1 introduction : kribb/kctc - wdcm status of kctc... · 2019-02-14 · grew well, but...
TRANSCRIPT
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!