Roles and Quality Management of Culture Collections in Genomic Era

21 November 2018

WDCM GCM2.0 Workshop

Ken-ichiro Suzuki Department of Fermentation Science

Faculty of Applied Bioscience Tokyo University of Agriculture (TUA)

鈴木健一朗 東京農業大学応用生物科学部醸造科学科

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Relationship between Culture Collection and Taxonomy (Summary of Today’s Talk)

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Culture Collections and the Network

Taxonomy

Scientific background

Providing Type strains

Academic Community

Social Infrastructure

Whole Genome Sequences – Summary of Today’s Talk –

• Research purpose

– Application

– Taxonomic comparison without transfer of strains

– Taxonomy for In silico hybridization

• Quality management of collection

– Trace the transfer at strain level

– Identity confirmation with the depositor

– Identity confirmation with other culture collections

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Whole Genome Sequence Analysis for

Taxonomic Studies

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Courtesy of NBRC

Culture Collection

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: Membrane filter method

: Renaturation method

: S1 nuclease method

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◎ Stackebrandt & Goebel, 1994

DNA-DNA reassociation (%)

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DNA threshold value

for species delineation

Relationship of 16s rRNA homology and DNA-DNA reassociation values

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Principle of DNA-DNA Hybridization

One of the most essential methods to elucidate the species level Identification.

Labeling (RI, fluorescent)

denatured

Ratio = Index

Hybridization reaction

Organism A (Reference)

Organism B

Washing Immobilized Heat

denatured (ds) (ss)

Heat Fragmen- tation

Judgement of the Results of DNA-DNA Hybridization

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A: Species

B: Subspecies

C: Other subspecies

in the same species

D: Other species

in different species

(J. L. Johnson 1973, 1984)

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The phylogenetic definition of u species generally would include strains with approximately 70% or greater DNA-DNA relatedness and with 5°C or less DTm.

(Wayne, et al. 1987)

Definition of Bacterial species Based on DDH The species is the basic unit of bacterial taxonomy and is defined as a group of strains, including the type strain, sharing 70% or greater DNA-DNA relatedness with 5ºC or less ΔTm (Vandamme et al. 1996, Wayne et al. 1987).

However, DNA-DNA hybridization (DDH) is …

There are several different methods.

There are many parameters such as salt concentration,

temperature, etc.

It is easily affected by experimental error.

It is required high-skilled techniques.

There are times that the values may be different between the

papers.

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In silico DNA-DNA Hybridization • Various methods have been developed for bacterial taxonomy using

genome sequences.

• The relationship between in silico DDH and traditional DDH was reported.

• Advantage of In silico DDH is based on the absolute data of WGS

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The average nucleotide identity (ANI) Konstantinidis & Tiedje, Proc Natl Acad Sci USA 2005, 102, 2567–2572 Goris et al. Int J Syst Evol Microbiol, 2007, 57, 81–91 Richter & Rosselló-Móra, Proc Natl Acad Sci USA, 2009, 106, 19126-19131.

95-96% ANI corresponds to 60-70% DDH. Genome-To-Genome Distance Calculator (GGDC) Auch et al., Stand Gen Sci, 2010, 2, 117-134 Auch et al., Stand Gen Sci, 2010, 2, 142-148

0.0412 GGDC formula (2) value corresponds to 70% DDH. DNA maximal unique matches index (MUMi) Deloger et al., J Bacterial 2009, 191, 91-99

0.33±0.03 MUMi corresponds to 95%±0.5% ANI.

Case 1: Proposal of New Species Based on DDH - Taxonomic Study of Novel Strains Belonging to the Family Demequinaceae Isolated Using SPPY Agar

21/11/2018 NBRC Culture Collection

Studied by Dr. Moriyuki Hamada, NBRC, Skerman Award Winner 2017

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Phylogenetic Tree of the Isolates Based on 16S rRNA Gene Sequences

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Brevibacterium linens DSM 20425T (X77451)

Oerskovia enterophila DSM 43852T (X83807)

Oerskovia turbata DSM 20577T (X83806)

Cellulomonas bogoriensis 69B4T (X92152)

Cellulomonas cellasea DSM 20118T (X83804)

Cellulomonas flavigena DSM 20109T (X83799)

Sanguibacter marinus 1-19T (AJ783958)

Sanguibacter keddieii ST-74T (X79450)

Actinotalea fermentans NBRC 105374T (AB639014)

Lysinimicrobium mangrovi NBRC 105856T (AB639012)

Demequina lutea NBRC 106155T (AB639016)

Demequina aestuarii NBRC 106260T (AB639015)

Demequina aurantiaca NBRC 106265T (AB639020)

Demequina oxidasica NBRC 106264T (AB639019)

Demequina salsinemoris NBRC 105323T (AB639017)

Demequina globuliformis NBRC 106266T (AB639018)

0.01 Knuc

Demequina sediminicola NBRC 105855T (AB674957)

Demequina flava NBRC 105854T (AB674956)

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Demequina cluster

Lysinimicrobium cluster

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Polyphasic Approach by Chemotaxonomy

Characteristic 13 isolates (Lysinimicrobium spp.)

Lysinimicrobium 7 isolates (Demequina spp.)

Demequina

Peptidoglycan type A4α A4α A4β A4β

Diamino acid L-Lys L-Lys L-Orn L-Orn

Interpeptide bridge D-Glu or

D-Ser–D-Glu

D-Glu L-Ser–D-Glu or

D-Glu

Ser–D-Asp or

Ser–D-Glu

Major menaquinone DMK-9(H4) DMK-9(H4) DMK-9(H4) DMK-9(H4)

Major fatty acids ai-C15:0, ai-C17:0,

C16:0

ai-C15:0, ai-C17:0,

C16:0

ai-C15:0, ai-C17:0,

C16:0

ai-C15:0, ai-C17:0,

C16:0

Polar lipids§ DPG, PG, PI, PIMs,

PL

DPG, PG, PI, PIMs,

PL

DPG, PG, PI,

PIMs, PL

DPG, PG, PI

Genome size 2.68–3.23 Mbp 2.97Mbp 2.50–3.35 Mbp 2.46–3.21 Mbp

DNA G+C content 71.4–72.4 71.8 68.9–71.1 62.7–70.2

§DPG, Diphosphatidylglycerol; PG, phosphatidylglycerol; PI, phosphatidylinositol; PIMs, phosphatidylinositol-mannosides;

PL, unknown polar lipid.

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ANIb Values and 16S rRNA Gene Sequence Similarities among the 13 Isolates and L. mangrovi NBRC 105856

Proposal of 9 New Species for 13 Isolates

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AN

Ib

16S rRNA Gene Sequence Similarity

Hamada et al. 2015

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D. lutea

D. aestuarii

D. aurantiaca

D. oxidasica

D. salsinemoris

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D. globuliformis

D. sediminicola

D. flava

L. mangrovi

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L. mangrovi

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D. globuliformis

D. sediminicola

D. flava

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D. aestuarii

D. salsinemoris

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D. aurantiaca

D. oxidasica

D. lutea

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L. mangrovi

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D. sediminicola

D. flava

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D. aurantiaca

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16S rRNA gene MLSA (Concatenated amino-acid sequences of atpD, gyrB, recA, rpoB and trpB genes)

ANI

Comparison of the Dendrograms by 16S, MLSA and ANI

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• 20 Strains which phylogenetically related to members of the family Demequinaceae were isolated from Iriomote Island, Japan, using the SPPY agar

• Of them, 13 strains formed a monophyletic cluster with Lysinimicrobium mangrovi and remaining 7 strains were included in Demequina cluster

• Major chemotaxonomic characteristics of the strains corresponded to those of the genera Lysinimicrobium and Demequina, respectively

• Results of in silico DNA-DNA hybridization suggested that 20 strains should be assigned to 9 new species of the genus Lysinimicrobium and 7 new species of the genus Demequina, respectively

Conclusion

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Case 2. Speciation of the Genus Nocardia using Whole Genome Sequences

Nocardia alba NBRC 108234 Nocardia caishijiensis NBRC 108228 Nocardia harenae NBRC 108248

The genus Nocardia is a large genus of actinomycetes. The species of the genus are known not only as human/animal pathogen but also artificial organic compound decomposer and producers of various bioactive compounds.

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Dr. Tomohiko Tamura NBRC

Nocardia inohanensis IFM 0092 T (AB092560) Nocardia yamanashiensis IFM 0265 T (AB092561)

Nocardia niigatensis DSM 44670 T (DQ659910) Nocardia concava IFM 0354 T (AB126880) Nocardia uniformis DSM 43136 T (AF430044)

Nocardia otitidiscaviarum DSM 43242 T (AF430067) Nocardia crassostreae JCM 10500 T (AF430049)

Nocardia nova JCM 6044 T (AF430028) Nocardia pseudobrasiliensis DSM 44290 T (AF430042)

Nocardia miyunensis 117 T (AY639901) Nocardia jiangxiensis 43401 T (AY639902)

Nocardia terpenica IFM 0706 T (AB201298) Nocardia mexicana DSM 44952 T (FR733723)

Nocardia anaemiae IFM 0323 T (AB162801) Nocardia pseudovaccinii DSM 43406 T (AF430046)

Nocardia vinacea MK703-102F1 T (AB024312) Nocardia caishijiensis F829 T (AF459443)

Nocardia alba YIM 30243 T (AY222321) Nocardia jejuensis N3-2 T (AY964666)

Nocardia ignorata DSM 44496 T (AJ303008) Nocardia coubleae OFNN11 T (DQ235688)

Nocardia salmonicida DSM 40472 T (AF430050) Nocardia soli DSM 44488 T (AF430051) Nocardia cummidelens DSM 44490 T (AF430052)

Nocardia gamkensis CZH20 T (DQ235272) Nocardia exalbida IFM 0803 T (AB187522)

Nocardia lijiangensis YIM 33378 T (AY779043) Nocardia xishanensis AS4.1860 T (AY333115) Nocardia brevicatena DSM 43024 T (AF430040)

Nocardia paucivorans DSM 44386 T (AF430041) Nocardia asteroides DSM 43757 T (AF430019)

Nocardia thailandica IFM 10145 T (AB126874) Nocardia abscessus IMMIBD-1592 T (AF218292)

Nocardia cyriacigeorgica DSM 44484 T (AF430027) Nocardia jinanensis 04-5195 T (DQ462650) Nocardia speluncae N2-11 T (AM422449)

Nocardia grenadensis GW5-5797 T (FR729900) Nocardia pigrifrangens 7031 T (AF219974)

Nocardia carnea DSM 43397 T (AF430035) Nocardia testacea JCM 12235 T (AB192415) Nocardia sienata IFM 10088 T (AB121770)

Nocardia rhamnosiphila 202GMO T (EF418604) Nocardia flavorosea JCM 3332 T (Z46754)

Nocardia transvalensis DSM 43405 T (AF430047) Nocardia harenae WS-26 T (DQ282122)

Nocardia takedensis MS1-3 T (AB158277) Nocardia tenerifensis (AJ556157)

Nocardia brasiliensis DSM 43758 T (AF430038) Nocardia altamirensis DSM 44997 T (EU006090)

Nocardia vaccinii DSM 43285 T (AF430045) Nocardia vermiculata IFM 0391 T (AB126873) Nocardia elegans IMMIBN-402 T (AJ854057)

Nocardia mikamii W8061DSM 45174 T (EU484388) Nocardia cerradoensis Y9 T (AF060790)

Nocardia aobensis IFM 0372 T (AB126876) Nocardia africana DSM 44491 T (AF430054)

Nocardia veterana DSM 44445 T (AF430055) Nocardia kruczakiae MB2876ATCC BAA-948 T (AY441974)

Nocardia pneumoniae IFM 0784 T (AB108780) Nocardia amamiensis TT00-78 T (AB275164)

Nocardia niwae W9241CCUG 57756 T (FJ765056) Nocardia beijingensis AS4.1521T T (AF154129)

Nocardia araoensis IFM 0575 T (AB108779) Nocardia arthritidis IFM 10035 T (AB108781) Nocardia puris IMMIBR-145 DSM 44599 T (AJ508748)

Nocardia asiatica IFM 0245 T (AB092566) Nocardia farcinica M.GoodfellowN898/ATCC 3318 T (Z36936)

Nocardia shimofusensis YZ-96 T (AB108775) Nocardia higoensis IFM 10084 T (AB108778)

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Rhodococcus erythropolis PR4 Nocardia africana NBRC 100379 Nocardia elegans NBRC 108235 Nocardia nova NBRC 15556 Nocardia aobensis NBRC 100429 "Nocardia violaceofusca" NBRC 14427 Nocardia kruczakiae NBRC 101016

Nocardia mikamii NBRC 108933 Nocardia cerradoensis NBRC 101014 Nocardia veterana NBRC 100344

Nocardia vermiculata NBRC 100427 Nocardia jiangxiensis NBRC 101359 Nocardia miyunensis NBRC 108239 Nocardia vaccinii NBRC 15922

Nocardia mexicana NBRC 108244 Nocardia transvalensis NBRC 15921 Nocardia pseudobrasiliensis NBRC 108224

Nocardia terpenica NBRC 100888 Nocardia acidivorans NBRC 108247 Nocardia crassostreae NBRC 100342 Nocardia jejuensis NBRC 103114 Nocardia concava NBRC 100430

Nocardia niigatensis NBRC 100131 Nocardia inohanensis NBRC 100128 Nocardia yamanashiensis NBRC 100130

Nocardia otitidiscaviarum NBRC 14405 Nocardia uniformis NBRC 13702

Nocardia abscessus NBRC 100374 Nocardia asiatica NBRC 100129 Nocardia araoensis NBRC 100135 Nocardia beijingensis NBRC 16342 Nocardia arthritidis NBRC 100137 Nocardia exalbida NBRC 100660 Nocardia gamkensis NBRC 108242 Nocardia niwae NBRC 108934 Nocardia amamiensis NBRC 102102

Nocardia pneumoniae NBRC 100136 Nocardia altamirensis NBRC 108246

Nocardia tenerifensis NBRC 101015 Nocardia brasiliensis NBRC 14402 Nocardia sp. NBRC 108936

Nocardia anaemiae NBRC 100462 Nocardia pseudovaccinii NBRC 100343 Nocardia vinacea NBRC 16497

Nocardia farcinica NBRC 15532 Nocardia higoensis NBRC 100133 Nocardia shimofusensis NBRC 100134

Nocardia lijiangensis NBRC 108240 Nocardia xishanensis NBRC 101358 Nocardia amikacinitolerans NBRC 108937 Nocardia puris NBRC 108233

Nocardia takedensis NBRC 100417 Nocardia sp. NBRC 108935

Nocardia brevicatena NBRC 12119 Nocardia paucivorans NBRC 100373

Nocardia carnea NBRC 14403 Nocardia flavorosea NBRC 108225 Nocardia speluncae NBRC 108251

"Nocardia fusca" NBRC 14340 Nocardia rhamnosiphila NBRC 108938 Nocardia sienata NBRC 100364 Nocardia grenadensis NBRC 108939 Nocardia testacea NBRC 100365

Nocardia jinanensis NBRC 108249 Nocardia cyriacigeorgica NBRC 100375

Nocardia harenae NBRC 108248 Nocardia thailandica NBRC 100428

Nocardia caishijiensis NBRC 108228 Nocardia coubleae NBRC 108252 Nocardia ignorata NBRC 108230

Nocardia alba NBRC 108234 Nocardia cummidelens NBRC 100378 Nocardia soli NBRC 100376 Nocardia salmonicida NBRC 13393

Nocardia asteroides NBRC 15531

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ANI

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Conclusion

• Draft sequences of type strains of 70 valid Nocardia species were analyzed.

• In silico DDH by mean of ANI gave results that agrees with the taxonomic relationships based on MLSA and Bidirectional Best Hit (BBH) in the genera Nocardia

• 98.9 -99.0 % BBH corresponds to 96-97 % ANI and 98.6-98.8 % similarity of concatenated sequence (atpD-groL1-groL2-recA-rpoA-secY-sodA-ychY) corresponds to 96-97 % ANI in the genus Nocardia.

• Possible synonymies of some species were shown from in silico DDH.

• In silico DDH, BBH and MLSA will be useful tool for actinomycete taxonomy by accumulating data

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Quality Management of Culture Collections

in Genomic Era

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NBRC

Culture Collection

Mission of Culture Collection

• Formerly, the task of a culture collection was to preserve microbial strains as they were deposited with the name that the depositor identified.

• Now the quality requested by the users is dependent on the purpose of use.

Culture collections are always responsible for the correct identification and updated names.

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Essential Functions of Culture Collections

1. Reference organisms for quality control and standardized tests Needs of specification of strains by national or international

regulations

2. Taxonomic type strains of prokaryotes (bacteria, archaea) and yeasts According to the Bacteriological Code of Nomenclature

Living culture is also recommended for fungi derived from the type according to the Botanical Code

3. Materials for research and development Characteristic for BRC and the original country for screening sources

Strains for large scale screening

Collection, Preservation and Supply of:

2. Quality Management of Culture Collections

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1. Viability and stability Growth on appropriate media Revival from the preserved stock Estimation of long-term preservation

2. Purity Colony appearance, cell morphology Molecular technique (fingerprint, primer amplification)

3. Identity (Depositor>Collection, In-house maintenance) 16S rRNA gene sequences for prokaryotes Molecular technique (functional genes) MALDI-TOM/MS

Case 1. Identity of P. subterranea SL1T & P. lettingae TMOT Revealed by Whole Genome Sequence Analysis

Pseudothermotoga subterranea (Jeanthon et al. 2000) Bhandari and Gupta 2014

NBRC 107924T <- DSM 9912T <- C. Jeanthon, SL1T

Pseudothermotoga lettingae (Balk et al. 2002) Bhandari and Gupta 2014

NBRC 107922T <- DSM 14385T <- M. Balk, TMOT

(Other collcetion No.: ATCC BAA-301T)

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Studied by Dr. Koji Mori, NBRC

Genomic Identity of Pseudothermotoga subterranea SL1T & Pseudothermotoga lettingae TMOT

Thermotoga subterranea Jeanthon et al. 2000 C. Jeanthon et al. Thermotoga subterranea sp. nov., a new thermophilic bacterium isolated from a continental oil reservoir. Arch. Microbiol. (1995) 164: 91-97

Thermotoga lettingae Balk et al. 2002 M. Balk et al. Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor. Int. J. Syst. Evol. Microbiol. (2002) 52: 1361-1368.

Pseudothermotoga subterranea (Jeanthon et al. 2000) Bhandari and Gupta 2014 Pseudothermotoga lettingae (Balk et al. 2002) Bhandari and Gupta 2014

V. Bhandari & R. S. Gupta. Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Antonie van Leeuwenhoek (2014) 105: 143-168

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Whole genome of P. subterranea SL1T & P. lettingae TMOT

P. lettingae DSM 14385T O. Zhaxybayeva et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc. Natl. Acad. Sci. USA (2009) 106: 5865-5870.

P. subterranea NBRC 107924T

K. Mori et al. Thermotoga profunda sp. nov., and Thermotoga caldifontis sp. nov., anaerobic thermophilic bacteria isolated from terrestrial hot springs. Int. J. Syst. Evol. Microbiol. (2014) 64: 2128-2136. (In this study, we determined the whole genome sequences of 5 strains of Thermotoga (Pseudothermotoga) species including P. subterranea NBRC 107924T but practically we did not describe the result of . subterranea NBRC 107924T.)

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Relationship Based on 16S rRNA and DDH (ANI)

T.profunda P.elfii P.subterranea P.lettingae T.caldifontis T.hypogea P.thermarum T.maritima

T. profunda 96.0 96.0 96.0 94.9 94.6 93.7 90.2 P. elfii 70.8 100.0 100.0 94.7 94.4 93.3 91.6 P. subterranea 70.5 99.1 100.0 94.7 94.4 93.3 91.6 P. lettingae 70.5 99.2 100.0 94.7 94.4 93.3 91.6 T. caldifontis 65.9 65.2 65.1 65.3 98.6 96.2 92.5 T. hypogea 66.1 65.4 65.3 65.5 76.6 95.7 92.5 P. thermarum 67.2 66.6 66.5 66.6 65.7 66.0 93.0 T. maritima 64.2 64.6 64.9 65.2 66.1 65.6 64.7

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Phylogenetic tree based on 16S rRNA gene sequences

16S rRNA

ANI

CONCLUSION

We concluded that P. subterranea NBRC 107924T and P. lettingae NBRC 107922T (=DSM 14385T) are the same strain.

The reason is that the whole genome sequence of P. subterranea NBRC 107924T is completely identical with that of P. lettingae DSM 14385T. Communication and custom of exchange among culture collection contributed to this solution. Different from wet DDH, WGS-based DDH provides absolute data accompanying with the strain of CC.

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Case 2: Response of Culture Collection to Reclassification

• Proposal of a new subspecies

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Proposal of a New Subspecies

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Differentiation Based on DNA-DNA Relatedness

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Description of the New Subspecies

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Reclassification by a Culture Collection

Publication (Taxonomic study)

Species A (strain 1T and strain 2)

Species A (strain 1T) + Species B (strain 2T)

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In response to this publication, culture collection must change the catalogue database (Strain-based database) as follows:

Before

Species A strain 1T

strain 2

After

Species A strain 1T

Species B strain 2T

strain 3

strain 4

?

?

Needs reidentification by CC

strain 3

strain 4

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On-Line Catalogue of NBRC

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16S rDNA

Determination of 16S rRNA gene Sequences by Culture Collections for

Quality Management

• Necessary condition to confirm the identity of the deposited strain to that the depositor studied.

• Not sufficient condition but the sequence data is a core of the proposal of a new species

• The possibility of new taxa can be estimated by the data of 16S rRNA sequences.

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• Many of old NBRC strains including former IFO strains that have been deposited since 1950s were bearing names identified only phenotypically.

• Classification has been drastically improved since 1980s, when molecular methods were introduced into the taxonomy.

We have to verify whether their scientific names are still correct now.

• NBRC is trying to determine 16S rRNA gene sequences (prokaryotes) and ITS and D1/D2 regions of 26S rRNA (eukaryotes) for all open NBRC strains (more than 15,000) deposited from 1950s.

• These sequence data are publicized and available at NBRC on-line catalogue.

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Re-identification of Strains in a Culture Collection (Updating of the Names)

QC Flow from Accession to Issuing Certificate

Depositor

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Culture Collection

First contact Reason of deposit Data sheet containing Taxon (possible name) Taxonomic information 16S rRNA gene sequence Source / location Terms & condition BSL

Material (Culture) Additional data (Special check points) Signed Accession form

•Notice of acceptance •Accession number •Certificate of availability •(Depositor’s check)

Check (Document level)

Check (material level) Preliminary check (viability, purity etc.) 16S rRNA gene sequence matching Y / N

Proposal of a New Species of the Prokaryotes (Published in IJSEM)

Author

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IJSEM Editor and Editorial Office

Manuscript Containing Proposing name with Description (Etymology and protologue) of taxon 16S rRNA gene sequence Assignment of type strain with CC Certificate (WGS)

•Review comments •Request of WGS

Check (Document level) Accepted!

Revised Manuscript WGS Added

Time and Cost for WGS

Can GCM2.0 support this

process?

Contribution of GCM2.0 Expected

1. If WGS is mandatory for proposal of a new species, all the published new species have WGS at publication.

2. Support of GCM2.0 in WGS determination for proposal of a new species before submission will be more valuable.

3. For that system, WDCM must evaluate the new species candidates before submission.

4. 16S rRNA gene sequence data are important especially confirmed by culture collections.

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Quality Management of JCM Accept of Deposit (Material Level)

Year Total

Deposit

Result Judgement

Dead Contamination

Non-identity of 16S

Withdrawal

OK NG NG Ratio

2010 870 4 3 9 1 853 17 2.0%

2011 999 17 11 22 2 947 52 5.2%

2012 471 15 7 17 3 429 42 8.9%

2013 744 29 13 41 5 656 88 11.8%

2014 1035 56 28 60 5 885 150 14.5%

Data: Courtesy of Dr. T. Kudo, JCM

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These data indicate how important the quality management of culture collections for the quality of taxonomy.

Advantage of WGS for Culture Collections

• The WGS information contributes to the quality management of culture collections

• The WGS information is valuable for the clients for their use of microbial resources

• The WGS information will contribute to the sales of cultures of culture collections.

• It may be worth for culture collections to collaborate with GCM2.0

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Second Stage of WGS for Culture Collections

• The WGS information will indicate the genome-based biodiversity of microbial resources.

• All microbiologists will recognize the usefulness of mirobial resources in culture collections

• Correct identification of the non-type strains

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Thank you very much for your attention.

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News : Genome sequencing data required with Taxonomic Descriptions.

• IJSEM will soon be asking authors to provide genome sequencing data with descriptions of novel taxa in Taxonomic Descriptions.

• Although not mandatory for publication, the inclusion of this data is highly recommended and will be expected to be included. If authors are unable to provide genome sequencing data for any reason this should be stated as such in their covering letter; exemptions will be considered on a case by case basis by the handling Editor.

• Genome sequences are of great value to the systematics of prokaryotes. In addition to improving the general understanding of the biology of microorganisms, they improve the identification of prokaryotic species, identification of functional characteristics useful for resolving taxonomic groups and the resolution of the phylogeny of higher taxa.

• This requirement will come into effect from January, 2018 and we ask that authors deposit the data in an established, freely available public database that does not require viewer registration (i.e. GenBank, ENA or DDBJ).

• For any queries regarding these requirements, please email.

21/11/2018 Website of IJSEM

Critical Issues of Use of Microorganisms from Culture Collection

1. Correct identification

2. Quality of materials satisfying purpose of use

3. Provision of sufficient information with materials

4. Terms and conditions of use especially for commercialization

5. Compliance with laws and regulations for transfer and use of materials

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• Whole genome analysis may find closely related species (type strain) for reclassification especially for the synonymy in such big genus without wet DNA-DNA hybridization.

• Whole genome analysis has made it possible to reveal the potential of strains for use as well as the taxonomic analysis.

• Whole genome sequences are essential data to develop differentiation with high resolution.

SUMMARY for Whole Genome Analysis

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