Morphological and physiologicalcharacteristics used in classification

• Oxygen relationship• Energy sources• Electron sources• Carbon sources• Fermentation products• Cell wall components• Temp and pH optima• Osmotic tolerance• Photosynthetic mechanism• Secondary metabolites• Sensitivity to antibiotics

• Colony morphology• Colony color• Cell shape• Staining results (Gram)• Endospore• Motility• Flagella• Size• Cellular inclusions• Ultrastructure

Oxygen requirements

• Aerobes• Anaerobes• Microaerophiles• Obligate aerobes• Obligate anaerobes• Facultative anaerobes

Numerical Taxonomy

Fig. 19.5

Molecular characteristics used inclassification

• Nucleic acid base composition (G+C %)• Nucleic acid hybridzation• Nucleic acid sequencing

– 16S rRNA– Signature sequences

• Nucleic acid/protein sequence comparisons• Complete genome sequencing

DNA melting curve (G+C %)

Fig. 19.6

Nucleic Acid Hybridization

Fig. 19.7

Hybridization based oncomplementarity of DNA sequences

Mem

bran

e Test DN

A

Small ribosomal subunit RNA

Fig. 19.9

DNA sequencing

Fig. 15.2

Fig. 11.6

Fig. 11.15

ddATP= stops DNA elongation

Fig. 15.1

Fig. 11.15

DNA sequencing

Fig. 15.2

Whole genome sequencing

Fig. 15.3

69 Complete Microbial Genomes(as of 12/17/01) [A] - Archaea - 12 species[B] - Bacteria - 57 species

224 Complete Microbial Genomes(as of 2/17/05) [A] - Archaea - 21 species[B] - Bacteria - 203 species

Map of Mycoplasma genitalium

Fig. 15.5

What do you get from sequencedata?

• Evolutionary relatedness based onseveral loci

• Infer function of proteins encoded bygenes

+ Consensus #1

- - - M - G Y R - - - - - - - S N V P K V R L T T D R I V L R L V H E R D A V R - L A D Y Y A E N R A F L E P W E P V R D E S H C Y R S G W Q A R L G M I - - S Consensus #1- - - M - G Y R - - - - - - - S N V P K V R L T T D R I V L R L V H E R D A V R - L A D Y Y A E N R A F L E P W E P V R D E S H C Y R S G W Q A R L G M I - - S Majority

10 20 30 40 50 60 70 80

- - - M F G Y R - - - - - - - S N V P K V R L T T D R L V V R L V H D R D A W R - L A D Y Y A E N R H F L K P W E P V R D E S H C Y P S G W Q A R L G M I - - N 1 rimJ-CDS- - - M F G Y R - - - - - - - S N V P K V R L T T D R L V V R L V H D R D A W R - L A D Y Y A E N K A F L K P W E P V R D D S H C Y P S G W Q A R L S M I - - A 1 rimJ-K. pneumoniae-CDS- - - M F G Y R - - - - - - - S N V P K V R L T T D R L V V R L V H E R D A W R - L A D Y Y A E N R H F L K P W E P V R D E S H C Y P S G W Q A R L G M I - - G 1 rimJ-S. typhi-CDS- - - M N G L N - - - - - - - S E C H F Y Q - T D G D I V V R C A Q I N D A E R - L S Q Y F V D N R S H L I E W E P R R E A E F F T E S G W L Q R L I K L - - N 1 rimJ-V.cholerae-CDS- - - L P G N R - - - - - - - R Q V P I L H R D A D - F L L R A L Q P D D F V R - T S R Y E N A N R E H L A P W E P L R D P G Y F S V D N A R A R T L L Q - - V 1 rimJ-P. aeruginosa-CDS/revcomp- - - M F G Y H - - - - - - - T A T P K V H L T T D R M S L R L V H E R D A Y R - L A E Y Y A E N Q V F L K P W E P V R D Q S H C M P S G W Q A R L G M I - - M 1 rimJ-Y. pestis-CDS- GOODV S V L L P F L - - - - - - - S P R P R L R L Q G R A V Y L R P P M Q R D Y A P - W A A L R S R S R A F L E P W E P T W P E H D L S R A A F R A R L A A Y - - A 1 rimJ-C. crescentus-CDS/revcompM - - - - - - - - - - - - - - - - - - - - - L K G K T I Y V R P L E V T D A E E - N L G L Q S E N R D F F E Q F S M I R A D D Y Y T V E G Q R K R I T E Y - - Q 1 rimJ-B. subtilis-CDS/revcompL V T L L R F N A R H P G W P S N V G P L R V P A G V I R L R A V R L R D G V Q - W S R I R L A D R A Y L E P W E P S T E G D W V V R H S V I A W Q V L C - - S 1 rimJ-M. leprae-CDSM P - - - H T P P R H L A E G P R V G I R H F S H A D A A E F T A R A R Q S K D - L H H P W L F P P E S V Q A Y E A Y A A - - R L I E D R T K A G F L V C - - E 1 rimJ-S. coelicolor-CDSM A - - - - - - - - - - - - - - - V G P L R V S A G V I R L R P V R M R D G V H - W S R I R L A D R A H L E P W E P S A D G E W T V R H T V A A W P A V C - - S 1 rimJ-M. tuberculosis-CDSM E T L - - Y T E - - - - - - - - - - - - - - - - - R L T L R K M - E L E D A D V L C Q Y W S D P E V T K Y M N I T P F T D V S Q A R D M I Q M I N D L - - - - 1 rimJ-B. lichenformis-CDSM I N I - G Y L H - - - - - - T T F P V F D L - - G N I V L R E L A E S D V Q D Y L C - Y M S R S E M G L Y I - - - - - T E S N R P K D L E E A R K E I F Y W S 1 rimj-R. prowezekki-CDS-revcomp

+ Consensus #1

E L H K Q G S A F Y F G L L D P E E - - G E I I G V A N F S N V V R G S F H A C Y L G Y S L G E A A Q G Q G L M T E A L T L A I R Y M F R T L G L H R I E A N V Consensus #1E L H K Q G S A F Y F G L L D P E E - - G E I I G V A N F S N V V R G S F H A C Y L G Y S L G E A A Q G Q G L M T E A L T L A I R Y M F R T L G L H R I E A N V Majority

90 100 110 120 130 140 150 160

E F H K Q G S A F Y F G L F D P D E - - K E I I G V A N F S N V V R G S F H A C Y L G Y S I G Q K W Q G K G L M F E A L T A A I R Y M Q R T Q H I H R I M A N Y 202 rimJ-CDSE F H K Q G S A F Y F A L L D P E E - - K E I I G V A N F S N V V R G S F H A C Y L G Y S I G E K W Q G Q G L M F E A L T S A I R Y M Q R T Q H I H R I M A N Y 202 rimJ-K. pneumoniae-CDSE F H K Q G S A F Y F A L L D P E E - - K E I I G V A N F S N V V R G S F H A C Y L G Y S I A Q E W Q G Q G L M F E A L T A A I R Y M Q R T Q H I H R I M A N Y 202 rimJ-S. typhi-CDSE L H K M K L G Y Y L L I L D A Q N - - D A M L G T I S F S N I I R F P F H A C N V G Y S L A Y E A Q G K G I M T R A L T M A C Q Y M F S E H N M H R I M A S Y 199 rimJ-V.cholerae-CDSA S M D E G E A L L L L L L D P D D - - G E V L G R C S Y T N I V R G V F Q A C H L G F S L A A A A Q G R G L M A R A L R V A N R Y C F E Q L G L H R I M A S H 199 rimJ-P. aeruginosa-CDS/revcompE L Q K Q G S A Y Y F I L L D P E E - - K E V R G V A N F S N V L R G S F H A C F L G Y S L G E R W Q G Q G L M F E A L Q P L I R Y M Q R Q E R M H R I M A N Y 202 rimJ-Y. pestis-CDS- GOODR E L E L G E A Y P F F I F R R E D - - D A L L G A I R L F H V R R G V S L T G T I G Y W L G E P Y V R Q G H M A D A V E T L I R F A F H G L G L H R L E A A C 211 rimJ-C. crescentus-CDS/revcompE R L E K D E E Y H F G I F T A S D - - D R L I G T V S L F Q I I R G A L Q T A F I G Y F L D K A H N G K G I M T E A V R L V V D Y A F H E L K L H R I E A G V 169 rimJ-B. subtilis-CDS/revcompS L R S E A R K G R M L P Y A - I E L D G N F C G Q L T I G N V T H G A L R S A W I G Y W V S S S A T G G G V A T G A L A L G L D H C F G P V M L H R V E A T V 232 rimJ-M. leprae-CDSK - D T E A T D G A G G P A G P V P D G G S I A G F V N I N N I V E G G F L S G A L G Y G A F A H A A G R G L M R E G L D L V V R Y A F G P M R L H R L E I N V 217 rimJ-S. coelicolor-CDSG L R S E A R N G R M L P Y V - I E L D G Q F C G Q L T I G N V T H G A L R S A W I G Y W V P S A A T G G G V A T G A L A L G L D H C F G P V M L H R V E A T V 187 rimJ-M. tuberculosis-CDSS L E G Q A N R F - - S I I - - V K E T D E V I G T C G F - N M I D Q E N G R A E I G Y D L G R N H W G K G F A S E A V Q K L I D Y G F T S L N L N R I E A K V 169 rimJ-B. lichenformis-CDSN L Y T L H R S F Y W G I A - - L K T D N K L I G T A G F - N I I N L E H H R A E I S Y D L D P N F W G Q G I M L K S I K N I L K F A - D C I G I I R V Q A T V 196 rimj-R. prowezekki-CDS-revcomp

+ Consensus #1

M P H N A R S G A L L A R L G F E K E G Y A K D Y L L I D G A W R D H V L T A L T T P E - - - - - - - - - - - - - - - - W - - - - - - Consensus #1M P H N A R S G A L L A R L G F E K E G Y A K D Y L L I D G A W R D H V L T A L T T P E - - - - - - - - - - - - - - - - W - - - - - - Majority

170 180 190 200 210 220

M P H N K R S G D L L A R L G F E K E G Y A K D Y L L I D G Q W R D H V L T A L T T P D - - - - - - - - - - - - - - - - W T P G R . 436 rimJ-CDSM P H N Q R S G A L - A R L G F E K E G Y A K D Y L L I D G Q W R D H V L T A L T T P D - - - - - - - - - - - - - - - - W S A G R . 436 rimJ-K. pneumoniae-CDSM P H N K R S G A L L A R L G F E K E G Y A K D Y L L I D G Q W R D H V L T A L T T P L - - - - - - - - - - - - - - - - W T P G R . D 436 rimJ-S. typhi-CDSI P H N K R S E N V L K R V G F V L E G H A K D Y L L I N G K W E D H N L T S L I N P N - - - - - - - - - - - - - - - - W K E . 433 rimJ-V.cholerae-CDSL P R N A R S E R L L E S L G F E K E G Y A R A Y L K I A G V W E D H V L R A L V D A - - - - - - - - - - - - - - - - - - - - P R . I 433 rimJ-P. aeruginosa-CDS/revcompM P H N H R S G N L L A R L G F E R E G Y A K D Y L M I D G Q W R D H V L T A L T N K E - - - - - - - - - - - - - - - - W A S T R . 436 rimJ-Y. pestis-CDS- GOODM P E N H A S A A L L A K C G F S E E G Y A H A Y L K I N G A W R D H R L F G L V A P E . 445 rimJ-C. crescentus-CDS/revcompM P R N L G S M R V L E K A G F H K E G I A R K N V K I N G V W E D H Q V L A I L N P D - - - - - - - - - - - - - - - - - - D E Q . 403 rimJ-B. subtilis-CDS/revcompR P A N V A S R A V L A K V G F R E E G L L R R Y L E V D R A W R D H L L M A L T I E E V S G S V T S N L V R A G R A S W L . I 469 rimJ-M. leprae-CDSQ P G N A A S I A L A R A C G F H L E G F S P R M L Y I D G A W R D H Q R W A I T A E T V T S - - - - - - - - - - - - - - - - - - G . 454 rimJ-S. coelicolor-CDSR P E N A A S R A V L A K V G F R E E G L L R R Y L E V D R A W R D H L L M A I T V E E V Y G S V A S T L V R A G H A S W P . 424 rimJ-M. tuberculosis-CDSE P E N T P S I K L L N S L S F Q K E G L L R D Y E K A K G R L I D V Y M F S L L K R E Y A G . 394 rimJ-B. lichenformis-CDSI T D N F R S V N L L E R C G F S K E G I L K K Y E I I A N K H K D Y Y M Y A R V - - - - - V . 424 rimj-R. prowezekki-CDS-revcomp

Consensus 'Consensus #1': When all match the residue of the Consensus show the residue of the Consensus, otherwise show '.'.

Decoration 'Decoration #1': Shade (with solid black) residues that match rimJ-CDS exactly.

Multiple sequence alignment

MFGYRSNVPKVRLTTDRLVVRLVHDRDAWRLADYYAENRH LKPWEPVRD

ESHCYPSGWQARLGMINEFHKQGSAFYFGLFDPDEKEIIGVANFSNVVRG

SFHACYLGYSIGQKWQGKGLMFEALTAAIRYMQRTQHIHRIMANYMPHNK

RSGDLLARLGFEKEGYAKDYLLIDGQWRDHVLTALTTPDWTPGR.

stop

L

rimJ-2::mTn10

rimJ-1::mTn10

Red= conserved in RimJ and 13 putative prokaryotic acetylasesYellow=conserved in RimJ and 11 putative prokaryotic acetylasesBl ue = rimJ mutations that cause a loss of papBA thermoregulationGr een= motifs conserved in N-acetyltransferase (GNAT) superfamily

The RimJ protein

Fig.15.6

Map of Haemophilus influenzae

Bergey’s Manuals

• Manual of Determinative Bacteriology– used for identification of bacterial species

• Manual of Systematic Bacteriology– more thorough taxonomic classification– 1st edition= phenetic classification– 2nd edition= phylogenetic classification