCGCMGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUG
An.margi GACUACGGUCGCAAGACUAMACUCAAAGGAAUUGACGGGGACnCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAAAACCWACCAC
CONS=90% UUGACAU -GA A - - ACAGGUG UGCAUGG UGUCGUCAGCUCGUG CGUGAG U
E. coli GUCUUGACAUCCACGGAA-GUUUUCA-GAGAUGAGAAU-GUGCCWCG-GGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGWGUGAAAU
An.margi UUCUUGACAUGGAGGCUAGAUCCUUCUUAACAGAAGGGCG-CAGUUCGGCUGGGCCUCGCACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAU
CONS-90% GUUGGGUUAAGUCCCGCAACGAGCGCAACCC GUU C A C G G ACUC ACUGCC G AA GGAGGAAGG
E. coli GUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUC-CGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGMAAGG
An.uargi GUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCAUCCUUAGUUACCAGCGGGUAAUGCCGGGCACUUUAAGGAAACUGCCAGUGAUAAACUGGAGGMGG
CONS-90% G GGA GACGUCAA UC UCAUG CCCUUA G GGGCUACACACGU CUACAAUGG ACA G G GC A G GA AGC AA C
E. coli UGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGGAAGCGACCUCGCGAGAAGCGGACC
An.nargi UGGGGAUGAUGUCAAGUCAGCACGGCCCUUAUGGGGUGGGCUACACACGUGCUACAAUGGCGACUACMUAGGUUGCAACGUCGCAAGGCUGAGCUAAUC
CONS-90% AAA UC AGU CGGAU G CUGCAACUCG C UGMG GGA U GCUAGUAAUCG AUCAG A CGGUGAAUACGUUC
E. coli UCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUC
An. argi CGU-AAAAGUCGUCUCAGUUCGGAUUGUCCUCUGUAACUCGAGGGCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGCAUGCCACGGUGAAUACGUUC
CONS=90% CGGG CUUGUACACACCGCCCGUCA CA G AG AAG AACC GGA C A GU G
E. coli CCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAGAAGUAGGUAGCUUMAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUG
An.suargi UCGGGUCUUGUACACACUGCCCGUCACGCCAUGGGMUUGGCUUCUCGAA GCUGGUGCGCCAACCGUMAGGAGGCAGCCAUUUAAGGUUGGGUCGGUG
CONS=90% A UGGG AAGUCGUAACAAGGUA CC UA GAA UG GG UGGAU ACCUCCUUU
E. coll ACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
An. argi ACUGGGGUGAAGUCGUAACAAGGUAGCUGUAGGUGAACCUGCggcuqgaucaccuccuu
rDl (---- (extend) 3'-CCGACCTAGTGGAGGAAttcgaacctagqgccc5'
rPl <---- 3'-TTCAGCATTGTTCCATTGCAttcgaacctaaagccc-5'
rP2 (---- 3'-TTCAGCATTGTTCCATCGGCAttcgaacctaqgqccc-5'
rP3 <---- 3'-TTCAGCATTGTTCCATAGGCAttcgaacctagggccc-5'
VOL. 173, 1991 16S rDNA AMPLIFICATION 699

TABLE 2. Primer combinations that have been proven to The primer pair designated fDl and rDl is capable of
produce an approximately l,500-bp fragment amplifying a wide variety of bacterial taxa. Replacing rDl
Species Primer pair with rPl extends the diversity of species even further, but
Neisseria gonorrhoeae .... ............. fDl + rDl from the perspective of amplifying the maximum number of
Coxiella burnetii ................. fDl + rDl nucleotides of 16S rDNA, rDl is preferable; it is closer to the
Anaplasma marginale .... ............. fDl + rDl 3' end.
Neisseria meningitidis ................. fDl + rDl Amplification of 16S rDNAs from several different bacte-
Bacteroides fragilis .................. fD + rP2 rial taxa by using different combinations of primers is shown
Borrelia burgdorferi ..................fD3 + rDl in Fig. 2. The PCR conditions used in this study were not
Borrelia hermsii ..................fD3 + rDl
Clostridium perfringens .... ............. fDl + rDl rigorously optimized for either specificity or low-input tar-
Mycoplasma pneumoniae ..... ............ fDl + rPl get. In general, these conditions seem to give a dependable
Mycoplasma hominis ................. fDl + rPl yield of full-sized product. Additional products of varying
Mycoplasma genitalium ................. fDl + rPl intensities were produced from some of the DNAs. As
Ureaplasma urealyticum .................i fD + rPl shown in Fig. 2, the smaller-sized band produced from
Campylobacterjejuni .................i tD + rPl Bacteroides fragilis DNA, derived from both culture and
Shigella flexneri .................fD2 + rPl lyophilized ampoule, is the most abundant spurious band
Shigella sonnei ................. fD2 + rPl within the bacterial strains examined. The occurrence of the
Chlamydia psittaci .................. f4 + rDl
additional PCR product in B. fragilis did not interfere with
Chlamydia trachomatis .... ............. f4 + rDl
Chlamydia pneumoniae .... ............. f4 + rDl the ability to clone the 16S rDNA. Of note is the fact that the
Mycobacterium bovis ................. fDl + rDl only reaction shown in which the rP2 primer was used was
Legionella pneumophila .... ............. fDl + rDl the B. fragilis amplification; in another experiment (not
shown), the same spurious band was produced when primer
rPl was substituted for rP2.
A. marginale 16S rRNA. To test the utility of these
(1; see Sequenase package insert), including the alkaline methods for phylogenetic study, A. marginale, a member of
denaturation method recommended by the manufacturer. the Rickettsiales, was used as an example. A. marginale is
For sequencing of amplified material directly, four identi- an obligate intracellular, erythrocytic, arthropod-transmitted
cal 100-RI amplification reactions were performed on each
sample, with the resultant material being pooled and purified parasite whose pathogenic range includes several ruminant
(see above). A 500-ng amount of template (amplification species (16). Previous attempts at sequencing directly from
product) was combined with 10 ng of primer, 2 ,ul of the RNA isolated from Renografin-purified A. marginale
Sequenase buffer, and water to 10 ,ul. This sample was held cells (supplied by J. Samuel, Pullman, Wash.) were unsuc-
at 98°C for 7 min and cooled to room temperature for 1 min, cessful (data not shown). Attempts at cloning into lambda
and then the labeling reaction was performed at either room phage vectors also were without success. A DNA prepara-
temperature or 37°C for 5 min. (These are slight modifica- tion (by standard phenol methods) (13, 14) from this same
tions of the procedures outlined in reference 19.) Chain gradient-purified material was used for amplification. By
elongation was terminated with sample loading buffer, and using the generally applicable primer pair, fDl + rDl,
sequencing was performed on buffer-gradient gels (1). amplification of the 16S rDNA of A. marginale was enabled.
Sequencing primers. Sequencing primers useful for con- The 16S rRNA sequence determined for A. marginale is
served regions within 16S rDNA genes, both forward and shown in Fig. 1, aligned with E. coli and with the primers.
reverse, have been described previously (11, 20). Forward Approximately 250 nucleotides of sequence were initially

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primers used in this study spanned positions (Escherichia determined directly from PCR-amplified material by using a
coli numbers) (4) as follows: 339 to 357, 785 to 805, 907 to primer located at position 519 (E. coli numbers) (4), reading
926, 1391 to 1406. Reverse primers included 357 to 342, 536 toward the 5' end of the molecule. After cloning the ampli-
to 519, 802 to 785, 926 to 907, 1115 to 1100, 1406 to 1392, and fication product into a pGEM vector, that same sequence
1513 to 1494. was again determined to validate the accuracy of the direct
sequencing, without disagreement. Aligning the sequence
RESULTS AND DISCUSSION with the accepted secondary structure (8, 25) indicated a
deleted helix within the 455 to 480 region (E. coli numbers)
Primers for 16S rDNA gene amplification. The primers (4) characteristic of a few bacterial groups (8, 25). The
used for amplification of bacterial 16S rDNA are displayed in complete A. marginale 16S rRNA sequence was determined
Table 1 as well as in an aligned format in Fig. 1. Their from the cloned amplification product. The structure of the
empirical and theoretical utility are described in Tables 2 and helices between positions 180 and 220 (E. coli numbers) (4)
3. Their implied hybridization is measured against the col- strongly suggested that this was a member of the alpha
lection of complete 16S rRNA sequences available to us at subdivision of the purple bacteria. Similarity and evolution-
the present time. It would be possible to introduce nucleo- ary distance data (Table 4) prove A. marginale to be related
tide ambiguities during the DNA synthesis of these primers to other Rickettsiales within the alpha subdivision of the
to obtain a smaller set of primers that would work on purple bacteria (19, 21), specifically related to the genera
virtually all bacteria, although it is likely that this would Rickettsia and Ehrlichia (19). A phylogenetic tree displaying
cause the appearance of spurious amplification products. this three-way relationship is shown in Fig. 3.

FIG. 1. Sequence alignment of the amplification primers with 16S rRNAs of E. coli, A. marginale, and a eubacterial consensus sequence.
The consensus shows positions that are greater than 90% conserved for a phylogenetically diverse collection of approximately 85 bacterial
sequences.
700 WEISBURG ET AL. J. BACTERIOL.

TABLE 3. Theoretical specificity of amplification primers for 16S rDNA

Primer Phylogenetic grouping and genera which should amplify with indicated primer'
Gram-positive bacteria and relatives
Bacillus, Clostridium, Staphylococcus, Listeria, Lactobacillus, Streptococcus, Mycoplasma, Spi-
roplasma, Ureaplasma, Acholeplasma, Erysipelothrix, Fusobacterium, Arthrobacter, Myco-
bacterium, Streptomyces
Purple bacteria and relatives (proteobacteria)
Rochalimaea, Brucella, Rhodopseudomonas, Agrobacterium, Rhodospirillum, Pseudomonas,
Neisseria, Caulobacter, Myxococcus, Campylobacter, Rickettsia, Ehrlichia
Cyanobacteria
Anacystis (Synechococcus)
Bacteroideslflavobacteria
Bacteroides, Flavobacterium
Deinococcus and relatives
Deinococcus, Thermus
Spirochetes
Treponema, Spirochaeta
Planctomyces and relatives
Planctomyces
Chlorobium-green sulfur bacteria
Chlorobium
Thermotoga
Thermotoga
fD2 Enteric members of gamma subdivision of proteobacteria
Escherichia, Shigella, Salmonella, Serratia, Erwinia, and Citrobacter, etc. (all the enterics);
Oceanospirillum, Haemophilus, Actinobacillus, Vibrio, Pasteurella
fD3 Spirochetes of the genus Borrelia
fD4 Genus Chlamydia
rDl Purple bacteria and relatives (proteobacteria)
Pseudomonas, Neisseria, Rochalimaea,
Agrobacterium, Myxococcus, Desulfovibrio
Gram-positive bacteria and relatives
Bacillus, Staphylococcus, Arthrobacter, Streptomyces,
Mycobacterium, Heliobacterium
Cyanobacteria
Anacystis (Synechococcus)
Spirochetes
Treponema, Leptospira
Planctomyces
Planctomyces

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Chlorobium
Chlorobium
Thermotoga
Thermotoga (plus selected archaebacteria)
rPl, rP2, or rP3 (probably all Should prime all bacteria, plus plant mitochondria, chloroplasts, archaebacteria, and Dictyostelium,
functionally equivalent) but not yeasts or vertebrates
a
Primers are considered applicable if there is a perfect match for approximately 15 bases at the 3' end of the primer. The list is definitive only in the sense that
the taxa mentioned represent the sequences available to the authors. The absence of a genus from the list does not imply that the primer will not work. Because
the majority of the available rRNA sequences are derived from direct sequencing of rRNAs with reverse transcriptase, there is far less information available about
the 3' end of the 16S. In some cases, the indicated genus is represented by numerous species; in other cases the indicated genus is represented by only one. The
sequence alignment from which these data were derived is unpublished (12, 24). Phylogenetic groupings are those of Woese (23).

A. marginale has historically been a difficult organism to As shown with A. marginale, a potential advantage of this
study (16) because of the lack of a culture system. Its technology in the study of bacterial phylogeny is the ability
phylogenetic placement, which was made possible by ampli- to work with relatively small numbers of cells. This ability is
fication with broad-specificity 16S rDNA PCR primers, has of greatest use when the target species is either extremely
implications which should shed light on the biology of this fastidious or highly pathogenic. In the case of A. marginale,
fastidious pathogen. Many properties found in the genera obtaining sufficient material for phylogenetic study would
Rickettsia or Ehrlichia, such as the utilization of host ATP have required the sacrifice of several cows; this is the only
(22), may also be characteristic of the genus Anaplasma. established culture system. It is also highly desirable to keep
Obviously, the sequence of the 16S rRNA of A. marginale culture volumes small when dealing with highly infectious
provides basic information useful for designing probes or organisms such as respiratory pathogens.
PCR primers specific for the detection of this veterinary 16S rDNA amplified from ATCC lyophilized ampoules. One
pathogen. obvious source of either fastidious or pathogenic organisms
VOL. 173, 1991 16S rDNA AMPLIFICATION 701

1 2 3 4 5 6 7 8 9 10 11 12 were amplified with the indicated primer pair (Fig. 2):

Streptococcus sanguis ATCC 10556 (fD1 + rDl), B. fragilis
23 1K bp ATCC 25285 (fD1 + rP2), Clostridium perfringens ATCC
13124 (fD1 + rDl), Peptostreptococcus magnus ATCC
9
K5 bp 29328 (fD1 + rDl), Yersinia enterocolitica ATCC 23715 (fD2
+ rPl), Mycobacterium smegmatis ATCC 14468 (fD1 +
2 .3K bp rPl), and Mycobacterium phlei ATCC 11758 (fD1 + rPl).
2. OK bp The last four species listed above were also amplified with a
forward primer similar to fD1; its rDNA-like sequence was
that of fDl, but the linker was replaced with a T7 promoter
sequence (see discussion of transcription below). The fact
that Y. enterocolitica amplified with this primer suggests
that, under the right conditions, one forward and one or two
reverse primers may amplify almost all of the eubacterial 16S
rDNAs. A similar interchangeability of primers was found
with Campylobacterjejuni rDNA (data not shown).
FIG. 2. Ethidium-bromide-stained 0.75% agarose gel displaying The lyophilized ampoules of S. sanguis actually had an
amplification products. Lanes: 1, B. fragilis DNA (fD1
perfringens DNA (fD1 + rD1); 3, C. psittaci DNA (fi
+ C.
4 rP2); 2, expiration date 8 months prior to these experiments. Meth-
B. burgdorferi DNA (fD3 + rD1); 5, lyophilized ampou I4 -derivd S. ods even simpler than the single phenol extraction or bead-
sanguis DNA (fD1 + rP2); 6, lyophilized ampoule-deriN ved B fragilis beating method were tested with S. sanguis-lyophilized
DNA (ff1 + rP2); 7, lyophilized ampoule-derived C '.perfringens ampoules. The simplest method involved resuspending a
DNA (ff1 + rD1); 8, lyophilized ampoule-derived Y. enterocolitica lyophilized ampoule in 100 ,ul of the buffer (described above)
DNA (fD2 + rPl); 9, lyophilized ampoule-derived P. A nagnus DNA containing 0.45% each of Tween 20 and Nonidet P-40
(fD1 + rD1); 10, lyophilized ampoule-derived M. sine ggmatis DNA detergents. This sample was boiled for 5 min, and 1 pl was
(fD1 + rP1); 11, lyophilized ampoule-derived M. phlie DNA + (fD1 used to prime an amplification reaction. Although success-
rD1); 12, Hindlll digest of lambda phage. Labeled b)ands include ful, this method was rejected from further exploration be-
23,130, 9,416, 6,557, 2,322, and 2,027 bp.
cause it is not likely to work for every bacterium, unlike the
bead-beating method.
Fidelity of amplification. To examine whether there were
which are in viable condition is such as
a culture coiledttion potential artifacts due to PCR amplification, portions of
the American Type Culture Collection (ATCC).. According several sequences were examined and compared with se-
to the Manual of Methods for General Bacterioology (7), a quences which had previously been determined by other
standard double-vial lyophilized ampoule Lins 2 x 105 conta methods. A comparison of a clone derived from PCR with
cells. Depending the quantitation of the inpiut cells (for
on one derived by conventional means should be the most
example, counting of cells in terms of viable CI FU) and the informative. The following numbers of bases were deter-
growth phase of the preserved cells, there could be several- mined from the clones indicated (all in pGEM vectors). (i)
fold moregenomes present in the lyophilize4d ampoule. An amplification clone-derived Borrelia burgdorferi se-
Factoring in the multicistronic nature of rRN'4A operons quence revealed one discrepancy within 1,517 bases as
(seven copies in E. coli) (10) contributes to e,ven greater compared with an RNA sequence (unpublished data), re-
target numbers available for gene amplification. solved in favor of the clone sequence, on the basis of
diverse taxa sequence composition of related species at this position. In

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Lyophilized ampoules of various types fromC
were selected to examine their potential to yield.IDNA
which addition, seven unresolved nucleotide assignments (Ns)
would initiate 16S rDNA amplification. DNAs from both from within the sequenceable region of the rRNA sequence
ATCC double-vial and single-vial preparations w'ere purified were determined from the clone, and several other bases
asdescribed in Materials and Methods. The follo,wing strains were determined from the 3' end of the rRNA. (Approxi-

TABLE 4. Percentage similarity and evolutionary distance (9) for nine bacteria belonging to the alpha subdivision of the purple bacteria
(23), plus E. coli (a gamma bacterium) as an outgroupa
% Similarity/evolutionary distance (x 100)"
Bacterium
E. coli R. palustris R. rubrum A. marginale E. risticii R. prowazekii R. rickettsii R. quintana B. abortus A. tumefaciens
Escherichia coli 81.0 84.0 81.2 78.6 80.5 80.3 81.2 81.9 81.2
Rhodopseudomonas palustris 21.8 - 88.5 83.3 82.1 85.4 85.3 89.3 90.0 89.3
Rhodospirillum rubrum 18.0 12.4 84.9 84.9 84.9 84.9 87.9 88.9 88.4
Anaplasma marginale 21.5 18.8 16.8 86.9 86.0 86.2 85.6 85.3 85.8
Ehrlichia risticii 25.2 20.4 20.0 14.3 84.6 84.6 83.2 83.8 84.2
Rickettsia prowazekii 22.7 16.2 16.8 15.4 17.2 99.0 87.0 87.1 86.9
Rickettsia rickettsii 22.7 16.3 16.8 15.2 17.1 0.9 87.1 87.1 86.9
Rochalimaea quintana 21.7 11.5 13.1 16.0 18.9 14.2 14.1 95.3 94.7
Brucella abortus 20.7 10.7 11.9 16.3 18.2 14.1 14.1 4.8 - 94.9
Agrobacterium tumefaciens 21.7 11.5 12.6 15.7 17.6 14.3 14.3 5.5 5.2
a
A mask was used which eliminated a small number of positions from consideration within the alignment; all positions in which base composition was not at
least 50% conserved were eliminated. All of the sequences represented may be obtained from Genbank except R. palustris which was used courtesy of C. R.
Woese.
b Numbers below the diagonal indicate evolutionary distance.
702 WEISBURG ET AL. J. BACTERIOL.
E. coli

I I I I I
'
0 0.02 0.04 0.06 0.08 0.10 0.12 0.14

Evoluony De
FIG. 3. Phylogenetic distance tree displaying the evolutionary origin of A. marginale within a lineage shared by the genera Rickettsia and
Ehrlichia. All species belonging to the order Rickettsiales are shown in boldface type. E. coli is used as an outgroup sequence.

mately 60 nucleotides at the 3' end of 16S rRNA cannot be highly recommend cloning the fragments if a near-perfect
sequenced directly from the rRNA.) (ii) A total of 226 bases sequence is desired.
were determined from a Neisseria gonorrhoeae PCR clone, Transcription of amplified material. One additional appli-

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with no disagreement with the RNA sequence or a published cation of primers similar to those described herein is the in
rDNA sequence (17). (iii) The sequence from the Neisseria vitro transcription of PCR-amplified material. We have tran-
meningitidis clone showed no disagreement with 250 bases scribed virtually full-length pseudo-rRNA from both cloned
of RNA-derived sequence. One N from the RNA sequence material and directly from amplified product (not shown).
was now determinable from the clone. (iv) In 212 bases of a Cloned rDNAs, in pGEM vectors, were transcribed by using
Chlamydia trachomatis sequence, there was no disagree- either T7 or SP6 polymerases, depending on clone orienta-
ment with the conventionally cloned sequence (unpublished tion. In addition, PCR primers similar to fDl, in which the
data). (v) In a C. jejuni PCR-derived clone, 328 bases were cloning linker was replaced with a T7 promoter sequence
inspected, and there was one discrepancy with the RNA- (5'-TTAATACGACTCACTATAGGG-followed by the 16S
derived sequence (an A-to-G transition) which may be the rDNA-like sequence), readily amplified and transcribed full-
result of minor cistron-to-cistron variation. Five N's were length pseudo-rRNA. This material can be used for sequenc-
resolved. ing, hybridization studies (data not shown), or potentially for
In summary, there appears to be no reason for more than reconstitution experiments.
the usual concern, because of Taq polymerase fidelity of Conclusion. The amplification by PCR of a taxonomically
replication, about sequence accuracy in this method. Several diverse collection of eubacterial 16S rDNA genes is possible
positions that had previously been scored as unknown or with a small number of primers. These products can readily
ambiguous are now determinable by taking advantage of be cloned for sequencing or they can be sequenced directly.
bidirectional gene sequencing and the absence of artifacts The ability to determine rRNA sequences from ATCC
due to rRNA secondary structure and posttranscriptionally lyophilized ampoules, without culture, enables the study of
modified nucleotides. As always, a cautious approach should fastidious or pathogenic species without employing tricky or
be taken by checking any sequence anomalies and con- expensive microbiological methods. While this should not be
firming known secondary structural constraints on se- a routine substitute for growing bacteria, picking individual
quences. colonies, and confirming their phenotypic and biochemical
Although we have spent considerable time optimizing and identities, it will enable experiments to be performed that
testing the direct sequencing of PCR-amplified rDNA, we were not previously possible.
VOL. 173, 1991 16S rDNA AMPLIFICATION 703

ACKNOWLEDGMENTS Escherichia coli. J. Bacteriol. 132:931-949.

We greatly appreciate the work of J. Samuel, who provided A. 11. Lane, D., B. Pace, G. J. Olsen, D. A. Stahl, M. L. Sogin, and
marginale cells purified from bovine erythrocytes. Carl Woese N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA
graciously provided unpublished rRNA sequences for analysis. sequences for phylogenetic analysis. Proc. Natl. Acad. Sci.
USA 82:6955-6959.
12. Lane, D. J., and W. G. Weisburg. Unpublished data.
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