DirectorKorean Collection for Type Cultures (KCTC)Biological Resource Center Korea Research Institute of Bioscience & Biotechnology

http://kctc.kribb.re.kr

21th Nov. 2018

1 Introduction : KRIBB/KCTC

KRIBB is the largest Government-funded Research

Institute for Biotechnology Research in Korea.

In accordance with the “Law on Establishment,

Management and Promotion of Government-supported

Research Institutes in the Science and Technology Sector”

Mission of KRIBB is to lead BT researches in KOREA

·R&D activities in bioscience and biotechnology

·Infrastructures to support research on bioscience

Fusion BT Pharma Green Bio National Agenda

Infrastructures

KCTC Functions

Collection and preservation of biological resources,

their distribution to industries, academia and institutes

Development of core technologies for

valuable bio-resources

Construction of local and international networks of

bioresources and their related information

Functions of KCTC

KCTC History…1985~

1985.02. Started CC with an official approval from the Ministry of

Science & Technology

1985.02. Became a member of the WFCC (World Federation of

Culture Collections) #597

1986.01.Became a member of the WDCM (World Data Center for

Microorganisms)

1990.06.Designated as an International Depositary Authority from

the WIPO (World Intellectual Property Organization) based on the

Budapest Treaty

2004.02.Obtained an ISO 9001:2000 certificate for Quality

Management System

2008.08.Designated as the National Repository for Bio-research

Products from the national R&D projects by the MSIT (Ministry of

Science & ICT)

2013.03.Biological Resource Center, Division of Biological Infrastructure

2016.01.Moved to Jeonbuk Branch Institute of KRIBB

2016.10. Took the Korean Gut Microbiome Bank (KGMB) Project

KCTC Organization

Director

Plant cell lines

Networks/

Bioinformatics

Patent resources

Animal cell linesYeast

Aerobes

Deposition/

Distribution

Virus Genetic materials Embryos

Extremophiles

Microalgae

ArchaeaAnaerobes, LABActinomycetes

Filamentous fungi

Six curators and ~30 researchers

General curators

Bio-research products

Preservation facilities

Preservation room

Lyophilized ampules

Preservation

room

LN2 Tanks

Preservation

room

Deep

Freezers

Back-upPreservation

room

2 MAJOR ACTIVITIES in 2018

Number of general and patent strains holding at KCTC

Total 34,352 strains4,313 1,658

1,692 185

255

178

7,567

2,168

1,068

4,870

6,440

5

700

585

2,668

Actinomycetes(4,313) Algae(1,658) Anaerobes(1,692)

Animal cells(185) Archaea(255) Extremophiles(178)

G(-) Bacteria(7,567) G(+) Bacteria(2,168) Lactic acid bacteria(1,068)

Molds(4,870) Patent(6,440) Phages(5)

Plant cells(700) Plasmids(585) Yeasts(2,668)

Number of microbial strains deposited at KCTC in 2018

◇ strains have been obtained at KCTC in 2015~2018.

G(-) Bacteria

Patents

Actinomycetes

Anaerobes

Animal cells

Archaea

Extremophiles

G(-) Bacteria

G(+) Bacteria

Lactic acid bacteria

Molds

Patent

Phages

Plant cells Plasmids

Yeasts

Actinomycetes(706)

Anaerobes(294)

Animal cells(27)

Archaea(61)

Extremophiles(5)

G(-) Bacteria(2,498)

G(+) Bacteria(390)

Lactic acid bacteria(116)

Molds(690)

Patent(1,356)

Phages(3)

Plant cells(386)

Plasmids (2)

Yeasts(224)

Number of KCTC strains reported in international taxonomy journals

263 229

337

406

349

221

100

150

200

250

300

350

400

450

2013 2014 2015 2016 2017 2018

Year KCTC type strains

~2012 1,203

2013 263

2014 229

2015 337

2016 406

2017 349

2018 221

Total 3,008

Numberof KCTC strains distributed

◇ KCTC strains have been distributed in 2015~2018.

-

4,000

8,000

12,000

2015 2016 2017 2018

G(-) BacteriaG(-) Bacteria

G(-) Bacteria

G(-) Bacteria

G(+) Bacteria G(+) Bacteria

G(+) Bacteria

G(+) Bacteria

Lactic acid bacteria

Lactic acid bacteria

Lactic acid bacteria

Lactic acid bacteria

Molds

Molds

Molds

Molds

Yeasts Yeasts

Yeasts

Yeasts

Yeasts

Plasmids

Plant cells

Phages

Molds

Lactic acid bacteria

G(+) Bacteria

G(-) Bacteria

Extremophiles

Archaea

Animal cells

Anaerobes

Algae

Actinomycetes

Number of KCTC strains distributed abroad

100

200

300

2015 2016 2017 2018

270

337319 393

Number of papers with KCTC strains is gradually increasing

0

100

200

300

400

2013 2014 2015 2016 2017 2018

269 267

338

396 436

285

www.scopus.com (ELSEVIER)

Pap

ers

0

50

100

150

200

250

2015 2016 2017 2018

105123

172189

0

10

20

30

40

50

2015 2016 2017 2018

17

36

42

13

Safety Deposit Ampoule service

Total 112 strains have been preserved 5248 ampoules were supplied for 5 years

Str

ain

s

No problem

Supplied

better … No growth

-

100

200

300

2015 2016 2017 2018

G(-) BacteriaG(-) Bacteria G(-) Bacteria G(-) Bacteria

Anaerobes

Anaerobes

Anaerobes

Anaerobes

LAB

LAB

LAB

LAB

Yeasts Yeasts

Yeasts

Yeasts

Archaea

Extremophiles

Animal cells

Yeasts

Molds

G(+) Bacteria

Actinomycetes

LAB

Anaerobes

G(-) Bacteria

No growth

Contami…

etc

USER claim KCTC response

Claims from users and response

out of ~34,000 strains distributed

Analyses of the claims Count (%)

Grew well, but re-distributed 871 96.8

No problems, but alternatives were re-

distributed 10 1.1

No growth 12 1.3

Contaminated, etc 7 0.8

Domestic Workshops

◆ Biological Resource Cultivation and Long-term Preservation

• One-day workshop

Lecture and practice sessions: about 40 participants in one-day workshop

Number of participants: ~ 120 - Aerobic bacteria/actinomycetes, Anaerobes, Fungi, Plant cell lines, Microalgae

• One-day workshop

Basic technique and understanding of

cellular fatty analysis for chemotaxonomy

Sample preparation and analysis by gas

chromatography (GC)

Maintenance of GC

Three times in 2018 (Mar., Jul., Sep.)

Seven times in 2018

Bacterial Cellular Fatty Acid Analysis (MIDI), Polar lipid, Dendrogram

Domestic Workshops

◆ Polar Lipid Analysis (Phospholipids)

• Two-day workshop

Basic technique and understanding of bacterial polar lipid analysis for

chemotaxonomy

Extraction, TLC development and detection by various reagents

• One-day workshop

Introduction to phylogenetics and taxonomy

DNA sequence preparation method

Understanding and practice of multiple sequence alignment

Practice of phylogenetic analysis using MEGA software

Twice in 2018 (May, Aug.)

Twice in 2018 (Jul., Nov.)

◆ Molecular Phylogenetic Analysis

ACM Microbial Taxonomy Training Course (since 2012)

Human Resource Development (HRD) Program for ACM members

ACM Asian Consortium for the conservation and sustainable use of Microbial resources

Participants: 7 people from 7 countries

Period: 6 weeks

1st Week: Introduction, phylogenetic tree

2nd Week: Fatty acids

3rd Week: Polar lipid

4rd Week: Quinone

5th Week: DNA G+C mol%, DNA-DNA hybridization

6th Week: Presentation of results and discussion

◆ Six-week training course on microbial taxonomy for ACM scientists

3 Research

Name1 Arachidicoccus rhizosphaerae

2 Erysipelothrix larvae

3 Draconibacterium filum

4 Geosporobacter ferrireducens

5 Hyunsoonleella udoensis

6 Jejuia marina

7 Fabibacter misakiensis

8 Sphingomonas vulcanisoli

9 Algoriphagus aestuarii

10 Sphingobium subterraneum

11 Arachidicoccus rhizosphaerae

12 Mucilaginibacter gotjawali

13 Anaerosolibacter carboniphilus

14 Polaribacter undariae

15 Leeuwenhoekiella polynyae

16 Pseudoseohaeicola caenipelagi

17 Demequina activiva

18 Palleronia soli

19 Lutibacter crassostreae

20 Sphingomonas morindae

21 Paenibacillus xanthinilyticus

22 Cohnella collisoli

23 Pseudoxanthomonas sangjuensis

24 Faecalibaculum rodentium

25 Weissella jogaejeotgali

26 Gaetbulibacter aquiaggeris

27 Paenibacillus baekrokdamisoli

28 Maliponia aquimaris

Name29 Loktanella marina

30 Fulvivirga lutimaris

31 Roseivirga maritima

32 Cribrihabitans pelagius

33 Taeania maliponensis

34 Nocardioides baekrokdamisoli

35 Lewinella aquimaris

36 Agarivorans aestuarii

37 Novosphingobium oryzae

38 Paenibacillus cathormii

39 Mucilaginibacter carri

40 Flavobacterium tistrianum

41 Calculibacillus koreensis

42 Spirosoma aerolatum

43 Rhodanobacter aciditrophus

44 Dermabacter vaginalis

45 Lacinutrix cladophorae

46 Actinotalea caeni

47 Pseudorhodobacter ponti

48 Algibacter aquaticus

49 Roseobacter ponti

50 Sphingomonas gotjawalisoli

51 Mucilaginibacter craterilacus

52 Altererythrobacter aquiaggeris

53 Paucibacter oligotrophus

54 Kiloniella antarctica

55 Olleya algicola

56 Oryzihumus soli

Name57 Roseomonas terricola

58 Psychrosphaera aquimarina

59 Bacillus ciccensis

60 Flavivirga eckloniae

61 Hymenobacter tenuis

62 Sphingomonas limnosediminicola

63 Lacinutrix chionocetis

64 Vibrio injenensis

65 Flagellimonas aquimarina

66 Hymenobacter defluvii

67 Lactobacillus porci

68 Tabrizicola fusiformis

69 Flavisolibacter carri

70 Lacinutrix salivirg

71 Zhongshania ponticola

72 Pseudoruegeria litorisediminis

73 Polaribacter staleyi

74 Aquimarina algiphila

75 Flavisolibacter metallilatus

76 Jatrophihabitans telluris

77 Sulfitobacter aestuarii

78 Pseudoruegeria insulae

79 Sphingomicrobium arenosum

80 Arenimonas halophila

81 Dokdonia aurantiaca

82 Pseudobizionia ponticola

83 Aestuariimonas insulae

84 Thalassotalea insulae

New bacterial names reported by KCTC (2015~2018)

◆ Korean Gut Microbiome Bank (KGMB) Project (2016.10. ~ 2021.05.)

Korean Gut Microbiome Bank (KGMB) Project

D

iag

n

o

sis

V

ir

u

le

nc

e

Bacterial Genomics

E

vo

l

u

ti

o

n

Epidem

iology

Biomarker

Discovery

M

et

a

bol

ism

Pathogen

Detection

Genomics

◆ Isolation, Cultivation, Identification and Preservation of Korean Gut Microbiome

Resource management via barcode system

10-2

10-4

~5,600 strains

Species Strain Species Strain Species Strain Species Strain

Bifidobacterium longum subsp. longum 461 Enterococcus faecalis 36 Enterococcus avium 15 Alistipes onderdonkii 8

Collinsella aerofaciens 441 Bacteroides caccae 35 Lactococcus lactis subsp. Hordniae 15 Barnesiella intestinihominis 8

Bifidobacterium pseudocatenulatum 370 Catenibacterium mitsuokai 35 Dorea formicigenerans 14 Bifidobacterium dentium 8

Eggerthella lenta 295 Dorea longicatena 34 Mitsuokella jalaludinii 14 Bilophila wadsworthia 8

Bacteroides vulgatus 263 Bacteroides dorei 32 Blautia wexlerae 13 Fusicatenibacter saccharivorans 8

Bifidobacterium adolescentis 217 Senegalimassilia anaerobia 30 Streptococcus lutetiensis 13 Lactobacillus sakei 8

Bifidobacterium faecale 173 Adlercreutzia equolifaciens 28 Streptococcus salivarius subsp. Salivarius 13 Streptococcus gallolyticus subsp. pasteurianus 8

Bacteroides uniformis 127 Clostridium perfringens 28 Clostridium ramosum 12 Asaccharobacter celatus 7

Bacteroides ovatus 121 Holdemanella biformis 28 Coprococcus comes 12 Bacteroides faecis 7

Enterococcus faecium 116 Prevotella copri 26 Lactococcus garvieae subsp. garvieae 12 Bifidobacterium stercoris 7

Escherichia coli 115 Ruminococcus faecis 24 Bacteroides plebeius 11 Catabacter hongkongensis 7

Bifidobacterium longum 105 Bifidobacterium animalis 23 Bifidobacterium 11 Citrobacter amalonaticus 7

Bifidobacterium longum subsp. infantis 93 Bifidobacterium breve 23 Lactobacillus curvatus 11 Clostridium baratii 7

Bacteroides fragilis 85 Flavonifractor plautii 23 Leuconostoc lactis 11 Clostridium hathewayi 7

Bifidobacterium bifidum 84 Bifidobacterium catenulatum 22 Proteus mirabilis 11 Eisenbergiella tayi 7

Enterococcus hirae 79 Bacteroides eggerthii 21 Bacteroides finegoldii 10 Eubacterium eligens 7

Bacteroides thetaiotaomicron 75 Bacteroides nordii 20 Bacteroides intestinalis 10 Lactobacillus pentosus 7

Shigella flexneri 71 Eubacterium limosum 20 Clostridium innocuum 10 Lactococcus lactis subsp. lactis 7

Bifidobacterium animalis subsp. Lactis 68 Parasutterella excrementihominis 20 Lactobacillus mucosae 10 Megasphaera elsdenii 7

Lactobacillus ruminis 55 Cutibacterium acnes 19 Ruminococcus obeum 10 Paraprevotella clara 7

Lactobacillus sakei subsp. sakei 54 Alistipes shahii 18 Veillonella seminalis 10 Ruminococcus lactaris 7

Enterococcus durans 53 Bacteroides cellulosilyticus 18 Weissella confusa 10 Slackia isoflavoniconvertens 7

Parabacteroides distasonis 51 Bacteroides stercoris 18 Bacillus paralicheniformis 9 Bacteroides coprocola 6

Bacteroides xylanisolvens 50 Blautia luti 18 Enterococcus mundtii 9 Bacteroides coprophilus 6

Eubacterium callanderi 49 Blautia obeum 17 Megamonas funiformis 9 Eubacterium tenue 6

Escherichia fergusonii 46 Alistipes indistinctus 16 Odoribacter splanchnicus 9 Lactobacillus johnsonii 6

Parabacteroides merdae 46 Shigella dysenteriae 16 Olsenella scatoligenes 9 Shigella sonnei 6

Alistipes putredinis 45 Staphylococcus epidermidis 16 Ruminococcus gnavus 9 Staphylococcus saprophyticus subsp. saprophyticus 6

Gordonibacter pamelaeae 41 Anaerostipes hadrus 15 Turicibacter sanguinis 9 Veillonella dispar 6

Sutterella wadsworthensis 40 Enterobacter aerogenes 15 Weissella cibaria 9 Others 361

Korean Gut Microbiome Bank (KGMB) Project

Domestic Microbiome Conference

Korean Gut Microbiome Bank (KGMB)

• From Healthy Korean

Intestinal Immune Cells, Gut Microbiota, and Metabolic

Homeostasis

Microbiome and Precision Medicine

Developing Effective Standard Operating Procedures for

Korean Gut Microbiome Studies

Development of Immune System Modulators in

Rheumatoid Arthritis via Gut Microbiome and Probiotics

Exploring Host-Microbiota Interactions by Use of Germ-

free and Gnotobiotic Mouse Model System

◆ Collection of Plant-associated Microbiome (Endophytes)

Plant-associated Microbiome (Endophytes) Research

Plant yield and Growth

Promotion

• Plant growth promoting/Phyt

ostimulation

• Nutrient solubilization/uptake

Phytoremediation

• Heavy metals

• Hazardous chemicals

Plant Health and

Protection

• Drought, cold, heat stress,

pathogens

• Anti-microbial compounds

Industrial and

Medical Application

• Antibiotics

• Antiviral

• Anticancer compounds

• Antioxidants

• Bioinsecticides

16S, 18S, ITS regionblack chokeberry

Bacteria

Plant tissue

Endophyte

- +

IAA

concentr

atio

n (mg/m

l)

Am

E-1

Am

E-2

Am

E-3

Am

E-4

Am

E-5

Am

E-6

Am

E-7

0

5

1 0

1 5

2 0

1 5 0

2 0 0

2 5 0

- T r p

+ T r p

IAA production ability

Endophyte

- +Anti-fungal

assayBacteria

Fungus

C. fimbriata

Cladosporium_herbarum_EF679363.1

Cladosporium_ramotenellum_DQ780403.1

Cladosporium_spinulosum_DQ780406.1

Cladosporium_subinflatum_DQ780405.1

Cladosporium_cladosporioides_AY213640.1

Cladosporium_fusiforme_DQ780388.1

Cladosporium_langeronii_DQ780379.1

Cladosporium_psychrotolerans_DQ780386.1

Cladosporium_dominicanum_DQ780353.1

Cladosporium_sphaerospermum_NR_111222.1

Cladosporium_cladosporioides_ATCC_64726_AY361968.1

Cladosporium_sphaerospermum_GU017501.1

Cladosporium_parahalotolerans_MF473169.1

Cladosporium_halotolerans_KM527111.1

PGPF1

Cladosporium_salinae_DQ780374.1

Cercospora_beticola_KF251298.1

100

77

56

98

91

66

95

95

68

83

68

66

69

100

0.02

MSBM M9 MEA PDA

NT

(co-incubation for 2 weeks)

1

23 4

56

7

89

1. Acetaldehyde (C2H4O)

2. Ethyl alchol (C2H6O)

3. Acetone (C2H6O)

4. 2-Propanol, 2-methyl (C4H10O)

5. Propanal, 2-methyl (C4H8O)

6. Acetic acid (C2H3O2)

7. 2,3 Butanedione (C4H6O2)

8. Butanal, 3-methyl-(C5H10O)

9. Butanal, 2-methyl (C5H10O)

PGPF1

C. fimbriata

w H2O

C. fimbriata

w P. dispersa

1 2 3 4 5

DiseaseIncidence 8/9 1/9

1. Control (water)

2. P. dispersa

3. C. fimbriata

4. C. fimbriata + P. dispersa (Pantoea 1-d pretreatment)5. C. fimbriata + P. dispersa (Pantoea 10 min pretreatment)

**

*

*

*

Plant protection by endophytic bacteria

against phytopathogenPlant growth promotion by plant-

associated fungi

wo

w

PGPF1

Kimchi cabbage

C. fimbriata w PantoeaC. fimbriata

SH-5

RO-21RO-20RO-18 SO-13

C. fimbriata w Pantoea

C. fimbriata w E.coli

E

.

c

o

li

KCTC_2564DH5a

Pantoea dispersa

C. fimbriata

* RO: isolated from root* SH: isolated from shoot* SO: isolated from soil

Storage roots

Shoot

Soil Bacillus

PantoeaPantoea

Relative distribution of microorganism

11 Pantoeaisolates

Sweetpotato

Plant-associated Microbiome (Endophytes) Research

Thank you for your attention!