KLASIFIKASI

Tujuan klasifikasi:
- Alat penyampaian informasi
- Sebagai dasar pengembangan sistem identifikasi
- Mengetahui sejarah evolusi mahluk hidup (mikrobia)
Alat penyampaian informasi
Klasifikasi:
. summarizing & cataloging information about microorganisms (database)
. Information retrieval system (large amount)
. Its position in the classification system is denoted by the use of a name.
. e.g. Bacillus: gram + bacteria, forms
endospore under aerobic
conditions
B. subtilis: secret extracellular enzymes,
amylase & protease, use nitrate,
competent to perform transformation e

1.

2. Dasar penyusunan sistem identifikasi

Microorganisms must be classified into groups before identification

system ca be devised

For recognition of new isolates

Without prior classification of strain into groups -> impossible to

assign new isolates to a taxon
3. Mengetahui sejarah evolusi mikroba:

Indicate the phylogenetic relationships

For some, phylogeny and classification are identical

Kriteria klasifikasi yang efektif

To serve the purposes effectively, a classification system should:
have high information content
be stable
be empirical
be scientifically based

Kelemahan Klasifikasi Tradisional

Tidak prediktif
Tidak stabil
Tidak objektif (subjektif)

Alasan kelemahan:

Apriory choice of characters (pengaruh Linnaeus)

Subjective -> disagreement between scientists
Lengthy discourse concerning the relative important of
characters e.g. misguided assumption:
morphological -> genera
physiological -> species
serological -> sub-species

Tipe-tipe Klasifikasi
1. Klasifikasi
. Useful
. Little

artifisial: tujuan khusus:

for the specialist

value to microbiology most bacteria are excluded

seldom display the natural relationship, e.g. Escherichia

coli & Shigella dysenteriae: strain of the taxa share great DNA
sequence relatedness, phenotypically are very similar, from every
view point they are single species.

. artificial

Bacillus cereus & Bacillus thuringiensis: plasmid coding for endotoxin

. E.g.

( single character) S. dysenteriae must cause dysentry

in human non-pathogenic strain can not be included in this taxa

. monothetic

Klasifikasi Artfisial

Based on restricted information: e.g. pathogenicity

Tend to be unstable: Erwinia herbicola (plant pathologist) and

Enterobacter agglomerans (clinical microbiologist) Erwinia
agglomerans.

Identification system derived from monothetic classification

missclassification !

Non-pathogenic isolates of S. dysenteriae genus Escherichia.

Non-toxic, plasmid deficient strain of B. thuringiensis

identified as B. cereus.

Conclussion: although artificial classification have their use, as

a general system of value to all microbiologists, their limitations
are severe !!

2. Klasifikasi alami
a. Fenetik
b. Filogenetik

a. Klasifikasi Alami Fenetik

General purpose classification

A system that is of value to all microbiologists
Encompass all bacteria and all aspects of them
Natural based on overall similarity (affinity)
containing all aspects (molecular physiological
habitat relationship)
Phenetic: refer to similarities based on the complete
organism (phenotype & genotype) as it exists at present
with no reference to the evolutionary pathways or ancestry
of the organism.
Contrast with the term natural used in evolutionary context
Polythetic: good predictivity

b. Klasifikasi Alami Filogenetik

Natural: a unique history of decent with modification

Based on phylogenetic relationship
This will be congruent with phenetic if there is no
parallel and convergent evolution and the rate of
changes proceed constantly in all lineages
Cladistic: the branching pattern that describes the
pathway of ancestry of a group of organism
monophyletic group (posses a homologous
characters: primitive or derived characters
Traditional evolutionist: classification is practised
with reference to the phylogeny but without the
requirement that all groups be monophyletic

Keunggulan klasifikasi fenetik vs filogenetik

1. Goodness of the classification:

Phylogenetic classification: reflect the evolutionary

pathway of the organisms it is impossible to compare
with the true cladogeny
Phenetic classification: less well defined, but represent
the similarities between and every organism. Various
statistical methods have been developed. The accuracy
of the classification cannot be evaluated difficult to
define the ultimate phenetic classification

Keunggulan Klasifikasi

2. Keterujian (Veriviability)
Phylogenetic approach : difficult to verify
Phenetic classification: more accesible to
verification, objective and can be repeated
3. Kepraktisan (Practicalities):
Phylogenetic approach: rely on gene sequences
data, hybridization technology offering simple
identification procedures molecular systematics
Phenetic approach: can be analised to select the
most diagnostic characters for delineation of
groups and provide reliable identification system

Pilihan antara Klasifikasi fenetik

dan Filogenetik
Jensen (1983) suggested that the classification what
is needed are:
Classification that reflect what is known about the
taxa
Procedures for generating hypothesis about
evolutionary relationships.
Many systematists now agree that the two
systems (phenetic & phylogenetic) should be
combined as far as possible

KLASIFIKASI NUMERIK FENETIK

(Taksonomi Adansonian)
Taksonomi Numerik:
pengelompokan unit takson dengan metode kuantitatif
berdasarkan keeadaan sifat-sifat
Perintis Aplikasi Sistematik Numerik : Peter H.A. Sneath
(1957)
Lima Prinsip Taksonomi Adansonian:

1. Taksonomi

alami ideal: taksonomi yang mengandung informasi terbesar

yaitu yang didasarkan atas sebanyak-banyaknya sifat.
2. Masing-masing sifat diberi nilai yang setara dalam mengkonstruksi
taksa alami.
3. Similaritas keseluruhan (afinitas) merupakan fungsi proporsi sifat yang
dimiliki bersama.
4. Taksa yang berbeda didasarkan atas sifat yang dimiliki.
5. Similaritas tidak besifat filogenetis.

Taksonomi Tradisional:
monotetik
karakter tunggal
dipilih secara subyektif
tidak dapat mengakomodasi variasi (mutan)
Taksonomi Numerik:
mengandung banyak informasi
sebanyak-banyak karakter (politetik)
dapat mengakomodasi variasi
sistem simpanan informasi yang berharga
sistem retrieval bagi para ilmuwan

Prosedur Taksonomi Numerik:

1. Pemilihan strain dan uji karakter
Pemilihan strain (OTU)
Pemilihan karakter
Akuisisi data secara tepat
Pengkodean data (data coding)

2. Evaluasi Eror
Estimasi test error
Komputasi resemblance
Konstruksi dendrogram (pengklasteran)
Evaluasi dendrogram (co-phenetic-correlation test)
3. Pendefinisian tingkat takson

Contoh: Tabel n x t
Karakter

Strain Mikroba (Operational Taxonomical Unit)

A

10

Komputasi nilai resemblance (similaritas):

Hasil uji Strain A

Hasil Uji Strain B

Indeks similaritas:

Simple matching coefficient

a + d
(SSM) = -------------------- x 100%
a +b +c +d

Jaccard coefficient
a
(SJ) = ----------------- x 100%
a +b +c

Contoh kalkulasi SSM

SSM (A-B) : a = 4; b = 2; c = 0; d = 4: SSM = 80%

SSM (A-C) : a = 2; b = 4; c = 3; d = 1: SSM = 30%
SSM (A-D) : a = 2; b = 4; c = 2; d = 2: SSM = 40%
SSM (A-E) : a = 3; b = 3; c = 4; d = 0: SSM = 30%
dan selanjutnya !!!

Matriks Similaritas
A

100

80

100

30

30

100

40

60

50

100

30

50

60

70

100

Clustring analysis (Analisis Kluster)

Strain Mikrobia (OTU)

Sim (%)
100

90

80

(A, B)

70

(A, B)

(D,E)

60

(A, B)

(D,E)

55

(A, B)

(C)(D,E)}

50

(A, B)

(C)(D,E)}

40

(A, B) } (C)(D,E)}]

30

(A, B) } (C)(D,E)}]

20

(A, B) } (C)(D,E)}]

10

(A, B) } (C)(D,E)}]

Algoritme Pengklasteran (Clustering

Algoritm)
1. Single linkage: fusi klaster dengan nilai
similaritas tertinggi
2. Average linkage: fusi klaster dengan nilai
similaritas rerata (UPGMA)
3. Complete linkage: fusi klaster dengan
nilai similaritas terkecil
UPGMA: Unweighted Paired Group Method with
Arithmetic Averages

Konstruksi dendrogram
Hasil klasifikasi:
A
B

C
30

40

50

60

70

80

90

100

Evaluasi dendrogram: Analisis korelasi ko-fenetik

Matriks Similaritas original (X)
A

100

80

100

30

30

100

40

60

50

100

30

50

60

70

100

Matriks similaritas derived from Dendrogram

(Y)
A

100

80

100

40

40

100

40

40

55

100

40

40

55

70

100

Analisis Kofenetik-korelasi
SSM

X2

Y2

XY

A-B
A-C
A-D
A-E
B-C
B-D
B-E
C-D
C-E
D-E

80
30
40
30
30
60
50
50
60
70
X

80
40
40
40
40
40
40
55
55
70
Y

X2

Y2

XY

Koefisien Korelasi (r)

(nXY XY)
r = ------------------------------------------(nX2 (X)2) (n (Y2) (Y)2)

r 60% (nilai r yang dapat diterima)