2023 - 1 - Mikrobiologi Umum - Pendahuluan - Taksonomi - Identifikasi - ESR - 13feb PDF

Mikrobiologi Umum
Somes Photos from Google
Prof. Dr. Retno Indrati (RI)

Prof. Dr. Endang Sutriswati Rahayu (ESR)
Dr. Lucia Dhiantika Witasari (LDW)
Stugestus Kurniawan Jati STP. MSc. (SKJ)
Endang S Rahayu
Universitas Gadjah Mada
1. Sejarah Mikrobiologi
The Historical Foundations of Microbiology
• The Development of the Microscope

• Robert Hooke (1635–1703)
• Antony van Leeuwenhoek (1632–1723)
• The Debate over Spontaneous Generation
• Francesco Redi (1626-1697)
• John Needham (1731–1781)
• Lazzaro Spallanzani 1729 –1799)
• Rudolf Virchow (1821 – 1902)
• Louis Pasteur (1822 – 1895)
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History of Microbiology
• Robert Hooke- First person to peer into the microbial world,
used compound lenses (1664)
• Anton van Leeuwenhoek- First true microbiologist / the
father of microbiology, Dutch -Simple Microscope
• single lens microscopes capable of 300 to 500X (1632 -
1723)
• drew and published (Proceeding of the Royal Society in
London) accurate pictures microscopic algae, protozoa,
bacteria, demonstrated “wee beasties” (“wee
animalcules”)
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Penemu Mikroskop
Gambar-gambar yang terdapat dalam slide ini,

diambil dari googling
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Perkembangan Mikroskop
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Spontaneous Generation
• Spontaneous Generation- the idea that life arose from
non-living matter - Abiogenesis
• Aristotle (384-322 BC) believed some simpler invertebrates
could arise by spontaneous generation
Abiogenesis - Biogenesis

diambil dari googling Endang S Rahayu
Spontaneous Generation Debate Endang S Rahayu
• Francesco Redi (1626-1697)

• belief at the time- maggots spontaneously arose
from rotting meat
• demonstrated that maggots were dependent on
the presence of fly eggs and of rotting meat

Spontaneous Generation
(continued debate)
• In 1748, English Priest John Needham
reported the results of his experiments
• boiled mutton broth and then tightly sealed
the flask
• eventually many of the sealed flask became
cloudy with microorganisms
• he proposed that organic matter possessed
a ‘vital force’ that could give rise to life

Spontaneous Generation disproved
• Lazzaro Spallanzani - improved on
Needham’s experimental design
• first- sealed seeds and water in glass flask
• second- boiled them
• no growth took place as long as the flasks
remained sealed
• proposed that air carried microbes to the
culture

Controversy finally settled
• 1859, one of the fathers of modern microbiology, Louis Pasteur offered strong
evidence against Spontaneous Generation
• Pasteur was a chemist by training but became interested in biology during his
early studies on fermentations.
• At that time virtually nothing was known about microorganisms – except that
they existed (this was discovered by Anton van Leeuwenhoek using home-made
microscopes in 1684).
• It was known that microorganisms could be found in decaying matter but it was
not clear what role they were playing in the decomposition process.
Louis Pasteur (1822-1895) Endang S Rahayu
"Do not put forward anything that you Gambar-gambar

yang terdapat dalam
cannot prove by experimentation" slide ini,
Pasteur’s Swan Neck

Flask Experiment
Drew out the necks of flasks

so that they remained open
• to the air
added broth and boiled it to
destroy any microbes present
flasks were incubated for
months and remained sterile
Rapid Advances 1857 -1914
• Rudolf Virchow introduced the concept of

biogenesis: living cells can arise only
from preexisting cells (1857).
• Louis Pasteur demonstrated that
microorganisms are in the air everywhere
and offered proof of biogenesis (1861).
• Agostino Bassi (1835) showed a causal
relationship between microorganisms
and disease.
The Recognition of the Microbial Role
in Disease
• Agostino Bassi (1773-1856)

• The "Father of Insect Pathology"
• 1835-6 showed that a silk worm disease was caused by
parasites/fungus (later named Beauveria bassiana in his honor
• The first animal pathogen to be understood was of insects, not humans!
• In 1844, he believed that "contagion by living organisms" also infected
humans with measles, syphilis, and the plague.

Pasteur’s Contributions to Science Endang S Rahayu
• 1800- French Government (Napoleon III)

enlisted his help in their Wine Industry
• showed the decline in quality was due to a
contaminating microbe
• process of pasteurization

Pasteur’s Contributions to Science
• Recognized that chickens became
immune to a bacterial pathogen if
injected with a weaken avirulent
strain.
Fig. 2. Louis Pasteur’s in

• Developed vaccines against rabies his laboratory performing
an experiment with rabies
and anthrax (rabbit spinal cord in jar)
in 1885.

Discovery of endospores of Bacillus
• Pasteur’s perplexing problem

• while working on spontaneous generation he
experienced an anomaly
• no matter how long some flasks were boiled, they
always produced growth
• German botanist - Ferdinand Cohn (1828–1898)
discovered the existence of heat resistant bacterial
spores
• Pasteur reasoned that the flask that produced
growth contained heat resistant bacterial spores
Tyndallization
• English physicist John Tyndall (1820-1893) dealt the

absolute final blow to Spontaneous Generation and
resolved Pasteur’s problem, he demonstrated the dust
did indeed carry microbes and if the dust were absent,
the broth remained sterile.
• He developed the process of tyndallization which is
fractional steam sterilization
• similar to the process we use today in the lab.

The Recognition of the Endang S Rahayu
Microbial Role in Disease

• Joseph Lister (1827 – 1912)
• English surgeon
• developed an antiseptic system of surgery and heat
sterilized his instruments as well as using phenol
with surgical dressing

Robert Koch (1843–1910)
The “father” of medical microbiology
• Direct evidence of the role of bacterial in
disease transmission
• established a relationship between anthrax
and the bacterium- Bacillus anthracis
• Koch’s techniques are still used today
• Today we know these as Koch’s Postulates
• Received the Nobel prize 1905 for his work on
tuberculosis

Koch’s Postulate
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Koch’s Postulate
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Koch’s Tuberculosis studies
• In 1881 Koch turned his attention to the study of a human disease – Tuberculosis (TBC).
• At that time TB killed 1 in 7 people and even today it accounts for more than 1 in 20 human
deaths worldwide. TBC was known to be contagious but no “contagion” had been identified.
• TBC is a disease of the lungs caused by the bacterium Mycobacterium tuberculosis. It is acquired
by inhalation of infected droplets or dust particles in the air.
• The bacterium can persist in the lungs for long periods. It survives and grows within macrophages.
• In individuals with a low resistance acute pulmonary infection can occur with extensive damage to
lung tissue. Spread of the bacterium to other parts of the body can then lead to death.
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Robert Koch – Pure Culture Technique
• Developing pure culture technique
• Use potato slices – first found individual bacterial
colonies growing with different appearance
• Microscopic examination revealed cells within a
single colony were similar
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Pure Culture Key to Studying Microbes
• Definition : Pure culture is a population of organisms, all of which are
the progeny of a single organism
• In nature, microbes almost never occur as pure cultures

Development of solidifying agents
and complex media
• Koch wanted to culture pathogens so he used something similar to the body
tissue
• Meat extracts
• Initially, gelatin (jell-o) was used to solidify beef extract broth but : (1) many
organisms can digest gelatin and (2) it melts at 37 oC, the favored incubation
temperature for most pathogens
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• Agar was suggested by Fannie Hesse wife of Walther Hesse
working in Koch Lab
• Story : Walther was working with gelatin plates in summer and
was having troubles
• Asked wife : Why do your jellies and pudding stay solid in
warm weather?
• Fannie learned to use agar from a Dutch neighbor in New York
who spent time in Asia
• Agar had been used as a gelling agent in Asia for centuries
Agar Endang S Rahayu
• Agar is complex polysaccharides derived from seaweed

• Its only melts at 100 oC, and solidifies at 45 oC
• Non-toxic to most microorganism
• Stable at sterilization temperature
• Only a very few bacteria have enzymes that digest it
Petri dish was invented in 1877
Petri - dish By an assistant of Koch – Endang S Rahayu
R.J. Petri (1852 – 1921)
Foto Koleksi ESR
Gambar ini diambil dari googling Foto Koleksi ESR

Key:
I. Gelatin stab culture
II. Agar stab culture
III. Colony appearance on gelatin plate
IV. Colony close up on gelatine plate
V. Gelatine Plate
VI. Agar Plate
VII. Colony appearance on agar plate
VIII. Appearance of growth on a slice of potato
IX. Microscopy
http://www.labnews.co.uk/printer_frien
dly.php/808/history-of-the-agar-plate
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Alexander Fleming Endang S Rahayu
(1881-1955) Universitas Gadjah Mada
Observed that the mold Penicillium inhibited

the growth of a bacterial culture.
Fleming's original culture plate http://fig.cox.miami.edu/~cmallery/255/255enz/penicillin.gif

Alexander Fleming’s original contaminated plate http://www.time.com/time/time100/scientist/profile/fleming.html
(1928), showing the zone of inhibited staphylococcal
growth around a Penicillium notatum colony.
Development of Penicillin
• Penicillin has been used clinically as an

antibiotic since the 1940s
Endang S Rahayu Gambar-gambar yang terdapat dalam slide ini,

Universitas Gadjah Mada diambil dari googling
Fermentasi Makanan Traditional
• Fermentasi makanan – perubahan bahan dasar ke
produk oleh aktivitas mikroorganisme / enzim yang
ditujukan untuk mendapatkan perubahan yang
dikehendaki
• Keberadaan makanan fermentasi sejak peradaban
manusia, contohnya: roti, anggur, dadih yang banyak
ditulis di dalam Kitab Suci.
• Banyak makanan fermentasi yang dihasilkan secara
spontan / fermentasi alami, dengan mikroorganisme
yang spesifik tergantung dari bahan dasar dan
lingkungan.
• Teknologi diperlukan untuk peningkatan proses dan hf.org/2014/03/beyond-sauerkraut-a-brief-history-
mutu produk, dan sebagai pangan fungsional of-fermented-foods/ Endang S Rahayu
Fermentasi susu
• Kemudian diambilnya dadih (curd) dan susu
serta anak lembu yang telah diolah itu, lalu
dihidangkannya ……. Kejadian 18:8 (Genesis
18:8)
D ad
ih
(Sum
Bar)
Preserving milk to souring

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Concept of Probiotics
•Metchnikoff’s (Rusia) theory –
longevity without aging by taking
yogurt (Metchnikoff, E. 1908. The
prolongation of life. G.P. Putnam’s
Sons. New York).
•Consumption of live cells – Pro
bio
tic P
have health beneficial rod
uc t
effects
The birth of probiotics –

probiotic food Lactic bacilli Pills produced by Le
Ferment Co
Gambar-gambar yang terdapat dalam slide ini, Endang S Rahayu (1905 – 1910) di Paris
diambil dari googling Universitas Gadjah Mada
Probiotics in Food (Functional Foods) Endang S Rahayu
38
●Genetic Engineering Herbert Boyer (1936 – now)
●Genetically Modified Microorganisms (GMO) Stanley N. Cohen (1935– now)
● Products from GMO
Paul Berg (1926-now) is

arguably most famous for his
pioneering work involving gene
splicing of recombinant DNA.[15]
Berg was the first scientist to
create a molecule containing
DNA from two different species
by inserting DNA from another
species into a molecule. This
gene-splicing technique was a
fundamental step in the
development of modern genetic
engineering. After developing
the technique, Berg used it for
his studies of viral Gambar-gambar yang terdapat dalam slide ini,
chromosomes.[16] diambil dari googling
Human Insulin Production

Rekayasa genetika pada Tanaman
• Mengapa Agrobacterium tumifaciens?
• Target gen from Baciilus thuringiensis
• Dapat melakukan transfer gen horizontal yaitu pada tanaman
• Mampu menghasilkan endotoksin yang dapat
sehingga menyebabkan penyakit galls (tumor pada akar)
membunuh beberapa inset
• Transfer gen ini dilakukan oleh plasmid Ti (tumor inducing plasmid)

Rekayasa genetika pada Tanaman
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Fermentation-Produced Chymosin (FPC)

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Genomics – transcriptomics – proteomics - metabolomics
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Whole Genome Sequence
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Whole Genome Sequence Probiotik Lokal
Lactiplantibacillus plantarum Dad-13
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• Adhesion Properties of Lactobacillus plantarum Dad-13 and Lactobacillus plantarum

Mut-7 on Sprague Dawley Rat Intestine. A Darmastuti, PN Hasan, R Wikandari, T Utami,
ES. Rahayu, and DA Suroto.
Microorganisms. 2021 Nov 11;9(11):2336.doi: 10.3390/microorganisms9112336.
• Genotypic and Phenotypic Analyses of Antibiotic Resistance in Indonesian Indigenous
Lactobacillus Probiotics. D Andriani, PN Hasan, T Utami, DA Suroto, R Wikandari, ES
Rahayu. Applied Food Biotechnology, 2021, 8 (4):267-274 https://journals.sbmu.ac.ir ›
article
• Genomic insight of two indigenous probiotics Lactobacillus plantarum Dad-13 and
Lactobacillus plantarum Mut-7 from different origins of Indonesian fermented foods.
DS Suroto, PN Hasan, ES Rahayu. Biodiversitas ISSN: 1412-033X, 22, 12, December 2021
E-ISSN: 2085-4722; Pages: 5491-5500
DOI: 10.13057/biodiv/d221233
Bakteriosin adalah anti-

bakteri yang dapat
membunuh patogen
Concept Check
Microorganisms can be both beneficial and harmful to humans.

Although we tend to emphasize the harmful microorganisms
(infectious and disease agents), many more microorganisms are
beneficial than harmful.
In what ways are microorganisms important in the food industries ?
Endang S Rahayu
2 and 3.
Taxonomy, Phylogeny,
Systematic of Microorganisms
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Taxonomy, Phylogeny,
Systematic of Microorganisms
Five Kingdom Classification
Photos from Google
Endang S Rahayu
Homework - 2
1. Dunia taksonomi terus berkembang sesuai dengan perkembangan ilmu dan peralatan
analisa yang semakin canggih. Taksonomi konvensional (didasarkan pada sifat penotipik)
telah berkembang menjadi taksonomi modern (systematic) yang didasarkan pada sifat
genotipik organism. Jelaskan masing-masing system ini serta alasan para peneliti di dalam
pengembangan ilmu taksonomi : dari 2 kingdom system (Linnaeus, 1766), menjadi 3
kingdom system (Hogg, 1860 dan Ernst Haeckel, 1866) serta 5 kingdom system (Whittaker,
1967)
2. Carl Woese (1988) menyampaikan systematic organisme yang disebut dengan three
domain system. Jelaskan tentang tiga domain ini serta dasar klasifikasi ke dalam domain
ini.
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Evolution: knowledge on Heredity and genetic :
Knowledge on the
the phylogeny of living
mechanisms of inheritance
organisms and variation of living
organisms
Taxonomy : Science of
identification, naming
and grouping of living
Morphology, physiology, organisms Environmental Biology :
development of Biology: Knowledge on the interaction
Knowledge on form and of living organisms with non
function of living organisms living, respond and behaviour
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Lecture 2
• Taksonomi mikroorganisme
• Penggolongan organisme dan taksonomi mikroorganisme:
• 2-, 3-, 5- kingdoms system dan 3 domain;
• Taksonomi modern (systematic), pilogeni dan evolusi
• Studi kasus – isolasi dan identifikasi mikroorganisme
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Taksonomi Endang S Rahayu
Photos from Google
• Pioneer dibidang taksonomi organisme adalah

Carolus Linnaeus, ahli fisika dan botani (1707 - 1778,
Sweden), yang pada tahun 1766 - 1768 mengajukan
konsep sistem pemberian nama untuk makhluk
hidup, yaitu nomenklatur binomial sebagai dasar
dari ilmu biologi.
Two Kingdom System
Diperkenalkan pada tahun 1766 oleh Linnaeus :
• Plantae dengan ciri utama fotosintetik terdiri dari tanaman tingkat tinggi,
berakar dan tidak bergerak - ahlinya disebut botanist
• Animalia dengan ciri utama mencerna makanan (food ingesting) terdiri dari
hewan tingkat tinggi dan bergerak - ahlinya disebut zoologist
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Three Kingdom System
• Plantae - fotosintetik - tanaman tingkat tinggi, berakar dan tidak bergerak - ahlinya
disebut botanist
• Animalia - mencerna makanan (food ingesting), hewan tingkat tinggi dan bergerak -
ahlinya disebut zoologist
• Protoctista (Hogg, 1860) atau protista (Ernst Haeckel, 1866) terdiri dari :
Uniseluler : bakteri
Multiseluler (namun tidak memiliki diferensiasi jaringan seperti hal tanaman/hewan
atau tidak membentuk jaringan) : algae dan fungi
Ahlinya disebut microbiologist (bacteriologist, food mycologist, dll)
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Haeckel's Tree of Life Endang S Rahayu
1. to be the first to describe the

evolutionary relationships among
Photos from Google
living organisms, a geneology of life,
as analogous to a tree
2. postulated a common origin for all
life (plants, animals and microbes)
3. described the third kingdom for
micro-organsims — the Protista.
Five Kingdom System Endang S Rahayu
The 5-Kingdom system is based

on three levels of organization-
procaryotic (Kingdom
Monera), eucaryotic
unicellular (Kingdom Protista),
and eucaryotic multicellular
(Kingdoms Plantae, Fungi and
Animalia).
Photos from Google
Whittaker's phylogenetic Tree of 1967

Five Kingdom System
R.H. Whittaker, 1959
• Kingdom Monera or Prokaryotes: Archaebacteria
(paling primitif) dan Eubacteria (bakteri)
• Kingdom Protista (uniseluler eukariot) contoh :
algae, protozoa, slime mold, organisme aquatic
dan parasit
• Kingdom Fungi (multiseluler eukariot) contohnya
: yeast, mold (micro fungi) and mushrom (macro
fungi)
• Kingdom Animalia
• Kingdom Plantae
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Carl Woese's Three Domain System (1988)
Erko Stackebrandt
Carl Woese
Photos from Google
Carl Woese's "universal" phylogenetic tree of 1988 determined from ribosomal RNA sequence comparisons. Note the three
major domains of living organisms: The Eubacteria (Bacteria), the Archaebacteria (Archaea) and the Eukaryotes (Eucarya). The
evolutionary distance between two groups of organisms is proportional to the cumulative distance between the end of the
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branch and the node that joins the two groups. Universitas Gadjah Mada
The Universal Phylogenetic Tree
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Taksonomi
• Ilmu yang berkembang sesuai dengan perkembangan metoda-metoda
penelitian, peralatan yang mendukung, komputer bersama
programnya, dll
• Taksonomi – Konvensional
• Klasifikasi
• Nomenklatur
• Identifikasi
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• Tata cara penulisan
• Rhizopus oligosporus
• Saccharomyces cerevisiae
• E. coli
• Tata cara penulisan ini dan perubahan penggolongan organisme
dikomunikasikan pada
• International Code of Nomenclature of Bacteria (ICNB) - International Code of
Nomenclature of Prokaryotes (ICNP)
• International Code of Botanical Nomenclature (ICBN)
• Journal of Systematics and Evolution (JSE)
• International Journal of Systematic and Evolutionary Microbiology
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Taxonomy groups organisms by:
• Penotypic characters – morphology, physiology –

conventional taxonomy
• Molecular composition –chemotaxonomy
taxonomy
• Genetics - macromolecul (DNA, RNA, Protein) –
molecular taxonomy
• Phylogenetic
• Systematic
• Evolutionary
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Phenotypic characteristics used in conventional
taxonomy
• Morphology (bentuk sel, motil/non motil, etc)
• Gram reaction (bakteri)
• Carbon source utilization
• Nitrogen source utilization
• Fermentation products (asam dan gas)
• Temperature range, pH range
• Aerob/Anaerob
• Pigment
• etc
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Kemotaksonomi
• Didasarkan pada komposisi kimia sel
• Asam lemak sel, asam mikolat, polar lipid
• Quinon – ubiquinon, poliamine
• Komposisi dinding sel – DAP, eksopolisakarida
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Molekular taksonomi
• Didasarkan pada makromolekul (DNA, RNA, protein)
• Dapat digunakan untuk menyusun pilogeni
• DNA DNA similariti/homologi;
• Mol % G+C;
• Pola restriksi (RLFP, PFGE); Ukuran genom
• Segmen DNA : PCR based DNA finger printing (ribotyping, ARDRA, RAPD, AFLP)
• DNA probe
• DNA sequensing
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Makromolekul yang lain
• RNA
• Sequen RNA
• LMW profil RNA
• Protein
• Pola elektroforesis protein sel
• Pola enzim
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Konsep spesies
• Dua strain dengan similaritas DNA di atas 70 % dapat dimasukkan ke dalam spesies yang
sama.
• Subspesies atau tipe yang mencerminkan klon spesifik dari sel.
• Biovar apabila subspesies ini dibedakan atas sifat fisiologinya,
• morfovar apabila dibedakan atas morfologinya, dan
• Serovar apabila dibedakan atas antigennya.
• Strain adalah populasi sel yang berasal dari strain tunggal.
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Kriteria klasifikasi yang didasarkan pada mol DNA/RNA
Spesies yg sama Genus yg sama Famili yg sama
Similariti DNA > 70 % > 20-30 %

Sekuen rRNA > 98 % > 93-95 % > 89-93 %
Often GC ratio of DNA is also used.

If 2 organisms that are thought to be closely related based on
phenotypic criteria do not have similar GC values, then they are
not in fact closely related.
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Strains of the same
species should have
values >70%
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Pilogeni
• Pilogeni – sejarah evolusi dari organisme. Istilah pilogeni berasal dari bahasa
Greek, phylon artinya tribe dan genesis artinya asal usul (origin).
• Zukerkandl dan Pauling (1965) yaitu dengan penjelasannya tentang Molecules

as documents of evolutionary history.
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Phylogenetic - Evolutionary
• Microorganisms……that all new species originate from preexisting species,

and that closely related organisms have similar features due to having
evolved from common ancestral forms
• Genetics - macromolecule (DNA, RNA, Protein)
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Molekul – Kronometer
• Bagaimana menentukan jarak evolusi seluruh makhluk di muka bumi ini ? –

diperlukan MOLEKUL yang digunakan sebagai KRONOMETER
• Perubahan sekuen nukleotida pada asam nukleat atau asam amino pada
protein dapat digunakan sebagai kronometer untuk menentukan waktu
evolusi.
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Endang S.Rahayu
Fak. Teknologi Pertanian UGM
Molekul Kronometer
• Terdistribusi (terdapat) di seluruh organisme
• Mempunyai fungsi yang sama dan konstan
• Berubah pada kecepatan tertentu
• Mudah diisolasi
• Molekul tersebut adalah ribosomal RNA
• Perubahan sekuen rRNA diperkirakan :
• 1% perubahan setiap 6,2 x 107 tahun selama billion (milyard) tahun pertama
• 1 % perubahan setiap 1,2–1,6 x 108 tahun selama beberapa billion (milyard) tahun
berikutnya
• 1-2 % perubahan setiap 5,0 x 107 tahun selama 500 million (juta) tahun akhir-akhir ini
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The Central Dogma of Molecular Biology
Virus
✓Ds DNA
✓ Ss DNA
✓ RNA
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Small Subunit
Ribosomal RNA
Type Size Large subunit Small subunit
prokaryotic 70S 50S (5S-115, 23S-2904) 30S (16S-1542)

eukaryotic 80S 60S (5S-115, 5.8S-153, 28S- 40S (18S- 2000)
Evolutionary chronometer
Hori H, Osawa S.
Evolutionary change in 5S RNA secondary structure and
a phylogenic tree of 54 5S RNA species. Proc. Natl. Acad.
Sci. U.S.A. 76, 381-385 (1979)
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rRNA gene sequence analysis - Endang S Rahayu
Phylogenetic Tree Universitas Gadjah Mada

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Endosymbiosis
Endosymbiosis
the hypothesis that
mitochondria and
chloroplast
are descendant of
ancient
prokaryotic
organisms from
domain bacteria
The probable events of endosymbiosis that
Endang S Rahayu gave rise to the chloroplasts and mitochondria
Universitas Gadjah Mada of eucaryotic cells
All cells of the present time organisms
share a common ancestor
An evolutionary phylogenetic tree:
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Evolusi – dari RNA – cellular life
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A Revolution in Microbiology Endang S Rahayu
1. Understanding of evolutionary relatednesss

(= phylogeny) between organisms
• quite different than what was originally
thought
2. Microbial Ecology
• ability to probe community structure
without the need for culturing
Genomics – Transcriptomics – Proteomics - Metabolomics
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Asian Microbiome Project
Gut microbiota
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Photos from Google
Gram positive
Bentuk batang, bulat
ISOLASI dan IDENTIFIKASI
Tidak membentuk spora BAKTERI ASAM LAKTAT
Katalase negatif
Menghasilkan asam laktat sebagai
produk utama fermentasi gula
Habitat : susu, buah-buahan, sayuran,
makanan fermentasi dan
saluran pencernaan
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Fermented Foods as Source of Microorganisms
Peda Asinan k
oya
p
Tem
Petis Dadih Asinan

(2003)
https://cfns.ugm.ac.id/2020/05/
28/download-materi-isolasi-
dan-identifikasi-bakteri-asam-
laktat/
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92
Endang S Rahayu
API Kit
50 CHL
https://cfns.ugm.
ac.id/wp-
content/uploads/
sites/861/2020/0
6/2020_Identifika
si-BAL-dengan-
API-KIT-dan-16S-
rRNA_ESR.pdf
https://cfns.ugm.ac.id/2020/05/29/dwnload-materi-
identifikasi-bakteri-asam-laktat-dengan-metode-molekuler/
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94
IDENTIFIKASI STRAIN
(yang telah diberi nama-
nomer), digunakan untuk
menentukan genus, Identifikasi berdasar
spesies atau subspesies
karakter GENOTIPIK
Strain yang akan diidentifikasi

• Bedasarkan similarity gen
16S rRNA, strain
indigenous (Dad-13; T-3;
Mut-7; Mut-13) memiliki
kesamaan >99%,
terhadap L. plantarum ss
plantarum, L. plantarum
ss argentoratensis, L.
pentosus
• Berdasar profile gen
RecA, ternyata seluruh
strain indigenous adalah
L. plantarum ss
✓ plantarum
✓
95
Nomenclature of the bacteria must conform to the current,
scientifically recognized names (FAO/WHO, 2002)
Strain Indigenous Dad-13, yang semula (2015)

berdasarkan kesamaan gen 16S rRNA dengan type strain
JCM 1149T (Accesion Number D79210), serta profile gen
RecA teridentifikasi sebagai Lactobacillus plantarum ss
plantarum.
Berdasarkan nomenclature baru (Zheng et al., 2020), Type
strain JCM 1149T ditetapkan sebagai Lactiplantibacillus
plantarum subsp. plantarum
maka kini Dad-13 kini menjadi Lactiplantibacillus
plantarum subsp. plantarum Dad-13
https://probiotics.wg.ugm.ac.id/2021/10/29/current-taxonomic-name-of-indigenous-probiotic-strains/
Endang S Rahayu 96
Paper I: Isolasi dan seleksi Lactobacillus yang berpotensi sebagai
agensia probiotik. SNP dan ESR, 2013, Agritech 23 (2): 75 - 84
Paper 1 (2003): strain SNP-2, sebagai

kandidat Probiotik, berdasarkan
Paper 2: Karakter GENOTIPIK
karakter penotipik, teridentifikasi
sebagai Lactobacillus acidophilus
Paper 2 (2015): Strain SNP-2

berdasarkan karakter genotipik,
similarity gen 16S rRNA dan profil
gen PepR, teridentifikasi sebagai
Lactobaciilus paracasei ss paracasei
Berdasarkan nomenclature baru

(Zheng et al., 2020), strain SNP-2
menjadi Lacticaseibacillus paracasei
subsp. paracasei SNP-2
Karakter PENOTIPIK
Photos from Google
Mold penghasil mikotoksin pada

biji kopi dan kakao
Endang S Rahayu
Occurrence of OTA in COFFEE and During After Indoor
CACAO, Yogyakarta, 2012 Fermentation Drying Mold
COCOA OTA COFFEE OTA
Samples (ppb) Samples (ppb)
F-1 7.85 F-1 11.21
F-2 13.19 F-2 3.37
F-3 29.49 F-3 8.58
F-4 10.61 F-4 2.34
F-5 6.68 F-5 5.26
F-6 19.83 F-6 3.49
F-7 17.29 F-7 8.38
F-8 8.50 F-8 2.55
F-9 17.09 F-9 2.64
F-10 12.31 F-10 2.77
C-11 17.95 C-11 4.16
C-12 10.67 C-12 3.48
Endang S Rahayu
Mycobiota of cocoa beans and indoor Universitas Gadjah Mada
Endang S Rahayu
Colonies of isolates in media MEA, CYA, and CZ

Grouping of the black Aspergillus based on macroscopic and microscopic characters
Colony on CYA Colony on MEA

Group Isolate diameter of diameter of
color reverse color reverse
colony colony
yellowish dark brown to black,
YAC-9, YAK-6, YAK- brown, white to
I 68-70 brown in the 60-65 white to yellow Pale
12 yellow mycelium
center mycelium
YAC-2, YAC-8, YAC-

12, YAC-13, YAC- brown, white dark brown, white
II 68-70 white 45-60 Pale
25, YAK-2, YAG-2, mycelium mycelium
YAG-8, YAG-11
YAC-4, YAK-3, YAG- dark brown, brown in the dark brown to black,
III 65-70 60-68 Yellow
3 white mycelium center white mycelium
IV YAK-1 68-70 grey to brown pale 44-47 brown Pale

Endang S Rahayu
Grouping of the black Aspergillus based on macroscopic and microscopic characters
microscopic features
OTA
Group Isolate veiscle conidia identified species as
seriation stipe (μm) (ppb)
(μm) (μm)
thick,
I YAC-9, YAK-6, YAK-12 biseriate 55-60 7-8 6-57 A.carbonarius
22-24
YAC-2, YAC-8, YAC-

12, YAC-13, YAC-25,
II biseriate 55-75 12-15 3-5 3 A.niger I
YAK-2, YAG-2, YAG-8,
YAG-11
III YAC-4, YAK-3, YAG-3 biseriate 45-50 12-15 3-5 <LOD A.niger II
IV YAK-1 uniseriate 50-55 11-12 3-5 <LOD A.aculeatus

Endang S Rahayu
Neighbor joining tree based on phylogenetic
analysis of ITS sequence
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Isolates this study were close related to four species of black Aspergilli
of
17
• A. tubingiensis (non OTA producer)
• A. carbonarius (OTA producer)
• A. niger (some OTA producer)
Endang S Rahayu
• A. aculeatus (non OTA producer) Universitas Gadjah Mada
Dari 545 urutan basa
nukeotida isolat,
mempunyai area yang
conserve (tidak
berubah) dari 189-346
Endang S Rahayu
Kesimpulan
q identifikasi black aspergili untuk dalam
kelompok spesies A.niger sangat susah
No Sampel isolat Uji OTA (ppb) identifikasi makroskopik identifikasi molekuler
1 Kakao 5 YAC-9 67,68 A.carbonarius A.carbonarius dibedakan secara morfologi
2 Kakao 6 YAC-26 tidak diuji - - q Beberapa kelompok yang dibedakan menjadi
3 kakao 7 YAC-27 tidak diuji - -
grup A.niger diidentifikasi secara molekuler
4 Kakao 10 YAC-8 <LOD A.niger II A. tubingensis
5 kakao 10 YAC-4 <LOD A.niger I A. tubingensis sebagai A.tubingensis
6 kakao 11 YAC-2 <LOD A.niger II A.niger q A. carbonarius adalah penghasil OTA dalam
7 kakao 11 YAC-13 <LOD A.niger II A.awamori
kelompok black aspergilli
8 kakao 11 YAC-25 <LOD A.niger II A.niger
9 kakao 12 YAC-12 <LOD A.niger II A.carbonarius
10 kopi 4 YAK-1 <LOD A. acuelatus A. acuelatus
11 kopi 5 YAK-2 <LOD A.niger II A. tubingensis
12 kopi 9 YAK-5 tidak diuji - -
13 kopi 10 YAK-3 <LOD A.niger I A. tubingensis
14 kopi 10 YAK-6 50,22 A.carbonarius A.carbonarius
15 kopi 10 YAK-12 6,04 A.carbonarius A.carbonarius
16 gaplek 4 YAG-11 <LOD A.niger II A.niger
17 gaplek 7 YAG-2 3,08 A.niger II A.niger
18 gaplek 8 YAG-3 <LOD A.niger I A. tubingensis
19 gaplek 10 YAG-10 tidak diuji - -
20 gaplek 16 YAG-8 <LOD A.niger II A.niger
Endang S Rahayu
TERIMA KASIH
Endang S Rahayu

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Mikrobiologi Umum

Somes Photos from Google

Prof. Dr. Retno Indrati (RI)

• The Development of the Microscope

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

• Francesco Redi (1626-1697)

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

"Do not put forward anything that you Gambar-gambar

Pasteur’s Swan Neck

Drew out the necks of flasks

• Rudolf Virchow introduced the concept of

• Agostino Bassi (1773-1856)

Gambar-gambar yang terdapat dalam slide ini,

• 1800- French Government (Napoleon III)

Gambar-gambar yang terdapat dalam slide ini,

Fig. 2. Louis Pasteur’s in

Gambar-gambar yang terdapat dalam slide ini,

• Pasteur’s perplexing problem

• English physicist John Tyndall (1820-1893) dealt the

Gambar-gambar yang terdapat dalam slide ini,

Microbial Role in Disease

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

• Agar is complex polysaccharides derived from seaweed

Foto Koleksi ESR

Gambar ini diambil dari googling Foto Koleksi ESR

(1881-1955) Universitas Gadjah Mada

Observed that the mold Penicillium inhibited

Fleming's original culture plate http://fig.cox.miami.edu/~cmallery/255/255enz/penicillin.gif

• Penicillin has been used clinically as an

Endang S Rahayu Gambar-gambar yang terdapat dalam slide ini,

Preserving milk to souring

The birth of probiotics –

Paul Berg (1926-now) is

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

Gambar-gambar yang terdapat dalam slide ini,

• Adhesion Properties of Lactobacillus plantarum Dad-13 and Lactobacillus plantarum

Bakteriosin adalah anti-

Microorganisms can be both beneficial and harmful to humans.

Five Kingdom Classification

Photos from Google

Photos from Google

• Pioneer dibidang taksonomi organisme adalah

1. to be the first to describe the

The 5-Kingdom system is based

Whittaker's phylogenetic Tree of 1967

Photos from Google

• Penotypic characters – morphology, physiology –

Spesies yg sama Genus yg sama Famili yg sama

Similariti DNA > 70 % > 20-30 %

Often GC ratio of DNA is also used.

• Zukerkandl dan Pauling (1965) yaitu dengan penjelasannya tentang Molecules

• Microorganisms……that all new species originate from preexisting species,

• Bagaimana menentukan jarak evolusi seluruh makhluk di muka bumi ini ? –

Type Size Large subunit Small subunit

prokaryotic 70S 50S (5S-115, 23S-2904) 30S (16S-1542)

Phylogenetic Tree Universitas Gadjah Mada